# Date 2008-01-16 Time 04:49:59 PST -0800 (1200487799.16 s)
#phil __OFF__

Command line arguments: "../481.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 14152
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 481

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.5475, 48.1033, 87.6859, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 48.1033, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0589 1.98081
Completeness in resolution range: 0.930417
Completeness with d_max=infinity: 0.927597

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0589
                             d_min =   1.9808

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 48.1033, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0589 1.98081
Completeness in resolution range: 0.930417
Completeness with d_max=infinity: 0.927597

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0593 -  4.2388 [2211/2239]  1988   223  10.1%
  bin  2:  4.2388 -  3.3769 [2116/2139]  1904   212  10.0%
  bin  3:  3.3769 -  2.9537 [2090/2115]  1881   209  10.0%
  bin  4:  2.9537 -  2.6853 [2083/2099]  1875   208  10.0%
  bin  5:  2.6853 -  2.4938 [2034/2078]  1829   205  10.1%
  bin  6:  2.4938 -  2.3473 [2066/2094]  1864   202   9.8%
  bin  7:  2.3473 -  2.2302 [2034/2070]  1830   204  10.0%
  bin  8:  2.2302 -  2.1334 [2033/2075]  1828   205  10.1%
  bin  9:  2.1334 -  2.0514 [2024/2070]  1829   195   9.6%
  bin 10:  2.0514 -  1.9808 [ 898/2075]   802    96  10.7%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_481/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:
        1.78 -     2.41: 25
        2.41 -     3.03: 2078
        3.03 -     3.65: 4593
        3.65 -     4.28: 8928
        4.28 -     4.90: 12321
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.783 3.040 -x+1,y-1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  81 " - " O   HOH Z 186 "  1.833 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.864 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  70 " - " O   HOH Z 296 "  1.935 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 27940 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_481/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_481/model_refine_001.geo

CPU time processing inputs: 9.10


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.5475 48.10325 87.68585 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 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4644   r_free= 0.4528   ksol= 0.00   Bsol= 0.00   scale= 0.881    |
|                                                                             |
| 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:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.278188                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0593 -  4.7279 0.99   1438  159 0.3718 0.3890      6.5659      6.5796|
|  2:  4.7279 -  3.7721 0.99   1383  155 0.4134 0.4265      6.8423      6.8572|
|  3:  3.7721 -  3.3010 0.99   1348  149 0.4473 0.4082      6.6762      6.6083|
|  4:  3.3010 -  3.0018 0.99   1349  144 0.4580 0.4215      6.5021      6.4612|
|  5:  3.0018 -  2.7881 0.98   1334  151 0.4983 0.4419      6.3614      6.3727|
|  6:  2.7881 -  2.6246 0.99   1332  148 0.5004 0.4886       6.274       6.153|
|  7:  2.6246 -  2.4938 0.98   1293  151 0.4857 0.4396      6.2143      6.1291|
|  8:  2.4938 -  2.3857 0.99   1334  139 0.4991 0.4826      6.1683      6.1432|
|  9:  2.3857 -  2.2942 0.99   1327  152 0.4941 0.4709      6.0975      6.1684|
| 10:  2.2942 -  2.2152 0.98   1317  141 0.5118 0.4910      6.0892      6.0678|
| 11:  2.2152 -  2.1462 0.97   1299  146 0.5226 0.5180      6.0264      6.0124|
| 12:  2.1462 -  2.0850 0.99   1297  153 0.5000 0.5304       5.936       5.986|
| 13:  2.0850 -  2.0302 0.92   1228  127 0.5129 0.5419      5.8621      5.8434|
| 14:  2.0302 -  1.9808 0.27    351   44 0.4692 0.4647       5.885      5.7102|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0593 -  4.7279  1438   159  0.68  35.60   0.82     0.71      75400.51|
|  2:  4.7279 -  3.7721  1383   155  0.70  35.09   0.90     0.79     104317.65|
|  3:  3.7721 -  3.3010  1348   149  0.61  42.69   0.88     0.78     107616.30|
|  4:  3.3010 -  3.0018  1349   144  0.54  48.75   0.90     0.71      91541.90|
|  5:  3.0018 -  2.7881  1334   151  0.47  54.27   0.87     0.65      72195.97|
|  6:  2.7881 -  2.6246  1332   148  0.45  55.82   0.88     0.61      60873.07|
|  7:  2.6246 -  2.4938  1293   151  0.45  56.22   0.91     0.60      56257.91|
|  8:  2.4938 -  2.3857  1334   139  0.44  56.84   0.90     0.60      50911.92|
|  9:  2.3857 -  2.2942  1327   152  0.43  57.46   0.90     0.62      48569.46|
| 10:  2.2942 -  2.2152  1317   141  0.43  57.78   0.92     0.62      43250.08|
| 11:  2.2152 -  2.1462  1299   146  0.38  61.80   0.92     0.58      44556.72|
| 12:  2.1462 -  2.0850  1297   153  0.32  66.25   0.91     0.50      43935.46|
| 13:  2.0850 -  2.0302  1228   127  0.26  70.44   0.90     0.42      40151.56|
| 14:  2.0302 -  1.9808   351    44  0.31  67.00   1.00     0.38      29702.98|
|alpha:            min =        0.38 max =            0.79 mean =         0.63|
|beta:             min =    29702.98 max =       107616.30 mean =     64396.58|
|figures of merit: min =        0.00 max =            1.00 mean =         0.48|
|phase err.(work): min =        0.00 max =           90.00 mean =        53.71|
|phase err.(test): min =        0.00 max =           89.93 mean =        53.86|
|-----------------------------------------------------------------------------|

============================== 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 = 13.308086             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 91.538   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.951790              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.925   (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 |  1.783 -  2.094:        9 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.094 -  2.406:       16 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.406 -  2.718:      148 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.718 -  3.030:     1930 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.030 -  3.341:     1841 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.341 -  3.653:     2752 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.653 -  3.965:     4644 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.965 -  4.277:     4284 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.277 -  4.588:     5594 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.588 -  4.900:     6727 |
|-----------------------------------------------------------------------------|
|-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 |        0.170 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.113    4.900  1.783 |       0.262 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.144)------------------------------------------|
|    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 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4644   r_free= 0.4528   ksol= 0.00   Bsol= 0.00   scale= 0.881    |
|                                                                             |
| 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:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.278188                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4559   r_free= 0.4411   ksol= 0.30   Bsol= 50.00   scale= 0.920   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.15,4.63,1.08,0.00,0.00,0.00); trace/3= 0.86                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.271256                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.543655             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 91.019   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.064330              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.632   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4559      final r-factor (work) = 0.3457          |
| start r-factor (free) = 0.4411      final r-factor (free) = 0.3732          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 36.3541 = 11.54 * 0.50 * 6.2691 + 1.00 * 0.1699                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 35.5844 = 11.54 * 0.50 * 6.1364 + 1.00 * 0.1662                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3457      final r-factor (work) = 0.3154          |
| start r-factor (free) = 0.3732      final r-factor (free) = 0.3881          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.5371 = 1.06 * 1.00 * 6.1364 + 1.00 * 0.0059                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.4421 = 1.06 * 1.00 * 6.0348 + 1.00 * 0.0190                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.144)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    105.42  18.75    None  None   None       |
|    all(noH): 2823   0      0.00    105.42  18.75    None  None   None       |
|    Sol.    : 438    0      0.00    105.42  38.57    None  None   None       |
|    Mac.    : 2385   0      0.00    82.01   15.11    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.542:  995   |   5:    52.710 -  63.252:   82        |
|      1:    10.542 -  21.084:  937   |   6:    63.252 -  73.794:   32        |
|      2:    21.084 -  31.626:  429   |   7:    73.794 -  84.335:   14        |
|      3:    31.626 -  42.168:  214   |   8:    84.335 -  94.877:    6        |
|      4:    42.168 -  52.710:  111   |   9:    94.877 - 105.419:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3154 r_free = 0.3881             target_work(ml) = 6.045         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3153 r_free = 0.3874             target_work(ml) = 6.044         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3153   r_free= 0.3874   ksol= 0.30   Bsol= 50.00   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.15,4.63,1.08,0.00,0.00,0.00); trace/3= 0.86                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.043766                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3137   r_free= 0.3845   ksol= 0.32   Bsol= 69.89   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.83,2.36,0.59,0.00,0.00,0.00); trace/3= 0.37                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.044132                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.176869             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 93.784   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.481954              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 150.481  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3137      final r-factor (work) = 0.2400          |
| start r-factor (free) = 0.3845      final r-factor (free) = 0.2955          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 36.9161 = 12.18 * 0.50 * 6.0360 + 1.00 * 0.1662                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 36.3535 = 12.18 * 0.50 * 5.9501 + 1.00 * 0.1264                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2400      final r-factor (work) = 0.2199          |
| start r-factor (free) = 0.2955      final r-factor (free) = 0.2750          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8867 = 0.48 * 1.00 * 5.9501 + 1.00 * 0.0190                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7895 = 0.48 * 1.00 * 5.7631 + 1.00 * 0.0120                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.144)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.33   17.97    None  None   None       |
|    all(noH): 2823   0      0.00    99.33   17.97    None  None   None       |
|    Sol.    : 438    0      2.46    99.33   40.18    None  None   None       |
|    Mac.    : 2385   0      0.00    82.71   13.90    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 -   9.933: 1028   |   5:    49.665 -  59.598:   90        |
|      1:     9.933 -  19.866:  996   |   6:    59.598 -  69.531:   41        |
|      2:    19.866 -  29.799:  317   |   7:    69.531 -  79.464:   23        |
|      3:    29.799 -  39.732:  195   |   8:    79.464 -  89.397:    7        |
|      4:    39.732 -  49.665:  122   |   9:    89.397 -  99.330:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2199 r_free = 0.2750             target_work(ml) = 5.733         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2196 r_free = 0.2751             target_work(ml) = 5.732         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2196   r_free= 0.2751   ksol= 0.32   Bsol= 69.89   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.83,2.36,0.59,0.00,0.00,0.00); trace/3= 0.37                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.732481                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2194   r_free= 0.2746   ksol= 0.33   Bsol= 66.42   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.99,0.72,0.06,0.00,0.00,0.00); trace/3= -0.41                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.732373                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.934092              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.741   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.746697              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 158.529  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2194      final r-factor (work) = 0.1638          |
| start r-factor (free) = 0.2746      final r-factor (free) = 0.2063          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.1103 = 6.93 * 0.50 * 5.7639 + 1.00 * 0.1264                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.5789 = 6.93 * 0.50 * 5.6217 + 1.00 * 0.0884                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1638      final r-factor (work) = 0.1467          |
| start r-factor (free) = 0.2063      final r-factor (free) = 0.1947          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2096 = 0.75 * 1.00 * 5.6217 + 1.00 * 0.0120                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0538 = 0.75 * 1.00 * 5.4116 + 1.00 * 0.0130                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.144)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    100.93  17.91    None  None   None       |
|    all(noH): 2823   0      0.00    100.93  17.91    None  None   None       |
|    Sol.    : 438    0      4.01    100.93  44.41    None  None   None       |
|    Mac.    : 2385   0      0.00    94.21   13.04    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.093: 1139   |   5:    50.467 -  60.560:   99        |
|      1:    10.093 -  20.187: 1004   |   6:    60.560 -  70.654:   66        |
|      2:    20.187 -  30.280:  226   |   7:    70.654 -  80.747:   33        |
|      3:    30.280 -  40.374:  126   |   8:    80.747 -  90.841:   11        |
|      4:    40.374 -  50.467:  114   |   9:    90.841 - 100.934:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1467 r_free = 0.1947             target_work(ml) = 5.381         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1467 r_free = 0.1947             target_work(ml) = 5.380         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1467   r_free= 0.1947   ksol= 0.33   Bsol= 66.42   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.99,0.72,0.06,0.00,0.00,0.00); trace/3= -0.41                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.380323                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1468   r_free= 0.1943   ksol= 0.34   Bsol= 75.04   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.27,-0.33,-0.22,-0.00,-0.00,-0.00); trace/3= -0.94                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.380907                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.915843              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 118.243  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.596505              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.607  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1468      final r-factor (work) = 0.1375          |
| start r-factor (free) = 0.1943      final r-factor (free) = 0.1844          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2751 = 1.92 * 0.50 * 5.4145 + 1.00 * 0.0884                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1833 = 1.92 * 0.50 * 5.3530 + 1.00 * 0.0555                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1375      final r-factor (work) = 0.1343          |
| start r-factor (free) = 0.1844      final r-factor (free) = 0.1817          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2059 = 0.60 * 1.00 * 5.3530 + 1.00 * 0.0129                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1836 = 0.60 * 1.00 * 5.3158 + 1.00 * 0.0127                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.144)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.47    104.80  17.64    None  None   None       |
|    all(noH): 2823   0      0.47    104.80  17.64    None  None   None       |
|    Sol.    : 438    0      3.87    101.58  44.66    None  None   None       |
|    Mac.    : 2385   0      0.47    104.80  12.68    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.473 -  10.906: 1326   |   5:    52.636 -  63.069:   82        |
|      1:    10.906 -  21.338:  905   |   6:    63.069 -  73.501:   58        |
|      2:    21.338 -  31.771:  175   |   7:    73.501 -  83.934:   34        |
|      3:    31.771 -  42.204:  119   |   8:    83.934 -  94.366:    9        |
|      4:    42.204 -  52.636:  110   |   9:    94.366 - 104.799:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1343 r_free = 0.1817             target_work(ml) = 5.306         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1342 r_free = 0.1819             target_work(ml) = 5.306         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1342   r_free= 0.1819   ksol= 0.34   Bsol= 75.04   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.27,-0.33,-0.22,-0.00,-0.00,-0.00); trace/3= -0.94                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.306223                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1341   r_free= 0.1820   ksol= 0.33   Bsol= 72.06   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.17,-0.53,-0.03,-0.00,-0.00,-0.00); trace/3= -0.91                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.306235                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.982407              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 135.259  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.437255              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 142.605  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1341      final r-factor (work) = 0.1203          |
| start r-factor (free) = 0.1820      final r-factor (free) = 0.1690          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.6400 = 3.98 * 0.50 * 5.3156 + 1.00 * 0.0555                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.5550 = 3.98 * 0.50 * 5.2586 + 1.00 * 0.0841                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1203      final r-factor (work) = 0.1188          |
| start r-factor (free) = 0.1690      final r-factor (free) = 0.1663          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3119 = 0.44 * 1.00 * 5.2586 + 1.00 * 0.0125                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2909 = 0.44 * 1.00 * 5.2131 + 1.00 * 0.0114                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.144)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    106.41  17.10    None  None   None       |
|    all(noH): 2823   0      0.00    106.41  17.10    None  None   None       |
|    Sol.    : 438    0      0.00    96.69   43.10    None  None   None       |
|    Mac.    : 2385   0      0.47    106.41  12.33    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.641: 1321   |   5:    53.203 -  63.844:   83        |
|      1:    10.641 -  21.281:  930   |   6:    63.844 -  74.484:   52        |
|      2:    21.281 -  31.922:  178   |   7:    74.484 -  85.125:   24        |
|      3:    31.922 -  42.562:  117   |   8:    85.125 -  95.765:    6        |
|      4:    42.562 -  53.203:  108   |   9:    95.765 - 106.406:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1188 r_free = 0.1663             target_work(ml) = 5.205         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1186 r_free = 0.1664             target_work(ml) = 5.205         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1186   r_free= 0.1664   ksol= 0.33   Bsol= 72.06   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.17,-0.53,-0.03,-0.00,-0.00,-0.00); trace/3= -0.91                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.204819                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0593 -  4.7279 0.99   1438  159 0.0970 0.1324      5.3946       5.591|
|  2:  4.7279 -  3.7721 0.99   1383  155 0.0830 0.1037      5.4264      5.6137|
|  3:  3.7721 -  3.3010 0.99   1348  149 0.1096 0.1628      5.4978      5.8985|
|  4:  3.3010 -  3.0018 0.99   1349  144 0.1316 0.1723      5.4992      5.6521|
|  5:  3.0018 -  2.7881 0.98   1334  151 0.1449 0.1825      5.4014      5.5697|
|  6:  2.7881 -  2.6246 0.99   1332  148 0.1379 0.2210      5.2976      5.5609|
|  7:  2.6246 -  2.4938 0.98   1293  151 0.1364 0.1741      5.2504      5.4406|
|  8:  2.4938 -  2.3857 0.99   1334  139 0.1279 0.1805      5.1717      5.3715|
|  9:  2.3857 -  2.2942 0.99   1327  152 0.1289 0.2031       5.102      5.4097|
| 10:  2.2942 -  2.2152 0.98   1317  141 0.1248 0.1737      5.0291      5.2078|
| 11:  2.2152 -  2.1462 0.97   1299  146 0.1222 0.1881      4.9592      5.2633|
| 12:  2.1462 -  2.0850 0.99   1297  153 0.1169 0.1627      4.8798      5.1165|
| 13:  2.0850 -  2.0302 0.92   1228  127 0.1191 0.1881      4.8029      5.0777|
| 14:  2.0302 -  1.9808 0.27    351   44 0.1012 0.1739       4.721      4.9391|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0593 -  4.7279  1438   159  0.94   9.41   0.97     0.94       7617.37|
|  2:  4.7279 -  3.7721  1383   155  0.95   8.40   1.01     0.99       9384.41|
|  3:  3.7721 -  3.3010  1348   149  0.93  11.88   1.02     1.02      11025.70|
|  4:  3.3010 -  3.0018  1349   144  0.91  14.95   1.01     1.00      11321.43|
|  5:  3.0018 -  2.7881  1334   151  0.89  17.35   1.00     0.98       9720.25|
|  6:  2.7881 -  2.6246  1332   148  0.88  18.34   0.98     0.95       8447.81|
|  7:  2.6246 -  2.4938  1293   151  0.89  17.56   0.99     0.96       7617.41|
|  8:  2.4938 -  2.3857  1334   139  0.89  17.64   0.99     0.95       6737.06|
|  9:  2.3857 -  2.2942  1327   152  0.89  17.31   0.99     0.93       5715.64|
| 10:  2.2942 -  2.2152  1317   141  0.89  17.45   0.99     0.95       5153.34|
| 11:  2.2152 -  2.1462  1299   146  0.89  17.00   0.98     0.94       4554.36|
| 12:  2.1462 -  2.0850  1297   153  0.90  16.30   1.00     0.98       3995.25|
| 13:  2.0850 -  2.0302  1228   127  0.90  16.90   0.98     0.96       3460.45|
| 14:  2.0302 -  1.9808   351    44  0.90  15.64   0.96     0.91       2953.23|
|alpha:            min =        0.91 max =            1.02 mean =         0.96|
|beta:             min =     2953.23 max =        11321.43 mean =      7253.49|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.85 mean =        15.35|
|phase err.(test): min =        0.00 max =           88.89 mean =        14.80|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1188   r_free= 0.1663   ksol= 0.33   Bsol= 67.29   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.17,-0.54,-0.03,-0.00,-0.00,-0.00); trace/3= -0.91                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.204105                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1188   r_free= 0.1663   ksol= 0.33   Bsol= 67.29   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.17,-0.54,-0.03,-0.00,-0.00,-0.00); trace/3= -0.91                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.204105                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0593 -  4.7279 0.99   1438  159 0.0979 0.1299      5.3806      5.5675|
|  2:  4.7279 -  3.7721 0.99   1383  155 0.0836 0.1042       5.425      5.6256|
|  3:  3.7721 -  3.3010 0.99   1348  149 0.1095 0.1630      5.5006      5.8951|
|  4:  3.3010 -  3.0018 0.99   1349  144 0.1321 0.1732      5.5015      5.6531|
|  5:  3.0018 -  2.7881 0.98   1334  151 0.1452 0.1832      5.4027       5.571|
|  6:  2.7881 -  2.6246 0.99   1332  148 0.1378 0.2213      5.2979      5.5623|
|  7:  2.6246 -  2.4938 0.98   1293  151 0.1365 0.1742      5.2512      5.4405|
|  8:  2.4938 -  2.3857 0.99   1334  139 0.1278 0.1807      5.1719      5.3718|
|  9:  2.3857 -  2.2942 0.99   1327  152 0.1288 0.2029      5.1018      5.4099|
| 10:  2.2942 -  2.2152 0.98   1317  141 0.1248 0.1736      5.0289      5.2069|
| 11:  2.2152 -  2.1462 0.97   1299  146 0.1222 0.1882      4.9591      5.2633|
| 12:  2.1462 -  2.0850 0.99   1297  153 0.1169 0.1629      4.8796      5.1164|
| 13:  2.0850 -  2.0302 0.92   1228  127 0.1190 0.1882      4.8029      5.0781|
| 14:  2.0302 -  1.9808 0.27    351   44 0.1013 0.1739      4.7211      4.9389|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0593 -  4.7279  1438   159  0.94   9.14   0.96     0.93       7130.15|
|  2:  4.7279 -  3.7721  1383   155  0.95   8.33   1.01     0.99       9222.64|
|  3:  3.7721 -  3.3010  1348   149  0.93  11.92   1.02     1.02      11124.18|
|  4:  3.3010 -  3.0018  1349   144  0.91  14.98   1.01     1.00      11355.34|
|  5:  3.0018 -  2.7881  1334   151  0.89  17.37   1.00     0.98       9737.42|
|  6:  2.7881 -  2.6246  1332   148  0.88  18.34   0.98     0.95       8453.70|
|  7:  2.6246 -  2.4938  1293   151  0.89  17.58   0.99     0.96       7633.11|
|  8:  2.4938 -  2.3857  1334   139  0.89  17.63   0.99     0.95       6739.18|
|  9:  2.3857 -  2.2942  1327   152  0.89  17.32   0.99     0.93       5720.23|
| 10:  2.2942 -  2.2152  1317   141  0.89  17.45   0.99     0.95       5149.67|
| 11:  2.2152 -  2.1462  1299   146  0.89  16.99   0.98     0.94       4552.59|
| 12:  2.1462 -  2.0850  1297   153  0.90  16.30   1.00     0.98       3994.93|
| 13:  2.0850 -  2.0302  1228   127  0.90  16.90   0.98     0.96       3461.05|
| 14:  2.0302 -  1.9808   351    44  0.90  15.65   0.96     0.91       2954.63|
|alpha:            min =        0.91 max =            1.02 mean =         0.96|
|beta:             min =     2954.63 max =        11355.34 mean =      7214.23|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.76 mean =        15.33|
|phase err.(test): min =        0.00 max =           88.98 mean =        14.74|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.144)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    106.41  17.10    None  None   None       |
|    all(noH): 2823   0      0.00    106.41  17.10    None  None   None       |
|    Sol.    : 438    0      0.00    96.69   43.10    None  None   None       |
|    Mac.    : 2385   0      0.47    106.41  12.33    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -  10.644: 1321   |   5:    53.206 -  63.847:   83        |
|      1:    10.644 -  21.284:  930   |   6:    63.847 -  74.487:   52        |
|      2:    21.284 -  31.925:  178   |   7:    74.487 -  85.128:   24        |
|      3:    31.925 -  42.565:  117   |   8:    85.128 -  95.768:    6        |
|      4:    42.565 -  53.206:  108   |   9:    95.768 - 106.409:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 322         
Filter by distance & map next to the model:
   mapped sites are within: 0.714 - 5.528
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 320 from: 322
   mapped sites are within: 0.714 - 5.528

peak=    5.987 closest distance to " O   HOH Z 210 " =    1.407
peak=    5.030 closest distance to " O   HOH Z 113 " =    1.942
peak=    4.956 closest distance to " O   HOH Z  49 " =    1.315
peak=    4.932 closest distance to " O   HOH Z  43 " =    2.153
peak=    4.888 closest distance to " O   HOH Z 403 " =    1.987
peak=    4.820 closest distance to " CB  SER A  63 " =    1.110
peak=    4.815 closest distance to " O   HOH Z 117 " =    1.255
peak=    4.775 closest distance to " CB  GLN A 183 " =    1.253
peak=    4.736 closest distance to " CD2 TRP A 179 " =    1.327
peak=    4.703 closest distance to " CA  TYR A  30 " =    0.947
peak=    4.633 closest distance to " CG  PRO A  54 " =    1.296
peak=    4.574 closest distance to " O   HOH Z 248 " =    1.464
peak=    4.535 closest distance to " O   HOH Z 214 " =    1.484
peak=    4.532 closest distance to " CB  GLN A 223 " =    1.458
peak=    4.524 closest distance to " O   HOH Z 433 " =    1.698
peak=    4.488 closest distance to " O   HOH Z 130 " =    2.658
peak=    4.450 closest distance to " O   HOH Z  63 " =    2.027
peak=    4.412 closest distance to " CG  PRO A  90 " =    1.281
peak=    4.358 closest distance to " O   HOH Z 369 " =    2.206
peak=    4.355 closest distance to " O   HOH Z 176 " =    1.824
peak=    4.313 closest distance to " O   HOH Z  40 " =    1.984
peak=    4.309 closest distance to " CA  ALA A  51 " =    1.029
peak=    4.302 closest distance to " CB  ARG A 275 " =    0.819
peak=    4.301 closest distance to " O   HOH Z 102 " =    1.411
peak=    4.292 closest distance to " O   HOH Z  44 " =    2.098
peak=    4.273 closest distance to " CB  ARG A 190 " =    1.807
peak=    4.272 closest distance to " CG  PRO A 280 " =    0.714
peak=    4.260 closest distance to " O   HOH Z 232 " =    2.436
peak=    4.232 closest distance to " CB  TRP A 179 " =    1.250
peak=    4.229 closest distance to " NE2 GLN A  11 " =    1.232
peak=    4.222 closest distance to " O   HOH Z 425 " =    1.554
peak=    4.212 closest distance to " O  BHOH Z  74 " =    1.341
peak=    4.210 closest distance to " O   HOH Z 402 " =    1.624
peak=    4.199 closest distance to " O   PRO A 198 " =    1.512
peak=    4.185 closest distance to " CB  GLU A 277 " =    3.787
peak=    4.166 closest distance to " CD  LYS A 166 " =    1.473
peak=    4.131 closest distance to " O   HOH Z 134 " =    1.928
peak=    4.129 closest distance to " CG1 ILE A  33 " =    1.203
peak=    4.124 closest distance to " O   HOH Z 431 " =    1.192
peak=    4.112 closest distance to " O   HOH Z 406 " =    1.606
peak=    4.100 closest distance to " O   HOH Z 124 " =    1.172
peak=    4.092 closest distance to " O   HOH Z 154 " =    2.255
peak=    4.090 closest distance to " CB  ARG A  79 " =    1.418
peak=    4.070 closest distance to " O   SER A  87 " =    2.260
peak=    4.066 closest distance to " CB  GLU A 152 " =    1.099
peak=    4.043 closest distance to " O   HOH Z   7 " =    1.165
peak=    4.038 closest distance to " O   HOH Z 154 " =    1.736
peak=    4.030 closest distance to " O   HOH Z 234 " =    3.629
peak=    4.029 closest distance to " O   HOH Z  65 " =    1.033
peak=    4.020 closest distance to " O   HOH Z 126 " =    1.609
peak=    4.013 closest distance to " O   HOH Z 203 " =    1.744
peak=    3.995 closest distance to " OE1 GLN A  55 " =    1.588
peak=    3.994 closest distance to " O   HOH Z 412 " =    3.390
peak=    3.983 closest distance to " ND2 ASN A 249 " =    2.071
peak=    3.953 closest distance to " O   HOH Z 368 " =    2.096
peak=    3.943 closest distance to " CG2BVAL A  41 " =    0.889
peak=    3.935 closest distance to " O   HOH Z 336 " =    1.938
peak=    3.933 closest distance to " O   HOH Z 423 " =    1.839
peak=    3.932 closest distance to " O   HOH Z 265 " =    1.927
peak=    3.932 closest distance to " O   HOH Z 345 " =    1.716
peak=    3.919 closest distance to " O   HOH Z 189 " =    2.872
peak=    3.918 closest distance to " OG BSER A 164 " =    2.220
peak=    3.918 closest distance to " O   HOH Z 298 " =    1.865
peak=    3.910 closest distance to " O   HOH Z 346 " =    1.542
peak=    3.902 closest distance to " O   HOH Z 394 " =    1.573
peak=    3.900 closest distance to " CA  ARG A  36 " =    1.102
peak=    3.894 closest distance to " O   ALA A 165 " =    1.382
peak=    3.884 closest distance to " CG2 VAL A 197 " =    1.167
peak=    3.872 closest distance to " O   HOH Z  80 " =    1.931
peak=    3.868 closest distance to " CA  ASN A 176 " =    1.785
peak=    3.864 closest distance to " CB  ASN A 285 " =    0.932
peak=    3.862 closest distance to " CB  SER A 141 " =    1.112
peak=    3.856 closest distance to " CG  PRO A 213 " =    1.260
peak=    3.853 closest distance to " O   HOH Z 132 " =    2.795
peak=    3.849 closest distance to " O   HOH Z 196 " =    1.471
peak=    3.831 closest distance to " O   HOH Z 418 " =    1.811
peak=    3.824 closest distance to " O   HOH Z 209 " =    2.327
peak=    3.818 closest distance to " CB  PRO A  54 " =    0.862
peak=    3.817 closest distance to " CB  ASN A 148 " =    1.464
peak=    3.811 closest distance to " O   HOH Z 261 " =    2.488
peak=    3.809 closest distance to " CA  ARG A 195 " =    1.161
peak=    3.804 closest distance to " O   HOH Z 258 " =    2.190
peak=    3.799 closest distance to " NE2 GLN A  77 " =    3.181
peak=    3.794 closest distance to " CG  GLN A  58 " =    0.993
peak=    3.786 closest distance to " O  BHOH Z 338 " =    1.124
peak=    3.777 closest distance to " OE1 GLN A  11 " =    2.144
peak=    3.774 closest distance to " O   HOH Z 144 " =    1.851
peak=    3.773 closest distance to " CB  SER A  26 " =    1.735
peak=    3.770 closest distance to " O   ASP A 124 " =    1.662
peak=    3.764 closest distance to " O   HOH Z 417 " =    2.954
peak=    3.763 closest distance to " O   HOH Z 132 " =    2.483
peak=    3.758 closest distance to " CB  THR A  52 " =    0.841
peak=    3.752 closest distance to " CG AARG A 275 " =    1.243
peak=    3.752 closest distance to " CD  PRO A  54 " =    1.017
peak=    3.744 closest distance to " O   HOH Z 414 " =    1.685
peak=    3.740 closest distance to " CB  VAL A 202 " =    1.524
peak=    3.736 closest distance to " O   HOH Z 437 " =    1.910
peak=    3.736 closest distance to " O   HOH Z 128 " =    2.044
peak=    3.735 closest distance to " CB  ASN A 142 " =    1.167
peak=    3.729 closest distance to " O   HOH Z 422 " =    2.547
peak=    3.727 closest distance to " CD  LYS A  76 " =    1.925
peak=    3.727 closest distance to " O   HOH Z  20 " =    1.631
peak=    3.727 closest distance to " O   HOH Z 362 " =    3.344
peak=    3.710 closest distance to " CZ3 TRP A 266 " =    1.064
peak=    3.704 closest distance to " CA  TYR A 116 " =    1.293
peak=    3.704 closest distance to " O   HOH Z 422 " =    0.783
peak=    3.696 closest distance to " O   HOH Z 147 " =    1.716
peak=    3.694 closest distance to " CB  GLU A 128 " =    1.155
peak=    3.692 closest distance to " CD  ARG A 269 " =    0.999
peak=    3.691 closest distance to " NH2 ARG A 156 " =    1.215
peak=    3.668 closest distance to " O   HOH Z  78 " =    1.653
peak=    3.666 closest distance to " O   HOH Z 357 " =    2.172
peak=    3.662 closest distance to " N   CYS A 260 " =    0.841
peak=    3.661 closest distance to " O   HOH Z  15 " =    2.225
peak=    3.652 closest distance to " CA  LEU A  83 " =    1.306
peak=    3.646 closest distance to " CB  ARG A  79 " =    0.951
peak=    3.645 closest distance to " O   HOH Z  39 " =    1.193
peak=    3.642 closest distance to " O   HOH Z 130 " =    2.360
peak=    3.636 closest distance to " O   HOH Z 156 " =    2.588
peak=    3.633 closest distance to " O   HOH Z 313 " =    1.823
peak=    3.631 closest distance to " OH  TYR A 116 " =    1.245
peak=    3.619 closest distance to " CB  TYR A 169 " =    0.854
peak=    3.619 closest distance to " CG1BVAL A  72 " =    1.910
peak=    3.604 closest distance to " O   HOH Z 251 " =    1.600
peak=    3.604 closest distance to " CB  SER A  62 " =    0.833
peak=    3.596 closest distance to " CA  ALA A 100 " =    1.094
peak=    3.591 closest distance to " O   HOH Z 139 " =    1.374
peak=    3.585 closest distance to " O   HOH Z 189 " =    2.551
peak=    3.582 closest distance to " O   HOH Z 146 " =    1.534
peak=    3.576 closest distance to " CA  ALA A 160 " =    0.932
peak=    3.574 closest distance to " CA  ILE A 106 " =    0.810
peak=    3.573 closest distance to " O   HOH Z 394 " =    3.863
peak=    3.571 closest distance to " O   HOH Z 365 " =    2.512
peak=    3.560 closest distance to " CG2 THR A 221 " =    1.023
peak=    3.558 closest distance to " NZ  LYS A 117 " =    2.899
peak=    3.558 closest distance to " O   HOH Z 146 " =    1.218
peak=    3.557 closest distance to " O   HOH Z 227 " =    1.721
peak=    3.556 closest distance to " O   HOH Z 291 " =    1.443
peak=    3.549 closest distance to " O   HOH Z 284 " =    2.933
peak=    3.549 closest distance to " ND2 ASN A 187 " =    1.469
peak=    3.547 closest distance to " O   HOH Z  61 " =    1.582
peak=    3.547 closest distance to " CA  ALA A 295 " =    1.025
peak=    3.545 closest distance to " CZ  PHE A  38 " =    1.211
peak=    3.539 closest distance to " CB  GLU A  46 " =    1.052
peak=    3.535 closest distance to " O   HOH Z 244 " =    1.705
peak=    3.529 closest distance to " CB  MET A 105 " =    1.150
peak=    3.528 closest distance to " O   HOH Z  30 " =    1.255
peak=    3.524 closest distance to " OE1 GLN A  58 " =    3.292
peak=    3.517 closest distance to " N   ASN A  39 " =    1.382
peak=    3.516 closest distance to " O   HOH Z 245 " =    1.346
peak=    3.510 closest distance to " CA  SER A  32 " =    1.655
peak=    3.507 closest distance to " NH2BARG A 145 " =    2.039
peak=    3.507 closest distance to " CB  LEU A  83 " =    0.848
peak=    3.505 closest distance to " O   HOH Z 316 " =    2.986
peak=    3.505 closest distance to " CB  TRP A 266 " =    1.034
peak=    3.499 closest distance to " OG  SER A 276 " =    1.609
peak=    3.497 closest distance to " CB  ASP A 124 " =    0.742
peak=    3.491 closest distance to " CD  ARG A 195 " =    0.982
peak=    3.485 closest distance to " O   HOH Z 150 " =    1.727
peak=    3.480 closest distance to " O   HOH Z 435 " =    1.782
peak=    3.471 closest distance to " O   HOH Z 247 " =    1.426
peak=    3.454 closest distance to " CA  GLU A 152 " =    0.874
peak=    3.451 closest distance to " CB  PHE A  16 " =    1.132
peak=    3.444 closest distance to " O   HOH Z 298 " =    4.357
peak=    3.442 closest distance to " CA  SER A  12 " =    1.529
peak=    3.440 closest distance to " CG  PRO A 243 " =    1.146
peak=    3.433 closest distance to " O   HOH Z 301 " =    1.654
peak=    3.430 closest distance to " O   HOH Z 359 " =    1.556
peak=    3.429 closest distance to " O   HOH Z  47 " =    2.378
peak=    3.423 closest distance to " O   HOH Z 358 " =    1.294
peak=    3.422 closest distance to " O   HOH Z 281 " =    5.021
peak=    3.422 closest distance to " CA  VAL A 125 " =    1.247
peak=    3.420 closest distance to " CB  THR A  31 " =    1.670
peak=    3.416 closest distance to " CA  GLY A 196 " =    1.116
peak=    3.413 closest distance to " O   HOH Z  35 " =    2.068
peak=    3.411 closest distance to " O   ASN A  74 " =    1.684
peak=    3.409 closest distance to " CG  GLN A  11 " =    1.233
peak=    3.407 closest distance to " O   HOH Z 185 " =    1.712
peak=    3.404 closest distance to " CA  ALA A 158 " =    1.318
peak=    3.404 closest distance to " CD  LYS A 119 " =    1.858
peak=    3.402 closest distance to " CB  ASN A  39 " =    0.835
peak=    3.394 closest distance to " O   HOH Z 427 " =    2.965
peak=    3.391 closest distance to " CB  PRO A  54 " =    1.278
peak=    3.390 closest distance to " O   HOH Z 285 " =    2.889
peak=    3.389 closest distance to " NZ  LYS A  48 " =    1.225
peak=    3.386 closest distance to " O   HOH Z 199 " =    1.708
peak=    3.382 closest distance to " CG2 ILE A  20 " =    1.451
peak=    3.381 closest distance to " O   HOH Z 213 " =    2.282
peak=    3.381 closest distance to " O   HOH Z 286 " =    2.080
peak=    3.377 closest distance to " O   HOH Z 299 " =    4.273
peak=    3.375 closest distance to " O   HOH Z 250 " =    1.361
peak=    3.374 closest distance to " CG  MET A 185 " =    1.079
peak=    3.372 closest distance to " O   HOH Z 383 " =    2.209
peak=    3.372 closest distance to " NH1AARG A 145 " =    1.406
peak=    3.367 closest distance to " O   HOH Z 234 " =    1.979
peak=    3.366 closest distance to " CA  THR A  82 " =    1.509
peak=    3.364 closest distance to " N   HIS A 108 " =    1.791
peak=    3.354 closest distance to " CB  LEU A   5 " =    1.132
peak=    3.354 closest distance to " O  BHOH Z 338 " =    2.025
peak=    3.352 closest distance to " O   HOH Z 327 " =    1.680
peak=    3.346 closest distance to " O   HOH Z 393 " =    3.288
peak=    3.341 closest distance to " O   HOH Z 299 " =    4.123
peak=    3.340 closest distance to " CZ  PHE A 218 " =    1.236
peak=    3.339 closest distance to " CA  GLU A  46 " =    0.976
peak=    3.339 closest distance to " OD1 ASN A  69 " =    2.406
peak=    3.339 closest distance to " O   HOH Z 128 " =    2.192
peak=    3.338 closest distance to " O   HOH Z 142 " =    1.450
peak=    3.335 closest distance to " CB  SER A   3 " =    1.409
peak=    3.335 closest distance to " CD  ARG A 159 " =    0.832
peak=    3.333 closest distance to " O   HOH Z 279 " =    2.114
peak=    3.329 closest distance to " CB  ALA A   9 " =    1.606
peak=    3.326 closest distance to " O   GLY A  91 " =    1.199
peak=    3.324 closest distance to " O   HOH Z 193 " =    1.787
peak=    3.324 closest distance to " O   HOH Z 271 " =    2.604
peak=    3.322 closest distance to " O   HOH Z 163 " =    1.426
peak=    3.318 closest distance to " O   HOH Z 339 " =    2.255
peak=    3.317 closest distance to " O   HOH Z 173 " =    2.193
peak=    3.313 closest distance to " O   HOH Z  68 " =    1.918
peak=    3.311 closest distance to " OD2 ASP A 298 " =    3.822
peak=    3.311 closest distance to " O   HOH Z  88 " =    1.584
peak=    3.310 closest distance to " CD1 LEU A  96 " =    0.739
peak=    3.309 closest distance to " O   HOH Z  63 " =    2.131
peak=    3.309 closest distance to " CB  GLU A 175 " =    1.365
peak=    3.308 closest distance to " CG  ARG A 219 " =    1.204
peak=    3.306 closest distance to " O   HOH Z 240 " =    2.372
peak=    3.305 closest distance to " O   HOH Z 130 " =    1.107
peak=    3.301 closest distance to " CB  ASP A 140 " =    0.996
peak=    3.300 closest distance to " CA  ASP A 191 " =    1.002
peak=    3.299 closest distance to " CB  ALA A 100 " =    1.298
peak=    3.298 closest distance to " O   HOH Z 139 " =    4.760
peak=    3.294 closest distance to " CE  LYS A  76 " =    0.801
peak=    3.288 closest distance to " CB  ALA A  10 " =    1.357
peak=    3.284 closest distance to " CG2 THR A 220 " =    0.737
peak=    3.282 closest distance to " O   HOH Z 298 " =    2.326
peak=    3.281 closest distance to " CB  LEU A 228 " =    1.130
peak=    3.281 closest distance to " CD1 LEU A 228 " =    1.645
peak=    3.278 closest distance to " O   HOH Z  21 " =    1.820
peak=    3.276 closest distance to " CE1 TYR A 186 " =    1.222
peak=    3.273 closest distance to " CG1 VAL A 153 " =    1.098
peak=    3.272 closest distance to " CB  VAL A 257 " =    0.863
peak=    3.270 closest distance to " CD2 TYR A 186 " =    0.990
peak=    3.270 closest distance to " CB  ALA A  71 " =    1.325
peak=    3.269 closest distance to " O   HOH Z 126 " =    2.000
peak=    3.269 closest distance to " O   HOH Z  88 " =    3.456
peak=    3.269 closest distance to " CA  SER A  87 " =    1.023
peak=    3.264 closest distance to " O   HOH Z  54 " =    1.208
peak=    3.260 closest distance to " O   TYR A 116 " =    1.441
peak=    3.259 closest distance to " O   HOH Z 435 " =    2.904
peak=    3.259 closest distance to " O   HOH Z  83 " =    1.669
peak=    3.258 closest distance to " O   HOH Z 285 " =    1.626
peak=    3.251 closest distance to " O   HOH Z 421 " =    1.949
peak=    3.246 closest distance to " CA  LYS A 166 " =    1.365
peak=    3.246 closest distance to " CA  ASP A 162 " =    1.133
peak=    3.240 closest distance to " O   HOH Z 216 " =    5.528
peak=    3.236 closest distance to " O   HOH Z 380 " =    1.798
peak=    3.236 closest distance to " O   HOH Z 272 " =    1.899
peak=    3.235 closest distance to " O   MET A 113 " =    1.632
peak=    3.231 closest distance to " CB  PRO A  90 " =    1.240
peak=    3.221 closest distance to " OE1 GLU A   2 " =    1.668
peak=    3.221 closest distance to " O   HOH Z 313 " =    1.757
peak=    3.221 closest distance to " CD  GLN A 194 " =    1.615
peak=    3.220 closest distance to " CZ3 TRP A  85 " =    0.933
peak=    3.217 closest distance to " CB  PRO A 280 " =    1.224
peak=    3.217 closest distance to " CA  ASP A 149 " =    1.220
peak=    3.214 closest distance to " OG1 THR A 221 " =    1.537
peak=    3.206 closest distance to " O   HOH Z 162 " =    1.493
peak=    3.200 closest distance to " CB  PHE A 204 " =    0.961
peak=    3.197 closest distance to " CB  PHE A 283 " =    0.798
peak=    3.196 closest distance to " CA  ALA A 299 " =    1.014
peak=    3.193 closest distance to " O   HOH Z 193 " =    1.922
peak=    3.193 closest distance to " CG2 ILE A 234 " =    1.214
peak=    3.188 closest distance to " CG  GLU A  37 " =    1.012
peak=    3.185 closest distance to " CB  PRO A 243 " =    1.353
peak=    3.185 closest distance to " O   HOH Z 195 " =    1.389
peak=    3.183 closest distance to " O   PRO A 213 " =    1.451
peak=    3.182 closest distance to " O   HOH Z 358 " =    2.030
peak=    3.181 closest distance to " O   HOH Z  90 " =    3.603
peak=    3.178 closest distance to " O   HOH Z 282 " =    2.108
peak=    3.177 closest distance to " CG2 THR A  29 " =    1.380
peak=    3.176 closest distance to " CG1 ILE A  20 " =    1.216
peak=    3.176 closest distance to " CA  LYS A 117 " =    1.283
peak=    3.175 closest distance to " CA  THR A 246 " =    1.011
peak=    3.166 closest distance to " NH2 ARG A  36 " =    1.702
peak=    3.164 closest distance to " CZ  ARG A  14 " =    1.366
peak=    3.157 closest distance to " CA  THR A 221 " =    1.693
peak=    3.157 closest distance to " CB  TYR A 116 " =    1.123
peak=    3.153 closest distance to " O   HOH Z 353 " =    2.788
peak=    3.152 closest distance to " NH2AARG A 275 " =    3.162
peak=    3.152 closest distance to " O   HOH Z 109 " =    1.864
peak=    3.148 closest distance to " O   HOH Z 413 " =    3.145
peak=    3.148 closest distance to " OE1 GLN A 223 " =    2.239
peak=    3.145 closest distance to " CG2 ILE A 120 " =    1.171
peak=    3.145 closest distance to " CB  SER A  97 " =    0.848
peak=    3.145 closest distance to " N   TYR A 247 " =    1.429
peak=    3.144 closest distance to " N   GLU A  44 " =    2.261
peak=    3.143 closest distance to " OG  SER A 135 " =    1.334
peak=    3.134 closest distance to " CG  ARG A 269 " =    1.352
peak=    3.133 closest distance to " O   HOH Z 420 " =    2.194
peak=    3.131 closest distance to " NZ  LYS A 117 " =    1.534
peak=    3.122 closest distance to " N   THR A  52 " =    1.180
peak=    3.121 closest distance to " CD1 LEU A 300 " =    1.078
peak=    3.121 closest distance to " O   PHE A  61 " =    1.446
peak=    3.120 closest distance to " CG  TRP A 179 " =    2.461
peak=    3.116 closest distance to " O   ALA A 158 " =    1.204
peak=    3.114 closest distance to " O   HOH Z 409 " =    3.516
peak=    3.113 closest distance to " CB  ALA A 291 " =    1.267
peak=    3.106 closest distance to " CE3 TRP A 150 " =    1.060
peak=    3.098 closest distance to " O   HOH Z 184 " =    1.127
peak=    3.094 closest distance to " O   HOH Z 374 " =    2.813
peak=    3.086 closest distance to " ND2 ASN A 249 " =    0.849
peak=    3.084 closest distance to " CB  ALA A  34 " =    0.977
peak=    3.082 closest distance to " O   HOH Z 189 " =    3.930
peak=    3.081 closest distance to " O   HOH Z 132 " =    1.008
peak=    3.078 closest distance to " CD  ARG A  66 " =    2.557
peak=    3.076 closest distance to " CA  ARG A 139 " =    1.382
peak=    3.074 closest distance to " NH1 ARG A  14 " =    1.252
peak=    3.056 closest distance to " OG  SER A 245 " =    1.605
peak=    3.051 closest distance to " O   ARG A  14 " =    1.703
peak=    3.047 closest distance to " O   THR A 251 " =    1.237
peak=    3.040 closest distance to " CG  MET A 185 " =    0.927

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 236         
Filter by distance & map next to the model:
   mapped sites are within: 0.681 - 5.910
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 234 from: 236
   mapped sites are within: 0.719 - 5.910

peak=   -4.683 closest distance to " O   HOH Z 266 " =    5.385
peak=   -4.560 closest distance to " CD  GLN A  58 " =    0.988
peak=   -4.452 closest distance to " CG2 ILE A  49 " =    2.716
peak=   -4.426 closest distance to " CD1 PHE A  59 " =    2.070
peak=   -4.201 closest distance to " CD2 LEU A 237 " =    2.684
peak=   -4.187 closest distance to " O   HOH Z 150 " =    0.841
peak=   -4.165 closest distance to " CD  ARG A  14 " =    3.429
peak=   -4.160 closest distance to " CD  ARG A 156 " =    2.113
peak=   -4.138 closest distance to " CA  VAL A  67 " =    3.080
peak=   -4.101 closest distance to " CD  GLN A  58 " =    0.852
peak=   -4.092 closest distance to " NE2 GLN A 223 " =    1.102
peak=   -4.091 closest distance to " CD  GLN A 223 " =    1.515
peak=   -4.046 closest distance to " O   HOH Z 377 " =    2.089
peak=   -4.044 closest distance to " O   PRO A 198 " =    1.375
peak=   -4.037 closest distance to " O   HOH Z   7 " =    1.067
peak=   -4.017 closest distance to " O   HOH Z  13 " =    1.873
peak=   -4.005 closest distance to " CD1 LEU A 101 " =    2.395
peak=   -3.989 closest distance to " O   HOH Z 166 " =    1.669
peak=   -3.987 closest distance to " OXT GLY A 302 " =    3.047
peak=   -3.960 closest distance to " CG  ARG A 269 " =    2.318
peak=   -3.927 closest distance to " O   VAL A  67 " =    2.875
peak=   -3.897 closest distance to " CB  PRO A 243 " =    2.764
peak=   -3.895 closest distance to " O   HOH Z 422 " =    1.468
peak=   -3.884 closest distance to " CG1 VAL A 112 " =    2.650
peak=   -3.883 closest distance to " O   HOH Z 407 " =    1.276
peak=   -3.875 closest distance to " CZ  TYR A 169 " =    1.940
peak=   -3.872 closest distance to " OG  SER A  97 " =    2.222
peak=   -3.851 closest distance to " O   HOH Z   5 " =    1.622
peak=   -3.839 closest distance to " CD2 TYR A 293 " =    1.831
peak=   -3.827 closest distance to " CB  SER A 210 " =    1.215
peak=   -3.818 closest distance to " ND2 ASN A  45 " =    2.005
peak=   -3.816 closest distance to " O   SER A 276 " =    1.640
peak=   -3.809 closest distance to " CE2 TYR A  30 " =    2.761
peak=   -3.798 closest distance to " O   HOH Z 234 " =    4.082
peak=   -3.786 closest distance to " CA  ASP A 298 " =    1.032
peak=   -3.778 closest distance to " O   HOH Z 392 " =    1.217
peak=   -3.774 closest distance to " CD2 PHE A  61 " =    2.100
peak=   -3.750 closest distance to " O   PRO A 163 " =    2.154
peak=   -3.749 closest distance to " O   PHE A 218 " =    1.441
peak=   -3.724 closest distance to " O   ALA A  34 " =    2.414
peak=   -3.715 closest distance to " CG  GLU A  53 " =    1.570
peak=   -3.711 closest distance to " O   HOH Z 165 " =    1.956
peak=   -3.707 closest distance to " CD  GLN A  88 " =    0.900
peak=   -3.696 closest distance to " OG BSER A 210 " =    1.227
peak=   -3.679 closest distance to " CG  GLN A  11 " =    1.488
peak=   -3.672 closest distance to " ND2BASN A 224 " =    1.891
peak=   -3.645 closest distance to " O   HOH Z 283 " =    2.154
peak=   -3.642 closest distance to " O   HOH Z 136 " =    2.405
peak=   -3.632 closest distance to " CH2 TRP A 179 " =    1.238
peak=   -3.616 closest distance to " OE1 GLN A 223 " =    2.535
peak=   -3.609 closest distance to " OD1 ASP A 171 " =    1.591
peak=   -3.605 closest distance to " O   HOH Z 290 " =    1.064
peak=   -3.590 closest distance to " CA  GLY A 203 " =    2.414
peak=   -3.586 closest distance to " O   HOH Z 374 " =    2.042
peak=   -3.586 closest distance to " CE2 PHE A  61 " =    2.652
peak=   -3.581 closest distance to " NH2 ARG A  79 " =    2.095
peak=   -3.577 closest distance to " O   GLN A 240 " =    2.767
peak=   -3.571 closest distance to " O   HOH Z 252 " =    3.684
peak=   -3.569 closest distance to " CG  GLN A 103 " =    2.491
peak=   -3.569 closest distance to " C   SER A 206 " =    1.395
peak=   -3.566 closest distance to " O   SER A 210 " =    1.748
peak=   -3.563 closest distance to " N   SER A 276 " =    1.491
peak=   -3.553 closest distance to " O   VAL A 174 " =    2.168
peak=   -3.541 closest distance to " CD  GLN A  73 " =    0.867
peak=   -3.536 closest distance to " OG1 THR A 157 " =    2.866
peak=   -3.531 closest distance to " O   HOH Z 185 " =    2.532
peak=   -3.515 closest distance to " C   HIS A 108 " =    1.124
peak=   -3.512 closest distance to " CG2 VAL A 189 " =    2.188
peak=   -3.509 closest distance to " O   HOH Z 196 " =    2.315
peak=   -3.507 closest distance to " O   HOH Z   6 " =    1.559
peak=   -3.500 closest distance to " SD  MET A 105 " =    2.479
peak=   -3.499 closest distance to " CB  ALA A 291 " =    2.407
peak=   -3.490 closest distance to " CB  ASP A 132 " =    2.414
peak=   -3.488 closest distance to " O   HOH Z  56 " =    1.240
peak=   -3.481 closest distance to " CB  ALA A  43 " =    2.563
peak=   -3.481 closest distance to " O   HOH Z 174 " =    2.262
peak=   -3.478 closest distance to " O   HOH Z 109 " =    3.304
peak=   -3.477 closest distance to " O   HOH Z 348 " =    2.273
peak=   -3.475 closest distance to " OD1 ASN A 148 " =    1.466
peak=   -3.475 closest distance to " O   HOH Z  90 " =    3.891
peak=   -3.472 closest distance to " CE3 TRP A 150 " =    2.398
peak=   -3.470 closest distance to " CD2 PHE A 225 " =    1.336
peak=   -3.469 closest distance to " O   HOH Z 418 " =    1.292
peak=   -3.466 closest distance to " C   ASN A 285 " =    2.282
peak=   -3.462 closest distance to " OD1 ASN A 301 " =    1.910
peak=   -3.460 closest distance to " CA  GLY A 241 " =    2.381
peak=   -3.459 closest distance to " O   HOH Z  15 " =    1.482
peak=   -3.457 closest distance to " C   THR A 279 " =    1.222
peak=   -3.457 closest distance to " O   ALA A  34 " =    2.081
peak=   -3.452 closest distance to " CD  ARG A 195 " =    5.180
peak=   -3.449 closest distance to " CA  GLY A 241 " =    3.099
peak=   -3.447 closest distance to " O   HOH Z 197 " =    2.042
peak=   -3.444 closest distance to " CG  LEU A  83 " =    2.066
peak=   -3.441 closest distance to " NE  ARG A  66 " =    4.529
peak=   -3.441 closest distance to " O   HOH Z 351 " =    1.552
peak=   -3.437 closest distance to " O   SER A 271 " =    2.071
peak=   -3.436 closest distance to " CD1 PHE A 130 " =    2.402
peak=   -3.427 closest distance to " O   HOH Z 200 " =    1.234
peak=   -3.424 closest distance to " O   HOH Z 331 " =    1.248
peak=   -3.420 closest distance to " O   TRP A  92 " =    1.970
peak=   -3.418 closest distance to " CD  LYS A 289 " =    2.313
peak=   -3.418 closest distance to " ND2 ASN A  69 " =    1.686
peak=   -3.417 closest distance to " O   HOH Z 102 " =    1.793
peak=   -3.417 closest distance to " OH  TYR A 172 " =    1.803
peak=   -3.407 closest distance to " O   HOH Z 157 " =    3.654
peak=   -3.397 closest distance to " CG1 VAL A 112 " =    2.581
peak=   -3.391 closest distance to " CB  TRP A  85 " =    2.536
peak=   -3.389 closest distance to " O   HOH Z   1 " =    4.395
peak=   -3.387 closest distance to " CB  ALA A 161 " =    2.556
peak=   -3.385 closest distance to " O   HOH Z  52 " =    1.780
peak=   -3.385 closest distance to " ND2 ASN A 249 " =    2.227
peak=   -3.379 closest distance to " O   HOH Z 301 " =    2.435
peak=   -3.374 closest distance to " ND2 ASN A  45 " =    1.214
peak=   -3.373 closest distance to " O   HOH Z 423 " =    2.378
peak=   -3.369 closest distance to " CA  VAL A 197 " =    0.969
peak=   -3.368 closest distance to " OD1 ASP A 191 " =    1.755
peak=   -3.354 closest distance to " O   HOH Z 285 " =    1.195
peak=   -3.350 closest distance to " CD1 ILE A 106 " =    2.147
peak=   -3.349 closest distance to " CG  PRO A 243 " =    1.671
peak=   -3.348 closest distance to " CD1 LEU A  25 " =    2.532
peak=   -3.335 closest distance to " O   HOH Z 366 " =    1.682
peak=   -3.331 closest distance to " O   HOH Z 109 " =    3.354
peak=   -3.329 closest distance to " CB  ALA A 291 " =    2.250
peak=   -3.327 closest distance to " CG  MET A 105 " =    0.959
peak=   -3.326 closest distance to " CG1 VAL A 189 " =    2.539
peak=   -3.324 closest distance to " CG1 VAL A  78 " =    2.607
peak=   -3.324 closest distance to " CE BMET A  47 " =    1.732
peak=   -3.324 closest distance to " ND2 ASN A 187 " =    1.697
peak=   -3.323 closest distance to " CZ  PHE A  38 " =    2.303
peak=   -3.321 closest distance to " CD2 PHE A  59 " =    2.347
peak=   -3.319 closest distance to " CB  ALA A 131 " =    2.341
peak=   -3.315 closest distance to " O   HOH Z 149 " =    2.057
peak=   -3.315 closest distance to " O   HOH Z  40 " =    2.986
peak=   -3.315 closest distance to " CG2 ILE A 263 " =    2.215
peak=   -3.313 closest distance to " C   GLY A  80 " =    2.749
peak=   -3.313 closest distance to " O   HOH Z 252 " =    3.972
peak=   -3.310 closest distance to " O   HOH Z 103 " =    1.750
peak=   -3.309 closest distance to " CB  ALA A  10 " =    2.176
peak=   -3.306 closest distance to " O   HOH Z 198 " =    1.650
peak=   -3.304 closest distance to " CE1 HIS A  81 " =    1.451
peak=   -3.303 closest distance to " O   HOH Z  91 " =    2.306
peak=   -3.301 closest distance to " O   HOH Z 264 " =    1.762
peak=   -3.296 closest distance to " O   HOH Z 146 " =    1.373
peak=   -3.293 closest distance to " CB  PRO A 163 " =    2.539
peak=   -3.292 closest distance to " OH  TYR A 247 " =    2.173
peak=   -3.287 closest distance to " CH2 TRP A 150 " =    1.109
peak=   -3.286 closest distance to " O   HOH Z 171 " =    2.489
peak=   -3.285 closest distance to " CG  ARG A 259 " =    2.397
peak=   -3.282 closest distance to " O   HOH Z 150 " =    1.739
peak=   -3.279 closest distance to " NE2 GLN A  88 " =    1.794
peak=   -3.279 closest distance to " O   HOH Z 210 " =    1.372
peak=   -3.279 closest distance to " NE2 GLN A 103 " =    1.637
peak=   -3.276 closest distance to " CD  GLN A  88 " =    0.959
peak=   -3.274 closest distance to " O   HOH Z  19 " =    2.344
peak=   -3.272 closest distance to " O   HOH Z 114 " =    3.647
peak=   -3.271 closest distance to " CE  MET A  93 " =    1.495
peak=   -3.267 closest distance to " O   HOH Z 198 " =    1.416
peak=   -3.259 closest distance to " CD2 LEU A 237 " =    2.601
peak=   -3.258 closest distance to " NH2 ARG A  66 " =    1.985
peak=   -3.258 closest distance to " CZ3 TRP A 274 " =    2.389
peak=   -3.255 closest distance to " O   HOH Z  30 " =    0.719
peak=   -3.255 closest distance to " O   HOH Z 128 " =    2.555
peak=   -3.253 closest distance to " O   HOH Z  78 " =    1.810
peak=   -3.249 closest distance to " OXT GLY A 302 " =    3.260
peak=   -3.246 closest distance to " CG2 THR A 182 " =    2.230
peak=   -3.245 closest distance to " CB  PHE A  16 " =    2.408
peak=   -3.245 closest distance to " O   HOH Z 145 " =    2.597
peak=   -3.243 closest distance to " O   HOH Z  71 " =    2.325
peak=   -3.243 closest distance to " N   ALA A  43 " =    2.765
peak=   -3.242 closest distance to " O   HOH Z 388 " =    2.139
peak=   -3.238 closest distance to " OG BSER A 134 " =    1.406
peak=   -3.238 closest distance to " O   ALA A  10 " =    1.786
peak=   -3.236 closest distance to " NE2 GLN A  94 " =    1.782
peak=   -3.231 closest distance to " CG  ASP A 132 " =    2.355
peak=   -3.229 closest distance to " CB  PHE A 192 " =    2.102
peak=   -3.228 closest distance to " CG2 THR A  18 " =    2.936
peak=   -3.228 closest distance to " O   ALA A 256 " =    1.748
peak=   -3.225 closest distance to " O   HOH Z 136 " =    0.932
peak=   -3.224 closest distance to " CE1 TYR A 247 " =    2.686
peak=   -3.223 closest distance to " O   HOH Z 166 " =    1.598
peak=   -3.221 closest distance to " O   HOH Z 196 " =    1.836
peak=   -3.218 closest distance to " C   ALA A 158 " =    1.449
peak=   -3.217 closest distance to " O   HOH Z 340 " =    1.994
peak=   -3.217 closest distance to " O   HOH Z 221 " =    1.101
peak=   -3.213 closest distance to " OD2 ASP A 171 " =    1.826
peak=   -3.205 closest distance to " O   HOH Z 394 " =    5.521
peak=   -3.203 closest distance to " O   HOH Z 131 " =    4.168
peak=   -3.203 closest distance to " CG2BVAL A  41 " =    1.999
peak=   -3.200 closest distance to " O   HOH Z 191 " =    5.910
peak=   -3.200 closest distance to " OG  SER A  26 " =    1.327
peak=   -3.199 closest distance to " O   HOH Z   7 " =    1.710
peak=   -3.198 closest distance to " N   ALA A 226 " =    1.954
peak=   -3.196 closest distance to " O   ASN A 301 " =    1.417
peak=   -3.191 closest distance to " CD1 TRP A 179 " =    1.135
peak=   -3.190 closest distance to " CB  ALA A 248 " =    2.164
peak=   -3.190 closest distance to " O   HOH Z  41 " =    2.148
peak=   -3.187 closest distance to " O   SER A 273 " =    1.393
peak=   -3.186 closest distance to " O   GLY A 196 " =    0.997
peak=   -3.185 closest distance to " N   ALA A 242 " =    1.962
peak=   -3.181 closest distance to " O   HOH Z 174 " =    3.594
peak=   -3.181 closest distance to " O   HOH Z 378 " =    1.264
peak=   -3.180 closest distance to " O   HOH Z 111 " =    2.224
peak=   -3.179 closest distance to " CB  ALA A 154 " =    2.725
peak=   -3.179 closest distance to " O   HOH Z  37 " =    1.528
peak=   -3.177 closest distance to " CG  PHE A 283 " =    2.784
peak=   -3.165 closest distance to " O   HOH Z 118 " =    1.283
peak=   -3.165 closest distance to " O   HOH Z 377 " =    1.125
peak=   -3.165 closest distance to " O   SER A 135 " =    1.627
peak=   -3.161 closest distance to " C   LEU A 143 " =    1.113
peak=   -3.160 closest distance to " O   HOH Z 111 " =    1.820
peak=   -3.159 closest distance to " OH  TYR A 172 " =    1.956
peak=   -3.159 closest distance to " CD2 LEU A 300 " =    2.842
peak=   -3.153 closest distance to " CG1AVAL A  41 " =    2.644
peak=   -3.152 closest distance to " O   HOH Z 371 " =    1.419
peak=   -3.150 closest distance to " O   HOH Z  40 " =    2.490
peak=   -3.149 closest distance to " NH2 ARG A 159 " =    2.422
peak=   -3.146 closest distance to " O   HOH Z 287 " =    1.971
peak=   -3.143 closest distance to " N   GLN A  58 " =    1.523
peak=   -3.125 closest distance to " CD2 HIS A 115 " =    0.981
peak=   -3.122 closest distance to " CB  SER A 146 " =    2.208
peak=   -3.117 closest distance to " O   SER A   3 " =    1.134
peak=   -3.110 closest distance to " O   PRO A 198 " =    1.694
peak=   -3.103 closest distance to " NH2 ARG A  66 " =    3.557
peak=   -3.098 closest distance to " OD2 ASP A 171 " =    2.290
peak=   -3.095 closest distance to " O   HOH Z 396 " =    2.252
peak=   -3.087 closest distance to " O   HOH Z 126 " =    1.987
peak=   -3.086 closest distance to " O   HOH Z 166 " =    1.468
peak=   -3.081 closest distance to " CD2 HIS A 207 " =    2.291
peak=   -3.080 closest distance to " O   HOH Z 336 " =    5.596
peak=   -3.065 closest distance to " O   HOH Z   2 " =    2.355
peak=   -3.063 closest distance to " O   HOH Z 350 " =    1.530
peak=   -3.055 closest distance to " O   HOH Z 259 " =    1.821
peak=   -3.048 closest distance to " O   ASP A 107 " =    1.909
peak=   -3.043 closest distance to " O   HOH Z 108 " =    2.168

================= 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    :  0.4644 0.4528   6.278188e+00   6.256566e+00
   1_bss:  0.4559 0.4411   6.271256e+00   6.245913e+00
   1_xyz:  0.3457 0.3732   6.088768e+00   6.142293e+00
   1_adp:  0.3154 0.3881   6.044580e+00   6.161207e+00
   1_occ:  0.3153 0.3874   6.043766e+00   6.160631e+00
   2_bss:  0.3137 0.3845   6.044132e+00   6.161502e+00
   2_xyz:  0.2400 0.2955   5.800189e+00   5.963436e+00
   2_adp:  0.2199 0.2750   5.733012e+00   5.907407e+00
   2_occ:  0.2196 0.2751   5.732481e+00   5.907733e+00
   3_bss:  0.2194 0.2746   5.732373e+00   5.907126e+00
   3_xyz:  0.1638 0.2063   5.462982e+00   5.659334e+00
   3_adp:  0.1467 0.1947   5.380542e+00   5.596373e+00
   3_occ:  0.1467 0.1947   5.380323e+00   5.596278e+00
   4_bss:  0.1468 0.1943   5.380907e+00   5.594931e+00
   4_xyz:  0.1375 0.1844   5.327188e+00   5.542900e+00
   4_adp:  0.1343 0.1817   5.306283e+00   5.521740e+00
   4_occ:  0.1342 0.1819   5.306223e+00   5.521800e+00
   5_bss:  0.1341 0.1820   5.306235e+00   5.521798e+00
   5_xyz:  0.1203 0.1690   5.217892e+00   5.452582e+00
   5_adp:  0.1188 0.1663   5.205188e+00   5.438361e+00
   5_occ:  0.1186 0.1664   5.204819e+00   5.438551e+00
   5_bss:  0.1188 0.1663   5.204105e+00   5.437585e+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:  0.300  50.000  -3.148   4.633   1.082   0.000   0.000   0.000
   1_xyz:  0.300  50.000  -3.148   4.633   1.082   0.000   0.000   0.000
   1_adp:  0.300  50.000  -3.148   4.633   1.082   0.000   0.000   0.000
   1_occ:  0.300  50.000  -3.148   4.633   1.082   0.000   0.000   0.000
   2_bss:  0.319  69.889  -1.825   2.357   0.588   0.000   0.000   0.000
   2_xyz:  0.319  69.889  -1.825   2.357   0.588   0.000   0.000   0.000
   2_adp:  0.319  69.889  -1.825   2.357   0.588   0.000   0.000   0.000
   2_occ:  0.319  69.889  -1.825   2.357   0.588   0.000   0.000   0.000
   3_bss:  0.327  66.418  -1.989   0.715   0.055   0.000   0.000   0.000
   3_xyz:  0.327  66.418  -1.989   0.715   0.055   0.000   0.000   0.000
   3_adp:  0.327  66.418  -1.989   0.715   0.055   0.000   0.000   0.000
   3_occ:  0.327  66.418  -1.989   0.715   0.055   0.000   0.000   0.000
   4_bss:  0.336  75.042  -2.272  -0.332  -0.220  -0.000  -0.000  -0.000
   4_xyz:  0.336  75.042  -2.272  -0.332  -0.220  -0.000  -0.000  -0.000
   4_adp:  0.336  75.042  -2.272  -0.332  -0.220  -0.000  -0.000  -0.000
   4_occ:  0.336  75.042  -2.272  -0.332  -0.220  -0.000  -0.000  -0.000
   5_bss:  0.332  72.061  -2.165  -0.534  -0.027  -0.000  -0.000  -0.000
   5_xyz:  0.332  72.061  -2.165  -0.534  -0.027  -0.000  -0.000  -0.000
   5_adp:  0.332  72.061  -2.165  -0.534  -0.027  -0.000  -0.000  -0.000
   5_occ:  0.332  72.061  -2.165  -0.534  -0.027  -0.000  -0.000  -0.000
   5_bss:  0.326  67.286  -2.168  -0.537  -0.030  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  53.722 0.4748  0.6269    64387.329
   1_bss:  52.445 0.4899  0.6677    61225.719
   1_xyz:  42.572 0.6115  0.8098    41689.319
   1_adp:  44.119 0.5922  0.7860    44403.060
   1_occ:  44.074 0.5927  0.7856    44280.232
   2_bss:  43.779 0.5963  0.7812    43951.330
   2_xyz:  31.728 0.7372  0.9333    23868.109
   2_adp:  28.791 0.7707  0.9469    20580.631
   2_occ:  28.794 0.7706  0.9464    20571.664
   3_bss:  28.684 0.7719  0.9237    20483.613
   3_xyz:  20.434 0.8567  0.9812    11040.683
   3_adp:  18.759 0.8732  0.9802     9808.486
   3_occ:  18.759 0.8732  0.9802     9809.333
   4_bss:  18.705 0.8737  0.9628     9762.296
   4_xyz:  17.406 0.8860  0.9680     8768.235
   4_adp:  16.936 0.8904  0.9626     8526.036
   4_occ:  16.939 0.8904  0.9625     8527.324
   5_bss:  16.941 0.8904  0.9639     8527.011
   5_xyz:  15.616 0.9016  0.9711     7435.163
   5_adp:  15.287 0.9045  0.9646     7252.825
   5_occ:  15.291 0.9045  0.9645     7252.216
   5_bss:  15.268 0.9046  0.9640     7212.958
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.113   1.6989e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.113   1.6989e-01
   1_xyz:   1.736  0.014  0.106 16.105  0.006  4.112   1.6616e-01
   1_adp:   1.736  0.014  0.106 16.105  0.006  4.112   1.6616e-01
   1_occ:   1.736  0.014  0.106 16.105  0.006  4.112   1.6616e-01
   2_bss:   1.736  0.014  0.106 16.105  0.006  4.112   1.6616e-01
   2_xyz:   1.485  0.013  0.096 15.195  0.007  4.116   1.2643e-01
   2_adp:   1.485  0.013  0.096 15.195  0.007  4.116   1.2643e-01
   2_occ:   1.485  0.013  0.096 15.195  0.007  4.116   1.2643e-01
   3_bss:   1.485  0.013  0.096 15.195  0.007  4.116   1.2643e-01
   3_xyz:   1.243  0.011  0.082 14.850  0.005  4.115   8.8384e-02
   3_adp:   1.243  0.011  0.082 14.850  0.005  4.115   8.8384e-02
   3_occ:   1.243  0.011  0.082 14.850  0.005  4.115   8.8384e-02
   4_bss:   1.243  0.011  0.082 14.850  0.005  4.115   8.8384e-02
   4_xyz:   0.975  0.006  0.071 14.391  0.003  4.123   5.5538e-02
   4_adp:   0.975  0.006  0.071 14.391  0.003  4.123   5.5538e-02
   4_occ:   0.975  0.006  0.071 14.391  0.003  4.123   5.5538e-02
   5_bss:   0.975  0.006  0.071 14.391  0.003  4.123   5.5538e-02
   5_xyz:   1.189  0.011  0.085 14.793  0.004  4.114   8.4051e-02
   5_adp:   1.189  0.011  0.085 14.793  0.004  4.114   8.4051e-02
   5_occ:   1.189  0.011  0.085 14.793  0.004  4.114   8.4051e-02
   5_bss:   1.189  0.011  0.085 14.793  0.004  4.114   8.4051e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.783   2.4352e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.783   2.4352e-01
   1_xyz:  10.873  0.073  0.448 81.971  0.028  1.972   2.4648e-01
   1_adp:  10.873  0.073  0.448 81.971  0.028  1.972   2.4648e-01
   1_occ:  10.873  0.073  0.448 81.971  0.028  1.972   2.4648e-01
   2_bss:  10.873  0.073  0.448 81.971  0.028  1.972   2.4648e-01
   2_xyz:   8.412  0.063  0.287 86.498  0.027  2.194   1.9523e-01
   2_adp:   8.412  0.063  0.287 86.498  0.027  2.194   1.9523e-01
   2_occ:   8.412  0.063  0.287 86.498  0.027  2.194   1.9523e-01
   3_bss:   8.412  0.063  0.287 86.498  0.027  2.194   1.9523e-01
   3_xyz:   8.103  0.062  0.227 81.982  0.039  2.142   6.5136e-02
   3_adp:   8.103  0.062  0.227 81.982  0.039  2.142   6.5136e-02
   3_occ:   8.103  0.062  0.227 81.982  0.039  2.142   6.5136e-02
   4_bss:   8.103  0.062  0.227 81.982  0.039  2.142   6.5136e-02
   4_xyz:   6.948  0.035  0.220 80.824  0.036  2.358   3.6375e-02
   4_adp:   6.948  0.035  0.220 80.824  0.036  2.358   3.6375e-02
   4_occ:   6.948  0.035  0.220 80.824  0.036  2.358   3.6375e-02
   5_bss:   6.948  0.035  0.220 80.824  0.036  2.358   3.6375e-02
   5_xyz:   8.775  0.053  0.299 82.040  0.034  2.270   6.5840e-02
   5_adp:   8.775  0.053  0.299 82.040  0.034  2.270   6.5840e-02
   5_occ:   8.775  0.053  0.299 82.040  0.034  2.270   6.5840e-02
   5_bss:   8.775  0.053  0.299 82.040  0.034  2.270   6.5840e-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: 105.42   0.00  18.75  82.01   0.00  15.11 105.42   0.00  38.57
   1_occ: 105.42   0.00  18.75  82.01   0.00  15.11 105.42   0.00  38.57
   2_bss: 105.42   0.00  18.75  82.01   0.00  15.11 105.42   0.00  38.57
   2_xyz: 105.42   0.00  18.75  82.01   0.00  15.11 105.42   0.00  38.57
   2_adp:  99.33   0.00  17.97  82.71   0.00  13.90  99.33   2.46  40.18
   2_occ:  99.33   0.00  17.97  82.71   0.00  13.90  99.33   2.46  40.18
   3_bss:  99.33   0.00  17.97  82.71   0.00  13.90  99.33   2.46  40.18
   3_xyz:  99.33   0.00  17.97  82.71   0.00  13.90  99.33   2.46  40.18
   3_adp: 100.93   0.00  17.91  94.21   0.00  13.04 100.93   4.01  44.41
   3_occ: 100.93   0.00  17.91  94.21   0.00  13.04 100.93   4.01  44.41
   4_bss: 100.93   0.00  17.91  94.21   0.00  13.04 100.93   4.01  44.41
   4_xyz: 100.93   0.00  17.91  94.21   0.00  13.04 100.93   4.01  44.41
   4_adp: 104.80   0.47  17.64 104.80   0.47  12.68 101.58   3.87  44.66
   4_occ: 104.80   0.47  17.64 104.80   0.47  12.68 101.58   3.87  44.66
   5_bss: 104.80   0.47  17.64 104.80   0.47  12.68 101.58   3.87  44.66
   5_xyz: 104.80   0.47  17.64 104.80   0.47  12.68 101.58   3.87  44.66
   5_adp: 106.41   0.00  17.10 106.41   0.47  12.33  96.69   0.00  43.10
   5_occ: 106.41   0.00  17.10 106.41   0.47  12.33  96.69   0.00  43.10
   5_bss: 106.41   0.00  17.10 106.41   0.47  12.33  96.69   0.00  43.10
------------------------------------------------------------------------
 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:    1.667    0.023    0.444
   1_adp:    1.667    0.023    0.444
   1_occ:    1.667    0.023    0.444
   2_bss:    1.667    0.023    0.444
   2_xyz:    1.522    0.041    0.634
   2_adp:    1.522    0.041    0.634
   2_occ:    1.522    0.041    0.634
   3_bss:    1.522    0.041    0.634
   3_xyz:    1.544    0.073    0.780
   3_adp:    1.544    0.073    0.780
   3_occ:    1.544    0.073    0.780
   4_bss:    1.544    0.073    0.780
   4_xyz:    1.607    0.094    0.804
   4_adp:    1.607    0.094    0.804
   4_occ:    1.607    0.094    0.804
   5_bss:    1.607    0.094    0.804
   5_xyz:    1.597    0.073    0.836
   5_adp:    1.597    0.073    0.836
   5_occ:    1.597    0.073    0.836
   5_bss:    1.597    0.073    0.836
------------------------------------------------------------------------

CPU time actual refinement: 332.06


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_481/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_481/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_481/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_481/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_481/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 331.91 
  Macro-tasks:
    bulk solvent and scale       = 44.10  
    individual site refinement   = 131.44 
    weights calculation          = 28.90  
    collect and process          = 6.50   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 211.04 
  Micro-tasks:
    mask                            = 2.36   
    f_calc                          = 104.43 
    alpha_beta                      = 8.27   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 112.47 
    fmodel                         = 7.12   
    r_factors                      = 0.19   
    phase_errors                   = 10.78  
    foms                           = 0.24   
    TOTAL for micro-tasks          = 247.01 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.776 micro seconds
Total CPU time: 5.76 minutes
from_scatterers_fft:    629 calls, 104.10 s
gradients_fft:          574 calls,  99.65 s

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

# Date 2008-01-16 Time 04:55:43 PST -0800 (1200488143.83 s)
Start R-work = 0.4644, R-free = 0.4528 (no bulk solvent and anisotropic scale)
Final R-work = 0.1382, R-free = 0.1818 (no bulk solvent and anisotropic scale)

Start R-work = 0.4559, R-free = 0.4411
Final R-work = 0.1188, R-free = 0.1663