# Date 2008-01-16 Time 06:22:33 PST -0800 (1200493353.25 s)
#phil __OFF__

Command line arguments: "../1116.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 16994
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1116

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (71.655, 46.2261, 86.39, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.655, 46.2261, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2108 1.97366
Completeness in resolution range: 0.942958
Completeness with d_max=infinity: 0.940242

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2108
                             d_min =   1.9737

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.655, 46.2261, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2108 1.97366
Completeness in resolution range: 0.942958
Completeness with d_max=infinity: 0.940242

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2112 -  4.2246 [2184/2211]  1967   217   9.9%
  bin  2:  4.2246 -  3.3651 [2089/2109]  1880   209  10.0%
  bin  3:  3.3651 -  2.9433 [2074/2093]  1864   210  10.1%
  bin  4:  2.9433 -  2.6758 [2033/2063]  1828   205  10.1%
  bin  5:  2.6758 -  2.4849 [2059/2078]  1860   199   9.7%
  bin  6:  2.4849 -  2.3389 [2008/2033]  1798   210  10.5%
  bin  7:  2.3389 -  2.2221 [2029/2057]  1827   202  10.0%
  bin  8:  2.2221 -  2.1257 [1997/2033]  1803   194   9.7%
  bin  9:  2.1257 -  2.0440 [2004/2046]  1803   201  10.0%
  bin 10:  2.0440 -  1.9737 [1112/2051]  1000   112  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1116/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 29
        2.42 -     3.04: 2182
        3.04 -     3.66: 4712
        3.66 -     4.28: 9032
        4.28 -     4.90: 12298
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 201 " - " O   HOH Z 349 "  1.967 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  2.091 3.040 x,y+1,z
  " O   HOH Z 208 " - " O   HOH Z 342 "  2.098 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 204 " - " O   HOH Z 296 "  2.128 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28248 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_1116/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1116/model_refine_001.geo

CPU time processing inputs: 9.10


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.655 46.22605 86.39 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: 1.97 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4057   r_free= 0.4007   ksol= 0.00   Bsol= 0.00   scale= 0.927    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.207003                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2112 -  4.7126 0.99   1416  159 0.3322 0.3224      6.4573       6.421|
|  2:  4.7126 -  3.7591 0.99   1355  151 0.3375 0.3200      6.6902      6.6305|
|  3:  3.7591 -  3.2894 0.99   1335  142 0.3568 0.3294      6.5279      6.5706|
|  4:  3.2894 -  2.9912 0.99   1335  155 0.3962 0.4210      6.4301       6.447|
|  5:  2.9912 -  2.7782 0.99   1330  149 0.4230 0.4030      6.2868      6.2957|
|  6:  2.7782 -  2.6152 0.99   1314  141 0.4170 0.4269      6.1905      6.1648|
|  7:  2.6152 -  2.4849 0.99   1314  143 0.4411 0.4194      6.1802      6.1335|
|  8:  2.4849 -  2.3771 0.98   1287  146 0.4471 0.4665      6.1096      6.1085|
|  9:  2.3771 -  2.2859 0.98   1290  150 0.4410 0.4496      6.0687      6.0982|
| 10:  2.2859 -  2.2073 1.00   1293  150 0.4613 0.4413      6.0438      6.0186|
| 11:  2.2073 -  2.1384 0.98   1309  131 0.4659 0.4735      6.0047      6.0217|
| 12:  2.1384 -  2.0775 0.98   1266  145 0.4733 0.4826      5.9271      5.9738|
| 13:  2.0775 -  2.0229 0.96   1270  134 0.4755 0.4729      5.8439      5.7725|
| 14:  2.0229 -  1.9737 0.39    516   63 0.4814 0.5093      5.8396      5.8211|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2112 -  4.7126  1416   159  0.76  28.81   0.84     0.80      52452.67|
|  2:  4.7126 -  3.7591  1355   151  0.78  27.76   0.94     0.88      70066.31|
|  3:  3.7591 -  3.2894  1335   142  0.70  35.38   0.96     0.87      77938.42|
|  4:  3.2894 -  2.9912  1335   155  0.63  41.40   0.94     0.82      73750.54|
|  5:  2.9912 -  2.7782  1330   149  0.55  48.07   0.92     0.74      62748.09|
|  6:  2.7782 -  2.6152  1314   141  0.54  48.58   0.94     0.73      53472.86|
|  7:  2.6152 -  2.4849  1314   143  0.53  49.82   0.95     0.71      48435.98|
|  8:  2.4849 -  2.3771  1287   146  0.53  49.82   0.94     0.72      43534.69|
|  9:  2.3771 -  2.2859  1290   150  0.52  50.82   0.97     0.71      40166.16|
| 10:  2.2859 -  2.2073  1293   150  0.51  51.75   0.97     0.72      37414.85|
| 11:  2.2073 -  2.1384  1309   131  0.48  53.81   0.98     0.70      37773.03|
| 12:  2.1384 -  2.0775  1266   145  0.45  56.49   0.95     0.67      35528.32|
| 13:  2.0775 -  2.0229  1270   134  0.40  60.04   0.97     0.62      32500.47|
| 14:  2.0229 -  1.9737   516    63  0.41  59.28   0.98     0.56      27656.60|
|alpha:            min =        0.56 max =            0.88 mean =         0.74|
|beta:             min =    27656.60 max =        77938.42 mean =     50781.16|
|figures of merit: min =        0.00 max =            1.00 mean =         0.57|
|phase err.(work): min =        0.00 max =           89.99 mean =        46.48|
|phase err.(test): min =        0.00 max =           89.89 mean =        46.44|
|-----------------------------------------------------------------------------|

============================== 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 = 8.294820              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.886   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.663022              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.564   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        4 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       25 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      193 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1989 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1872 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2840 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4637 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4395 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5610 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6688 |
|-----------------------------------------------------------------------------|
|-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 |        0.165 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.806 |       0.217 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.952)------------------------------------------|
|    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: 1.97 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4057   r_free= 0.4007   ksol= 0.00   Bsol= 0.00   scale= 0.927    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.207003                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3953   r_free= 0.3914   ksol= 0.34   Bsol= 53.67   scale= 0.955   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.08,1.28,-2.08,0.00,-0.00,-0.00); trace/3= 0.09                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.195658                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.238372              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.096   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.783347              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.306   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3953      final r-factor (work) = 0.2461          |
| start r-factor (free) = 0.3914      final r-factor (free) = 0.2808          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.5832 = 7.24 * 0.50 * 6.1942 + 1.00 * 0.1653                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.7694 = 7.24 * 0.50 * 5.9896 + 1.00 * 0.0919                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2461      final r-factor (work) = 0.2249          |
| start r-factor (free) = 0.2808      final r-factor (free) = 0.2930          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6982 = 0.78 * 1.00 * 5.9896 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5137 = 0.78 * 1.00 * 5.7444 + 1.00 * 0.0138                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.952)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    100.69  18.12    None  None   None       |
|    all(noH): 2823   0      0.00    100.69  18.12    None  None   None       |
|    Sol.    : 438    0      3.31    100.69  42.54    None  None   None       |
|    Mac.    : 2385   0      0.00    81.54   13.63    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 -  10.069:  976   |   5:    50.346 -  60.415:   94        |
|      1:    10.069 -  20.139: 1070   |   6:    60.415 -  70.485:   41        |
|      2:    20.139 -  30.208:  322   |   7:    70.485 -  80.554:   23        |
|      3:    30.208 -  40.277:  154   |   8:    80.554 -  90.623:    5        |
|      4:    40.277 -  50.346:  137   |   9:    90.623 - 100.692:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2249 r_free = 0.2930             target_work(ml) = 5.764         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2246 r_free = 0.2928             target_work(ml) = 5.762         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2246   r_free= 0.2928   ksol= 0.34   Bsol= 53.67   scale= 1.033   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.08,1.28,-2.08,0.00,-0.00,-0.00); trace/3= 0.09                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.762472                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2225   r_free= 0.2896   ksol= 0.35   Bsol= 69.27   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.13,-1.47,-1.65,-0.00,-0.00,-0.00); trace/3= -1.42                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.756257                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.369577              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.268   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.255955              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.740  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2225      final r-factor (work) = 0.1703          |
| start r-factor (free) = 0.2896      final r-factor (free) = 0.2238          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9049 = 2.37 * 0.50 * 5.7504 + 1.00 * 0.0919                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7455 = 2.37 * 0.50 * 5.6500 + 1.00 * 0.0515                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1703      final r-factor (work) = 0.1596          |
| start r-factor (free) = 0.2238      final r-factor (free) = 0.2082          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4599 = 0.26 * 1.00 * 5.6500 + 1.00 * 0.0138                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4130 = 0.26 * 1.00 * 5.4855 + 1.00 * 0.0089                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.952)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.25    96.93   17.54    None  None   None       |
|    all(noH): 2823   0      1.25    96.93   17.54    None  None   None       |
|    Sol.    : 438    0      6.07    96.93   40.99    None  None   None       |
|    Mac.    : 2385   0      1.25    79.96   13.23    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:     1.250 -  10.818: 1128   |   5:    49.088 -  58.655:   94        |
|      1:    10.818 -  20.385: 1029   |   6:    58.655 -  68.223:   49        |
|      2:    20.385 -  29.953:  234   |   7:    68.223 -  77.790:   15        |
|      3:    29.953 -  39.520:  143   |   8:    77.790 -  87.358:    5        |
|      4:    39.520 -  49.088:  124   |   9:    87.358 -  96.925:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1596 r_free = 0.2082             target_work(ml) = 5.451         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1595 r_free = 0.2082             target_work(ml) = 5.451         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1595   r_free= 0.2082   ksol= 0.35   Bsol= 69.27   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.13,-1.47,-1.65,-0.00,-0.00,-0.00); trace/3= -1.42                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.450989                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1595   r_free= 0.2075   ksol= 0.35   Bsol= 69.27   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.72,-2.26,-1.36,-0.00,-0.00,-0.00); trace/3= -1.78                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.449036                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.675322              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.933  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.500708              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 142.206  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1595      final r-factor (work) = 0.1265          |
| start r-factor (free) = 0.2075      final r-factor (free) = 0.1735          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.1315 = 3.68 * 0.50 * 5.4852 + 1.00 * 0.0516                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.8967 = 3.68 * 0.50 * 5.3509 + 1.00 * 0.0636                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1265      final r-factor (work) = 0.1199          |
| start r-factor (free) = 0.1735      final r-factor (free) = 0.1668          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6881 = 0.50 * 1.00 * 5.3509 + 1.00 * 0.0089                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6244 = 0.50 * 1.00 * 5.2226 + 1.00 * 0.0094                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.952)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.38   17.61    None  None   None       |
|    all(noH): 2823   0      0.00    92.38   17.61    None  None   None       |
|    Sol.    : 438    0      6.06    92.38   42.11    None  None   None       |
|    Mac.    : 2385   0      0.00    85.15   13.11    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.238:  812   |   5:    46.190 -  55.427:  108        |
|      1:     9.238 -  18.476: 1278   |   6:    55.427 -  64.665:   72        |
|      2:    18.476 -  27.714:  269   |   7:    64.665 -  73.903:   32        |
|      3:    27.714 -  36.952:  133   |   8:    73.903 -  83.141:   11        |
|      4:    36.952 -  46.190:  102   |   9:    83.141 -  92.379:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1199 r_free = 0.1668             target_work(ml) = 5.202         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1199 r_free = 0.1668             target_work(ml) = 5.202         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1199   r_free= 0.1668   ksol= 0.35   Bsol= 69.27   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.72,-2.26,-1.36,-0.00,-0.00,-0.00); trace/3= -1.78                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.202013                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1202   r_free= 0.1663   ksol= 0.32   Bsol= 59.19   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.13,-2.72,-1.53,-0.00,-0.00,-0.00); trace/3= -2.13                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.201480                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.560270              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 138.226  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.274701              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 145.063  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1202      final r-factor (work) = 0.1179          |
| start r-factor (free) = 0.1663      final r-factor (free) = 0.1622          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.1393 = 1.56 * 0.50 * 5.2244 + 1.00 * 0.0636                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.1024 = 1.56 * 0.50 * 5.1950 + 1.00 * 0.0496                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1179      final r-factor (work) = 0.1171          |
| start r-factor (free) = 0.1622      final r-factor (free) = 0.1616          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4364 = 0.27 * 1.00 * 5.1950 + 1.00 * 0.0093                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4327 = 0.27 * 1.00 * 5.1833 + 1.00 * 0.0088                               |
|-----------------------------------------------------------------------------|
| number of iterations = 14      |    number of function evaluations = 18     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.952)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.57    89.88   17.40    None  None   None       |
|    all(noH): 2823   0      0.57    89.88   17.40    None  None   None       |
|    Sol.    : 438    0      5.77    89.88   41.20    None  None   None       |
|    Mac.    : 2385   0      0.57    86.41   13.03    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:     0.573 -   9.504:  881   |   5:    45.228 -  54.159:  101        |
|      1:     9.504 -  18.435: 1220   |   6:    54.159 -  63.090:   72        |
|      2:    18.435 -  27.366:  264   |   7:    63.090 -  72.021:   32        |
|      3:    27.366 -  36.297:  128   |   8:    72.021 -  80.952:   11        |
|      4:    36.297 -  45.228:  106   |   9:    80.952 -  89.883:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1171 r_free = 0.1616             target_work(ml) = 5.181         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1171 r_free = 0.1615             target_work(ml) = 5.180         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1171   r_free= 0.1615   ksol= 0.32   Bsol= 59.19   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.13,-2.72,-1.53,-0.00,-0.00,-0.00); trace/3= -2.13                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.180382                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1171   r_free= 0.1615   ksol= 0.32   Bsol= 59.19   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.19,-2.80,-1.48,-0.00,-0.00,-0.00); trace/3= -2.15                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.180235                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.132710              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 126.778  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.034336              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 151.178  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1171      final r-factor (work) = 0.1120          |
| start r-factor (free) = 0.1615      final r-factor (free) = 0.1591          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5766 = 2.13 * 0.50 * 5.1831 + 1.00 * 0.0496                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5625 = 2.13 * 0.50 * 5.1598 + 1.00 * 0.0603                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1120      final r-factor (work) = 0.1113          |
| start r-factor (free) = 0.1591      final r-factor (free) = 0.1602          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.5057 = 2.03 * 1.00 * 5.1598 + 1.00 * 0.0088                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.4794 = 2.03 * 1.00 * 5.1462 + 1.00 * 0.0104                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.952)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.54   17.59    None  None   None       |
|    all(noH): 2823   0      0.00    99.54   17.59    None  None   None       |
|    Sol.    : 438    0      5.74    99.54   42.08    None  None   None       |
|    Mac.    : 2385   0      0.00    97.66   13.09    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.954: 1029   |   5:    49.770 -  59.724:   93        |
|      1:     9.954 -  19.908: 1138   |   6:    59.724 -  69.678:   51        |
|      2:    19.908 -  29.862:  224   |   7:    69.678 -  79.632:   23        |
|      3:    29.862 -  39.816:  132   |   8:    79.632 -  89.586:   11        |
|      4:    39.816 -  49.770:  115   |   9:    89.586 -  99.539:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1113 r_free = 0.1602             target_work(ml) = 5.151         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1113 r_free = 0.1602             target_work(ml) = 5.150         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1113   r_free= 0.1602   ksol= 0.32   Bsol= 59.19   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.19,-2.80,-1.48,-0.00,-0.00,-0.00); trace/3= -2.15                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.150475                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2112 -  4.7126 0.99   1416  159 0.0947 0.1321      5.3595       5.574|
|  2:  4.7126 -  3.7591 0.99   1355  151 0.0831 0.1030      5.4256      5.5889|
|  3:  3.7591 -  3.2894 0.99   1335  142 0.1069 0.1601      5.4739      5.8589|
|  4:  3.2894 -  2.9912 0.99   1335  155 0.1233 0.1730      5.4627      5.6279|
|  5:  2.9912 -  2.7782 0.99   1330  149 0.1325 0.1744      5.3177      5.5761|
|  6:  2.7782 -  2.6152 0.99   1314  141 0.1200 0.1783      5.1981      5.4202|
|  7:  2.6152 -  2.4849 0.99   1314  143 0.1271 0.1719       5.166      5.3633|
|  8:  2.4849 -  2.3771 0.98   1287  146 0.1155 0.1804      5.0627      5.3666|
|  9:  2.3771 -  2.2859 0.98   1290  150 0.1185 0.1837      5.0521      5.3409|
| 10:  2.2859 -  2.2073 1.00   1293  150 0.1115 0.1673      4.9461      5.1803|
| 11:  2.2073 -  2.1384 0.98   1309  131 0.1121 0.1825      4.9511      5.3322|
| 12:  2.1384 -  2.0775 0.98   1266  145 0.1128 0.1644      4.8711      5.1088|
| 13:  2.0775 -  2.0229 0.96   1270  134 0.1137 0.1757       4.799      5.0521|
| 14:  2.0229 -  1.9737 0.39    516   63 0.0997 0.1674      4.6514      4.9343|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2112 -  4.7126  1416   159  0.94   9.04   0.97     0.94       7070.91|
|  2:  4.7126 -  3.7591  1355   151  0.95   7.85   1.01     1.00       9039.33|
|  3:  3.7591 -  3.2894  1335   142  0.93  11.35   1.02     1.02      10309.04|
|  4:  3.2894 -  2.9912  1335   155  0.91  14.42   1.01     0.98      10703.85|
|  5:  2.9912 -  2.7782  1330   149  0.90  15.77   0.99     0.97       8210.51|
|  6:  2.7782 -  2.6152  1314   141  0.90  15.99   0.98     0.96       6982.55|
|  7:  2.6152 -  2.4849  1314   143  0.90  15.73   0.99     0.97       6298.60|
|  8:  2.4849 -  2.3771  1287   146  0.90  15.62   0.98     0.95       5314.99|
|  9:  2.3771 -  2.2859  1290   150  0.90  15.80   0.99     0.95       5212.01|
| 10:  2.2859 -  2.2073  1293   150  0.90  15.62   0.99     0.96       4359.81|
| 11:  2.2073 -  2.1384  1309   131  0.90  16.18   0.98     0.93       4450.45|
| 12:  2.1384 -  2.0775  1266   145  0.90  15.99   1.00     0.99       4031.89|
| 13:  2.0775 -  2.0229  1270   134  0.90  16.51   0.99     0.97       3483.18|
| 14:  2.0229 -  1.9737   516    63  0.91  14.78   0.96     0.93       2607.75|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2607.75 max =        10703.85 mean =      6499.42|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.94 mean =        14.25|
|phase err.(test): min =        0.00 max =           88.89 mean =        13.82|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1112   r_free= 0.1601   ksol= 0.32   Bsol= 59.20   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.99,-2.64,-1.29,-0.00,-0.00,-0.00); trace/3= -1.97                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.150572                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1112   r_free= 0.1601   ksol= 0.32   Bsol= 59.20   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.99,-2.64,-1.29,-0.00,-0.00,-0.00); trace/3= -1.97                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.150572                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2112 -  4.7126 0.99   1416  159 0.0948 0.1323      5.3604      5.5755|
|  2:  4.7126 -  3.7591 0.99   1355  151 0.0832 0.1030       5.426      5.5891|
|  3:  3.7591 -  3.2894 0.99   1335  142 0.1069 0.1601      5.4739      5.8591|
|  4:  3.2894 -  2.9912 0.99   1335  155 0.1233 0.1731      5.4627      5.6278|
|  5:  2.9912 -  2.7782 0.99   1330  149 0.1324 0.1744      5.3176      5.5759|
|  6:  2.7782 -  2.6152 0.99   1314  141 0.1200 0.1783       5.198      5.4199|
|  7:  2.6152 -  2.4849 0.99   1314  143 0.1271 0.1719       5.166      5.3633|
|  8:  2.4849 -  2.3771 0.98   1287  146 0.1155 0.1804      5.0627      5.3666|
|  9:  2.3771 -  2.2859 0.98   1290  150 0.1185 0.1836      5.0522      5.3407|
| 10:  2.2859 -  2.2073 1.00   1293  150 0.1115 0.1675      4.9462      5.1808|
| 11:  2.2073 -  2.1384 0.98   1309  131 0.1121 0.1825      4.9513      5.3323|
| 12:  2.1384 -  2.0775 0.98   1266  145 0.1127 0.1643      4.8709      5.1087|
| 13:  2.0775 -  2.0229 0.96   1270  134 0.1137 0.1757      4.7988      5.0516|
| 14:  2.0229 -  1.9737 0.39    516   63 0.0997 0.1674      4.6511      4.9339|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2112 -  4.7126  1416   159  0.94   9.06   0.97     0.95       7086.51|
|  2:  4.7126 -  3.7591  1355   151  0.95   7.86   1.01     1.01       9050.47|
|  3:  3.7591 -  3.2894  1335   142  0.93  11.35   1.03     1.03      10311.35|
|  4:  3.2894 -  2.9912  1335   155  0.91  14.43   1.01     0.99      10704.86|
|  5:  2.9912 -  2.7782  1330   149  0.90  15.77   1.00     0.98       8208.27|
|  6:  2.7782 -  2.6152  1314   141  0.90  15.99   0.99     0.97       6981.32|
|  7:  2.6152 -  2.4849  1314   143  0.90  15.73   1.00     0.97       6298.64|
|  8:  2.4849 -  2.3771  1287   146  0.90  15.62   0.99     0.96       5314.03|
|  9:  2.3771 -  2.2859  1290   150  0.90  15.81   1.00     0.96       5211.35|
| 10:  2.2859 -  2.2073  1293   150  0.90  15.63   1.00     0.97       4361.26|
| 11:  2.2073 -  2.1384  1309   131  0.90  16.19   0.99     0.94       4452.73|
| 12:  2.1384 -  2.0775  1266   145  0.90  15.99   1.01     1.00       4031.99|
| 13:  2.0775 -  2.0229  1270   134  0.90  16.51   1.00     0.98       3481.65|
| 14:  2.0229 -  1.9737   516    63  0.91  14.78   0.97     0.94       2605.97|
|alpha:            min =        0.94 max =            1.03 mean =         0.98|
|beta:             min =     2605.97 max =        10704.86 mean =      6501.52|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.94 mean =        14.25|
|phase err.(test): min =        0.00 max =           88.89 mean =        13.82|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.952)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.54   17.59    None  None   None       |
|    all(noH): 2823   0      0.00    99.54   17.59    None  None   None       |
|    Sol.    : 438    0      5.74    99.54   42.08    None  None   None       |
|    Mac.    : 2385   0      0.00    97.67   13.09    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   9.957: 1029   |   5:    49.773 -  59.727:   93        |
|      1:     9.957 -  19.911: 1138   |   6:    59.727 -  69.681:   51        |
|      2:    19.911 -  29.865:  224   |   7:    69.681 -  79.635:   23        |
|      3:    29.865 -  39.819:  132   |   8:    79.635 -  89.589:   11        |
|      4:    39.819 -  49.773:  115   |   9:    89.589 -  99.542:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 313         
Filter by distance & map next to the model:
   mapped sites are within: 0.539 - 4.606
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 310 from: 313
   mapped sites are within: 0.720 - 4.606

peak=    6.136 closest distance to " NE2 GLN A  11 " =    1.226
peak=    5.372 closest distance to " O   HOH Z 111 " =    2.020
peak=    5.352 closest distance to " CB  GLN A 223 " =    1.495
peak=    5.334 closest distance to " CG  PRO A  54 " =    1.230
peak=    5.205 closest distance to " O   HOH Z 232 " =    2.247
peak=    5.030 closest distance to " O   HOH Z 126 " =    2.028
peak=    5.000 closest distance to " O   HOH Z 144 " =    1.761
peak=    4.927 closest distance to " CB  SER A  63 " =    1.274
peak=    4.827 closest distance to " O   HOH Z 423 " =    1.848
peak=    4.802 closest distance to " CB  PRO A  54 " =    0.963
peak=    4.778 closest distance to " CG  PRO A 213 " =    1.275
peak=    4.775 closest distance to " CB  GLN A 183 " =    1.252
peak=    4.757 closest distance to " CG  PRO A 198 " =    1.252
peak=    4.748 closest distance to " O   HOH Z 298 " =    2.075
peak=    4.715 closest distance to " O   HOH Z  78 " =    1.998
peak=    4.631 closest distance to " CB  ASN A 148 " =    1.374
peak=    4.603 closest distance to " O   HOH Z 369 " =    2.130
peak=    4.577 closest distance to " C   PRO A 198 " =    1.516
peak=    4.551 closest distance to " O   HOH Z 427 " =    2.748
peak=    4.499 closest distance to " CA  TYR A  30 " =    1.008
peak=    4.437 closest distance to " O   HOH Z 287 " =    2.144
peak=    4.350 closest distance to " CD  ARG A 159 " =    0.818
peak=    4.333 closest distance to " O   HOH Z 425 " =    1.344
peak=    4.314 closest distance to " CB  GLU A 128 " =    1.076
peak=    4.307 closest distance to " O   HOH Z   2 " =    1.529
peak=    4.283 closest distance to " O   HOH Z   9 " =    2.228
peak=    4.270 closest distance to " ND1 HIS A  86 " =    1.765
peak=    4.270 closest distance to " CB  LEU A 228 " =    1.113
peak=    4.219 closest distance to " CB  ARG A 275 " =    0.946
peak=    4.192 closest distance to " O   HOH Z 417 " =    1.197
peak=    4.154 closest distance to " CB  TRP A 266 " =    1.028
peak=    4.129 closest distance to " O   HOH Z 437 " =    1.689
peak=    4.106 closest distance to " CG  LEU A 167 " =    1.262
peak=    4.094 closest distance to " CB  SER A   3 " =    1.437
peak=    4.073 closest distance to " O   HOH Z  63 " =    1.429
peak=    4.067 closest distance to " O   HOH Z 193 " =    1.758
peak=    4.056 closest distance to " ND2 ASN A 187 " =    1.403
peak=    4.054 closest distance to " O   HOH Z 133 " =    2.480
peak=    4.053 closest distance to " O   HOH Z 261 " =    1.691
peak=    4.047 closest distance to " CG2 VAL A 257 " =    0.951
peak=    4.045 closest distance to " O   HOH Z 132 " =    2.345
peak=    4.043 closest distance to " O   HOH Z   1 " =    1.810
peak=    4.038 closest distance to " O   HOH Z 180 " =    2.094
peak=    4.022 closest distance to " CB  ARG A  79 " =    1.404
peak=    4.012 closest distance to " O   HOH Z   1 " =    1.828
peak=    4.009 closest distance to " O   HOH Z 214 " =    2.049
peak=    4.006 closest distance to " O   HOH Z 193 " =    1.776
peak=    3.985 closest distance to " CB  ARG A 190 " =    1.623
peak=    3.984 closest distance to " CD  ARG A  66 " =    2.113
peak=    3.980 closest distance to " CE  LYS A  76 " =    0.859
peak=    3.974 closest distance to " CG2 THR A 221 " =    1.031
peak=    3.964 closest distance to " CB  GLU A 152 " =    1.330
peak=    3.961 closest distance to " CD BLYS A 290 " =    1.003
peak=    3.948 closest distance to " NH1AARG A 145 " =    1.162
peak=    3.948 closest distance to " O   HOH Z 316 " =    3.100
peak=    3.922 closest distance to " CB  SER A 212 " =    1.111
peak=    3.919 closest distance to " O   HOH Z 272 " =    1.822
peak=    3.916 closest distance to " O   HOH Z   7 " =    1.293
peak=    3.912 closest distance to " CG  TRP A 179 " =    2.272
peak=    3.911 closest distance to " CG  PRO A  90 " =    1.096
peak=    3.906 closest distance to " CB  ASN A 187 " =    1.092
peak=    3.889 closest distance to " CZ  PHE A 218 " =    1.043
peak=    3.886 closest distance to " O   HOH Z  58 " =    1.734
peak=    3.876 closest distance to " CB  SER A 216 " =    0.905
peak=    3.873 closest distance to " O   HOH Z 411 " =    3.658
peak=    3.868 closest distance to " O   HOH Z  61 " =    1.634
peak=    3.856 closest distance to " OD1 ASN A  69 " =    2.679
peak=    3.853 closest distance to " O   HOH Z  88 " =    3.655
peak=    3.846 closest distance to " O   HOH Z 250 " =    1.466
peak=    3.843 closest distance to " CA  MET A  40 " =    1.191
peak=    3.837 closest distance to " O   HOH Z 380 " =    1.632
peak=    3.827 closest distance to " CB  VAL A 265 " =    1.300
peak=    3.817 closest distance to " O   HOH Z 234 " =    3.803
peak=    3.807 closest distance to " O   HOH Z  10 " =    1.772
peak=    3.807 closest distance to " O   HOH Z 158 " =    2.933
peak=    3.800 closest distance to " O   HOH Z 126 " =    1.452
peak=    3.783 closest distance to " O   HOH Z 209 " =    2.264
peak=    3.774 closest distance to " N   PHE A 130 " =    1.190
peak=    3.772 closest distance to " O   HOH Z 419 " =    2.079
peak=    3.771 closest distance to " CA  SER A  87 " =    1.056
peak=    3.769 closest distance to " O   HOH Z 217 " =    3.034
peak=    3.769 closest distance to " CD2 LEU A 255 " =    1.653
peak=    3.763 closest distance to " CB  ASP A 124 " =    0.720
peak=    3.759 closest distance to " CB  ALA A  34 " =    1.189
peak=    3.758 closest distance to " O   HOH Z  40 " =    2.058
peak=    3.749 closest distance to " O   HOH Z 391 " =    2.941
peak=    3.742 closest distance to " CG1 ILE A  33 " =    1.207
peak=    3.738 closest distance to " O   HOH Z 213 " =    2.025
peak=    3.730 closest distance to " O   HOH Z  61 " =    1.518
peak=    3.716 closest distance to " N   ASN A 127 " =    1.279
peak=    3.711 closest distance to " CA  ARG A 195 " =    1.377
peak=    3.711 closest distance to " O   HOH Z 135 " =    1.713
peak=    3.707 closest distance to " O   HOH Z 371 " =    2.018
peak=    3.702 closest distance to " OD2 ASP A 286 " =    2.839
peak=    3.702 closest distance to " CA  ASN A 215 " =    1.256
peak=    3.686 closest distance to " CG  PRO A 243 " =    1.109
peak=    3.675 closest distance to " O   HOH Z 183 " =    1.469
peak=    3.673 closest distance to " O   THR A 220 " =    1.461
peak=    3.659 closest distance to " CA  ILE A 234 " =    1.056
peak=    3.638 closest distance to " O   HOH Z 352 " =    1.712
peak=    3.634 closest distance to " O   HOH Z 368 " =    2.029
peak=    3.633 closest distance to " O   HOH Z  21 " =    1.714
peak=    3.628 closest distance to " O   HOH Z 409 " =    2.411
peak=    3.622 closest distance to " CA  THR A 264 " =    0.860
peak=    3.615 closest distance to " CA  TYR A  30 " =    1.068
peak=    3.614 closest distance to " O   HOH Z 108 " =    2.293
peak=    3.613 closest distance to " CA  ALA A 158 " =    1.127
peak=    3.604 closest distance to " O   HOH Z 130 " =    3.800
peak=    3.604 closest distance to " CB  TYR A 169 " =    0.788
peak=    3.601 closest distance to " O   HOH Z  55 " =    2.280
peak=    3.596 closest distance to " CB  ALA A   1 " =    4.606
peak=    3.594 closest distance to " CG  GLN A  88 " =    1.091
peak=    3.591 closest distance to " N   TYR A  15 " =    0.861
peak=    3.589 closest distance to " OG  SER A  62 " =    3.053
peak=    3.588 closest distance to " CB  LEU A 237 " =    0.789
peak=    3.583 closest distance to " CB  VAL A 202 " =    1.619
peak=    3.580 closest distance to " CG  MET A 113 " =    1.484
peak=    3.575 closest distance to " O   HOH Z 289 " =    1.669
peak=    3.573 closest distance to " O   HOH Z 193 " =    2.135
peak=    3.573 closest distance to " CD1 LEU A 300 " =    1.201
peak=    3.564 closest distance to " O   HOH Z 327 " =    1.759
peak=    3.558 closest distance to " O   HOH Z 368 " =    3.670
peak=    3.554 closest distance to " CB  GLU A 236 " =    1.228
peak=    3.550 closest distance to " O   HOH Z 365 " =    2.836
peak=    3.550 closest distance to " O   HOH Z 116 " =    3.052
peak=    3.547 closest distance to " O   HOH Z 285 " =    2.684
peak=    3.546 closest distance to " O   MET A 105 " =    1.803
peak=    3.544 closest distance to " O   HOH Z 389 " =    1.929
peak=    3.538 closest distance to " CB  THR A  82 " =    1.313
peak=    3.536 closest distance to " O   HOH Z 344 " =    3.407
peak=    3.531 closest distance to " O   HOH Z 109 " =    2.501
peak=    3.528 closest distance to " CB  GLU A 277 " =    3.659
peak=    3.524 closest distance to " O   HOH Z  44 " =    2.855
peak=    3.518 closest distance to " O   HOH Z 405 " =    1.363
peak=    3.516 closest distance to " CA  ALA A 291 " =    0.900
peak=    3.514 closest distance to " O   HOH Z 207 " =    2.158
peak=    3.509 closest distance to " N   ALA A   1 " =    2.092
peak=    3.505 closest distance to " CB  ARG A 139 " =    0.998
peak=    3.493 closest distance to " CA  TYR A 116 " =    1.354
peak=    3.488 closest distance to " O   HOH Z  59 " =    1.894
peak=    3.487 closest distance to " CB  MET A  47 " =    1.073
peak=    3.486 closest distance to " CA  ALA A 154 " =    1.025
peak=    3.482 closest distance to " CA  GLY A 267 " =    1.298
peak=    3.480 closest distance to " O  BHOH Z 338 " =    2.380
peak=    3.477 closest distance to " CB  VAL A 265 " =    1.705
peak=    3.474 closest distance to " O   HOH Z 219 " =    2.151
peak=    3.469 closest distance to " O   HOH Z 115 " =    1.785
peak=    3.466 closest distance to " CB  MET A  40 " =    0.785
peak=    3.464 closest distance to " O   HOH Z  59 " =    1.671
peak=    3.464 closest distance to " O   HOH Z 305 " =    3.638
peak=    3.461 closest distance to " O   TYR A 116 " =    1.294
peak=    3.460 closest distance to " O   HOH Z 133 " =    1.684
peak=    3.453 closest distance to " CB  ASN A  39 " =    0.978
peak=    3.453 closest distance to " CB  ASN A 142 " =    0.911
peak=    3.451 closest distance to " O   HOH Z 175 " =    2.182
peak=    3.450 closest distance to " O   HOH Z 258 " =    2.150
peak=    3.450 closest distance to " CB  SER A 276 " =    1.145
peak=    3.449 closest distance to " CG BARG A 275 " =    1.516
peak=    3.448 closest distance to " OD1BASN A 224 " =    2.334
peak=    3.434 closest distance to " O   HOH Z 211 " =    2.749
peak=    3.431 closest distance to " CA  ARG A 102 " =    1.204
peak=    3.430 closest distance to " O   HOH Z 286 " =    2.344
peak=    3.425 closest distance to " CB  ASP A 140 " =    0.889
peak=    3.419 closest distance to " O   ASN A 209 " =    1.431
peak=    3.419 closest distance to " CG1 VAL A 189 " =    2.035
peak=    3.419 closest distance to " O   SER A  87 " =    2.434
peak=    3.417 closest distance to " O   HOH Z 280 " =    3.117
peak=    3.401 closest distance to " NE2 GLN A  73 " =    3.818
peak=    3.400 closest distance to " CA  ALA A 233 " =    1.354
peak=    3.399 closest distance to " O   HOH Z 188 " =    2.316
peak=    3.397 closest distance to " CB  ALA A 104 " =    0.726
peak=    3.397 closest distance to " CB  TYR A 116 " =    0.868
peak=    3.393 closest distance to " O   HOH Z 147 " =    1.782
peak=    3.391 closest distance to " OG  SER A  62 " =    3.039
peak=    3.391 closest distance to " CB  TRP A 179 " =    1.544
peak=    3.391 closest distance to " O   HOH Z 371 " =    2.872
peak=    3.389 closest distance to " CG  GLN A  89 " =    1.400
peak=    3.388 closest distance to " CA  THR A 221 " =    0.975
peak=    3.380 closest distance to " CA  LEU A 101 " =    1.486
peak=    3.378 closest distance to " O   HOH Z 189 " =    2.524
peak=    3.378 closest distance to " O   HOH Z 172 " =    3.065
peak=    3.377 closest distance to " O   HOH Z  68 " =    2.055
peak=    3.375 closest distance to " N   SER A 146 " =    1.764
peak=    3.373 closest distance to " CB  ASN A 110 " =    1.176
peak=    3.369 closest distance to " CD  LYS A 166 " =    1.378
peak=    3.362 closest distance to " CG  ARG A 159 " =    0.883
peak=    3.362 closest distance to " O   HOH Z 394 " =    1.636
peak=    3.352 closest distance to " CB  THR A 157 " =    1.163
peak=    3.352 closest distance to " CA  MET A 105 " =    0.960
peak=    3.348 closest distance to " CG1 VAL A 153 " =    0.945
peak=    3.347 closest distance to " CD  PRO A 243 " =    1.732
peak=    3.342 closest distance to " CA  LYS A 290 " =    1.373
peak=    3.342 closest distance to " O   HOH Z  20 " =    1.756
peak=    3.330 closest distance to " CB  LYS A 117 " =    1.193
peak=    3.328 closest distance to " N   GLN A 278 " =    1.140
peak=    3.328 closest distance to " O   HOH Z 302 " =    1.698
peak=    3.324 closest distance to " O   HOH Z 345 " =    1.674
peak=    3.324 closest distance to " O   HOH Z 362 " =    2.380
peak=    3.323 closest distance to " O   HOH Z 290 " =    0.923
peak=    3.323 closest distance to " O   HOH Z 373 " =    1.459
peak=    3.322 closest distance to " O   HOH Z 207 " =    1.828
peak=    3.322 closest distance to " O   HOH Z 238 " =    3.685
peak=    3.320 closest distance to " O   HOH Z 386 " =    3.114
peak=    3.317 closest distance to " O   HOH Z 423 " =    2.226
peak=    3.314 closest distance to " O   ALA A 291 " =    1.372
peak=    3.310 closest distance to " O   HOH Z  64 " =    2.107
peak=    3.308 closest distance to " O   THR A 251 " =    1.245
peak=    3.306 closest distance to " CA  ALA A 160 " =    0.885
peak=    3.302 closest distance to " O   HOH Z 392 " =    1.295
peak=    3.302 closest distance to " O   HOH Z 313 " =    1.856
peak=    3.301 closest distance to " ND1 HIS A  81 " =    1.601
peak=    3.300 closest distance to " O   HOH Z 425 " =    1.914
peak=    3.298 closest distance to " CB  GLU A 152 " =    1.433
peak=    3.294 closest distance to " O   HOH Z   3 " =    1.892
peak=    3.291 closest distance to " O   HOH Z 407 " =    2.090
peak=    3.289 closest distance to " CA  ALA A 299 " =    0.930
peak=    3.289 closest distance to " CD1 ILE A  33 " =    1.638
peak=    3.282 closest distance to " O   HOH Z 128 " =    2.268
peak=    3.281 closest distance to " O   HOH Z 345 " =    3.553
peak=    3.275 closest distance to " O   HOH Z 146 " =    1.716
peak=    3.274 closest distance to " OH  TYR A 186 " =    1.111
peak=    3.272 closest distance to " O   HOH Z 329 " =    3.871
peak=    3.270 closest distance to " CG  GLN A  55 " =    2.091
peak=    3.269 closest distance to " CB  HIS A 108 " =    0.787
peak=    3.261 closest distance to " O   HOH Z 326 " =    2.372
peak=    3.256 closest distance to " NE AARG A 275 " =    1.385
peak=    3.256 closest distance to " CB  LEU A 143 " =    1.137
peak=    3.255 closest distance to " O   HOH Z 386 " =    2.850
peak=    3.254 closest distance to " CE2 TYR A 186 " =    0.878
peak=    3.253 closest distance to " O   HOH Z 271 " =    2.503
peak=    3.252 closest distance to " CB  TYR A 169 " =    0.937
peak=    3.251 closest distance to " O   HOH Z 403 " =    1.393
peak=    3.244 closest distance to " CG  GLN A 278 " =    1.324
peak=    3.238 closest distance to " CB  SER A  62 " =    1.190
peak=    3.237 closest distance to " NH2BARG A 145 " =    2.029
peak=    3.235 closest distance to " O   HOH Z 236 " =    1.568
peak=    3.234 closest distance to " NE  ARG A  79 " =    1.178
peak=    3.231 closest distance to " O   HOH Z 356 " =    2.732
peak=    3.231 closest distance to " O   HOH Z 153 " =    1.601
peak=    3.227 closest distance to " OE1 GLN A 240 " =    1.679
peak=    3.226 closest distance to " O   HOH Z 185 " =    1.911
peak=    3.224 closest distance to " O   HOH Z 325 " =    3.755
peak=    3.220 closest distance to " CB  ILE A 120 " =    1.291
peak=    3.220 closest distance to " CB  ALA A 114 " =    0.819
peak=    3.220 closest distance to " CD2 TRP A 179 " =    1.283
peak=    3.219 closest distance to " O   HOH Z 184 " =    1.586
peak=    3.219 closest distance to " OG BSER A 164 " =    2.404
peak=    3.215 closest distance to " CG  GLU A 277 " =    1.958
peak=    3.214 closest distance to " CG  GLN A 144 " =    0.918
peak=    3.212 closest distance to " O   HOH Z 218 " =    4.447
peak=    3.208 closest distance to " NE2 HIS A 207 " =    1.365
peak=    3.207 closest distance to " OG BSER A 212 " =    2.691
peak=    3.204 closest distance to " O   HOH Z 282 " =    2.065
peak=    3.199 closest distance to " O   HOH Z 213 " =    2.929
peak=    3.198 closest distance to " CD2 LEU A 297 " =    0.934
peak=    3.197 closest distance to " O   ALA A 158 " =    1.383
peak=    3.195 closest distance to " O   HOH Z 148 " =    3.478
peak=    3.193 closest distance to " O   HOH Z 175 " =    3.633
peak=    3.190 closest distance to " CB  ALA A 114 " =    1.456
peak=    3.188 closest distance to " N   SER A 134 " =    1.391
peak=    3.188 closest distance to " CG1 ILE A 151 " =    1.036
peak=    3.187 closest distance to " CB  ASP A 253 " =    0.899
peak=    3.187 closest distance to " OG  SER A  22 " =    2.847
peak=    3.182 closest distance to " N   ASN A  39 " =    1.401
peak=    3.181 closest distance to " CA  SER A  95 " =    1.035
peak=    3.181 closest distance to " NZ  LYS A  76 " =    1.587
peak=    3.180 closest distance to " CA  ALA A  51 " =    1.000
peak=    3.179 closest distance to " O   GLY A  57 " =    2.642
peak=    3.178 closest distance to " CB  TRP A 150 " =    1.045
peak=    3.175 closest distance to " CA  GLU A  46 " =    0.903
peak=    3.174 closest distance to " NH2 ARG A 219 " =    1.791
peak=    3.174 closest distance to " N   ARG A 156 " =    1.326
peak=    3.172 closest distance to " O   HOH Z 227 " =    1.733
peak=    3.172 closest distance to " CA  TYR A 186 " =    1.568
peak=    3.170 closest distance to " NZ ALYS A 290 " =    1.056
peak=    3.163 closest distance to " CB  ASP A 171 " =    0.957
peak=    3.161 closest distance to " CD  ARG A 219 " =    1.119
peak=    3.161 closest distance to " OD1 ASN A 217 " =    1.554
peak=    3.161 closest distance to " O   HOH Z  64 " =    2.167
peak=    3.160 closest distance to " O   HOH Z 286 " =    2.254
peak=    3.160 closest distance to " O   HOH Z 291 " =    2.041
peak=    3.156 closest distance to " O   HOH Z  97 " =    2.134
peak=    3.156 closest distance to " O   HOH Z 426 " =    1.831
peak=    3.151 closest distance to " CA  ASP A 140 " =    1.229
peak=    3.149 closest distance to " CG2 VAL A 197 " =    1.096
peak=    3.146 closest distance to " NE2 GLN A  58 " =    3.624
peak=    3.146 closest distance to " O   HOH Z  53 " =    2.500
peak=    3.140 closest distance to " O   PRO A 213 " =    1.654
peak=    3.140 closest distance to " O   HOH Z 116 " =    1.751
peak=    3.135 closest distance to " O   HOH Z 368 " =    4.280
peak=    3.133 closest distance to " CB  GLU A  46 " =    0.995
peak=    3.131 closest distance to " OE2 GLU A  53 " =    2.130
peak=    3.131 closest distance to " CB  PRO A 163 " =    4.135
peak=    3.131 closest distance to " O   THR A 294 " =    1.071
peak=    3.123 closest distance to " CB  ARG A 138 " =    0.931
peak=    3.118 closest distance to " CA  ASN A 217 " =    1.166
peak=    3.113 closest distance to " CD1 ILE A 106 " =    0.797
peak=    3.111 closest distance to " O   HOH Z 217 " =    1.537
peak=    3.110 closest distance to " CD1AILE A 234 " =    0.963
peak=    3.109 closest distance to " OG BSER A  99 " =    2.262
peak=    3.101 closest distance to " O   HOH Z 303 " =    1.783
peak=    3.100 closest distance to " O   HOH Z  85 " =    2.074
peak=    3.091 closest distance to " O   HOH Z  44 " =    1.605
peak=    3.088 closest distance to " O   HOH Z 273 " =    2.795
peak=    3.084 closest distance to " O   HOH Z 303 " =    2.626
peak=    3.083 closest distance to " CG  LYS A  76 " =    1.015
peak=    3.078 closest distance to " O   HOH Z 295 " =    1.539
peak=    3.073 closest distance to " CB  TYR A  30 " =    1.404
peak=    3.073 closest distance to " O   HOH Z 128 " =    2.087
peak=    3.014 closest distance to " O   HOH Z 213 " =    2.107

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 208         
Filter by distance & map next to the model:
   mapped sites are within: 0.712 - 5.880
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 208 from: 208
   mapped sites are within: 0.712 - 5.880

peak=   -4.628 closest distance to " O   HOH Z 377 " =    1.909
peak=   -4.548 closest distance to " CB  PRO A 243 " =    2.529
peak=   -4.280 closest distance to " CD  ARG A  14 " =    3.401
peak=   -4.269 closest distance to " CD  ARG A 156 " =    2.049
peak=   -4.186 closest distance to " O   PRO A 198 " =    1.301
peak=   -4.152 closest distance to " CG  GLN A 223 " =    2.082
peak=   -4.122 closest distance to " O   HOH Z 389 " =    2.007
peak=   -4.109 closest distance to " O   HOH Z 231 " =    2.039
peak=   -4.099 closest distance to " O   HOH Z 266 " =    5.042
peak=   -4.050 closest distance to " N   ALA A  43 " =    2.559
peak=   -4.024 closest distance to " O   HOH Z  52 " =    1.350
peak=   -3.962 closest distance to " O   HOH Z 407 " =    3.314
peak=   -3.950 closest distance to " OG BSER A 134 " =    1.247
peak=   -3.928 closest distance to " O   HOH Z  38 " =    1.392
peak=   -3.867 closest distance to " CB  ALA A  43 " =    2.499
peak=   -3.847 closest distance to " O   HOH Z 351 " =    1.579
peak=   -3.840 closest distance to " O   HOH Z 435 " =    2.924
peak=   -3.827 closest distance to " C   ALA A 158 " =    1.518
peak=   -3.824 closest distance to " CA  GLY A  98 " =    1.892
peak=   -3.819 closest distance to " O   HOH Z 185 " =    2.077
peak=   -3.811 closest distance to " CZ3 TRP A 179 " =    1.110
peak=   -3.808 closest distance to " O   TYR A 247 " =    2.884
peak=   -3.792 closest distance to " O   HOH Z 290 " =    1.266
peak=   -3.787 closest distance to " O   HOH Z 372 " =    2.468
peak=   -3.785 closest distance to " O   HOH Z 152 " =    5.133
peak=   -3.772 closest distance to " CA  GLY A 203 " =    2.283
peak=   -3.771 closest distance to " CG1 VAL A 112 " =    2.955
peak=   -3.762 closest distance to " CB  ASP A  27 " =    2.484
peak=   -3.762 closest distance to " O   HOH Z 313 " =    1.765
peak=   -3.723 closest distance to " C   LEU A 222 " =    0.713
peak=   -3.716 closest distance to " OD1 ASP A 191 " =    1.867
peak=   -3.714 closest distance to " CG  MET A 105 " =    0.951
peak=   -3.713 closest distance to " ND2 ASN A  45 " =    1.956
peak=   -3.711 closest distance to " CE2 TYR A  30 " =    2.603
peak=   -3.699 closest distance to " OD1 ASN A 187 " =    1.552
peak=   -3.698 closest distance to " CZ BARG A 275 " =    1.671
peak=   -3.687 closest distance to " ND2 ASN A  45 " =    1.220
peak=   -3.685 closest distance to " O   VAL A  67 " =    2.640
peak=   -3.683 closest distance to " CB  PRO A  54 " =    2.469
peak=   -3.663 closest distance to " O   VAL A 189 " =    2.471
peak=   -3.650 closest distance to " O   HOH Z 198 " =    1.976
peak=   -3.626 closest distance to " NH2AARG A 275 " =    5.587
peak=   -3.624 closest distance to " CG  ARG A 269 " =    2.618
peak=   -3.622 closest distance to " O   HOH Z 111 " =    1.854
peak=   -3.622 closest distance to " O   HOH Z 198 " =    1.672
peak=   -3.611 closest distance to " OD1 ASN A 148 " =    1.593
peak=   -3.603 closest distance to " OG  SER A  87 " =    1.301
peak=   -3.602 closest distance to " CB  TRP A  85 " =    2.445
peak=   -3.596 closest distance to " CB  ALA A   9 " =    2.469
peak=   -3.594 closest distance to " CB  ALA A 291 " =    2.195
peak=   -3.593 closest distance to " CB  CYS A 254 " =    2.115
peak=   -3.589 closest distance to " CG  PHE A 283 " =    2.745
peak=   -3.572 closest distance to " CD2 LEU A 143 " =    2.588
peak=   -3.566 closest distance to " CG  GLN A  88 " =    0.854
peak=   -3.557 closest distance to " CG2 THR A  18 " =    2.821
peak=   -3.551 closest distance to " O   PRO A 243 " =    2.389
peak=   -3.547 closest distance to " C   ASN A 285 " =    2.464
peak=   -3.541 closest distance to " O   HOH Z  65 " =    1.290
peak=   -3.536 closest distance to " O   PHE A 218 " =    1.407
peak=   -3.532 closest distance to " O   SER A 135 " =    1.452
peak=   -3.530 closest distance to " OD1 ASP A 191 " =    1.566
peak=   -3.520 closest distance to " CE2 PHE A 218 " =    2.461
peak=   -3.520 closest distance to " CD1 PHE A  59 " =    1.927
peak=   -3.514 closest distance to " C   HIS A 108 " =    1.158
peak=   -3.511 closest distance to " NE  ARG A  36 " =    1.981
peak=   -3.503 closest distance to " C   ASN A 187 " =    1.808
peak=   -3.501 closest distance to " O   HOH Z 281 " =    2.728
peak=   -3.501 closest distance to " O   PRO A 163 " =    1.998
peak=   -3.500 closest distance to " N   THR A 157 " =    1.510
peak=   -3.494 closest distance to " ND2 ASN A 249 " =    2.270
peak=   -3.494 closest distance to " C   GLY A  13 " =    1.021
peak=   -3.494 closest distance to " C   LEU A 143 " =    1.438
peak=   -3.493 closest distance to " CD1 LEU A 101 " =    2.323
peak=   -3.491 closest distance to " O   HOH Z  43 " =    1.567
peak=   -3.481 closest distance to " CZ  PHE A  59 " =    1.546
peak=   -3.463 closest distance to " O   HOH Z  73 " =    1.996
peak=   -3.463 closest distance to " CB  ALA A 131 " =    2.038
peak=   -3.461 closest distance to " O   GLY A 211 " =    1.298
peak=   -3.459 closest distance to " CE  MET A 105 " =    2.265
peak=   -3.458 closest distance to " CB  ASN A  39 " =    2.277
peak=   -3.457 closest distance to " CB  ALA A 291 " =    2.305
peak=   -3.449 closest distance to " O   HOH Z 102 " =    1.614
peak=   -3.427 closest distance to " O   HOH Z 184 " =    1.867
peak=   -3.425 closest distance to " N   ASP A 171 " =    2.377
peak=   -3.420 closest distance to " O   HOH Z  90 " =    2.909
peak=   -3.416 closest distance to " CG  PRO A 163 " =    2.386
peak=   -3.416 closest distance to " CA  GLY A 241 " =    2.241
peak=   -3.414 closest distance to " CG  ARG A 269 " =    2.970
peak=   -3.409 closest distance to " O   HOH Z 298 " =    1.137
peak=   -3.406 closest distance to " O   SER A  62 " =    2.229
peak=   -3.403 closest distance to " O   HOH Z 345 " =    2.290
peak=   -3.399 closest distance to " O   HOH Z  22 " =    2.559
peak=   -3.391 closest distance to " O   HOH Z 417 " =    3.046
peak=   -3.389 closest distance to " CD2 TYR A 293 " =    1.942
peak=   -3.389 closest distance to " NH2 ARG A  79 " =    1.945
peak=   -3.386 closest distance to " O   HOH Z  53 " =    1.749
peak=   -3.379 closest distance to " O   PRO A 198 " =    1.368
peak=   -3.374 closest distance to " CG2 THR A 178 " =    2.206
peak=   -3.372 closest distance to " CD1 LEU A 228 " =    2.369
peak=   -3.370 closest distance to " CB  ALA A 248 " =    2.384
peak=   -3.367 closest distance to " O   ALA A 180 " =    1.226
peak=   -3.366 closest distance to " CE3 TRP A 123 " =    1.363
peak=   -3.361 closest distance to " CG  ASP A 231 " =    0.764
peak=   -3.360 closest distance to " OE1 GLN A  88 " =    1.193
peak=   -3.360 closest distance to " O   GLY A  17 " =    1.218
peak=   -3.360 closest distance to " O   HOH Z  11 " =    1.893
peak=   -3.360 closest distance to " O   HOH Z 298 " =    2.431
peak=   -3.359 closest distance to " CG1 VAL A 197 " =    2.258
peak=   -3.356 closest distance to " OXT GLY A 302 " =    3.099
peak=   -3.355 closest distance to " O   HOH Z 292 " =    1.667
peak=   -3.352 closest distance to " CD  LYS A 289 " =    2.378
peak=   -3.350 closest distance to " O   ILE A  49 " =    1.734
peak=   -3.349 closest distance to " NH1AARG A 275 " =    1.915
peak=   -3.346 closest distance to " O   HOH Z 426 " =    1.666
peak=   -3.342 closest distance to " CB  ALA A 248 " =    1.996
peak=   -3.341 closest distance to " O   HOH Z  51 " =    1.200
peak=   -3.341 closest distance to " NZ  LYS A 166 " =    1.234
peak=   -3.339 closest distance to " O   VAL A 197 " =    1.617
peak=   -3.334 closest distance to " O   HOH Z 131 " =    4.117
peak=   -3.333 closest distance to " O   HOH Z 353 " =    2.046
peak=   -3.332 closest distance to " O   HOH Z 166 " =    1.249
peak=   -3.330 closest distance to " O   SER A  22 " =    2.550
peak=   -3.329 closest distance to " CE1 TYR A 169 " =    2.497
peak=   -3.325 closest distance to " CB  PHE A 192 " =    1.804
peak=   -3.322 closest distance to " OD2 ASP A 171 " =    1.761
peak=   -3.319 closest distance to " O   HOH Z 174 " =    2.597
peak=   -3.311 closest distance to " CB  ALA A   7 " =    2.220
peak=   -3.308 closest distance to " OG  SER A  97 " =    2.182
peak=   -3.299 closest distance to " SG  CYS A 168 " =    1.084
peak=   -3.298 closest distance to " CD2 PHE A 225 " =    1.101
peak=   -3.294 closest distance to " OG BSER A 134 " =    1.640
peak=   -3.289 closest distance to " CG1 VAL A 250 " =    2.582
peak=   -3.288 closest distance to " ND2BASN A 224 " =    1.694
peak=   -3.286 closest distance to " CD  ARG A 139 " =    1.587
peak=   -3.284 closest distance to " O   ASN A 301 " =    1.436
peak=   -3.281 closest distance to " O   HOH Z 231 " =    1.061
peak=   -3.280 closest distance to " O   HOH Z 191 " =    5.522
peak=   -3.280 closest distance to " O   GLY A  80 " =    2.381
peak=   -3.278 closest distance to " O   HOH Z 409 " =    5.880
peak=   -3.277 closest distance to " O   HOH Z 275 " =    1.788
peak=   -3.276 closest distance to " O   HOH Z 255 " =    2.248
peak=   -3.269 closest distance to " CZ  TYR A 169 " =    1.669
peak=   -3.267 closest distance to " CE  MET A  93 " =    1.193
peak=   -3.265 closest distance to " CG  TRP A 266 " =    1.676
peak=   -3.261 closest distance to " O   HOH Z   1 " =    1.535
peak=   -3.251 closest distance to " O   HOH Z 207 " =    2.152
peak=   -3.248 closest distance to " CG  ASN A  39 " =    1.728
peak=   -3.246 closest distance to " ND2 ASN A  69 " =    1.710
peak=   -3.243 closest distance to " CE2 PHE A  61 " =    2.690
peak=   -3.243 closest distance to " O   TYR A  30 " =    2.787
peak=   -3.241 closest distance to " O   ARG A 145 " =    1.470
peak=   -3.238 closest distance to " OD1 ASP A 171 " =    1.601
peak=   -3.236 closest distance to " O   HOH Z 385 " =    2.128
peak=   -3.236 closest distance to " O   HOH Z 266 " =    4.745
peak=   -3.226 closest distance to " O   HOH Z 384 " =    2.770
peak=   -3.223 closest distance to " O   HOH Z 211 " =    1.416
peak=   -3.223 closest distance to " O   HOH Z 189 " =    2.042
peak=   -3.222 closest distance to " OH  TYR A 247 " =    1.815
peak=   -3.222 closest distance to " O   HOH Z 140 " =    1.524
peak=   -3.213 closest distance to " O   ILE A 109 " =    2.627
peak=   -3.210 closest distance to " O   HOH Z 352 " =    2.202
peak=   -3.208 closest distance to " O   VAL A  67 " =    2.799
peak=   -3.205 closest distance to " OE1 GLN A  58 " =    3.087
peak=   -3.204 closest distance to " O   HOH Z  13 " =    1.861
peak=   -3.202 closest distance to " O   ALA A  10 " =    1.674
peak=   -3.202 closest distance to " CA  GLY A 133 " =    1.975
peak=   -3.198 closest distance to " O   HOH Z  10 " =    1.520
peak=   -3.192 closest distance to " OG  SER A 245 " =    1.249
peak=   -3.192 closest distance to " CD  GLN A 223 " =    1.398
peak=   -3.190 closest distance to " O   TRP A  70 " =    1.448
peak=   -3.188 closest distance to " OD2 ASP A 171 " =    1.984
peak=   -3.182 closest distance to " CE BMET A  47 " =    1.676
peak=   -3.181 closest distance to " CG2BVAL A  41 " =    1.129
peak=   -3.179 closest distance to " O   HOH Z 114 " =    0.712
peak=   -3.178 closest distance to " O   HOH Z 359 " =    3.256
peak=   -3.174 closest distance to " O   ASP A 162 " =    2.291
peak=   -3.173 closest distance to " ND2 ASN A 187 " =    1.582
peak=   -3.170 closest distance to " O   HOH Z 282 " =    4.693
peak=   -3.164 closest distance to " O   HOH Z   9 " =    1.830
peak=   -3.160 closest distance to " O   HOH Z 324 " =    2.190
peak=   -3.160 closest distance to " OE2 GLU A 152 " =    1.075
peak=   -3.158 closest distance to " CB  ALA A 100 " =    2.183
peak=   -3.154 closest distance to " CD1 LEU A 297 " =    2.603
peak=   -3.145 closest distance to " CE3 TRP A 274 " =    2.449
peak=   -3.137 closest distance to " N   THR A 235 " =    1.271
peak=   -3.135 closest distance to " CD  GLN A  58 " =    0.973
peak=   -3.134 closest distance to " O   HOH Z 409 " =    4.469
peak=   -3.132 closest distance to " ND2 ASN A 285 " =    2.120
peak=   -3.129 closest distance to " O   HOH Z  90 " =    1.664
peak=   -3.126 closest distance to " O   HOH Z 263 " =    5.202
peak=   -3.125 closest distance to " CB  ASP A 286 " =    2.298
peak=   -3.110 closest distance to " O   HOH Z 118 " =    1.636
peak=   -3.103 closest distance to " O   HOH Z 176 " =    0.825
peak=   -3.102 closest distance to " CB  PRO A 163 " =    2.457
peak=   -3.097 closest distance to " N   SER A 276 " =    1.222
peak=   -3.097 closest distance to " OXT GLY A 302 " =    3.297
peak=   -3.094 closest distance to " O   HOH Z 118 " =    1.492
peak=   -3.093 closest distance to " O   HOH Z 247 " =    1.913
peak=   -3.093 closest distance to " O   HOH Z 383 " =    1.111
peak=   -3.081 closest distance to " O   VAL A 125 " =    2.272
peak=   -3.079 closest distance to " O   HOH Z 337 " =    1.577
peak=   -3.078 closest distance to " ND2 ASN A 215 " =    2.255
peak=   -3.077 closest distance to " CA  ASP A 298 " =    1.030
peak=   -3.074 closest distance to " CB  TYR A  15 " =    2.148
peak=   -3.070 closest distance to " O   HOH Z 350 " =    1.893
peak=   -3.037 closest distance to " O   HOH Z 198 " =    1.831
peak=   -3.036 closest distance to " O   HOH Z 410 " =    2.216
peak=   -3.013 closest distance to " NH2 ARG A 219 " =    1.788

================= 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    :  0.4057 0.4007   6.207003e+00   6.198832e+00
   1_bss:  0.3953 0.3914   6.195658e+00   6.184098e+00
   1_xyz:  0.2461 0.2808   5.809131e+00   5.887846e+00
   1_adp:  0.2249 0.2930   5.763616e+00   5.929212e+00
   1_occ:  0.2246 0.2928   5.762472e+00   5.928327e+00
   2_bss:  0.2225 0.2896   5.756257e+00   5.920037e+00
   2_xyz:  0.1703 0.2238   5.510101e+00   5.713903e+00
   2_adp:  0.1596 0.2082   5.451386e+00   5.648290e+00
   2_occ:  0.1595 0.2082   5.450989e+00   5.648088e+00
   3_bss:  0.1595 0.2075   5.449036e+00   5.645564e+00
   3_xyz:  0.1265 0.1735   5.247025e+00   5.474143e+00
   3_adp:  0.1199 0.1668   5.202218e+00   5.437981e+00
   3_occ:  0.1199 0.1668   5.202013e+00   5.437794e+00
   4_bss:  0.1202 0.1663   5.201480e+00   5.435609e+00
   4_xyz:  0.1179 0.1622   5.185474e+00   5.417255e+00
   4_adp:  0.1171 0.1616   5.180780e+00   5.413859e+00
   4_occ:  0.1171 0.1615   5.180382e+00   5.413450e+00
   5_bss:  0.1171 0.1615   5.180235e+00   5.413257e+00
   5_xyz:  0.1120 0.1591   5.150298e+00   5.397794e+00
   5_adp:  0.1113 0.1602   5.150604e+00   5.403487e+00
   5_occ:  0.1113 0.1602   5.150475e+00   5.403442e+00
   5_bss:  0.1112 0.1601   5.150572e+00   5.403527e+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:  0.336  53.670   1.079   1.284  -2.085   0.000  -0.000  -0.000
   1_xyz:  0.336  53.670   1.079   1.284  -2.085   0.000  -0.000  -0.000
   1_adp:  0.336  53.670   1.079   1.284  -2.085   0.000  -0.000  -0.000
   1_occ:  0.336  53.670   1.079   1.284  -2.085   0.000  -0.000  -0.000
   2_bss:  0.346  69.268  -1.131  -1.474  -1.646  -0.000  -0.000  -0.000
   2_xyz:  0.346  69.268  -1.131  -1.474  -1.646  -0.000  -0.000  -0.000
   2_adp:  0.346  69.268  -1.131  -1.474  -1.646  -0.000  -0.000  -0.000
   2_occ:  0.346  69.268  -1.131  -1.474  -1.646  -0.000  -0.000  -0.000
   3_bss:  0.346  69.268  -1.719  -2.262  -1.365  -0.000  -0.000  -0.000
   3_xyz:  0.346  69.268  -1.719  -2.262  -1.365  -0.000  -0.000  -0.000
   3_adp:  0.346  69.268  -1.719  -2.262  -1.365  -0.000  -0.000  -0.000
   3_occ:  0.346  69.268  -1.719  -2.262  -1.365  -0.000  -0.000  -0.000
   4_bss:  0.325  59.194  -2.127  -2.719  -1.533  -0.000  -0.000  -0.000
   4_xyz:  0.325  59.194  -2.127  -2.719  -1.533  -0.000  -0.000  -0.000
   4_adp:  0.325  59.194  -2.127  -2.719  -1.533  -0.000  -0.000  -0.000
   4_occ:  0.325  59.194  -2.127  -2.719  -1.533  -0.000  -0.000  -0.000
   5_bss:  0.325  59.194  -2.187  -2.800  -1.477  -0.000  -0.000  -0.000
   5_xyz:  0.325  59.194  -2.187  -2.800  -1.477  -0.000  -0.000  -0.000
   5_adp:  0.325  59.194  -2.187  -2.800  -1.477  -0.000  -0.000  -0.000
   5_occ:  0.325  59.194  -2.187  -2.800  -1.477  -0.000  -0.000  -0.000
   5_bss:  0.325  59.197  -1.992  -2.643  -1.289  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  46.480 0.5653  0.7418    50778.313
   1_bss:  45.634 0.5742  0.7602    48368.297
   1_xyz:  27.598 0.7854  0.9743    20226.336
   1_adp:  29.552 0.7628  0.9541    22079.417
   1_occ:  29.538 0.7628  0.9536    22028.822
   2_bss:  29.078 0.7679  0.9111    21556.415
   2_xyz:  21.863 0.8429  0.9691    12717.708
   2_adp:  19.820 0.8639  0.9790    11110.133
   2_occ:  19.819 0.8639  0.9788    11103.822
   3_bss:  19.733 0.8647  0.9664    11009.542
   3_xyz:  15.851 0.8992  0.9878     7535.242
   3_adp:  15.018 0.9065  0.9881     7044.945
   3_occ:  15.013 0.9066  0.9881     7040.567
   4_bss:  14.985 0.9067  0.9760     6989.895
   4_xyz:  14.514 0.9110  0.9756     6681.800
   4_adp:  14.385 0.9123  0.9735     6651.165
   4_occ:  14.377 0.9123  0.9734     6639.212
   5_bss:  14.372 0.9124  0.9725     6636.562
   5_xyz:  14.091 0.9145  0.9740     6444.335
   5_adp:  14.205 0.9136  0.9688     6500.868
   5_occ:  14.205 0.9136  0.9688     6499.359
   5_bss:  14.210 0.9136  0.9751     6501.462
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.6533e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.6533e-01
   1_xyz:   1.228  0.010  0.087 15.565  0.006  4.112   9.1923e-02
   1_adp:   1.228  0.010  0.087 15.565  0.006  4.112   9.1923e-02
   1_occ:   1.228  0.010  0.087 15.565  0.006  4.112   9.1923e-02
   2_bss:   1.228  0.010  0.087 15.565  0.006  4.112   9.1923e-02
   2_xyz:   0.948  0.006  0.068 14.062  0.003  4.123   5.1527e-02
   2_adp:   0.948  0.006  0.068 14.062  0.003  4.123   5.1527e-02
   2_occ:   0.948  0.006  0.068 14.062  0.003  4.123   5.1527e-02
   3_bss:   0.948  0.006  0.068 14.062  0.003  4.123   5.1527e-02
   3_xyz:   1.042  0.008  0.078 14.625  0.004  4.121   6.3552e-02
   3_adp:   1.042  0.008  0.078 14.625  0.004  4.121   6.3552e-02
   3_occ:   1.042  0.008  0.078 14.625  0.004  4.121   6.3552e-02
   4_bss:   1.042  0.008  0.078 14.625  0.004  4.121   6.3552e-02
   4_xyz:   0.891  0.006  0.068 14.327  0.004  4.123   4.9616e-02
   4_adp:   0.891  0.006  0.068 14.327  0.004  4.123   4.9616e-02
   4_occ:   0.891  0.006  0.068 14.327  0.004  4.123   4.9616e-02
   5_bss:   0.891  0.006  0.068 14.327  0.004  4.123   4.9616e-02
   5_xyz:   1.010  0.008  0.075 14.556  0.004  4.126   6.0285e-02
   5_adp:   1.010  0.008  0.075 14.556  0.004  4.126   6.0285e-02
   5_occ:   1.010  0.008  0.075 14.556  0.004  4.126   6.0285e-02
   5_bss:   1.010  0.008  0.075 14.556  0.004  4.126   6.0285e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4124e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4124e-01
   1_xyz:   8.930  0.082  0.299 87.779  0.045  2.165   9.8945e-02
   1_adp:   8.930  0.082  0.299 87.779  0.045  2.165   9.8945e-02
   1_occ:   8.930  0.082  0.299 87.779  0.045  2.165   9.8945e-02
   2_bss:   8.930  0.082  0.299 87.779  0.045  2.165   9.8945e-02
   2_xyz:   7.791  0.037  0.250 83.926  0.036  2.388   3.8231e-02
   2_adp:   7.791  0.037  0.250 83.926  0.036  2.388   3.8231e-02
   2_occ:   7.791  0.037  0.250 83.926  0.036  2.388   3.8231e-02
   3_bss:   7.791  0.037  0.250 83.926  0.036  2.388   3.8231e-02
   3_xyz:   8.578  0.044  0.224 85.370  0.033  2.267   4.7655e-02
   3_adp:   8.578  0.044  0.224 85.370  0.033  2.267   4.7655e-02
   3_occ:   8.578  0.044  0.224 85.370  0.033  2.267   4.7655e-02
   4_bss:   8.578  0.044  0.224 85.370  0.033  2.267   4.7655e-02
   4_xyz:   7.985  0.039  0.192 83.659  0.039  2.387   4.3904e-02
   4_adp:   7.985  0.039  0.192 83.659  0.039  2.387   4.3904e-02
   4_occ:   7.985  0.039  0.192 83.659  0.039  2.387   4.3904e-02
   5_bss:   7.985  0.039  0.192 83.659  0.039  2.387   4.3904e-02
   5_xyz:   8.172  0.041  0.226 85.394  0.036  2.306   4.1815e-02
   5_adp:   8.172  0.041  0.226 85.394  0.036  2.306   4.1815e-02
   5_occ:   8.172  0.041  0.226 85.394  0.036  2.306   4.1815e-02
   5_bss:   8.172  0.041  0.226 85.394  0.036  2.306   4.1815e-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: 100.69   0.00  18.12  81.54   0.00  13.63 100.69   3.31  42.54
   1_occ: 100.69   0.00  18.12  81.54   0.00  13.63 100.69   3.31  42.54
   2_bss: 100.69   0.00  18.12  81.54   0.00  13.63 100.69   3.31  42.54
   2_xyz: 100.69   0.00  18.12  81.54   0.00  13.63 100.69   3.31  42.54
   2_adp:  96.93   1.25  17.54  79.96   1.25  13.23  96.93   6.07  40.99
   2_occ:  96.93   1.25  17.54  79.96   1.25  13.23  96.93   6.07  40.99
   3_bss:  96.93   1.25  17.54  79.96   1.25  13.23  96.93   6.07  40.99
   3_xyz:  96.93   1.25  17.54  79.96   1.25  13.23  96.93   6.07  40.99
   3_adp:  92.38   0.00  17.61  85.15   0.00  13.11  92.38   6.06  42.11
   3_occ:  92.38   0.00  17.61  85.15   0.00  13.11  92.38   6.06  42.11
   4_bss:  92.38   0.00  17.61  85.15   0.00  13.11  92.38   6.06  42.11
   4_xyz:  92.38   0.00  17.61  85.15   0.00  13.11  92.38   6.06  42.11
   4_adp:  89.88   0.57  17.40  86.41   0.57  13.03  89.88   5.77  41.20
   4_occ:  89.88   0.57  17.40  86.41   0.57  13.03  89.88   5.77  41.20
   5_bss:  89.88   0.57  17.40  86.41   0.57  13.03  89.88   5.77  41.20
   5_xyz:  89.88   0.57  17.40  86.41   0.57  13.03  89.88   5.77  41.20
   5_adp:  99.54   0.00  17.59  97.66   0.00  13.09  99.54   5.74  42.08
   5_occ:  99.54   0.00  17.59  97.66   0.00  13.09  99.54   5.74  42.08
   5_bss:  99.54   0.00  17.59  97.67   0.00  13.09  99.54   5.74  42.08
------------------------------------------------------------------------
 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:    1.511    0.032    0.402
   1_adp:    1.511    0.032    0.402
   1_occ:    1.511    0.032    0.402
   2_bss:    1.511    0.032    0.402
   2_xyz:    1.153    0.035    0.473
   2_adp:    1.153    0.035    0.473
   2_occ:    1.153    0.035    0.473
   3_bss:    1.153    0.035    0.473
   3_xyz:    1.131    0.044    0.564
   3_adp:    1.131    0.044    0.564
   3_occ:    1.131    0.044    0.564
   4_bss:    1.131    0.044    0.564
   4_xyz:    1.211    0.028    0.576
   4_adp:    1.211    0.028    0.576
   4_occ:    1.211    0.028    0.576
   5_bss:    1.211    0.028    0.576
   5_xyz:    1.268    0.026    0.591
   5_adp:    1.268    0.026    0.591
   5_occ:    1.268    0.026    0.591
   5_bss:    1.268    0.026    0.591
------------------------------------------------------------------------

CPU time actual refinement: 352.34


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1116/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_1116/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1116/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1116/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1116/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 352.18 
  Macro-tasks:
    bulk solvent and scale       = 36.72  
    individual site refinement   = 148.68 
    weights calculation          = 31.23  
    collect and process          = 6.74   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 223.50 
  Micro-tasks:
    mask                            = 1.83   
    f_calc                          = 116.97 
    alpha_beta                      = 8.07   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 124.82 
    fmodel                         = 6.75   
    r_factors                      = 0.20   
    phase_errors                   = 10.96  
    foms                           = 0.33   
    TOTAL for micro-tasks          = 271.07 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.958 micro seconds
Total CPU time: 6.10 minutes
from_scatterers_fft:    653 calls, 116.45 s
gradients_fft:          598 calls, 110.98 s

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

# Date 2008-01-16 Time 06:28:38 PST -0800 (1200493718.62 s)
Start R-work = 0.4057, R-free = 0.4007 (no bulk solvent and anisotropic scale)
Final R-work = 0.1351, R-free = 0.1797 (no bulk solvent and anisotropic scale)

Start R-work = 0.3953, R-free = 0.3914
Final R-work = 0.1112, R-free = 0.1601