# Date 2008-01-16 Time 05:47:33 PST -0800 (1200491253.28 s)
#phil __OFF__

Command line arguments: "../879.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 14762
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 879

-------------------------------------------------------------------------------
  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: (70.9525, 46.2261, 88.5498, 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: 3.27, per 1000 atoms: 1.16


================================== 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: (70.9525, 46.2261, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2039 1.97353
Completeness in resolution range: 0.929799
Completeness with d_max=infinity: 0.927114

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2039
                             d_min =   1.9735

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: (70.9525, 46.2261, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2039 1.97353
Completeness in resolution range: 0.929799
Completeness with d_max=infinity: 0.927114

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2044 -  4.2243 [2211/2237]  1989   222  10.0%
  bin  2:  4.2243 -  3.3649 [2136/2156]  1925   211   9.9%
  bin  3:  3.3649 -  2.9431 [2091/2110]  1882   209  10.0%
  bin  4:  2.9431 -  2.6756 [2085/2115]  1868   217  10.4%
  bin  5:  2.6756 -  2.4847 [2064/2083]  1864   200   9.7%
  bin  6:  2.4847 -  2.3387 [2068/2093]  1859   209  10.1%
  bin  7:  2.3387 -  2.2220 [2024/2052]  1820   204  10.1%
  bin  8:  2.2220 -  2.1255 [2051/2087]  1842   209  10.2%
  bin  9:  2.1255 -  2.0439 [2032/2079]  1841   191   9.4%
  bin 10:  2.0439 -  1.9735 [ 827/2056]   740    87  10.5%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_879/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: 33
        2.42 -     3.04: 2178
        3.04 -     3.66: 4663
        3.66 -     4.28: 8938
        4.28 -     4.90: 12237
  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  42 " - " O   HOH Z 183 "  1.821 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  95 " - " O   HOH Z  50 "  1.900 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  50 " - " O   HOH Z  95 "  1.900 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.902 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28044 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_879/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_879/model_refine_001.geo

CPU time processing inputs: 9.13


============================ 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 = 70.9525 46.22605 88.54975 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4548   r_free= 0.4511   ksol= 0.00   Bsol= 0.00   scale= 0.892    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.267581                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2044 -  4.7122 0.99   1433  157 0.3649 0.3344      6.5668      6.4636|
|  2:  4.7122 -  3.7588 0.99   1384  158 0.3831 0.3831      6.7832      6.7631|
|  3:  3.7588 -  3.2892 0.99   1365  148 0.4097 0.3771      6.6255      6.6014|
|  4:  3.2892 -  2.9910 0.99   1338  152 0.4479 0.4750      6.5014       6.511|
|  5:  2.9910 -  2.7780 0.99   1349  150 0.4946 0.4553      6.3433      6.3639|
|  6:  2.7780 -  2.6150 0.99   1323  144 0.4727 0.5132       6.236      6.1969|
|  7:  2.6150 -  2.4847 0.99   1336  150 0.4849 0.4715      6.2225      6.1801|
|  8:  2.4847 -  2.3769 0.98   1315  150 0.5181 0.5208      6.1667      6.1507|
|  9:  2.3769 -  2.2857 0.98   1303  142 0.5049 0.4960      6.1151      6.1763|
| 10:  2.2857 -  2.2071 1.00   1346  148 0.5154 0.5315      6.0703      6.0639|
| 11:  2.2071 -  2.1383 0.98   1314  146 0.5079 0.5125      6.0268      6.0148|
| 12:  2.1383 -  2.0773 0.98   1293  137 0.5212 0.5087      5.9347      5.9444|
| 13:  2.0773 -  2.0228 0.91   1211  136 0.5028 0.5203       5.878      5.8046|
| 14:  2.0228 -  1.9735 0.24    320   41 0.5389 0.4865      5.8661       5.854|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2044 -  4.7122  1433   157  0.76  28.87   0.82     0.80      54412.28|
|  2:  4.7122 -  3.7588  1384   158  0.75  30.85   0.90     0.85      89205.69|
|  3:  3.7588 -  3.2892  1365   148  0.63  41.36   0.93     0.81     100077.13|
|  4:  3.2892 -  2.9910  1338   152  0.53  49.53   0.90     0.71      95994.03|
|  5:  2.9910 -  2.7780  1349   150  0.44  56.91   0.88     0.61      77297.26|
|  6:  2.7780 -  2.6150  1323   144  0.40  59.46   0.90     0.55      68277.96|
|  7:  2.6150 -  2.4847  1336   150  0.39  60.26   0.91     0.53      61825.20|
|  8:  2.4847 -  2.3769  1315   150  0.37  62.26   0.89     0.53      56163.22|
|  9:  2.3769 -  2.2857  1303   142  0.39  61.00   0.91     0.56      52552.44|
| 10:  2.2857 -  2.2071  1346   148  0.38  61.33   0.93     0.56      45968.01|
| 11:  2.2071 -  2.1383  1314   146  0.37  62.55   0.94     0.55      46098.83|
| 12:  2.1383 -  2.0773  1293   137  0.34  64.64   0.91     0.53      41612.79|
| 13:  2.0773 -  2.0228  1211   136  0.32  66.52   0.93     0.51      37971.96|
| 14:  2.0228 -  1.9735   320    41  0.37  62.72   0.92     0.52      30057.40|
|alpha:            min =        0.51 max =            0.85 mean =         0.63|
|beta:             min =    30057.40 max =       100077.13 mean =     63407.15|
|figures of merit: min =        0.00 max =            1.00 mean =         0.47|
|phase err.(work): min =        0.00 max =           89.98 mean =        54.06|
|phase err.(test): min =        0.00 max =           89.95 mean =        54.16|
|-----------------------------------------------------------------------------|

============================== 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 = 15.698690             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.064   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.444153              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.722   (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:        7 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       26 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      192 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1986 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1852 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2811 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4588 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4350 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5573 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6664 |
|-----------------------------------------------------------------------------|
|-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 |        0.169 |
| 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 |       0.250 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.059)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4548   r_free= 0.4511   ksol= 0.00   Bsol= 0.00   scale= 0.892    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.267581                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4446   r_free= 0.4454   ksol= 0.30   Bsol= 50.00   scale= 0.938   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.27,0.35,4.50,0.00,0.00,0.00); trace/3= 0.86                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.260852                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.882606             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.909   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.094963              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.393   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4446      final r-factor (work) = 0.2900          |
| start r-factor (free) = 0.4454      final r-factor (free) = 0.3240          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 40.4473 = 12.88 * 0.50 * 6.2532 + 1.00 * 0.1686                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 39.3955 = 12.88 * 0.50 * 6.0889 + 1.00 * 0.1751                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2900      final r-factor (work) = 0.2611          |
| start r-factor (free) = 0.3240      final r-factor (free) = 0.3345          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.6736 = 1.09 * 1.00 * 6.0889 + 1.00 * 0.0064                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.4510 = 1.09 * 1.00 * 5.8695 + 1.00 * 0.0241                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.059)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.78  19.00    None  None   None       |
|    all(noH): 2823   0      0.00    104.78  19.00    None  None   None       |
|    Sol.    : 438    0      1.74    104.78  45.11    None  None   None       |
|    Mac.    : 2385   0      0.00    86.71   14.20    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.478: 1024   |   5:    52.390 -  62.868:   78        |
|      1:    10.478 -  20.956:  974   |   6:    62.868 -  73.345:   65        |
|      2:    20.956 -  31.434:  349   |   7:    73.345 -  83.823:   24        |
|      3:    31.434 -  41.912:  181   |   8:    83.823 -  94.301:    8        |
|      4:    41.912 -  52.390:  116   |   9:    94.301 - 104.779:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2611 r_free = 0.3345             target_work(ml) = 5.882         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2607 r_free = 0.3343             target_work(ml) = 5.882         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2607   r_free= 0.3343   ksol= 0.30   Bsol= 50.00   scale= 1.033   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.27,0.35,4.50,0.00,0.00,0.00); trace/3= 0.86                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.882099                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2585   r_free= 0.3324   ksol= 0.35   Bsol= 85.88   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.93,-1.29,1.72,-0.00,0.00,0.00); trace/3= -0.50                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.882575                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.752888              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 92.370   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.409378              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 101.459  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2585      final r-factor (work) = 0.2023          |
| start r-factor (free) = 0.3324      final r-factor (free) = 0.2659          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.1930 = 3.75 * 0.50 * 5.8718 + 1.00 * 0.1749                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.9312 = 3.75 * 0.50 * 5.7935 + 1.00 * 0.0600                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2023      final r-factor (work) = 0.1896          |
| start r-factor (free) = 0.2659      final r-factor (free) = 0.2463          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3928 = 0.41 * 1.00 * 5.7935 + 1.00 * 0.0211                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3205 = 0.41 * 1.00 * 5.6388 + 1.00 * 0.0121                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.059)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    103.91  18.40    None  None   None       |
|    all(noH): 2823   0      0.00    103.91  18.40    None  None   None       |
|    Sol.    : 438    0      3.52    103.91  44.96    None  None   None       |
|    Mac.    : 2385   0      0.00    89.03   13.52    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.391: 1078   |   5:    51.956 -  62.347:   91        |
|      1:    10.391 -  20.782: 1024   |   6:    62.347 -  72.738:   61        |
|      2:    20.782 -  31.174:  272   |   7:    72.738 -  83.130:   21        |
|      3:    31.174 -  41.565:  134   |   8:    83.130 -  93.521:    8        |
|      4:    41.565 -  51.956:  132   |   9:    93.521 - 103.912:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1896 r_free = 0.2463             target_work(ml) = 5.604         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1896 r_free = 0.2465             target_work(ml) = 5.603         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1896   r_free= 0.2465   ksol= 0.35   Bsol= 85.88   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.93,-1.29,1.72,-0.00,0.00,0.00); trace/3= -0.50                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.603495                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1894   r_free= 0.2466   ksol= 0.34   Bsol= 78.27   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.98,-1.87,0.63,-0.00,0.00,0.00); trace/3= -1.07                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.603795                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.855052              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.635  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.227649              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.672  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1894      final r-factor (work) = 0.1506          |
| start r-factor (free) = 0.2466      final r-factor (free) = 0.2032          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.1102 = 2.86 * 0.50 * 5.6393 + 1.00 * 0.0600                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9178 = 2.86 * 0.50 * 5.5044 + 1.00 * 0.0602                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1506      final r-factor (work) = 0.1436          |
| start r-factor (free) = 0.2032      final r-factor (free) = 0.1928          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2652 = 0.23 * 1.00 * 5.5044 + 1.00 * 0.0121                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2350 = 0.23 * 1.00 * 5.3827 + 1.00 * 0.0096                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.059)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.15    95.46   17.62    None  None   None       |
|    all(noH): 2823   0      1.15    95.46   17.62    None  None   None       |
|    Sol.    : 438    0      5.04    95.46   43.37    None  None   None       |
|    Mac.    : 2385   0      1.15    84.95   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:     1.150 -  10.581: 1179   |   5:    48.303 -  57.734:   89        |
|      1:    10.581 -  20.011:  979   |   6:    57.734 -  67.164:   70        |
|      2:    20.011 -  29.442:  222   |   7:    67.164 -  76.595:   32        |
|      3:    29.442 -  38.873:  119   |   8:    76.595 -  86.026:   10        |
|      4:    38.873 -  48.303:  121   |   9:    86.026 -  95.456:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1436 r_free = 0.1928             target_work(ml) = 5.356         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1435 r_free = 0.1929             target_work(ml) = 5.356         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1435   r_free= 0.1929   ksol= 0.34   Bsol= 78.27   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.98,-1.87,0.63,-0.00,0.00,0.00); trace/3= -1.07                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.355526                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1438   r_free= 0.1926   ksol= 0.33   Bsol= 70.68   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.33,-2.43,-0.14,-0.00,-0.00,-0.00); trace/3= -1.63                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.354778                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.828434              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 115.146  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.387976              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 157.021  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1438      final r-factor (work) = 0.1242          |
| start r-factor (free) = 0.1926      final r-factor (free) = 0.1709          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.3681 = 3.83 * 0.50 * 5.3850 + 1.00 * 0.0602                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.2106 = 3.83 * 0.50 * 5.2947 + 1.00 * 0.0755                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1242      final r-factor (work) = 0.1203          |
| start r-factor (free) = 0.1709      final r-factor (free) = 0.1686          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0637 = 0.39 * 1.00 * 5.2947 + 1.00 * 0.0095                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0329 = 0.39 * 1.00 * 5.2141 + 1.00 * 0.0099                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.059)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.59    93.61   17.51    None  None   None       |
|    all(noH): 2823   0      0.59    93.61   17.51    None  None   None       |
|    Sol.    : 438    0      3.69    93.61   43.00    None  None   None       |
|    Mac.    : 2385   0      0.59    88.36   12.83    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:     0.594 -   9.896: 1036   |   5:    47.101 -  56.402:   95        |
|      1:     9.896 -  19.197: 1104   |   6:    56.402 -  65.704:   65        |
|      2:    19.197 -  28.498:  232   |   7:    65.704 -  75.005:   38        |
|      3:    28.498 -  37.800:  127   |   8:    75.005 -  84.306:   13        |
|      4:    37.800 -  47.101:  105   |   9:    84.306 -  93.608:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1203 r_free = 0.1686             target_work(ml) = 5.206         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1202 r_free = 0.1686             target_work(ml) = 5.206         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1202   r_free= 0.1686   ksol= 0.33   Bsol= 70.68   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.33,-2.43,-0.14,-0.00,-0.00,-0.00); trace/3= -1.63                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.206075                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1201   r_free= 0.1686   ksol= 0.32   Bsol= 63.52   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.22,-2.41,-0.25,-0.00,-0.00,-0.00); trace/3= -1.62                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.206024                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.017879              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 138.917  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.217708              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 143.787  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1201      final r-factor (work) = 0.1199          |
| start r-factor (free) = 0.1686      final r-factor (free) = 0.1670          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3359 = 2.02 * 0.50 * 5.2139 + 1.00 * 0.0755                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3116 = 2.02 * 0.50 * 5.2070 + 1.00 * 0.0581                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1199      final r-factor (work) = 0.1199          |
| start r-factor (free) = 0.1670      final r-factor (free) = 0.1662          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1434 = 0.22 * 1.00 * 5.2070 + 1.00 * 0.0099                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1424 = 0.22 * 1.00 * 5.2065 + 1.00 * 0.0089                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.059)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.97    91.69   17.03    None  None   None       |
|    all(noH): 2823   0      0.97    91.69   17.03    None  None   None       |
|    Sol.    : 438    0      5.68    91.69   41.03    None  None   None       |
|    Mac.    : 2385   0      0.97    87.78   12.63    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.973 -  10.044: 1106   |   5:    46.330 -  55.402:  101        |
|      1:    10.044 -  19.116: 1038   |   6:    55.402 -  64.473:   56        |
|      2:    19.116 -  28.187:  248   |   7:    64.473 -  73.545:   30        |
|      3:    28.187 -  37.259:  133   |   8:    73.545 -  82.616:   14        |
|      4:    37.259 -  46.330:   89   |   9:    82.616 -  91.688:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1199 r_free = 0.1662             target_work(ml) = 5.206         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1198 r_free = 0.1662             target_work(ml) = 5.206         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1198   r_free= 0.1662   ksol= 0.32   Bsol= 63.52   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.22,-2.41,-0.25,-0.00,-0.00,-0.00); trace/3= -1.62                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.206157                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2044 -  4.7122 0.99   1433  157 0.0995 0.1323      5.4094      5.6018|
|  2:  4.7122 -  3.7588 0.99   1384  158 0.0888 0.1191      5.4786      5.6951|
|  3:  3.7588 -  3.2892 0.99   1365  148 0.1145 0.1644      5.5325      5.8435|
|  4:  3.2892 -  2.9910 0.99   1338  152 0.1344 0.1795      5.5153      5.6557|
|  5:  2.9910 -  2.7780 0.99   1349  150 0.1471 0.1801      5.3898      5.6023|
|  6:  2.7780 -  2.6150 0.99   1323  144 0.1333 0.2061      5.2555      5.5043|
|  7:  2.6150 -  2.4847 0.99   1336  150 0.1372 0.1622      5.2352      5.3686|
|  8:  2.4847 -  2.3769 0.98   1315  150 0.1298 0.1790      5.1332      5.3968|
|  9:  2.3769 -  2.2857 0.98   1303  142 0.1271 0.1982      5.0954      5.3849|
| 10:  2.2857 -  2.2071 1.00   1346  148 0.1191 0.1706      4.9704      5.2089|
| 11:  2.2071 -  2.1383 0.98   1314  146 0.1175 0.1875      4.9764      5.3415|
| 12:  2.1383 -  2.0773 0.98   1293  137 0.1266 0.1864      4.9206      5.1761|
| 13:  2.0773 -  2.0228 0.91   1211  136 0.1146 0.1628      4.8072      5.0087|
| 14:  2.0228 -  1.9735 0.24    320   41 0.1005 0.1635      4.6834      4.9378|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2044 -  4.7122  1433   157  0.94   9.22   0.97     0.94       7440.86|
|  2:  4.7122 -  3.7588  1384   158  0.95   8.48   1.01     0.99       9898.12|
|  3:  3.7588 -  3.2892  1365   148  0.93  12.35   1.02     1.02      11558.53|
|  4:  3.2892 -  2.9910  1338   152  0.91  15.06   1.00     0.97      11381.65|
|  5:  2.9910 -  2.7780  1349   150  0.90  16.63   0.99     0.98       8920.58|
|  6:  2.7780 -  2.6150  1323   144  0.89  16.99   0.98     0.95       7523.69|
|  7:  2.6150 -  2.4847  1336   150  0.90  16.38   0.99     0.95       6955.01|
|  8:  2.4847 -  2.3769  1315   150  0.90  16.78   0.99     0.96       5923.70|
|  9:  2.3769 -  2.2857  1303   142  0.90  16.90   0.99     0.95       5669.54|
| 10:  2.2857 -  2.2071  1346   148  0.90  16.05   1.00     0.97       4483.17|
| 11:  2.2071 -  2.1383  1314   146  0.90  16.51   0.98     0.92       4535.35|
| 12:  2.1383 -  2.0773  1293   137  0.90  16.56   0.99     0.99       4202.15|
| 13:  2.0773 -  2.0228  1211   136  0.89  17.57   0.98     0.96       3606.51|
| 14:  2.0228 -  1.9735   320    41  0.93  12.90   0.97     0.95       2624.77|
|alpha:            min =        0.92 max =            1.02 mean =         0.97|
|beta:             min =     2624.77 max =        11558.53 mean =      7059.50|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.96 mean =        14.92|
|phase err.(test): min =        0.00 max =           89.79 mean =        14.35|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1200   r_free= 0.1658   ksol= 0.32   Bsol= 62.00   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.15,-2.39,-0.20,-0.00,-0.00,-0.00); trace/3= -1.58                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.203834                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1200   r_free= 0.1658   ksol= 0.32   Bsol= 62.00   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.15,-2.39,-0.20,-0.00,-0.00,-0.00); trace/3= -1.58                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.203834                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2044 -  4.7122 0.99   1433  157 0.0997 0.1284      5.3835       5.564|
|  2:  4.7122 -  3.7588 0.99   1384  158 0.0892 0.1170      5.4714      5.6857|
|  3:  3.7588 -  3.2892 0.99   1365  148 0.1152 0.1632      5.5322      5.8397|
|  4:  3.2892 -  2.9910 0.99   1338  152 0.1345 0.1807      5.5164      5.6618|
|  5:  2.9910 -  2.7780 0.99   1349  150 0.1471 0.1808       5.391      5.6037|
|  6:  2.7780 -  2.6150 0.99   1323  144 0.1331 0.2061      5.2557      5.5049|
|  7:  2.6150 -  2.4847 0.99   1336  150 0.1373 0.1631      5.2363      5.3717|
|  8:  2.4847 -  2.3769 0.98   1315  150 0.1297 0.1793      5.1337      5.3968|
|  9:  2.3769 -  2.2857 0.98   1303  142 0.1271 0.1984      5.0958      5.3856|
| 10:  2.2857 -  2.2071 1.00   1346  148 0.1190 0.1710      4.9704      5.2108|
| 11:  2.2071 -  2.1383 0.98   1314  146 0.1174 0.1874      4.9767      5.3413|
| 12:  2.1383 -  2.0773 0.98   1293  137 0.1266 0.1866       4.921      5.1768|
| 13:  2.0773 -  2.0228 0.91   1211  136 0.1145 0.1626      4.8069      5.0081|
| 14:  2.0228 -  1.9735 0.24    320   41 0.1004 0.1635      4.6828      4.9377|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2044 -  4.7122  1433   157  0.94   8.85   0.97     0.94       6812.53|
|  2:  4.7122 -  3.7588  1384   158  0.95   8.19   1.01     0.99       9405.84|
|  3:  3.7588 -  3.2892  1365   148  0.93  12.31   1.02     1.02      11447.96|
|  4:  3.2892 -  2.9910  1338   152  0.91  15.10   1.00     0.97      11432.68|
|  5:  2.9910 -  2.7780  1349   150  0.89  16.67   0.99     0.98       8970.90|
|  6:  2.7780 -  2.6150  1323   144  0.89  17.02   0.98     0.95       7546.75|
|  7:  2.6150 -  2.4847  1336   150  0.90  16.41   0.99     0.95       6981.07|
|  8:  2.4847 -  2.3769  1315   150  0.90  16.80   0.99     0.96       5932.71|
|  9:  2.3769 -  2.2857  1303   142  0.89  16.92   0.99     0.95       5680.88|
| 10:  2.2857 -  2.2071  1346   148  0.90  16.06   1.00     0.97       4489.29|
| 11:  2.2071 -  2.1383  1314   146  0.90  16.53   0.98     0.92       4543.46|
| 12:  2.1383 -  2.0773  1293   137  0.90  16.57   0.99     0.99       4207.24|
| 13:  2.0773 -  2.0228  1211   136  0.89  17.58   0.98     0.96       3606.83|
| 14:  2.0228 -  1.9735   320    41  0.93  12.88   0.97     0.95       2622.92|
|alpha:            min =        0.92 max =            1.02 mean =         0.97|
|beta:             min =     2622.92 max =        11447.96 mean =      6975.60|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.96 mean =        14.88|
|phase err.(test): min =        0.00 max =           89.95 mean =        14.27|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.059)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.94    91.65   17.00    None  None   None       |
|    all(noH): 2823   0      0.94    91.65   17.00    None  None   None       |
|    Sol.    : 438    0      5.65    91.65   41.00    None  None   None       |
|    Mac.    : 2385   0      0.94    87.75   12.59    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:     0.939 -  10.011: 1106   |   5:    46.297 -  55.368:  101        |
|      1:    10.011 -  19.082: 1038   |   6:    55.368 -  64.440:   56        |
|      2:    19.082 -  28.154:  248   |   7:    64.440 -  73.511:   30        |
|      3:    28.154 -  37.225:  133   |   8:    73.511 -  82.583:   14        |
|      4:    37.225 -  46.297:   89   |   9:    82.583 -  91.654:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 314         
Filter by distance & map next to the model:
   mapped sites are within: 0.576 - 5.059
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 310 from: 314
   mapped sites are within: 0.703 - 5.059

peak=    5.590 closest distance to " NE2 GLN A  11 " =    1.208
peak=    5.558 closest distance to " CG  PRO A  54 " =    1.435
peak=    5.331 closest distance to " O   HOH Z 144 " =    2.097
peak=    5.282 closest distance to " CG  PRO A 280 " =    0.900
peak=    5.219 closest distance to " O   HOH Z 423 " =    2.011
peak=    5.015 closest distance to " CB  GLN A 223 " =    1.517
peak=    5.007 closest distance to " O   HOH Z 417 " =    1.668
peak=    5.001 closest distance to " O   HOH Z   7 " =    1.488
peak=    4.873 closest distance to " O   HOH Z 369 " =    2.107
peak=    4.854 closest distance to " O   HOH Z  63 " =    1.534
peak=    4.791 closest distance to " O   HOH Z 287 " =    2.125
peak=    4.757 closest distance to " CB  ASN A 148 " =    1.438
peak=    4.745 closest distance to " O   HOH Z 222 " =    1.238
peak=    4.710 closest distance to " NH2 ARG A  56 " =    2.081
peak=    4.674 closest distance to " O   HOH Z   9 " =    1.791
peak=    4.602 closest distance to " CB  PRO A  54 " =    1.070
peak=    4.602 closest distance to " CZ  PHE A 218 " =    1.101
peak=    4.593 closest distance to " CG  PRO A  90 " =    1.380
peak=    4.579 closest distance to " O   HOH Z 232 " =    2.255
peak=    4.545 closest distance to " CG  PRO A 213 " =    1.313
peak=    4.537 closest distance to " ND2 ASN A 187 " =    1.621
peak=    4.479 closest distance to " CB  ARG A 275 " =    0.931
peak=    4.395 closest distance to " O   HOH Z  78 " =    1.660
peak=    4.358 closest distance to " CB  ARG A 190 " =    1.702
peak=    4.352 closest distance to " O   HOH Z 126 " =    1.550
peak=    4.341 closest distance to " O   HOH Z 126 " =    1.999
peak=    4.337 closest distance to " CB  SER A  63 " =    1.298
peak=    4.335 closest distance to " O   HOH Z  49 " =    1.145
peak=    4.308 closest distance to " CD  ARG A 159 " =    0.773
peak=    4.303 closest distance to " CG  PRO A 198 " =    1.279
peak=    4.302 closest distance to " O   HOH Z 380 " =    1.715
peak=    4.286 closest distance to " CZ3 TRP A 266 " =    1.099
peak=    4.269 closest distance to " O   HOH Z 298 " =    2.148
peak=    4.257 closest distance to " CB  ARG A  79 " =    1.336
peak=    4.234 closest distance to " O   HOH Z  69 " =    1.105
peak=    4.205 closest distance to " O   HOH Z 406 " =    1.700
peak=    4.197 closest distance to " O   HOH Z 183 " =    1.541
peak=    4.156 closest distance to " CG2 VAL A 257 " =    0.886
peak=    4.156 closest distance to " CG  TRP A 179 " =    2.237
peak=    4.154 closest distance to " CB  ASN A 142 " =    0.926
peak=    4.148 closest distance to " CG  LEU A 167 " =    1.248
peak=    4.143 closest distance to " CA  TYR A  30 " =    1.017
peak=    4.073 closest distance to " O   HOH Z 427 " =    2.743
peak=    4.066 closest distance to " CA  ARG A 195 " =    1.322
peak=    4.064 closest distance to " CA  SER A  87 " =    0.961
peak=    4.057 closest distance to " O   HOH Z 425 " =    1.419
peak=    4.023 closest distance to " CB  ASN A 187 " =    1.028
peak=    4.014 closest distance to " O   TYR A 116 " =    1.307
peak=    4.014 closest distance to " CB  ASP A 124 " =    0.790
peak=    4.012 closest distance to " O   HOH Z 188 " =    2.708
peak=    4.009 closest distance to " NH2AARG A 190 " =    2.055
peak=    4.008 closest distance to " NE2 HIS A 207 " =    1.093
peak=    3.998 closest distance to " O   HOH Z 419 " =    2.129
peak=    3.971 closest distance to " O  BHOH Z  74 " =    1.275
peak=    3.955 closest distance to " CB  GLN A 183 " =    1.205
peak=    3.952 closest distance to " CG  PRO A 243 " =    1.097
peak=    3.934 closest distance to " CB  ALA A 160 " =    1.385
peak=    3.918 closest distance to " O   PRO A 198 " =    1.588
peak=    3.895 closest distance to " CE  LYS A  76 " =    0.911
peak=    3.892 closest distance to " CB  SER A 210 " =    0.819
peak=    3.891 closest distance to " CB  SER A 212 " =    1.285
peak=    3.879 closest distance to " O   HOH Z 316 " =    3.088
peak=    3.878 closest distance to " CD1 LEU A 300 " =    1.134
peak=    3.874 closest distance to " O   HOH Z 362 " =    2.415
peak=    3.865 closest distance to " CB  LEU A 228 " =    1.070
peak=    3.853 closest distance to " CB  VAL A 265 " =    1.291
peak=    3.853 closest distance to " O   HOH Z 180 " =    2.160
peak=    3.843 closest distance to " CD2 TRP A 179 " =    1.220
peak=    3.837 closest distance to " CB  GLU A  46 " =    1.036
peak=    3.824 closest distance to " CA  ALA A  51 " =    0.960
peak=    3.822 closest distance to " O   HOH Z 403 " =    1.556
peak=    3.822 closest distance to " O   ASN A  74 " =    1.385
peak=    3.819 closest distance to " O   HOH Z 214 " =    2.250
peak=    3.814 closest distance to " CA  VAL A 125 " =    1.163
peak=    3.810 closest distance to " NZ  LYS A 119 " =    2.687
peak=    3.805 closest distance to " CG1 ILE A 151 " =    1.068
peak=    3.805 closest distance to " O   HOH Z  88 " =    3.997
peak=    3.801 closest distance to " O   HOH Z   1 " =    1.878
peak=    3.800 closest distance to " CB  SER A 216 " =    0.964
peak=    3.797 closest distance to " CD  ARG A 269 " =    0.914
peak=    3.791 closest distance to " CB  ASN A  39 " =    0.942
peak=    3.766 closest distance to " O   HOH Z 368 " =    3.596
peak=    3.760 closest distance to " CB  TRP A 266 " =    1.010
peak=    3.753 closest distance to " O   HOH Z 145 " =    1.491
peak=    3.734 closest distance to " O   HOH Z  61 " =    1.616
peak=    3.731 closest distance to " NH1AARG A 145 " =    1.273
peak=    3.723 closest distance to " CD  ARG A  66 " =    2.075
peak=    3.719 closest distance to " ND1 HIS A  86 " =    1.787
peak=    3.718 closest distance to " OG  SER A  62 " =    3.043
peak=    3.709 closest distance to " CZ  PHE A  38 " =    1.197
peak=    3.709 closest distance to " CA  THR A 264 " =    0.859
peak=    3.707 closest distance to " O   HOH Z 272 " =    1.761
peak=    3.705 closest distance to " O   HOH Z  21 " =    1.793
peak=    3.703 closest distance to " CB  VAL A 202 " =    1.601
peak=    3.700 closest distance to " O   SER A  87 " =    2.355
peak=    3.697 closest distance to " O   HOH Z 437 " =    1.398
peak=    3.663 closest distance to " O   HOH Z 145 " =    1.884
peak=    3.655 closest distance to " O   HOH Z 286 " =    2.303
peak=    3.651 closest distance to " ND2BASN A 224 " =    0.928
peak=    3.646 closest distance to " O   HOH Z 211 " =    1.212
peak=    3.641 closest distance to " O   HOH Z 258 " =    2.107
peak=    3.636 closest distance to " O   HOH Z 218 " =    1.744
peak=    3.635 closest distance to " O   HOH Z 394 " =    1.771
peak=    3.633 closest distance to " CB  SER A   3 " =    1.447
peak=    3.631 closest distance to " O   HOH Z 422 " =    2.698
peak=    3.611 closest distance to " CA  TYR A 116 " =    1.394
peak=    3.611 closest distance to " O   HOH Z 368 " =    1.789
peak=    3.610 closest distance to " N   CYS A 260 " =    0.830
peak=    3.609 closest distance to " O   HOH Z 368 " =    4.266
peak=    3.609 closest distance to " CA  ASN A 127 " =    1.095
peak=    3.608 closest distance to " CG2 THR A 221 " =    0.958
peak=    3.604 closest distance to " O   HOH Z 215 " =    1.520
peak=    3.592 closest distance to " O   HOH Z 394 " =    3.998
peak=    3.589 closest distance to " NZ  LYS A 117 " =    2.982
peak=    3.589 closest distance to " O   HOH Z 434 " =    1.520
peak=    3.579 closest distance to " O   HOH Z 294 " =    1.539
peak=    3.578 closest distance to " CB  GLU A 128 " =    0.824
peak=    3.571 closest distance to " CB  PRO A  90 " =    1.086
peak=    3.565 closest distance to " O   HOH Z 365 " =    2.784
peak=    3.564 closest distance to " ND2 ASN A 249 " =    0.860
peak=    3.552 closest distance to " O   ASN A  74 " =    2.054
peak=    3.551 closest distance to " O   HOH Z   2 " =    1.631
peak=    3.548 closest distance to " CB  ALA A 114 " =    0.754
peak=    3.546 closest distance to " CB  GLU A 277 " =    3.689
peak=    3.544 closest distance to " O   HOH Z   1 " =    1.710
peak=    3.538 closest distance to " CE3 TRP A 150 " =    1.111
peak=    3.535 closest distance to " O   HOH Z  10 " =    1.705
peak=    3.527 closest distance to " O   HOH Z 421 " =    2.258
peak=    3.524 closest distance to " OE2 GLU A  53 " =    1.861
peak=    3.523 closest distance to " CB  LYS A 117 " =    1.201
peak=    3.522 closest distance to " CA  ALA A 158 " =    1.136
peak=    3.522 closest distance to " CA  ALA A 160 " =    1.050
peak=    3.521 closest distance to " CB  ILE A 120 " =    1.304
peak=    3.518 closest distance to " O   HOH Z  61 " =    1.700
peak=    3.511 closest distance to " O   THR A 220 " =    1.429
peak=    3.506 closest distance to " O   HOH Z 193 " =    2.138
peak=    3.500 closest distance to " O   HOH Z 405 " =    1.503
peak=    3.499 closest distance to " O   HOH Z 193 " =    1.661
peak=    3.493 closest distance to " O   HOH Z  68 " =    2.037
peak=    3.492 closest distance to " CA  ILE A 106 " =    0.808
peak=    3.492 closest distance to " CA  MET A 105 " =    0.895
peak=    3.490 closest distance to " CB  LEU A  83 " =    0.705
peak=    3.490 closest distance to " O   HOH Z 116 " =    3.226
peak=    3.489 closest distance to " CA  ILE A 234 " =    1.017
peak=    3.476 closest distance to " CG1BVAL A  72 " =    1.600
peak=    3.465 closest distance to " CG AARG A 275 " =    1.245
peak=    3.465 closest distance to " O   HOH Z 359 " =    1.474
peak=    3.463 closest distance to " O   ASN A 209 " =    1.330
peak=    3.461 closest distance to " CG2 ILE A 120 " =    1.298
peak=    3.460 closest distance to " CA  ALA A 233 " =    1.287
peak=    3.456 closest distance to " O   HOH Z 411 " =    3.739
peak=    3.453 closest distance to " O   HOH Z 216 " =    4.012
peak=    3.453 closest distance to " O   HOH Z 112 " =    0.961
peak=    3.447 closest distance to " O   HOH Z 132 " =    2.579
peak=    3.443 closest distance to " CB  GLN A  88 " =    1.266
peak=    3.440 closest distance to " OE2 GLU A  53 " =    1.319
peak=    3.437 closest distance to " CB  ARG A 102 " =    0.733
peak=    3.431 closest distance to " CB  MET A  40 " =    0.733
peak=    3.426 closest distance to " CB  ALA A  43 " =    0.818
peak=    3.419 closest distance to " CB  THR A  31 " =    1.648
peak=    3.418 closest distance to " O   HOH Z 325 " =    2.368
peak=    3.413 closest distance to " O   HOH Z 154 " =    2.046
peak=    3.409 closest distance to " O   HOH Z 128 " =    1.821
peak=    3.405 closest distance to " CB  ASN A 110 " =    1.062
peak=    3.404 closest distance to " O   HOH Z 248 " =    1.641
peak=    3.403 closest distance to " O   HOH Z 148 " =    3.553
peak=    3.400 closest distance to " N   VAL A 296 " =    1.724
peak=    3.397 closest distance to " CD  LYS A 166 " =    1.269
peak=    3.393 closest distance to " N   PHE A 130 " =    1.232
peak=    3.391 closest distance to " CA  ARG A  36 " =    1.083
peak=    3.389 closest distance to " OD1 ASN A  69 " =    2.629
peak=    3.386 closest distance to " O   HOH Z  58 " =    1.723
peak=    3.386 closest distance to " O   HOH Z 359 " =    4.254
peak=    3.382 closest distance to " O   HOH Z 128 " =    2.187
peak=    3.382 closest distance to " O   HOH Z 156 " =    2.775
peak=    3.377 closest distance to " OG  SER A 135 " =    1.217
peak=    3.374 closest distance to " O   THR A 182 " =    1.414
peak=    3.373 closest distance to " O   HOH Z 352 " =    1.827
peak=    3.372 closest distance to " CB  ARG A 138 " =    1.024
peak=    3.371 closest distance to " O   HOH Z 158 " =    2.962
peak=    3.368 closest distance to " CA  GLN A  94 " =    0.762
peak=    3.368 closest distance to " CA  ASP A 162 " =    0.958
peak=    3.366 closest distance to " OG BSER A 134 " =    2.856
peak=    3.365 closest distance to " O   HOH Z 391 " =    2.995
peak=    3.365 closest distance to " CG  GLN A  58 " =    1.092
peak=    3.357 closest distance to " CG2 ILE A 239 " =    0.778
peak=    3.352 closest distance to " O   THR A 294 " =    1.052
peak=    3.351 closest distance to " CB  GLU A 152 " =    1.172
peak=    3.351 closest distance to " OG BSER A 164 " =    2.511
peak=    3.348 closest distance to " CB  TRP A 179 " =    1.402
peak=    3.342 closest distance to " O   HOH Z  90 " =    2.200
peak=    3.341 closest distance to " O   MET A 105 " =    1.728
peak=    3.339 closest distance to " O   HOH Z 172 " =    2.660
peak=    3.336 closest distance to " O   HOH Z 238 " =    3.454
peak=    3.332 closest distance to " CB  SER A  62 " =    0.949
peak=    3.331 closest distance to " CB  GLN A  89 " =    1.293
peak=    3.330 closest distance to " N   ARG A 156 " =    1.320
peak=    3.329 closest distance to " CB  ALA A 291 " =    1.168
peak=    3.327 closest distance to " O   HOH Z 285 " =    2.476
peak=    3.325 closest distance to " O   HOH Z 153 " =    3.753
peak=    3.324 closest distance to " NH2 ARG A  56 " =    1.130
peak=    3.322 closest distance to " CA  SER A  95 " =    0.948
peak=    3.319 closest distance to " O   HOH Z  40 " =    2.034
peak=    3.317 closest distance to " N   TYR A 116 " =    1.360
peak=    3.313 closest distance to " O   HOH Z 299 " =    2.517
peak=    3.312 closest distance to " O   PHE A 192 " =    1.364
peak=    3.303 closest distance to " CG2 ILE A  20 " =    1.537
peak=    3.303 closest distance to " O   HOH Z 234 " =    3.882
peak=    3.303 closest distance to " CE  LYS A 119 " =    1.155
peak=    3.302 closest distance to " CG  MET A 113 " =    1.295
peak=    3.297 closest distance to " CB  ASN A 215 " =    1.103
peak=    3.296 closest distance to " CB  ALA A 242 " =    0.912
peak=    3.295 closest distance to " O   HOH Z 380 " =    5.059
peak=    3.293 closest distance to " CB  ALA A   1 " =    4.642
peak=    3.288 closest distance to " O   HOH Z 152 " =    2.575
peak=    3.287 closest distance to " CB  TYR A 116 " =    0.958
peak=    3.283 closest distance to " O   HOH Z 278 " =    1.193
peak=    3.280 closest distance to " CA  ARG A 102 " =    1.164
peak=    3.280 closest distance to " CB  ALA A 291 " =    0.820
peak=    3.278 closest distance to " O   HOH Z 291 " =    1.508
peak=    3.276 closest distance to " NE AARG A 275 " =    1.415
peak=    3.275 closest distance to " N   ASN A 127 " =    1.358
peak=    3.274 closest distance to " O   HOH Z 369 " =    1.758
peak=    3.273 closest distance to " O   HOH Z 106 " =    2.217
peak=    3.272 closest distance to " O   PRO A 198 " =    1.316
peak=    3.265 closest distance to " CB  SER A 273 " =    0.899
peak=    3.263 closest distance to " NH1 ARG A 138 " =    1.064
peak=    3.261 closest distance to " CB  TYR A  30 " =    1.405
peak=    3.260 closest distance to " OG BSER A  99 " =    2.328
peak=    3.260 closest distance to " CE3 TRP A  85 " =    1.002
peak=    3.254 closest distance to " O   HOH Z 402 " =    1.495
peak=    3.252 closest distance to " O   HOH Z 371 " =    2.798
peak=    3.251 closest distance to " O   HOH Z  88 " =    3.348
peak=    3.251 closest distance to " CA  ALA A 154 " =    1.058
peak=    3.246 closest distance to " CB  GLU A 128 " =    0.703
peak=    3.238 closest distance to " CB  PHE A 204 " =    0.730
peak=    3.236 closest distance to " CB  GLU A  37 " =    0.918
peak=    3.233 closest distance to " O   HOH Z  24 " =    1.812
peak=    3.228 closest distance to " O   HOH Z 213 " =    2.707
peak=    3.218 closest distance to " OD2 ASP A 286 " =    3.263
peak=    3.217 closest distance to " O   HOH Z 305 " =    3.666
peak=    3.215 closest distance to " O   HOH Z 357 " =    2.069
peak=    3.215 closest distance to " N   TYR A  15 " =    0.813
peak=    3.212 closest distance to " O   HOH Z 290 " =    1.083
peak=    3.211 closest distance to " O   HOH Z 310 " =    2.221
peak=    3.210 closest distance to " N   GLN A 278 " =    1.165
peak=    3.203 closest distance to " CA  ALA A 129 " =    1.224
peak=    3.200 closest distance to " CG  PHE A 204 " =    0.921
peak=    3.198 closest distance to " CD1 ILE A  33 " =    1.760
peak=    3.198 closest distance to " O   HOH Z 415 " =    3.932
peak=    3.197 closest distance to " CG  GLN A 278 " =    1.253
peak=    3.197 closest distance to " O   HOH Z 383 " =    1.835
peak=    3.195 closest distance to " CA  ARG A 156 " =    1.092
peak=    3.193 closest distance to " CA  ILE A 263 " =    1.032
peak=    3.193 closest distance to " CG  LYS A 119 " =    1.095
peak=    3.192 closest distance to " O   HOH Z 302 " =    1.853
peak=    3.186 closest distance to " CB  SER A  99 " =    0.941
peak=    3.178 closest distance to " N   ALA A   1 " =    1.983
peak=    3.175 closest distance to " O   HOH Z 285 " =    2.130
peak=    3.175 closest distance to " OE2 GLU A  44 " =    1.098
peak=    3.175 closest distance to " CG  GLN A 144 " =    0.831
peak=    3.165 closest distance to " CA  ARG A 159 " =    1.270
peak=    3.157 closest distance to " O   HOH Z 213 " =    2.131
peak=    3.156 closest distance to " CA  ASN A  74 " =    1.338
peak=    3.155 closest distance to " O   PRO A 213 " =    1.406
peak=    3.153 closest distance to " CB  ALA A 180 " =    1.359
peak=    3.153 closest distance to " O   HOH Z 327 " =    1.750
peak=    3.143 closest distance to " CB  ASN A 285 " =    0.951
peak=    3.141 closest distance to " CG  GLU A 277 " =    2.029
peak=    3.140 closest distance to " CG1 VAL A 153 " =    0.950
peak=    3.140 closest distance to " N   SER A 135 " =    1.351
peak=    3.139 closest distance to " CA  GLY A 136 " =    0.929
peak=    3.138 closest distance to " O   HOH Z 106 " =    4.172
peak=    3.131 closest distance to " OG  SER A  26 " =    1.634
peak=    3.131 closest distance to " O   HOH Z 438 " =    1.977
peak=    3.131 closest distance to " O   HOH Z 128 " =    1.925
peak=    3.129 closest distance to " NH1 ARG A  14 " =    1.113
peak=    3.123 closest distance to " O   HOH Z 124 " =    2.038
peak=    3.123 closest distance to " O   HOH Z 153 " =    1.646
peak=    3.122 closest distance to " O   HOH Z   3 " =    2.116
peak=    3.122 closest distance to " CG2 ILE A 151 " =    0.790
peak=    3.119 closest distance to " CB  LEU A 255 " =    1.418
peak=    3.114 closest distance to " CA  ALA A 100 " =    1.044
peak=    3.113 closest distance to " CE3 TRP A 274 " =    1.371
peak=    3.113 closest distance to " O   HOH Z  80 " =    1.558
peak=    3.112 closest distance to " O   HOH Z  59 " =    1.734
peak=    3.112 closest distance to " CB  THR A 157 " =    1.142
peak=    3.111 closest distance to " O   HOH Z  49 " =    3.538
peak=    3.106 closest distance to " CG  ARG A 138 " =    1.239
peak=    3.103 closest distance to " CA  GLY A  35 " =    1.035
peak=    3.102 closest distance to " CB  ALA A 248 " =    1.001
peak=    3.096 closest distance to " CB  GLU A 152 " =    1.344
peak=    3.093 closest distance to " O   HOH Z 188 " =    1.932
peak=    3.090 closest distance to " CD1 ILE A 199 " =    1.091
peak=    3.089 closest distance to " OE1 GLU A  37 " =    1.382
peak=    3.089 closest distance to " CB  PRO A 243 " =    1.404
peak=    3.083 closest distance to " CA  THR A 221 " =    0.945
peak=    3.080 closest distance to " OG1 THR A 264 " =    0.711
peak=    3.077 closest distance to " CB  ALA A 114 " =    1.020
peak=    3.073 closest distance to " CD BLYS A 290 " =    0.949
peak=    3.072 closest distance to " CG  GLN A  89 " =    1.508
peak=    3.071 closest distance to " O   HOH Z 225 " =    1.663
peak=    3.068 closest distance to " O   HOH Z 194 " =    2.288
peak=    3.059 closest distance to " CB  LEU A 300 " =    0.963
peak=    3.058 closest distance to " CE2 PHE A  16 " =    0.934
peak=    3.058 closest distance to " O   HOH Z 332 " =    1.527
peak=    3.047 closest distance to " CA  LEU A 282 " =    1.105
peak=    3.041 closest distance to " O   HOH Z 389 " =    1.805
peak=    3.032 closest distance to " CA  ALA A 299 " =    0.867
peak=    3.018 closest distance to " N   GLU A 152 " =    1.447

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 214         
Filter by distance & map next to the model:
   mapped sites are within: 0.499 - 5.969
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 211 from: 214
   mapped sites are within: 0.827 - 5.969

peak=   -4.565 closest distance to " CD  ARG A  14 " =    3.297
peak=   -4.421 closest distance to " CG2 ILE A  49 " =    2.862
peak=   -4.364 closest distance to " O   PRO A 198 " =    1.196
peak=   -4.352 closest distance to " O   HOH Z 377 " =    1.854
peak=   -4.325 closest distance to " CB  PRO A 243 " =    2.650
peak=   -4.225 closest distance to " CD  ARG A 156 " =    2.107
peak=   -4.195 closest distance to " CG1 VAL A 112 " =    2.640
peak=   -4.134 closest distance to " O   HOH Z  60 " =    1.352
peak=   -4.071 closest distance to " O   HOH Z 231 " =    0.948
peak=   -4.050 closest distance to " O   HOH Z 290 " =    0.994
peak=   -4.047 closest distance to " OG BSER A 134 " =    1.450
peak=   -4.012 closest distance to " CB  ALA A  43 " =    2.560
peak=   -3.978 closest distance to " CZ3 TRP A 179 " =    1.200
peak=   -3.956 closest distance to " O   HOH Z 351 " =    1.560
peak=   -3.876 closest distance to " O   HOH Z 131 " =    4.023
peak=   -3.863 closest distance to " O   HOH Z 216 " =    1.184
peak=   -3.861 closest distance to " CA  GLY A  98 " =    1.904
peak=   -3.860 closest distance to " CB  ALA A 291 " =    2.292
peak=   -3.855 closest distance to " CD2 TYR A 293 " =    1.919
peak=   -3.828 closest distance to " O   HOH Z 231 " =    2.128
peak=   -3.823 closest distance to " O   ALA A  10 " =    1.615
peak=   -3.810 closest distance to " CG1 VAL A 250 " =    2.694
peak=   -3.807 closest distance to " O   HOH Z  73 " =    2.143
peak=   -3.768 closest distance to " CE BMET A  47 " =    1.446
peak=   -3.755 closest distance to " OE1 GLN A  88 " =    1.094
peak=   -3.736 closest distance to " ND2 ASN A 249 " =    2.200
peak=   -3.736 closest distance to " O   HOH Z  69 " =    1.643
peak=   -3.734 closest distance to " CG  GLN A  88 " =    0.827
peak=   -3.720 closest distance to " CD1 TYR A 247 " =    2.836
peak=   -3.712 closest distance to " OG BSER A 134 " =    1.830
peak=   -3.710 closest distance to " CA  GLY A 241 " =    2.316
peak=   -3.708 closest distance to " O   GLU A 152 " =    1.368
peak=   -3.698 closest distance to " O   PRO A 163 " =    1.902
peak=   -3.672 closest distance to " N   THR A 157 " =    1.561
peak=   -3.661 closest distance to " O   HOH Z 111 " =    1.453
peak=   -3.658 closest distance to " CG  LEU A 167 " =    0.999
peak=   -3.654 closest distance to " O   HOH Z 140 " =    1.183
peak=   -3.649 closest distance to " CA  ASP A  27 " =    2.460
peak=   -3.646 closest distance to " C   HIS A 108 " =    1.135
peak=   -3.637 closest distance to " O   HOH Z 185 " =    2.247
peak=   -3.629 closest distance to " CG2 THR A  18 " =    2.842
peak=   -3.624 closest distance to " O   HOH Z 275 " =    1.724
peak=   -3.620 closest distance to " CG  GLN A  58 " =    1.059
peak=   -3.617 closest distance to " CE2 TYR A  30 " =    2.569
peak=   -3.608 closest distance to " O   HOH Z 298 " =    2.468
peak=   -3.597 closest distance to " OG  SER A  97 " =    2.210
peak=   -3.595 closest distance to " CD  GLU A 277 " =    1.184
peak=   -3.589 closest distance to " CG  MET A 105 " =    0.991
peak=   -3.585 closest distance to " CB  GLN A  55 " =    1.307
peak=   -3.585 closest distance to " O   HOH Z  52 " =    1.404
peak=   -3.581 closest distance to " O   HOH Z 313 " =    1.735
peak=   -3.572 closest distance to " CE  MET A 105 " =    2.583
peak=   -3.569 closest distance to " CB  ASP A 200 " =    2.583
peak=   -3.564 closest distance to " N   ALA A  43 " =    2.532
peak=   -3.559 closest distance to " O   HOH Z 278 " =    1.187
peak=   -3.557 closest distance to " O   HOH Z 412 " =    4.491
peak=   -3.555 closest distance to " O   HOH Z 407 " =    3.202
peak=   -3.551 closest distance to " O   SER A  22 " =    2.664
peak=   -3.542 closest distance to " O   HOH Z 411 " =    5.327
peak=   -3.541 closest distance to " CD1 LEU A 255 " =    3.002
peak=   -3.536 closest distance to " O   HOH Z 100 " =    0.897
peak=   -3.533 closest distance to " CG2 THR A 178 " =    2.284
peak=   -3.533 closest distance to " O   HOH Z 359 " =    3.120
peak=   -3.532 closest distance to " O   HOH Z 198 " =    1.542
peak=   -3.526 closest distance to " CA  GLY A 133 " =    2.054
peak=   -3.523 closest distance to " O   HOH Z 389 " =    2.200
peak=   -3.513 closest distance to " O   VAL A  67 " =    2.667
peak=   -3.513 closest distance to " O   HOH Z  11 " =    1.653
peak=   -3.508 closest distance to " CG2 ILE A 263 " =    2.417
peak=   -3.500 closest distance to " O   HOH Z  22 " =    2.219
peak=   -3.498 closest distance to " CD1 LEU A 101 " =    2.301
peak=   -3.495 closest distance to " CE1 TYR A 172 " =    1.900
peak=   -3.491 closest distance to " O   HOH Z 211 " =    0.898
peak=   -3.487 closest distance to " CD2 LEU A 143 " =    2.577
peak=   -3.467 closest distance to " CB  ALA A   9 " =    2.468
peak=   -3.464 closest distance to " CB  TRP A  85 " =    2.479
peak=   -3.459 closest distance to " O   HOH Z  53 " =    1.718
peak=   -3.456 closest distance to " O   HOH Z  38 " =    1.560
peak=   -3.453 closest distance to " CB  PRO A  54 " =    2.518
peak=   -3.451 closest distance to " O   HOH Z 351 " =    1.710
peak=   -3.445 closest distance to " CG  GLN A 223 " =    2.441
peak=   -3.442 closest distance to " O   GLY A  17 " =    1.192
peak=   -3.438 closest distance to " OD1 ASP A 191 " =    1.721
peak=   -3.436 closest distance to " O   ILE A  49 " =    1.692
peak=   -3.431 closest distance to " O   HOH Z 394 " =    1.573
peak=   -3.431 closest distance to " ND2 ASN A  45 " =    2.236
peak=   -3.428 closest distance to " CZ  PHE A 155 " =    1.152
peak=   -3.424 closest distance to " O   HOH Z 219 " =    4.245
peak=   -3.423 closest distance to " O   HOH Z 174 " =    2.689
peak=   -3.412 closest distance to " CD2 PHE A  61 " =    2.098
peak=   -3.410 closest distance to " CA  ASP A 298 " =    1.186
peak=   -3.404 closest distance to " NZ  LYS A 166 " =    1.162
peak=   -3.401 closest distance to " CD  ARG A  79 " =    1.122
peak=   -3.400 closest distance to " O   HOH Z 139 " =    0.954
peak=   -3.395 closest distance to " CG1 VAL A 112 " =    3.091
peak=   -3.393 closest distance to " O   HOH Z  65 " =    1.262
peak=   -3.389 closest distance to " CG2 ILE A  20 " =    2.928
peak=   -3.387 closest distance to " O   HOH Z 191 " =    5.619
peak=   -3.377 closest distance to " OD1 ASP A 171 " =    1.627
peak=   -3.370 closest distance to " CG2 ILE A 151 " =    2.563
peak=   -3.370 closest distance to " N   SER A 212 " =    1.946
peak=   -3.369 closest distance to " O   HOH Z 152 " =    4.943
peak=   -3.368 closest distance to " ND2 ASN A  60 " =    4.051
peak=   -3.361 closest distance to " CB  ALA A 158 " =    1.611
peak=   -3.349 closest distance to " CB  ASP A 132 " =    2.344
peak=   -3.349 closest distance to " O   PRO A 243 " =    2.556
peak=   -3.349 closest distance to " O   ARG A  24 " =    1.773
peak=   -3.347 closest distance to " O   TYR A 186 " =    1.710
peak=   -3.344 closest distance to " CE3 TRP A 274 " =    0.968
peak=   -3.338 closest distance to " O   VAL A 189 " =    2.551
peak=   -3.334 closest distance to " CB  GLN A  11 " =    1.634
peak=   -3.326 closest distance to " O   ALA A   7 " =    1.477
peak=   -3.325 closest distance to " O   HOH Z  64 " =    1.145
peak=   -3.324 closest distance to " CE2 PHE A 218 " =    2.507
peak=   -3.323 closest distance to " CA  GLY A 241 " =    3.324
peak=   -3.323 closest distance to " O   HOH Z  28 " =    1.579
peak=   -3.322 closest distance to " O   HOH Z   9 " =    1.124
peak=   -3.321 closest distance to " O   HOH Z 276 " =    1.324
peak=   -3.318 closest distance to " O   SER A 135 " =    1.393
peak=   -3.317 closest distance to " O   GLN A 240 " =    2.027
peak=   -3.309 closest distance to " O   HOH Z  26 " =    1.056
peak=   -3.308 closest distance to " O   ILE A 106 " =    2.131
peak=   -3.308 closest distance to " O   HOH Z 252 " =    3.839
peak=   -3.306 closest distance to " O   HOH Z 372 " =    2.490
peak=   -3.304 closest distance to " CG2BVAL A  41 " =    1.115
peak=   -3.300 closest distance to " O   HOH Z 281 " =    2.770
peak=   -3.297 closest distance to " O   HOH Z 191 " =    3.278
peak=   -3.296 closest distance to " CB  PHE A 192 " =    1.921
peak=   -3.296 closest distance to " O   HOH Z 389 " =    1.526
peak=   -3.295 closest distance to " O   HOH Z 100 " =    1.188
peak=   -3.293 closest distance to " O   ARG A  56 " =    4.399
peak=   -3.292 closest distance to " CA  GLY A 203 " =    2.478
peak=   -3.290 closest distance to " CE2 PHE A  61 " =    2.768
peak=   -3.289 closest distance to " NH2AARG A 275 " =    5.523
peak=   -3.286 closest distance to " O   HOH Z 232 " =    1.789
peak=   -3.282 closest distance to " CB  ASP A 286 " =    2.156
peak=   -3.281 closest distance to " CE  LYS A  76 " =    2.749
peak=   -3.277 closest distance to " O   HOH Z 108 " =    1.297
peak=   -3.275 closest distance to " ND2 ASN A  45 " =    1.330
peak=   -3.273 closest distance to " CB  ASN A  39 " =    2.286
peak=   -3.269 closest distance to " O   HOH Z 384 " =    3.088
peak=   -3.264 closest distance to " O   HOH Z 348 " =    2.214
peak=   -3.261 closest distance to " C   MET A 188 " =    1.591
peak=   -3.260 closest distance to " O   HOH Z 295 " =    1.833
peak=   -3.257 closest distance to " CB  ALA A 114 " =    2.543
peak=   -3.256 closest distance to " N   ASP A 270 " =    1.393
peak=   -3.254 closest distance to " NE2 GLN A 278 " =    1.593
peak=   -3.253 closest distance to " O   SER A 141 " =    1.658
peak=   -3.247 closest distance to " O   HOH Z 357 " =    2.075
peak=   -3.246 closest distance to " O   HOH Z  24 " =    1.168
peak=   -3.244 closest distance to " CD2 HIS A 207 " =    2.195
peak=   -3.242 closest distance to " ND2 ASN A 187 " =    1.534
peak=   -3.240 closest distance to " O   HOH Z 145 " =    1.354
peak=   -3.234 closest distance to " O   HOH Z 318 " =    1.831
peak=   -3.234 closest distance to " O   HOH Z  51 " =    0.994
peak=   -3.233 closest distance to " CD  LYS A 289 " =    2.318
peak=   -3.233 closest distance to " O   HOH Z  32 " =    1.944
peak=   -3.230 closest distance to " O   HOH Z 364 " =    2.388
peak=   -3.227 closest distance to " O   HOH Z 290 " =    0.937
peak=   -3.226 closest distance to " CG  ASN A  39 " =    1.784
peak=   -3.224 closest distance to " C   PHE A  59 " =    1.182
peak=   -3.223 closest distance to " O   PHE A 218 " =    1.454
peak=   -3.220 closest distance to " CB  PRO A 163 " =    2.513
peak=   -3.215 closest distance to " OG  SER A  87 " =    1.375
peak=   -3.214 closest distance to " O   LYS A 181 " =    2.887
peak=   -3.214 closest distance to " O   HOH Z 409 " =    5.969
peak=   -3.211 closest distance to " O   HOH Z   1 " =    1.348
peak=   -3.198 closest distance to " O   ARG A  56 " =    1.910
peak=   -3.197 closest distance to " O   HOH Z  10 " =    1.534
peak=   -3.196 closest distance to " O   HOH Z  49 " =    1.415
peak=   -3.195 closest distance to " O   HOH Z 247 " =    0.857
peak=   -3.192 closest distance to " O   HOH Z 103 " =    1.623
peak=   -3.190 closest distance to " CG1 VAL A 125 " =    2.320
peak=   -3.187 closest distance to " OH  TYR A 247 " =    2.205
peak=   -3.184 closest distance to " O   HOH Z 166 " =    2.060
peak=   -3.184 closest distance to " O   ARG A 145 " =    1.415
peak=   -3.181 closest distance to " CG  LEU A  83 " =    2.083
peak=   -3.181 closest distance to " CG  LEU A 282 " =    2.476
peak=   -3.180 closest distance to " O   GLN A  94 " =    2.231
peak=   -3.176 closest distance to " NE2 GLN A  55 " =    1.179
peak=   -3.174 closest distance to " CA  ASN A 127 " =    1.494
peak=   -3.167 closest distance to " N   ASP A 171 " =    2.531
peak=   -3.162 closest distance to " CZ  PHE A  16 " =    2.323
peak=   -3.161 closest distance to " O   HOH Z 364 " =    1.640
peak=   -3.158 closest distance to " SG BCYS A 201 " =    2.012
peak=   -3.152 closest distance to " CG1 VAL A 125 " =    1.797
peak=   -3.151 closest distance to " CG1 VAL A  78 " =    2.751
peak=   -3.149 closest distance to " O   HOH Z 193 " =    1.325
peak=   -3.148 closest distance to " CB  ALA A 100 " =    2.298
peak=   -3.145 closest distance to " OE1 GLU A  44 " =    1.041
peak=   -3.143 closest distance to " N   ASP A 191 " =    1.132
peak=   -3.142 closest distance to " OXT GLY A 302 " =    3.297
peak=   -3.142 closest distance to " CB  ALA A 291 " =    1.920
peak=   -3.141 closest distance to " CB  CYS A 254 " =    2.140
peak=   -3.126 closest distance to " O   HOH Z 368 " =    1.662
peak=   -3.126 closest distance to " O   HOH Z 241 " =    1.376
peak=   -3.122 closest distance to " CA  GLY A  57 " =    2.082
peak=   -3.121 closest distance to " CB  ASP A  65 " =    1.612
peak=   -3.111 closest distance to " O   HOH Z  60 " =    1.274
peak=   -3.106 closest distance to " O   HOH Z 323 " =    1.612
peak=   -3.102 closest distance to " O   ALA A 180 " =    1.236
peak=   -3.089 closest distance to " CE1 TYR A 247 " =    2.742
peak=   -3.089 closest distance to " O   HOH Z 144 " =    1.092
peak=   -3.086 closest distance to " CD2 TYR A 293 " =    2.114
peak=   -3.085 closest distance to " N   ALA A 226 " =    2.072
peak=   -3.070 closest distance to " CG1 VAL A  67 " =    2.813
peak=   -3.062 closest distance to " OE1 GLN A 183 " =    1.645
peak=   -3.054 closest distance to " O   PRO A 198 " =    1.404
peak=   -3.047 closest distance to " CG  TRP A 266 " =    1.813
peak=   -3.045 closest distance to " O   HOH Z  86 " =    2.741
peak=   -3.036 closest distance to " O   HOH Z 250 " =    1.286

================= 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    :  0.4548 0.4511   6.267581e+00   6.249653e+00
   1_bss:  0.4446 0.4454   6.260852e+00   6.242253e+00
   1_xyz:  0.2900 0.3240   5.935246e+00   6.014920e+00
   1_adp:  0.2611 0.3345   5.882072e+00   6.039378e+00
   1_occ:  0.2607 0.3343   5.882099e+00   6.040211e+00
   2_bss:  0.2585 0.3324   5.882575e+00   6.040204e+00
   2_xyz:  0.2023 0.2659   5.663587e+00   5.856963e+00
   2_adp:  0.1896 0.2463   5.603670e+00   5.792139e+00
   2_occ:  0.1896 0.2465   5.603495e+00   5.792716e+00
   3_bss:  0.1894 0.2466   5.603795e+00   5.793383e+00
   3_xyz:  0.1506 0.2032   5.402265e+00   5.621570e+00
   3_adp:  0.1436 0.1928   5.355503e+00   5.568534e+00
   3_occ:  0.1435 0.1929   5.355526e+00   5.569110e+00
   4_bss:  0.1438 0.1926   5.354778e+00   5.567903e+00
   4_xyz:  0.1242 0.1709   5.228976e+00   5.463430e+00
   4_adp:  0.1203 0.1686   5.206187e+00   5.445390e+00
   4_occ:  0.1202 0.1686   5.206075e+00   5.445336e+00
   5_bss:  0.1201 0.1686   5.206024e+00   5.445375e+00
   5_xyz:  0.1199 0.1670   5.205763e+00   5.441782e+00
   5_adp:  0.1199 0.1662   5.206093e+00   5.441256e+00
   5_occ:  0.1198 0.1662   5.206157e+00   5.441444e+00
   5_bss:  0.1200 0.1658   5.203834e+00   5.438404e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.300  50.000  -2.273   0.353   4.500   0.000   0.000   0.000
   1_xyz:  0.300  50.000  -2.273   0.353   4.500   0.000   0.000   0.000
   1_adp:  0.300  50.000  -2.273   0.353   4.500   0.000   0.000   0.000
   1_occ:  0.300  50.000  -2.273   0.353   4.500   0.000   0.000   0.000
   2_bss:  0.346  85.876  -1.932  -1.292   1.720  -0.000   0.000   0.000
   2_xyz:  0.346  85.876  -1.932  -1.292   1.720  -0.000   0.000   0.000
   2_adp:  0.346  85.876  -1.932  -1.292   1.720  -0.000   0.000   0.000
   2_occ:  0.346  85.876  -1.932  -1.292   1.720  -0.000   0.000   0.000
   3_bss:  0.336  78.275  -1.980  -1.868   0.630  -0.000   0.000   0.000
   3_xyz:  0.336  78.275  -1.980  -1.868   0.630  -0.000   0.000   0.000
   3_adp:  0.336  78.275  -1.980  -1.868   0.630  -0.000   0.000   0.000
   3_occ:  0.336  78.275  -1.980  -1.868   0.630  -0.000   0.000   0.000
   4_bss:  0.327  70.683  -2.330  -2.431  -0.141  -0.000  -0.000  -0.000
   4_xyz:  0.327  70.683  -2.330  -2.431  -0.141  -0.000  -0.000  -0.000
   4_adp:  0.327  70.683  -2.330  -2.431  -0.141  -0.000  -0.000  -0.000
   4_occ:  0.327  70.683  -2.330  -2.431  -0.141  -0.000  -0.000  -0.000
   5_bss:  0.319  63.516  -2.215  -2.411  -0.245  -0.000  -0.000  -0.000
   5_xyz:  0.319  63.516  -2.215  -2.411  -0.245  -0.000  -0.000  -0.000
   5_adp:  0.319  63.516  -2.215  -2.411  -0.245  -0.000  -0.000  -0.000
   5_occ:  0.319  63.516  -2.215  -2.411  -0.245  -0.000  -0.000  -0.000
   5_bss:  0.319  61.999  -2.155  -2.388  -0.203  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  54.068 0.4691  0.6256    63409.374
   1_bss:  53.114 0.4801  0.6647    61295.865
   1_xyz:  33.376 0.7206  0.9321    27895.586
   1_adp:  34.996 0.7008  0.9128    30011.686
   1_occ:  35.073 0.6998  0.9110    30058.463
   2_bss:  34.892 0.7022  0.8750    30087.105
   2_xyz:  26.629 0.7929  0.9569    17921.775
   2_adp:  23.992 0.8217  0.9692    15511.683
   2_occ:  24.020 0.8214  0.9686    15515.074
   3_bss:  24.009 0.8215  0.9493    15556.544
   3_xyz:  19.402 0.8667  0.9801    10502.630
   3_adp:  18.028 0.8802  0.9814     9487.313
   3_occ:  18.041 0.8801  0.9812     9494.837
   4_bss:  17.998 0.8805  0.9626     9453.618
   4_xyz:  15.448 0.9029  0.9741     7378.259
   4_adp:  15.060 0.9065  0.9698     7152.386
   4_occ:  15.061 0.9065  0.9698     7148.662
   5_bss:  15.063 0.9065  0.9701     7149.131
   5_xyz:  14.912 0.9080  0.9701     7057.080
   5_adp:  14.851 0.9087  0.9654     7060.453
   5_occ:  14.859 0.9086  0.9654     7059.559
   5_bss:  14.815 0.9088  0.9658     6975.644
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.6855e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.6855e-01
   1_xyz:   1.625  0.015  0.103 16.237  0.007  4.113   1.7505e-01
   1_adp:   1.625  0.015  0.103 16.237  0.007  4.113   1.7505e-01
   1_occ:   1.625  0.015  0.103 16.237  0.007  4.113   1.7505e-01
   2_bss:   1.625  0.015  0.103 16.237  0.007  4.113   1.7505e-01
   2_xyz:   1.043  0.006  0.077 14.603  0.004  4.120   6.0050e-02
   2_adp:   1.043  0.006  0.077 14.603  0.004  4.120   6.0050e-02
   2_occ:   1.043  0.006  0.077 14.603  0.004  4.120   6.0050e-02
   3_bss:   1.043  0.006  0.077 14.603  0.004  4.120   6.0050e-02
   3_xyz:   1.016  0.008  0.074 14.562  0.004  4.132   6.0154e-02
   3_adp:   1.016  0.008  0.074 14.562  0.004  4.132   6.0154e-02
   3_occ:   1.016  0.008  0.074 14.562  0.004  4.132   6.0154e-02
   4_bss:   1.016  0.008  0.074 14.562  0.004  4.132   6.0154e-02
   4_xyz:   1.129  0.010  0.082 14.829  0.004  4.117   7.5461e-02
   4_adp:   1.129  0.010  0.082 14.829  0.004  4.117   7.5461e-02
   4_occ:   1.129  0.010  0.082 14.829  0.004  4.117   7.5461e-02
   5_bss:   1.129  0.010  0.082 14.829  0.004  4.117   7.5461e-02
   5_xyz:   0.981  0.008  0.074 14.341  0.004  4.118   5.8065e-02
   5_adp:   0.981  0.008  0.074 14.341  0.004  4.118   5.8065e-02
   5_occ:   0.981  0.008  0.074 14.341  0.004  4.118   5.8065e-02
   5_bss:   0.981  0.008  0.074 14.341  0.004  4.118   5.8065e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4271e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4271e-01
   1_xyz:  10.144  0.131  0.347 81.228  0.056  2.060   3.7464e-01
   1_adp:  10.144  0.131  0.347 81.228  0.056  2.060   3.7464e-01
   1_occ:  10.144  0.131  0.347 81.228  0.056  2.060   3.7464e-01
   2_bss:  10.144  0.131  0.347 81.228  0.056  2.060   3.7464e-01
   2_xyz:   6.960  0.045  0.275 78.511  0.041  2.317   5.0242e-02
   2_adp:   6.960  0.045  0.275 78.511  0.041  2.317   5.0242e-02
   2_occ:   6.960  0.045  0.275 78.511  0.041  2.317   5.0242e-02
   3_bss:   6.960  0.045  0.275 78.511  0.041  2.317   5.0242e-02
   3_xyz:   7.761  0.042  0.229 81.385  0.038  2.319   4.9270e-02
   3_adp:   7.761  0.042  0.229 81.385  0.038  2.319   4.9270e-02
   3_occ:   7.761  0.042  0.229 81.385  0.038  2.319   4.9270e-02
   4_bss:   7.761  0.042  0.229 81.385  0.038  2.319   4.9270e-02
   4_xyz:   7.882  0.057  0.269 82.716  0.033  2.303   6.1652e-02
   4_adp:   7.882  0.057  0.269 82.716  0.033  2.303   6.1652e-02
   4_occ:   7.882  0.057  0.269 82.716  0.033  2.303   6.1652e-02
   5_bss:   7.882  0.057  0.269 82.716  0.033  2.303   6.1652e-02
   5_xyz:   7.704  0.047  0.235 83.787  0.034  2.408   4.0544e-02
   5_adp:   7.704  0.047  0.235 83.787  0.034  2.408   4.0544e-02
   5_occ:   7.704  0.047  0.235 83.787  0.034  2.408   4.0544e-02
   5_bss:   7.704  0.047  0.235 83.787  0.034  2.408   4.0544e-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: 104.78   0.00  19.00  86.71   0.00  14.20 104.78   1.74  45.11
   1_occ: 104.78   0.00  19.00  86.71   0.00  14.20 104.78   1.74  45.11
   2_bss: 104.78   0.00  19.00  86.71   0.00  14.20 104.78   1.74  45.11
   2_xyz: 104.78   0.00  19.00  86.71   0.00  14.20 104.78   1.74  45.11
   2_adp: 103.91   0.00  18.40  89.03   0.00  13.52 103.91   3.52  44.96
   2_occ: 103.91   0.00  18.40  89.03   0.00  13.52 103.91   3.52  44.96
   3_bss: 103.91   0.00  18.40  89.03   0.00  13.52 103.91   3.52  44.96
   3_xyz: 103.91   0.00  18.40  89.03   0.00  13.52 103.91   3.52  44.96
   3_adp:  95.46   1.15  17.62  84.95   1.15  12.89  95.46   5.04  43.37
   3_occ:  95.46   1.15  17.62  84.95   1.15  12.89  95.46   5.04  43.37
   4_bss:  95.46   1.15  17.62  84.95   1.15  12.89  95.46   5.04  43.37
   4_xyz:  95.46   1.15  17.62  84.95   1.15  12.89  95.46   5.04  43.37
   4_adp:  93.61   0.59  17.51  88.36   0.59  12.83  93.61   3.69  43.00
   4_occ:  93.61   0.59  17.51  88.36   0.59  12.83  93.61   3.69  43.00
   5_bss:  93.61   0.59  17.51  88.36   0.59  12.83  93.61   3.69  43.00
   5_xyz:  93.61   0.59  17.51  88.36   0.59  12.83  93.61   3.69  43.00
   5_adp:  91.69   0.97  17.03  87.78   0.97  12.63  91.69   5.68  41.03
   5_occ:  91.69   0.97  17.03  87.78   0.97  12.63  91.69   5.68  41.03
   5_bss:  91.65   0.94  17.00  87.75   0.94  12.59  91.65   5.65  41.00
------------------------------------------------------------------------
 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:    1.571    0.029    0.493
   1_adp:    1.571    0.029    0.493
   1_occ:    1.571    0.029    0.493
   2_bss:    1.571    0.029    0.493
   2_xyz:    1.359    0.050    0.563
   2_adp:    1.359    0.050    0.563
   2_occ:    1.359    0.050    0.563
   3_bss:    1.359    0.050    0.563
   3_xyz:    1.287    0.060    0.664
   3_adp:    1.287    0.060    0.664
   3_occ:    1.287    0.060    0.664
   4_bss:    1.287    0.060    0.664
   4_xyz:    1.433    0.118    0.704
   4_adp:    1.433    0.118    0.704
   4_occ:    1.433    0.118    0.704
   5_bss:    1.433    0.118    0.704
   5_xyz:    1.559    0.112    0.713
   5_adp:    1.559    0.112    0.713
   5_occ:    1.559    0.112    0.713
   5_bss:    1.559    0.112    0.713
------------------------------------------------------------------------

CPU time actual refinement: 334.55


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_879/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_879/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_879/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_879/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_879/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 334.40 
  Macro-tasks:
    bulk solvent and scale       = 50.14  
    individual site refinement   = 130.79 
    weights calculation          = 30.23  
    collect and process          = 6.63   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 217.92 
  Micro-tasks:
    mask                            = 2.35   
    f_calc                          = 101.48 
    alpha_beta                      = 8.39   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 109.57 
    fmodel                         = 7.92   
    r_factors                      = 0.27   
    phase_errors                   = 10.73  
    foms                           = 0.22   
    TOTAL for micro-tasks          = 242.11 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.769 micro seconds
Total CPU time: 5.80 minutes
from_scatterers_fft:    625 calls, 101.22 s
gradients_fft:          570 calls,  96.66 s

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

# Date 2008-01-16 Time 05:53:20 PST -0800 (1200491600.34 s)
Start R-work = 0.4548, R-free = 0.4511 (no bulk solvent and anisotropic scale)
Final R-work = 0.1419, R-free = 0.1844 (no bulk solvent and anisotropic scale)

Start R-work = 0.4446, R-free = 0.4454
Final R-work = 0.1200, R-free = 0.1658