# Date 2008-01-16 Time 04:50:10 PST -0800 (1200487810.29 s)
#phil __OFF__

Command line arguments: "../482.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 30727
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 482

-------------------------------------------------------------------------------
  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, 88.1178, 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: 3.41, per 1000 atoms: 1.21


================================== 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, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0676 1.98086
Completeness in resolution range: 0.926062
Completeness with d_max=infinity: 0.923269

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0676
                             d_min =   1.9809

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, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0676 1.98086
Completeness in resolution range: 0.926062
Completeness with d_max=infinity: 0.923269

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0680 -  4.2389 [2221/2249]  1997   224  10.1%
  bin  2:  4.2389 -  3.3770 [2125/2148]  1909   216  10.2%
  bin  3:  3.3770 -  2.9538 [2097/2122]  1892   205   9.8%
  bin  4:  2.9538 -  2.6854 [2089/2105]  1879   210  10.1%
  bin  5:  2.6854 -  2.4938 [2055/2099]  1844   211  10.3%
  bin  6:  2.4938 -  2.3474 [2072/2100]  1869   203   9.8%
  bin  7:  2.3474 -  2.2302 [2043/2079]  1844   199   9.7%
  bin  8:  2.2302 -  2.1334 [2054/2096]  1847   207  10.1%
  bin  9:  2.1334 -  2.0515 [2020/2066]  1818   202  10.0%
  bin 10:  2.0515 -  1.9809 [ 813/2089]   731    82  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_482/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:
        1.66 -     2.31: 21
        2.31 -     2.95: 1635
        2.95 -     3.60: 4457
        3.60 -     4.25: 9038
        4.25 -     4.90: 12733
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.657 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.804 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 "  1.861 3.040 -x+1,y+1/2,-z+1/2
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.891 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 27879 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_482/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_482/model_refine_001.geo

CPU time processing inputs: 9.31


============================ 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 88.1178 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 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4802   r_free= 0.4737   ksol= 0.00   Bsol= 0.00   scale= 0.867    |
|                                                                             |
| 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:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.290913                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0680 -  4.7281 0.99   1442  159 0.3850 0.3932       6.588       6.589|
|  2:  4.7281 -  3.7722 0.99   1396  155 0.4325 0.4603       6.864      6.9036|
|  3:  3.7722 -  3.3011 0.99   1350  149 0.4680 0.4308      6.6992      6.6357|
|  4:  3.3011 -  3.0019 0.99   1357  148 0.4724 0.4437      6.5136      6.4818|
|  5:  3.0019 -  2.7881 0.98   1327  153 0.5137 0.4736      6.3711      6.3936|
|  6:  2.7881 -  2.6247 0.99   1357  146 0.5150 0.5173       6.278        6.17|
|  7:  2.6247 -  2.4938 0.98   1292  156 0.4992 0.4554      6.2326      6.1537|
|  8:  2.4938 -  2.3857 0.99   1343  134 0.5192 0.5003      6.1732      6.1509|
|  9:  2.3857 -  2.2942 0.99   1340  151 0.5131 0.4969      6.1091      6.1874|
| 10:  2.2942 -  2.2153 0.98   1316  146 0.5219 0.5102      6.0881      6.0881|
| 11:  2.2153 -  2.1462 0.97   1281  149 0.5392 0.5292      6.0318      6.0265|
| 12:  2.1462 -  2.0850 0.99   1329  148 0.5091 0.5698      5.9379      5.9654|
| 13:  2.0850 -  2.0303 0.88   1196  127 0.5273 0.5521      5.8681      5.8413|
| 14:  2.0303 -  1.9809 0.23    304   38 0.4828 0.4262      5.8952      5.7335|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0680 -  4.7281  1442   159  0.68  35.69   0.81     0.71      76592.08|
|  2:  4.7281 -  3.7722  1396   155  0.68  37.14   0.88     0.77     113913.69|
|  3:  3.7722 -  3.3011  1350   149  0.57  45.99   0.86     0.74     119927.10|
|  4:  3.3011 -  3.0019  1357   148  0.48  53.15   0.88     0.65     103582.25|
|  5:  3.0019 -  2.7881  1327   153  0.42  58.50   0.85     0.59      80242.51|
|  6:  2.7881 -  2.6247  1357   146  0.40  60.18   0.86     0.55      67539.18|
|  7:  2.6247 -  2.4938  1292   156  0.39  60.52   0.91     0.53      62310.60|
|  8:  2.4938 -  2.3857  1343   134  0.37  61.90   0.88     0.52      56237.55|
|  9:  2.3857 -  2.2942  1340   151  0.37  62.51   0.89     0.54      53736.39|
| 10:  2.2942 -  2.2153  1316   146  0.37  61.95   0.91     0.55      47224.73|
| 11:  2.2153 -  2.1462  1281   149  0.31  66.56   0.90     0.49      48259.71|
| 12:  2.1462 -  2.0850  1329   148  0.26  70.84   0.90     0.40      46561.09|
| 13:  2.0850 -  2.0303  1196   127  0.21  74.09   0.89     0.34      42211.10|
| 14:  2.0303 -  1.9809   304    38  0.29  68.05   0.99     0.38      30971.86|
|alpha:            min =        0.34 max =            0.77 mean =         0.57|
|beta:             min =    30971.86 max =       119927.10 mean =     70553.13|
|figures of merit: min =        0.00 max =            1.00 mean =         0.43|
|phase err.(work): min =        0.00 max =           89.98 mean =        57.41|
|phase err.(test): min =        0.00 max =           89.95 mean =        57.62|
|-----------------------------------------------------------------------------|

============================== 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 = 14.001972             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 91.544   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.655642              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.948   (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 |  1.657 -  1.981:        7 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.981 -  2.305:       14 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.305 -  2.630:       45 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.630 -  2.954:     1590 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.954 -  3.278:     1892 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.278 -  3.603:     2565 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.603 -  3.927:     4702 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.927 -  4.251:     4336 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.251 -  4.576:     5756 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.576 -  4.900:     6977 |
|-----------------------------------------------------------------------------|
|-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 |        0.174 |
| 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  1.657 |       0.315 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.186)------------------------------------------|
|    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 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4802   r_free= 0.4737   ksol= 0.00   Bsol= 0.00   scale= 0.867    |
|                                                                             |
| 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:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.290913                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4721   r_free= 0.4633   ksol= 0.29   Bsol= 33.01   scale= 0.911   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.29,3.96,2.37,0.00,0.00,0.00); trace/3= 1.01                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.286162                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.656501             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.972   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.364823              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.572   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4721      final r-factor (work) = 0.3804          |
| start r-factor (free) = 0.4633      final r-factor (free) = 0.4100          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 36.7912 = 11.66 * 0.50 * 6.2827 + 1.00 * 0.1738                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 36.1704 = 11.66 * 0.50 * 6.1825 + 1.00 * 0.1373                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3804      final r-factor (work) = 0.3482          |
| start r-factor (free) = 0.4100      final r-factor (free) = 0.4205          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.4439 = 1.36 * 1.00 * 6.1825 + 1.00 * 0.0059                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.3575 = 1.36 * 1.00 * 6.1062 + 1.00 * 0.0235                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.186)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    117.50  19.66    None  None   None       |
|    all(noH): 2823   0      0.00    117.50  19.66    None  None   None       |
|    Sol.    : 438    0      0.00    117.50  38.21    None  None   None       |
|    Mac.    : 2385   0      0.00    95.66   16.25    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 -  11.750: 1029   |   5:    58.752 -  70.502:   51        |
|      1:    11.750 -  23.501:  929   |   6:    70.502 -  82.252:   21        |
|      2:    23.501 -  35.251:  455   |   7:    82.252 -  94.002:   12        |
|      3:    35.251 -  47.001:  221   |   8:    94.002 - 105.753:    3        |
|      4:    47.001 -  58.752:  101   |   9:   105.753 - 117.503:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3482 r_free = 0.4205             target_work(ml) = 6.109         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3480 r_free = 0.4199             target_work(ml) = 6.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3480   r_free= 0.4199   ksol= 0.29   Bsol= 33.01   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.29,3.96,2.37,0.00,0.00,0.00); trace/3= 1.01                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.107878                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3473   r_free= 0.4184   ksol= 0.30   Bsol= 48.94   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.67,2.46,1.39,0.00,0.00,0.00); trace/3= 0.73                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.109831                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.509535             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.982   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.513285              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 110.074  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3473      final r-factor (work) = 0.2762          |
| start r-factor (free) = 0.4184      final r-factor (free) = 0.3387          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 38.3426 = 12.51 * 0.50 * 6.1082 + 1.00 * 0.1373                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 37.8363 = 12.51 * 0.50 * 6.0287 + 1.00 * 0.1281                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2762      final r-factor (work) = 0.2563          |
| start r-factor (free) = 0.3387      final r-factor (free) = 0.3228          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1223 = 0.51 * 1.00 * 6.0287 + 1.00 * 0.0279                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0541 = 0.51 * 1.00 * 5.8912 + 1.00 * 0.0302                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.186)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    111.70  18.32    None  None   None       |
|    all(noH): 2823   0      0.00    111.70  18.32    None  None   None       |
|    Sol.    : 438    0      0.00    111.70  37.95    None  None   None       |
|    Mac.    : 2385   0      0.00    82.02   14.71    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 -  11.170: 1094   |   5:    55.852 -  67.022:   52        |
|      1:    11.170 -  22.341:  972   |   6:    67.022 -  78.193:   26        |
|      2:    22.341 -  33.511:  378   |   7:    78.193 -  89.363:    7        |
|      3:    33.511 -  44.682:  178   |   8:    89.363 - 100.534:    2        |
|      4:    44.682 -  55.852:  112   |   9:   100.534 - 111.704:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2563 r_free = 0.3228             target_work(ml) = 5.872         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2560 r_free = 0.3228             target_work(ml) = 5.872         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2560   r_free= 0.3228   ksol= 0.30   Bsol= 48.94   scale= 1.025   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.67,2.46,1.39,0.00,0.00,0.00); trace/3= 0.73                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.871685                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2558   r_free= 0.3216   ksol= 0.33   Bsol= 65.70   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.93,1.00,0.29,0.00,0.00,0.00); trace/3= -0.21                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.872590                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.492595              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.429   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.562389              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.403   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2558      final r-factor (work) = 0.1964          |
| start r-factor (free) = 0.3216      final r-factor (free) = 0.2461          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.2013 = 7.49 * 0.50 * 5.8920 + 1.00 * 0.1281                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.7218 = 7.49 * 0.50 * 5.7755 + 1.00 * 0.0852                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1964      final r-factor (work) = 0.1771          |
| start r-factor (free) = 0.2461      final r-factor (free) = 0.2298          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2625 = 0.56 * 1.00 * 5.7755 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1488 = 0.56 * 1.00 * 5.5766 + 1.00 * 0.0126                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.186)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    107.97  18.33    None  None   None       |
|    all(noH): 2823   0      0.00    107.97  18.33    None  None   None       |
|    Sol.    : 438    0      3.63    107.97  43.32    None  None   None       |
|    Mac.    : 2385   0      0.00    84.85   13.74    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 -  10.797: 1196   |   5:    53.986 -  64.783:   84        |
|      1:    10.797 -  21.594:  939   |   6:    64.783 -  75.580:   48        |
|      2:    21.594 -  32.392:  249   |   7:    75.580 -  86.377:   15        |
|      3:    32.392 -  43.189:  149   |   8:    86.377 -  97.175:    4        |
|      4:    43.189 -  53.986:  137   |   9:    97.175 - 107.972:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1771 r_free = 0.2298             target_work(ml) = 5.544         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1769 r_free = 0.2295             target_work(ml) = 5.543         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1769   r_free= 0.2295   ksol= 0.33   Bsol= 65.70   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.93,1.00,0.29,0.00,0.00,0.00); trace/3= -0.21                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.543094                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1764   r_free= 0.2288   ksol= 0.33   Bsol= 75.25   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.52,-0.44,-0.36,-0.00,-0.00,-0.00); trace/3= -1.10                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.541695                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.401887              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.261  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.590766              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.497  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1764      final r-factor (work) = 0.1477          |
| start r-factor (free) = 0.2288      final r-factor (free) = 0.1956          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.5759 = 3.40 * 0.50 * 5.5797 + 1.00 * 0.0852                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.3726 = 3.40 * 0.50 * 5.4682 + 1.00 * 0.0714                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1477      final r-factor (work) = 0.1393          |
| start r-factor (free) = 0.1956      final r-factor (free) = 0.1894          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2429 = 0.59 * 1.00 * 5.4682 + 1.00 * 0.0125                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1777 = 0.59 * 1.00 * 5.3575 + 1.00 * 0.0127                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.186)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.84    100.54  18.10    None  None   None       |
|    all(noH): 2823   0      0.84    100.54  18.10    None  None   None       |
|    Sol.    : 438    0      3.83    100.54  45.27    None  None   None       |
|    Mac.    : 2385   0      0.84    94.68   13.11    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.836 -  10.806: 1245   |   5:    50.686 -  60.655:   80        |
|      1:    10.806 -  20.776:  920   |   6:    60.655 -  70.625:   71        |
|      2:    20.776 -  30.746:  214   |   7:    70.625 -  80.595:   43        |
|      3:    30.746 -  40.716:  124   |   8:    80.595 -  90.565:   10        |
|      4:    40.716 -  50.686:  108   |   9:    90.565 - 100.535:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1393 r_free = 0.1894             target_work(ml) = 5.340         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1392 r_free = 0.1894             target_work(ml) = 5.339         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1392   r_free= 0.1894   ksol= 0.33   Bsol= 75.25   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.52,-0.44,-0.36,-0.00,-0.00,-0.00); trace/3= -1.10                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.339205                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1397   r_free= 0.1893   ksol= 0.34   Bsol= 75.96   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.46,-0.81,-0.22,-0.00,-0.00,-0.00); trace/3= -1.16                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.340400                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.021164              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 127.284  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.129099              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 142.602  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1397      final r-factor (work) = 0.1320          |
| start r-factor (free) = 0.1893      final r-factor (free) = 0.1803          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4865 = 2.02 * 0.50 * 5.3584 + 1.00 * 0.0714                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4320 = 2.02 * 0.50 * 5.3170 + 1.00 * 0.0588                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1320      final r-factor (work) = 0.1338          |
| start r-factor (free) = 0.1803      final r-factor (free) = 0.1755          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6990 = 0.13 * 1.00 * 5.3170 + 1.00 * 0.0125                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6934 = 0.13 * 1.00 * 5.3046 + 1.00 * 0.0086                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.186)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.95    93.83   17.08    None  None   None       |
|    all(noH): 2823   0      1.95    93.83   17.08    None  None   None       |
|    Sol.    : 438    0      3.82    93.83   41.02    None  None   None       |
|    Mac.    : 2385   0      1.95    89.40   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:     1.950 -  11.138: 1330   |   5:    47.890 -  57.078:   84        |
|      1:    11.138 -  20.326:  897   |   6:    57.078 -  66.266:   56        |
|      2:    20.326 -  29.514:  184   |   7:    66.266 -  75.454:   33        |
|      3:    29.514 -  38.702:  125   |   8:    75.454 -  84.642:    7        |
|      4:    38.702 -  47.890:   97   |   9:    84.642 -  93.830:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1338 r_free = 0.1755             target_work(ml) = 5.293         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1336 r_free = 0.1756             target_work(ml) = 5.293         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1336   r_free= 0.1756   ksol= 0.34   Bsol= 75.96   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.46,-0.81,-0.22,-0.00,-0.00,-0.00); trace/3= -1.16                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.292811                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0680 -  4.7281 0.99   1442  159 0.1040 0.1348        5.44      5.6087|
|  2:  4.7281 -  3.7722 0.99   1396  155 0.0928 0.1064      5.4998      5.6675|
|  3:  3.7722 -  3.3011 0.99   1350  149 0.1242 0.1739      5.5938      5.9615|
|  4:  3.3011 -  3.0019 0.99   1357  148 0.1488 0.1802      5.5879      5.7051|
|  5:  3.0019 -  2.7881 0.98   1327  153 0.1646 0.1858      5.4963      5.6291|
|  6:  2.7881 -  2.6247 0.99   1357  146 0.1567 0.2379      5.3906      5.6167|
|  7:  2.6247 -  2.4938 0.98   1292  156 0.1545 0.1952      5.3494      5.5516|
|  8:  2.4938 -  2.3857 0.99   1343  134 0.1493 0.2020      5.2803      5.4491|
|  9:  2.3857 -  2.2942 0.99   1340  151 0.1455 0.2206      5.1927      5.4807|
| 10:  2.2942 -  2.2153 0.98   1316  146 0.1412 0.1879      5.1168      5.2684|
| 11:  2.2153 -  2.1462 0.97   1281  149 0.1399 0.1939      5.0382      5.3254|
| 12:  2.1462 -  2.0850 0.99   1329  148 0.1361 0.1647      4.9688      5.1347|
| 13:  2.0850 -  2.0303 0.88   1196  127 0.1357 0.1979      4.8812      5.1118|
| 14:  2.0303 -  1.9809 0.23    304   38 0.1152 0.1817      4.7914      5.0126|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0680 -  4.7281  1442   159  0.94   9.38   0.96     0.93       7497.72|
|  2:  4.7281 -  3.7722  1396   155  0.95   8.82   1.00     0.99       9975.17|
|  3:  3.7722 -  3.3011  1350   149  0.92  12.88   1.02     1.02      12471.94|
|  4:  3.3011 -  3.0019  1357   148  0.90  16.36   1.00     0.99      13007.51|
|  5:  3.0019 -  2.7881  1327   153  0.88  18.81   1.00     0.98      11209.35|
|  6:  2.7881 -  2.6247  1357   146  0.87  19.83   0.98     0.95       9839.01|
|  7:  2.6247 -  2.4938  1292   156  0.88  19.15   1.00     0.96       8907.40|
|  8:  2.4938 -  2.3857  1343   134  0.87  19.75   1.00     0.95       8195.17|
|  9:  2.3857 -  2.2942  1340   151  0.87  19.19   1.00     0.94       6808.04|
| 10:  2.2942 -  2.2153  1316   146  0.88  18.84   1.00     0.96       5924.47|
| 11:  2.2153 -  2.1462  1281   149  0.88  18.12   0.99     0.95       5038.83|
| 12:  2.1462 -  2.0850  1329   148  0.90  17.04   1.00     1.00       4398.72|
| 13:  2.0850 -  2.0303  1196   127  0.89  17.70   0.98     0.98       3769.65|
| 14:  2.0303 -  1.9809   304    38  0.90  15.91   0.97     0.92       3162.27|
|alpha:            min =        0.92 max =            1.02 mean =         0.97|
|beta:             min =     3162.27 max =        13007.51 mean =      8205.11|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.97 mean =        16.50|
|phase err.(test): min =        0.00 max =           89.26 mean =        15.87|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1335   r_free= 0.1756   ksol= 0.33   Bsol= 66.62   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.62,-1.15,-0.36,-0.00,-0.00,-0.00); trace/3= -1.38                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.292678                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1335   r_free= 0.1756   ksol= 0.33   Bsol= 66.62   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.62,-1.15,-0.36,-0.00,-0.00,-0.00); trace/3= -1.38                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.292678                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0680 -  4.7281 0.99   1442  159 0.1036 0.1344      5.4369       5.602|
|  2:  4.7281 -  3.7722 0.99   1396  155 0.0922 0.1059      5.4947      5.6632|
|  3:  3.7722 -  3.3011 0.99   1350  149 0.1241 0.1735       5.592       5.963|
|  4:  3.3011 -  3.0019 0.99   1357  148 0.1492 0.1804      5.5895      5.7061|
|  5:  3.0019 -  2.7881 0.98   1327  153 0.1649 0.1863      5.4985      5.6311|
|  6:  2.7881 -  2.6247 0.99   1357  146 0.1567 0.2379      5.3915      5.6172|
|  7:  2.6247 -  2.4938 0.98   1292  156 0.1546 0.1954      5.3506      5.5524|
|  8:  2.4938 -  2.3857 0.99   1343  134 0.1493 0.2021       5.281      5.4504|
|  9:  2.3857 -  2.2942 0.99   1340  151 0.1455 0.2211      5.1932      5.4818|
| 10:  2.2942 -  2.2153 0.98   1316  146 0.1412 0.1885      5.1172      5.2699|
| 11:  2.2153 -  2.1462 0.97   1281  149 0.1399 0.1941      5.0384      5.3249|
| 12:  2.1462 -  2.0850 0.99   1329  148 0.1362 0.1648      4.9695      5.1357|
| 13:  2.0850 -  2.0303 0.88   1196  127 0.1359 0.1977      4.8818      5.1114|
| 14:  2.0303 -  1.9809 0.23    304   38 0.1151 0.1819       4.792      5.0135|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0680 -  4.7281  1442   159  0.94   9.34   0.96     0.93       7461.09|
|  2:  4.7281 -  3.7722  1396   155  0.95   8.75   1.00     0.99       9884.01|
|  3:  3.7722 -  3.3011  1350   149  0.92  12.80   1.01     1.01      12374.82|
|  4:  3.3011 -  3.0019  1357   148  0.90  16.38   1.00     0.98      13039.33|
|  5:  3.0019 -  2.7881  1327   153  0.88  18.84   0.99     0.97      11257.69|
|  6:  2.7881 -  2.6247  1357   146  0.87  19.86   0.97     0.94       9872.04|
|  7:  2.6247 -  2.4938  1292   156  0.87  19.17   0.99     0.95       8929.07|
|  8:  2.4938 -  2.3857  1343   134  0.87  19.77   0.99     0.94       8214.64|
|  9:  2.3857 -  2.2942  1340   151  0.87  19.21   0.98     0.92       6825.60|
| 10:  2.2942 -  2.2153  1316   146  0.88  18.85   0.99     0.94       5937.11|
| 11:  2.2153 -  2.1462  1281   149  0.88  18.13   0.98     0.94       5047.04|
| 12:  2.1462 -  2.0850  1329   148  0.90  17.04   0.99     0.99       4401.75|
| 13:  2.0850 -  2.0303  1196   127  0.89  17.69   0.97     0.96       3768.65|
| 14:  2.0303 -  1.9809   304    38  0.90  15.92   0.96     0.90       3163.28|
|alpha:            min =        0.90 max =            1.01 mean =         0.96|
|beta:             min =     3163.28 max =        13039.33 mean =      8202.21|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.95 mean =        16.50|
|phase err.(test): min =        0.00 max =           89.29 mean =        15.87|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.186)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.88    93.76   17.01    None  None   None       |
|    all(noH): 2823   0      1.88    93.76   17.01    None  None   None       |
|    Sol.    : 438    0      3.75    93.76   40.95    None  None   None       |
|    Mac.    : 2385   0      1.88    89.33   12.61    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.880 -  11.068: 1330   |   5:    47.820 -  57.008:   84        |
|      1:    11.068 -  20.256:  897   |   6:    57.008 -  66.196:   56        |
|      2:    20.256 -  29.444:  184   |   7:    66.196 -  75.384:   33        |
|      3:    29.444 -  38.632:  125   |   8:    75.384 -  84.572:    7        |
|      4:    38.632 -  47.820:   97   |   9:    84.572 -  93.760:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 324         
Filter by distance & map next to the model:
   mapped sites are within: 0.422 - 5.176
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 319 from: 324
   mapped sites are within: 0.710 - 5.176

peak=    7.907 closest distance to " O   HOH Z 203 " =    1.147
peak=    7.628 closest distance to " O  BHOH Z  74 " =    1.131
peak=    5.858 closest distance to " O   HOH Z 117 " =    1.514
peak=    5.382 closest distance to " O   HOH Z 210 " =    1.469
peak=    5.206 closest distance to " O   HOH Z 248 " =    1.592
peak=    5.151 closest distance to " O   HOH Z  54 " =    1.421
peak=    5.060 closest distance to " O   GLN A  11 " =    1.094
peak=    5.025 closest distance to " CG  PRO A 280 " =    0.896
peak=    5.000 closest distance to " CD2 TRP A 179 " =    1.253
peak=    4.918 closest distance to " O   HOH Z  49 " =    1.596
peak=    4.918 closest distance to " O   HOH Z  69 " =    1.525
peak=    4.878 closest distance to " CG  PRO A  90 " =    1.449
peak=    4.813 closest distance to " O   HOH Z  65 " =    1.264
peak=    4.800 closest distance to " CG  PRO A  54 " =    1.457
peak=    4.705 closest distance to " CB  GLN A 223 " =    1.362
peak=    4.697 closest distance to " O   HOH Z 113 " =    1.935
peak=    4.697 closest distance to " CG  GLN A  11 " =    1.013
peak=    4.682 closest distance to " O   HOH Z 255 " =    1.046
peak=    4.661 closest distance to " O   HOH Z 403 " =    2.051
peak=    4.512 closest distance to " CZ3 TRP A 266 " =    1.088
peak=    4.508 closest distance to " CA  TYR A  30 " =    0.979
peak=    4.457 closest distance to " O   HOH Z 130 " =    2.697
peak=    4.398 closest distance to " CB  SER A  63 " =    1.104
peak=    4.396 closest distance to " CB  TRP A 179 " =    1.285
peak=    4.385 closest distance to " CB  PRO A  54 " =    0.981
peak=    4.342 closest distance to " O   HOH Z 402 " =    1.690
peak=    4.323 closest distance to " O   PRO A 198 " =    1.556
peak=    4.275 closest distance to " CB  ARG A 275 " =    0.802
peak=    4.272 closest distance to " O   HOH Z 412 " =    3.421
peak=    4.264 closest distance to " OD1 ASN A 301 " =    1.077
peak=    4.228 closest distance to " CB  GLN A 183 " =    1.209
peak=    4.174 closest distance to " O   HOH Z 176 " =    2.401
peak=    4.150 closest distance to " O  BHOH Z 338 " =    1.203
peak=    4.145 closest distance to " CB  ASN A 142 " =    1.046
peak=    4.132 closest distance to " NH2 ARG A 156 " =    1.206
peak=    4.071 closest distance to " CB  GLU A 152 " =    1.250
peak=    4.070 closest distance to " CD  LYS A 166 " =    1.572
peak=    4.063 closest distance to " O   HOH Z 433 " =    1.910
peak=    4.058 closest distance to " O   HOH Z 144 " =    1.885
peak=    4.052 closest distance to " CG AARG A 275 " =    1.183
peak=    4.048 closest distance to " O   HOH Z 124 " =    1.183
peak=    4.034 closest distance to " OE1 GLN A  55 " =    1.653
peak=    3.999 closest distance to " O   HOH Z 189 " =    2.966
peak=    3.991 closest distance to " O   HOH Z 425 " =    1.610
peak=    3.984 closest distance to " CZ  PHE A 218 " =    1.201
peak=    3.977 closest distance to " CZ  PHE A  38 " =    1.134
peak=    3.974 closest distance to " O   HOH Z 394 " =    1.664
peak=    3.971 closest distance to " CB  ASN A 148 " =    1.438
peak=    3.970 closest distance to " O   HOH Z  40 " =    1.959
peak=    3.966 closest distance to " CB  ASN A 187 " =    1.201
peak=    3.961 closest distance to " O   HOH Z 261 " =    2.505
peak=    3.952 closest distance to " CA  ARG A  36 " =    1.066
peak=    3.943 closest distance to " CB  SER A  62 " =    0.872
peak=    3.935 closest distance to " CB  ASN A  39 " =    0.757
peak=    3.918 closest distance to " O   HOH Z 404 " =    1.681
peak=    3.916 closest distance to " CG2 VAL A 197 " =    1.186
peak=    3.900 closest distance to " O   ALA A 165 " =    1.350
peak=    3.899 closest distance to " O   HOH Z  44 " =    2.189
peak=    3.890 closest distance to " CG  PRO A 243 " =    1.173
peak=    3.890 closest distance to " O   HOH Z 134 " =    1.897
peak=    3.889 closest distance to " NE2 GLN A  11 " =    1.222
peak=    3.874 closest distance to " O   HOH Z 126 " =    1.592
peak=    3.869 closest distance to " CG2AVAL A 121 " =    2.037
peak=    3.864 closest distance to " O   HOH Z  76 " =    1.287
peak=    3.864 closest distance to " CG2BVAL A  41 " =    0.895
peak=    3.863 closest distance to " O   HOH Z  80 " =    2.080
peak=    3.862 closest distance to " CA  GLU A 152 " =    0.891
peak=    3.854 closest distance to " CB  GLU A  46 " =    1.129
peak=    3.853 closest distance to " O   HOH Z 336 " =    1.963
peak=    3.852 closest distance to " CD  ARG A 195 " =    1.025
peak=    3.845 closest distance to " O   HOH Z 128 " =    1.546
peak=    3.844 closest distance to " CA  THR A 246 " =    1.038
peak=    3.829 closest distance to " CA  ALA A 100 " =    1.071
peak=    3.818 closest distance to " CG1AVAL A 121 " =    0.830
peak=    3.816 closest distance to " O   HOH Z 234 " =    3.764
peak=    3.811 closest distance to " O   HOH Z 298 " =    1.835
peak=    3.809 closest distance to " O   HOH Z 437 " =    2.093
peak=    3.808 closest distance to " O   HOH Z 132 " =    2.857
peak=    3.807 closest distance to " CB  GLU A 277 " =    3.817
peak=    3.806 closest distance to " O   HOH Z 369 " =    1.753
peak=    3.788 closest distance to " CB  ASP A 191 " =    1.115
peak=    3.769 closest distance to " O   HOH Z 147 " =    1.610
peak=    3.766 closest distance to " CB  LEU A  83 " =    0.734
peak=    3.760 closest distance to " CA  ARG A 195 " =    1.171
peak=    3.754 closest distance to " CG1 ILE A  20 " =    1.240
peak=    3.736 closest distance to " CG  PRO A 198 " =    1.183
peak=    3.724 closest distance to " CA  ILE A 106 " =    0.748
peak=    3.719 closest distance to " O   HOH Z 102 " =    1.370
peak=    3.714 closest distance to " N   SER A 164 " =    0.984
peak=    3.709 closest distance to " NE2 GLN A  77 " =    3.177
peak=    3.709 closest distance to " CA  TYR A 116 " =    1.434
peak=    3.708 closest distance to " CA  ALA A  51 " =    1.012
peak=    3.702 closest distance to " CB  ARG A 190 " =    1.913
peak=    3.699 closest distance to " O   HOH Z 176 " =    1.776
peak=    3.696 closest distance to " O   HOH Z 406 " =    1.661
peak=    3.688 closest distance to " ND2 ASN A 249 " =    0.930
peak=    3.684 closest distance to " O   HOH Z 431 " =    1.340
peak=    3.680 closest distance to " CB  PRO A 243 " =    1.485
peak=    3.680 closest distance to " O   HOH Z 139 " =    1.454
peak=    3.669 closest distance to " CG1 ILE A  33 " =    1.302
peak=    3.666 closest distance to " CB  GLU A 128 " =    1.026
peak=    3.657 closest distance to " ND2 ASN A 187 " =    1.577
peak=    3.653 closest distance to " OE1 GLN A  11 " =    2.292
peak=    3.648 closest distance to " O   ASN A  74 " =    1.921
peak=    3.642 closest distance to " O   HOH Z 214 " =    1.522
peak=    3.641 closest distance to " CB  ARG A  79 " =    0.856
peak=    3.634 closest distance to " O   HOH Z  67 " =    1.047
peak=    3.633 closest distance to " O   HOH Z 423 " =    1.814
peak=    3.630 closest distance to " O   HOH Z 232 " =    2.542
peak=    3.627 closest distance to " O   HOH Z  63 " =    1.787
peak=    3.619 closest distance to " OG BSER A 212 " =    2.428
peak=    3.615 closest distance to " CB  ASN A 285 " =    0.883
peak=    3.614 closest distance to " CA  SER A  12 " =    1.607
peak=    3.610 closest distance to " O   HOH Z 146 " =    1.641
peak=    3.608 closest distance to " O   HOH Z  20 " =    1.701
peak=    3.605 closest distance to " CB  SER A 141 " =    1.103
peak=    3.584 closest distance to " CB  PRO A 198 " =    0.956
peak=    3.584 closest distance to " CB  ALA A 291 " =    1.042
peak=    3.584 closest distance to " O   HOH Z 346 " =    1.507
peak=    3.579 closest distance to " CB  PRO A  90 " =    1.208
peak=    3.575 closest distance to " O   HOH Z 196 " =    1.338
peak=    3.565 closest distance to " O   HOH Z 414 " =    1.695
peak=    3.564 closest distance to " CB  ARG A  79 " =    1.054
peak=    3.561 closest distance to " CA  ASN A 217 " =    1.385
peak=    3.557 closest distance to " O   HOH Z 128 " =    1.965
peak=    3.554 closest distance to " O   HOH Z 394 " =    4.052
peak=    3.553 closest distance to " O   HOH Z 417 " =    2.811
peak=    3.552 closest distance to " CB  TYR A 169 " =    0.806
peak=    3.551 closest distance to " N   ASN A  39 " =    1.228
peak=    3.551 closest distance to " CD  PRO A  54 " =    0.988
peak=    3.551 closest distance to " O   SER A  87 " =    2.282
peak=    3.549 closest distance to " CG  GLN A  77 " =    0.771
peak=    3.546 closest distance to " CB  ASN A  45 " =    1.163
peak=    3.543 closest distance to " O   HOH Z 345 " =    1.685
peak=    3.542 closest distance to " O   HOH Z 368 " =    2.015
peak=    3.536 closest distance to " O   ASP A 124 " =    1.610
peak=    3.533 closest distance to " CB  PHE A  16 " =    1.293
peak=    3.533 closest distance to " CE1 TYR A  30 " =    1.094
peak=    3.530 closest distance to " CB  PRO A 213 " =    1.386
peak=    3.528 closest distance to " CD1 ILE A 199 " =    1.339
peak=    3.524 closest distance to " CA  SER A  87 " =    0.993
peak=    3.523 closest distance to " CG1 ILE A 120 " =    1.131
peak=    3.521 closest distance to " O   HOH Z 126 " =    2.048
peak=    3.520 closest distance to " O   HOH Z 389 " =    2.130
peak=    3.513 closest distance to " ND2BASN A 224 " =    0.806
peak=    3.508 closest distance to " CG  ARG A 138 " =    1.396
peak=    3.503 closest distance to " OD1 ASN A 217 " =    1.592
peak=    3.502 closest distance to " OE1 GLN A  58 " =    3.406
peak=    3.501 closest distance to " O   HOH Z 209 " =    2.173
peak=    3.496 closest distance to " CD  ARG A 269 " =    1.053
peak=    3.493 closest distance to " O   HOH Z 195 " =    1.270
peak=    3.489 closest distance to " O   HOH Z 251 " =    1.597
peak=    3.488 closest distance to " CA  ASP A 162 " =    1.071
peak=    3.487 closest distance to " CA  ASN A 249 " =    1.395
peak=    3.482 closest distance to " CB  VAL A 202 " =    1.477
peak=    3.479 closest distance to " N   TYR A 116 " =    1.667
peak=    3.476 closest distance to " CD  ARG A 159 " =    0.810
peak=    3.470 closest distance to " CA  GLY A 196 " =    0.910
peak=    3.466 closest distance to " O   HOH Z 435 " =    1.969
peak=    3.463 closest distance to " O   HOH Z   7 " =    1.223
peak=    3.461 closest distance to " O   HOH Z 246 " =    1.474
peak=    3.457 closest distance to " N   THR A  52 " =    1.142
peak=    3.451 closest distance to " O   THR A 251 " =    1.276
peak=    3.450 closest distance to " N   ASP A 132 " =    0.975
peak=    3.449 closest distance to " CB  LEU A   5 " =    1.171
peak=    3.447 closest distance to " O   HOH Z 285 " =    1.932
peak=    3.444 closest distance to " O   HOH Z 139 " =    4.948
peak=    3.432 closest distance to " O   HOH Z 265 " =    1.951
peak=    3.420 closest distance to " O   HOH Z  35 " =    1.920
peak=    3.412 closest distance to " CD2 LEU A 297 " =    1.051
peak=    3.406 closest distance to " CA  ALA A 295 " =    0.941
peak=    3.404 closest distance to " CE1 TYR A 186 " =    1.352
peak=    3.402 closest distance to " O   HOH Z 301 " =    1.532
peak=    3.400 closest distance to " OE1 GLU A   2 " =    1.346
peak=    3.393 closest distance to " CG2 THR A 220 " =    0.836
peak=    3.390 closest distance to " O   HOH Z 146 " =    1.252
peak=    3.389 closest distance to " CZ3 TRP A  85 " =    0.988
peak=    3.388 closest distance to " O   HOH Z 358 " =    1.370
peak=    3.387 closest distance to " NZ  LYS A 117 " =    2.991
peak=    3.385 closest distance to " O   HOH Z 132 " =    2.641
peak=    3.384 closest distance to " O   HOH Z 258 " =    2.166
peak=    3.382 closest distance to " CA  VAL A  41 " =    0.809
peak=    3.382 closest distance to " O   HOH Z 116 " =    1.355
peak=    3.378 closest distance to " N   CYS A 260 " =    0.769
peak=    3.376 closest distance to " O   HOH Z 298 " =    2.256
peak=    3.369 closest distance to " O   HOH Z 299 " =    4.048
peak=    3.366 closest distance to " CB  VAL A 265 " =    1.192
peak=    3.366 closest distance to " CA  ALA A 160 " =    1.034
peak=    3.361 closest distance to " CB  GLU A 175 " =    1.355
peak=    3.356 closest distance to " CG  GLU A  37 " =    1.073
peak=    3.356 closest distance to " CB  THR A  52 " =    0.909
peak=    3.356 closest distance to " O   HOH Z 250 " =    1.569
peak=    3.354 closest distance to " CB  TYR A 116 " =    1.182
peak=    3.345 closest distance to " O   HOH Z 162 " =    1.609
peak=    3.333 closest distance to " OG BSER A 164 " =    2.259
peak=    3.333 closest distance to " O   HOH Z  21 " =    1.801
peak=    3.333 closest distance to " OG1 THR A 221 " =    1.749
peak=    3.331 closest distance to " O   HOH Z 185 " =    1.717
peak=    3.329 closest distance to " CE  LYS A  76 " =    0.875
peak=    3.329 closest distance to " CA  GLN A 223 " =    0.773
peak=    3.328 closest distance to " O   HOH Z 193 " =    2.012
peak=    3.326 closest distance to " O   HOH Z  88 " =    1.618
peak=    3.324 closest distance to " O   HOH Z 362 " =    3.283
peak=    3.323 closest distance to " O   HOH Z 244 " =    1.704
peak=    3.323 closest distance to " CB  ARG A 269 " =    1.105
peak=    3.322 closest distance to " CB  MET A 105 " =    1.039
peak=    3.321 closest distance to " O   HOH Z 130 " =    1.172
peak=    3.315 closest distance to " O   HOH Z 316 " =    2.924
peak=    3.314 closest distance to " CB  SER A 210 " =    0.883
peak=    3.313 closest distance to " O   HOH Z 156 " =    2.538
peak=    3.311 closest distance to " CG2 THR A 221 " =    1.044
peak=    3.310 closest distance to " CB  GLN A 194 " =    0.872
peak=    3.306 closest distance to " CE1 HIS A  81 " =    1.563
peak=    3.306 closest distance to " O   HOH Z  51 " =    1.652
peak=    3.305 closest distance to " O   ASP A 200 " =    1.517
peak=    3.303 closest distance to " O   HOH Z 259 " =    2.132
peak=    3.303 closest distance to " CA  ALA A   9 " =    1.066
peak=    3.302 closest distance to " CG2AVAL A  72 " =    1.843
peak=    3.298 closest distance to " CG2 THR A  29 " =    1.295
peak=    3.295 closest distance to " O   HOH Z 357 " =    2.240
peak=    3.294 closest distance to " O   HOH Z 141 " =    1.746
peak=    3.289 closest distance to " O   HOH Z  30 " =    2.277
peak=    3.279 closest distance to " CB  PHE A 204 " =    0.930
peak=    3.276 closest distance to " CG2 ILE A  20 " =    1.370
peak=    3.272 closest distance to " O   HOH Z  85 " =    2.382
peak=    3.270 closest distance to " CB  ASP A 124 " =    0.823
peak=    3.267 closest distance to " CB  ARG A 156 " =    1.018
peak=    3.265 closest distance to " O   HOH Z 234 " =    1.916
peak=    3.264 closest distance to " CB  ASP A 253 " =    0.965
peak=    3.264 closest distance to " O   HOH Z 313 " =    1.797
peak=    3.258 closest distance to " CA  ASP A 191 " =    0.865
peak=    3.257 closest distance to " O   PRO A 213 " =    1.310
peak=    3.256 closest distance to " O   HOH Z  88 " =    3.140
peak=    3.254 closest distance to " O   HOH Z  83 " =    1.748
peak=    3.253 closest distance to " NH2AARG A 145 " =    1.021
peak=    3.250 closest distance to " OD2 ASP A 298 " =    3.622
peak=    3.247 closest distance to " NH1AARG A 145 " =    1.272
peak=    3.245 closest distance to " CA  SER A  32 " =    1.598
peak=    3.245 closest distance to " NE AARG A 275 " =    1.204
peak=    3.245 closest distance to " O   HOH Z  27 " =    1.091
peak=    3.242 closest distance to " CB  SER A  32 " =    1.286
peak=    3.241 closest distance to " O   HOH Z  15 " =    2.338
peak=    3.239 closest distance to " O   HOH Z 199 " =    1.706
peak=    3.238 closest distance to " CB  ALA A 248 " =    1.332
peak=    3.232 closest distance to " OD1 ASN A  69 " =    2.255
peak=    3.230 closest distance to " O   HOH Z 293 " =    1.900
peak=    3.227 closest distance to " O   HOH Z 298 " =    4.361
peak=    3.227 closest distance to " O   HOH Z 395 " =    1.522
peak=    3.227 closest distance to " CB  LYS A 289 " =    1.163
peak=    3.224 closest distance to " CB  SER A  26 " =    1.719
peak=    3.224 closest distance to " CB  TRP A 266 " =    0.989
peak=    3.222 closest distance to " CE1 HIS A 115 " =    1.023
peak=    3.219 closest distance to " NH2BARG A 145 " =    2.001
peak=    3.217 closest distance to " O   GLY A  91 " =    1.132
peak=    3.217 closest distance to " OG  SER A  28 " =    1.714
peak=    3.215 closest distance to " O   HOH Z 343 " =    2.481
peak=    3.209 closest distance to " O   HOH Z  39 " =    1.301
peak=    3.207 closest distance to " O   HOH Z 383 " =    1.982
peak=    3.205 closest distance to " CB  ALA A  34 " =    0.742
peak=    3.205 closest distance to " CB  GLN A 103 " =    0.870
peak=    3.205 closest distance to " CB  THR A  31 " =    1.514
peak=    3.202 closest distance to " O   HOH Z 284 " =    2.952
peak=    3.202 closest distance to " O   THR A 220 " =    1.120
peak=    3.201 closest distance to " CD  GLN A 194 " =    1.667
peak=    3.199 closest distance to " O   HOH Z 421 " =    1.919
peak=    3.198 closest distance to " O   HOH Z 173 " =    2.204
peak=    3.196 closest distance to " CG  MET A 185 " =    1.070
peak=    3.192 closest distance to " O   HOH Z 364 " =    2.132
peak=    3.190 closest distance to " O   HOH Z  78 " =    1.669
peak=    3.189 closest distance to " O   HOH Z 219 " =    2.253
peak=    3.184 closest distance to " CG2 THR A  42 " =    0.769
peak=    3.183 closest distance to " NH1 ARG A 269 " =    0.757
peak=    3.179 closest distance to " CD  ARG A 139 " =    1.249
peak=    3.178 closest distance to " CB  MET A  40 " =    1.006
peak=    3.173 closest distance to " O   HOH Z  22 " =    2.355
peak=    3.173 closest distance to " CB  SER A  28 " =    0.954
peak=    3.171 closest distance to " NH2AARG A 190 " =    2.084
peak=    3.171 closest distance to " O   THR A 182 " =    1.398
peak=    3.166 closest distance to " N   ARG A 190 " =    1.020
peak=    3.161 closest distance to " O   HOH Z 213 " =    1.799
peak=    3.158 closest distance to " CB  ALA A  10 " =    1.328
peak=    3.158 closest distance to " CG  MET A 188 " =    0.921
peak=    3.154 closest distance to " O   HOH Z 154 " =    1.658
peak=    3.153 closest distance to " N   GLU A  44 " =    1.521
peak=    3.152 closest distance to " CE  MET A  40 " =    1.261
peak=    3.144 closest distance to " CB  ASP A 140 " =    0.862
peak=    3.143 closest distance to " O   HOH Z   6 " =    1.284
peak=    3.139 closest distance to " NH1 ARG A  14 " =    1.143
peak=    3.139 closest distance to " CB  ALA A  71 " =    1.347
peak=    3.137 closest distance to " CG2 VAL A 126 " =    0.938
peak=    3.134 closest distance to " CG  LYS A  76 " =    1.125
peak=    3.133 closest distance to " CB  SER A   3 " =    1.396
peak=    3.130 closest distance to " CA  ALA A  21 " =    1.204
peak=    3.130 closest distance to " CG  GLN A  58 " =    1.090
peak=    3.128 closest distance to " O   HOH Z 303 " =    2.423
peak=    3.127 closest distance to " CA  THR A  82 " =    1.502
peak=    3.121 closest distance to " CD1 LEU A 222 " =    0.710
peak=    3.117 closest distance to " O   HOH Z 258 " =    1.908
peak=    3.111 closest distance to " O   HOH Z 420 " =    4.969
peak=    3.106 closest distance to " CG  LEU A 237 " =    1.272
peak=    3.105 closest distance to " CB  ARG A 219 " =    1.278
peak=    3.102 closest distance to " O   HOH Z 240 " =    2.324
peak=    3.100 closest distance to " O   HOH Z 184 " =    1.189
peak=    3.098 closest distance to " O   HOH Z 216 " =    5.176
peak=    3.097 closest distance to " O   HOH Z 227 " =    1.639
peak=    3.085 closest distance to " CG1 VAL A 153 " =    1.142
peak=    3.081 closest distance to " CB  TYR A 172 " =    0.897
peak=    3.080 closest distance to " CA  ALA A 248 " =    1.254
peak=    3.077 closest distance to " O   HOH Z 154 " =    2.374
peak=    3.074 closest distance to " CG2 ILE A 120 " =    1.192
peak=    3.074 closest distance to " CB  ASN A 173 " =    0.879
peak=    3.067 closest distance to " NE2 GLN A  58 " =    4.880
peak=    3.062 closest distance to " OE1 GLN A 223 " =    2.327
peak=    3.056 closest distance to " O   HOH Z  47 " =    2.321
peak=    3.053 closest distance to " CD1 ILE A 199 " =    1.959
peak=    3.047 closest distance to " CG2 VAL A 268 " =    1.206
peak=    3.039 closest distance to " CA  PRO A  90 " =    0.975
peak=    3.034 closest distance to " CA  ASP A 149 " =    1.147
peak=    3.016 closest distance to " O   HOH Z 214 " =    2.986

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 222         
Filter by distance & map next to the model:
   mapped sites are within: 0.501 - 5.862
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 210 from: 222
   mapped sites are within: 0.706 - 5.862

peak=   -4.679 closest distance to " CD  GLN A  58 " =    0.859
peak=   -4.489 closest distance to " CD  GLN A 223 " =    1.390
peak=   -4.404 closest distance to " CD1 PHE A  59 " =    2.100
peak=   -4.388 closest distance to " CG  GLN A  11 " =    1.266
peak=   -4.352 closest distance to " O   PRO A 198 " =    1.297
peak=   -4.309 closest distance to " CD2 LEU A 237 " =    2.527
peak=   -4.304 closest distance to " O   HOH Z 290 " =    0.840
peak=   -4.204 closest distance to " O   GLN A  11 " =    0.956
peak=   -4.164 closest distance to " O   HOH Z 411 " =    5.499
peak=   -4.146 closest distance to " CD  ARG A  14 " =    3.262
peak=   -4.134 closest distance to " CD  GLN A 223 " =    0.989
peak=   -4.126 closest distance to " O   HOH Z 166 " =    1.460
peak=   -4.107 closest distance to " CD1 LEU A 101 " =    2.399
peak=   -4.103 closest distance to " O   HOH Z 422 " =    1.165
peak=   -4.081 closest distance to " O   HOH Z   7 " =    0.986
peak=   -4.077 closest distance to " CD2 TYR A  30 " =    2.885
peak=   -4.011 closest distance to " CG2 ILE A  49 " =    2.769
peak=   -4.009 closest distance to " O   VAL A  67 " =    2.844
peak=   -3.964 closest distance to " CB  PRO A 243 " =    2.837
peak=   -3.930 closest distance to " CD  GLN A  88 " =    0.878
peak=   -3.928 closest distance to " O   HOH Z 221 " =    0.871
peak=   -3.927 closest distance to " O  BHOH Z  74 " =    0.907
peak=   -3.905 closest distance to " CG  GLU A  53 " =    1.429
peak=   -3.900 closest distance to " OE1 GLN A  88 " =    0.947
peak=   -3.829 closest distance to " O   HOH Z 377 " =    2.022
peak=   -3.823 closest distance to " CG  GLN A 103 " =    2.411
peak=   -3.803 closest distance to " NH2 ARG A  79 " =    1.571
peak=   -3.792 closest distance to " O   HOH Z 331 " =    1.062
peak=   -3.782 closest distance to " O   HOH Z   5 " =    1.546
peak=   -3.781 closest distance to " C   THR A 279 " =    1.218
peak=   -3.766 closest distance to " CD2 TYR A 293 " =    1.912
peak=   -3.740 closest distance to " O   HOH Z 407 " =    1.019
peak=   -3.723 closest distance to " CE2 PHE A  61 " =    2.754
peak=   -3.721 closest distance to " O   HOH Z 392 " =    1.077
peak=   -3.715 closest distance to " O   HOH Z 136 " =    2.455
peak=   -3.714 closest distance to " NE  ARG A  36 " =    0.933
peak=   -3.704 closest distance to " O   SER A 271 " =    1.971
peak=   -3.701 closest distance to " CG2 ILE A  20 " =    2.875
peak=   -3.688 closest distance to " CG  ARG A 269 " =    2.315
peak=   -3.687 closest distance to " CD2 PHE A  61 " =    2.097
peak=   -3.681 closest distance to " CB  ALA A 291 " =    2.504
peak=   -3.674 closest distance to " CD1 ILE A 109 " =    2.791
peak=   -3.670 closest distance to " CG1 VAL A 112 " =    2.726
peak=   -3.663 closest distance to " CD  ARG A 156 " =    2.095
peak=   -3.662 closest distance to " OD1 ASP A 171 " =    1.536
peak=   -3.654 closest distance to " OH  TYR A 172 " =    1.938
peak=   -3.645 closest distance to " CB  ALA A  10 " =    2.138
peak=   -3.627 closest distance to " CZ  TYR A 169 " =    2.102
peak=   -3.623 closest distance to " OXT GLY A 302 " =    2.980
peak=   -3.621 closest distance to " O   HOH Z  52 " =    1.997
peak=   -3.620 closest distance to " O   HOH Z 155 " =    1.892
peak=   -3.614 closest distance to " O   VAL A 174 " =    2.093
peak=   -3.612 closest distance to " O   HOH Z 203 " =    1.033
peak=   -3.598 closest distance to " O   ARG A  79 " =    1.045
peak=   -3.593 closest distance to " O   TRP A  92 " =    2.093
peak=   -3.588 closest distance to " O   HOH Z 377 " =    0.927
peak=   -3.587 closest distance to " O   HOH Z 423 " =    2.647
peak=   -3.586 closest distance to " SD  MET A 105 " =    2.384
peak=   -3.583 closest distance to " CG  PRO A 243 " =    1.650
peak=   -3.573 closest distance to " OD1 ASN A 148 " =    1.292
peak=   -3.570 closest distance to " O   HOH Z 368 " =    2.023
peak=   -3.563 closest distance to " O   HOH Z 394 " =    1.675
peak=   -3.559 closest distance to " OD2 ASP A 298 " =    0.870
peak=   -3.551 closest distance to " CA  PRO A 280 " =    1.025
peak=   -3.551 closest distance to " O   HOH Z 156 " =    3.679
peak=   -3.543 closest distance to " O   HOH Z  67 " =    1.339
peak=   -3.536 closest distance to " SG  CYS A 168 " =    1.136
peak=   -3.532 closest distance to " CZ  PHE A  38 " =    2.344
peak=   -3.526 closest distance to " C   ASN A 285 " =    2.278
peak=   -3.512 closest distance to " CH2 TRP A 150 " =    1.134
peak=   -3.504 closest distance to " O   HOH Z 418 " =    1.217
peak=   -3.502 closest distance to " CG  MET A 105 " =    0.975
peak=   -3.499 closest distance to " O   HOH Z  65 " =    2.007
peak=   -3.496 closest distance to " O   HOH Z 198 " =    0.757
peak=   -3.491 closest distance to " NE2 GLN A 194 " =    2.108
peak=   -3.486 closest distance to " CG2 THR A 182 " =    2.217
peak=   -3.485 closest distance to " CA  GLY A 241 " =    3.370
peak=   -3.480 closest distance to " CG1 VAL A 112 " =    2.566
peak=   -3.475 closest distance to " OG  SER A  97 " =    2.240
peak=   -3.473 closest distance to " O   HOH Z  56 " =    0.995
peak=   -3.472 closest distance to " CD  ARG A  79 " =    1.254
peak=   -3.471 closest distance to " CD1 LEU A  25 " =    2.488
peak=   -3.462 closest distance to " CZ  ARG A 259 " =    0.764
peak=   -3.461 closest distance to " ND2 ASN A  45 " =    1.887
peak=   -3.458 closest distance to " OD2 ASP A 171 " =    1.807
peak=   -3.449 closest distance to " O   HOH Z 366 " =    1.564
peak=   -3.448 closest distance to " O   HOH Z 211 " =    1.133
peak=   -3.448 closest distance to " O   ALA A  34 " =    2.633
peak=   -3.447 closest distance to " O   SER A 206 " =    1.375
peak=   -3.447 closest distance to " CG2 VAL A 189 " =    2.164
peak=   -3.439 closest distance to " CA  GLY A 241 " =    2.380
peak=   -3.435 closest distance to " CB  ALA A 248 " =    2.237
peak=   -3.428 closest distance to " C   HIS A 108 " =    1.048
peak=   -3.420 closest distance to " C   VAL A 265 " =    0.932
peak=   -3.418 closest distance to " CA  VAL A 197 " =    0.984
peak=   -3.404 closest distance to " O   HOH Z 165 " =    1.800
peak=   -3.397 closest distance to " CA  GLU A 277 " =    1.249
peak=   -3.393 closest distance to " CG1 VAL A 189 " =    2.502
peak=   -3.391 closest distance to " N   ARG A 275 " =    1.589
peak=   -3.391 closest distance to " O   SER A 210 " =    1.635
peak=   -3.385 closest distance to " O   HOH Z 185 " =    2.616
peak=   -3.378 closest distance to " CE3 TRP A 150 " =    2.486
peak=   -3.374 closest distance to " NH2 ARG A  66 " =    2.097
peak=   -3.372 closest distance to " CG  LEU A  83 " =    2.080
peak=   -3.370 closest distance to " OH  TYR A 247 " =    2.235
peak=   -3.368 closest distance to " CZ  TYR A  68 " =    1.041
peak=   -3.363 closest distance to " CD1 TRP A 179 " =    0.888
peak=   -3.360 closest distance to " O   ARG A 275 " =    1.862
peak=   -3.359 closest distance to " O   VAL A  67 " =    2.632
peak=   -3.359 closest distance to " N   ALA A  43 " =    2.788
peak=   -3.354 closest distance to " O   HOH Z 197 " =    1.946
peak=   -3.351 closest distance to " CA  ASP A  65 " =    1.432
peak=   -3.348 closest distance to " CD1 LEU A 167 " =    1.998
peak=   -3.337 closest distance to " CG2 THR A  18 " =    2.892
peak=   -3.336 closest distance to " O   HOH Z  88 " =    2.787
peak=   -3.335 closest distance to " O   HOH Z 210 " =    0.758
peak=   -3.335 closest distance to " CG  ARG A 139 " =    1.107
peak=   -3.332 closest distance to " CB  ASP A 162 " =    2.546
peak=   -3.327 closest distance to " N   ALA A 226 " =    2.023
peak=   -3.323 closest distance to " CB  ASP A 286 " =    1.940
peak=   -3.322 closest distance to " O   HOH Z 198 " =    1.313
peak=   -3.321 closest distance to " O   HOH Z 191 " =    5.862
peak=   -3.319 closest distance to " O   SER A   3 " =    1.056
peak=   -3.316 closest distance to " O   HOH Z 297 " =    0.874
peak=   -3.312 closest distance to " CD2 LEU A 237 " =    2.697
peak=   -3.309 closest distance to " NH2 ARG A  79 " =    2.099
peak=   -3.307 closest distance to " O   HOH Z 326 " =    4.998
peak=   -3.299 closest distance to " O   HOH Z 340 " =    1.638
peak=   -3.298 closest distance to " N   ALA A 242 " =    1.917
peak=   -3.297 closest distance to " CE BMET A  47 " =    1.684
peak=   -3.295 closest distance to " CB  ALA A 161 " =    2.525
peak=   -3.294 closest distance to " O   HOH Z   6 " =    1.366
peak=   -3.291 closest distance to " CG  ASP A  50 " =    2.249
peak=   -3.288 closest distance to " O   HOH Z 313 " =    1.411
peak=   -3.287 closest distance to " O   HOH Z 154 " =    1.419
peak=   -3.286 closest distance to " CA  GLY A 203 " =    2.367
peak=   -3.279 closest distance to " O   HOH Z  90 " =    3.773
peak=   -3.276 closest distance to " O   HOH Z 149 " =    1.912
peak=   -3.273 closest distance to " CG  ASP A 231 " =    0.711
peak=   -3.273 closest distance to " NE2 GLN A 103 " =    2.022
peak=   -3.269 closest distance to " O   HOH Z 397 " =    1.185
peak=   -3.266 closest distance to " CD1 ILE A 263 " =    2.034
peak=   -3.265 closest distance to " O   HOH Z  69 " =    1.343
peak=   -3.264 closest distance to " CG  ASP A 286 " =    1.356
peak=   -3.263 closest distance to " CA  ASP A 298 " =    1.083
peak=   -3.261 closest distance to " CB  ALA A  43 " =    2.622
peak=   -3.257 closest distance to " CB  ASP A 132 " =    2.507
peak=   -3.255 closest distance to " O   HOH Z 174 " =    3.473
peak=   -3.251 closest distance to " O  BHOH Z 338 " =    1.140
peak=   -3.242 closest distance to " O   GLY A  80 " =    2.749
peak=   -3.223 closest distance to " CE1 TYR A 247 " =    2.715
peak=   -3.221 closest distance to " O   HOH Z 109 " =    3.386
peak=   -3.218 closest distance to " NH2 ARG A 159 " =    2.408
peak=   -3.215 closest distance to " ND2 ASN A 249 " =    2.180
peak=   -3.214 closest distance to " O   HOH Z  41 " =    2.094
peak=   -3.213 closest distance to " O   HOH Z 246 " =    1.080
peak=   -3.211 closest distance to " O   HOH Z 351 " =    1.689
peak=   -3.210 closest distance to " O   HOH Z 403 " =    1.117
peak=   -3.210 closest distance to " O   HOH Z  13 " =    0.769
peak=   -3.208 closest distance to " O   HOH Z 345 " =    3.027
peak=   -3.203 closest distance to " CG  PRO A 198 " =    2.007
peak=   -3.201 closest distance to " O   HOH Z 198 " =    1.007
peak=   -3.195 closest distance to " O   HOH Z 174 " =    2.296
peak=   -3.191 closest distance to " O   PRO A 163 " =    2.182
peak=   -3.184 closest distance to " O   HOH Z 108 " =    2.334
peak=   -3.178 closest distance to " O   HOH Z 100 " =    0.849
peak=   -3.177 closest distance to " O   PHE A 218 " =    1.423
peak=   -3.177 closest distance to " O   HOH Z 283 " =    2.302
peak=   -3.177 closest distance to " CE AMET A  47 " =    2.930
peak=   -3.175 closest distance to " CA  TRP A 274 " =    1.128
peak=   -3.171 closest distance to " CE  MET A  93 " =    2.188
peak=   -3.170 closest distance to " NE2 GLN A  88 " =    1.024
peak=   -3.168 closest distance to " O   ARG A  79 " =    1.751
peak=   -3.160 closest distance to " O   HOH Z 215 " =    2.284
peak=   -3.157 closest distance to " O   HOH Z   7 " =    1.522
peak=   -3.156 closest distance to " CG2BVAL A  41 " =    1.560
peak=   -3.156 closest distance to " O   HOH Z 348 " =    2.248
peak=   -3.156 closest distance to " O   GLN A  94 " =    2.255
peak=   -3.155 closest distance to " O   HOH Z 193 " =    1.605
peak=   -3.154 closest distance to " O   VAL A 257 " =    1.358
peak=   -3.150 closest distance to " OD2 ASP A 270 " =    1.041
peak=   -3.145 closest distance to " C   ALA A 158 " =    1.672
peak=   -3.144 closest distance to " O   ALA A  34 " =    2.025
peak=   -3.141 closest distance to " O   HOH Z  60 " =    0.879
peak=   -3.139 closest distance to " O   HOH Z  17 " =    1.355
peak=   -3.132 closest distance to " O   HOH Z 128 " =    2.488
peak=   -3.130 closest distance to " CB  SER A 210 " =    1.122
peak=   -3.126 closest distance to " O   HOH Z  39 " =    2.471
peak=   -3.125 closest distance to " C   GLY A 133 " =    1.191
peak=   -3.119 closest distance to " CB  ALA A   9 " =    2.627
peak=   -3.112 closest distance to " OE2 GLU A 277 " =    2.744
peak=   -3.112 closest distance to " CG  ARG A 259 " =    2.411
peak=   -3.111 closest distance to " O   HOH Z   1 " =    4.363
peak=   -3.106 closest distance to " CD1 ILE A 106 " =    2.135
peak=   -3.098 closest distance to " O   LEU A 282 " =    2.348
peak=   -3.091 closest distance to " O   HOH Z 250 " =    2.147
peak=   -3.091 closest distance to " CD  LYS A 289 " =    2.361
peak=   -3.087 closest distance to " O   HOH Z 234 " =    4.224
peak=   -3.085 closest distance to " OE1 GLN A 223 " =    2.357
peak=   -3.083 closest distance to " OE2 GLU A 152 " =    1.487
peak=   -3.082 closest distance to " O   HOH Z 265 " =    1.270
peak=   -3.082 closest distance to " O   HOH Z  54 " =    1.667
peak=   -3.081 closest distance to " CD2 PHE A  59 " =    2.376
peak=   -3.074 closest distance to " OE1 GLN A  88 " =    0.931
peak=   -3.073 closest distance to " OG1 THR A  82 " =    1.028
peak=   -3.058 closest distance to " O   HOH Z 412 " =    2.071
peak=   -3.050 closest distance to " O   HOH Z 232 " =    0.706
peak=   -3.049 closest distance to " O   HOH Z  40 " =    3.038
peak=   -3.040 closest distance to " O   HOH Z  31 " =    2.172
peak=   -3.007 closest distance to " O   HOH Z 265 " =    1.913

================= 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    :  0.4802 0.4737   6.290913e+00   6.274979e+00
   1_bss:  0.4721 0.4633   6.286162e+00   6.267429e+00
   1_xyz:  0.3804 0.4100   6.152914e+00   6.197018e+00
   1_adp:  0.3482 0.4205   6.108514e+00   6.207524e+00
   1_occ:  0.3480 0.4199   6.107878e+00   6.207580e+00
   2_bss:  0.3473 0.4184   6.109831e+00   6.208940e+00
   2_xyz:  0.2762 0.3387   5.918401e+00   6.071020e+00
   2_adp:  0.2563 0.3228   5.872078e+00   6.033272e+00
   2_occ:  0.2560 0.3228   5.871685e+00   6.033653e+00
   3_bss:  0.2558 0.3216   5.872590e+00   6.032704e+00
   3_xyz:  0.1964 0.2461   5.624591e+00   5.810048e+00
   3_adp:  0.1771 0.2298   5.544015e+00   5.747114e+00
   3_occ:  0.1769 0.2295   5.543094e+00   5.746697e+00
   4_bss:  0.1764 0.2288   5.541695e+00   5.744990e+00
   4_xyz:  0.1477 0.1956   5.384588e+00   5.600407e+00
   4_adp:  0.1393 0.1894   5.339535e+00   5.561680e+00
   4_occ:  0.1392 0.1894   5.339205e+00   5.561448e+00
   5_bss:  0.1397 0.1893   5.340400e+00   5.561064e+00
   5_xyz:  0.1320 0.1803   5.294546e+00   5.518393e+00
   5_adp:  0.1338 0.1755   5.293415e+00   5.498021e+00
   5_occ:  0.1336 0.1756   5.292811e+00   5.497835e+00
   5_bss:  0.1335 0.1756   5.292678e+00   5.497712e+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:  0.288  33.005  -3.290   3.955   2.372   0.000   0.000   0.000
   1_xyz:  0.288  33.005  -3.290   3.955   2.372   0.000   0.000   0.000
   1_adp:  0.288  33.005  -3.290   3.955   2.372   0.000   0.000   0.000
   1_occ:  0.288  33.005  -3.290   3.955   2.372   0.000   0.000   0.000
   2_bss:  0.299  48.935  -1.668   2.463   1.394   0.000   0.000   0.000
   2_xyz:  0.299  48.935  -1.668   2.463   1.394   0.000   0.000   0.000
   2_adp:  0.299  48.935  -1.668   2.463   1.394   0.000   0.000   0.000
   2_occ:  0.299  48.935  -1.668   2.463   1.394   0.000   0.000   0.000
   3_bss:  0.328  65.699  -1.934   0.998   0.292   0.000   0.000   0.000
   3_xyz:  0.328  65.699  -1.934   0.998   0.292   0.000   0.000   0.000
   3_adp:  0.328  65.699  -1.934   0.998   0.292   0.000   0.000   0.000
   3_occ:  0.328  65.699  -1.934   0.998   0.292   0.000   0.000   0.000
   4_bss:  0.333  75.247  -2.517  -0.442  -0.355  -0.000  -0.000  -0.000
   4_xyz:  0.333  75.247  -2.517  -0.442  -0.355  -0.000  -0.000  -0.000
   4_adp:  0.333  75.247  -2.517  -0.442  -0.355  -0.000  -0.000  -0.000
   4_occ:  0.333  75.247  -2.517  -0.442  -0.355  -0.000  -0.000  -0.000
   5_bss:  0.336  75.963  -2.457  -0.810  -0.215  -0.000  -0.000  -0.000
   5_xyz:  0.336  75.963  -2.457  -0.810  -0.215  -0.000  -0.000  -0.000
   5_adp:  0.336  75.963  -2.457  -0.810  -0.215  -0.000  -0.000  -0.000
   5_occ:  0.336  75.963  -2.457  -0.810  -0.215  -0.000  -0.000  -0.000
   5_bss:  0.327  66.619  -2.625  -1.148  -0.360  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  57.431 0.4271  0.5684    70545.115
   1_bss:  56.234 0.4412  0.6090    67674.885
   1_xyz:  48.020 0.5442  0.7346    51122.473
   1_adp:  48.387 0.5396  0.7380    52530.634
   1_occ:  48.389 0.5395  0.7367    52449.740
   2_bss:  48.221 0.5417  0.7360    52335.870
   2_xyz:  37.092 0.6761  0.8982    32627.278
   2_adp:  34.776 0.7035  0.9096    29297.918
   2_occ:  34.780 0.7034  0.9090    29306.997
   3_bss:  34.653 0.7051  0.8835    29244.110
   3_xyz:  25.026 0.8106  0.9732    15889.917
   3_adp:  22.783 0.8342  0.9785    13874.451
   3_occ:  22.754 0.8345  0.9787    13842.974
   4_bss:  22.639 0.8355  0.9502    13725.233
   4_xyz:  18.804 0.8730  0.9689     9876.356
   4_adp:  17.866 0.8818  0.9639     9266.997
   4_occ:  17.860 0.8819  0.9639     9262.970
   5_bss:  17.849 0.8820  0.9622     9249.163
   5_xyz:  16.887 0.8906  0.9668     8418.185
   5_adp:  16.434 0.8949  0.9666     8208.240
   5_occ:  16.439 0.8948  0.9665     8204.128
   5_bss:  16.437 0.8948  0.9571     8201.244
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.113   1.7379e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.113   1.7379e-01
   1_xyz:   1.620  0.012  0.101 15.954  0.006  4.111   1.3726e-01
   1_adp:   1.620  0.012  0.101 15.954  0.006  4.111   1.3726e-01
   1_occ:   1.620  0.012  0.101 15.954  0.006  4.111   1.3726e-01
   2_bss:   1.620  0.012  0.101 15.954  0.006  4.111   1.3726e-01
   2_xyz:   1.472  0.012  0.095 15.683  0.006  4.114   1.2809e-01
   2_adp:   1.472  0.012  0.095 15.683  0.006  4.114   1.2809e-01
   2_occ:   1.472  0.012  0.095 15.683  0.006  4.114   1.2809e-01
   3_bss:   1.472  0.012  0.095 15.683  0.006  4.114   1.2809e-01
   3_xyz:   1.214  0.010  0.080 15.024  0.005  4.114   8.5211e-02
   3_adp:   1.214  0.010  0.080 15.024  0.005  4.114   8.5211e-02
   3_occ:   1.214  0.010  0.080 15.024  0.005  4.114   8.5211e-02
   4_bss:   1.214  0.010  0.080 15.024  0.005  4.114   8.5211e-02
   4_xyz:   1.114  0.009  0.079 14.557  0.004  4.112   7.1442e-02
   4_adp:   1.114  0.009  0.079 14.557  0.004  4.112   7.1442e-02
   4_occ:   1.114  0.009  0.079 14.557  0.004  4.112   7.1442e-02
   5_bss:   1.114  0.009  0.079 14.557  0.004  4.112   7.1442e-02
   5_xyz:   1.002  0.008  0.073 14.352  0.004  4.118   5.8795e-02
   5_adp:   1.002  0.008  0.073 14.352  0.004  4.118   5.8795e-02
   5_occ:   1.002  0.008  0.073 14.352  0.004  4.118   5.8795e-02
   5_bss:   1.002  0.008  0.073 14.352  0.004  4.118   5.8795e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.657   2.4413e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.657   2.4413e-01
   1_xyz:   8.967  0.076  0.366 80.707  0.033  1.833   1.1085e-01
   1_adp:   8.967  0.076  0.366 80.707  0.033  1.833   1.1085e-01
   1_occ:   8.967  0.076  0.366 80.707  0.033  1.833   1.1085e-01
   2_bss:   8.967  0.076  0.366 80.707  0.033  1.833   1.1085e-01
   2_xyz:   8.943  0.076  0.311 85.097  0.027  2.182   2.1136e-01
   2_adp:   8.943  0.076  0.311 85.097  0.027  2.182   2.1136e-01
   2_occ:   8.943  0.076  0.311 85.097  0.027  2.182   2.1136e-01
   3_bss:   8.943  0.076  0.311 85.097  0.027  2.182   2.1136e-01
   3_xyz:   7.891  0.078  0.282 82.459  0.055  2.153   7.4002e-02
   3_adp:   7.891  0.078  0.282 82.459  0.055  2.153   7.4002e-02
   3_occ:   7.891  0.078  0.282 82.459  0.055  2.153   7.4002e-02
   4_bss:   7.891  0.078  0.282 82.459  0.055  2.153   7.4002e-02
   4_xyz:   8.028  0.056  0.229 83.248  0.032  2.292   5.0697e-02
   4_adp:   8.028  0.056  0.229 83.248  0.032  2.292   5.0697e-02
   4_occ:   8.028  0.056  0.229 83.248  0.032  2.292   5.0697e-02
   5_bss:   8.028  0.056  0.229 83.248  0.032  2.292   5.0697e-02
   5_xyz:   7.290  0.041  0.234 81.300  0.035  2.348   3.9203e-02
   5_adp:   7.290  0.041  0.234 81.300  0.035  2.348   3.9203e-02
   5_occ:   7.290  0.041  0.234 81.300  0.035  2.348   3.9203e-02
   5_bss:   7.290  0.041  0.234 81.300  0.035  2.348   3.9203e-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: 117.50   0.00  19.66  95.66   0.00  16.25 117.50   0.00  38.21
   1_occ: 117.50   0.00  19.66  95.66   0.00  16.25 117.50   0.00  38.21
   2_bss: 117.50   0.00  19.66  95.66   0.00  16.25 117.50   0.00  38.21
   2_xyz: 117.50   0.00  19.66  95.66   0.00  16.25 117.50   0.00  38.21
   2_adp: 111.70   0.00  18.32  82.02   0.00  14.71 111.70   0.00  37.95
   2_occ: 111.70   0.00  18.32  82.02   0.00  14.71 111.70   0.00  37.95
   3_bss: 111.70   0.00  18.32  82.02   0.00  14.71 111.70   0.00  37.95
   3_xyz: 111.70   0.00  18.32  82.02   0.00  14.71 111.70   0.00  37.95
   3_adp: 107.97   0.00  18.33  84.85   0.00  13.74 107.97   3.63  43.32
   3_occ: 107.97   0.00  18.33  84.85   0.00  13.74 107.97   3.63  43.32
   4_bss: 107.97   0.00  18.33  84.85   0.00  13.74 107.97   3.63  43.32
   4_xyz: 107.97   0.00  18.33  84.85   0.00  13.74 107.97   3.63  43.32
   4_adp: 100.54   0.84  18.10  94.68   0.84  13.11 100.54   3.83  45.27
   4_occ: 100.54   0.84  18.10  94.68   0.84  13.11 100.54   3.83  45.27
   5_bss: 100.54   0.84  18.10  94.68   0.84  13.11 100.54   3.83  45.27
   5_xyz: 100.54   0.84  18.10  94.68   0.84  13.11 100.54   3.83  45.27
   5_adp:  93.83   1.95  17.08  89.40   1.95  12.68  93.83   3.82  41.02
   5_occ:  93.83   1.95  17.08  89.40   1.95  12.68  93.83   3.82  41.02
   5_bss:  93.76   1.88  17.01  89.33   1.88  12.61  93.76   3.75  40.95
------------------------------------------------------------------------
 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:    1.685    0.022    0.367
   1_adp:    1.685    0.022    0.367
   1_occ:    1.685    0.022    0.367
   2_bss:    1.685    0.022    0.367
   2_xyz:    1.712    0.021    0.616
   2_adp:    1.712    0.021    0.616
   2_occ:    1.712    0.021    0.616
   3_bss:    1.712    0.021    0.616
   3_xyz:    1.544    0.079    0.774
   3_adp:    1.544    0.079    0.774
   3_occ:    1.544    0.079    0.774
   4_bss:    1.544    0.079    0.774
   4_xyz:    1.730    0.098    0.846
   4_adp:    1.730    0.098    0.846
   4_occ:    1.730    0.098    0.846
   5_bss:    1.730    0.098    0.846
   5_xyz:    1.637    0.090    0.870
   5_adp:    1.637    0.090    0.870
   5_occ:    1.637    0.090    0.870
   5_bss:    1.637    0.090    0.870
------------------------------------------------------------------------

CPU time actual refinement: 359.56


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_482/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_482/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_482/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_482/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_482/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 359.41 
  Macro-tasks:
    bulk solvent and scale       = 49.69  
    individual site refinement   = 148.45 
    weights calculation          = 29.38  
    collect and process          = 6.51   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 234.12 
  Micro-tasks:
    mask                            = 2.44   
    f_calc                          = 113.52 
    alpha_beta                      = 8.34   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 123.21 
    fmodel                         = 8.08   
    r_factors                      = 0.17   
    phase_errors                   = 10.23  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 267.41 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 5.035 micro seconds
Total CPU time: 6.22 minutes
from_scatterers_fft:    657 calls, 113.27 s
gradients_fft:          602 calls, 109.66 s

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

# Date 2008-01-16 Time 04:56:23 PST -0800 (1200488183.97 s)
Start R-work = 0.4802, R-free = 0.4737 (no bulk solvent and anisotropic scale)
Final R-work = 0.1544, R-free = 0.1935 (no bulk solvent and anisotropic scale)

Start R-work = 0.4721, R-free = 0.4633
Final R-work = 0.1335, R-free = 0.1756