# Date 2008-01-16 Time 06:23:58 PST -0800 (1200493438.07 s)
#phil __OFF__

Command line arguments: "../1129.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 14886
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1129

-------------------------------------------------------------------------------
  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: (71.655, 46.4607, 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: 3.29, per 1000 atoms: 1.17


================================== 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: (71.655, 46.4607, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2528 1.98349
Completeness in resolution range: 0.944094
Completeness with d_max=infinity: 0.941372

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2528
                             d_min =   1.9835

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: (71.655, 46.4607, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2528 1.98349
Completeness in resolution range: 0.944094
Completeness with d_max=infinity: 0.941372

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2532 -  4.2455 [2184/2211]  1964   220  10.1%
  bin  2:  4.2455 -  3.3818 [2096/2116]  1889   207   9.9%
  bin  3:  3.3818 -  2.9579 [2069/2088]  1860   209  10.1%
  bin  4:  2.9579 -  2.6891 [2049/2079]  1843   206  10.1%
  bin  5:  2.6891 -  2.4972 [2033/2052]  1838   195   9.6%
  bin  6:  2.4972 -  2.3505 [2024/2049]  1812   212  10.5%
  bin  7:  2.3505 -  2.2332 [2014/2042]  1816   198   9.8%
  bin  8:  2.2332 -  2.1363 [2001/2037]  1800   201  10.0%
  bin  9:  2.1363 -  2.0542 [2010/2052]  1814   196   9.8%
  bin 10:  2.0542 -  1.9835 [1109/2023]   994   115  10.4%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1129/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 17
        2.42 -     3.04: 2168
        3.04 -     3.66: 4660
        3.66 -     4.28: 8955
        4.28 -     4.90: 12251
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 208 " - " O   HOH Z 342 "  2.198 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z 341 " - " O   HOH Z 207 "  2.241 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.241 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28046 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_1129/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1129/model_refine_001.geo

CPU time processing inputs: 9.67


============================ 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 = 71.655 46.4607 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: 1.98 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3934   r_free= 0.3860   ksol= 0.00   Bsol= 0.00   scale= 0.931    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.176649                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2532 -  4.7358 0.99   1414  158 0.3166 0.2947      6.4272      6.3415|
|  2:  4.7358 -  3.7777 0.99   1357  152 0.3214 0.2991      6.6415      6.5704|
|  3:  3.7777 -  3.3057 0.99   1345  143 0.3410 0.3309      6.4773      6.4874|
|  4:  3.3057 -  3.0060 0.99   1330  155 0.3750 0.3968      6.3782      6.4036|
|  5:  3.0060 -  2.7920 0.99   1322  149 0.4187 0.3786      6.2502      6.2481|
|  6:  2.7920 -  2.6282 0.99   1306  143 0.3959 0.4181      6.1432      6.1246|
|  7:  2.6282 -  2.4972 0.99   1320  137 0.4377 0.4098      6.1629      6.1225|
|  8:  2.4972 -  2.3889 0.98   1290  148 0.4454 0.4262      6.0958      6.0895|
|  9:  2.3889 -  2.2973 0.98   1282  152 0.4456 0.4520      6.0457      6.0517|
| 10:  2.2973 -  2.2183 1.00   1315  141 0.4537 0.4484      6.0329      5.9979|
| 11:  2.2183 -  2.1491 0.98   1294  136 0.4580 0.4674      5.9931      6.0002|
| 12:  2.1491 -  2.0878 0.98   1283  147 0.4571 0.4724      5.8973      5.9547|
| 13:  2.0878 -  2.0330 0.98   1272  139 0.4667 0.4532      5.8203       5.755|
| 14:  2.0330 -  1.9835 0.38    500   59 0.4609 0.4731      5.8116      5.8031|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2532 -  4.7358  1414   158  0.79  26.39   0.84     0.82      44254.19|
|  2:  4.7358 -  3.7777  1357   152  0.82  24.67   0.94     0.89      57784.81|
|  3:  3.7777 -  3.3057  1345   143  0.74  31.75   0.96     0.90      64346.31|
|  4:  3.3057 -  3.0060  1330   155  0.69  36.70   0.95     0.85      60360.21|
|  5:  3.0060 -  2.7920  1322   149  0.60  44.03   0.94     0.80      52284.52|
|  6:  2.7920 -  2.6282  1306   143  0.60  44.40   0.95     0.78      44547.28|
|  7:  2.6282 -  2.4972  1320   137  0.58  45.54   0.95     0.75      41897.60|
|  8:  2.4972 -  2.3889  1290   148  0.57  46.82   0.94     0.75      38421.28|
|  9:  2.3889 -  2.2973  1282   152  0.55  48.10   0.97     0.75      36873.40|
| 10:  2.2973 -  2.2183  1315   141  0.54  49.09   0.98     0.74      34466.75|
| 11:  2.2183 -  2.1491  1294   136  0.51  51.36   0.98     0.73      35080.44|
| 12:  2.1491 -  2.0878  1283   147  0.49  53.03   0.97     0.70      31985.08|
| 13:  2.0878 -  2.0330  1272   139  0.48  54.02   0.95     0.72      28101.05|
| 14:  2.0330 -  1.9835   500    59  0.55  48.54   1.00     0.74      21628.44|
|alpha:            min =        0.70 max =            0.90 mean =         0.78|
|beta:             min =    21628.44 max =        64346.31 mean =     43424.09|
|figures of merit: min =        0.00 max =            1.00 mean =         0.61|
|phase err.(work): min =        0.00 max =           89.95 mean =        42.69|
|phase err.(test): min =        0.00 max =           89.91 mean =        42.34|
|-----------------------------------------------------------------------------|

============================== 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 = 7.273731              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.803   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.250374              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.333   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        1 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       16 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      192 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1976 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1847 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2813 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4606 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4349 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5595 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6656 |
|-----------------------------------------------------------------------------|
|-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 |        0.162 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.112    4.900  1.806 |       0.158 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.128)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.98 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3934   r_free= 0.3860   ksol= 0.00   Bsol= 0.00   scale= 0.931    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.176649                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3840   r_free= 0.3785   ksol= 0.34   Bsol= 68.30   scale= 0.959   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.14,-0.98,-0.12,-0.00,-0.00,-0.00); trace/3= 0.02                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.165541                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.314630              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.979   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.631032              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.059   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3840      final r-factor (work) = 0.2168          |
| start r-factor (free) = 0.3785      final r-factor (free) = 0.2456          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.6230 = 6.31 * 0.50 * 6.1637 + 1.00 * 0.1622                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.7653 = 6.31 * 0.50 * 5.9160 + 1.00 * 0.0866                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2168      final r-factor (work) = 0.1963          |
| start r-factor (free) = 0.2456      final r-factor (free) = 0.2551          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7394 = 0.63 * 1.00 * 5.9160 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5568 = 0.63 * 1.00 * 5.6176 + 1.00 * 0.0119                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.128)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.72   17.88    None  None   None       |
|    all(noH): 2823   0      0.00    89.72   17.88    None  None   None       |
|    Sol.    : 438    0      2.22    89.72   42.47    None  None   None       |
|    Mac.    : 2385   0      0.00    71.90   13.36    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.972:  755   |   5:    44.858 -  53.829:   94        |
|      1:     8.972 -  17.943: 1234   |   6:    53.829 -  62.801:   90        |
|      2:    17.943 -  26.915:  346   |   7:    62.801 -  71.772:   35        |
|      3:    26.915 -  35.886:  140   |   8:    71.772 -  80.744:   17        |
|      4:    35.886 -  44.858:  110   |   9:    80.744 -  89.715:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1963 r_free = 0.2551             target_work(ml) = 5.632         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1959 r_free = 0.2546             target_work(ml) = 5.631         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1959   r_free= 0.2546   ksol= 0.34   Bsol= 68.30   scale= 1.034   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.14,-0.98,-0.12,-0.00,-0.00,-0.00); trace/3= 0.02                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.630943                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1944   r_free= 0.2532   ksol= 0.34   Bsol= 75.43   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.31,-2.44,-1.07,-0.00,-0.00,-0.00); trace/3= -1.61                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.630609                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.085981              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.417   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.242080              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.210  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1944      final r-factor (work) = 0.1508          |
| start r-factor (free) = 0.2532      final r-factor (free) = 0.1988          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9633 = 2.09 * 0.50 * 5.6345 + 1.00 * 0.0866                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8179 = 2.09 * 0.50 * 5.5276 + 1.00 * 0.0526                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1508      final r-factor (work) = 0.1437          |
| start r-factor (free) = 0.1988      final r-factor (free) = 0.1883          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3500 = 0.24 * 1.00 * 5.5276 + 1.00 * 0.0119                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3738 = 0.24 * 1.00 * 5.3823 + 1.00 * 0.0708                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.128)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.55   17.68    None  None   None       |
|    all(noH): 2823   0      0.00    88.55   17.68    None  None   None       |
|    Sol.    : 438    0      5.53    88.55   41.88    None  None   None       |
|    Mac.    : 2385   0      0.00    72.00   13.24    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.856:  725   |   5:    44.277 -  53.133:   94        |
|      1:     8.856 -  17.711: 1284   |   6:    53.133 -  61.988:   90        |
|      2:    17.711 -  26.566:  321   |   7:    61.988 -  70.844:   37        |
|      3:    26.566 -  35.422:  141   |   8:    70.844 -  79.699:   14        |
|      4:    35.422 -  44.277:  114   |   9:    79.699 -  88.555:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1437 r_free = 0.1883             target_work(ml) = 5.355         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1435 r_free = 0.1884             target_work(ml) = 5.355         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1435   r_free= 0.1884   ksol= 0.34   Bsol= 75.43   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.31,-2.44,-1.07,-0.00,-0.00,-0.00); trace/3= -1.61                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.354517                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1435   r_free= 0.1882   ksol= 0.33   Bsol= 66.83   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.82,-2.57,-0.91,-0.00,-0.00,-0.00); trace/3= -1.77                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.353521                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.683308              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 109.010  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.329855              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.812   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1435      final r-factor (work) = 0.1204          |
| start r-factor (free) = 0.1882      final r-factor (free) = 0.1673          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.9629 = 3.68 * 0.50 * 5.3812 + 1.00 * 0.0526                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.7931 = 3.68 * 0.50 * 5.2781 + 1.00 * 0.0727                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1204      final r-factor (work) = 0.1154          |
| start r-factor (free) = 0.1673      final r-factor (free) = 0.1637          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 17.5872 = 3.33 * 1.00 * 5.2781 + 1.00 * 0.0119                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 17.2959 = 3.33 * 1.00 * 5.1909 + 1.00 * 0.0110                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.128)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.93   17.99    None  None   None       |
|    all(noH): 2823   0      0.00    95.93   17.99    None  None   None       |
|    Sol.    : 438    0      5.86    95.93   43.62    None  None   None       |
|    Mac.    : 2385   0      0.00    86.16   13.28    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 -   9.593:  904   |   5:    47.963 -  57.555:   86        |
|      1:     9.593 -  19.185: 1209   |   6:    57.555 -  67.148:   76        |
|      2:    19.185 -  28.778:  248   |   7:    67.148 -  76.741:   34        |
|      3:    28.778 -  38.370:  136   |   8:    76.741 -  86.333:   17        |
|      4:    38.370 -  47.963:  107   |   9:    86.333 -  95.926:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1154 r_free = 0.1637             target_work(ml) = 5.178         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1154 r_free = 0.1638             target_work(ml) = 5.178         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1154   r_free= 0.1638   ksol= 0.33   Bsol= 66.83   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.82,-2.57,-0.91,-0.00,-0.00,-0.00); trace/3= -1.77                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.178327                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1158   r_free= 0.1635   ksol= 0.33   Bsol= 66.83   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.14,-2.74,-1.14,-0.00,-0.00,-0.00); trace/3= -2.01                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.178548                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.597228              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 140.657  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.148744              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 119.805  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1158      final r-factor (work) = 0.1171          |
| start r-factor (free) = 0.1635      final r-factor (free) = 0.1640          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.2195 = 1.60 * 0.50 * 5.1925 + 1.00 * 0.0727                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.1950 = 1.60 * 0.50 * 5.1848 + 1.00 * 0.0543                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1171      final r-factor (work) = 0.1179          |
| start r-factor (free) = 0.1640      final r-factor (free) = 0.1609          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7822 = 0.15 * 1.00 * 5.1848 + 1.00 * 0.0110                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7813 = 0.15 * 1.00 * 5.1936 + 1.00 * 0.0088                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 35     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.128)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.98    93.78   17.58    None  None   None       |
|    all(noH): 2823   0      0.98    93.78   17.58    None  None   None       |
|    Sol.    : 438    0      6.04    93.78   41.87    None  None   None       |
|    Mac.    : 2385   0      0.98    85.11   13.12    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:     0.983 -  10.263: 1061   |   5:    47.380 -  56.659:   87        |
|      1:    10.263 -  19.542: 1105   |   6:    56.659 -  65.939:   70        |
|      2:    19.542 -  28.821:  225   |   7:    65.939 -  75.218:   30        |
|      3:    28.821 -  38.101:  123   |   8:    75.218 -  84.497:   16        |
|      4:    38.101 -  47.380:  100   |   9:    84.497 -  93.777:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1179 r_free = 0.1609             target_work(ml) = 5.183         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1178 r_free = 0.1607             target_work(ml) = 5.183         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1178   r_free= 0.1607   ksol= 0.33   Bsol= 66.83   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.14,-2.74,-1.14,-0.00,-0.00,-0.00); trace/3= -2.01                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.182857                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1178   r_free= 0.1608   ksol= 0.32   Bsol= 61.36   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.27,-2.79,-1.18,-0.00,-0.00,-0.00); trace/3= -2.08                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.182714                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.077014              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 156.836  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.900600              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 124.592  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1178      final r-factor (work) = 0.1136          |
| start r-factor (free) = 0.1608      final r-factor (free) = 0.1585          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4473 = 2.08 * 0.50 * 5.1931 + 1.00 * 0.0543                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4283 = 2.08 * 0.50 * 5.1656 + 1.00 * 0.0638                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1136      final r-factor (work) = 0.1126          |
| start r-factor (free) = 0.1585      final r-factor (free) = 0.1604          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 20.1576 = 3.90 * 1.00 * 5.1656 + 1.00 * 0.0087                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 20.1068 = 3.90 * 1.00 * 5.1521 + 1.00 * 0.0105                              |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 18     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.128)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.11   17.63    None  None   None       |
|    all(noH): 2823   0      0.00    98.11   17.63    None  None   None       |
|    Sol.    : 438    0      5.76    98.11   42.30    None  None   None       |
|    Mac.    : 2385   0      0.00    89.47   13.10    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 -   9.811: 1002   |   5:    49.053 -  58.864:   89        |
|      1:     9.811 -  19.621: 1142   |   6:    58.864 -  68.674:   56        |
|      2:    19.621 -  29.432:  227   |   7:    68.674 -  78.485:   32        |
|      3:    29.432 -  39.243:  154   |   8:    78.485 -  88.296:   10        |
|      4:    39.243 -  49.053:  106   |   9:    88.296 -  98.106:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1126 r_free = 0.1604             target_work(ml) = 5.160         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1125 r_free = 0.1604             target_work(ml) = 5.160         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1125   r_free= 0.1604   ksol= 0.32   Bsol= 61.36   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.27,-2.79,-1.18,-0.00,-0.00,-0.00); trace/3= -2.08                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.159557                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2532 -  4.7358 0.99   1414  158 0.0955 0.1295      5.3575      5.5486|
|  2:  4.7358 -  3.7777 0.99   1357  152 0.0841 0.1044      5.4273      5.5947|
|  3:  3.7777 -  3.3057 0.99   1345  143 0.1069 0.1580      5.4793      5.8583|
|  4:  3.3057 -  3.0060 0.99   1330  155 0.1233 0.1727      5.4685      5.6406|
|  5:  3.0060 -  2.7920 0.99   1322  149 0.1363 0.1764      5.3342      5.5832|
|  6:  2.7920 -  2.6282 0.99   1306  143 0.1238 0.1940      5.2166      5.4837|
|  7:  2.6282 -  2.4972 0.99   1320  137 0.1275 0.1580      5.1846      5.3185|
|  8:  2.4972 -  2.3889 0.98   1290  148 0.1176 0.1731      5.0751      5.3576|
|  9:  2.3889 -  2.2973 0.98   1282  152 0.1208 0.1874      5.0591      5.3315|
| 10:  2.2973 -  2.2183 1.00   1315  141 0.1119 0.1706      4.9484      5.1976|
| 11:  2.2183 -  2.1491 0.98   1294  136 0.1124 0.1856      4.9537      5.3461|
| 12:  2.1491 -  2.0878 0.98   1283  147 0.1132 0.1716      4.8762       5.135|
| 13:  2.0878 -  2.0330 0.98   1272  139 0.1145 0.1687      4.8043       5.027|
| 14:  2.0330 -  1.9835 0.38    500   59 0.1047 0.1686      4.7089      4.9395|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2532 -  4.7358  1414   158  0.94   8.92   0.97     0.94       6865.96|
|  2:  4.7358 -  3.7777  1357   152  0.95   7.81   1.00     0.99       8936.16|
|  3:  3.7777 -  3.3057  1345   143  0.93  11.26   1.02     1.02      10347.50|
|  4:  3.3057 -  3.0060  1330   155  0.91  14.28   1.00     0.98      10770.77|
|  5:  3.0060 -  2.7920  1322   149  0.90  16.21   0.99     0.97       8501.21|
|  6:  2.7920 -  2.6282  1306   143  0.89  16.55   0.98     0.96       7288.69|
|  7:  2.6282 -  2.4972  1320   137  0.90  15.66   0.99     0.96       6466.77|
|  8:  2.4972 -  2.3889  1290   148  0.90  15.81   0.98     0.95       5471.12|
|  9:  2.3889 -  2.2973  1282   152  0.90  15.92   0.99     0.94       5183.90|
| 10:  2.2973 -  2.2183  1315   141  0.90  15.85   0.99     0.96       4396.46|
| 11:  2.2183 -  2.1491  1294   136  0.90  15.83   0.97     0.92       4360.62|
| 12:  2.1491 -  2.0878  1283   147  0.91  15.87   0.99     0.99       4034.22|
| 13:  2.0878 -  2.0330  1272   139  0.89  17.12   0.97     0.95       3582.61|
| 14:  2.0330 -  1.9835   500    59  0.91  15.28   0.95     0.92       2885.55|
|alpha:            min =        0.92 max =            1.02 mean =         0.96|
|beta:             min =     2885.55 max =        10770.77 mean =      6561.22|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.87 mean =        14.35|
|phase err.(test): min =        0.00 max =           89.33 mean =        13.87|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1124   r_free= 0.1604   ksol= 0.32   Bsol= 61.36   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.11,-2.64,-1.04,-0.00,-0.00,-0.00); trace/3= -1.93                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.159574                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1124   r_free= 0.1604   ksol= 0.32   Bsol= 61.36   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.11,-2.64,-1.04,-0.00,-0.00,-0.00); trace/3= -1.93                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.159574                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2532 -  4.7358 0.99   1414  158 0.0954 0.1295      5.3573      5.5501|
|  2:  4.7358 -  3.7777 0.99   1357  152 0.0841 0.1044      5.4279      5.5951|
|  3:  3.7777 -  3.3057 0.99   1345  143 0.1069 0.1580      5.4794      5.8586|
|  4:  3.3057 -  3.0060 0.99   1330  155 0.1233 0.1727      5.4685      5.6405|
|  5:  3.0060 -  2.7920 0.99   1322  149 0.1363 0.1763       5.334      5.5828|
|  6:  2.7920 -  2.6282 0.99   1306  143 0.1237 0.1941      5.2165      5.4839|
|  7:  2.6282 -  2.4972 0.99   1320  137 0.1275 0.1580      5.1846      5.3185|
|  8:  2.4972 -  2.3889 0.98   1290  148 0.1176 0.1731      5.0752      5.3574|
|  9:  2.3889 -  2.2973 0.98   1282  152 0.1208 0.1874      5.0592      5.3318|
| 10:  2.2973 -  2.2183 1.00   1315  141 0.1119 0.1706      4.9484       5.197|
| 11:  2.2183 -  2.1491 0.98   1294  136 0.1124 0.1855      4.9538      5.3462|
| 12:  2.1491 -  2.0878 0.98   1283  147 0.1132 0.1716      4.8759      5.1348|
| 13:  2.0878 -  2.0330 0.98   1272  139 0.1145 0.1687      4.8042      5.0268|
| 14:  2.0330 -  1.9835 0.38    500   59 0.1047 0.1686      4.7091      4.9396|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2532 -  4.7358  1414   158  0.94   8.92   0.97     0.94       6871.15|
|  2:  4.7358 -  3.7777  1357   152  0.95   7.82   1.00     1.00       8945.11|
|  3:  3.7777 -  3.3057  1345   143  0.93  11.27   1.02     1.02      10351.87|
|  4:  3.3057 -  3.0060  1330   155  0.91  14.28   1.01     0.98      10769.92|
|  5:  3.0060 -  2.7920  1322   149  0.90  16.21   1.00     0.98       8499.79|
|  6:  2.7920 -  2.6282  1306   143  0.89  16.55   0.99     0.97       7287.72|
|  7:  2.6282 -  2.4972  1320   137  0.90  15.66   0.99     0.97       6467.60|
|  8:  2.4972 -  2.3889  1290   148  0.90  15.81   0.98     0.96       5471.15|
|  9:  2.3889 -  2.2973  1282   152  0.90  15.93   0.99     0.95       5184.35|
| 10:  2.2973 -  2.2183  1315   141  0.90  15.86   0.99     0.96       4395.85|
| 11:  2.2183 -  2.1491  1294   136  0.90  15.83   0.98     0.93       4359.32|
| 12:  2.1491 -  2.0878  1283   147  0.91  15.87   1.00     1.00       4032.32|
| 13:  2.0878 -  2.0330  1272   139  0.89  17.12   0.98     0.96       3582.14|
| 14:  2.0330 -  1.9835   500    59  0.91  15.30   0.96     0.93       2886.68|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2886.68 max =        10769.92 mean =      6562.24|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.87 mean =        14.35|
|phase err.(test): min =        0.00 max =           89.34 mean =        13.87|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.128)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.11   17.64    None  None   None       |
|    all(noH): 2823   0      0.00    98.11   17.64    None  None   None       |
|    Sol.    : 438    0      5.76    98.11   42.30    None  None   None       |
|    Mac.    : 2385   0      0.00    89.48   13.11    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   9.814: 1002   |   5:    49.056 -  58.867:   89        |
|      1:     9.814 -  19.624: 1142   |   6:    58.867 -  68.677:   56        |
|      2:    19.624 -  29.435:  227   |   7:    68.677 -  78.488:   32        |
|      3:    29.435 -  39.246:  154   |   8:    78.488 -  88.299:   10        |
|      4:    39.246 -  49.056:  106   |   9:    88.299 -  98.109:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 309         
Filter by distance & map next to the model:
   mapped sites are within: 0.538 - 4.717
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 306 from: 309
   mapped sites are within: 0.712 - 4.717

peak=    5.614 closest distance to " CB  GLN A 223 " =    1.458
peak=    5.601 closest distance to " NE2 GLN A  11 " =    1.190
peak=    5.429 closest distance to " O   HOH Z 111 " =    1.991
peak=    5.328 closest distance to " O   HOH Z 232 " =    2.305
peak=    5.171 closest distance to " CG  PRO A  54 " =    1.275
peak=    4.992 closest distance to " O   HOH Z 144 " =    1.802
peak=    4.850 closest distance to " CG  PRO A 213 " =    1.218
peak=    4.820 closest distance to " CB  SER A  63 " =    1.253
peak=    4.805 closest distance to " CB  GLN A 183 " =    1.255
peak=    4.762 closest distance to " O   HOH Z 298 " =    2.138
peak=    4.759 closest distance to " O   HOH Z 126 " =    1.978
peak=    4.680 closest distance to " CG  PRO A 198 " =    1.236
peak=    4.594 closest distance to " O   HOH Z 369 " =    2.098
peak=    4.589 closest distance to " CB  ARG A 190 " =    1.573
peak=    4.587 closest distance to " CB  ASN A 148 " =    1.409
peak=    4.566 closest distance to " CB  PRO A  54 " =    0.978
peak=    4.547 closest distance to " C   PRO A 198 " =    1.545
peak=    4.522 closest distance to " O   HOH Z  78 " =    1.785
peak=    4.495 closest distance to " CD  ARG A 159 " =    0.808
peak=    4.419 closest distance to " CB  LEU A 228 " =    1.110
peak=    4.414 closest distance to " O   HOH Z 287 " =    2.158
peak=    4.407 closest distance to " O   HOH Z 427 " =    2.911
peak=    4.343 closest distance to " O   HOH Z 423 " =    1.598
peak=    4.336 closest distance to " CB  ARG A 275 " =    0.970
peak=    4.333 closest distance to " NH1AARG A 145 " =    1.244
peak=    4.320 closest distance to " CB  ARG A  79 " =    1.472
peak=    4.296 closest distance to " O   HOH Z   9 " =    2.194
peak=    4.287 closest distance to " O   HOH Z 133 " =    2.467
peak=    4.281 closest distance to " CZ  PHE A 218 " =    1.065
peak=    4.248 closest distance to " ND1 HIS A  86 " =    1.797
peak=    4.247 closest distance to " CE  LYS A  76 " =    0.874
peak=    4.182 closest distance to " CG2 VAL A 257 " =    0.965
peak=    4.168 closest distance to " CA  TYR A  30 " =    1.013
peak=    4.140 closest distance to " CB  SER A 212 " =    1.134
peak=    4.086 closest distance to " CB  VAL A 265 " =    1.277
peak=    4.082 closest distance to " CD  ARG A  66 " =    2.229
peak=    4.073 closest distance to " O   HOH Z 425 " =    1.335
peak=    4.041 closest distance to " CB  TRP A 266 " =    1.037
peak=    4.039 closest distance to " O   HOH Z  54 " =    2.368
peak=    4.034 closest distance to " O   HOH Z 180 " =    2.087
peak=    4.031 closest distance to " CD BLYS A 290 " =    0.962
peak=    4.031 closest distance to " CG  LEU A 167 " =    1.265
peak=    4.022 closest distance to " O   HOH Z 303 " =    2.212
peak=    4.000 closest distance to " ND2 ASN A 187 " =    1.413
peak=    3.997 closest distance to " O   HOH Z 250 " =    1.447
peak=    3.978 closest distance to " O   HOH Z 193 " =    1.797
peak=    3.962 closest distance to " O   HOH Z 272 " =    1.827
peak=    3.952 closest distance to " CG2 THR A 221 " =    1.008
peak=    3.946 closest distance to " CB  GLU A 128 " =    1.042
peak=    3.931 closest distance to " O   HOH Z 316 " =    3.072
peak=    3.930 closest distance to " CB  ASP A 124 " =    0.730
peak=    3.922 closest distance to " CG  PRO A 243 " =    1.069
peak=    3.915 closest distance to " CA  MET A  40 " =    1.234
peak=    3.911 closest distance to " O   HOH Z 214 " =    2.098
peak=    3.902 closest distance to " CA  SER A  87 " =    1.038
peak=    3.886 closest distance to " O   HOH Z  21 " =    1.773
peak=    3.885 closest distance to " O   HOH Z 158 " =    2.976
peak=    3.878 closest distance to " CA  ARG A 195 " =    1.343
peak=    3.874 closest distance to " O   HOH Z  61 " =    1.632
peak=    3.862 closest distance to " CB  TYR A 169 " =    0.771
peak=    3.842 closest distance to " CB  ASP A 140 " =    0.974
peak=    3.841 closest distance to " O   HOH Z 368 " =    2.077
peak=    3.825 closest distance to " O   HOH Z 290 " =    1.045
peak=    3.815 closest distance to " CB  VAL A 202 " =    1.632
peak=    3.815 closest distance to " O   HOH Z 234 " =    3.840
peak=    3.807 closest distance to " O   HOH Z   1 " =    1.880
peak=    3.804 closest distance to " O   HOH Z 261 " =    2.082
peak=    3.793 closest distance to " O   HOH Z 437 " =    1.385
peak=    3.790 closest distance to " O   HOH Z 411 " =    3.665
peak=    3.762 closest distance to " N   PHE A 130 " =    1.212
peak=    3.750 closest distance to " O   HOH Z 189 " =    2.816
peak=    3.746 closest distance to " OD1 ASN A  69 " =    2.673
peak=    3.744 closest distance to " CB  GLU A 152 " =    1.288
peak=    3.741 closest distance to " O   HOH Z   2 " =    1.438
peak=    3.741 closest distance to " O   HOH Z  10 " =    1.791
peak=    3.737 closest distance to " CB  SER A   3 " =    1.445
peak=    3.732 closest distance to " O   HOH Z 213 " =    2.099
peak=    3.727 closest distance to " CA  ASN A 215 " =    1.225
peak=    3.718 closest distance to " CD2 TRP A 179 " =    1.304
peak=    3.718 closest distance to " CD1 LEU A 300 " =    1.192
peak=    3.711 closest distance to " CB  ASN A  39 " =    0.937
peak=    3.706 closest distance to " CB  GLU A 277 " =    3.702
peak=    3.699 closest distance to " O   HOH Z 135 " =    1.742
peak=    3.696 closest distance to " CB  ASP A 132 " =    4.027
peak=    3.695 closest distance to " CB  SER A 216 " =    0.927
peak=    3.676 closest distance to " CD  ARG A 269 " =    0.916
peak=    3.676 closest distance to " O   HOH Z  58 " =    1.707
peak=    3.672 closest distance to " O   HOH Z 346 " =    1.681
peak=    3.671 closest distance to " CB  ASN A 187 " =    1.173
peak=    3.666 closest distance to " CG1 ILE A  33 " =    1.203
peak=    3.656 closest distance to " O   HOH Z 285 " =    2.469
peak=    3.652 closest distance to " N   ASN A 127 " =    1.259
peak=    3.644 closest distance to " CB  ASN A 110 " =    1.186
peak=    3.638 closest distance to " O   HOH Z 132 " =    2.452
peak=    3.624 closest distance to " O   HOH Z 217 " =    3.129
peak=    3.609 closest distance to " CA  ARG A 102 " =    1.194
peak=    3.608 closest distance to " O   HOH Z 183 " =    1.392
peak=    3.601 closest distance to " ND2 ASN A 249 " =    0.834
peak=    3.592 closest distance to " O   HOH Z  53 " =    2.500
peak=    3.592 closest distance to " O   HOH Z 391 " =    2.920
peak=    3.589 closest distance to " CA  ALA A 158 " =    1.182
peak=    3.583 closest distance to " CB  MET A  40 " =    0.789
peak=    3.582 closest distance to " CD2 LEU A 255 " =    1.690
peak=    3.579 closest distance to " CA  PRO A  54 " =    1.372
peak=    3.576 closest distance to " CB  ASN A 142 " =    0.966
peak=    3.566 closest distance to " OG  SER A  62 " =    3.048
peak=    3.563 closest distance to " O   HOH Z 406 " =    1.603
peak=    3.561 closest distance to " CB  TYR A 116 " =    0.807
peak=    3.555 closest distance to " O   HOH Z 286 " =    2.364
peak=    3.550 closest distance to " CB  SER A 276 " =    1.103
peak=    3.549 closest distance to " CB  ALA A 104 " =    0.765
peak=    3.549 closest distance to " CA  ALA A 291 " =    0.860
peak=    3.546 closest distance to " CA  ILE A 234 " =    1.040
peak=    3.545 closest distance to " O   HOH Z 365 " =    2.874
peak=    3.535 closest distance to " CD  LYS A 166 " =    1.314
peak=    3.533 closest distance to " CG1 VAL A 153 " =    0.970
peak=    3.529 closest distance to " CA  THR A 221 " =    0.973
peak=    3.528 closest distance to " CA  TYR A 116 " =    1.370
peak=    3.524 closest distance to " O   THR A 220 " =    1.319
peak=    3.523 closest distance to " O   HOH Z 405 " =    1.297
peak=    3.517 closest distance to " CA  ARG A  36 " =    1.150
peak=    3.517 closest distance to " O   HOH Z 193 " =    1.835
peak=    3.517 closest distance to " O   HOH Z 172 " =    3.140
peak=    3.514 closest distance to " O   HOH Z 209 " =    2.302
peak=    3.513 closest distance to " O   TYR A 116 " =    1.325
peak=    3.512 closest distance to " O   HOH Z 108 " =    2.619
peak=    3.511 closest distance to " CB  LEU A 237 " =    0.776
peak=    3.509 closest distance to " O   HOH Z 409 " =    2.535
peak=    3.501 closest distance to " O   HOH Z 193 " =    2.168
peak=    3.493 closest distance to " O   HOH Z 325 " =    2.455
peak=    3.491 closest distance to " CB  ALA A  34 " =    1.104
peak=    3.487 closest distance to " O   HOH Z  59 " =    1.801
peak=    3.481 closest distance to " O   MET A 105 " =    1.877
peak=    3.480 closest distance to " O   HOH Z   1 " =    1.707
peak=    3.480 closest distance to " O   HOH Z 352 " =    1.705
peak=    3.479 closest distance to " O   HOH Z 329 " =    4.010
peak=    3.478 closest distance to " CB  ALA A   1 " =    4.717
peak=    3.473 closest distance to " CA  THR A 264 " =    0.888
peak=    3.468 closest distance to " O   THR A 251 " =    1.212
peak=    3.466 closest distance to " O   HOH Z 389 " =    1.947
peak=    3.464 closest distance to " O   HOH Z 386 " =    3.010
peak=    3.462 closest distance to " CB  TYR A 169 " =    0.848
peak=    3.462 closest distance to " O   HOH Z 218 " =    4.564
peak=    3.458 closest distance to " CB  GLU A  46 " =    0.973
peak=    3.456 closest distance to " O   HOH Z  61 " =    1.495
peak=    3.456 closest distance to " CB  SER A 210 " =    0.783
peak=    3.456 closest distance to " O   HOH Z 130 " =    3.797
peak=    3.454 closest distance to " O   HOH Z 419 " =    1.955
peak=    3.452 closest distance to " O   HOH Z 371 " =    2.894
peak=    3.450 closest distance to " CA  MET A 105 " =    0.992
peak=    3.437 closest distance to " CG1 VAL A 189 " =    1.996
peak=    3.437 closest distance to " CG  MET A 113 " =    1.614
peak=    3.436 closest distance to " NH2AARG A 190 " =    1.940
peak=    3.435 closest distance to " O   HOH Z 327 " =    1.937
peak=    3.433 closest distance to " NE2 HIS A 207 " =    1.259
peak=    3.433 closest distance to " O   HOH Z  88 " =    3.347
peak=    3.429 closest distance to " N   TYR A  15 " =    0.824
peak=    3.425 closest distance to " CA  LYS A 290 " =    1.338
peak=    3.424 closest distance to " O   HOH Z 353 " =    2.653
peak=    3.423 closest distance to " O   HOH Z   7 " =    1.302
peak=    3.418 closest distance to " O   HOH Z 325 " =    3.959
peak=    3.418 closest distance to " O   HOH Z 124 " =    1.982
peak=    3.417 closest distance to " CB  THR A  82 " =    1.331
peak=    3.414 closest distance to " CG  ARG A 159 " =    0.923
peak=    3.410 closest distance to " O   HOH Z 148 " =    3.415
peak=    3.402 closest distance to " CZ3 TRP A 266 " =    1.128
peak=    3.401 closest distance to " N   ARG A 156 " =    1.360
peak=    3.401 closest distance to " O   HOH Z 373 " =    1.554
peak=    3.400 closest distance to " CB  GLU A 236 " =    1.200
peak=    3.398 closest distance to " CA  VAL A 125 " =    1.198
peak=    3.397 closest distance to " CA  ALA A  51 " =    0.962
peak=    3.396 closest distance to " CA  ASN A 217 " =    1.195
peak=    3.396 closest distance to " O   HOH Z 368 " =    3.666
peak=    3.395 closest distance to " OE1 GLN A  11 " =    2.173
peak=    3.395 closest distance to " O   HOH Z  40 " =    1.842
peak=    3.393 closest distance to " CA  ALA A 154 " =    1.044
peak=    3.388 closest distance to " O  BHOH Z 338 " =    2.361
peak=    3.385 closest distance to " O   HOH Z 380 " =    1.616
peak=    3.382 closest distance to " O   HOH Z 238 " =    3.661
peak=    3.382 closest distance to " O   HOH Z 280 " =    3.065
peak=    3.380 closest distance to " O   HOH Z 371 " =    1.929
peak=    3.374 closest distance to " CA  GLY A 267 " =    1.263
peak=    3.368 closest distance to " O   HOH Z 128 " =    2.341
peak=    3.364 closest distance to " NH2 ARG A 156 " =    1.195
peak=    3.363 closest distance to " CE1 TYR A 186 " =    1.386
peak=    3.352 closest distance to " CB  ILE A 120 " =    1.353
peak=    3.352 closest distance to " CA  ALA A 160 " =    0.916
peak=    3.349 closest distance to " CB  PRO A  90 " =    1.209
peak=    3.348 closest distance to " CG  GLN A  88 " =    1.016
peak=    3.348 closest distance to " O   HOH Z 258 " =    2.170
peak=    3.346 closest distance to " O   SER A  87 " =    2.418
peak=    3.344 closest distance to " CB  ARG A 138 " =    0.966
peak=    3.339 closest distance to " O   HOH Z 116 " =    3.152
peak=    3.338 closest distance to " O   HOH Z 188 " =    2.458
peak=    3.337 closest distance to " OD2 ASP A 286 " =    2.884
peak=    3.335 closest distance to " CG  GLU A 277 " =    2.004
peak=    3.330 closest distance to " CA  GLU A  46 " =    0.933
peak=    3.329 closest distance to " O   HOH Z  68 " =    2.072
peak=    3.329 closest distance to " CB  MET A  47 " =    0.975
peak=    3.326 closest distance to " O   ASN A  74 " =    1.557
peak=    3.325 closest distance to " O   HOH Z  44 " =    2.842
peak=    3.318 closest distance to " O   HOH Z  20 " =    1.806
peak=    3.316 closest distance to " CD  ARG A  14 " =    1.181
peak=    3.306 closest distance to " CB  LYS A 117 " =    1.200
peak=    3.300 closest distance to " CA  SER A  95 " =    1.016
peak=    3.298 closest distance to " O   HOH Z 109 " =    2.698
peak=    3.297 closest distance to " O   HOH Z 147 " =    1.784
peak=    3.297 closest distance to " CG2 ILE A 151 " =    0.961
peak=    3.296 closest distance to " O   ALA A 291 " =    1.461
peak=    3.295 closest distance to " CE2 TYR A 186 " =    0.879
peak=    3.294 closest distance to " CG BARG A 275 " =    1.516
peak=    3.292 closest distance to " CB  TRP A 150 " =    1.252
peak=    3.292 closest distance to " N   SER A 146 " =    1.771
peak=    3.291 closest distance to " NH2 ARG A 219 " =    1.800
peak=    3.290 closest distance to " CB  ALA A 114 " =    0.712
peak=    3.288 closest distance to " OG  SER A  22 " =    2.900
peak=    3.287 closest distance to " O   HOH Z 227 " =    1.763
peak=    3.283 closest distance to " O   HOH Z 422 " =    2.701
peak=    3.279 closest distance to " CA  ALA A 233 " =    1.473
peak=    3.272 closest distance to " OG BSER A 164 " =    2.408
peak=    3.271 closest distance to " CG1 ILE A 151 " =    1.096
peak=    3.266 closest distance to " CZ  PHE A  38 " =    1.271
peak=    3.265 closest distance to " O   HOH Z 368 " =    4.211
peak=    3.261 closest distance to " O   HOH Z 344 " =    3.306
peak=    3.260 closest distance to " O   HOH Z 403 " =    1.616
peak=    3.256 closest distance to " O   HOH Z 305 " =    3.578
peak=    3.251 closest distance to " O   HOH Z 294 " =    1.593
peak=    3.250 closest distance to " CB  GLN A  88 " =    1.277
peak=    3.246 closest distance to " NH1 ARG A 138 " =    1.057
peak=    3.245 closest distance to " CB  ARG A 139 " =    1.007
peak=    3.242 closest distance to " NE  ARG A  79 " =    1.125
peak=    3.241 closest distance to " O   HOH Z 426 " =    1.762
peak=    3.233 closest distance to " O   HOH Z 166 " =    3.880
peak=    3.233 closest distance to " CD1 ILE A 106 " =    0.789
peak=    3.231 closest distance to " N   VAL A 126 " =    1.283
peak=    3.228 closest distance to " O   PRO A 213 " =    1.616
peak=    3.228 closest distance to " CB  ALA A   9 " =    1.627
peak=    3.214 closest distance to " O   HOH Z 188 " =    1.915
peak=    3.208 closest distance to " O   HOH Z 282 " =    1.979
peak=    3.208 closest distance to " CB  GLN A 103 " =    1.019
peak=    3.207 closest distance to " O   HOH Z 345 " =    1.693
peak=    3.206 closest distance to " O   HOH Z 285 " =    1.853
peak=    3.206 closest distance to " CE  LYS A  48 " =    1.110
peak=    3.204 closest distance to " CD1AILE A 234 " =    1.000
peak=    3.204 closest distance to " CD2 LEU A 297 " =    0.915
peak=    3.204 closest distance to " OD1BASN A 224 " =    2.393
peak=    3.203 closest distance to " CG  GLN A 278 " =    1.426
peak=    3.202 closest distance to " O   HOH Z 327 " =    2.621
peak=    3.201 closest distance to " O   HOH Z 116 " =    1.798
peak=    3.200 closest distance to " CB  PRO A 243 " =    1.194
peak=    3.198 closest distance to " O   HOH Z 425 " =    2.060
peak=    3.198 closest distance to " CA  ASN A  74 " =    1.407
peak=    3.195 closest distance to " O   ASN A 209 " =    1.347
peak=    3.195 closest distance to " CD1 ILE A  33 " =    1.649
peak=    3.194 closest distance to " CA  ARG A 159 " =    1.376
peak=    3.194 closest distance to " ND1 HIS A  81 " =    1.671
peak=    3.193 closest distance to " O   HOH Z 359 " =    4.051
peak=    3.189 closest distance to " CD1 LEU A  96 " =    0.776
peak=    3.182 closest distance to " O   HOH Z 185 " =    1.900
peak=    3.182 closest distance to " O   HOH Z 299 " =    2.651
peak=    3.180 closest distance to " ND2 ASN A 110 " =    1.739
peak=    3.180 closest distance to " CA  LEU A 101 " =    1.477
peak=    3.177 closest distance to " CG2 ILE A  20 " =    1.276
peak=    3.175 closest distance to " O   HOH Z 273 " =    2.805
peak=    3.174 closest distance to " O   HOH Z 175 " =    2.247
peak=    3.173 closest distance to " O   HOH Z  80 " =    1.470
peak=    3.172 closest distance to " CA  ARG A 156 " =    1.032
peak=    3.168 closest distance to " CB  SER A  62 " =    1.077
peak=    3.166 closest distance to " O   HOH Z 126 " =    1.511
peak=    3.166 closest distance to " CA  LYS A 117 " =    1.149
peak=    3.164 closest distance to " O   HOH Z 407 " =    2.214
peak=    3.159 closest distance to " O   HOH Z 345 " =    3.603
peak=    3.151 closest distance to " O   HOH Z 302 " =    1.830
peak=    3.150 closest distance to " O   ALA A 158 " =    1.397
peak=    3.148 closest distance to " O   HOH Z 417 " =    3.551
peak=    3.144 closest distance to " OD1 ASN A 217 " =    1.568
peak=    3.143 closest distance to " CA  GLY A 136 " =    1.026
peak=    3.142 closest distance to " CB  THR A 157 " =    1.174
peak=    3.139 closest distance to " O   HOH Z  64 " =    2.420
peak=    3.136 closest distance to " CB  TRP A 179 " =    1.581
peak=    3.134 closest distance to " CB  ALA A 114 " =    0.981
peak=    3.133 closest distance to " CD  LYS A  76 " =    1.938
peak=    3.131 closest distance to " O   HOH Z 219 " =    1.633
peak=    3.131 closest distance to " CB  HIS A 108 " =    0.773
peak=    3.121 closest distance to " CE2 TYR A 293 " =    1.075
peak=    3.120 closest distance to " CB  VAL A 265 " =    2.134
peak=    3.116 closest distance to " CG  GLU A  37 " =    0.845
peak=    3.115 closest distance to " CA  TYR A 186 " =    1.593
peak=    3.111 closest distance to " CA  ARG A 139 " =    1.029
peak=    3.109 closest distance to " O   HOH Z  85 " =    2.208
peak=    3.108 closest distance to " CA  ASP A 140 " =    1.275
peak=    3.102 closest distance to " OG  SER A  62 " =    3.056
peak=    3.100 closest distance to " CG  LYS A  76 " =    0.985
peak=    3.100 closest distance to " CA  ALA A 299 " =    0.920
peak=    3.099 closest distance to " O   HOH Z 303 " =    3.004
peak=    3.098 closest distance to " O   HOH Z 271 " =    2.487
peak=    3.097 closest distance to " CB  PRO A 163 " =    4.233
peak=    3.095 closest distance to " CD2 TYR A 186 " =    1.042
peak=    3.091 closest distance to " CB  PHE A 204 " =    0.797
peak=    3.086 closest distance to " O   HOH Z  97 " =    1.987
peak=    3.086 closest distance to " O   HOH Z 303 " =    2.570
peak=    3.084 closest distance to " N   CYS A 260 " =    0.929
peak=    3.080 closest distance to " CB  ALA A  43 " =    0.826
peak=    3.076 closest distance to " O   HOH Z 386 " =    3.159
peak=    3.068 closest distance to " O   HOH Z 286 " =    2.373
peak=    3.054 closest distance to " O   HOH Z 369 " =    1.670

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 205         
Filter by distance & map next to the model:
   mapped sites are within: 0.749 - 5.690
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 205 from: 205
   mapped sites are within: 0.749 - 5.690

peak=   -4.469 closest distance to " O   HOH Z 377 " =    2.003
peak=   -4.405 closest distance to " CD  ARG A 156 " =    2.084
peak=   -4.364 closest distance to " CD  ARG A  14 " =    3.506
peak=   -4.303 closest distance to " CB  PRO A 243 " =    2.566
peak=   -4.257 closest distance to " O   HOH Z 231 " =    2.121
peak=   -4.256 closest distance to " O   PRO A 198 " =    1.273
peak=   -4.096 closest distance to " O   HOH Z  38 " =    1.307
peak=   -4.074 closest distance to " N   ALA A  43 " =    2.595
peak=   -4.050 closest distance to " CB  ALA A  43 " =    2.596
peak=   -4.013 closest distance to " CG  GLN A 223 " =    2.103
peak=   -3.991 closest distance to " OG BSER A 134 " =    1.288
peak=   -3.987 closest distance to " O   HOH Z 266 " =    5.364
peak=   -3.967 closest distance to " O   HOH Z 389 " =    2.093
peak=   -3.962 closest distance to " O   HOH Z 407 " =    3.334
peak=   -3.955 closest distance to " CZ3 TRP A 179 " =    1.089
peak=   -3.918 closest distance to " CA  GLY A 203 " =    2.367
peak=   -3.811 closest distance to " CG  MET A 105 " =    0.946
peak=   -3.807 closest distance to " O   HOH Z 351 " =    1.509
peak=   -3.801 closest distance to " CG1 VAL A 112 " =    3.073
peak=   -3.789 closest distance to " O   VAL A  67 " =    2.652
peak=   -3.774 closest distance to " CE2 TYR A  30 " =    2.762
peak=   -3.761 closest distance to " CB  ASP A  27 " =    2.509
peak=   -3.728 closest distance to " O   HOH Z 198 " =    1.974
peak=   -3.726 closest distance to " O   HOH Z 372 " =    2.484
peak=   -3.723 closest distance to " O   TYR A 247 " =    2.895
peak=   -3.700 closest distance to " ND2 ASN A  45 " =    2.028
peak=   -3.694 closest distance to " O   ALA A  10 " =    1.645
peak=   -3.687 closest distance to " C   LEU A 222 " =    0.760
peak=   -3.679 closest distance to " CB  TRP A  85 " =    2.460
peak=   -3.679 closest distance to " O   HOH Z  73 " =    1.958
peak=   -3.673 closest distance to " O   HOH Z  52 " =    1.325
peak=   -3.662 closest distance to " CD2 LEU A 143 " =    2.625
peak=   -3.655 closest distance to " CG1 VAL A 112 " =    2.606
peak=   -3.653 closest distance to " CG2 ILE A  49 " =    2.690
peak=   -3.648 closest distance to " O   HOH Z 435 " =    2.828
peak=   -3.648 closest distance to " CD2 TYR A 293 " =    1.957
peak=   -3.646 closest distance to " CE  MET A 105 " =    2.305
peak=   -3.644 closest distance to " CA  GLY A 241 " =    2.310
peak=   -3.644 closest distance to " ND2 ASN A 249 " =    2.099
peak=   -3.641 closest distance to " CD1 PHE A  59 " =    1.901
peak=   -3.636 closest distance to " O   VAL A 189 " =    2.526
peak=   -3.635 closest distance to " CG1 VAL A 250 " =    2.607
peak=   -3.632 closest distance to " O   HOH Z 313 " =    1.809
peak=   -3.626 closest distance to " NH2AARG A 275 " =    5.568
peak=   -3.624 closest distance to " CG  GLN A  88 " =    0.850
peak=   -3.608 closest distance to " O   HOH Z 111 " =    1.813
peak=   -3.601 closest distance to " OD1 ASN A 148 " =    1.516
peak=   -3.598 closest distance to " O   HOH Z 185 " =    2.175
peak=   -3.588 closest distance to " CD  ARG A 195 " =    5.149
peak=   -3.584 closest distance to " N   THR A 157 " =    1.500
peak=   -3.580 closest distance to " O   GLY A 203 " =    2.400
peak=   -3.578 closest distance to " OG  SER A  97 " =    2.148
peak=   -3.573 closest distance to " O   HOH Z 290 " =    1.203
peak=   -3.568 closest distance to " O   GLY A  17 " =    1.210
peak=   -3.567 closest distance to " CB  PRO A  54 " =    2.522
peak=   -3.565 closest distance to " C   ASN A 285 " =    2.489
peak=   -3.561 closest distance to " O   HOH Z 198 " =    1.666
peak=   -3.559 closest distance to " OD1 ASP A 171 " =    1.626
peak=   -3.558 closest distance to " C   HIS A 108 " =    1.115
peak=   -3.557 closest distance to " O   PRO A 163 " =    1.994
peak=   -3.555 closest distance to " CB  ALA A 291 " =    2.273
peak=   -3.548 closest distance to " CG  ARG A 269 " =    2.573
peak=   -3.533 closest distance to " O   HOH Z 394 " =    1.514
peak=   -3.532 closest distance to " O   HOH Z  10 " =    1.501
peak=   -3.523 closest distance to " CG2 THR A 178 " =    2.290
peak=   -3.522 closest distance to " CD  GLN A  58 " =    0.941
peak=   -3.519 closest distance to " CA  GLY A 241 " =    3.145
peak=   -3.518 closest distance to " CD1 LEU A 101 " =    2.312
peak=   -3.515 closest distance to " ND2 ASN A  45 " =    1.187
peak=   -3.510 closest distance to " O   GLY A 211 " =    1.297
peak=   -3.510 closest distance to " OE1 GLN A  88 " =    1.141
peak=   -3.506 closest distance to " CB  ALA A   9 " =    2.435
peak=   -3.506 closest distance to " OD1 ASN A 187 " =    1.449
peak=   -3.499 closest distance to " CD  ARG A 139 " =    1.512
peak=   -3.492 closest distance to " O   HOH Z 275 " =    1.806
peak=   -3.484 closest distance to " CZ BARG A 275 " =    1.802
peak=   -3.484 closest distance to " O   HOH Z 426 " =    1.585
peak=   -3.483 closest distance to " OG  SER A  87 " =    1.331
peak=   -3.483 closest distance to " O   HOH Z 176 " =    0.749
peak=   -3.480 closest distance to " O   HOH Z 102 " =    1.653
peak=   -3.475 closest distance to " OD1 ASP A 191 " =    1.867
peak=   -3.474 closest distance to " O   ALA A 180 " =    1.217
peak=   -3.469 closest distance to " O   HOH Z 359 " =    3.223
peak=   -3.461 closest distance to " O   HOH Z 281 " =    2.648
peak=   -3.454 closest distance to " O   PHE A 218 " =    1.460
peak=   -3.450 closest distance to " OG BSER A 134 " =    1.724
peak=   -3.450 closest distance to " CB  ASN A  39 " =    2.300
peak=   -3.444 closest distance to " NZ  LYS A 166 " =    1.196
peak=   -3.433 closest distance to " CA  GLY A  98 " =    1.921
peak=   -3.427 closest distance to " O   HOH Z  65 " =    1.279
peak=   -3.425 closest distance to " O   SER A 135 " =    1.448
peak=   -3.424 closest distance to " O   HOH Z 292 " =    1.835
peak=   -3.421 closest distance to " C   ALA A 158 " =    1.563
peak=   -3.420 closest distance to " CB  ALA A 100 " =    2.242
peak=   -3.409 closest distance to " O   SER A  62 " =    2.301
peak=   -3.408 closest distance to " CB  ALA A 131 " =    2.092
peak=   -3.403 closest distance to " O   HOH Z 118 " =    1.458
peak=   -3.401 closest distance to " CE BMET A  47 " =    1.538
peak=   -3.401 closest distance to " NE  ARG A  36 " =    2.011
peak=   -3.389 closest distance to " O   HOH Z  43 " =    1.639
peak=   -3.376 closest distance to " ND2BASN A 224 " =    1.732
peak=   -3.363 closest distance to " CG  PHE A 283 " =    2.733
peak=   -3.359 closest distance to " C   ASN A 187 " =    1.829
peak=   -3.354 closest distance to " C   LEU A 143 " =    1.352
peak=   -3.351 closest distance to " CG  GLU A  53 " =    1.377
peak=   -3.350 closest distance to " N   ALA A 248 " =    1.609
peak=   -3.346 closest distance to " CG  HIS A  86 " =    0.939
peak=   -3.344 closest distance to " OXT GLY A 302 " =    3.138
peak=   -3.343 closest distance to " O   ILE A 109 " =    2.623
peak=   -3.338 closest distance to " N   SER A 212 " =    2.010
peak=   -3.331 closest distance to " CE2 PHE A  61 " =    2.683
peak=   -3.329 closest distance to " O   HOH Z 345 " =    2.352
peak=   -3.322 closest distance to " O   HOH Z 114 " =    3.358
peak=   -3.321 closest distance to " CB  ALA A 248 " =    2.452
peak=   -3.320 closest distance to " O   HOH Z 191 " =    5.600
peak=   -3.319 closest distance to " O   GLY A  80 " =    2.440
peak=   -3.317 closest distance to " O   HOH Z 409 " =    4.535
peak=   -3.314 closest distance to " OH  TYR A 172 " =    1.720
peak=   -3.314 closest distance to " CD  LYS A 289 " =    2.362
peak=   -3.307 closest distance to " O   HOH Z 298 " =    1.160
peak=   -3.305 closest distance to " CD1 LEU A 228 " =    2.418
peak=   -3.302 closest distance to " CG  TRP A 266 " =    1.701
peak=   -3.299 closest distance to " CB  ALA A 291 " =    2.253
peak=   -3.299 closest distance to " O   ILE A  49 " =    1.770
peak=   -3.295 closest distance to " O   PRO A 198 " =    1.379
peak=   -3.286 closest distance to " O   HOH Z 275 " =    1.505
peak=   -3.285 closest distance to " CB  PRO A 163 " =    2.498
peak=   -3.285 closest distance to " O   HOH Z 247 " =    1.976
peak=   -3.284 closest distance to " O   HOH Z  22 " =    2.449
peak=   -3.282 closest distance to " O   HOH Z 353 " =    2.106
peak=   -3.281 closest distance to " CB  PHE A 192 " =    1.878
peak=   -3.274 closest distance to " CE2 PHE A 218 " =    2.445
peak=   -3.274 closest distance to " O   HOH Z 317 " =    1.603
peak=   -3.271 closest distance to " O   HOH Z  51 " =    1.750
peak=   -3.269 closest distance to " C   GLY A  13 " =    0.990
peak=   -3.268 closest distance to " CD2 PHE A 192 " =    2.272
peak=   -3.264 closest distance to " O   HOH Z 417 " =    2.827
peak=   -3.264 closest distance to " NE2 GLN A 194 " =    1.840
peak=   -3.263 closest distance to " CB  ASP A 286 " =    2.144
peak=   -3.252 closest distance to " O   HOH Z 350 " =    1.337
peak=   -3.252 closest distance to " O   VAL A  67 " =    2.899
peak=   -3.252 closest distance to " O   PRO A 243 " =    2.451
peak=   -3.252 closest distance to " O   HOH Z 123 " =    2.570
peak=   -3.252 closest distance to " O   HOH Z 196 " =    2.244
peak=   -3.251 closest distance to " CD2 PHE A  61 " =    1.998
peak=   -3.248 closest distance to " CG1 VAL A  67 " =    2.916
peak=   -3.247 closest distance to " NE2 GLN A 278 " =    1.825
peak=   -3.233 closest distance to " CG  PRO A 163 " =    2.372
peak=   -3.233 closest distance to " CE3 TRP A 150 " =    2.210
peak=   -3.231 closest distance to " O   HOH Z 252 " =    4.238
peak=   -3.230 closest distance to " O   HOH Z 298 " =    2.429
peak=   -3.230 closest distance to " O   HOH Z  70 " =    2.165
peak=   -3.228 closest distance to " O   HOH Z  90 " =    1.584
peak=   -3.224 closest distance to " N   SER A 276 " =    1.264
peak=   -3.222 closest distance to " CB  CYS A 254 " =    2.155
peak=   -3.217 closest distance to " O   HOH Z 174 " =    2.648
peak=   -3.217 closest distance to " O   HOH Z 189 " =    2.126
peak=   -3.212 closest distance to " O   ASN A 301 " =    1.360
peak=   -3.211 closest distance to " OD2 ASP A 171 " =    1.790
peak=   -3.207 closest distance to " O   HOH Z  11 " =    1.809
peak=   -3.200 closest distance to " O   HOH Z 231 " =    1.242
peak=   -3.194 closest distance to " O   HOH Z 348 " =    2.266
peak=   -3.192 closest distance to " N   ASN A  60 " =    1.233
peak=   -3.187 closest distance to " NH1AARG A 275 " =    1.947
peak=   -3.182 closest distance to " O   HOH Z 184 " =    1.752
peak=   -3.181 closest distance to " O   HOH Z  53 " =    1.666
peak=   -3.179 closest distance to " CG2 THR A  18 " =    2.861
peak=   -3.179 closest distance to " O   HOH Z 211 " =    1.407
peak=   -3.178 closest distance to " O   HOH Z 337 " =    1.483
peak=   -3.177 closest distance to " CB  TYR A  15 " =    2.257
peak=   -3.174 closest distance to " CG2 VAL A 189 " =    1.928
peak=   -3.169 closest distance to " O   TRP A  70 " =    1.410
peak=   -3.163 closest distance to " ND2 ASN A  60 " =    1.983
peak=   -3.161 closest distance to " CA  SER A 135 " =    1.312
peak=   -3.159 closest distance to " O   HOH Z 118 " =    1.604
peak=   -3.157 closest distance to " CZ  TYR A 169 " =    1.670
peak=   -3.154 closest distance to " O   HOH Z   6 " =    1.517
peak=   -3.148 closest distance to " CA  ASP A 298 " =    1.037
peak=   -3.146 closest distance to " O   HOH Z  63 " =    1.624
peak=   -3.144 closest distance to " N   LYS A 166 " =    1.888
peak=   -3.143 closest distance to " ND2 ASN A 187 " =    1.537
peak=   -3.143 closest distance to " CZ  PHE A  59 " =    1.627
peak=   -3.139 closest distance to " O   HOH Z 114 " =    0.869
peak=   -3.134 closest distance to " O   HOH Z 166 " =    1.988
peak=   -3.134 closest distance to " OD2 ASP A 140 " =    1.730
peak=   -3.130 closest distance to " O   HOH Z 282 " =    4.772
peak=   -3.129 closest distance to " NH2 ARG A  79 " =    1.515
peak=   -3.129 closest distance to " CD1 LEU A   5 " =    2.656
peak=   -3.122 closest distance to " O   HOH Z 166 " =    1.380
peak=   -3.122 closest distance to " OE1 GLN A  58 " =    3.165
peak=   -3.117 closest distance to " CD1 PHE A  61 " =    2.999
peak=   -3.104 closest distance to " O   VAL A 125 " =    2.326
peak=   -3.104 closest distance to " CD2 TYR A 293 " =    2.157
peak=   -3.095 closest distance to " O   ARG A  56 " =    1.846
peak=   -3.093 closest distance to " O   HOH Z 140 " =    1.610
peak=   -3.092 closest distance to " CA  GLY A 241 " =    2.871
peak=   -3.085 closest distance to " O   ASP A  27 " =    1.917
peak=   -3.082 closest distance to " CA  HIS A  86 " =    2.256
peak=   -3.072 closest distance to " O   HOH Z 357 " =    2.009
peak=   -3.066 closest distance to " O   HOH Z 336 " =    5.690
peak=   -3.064 closest distance to " ND2BASN A 224 " =    1.769
peak=   -3.058 closest distance to " CD1 LEU A 297 " =    2.562
peak=   -3.057 closest distance to " N   ALA A 226 " =    2.148
peak=   -3.037 closest distance to " O   HOH Z 383 " =    1.116
peak=   -3.030 closest distance to " C   GLY A 262 " =    2.149

================= 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    :  0.3934 0.3860   6.176649e+00   6.159752e+00
   1_bss:  0.3840 0.3785   6.165541e+00   6.145115e+00
   1_xyz:  0.2168 0.2456   5.685283e+00   5.771961e+00
   1_adp:  0.1963 0.2551   5.632300e+00   5.807768e+00
   1_occ:  0.1959 0.2546   5.630943e+00   5.807051e+00
   2_bss:  0.1944 0.2532   5.630609e+00   5.804358e+00
   2_xyz:  0.1508 0.1988   5.402430e+00   5.604807e+00
   2_adp:  0.1437 0.1883   5.354907e+00   5.555118e+00
   2_occ:  0.1435 0.1884   5.354517e+00   5.555615e+00
   3_bss:  0.1435 0.1882   5.353521e+00   5.554398e+00
   3_xyz:  0.1204 0.1673   5.209936e+00   5.441862e+00
   3_adp:  0.1154 0.1637   5.178147e+00   5.420870e+00
   3_occ:  0.1154 0.1638   5.178327e+00   5.421361e+00
   4_bss:  0.1158 0.1635   5.178548e+00   5.419685e+00
   4_xyz:  0.1171 0.1640   5.188679e+00   5.425023e+00
   4_adp:  0.1179 0.1609   5.183398e+00   5.408710e+00
   4_occ:  0.1178 0.1607   5.182857e+00   5.408147e+00
   5_bss:  0.1178 0.1608   5.182714e+00   5.408173e+00
   5_xyz:  0.1136 0.1585   5.158197e+00   5.395780e+00
   5_adp:  0.1126 0.1604   5.159540e+00   5.406753e+00
   5_occ:  0.1125 0.1604   5.159557e+00   5.406887e+00
   5_bss:  0.1124 0.1604   5.159574e+00   5.406975e+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:  0.337  68.296   1.143  -0.981  -0.115  -0.000  -0.000  -0.000
   1_xyz:  0.337  68.296   1.143  -0.981  -0.115  -0.000  -0.000  -0.000
   1_adp:  0.337  68.296   1.143  -0.981  -0.115  -0.000  -0.000  -0.000
   1_occ:  0.337  68.296   1.143  -0.981  -0.115  -0.000  -0.000  -0.000
   2_bss:  0.342  75.431  -1.314  -2.437  -1.074  -0.000  -0.000  -0.000
   2_xyz:  0.342  75.431  -1.314  -2.437  -1.074  -0.000  -0.000  -0.000
   2_adp:  0.342  75.431  -1.314  -2.437  -1.074  -0.000  -0.000  -0.000
   2_occ:  0.342  75.431  -1.314  -2.437  -1.074  -0.000  -0.000  -0.000
   3_bss:  0.332  66.826  -1.816  -2.569  -0.912  -0.000  -0.000  -0.000
   3_xyz:  0.332  66.826  -1.816  -2.569  -0.912  -0.000  -0.000  -0.000
   3_adp:  0.332  66.826  -1.816  -2.569  -0.912  -0.000  -0.000  -0.000
   3_occ:  0.332  66.826  -1.816  -2.569  -0.912  -0.000  -0.000  -0.000
   4_bss:  0.332  66.826  -2.144  -2.736  -1.136  -0.000  -0.000  -0.000
   4_xyz:  0.332  66.826  -2.144  -2.736  -1.136  -0.000  -0.000  -0.000
   4_adp:  0.332  66.826  -2.144  -2.736  -1.136  -0.000  -0.000  -0.000
   4_occ:  0.332  66.826  -2.144  -2.736  -1.136  -0.000  -0.000  -0.000
   5_bss:  0.320  61.360  -2.274  -2.786  -1.176  -0.000  -0.000  -0.000
   5_xyz:  0.320  61.360  -2.274  -2.786  -1.176  -0.000  -0.000  -0.000
   5_adp:  0.320  61.360  -2.274  -2.786  -1.176  -0.000  -0.000  -0.000
   5_occ:  0.320  61.360  -2.274  -2.786  -1.176  -0.000  -0.000  -0.000
   5_bss:  0.317  61.363  -2.108  -2.637  -1.044  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  42.659 0.6122  0.7826    43422.628
   1_bss:  41.902 0.6199  0.7988    41406.530
   1_xyz:  23.652 0.8266  0.9971    15167.197
   1_adp:  24.849 0.8132  0.9881    16164.612
   1_occ:  24.814 0.8135  0.9877    16093.580
   2_bss:  24.710 0.8147  0.9340    16009.123
   2_xyz:  19.078 0.8699  0.9718    10018.265
   2_adp:  17.679 0.8837  0.9779     9081.038
   2_occ:  17.694 0.8836  0.9774     9087.796
   3_bss:  17.667 0.8837  0.9714     9040.873
   3_xyz:  15.180 0.9051  0.9844     7092.012
   3_adp:  14.663 0.9095  0.9812     6756.274
   3_occ:  14.671 0.9095  0.9810     6761.130
   4_bss:  14.665 0.9095  0.9728     6731.376
   4_xyz:  14.696 0.9096  0.9711     6793.630
   4_adp:  14.333 0.9127  0.9705     6616.130
   4_occ:  14.320 0.9128  0.9706     6600.993
   5_bss:  14.320 0.9128  0.9679     6596.517
   5_xyz:  14.083 0.9146  0.9695     6452.006
   5_adp:  14.301 0.9128  0.9637     6560.524
   5_occ:  14.301 0.9128  0.9636     6561.513
   5_bss:  14.304 0.9128  0.9687     6562.522
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.112   1.6220e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.112   1.6220e-01
   1_xyz:   1.233  0.010  0.084 15.724  0.006  4.113   8.6576e-02
   1_adp:   1.233  0.010  0.084 15.724  0.006  4.113   8.6576e-02
   1_occ:   1.233  0.010  0.084 15.724  0.006  4.113   8.6576e-02
   2_bss:   1.233  0.010  0.084 15.724  0.006  4.113   8.6576e-02
   2_xyz:   0.948  0.006  0.071 14.498  0.003  4.127   5.2643e-02
   2_adp:   0.948  0.006  0.071 14.498  0.003  4.127   5.2643e-02
   2_occ:   0.948  0.006  0.071 14.498  0.003  4.127   5.2643e-02
   3_bss:   0.948  0.006  0.071 14.498  0.003  4.127   5.2643e-02
   3_xyz:   1.101  0.010  0.083 14.934  0.004  4.136   7.2683e-02
   3_adp:   1.101  0.010  0.083 14.934  0.004  4.136   7.2683e-02
   3_occ:   1.101  0.010  0.083 14.934  0.004  4.136   7.2683e-02
   4_bss:   1.101  0.010  0.083 14.934  0.004  4.136   7.2683e-02
   4_xyz:   0.931  0.007  0.071 14.625  0.003  4.113   5.4302e-02
   4_adp:   0.931  0.007  0.071 14.625  0.003  4.113   5.4302e-02
   4_occ:   0.931  0.007  0.071 14.625  0.003  4.113   5.4302e-02
   5_bss:   0.931  0.007  0.071 14.625  0.003  4.113   5.4302e-02
   5_xyz:   1.031  0.009  0.078 14.755  0.004  4.116   6.3800e-02
   5_adp:   1.031  0.009  0.078 14.755  0.004  4.116   6.3800e-02
   5_occ:   1.031  0.009  0.078 14.755  0.004  4.116   6.3800e-02
   5_bss:   1.031  0.009  0.078 14.755  0.004  4.116   6.3800e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4254e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4254e-01
   1_xyz:  10.088  0.069  0.302 84.869  0.051  2.205   8.1690e-02
   1_adp:  10.088  0.069  0.302 84.869  0.051  2.205   8.1690e-02
   1_occ:  10.088  0.069  0.302 84.869  0.051  2.205   8.1690e-02
   2_bss:  10.088  0.069  0.302 84.869  0.051  2.205   8.1690e-02
   2_xyz:   8.338  0.038  0.233 81.176  0.032  2.364   4.9067e-02
   2_adp:   8.338  0.038  0.233 81.176  0.032  2.364   4.9067e-02
   2_occ:   8.338  0.038  0.233 81.176  0.032  2.364   4.9067e-02
   3_bss:   8.338  0.038  0.233 81.176  0.032  2.364   4.9067e-02
   3_xyz:   8.485  0.047  0.257 83.883  0.036  2.287   5.9483e-02
   3_adp:   8.485  0.047  0.257 83.883  0.036  2.287   5.9483e-02
   3_occ:   8.485  0.047  0.257 83.883  0.036  2.287   5.9483e-02
   4_bss:   8.485  0.047  0.257 83.883  0.036  2.287   5.9483e-02
   4_xyz:   8.178  0.040  0.211 83.497  0.037  2.400   3.4752e-02
   4_adp:   8.178  0.040  0.211 83.497  0.037  2.400   3.4752e-02
   4_occ:   8.178  0.040  0.211 83.497  0.037  2.400   3.4752e-02
   5_bss:   8.178  0.040  0.211 83.497  0.037  2.400   3.4752e-02
   5_xyz:   8.347  0.043  0.238 85.154  0.036  2.325   4.2248e-02
   5_adp:   8.347  0.043  0.238 85.154  0.036  2.325   4.2248e-02
   5_occ:   8.347  0.043  0.238 85.154  0.036  2.325   4.2248e-02
   5_bss:   8.347  0.043  0.238 85.154  0.036  2.325   4.2248e-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:  89.72   0.00  17.88  71.90   0.00  13.36  89.72   2.22  42.47
   1_occ:  89.72   0.00  17.88  71.90   0.00  13.36  89.72   2.22  42.47
   2_bss:  89.72   0.00  17.88  71.90   0.00  13.36  89.72   2.22  42.47
   2_xyz:  89.72   0.00  17.88  71.90   0.00  13.36  89.72   2.22  42.47
   2_adp:  88.55   0.00  17.68  72.00   0.00  13.24  88.55   5.53  41.88
   2_occ:  88.55   0.00  17.68  72.00   0.00  13.24  88.55   5.53  41.88
   3_bss:  88.55   0.00  17.68  72.00   0.00  13.24  88.55   5.53  41.88
   3_xyz:  88.55   0.00  17.68  72.00   0.00  13.24  88.55   5.53  41.88
   3_adp:  95.93   0.00  17.99  86.16   0.00  13.28  95.93   5.86  43.62
   3_occ:  95.93   0.00  17.99  86.16   0.00  13.28  95.93   5.86  43.62
   4_bss:  95.93   0.00  17.99  86.16   0.00  13.28  95.93   5.86  43.62
   4_xyz:  95.93   0.00  17.99  86.16   0.00  13.28  95.93   5.86  43.62
   4_adp:  93.78   0.98  17.58  85.11   0.98  13.12  93.78   6.04  41.87
   4_occ:  93.78   0.98  17.58  85.11   0.98  13.12  93.78   6.04  41.87
   5_bss:  93.78   0.98  17.58  85.11   0.98  13.12  93.78   6.04  41.87
   5_xyz:  93.78   0.98  17.58  85.11   0.98  13.12  93.78   6.04  41.87
   5_adp:  98.11   0.00  17.63  89.47   0.00  13.10  98.11   5.76  42.30
   5_occ:  98.11   0.00  17.63  89.47   0.00  13.10  98.11   5.76  42.30
   5_bss:  98.11   0.00  17.64  89.48   0.00  13.11  98.11   5.76  42.30
------------------------------------------------------------------------
 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:    1.224    0.027    0.393
   1_adp:    1.224    0.027    0.393
   1_occ:    1.224    0.027    0.393
   2_bss:    1.224    0.027    0.393
   2_xyz:    1.119    0.034    0.442
   2_adp:    1.119    0.034    0.442
   2_occ:    1.119    0.034    0.442
   3_bss:    1.119    0.034    0.442
   3_xyz:    1.129    0.038    0.507
   3_adp:    1.129    0.038    0.507
   3_occ:    1.129    0.038    0.507
   4_bss:    1.129    0.038    0.507
   4_xyz:    1.206    0.050    0.514
   4_adp:    1.206    0.050    0.514
   4_occ:    1.206    0.050    0.514
   5_bss:    1.206    0.050    0.514
   5_xyz:    1.347    0.056    0.527
   5_adp:    1.347    0.056    0.527
   5_occ:    1.347    0.056    0.527
   5_bss:    1.347    0.056    0.527
------------------------------------------------------------------------

CPU time actual refinement: 345.69


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1129/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_1129/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1129/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1129/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1129/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 345.53 
  Macro-tasks:
    bulk solvent and scale       = 42.05  
    individual site refinement   = 145.49 
    weights calculation          = 29.73  
    collect and process          = 6.48   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 223.84 
  Micro-tasks:
    mask                            = 1.84   
    f_calc                          = 112.08 
    alpha_beta                      = 8.15   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 120.34 
    fmodel                         = 7.07   
    r_factors                      = 0.31   
    phase_errors                   = 10.75  
    foms                           = 0.23   
    TOTAL for micro-tasks          = 261.92 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.897 micro seconds
Total CPU time: 5.99 minutes
from_scatterers_fft:    633 calls, 111.79 s
gradients_fft:          578 calls, 107.11 s

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

# Date 2008-01-16 Time 06:29:55 PST -0800 (1200493795.91 s)
Start R-work = 0.3934, R-free = 0.3860 (no bulk solvent and anisotropic scale)
Final R-work = 0.1359, R-free = 0.1799 (no bulk solvent and anisotropic scale)

Start R-work = 0.3840, R-free = 0.3785
Final R-work = 0.1124, R-free = 0.1604