# Date 2008-01-16 Time 06:04:44 PST -0800 (1200492284.70 s)
#phil __OFF__

Command line arguments: "../996.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 8379
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 996

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (71.3037, 46.2261, 86.822, 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: 3.25, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 46.2261, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1778 1.97348
Completeness in resolution range: 0.943912
Completeness with d_max=infinity: 0.941191

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1778
                             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: (71.3037, 46.2261, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1778 1.97348
Completeness in resolution range: 0.943912
Completeness with d_max=infinity: 0.941191

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1782 -  4.2241 [2185/2212]  1965   220  10.1%
  bin  2:  4.2241 -  3.3648 [2096/2116]  1889   207   9.9%
  bin  3:  3.3648 -  2.9430 [2069/2088]  1860   209  10.1%
  bin  4:  2.9430 -  2.6755 [2048/2078]  1842   206  10.1%
  bin  5:  2.6755 -  2.4846 [2036/2055]  1840   196   9.6%
  bin  6:  2.4846 -  2.3387 [2023/2048]  1812   211  10.4%
  bin  7:  2.3387 -  2.2219 [2016/2044]  1817   199   9.9%
  bin  8:  2.2219 -  2.1255 [1998/2034]  1798   200  10.0%
  bin  9:  2.1255 -  2.0439 [2010/2052]  1814   196   9.8%
  bin 10:  2.0439 -  1.9735 [1108/2026]   993   115  10.4%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_996/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: 0.15 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 26
        2.42 -     3.04: 2180
        3.04 -     3.66: 4704
        3.66 -     4.28: 9008
        4.28 -     4.90: 12301
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 201 " - " O   HOH Z 349 "  2.024 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  2.091 3.040 x,y+1,z
  " O   HOH Z  61 " - " O   HOH Z 246 "  2.148 3.040 x,y+1,z
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  ... (remaining 28214 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_996/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_996/model_refine_001.geo

CPU time processing inputs: 9.20


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.30375 46.22605 86.82195 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 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3908   r_free= 0.3865   ksol= 0.00   Bsol= 0.00   scale= 0.936    |
|                                                                             |
| 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:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.182917                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1782 -  4.7119 0.99   1414  158 0.3228 0.3102      6.4377      6.3833|
|  2:  4.7119 -  3.7587 0.99   1357  152 0.3182 0.2905      6.6431      6.5539|
|  3:  3.7587 -  3.2891 0.99   1345  143 0.3359 0.3157       6.486      6.5186|
|  4:  3.2891 -  2.9909 0.99   1331  155 0.3777 0.4138      6.3973        6.45|
|  5:  2.9909 -  2.7779 0.99   1323  149 0.4121 0.3685      6.2568      6.2294|
|  6:  2.7779 -  2.6150 0.99   1306  143 0.3994 0.4309      6.1569      6.1356|
|  7:  2.6150 -  2.4846 0.99   1320  138 0.4239 0.3936      6.1605      6.1099|
|  8:  2.4846 -  2.3769 0.98   1290  147 0.4376 0.4399      6.0911      6.1148|
|  9:  2.3769 -  2.2857 0.98   1282  152 0.4325 0.4502      6.0485      6.0544|
| 10:  2.2857 -  2.2071 1.00   1315  141 0.4490 0.4346      6.0354      5.9911|
| 11:  2.2071 -  2.1382 0.98   1294  138 0.4482 0.4759       5.989      6.0113|
| 12:  2.1382 -  2.0773 0.98   1287  146 0.4598 0.4758      5.9097      5.9613|
| 13:  2.0773 -  2.0227 0.98   1271  139 0.4578 0.4678      5.8227      5.7665|
| 14:  2.0227 -  1.9735 0.38    495   58 0.4896 0.4972      5.8461      5.8376|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1782 -  4.7119  1414   158  0.77  27.47   0.84     0.81      47782.62|
|  2:  4.7119 -  3.7587  1357   152  0.81  25.62   0.94     0.90      61223.79|
|  3:  3.7587 -  3.2891  1345   143  0.73  32.59   0.97     0.90      67787.12|
|  4:  3.2891 -  2.9909  1331   155  0.67  37.92   0.95     0.86      63599.37|
|  5:  2.9909 -  2.7779  1323   149  0.59  44.34   0.94     0.81      54438.74|
|  6:  2.7779 -  2.6150  1306   143  0.60  44.35   0.95     0.79      46179.74|
|  7:  2.6150 -  2.4846  1320   138  0.57  46.37   0.96     0.75      43793.29|
|  8:  2.4846 -  2.3769  1290   147  0.55  48.14   0.95     0.74      40186.69|
|  9:  2.3769 -  2.2857  1282   152  0.55  48.40   0.98     0.75      37763.67|
| 10:  2.2857 -  2.2071  1315   141  0.55  48.39   0.98     0.76      34032.72|
| 11:  2.2071 -  2.1382  1294   138  0.52  50.50   1.00     0.76      34848.38|
| 12:  2.1382 -  2.0773  1287   146  0.48  53.67   0.97     0.70      32817.48|
| 13:  2.0773 -  2.0227  1271   139  0.43  57.67   0.97     0.67      30879.29|
| 14:  2.0227 -  1.9735   495    58  0.45  55.93   0.98     0.63      26351.42|
|alpha:            min =        0.63 max =            0.90 mean =         0.78|
|beta:             min =    26351.42 max =        67787.12 mean =     45447.44|
|figures of merit: min =        0.00 max =            1.00 mean =         0.60|
|phase err.(work): min =        0.00 max =           89.99 mean =        43.61|
|phase err.(test): min =        0.00 max =           89.93 mean =        43.61|
|-----------------------------------------------------------------------------|

============================== 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 = 4.750131              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.058   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.380251              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.653   (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:        3 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       23 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      195 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1985 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1863 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2841 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4628 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4380 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5630 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6671 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.165 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.806 |       0.206 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.952)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.97 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3908   r_free= 0.3865   ksol= 0.00   Bsol= 0.00   scale= 0.936    |
|                                                                             |
| 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:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.182917                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3801   r_free= 0.3803   ksol= 0.33   Bsol= 45.50   scale= 0.965   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.25,1.69,-1.19,0.00,-0.00,-0.00); trace/3= 0.08                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.170544                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.163259              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.266   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.678228              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.441   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3801      final r-factor (work) = 0.2572          |
| start r-factor (free) = 0.3803      final r-factor (free) = 0.2896          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.0063 = 4.16 * 0.50 * 6.1690 + 1.00 * 0.1647                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.5274 = 4.16 * 0.50 * 5.9773 + 1.00 * 0.0848                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2572      final r-factor (work) = 0.2345          |
| start r-factor (free) = 0.2896      final r-factor (free) = 0.3030          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0601 = 0.68 * 1.00 * 5.9773 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9398 = 0.68 * 1.00 * 5.7894 + 1.00 * 0.0133                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.952)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.31   17.95    None  None   None       |
|    all(noH): 2823   0      0.00    96.31   17.95    None  None   None       |
|    Sol.    : 438    0      3.59    96.31   40.41    None  None   None       |
|    Mac.    : 2385   0      0.00    73.47   13.82    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.631:  888   |   5:    48.153 -  57.784:  103        |
|      1:     9.631 -  19.261: 1093   |   6:    57.784 -  67.414:   40        |
|      2:    19.261 -  28.892:  370   |   7:    67.414 -  77.045:   17        |
|      3:    28.892 -  38.523:  164   |   8:    77.045 -  86.676:    6        |
|      4:    38.523 -  48.153:  141   |   9:    86.676 -  96.306:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2345 r_free = 0.3030             target_work(ml) = 5.808         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2341 r_free = 0.3021             target_work(ml) = 5.807         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2341   r_free= 0.3021   ksol= 0.33   Bsol= 45.50   scale= 1.032   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.25,1.69,-1.19,0.00,-0.00,-0.00); trace/3= 0.08                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.806786                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2332   r_free= 0.3004   ksol= 0.34   Bsol= 64.61   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.59,-1.09,-1.26,-0.00,-0.00,-0.00); trace/3= -1.31                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.804313                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.603289              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.486   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.268879              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 142.729  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2332      final r-factor (work) = 0.1762          |
| start r-factor (free) = 0.3004      final r-factor (free) = 0.2292          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6280 = 2.60 * 0.50 * 5.7951 + 1.00 * 0.0848                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.4598 = 2.60 * 0.50 * 5.6868 + 1.00 * 0.0576                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1762      final r-factor (work) = 0.1652          |
| start r-factor (free) = 0.2292      final r-factor (free) = 0.2149          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5424 = 0.27 * 1.00 * 5.6868 + 1.00 * 0.0133                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4919 = 0.27 * 1.00 * 5.5146 + 1.00 * 0.0092                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.952)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.29    94.94   17.48    None  None   None       |
|    all(noH): 2823   0      1.29    94.94   17.48    None  None   None       |
|    Sol.    : 438    0      5.76    94.94   40.16    None  None   None       |
|    Mac.    : 2385   0      1.29    74.74   13.31    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:     1.293 -  10.658: 1087   |   5:    48.118 -  57.483:  100        |
|      1:    10.658 -  20.023: 1032   |   6:    57.483 -  66.848:   35        |
|      2:    20.023 -  29.388:  258   |   7:    66.848 -  76.213:   17        |
|      3:    29.388 -  38.753:  154   |   8:    76.213 -  85.578:    4        |
|      4:    38.753 -  48.118:  135   |   9:    85.578 -  94.943:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1652 r_free = 0.2149             target_work(ml) = 5.484         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1651 r_free = 0.2148             target_work(ml) = 5.484         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1651   r_free= 0.2148   ksol= 0.34   Bsol= 64.61   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.59,-1.09,-1.26,-0.00,-0.00,-0.00); trace/3= -1.31                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.483698                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1653   r_free= 0.2139   ksol= 0.34   Bsol= 64.61   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.92,-2.03,-1.05,-0.00,-0.00,-0.00); trace/3= -1.67                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.482333                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.874876              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.654   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.366556              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 119.205  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1653      final r-factor (work) = 0.1307          |
| start r-factor (free) = 0.2139      final r-factor (free) = 0.1783          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9850 = 2.87 * 0.50 * 5.5149 + 1.00 * 0.0577                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7884 = 2.87 * 0.50 * 5.3789 + 1.00 * 0.0565                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1307      final r-factor (work) = 0.1224          |
| start r-factor (free) = 0.1783      final r-factor (free) = 0.1708          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.7385 = 2.37 * 1.00 * 5.3789 + 1.00 * 0.0091                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.4350 = 2.37 * 1.00 * 5.2498 + 1.00 * 0.0110                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.952)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.81   17.89    None  None   None       |
|    all(noH): 2823   0      0.00    96.81   17.89    None  None   None       |
|    Sol.    : 438    0      6.07    96.81   43.70    None  None   None       |
|    Mac.    : 2385   0      0.00    87.76   13.15    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.681:  975   |   5:    48.406 -  58.087:  111        |
|      1:     9.681 -  19.362: 1141   |   6:    58.087 -  67.768:   70        |
|      2:    19.362 -  29.043:  252   |   7:    67.768 -  77.449:   38        |
|      3:    29.043 -  38.724:  135   |   8:    77.449 -  87.130:   10        |
|      4:    38.724 -  48.406:   86   |   9:    87.130 -  96.811:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1224 r_free = 0.1708             target_work(ml) = 5.228         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1224 r_free = 0.1708             target_work(ml) = 5.228         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1224   r_free= 0.1708   ksol= 0.34   Bsol= 64.61   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.92,-2.03,-1.05,-0.00,-0.00,-0.00); trace/3= -1.67                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.227894                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1227   r_free= 0.1708   ksol= 0.33   Bsol= 64.61   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.13,-2.47,-1.18,-0.00,-0.00,-0.00); trace/3= -1.93                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.228152                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.856768              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 131.002  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.664903              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 122.174  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1227      final r-factor (work) = 0.1137          |
| start r-factor (free) = 0.1708      final r-factor (free) = 0.1623          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5571 = 2.86 * 0.50 * 5.2511 + 1.00 * 0.0565                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.4858 = 2.86 * 0.50 * 5.1961 + 1.00 * 0.0638                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1137      final r-factor (work) = 0.1121          |
| start r-factor (free) = 0.1623      final r-factor (free) = 0.1600          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4658 = 0.66 * 1.00 * 5.1961 + 1.00 * 0.0109                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4424 = 0.66 * 1.00 * 5.1617 + 1.00 * 0.0103                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.952)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    94.46   17.55    None  None   None       |
|    all(noH): 2823   0      0.00    94.46   17.55    None  None   None       |
|    Sol.    : 438    0      5.67    94.46   42.42    None  None   None       |
|    Mac.    : 2385   0      0.00    92.82   12.98    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.446:  940   |   5:    47.232 -  56.678:   94        |
|      1:     9.446 -  18.893: 1182   |   6:    56.678 -  66.125:   64        |
|      2:    18.893 -  28.339:  243   |   7:    66.125 -  75.571:   29        |
|      3:    28.339 -  37.786:  139   |   8:    75.571 -  85.017:   17        |
|      4:    37.786 -  47.232:  107   |   9:    85.017 -  94.464:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1121 r_free = 0.1600             target_work(ml) = 5.154         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1120 r_free = 0.1599             target_work(ml) = 5.154         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1120   r_free= 0.1599   ksol= 0.33   Bsol= 64.61   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.13,-2.47,-1.18,-0.00,-0.00,-0.00); trace/3= -1.93                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.153961                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1120   r_free= 0.1599   ksol= 0.33   Bsol= 64.61   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.05,-2.50,-1.05,-0.00,-0.00,-0.00); trace/3= -1.87                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.153824                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.806123              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 152.099  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.195865              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.234  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1120      final r-factor (work) = 0.1096          |
| start r-factor (free) = 0.1599      final r-factor (free) = 0.1588          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3059 = 2.81 * 0.50 * 5.1617 + 1.00 * 0.0638                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.2838 = 2.81 * 0.50 * 5.1449 + 1.00 * 0.0652                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1096      final r-factor (work) = 0.1104          |
| start r-factor (free) = 0.1588      final r-factor (free) = 0.1574          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0180 = 0.20 * 1.00 * 5.1449 + 1.00 * 0.0103                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0159 = 0.20 * 1.00 * 5.1465 + 1.00 * 0.0079                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.952)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.05    88.08   16.71    None  None   None       |
|    all(noH): 2823   0      1.05    88.08   16.71    None  None   None       |
|    Sol.    : 438    0      6.05    88.08   38.70    None  None   None       |
|    Mac.    : 2385   0      1.05    87.66   12.67    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:     1.054 -   9.757: 1011   |   5:    44.565 -  53.267:   88        |
|      1:     9.757 -  18.459: 1117   |   6:    53.267 -  61.969:   55        |
|      2:    18.459 -  27.161:  242   |   7:    61.969 -  70.672:   23        |
|      3:    27.161 -  35.863:  142   |   8:    70.672 -  79.374:    9        |
|      4:    35.863 -  44.565:  129   |   9:    79.374 -  88.076:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1104 r_free = 0.1574             target_work(ml) = 5.142         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1103 r_free = 0.1572             target_work(ml) = 5.142         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1103   r_free= 0.1572   ksol= 0.33   Bsol= 64.61   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.05,-2.50,-1.05,-0.00,-0.00,-0.00); trace/3= -1.87                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.142018                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1782 -  4.7119 0.99   1414  158 0.0959 0.1314      5.3624      5.5791|
|  2:  4.7119 -  3.7587 0.99   1357  152 0.0848 0.1078      5.4421      5.6199|
|  3:  3.7587 -  3.2891 0.99   1345  143 0.1068 0.1600      5.4781      5.8511|
|  4:  3.2891 -  2.9909 0.99   1331  155 0.1207 0.1660      5.4533      5.6092|
|  5:  2.9909 -  2.7779 0.99   1323  149 0.1326 0.1737      5.3138      5.5778|
|  6:  2.7779 -  2.6150 0.99   1306  143 0.1182 0.1892      5.1836      5.4552|
|  7:  2.6150 -  2.4846 0.99   1320  138 0.1232 0.1576      5.1567      5.3104|
|  8:  2.4846 -  2.3769 0.98   1290  147 0.1152 0.1654      5.0462      5.3174|
|  9:  2.3769 -  2.2857 0.98   1282  152 0.1178 0.1795      5.0342      5.3074|
| 10:  2.2857 -  2.2071 1.00   1315  141 0.1103 0.1694       4.927      5.1936|
| 11:  2.2071 -  2.1382 0.98   1294  138 0.1087 0.1796      4.9278      5.3054|
| 12:  2.1382 -  2.0773 0.98   1287  146 0.1114 0.1589      4.8511      5.0981|
| 13:  2.0773 -  2.0227 0.98   1271  139 0.1143 0.1667      4.7803       5.017|
| 14:  2.0227 -  1.9735 0.38    495   58 0.1036 0.1485       4.677      4.8687|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1782 -  4.7119  1414   158  0.94   9.08   0.97     0.95       7054.00|
|  2:  4.7119 -  3.7587  1357   152  0.95   7.94   1.01     1.00       9290.91|
|  3:  3.7587 -  3.2891  1345   143  0.93  11.33   1.02     1.02      10468.81|
|  4:  3.2891 -  2.9909  1331   155  0.92  14.12   1.00     0.98      10540.56|
|  5:  2.9909 -  2.7779  1323   149  0.90  15.92   0.99     0.98       8179.07|
|  6:  2.7779 -  2.6150  1306   143  0.90  15.90   0.99     0.97       6824.58|
|  7:  2.6150 -  2.4846  1320   138  0.91  15.13   1.00     0.97       6097.96|
|  8:  2.4846 -  2.3769  1290   147  0.91  15.21   0.98     0.96       5063.14|
|  9:  2.3769 -  2.2857  1282   152  0.91  15.42   1.00     0.96       4940.44|
| 10:  2.2857 -  2.2071  1315   141  0.91  15.35   1.00     0.97       4185.88|
| 11:  2.2071 -  2.1382  1294   138  0.91  15.56   0.98     0.94       4198.56|
| 12:  2.1382 -  2.0773  1287   146  0.91  15.41   1.01     1.01       3820.14|
| 13:  2.0773 -  2.0227  1271   139  0.90  16.42   0.99     0.98       3327.22|
| 14:  2.0227 -  1.9735   495    58  0.92  14.36   0.97     0.95       2649.50|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2649.50 max =        10540.56 mean =      6394.48|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.86 mean =        14.01|
|phase err.(test): min =        0.00 max =           89.41 mean =        13.56|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1103   r_free= 0.1572   ksol= 0.32   Bsol= 53.46   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.99,-2.48,-0.92,-0.00,-0.00,-0.00); trace/3= -1.79                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.141857                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1103   r_free= 0.1572   ksol= 0.32   Bsol= 53.46   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.99,-2.48,-0.92,-0.00,-0.00,-0.00); trace/3= -1.79                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.141857                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1782 -  4.7119 0.99   1414  158 0.0953 0.1307      5.3573      5.5736|
|  2:  4.7119 -  3.7587 0.99   1357  152 0.0840 0.1075      5.4351      5.6152|
|  3:  3.7587 -  3.2891 0.99   1345  143 0.1063 0.1595      5.4749      5.8484|
|  4:  3.2891 -  2.9909 0.99   1331  155 0.1207 0.1664      5.4539       5.611|
|  5:  2.9909 -  2.7779 0.99   1323  149 0.1330 0.1743      5.3162      5.5809|
|  6:  2.7779 -  2.6150 0.99   1306  143 0.1186 0.1893      5.1863       5.457|
|  7:  2.6150 -  2.4846 0.99   1320  138 0.1235 0.1578      5.1591      5.3126|
|  8:  2.4846 -  2.3769 0.98   1290  147 0.1155 0.1658      5.0476      5.3188|
|  9:  2.3769 -  2.2857 0.98   1282  152 0.1179 0.1794      5.0353      5.3067|
| 10:  2.2857 -  2.2071 1.00   1315  141 0.1105 0.1702      4.9284       5.197|
| 11:  2.2071 -  2.1382 0.98   1294  138 0.1087 0.1796      4.9289      5.3054|
| 12:  2.1382 -  2.0773 0.98   1287  146 0.1113 0.1590      4.8516      5.0994|
| 13:  2.0773 -  2.0227 0.98   1271  139 0.1144 0.1663      4.7808      5.0165|
| 14:  2.0227 -  1.9735 0.38    495   58 0.1035 0.1490      4.6765      4.8697|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1782 -  4.7119  1414   158  0.94   9.01   0.97     0.95       6960.27|
|  2:  4.7119 -  3.7587  1357   152  0.95   7.88   1.01     1.00       9200.53|
|  3:  3.7587 -  3.2891  1345   143  0.93  11.28   1.02     1.02      10403.53|
|  4:  3.2891 -  2.9909  1331   155  0.92  14.12   1.01     0.98      10539.27|
|  5:  2.9909 -  2.7779  1323   149  0.90  15.96   0.99     0.98       8211.16|
|  6:  2.7779 -  2.6150  1306   143  0.90  15.96   0.99     0.97       6860.74|
|  7:  2.6150 -  2.4846  1320   138  0.91  15.18   1.00     0.97       6132.75|
|  8:  2.4846 -  2.3769  1290   147  0.91  15.23   0.98     0.96       5076.66|
|  9:  2.3769 -  2.2857  1282   152  0.91  15.44   1.00     0.96       4950.71|
| 10:  2.2857 -  2.2071  1315   141  0.91  15.39   1.00     0.97       4197.93|
| 11:  2.2071 -  2.1382  1294   138  0.91  15.59   0.99     0.94       4215.04|
| 12:  2.1382 -  2.0773  1287   146  0.91  15.45   1.01     1.01       3829.79|
| 13:  2.0773 -  2.0227  1271   139  0.90  16.43   1.00     0.98       3330.50|
| 14:  2.0227 -  1.9735   495    58  0.92  14.35   0.97     0.95       2647.03|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2647.03 max =        10539.27 mean =      6387.33|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.95 mean =        14.02|
|phase err.(test): min =        0.00 max =           89.31 mean =        13.57|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.952)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.02    88.04   16.67    None  None   None       |
|    all(noH): 2823   0      1.02    88.04   16.67    None  None   None       |
|    Sol.    : 438    0      6.02    88.04   38.66    None  None   None       |
|    Mac.    : 2385   0      1.02    87.63   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:     1.018 -   9.720: 1011   |   5:    44.529 -  53.231:   88        |
|      1:     9.720 -  18.422: 1117   |   6:    53.231 -  61.933:   55        |
|      2:    18.422 -  27.124:  242   |   7:    61.933 -  70.635:   23        |
|      3:    27.124 -  35.826:  142   |   8:    70.635 -  79.337:    9        |
|      4:    35.826 -  44.529:  129   |   9:    79.337 -  88.039:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 308         
Filter by distance & map next to the model:
   mapped sites are within: 0.444 - 4.698
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 304 from: 308
   mapped sites are within: 0.715 - 4.698

peak=    6.127 closest distance to " NE2 GLN A  11 " =    1.266
peak=    5.605 closest distance to " NH2 ARG A  56 " =    2.095
peak=    5.382 closest distance to " CG  PRO A  54 " =    1.295
peak=    5.203 closest distance to " O   HOH Z 126 " =    1.966
peak=    5.169 closest distance to " O   HOH Z 144 " =    1.753
peak=    5.149 closest distance to " CB  GLN A 223 " =    1.465
peak=    5.149 closest distance to " O   HOH Z 232 " =    2.249
peak=    4.925 closest distance to " CB  SER A  63 " =    1.224
peak=    4.685 closest distance to " O   HOH Z 423 " =    1.795
peak=    4.675 closest distance to " O   HOH Z 236 " =    2.223
peak=    4.662 closest distance to " O   HOH Z 298 " =    2.065
peak=    4.655 closest distance to " CG  PRO A 213 " =    1.263
peak=    4.626 closest distance to " O   HOH Z 369 " =    2.114
peak=    4.625 closest distance to " ND2 ASN A 187 " =    1.523
peak=    4.605 closest distance to " CB  GLN A 183 " =    1.204
peak=    4.585 closest distance to " CB  PRO A  54 " =    0.925
peak=    4.582 closest distance to " C   PRO A 198 " =    1.531
peak=    4.474 closest distance to " O   HOH Z 427 " =    2.763
peak=    4.435 closest distance to " CB  ASN A 148 " =    1.367
peak=    4.412 closest distance to " CB  LEU A 228 " =    1.089
peak=    4.398 closest distance to " CB  ARG A 275 " =    0.923
peak=    4.382 closest distance to " CB  ARG A  79 " =    1.486
peak=    4.345 closest distance to " O   HOH Z  78 " =    1.985
peak=    4.331 closest distance to " CG  TRP A 179 " =    2.226
peak=    4.322 closest distance to " CB  ARG A 190 " =    1.535
peak=    4.300 closest distance to " O   HOH Z   1 " =    1.812
peak=    4.294 closest distance to " O   HOH Z  63 " =    1.442
peak=    4.215 closest distance to " CB  ASN A 187 " =    1.060
peak=    4.212 closest distance to " CD  ARG A 159 " =    0.774
peak=    4.208 closest distance to " CB  GLU A 152 " =    1.237
peak=    4.183 closest distance to " CG  PRO A 198 " =    1.296
peak=    4.140 closest distance to " O   HOH Z   9 " =    2.090
peak=    4.136 closest distance to " O   HOH Z 214 " =    2.103
peak=    4.130 closest distance to " O   HOH Z 133 " =    2.446
peak=    4.127 closest distance to " CB  GLU A 128 " =    1.055
peak=    4.118 closest distance to " CD  ARG A  66 " =    2.107
peak=    4.101 closest distance to " O   HOH Z  10 " =    1.853
peak=    4.096 closest distance to " ND1 HIS A  86 " =    1.648
peak=    4.093 closest distance to " O   HOH Z  40 " =    1.992
peak=    4.046 closest distance to " O   HOH Z 419 " =    2.087
peak=    4.044 closest distance to " O   HOH Z 425 " =    1.354
peak=    4.030 closest distance to " CB  SER A 212 " =    1.183
peak=    4.013 closest distance to " CB  TRP A 266 " =    0.985
peak=    4.001 closest distance to " O   HOH Z 265 " =    2.302
peak=    3.981 closest distance to " O   HOH Z  21 " =    1.710
peak=    3.978 closest distance to " CA  TYR A  30 " =    0.986
peak=    3.972 closest distance to " CA  SER A  87 " =    0.992
peak=    3.959 closest distance to " CE  LYS A  76 " =    0.886
peak=    3.953 closest distance to " O   HOH Z 132 " =    2.416
peak=    3.953 closest distance to " CG2 VAL A 257 " =    0.950
peak=    3.951 closest distance to " O   HOH Z 261 " =    1.896
peak=    3.946 closest distance to " O   HOH Z 316 " =    3.096
peak=    3.945 closest distance to " O   HOH Z 193 " =    1.700
peak=    3.930 closest distance to " CG2 THR A 221 " =    0.984
peak=    3.928 closest distance to " O   HOH Z 250 " =    1.500
peak=    3.928 closest distance to " O   HOH Z 158 " =    3.011
peak=    3.921 closest distance to " N   PHE A 130 " =    1.220
peak=    3.918 closest distance to " CG  LEU A 167 " =    1.266
peak=    3.912 closest distance to " NH1AARG A 145 " =    1.259
peak=    3.906 closest distance to " O   HOH Z 213 " =    1.836
peak=    3.895 closest distance to " CD1 LEU A 300 " =    1.200
peak=    3.892 closest distance to " CB  VAL A 265 " =    1.321
peak=    3.883 closest distance to " O   HOH Z 193 " =    1.868
peak=    3.880 closest distance to " O   HOH Z 209 " =    2.352
peak=    3.870 closest distance to " CG  PRO A 243 " =    1.087
peak=    3.868 closest distance to " CZ  PHE A 218 " =    1.049
peak=    3.865 closest distance to " CB  ASN A  39 " =    0.923
peak=    3.861 closest distance to " O   HOH Z  61 " =    1.599
peak=    3.859 closest distance to " O   ASN A 209 " =    1.367
peak=    3.857 closest distance to " O   HOH Z 371 " =    1.959
peak=    3.846 closest distance to " CG  PRO A  90 " =    1.215
peak=    3.836 closest distance to " O   HOH Z 272 " =    1.818
peak=    3.836 closest distance to " O   HOH Z   7 " =    1.335
peak=    3.832 closest distance to " O   HOH Z 417 " =    1.203
peak=    3.822 closest distance to " O   HOH Z 217 " =    3.151
peak=    3.821 closest distance to " O   HOH Z 380 " =    1.693
peak=    3.814 closest distance to " CD2 TRP A 179 " =    1.249
peak=    3.807 closest distance to " O   HOH Z   2 " =    1.571
peak=    3.796 closest distance to " O   HOH Z 234 " =    3.755
peak=    3.791 closest distance to " OD1 ASN A  69 " =    2.682
peak=    3.763 closest distance to " O   HOH Z   1 " =    1.809
peak=    3.753 closest distance to " O   HOH Z 180 " =    2.014
peak=    3.753 closest distance to " CB  SER A   3 " =    1.464
peak=    3.745 closest distance to " CB  ASP A 124 " =    0.883
peak=    3.743 closest distance to " CB  ASN A 142 " =    0.934
peak=    3.731 closest distance to " CD1 LEU A 255 " =    1.755
peak=    3.727 closest distance to " O   HOH Z 346 " =    1.659
peak=    3.727 closest distance to " O   HOH Z 437 " =    1.632
peak=    3.721 closest distance to " CB  ALA A  34 " =    1.132
peak=    3.719 closest distance to " CA  THR A 264 " =    0.881
peak=    3.699 closest distance to " CB  SER A 216 " =    0.821
peak=    3.695 closest distance to " O   HOH Z 426 " =    1.905
peak=    3.682 closest distance to " O   HOH Z 368 " =    3.623
peak=    3.677 closest distance to " O   HOH Z  88 " =    3.619
peak=    3.668 closest distance to " O   HOH Z 116 " =    3.085
peak=    3.663 closest distance to " O   HOH Z 389 " =    1.954
peak=    3.659 closest distance to " O   HOH Z  58 " =    1.778
peak=    3.656 closest distance to " O   HOH Z 411 " =    3.732
peak=    3.647 closest distance to " CA  ALA A 233 " =    1.249
peak=    3.639 closest distance to " CB  ALA A   1 " =    4.698
peak=    3.627 closest distance to " O   HOH Z 362 " =    2.309
peak=    3.627 closest distance to " CB  GLU A 277 " =    3.630
peak=    3.623 closest distance to " O   HOH Z 327 " =    1.680
peak=    3.609 closest distance to " O   HOH Z 147 " =    1.832
peak=    3.600 closest distance to " CD BLYS A 290 " =    1.037
peak=    3.588 closest distance to " CB  TYR A 169 " =    0.859
peak=    3.581 closest distance to " O   HOH Z 258 " =    2.258
peak=    3.579 closest distance to " O   HOH Z 219 " =    2.068
peak=    3.576 closest distance to " O   HOH Z 403 " =    1.647
peak=    3.574 closest distance to " O   HOH Z 345 " =    1.743
peak=    3.571 closest distance to " O   HOH Z 423 " =    2.237
peak=    3.571 closest distance to " O   HOH Z  61 " =    1.489
peak=    3.567 closest distance to " CB  TYR A 169 " =    0.715
peak=    3.565 closest distance to " CA  ASN A 215 " =    1.208
peak=    3.565 closest distance to " O   HOH Z 175 " =    2.155
peak=    3.564 closest distance to " O   HOH Z 386 " =    2.950
peak=    3.561 closest distance to " CB  ASP A 140 " =    0.858
peak=    3.552 closest distance to " O   HOH Z 291 " =    1.505
peak=    3.552 closest distance to " O   HOH Z 193 " =    2.063
peak=    3.541 closest distance to " CA  TYR A 116 " =    1.353
peak=    3.537 closest distance to " CB  TRP A 150 " =    1.293
peak=    3.535 closest distance to " CG  MET A 113 " =    1.403
peak=    3.532 closest distance to " CA  ARG A 195 " =    1.288
peak=    3.526 closest distance to " CA  PRO A  54 " =    1.346
peak=    3.525 closest distance to " O   SER A  87 " =    2.416
peak=    3.520 closest distance to " NH2AARG A 190 " =    1.874
peak=    3.517 closest distance to " O   HOH Z 133 " =    1.671
peak=    3.512 closest distance to " CG1 ILE A  33 " =    1.252
peak=    3.511 closest distance to " NZ  LYS A  76 " =    1.572
peak=    3.510 closest distance to " CA  ALA A 158 " =    1.146
peak=    3.509 closest distance to " O   HOH Z 286 " =    2.187
peak=    3.505 closest distance to " CD  ARG A 269 " =    0.942
peak=    3.500 closest distance to " CB  ASN A 110 " =    1.079
peak=    3.489 closest distance to " OD2 ASP A 286 " =    2.848
peak=    3.487 closest distance to " CB  GLN A  88 " =    1.240
peak=    3.481 closest distance to " NH2 ARG A 156 " =    1.203
peak=    3.474 closest distance to " CB  SER A  62 " =    1.134
peak=    3.471 closest distance to " O   HOH Z 128 " =    1.897
peak=    3.467 closest distance to " CG2AVAL A  72 " =    1.532
peak=    3.464 closest distance to " O   HOH Z 373 " =    1.570
peak=    3.463 closest distance to " CB  MET A  47 " =    1.086
peak=    3.457 closest distance to " O   HOH Z 371 " =    2.772
peak=    3.452 closest distance to " O   HOH Z 368 " =    1.982
peak=    3.452 closest distance to " O   HOH Z  44 " =    2.858
peak=    3.446 closest distance to " OD1BASN A 224 " =    2.347
peak=    3.441 closest distance to " CB  ARG A 139 " =    1.019
peak=    3.434 closest distance to " CB  ILE A 120 " =    1.320
peak=    3.432 closest distance to " O   HOH Z 305 " =    3.621
peak=    3.429 closest distance to " O   HOH Z 391 " =    2.901
peak=    3.429 closest distance to " CB  ALA A 248 " =    0.964
peak=    3.426 closest distance to " N   GLN A 278 " =    1.257
peak=    3.425 closest distance to " CB  VAL A 202 " =    1.636
peak=    3.425 closest distance to " O   HOH Z 189 " =    2.529
peak=    3.420 closest distance to " CB  GLU A  46 " =    0.937
peak=    3.418 closest distance to " CD  PRO A 243 " =    1.682
peak=    3.416 closest distance to " O   TYR A 116 " =    1.376
peak=    3.416 closest distance to " O   HOH Z 365 " =    2.796
peak=    3.407 closest distance to " CB  MET A  40 " =    0.784
peak=    3.406 closest distance to " CD  LYS A 166 " =    1.273
peak=    3.406 closest distance to " NE2 GLN A  73 " =    3.830
peak=    3.404 closest distance to " O   HOH Z 285 " =    2.531
peak=    3.401 closest distance to " NH2BARG A 145 " =    2.054
peak=    3.397 closest distance to " O   HOH Z 352 " =    1.746
peak=    3.392 closest distance to " CA  MET A  40 " =    1.216
peak=    3.392 closest distance to " CG1 VAL A 189 " =    1.838
peak=    3.387 closest distance to " O   HOH Z 425 " =    1.911
peak=    3.381 closest distance to " O  BHOH Z 338 " =    2.385
peak=    3.378 closest distance to " O   HOH Z  59 " =    1.907
peak=    3.376 closest distance to " N   ALA A   1 " =    2.035
peak=    3.375 closest distance to " N   ASN A 127 " =    1.268
peak=    3.374 closest distance to " O   HOH Z  68 " =    2.090
peak=    3.373 closest distance to " CD1 ILE A 263 " =    1.309
peak=    3.372 closest distance to " CB  SER A 210 " =    0.725
peak=    3.369 closest distance to " CB  LEU A 143 " =    1.110
peak=    3.367 closest distance to " ND2 ASN A 249 " =    0.869
peak=    3.366 closest distance to " CA  ALA A 154 " =    0.966
peak=    3.360 closest distance to " O   HOH Z 128 " =    2.193
peak=    3.359 closest distance to " O   HOH Z   3 " =    1.886
peak=    3.359 closest distance to " NE2 HIS A 207 " =    1.315
peak=    3.353 closest distance to " CD2 LEU A 297 " =    0.945
peak=    3.351 closest distance to " CB  TYR A 116 " =    0.892
peak=    3.350 closest distance to " CA  ALA A 291 " =    0.899
peak=    3.349 closest distance to " O   HOH Z 128 " =    2.086
peak=    3.348 closest distance to " CA  ARG A 102 " =    1.137
peak=    3.348 closest distance to " CG  GLN A 278 " =    1.385
peak=    3.343 closest distance to " O   HOH Z 188 " =    2.258
peak=    3.343 closest distance to " N   CYS A 260 " =    0.799
peak=    3.343 closest distance to " CA  THR A 221 " =    0.972
peak=    3.341 closest distance to " O   HOH Z 409 " =    2.336
peak=    3.340 closest distance to " O   HOH Z 172 " =    2.983
peak=    3.339 closest distance to " CB  THR A 157 " =    1.182
peak=    3.332 closest distance to " O   HOH Z 238 " =    3.687
peak=    3.331 closest distance to " CB  GLU A 236 " =    1.078
peak=    3.328 closest distance to " CB  ASP A 171 " =    0.716
peak=    3.325 closest distance to " O   HOH Z 126 " =    1.446
peak=    3.324 closest distance to " O   MET A 105 " =    1.630
peak=    3.319 closest distance to " CZ3 TRP A 123 " =    1.376
peak=    3.317 closest distance to " CB  LYS A 117 " =    1.243
peak=    3.312 closest distance to " O   HOH Z 148 " =    3.384
peak=    3.306 closest distance to " O   HOH Z 345 " =    3.437
peak=    3.304 closest distance to " CD  ARG A 219 " =    1.092
peak=    3.303 closest distance to " CB  ALA A 114 " =    1.063
peak=    3.302 closest distance to " O   HOH Z 135 " =    1.709
peak=    3.301 closest distance to " O   HOH Z 273 " =    2.842
peak=    3.300 closest distance to " O   HOH Z 146 " =    1.647
peak=    3.300 closest distance to " O   HOH Z 218 " =    4.465
peak=    3.296 closest distance to " O   HOH Z 145 " =    2.249
peak=    3.295 closest distance to " O   HOH Z  85 " =    2.208
peak=    3.289 closest distance to " O   HOH Z 405 " =    1.374
peak=    3.289 closest distance to " CD2 TYR A 186 " =    1.003
peak=    3.285 closest distance to " O   HOH Z 207 " =    1.799
peak=    3.282 closest distance to " CA  ASP A 162 " =    1.017
peak=    3.282 closest distance to " CG2 ILE A 151 " =    0.845
peak=    3.273 closest distance to " CB  THR A  82 " =    1.403
peak=    3.272 closest distance to " CG BARG A 275 " =    1.439
peak=    3.269 closest distance to " CB  ALA A 233 " =    1.339
peak=    3.267 closest distance to " CG1 ILE A 151 " =    1.126
peak=    3.266 closest distance to " CD1 ILE A 106 " =    0.809
peak=    3.265 closest distance to " O   ARG A 145 " =    1.693
peak=    3.257 closest distance to " O   HOH Z 386 " =    2.938
peak=    3.255 closest distance to " O   HOH Z 286 " =    2.295
peak=    3.254 closest distance to " CB  ALA A 114 " =    1.433
peak=    3.253 closest distance to " O   HOH Z  53 " =    2.535
peak=    3.253 closest distance to " ND1 HIS A  81 " =    1.617
peak=    3.248 closest distance to " O   HOH Z 294 " =    1.501
peak=    3.247 closest distance to " N   ARG A 156 " =    1.345
peak=    3.246 closest distance to " OG  SER A  22 " =    2.864
peak=    3.244 closest distance to " O   HOH Z 406 " =    1.642
peak=    3.243 closest distance to " OG  SER A  62 " =    3.008
peak=    3.243 closest distance to " CA  GLU A  46 " =    0.831
peak=    3.240 closest distance to " O   HOH Z 329 " =    3.855
peak=    3.239 closest distance to " CA  ASN A 217 " =    1.149
peak=    3.235 closest distance to " CB  TRP A 179 " =    1.498
peak=    3.232 closest distance to " CA  SER A  95 " =    0.995
peak=    3.232 closest distance to " CA  TYR A  30 " =    1.050
peak=    3.230 closest distance to " O   HOH Z 344 " =    3.191
peak=    3.228 closest distance to " O   HOH Z 213 " =    2.127
peak=    3.226 closest distance to " O   HOH Z 356 " =    2.862
peak=    3.224 closest distance to " O   HOH Z 116 " =    1.721
peak=    3.223 closest distance to " O   THR A 251 " =    1.184
peak=    3.221 closest distance to " O   HOH Z 325 " =    3.900
peak=    3.219 closest distance to " CG1 VAL A 153 " =    0.925
peak=    3.218 closest distance to " CB  SER A 276 " =    1.122
peak=    3.218 closest distance to " O   HOH Z 302 " =    1.810
peak=    3.218 closest distance to " CA  LYS A 290 " =    1.297
peak=    3.216 closest distance to " O   HOH Z  88 " =    2.760
peak=    3.213 closest distance to " CG2 ILE A  20 " =    1.357
peak=    3.212 closest distance to " CD  ARG A 138 " =    0.781
peak=    3.210 closest distance to " O   HOH Z  64 " =    2.227
peak=    3.208 closest distance to " CA  ALA A 299 " =    0.866
peak=    3.205 closest distance to " O   HOH Z 109 " =    2.587
peak=    3.202 closest distance to " O   HOH Z 359 " =    4.114
peak=    3.201 closest distance to " O   HOH Z 407 " =    2.160
peak=    3.201 closest distance to " O   HOH Z 153 " =    1.656
peak=    3.200 closest distance to " O   THR A 294 " =    1.031
peak=    3.200 closest distance to " CG  ARG A 159 " =    0.837
peak=    3.198 closest distance to " N   SER A 134 " =    1.331
peak=    3.197 closest distance to " NH2 ARG A 219 " =    1.846
peak=    3.197 closest distance to " CZ  PHE A  38 " =    1.280
peak=    3.196 closest distance to " O   HOH Z 227 " =    2.037
peak=    3.195 closest distance to " O   HOH Z  20 " =    1.766
peak=    3.194 closest distance to " O   HOH Z 149 " =    2.135
peak=    3.185 closest distance to " CG BARG A 102 " =    1.912
peak=    3.182 closest distance to " O   HOH Z 130 " =    2.116
peak=    3.182 closest distance to " O   HOH Z 368 " =    4.255
peak=    3.180 closest distance to " CG2 ILE A 120 " =    1.204
peak=    3.179 closest distance to " CD  GLN A 240 " =    1.639
peak=    3.178 closest distance to " O   HOH Z 274 " =    2.076
peak=    3.178 closest distance to " O   HOH Z 217 " =    1.567
peak=    3.178 closest distance to " CB  ARG A 138 " =    0.961
peak=    3.178 closest distance to " CA  MET A 105 " =    0.893
peak=    3.175 closest distance to " CA  ALA A  21 " =    1.219
peak=    3.171 closest distance to " CZ3 TRP A 266 " =    1.120
peak=    3.169 closest distance to " CB  ASN A 215 " =    1.098
peak=    3.167 closest distance to " O   HOH Z 291 " =    1.941
peak=    3.166 closest distance to " O   HOH Z 422 " =    2.692
peak=    3.158 closest distance to " CA  ILE A 234 " =    0.963
peak=    3.156 closest distance to " NE2 GLN A  58 " =    3.808
peak=    3.153 closest distance to " CG  GLN A 278 " =    3.567
peak=    3.146 closest distance to " O   HOH Z 115 " =    1.862
peak=    3.144 closest distance to " O   HOH Z 113 " =    1.998
peak=    3.143 closest distance to " CG  GLU A 277 " =    2.065
peak=    3.142 closest distance to " CG  GLN A  77 " =    2.297
peak=    3.134 closest distance to " O   HOH Z 130 " =    3.796
peak=    3.133 closest distance to " CG  LYS A  76 " =    0.934
peak=    3.132 closest distance to " OG BSER A 164 " =    2.404
peak=    3.128 closest distance to " O   HOH Z 280 " =    3.079
peak=    3.122 closest distance to " NH1 ARG A 138 " =    1.095
peak=    3.105 closest distance to " O   HOH Z  44 " =    1.585
peak=    3.104 closest distance to " CB  PRO A 243 " =    1.149
peak=    3.103 closest distance to " CB  HIS A 108 " =    0.760
peak=    3.091 closest distance to " O   HOH Z  50 " =    1.579
peak=    3.090 closest distance to " O   HOH Z  30 " =    1.669
peak=    3.080 closest distance to " O   HOH Z 415 " =    3.802
peak=    3.079 closest distance to " CB  ASN A 224 " =    1.041
peak=    3.077 closest distance to " O   HOH Z 295 " =    1.565
peak=    3.068 closest distance to " NH1BARG A 145 " =    1.285
peak=    3.068 closest distance to " O   HOH Z 271 " =    2.518
peak=    3.066 closest distance to " CA  ILE A 106 " =    0.789
peak=    3.064 closest distance to " O   HOH Z  97 " =    2.024
peak=    3.062 closest distance to " CB  ALA A  43 " =    0.836
peak=    3.051 closest distance to " O   HOH Z 132 " =    3.685
peak=    3.048 closest distance to " CA  ASP A 140 " =    1.264
peak=    3.033 closest distance to " OD1 ASN A 217 " =    1.562

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 215         
Filter by distance & map next to the model:
   mapped sites are within: 0.468 - 5.913
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 213 from: 215
   mapped sites are within: 0.712 - 5.913

peak=   -4.884 closest distance to " CB  PRO A 243 " =    2.561
peak=   -4.550 closest distance to " O   HOH Z 290 " =    1.068
peak=   -4.460 closest distance to " O   HOH Z 377 " =    1.963
peak=   -4.293 closest distance to " O   HOH Z 389 " =    2.015
peak=   -4.289 closest distance to " O   HOH Z 266 " =    5.113
peak=   -4.270 closest distance to " CD  ARG A 156 " =    2.109
peak=   -4.251 closest distance to " O   HOH Z 435 " =    2.946
peak=   -4.190 closest distance to " CD  ARG A  14 " =    3.468
peak=   -4.186 closest distance to " O   PRO A 198 " =    1.285
peak=   -4.184 closest distance to " O   HOH Z 231 " =    2.118
peak=   -4.075 closest distance to " O   HOH Z  38 " =    1.403
peak=   -4.057 closest distance to " O   VAL A  67 " =    2.656
peak=   -4.036 closest distance to " CG  GLN A 223 " =    1.995
peak=   -3.999 closest distance to " O   HOH Z 407 " =    3.275
peak=   -3.987 closest distance to " CB  ALA A  43 " =    2.533
peak=   -3.979 closest distance to " CZ3 TRP A 179 " =    1.142
peak=   -3.965 closest distance to " N   ALA A  43 " =    2.630
peak=   -3.948 closest distance to " O   HOH Z 351 " =    1.552
peak=   -3.920 closest distance to " O   HOH Z 231 " =    0.991
peak=   -3.901 closest distance to " O   HOH Z  52 " =    1.264
peak=   -3.870 closest distance to " CG1 VAL A 112 " =    2.948
peak=   -3.863 closest distance to " O   HOH Z 176 " =    0.712
peak=   -3.821 closest distance to " OG BSER A 134 " =    1.324
peak=   -3.816 closest distance to " O   HOH Z 185 " =    2.141
peak=   -3.808 closest distance to " CD  ARG A 195 " =    5.150
peak=   -3.769 closest distance to " CA  GLY A  98 " =    1.854
peak=   -3.763 closest distance to " C   HIS A 108 " =    1.222
peak=   -3.760 closest distance to " O   HOH Z 282 " =    0.844
peak=   -3.755 closest distance to " N   THR A 157 " =    1.564
peak=   -3.737 closest distance to " ND2 ASN A 249 " =    2.128
peak=   -3.729 closest distance to " OD1 ASP A 191 " =    1.837
peak=   -3.723 closest distance to " ND2 ASN A  45 " =    1.974
peak=   -3.717 closest distance to " CB  TRP A  85 " =    2.453
peak=   -3.717 closest distance to " OG BSER A 134 " =    1.662
peak=   -3.710 closest distance to " N   ASP A 171 " =    2.424
peak=   -3.709 closest distance to " O   VAL A 189 " =    2.503
peak=   -3.701 closest distance to " CA  GLY A 241 " =    2.294
peak=   -3.697 closest distance to " CG  PHE A 283 " =    2.695
peak=   -3.692 closest distance to " O   HOH Z 372 " =    2.488
peak=   -3.689 closest distance to " O   HOH Z 211 " =    1.446
peak=   -3.687 closest distance to " CE2 PHE A 218 " =    2.468
peak=   -3.684 closest distance to " CE2 TYR A  30 " =    2.596
peak=   -3.666 closest distance to " O   HOH Z 377 " =    0.736
peak=   -3.658 closest distance to " O   HOH Z 313 " =    1.774
peak=   -3.633 closest distance to " CG  MET A 105 " =    0.991
peak=   -3.625 closest distance to " O   PRO A 198 " =    1.321
peak=   -3.625 closest distance to " O   HOH Z 359 " =    3.263
peak=   -3.622 closest distance to " O   TYR A 247 " =    2.878
peak=   -3.598 closest distance to " CB  CYS A 254 " =    2.165
peak=   -3.591 closest distance to " CB  ASP A  27 " =    2.441
peak=   -3.589 closest distance to " O   HOH Z  73 " =    2.078
peak=   -3.588 closest distance to " C   ASN A 285 " =    2.401
peak=   -3.587 closest distance to " C   ALA A 158 " =    1.587
peak=   -3.582 closest distance to " CB  ALA A 291 " =    2.186
peak=   -3.579 closest distance to " O   HOH Z  51 " =    1.056
peak=   -3.573 closest distance to " O   PHE A 218 " =    1.522
peak=   -3.565 closest distance to " CB  ALA A   9 " =    2.413
peak=   -3.561 closest distance to " O   HOH Z 351 " =    1.701
peak=   -3.550 closest distance to " NH2 ARG A  79 " =    1.955
peak=   -3.543 closest distance to " CB  ALA A 248 " =    2.432
peak=   -3.543 closest distance to " CG2 THR A  18 " =    2.865
peak=   -3.539 closest distance to " CG1 VAL A 197 " =    2.229
peak=   -3.536 closest distance to " CB  PRO A 163 " =    2.486
peak=   -3.536 closest distance to " CB  PRO A  54 " =    2.468
peak=   -3.524 closest distance to " CD1 PHE A  59 " =    1.969
peak=   -3.522 closest distance to " O   HOH Z 140 " =    1.370
peak=   -3.520 closest distance to " NH2AARG A 275 " =    5.449
peak=   -3.514 closest distance to " O   PRO A 163 " =    1.961
peak=   -3.513 closest distance to " O   HOH Z 298 " =    2.459
peak=   -3.493 closest distance to " O   PRO A 243 " =    2.454
peak=   -3.493 closest distance to " CD  GLU A 277 " =    1.108
peak=   -3.492 closest distance to " CD2 LEU A 143 " =    2.594
peak=   -3.488 closest distance to " OD1 ASN A 148 " =    1.585
peak=   -3.481 closest distance to " CG  TRP A 266 " =    1.713
peak=   -3.479 closest distance to " CZ BARG A 275 " =    1.690
peak=   -3.474 closest distance to " ND2 ASN A  45 " =    1.272
peak=   -3.469 closest distance to " OD1 ASP A 171 " =    1.671
peak=   -3.461 closest distance to " CA  GLY A 203 " =    2.328
peak=   -3.460 closest distance to " CD2 PHE A  61 " =    2.004
peak=   -3.460 closest distance to " CD  GLN A  58 " =    0.947
peak=   -3.457 closest distance to " CE  MET A 105 " =    2.364
peak=   -3.451 closest distance to " O   HOH Z 337 " =    1.393
peak=   -3.450 closest distance to " NH1AARG A 275 " =    1.873
peak=   -3.449 closest distance to " O   HOH Z 394 " =    1.418
peak=   -3.446 closest distance to " O   HOH Z 111 " =    1.773
peak=   -3.446 closest distance to " CE2 PHE A  61 " =    2.662
peak=   -3.439 closest distance to " CD1 LEU A 101 " =    2.285
peak=   -3.433 closest distance to " O   HOH Z 281 " =    2.685
peak=   -3.432 closest distance to " OG  SER A  87 " =    1.287
peak=   -3.417 closest distance to " CG  PRO A 163 " =    2.508
peak=   -3.391 closest distance to " CD  GLN A  88 " =    0.852
peak=   -3.390 closest distance to " O   VAL A  67 " =    2.865
peak=   -3.382 closest distance to " O   HOH Z 198 " =    1.577
peak=   -3.380 closest distance to " CB  PHE A 192 " =    1.966
peak=   -3.377 closest distance to " O   HOH Z  11 " =    1.917
peak=   -3.376 closest distance to " O   HOH Z  65 " =    1.191
peak=   -3.374 closest distance to " O   HOH Z 377 " =    0.999
peak=   -3.373 closest distance to " C   LEU A 222 " =    0.746
peak=   -3.373 closest distance to " O   ALA A  10 " =    1.685
peak=   -3.372 closest distance to " CB  ALA A 161 " =    2.640
peak=   -3.369 closest distance to " CA  GLY A 133 " =    2.077
peak=   -3.359 closest distance to " CG2 THR A 178 " =    2.242
peak=   -3.358 closest distance to " NE2 GLN A 278 " =    1.770
peak=   -3.355 closest distance to " ND2 ASN A 285 " =    2.090
peak=   -3.354 closest distance to " O   GLY A  17 " =    1.228
peak=   -3.352 closest distance to " O   ILE A  49 " =    1.750
peak=   -3.350 closest distance to " O   SER A  22 " =    2.533
peak=   -3.350 closest distance to " CG1 VAL A 250 " =    2.651
peak=   -3.348 closest distance to " O   HOH Z 266 " =    4.859
peak=   -3.346 closest distance to " N   GLN A  58 " =    1.810
peak=   -3.345 closest distance to " CG  ASP A 231 " =    0.730
peak=   -3.343 closest distance to " OG  SER A  97 " =    2.147
peak=   -3.341 closest distance to " O   HOH Z  10 " =    1.410
peak=   -3.339 closest distance to " CZ  TYR A 169 " =    1.618
peak=   -3.338 closest distance to " O   HOH Z 174 " =    2.573
peak=   -3.334 closest distance to " CD2 TYR A 293 " =    1.973
peak=   -3.328 closest distance to " CG  ARG A 269 " =    2.622
peak=   -3.325 closest distance to " O   HOH Z 368 " =    1.662
peak=   -3.323 closest distance to " CA  GLY A 241 " =    3.101
peak=   -3.323 closest distance to " O   HOH Z 168 " =    1.807
peak=   -3.322 closest distance to " CB  ASN A  39 " =    2.275
peak=   -3.311 closest distance to " CG1 VAL A 112 " =    2.583
peak=   -3.300 closest distance to " CD  GLU A 152 " =    0.888
peak=   -3.299 closest distance to " CD1 LEU A 228 " =    2.309
peak=   -3.297 closest distance to " O   HOH Z 191 " =    5.569
peak=   -3.290 closest distance to " CB  ALA A 248 " =    2.000
peak=   -3.286 closest distance to " CG2 ILE A  49 " =    2.678
peak=   -3.285 closest distance to " CE1 TYR A 169 " =    2.554
peak=   -3.284 closest distance to " O   HOH Z 166 " =    1.301
peak=   -3.276 closest distance to " O   GLY A 211 " =    1.329
peak=   -3.275 closest distance to " CE3 TRP A 274 " =    2.462
peak=   -3.274 closest distance to " O   HOH Z 298 " =    1.149
peak=   -3.274 closest distance to " O   ARG A 145 " =    1.507
peak=   -3.272 closest distance to " CE  LYS A  76 " =    2.814
peak=   -3.272 closest distance to " OE1 GLN A  88 " =    1.215
peak=   -3.271 closest distance to " O   HOH Z 275 " =    1.742
peak=   -3.268 closest distance to " O   SER A 135 " =    1.436
peak=   -3.268 closest distance to " OXT GLY A 302 " =    3.168
peak=   -3.265 closest distance to " O   HOH Z   9 " =    1.762
peak=   -3.265 closest distance to " O   HOH Z 243 " =    2.022
peak=   -3.264 closest distance to " O   ALA A 180 " =    1.201
peak=   -3.264 closest distance to " CG2 THR A 157 " =    2.203
peak=   -3.262 closest distance to " ND2BASN A 224 " =    1.718
peak=   -3.258 closest distance to " O   HOH Z  90 " =    2.706
peak=   -3.258 closest distance to " O   HOH Z 390 " =    2.398
peak=   -3.257 closest distance to " O   HOH Z 198 " =    2.019
peak=   -3.257 closest distance to " CD  ARG A 139 " =    1.555
peak=   -3.257 closest distance to " O   HOH Z 357 " =    2.032
peak=   -3.255 closest distance to " O   HOH Z 384 " =    2.729
peak=   -3.252 closest distance to " ND2 ASN A  60 " =    1.446
peak=   -3.250 closest distance to " O   HOH Z 409 " =    5.913
peak=   -3.250 closest distance to " O   HOH Z 426 " =    1.634
peak=   -3.243 closest distance to " C   GLY A  13 " =    0.961
peak=   -3.239 closest distance to " O   HOH Z  43 " =    1.663
peak=   -3.237 closest distance to " O   HOH Z 353 " =    2.088
peak=   -3.235 closest distance to " NE  ARG A  36 " =    2.004
peak=   -3.234 closest distance to " O   HOH Z 317 " =    1.554
peak=   -3.232 closest distance to " OH  TYR A 172 " =    1.752
peak=   -3.230 closest distance to " O   HOH Z 198 " =    0.837
peak=   -3.229 closest distance to " O   HOH Z 348 " =    1.757
peak=   -3.221 closest distance to " O   SER A 210 " =    1.967
peak=   -3.210 closest distance to " O   HOH Z 218 " =    3.563
peak=   -3.200 closest distance to " CG2 ILE A  20 " =    2.885
peak=   -3.196 closest distance to " C   ASN A 187 " =    1.878
peak=   -3.189 closest distance to " O   HOH Z 383 " =    1.106
peak=   -3.188 closest distance to " O   HOH Z 356 " =    2.348
peak=   -3.185 closest distance to " O   HOH Z 323 " =    1.472
peak=   -3.180 closest distance to " CB  PHE A 208 " =    2.285
peak=   -3.179 closest distance to " CD1 LEU A 297 " =    2.528
peak=   -3.174 closest distance to " CB  TYR A  15 " =    2.244
peak=   -3.174 closest distance to " CE BMET A  47 " =    1.629
peak=   -3.165 closest distance to " O   HOH Z 292 " =    1.624
peak=   -3.165 closest distance to " O   HOH Z 118 " =    1.344
peak=   -3.163 closest distance to " CB  ALA A 291 " =    2.311
peak=   -3.161 closest distance to " CE3 TRP A 274 " =    1.004
peak=   -3.159 closest distance to " CD  LYS A 289 " =    2.358
peak=   -3.158 closest distance to " CE3 TRP A 123 " =    1.326
peak=   -3.157 closest distance to " CZ  PHE A  59 " =    1.591
peak=   -3.156 closest distance to " CE  MET A  93 " =    1.207
peak=   -3.155 closest distance to " O   TRP A  70 " =    1.477
peak=   -3.155 closest distance to " O   ASP A 162 " =    2.254
peak=   -3.154 closest distance to " CG  GLN A 240 " =    2.448
peak=   -3.154 closest distance to " O   HOH Z  60 " =    0.996
peak=   -3.154 closest distance to " O   HOH Z 111 " =    1.206
peak=   -3.148 closest distance to " CB  CYS A 201 " =    2.475
peak=   -3.148 closest distance to " OD2 ASP A 171 " =    2.157
peak=   -3.147 closest distance to " O   HOH Z 345 " =    2.220
peak=   -3.146 closest distance to " O   HOH Z  13 " =    1.668
peak=   -3.141 closest distance to " O   HOH Z 253 " =    4.009
peak=   -3.139 closest distance to " CD2 PHE A 225 " =    1.090
peak=   -3.138 closest distance to " O   HOH Z  53 " =    1.677
peak=   -3.138 closest distance to " OG  SER A 245 " =    1.244
peak=   -3.136 closest distance to " O   VAL A 197 " =    1.727
peak=   -3.129 closest distance to " O   HOH Z 371 " =    1.457
peak=   -3.117 closest distance to " CD1 ILE A 199 " =    2.706
peak=   -3.113 closest distance to " CH2 TRP A 177 " =    2.214
peak=   -3.110 closest distance to " O   HOH Z 282 " =    4.727
peak=   -3.109 closest distance to " O   ASN A 301 " =    1.428
peak=   -3.105 closest distance to " CD1 TYR A 247 " =    2.944
peak=   -3.090 closest distance to " O   HOH Z 241 " =    1.326
peak=   -3.084 closest distance to " O   HOH Z 247 " =    0.827
peak=   -3.083 closest distance to " C   MET A 188 " =    1.565
peak=   -3.080 closest distance to " OE1 GLN A  58 " =    3.125
peak=   -3.079 closest distance to " O   HOH Z  60 " =    1.971
peak=   -3.074 closest distance to " CB  ASP A 132 " =    2.361
peak=   -3.072 closest distance to " O   HOH Z 252 " =    4.248
peak=   -3.068 closest distance to " N   ASP A 270 " =    1.379
peak=   -3.066 closest distance to " O   HOH Z 193 " =    1.496
peak=   -3.057 closest distance to " C   ALA A 114 " =    2.335
peak=   -3.057 closest distance to " O   LYS A 289 " =    3.141
peak=   -3.047 closest distance to " N   ALA A 226 " =    2.133
peak=   -3.043 closest distance to " CG1 VAL A 197 " =    2.138
peak=   -3.039 closest distance to " OD2 ASP A 171 " =    1.858

================= 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    :  0.3908 0.3865   6.182917e+00   6.171181e+00
   1_bss:  0.3801 0.3803   6.170544e+00   6.156687e+00
   1_xyz:  0.2572 0.2896   5.855466e+00   5.922357e+00
   1_adp:  0.2345 0.3030   5.808026e+00   5.959826e+00
   1_occ:  0.2341 0.3021   5.806786e+00   5.958861e+00
   2_bss:  0.2332 0.3004   5.804313e+00   5.953821e+00
   2_xyz:  0.1762 0.2292   5.543101e+00   5.732406e+00
   2_adp:  0.1652 0.2149   5.484067e+00   5.676224e+00
   2_occ:  0.1651 0.2148   5.483698e+00   5.675997e+00
   3_bss:  0.1653 0.2139   5.482333e+00   5.672823e+00
   3_xyz:  0.1307 0.1783   5.280813e+00   5.501695e+00
   3_adp:  0.1224 0.1708   5.228005e+00   5.460319e+00
   3_occ:  0.1224 0.1708   5.227894e+00   5.460221e+00
   4_bss:  0.1227 0.1708   5.228152e+00   5.459813e+00
   4_xyz:  0.1137 0.1623   5.166598e+00   5.415064e+00
   4_adp:  0.1121 0.1600   5.154163e+00   5.403056e+00
   4_occ:  0.1120 0.1599   5.153961e+00   5.402811e+00
   5_bss:  0.1120 0.1599   5.153824e+00   5.402693e+00
   5_xyz:  0.1096 0.1588   5.141874e+00   5.397895e+00
   5_adp:  0.1104 0.1574   5.142497e+00   5.392464e+00
   5_occ:  0.1103 0.1572   5.142018e+00   5.391913e+00
   5_bss:  0.1103 0.1572   5.141857e+00   5.391967e+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:  0.333  45.497  -0.247   1.688  -1.188   0.000  -0.000  -0.000
   1_xyz:  0.333  45.497  -0.247   1.688  -1.188   0.000  -0.000  -0.000
   1_adp:  0.333  45.497  -0.247   1.688  -1.188   0.000  -0.000  -0.000
   1_occ:  0.333  45.497  -0.247   1.688  -1.188   0.000  -0.000  -0.000
   2_bss:  0.340  64.613  -1.586  -1.086  -1.256  -0.000  -0.000  -0.000
   2_xyz:  0.340  64.613  -1.586  -1.086  -1.256  -0.000  -0.000  -0.000
   2_adp:  0.340  64.613  -1.586  -1.086  -1.256  -0.000  -0.000  -0.000
   2_occ:  0.340  64.613  -1.586  -1.086  -1.256  -0.000  -0.000  -0.000
   3_bss:  0.340  64.613  -1.916  -2.034  -1.051  -0.000  -0.000  -0.000
   3_xyz:  0.340  64.613  -1.916  -2.034  -1.051  -0.000  -0.000  -0.000
   3_adp:  0.340  64.613  -1.916  -2.034  -1.051  -0.000  -0.000  -0.000
   3_occ:  0.340  64.613  -1.916  -2.034  -1.051  -0.000  -0.000  -0.000
   4_bss:  0.328  64.613  -2.132  -2.474  -1.176  -0.000  -0.000  -0.000
   4_xyz:  0.328  64.613  -2.132  -2.474  -1.176  -0.000  -0.000  -0.000
   4_adp:  0.328  64.613  -2.132  -2.474  -1.176  -0.000  -0.000  -0.000
   4_occ:  0.328  64.613  -2.132  -2.474  -1.176  -0.000  -0.000  -0.000
   5_bss:  0.328  64.613  -2.048  -2.503  -1.051  -0.000  -0.000  -0.000
   5_xyz:  0.328  64.613  -2.048  -2.503  -1.051  -0.000  -0.000  -0.000
   5_adp:  0.328  64.613  -2.048  -2.503  -1.051  -0.000  -0.000  -0.000
   5_occ:  0.328  64.613  -2.048  -2.503  -1.051  -0.000  -0.000  -0.000
   5_bss:  0.317  53.460  -1.990  -2.476  -0.918  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  43.612 0.6005  0.7814    45447.510
   1_bss:  42.991 0.6065  0.7955    43458.538
   1_xyz:  28.576 0.7751  0.9636    21668.618
   1_adp:  30.629 0.7511  0.9433    23930.416
   1_occ:  30.587 0.7515  0.9430    23846.906
   2_bss:  30.229 0.7554  0.9034    23447.035
   2_xyz:  22.478 0.8364  0.9679    13262.800
   2_adp:  20.512 0.8569  0.9749    11651.947
   2_occ:  20.507 0.8570  0.9747    11647.973
   3_bss:  20.401 0.8579  0.9630    11532.297
   3_xyz:  16.581 0.8927  0.9856     7980.175
   3_adp:  15.626 0.9014  0.9831     7372.432
   3_occ:  15.628 0.9014  0.9831     7373.244
   4_bss:  15.623 0.9014  0.9741     7369.020
   4_xyz:  14.546 0.9105  0.9780     6630.403
   4_adp:  14.238 0.9131  0.9741     6478.434
   4_occ:  14.234 0.9132  0.9741     6471.719
   5_bss:  14.231 0.9132  0.9763     6470.791
   5_xyz:  14.116 0.9143  0.9763     6442.008
   5_adp:  13.973 0.9155  0.9732     6408.125
   5_occ:  13.963 0.9156  0.9732     6394.768
   5_bss:  13.971 0.9155  0.9742     6387.618
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.6471e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.6471e-01
   1_xyz:   1.222  0.009  0.083 15.390  0.005  4.109   8.4843e-02
   1_adp:   1.222  0.009  0.083 15.390  0.005  4.109   8.4843e-02
   1_occ:   1.222  0.009  0.083 15.390  0.005  4.109   8.4843e-02
   2_bss:   1.222  0.009  0.083 15.390  0.005  4.109   8.4843e-02
   2_xyz:   1.014  0.006  0.071 14.150  0.004  4.121   5.7587e-02
   2_adp:   1.014  0.006  0.071 14.150  0.004  4.121   5.7587e-02
   2_occ:   1.014  0.006  0.071 14.150  0.004  4.121   5.7587e-02
   3_bss:   1.014  0.006  0.071 14.150  0.004  4.121   5.7587e-02
   3_xyz:   0.978  0.007  0.073 14.514  0.003  4.119   5.6545e-02
   3_adp:   0.978  0.007  0.073 14.514  0.003  4.119   5.6545e-02
   3_occ:   0.978  0.007  0.073 14.514  0.003  4.119   5.6545e-02
   4_bss:   0.978  0.007  0.073 14.514  0.003  4.119   5.6545e-02
   4_xyz:   1.032  0.008  0.077 14.636  0.004  4.124   6.3810e-02
   4_adp:   1.032  0.008  0.077 14.636  0.004  4.124   6.3810e-02
   4_occ:   1.032  0.008  0.077 14.636  0.004  4.124   6.3810e-02
   5_bss:   1.032  0.008  0.077 14.636  0.004  4.124   6.3810e-02
   5_xyz:   1.044  0.009  0.078 14.661  0.004  4.126   6.5158e-02
   5_adp:   1.044  0.009  0.078 14.661  0.004  4.126   6.5158e-02
   5_occ:   1.044  0.009  0.078 14.661  0.004  4.126   6.5158e-02
   5_bss:   1.044  0.009  0.078 14.661  0.004  4.126   6.5158e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4145e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4145e-01
   1_xyz:   8.621  0.050  0.293 85.136  0.046  2.118   8.4031e-02
   1_adp:   8.621  0.050  0.293 85.136  0.046  2.118   8.4031e-02
   1_occ:   8.621  0.050  0.293 85.136  0.046  2.118   8.4031e-02
   2_bss:   8.621  0.050  0.293 85.136  0.046  2.118   8.4031e-02
   2_xyz:   7.642  0.036  0.255 82.096  0.034  2.418   8.3187e-02
   2_adp:   7.642  0.036  0.255 82.096  0.034  2.418   8.3187e-02
   2_occ:   7.642  0.036  0.255 82.096  0.034  2.418   8.3187e-02
   3_bss:   7.642  0.036  0.255 82.096  0.034  2.418   8.3187e-02
   3_xyz:   7.974  0.040  0.223 83.818  0.027  2.322   4.0639e-02
   3_adp:   7.974  0.040  0.223 83.818  0.027  2.322   4.0639e-02
   3_occ:   7.974  0.040  0.223 83.818  0.027  2.322   4.0639e-02
   4_bss:   7.974  0.040  0.223 83.818  0.027  2.322   4.0639e-02
   4_xyz:   8.075  0.042  0.246 83.804  0.039  2.304   4.9562e-02
   4_adp:   8.075  0.042  0.246 83.804  0.039  2.304   4.9562e-02
   4_occ:   8.075  0.042  0.246 83.804  0.039  2.304   4.9562e-02
   5_bss:   8.075  0.042  0.246 83.804  0.039  2.304   4.9562e-02
   5_xyz:   8.064  0.045  0.257 84.775  0.038  2.311   5.0973e-02
   5_adp:   8.064  0.045  0.257 84.775  0.038  2.311   5.0973e-02
   5_occ:   8.064  0.045  0.257 84.775  0.038  2.311   5.0973e-02
   5_bss:   8.064  0.045  0.257 84.775  0.038  2.311   5.0973e-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:  96.31   0.00  17.95  73.47   0.00  13.82  96.31   3.59  40.41
   1_occ:  96.31   0.00  17.95  73.47   0.00  13.82  96.31   3.59  40.41
   2_bss:  96.31   0.00  17.95  73.47   0.00  13.82  96.31   3.59  40.41
   2_xyz:  96.31   0.00  17.95  73.47   0.00  13.82  96.31   3.59  40.41
   2_adp:  94.94   1.29  17.48  74.74   1.29  13.31  94.94   5.76  40.16
   2_occ:  94.94   1.29  17.48  74.74   1.29  13.31  94.94   5.76  40.16
   3_bss:  94.94   1.29  17.48  74.74   1.29  13.31  94.94   5.76  40.16
   3_xyz:  94.94   1.29  17.48  74.74   1.29  13.31  94.94   5.76  40.16
   3_adp:  96.81   0.00  17.89  87.76   0.00  13.15  96.81   6.07  43.70
   3_occ:  96.81   0.00  17.89  87.76   0.00  13.15  96.81   6.07  43.70
   4_bss:  96.81   0.00  17.89  87.76   0.00  13.15  96.81   6.07  43.70
   4_xyz:  96.81   0.00  17.89  87.76   0.00  13.15  96.81   6.07  43.70
   4_adp:  94.46   0.00  17.55  92.82   0.00  12.98  94.46   5.67  42.42
   4_occ:  94.46   0.00  17.55  92.82   0.00  12.98  94.46   5.67  42.42
   5_bss:  94.46   0.00  17.55  92.82   0.00  12.98  94.46   5.67  42.42
   5_xyz:  94.46   0.00  17.55  92.82   0.00  12.98  94.46   5.67  42.42
   5_adp:  88.08   1.05  16.71  87.66   1.05  12.67  88.08   6.05  38.70
   5_occ:  88.08   1.05  16.71  87.66   1.05  12.67  88.08   6.05  38.70
   5_bss:  88.04   1.02  16.67  87.63   1.02  12.63  88.04   6.02  38.66
------------------------------------------------------------------------
 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:    1.556    0.011    0.302
   1_adp:    1.556    0.011    0.302
   1_occ:    1.556    0.011    0.302
   2_bss:    1.556    0.011    0.302
   2_xyz:    1.131    0.019    0.412
   2_adp:    1.131    0.019    0.412
   2_occ:    1.131    0.019    0.412
   3_bss:    1.131    0.019    0.412
   3_xyz:    1.129    0.032    0.518
   3_adp:    1.129    0.032    0.518
   3_occ:    1.129    0.032    0.518
   4_bss:    1.129    0.032    0.518
   4_xyz:    1.235    0.047    0.537
   4_adp:    1.235    0.047    0.537
   4_occ:    1.235    0.047    0.537
   5_bss:    1.235    0.047    0.537
   5_xyz:    1.314    0.028    0.554
   5_adp:    1.314    0.028    0.554
   5_occ:    1.314    0.028    0.554
   5_bss:    1.314    0.028    0.554
------------------------------------------------------------------------

CPU time actual refinement: 361.60


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_996/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_996/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_996/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_996/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_996/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 361.45 
  Macro-tasks:
    bulk solvent and scale       = 35.97  
    individual site refinement   = 162.10 
    weights calculation          = 30.39  
    collect and process          = 6.62   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 235.18 
  Micro-tasks:
    mask                            = 1.85   
    f_calc                          = 120.05 
    alpha_beta                      = 8.49   
    target                          = 1.20   
    gradients_wrt_atomic_parameters = 131.38 
    fmodel                         = 6.91   
    r_factors                      = 0.22   
    phase_errors                   = 10.96  
    foms                           = 0.21   
    TOTAL for micro-tasks          = 281.27 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.940 micro seconds
Total CPU time: 6.25 minutes
from_scatterers_fft:    683 calls, 119.74 s
gradients_fft:          628 calls, 116.35 s

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

# Date 2008-01-16 Time 06:10:59 PST -0800 (1200492659.03 s)
Start R-work = 0.3908, R-free = 0.3865 (no bulk solvent and anisotropic scale)
Final R-work = 0.1339, R-free = 0.1774 (no bulk solvent and anisotropic scale)

Start R-work = 0.3801, R-free = 0.3803
Final R-work = 0.1103, R-free = 0.1572