# Date 2008-01-16 Time 04:55:40 PST -0800 (1200488140.39 s)
#phil __OFF__

Command line arguments: "../520.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 5778
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 520

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.8988, 46.4607, 85.5261, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 46.4607, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8986 1.98037
Completeness in resolution range: 0.981167
Completeness with d_max=infinity: 0.978081

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8986
                             d_min =   1.9804

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 46.4607, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8986 1.98037
Completeness in resolution range: 0.981167
Completeness with d_max=infinity: 0.978081

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8990 -  4.2369 [2095/2119]  1886   209  10.0%
  bin  2:  4.2369 -  3.3759 [2023/2043]  1820   203  10.0%
  bin  3:  3.3759 -  2.9529 [1982/2001]  1783   199  10.0%
  bin  4:  2.9529 -  2.6846 [1954/1984]  1759   195  10.0%
  bin  5:  2.6846 -  2.4932 [1964/1983]  1770   194   9.9%
  bin  6:  2.4932 -  2.3468 [1955/1980]  1759   196  10.0%
  bin  7:  2.3468 -  2.2296 [1950/1978]  1752   198  10.2%
  bin  8:  2.2296 -  2.1329 [1917/1953]  1726   191  10.0%
  bin  9:  2.1329 -  2.0510 [1917/1959]  1727   190   9.9%
  bin 10:  2.0510 -  1.9804 [1832/1965]  1648   184  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_520/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 26
        2.42 -     3.04: 2228
        3.04 -     3.66: 4767
        3.66 -     4.28: 9141
        4.28 -     4.90: 12479
  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  52 " - " O   HOH Z 183 "  1.976 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 110 " - " O   HOH Z 355 "  2.146 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 271 " - " O   HOH Z 342 "  2.164 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  2.174 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28636 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_520/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_520/model_refine_001.geo

CPU time processing inputs: 9.12


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.89875 46.4607 85.5261 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3234   r_free= 0.3242   ksol= 0.00   Bsol= 0.00   scale= 0.983    |
|                                                                             |
| 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:   0.35 A                  |
| x-ray target function (ml) for work reflections: 6.035760                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8990 -  4.7254 0.99   1367  152 0.2866 0.2832      6.3502      6.3067|
|  2:  4.7254 -  3.7707 0.99   1310  145 0.2577 0.2436      6.4275      6.3864|
|  3:  3.7707 -  3.3000 0.99   1274  143 0.2732 0.2756      6.3283      6.4196|
|  4:  3.3000 -  3.0009 0.99   1280  144 0.2889 0.3192      6.2126       6.259|
|  5:  3.0009 -  2.7873 0.99   1263  138 0.3254 0.3050      6.0993      6.0315|
|  6:  2.7873 -  2.6239 0.99   1265  141 0.3300 0.3663      6.0298      6.0371|
|  7:  2.6239 -  2.4932 0.99   1259  137 0.3451 0.3117       6.004      5.8991|
|  8:  2.4932 -  2.3851 0.98   1258  140 0.3511 0.3745      5.9763      6.0491|
|  9:  2.3851 -  2.2936 0.98   1241  136 0.3562 0.3662      5.9255       5.891|
| 10:  2.2936 -  2.2147 1.00   1240  140 0.3590 0.3630      5.8989      5.8545|
| 11:  2.2147 -  2.1457 0.97   1249  142 0.3749 0.3603      5.8564      5.9164|
| 12:  2.1457 -  2.0845 0.97   1231  133 0.3790 0.3889       5.842      5.8399|
| 13:  2.0845 -  2.0298 0.99   1228  141 0.3764 0.3586      5.7392      5.7125|
| 14:  2.0298 -  1.9804 0.91   1165  127 0.3934 0.3552      5.7211       5.548|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8990 -  4.7254  1367   152  0.79  26.17   0.87     0.81      42567.50|
|  2:  4.7254 -  3.7707  1310   145  0.84  21.94   0.98     0.93      46154.72|
|  3:  3.7707 -  3.3000  1274   143  0.81  25.25   1.01     0.98      45372.89|
|  4:  3.3000 -  3.0009  1280   144  0.78  28.62   1.01     0.96      40646.40|
|  5:  3.0009 -  2.7873  1263   138  0.74  32.02   1.00     0.94      32919.44|
|  6:  2.7873 -  2.6239  1265   141  0.74  32.38   1.00     0.94      28427.98|
|  7:  2.6239 -  2.4932  1259   137  0.73  32.89   1.01     0.95      25237.96|
|  8:  2.4932 -  2.3851  1258   140  0.72  34.20   1.02     0.94      24684.59|
|  9:  2.3851 -  2.2936  1241   136  0.71  34.55   1.03     0.92      22855.11|
| 10:  2.2936 -  2.2147  1240   140  0.69  36.51   1.06     0.94      22458.76|
| 11:  2.2147 -  2.1457  1249   142  0.68  37.70   1.05     0.94      21105.26|
| 12:  2.1457 -  2.0845  1231   133  0.69  37.16   1.07     0.95      19379.54|
| 13:  2.0845 -  2.0298  1228   141  0.69  37.12   1.06     0.94      16080.15|
| 14:  2.0298 -  1.9804  1165   127  0.71  34.74   1.05     0.91      12114.44|
|alpha:            min =        0.81 max =            0.98 mean =         0.93|
|beta:             min =    12114.44 max =        46154.72 mean =     28879.17|
|figures of merit: min =        0.00 max =            1.00 mean =         0.74|
|phase err.(work): min =        0.00 max =           89.98 mean =        32.11|
|phase err.(test): min =        0.00 max =           89.95 mean =        32.31|
|-----------------------------------------------------------------------------|

============================== 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 = 3.581104              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.552   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.664419              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.897   (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:        2 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       24 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      213 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2015 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1891 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2876 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4696 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4445 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5686 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6793 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.162 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.806 |       0.199 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.620)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3234   r_free= 0.3242   ksol= 0.00   Bsol= 0.00   scale= 0.983    |
|                                                                             |
| 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:   0.35 A                  |
| x-ray target function (ml) for work reflections: 6.035760                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3085   r_free= 0.3057   ksol= 0.33   Bsol= 34.11   scale= 0.981   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.00,0.13,-0.50,0.00,-0.00,-0.00); trace/3= -1.13                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 6.015953                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.116923              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.540   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.338674              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.805   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3085      final r-factor (work) = 0.1751          |
| start r-factor (free) = 0.3057      final r-factor (free) = 0.1979          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.5513 = 3.12 * 0.50 * 6.0245 + 1.00 * 0.1624                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.9467 = 3.12 * 0.50 * 5.7014 + 1.00 * 0.0613                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1751      final r-factor (work) = 0.1603          |
| start r-factor (free) = 0.1979      final r-factor (free) = 0.2053          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9369 = 0.34 * 1.00 * 5.7014 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8456 = 0.34 * 1.00 * 5.4242 + 1.00 * 0.0086                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.620)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    71.57   17.07    None  None   None       |
|    all(noH): 2823   0      0.00    71.57   17.07    None  None   None       |
|    Sol.    : 438    0      8.29    71.57   38.86    None  None   None       |
|    Mac.    : 2385   0      0.00    65.62   13.07    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 -   7.157:  360   |   5:    35.787 -  42.944:  119        |
|      1:     7.157 -  14.315: 1355   |   6:    42.944 -  50.101:  104        |
|      2:    14.315 -  21.472:  508   |   7:    50.101 -  57.259:   74        |
|      3:    21.472 -  28.629:  160   |   8:    57.259 -  64.416:   32        |
|      4:    28.629 -  35.787:  102   |   9:    64.416 -  71.573:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1603 r_free = 0.2053             target_work(ml) = 5.441         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1601 r_free = 0.2052             target_work(ml) = 5.440         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1601   r_free= 0.2052   ksol= 0.33   Bsol= 34.11   scale= 1.028   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.00,0.13,-0.50,0.00,-0.00,-0.00); trace/3= -1.13                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.439654                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1589   r_free= 0.2026   ksol= 0.32   Bsol= 39.82   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.98,-2.01,-1.50,-0.00,-0.00,-0.00); trace/3= -2.17                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.432582                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.410586              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.434   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.134444              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.117  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1589      final r-factor (work) = 0.1224          |
| start r-factor (free) = 0.2026      final r-factor (free) = 0.1633          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6107 = 2.41 * 0.50 * 5.4339 + 1.00 * 0.0613                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4654 = 2.41 * 0.50 * 5.3208 + 1.00 * 0.0523                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1224      final r-factor (work) = 0.1180          |
| start r-factor (free) = 0.1633      final r-factor (free) = 0.1558          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7240 = 0.13 * 1.00 * 5.3208 + 1.00 * 0.0086                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7033 = 0.13 * 1.00 * 5.1807 + 1.00 * 0.0067                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.620)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.80    68.03   16.72    None  None   None       |
|    all(noH): 2823   0      1.80    68.03   16.72    None  None   None       |
|    Sol.    : 438    0      5.50    67.65   37.58    None  None   None       |
|    Mac.    : 2385   0      1.80    68.03   12.89    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:     1.801 -   8.424:  556   |   5:    34.915 -  41.538:  119        |
|      1:     8.424 -  15.047: 1308   |   6:    41.538 -  48.161:   96        |
|      2:    15.047 -  21.670:  395   |   7:    48.161 -  54.784:   68        |
|      3:    21.670 -  28.292:  129   |   8:    54.784 -  61.407:   36        |
|      4:    28.292 -  34.915:   98   |   9:    61.407 -  68.030:   18        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1180 r_free = 0.1558             target_work(ml) = 5.157         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1179 r_free = 0.1559             target_work(ml) = 5.156         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1179   r_free= 0.1559   ksol= 0.32   Bsol= 39.82   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.98,-2.01,-1.50,-0.00,-0.00,-0.00); trace/3= -2.17                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.156462                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1182   r_free= 0.1560   ksol= 0.32   Bsol= 39.82   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.83,-2.37,-1.49,-0.00,-0.00,-0.00); trace/3= -2.23                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.156793                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.620180              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 132.250  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.065615              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.761  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1182      final r-factor (work) = 0.1087          |
| start r-factor (free) = 0.1560      final r-factor (free) = 0.1507          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8395 = 2.62 * 0.50 * 5.1807 + 1.00 * 0.0523                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7667 = 2.62 * 0.50 * 5.1173 + 1.00 * 0.0626                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1087      final r-factor (work) = 0.1063          |
| start r-factor (free) = 0.1507      final r-factor (free) = 0.1510          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.4598 = 1.07 * 1.00 * 5.1173 + 1.00 * 0.0067                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.4308 = 1.07 * 1.00 * 5.0884 + 1.00 * 0.0085                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.620)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.67    80.21   16.97    None  None   None       |
|    all(noH): 2823   0      0.67    80.21   16.97    None  None   None       |
|    Sol.    : 438    0      4.18    74.95   39.26    None  None   None       |
|    Mac.    : 2385   0      0.67    80.21   12.88    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:     0.674 -   8.628:  679   |   5:    40.441 -  48.394:  116        |
|      1:     8.628 -  16.581: 1312   |   6:    48.394 -  56.347:   82        |
|      2:    16.581 -  24.534:  330   |   7:    56.347 -  64.300:   50        |
|      3:    24.534 -  32.487:  121   |   8:    64.300 -  72.254:   21        |
|      4:    32.487 -  40.441:  107   |   9:    72.254 -  80.207:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1063 r_free = 0.1510             target_work(ml) = 5.091         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1062 r_free = 0.1511             target_work(ml) = 5.091         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1062   r_free= 0.1511   ksol= 0.32   Bsol= 39.82   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.83,-2.37,-1.49,-0.00,-0.00,-0.00); trace/3= -2.23                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.091238                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1062   r_free= 0.1510   ksol= 0.32   Bsol= 41.56   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.63,-2.33,-1.40,-0.00,-0.00,-0.00); trace/3= -2.12                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.090673                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.544496              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 152.972  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.804315              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 121.507  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1062      final r-factor (work) = 0.1077          |
| start r-factor (free) = 0.1510      final r-factor (free) = 0.1514          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.9921 = 1.54 * 0.50 * 5.0884 + 1.00 * 0.0626                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.9873 = 1.54 * 0.50 * 5.0982 + 1.00 * 0.0502                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1077      final r-factor (work) = 0.1074          |
| start r-factor (free) = 0.1514      final r-factor (free) = 0.1521          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1091 = 0.80 * 1.00 * 5.0982 + 1.00 * 0.0085                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1098 = 0.80 * 1.00 * 5.0986 + 1.00 * 0.0089                               |
|-----------------------------------------------------------------------------|
| number of iterations = 19      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.620)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.26    83.11   16.85    None  None   None       |
|    all(noH): 2823   0      0.26    83.11   16.85    None  None   None       |
|    Sol.    : 438    0      5.61    76.76   39.25    None  None   None       |
|    Mac.    : 2385   0      0.26    83.11   12.74    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.256 -   8.541:  707   |   5:    41.684 -  49.970:  113        |
|      1:     8.541 -  16.827: 1309   |   6:    49.970 -  58.256:   77        |
|      2:    16.827 -  25.113:  313   |   7:    58.256 -  66.541:   42        |
|      3:    25.113 -  33.398:  127   |   8:    66.541 -  74.827:   15        |
|      4:    33.398 -  41.684:  116   |   9:    74.827 -  83.113:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1074 r_free = 0.1521             target_work(ml) = 5.103         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1074 r_free = 0.1522             target_work(ml) = 5.103         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1074   r_free= 0.1522   ksol= 0.32   Bsol= 41.56   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.63,-2.33,-1.40,-0.00,-0.00,-0.00); trace/3= -2.12                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.102828                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1073   r_free= 0.1522   ksol= 0.32   Bsol= 42.90   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.40,-2.17,-1.20,-0.00,-0.00,-0.00); trace/3= -1.92                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.102737                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.041510              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 163.764  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.258325              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 124.792  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1073      final r-factor (work) = 0.1051          |
| start r-factor (free) = 0.1522      final r-factor (free) = 0.1528          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2555 = 2.04 * 0.50 * 5.0995 + 1.00 * 0.0502                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2550 = 2.04 * 0.50 * 5.0932 + 1.00 * 0.0562                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1051      final r-factor (work) = 0.1051          |
| start r-factor (free) = 0.1528      final r-factor (free) = 0.1536          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.5109 = 2.26 * 1.00 * 5.0932 + 1.00 * 0.0089                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.5101 = 2.26 * 1.00 * 5.0926 + 1.00 * 0.0093                              |
|-----------------------------------------------------------------------------|
| number of iterations = 10      |    number of function evaluations = 11     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.620)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.69   16.71    None  None   None       |
|    all(noH): 2823   0      0.00    84.69   16.71    None  None   None       |
|    Sol.    : 438    0      6.18    77.86   39.28    None  None   None       |
|    Mac.    : 2385   0      0.00    84.69   12.56    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.469:  754   |   5:    42.346 -  50.815:  115        |
|      1:     8.469 -  16.938: 1283   |   6:    50.815 -  59.284:   74        |
|      2:    16.938 -  25.407:  295   |   7:    59.284 -  67.753:   36        |
|      3:    25.407 -  33.876:  133   |   8:    67.753 -  76.222:   15        |
|      4:    33.876 -  42.346:  114   |   9:    76.222 -  84.691:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1051 r_free = 0.1536             target_work(ml) = 5.096         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1050 r_free = 0.1536             target_work(ml) = 5.096         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1050   r_free= 0.1536   ksol= 0.32   Bsol= 42.90   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.40,-2.17,-1.20,-0.00,-0.00,-0.00); trace/3= -1.92                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.096067                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8990 -  4.7254 0.99   1367  152 0.0965 0.1231      5.3556      5.4927|
|  2:  4.7254 -  3.7707 0.99   1310  145 0.0816 0.1114      5.4045      5.6199|
|  3:  3.7707 -  3.3000 0.99   1274  143 0.1004 0.1489      5.4456      5.8287|
|  4:  3.3000 -  3.0009 0.99   1280  144 0.1150 0.1509       5.419      5.5664|
|  5:  3.0009 -  2.7873 0.99   1263  138 0.1209 0.1717      5.2774      5.5175|
|  6:  2.7873 -  2.6239 0.99   1265  141 0.1110 0.1714       5.165      5.3901|
|  7:  2.6239 -  2.4932 0.99   1259  137 0.1183 0.1642       5.112      5.3624|
|  8:  2.4932 -  2.3851 0.98   1258  140 0.1078 0.1639      5.0169      5.3212|
|  9:  2.3851 -  2.2936 0.98   1241  136 0.1089 0.1587      4.9845      5.1968|
| 10:  2.2936 -  2.2147 1.00   1240  140 0.1016 0.1911      4.9208      5.2905|
| 11:  2.2147 -  2.1457 0.97   1249  142 0.1071 0.1552      4.9126      5.1932|
| 12:  2.1457 -  2.0845 0.97   1231  133 0.1060 0.1798      4.8492      5.2586|
| 13:  2.0845 -  2.0298 0.99   1228  141 0.1016 0.1554      4.7588      4.9949|
| 14:  2.0298 -  1.9804 0.91   1165  127 0.0991 0.1737       4.623      4.9316|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8990 -  4.7254  1367   152  0.94   8.80   0.98     0.95       6634.50|
|  2:  4.7254 -  3.7707  1310   145  0.95   7.64   1.02     1.01       8619.31|
|  3:  3.7707 -  3.3000  1274   143  0.94  10.59   1.03     1.02       9833.29|
|  4:  3.3000 -  3.0009  1280   144  0.93  12.84   1.02     1.01       9703.44|
|  5:  3.0009 -  2.7873  1263   138  0.91  14.96   1.00     0.97       7721.59|
|  6:  2.7873 -  2.6239  1265   141  0.91  15.03   0.99     0.96       6605.34|
|  7:  2.6239 -  2.4932  1259   137  0.91  15.05   0.99     0.96       5696.55|
|  8:  2.4932 -  2.3851  1258   140  0.92  13.88   0.99     0.97       4768.33|
|  9:  2.3851 -  2.2936  1241   136  0.92  14.34   1.00     0.98       4599.27|
| 10:  2.2936 -  2.2147  1240   140  0.91  14.38   1.00     0.96       4059.94|
| 11:  2.2147 -  2.1457  1249   142  0.90  15.91   1.00     0.97       4287.25|
| 12:  2.1457 -  2.0845  1231   133  0.92  14.68   1.00     0.98       3738.07|
| 13:  2.0845 -  2.0298  1228   141  0.91  14.68   1.00     0.99       3193.70|
| 14:  2.0298 -  1.9804  1165   127  0.92  13.86   0.98     0.95       2359.31|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2359.31 max =         9833.29 mean =      5896.55|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.84 mean =        13.27|
|phase err.(test): min =        0.00 max =           88.13 mean =        12.83|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1049   r_free= 0.1536   ksol= 0.32   Bsol= 43.16   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.17,-1.98,-1.00,-0.00,-0.00,-0.00); trace/3= -1.72                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.096194                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1049   r_free= 0.1536   ksol= 0.32   Bsol= 43.16   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.17,-1.98,-1.00,-0.00,-0.00,-0.00); trace/3= -1.72                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.096194                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8990 -  4.7254 0.99   1367  152 0.0966 0.1234      5.3574       5.495|
|  2:  4.7254 -  3.7707 0.99   1310  145 0.0817 0.1114      5.4051      5.6198|
|  3:  3.7707 -  3.3000 0.99   1274  143 0.1004 0.1490      5.4457      5.8291|
|  4:  3.3000 -  3.0009 0.99   1280  144 0.1150 0.1509      5.4189      5.5664|
|  5:  3.0009 -  2.7873 0.99   1263  138 0.1208 0.1716      5.2772      5.5171|
|  6:  2.7873 -  2.6239 0.99   1265  141 0.1109 0.1713      5.1648      5.3898|
|  7:  2.6239 -  2.4932 0.99   1259  137 0.1183 0.1642       5.112      5.3626|
|  8:  2.4932 -  2.3851 0.98   1258  140 0.1078 0.1638      5.0169      5.3208|
|  9:  2.3851 -  2.2936 0.98   1241  136 0.1089 0.1586      4.9846      5.1967|
| 10:  2.2936 -  2.2147 1.00   1240  140 0.1016 0.1911      4.9209      5.2911|
| 11:  2.2147 -  2.1457 0.97   1249  142 0.1071 0.1552      4.9126      5.1931|
| 12:  2.1457 -  2.0845 0.97   1231  133 0.1060 0.1798       4.849      5.2584|
| 13:  2.0845 -  2.0298 0.99   1228  141 0.1016 0.1553      4.7586      4.9947|
| 14:  2.0298 -  1.9804 0.91   1165  127 0.0991 0.1736      4.6228      4.9312|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8990 -  4.7254  1367   152  0.94   8.82   0.98     0.96       6666.55|
|  2:  4.7254 -  3.7707  1310   145  0.95   7.65   1.03     1.01       8638.71|
|  3:  3.7707 -  3.3000  1274   143  0.94  10.60   1.04     1.03       9834.55|
|  4:  3.3000 -  3.0009  1280   144  0.93  12.83   1.02     1.01       9700.43|
|  5:  3.0009 -  2.7873  1263   138  0.91  14.96   1.00     0.97       7717.30|
|  6:  2.7873 -  2.6239  1265   141  0.91  15.02   1.00     0.97       6602.05|
|  7:  2.6239 -  2.4932  1259   137  0.91  15.05   0.99     0.97       5695.34|
|  8:  2.4932 -  2.3851  1258   140  0.92  13.88   1.00     0.98       4766.86|
|  9:  2.3851 -  2.2936  1241   136  0.92  14.34   1.01     0.99       4600.44|
| 10:  2.2936 -  2.2147  1240   140  0.91  14.38   1.01     0.97       4060.20|
| 11:  2.2147 -  2.1457  1249   142  0.90  15.91   1.01     0.98       4288.41|
| 12:  2.1457 -  2.0845  1231   133  0.92  14.67   1.01     0.99       3736.60|
| 13:  2.0845 -  2.0298  1228   141  0.91  14.67   1.02     1.00       3191.61|
| 14:  2.0298 -  1.9804  1165   127  0.92  13.86   0.99     0.96       2357.66|
|alpha:            min =        0.96 max =            1.03 mean =         0.98|
|beta:             min =     2357.66 max =         9834.55 mean =      5899.44|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.85 mean =        13.28|
|phase err.(test): min =        0.00 max =           88.14 mean =        12.84|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.620)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.69   16.71    None  None   None       |
|    all(noH): 2823   0      0.00    84.69   16.71    None  None   None       |
|    Sol.    : 438    0      6.18    77.86   39.28    None  None   None       |
|    Mac.    : 2385   0      0.00    84.69   12.57    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 -   8.472:  754   |   5:    42.349 -  50.818:  115        |
|      1:     8.472 -  16.941: 1283   |   6:    50.818 -  59.287:   74        |
|      2:    16.941 -  25.410:  295   |   7:    59.287 -  67.756:   36        |
|      3:    25.410 -  33.879:  133   |   8:    67.756 -  76.225:   15        |
|      4:    33.879 -  42.349:  114   |   9:    76.225 -  84.694:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 283         
Filter by distance & map next to the model:
   mapped sites are within: 0.414 - 4.548
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 277 from: 283
   mapped sites are within: 0.707 - 4.548

peak=    5.883 closest distance to " NE2 GLN A  11 " =    1.174
peak=    5.615 closest distance to " O   HOH Z 126 " =    1.939
peak=    5.507 closest distance to " NH2 ARG A  56 " =    2.181
peak=    5.436 closest distance to " O   HOH Z 144 " =    1.755
peak=    5.348 closest distance to " CG  PRO A  54 " =    1.233
peak=    5.110 closest distance to " CB  GLN A 223 " =    1.478
peak=    5.072 closest distance to " CB  ARG A 275 " =    0.897
peak=    5.069 closest distance to " CG  PRO A 213 " =    1.248
peak=    5.064 closest distance to " CB  SER A  63 " =    1.166
peak=    5.060 closest distance to " O   HOH Z 232 " =    2.349
peak=    4.986 closest distance to " CB  GLN A 183 " =    1.234
peak=    4.715 closest distance to " O   HOH Z 427 " =    2.773
peak=    4.690 closest distance to " C   PRO A 198 " =    1.449
peak=    4.639 closest distance to " O   HOH Z  78 " =    1.791
peak=    4.584 closest distance to " CB  GLU A 152 " =    1.255
peak=    4.525 closest distance to " O   HOH Z 193 " =    1.811
peak=    4.489 closest distance to " O   HOH Z  15 " =    2.390
peak=    4.468 closest distance to " O   HOH Z 236 " =    2.139
peak=    4.354 closest distance to " O   HOH Z 272 " =    1.833
peak=    4.347 closest distance to " O   HOH Z 303 " =    2.125
peak=    4.344 closest distance to " CA  TYR A  30 " =    0.916
peak=    4.335 closest distance to " O   HOH Z 298 " =    1.898
peak=    4.333 closest distance to " O   HOH Z 209 " =    2.251
peak=    4.328 closest distance to " CB  ASN A 148 " =    1.390
peak=    4.321 closest distance to " O   HOH Z 369 " =    2.029
peak=    4.310 closest distance to " CB  ARG A  79 " =    1.428
peak=    4.276 closest distance to " ND2 ASN A 187 " =    1.497
peak=    4.273 closest distance to " CB  PRO A  54 " =    0.943
peak=    4.263 closest distance to " O   HOH Z  44 " =    1.815
peak=    4.257 closest distance to " O   HOH Z 234 " =    3.591
peak=    4.231 closest distance to " CG  PRO A  90 " =    1.037
peak=    4.209 closest distance to " CG2 VAL A 257 " =    0.862
peak=    4.205 closest distance to " O   HOH Z 203 " =    1.781
peak=    4.176 closest distance to " CB  VAL A 265 " =    1.356
peak=    4.156 closest distance to " O   HOH Z 316 " =    3.076
peak=    4.154 closest distance to " O   HOH Z 132 " =    2.286
peak=    4.146 closest distance to " O   HOH Z  78 " =    2.109
peak=    4.115 closest distance to " O   HOH Z 158 " =    2.959
peak=    4.091 closest distance to " CB  SER A   3 " =    1.303
peak=    4.074 closest distance to " O   HOH Z 144 " =    2.220
peak=    4.064 closest distance to " CG1 ILE A  33 " =    1.213
peak=    4.054 closest distance to " O   HOH Z 346 " =    1.736
peak=    4.053 closest distance to " NZ  LYS A 117 " =    3.206
peak=    4.022 closest distance to " CB  TYR A 169 " =    0.763
peak=    4.018 closest distance to " CG  ARG A  66 " =    2.347
peak=    4.015 closest distance to " O   HOH Z   1 " =    1.871
peak=    4.002 closest distance to " CB  GLU A 128 " =    1.074
peak=    3.998 closest distance to " O   HOH Z   9 " =    2.053
peak=    3.996 closest distance to " OG BSER A 164 " =    2.284
peak=    3.981 closest distance to " O   HOH Z 250 " =    1.407
peak=    3.980 closest distance to " O   HOH Z 344 " =    3.308
peak=    3.958 closest distance to " O   HOH Z  61 " =    1.642
peak=    3.952 closest distance to " O   HOH Z  66 " =    2.106
peak=    3.947 closest distance to " OD1 ASN A  69 " =    2.615
peak=    3.938 closest distance to " O   HOH Z  59 " =    1.734
peak=    3.938 closest distance to " CB  LEU A 228 " =    1.104
peak=    3.937 closest distance to " O   HOH Z 371 " =    1.641
peak=    3.932 closest distance to " O   HOH Z 407 " =    2.335
peak=    3.925 closest distance to " O   HOH Z 128 " =    2.127
peak=    3.919 closest distance to " CD2 TRP A 179 " =    1.384
peak=    3.916 closest distance to " O   HOH Z 425 " =    2.066
peak=    3.901 closest distance to " O   HOH Z 392 " =    3.097
peak=    3.895 closest distance to " CG  PRO A 243 " =    1.102
peak=    3.893 closest distance to " CB  ARG A 190 " =    1.642
peak=    3.889 closest distance to " O   HOH Z  61 " =    1.544
peak=    3.887 closest distance to " O   SER A  87 " =    2.162
peak=    3.878 closest distance to " CA  ASN A 215 " =    1.195
peak=    3.876 closest distance to " CB  ARG A 139 " =    0.996
peak=    3.875 closest distance to " O   HOH Z 402 " =    1.412
peak=    3.853 closest distance to " O   HOH Z 403 " =    1.706
peak=    3.848 closest distance to " O   HOH Z 389 " =    1.766
peak=    3.843 closest distance to " CE  LYS A  76 " =    0.854
peak=    3.839 closest distance to " CG  PRO A 198 " =    1.231
peak=    3.831 closest distance to " O   HOH Z 368 " =    3.590
peak=    3.810 closest distance to " O   HOH Z 189 " =    2.089
peak=    3.796 closest distance to " CB  TRP A 179 " =    1.314
peak=    3.784 closest distance to " O   HOH Z  64 " =    2.316
peak=    3.771 closest distance to " O   HOH Z  93 " =    2.350
peak=    3.757 closest distance to " O   HOH Z 327 " =    1.642
peak=    3.748 closest distance to " O   HOH Z 368 " =    1.949
peak=    3.739 closest distance to " O   HOH Z 371 " =    3.043
peak=    3.729 closest distance to " O   HOH Z 207 " =    1.755
peak=    3.723 closest distance to " O   HOH Z 419 " =    2.113
peak=    3.705 closest distance to " O   HOH Z 245 " =    1.284
peak=    3.683 closest distance to " OD2 ASP A 286 " =    2.784
peak=    3.682 closest distance to " O   HOH Z 298 " =    2.529
peak=    3.676 closest distance to " CD2 LEU A 297 " =    0.923
peak=    3.666 closest distance to " O   HOH Z 214 " =    2.119
peak=    3.659 closest distance to " O   HOH Z 248 " =    1.614
peak=    3.655 closest distance to " CD BLYS A 290 " =    1.243
peak=    3.638 closest distance to " CB  VAL A 202 " =    1.606
peak=    3.628 closest distance to " CB  SER A  26 " =    1.598
peak=    3.624 closest distance to " O   HOH Z 193 " =    1.653
peak=    3.617 closest distance to " CB  GLU A 277 " =    3.506
peak=    3.613 closest distance to " NH1AARG A 145 " =    1.162
peak=    3.606 closest distance to " O   HOH Z 305 " =    3.509
peak=    3.603 closest distance to " CB  THR A 157 " =    1.080
peak=    3.600 closest distance to " CB  TRP A 266 " =    1.021
peak=    3.597 closest distance to " CG2 ILE A 120 " =    1.065
peak=    3.592 closest distance to " O   HOH Z   1 " =    1.632
peak=    3.591 closest distance to " O   HOH Z  43 " =    1.791
peak=    3.587 closest distance to " O   HOH Z 284 " =    2.943
peak=    3.587 closest distance to " ND1 HIS A  86 " =    1.844
peak=    3.583 closest distance to " O   HOH Z 286 " =    2.336
peak=    3.580 closest distance to " CA  ALA A  21 " =    1.133
peak=    3.580 closest distance to " O   HOH Z  54 " =    1.656
peak=    3.575 closest distance to " CZ  PHE A 218 " =    1.010
peak=    3.574 closest distance to " O   HOH Z  40 " =    1.501
peak=    3.565 closest distance to " O   HOH Z 172 " =    3.314
peak=    3.563 closest distance to " CB  ASP A 140 " =    0.934
peak=    3.550 closest distance to " O   HOH Z  10 " =    1.827
peak=    3.544 closest distance to " NH2BARG A 145 " =    2.119
peak=    3.540 closest distance to " CB  ALA A 291 " =    1.416
peak=    3.537 closest distance to " O   HOH Z 180 " =    2.196
peak=    3.534 closest distance to " CB  SER A 216 " =    0.818
peak=    3.533 closest distance to " O   HOH Z 426 " =    1.534
peak=    3.528 closest distance to " CA  THR A 264 " =    0.865
peak=    3.527 closest distance to " O   HOH Z  40 " =    1.925
peak=    3.526 closest distance to " CG1BVAL A  72 " =    1.424
peak=    3.526 closest distance to " CB  GLN A  89 " =    1.406
peak=    3.515 closest distance to " CB  ALA A  34 " =    1.158
peak=    3.514 closest distance to " O   HOH Z  71 " =    2.132
peak=    3.512 closest distance to " O   HOH Z 147 " =    1.747
peak=    3.511 closest distance to " O   HOH Z   3 " =    1.853
peak=    3.509 closest distance to " O   HOH Z 423 " =    2.764
peak=    3.507 closest distance to " CB  LYS A 117 " =    1.190
peak=    3.503 closest distance to " O   HOH Z 108 " =    2.269
peak=    3.497 closest distance to " NH1BARG A 145 " =    1.259
peak=    3.487 closest distance to " CG  MET A 113 " =    1.113
peak=    3.486 closest distance to " O   HOH Z 250 " =    1.886
peak=    3.473 closest distance to " O   HOH Z 236 " =    1.436
peak=    3.470 closest distance to " O   HOH Z 337 " =    3.639
peak=    3.463 closest distance to " O   HOH Z 366 " =    2.967
peak=    3.461 closest distance to " O   HOH Z 219 " =    2.214
peak=    3.461 closest distance to " O   HOH Z 353 " =    2.659
peak=    3.461 closest distance to " O   HOH Z 128 " =    2.052
peak=    3.455 closest distance to " O   MET A 105 " =    1.850
peak=    3.452 closest distance to " CA  MET A  40 " =    1.066
peak=    3.443 closest distance to " N   PHE A 130 " =    1.234
peak=    3.441 closest distance to " CB  SER A 212 " =    1.024
peak=    3.441 closest distance to " O   HOH Z 380 " =    1.928
peak=    3.438 closest distance to " CA  ALA A 233 " =    1.013
peak=    3.433 closest distance to " CD  ARG A 159 " =    0.742
peak=    3.433 closest distance to " O   HOH Z 173 " =    1.849
peak=    3.410 closest distance to " O   HOH Z   6 " =    2.126
peak=    3.408 closest distance to " O   HOH Z 345 " =    3.380
peak=    3.408 closest distance to " CD2 LEU A 255 " =    1.439
peak=    3.404 closest distance to " CG2 THR A 221 " =    1.123
peak=    3.400 closest distance to " N   ARG A 156 " =    1.270
peak=    3.400 closest distance to " CB  SER A  62 " =    1.296
peak=    3.399 closest distance to " OD1BASN A 224 " =    2.259
peak=    3.399 closest distance to " O   HOH Z 234 " =    1.780
peak=    3.394 closest distance to " CD1 ILE A 106 " =    0.902
peak=    3.394 closest distance to " O   HOH Z  88 " =    2.577
peak=    3.394 closest distance to " O   HOH Z 193 " =    1.984
peak=    3.393 closest distance to " O  BHOH Z 338 " =    2.372
peak=    3.391 closest distance to " CA  PHE A 283 " =    1.325
peak=    3.390 closest distance to " OG BSER A 134 " =    2.824
peak=    3.386 closest distance to " O   HOH Z  40 " =    2.279
peak=    3.385 closest distance to " O   HOH Z  97 " =    1.976
peak=    3.384 closest distance to " N   ASN A  39 " =    1.234
peak=    3.383 closest distance to " CB  TYR A 116 " =    0.804
peak=    3.381 closest distance to " OH  TYR A 116 " =    1.068
peak=    3.378 closest distance to " O   HOH Z 213 " =    2.062
peak=    3.378 closest distance to " O   HOH Z 128 " =    2.014
peak=    3.377 closest distance to " O   HOH Z 417 " =    3.176
peak=    3.372 closest distance to " O   HOH Z 433 " =    1.797
peak=    3.364 closest distance to " CB  MET A  47 " =    1.175
peak=    3.361 closest distance to " O   HOH Z 336 " =    1.986
peak=    3.360 closest distance to " O   HOH Z 227 " =    1.718
peak=    3.357 closest distance to " O   HOH Z 329 " =    3.778
peak=    3.346 closest distance to " O   HOH Z  21 " =    1.703
peak=    3.344 closest distance to " O   HOH Z 135 " =    1.660
peak=    3.342 closest distance to " OG  SER A  62 " =    2.845
peak=    3.339 closest distance to " O   HOH Z 437 " =    1.456
peak=    3.338 closest distance to " OG  SER A  22 " =    2.685
peak=    3.326 closest distance to " ND1 HIS A  81 " =    1.564
peak=    3.326 closest distance to " O   HOH Z 227 " =    2.140
peak=    3.321 closest distance to " O   HOH Z 261 " =    2.207
peak=    3.321 closest distance to " O   HOH Z 291 " =    1.546
peak=    3.318 closest distance to " CB  ASN A 110 " =    1.127
peak=    3.317 closest distance to " CB  LEU A 255 " =    0.779
peak=    3.315 closest distance to " CG  LEU A 167 " =    1.218
peak=    3.310 closest distance to " O   HOH Z 409 " =    2.632
peak=    3.306 closest distance to " CA  THR A 221 " =    0.991
peak=    3.298 closest distance to " CA  ALA A 291 " =    0.871
peak=    3.296 closest distance to " CG AARG A 275 " =    1.027
peak=    3.290 closest distance to " O   HOH Z 435 " =    1.856
peak=    3.288 closest distance to " CA  ASP A 162 " =    1.096
peak=    3.287 closest distance to " CB  ILE A 120 " =    1.317
peak=    3.285 closest distance to " O   ALA A   1 " =    1.684
peak=    3.285 closest distance to " NE2 GLN A  73 " =    3.667
peak=    3.283 closest distance to " CB  THR A 279 " =    1.693
peak=    3.283 closest distance to " O   HOH Z 153 " =    1.594
peak=    3.279 closest distance to " CA  LYS A 290 " =    1.343
peak=    3.278 closest distance to " O   HOH Z 421 " =    1.811
peak=    3.278 closest distance to " CB  ALA A 248 " =    0.906
peak=    3.272 closest distance to " O   HOH Z 279 " =    2.183
peak=    3.270 closest distance to " O   HOH Z 423 " =    1.827
peak=    3.269 closest distance to " O   HOH Z 273 " =    2.713
peak=    3.268 closest distance to " CB  GLN A  88 " =    1.204
peak=    3.267 closest distance to " O   HOH Z 133 " =    2.655
peak=    3.266 closest distance to " CB  ASN A  39 " =    0.851
peak=    3.266 closest distance to " O   HOH Z 411 " =    3.744
peak=    3.264 closest distance to " O   HOH Z 271 " =    2.338
peak=    3.262 closest distance to " CA  ALA A 158 " =    1.180
peak=    3.261 closest distance to " CB  LYS A 290 " =    1.092
peak=    3.249 closest distance to " CB  ALA A   1 " =    4.548
peak=    3.249 closest distance to " N   ASN A 127 " =    1.263
peak=    3.241 closest distance to " O  BHOH Z  74 " =    1.377
peak=    3.239 closest distance to " O   HOH Z 257 " =    2.240
peak=    3.235 closest distance to " CB  SER A 141 " =    0.986
peak=    3.234 closest distance to " O   HOH Z 148 " =    3.329
peak=    3.231 closest distance to " CG  LYS A  76 " =    1.009
peak=    3.231 closest distance to " CB  ALA A 248 " =    1.455
peak=    3.230 closest distance to " CB  HIS A 108 " =    0.789
peak=    3.229 closest distance to " CB  LEU A 143 " =    1.135
peak=    3.225 closest distance to " CD  PRO A 243 " =    1.537
peak=    3.224 closest distance to " CB  ASN A 224 " =    0.962
peak=    3.217 closest distance to " CG2 VAL A 197 " =    1.117
peak=    3.217 closest distance to " CA  MET A 105 " =    0.974
peak=    3.216 closest distance to " O   HOH Z  47 " =    1.813
peak=    3.215 closest distance to " CD1 LEU A 300 " =    1.306
peak=    3.215 closest distance to " O   HOH Z 357 " =    1.830
peak=    3.213 closest distance to " CZ  ARG A  14 " =    1.905
peak=    3.206 closest distance to " CA  ALA A  84 " =    1.345
peak=    3.206 closest distance to " O   HOH Z 266 " =    3.116
peak=    3.206 closest distance to " CE AMET A  47 " =    1.374
peak=    3.197 closest distance to " O   HOH Z 133 " =    1.404
peak=    3.197 closest distance to " CA  GLY A  80 " =    0.707
peak=    3.196 closest distance to " CB  ALA A  21 " =    1.910
peak=    3.194 closest distance to " O   HOH Z 261 " =    1.463
peak=    3.191 closest distance to " CG  GLN A  89 " =    1.488
peak=    3.190 closest distance to " O   HOH Z 391 " =    2.962
peak=    3.188 closest distance to " O   HOH Z  53 " =    2.537
peak=    3.188 closest distance to " O   HOH Z 313 " =    1.939
peak=    3.186 closest distance to " CZ2 TRP A 179 " =    1.650
peak=    3.185 closest distance to " O   HOH Z 163 " =    1.607
peak=    3.182 closest distance to " O   HOH Z 290 " =    0.954
peak=    3.180 closest distance to " CA  ARG A  36 " =    0.988
peak=    3.177 closest distance to " CB  VAL A 126 " =    1.107
peak=    3.177 closest distance to " CG1 ILE A 151 " =    0.917
peak=    3.171 closest distance to " O   HOH Z 291 " =    1.811
peak=    3.167 closest distance to " CA  ARG A 195 " =    1.192
peak=    3.167 closest distance to " O   HOH Z 406 " =    1.627
peak=    3.167 closest distance to " OG BSER A  99 " =    2.197
peak=    3.163 closest distance to " CA  SER A 146 " =    1.699
peak=    3.163 closest distance to " CB  SER A  62 " =    0.871
peak=    3.162 closest distance to " CG  GLN A  77 " =    2.271
peak=    3.161 closest distance to " CB  MET A  40 " =    0.845
peak=    3.157 closest distance to " O   HOH Z  54 " =    2.464
peak=    3.156 closest distance to " CB  VAL A 268 " =    0.844
peak=    3.152 closest distance to " O   HOH Z 175 " =    2.097
peak=    3.132 closest distance to " O   HOH Z  66 " =    1.906
peak=    3.128 closest distance to " O   HOH Z 425 " =    1.208
peak=    3.125 closest distance to " N   GLN A 278 " =    1.156
peak=    3.119 closest distance to " CH2 TRP A  92 " =    2.144
peak=    3.118 closest distance to " CA  ALA A  51 " =    0.891
peak=    3.115 closest distance to " O   HOH Z 325 " =    3.699
peak=    3.099 closest distance to " CD1 LEU A 228 " =    1.593
peak=    3.099 closest distance to " O   HOH Z 124 " =    1.270
peak=    3.095 closest distance to " CA  ALA A 248 " =    1.240
peak=    3.091 closest distance to " O   HOH Z  88 " =    2.457
peak=    3.089 closest distance to " O   HOH Z 124 " =    2.070
peak=    3.085 closest distance to " CG  MET A 185 " =    1.198
peak=    3.081 closest distance to " CB  ASN A 215 " =    1.137
peak=    3.080 closest distance to " CB  GLN A 278 " =    0.872
peak=    3.076 closest distance to " CD1AILE A 234 " =    0.877
peak=    3.073 closest distance to " N   ASP A 162 " =    1.287
peak=    3.070 closest distance to " CD  LYS A 119 " =    1.224
peak=    3.067 closest distance to " O   HOH Z  85 " =    2.300
peak=    3.065 closest distance to " CA  ARG A 102 " =    1.070
peak=    3.060 closest distance to " O   THR A 220 " =    1.353
peak=    3.050 closest distance to " O   HOH Z 192 " =    1.999
peak=    3.041 closest distance to " O   HOH Z 286 " =    2.318
peak=    3.020 closest distance to " O   HOH Z 218 " =    2.344
peak=    3.001 closest distance to " O   HOH Z  88 " =    3.137

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 209         
Filter by distance & map next to the model:
   mapped sites are within: 0.790 - 5.206
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 208 from: 209
   mapped sites are within: 0.790 - 5.206

peak=   -4.852 closest distance to " O   HOH Z 266 " =    4.757
peak=   -4.536 closest distance to " CD  ARG A 156 " =    2.003
peak=   -4.535 closest distance to " CB  PRO A 243 " =    2.586
peak=   -4.513 closest distance to " O   HOH Z 377 " =    2.100
peak=   -4.396 closest distance to " CG  GLN A 223 " =    1.918
peak=   -4.390 closest distance to " C   HIS A 108 " =    1.082
peak=   -4.380 closest distance to " OG BSER A 134 " =    1.259
peak=   -4.249 closest distance to " SG  CYS A 254 " =    3.382
peak=   -4.238 closest distance to " O   HOH Z 389 " =    1.893
peak=   -4.215 closest distance to " CG1 VAL A 112 " =    2.844
peak=   -4.136 closest distance to " CE  MET A 105 " =    2.303
peak=   -4.128 closest distance to " O   VAL A  67 " =    2.704
peak=   -4.128 closest distance to " CE2 PHE A 218 " =    2.443
peak=   -4.084 closest distance to " O   HOH Z 290 " =    1.143
peak=   -4.074 closest distance to " CA  VAL A  67 " =    2.737
peak=   -4.073 closest distance to " O   HOH Z 435 " =    2.735
peak=   -4.044 closest distance to " CE2 TYR A  30 " =    2.783
peak=   -4.006 closest distance to " O   HOH Z 313 " =    1.885
peak=   -3.997 closest distance to " CZ  PHE A  59 " =    1.507
peak=   -3.988 closest distance to " CZ  TYR A 169 " =    1.697
peak=   -3.975 closest distance to " O   HOH Z 198 " =    1.993
peak=   -3.971 closest distance to " O   HOH Z 372 " =    2.435
peak=   -3.970 closest distance to " ND2 ASN A  45 " =    1.695
peak=   -3.917 closest distance to " O   HOH Z 231 " =    2.266
peak=   -3.898 closest distance to " N   GLN A  58 " =    1.581
peak=   -3.895 closest distance to " O   PRO A 198 " =    1.294
peak=   -3.879 closest distance to " OXT GLY A 302 " =    2.796
peak=   -3.867 closest distance to " CZ3 TRP A 179 " =    1.208
peak=   -3.855 closest distance to " NE  ARG A 156 " =    1.865
peak=   -3.846 closest distance to " O   SER A 135 " =    1.463
peak=   -3.833 closest distance to " CD  GLN A  58 " =    1.117
peak=   -3.827 closest distance to " O   ARG A 145 " =    1.545
peak=   -3.821 closest distance to " CB  ASN A  39 " =    2.283
peak=   -3.816 closest distance to " CB  TYR A  15 " =    2.156
peak=   -3.802 closest distance to " CG  PHE A 283 " =    2.724
peak=   -3.799 closest distance to " CB  ALA A 291 " =    2.170
peak=   -3.779 closest distance to " OD1 ASN A 187 " =    1.571
peak=   -3.770 closest distance to " O   ILE A 109 " =    2.548
peak=   -3.766 closest distance to " O   HOH Z 407 " =    3.010
peak=   -3.756 closest distance to " CD  ARG A 139 " =    1.541
peak=   -3.751 closest distance to " O   HOH Z  52 " =    1.367
peak=   -3.745 closest distance to " O   ALA A 161 " =    1.585
peak=   -3.738 closest distance to " O   HOH Z 351 " =    1.565
peak=   -3.731 closest distance to " N   ALA A  43 " =    2.565
peak=   -3.727 closest distance to " O   HOH Z  43 " =    1.721
peak=   -3.719 closest distance to " CD1 PHE A  59 " =    1.892
peak=   -3.718 closest distance to " O   HOH Z 185 " =    2.202
peak=   -3.718 closest distance to " O   HOH Z 126 " =    1.834
peak=   -3.712 closest distance to " NH1 ARG A 195 " =    2.603
peak=   -3.704 closest distance to " O   HOH Z 114 " =    3.057
peak=   -3.691 closest distance to " O   HOH Z 198 " =    1.489
peak=   -3.687 closest distance to " CB  PHE A 192 " =    1.923
peak=   -3.686 closest distance to " ND2 ASN A  45 " =    1.049
peak=   -3.678 closest distance to " OD2 ASP A 191 " =    1.412
peak=   -3.674 closest distance to " O   HOH Z  13 " =    1.543
peak=   -3.673 closest distance to " N   ALA A 248 " =    1.577
peak=   -3.672 closest distance to " CB  ALA A 291 " =    2.332
peak=   -3.668 closest distance to " OD2 ASP A 171 " =    2.296
peak=   -3.608 closest distance to " OD1 ASP A 171 " =    1.566
peak=   -3.603 closest distance to " CA  GLY A  98 " =    1.862
peak=   -3.598 closest distance to " CD1 LEU A 228 " =    2.126
peak=   -3.593 closest distance to " CA  GLY A 203 " =    2.198
peak=   -3.592 closest distance to " CG  ASP A 231 " =    0.790
peak=   -3.589 closest distance to " O   HOH Z 263 " =    2.900
peak=   -3.582 closest distance to " O   HOH Z 395 " =    5.166
peak=   -3.581 closest distance to " O   HOH Z 211 " =    1.652
peak=   -3.581 closest distance to " O   HOH Z 353 " =    2.164
peak=   -3.577 closest distance to " O   HOH Z 102 " =    1.546
peak=   -3.572 closest distance to " O   HOH Z 385 " =    1.895
peak=   -3.570 closest distance to " OD1 ASN A 148 " =    1.565
peak=   -3.549 closest distance to " O   HOH Z 298 " =    1.251
peak=   -3.544 closest distance to " O   PRO A 163 " =    1.959
peak=   -3.540 closest distance to " NH2BARG A 275 " =    1.869
peak=   -3.497 closest distance to " C   ALA A 158 " =    1.297
peak=   -3.491 closest distance to " O   PHE A 218 " =    1.577
peak=   -3.488 closest distance to " O   PRO A 243 " =    2.505
peak=   -3.485 closest distance to " C   LEU A 143 " =    1.081
peak=   -3.481 closest distance to " O   HOH Z  60 " =    2.287
peak=   -3.480 closest distance to " ND2 ASN A 187 " =    1.551
peak=   -3.479 closest distance to " N   SER A 212 " =    1.987
peak=   -3.473 closest distance to " CG1 VAL A 230 " =    1.970
peak=   -3.471 closest distance to " O   PRO A 198 " =    1.249
peak=   -3.467 closest distance to " NE  ARG A  36 " =    1.911
peak=   -3.458 closest distance to " CB  PHE A 208 " =    2.194
peak=   -3.454 closest distance to " OG  SER A  97 " =    2.091
peak=   -3.452 closest distance to " OD1 ASP A 191 " =    1.882
peak=   -3.451 closest distance to " CG  ARG A 269 " =    2.339
peak=   -3.448 closest distance to " N   ASP A 286 " =    2.379
peak=   -3.447 closest distance to " OH  TYR A 214 " =    1.263
peak=   -3.446 closest distance to " CB  ASP A 132 " =    2.361
peak=   -3.438 closest distance to " O   HOH Z  10 " =    1.427
peak=   -3.435 closest distance to " SG ACYS A 201 " =    1.894
peak=   -3.433 closest distance to " CB  ALA A   7 " =    2.081
peak=   -3.430 closest distance to " O   SER A  95 " =    1.464
peak=   -3.427 closest distance to " O   VAL A 174 " =    2.101
peak=   -3.420 closest distance to " CA  GLY A 133 " =    1.947
peak=   -3.414 closest distance to " O   HOH Z  63 " =    1.637
peak=   -3.414 closest distance to " CB  ALA A 248 " =    2.298
peak=   -3.410 closest distance to " OD1 ASN A 176 " =    1.290
peak=   -3.410 closest distance to " CB  ALA A 248 " =    2.004
peak=   -3.403 closest distance to " ND2 ASN A 249 " =    2.070
peak=   -3.401 closest distance to " CB  ASP A 286 " =    2.181
peak=   -3.399 closest distance to " CG2 ILE A 263 " =    2.235
peak=   -3.395 closest distance to " O   HOH Z 266 " =    4.538
peak=   -3.384 closest distance to " O   HOH Z 253 " =    3.770
peak=   -3.382 closest distance to " NH2 ARG A  79 " =    1.952
peak=   -3.375 closest distance to " O   ALA A  51 " =    1.304
peak=   -3.371 closest distance to " O   HOH Z 111 " =    2.309
peak=   -3.369 closest distance to " NH2AARG A 275 " =    5.206
peak=   -3.366 closest distance to " OD1 ASP A 191 " =    1.471
peak=   -3.362 closest distance to " CG  GLU A   2 " =    2.054
peak=   -3.361 closest distance to " O   ALA A 180 " =    1.216
peak=   -3.357 closest distance to " CD  LYS A 289 " =    2.368
peak=   -3.356 closest distance to " OG BSER A 134 " =    1.615
peak=   -3.346 closest distance to " CD2 LEU A 300 " =    2.858
peak=   -3.343 closest distance to " CB  ASP A 286 " =    1.810
peak=   -3.339 closest distance to " N   THR A 235 " =    1.375
peak=   -3.339 closest distance to " O   HOH Z  38 " =    1.673
peak=   -3.338 closest distance to " O   HOH Z  37 " =    1.787
peak=   -3.324 closest distance to " C   PRO A  90 " =    1.487
peak=   -3.322 closest distance to " CE3 TRP A 274 " =    2.306
peak=   -3.316 closest distance to " O   HOH Z 165 " =    2.105
peak=   -3.307 closest distance to " O   HOH Z  24 " =    1.389
peak=   -3.305 closest distance to " OXT GLY A 302 " =    3.518
peak=   -3.299 closest distance to " O   VAL A 189 " =    2.537
peak=   -3.298 closest distance to " O   TRP A  70 " =    1.458
peak=   -3.298 closest distance to " O   HOH Z 388 " =    2.045
peak=   -3.288 closest distance to " NZ  LYS A 119 " =    3.414
peak=   -3.286 closest distance to " O   HOH Z 339 " =    1.846
peak=   -3.284 closest distance to " O   SER A  22 " =    2.350
peak=   -3.282 closest distance to " O   GLY A  80 " =    2.489
peak=   -3.282 closest distance to " O   HOH Z  11 " =    1.825
peak=   -3.280 closest distance to " O   SER A 146 " =    1.090
peak=   -3.280 closest distance to " O   HOH Z 196 " =    2.160
peak=   -3.274 closest distance to " CA  GLY A  57 " =    2.169
peak=   -3.274 closest distance to " N   HIS A 115 " =    2.126
peak=   -3.272 closest distance to " CD2 PHE A 225 " =    1.134
peak=   -3.271 closest distance to " O   HOH Z 322 " =    1.661
peak=   -3.267 closest distance to " CB  CYS A 254 " =    2.291
peak=   -3.262 closest distance to " O   ALA A 292 " =    1.891
peak=   -3.261 closest distance to " OD2 ASP A  50 " =    1.581
peak=   -3.260 closest distance to " O   HOH Z 351 " =    1.672
peak=   -3.259 closest distance to " CB  ALA A 244 " =    2.074
peak=   -3.254 closest distance to " CB  PRO A 163 " =    2.433
peak=   -3.254 closest distance to " O   HOH Z 166 " =    1.462
peak=   -3.250 closest distance to " CA  ASP A 298 " =    1.052
peak=   -3.250 closest distance to " O   HOH Z 359 " =    3.295
peak=   -3.249 closest distance to " OG  SER A  26 " =    1.224
peak=   -3.247 closest distance to " O   ASN A 249 " =    1.442
peak=   -3.245 closest distance to " CG  PHE A 283 " =    2.639
peak=   -3.243 closest distance to " O   HOH Z 244 " =    2.019
peak=   -3.241 closest distance to " CB  TRP A  85 " =    2.475
peak=   -3.238 closest distance to " O   MET A  40 " =    2.704
peak=   -3.236 closest distance to " O   HOH Z  90 " =    2.479
peak=   -3.236 closest distance to " O   ALA A 180 " =    1.046
peak=   -3.235 closest distance to " ND2 ASN A  69 " =    1.524
peak=   -3.230 closest distance to " O   HOH Z 123 " =    2.314
peak=   -3.224 closest distance to " O   HOH Z 250 " =    1.445
peak=   -3.222 closest distance to " O   HOH Z 131 " =    4.101
peak=   -3.221 closest distance to " CB  ALA A 131 " =    1.996
peak=   -3.215 closest distance to " CB  ASP A 132 " =    2.243
peak=   -3.214 closest distance to " CG2 VAL A 189 " =    2.010
peak=   -3.211 closest distance to " O   HOH Z 137 " =    1.427
peak=   -3.205 closest distance to " CD  GLU A 236 " =    1.053
peak=   -3.205 closest distance to " CD1 ILE A 151 " =    2.156
peak=   -3.202 closest distance to " CG  PRO A 243 " =    1.628
peak=   -3.202 closest distance to " OG  SER A  62 " =    1.609
peak=   -3.199 closest distance to " O   HOH Z 137 " =    1.427
peak=   -3.197 closest distance to " C   LYS A  76 " =    1.621
peak=   -3.197 closest distance to " OE1 GLN A 223 " =    1.954
peak=   -3.195 closest distance to " O   PRO A 198 " =    1.629
peak=   -3.193 closest distance to " OD2 ASP A 171 " =    1.696
peak=   -3.191 closest distance to " ND2 ASN A 252 " =    1.652
peak=   -3.188 closest distance to " O   HOH Z  93 " =    1.946
peak=   -3.188 closest distance to " CE  MET A  93 " =    1.221
peak=   -3.187 closest distance to " CB  LEU A  83 " =    2.360
peak=   -3.187 closest distance to " O   HOH Z  44 " =    2.240
peak=   -3.174 closest distance to " CG  GLU A 152 " =    1.064
peak=   -3.174 closest distance to " CB  CYS A 201 " =    2.560
peak=   -3.173 closest distance to " O   HOH Z 369 " =    2.148
peak=   -3.170 closest distance to " O   HOH Z 281 " =    2.689
peak=   -3.168 closest distance to " CA  GLY A 241 " =    3.126
peak=   -3.166 closest distance to " CB  ILE A  33 " =    2.868
peak=   -3.164 closest distance to " OG1 THR A 178 " =    1.285
peak=   -3.160 closest distance to " O   ILE A 120 " =    1.496
peak=   -3.159 closest distance to " O   ASN A 127 " =    2.141
peak=   -3.151 closest distance to " O   GLN A 240 " =    2.362
peak=   -3.151 closest distance to " O   HOH Z 394 " =    1.454
peak=   -3.146 closest distance to " CG  PRO A 163 " =    2.601
peak=   -3.145 closest distance to " O   HOH Z 311 " =    3.575
peak=   -3.141 closest distance to " CG  MET A 105 " =    0.937
peak=   -3.123 closest distance to " OE1 GLN A  88 " =    1.107
peak=   -3.122 closest distance to " CD2 PHE A  61 " =    2.246
peak=   -3.120 closest distance to " N   SER A 276 " =    1.199
peak=   -3.118 closest distance to " CD2 LEU A 237 " =    2.663
peak=   -3.115 closest distance to " CG1 VAL A  78 " =    2.899
peak=   -3.110 closest distance to " C   MET A 188 " =    1.447
peak=   -3.109 closest distance to " O   GLN A 240 " =    1.846
peak=   -3.106 closest distance to " O   GLN A 144 " =    1.434
peak=   -3.105 closest distance to " CZ2 TRP A 274 " =    0.992
peak=   -3.094 closest distance to " OD1AASN A 224 " =    1.839
peak=   -3.079 closest distance to " OG1 THR A 246 " =    1.403
peak=   -3.073 closest distance to " OE2 GLU A 152 " =    1.142
peak=   -3.070 closest distance to " O   HOH Z 361 " =    3.411
peak=   -3.066 closest distance to " O   HOH Z 414 " =    1.798
peak=   -3.060 closest distance to " O   HOH Z 298 " =    2.331
peak=   -3.038 closest distance to " CG1 VAL A 197 " =    2.140
peak=   -3.031 closest distance to " CG  ARG A 269 " =    2.021

================= 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    :  0.3234 0.3242   6.035760e+00   6.018522e+00
   1_bss:  0.3085 0.3057   6.015953e+00   5.983012e+00
   1_xyz:  0.1751 0.1979   5.490811e+00   5.595321e+00
   1_adp:  0.1603 0.2053   5.441274e+00   5.636093e+00
   1_occ:  0.1601 0.2052   5.439654e+00   5.634814e+00
   2_bss:  0.1589 0.2026   5.432582e+00   5.625640e+00
   2_xyz:  0.1224 0.1633   5.197563e+00   5.418453e+00
   2_adp:  0.1180 0.1558   5.156993e+00   5.371302e+00
   2_occ:  0.1179 0.1559   5.156462e+00   5.371101e+00
   3_bss:  0.1182 0.1560   5.156793e+00   5.370267e+00
   3_xyz:  0.1087 0.1507   5.100005e+00   5.339422e+00
   3_adp:  0.1063 0.1510   5.091077e+00   5.341660e+00
   3_occ:  0.1062 0.1511   5.091238e+00   5.342089e+00
   4_bss:  0.1062 0.1510   5.090673e+00   5.341534e+00
   4_xyz:  0.1077 0.1514   5.101039e+00   5.346571e+00
   4_adp:  0.1074 0.1521   5.102723e+00   5.352386e+00
   4_occ:  0.1074 0.1522   5.102828e+00   5.352728e+00
   5_bss:  0.1073 0.1522   5.102737e+00   5.352570e+00
   5_xyz:  0.1051 0.1528   5.094371e+00   5.356308e+00
   5_adp:  0.1051 0.1536   5.095938e+00   5.360016e+00
   5_occ:  0.1050 0.1536   5.096067e+00   5.360252e+00
   5_bss:  0.1049 0.1536   5.096194e+00   5.360361e+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:  0.330  34.113  -3.002   0.129  -0.504   0.000  -0.000  -0.000
   1_xyz:  0.330  34.113  -3.002   0.129  -0.504   0.000  -0.000  -0.000
   1_adp:  0.330  34.113  -3.002   0.129  -0.504   0.000  -0.000  -0.000
   1_occ:  0.330  34.113  -3.002   0.129  -0.504   0.000  -0.000  -0.000
   2_bss:  0.322  39.816  -2.983  -2.008  -1.505  -0.000  -0.000  -0.000
   2_xyz:  0.322  39.816  -2.983  -2.008  -1.505  -0.000  -0.000  -0.000
   2_adp:  0.322  39.816  -2.983  -2.008  -1.505  -0.000  -0.000  -0.000
   2_occ:  0.322  39.816  -2.983  -2.008  -1.505  -0.000  -0.000  -0.000
   3_bss:  0.322  39.816  -2.827  -2.367  -1.490  -0.000  -0.000  -0.000
   3_xyz:  0.322  39.816  -2.827  -2.367  -1.490  -0.000  -0.000  -0.000
   3_adp:  0.322  39.816  -2.827  -2.367  -1.490  -0.000  -0.000  -0.000
   3_occ:  0.322  39.816  -2.827  -2.367  -1.490  -0.000  -0.000  -0.000
   4_bss:  0.321  41.558  -2.634  -2.334  -1.404  -0.000  -0.000  -0.000
   4_xyz:  0.321  41.558  -2.634  -2.334  -1.404  -0.000  -0.000  -0.000
   4_adp:  0.321  41.558  -2.634  -2.334  -1.404  -0.000  -0.000  -0.000
   4_occ:  0.321  41.558  -2.634  -2.334  -1.404  -0.000  -0.000  -0.000
   5_bss:  0.321  42.895  -2.399  -2.166  -1.205  -0.000  -0.000  -0.000
   5_xyz:  0.321  42.895  -2.399  -2.166  -1.205  -0.000  -0.000  -0.000
   5_adp:  0.321  42.895  -2.399  -2.166  -1.205  -0.000  -0.000  -0.000
   5_occ:  0.321  42.895  -2.399  -2.166  -1.205  -0.000  -0.000  -0.000
   5_bss:  0.322  43.157  -2.173  -1.984  -0.998  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  32.134 0.7380  0.9318    28880.564
   1_bss:  30.609 0.7527  0.9100    24996.848
   1_xyz:  18.180 0.8805  1.0073     9860.975
   1_adp:  19.240 0.8700  1.0000    10603.797
   1_occ:  19.211 0.8703  0.9999    10553.102
   2_bss:  18.906 0.8729  0.9666    10250.915
   2_xyz:  14.608 0.9095  0.9874     6613.770
   2_adp:  13.621 0.9177  0.9880     6120.894
   2_occ:  13.617 0.9177  0.9879     6110.450
   3_bss:  13.602 0.9178  0.9861     6106.455
   3_xyz:  12.940 0.9231  0.9878     5675.337
   3_adp:  12.946 0.9232  0.9817     5672.733
   3_occ:  12.954 0.9232  0.9816     5676.959
   4_bss:  12.941 0.9233  0.9857     5669.945
   4_xyz:  13.006 0.9229  0.9847     5741.605
   4_adp:  13.103 0.9223  0.9777     5800.729
   4_occ:  13.109 0.9222  0.9776     5805.265
   5_bss:  13.104 0.9223  0.9850     5804.406
   5_xyz:  13.153 0.9219  0.9848     5863.487
   5_adp:  13.226 0.9213  0.9774     5894.032
   5_occ:  13.230 0.9213  0.9773     5896.806
   5_bss:  13.232 0.9213  0.9849     5899.697
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.6235e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.6235e-01
   1_xyz:   1.030  0.007  0.067 14.709  0.005  4.107   6.1350e-02
   1_adp:   1.030  0.007  0.067 14.709  0.005  4.107   6.1350e-02
   1_occ:   1.030  0.007  0.067 14.709  0.005  4.107   6.1350e-02
   2_bss:   1.030  0.007  0.067 14.709  0.005  4.107   6.1350e-02
   2_xyz:   0.952  0.005  0.070 14.434  0.004  4.110   5.2317e-02
   2_adp:   0.952  0.005  0.070 14.434  0.004  4.110   5.2317e-02
   2_occ:   0.952  0.005  0.070 14.434  0.004  4.110   5.2317e-02
   3_bss:   0.952  0.005  0.070 14.434  0.004  4.110   5.2317e-02
   3_xyz:   1.020  0.007  0.077 14.842  0.004  4.110   6.2608e-02
   3_adp:   1.020  0.007  0.077 14.842  0.004  4.110   6.2608e-02
   3_occ:   1.020  0.007  0.077 14.842  0.004  4.110   6.2608e-02
   4_bss:   1.020  0.007  0.077 14.842  0.004  4.110   6.2608e-02
   4_xyz:   0.895  0.005  0.069 14.376  0.004  4.110   5.0167e-02
   4_adp:   0.895  0.005  0.069 14.376  0.004  4.110   5.0167e-02
   4_occ:   0.895  0.005  0.069 14.376  0.004  4.110   5.0167e-02
   5_bss:   0.895  0.005  0.069 14.376  0.004  4.110   5.0167e-02
   5_xyz:   0.969  0.006  0.073 14.537  0.004  4.109   5.6155e-02
   5_adp:   0.969  0.006  0.073 14.537  0.004  4.109   5.6155e-02
   5_occ:   0.969  0.006  0.073 14.537  0.004  4.109   5.6155e-02
   5_bss:   0.969  0.006  0.073 14.537  0.004  4.109   5.6155e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.3862e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.3862e-01
   1_xyz:   7.709  0.042  0.322 89.727  0.043  2.241   6.6894e-02
   1_adp:   7.709  0.042  0.322 89.727  0.043  2.241   6.6894e-02
   1_occ:   7.709  0.042  0.322 89.727  0.043  2.241   6.6894e-02
   2_bss:   7.709  0.042  0.322 89.727  0.043  2.241   6.6894e-02
   2_xyz:   6.912  0.035  0.208 83.547  0.044  2.361   3.7336e-02
   2_adp:   6.912  0.035  0.208 83.547  0.044  2.361   3.7336e-02
   2_occ:   6.912  0.035  0.208 83.547  0.044  2.361   3.7336e-02
   3_bss:   6.912  0.035  0.208 83.547  0.044  2.361   3.7336e-02
   3_xyz:   6.365  0.032  0.257 85.118  0.036  2.265   5.2714e-02
   3_adp:   6.365  0.032  0.257 85.118  0.036  2.265   5.2714e-02
   3_occ:   6.365  0.032  0.257 85.118  0.036  2.265   5.2714e-02
   4_bss:   6.365  0.032  0.257 85.118  0.036  2.265   5.2714e-02
   4_xyz:   6.227  0.039  0.215 83.694  0.043  2.359   3.4727e-02
   4_adp:   6.227  0.039  0.215 83.694  0.043  2.359   3.4727e-02
   4_occ:   6.227  0.039  0.215 83.694  0.043  2.359   3.4727e-02
   5_bss:   6.227  0.039  0.215 83.694  0.043  2.359   3.4727e-02
   5_xyz:   6.270  0.035  0.237 83.539  0.037  2.290   4.4517e-02
   5_adp:   6.270  0.035  0.237 83.539  0.037  2.290   4.4517e-02
   5_occ:   6.270  0.035  0.237 83.539  0.037  2.290   4.4517e-02
   5_bss:   6.270  0.035  0.237 83.539  0.037  2.290   4.4517e-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:  71.57   0.00  17.07  65.62   0.00  13.07  71.57   8.29  38.86
   1_occ:  71.57   0.00  17.07  65.62   0.00  13.07  71.57   8.29  38.86
   2_bss:  71.57   0.00  17.07  65.62   0.00  13.07  71.57   8.29  38.86
   2_xyz:  71.57   0.00  17.07  65.62   0.00  13.07  71.57   8.29  38.86
   2_adp:  68.03   1.80  16.72  68.03   1.80  12.89  67.65   5.50  37.58
   2_occ:  68.03   1.80  16.72  68.03   1.80  12.89  67.65   5.50  37.58
   3_bss:  68.03   1.80  16.72  68.03   1.80  12.89  67.65   5.50  37.58
   3_xyz:  68.03   1.80  16.72  68.03   1.80  12.89  67.65   5.50  37.58
   3_adp:  80.21   0.67  16.97  80.21   0.67  12.88  74.95   4.18  39.26
   3_occ:  80.21   0.67  16.97  80.21   0.67  12.88  74.95   4.18  39.26
   4_bss:  80.21   0.67  16.97  80.21   0.67  12.88  74.95   4.18  39.26
   4_xyz:  80.21   0.67  16.97  80.21   0.67  12.88  74.95   4.18  39.26
   4_adp:  83.11   0.26  16.85  83.11   0.26  12.74  76.76   5.61  39.25
   4_occ:  83.11   0.26  16.85  83.11   0.26  12.74  76.76   5.61  39.25
   5_bss:  83.11   0.26  16.85  83.11   0.26  12.74  76.76   5.61  39.25
   5_xyz:  83.11   0.26  16.85  83.11   0.26  12.74  76.76   5.61  39.25
   5_adp:  84.69   0.00  16.71  84.69   0.00  12.56  77.86   6.18  39.28
   5_occ:  84.69   0.00  16.71  84.69   0.00  12.56  77.86   6.18  39.28
   5_bss:  84.69   0.00  16.71  84.69   0.00  12.57  77.86   6.18  39.28
------------------------------------------------------------------------
 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:    1.215    0.018    0.300
   1_adp:    1.215    0.018    0.300
   1_occ:    1.215    0.018    0.300
   2_bss:    1.215    0.018    0.300
   2_xyz:    0.802    0.030    0.356
   2_adp:    0.802    0.030    0.356
   2_occ:    0.802    0.030    0.356
   3_bss:    0.802    0.030    0.356
   3_xyz:    0.829    0.021    0.388
   3_adp:    0.829    0.021    0.388
   3_occ:    0.829    0.021    0.388
   4_bss:    0.829    0.021    0.388
   4_xyz:    0.930    0.009    0.393
   4_adp:    0.930    0.009    0.393
   4_occ:    0.930    0.009    0.393
   5_bss:    0.930    0.009    0.393
   5_xyz:    1.098    0.019    0.402
   5_adp:    1.098    0.019    0.402
   5_occ:    1.098    0.019    0.402
   5_bss:    1.098    0.019    0.402
------------------------------------------------------------------------

CPU time actual refinement: 319.98


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_520/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_520/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_520/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_520/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_520/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 319.83 
  Macro-tasks:
    bulk solvent and scale       = 36.36  
    individual site refinement   = 132.19 
    weights calculation          = 29.21  
    collect and process          = 6.59   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 204.48 
  Micro-tasks:
    mask                            = 1.20   
    f_calc                          = 101.70 
    alpha_beta                      = 7.83   
    target                          = 1.13   
    gradients_wrt_atomic_parameters = 110.50 
    fmodel                         = 6.73   
    r_factors                      = 0.20   
    phase_errors                   = 11.13  
    foms                           = 0.23   
    TOTAL for micro-tasks          = 240.65 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.552 micro seconds
Total CPU time: 5.55 minutes
from_scatterers_fft:    640 calls, 101.30 s
gradients_fft:          585 calls,  97.12 s

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

# Date 2008-01-16 Time 05:01:12 PST -0800 (1200488472.80 s)
Start R-work = 0.3234, R-free = 0.3242 (no bulk solvent and anisotropic scale)
Final R-work = 0.1288, R-free = 0.1726 (no bulk solvent and anisotropic scale)

Start R-work = 0.3085, R-free = 0.3057
Final R-work = 0.1049, R-free = 0.1536