# Date 2008-01-16 Time 04:36:08 PST -0800 (1200486968.23 s)
#phil __OFF__

Command line arguments: "../381.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 26406
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 381

-------------------------------------------------------------------------------
  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: (69.5475, 45.9914, 87.2539, 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: 3.27, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 45.9914, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9236 1.96253
Completeness in resolution range: 0.950277
Completeness with d_max=infinity: 0.947381

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9236
                             d_min =   1.9625

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: (69.5475, 45.9914, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9236 1.96253
Completeness in resolution range: 0.950277
Completeness with d_max=infinity: 0.947381

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9240 -  4.1997 [2166/2190]  1946   220  10.2%
  bin  2:  4.1997 -  3.3458 [2069/2089]  1865   204   9.9%
  bin  3:  3.3458 -  2.9265 [2069/2088]  1864   205   9.9%
  bin  4:  2.9265 -  2.6605 [2021/2051]  1816   205  10.1%
  bin  5:  2.6605 -  2.4708 [2022/2041]  1822   200   9.9%
  bin  6:  2.4708 -  2.3257 [2006/2031]  1801   205  10.2%
  bin  7:  2.3257 -  2.2096 [2012/2040]  1811   201  10.0%
  bin  8:  2.2096 -  2.1137 [1984/2020]  1789   195   9.8%
  bin  9:  2.1137 -  2.0325 [1990/2032]  1793   197   9.9%
  bin 10:  2.0325 -  1.9625 [1250/2032]  1123   127  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_381/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:
        1.62 -     2.27: 30
        2.27 -     2.93: 1571
        2.93 -     3.59: 4559
        3.59 -     4.24: 9318
        4.24 -     4.90: 13131
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.615 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  70 " - " O   HOH Z 302 "  1.680 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.883 3.040 x,y+1,z
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.941 3.040 x,y+1,z
  ... (remaining 28604 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_381/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_381/model_refine_001.geo

CPU time processing inputs: 9.09


============================ 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 = 69.5475 45.9914 87.2539 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4209   r_free= 0.4182   ksol= 0.00   Bsol= 0.00   scale= 0.927    |
|                                                                             |
| 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:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.231463                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9240 -  4.6843 0.99   1406  154 0.3399 0.3296      6.5073       6.459|
|  2:  4.6843 -  3.7373 0.99   1357  153 0.3448 0.3293      6.7003      6.6439|
|  3:  3.7373 -  3.2705 0.99   1321  144 0.3836 0.3560      6.6165      6.6153|
|  4:  3.2705 -  2.9741 0.99   1321  152 0.4048 0.4248      6.4639      6.5134|
|  5:  2.9741 -  2.7623 0.99   1304  145 0.4493 0.3758      6.3085      6.2663|
|  6:  2.7623 -  2.6004 0.99   1309  141 0.4482 0.4888      6.2241      6.1549|
|  7:  2.6004 -  2.4708 0.99   1295  145 0.4510 0.4404      6.1777       6.112|
|  8:  2.4708 -  2.3636 0.98   1296  146 0.4810 0.5085      6.1655       6.183|
|  9:  2.3636 -  2.2730 0.98   1279  140 0.4584 0.4808      6.0733      6.1344|
| 10:  2.2730 -  2.1948 1.00   1280  144 0.4707 0.4728      6.0669       6.055|
| 11:  2.1948 -  2.1264 0.98   1290  144 0.4693 0.5172      5.9963       6.046|
| 12:  2.1264 -  2.0657 0.98   1268  143 0.4791 0.4495      5.9558      5.9488|
| 13:  2.0657 -  2.0115 0.98   1282  138 0.4687 0.4634      5.8439      5.7872|
| 14:  2.0115 -  1.9625 0.47    622   70 0.5220 0.4931      5.8892       5.791|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9240 -  4.6843  1406   154  0.76  28.95   0.84     0.81      54434.02|
|  2:  4.6843 -  3.7373  1357   153  0.77  29.29   0.94     0.88      79655.96|
|  3:  3.7373 -  3.2705  1321   144  0.68  36.79   0.96     0.86      85845.58|
|  4:  3.2705 -  2.9741  1321   152  0.61  42.90   0.95     0.81      79926.97|
|  5:  2.9741 -  2.7623  1304   145  0.54  48.60   0.93     0.75      61357.09|
|  6:  2.7623 -  2.6004  1309   141  0.52  50.10   0.93     0.71      54495.78|
|  7:  2.6004 -  2.4708  1295   145  0.49  52.55   0.95     0.67      51625.85|
|  8:  2.4708 -  2.3636  1296   146  0.46  55.07   0.94     0.64      49604.26|
|  9:  2.3636 -  2.2730  1279   140  0.45  55.72   0.96     0.64      46291.27|
| 10:  2.2730 -  2.1948  1280   144  0.46  55.31   0.98     0.66      41638.87|
| 11:  2.1948 -  2.1264  1290   144  0.44  56.95   0.97     0.67      41461.25|
| 12:  2.1264 -  2.0657  1268   143  0.43  57.98   0.99     0.66      37651.92|
| 13:  2.0657 -  2.0115  1282   138  0.41  59.48   0.97     0.63      32722.42|
| 14:  2.0115 -  1.9625   622    70  0.44  56.91   1.01     0.63      26056.64|
|alpha:            min =        0.63 max =            0.88 mean =         0.72|
|beta:             min =    26056.64 max =        85845.58 mean =     54338.59|
|figures of merit: min =        0.00 max =            1.00 mean =         0.54|
|phase err.(work): min =        0.00 max =           90.00 mean =        48.49|
|phase err.(test): min =        0.00 max =           89.92 mean =        48.74|
|-----------------------------------------------------------------------------|

============================== 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 = 9.174117              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.037   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.587092              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.866   (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 |  1.615 -  1.944:        5 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.944 -  2.272:       25 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.272 -  2.600:       56 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.600 -  2.929:     1515 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.929 -  3.257:     1936 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.257 -  3.586:     2623 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.586 -  3.914:     4775 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.914 -  4.243:     4543 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.243 -  4.571:     5998 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.571 -  4.900:     7133 |
|-----------------------------------------------------------------------------|
|-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 |        0.177 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.108    4.900  1.615 |       0.410 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.602)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.96 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4209   r_free= 0.4182   ksol= 0.00   Bsol= 0.00   scale= 0.927    |
|                                                                             |
| 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:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.231463                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4093   r_free= 0.4080   ksol= 0.34   Bsol= 31.68   scale= 0.958   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.48,2.97,0.10,0.00,0.00,0.00); trace/3= 0.20                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.221683                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.359900              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.963   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.833822              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.642   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4093      final r-factor (work) = 0.2928          |
| start r-factor (free) = 0.4080      final r-factor (free) = 0.3308          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.0501 = 7.36 * 0.50 * 6.2157 + 1.00 * 0.1767                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.3861 = 7.36 * 0.50 * 6.0504 + 1.00 * 0.1207                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2928      final r-factor (work) = 0.2655          |
| start r-factor (free) = 0.3308      final r-factor (free) = 0.3443          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.0511 = 0.83 * 1.00 * 6.0504 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9336 = 0.83 * 1.00 * 5.8989 + 1.00 * 0.0150                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.602)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    94.78   17.98    None  None   None       |
|    all(noH): 2823   0      0.00    94.78   17.98    None  None   None       |
|    Sol.    : 438    0      2.25    94.78   38.85    None  None   None       |
|    Mac.    : 2385   0      0.00    66.26   14.15    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 -   9.478:  848   |   5:    47.388 -  56.866:   97        |
|      1:     9.478 -  18.955: 1017   |   6:    56.866 -  66.343:   43        |
|      2:    18.955 -  28.433:  442   |   7:    66.343 -  75.821:   14        |
|      3:    28.433 -  37.911:  233   |   8:    75.821 -  85.299:    3        |
|      4:    37.911 -  47.388:  125   |   9:    85.299 -  94.776:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2655 r_free = 0.3443             target_work(ml) = 5.914         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2651 r_free = 0.3453             target_work(ml) = 5.914         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2651   r_free= 0.3453   ksol= 0.34   Bsol= 31.68   scale= 1.031   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.48,2.97,0.10,0.00,0.00,0.00); trace/3= 0.20                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.914353                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2641   r_free= 0.3411   ksol= 0.34   Bsol= 57.17   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.34,0.02,-0.26,0.00,-0.00,-0.00); trace/3= -0.86                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.910573                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.308710              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.495   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.297044              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 142.831  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2641      final r-factor (work) = 0.2106          |
| start r-factor (free) = 0.3411      final r-factor (free) = 0.2726          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.8804 = 3.31 * 0.50 * 5.8998 + 1.00 * 0.1200                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.6895 = 3.31 * 0.50 * 5.8214 + 1.00 * 0.0588                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2106      final r-factor (work) = 0.1990          |
| start r-factor (free) = 0.2726      final r-factor (free) = 0.2552          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7440 = 0.30 * 1.00 * 5.8214 + 1.00 * 0.0148                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6970 = 0.30 * 1.00 * 5.6822 + 1.00 * 0.0091                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.602)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.70   17.44    None  None   None       |
|    all(noH): 2823   0      0.00    92.70   17.44    None  None   None       |
|    Sol.    : 438    0      4.56    92.70   38.82    None  None   None       |
|    Mac.    : 2385   0      0.00    72.06   13.51    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 -   9.270:  833   |   5:    46.348 -  55.618:  108        |
|      1:     9.270 -  18.539: 1151   |   6:    55.618 -  64.888:   34        |
|      2:    18.539 -  27.809:  352   |   7:    64.888 -  74.157:   19        |
|      3:    27.809 -  37.079:  181   |   8:    74.157 -  83.427:    1        |
|      4:    37.079 -  46.348:  143   |   9:    83.427 -  92.697:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1990 r_free = 0.2552             target_work(ml) = 5.655         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1989 r_free = 0.2551             target_work(ml) = 5.654         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1989   r_free= 0.2551   ksol= 0.34   Bsol= 57.17   scale= 1.026   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.34,0.02,-0.26,0.00,-0.00,-0.00); trace/3= -0.86                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.654296                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1984   r_free= 0.2542   ksol= 0.33   Bsol= 53.06   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.64,-1.23,-0.43,-0.00,-0.00,-0.00); trace/3= -1.43                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.651224                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.090090              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.199   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.576441              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 150.299  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1984      final r-factor (work) = 0.1575          |
| start r-factor (free) = 0.2542      final r-factor (free) = 0.2050          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9961 = 2.09 * 0.50 * 5.6814 + 1.00 * 0.0588                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8407 = 2.09 * 0.50 * 5.5407 + 1.00 * 0.0504                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1575      final r-factor (work) = 0.1459          |
| start r-factor (free) = 0.2050      final r-factor (free) = 0.1973          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2030 = 0.58 * 1.00 * 5.5407 + 1.00 * 0.0091                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1209 = 0.58 * 1.00 * 5.3958 + 1.00 * 0.0105                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.602)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    94.28   17.73    None  None   None       |
|    all(noH): 2823   0      0.00    94.28   17.73    None  None   None       |
|    Sol.    : 438    0      6.20    94.28   43.16    None  None   None       |
|    Mac.    : 2385   0      0.00    85.58   13.06    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 -   9.428:  932   |   5:    47.139 -  56.567:  105        |
|      1:     9.428 -  18.856: 1153   |   6:    56.567 -  65.995:   74        |
|      2:    18.856 -  28.284:  266   |   7:    65.995 -  75.423:   34        |
|      3:    28.284 -  37.711:  129   |   8:    75.423 -  84.851:   11        |
|      4:    37.711 -  47.139:  116   |   9:    84.851 -  94.279:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1459 r_free = 0.1973             target_work(ml) = 5.378         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1457 r_free = 0.1970             target_work(ml) = 5.377         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1457   r_free= 0.1970   ksol= 0.33   Bsol= 53.06   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.64,-1.23,-0.43,-0.00,-0.00,-0.00); trace/3= -1.43                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.376920                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1459   r_free= 0.1967   ksol= 0.32   Bsol= 53.06   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.59,-2.03,-0.59,-0.00,-0.00,-0.00); trace/3= -1.74                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.374234                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.533279              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.442  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.150933              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 142.460  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1459      final r-factor (work) = 0.1246          |
| start r-factor (free) = 0.1967      final r-factor (free) = 0.1733          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8857 = 2.53 * 0.50 * 5.3964 + 1.00 * 0.0504                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7779 = 2.53 * 0.50 * 5.3078 + 1.00 * 0.0548                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1246      final r-factor (work) = 0.1224          |
| start r-factor (free) = 0.1733      final r-factor (free) = 0.1663          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8116 = 0.15 * 1.00 * 5.3078 + 1.00 * 0.0105                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7973 = 0.15 * 1.00 * 5.2295 + 1.00 * 0.0080                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 34     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.602)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.36    90.36   17.02    None  None   None       |
|    all(noH): 2823   0      1.36    90.36   17.02    None  None   None       |
|    Sol.    : 438    0      4.84    90.36   40.57    None  None   None       |
|    Mac.    : 2385   0      1.36    85.91   12.70    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.364 -  10.263: 1143   |   5:    45.860 -  54.759:   91        |
|      1:    10.263 -  19.162: 1022   |   6:    54.759 -  63.658:   63        |
|      2:    19.162 -  28.061:  217   |   7:    63.658 -  72.557:   30        |
|      3:    28.061 -  36.960:  125   |   8:    72.557 -  81.456:   10        |
|      4:    36.960 -  45.860:  118   |   9:    81.456 -  90.355:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1224 r_free = 0.1663             target_work(ml) = 5.207         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1222 r_free = 0.1662             target_work(ml) = 5.207         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1222   r_free= 0.1662   ksol= 0.32   Bsol= 53.06   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.59,-2.03,-0.59,-0.00,-0.00,-0.00); trace/3= -1.74                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.206850                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1222   r_free= 0.1662   ksol= 0.32   Bsol= 48.03   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.62,-2.28,-0.62,-0.00,-0.00,-0.00); trace/3= -1.84                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.206490                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.385401              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 127.091  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 4.733116              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 151.929  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1222      final r-factor (work) = 0.1188          |
| start r-factor (free) = 0.1662      final r-factor (free) = 0.1611          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.6768 = 1.39 * 0.50 * 5.2288 + 1.00 * 0.0548                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.6453 = 1.39 * 0.50 * 5.1957 + 1.00 * 0.0463                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1188      final r-factor (work) = 0.1168          |
| start r-factor (free) = 0.1611      final r-factor (free) = 0.1631          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 24.5995 = 4.73 * 1.00 * 5.1957 + 1.00 * 0.0079                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 24.4859 = 4.73 * 1.00 * 5.1712 + 1.00 * 0.0102                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.602)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.70   17.28    None  None   None       |
|    all(noH): 2823   0      0.00    92.70   17.28    None  None   None       |
|    Sol.    : 438    0      5.52    92.70   42.25    None  None   None       |
|    Mac.    : 2385   0      0.00    92.68   12.70    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 -   9.270:  929   |   5:    46.352 -  55.622:   99        |
|      1:     9.270 -  18.541: 1192   |   6:    55.622 -  64.892:   73        |
|      2:    18.541 -  27.811:  245   |   7:    64.892 -  74.162:   42        |
|      3:    27.811 -  37.081:  120   |   8:    74.162 -  83.433:   10        |
|      4:    37.081 -  46.352:  107   |   9:    83.433 -  92.703:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1168 r_free = 0.1631             target_work(ml) = 5.179         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1168 r_free = 0.1631             target_work(ml) = 5.179         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1168   r_free= 0.1631   ksol= 0.32   Bsol= 48.03   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.62,-2.28,-0.62,-0.00,-0.00,-0.00); trace/3= -1.84                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.178801                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9240 -  4.6843 0.99   1406  154 0.1001 0.1245      5.3854       5.539|
|  2:  4.6843 -  3.7373 0.99   1357  153 0.0872 0.1153      5.4494      5.6478|
|  3:  3.7373 -  3.2705 0.99   1321  144 0.1125 0.1521      5.5236      5.8283|
|  4:  3.2705 -  2.9741 0.99   1321  152 0.1303 0.1794      5.4887       5.652|
|  5:  2.9741 -  2.7623 0.99   1304  145 0.1408 0.1771      5.3708       5.586|
|  6:  2.7623 -  2.6004 0.99   1309  141 0.1280 0.2009      5.2365      5.4875|
|  7:  2.6004 -  2.4708 0.99   1295  145 0.1359 0.1686      5.2185      5.3756|
|  8:  2.4708 -  2.3636 0.98   1296  146 0.1225 0.1714      5.1164       5.359|
|  9:  2.3636 -  2.2730 0.98   1279  140 0.1233 0.1834       5.064      5.3416|
| 10:  2.2730 -  2.1948 1.00   1280  144 0.1156 0.1684       4.976      5.1719|
| 11:  2.1948 -  2.1264 0.98   1290  144 0.1148 0.1960      4.9638      5.3458|
| 12:  2.1264 -  2.0657 0.98   1268  143 0.1225 0.1779      4.9333      5.2348|
| 13:  2.0657 -  2.0115 0.98   1282  138 0.1127 0.1862      4.7988      5.0401|
| 14:  2.0115 -  1.9625 0.47    622   70 0.0948 0.1515      4.6375      4.8492|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9240 -  4.6843  1406   154  0.94   8.95   0.98     0.95       6824.06|
|  2:  4.6843 -  3.7373  1357   153  0.95   7.80   1.02     1.01       9007.59|
|  3:  3.7373 -  3.2705  1321   144  0.93  11.73   1.04     1.04      11039.02|
|  4:  3.2705 -  2.9741  1321   152  0.91  14.27   1.01     0.99      10626.34|
|  5:  2.9741 -  2.7623  1304   145  0.90  16.04   1.01     0.99       8805.21|
|  6:  2.7623 -  2.6004  1309   141  0.89  16.65   0.98     0.95       7291.65|
|  7:  2.6004 -  2.4708  1295   145  0.90  16.59   0.99     0.96       6758.70|
|  8:  2.4708 -  2.3636  1296   146  0.90  15.85   1.00     0.97       5781.96|
|  9:  2.3636 -  2.2730  1279   140  0.91  15.68   1.00     0.95       5187.90|
| 10:  2.2730 -  2.1948  1280   144  0.90  15.95   1.01     0.97       4589.60|
| 11:  2.1948 -  2.1264  1290   144  0.90  16.84   1.00     0.96       4676.77|
| 12:  2.1264 -  2.0657  1268   143  0.90  16.81   1.01     1.00       4415.08|
| 13:  2.0657 -  2.0115  1282   138  0.90  16.63   1.00     0.98       3508.64|
| 14:  2.0115 -  1.9625   622    70  0.93  13.24   0.99     0.96       2484.09|
|alpha:            min =        0.95 max =            1.04 mean =         0.98|
|beta:             min =     2484.09 max =        11039.02 mean =      6687.19|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.92 mean =        14.48|
|phase err.(test): min =        0.00 max =           89.28 mean =        14.13|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1170   r_free= 0.1627   ksol= 0.32   Bsol= 51.16   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.53,-2.32,-0.57,-0.00,-0.00,-0.00); trace/3= -1.81                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.178567                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1170   r_free= 0.1627   ksol= 0.32   Bsol= 51.16   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.53,-2.32,-0.57,-0.00,-0.00,-0.00); trace/3= -1.81                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.178567                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9240 -  4.6843 0.99   1406  154 0.1009 0.1241      5.3805      5.5294|
|  2:  4.6843 -  3.7373 0.99   1357  153 0.0881 0.1137      5.4553      5.6467|
|  3:  3.7373 -  3.2705 0.99   1321  144 0.1135 0.1512      5.5281      5.8273|
|  4:  3.2705 -  2.9741 0.99   1321  152 0.1301 0.1803      5.4893       5.656|
|  5:  2.9741 -  2.7623 0.99   1304  145 0.1409 0.1760      5.3712      5.5821|
|  6:  2.7623 -  2.6004 0.99   1309  141 0.1282 0.2011      5.2361      5.4875|
|  7:  2.6004 -  2.4708 0.99   1295  145 0.1358 0.1689      5.2173      5.3777|
|  8:  2.4708 -  2.3636 0.98   1296  146 0.1222 0.1709      5.1146      5.3563|
|  9:  2.3636 -  2.2730 0.98   1279  140 0.1232 0.1834      5.0624      5.3414|
| 10:  2.2730 -  2.1948 1.00   1280  144 0.1153 0.1682      4.9747      5.1731|
| 11:  2.1948 -  2.1264 0.98   1290  144 0.1146 0.1954      4.9631       5.345|
| 12:  2.1264 -  2.0657 0.98   1268  143 0.1223 0.1777      4.9331      5.2336|
| 13:  2.0657 -  2.0115 0.98   1282  138 0.1125 0.1860      4.7971      5.0399|
| 14:  2.0115 -  1.9625 0.47    622   70 0.0947 0.1506      4.6356      4.8444|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9240 -  4.6843  1406   154  0.94   8.73   0.98     0.95       6664.23|
|  2:  4.6843 -  3.7373  1357   153  0.95   7.74   1.02     1.01       8919.21|
|  3:  3.7373 -  3.2705  1321   144  0.93  11.77   1.04     1.04      11054.71|
|  4:  3.2705 -  2.9741  1321   152  0.91  14.33   1.02     0.99      10669.52|
|  5:  2.9741 -  2.7623  1304   145  0.90  16.01   1.01     0.99       8782.97|
|  6:  2.7623 -  2.6004  1309   141  0.89  16.62   0.98     0.96       7282.58|
|  7:  2.6004 -  2.4708  1295   145  0.90  16.59   1.00     0.96       6751.05|
|  8:  2.4708 -  2.3636  1296   146  0.90  15.85   1.00     0.98       5770.22|
|  9:  2.3636 -  2.2730  1279   140  0.91  15.65   1.00     0.96       5175.46|
| 10:  2.2730 -  2.1948  1280   144  0.90  15.92   1.01     0.97       4583.35|
| 11:  2.1948 -  2.1264  1290   144  0.90  16.84   1.00     0.96       4674.97|
| 12:  2.1264 -  2.0657  1268   143  0.90  16.81   1.01     1.01       4415.13|
| 13:  2.0657 -  2.0115  1282   138  0.90  16.60   1.01     0.99       3496.35|
| 14:  2.0115 -  1.9625   622    70  0.93  13.18   0.99     0.96       2469.36|
|alpha:            min =        0.95 max =            1.04 mean =         0.98|
|beta:             min =     2469.36 max =        11054.71 mean =      6665.41|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           90.00 mean =        14.45|
|phase err.(test): min =        0.00 max =           89.21 mean =        14.13|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.602)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.71   17.29    None  None   None       |
|    all(noH): 2823   0      0.00    92.71   17.29    None  None   None       |
|    Sol.    : 438    0      5.52    92.71   42.25    None  None   None       |
|    Mac.    : 2385   0      0.00    92.69   12.70    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   9.273:  929   |   5:    46.354 -  55.625:   99        |
|      1:     9.273 -  18.544: 1192   |   6:    55.625 -  64.895:   73        |
|      2:    18.544 -  27.814:  245   |   7:    64.895 -  74.165:   42        |
|      3:    27.814 -  37.084:  120   |   8:    74.165 -  83.436:   10        |
|      4:    37.084 -  46.354:  107   |   9:    83.436 -  92.706:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 309         
Filter by distance & map next to the model:
   mapped sites are within: 0.578 - 4.258
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 305 from: 309
   mapped sites are within: 0.709 - 4.258

peak=    5.765 closest distance to " NE2 GLN A  11 " =    1.257
peak=    5.726 closest distance to " O   HOH Z 142 " =    2.007
peak=    5.605 closest distance to " O   HOH Z 287 " =    1.926
peak=    5.557 closest distance to " O   HOH Z 423 " =    1.788
peak=    5.460 closest distance to " O   HOH Z 375 " =    1.266
peak=    5.433 closest distance to " CG  PRO A  54 " =    1.353
peak=    5.341 closest distance to " O   HOH Z 126 " =    2.167
peak=    5.134 closest distance to " O   HOH Z 417 " =    2.015
peak=    5.051 closest distance to " O   HOH Z   9 " =    1.610
peak=    4.976 closest distance to " CB  PRO A  54 " =    1.076
peak=    4.938 closest distance to " O   HOH Z  63 " =    1.611
peak=    4.929 closest distance to " O   HOH Z 371 " =    2.100
peak=    4.921 closest distance to " NH2 ARG A  56 " =    2.080
peak=    4.912 closest distance to " O   HOH Z  65 " =    1.052
peak=    4.887 closest distance to " O   HOH Z 112 " =    1.277
peak=    4.879 closest distance to " O   HOH Z 427 " =    2.319
peak=    4.823 closest distance to " O   HOH Z  57 " =    2.393
peak=    4.821 closest distance to " CB  ARG A 275 " =    0.999
peak=    4.799 closest distance to " O   HOH Z  78 " =    1.609
peak=    4.792 closest distance to " O   HOH Z 245 " =    1.148
peak=    4.750 closest distance to " O   HOH Z 236 " =    1.464
peak=    4.737 closest distance to " O   HOH Z 232 " =    2.278
peak=    4.710 closest distance to " O   HOH Z 380 " =    1.852
peak=    4.689 closest distance to " CG2 VAL A 257 " =    0.926
peak=    4.684 closest distance to " O   HOH Z 403 " =    1.541
peak=    4.671 closest distance to " CB  GLN A 223 " =    1.502
peak=    4.652 closest distance to " O   HOH Z  39 " =    1.208
peak=    4.560 closest distance to " CG  PRO A 198 " =    1.272
peak=    4.556 closest distance to " O   HOH Z   1 " =    1.854
peak=    4.547 closest distance to " O   HOH Z  49 " =    1.216
peak=    4.500 closest distance to " NZ  LYS A 119 " =    2.374
peak=    4.455 closest distance to " CG  PRO A  90 " =    1.165
peak=    4.444 closest distance to " CB  SER A  63 " =    1.225
peak=    4.433 closest distance to " O   HOH Z 298 " =    1.873
peak=    4.350 closest distance to " CB  ASN A 148 " =    1.389
peak=    4.312 closest distance to " CG  PRO A 213 " =    1.271
peak=    4.242 closest distance to " O   HOH Z 422 " =    0.859
peak=    4.230 closest distance to " CB  SER A   3 " =    1.252
peak=    4.225 closest distance to " O   HOH Z 425 " =    1.363
peak=    4.195 closest distance to " CB  GLU A 277 " =    3.531
peak=    4.190 closest distance to " O   HOH Z 427 " =    1.196
peak=    4.153 closest distance to " CA  TYR A  30 " =    1.026
peak=    4.148 closest distance to " O   HOH Z   7 " =    1.347
peak=    4.124 closest distance to " CB  SER A 216 " =    0.952
peak=    4.101 closest distance to " O   HOH Z 327 " =    1.707
peak=    4.100 closest distance to " CG  TRP A 179 " =    2.105
peak=    4.087 closest distance to " O   HOH Z  61 " =    1.551
peak=    4.084 closest distance to " CB  GLN A 183 " =    1.192
peak=    4.080 closest distance to " CE  LYS A 119 " =    1.271
peak=    4.070 closest distance to " NH1AARG A 145 " =    1.192
peak=    4.067 closest distance to " CB  ARG A 190 " =    1.660
peak=    4.036 closest distance to " CZ  PHE A 218 " =    1.082
peak=    4.031 closest distance to " CB  VAL A 265 " =    1.254
peak=    4.030 closest distance to " O   HOH Z 209 " =    2.213
peak=    4.028 closest distance to " CB  GLU A 128 " =    0.981
peak=    4.027 closest distance to " O   SER A  87 " =    2.412
peak=    4.018 closest distance to " NH2AARG A 190 " =    1.789
peak=    3.999 closest distance to " O   HOH Z 352 " =    1.795
peak=    3.989 closest distance to " O  BHOH Z  74 " =    1.275
peak=    3.985 closest distance to " CB  ARG A  79 " =    1.308
peak=    3.975 closest distance to " O   HOH Z 365 " =    2.684
peak=    3.947 closest distance to " CD  ARG A 159 " =    0.839
peak=    3.941 closest distance to " O   HOH Z 158 " =    2.819
peak=    3.938 closest distance to " OG ASER A 258 " =    3.060
peak=    3.936 closest distance to " CE  LYS A  76 " =    0.865
peak=    3.925 closest distance to " O   HOH Z  24 " =    1.787
peak=    3.913 closest distance to " O   HOH Z  68 " =    2.160
peak=    3.903 closest distance to " O   HOH Z 405 " =    1.436
peak=    3.894 closest distance to " CA  ASN A 215 " =    1.060
peak=    3.892 closest distance to " O   HOH Z 394 " =    1.775
peak=    3.875 closest distance to " O   HOH Z  44 " =    1.781
peak=    3.863 closest distance to " CA  ARG A 195 " =    1.312
peak=    3.833 closest distance to " O   HOH Z 437 " =    1.779
peak=    3.832 closest distance to " O   HOH Z  40 " =    1.645
peak=    3.816 closest distance to " O   HOH Z 261 " =    2.168
peak=    3.788 closest distance to " CG1 ILE A 120 " =    1.431
peak=    3.780 closest distance to " O   HOH Z 425 " =    1.949
peak=    3.776 closest distance to " O   HOH Z 346 " =    1.711
peak=    3.775 closest distance to " O   HOH Z 362 " =    2.037
peak=    3.773 closest distance to " CB  THR A  31 " =    1.606
peak=    3.767 closest distance to " O   HOH Z   3 " =    1.949
peak=    3.765 closest distance to " O   HOH Z 272 " =    1.814
peak=    3.756 closest distance to " CB  VAL A 202 " =    1.667
peak=    3.755 closest distance to " CD  ARG A  66 " =    2.591
peak=    3.749 closest distance to " O   HOH Z  61 " =    1.658
peak=    3.742 closest distance to " N   GLN A 278 " =    1.291
peak=    3.735 closest distance to " CA  ASN A 127 " =    1.032
peak=    3.730 closest distance to " O   HOH Z  78 " =    1.826
peak=    3.718 closest distance to " CB  LYS A 117 " =    1.239
peak=    3.713 closest distance to " O   ASN A  74 " =    1.456
peak=    3.711 closest distance to " O   HOH Z 419 " =    1.685
peak=    3.703 closest distance to " OG BSER A 164 " =    2.127
peak=    3.699 closest distance to " CZ3 TRP A 266 " =    1.168
peak=    3.698 closest distance to " O   HOH Z 344 " =    3.173
peak=    3.697 closest distance to " ND2 ASN A 187 " =    1.618
peak=    3.694 closest distance to " CG  LEU A 167 " =    1.269
peak=    3.693 closest distance to " NZ  LYS A 117 " =    2.874
peak=    3.684 closest distance to " O   HOH Z 286 " =    2.362
peak=    3.674 closest distance to " O   HOH Z   2 " =    1.768
peak=    3.674 closest distance to " CB  ASN A  39 " =    0.895
peak=    3.660 closest distance to " N   GLU A   2 " =    1.392
peak=    3.654 closest distance to " CB  GLU A 152 " =    1.327
peak=    3.650 closest distance to " OG  SER A  62 " =    2.950
peak=    3.636 closest distance to " O   HOH Z 214 " =    2.412
peak=    3.610 closest distance to " O   PRO A 198 " =    1.173
peak=    3.608 closest distance to " O   HOH Z 139 " =    1.116
peak=    3.605 closest distance to " CB  LEU A 228 " =    1.093
peak=    3.604 closest distance to " CG  PRO A 243 " =    1.043
peak=    3.602 closest distance to " O   HOH Z 290 " =    1.048
peak=    3.593 closest distance to " O   HOH Z 368 " =    3.601
peak=    3.590 closest distance to " CB  TRP A 266 " =    1.110
peak=    3.589 closest distance to " CA  VAL A 125 " =    1.184
peak=    3.588 closest distance to " O   HOH Z 172 " =    2.566
peak=    3.588 closest distance to " O   HOH Z 117 " =    1.204
peak=    3.588 closest distance to " O   HOH Z 392 " =    1.192
peak=    3.587 closest distance to " CB  TYR A 169 " =    0.816
peak=    3.583 closest distance to " CG1 ILE A  33 " =    1.294
peak=    3.583 closest distance to " CB  SER A 212 " =    1.245
peak=    3.573 closest distance to " CB  ALA A 114 " =    0.978
peak=    3.570 closest distance to " O   HOH Z 189 " =    2.577
peak=    3.565 closest distance to " O   HOH Z 422 " =    2.457
peak=    3.560 closest distance to " OD1 ASN A  69 " =    2.449
peak=    3.557 closest distance to " O   HOH Z 116 " =    2.873
peak=    3.556 closest distance to " O   HOH Z   1 " =    1.751
peak=    3.551 closest distance to " O   HOH Z 371 " =    2.025
peak=    3.545 closest distance to " O   HOH Z 305 " =    3.445
peak=    3.545 closest distance to " ND1 HIS A  86 " =    1.815
peak=    3.543 closest distance to " CB  GLN A  88 " =    1.254
peak=    3.540 closest distance to " O   HOH Z 406 " =    1.570
peak=    3.537 closest distance to " O   HOH Z  59 " =    1.543
peak=    3.535 closest distance to " O   HOH Z 145 " =    1.207
peak=    3.533 closest distance to " CG2 ILE A 120 " =    1.164
peak=    3.528 closest distance to " CB  SER A 210 " =    0.748
peak=    3.520 closest distance to " O   HOH Z 153 " =    3.728
peak=    3.516 closest distance to " O   HOH Z 357 " =    1.965
peak=    3.513 closest distance to " O   HOH Z 146 " =    1.519
peak=    3.512 closest distance to " CA  ALA A  51 " =    1.002
peak=    3.510 closest distance to " O   HOH Z 234 " =    3.605
peak=    3.505 closest distance to " CB  ALA A 114 " =    0.873
peak=    3.503 closest distance to " O   HOH Z 359 " =    1.385
peak=    3.502 closest distance to " CB  ARG A 139 " =    1.147
peak=    3.491 closest distance to " O   HOH Z 434 " =    1.434
peak=    3.490 closest distance to " CB  SER A 276 " =    1.242
peak=    3.483 closest distance to " O   HOH Z 421 " =    2.071
peak=    3.479 closest distance to " CB  TRP A 179 " =    1.350
peak=    3.478 closest distance to " CG  LYS A  76 " =    1.667
peak=    3.478 closest distance to " CB  GLU A  46 " =    1.137
peak=    3.478 closest distance to " CG2 THR A 221 " =    1.253
peak=    3.476 closest distance to " O   HOH Z 128 " =    2.097
peak=    3.473 closest distance to " N   PHE A 130 " =    1.225
peak=    3.473 closest distance to " O   HOH Z 175 " =    2.092
peak=    3.471 closest distance to " N   TYR A 116 " =    1.381
peak=    3.468 closest distance to " ND2 ASN A 249 " =    0.869
peak=    3.467 closest distance to " CB  PHE A 130 " =    0.917
peak=    3.465 closest distance to " NH1BARG A 145 " =    1.332
peak=    3.464 closest distance to " O   HOH Z 124 " =    2.113
peak=    3.462 closest distance to " O   HOH Z 130 " =    2.461
peak=    3.461 closest distance to " O   HOH Z 378 " =    0.905
peak=    3.452 closest distance to " O   HOH Z 272 " =    2.064
peak=    3.448 closest distance to " O   HOH Z 132 " =    2.356
peak=    3.445 closest distance to " CB  ASN A 110 " =    1.068
peak=    3.440 closest distance to " O   HOH Z 411 " =    3.744
peak=    3.434 closest distance to " O   HOH Z  10 " =    1.736
peak=    3.431 closest distance to " O   HOH Z 193 " =    1.673
peak=    3.425 closest distance to " O   HOH Z 124 " =    1.317
peak=    3.424 closest distance to " CB  THR A 157 " =    1.092
peak=    3.423 closest distance to " O   HOH Z  88 " =    2.560
peak=    3.422 closest distance to " CB  HIS A 108 " =    0.843
peak=    3.421 closest distance to " CG2 VAL A 197 " =    1.029
peak=    3.420 closest distance to " CG  GLN A  58 " =    0.937
peak=    3.419 closest distance to " O   HOH Z 193 " =    1.665
peak=    3.416 closest distance to " CB  SER A  62 " =    1.135
peak=    3.411 closest distance to " NH1 ARG A  14 " =    1.089
peak=    3.410 closest distance to " O   THR A 220 " =    1.215
peak=    3.407 closest distance to " O   HOH Z 225 " =    1.466
peak=    3.399 closest distance to " NZ  LYS A 119 " =    1.388
peak=    3.399 closest distance to " O   HOH Z 222 " =    1.273
peak=    3.392 closest distance to " CB  ASN A 142 " =    1.017
peak=    3.392 closest distance to " CB  SER A  26 " =    1.704
peak=    3.383 closest distance to " CB  ASN A 187 " =    1.259
peak=    3.382 closest distance to " CD2 TRP A 179 " =    1.309
peak=    3.376 closest distance to " CG1BVAL A  72 " =    1.388
peak=    3.374 closest distance to " CA  ILE A 234 " =    0.998
peak=    3.371 closest distance to " CB  ASP A 191 " =    1.235
peak=    3.369 closest distance to " O   HOH Z  44 " =    2.862
peak=    3.366 closest distance to " O   HOH Z 215 " =    1.541
peak=    3.365 closest distance to " O   HOH Z 213 " =    2.055
peak=    3.362 closest distance to " O   HOH Z 368 " =    4.235
peak=    3.361 closest distance to " O   HOH Z 257 " =    2.155
peak=    3.355 closest distance to " O   HOH Z 402 " =    1.415
peak=    3.351 closest distance to " O   HOH Z 244 " =    1.713
peak=    3.347 closest distance to " N   SER A 134 " =    1.244
peak=    3.342 closest distance to " CA  SER A  87 " =    1.069
peak=    3.340 closest distance to " O   HOH Z  55 " =    2.045
peak=    3.339 closest distance to " CA  ARG A 156 " =    0.989
peak=    3.338 closest distance to " O   HOH Z 352 " =    1.371
peak=    3.336 closest distance to " CB  PRO A  90 " =    1.018
peak=    3.334 closest distance to " O   HOH Z 128 " =    1.921
peak=    3.332 closest distance to " O   HOH Z 222 " =    2.241
peak=    3.330 closest distance to " CA  ARG A 102 " =    1.191
peak=    3.330 closest distance to " CG AARG A 275 " =    1.136
peak=    3.326 closest distance to " CD  PRO A 243 " =    1.739
peak=    3.325 closest distance to " N   ARG A 156 " =    1.290
peak=    3.324 closest distance to " O   TYR A 116 " =    1.281
peak=    3.324 closest distance to " O   HOH Z  90 " =    2.065
peak=    3.321 closest distance to " CG2 VAL A 232 " =    0.748
peak=    3.321 closest distance to " CD1 ILE A 263 " =    1.341
peak=    3.321 closest distance to " O   HOH Z 365 " =    1.461
peak=    3.315 closest distance to " O   HOH Z 128 " =    2.736
peak=    3.314 closest distance to " O   HOH Z  26 " =    1.378
peak=    3.313 closest distance to " O   HOH Z 109 " =    2.255
peak=    3.313 closest distance to " CB  SER A  99 " =    0.858
peak=    3.312 closest distance to " O   HOH Z 414 " =    1.316
peak=    3.308 closest distance to " CB  PRO A 243 " =    1.164
peak=    3.305 closest distance to " N   SER A  97 " =    0.825
peak=    3.303 closest distance to " CB  LEU A 300 " =    0.896
peak=    3.301 closest distance to " O   HOH Z 345 " =    1.734
peak=    3.296 closest distance to " OG BSER A  99 " =    2.374
peak=    3.294 closest distance to " CB  SER A 273 " =    0.840
peak=    3.294 closest distance to " O   HOH Z 166 " =    1.511
peak=    3.288 closest distance to " O   HOH Z 180 " =    2.276
peak=    3.288 closest distance to " CB  ALA A 160 " =    1.496
peak=    3.286 closest distance to " O   HOH Z 391 " =    2.943
peak=    3.279 closest distance to " CB  ARG A 138 " =    0.822
peak=    3.278 closest distance to " CZ  PHE A  38 " =    1.225
peak=    3.275 closest distance to " O   HOH Z 337 " =    3.553
peak=    3.272 closest distance to " O   HOH Z 389 " =    1.753
peak=    3.270 closest distance to " CA  ALA A  84 " =    1.237
peak=    3.268 closest distance to " NZ  LYS A 117 " =    1.271
peak=    3.266 closest distance to " CE AMET A  47 " =    1.407
peak=    3.266 closest distance to " O   HOH Z 371 " =    3.066
peak=    3.253 closest distance to " O   HOH Z 128 " =    2.005
peak=    3.252 closest distance to " O   HOH Z   9 " =    1.806
peak=    3.248 closest distance to " O   PRO A  90 " =    1.745
peak=    3.248 closest distance to " CG1 ILE A 151 " =    0.992
peak=    3.247 closest distance to " O   HOH Z 207 " =    2.297
peak=    3.244 closest distance to " O   HOH Z 248 " =    1.612
peak=    3.243 closest distance to " O   HOH Z  66 " =    1.255
peak=    3.241 closest distance to " O   HOH Z 130 " =    3.486
peak=    3.239 closest distance to " CE3 TRP A 150 " =    1.107
peak=    3.238 closest distance to " N   CYS A 260 " =    0.820
peak=    3.231 closest distance to " O   HOH Z 218 " =    1.613
peak=    3.230 closest distance to " O   HOH Z 148 " =    3.424
peak=    3.221 closest distance to " OG BSER A 134 " =    3.051
peak=    3.221 closest distance to " O   HOH Z 181 " =    2.179
peak=    3.221 closest distance to " NE2 GLN A  58 " =    4.123
peak=    3.220 closest distance to " CZ3 TRP A 274 " =    1.320
peak=    3.215 closest distance to " O   HOH Z 126 " =    1.463
peak=    3.214 closest distance to " CB  ASN A 215 " =    1.047
peak=    3.213 closest distance to " O   HOH Z 393 " =    1.296
peak=    3.211 closest distance to " O   PHE A 192 " =    1.408
peak=    3.205 closest distance to " O   HOH Z  48 " =    1.606
peak=    3.198 closest distance to " CA  LEU A 101 " =    1.560
peak=    3.197 closest distance to " CB  ASP A 124 " =    0.888
peak=    3.197 closest distance to " CG2 ILE A  20 " =    1.627
peak=    3.196 closest distance to " OD1BASN A 224 " =    2.219
peak=    3.194 closest distance to " CD1AILE A 234 " =    0.901
peak=    3.192 closest distance to " O   HOH Z  93 " =    2.322
peak=    3.191 closest distance to " O   HOH Z 250 " =    1.449
peak=    3.187 closest distance to " CB  ALA A 291 " =    1.219
peak=    3.184 closest distance to " CA  ASN A 217 " =    1.174
peak=    3.183 closest distance to " O   HOH Z 119 " =    4.258
peak=    3.180 closest distance to " CG2 ILE A  20 " =    1.199
peak=    3.179 closest distance to " CB  ARG A 219 " =    0.878
peak=    3.176 closest distance to " O   HOH Z 151 " =    1.339
peak=    3.169 closest distance to " N   VAL A 296 " =    1.776
peak=    3.168 closest distance to " CB  TYR A 116 " =    0.913
peak=    3.165 closest distance to " CA  ALA A 129 " =    1.221
peak=    3.163 closest distance to " CA  THR A 264 " =    0.784
peak=    3.157 closest distance to " CD2 TYR A 186 " =    1.074
peak=    3.154 closest distance to " NH2BARG A 145 " =    1.874
peak=    3.154 closest distance to " CD  LYS A 166 " =    1.376
peak=    3.153 closest distance to " OE2 GLU A  53 " =    1.940
peak=    3.152 closest distance to " O   HOH Z  47 " =    1.747
peak=    3.151 closest distance to " CB  TYR A  30 " =    1.457
peak=    3.148 closest distance to " NE2 GLN A  73 " =    2.286
peak=    3.146 closest distance to " CG1 VAL A 153 " =    0.893
peak=    3.145 closest distance to " O   HOH Z 343 " =    3.184
peak=    3.144 closest distance to " CA  SER A  95 " =    1.058
peak=    3.144 closest distance to " CA  ALA A 158 " =    1.224
peak=    3.142 closest distance to " NE1 TRP A 274 " =    0.989
peak=    3.133 closest distance to " O   HOH Z   6 " =    1.967
peak=    3.126 closest distance to " N   ASN A  39 " =    1.168
peak=    3.124 closest distance to " O   HOH Z  40 " =    2.108
peak=    3.118 closest distance to " CA  ALA A 291 " =    0.812
peak=    3.113 closest distance to " O   HOH Z  90 " =    3.961
peak=    3.107 closest distance to " O   HOH Z 298 " =    2.466
peak=    3.106 closest distance to " CB  GLU A 152 " =    0.983
peak=    3.099 closest distance to " CA  ALA A 299 " =    0.927
peak=    3.097 closest distance to " N   TYR A  15 " =    1.118
peak=    3.094 closest distance to " CG  MET A 113 " =    1.043
peak=    3.090 closest distance to " O   HOH Z   3 " =    2.598
peak=    3.087 closest distance to " O   HOH Z 219 " =    2.291
peak=    3.084 closest distance to " CB  MET A 188 " =    1.700
peak=    3.083 closest distance to " O   HOH Z  47 " =    1.495
peak=    3.077 closest distance to " O   HOH Z 227 " =    2.067
peak=    3.072 closest distance to " CA  MET A 105 " =    0.883
peak=    3.066 closest distance to " O   HOH Z 260 " =    2.418
peak=    3.059 closest distance to " O   HOH Z 267 " =    1.941
peak=    3.055 closest distance to " O   HOH Z 173 " =    1.879
peak=    3.052 closest distance to " CB  PHE A 204 " =    0.709
peak=    3.051 closest distance to " O   HOH Z 154 " =    1.829
peak=    3.026 closest distance to " CB  ARG A  79 " =    0.861
peak=    3.023 closest distance to " OG BSER A 258 " =    0.822
peak=    3.021 closest distance to " ND1 HIS A  81 " =    1.600

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 195         
Filter by distance & map next to the model:
   mapped sites are within: 0.734 - 5.563
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 195 from: 195
   mapped sites are within: 0.734 - 5.563

peak=   -4.441 closest distance to " O   HOH Z 185 " =    2.044
peak=   -4.412 closest distance to " O   PRO A 198 " =    1.208
peak=   -4.334 closest distance to " CD  ARG A  14 " =    3.363
peak=   -4.321 closest distance to " CB  PRO A 243 " =    2.576
peak=   -4.295 closest distance to " O   HOH Z 385 " =    1.302
peak=   -4.267 closest distance to " CD  ARG A 156 " =    2.074
peak=   -4.265 closest distance to " CZ2 TRP A 274 " =    0.881
peak=   -4.136 closest distance to " CB  ALA A  43 " =    2.354
peak=   -4.111 closest distance to " O   HOH Z 377 " =    1.971
peak=   -4.083 closest distance to " OG BSER A 134 " =    1.294
peak=   -4.053 closest distance to " N   THR A 157 " =    1.509
peak=   -4.052 closest distance to " O   HOH Z  24 " =    1.122
peak=   -4.004 closest distance to " OD2 ASP A 191 " =    1.310
peak=   -3.948 closest distance to " CB  ALA A 248 " =    2.117
peak=   -3.943 closest distance to " CD1 LEU A 255 " =    2.848
peak=   -3.941 closest distance to " O   HOH Z  60 " =    1.644
peak=   -3.905 closest distance to " O   HOH Z 351 " =    1.538
peak=   -3.903 closest distance to " O   HOH Z  65 " =    1.067
peak=   -3.896 closest distance to " O   HOH Z 231 " =    1.994
peak=   -3.889 closest distance to " O   HOH Z 131 " =    4.002
peak=   -3.888 closest distance to " O   PRO A 243 " =    2.485
peak=   -3.870 closest distance to " CG  GLN A  58 " =    1.033
peak=   -3.869 closest distance to " O   VAL A  67 " =    2.631
peak=   -3.833 closest distance to " O   HOH Z 286 " =    1.604
peak=   -3.828 closest distance to " CZ  PHE A  59 " =    1.412
peak=   -3.824 closest distance to " CB  ALA A 291 " =    2.201
peak=   -3.812 closest distance to " O   SER A 135 " =    1.468
peak=   -3.788 closest distance to " CA  GLY A  98 " =    1.697
peak=   -3.784 closest distance to " CB  PHE A 192 " =    1.957
peak=   -3.765 closest distance to " O   ALA A  10 " =    1.632
peak=   -3.761 closest distance to " O   SER A  22 " =    2.546
peak=   -3.755 closest distance to " O   HOH Z 266 " =    5.006
peak=   -3.748 closest distance to " CD2 TYR A 293 " =    1.820
peak=   -3.718 closest distance to " O   HOH Z 372 " =    2.406
peak=   -3.715 closest distance to " CD2 LEU A 237 " =    2.844
peak=   -3.699 closest distance to " C   HIS A 108 " =    1.076
peak=   -3.692 closest distance to " O   HOH Z 298 " =    2.544
peak=   -3.686 closest distance to " CB  GLN A  55 " =    1.110
peak=   -3.682 closest distance to " CE BMET A  47 " =    1.093
peak=   -3.682 closest distance to " O   HOH Z  28 " =    1.524
peak=   -3.673 closest distance to " O   HOH Z 290 " =    1.018
peak=   -3.660 closest distance to " O   HOH Z 198 " =    1.576
peak=   -3.648 closest distance to " CB  ASN A  39 " =    2.323
peak=   -3.642 closest distance to " O   HOH Z 348 " =    2.103
peak=   -3.636 closest distance to " O   TYR A 186 " =    1.361
peak=   -3.631 closest distance to " CG1 VAL A 112 " =    3.071
peak=   -3.621 closest distance to " OG  SER A  97 " =    2.073
peak=   -3.616 closest distance to " CD1 LEU A 101 " =    2.228
peak=   -3.605 closest distance to " CA  GLY A 241 " =    2.196
peak=   -3.602 closest distance to " N   ALA A  43 " =    2.468
peak=   -3.590 closest distance to " CB  ASP A 132 " =    2.395
peak=   -3.590 closest distance to " O   GLU A 152 " =    1.346
peak=   -3.585 closest distance to " OG  SER A   3 " =    1.617
peak=   -3.583 closest distance to " CG  GLN A 223 " =    1.892
peak=   -3.569 closest distance to " CG2 THR A  18 " =    2.795
peak=   -3.561 closest distance to " O   HOH Z 276 " =    1.539
peak=   -3.561 closest distance to " CE2 TYR A  30 " =    2.744
peak=   -3.558 closest distance to " O   HOH Z 313 " =    1.652
peak=   -3.540 closest distance to " O   HOH Z 298 " =    1.081
peak=   -3.538 closest distance to " CG2 ILE A  20 " =    2.954
peak=   -3.529 closest distance to " CZ3 TRP A 179 " =    1.291
peak=   -3.529 closest distance to " O   ASP A 191 " =    1.888
peak=   -3.524 closest distance to " O   HOH Z  69 " =    2.014
peak=   -3.524 closest distance to " O   HOH Z 256 " =    1.332
peak=   -3.522 closest distance to " CE  MET A 105 " =    2.471
peak=   -3.518 closest distance to " O   PRO A 163 " =    1.236
peak=   -3.515 closest distance to " CD  GLN A  77 " =    1.299
peak=   -3.514 closest distance to " O   ILE A  49 " =    1.648
peak=   -3.514 closest distance to " CG  LEU A  83 " =    2.120
peak=   -3.508 closest distance to " CG2 ILE A  49 " =    2.766
peak=   -3.499 closest distance to " O   ALA A   1 " =    1.630
peak=   -3.487 closest distance to " O   HOH Z 415 " =    1.599
peak=   -3.483 closest distance to " OD1 ASN A 148 " =    1.464
peak=   -3.476 closest distance to " CA  GLY A 133 " =    1.983
peak=   -3.475 closest distance to " O   HOH Z 165 " =    2.353
peak=   -3.470 closest distance to " CG  ASN A  39 " =    1.618
peak=   -3.468 closest distance to " O   HOH Z 385 " =    0.804
peak=   -3.465 closest distance to " O   HOH Z 211 " =    1.384
peak=   -3.460 closest distance to " O   HOH Z  90 " =    2.513
peak=   -3.457 closest distance to " O   PHE A 218 " =    1.385
peak=   -3.456 closest distance to " CA  GLY A 203 " =    2.287
peak=   -3.453 closest distance to " N   GLN A  58 " =    1.302
peak=   -3.447 closest distance to " O   HOH Z  39 " =    1.189
peak=   -3.445 closest distance to " O   HOH Z  11 " =    1.721
peak=   -3.440 closest distance to " OG  SER A  87 " =    1.372
peak=   -3.433 closest distance to " CZ  TYR A 169 " =    1.747
peak=   -3.428 closest distance to " N   GLN A  58 " =    1.645
peak=   -3.426 closest distance to " O   HOH Z  49 " =    1.104
peak=   -3.425 closest distance to " ND2 ASN A 187 " =    1.467
peak=   -3.422 closest distance to " CE2 PHE A 218 " =    2.320
peak=   -3.417 closest distance to " CG  ASP A 231 " =    0.734
peak=   -3.416 closest distance to " O   ALA A 161 " =    1.579
peak=   -3.413 closest distance to " O   HOH Z 213 " =    1.517
peak=   -3.411 closest distance to " O   SER A  95 " =    1.454
peak=   -3.408 closest distance to " O   HOH Z 166 " =    1.929
peak=   -3.402 closest distance to " OE2 GLU A 152 " =    1.124
peak=   -3.402 closest distance to " O   ASP A 162 " =    2.006
peak=   -3.399 closest distance to " O   HOH Z   1 " =    1.414
peak=   -3.386 closest distance to " O   HOH Z 407 " =    2.866
peak=   -3.385 closest distance to " O   HOH Z 282 " =    4.753
peak=   -3.383 closest distance to " OD2 ASP A 171 " =    1.507
peak=   -3.380 closest distance to " O   HOH Z 196 " =    1.930
peak=   -3.378 closest distance to " C   GLU A 236 " =    0.877
peak=   -3.372 closest distance to " NE2 GLN A 278 " =    1.553
peak=   -3.365 closest distance to " O   HOH Z 389 " =    1.282
peak=   -3.364 closest distance to " ND2 ASN A 285 " =    2.061
peak=   -3.357 closest distance to " O   HOH Z 147 " =    1.153
peak=   -3.356 closest distance to " CB  TYR A  15 " =    2.199
peak=   -3.354 closest distance to " O   HOH Z 102 " =    1.541
peak=   -3.347 closest distance to " CG  MET A 105 " =    0.953
peak=   -3.347 closest distance to " O   ALA A 180 " =    1.174
peak=   -3.345 closest distance to " C   ALA A 114 " =    2.212
peak=   -3.337 closest distance to " N   ARG A 159 " =    1.848
peak=   -3.335 closest distance to " ND2 ASN A 249 " =    2.339
peak=   -3.333 closest distance to " OXT GLY A 302 " =    3.122
peak=   -3.321 closest distance to " O   HOH Z 263 " =    3.082
peak=   -3.319 closest distance to " N   MET A 188 " =    1.924
peak=   -3.310 closest distance to " N   GLN A 122 " =    1.280
peak=   -3.299 closest distance to " O   HOH Z 292 " =    1.554
peak=   -3.297 closest distance to " O   HOH Z 348 " =    1.793
peak=   -3.297 closest distance to " O   HOH Z 201 " =    1.955
peak=   -3.294 closest distance to " CB  ALA A 114 " =    2.530
peak=   -3.294 closest distance to " N   HIS A 207 " =    1.159
peak=   -3.289 closest distance to " CG1 VAL A 230 " =    1.976
peak=   -3.288 closest distance to " N   ASN A 127 " =    1.474
peak=   -3.287 closest distance to " OE1 GLN A 183 " =    1.582
peak=   -3.287 closest distance to " O   HOH Z  52 " =    1.337
peak=   -3.283 closest distance to " CE3 TRP A 274 " =    2.310
peak=   -3.280 closest distance to " O   PRO A 198 " =    1.295
peak=   -3.277 closest distance to " OG  SER A 245 " =    1.423
peak=   -3.273 closest distance to " O   HOH Z 250 " =    1.331
peak=   -3.268 closest distance to " O   HOH Z 389 " =    2.090
peak=   -3.268 closest distance to " CB  ASP A  27 " =    2.298
peak=   -3.262 closest distance to " O   HOH Z 384 " =    1.702
peak=   -3.262 closest distance to " O   HOH Z 166 " =    1.216
peak=   -3.259 closest distance to " CB  PRO A 213 " =    2.183
peak=   -3.259 closest distance to " O   GLN A 240 " =    1.860
peak=   -3.258 closest distance to " C   LEU A   5 " =    0.894
peak=   -3.252 closest distance to " O   HOH Z  37 " =    1.566
peak=   -3.251 closest distance to " O   HOH Z 191 " =    5.563
peak=   -3.249 closest distance to " O   VAL A 189 " =    2.551
peak=   -3.242 closest distance to " CD1 TYR A 169 " =    2.561
peak=   -3.240 closest distance to " CG1 VAL A 112 " =    2.572
peak=   -3.240 closest distance to " NZ  LYS A 119 " =    0.774
peak=   -3.239 closest distance to " CA  GLY A  57 " =    2.105
peak=   -3.238 closest distance to " CB  CYS A 201 " =    2.395
peak=   -3.238 closest distance to " OD1 ASN A 301 " =    1.686
peak=   -3.238 closest distance to " CD  GLU A 277 " =    1.284
peak=   -3.231 closest distance to " O   HOH Z 369 " =    2.256
peak=   -3.225 closest distance to " CZ3 TRP A 123 " =    1.534
peak=   -3.216 closest distance to " O   HOH Z 111 " =    2.319
peak=   -3.215 closest distance to " ND2BASN A 224 " =    1.777
peak=   -3.215 closest distance to " CA  ILE A 263 " =    0.903
peak=   -3.215 closest distance to " OE1 GLN A  88 " =    1.132
peak=   -3.215 closest distance to " O   HOH Z 317 " =    1.518
peak=   -3.210 closest distance to " CB  ASN A  45 " =    2.071
peak=   -3.205 closest distance to " CG  GLN A  88 " =    0.873
peak=   -3.204 closest distance to " O   ASN A 249 " =    1.638
peak=   -3.200 closest distance to " CG  PHE A 283 " =    2.594
peak=   -3.200 closest distance to " OD1 ASP A 171 " =    1.567
peak=   -3.199 closest distance to " N   VAL A 232 " =    2.041
peak=   -3.198 closest distance to " NH2 ARG A 219 " =    1.660
peak=   -3.195 closest distance to " CD2 PHE A  61 " =    2.325
peak=   -3.194 closest distance to " CE1 PHE A  59 " =    2.138
peak=   -3.187 closest distance to " CA  ASP A 298 " =    1.094
peak=   -3.187 closest distance to " O   HOH Z 288 " =    1.346
peak=   -3.186 closest distance to " C   LEU A 143 " =    1.052
peak=   -3.184 closest distance to " CB  ALA A 291 " =    2.258
peak=   -3.183 closest distance to " O   LEU A 101 " =    2.135
peak=   -3.181 closest distance to " OG BSER A 210 " =    2.308
peak=   -3.176 closest distance to " O   HOH Z 140 " =    1.381
peak=   -3.176 closest distance to " O   ARG A 145 " =    1.181
peak=   -3.169 closest distance to " CB  ASP A 132 " =    2.328
peak=   -3.166 closest distance to " CG2 THR A 178 " =    2.118
peak=   -3.162 closest distance to " OG1 THR A  82 " =    1.928
peak=   -3.161 closest distance to " ND2 ASN A  45 " =    2.056
peak=   -3.157 closest distance to " O   TRP A  70 " =    1.353
peak=   -3.155 closest distance to " N   ALA A 226 " =    2.037
peak=   -3.154 closest distance to " O   HOH Z 390 " =    2.464
peak=   -3.152 closest distance to " CG1 VAL A  78 " =    2.496
peak=   -3.152 closest distance to " CB  SER A 210 " =    1.079
peak=   -3.146 closest distance to " O   HOH Z 364 " =    2.346
peak=   -3.146 closest distance to " NE2 GLN A 223 " =    1.836
peak=   -3.143 closest distance to " O   HOH Z 134 " =    3.955
peak=   -3.143 closest distance to " O   HOH Z 231 " =    1.245
peak=   -3.141 closest distance to " O   HOH Z 359 " =    3.234
peak=   -3.134 closest distance to " O   HOH Z 414 " =    1.972
peak=   -3.134 closest distance to " O   HOH Z 317 " =    0.941
peak=   -3.131 closest distance to " OG  SER A  97 " =    1.652
peak=   -3.118 closest distance to " O   HOH Z 174 " =    2.707
peak=   -3.114 closest distance to " CB  GLN A  11 " =    1.802
peak=   -3.103 closest distance to " CZ  PHE A  38 " =    2.547
peak=   -3.100 closest distance to " OD1 ASP A 200 " =    1.360
peak=   -3.092 closest distance to " O   HOH Z 171 " =    1.606
peak=   -3.044 closest distance to " O   HOH Z 412 " =    3.616

================= 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    :  0.4209 0.4182   6.231463e+00   6.215060e+00
   1_bss:  0.4093 0.4080   6.221683e+00   6.199316e+00
   1_xyz:  0.2928 0.3308   5.962492e+00   6.035055e+00
   1_adp:  0.2655 0.3443   5.913680e+00   6.065279e+00
   1_occ:  0.2651 0.3453   5.914353e+00   6.066644e+00
   2_bss:  0.2641 0.3411   5.910573e+00   6.062238e+00
   2_xyz:  0.2106 0.2726   5.705559e+00   5.892505e+00
   2_adp:  0.1990 0.2552   5.655323e+00   5.838487e+00
   2_occ:  0.1989 0.2551   5.654296e+00   5.837686e+00
   3_bss:  0.1984 0.2542   5.651224e+00   5.835564e+00
   3_xyz:  0.1575 0.2050   5.435701e+00   5.636643e+00
   3_adp:  0.1459 0.1973   5.377894e+00   5.598492e+00
   3_occ:  0.1457 0.1970   5.376920e+00   5.597024e+00
   4_bss:  0.1459 0.1967   5.374234e+00   5.593351e+00
   4_xyz:  0.1246 0.1733   5.235266e+00   5.471307e+00
   4_adp:  0.1224 0.1663   5.207287e+00   5.431519e+00
   4_occ:  0.1222 0.1662   5.206850e+00   5.431090e+00
   5_bss:  0.1222 0.1662   5.206490e+00   5.430653e+00
   5_xyz:  0.1188 0.1611   5.180791e+00   5.403618e+00
   5_adp:  0.1168 0.1631   5.179105e+00   5.414851e+00
   5_occ:  0.1168 0.1631   5.178801e+00   5.414488e+00
   5_bss:  0.1170 0.1627   5.178567e+00   5.413312e+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:  0.338  31.679  -2.477   2.968   0.100   0.000   0.000   0.000
   1_xyz:  0.338  31.679  -2.477   2.968   0.100   0.000   0.000   0.000
   1_adp:  0.338  31.679  -2.477   2.968   0.100   0.000   0.000   0.000
   1_occ:  0.338  31.679  -2.477   2.968   0.100   0.000   0.000   0.000
   2_bss:  0.342  57.169  -2.345   0.016  -0.264   0.000  -0.000  -0.000
   2_xyz:  0.342  57.169  -2.345   0.016  -0.264   0.000  -0.000  -0.000
   2_adp:  0.342  57.169  -2.345   0.016  -0.264   0.000  -0.000  -0.000
   2_occ:  0.342  57.169  -2.345   0.016  -0.264   0.000  -0.000  -0.000
   3_bss:  0.332  53.065  -2.639  -1.233  -0.427  -0.000  -0.000  -0.000
   3_xyz:  0.332  53.065  -2.639  -1.233  -0.427  -0.000  -0.000  -0.000
   3_adp:  0.332  53.065  -2.639  -1.233  -0.427  -0.000  -0.000  -0.000
   3_occ:  0.332  53.065  -2.639  -1.233  -0.427  -0.000  -0.000  -0.000
   4_bss:  0.322  53.065  -2.586  -2.032  -0.595  -0.000  -0.000  -0.000
   4_xyz:  0.322  53.065  -2.586  -2.032  -0.595  -0.000  -0.000  -0.000
   4_adp:  0.322  53.065  -2.586  -2.032  -0.595  -0.000  -0.000  -0.000
   4_occ:  0.322  53.065  -2.586  -2.032  -0.595  -0.000  -0.000  -0.000
   5_bss:  0.318  48.026  -2.620  -2.280  -0.623  -0.000  -0.000  -0.000
   5_xyz:  0.318  48.026  -2.620  -2.280  -0.623  -0.000  -0.000  -0.000
   5_adp:  0.318  48.026  -2.620  -2.280  -0.623  -0.000  -0.000  -0.000
   5_occ:  0.318  48.026  -2.620  -2.280  -0.623  -0.000  -0.000  -0.000
   5_bss:  0.317  51.157  -2.528  -2.322  -0.574  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  48.511 0.5400  0.7205    54344.275
   1_bss:  47.504 0.5507  0.7407    51192.884
   1_xyz:  34.011 0.7136  0.9237    29447.244
   1_adp:  35.874 0.6912  0.9021    32409.073
   1_occ:  36.035 0.6893  0.8990    32589.438
   2_bss:  35.522 0.6950  0.8746    31784.306
   2_xyz:  27.342 0.7859  0.9593    19415.178
   2_adp:  25.037 0.8113  0.9722    16919.711
   2_occ:  24.995 0.8117  0.9723    16859.425
   3_bss:  24.842 0.8130  0.9535    16646.738
   3_xyz:  19.764 0.8634  0.9856    10745.602
   3_adp:  18.741 0.8735  0.9820     9933.286
   3_occ:  18.700 0.8738  0.9819     9887.703
   4_bss:  18.579 0.8748  0.9722     9771.320
   4_xyz:  15.846 0.8992  0.9858     7502.568
   4_adp:  14.910 0.9075  0.9858     7005.017
   4_occ:  14.903 0.9075  0.9857     6991.597
   5_bss:  14.898 0.9076  0.9819     6986.874
   5_xyz:  14.262 0.9130  0.9845     6583.920
   5_adp:  14.455 0.9116  0.9787     6694.503
   5_occ:  14.446 0.9117  0.9787     6687.843
   5_bss:  14.422 0.9118  0.9805     6666.086
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.108   1.7674e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.108   1.7674e-01
   1_xyz:   1.490  0.011  0.098 15.775  0.007  4.108   1.2071e-01
   1_adp:   1.490  0.011  0.098 15.775  0.007  4.108   1.2071e-01
   1_occ:   1.490  0.011  0.098 15.775  0.007  4.108   1.2071e-01
   2_bss:   1.490  0.011  0.098 15.775  0.007  4.108   1.2071e-01
   2_xyz:   1.002  0.007  0.071 14.553  0.004  4.107   5.8795e-02
   2_adp:   1.002  0.007  0.071 14.553  0.004  4.107   5.8795e-02
   2_occ:   1.002  0.007  0.071 14.553  0.004  4.107   5.8795e-02
   3_bss:   1.002  0.007  0.071 14.553  0.004  4.107   5.8795e-02
   3_xyz:   0.912  0.005  0.065 14.496  0.003  4.110   5.0379e-02
   3_adp:   0.912  0.005  0.065 14.496  0.003  4.110   5.0379e-02
   3_occ:   0.912  0.005  0.065 14.496  0.003  4.110   5.0379e-02
   4_bss:   0.912  0.005  0.065 14.496  0.003  4.110   5.0379e-02
   4_xyz:   0.952  0.006  0.069 14.606  0.004  4.108   5.4820e-02
   4_adp:   0.952  0.006  0.069 14.606  0.004  4.108   5.4820e-02
   4_occ:   0.952  0.006  0.069 14.606  0.004  4.108   5.4820e-02
   5_bss:   0.952  0.006  0.069 14.606  0.004  4.108   5.4820e-02
   5_xyz:   0.850  0.005  0.065 14.285  0.003  4.110   4.6290e-02
   5_adp:   0.850  0.005  0.065 14.285  0.003  4.110   4.6290e-02
   5_occ:   0.850  0.005  0.065 14.285  0.003  4.110   4.6290e-02
   5_bss:   0.850  0.005  0.065 14.285  0.003  4.110   4.6290e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.615   2.3936e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.615   2.3936e-01
   1_xyz:   9.560  0.070  0.324 84.843  0.065  2.020   1.0960e-01
   1_adp:   9.560  0.070  0.324 84.843  0.065  2.020   1.0960e-01
   1_occ:   9.560  0.070  0.324 84.843  0.065  2.020   1.0960e-01
   2_bss:   9.560  0.070  0.324 84.843  0.065  2.020   1.0960e-01
   2_xyz:   6.841  0.033  0.221 80.693  0.031  2.299   6.0994e-02
   2_adp:   6.841  0.033  0.221 80.693  0.031  2.299   6.0994e-02
   2_occ:   6.841  0.033  0.221 80.693  0.031  2.299   6.0994e-02
   3_bss:   6.841  0.033  0.221 80.693  0.031  2.299   6.0994e-02
   3_xyz:   6.179  0.040  0.180 82.110  0.033  2.344   4.6340e-02
   3_adp:   6.179  0.040  0.180 82.110  0.033  2.344   4.6340e-02
   3_occ:   6.179  0.040  0.180 82.110  0.033  2.344   4.6340e-02
   4_bss:   6.179  0.040  0.180 82.110  0.033  2.344   4.6340e-02
   4_xyz:   6.838  0.041  0.208 81.952  0.033  2.296   4.6188e-02
   4_adp:   6.838  0.041  0.208 81.952  0.033  2.296   4.6188e-02
   4_occ:   6.838  0.041  0.208 81.952  0.033  2.296   4.6188e-02
   5_bss:   6.838  0.041  0.208 81.952  0.033  2.296   4.6188e-02
   5_xyz:   6.464  0.040  0.199 83.260  0.033  2.365   2.8953e-02
   5_adp:   6.464  0.040  0.199 83.260  0.033  2.365   2.8953e-02
   5_occ:   6.464  0.040  0.199 83.260  0.033  2.365   2.8953e-02
   5_bss:   6.464  0.040  0.199 83.260  0.033  2.365   2.8953e-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:  94.78   0.00  17.98  66.26   0.00  14.15  94.78   2.25  38.85
   1_occ:  94.78   0.00  17.98  66.26   0.00  14.15  94.78   2.25  38.85
   2_bss:  94.78   0.00  17.98  66.26   0.00  14.15  94.78   2.25  38.85
   2_xyz:  94.78   0.00  17.98  66.26   0.00  14.15  94.78   2.25  38.85
   2_adp:  92.70   0.00  17.44  72.06   0.00  13.51  92.70   4.56  38.82
   2_occ:  92.70   0.00  17.44  72.06   0.00  13.51  92.70   4.56  38.82
   3_bss:  92.70   0.00  17.44  72.06   0.00  13.51  92.70   4.56  38.82
   3_xyz:  92.70   0.00  17.44  72.06   0.00  13.51  92.70   4.56  38.82
   3_adp:  94.28   0.00  17.73  85.58   0.00  13.06  94.28   6.20  43.16
   3_occ:  94.28   0.00  17.73  85.58   0.00  13.06  94.28   6.20  43.16
   4_bss:  94.28   0.00  17.73  85.58   0.00  13.06  94.28   6.20  43.16
   4_xyz:  94.28   0.00  17.73  85.58   0.00  13.06  94.28   6.20  43.16
   4_adp:  90.36   1.36  17.02  85.91   1.36  12.70  90.36   4.84  40.57
   4_occ:  90.36   1.36  17.02  85.91   1.36  12.70  90.36   4.84  40.57
   5_bss:  90.36   1.36  17.02  85.91   1.36  12.70  90.36   4.84  40.57
   5_xyz:  90.36   1.36  17.02  85.91   1.36  12.70  90.36   4.84  40.57
   5_adp:  92.70   0.00  17.28  92.68   0.00  12.70  92.70   5.52  42.25
   5_occ:  92.70   0.00  17.28  92.68   0.00  12.70  92.70   5.52  42.25
   5_bss:  92.71   0.00  17.29  92.69   0.00  12.70  92.71   5.52  42.25
------------------------------------------------------------------------
 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:    1.752    0.023    0.403
   1_adp:    1.752    0.023    0.403
   1_occ:    1.752    0.023    0.403
   2_bss:    1.752    0.023    0.403
   2_xyz:    1.637    0.037    0.483
   2_adp:    1.637    0.037    0.483
   2_occ:    1.637    0.037    0.483
   3_bss:    1.637    0.037    0.483
   3_xyz:    1.544    0.037    0.603
   3_adp:    1.544    0.037    0.603
   3_occ:    1.544    0.037    0.603
   4_bss:    1.544    0.037    0.603
   4_xyz:    1.317    0.019    0.647
   4_adp:    1.317    0.019    0.647
   4_occ:    1.317    0.019    0.647
   5_bss:    1.317    0.019    0.647
   5_xyz:    1.456    0.036    0.663
   5_adp:    1.456    0.036    0.663
   5_occ:    1.456    0.036    0.663
   5_bss:    1.456    0.036    0.663
------------------------------------------------------------------------

CPU time actual refinement: 338.56


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_381/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_381/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_381/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_381/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_381/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 338.40 
  Macro-tasks:
    bulk solvent and scale       = 39.70  
    individual site refinement   = 139.98 
    weights calculation          = 30.34  
    collect and process          = 6.78   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 216.90 
  Micro-tasks:
    mask                            = 2.36   
    f_calc                          = 107.05 
    alpha_beta                      = 8.53   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 116.10 
    fmodel                         = 6.69   
    r_factors                      = 0.28   
    phase_errors                   = 10.82  
    foms                           = 0.26   
    TOTAL for micro-tasks          = 253.27 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.770 micro seconds
Total CPU time: 5.86 minutes
from_scatterers_fft:    657 calls, 106.70 s
gradients_fft:          602 calls, 102.44 s

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

# Date 2008-01-16 Time 04:41:59 PST -0800 (1200487319.56 s)
Start R-work = 0.4209, R-free = 0.4182 (no bulk solvent and anisotropic scale)
Final R-work = 0.1396, R-free = 0.1811 (no bulk solvent and anisotropic scale)

Start R-work = 0.4093, R-free = 0.4080
Final R-work = 0.1170, R-free = 0.1627