# Date 2008-01-16 Time 05:46:43 PST -0800 (1200491203.15 s)
#phil __OFF__

Command line arguments: "../873.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 27656
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 873

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.9525, 46.2261, 85.9581, 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: 2.75, per 1000 atoms: 0.97


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 46.2261, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0819 1.97275
Completeness in resolution range: 0.956307
Completeness with d_max=infinity: 0.953468

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0819
                             d_min =   1.9728

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 46.2261, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0819 1.97275
Completeness in resolution range: 0.956307
Completeness with d_max=infinity: 0.953468

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0824 -  4.2220 [2147/2173]  1934   213   9.9%
  bin  2:  4.2220 -  3.3634 [2068/2088]  1859   209  10.1%
  bin  3:  3.3634 -  2.9418 [2043/2062]  1841   202   9.9%
  bin  4:  2.9418 -  2.6744 [2027/2057]  1822   205  10.1%
  bin  5:  2.6744 -  2.4837 [2015/2034]  1820   195   9.7%
  bin  6:  2.4837 -  2.3378 [1988/2013]  1778   210  10.6%
  bin  7:  2.3378 -  2.2211 [2000/2028]  1803   197   9.8%
  bin  8:  2.2211 -  2.1247 [1975/2011]  1778   197  10.0%
  bin  9:  2.1247 -  2.0431 [1963/2005]  1766   197  10.0%
  bin 10:  2.0431 -  1.9728 [1363/2013]  1229   134   9.8%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_873/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: 0.11 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 29
        2.42 -     3.04: 2198
        3.04 -     3.66: 4735
        3.66 -     4.28: 9098
        4.28 -     4.90: 12346
  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 204 " - " O   HOH Z 296 "  2.046 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 201 " - " O   HOH Z 349 "  2.052 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
  ... (remaining 28401 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_873/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_873/model_refine_001.geo

CPU time processing inputs: 7.93


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.9525 46.22605 85.95805 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 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3677   r_free= 0.3658   ksol= 0.00   Bsol= 0.00   scale= 0.953    |
|                                                                             |
| 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:   0.46 A                  |
| x-ray target function (ml) for work reflections: 6.145707                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0824 -  4.7094 0.99   1395  157 0.3106 0.3073       6.413      6.3896|
|  2:  4.7094 -  3.7570 0.99   1345  148 0.2954 0.2883      6.5791      6.4928|
|  3:  3.7570 -  3.2877 0.99   1326  144 0.3179 0.2821      6.4555      6.5297|
|  4:  3.2877 -  2.9897 0.99   1313  153 0.3427 0.3853      6.3574      6.3833|
|  5:  2.9897 -  2.7768 0.99   1298  143 0.3851 0.3526      6.2229      6.1978|
|  6:  2.7768 -  2.6140 0.99   1303  140 0.3837 0.3859      6.1362      6.1085|
|  7:  2.6140 -  2.4837 0.99   1296  139 0.3912 0.3886      6.1151      6.0995|
|  8:  2.4837 -  2.3760 0.98   1255  147 0.4098 0.3919      6.0566      6.0455|
|  9:  2.3760 -  2.2848 0.98   1276  148 0.4023 0.4111      6.0131      6.0299|
| 10:  2.2848 -  2.2062 1.00   1294  140 0.4168 0.4140      5.9982      5.9671|
| 11:  2.2062 -  2.1375 0.98   1294  136 0.4188 0.4460      5.9545       5.994|
| 12:  2.1375 -  2.0765 0.98   1247  145 0.4341 0.4415      5.9104      5.9336|
| 13:  2.0765 -  2.0220 0.99   1279  137 0.4274 0.4399      5.7988      5.7438|
| 14:  2.0220 -  1.9728 0.55    709   82 0.4652 0.4672      5.8126      5.7915|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0824 -  4.7094  1395   157  0.78  27.37   0.85     0.81      47625.29|
|  2:  4.7094 -  3.7570  1345   148  0.81  25.11   0.96     0.90      58712.21|
|  3:  3.7570 -  3.2877  1326   144  0.75  30.88   0.99     0.93      62451.97|
|  4:  3.2877 -  2.9897  1313   153  0.70  35.42   0.98     0.89      58205.78|
|  5:  2.9897 -  2.7768  1298   143  0.63  41.19   0.95     0.84      48868.24|
|  6:  2.7768 -  2.6140  1303   140  0.63  41.40   0.97     0.83      42224.89|
|  7:  2.6140 -  2.4837  1296   139  0.62  42.11   0.99     0.82      38332.64|
|  8:  2.4837 -  2.3760  1255   147  0.61  43.38   0.98     0.83      35089.51|
|  9:  2.3760 -  2.2848  1276   148  0.62  42.68   0.99     0.83      31861.78|
| 10:  2.2848 -  2.2062  1294   140  0.61  43.27   1.01     0.85      29369.13|
| 11:  2.2062 -  2.1375  1294   136  0.59  44.99   1.03     0.85      29461.11|
| 12:  2.1375 -  2.0765  1247   145  0.56  47.26   1.00     0.81      28097.52|
| 13:  2.0765 -  2.0220  1279   137  0.51  51.78   1.01     0.75      26044.13|
| 14:  2.0220 -  1.9728   709    82  0.51  51.45   0.99     0.70      22658.13|
|alpha:            min =        0.70 max =            0.93 mean =         0.84|
|beta:             min =    22658.13 max =        62451.97 mean =     40726.14|
|figures of merit: min =        0.00 max =            1.00 mean =         0.64|
|phase err.(work): min =        0.00 max =           89.99 mean =        40.05|
|phase err.(test): min =        0.00 max =           89.76 mean =        40.14|
|-----------------------------------------------------------------------------|

============================== Outliers rejection =============================

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 0
total                    = 0

====================== Target weights (before refinement) =====================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.487282              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.257   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.124047              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.898   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        4 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       25 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      202 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1996 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1891 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2844 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4653 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4445 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5621 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6725 |
|-----------------------------------------------------------------------------|
|-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 |        0.164 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.110    4.900  1.806 |       0.214 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.796)------------------------------------------|
|    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 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3677   r_free= 0.3658   ksol= 0.00   Bsol= 0.00   scale= 0.953    |
|                                                                             |
| 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:   0.46 A                  |
| x-ray target function (ml) for work reflections: 6.145707                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3550   r_free= 0.3567   ksol= 0.34   Bsol= 41.10   scale= 0.971   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.51,2.08,-1.59,0.00,-0.00,-0.00); trace/3= -0.34                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 6.129243                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.512944              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.426   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.557789              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.721   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3550      final r-factor (work) = 0.1955          |
| start r-factor (free) = 0.3567      final r-factor (free) = 0.2206          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.1948 = 7.51 * 0.50 * 6.1309 + 1.00 * 0.1644                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.1350 = 7.51 * 0.50 * 5.8608 + 1.00 * 0.1193                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1955      final r-factor (work) = 0.1779          |
| start r-factor (free) = 0.2206      final r-factor (free) = 0.2301          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2750 = 0.56 * 1.00 * 5.8608 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0932 = 0.56 * 1.00 * 5.5262 + 1.00 * 0.0107                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.796)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.67   17.44    None  None   None       |
|    all(noH): 2823   0      0.00    85.67   17.44    None  None   None       |
|    Sol.    : 438    0      6.30    85.67   40.97    None  None   None       |
|    Mac.    : 2385   0      0.00    74.15   13.11    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.567:  702   |   5:    42.834 -  51.400:  112        |
|      1:     8.567 -  17.133: 1274   |   6:    51.400 -  59.967:   72        |
|      2:    17.133 -  25.700:  332   |   7:    59.967 -  68.534:   40        |
|      3:    25.700 -  34.267:  146   |   8:    68.534 -  77.100:   18        |
|      4:    34.267 -  42.834:  125   |   9:    77.100 -  85.667:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1779 r_free = 0.2301             target_work(ml) = 5.542         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1776 r_free = 0.2299             target_work(ml) = 5.541         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1776   r_free= 0.2299   ksol= 0.34   Bsol= 41.10   scale= 1.038   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.51,2.08,-1.59,0.00,-0.00,-0.00); trace/3= -0.34                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.541155                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1748   r_free= 0.2261   ksol= 0.33   Bsol= 49.45   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.22,-1.47,-1.69,-0.00,-0.00,-0.00); trace/3= -1.79                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.525825                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.885540              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.682   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.128414              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 121.175  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1748      final r-factor (work) = 0.1337          |
| start r-factor (free) = 0.2261      final r-factor (free) = 0.1823          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.1084 = 2.89 * 0.50 * 5.5374 + 1.00 * 0.1193                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.8729 = 2.89 * 0.50 * 5.4180 + 1.00 * 0.0560                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1337      final r-factor (work) = 0.1288          |
| start r-factor (free) = 0.1823      final r-factor (free) = 0.1707          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7065 = 0.13 * 1.00 * 5.4180 + 1.00 * 0.0107                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6851 = 0.13 * 1.00 * 5.2837 + 1.00 * 0.0066                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.796)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.93    74.99   16.70    None  None   None       |
|    all(noH): 2823   0      1.93    74.99   16.70    None  None   None       |
|    Sol.    : 438    0      6.85    74.81   37.65    None  None   None       |
|    Mac.    : 2385   0      1.93    74.99   12.86    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:     1.929 -   9.235:  757   |   5:    38.460 -  45.767:  101        |
|      1:     9.235 -  16.542: 1237   |   6:    45.767 -  53.073:   85        |
|      2:    16.542 -  23.848:  325   |   7:    53.073 -  60.379:   33        |
|      3:    23.848 -  31.154:  125   |   8:    60.379 -  67.685:   23        |
|      4:    31.154 -  38.460:  130   |   9:    67.685 -  74.991:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1288 r_free = 0.1707             target_work(ml) = 5.249         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1286 r_free = 0.1708             target_work(ml) = 5.248         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1286   r_free= 0.1708   ksol= 0.33   Bsol= 49.45   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.22,-1.47,-1.69,-0.00,-0.00,-0.00); trace/3= -1.79                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.248477                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1286   r_free= 0.1702   ksol= 0.33   Bsol= 49.45   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.41,-2.38,-1.54,-0.00,-0.00,-0.00); trace/3= -2.11                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.245386                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.973181              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 123.121  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.260980              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.172  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1286      final r-factor (work) = 0.1137          |
| start r-factor (free) = 0.1702      final r-factor (free) = 0.1570          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9089 = 2.97 * 0.50 * 5.2825 + 1.00 * 0.0560                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7815 = 2.97 * 0.50 * 5.1904 + 1.00 * 0.0655                               |
|-----------------------------------------------------------------------------|
| 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) = 0.1105          |
| start r-factor (free) = 0.1570      final r-factor (free) = 0.1546          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3612 = 0.26 * 1.00 * 5.1904 + 1.00 * 0.0066                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3470 = 0.26 * 1.00 * 5.1326 + 1.00 * 0.0075                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.796)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.03    80.01   16.81    None  None   None       |
|    all(noH): 2823   0      1.03    80.01   16.81    None  None   None       |
|    Sol.    : 438    0      6.81    76.74   38.49    None  None   None       |
|    Mac.    : 2385   0      1.03    80.01   12.83    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.026 -   8.925:  723   |   5:    40.519 -  48.418:  113        |
|      1:     8.925 -  16.823: 1298   |   6:    48.418 -  56.316:   74        |
|      2:    16.823 -  24.722:  316   |   7:    56.316 -  64.215:   42        |
|      3:    24.722 -  32.621:  121   |   8:    64.215 -  72.114:   15        |
|      4:    32.621 -  40.519:  116   |   9:    72.114 -  80.012:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1105 r_free = 0.1546             target_work(ml) = 5.127         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1104 r_free = 0.1546             target_work(ml) = 5.127         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1104   r_free= 0.1546   ksol= 0.33   Bsol= 49.45   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.41,-2.38,-1.54,-0.00,-0.00,-0.00); trace/3= -2.11                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.126722                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1104   r_free= 0.1545   ksol= 0.33   Bsol= 49.45   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.38,-2.59,-1.48,-0.00,-0.00,-0.00); trace/3= -2.15                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.126260                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.491496              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 143.182  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.347814              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.974  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1104      final r-factor (work) = 0.1087          |
| start r-factor (free) = 0.1545      final r-factor (free) = 0.1540          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4587 = 2.49 * 0.50 * 5.1323 + 1.00 * 0.0652                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4392 = 2.49 * 0.50 * 5.1195 + 1.00 * 0.0617                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1087      final r-factor (work) = 0.1079          |
| start r-factor (free) = 0.1540      final r-factor (free) = 0.1542          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7881 = 0.35 * 1.00 * 5.1195 + 1.00 * 0.0074                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7871 = 0.35 * 1.00 * 5.1151 + 1.00 * 0.0080                               |
|-----------------------------------------------------------------------------|
| number of iterations = 16      |    number of function evaluations = 17     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.796)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.86    82.43   16.75    None  None   None       |
|    all(noH): 2823   0      0.86    82.43   16.75    None  None   None       |
|    Sol.    : 438    0      6.58    78.72   38.60    None  None   None       |
|    Mac.    : 2385   0      0.86    82.43   12.74    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.863 -   9.020:  789   |   5:    41.648 -  49.805:  105        |
|      1:     9.020 -  17.177: 1252   |   6:    49.805 -  57.962:   79        |
|      2:    17.177 -  25.334:  301   |   7:    57.962 -  66.119:   33        |
|      3:    25.334 -  33.491:  131   |   8:    66.119 -  74.276:   12        |
|      4:    33.491 -  41.648:  117   |   9:    74.276 -  82.433:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1079 r_free = 0.1542             target_work(ml) = 5.118         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1079 r_free = 0.1543             target_work(ml) = 5.119         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1079   r_free= 0.1543   ksol= 0.33   Bsol= 49.45   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.38,-2.59,-1.48,-0.00,-0.00,-0.00); trace/3= -2.15                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.118559                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1078   r_free= 0.1543   ksol= 0.33   Bsol= 49.45   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.19,-2.49,-1.27,-0.00,-0.00,-0.00); trace/3= -1.98                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.118543                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.605968              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 164.869  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.311208              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.011  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1078      final r-factor (work) = 0.1068          |
| start r-factor (free) = 0.1543      final r-factor (free) = 0.1546          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7274 = 2.61 * 0.50 * 5.1158 + 1.00 * 0.0617                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7275 = 2.61 * 0.50 * 5.1142 + 1.00 * 0.0638                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1068      final r-factor (work) = 0.1068          |
| start r-factor (free) = 0.1546      final r-factor (free) = 0.1544          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5995 = 0.31 * 1.00 * 5.1142 + 1.00 * 0.0080                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5990 = 0.31 * 1.00 * 5.1126 + 1.00 * 0.0079                               |
|-----------------------------------------------------------------------------|
| number of iterations = 18      |    number of function evaluations = 20     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.796)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.77    84.16   16.56    None  None   None       |
|    all(noH): 2823   0      0.77    84.16   16.56    None  None   None       |
|    Sol.    : 438    0      6.54    80.68   38.19    None  None   None       |
|    Mac.    : 2385   0      0.77    84.16   12.59    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.767 -   9.106:  857   |   5:    42.463 -  50.802:   95        |
|      1:     9.106 -  17.445: 1228   |   6:    50.802 -  59.141:   69        |
|      2:    17.445 -  25.784:  267   |   7:    59.141 -  67.480:   30        |
|      3:    25.784 -  34.123:  142   |   8:    67.480 -  75.819:   10        |
|      4:    34.123 -  42.463:  121   |   9:    75.819 -  84.158:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1068 r_free = 0.1544             target_work(ml) = 5.112         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1068 r_free = 0.1543             target_work(ml) = 5.112         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1068   r_free= 0.1543   ksol= 0.33   Bsol= 49.45   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.19,-2.49,-1.27,-0.00,-0.00,-0.00); trace/3= -1.98                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.112050                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0824 -  4.7094 0.99   1395  157 0.0983 0.1246      5.3769      5.5461|
|  2:  4.7094 -  3.7570 0.99   1345  148 0.0839 0.1166      5.4326      5.6356|
|  3:  3.7570 -  3.2877 0.99   1326  144 0.1043 0.1516      5.4625      5.8523|
|  4:  3.2877 -  2.9897 0.99   1313  153 0.1151 0.1596      5.4266      5.5694|
|  5:  2.9897 -  2.7768 0.99   1298  143 0.1279 0.1740      5.2972      5.5505|
|  6:  2.7768 -  2.6140 0.99   1303  140 0.1137 0.1712       5.168      5.4082|
|  7:  2.6140 -  2.4837 0.99   1296  139 0.1190 0.1547      5.1261      5.3065|
|  8:  2.4837 -  2.3760 0.98   1255  147 0.1087 0.1683      4.9917      5.3142|
|  9:  2.3760 -  2.2848 0.98   1276  148 0.1083 0.1720      4.9812      5.3031|
| 10:  2.2848 -  2.2062 1.00   1294  140 0.1050 0.1647      4.9034      5.1644|
| 11:  2.2062 -  2.1375 0.98   1294  136 0.1059 0.1738        4.91      5.2408|
| 12:  2.1375 -  2.0765 0.98   1247  145 0.1041 0.1600      4.8385      5.1102|
| 13:  2.0765 -  2.0220 0.99   1279  137 0.1071 0.1745      4.7459      5.0429|
| 14:  2.0220 -  1.9728 0.55    709   82 0.0975 0.1604      4.6174      4.8798|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0824 -  4.7094  1395   157  0.94   8.90   0.98     0.95       6889.31|
|  2:  4.7094 -  3.7570  1345   148  0.95   7.99   1.02     1.01       9156.91|
|  3:  3.7570 -  3.2877  1326   144  0.93  11.25   1.02     1.02      10213.47|
|  4:  3.2877 -  2.9897  1313   153  0.92  13.39   1.01     0.98      10015.95|
|  5:  2.9897 -  2.7768  1298   143  0.90  15.71   0.99     0.97       8004.29|
|  6:  2.7768 -  2.6140  1303   140  0.91  15.38   0.99     0.96       6664.68|
|  7:  2.6140 -  2.4837  1296   139  0.91  14.88   0.99     0.96       5848.52|
|  8:  2.4837 -  2.3760  1255   147  0.91  14.36   0.98     0.96       4564.34|
|  9:  2.3760 -  2.2848  1276   148  0.92  14.33   1.00     0.98       4548.73|
| 10:  2.2848 -  2.2062  1294   140  0.91  14.81   1.00     0.97       3984.12|
| 11:  2.2062 -  2.1375  1294   136  0.91  15.46   0.99     0.95       4134.90|
| 12:  2.1375 -  2.0765  1247   145  0.92  14.66   1.01     1.00       3788.03|
| 13:  2.0765 -  2.0220  1279   137  0.90  15.77   1.00     0.98       3134.68|
| 14:  2.0220 -  1.9728   709    82  0.92  13.78   0.98     0.95       2387.26|
|alpha:            min =        0.95 max =            1.02 mean =         0.97|
|beta:             min =     2387.26 max =        10213.47 mean =      6111.05|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.92 mean =        13.56|
|phase err.(test): min =        0.00 max =           89.71 mean =        13.11|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1068   r_free= 0.1538   ksol= 0.32   Bsol= 49.43   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.04,-2.38,-1.12,-0.00,-0.00,-0.00); trace/3= -1.85                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.110691                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1068   r_free= 0.1538   ksol= 0.32   Bsol= 49.43   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.04,-2.38,-1.12,-0.00,-0.00,-0.00); trace/3= -1.85                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.110691                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0824 -  4.7094 0.99   1395  157 0.0983 0.1226      5.3676      5.5161|
|  2:  4.7094 -  3.7570 0.99   1345  148 0.0845 0.1133      5.4267      5.6161|
|  3:  3.7570 -  3.2877 0.99   1326  144 0.1042 0.1491       5.457      5.8384|
|  4:  3.2877 -  2.9897 0.99   1313  153 0.1150 0.1611      5.4246      5.5741|
|  5:  2.9897 -  2.7768 0.99   1298  143 0.1282 0.1728      5.2984      5.5463|
|  6:  2.7768 -  2.6140 0.99   1303  140 0.1140 0.1728       5.168      5.4106|
|  7:  2.6140 -  2.4837 0.99   1296  139 0.1190 0.1543      5.1261      5.3055|
|  8:  2.4837 -  2.3760 0.98   1255  147 0.1085 0.1686      4.9916      5.3145|
|  9:  2.3760 -  2.2848 0.98   1276  148 0.1083 0.1723      4.9826      5.3066|
| 10:  2.2848 -  2.2062 1.00   1294  140 0.1050 0.1653      4.9045      5.1674|
| 11:  2.2062 -  2.1375 0.98   1294  136 0.1058 0.1737      4.9107      5.2407|
| 12:  2.1375 -  2.0765 0.98   1247  145 0.1041 0.1601       4.839      5.1108|
| 13:  2.0765 -  2.0220 0.99   1279  137 0.1069 0.1749      4.7463      5.0442|
| 14:  2.0220 -  1.9728 0.55    709   82 0.0974 0.1604      4.6176      4.8809|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0824 -  4.7094  1395   157  0.94   8.66   0.98     0.95       6509.16|
|  2:  4.7094 -  3.7570  1345   148  0.95   7.76   1.02     1.01       8751.77|
|  3:  3.7570 -  3.2877  1326   144  0.94  11.07   1.02     1.02       9991.64|
|  4:  3.2877 -  2.9897  1313   153  0.92  13.36   1.01     0.99       9966.57|
|  5:  2.9897 -  2.7768  1298   143  0.90  15.71   0.99     0.97       8010.71|
|  6:  2.7768 -  2.6140  1303   140  0.91  15.37   0.99     0.97       6662.96|
|  7:  2.6140 -  2.4837  1296   139  0.91  14.86   1.00     0.97       5846.09|
|  8:  2.4837 -  2.3760  1255   147  0.91  14.38   0.99     0.96       4575.48|
|  9:  2.3760 -  2.2848  1276   148  0.92  14.37   1.01     0.98       4568.97|
| 10:  2.2848 -  2.2062  1294   140  0.91  14.84   1.00     0.97       4001.29|
| 11:  2.2062 -  2.1375  1294   136  0.91  15.50   0.99     0.95       4145.28|
| 12:  2.1375 -  2.0765  1247   145  0.92  14.68   1.01     1.01       3795.12|
| 13:  2.0765 -  2.0220  1279   137  0.90  15.79   1.00     0.98       3143.01|
| 14:  2.0220 -  1.9728   709    82  0.92  13.80   0.99     0.96       2390.75|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2390.75 max =         9991.64 mean =      6035.40|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.95 mean =        13.52|
|phase err.(test): min =        0.00 max =           89.96 mean =        13.07|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.796)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.74    84.13   16.54    None  None   None       |
|    all(noH): 2823   0      0.74    84.13   16.54    None  None   None       |
|    Sol.    : 438    0      6.51    80.66   38.16    None  None   None       |
|    Mac.    : 2385   0      0.74    84.13   12.57    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.741 -   9.080:  857   |   5:    42.437 -  50.776:   95        |
|      1:     9.080 -  17.419: 1228   |   6:    50.776 -  59.115:   69        |
|      2:    17.419 -  25.758:  267   |   7:    59.115 -  67.454:   30        |
|      3:    25.758 -  34.098:  142   |   8:    67.454 -  75.793:   10        |
|      4:    34.098 -  42.437:  121   |   9:    75.793 -  84.133:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 302         
Filter by distance & map next to the model:
   mapped sites are within: 0.494 - 4.623
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 296 from: 302
   mapped sites are within: 0.714 - 4.623

peak=    6.089 closest distance to " NE2 GLN A  11 " =    1.225
peak=    5.813 closest distance to " NH2 ARG A  56 " =    2.124
peak=    5.650 closest distance to " O   HOH Z 126 " =    1.838
peak=    5.479 closest distance to " CG  PRO A  54 " =    1.255
peak=    5.130 closest distance to " CB  SER A  63 " =    1.248
peak=    5.104 closest distance to " O   HOH Z 144 " =    1.728
peak=    4.869 closest distance to " CB  GLN A 223 " =    1.463
peak=    4.849 closest distance to " C   PRO A 198 " =    1.468
peak=    4.789 closest distance to " O   HOH Z 369 " =    2.141
peak=    4.788 closest distance to " O   HOH Z 232 " =    2.377
peak=    4.744 closest distance to " CB  GLN A 183 " =    1.196
peak=    4.721 closest distance to " CB  PRO A  54 " =    0.949
peak=    4.631 closest distance to " CB  ARG A 275 " =    0.900
peak=    4.498 closest distance to " O   HOH Z 419 " =    2.064
peak=    4.496 closest distance to " ND2 ASN A 187 " =    1.521
peak=    4.477 closest distance to " CB  GLU A 152 " =    1.235
peak=    4.465 closest distance to " O   HOH Z  15 " =    2.287
peak=    4.452 closest distance to " CB  ARG A  79 " =    1.403
peak=    4.425 closest distance to " O   HOH Z  63 " =    1.507
peak=    4.416 closest distance to " O   HOH Z 298 " =    1.850
peak=    4.409 closest distance to " O   HOH Z  78 " =    1.783
peak=    4.396 closest distance to " CG  TRP A 179 " =    2.226
peak=    4.377 closest distance to " O   HOH Z 236 " =    2.080
peak=    4.355 closest distance to " CB  ASN A 148 " =    1.489
peak=    4.325 closest distance to " CA  TYR A  30 " =    0.958
peak=    4.280 closest distance to " O   HOH Z 427 " =    2.789
peak=    4.231 closest distance to " O   HOH Z 423 " =    1.480
peak=    4.220 closest distance to " CB  GLU A 128 " =    0.987
peak=    4.184 closest distance to " O   HOH Z 209 " =    2.288
peak=    4.163 closest distance to " O   HOH Z 217 " =    3.032
peak=    4.158 closest distance to " CB  LEU A 228 " =    1.072
peak=    4.135 closest distance to " O   HOH Z 203 " =    1.907
peak=    4.120 closest distance to " O   HOH Z 261 " =    2.136
peak=    4.117 closest distance to " O   HOH Z 193 " =    1.842
peak=    4.077 closest distance to " O   HOH Z 234 " =    3.720
peak=    4.076 closest distance to " CB  ARG A 190 " =    1.591
peak=    4.072 closest distance to " O   HOH Z 158 " =    3.080
peak=    4.071 closest distance to " CB  SER A   3 " =    1.362
peak=    4.065 closest distance to " O   HOH Z  61 " =    1.587
peak=    4.053 closest distance to " CB  ASN A 187 " =    1.042
peak=    4.041 closest distance to " O   HOH Z  40 " =    2.231
peak=    4.030 closest distance to " CG2 VAL A 257 " =    0.930
peak=    4.029 closest distance to " OD1 ASN A  69 " =    2.703
peak=    4.028 closest distance to " O   HOH Z   1 " =    1.981
peak=    3.982 closest distance to " CB  SER A 212 " =    1.106
peak=    3.978 closest distance to " O   HOH Z  61 " =    1.530
peak=    3.950 closest distance to " O   HOH Z 133 " =    2.400
peak=    3.934 closest distance to " O   HOH Z  68 " =    2.136
peak=    3.927 closest distance to " CG  PRO A 198 " =    1.273
peak=    3.924 closest distance to " O   HOH Z 368 " =    2.041
peak=    3.920 closest distance to " O   HOH Z 180 " =    2.137
peak=    3.909 closest distance to " ND1 HIS A  86 " =    1.762
peak=    3.906 closest distance to " O   SER A  87 " =    2.166
peak=    3.904 closest distance to " O   HOH Z 132 " =    2.468
peak=    3.885 closest distance to " CE  LYS A  76 " =    0.897
peak=    3.878 closest distance to " CG  PRO A 243 " =    1.104
peak=    3.871 closest distance to " O   HOH Z 189 " =    2.333
peak=    3.871 closest distance to " CB  SER A 216 " =    0.810
peak=    3.859 closest distance to " CB  TRP A 266 " =    1.013
peak=    3.858 closest distance to " O   HOH Z  21 " =    1.712
peak=    3.854 closest distance to " CA  ASN A 215 " =    1.192
peak=    3.846 closest distance to " OG ASER A 258 " =    3.115
peak=    3.838 closest distance to " O   HOH Z 193 " =    1.667
peak=    3.831 closest distance to " O   HOH Z 425 " =    2.045
peak=    3.826 closest distance to " O   HOH Z  10 " =    1.834
peak=    3.818 closest distance to " CB  VAL A 265 " =    1.320
peak=    3.817 closest distance to " O   HOH Z 437 " =    1.698
peak=    3.808 closest distance to " CB  ARG A 139 " =    0.998
peak=    3.800 closest distance to " O   HOH Z 371 " =    2.877
peak=    3.797 closest distance to " CA  ALA A 233 " =    1.074
peak=    3.789 closest distance to " CD  ARG A 159 " =    0.767
peak=    3.788 closest distance to " O   HOH Z 344 " =    3.161
peak=    3.763 closest distance to " O   HOH Z 327 " =    1.656
peak=    3.748 closest distance to " O   HOH Z 368 " =    3.606
peak=    3.748 closest distance to " O   HOH Z 250 " =    1.506
peak=    3.725 closest distance to " O   HOH Z 272 " =    1.807
peak=    3.721 closest distance to " OD1BASN A 224 " =    2.295
peak=    3.717 closest distance to " O   HOH Z  44 " =    1.691
peak=    3.717 closest distance to " CG1 ILE A  33 " =    1.232
peak=    3.714 closest distance to " OD2 ASP A 286 " =    2.829
peak=    3.714 closest distance to " CB  TYR A 169 " =    0.796
peak=    3.708 closest distance to " CB  ALA A   1 " =    4.623
peak=    3.706 closest distance to " CD BLYS A 290 " =    1.205
peak=    3.706 closest distance to " CB  TRP A 179 " =    1.438
peak=    3.699 closest distance to " O   HOH Z 175 " =    2.178
peak=    3.692 closest distance to " OE1 GLN A  11 " =    2.172
peak=    3.690 closest distance to " CA  MET A  40 " =    1.130
peak=    3.687 closest distance to " O   HOH Z   9 " =    1.932
peak=    3.682 closest distance to " O   HOH Z  64 " =    2.313
peak=    3.674 closest distance to " CZ  PHE A 218 " =    1.009
peak=    3.662 closest distance to " O   HOH Z   1 " =    1.761
peak=    3.661 closest distance to " CA  THR A 264 " =    0.850
peak=    3.655 closest distance to " O   HOH Z 380 " =    1.651
peak=    3.652 closest distance to " O   HOH Z 405 " =    1.226
peak=    3.648 closest distance to " CB  ASN A  39 " =    0.892
peak=    3.643 closest distance to " N   PHE A 130 " =    1.255
peak=    3.642 closest distance to " CG2 THR A 221 " =    1.015
peak=    3.632 closest distance to " CD2 LEU A 255 " =    1.511
peak=    3.630 closest distance to " O   HOH Z 346 " =    1.709
peak=    3.626 closest distance to " CG  PRO A  90 " =    1.043
peak=    3.613 closest distance to " O   HOH Z 426 " =    1.868
peak=    3.602 closest distance to " O   HOH Z 392 " =    3.217
peak=    3.596 closest distance to " CA  SER A  87 " =    0.982
peak=    3.595 closest distance to " CB  ALA A  34 " =    1.101
peak=    3.593 closest distance to " CG  GLN A  89 " =    1.469
peak=    3.587 closest distance to " O   HOH Z 188 " =    1.991
peak=    3.582 closest distance to " CB  ASN A 142 " =    0.920
peak=    3.580 closest distance to " O   HOH Z  43 " =    1.937
peak=    3.576 closest distance to " CB  TYR A 116 " =    0.835
peak=    3.573 closest distance to " O   HOH Z 128 " =    2.188
peak=    3.564 closest distance to " O   HOH Z 133 " =    1.615
peak=    3.560 closest distance to " O   HOH Z 403 " =    1.637
peak=    3.539 closest distance to " CD2 TRP A 179 " =    1.309
peak=    3.536 closest distance to " O   HOH Z 207 " =    1.732
peak=    3.535 closest distance to " CG  LEU A 167 " =    1.249
peak=    3.531 closest distance to " O   HOH Z 128 " =    2.031
peak=    3.530 closest distance to " O   HOH Z 248 " =    1.626
peak=    3.529 closest distance to " CG  GLN A  11 " =    1.873
peak=    3.528 closest distance to " O   HOH Z 362 " =    2.609
peak=    3.525 closest distance to " CB  ASP A 140 " =    0.917
peak=    3.523 closest distance to " O   HOH Z 425 " =    1.278
peak=    3.518 closest distance to " O   HOH Z 261 " =    2.271
peak=    3.515 closest distance to " NH2AARG A 190 " =    1.936
peak=    3.514 closest distance to " O   HOH Z 371 " =    1.874
peak=    3.505 closest distance to " CD1 LEU A 300 " =    1.256
peak=    3.503 closest distance to " NH1BARG A 145 " =    1.253
peak=    3.500 closest distance to " O   HOH Z 391 " =    2.920
peak=    3.497 closest distance to " O   HOH Z 291 " =    1.577
peak=    3.491 closest distance to " O   HOH Z 214 " =    2.037
peak=    3.489 closest distance to " CA  GLY A 241 " =    3.802
peak=    3.486 closest distance to " O   HOH Z 147 " =    1.816
peak=    3.475 closest distance to " O   HOH Z  40 " =    2.018
peak=    3.473 closest distance to " O   HOH Z  88 " =    4.013
peak=    3.467 closest distance to " NE2 GLN A  73 " =    3.721
peak=    3.463 closest distance to " O   HOH Z 172 " =    2.960
peak=    3.459 closest distance to " OG BSER A 164 " =    2.278
peak=    3.459 closest distance to " O   HOH Z 409 " =    2.496
peak=    3.459 closest distance to " CA  ALA A  21 " =    1.144
peak=    3.458 closest distance to " O   HOH Z 193 " =    2.019
peak=    3.456 closest distance to " O   HOH Z 219 " =    2.228
peak=    3.453 closest distance to " O   HOH Z 417 " =    3.494
peak=    3.448 closest distance to " O   HOH Z 135 " =    1.713
peak=    3.442 closest distance to " NH1AARG A 145 " =    1.151
peak=    3.441 closest distance to " CD1 ILE A 263 " =    1.346
peak=    3.439 closest distance to " O   HOH Z 183 " =    1.375
peak=    3.425 closest distance to " O   HOH Z  85 " =    2.157
peak=    3.425 closest distance to " CB  GLU A 277 " =    3.534
peak=    3.424 closest distance to " CB  THR A 157 " =    1.117
peak=    3.423 closest distance to " CA  GLY A 267 " =    1.210
peak=    3.422 closest distance to " O   HOH Z 217 " =    1.592
peak=    3.420 closest distance to " O   HOH Z 407 " =    2.208
peak=    3.417 closest distance to " O   HOH Z 245 " =    1.304
peak=    3.413 closest distance to " ND2 ASN A 249 " =    1.861
peak=    3.410 closest distance to " O   HOH Z 303 " =    1.917
peak=    3.410 closest distance to " O   HOH Z 265 " =    2.275
peak=    3.409 closest distance to " O   HOH Z 302 " =    1.771
peak=    3.406 closest distance to " CG  ARG A 159 " =    0.798
peak=    3.405 closest distance to " O   HOH Z  88 " =    3.286
peak=    3.405 closest distance to " N   SER A 134 " =    1.310
peak=    3.405 closest distance to " O   HOH Z 280 " =    3.064
peak=    3.404 closest distance to " O   HOH Z 152 " =    1.901
peak=    3.404 closest distance to " O   HOH Z 271 " =    2.531
peak=    3.401 closest distance to " CB  ALA A 114 " =    1.442
peak=    3.397 closest distance to " CB  SER A  62 " =    1.201
peak=    3.391 closest distance to " O   HOH Z 286 " =    2.383
peak=    3.387 closest distance to " NE2 HIS A 207 " =    1.424
peak=    3.378 closest distance to " O   HOH Z 128 " =    2.046
peak=    3.376 closest distance to " CA  ALA A  84 " =    1.381
peak=    3.372 closest distance to " O   HOH Z  64 " =    2.130
peak=    3.371 closest distance to " O   HOH Z 329 " =    3.792
peak=    3.371 closest distance to " CA  ALA A 291 " =    0.920
peak=    3.369 closest distance to " CA  THR A 221 " =    0.987
peak=    3.369 closest distance to " CA  ALA A 158 " =    1.137
peak=    3.368 closest distance to " O   MET A 105 " =    1.776
peak=    3.364 closest distance to " CB  LEU A 143 " =    1.112
peak=    3.364 closest distance to " CB  VAL A 202 " =    1.629
peak=    3.362 closest distance to " CD  LYS A 166 " =    1.227
peak=    3.361 closest distance to " CB  ALA A 291 " =    1.364
peak=    3.359 closest distance to " O   HOH Z 295 " =    1.609
peak=    3.357 closest distance to " O   HOH Z 305 " =    3.567
peak=    3.354 closest distance to " CA  TYR A 116 " =    1.292
peak=    3.345 closest distance to " CG1 ILE A 151 " =    0.992
peak=    3.338 closest distance to " CA  ILE A 234 " =    0.951
peak=    3.329 closest distance to " O   HOH Z 213 " =    2.675
peak=    3.327 closest distance to " O   ASN A 209 " =    1.327
peak=    3.325 closest distance to " CE1 TYR A 186 " =    1.372
peak=    3.321 closest distance to " O   ARG A 145 " =    1.702
peak=    3.318 closest distance to " CB  ASN A 224 " =    0.949
peak=    3.317 closest distance to " CA  ARG A 195 " =    1.247
peak=    3.314 closest distance to " O   HOH Z 345 " =    3.501
peak=    3.312 closest distance to " CA  ALA A  51 " =    0.907
peak=    3.312 closest distance to " O   HOH Z  93 " =    2.438
peak=    3.310 closest distance to " O   HOH Z  44 " =    2.973
peak=    3.310 closest distance to " O   HOH Z 266 " =    3.334
peak=    3.300 closest distance to " OG  SER A  22 " =    2.794
peak=    3.298 closest distance to " O   HOH Z 402 " =    1.422
peak=    3.296 closest distance to " O   HOH Z 406 " =    1.606
peak=    3.292 closest distance to " CB  GLN A  88 " =    1.258
peak=    3.290 closest distance to " O   TYR A 116 " =    1.343
peak=    3.288 closest distance to " O   HOH Z 213 " =    1.840
peak=    3.286 closest distance to " NH2BARG A 145 " =    2.007
peak=    3.285 closest distance to " NH2BARG A 190 " =    1.572
peak=    3.284 closest distance to " CB  ILE A 120 " =    1.275
peak=    3.284 closest distance to " O   HOH Z 325 " =    3.832
peak=    3.281 closest distance to " N   ARG A 156 " =    1.282
peak=    3.279 closest distance to " CA  LYS A 290 " =    1.390
peak=    3.277 closest distance to " O   ALA A 165 " =    1.403
peak=    3.268 closest distance to " O   HOH Z 435 " =    1.863
peak=    3.266 closest distance to " O   HOH Z 292 " =    1.731
peak=    3.265 closest distance to " O   HOH Z 285 " =    2.725
peak=    3.264 closest distance to " O   HOH Z 116 " =    2.959
peak=    3.260 closest distance to " CG  LYS A  76 " =    0.978
peak=    3.258 closest distance to " O   HOH Z 146 " =    1.711
peak=    3.254 closest distance to " O   HOH Z 310 " =    2.248
peak=    3.249 closest distance to " CB  ARG A 138 " =    0.999
peak=    3.247 closest distance to " O   HOH Z 153 " =    1.729
peak=    3.246 closest distance to " CB  VAL A 126 " =    1.096
peak=    3.246 closest distance to " OG  SER A  97 " =    3.529
peak=    3.246 closest distance to " CB  LYS A 117 " =    1.220
peak=    3.244 closest distance to " CB  TRP A 150 " =    1.325
peak=    3.242 closest distance to " O   HOH Z 185 " =    2.202
peak=    3.242 closest distance to " CD1 ILE A 106 " =    0.793
peak=    3.240 closest distance to " CB  GLU A  46 " =    0.983
peak=    3.237 closest distance to " O   HOH Z 148 " =    3.410
peak=    3.234 closest distance to " O   HOH Z 162 " =    2.047
peak=    3.233 closest distance to " NE AARG A 275 " =    1.346
peak=    3.231 closest distance to " CA  LYS A 117 " =    1.192
peak=    3.231 closest distance to " CG  MET A 113 " =    1.280
peak=    3.229 closest distance to " CA  ALA A 299 " =    0.877
peak=    3.226 closest distance to " O   HOH Z 403 " =    1.360
peak=    3.220 closest distance to " NH2AARG A 275 " =    3.604
peak=    3.213 closest distance to " O   HOH Z 257 " =    2.264
peak=    3.212 closest distance to " N   ASN A 127 " =    1.297
peak=    3.211 closest distance to " OG  SER A  62 " =    2.958
peak=    3.209 closest distance to " CE BLYS A 290 " =    1.254
peak=    3.206 closest distance to " O   HOH Z 109 " =    2.612
peak=    3.203 closest distance to " CG1 VAL A 153 " =    0.939
peak=    3.202 closest distance to " O   HOH Z  97 " =    1.968
peak=    3.198 closest distance to " CB  THR A 235 " =    1.028
peak=    3.195 closest distance to " O   HOH Z  53 " =    2.571
peak=    3.193 closest distance to " CA  GLU A  46 " =    0.808
peak=    3.193 closest distance to " O   HOH Z 132 " =    3.441
peak=    3.191 closest distance to " CB  ALA A 248 " =    0.899
peak=    3.191 closest distance to " CB  MET A  47 " =    1.214
peak=    3.187 closest distance to " O   HOH Z 365 " =    2.854
peak=    3.186 closest distance to " O   HOH Z 108 " =    2.208
peak=    3.185 closest distance to " CD  PRO A 243 " =    1.625
peak=    3.184 closest distance to " NH1 ARG A 138 " =    1.116
peak=    3.184 closest distance to " CB  LEU A 300 " =    0.921
peak=    3.183 closest distance to " OD1 ASN A 217 " =    1.667
peak=    3.182 closest distance to " O   HOH Z 359 " =    1.487
peak=    3.180 closest distance to " N   CYS A 260 " =    0.875
peak=    3.179 closest distance to " CB  MET A  40 " =    0.786
peak=    3.178 closest distance to " CB  GLN A  89 " =    1.352
peak=    3.177 closest distance to " CG BARG A 275 " =    1.491
peak=    3.176 closest distance to " O  BHOH Z 338 " =    2.351
peak=    3.176 closest distance to " CD2 LEU A 297 " =    0.892
peak=    3.174 closest distance to " O   HOH Z 411 " =    1.799
peak=    3.174 closest distance to " O   HOH Z 374 " =    2.716
peak=    3.172 closest distance to " O   HOH Z  66 " =    2.147
peak=    3.166 closest distance to " O   HOH Z 386 " =    2.890
peak=    3.166 closest distance to " O   HOH Z  88 " =    2.571
peak=    3.160 closest distance to " O   HOH Z 291 " =    1.919
peak=    3.156 closest distance to " O   HOH Z 116 " =    1.721
peak=    3.151 closest distance to " CA  ASN A 217 " =    1.228
peak=    3.151 closest distance to " O   HOH Z 227 " =    2.120
peak=    3.145 closest distance to " O   HOH Z 236 " =    1.522
peak=    3.143 closest distance to " CG  PRO A 213 " =    0.980
peak=    3.140 closest distance to " O   HOH Z 130 " =    3.807
peak=    3.138 closest distance to " O   HOH Z 357 " =    1.919
peak=    3.137 closest distance to " ND1 HIS A  81 " =    1.705
peak=    3.137 closest distance to " CA  TYR A 186 " =    1.542
peak=    3.137 closest distance to " CG1 VAL A 189 " =    1.866
peak=    3.136 closest distance to " OG  SER A  62 " =    3.042
peak=    3.136 closest distance to " O   HOH Z 417 " =    1.174
peak=    3.136 closest distance to " CD2 HIS A  81 " =    1.175
peak=    3.134 closest distance to " O   HOH Z  59 " =    1.900
peak=    3.126 closest distance to " CG1BVAL A  72 " =    1.533
peak=    3.122 closest distance to " O   HOH Z 422 " =    2.639
peak=    3.117 closest distance to " O   GLY A 302 " =    1.855
peak=    3.106 closest distance to " N   TYR A  15 " =    0.714
peak=    3.103 closest distance to " O   HOH Z 359 " =    4.252
peak=    3.099 closest distance to " O   HOH Z 336 " =    1.964
peak=    3.096 closest distance to " CB  ALA A   9 " =    1.560
peak=    3.096 closest distance to " O   HOH Z  20 " =    1.639
peak=    3.096 closest distance to " CD  ARG A 219 " =    1.141
peak=    3.082 closest distance to " CB  ILE A 234 " =    1.108
peak=    3.075 closest distance to " O   HOH Z  50 " =    1.590
peak=    3.073 closest distance to " O   HOH Z 423 " =    2.518
peak=    3.072 closest distance to " OG BSER A 134 " =    3.137
peak=    3.071 closest distance to " O   HOH Z  88 " =    2.328
peak=    3.066 closest distance to " CG  GLU A 277 " =    3.451
peak=    3.059 closest distance to " O   HOH Z 263 " =    1.720
peak=    3.034 closest distance to " CA  GLY A 136 " =    0.982
peak=    3.026 closest distance to " O   HOH Z 151 " =    2.335
peak=    3.009 closest distance to " O   HOH Z 214 " =    2.297

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 193         
Filter by distance & map next to the model:
   mapped sites are within: 0.561 - 5.989
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 192 from: 193
   mapped sites are within: 0.702 - 5.989

peak=   -4.795 closest distance to " CB  PRO A 243 " =    2.585
peak=   -4.534 closest distance to " CD  ARG A 156 " =    2.020
peak=   -4.514 closest distance to " O   HOH Z 377 " =    2.093
peak=   -4.488 closest distance to " O   HOH Z 266 " =    4.892
peak=   -4.305 closest distance to " O   VAL A  67 " =    2.634
peak=   -4.224 closest distance to " CG  GLN A 223 " =    1.855
peak=   -4.204 closest distance to " OG BSER A 134 " =    1.283
peak=   -4.088 closest distance to " O   HOH Z 435 " =    2.899
peak=   -4.068 closest distance to " O   HOH Z 372 " =    2.435
peak=   -4.048 closest distance to " CZ3 TRP A 179 " =    1.153
peak=   -4.021 closest distance to " C   HIS A 108 " =    1.159
peak=   -4.012 closest distance to " SG  CYS A 254 " =    3.462
peak=   -3.991 closest distance to " O   HOH Z 290 " =    1.193
peak=   -3.974 closest distance to " O   PRO A 198 " =    1.277
peak=   -3.962 closest distance to " CG1 VAL A 112 " =    2.847
peak=   -3.962 closest distance to " O   HOH Z 351 " =    1.509
peak=   -3.945 closest distance to " O   HOH Z 389 " =    1.966
peak=   -3.944 closest distance to " O   HOH Z 313 " =    1.885
peak=   -3.937 closest distance to " O   HOH Z 185 " =    2.156
peak=   -3.929 closest distance to " O   HOH Z 231 " =    2.166
peak=   -3.895 closest distance to " N   ALA A  43 " =    2.583
peak=   -3.860 closest distance to " O   VAL A  67 " =    2.718
peak=   -3.840 closest distance to " CA  GLY A  98 " =    1.897
peak=   -3.838 closest distance to " CB  ALA A 291 " =    2.194
peak=   -3.830 closest distance to " CB  ALA A  43 " =    2.491
peak=   -3.819 closest distance to " CE2 PHE A 218 " =    2.408
peak=   -3.814 closest distance to " CE2 TYR A  30 " =    2.750
peak=   -3.805 closest distance to " ND2 ASN A  45 " =    1.127
peak=   -3.805 closest distance to " O   HOH Z  60 " =    2.429
peak=   -3.782 closest distance to " O   PRO A 198 " =    1.257
peak=   -3.781 closest distance to " ND2 ASN A  45 " =    1.786
peak=   -3.772 closest distance to " CB  ALA A 291 " =    2.259
peak=   -3.765 closest distance to " CA  GLY A 203 " =    2.210
peak=   -3.761 closest distance to " O   HOH Z  43 " =    1.679
peak=   -3.760 closest distance to " O   HOH Z 198 " =    1.939
peak=   -3.745 closest distance to " O   ILE A 109 " =    2.565
peak=   -3.722 closest distance to " O   HOH Z 152 " =    5.098
peak=   -3.706 closest distance to " CB  TRP A  85 " =    2.441
peak=   -3.700 closest distance to " CD1 PHE A  59 " =    1.919
peak=   -3.695 closest distance to " CD  GLN A  58 " =    1.015
peak=   -3.689 closest distance to " CB  CYS A 254 " =    2.254
peak=   -3.679 closest distance to " OD1 ASP A 171 " =    1.598
peak=   -3.674 closest distance to " OG BSER A 134 " =    1.658
peak=   -3.654 closest distance to " O   HOH Z 407 " =    3.129
peak=   -3.651 closest distance to " CD1 LEU A 228 " =    2.277
peak=   -3.648 closest distance to " CG  PHE A 283 " =    2.643
peak=   -3.638 closest distance to " CD  ARG A 139 " =    1.547
peak=   -3.635 closest distance to " C   ALA A 158 " =    1.397
peak=   -3.635 closest distance to " O   VAL A 189 " =    2.532
peak=   -3.633 closest distance to " O   SER A 135 " =    1.450
peak=   -3.627 closest distance to " CZ  PHE A  59 " =    1.485
peak=   -3.624 closest distance to " O   PRO A 163 " =    1.981
peak=   -3.605 closest distance to " O   HOH Z 298 " =    1.238
peak=   -3.599 closest distance to " CE  MET A 105 " =    2.251
peak=   -3.595 closest distance to " CG  ASP A 231 " =    0.734
peak=   -3.594 closest distance to " CB  PHE A 192 " =    2.053
peak=   -3.591 closest distance to " CZ  TYR A 169 " =    1.569
peak=   -3.583 closest distance to " N   ASP A 286 " =    2.411
peak=   -3.571 closest distance to " CZ BARG A 275 " =    1.724
peak=   -3.556 closest distance to " CB  PRO A 163 " =    2.506
peak=   -3.554 closest distance to " CB  ASN A  39 " =    2.205
peak=   -3.543 closest distance to " OG  SER A  97 " =    2.195
peak=   -3.541 closest distance to " O   HOH Z  38 " =    1.581
peak=   -3.540 closest distance to " N   GLN A  58 " =    1.700
peak=   -3.540 closest distance to " O   HOH Z 198 " =    1.437
peak=   -3.520 closest distance to " O   HOH Z 211 " =    1.654
peak=   -3.520 closest distance to " CG  MET A 105 " =    0.952
peak=   -3.511 closest distance to " CD1 LEU A 101 " =    2.286
peak=   -3.506 closest distance to " O   HOH Z 409 " =    5.989
peak=   -3.500 closest distance to " O   HOH Z 359 " =    3.253
peak=   -3.500 closest distance to " CD2 LEU A 237 " =    2.831
peak=   -3.486 closest distance to " O   ARG A 145 " =    1.479
peak=   -3.474 closest distance to " O   HOH Z 353 " =    2.193
peak=   -3.464 closest distance to " O   HOH Z 385 " =    1.996
peak=   -3.462 closest distance to " C   LEU A 143 " =    1.259
peak=   -3.454 closest distance to " CD1 LEU A 297 " =    2.467
peak=   -3.453 closest distance to " OG  SER A  87 " =    1.320
peak=   -3.451 closest distance to " OD2 ASP A 171 " =    2.108
peak=   -3.451 closest distance to " NH2AARG A 275 " =    5.416
peak=   -3.450 closest distance to " O   HOH Z 316 " =    1.774
peak=   -3.449 closest distance to " CG  TRP A 266 " =    1.793
peak=   -3.448 closest distance to " O   HOH Z 426 " =    1.631
peak=   -3.446 closest distance to " O   SER A  95 " =    1.445
peak=   -3.437 closest distance to " O   HOH Z  13 " =    1.524
peak=   -3.436 closest distance to " O   HOH Z  11 " =    1.751
peak=   -3.422 closest distance to " O   HOH Z  63 " =    1.897
peak=   -3.415 closest distance to " C   LEU A 222 " =    0.702
peak=   -3.408 closest distance to " O   SER A  22 " =    2.466
peak=   -3.407 closest distance to " O   ALA A 161 " =    1.551
peak=   -3.399 closest distance to " O   HOH Z 131 " =    4.164
peak=   -3.397 closest distance to " CG1 VAL A 197 " =    2.176
peak=   -3.397 closest distance to " O   PRO A 243 " =    2.541
peak=   -3.396 closest distance to " N   MET A 188 " =    1.889
peak=   -3.395 closest distance to " O   HOH Z  52 " =    1.165
peak=   -3.391 closest distance to " CB  ALA A 248 " =    2.015
peak=   -3.387 closest distance to " O   HOH Z 377 " =    0.848
peak=   -3.369 closest distance to " O   HOH Z 102 " =    1.559
peak=   -3.367 closest distance to " NH1 ARG A 195 " =    2.588
peak=   -3.366 closest distance to " O   HOH Z 282 " =    1.094
peak=   -3.359 closest distance to " ND2 ASN A 187 " =    1.430
peak=   -3.356 closest distance to " CG2 THR A 178 " =    2.189
peak=   -3.356 closest distance to " O   HOH Z 137 " =    1.538
peak=   -3.352 closest distance to " CA  ASP A  27 " =    2.460
peak=   -3.348 closest distance to " CB  ASP A 286 " =    2.095
peak=   -3.346 closest distance to " O   HOH Z 114 " =    3.011
peak=   -3.340 closest distance to " OD1 ASN A 187 " =    1.590
peak=   -3.339 closest distance to " CB  PHE A 208 " =    2.227
peak=   -3.336 closest distance to " CG1 VAL A 250 " =    2.699
peak=   -3.330 closest distance to " CA  GLY A 133 " =    1.965
peak=   -3.329 closest distance to " O   HOH Z 111 " =    2.016
peak=   -3.327 closest distance to " O   HOH Z 348 " =    1.754
peak=   -3.325 closest distance to " O   HOH Z 244 " =    2.045
peak=   -3.323 closest distance to " O   HOH Z 193 " =    1.922
peak=   -3.323 closest distance to " OXT GLY A 302 " =    3.433
peak=   -3.322 closest distance to " O   HOH Z 417 " =    2.339
peak=   -3.319 closest distance to " NE  ARG A  36 " =    1.883
peak=   -3.318 closest distance to " CE  LYS A  76 " =    2.772
peak=   -3.316 closest distance to " N   THR A 157 " =    1.509
peak=   -3.312 closest distance to " OD1 ASN A 148 " =    1.647
peak=   -3.310 closest distance to " O   HOH Z  51 " =    1.220
peak=   -3.309 closest distance to " CG2 ILE A 263 " =    2.280
peak=   -3.308 closest distance to " NH1AARG A 275 " =    1.783
peak=   -3.296 closest distance to " N   SER A 212 " =    1.877
peak=   -3.294 closest distance to " CB  ASP A 132 " =    2.336
peak=   -3.290 closest distance to " CG  GLN A  88 " =    0.870
peak=   -3.281 closest distance to " O   GLY A 211 " =    1.318
peak=   -3.280 closest distance to " O   HOH Z 317 " =    1.587
peak=   -3.279 closest distance to " CE3 TRP A 274 " =    1.046
peak=   -3.274 closest distance to " CA  GLY A 241 " =    2.220
peak=   -3.272 closest distance to " CG1 VAL A 268 " =    2.419
peak=   -3.269 closest distance to " O   PHE A 218 " =    1.552
peak=   -3.267 closest distance to " O   HOH Z  73 " =    2.183
peak=   -3.266 closest distance to " O   HOH Z 266 " =    4.711
peak=   -3.257 closest distance to " CG  GLU A 152 " =    1.092
peak=   -3.256 closest distance to " CB  ALA A 131 " =    2.010
peak=   -3.256 closest distance to " CB  TYR A  15 " =    2.185
peak=   -3.256 closest distance to " O   GLY A  80 " =    2.412
peak=   -3.256 closest distance to " O   HOH Z 263 " =    3.099
peak=   -3.252 closest distance to " O   HOH Z 414 " =    2.367
peak=   -3.243 closest distance to " O   HOH Z 191 " =    5.570
peak=   -3.241 closest distance to " OXT GLY A 302 " =    2.892
peak=   -3.240 closest distance to " O   HOH Z  10 " =    1.458
peak=   -3.239 closest distance to " CG  PRO A 163 " =    2.497
peak=   -3.238 closest distance to " ND2 ASN A  69 " =    1.607
peak=   -3.238 closest distance to " O   GLY A  17 " =    1.163
peak=   -3.236 closest distance to " O   VAL A 174 " =    2.202
peak=   -3.235 closest distance to " NH2 ARG A  79 " =    1.927
peak=   -3.235 closest distance to " CE3 TRP A 123 " =    1.300
peak=   -3.229 closest distance to " ND2 ASN A  60 " =    1.952
peak=   -3.229 closest distance to " O   HOH Z 324 " =    2.163
peak=   -3.223 closest distance to " CE3 TRP A 274 " =    2.348
peak=   -3.221 closest distance to " O   HOH Z 111 " =    1.233
peak=   -3.219 closest distance to " N   ALA A 248 " =    1.551
peak=   -3.212 closest distance to " CB  ALA A 248 " =    2.414
peak=   -3.210 closest distance to " O   VAL A 189 " =    1.596
peak=   -3.206 closest distance to " ND2 ASN A 249 " =    2.294
peak=   -3.205 closest distance to " N   THR A 235 " =    1.336
peak=   -3.195 closest distance to " OG  SER A 245 " =    1.163
peak=   -3.193 closest distance to " O   HOH Z 222 " =    1.172
peak=   -3.192 closest distance to " O   HOH Z 184 " =    1.773
peak=   -3.191 closest distance to " CA  GLY A 241 " =    3.189
peak=   -3.188 closest distance to " O   HOH Z 140 " =    1.649
peak=   -3.186 closest distance to " CD  GLU A 277 " =    1.160
peak=   -3.184 closest distance to " O   HOH Z   6 " =    1.433
peak=   -3.179 closest distance to " O   HOH Z 149 " =    2.233
peak=   -3.177 closest distance to " CD2 PHE A 225 " =    1.112
peak=   -3.175 closest distance to " O   HOH Z 282 " =    4.741
peak=   -3.171 closest distance to " O   HOH Z 281 " =    3.043
peak=   -3.164 closest distance to " CD2 PHE A  61 " =    1.996
peak=   -3.164 closest distance to " C   LYS A  76 " =    1.723
peak=   -3.147 closest distance to " O   HOH Z 250 " =    1.426
peak=   -3.139 closest distance to " CA  TRP A 274 " =    1.409
peak=   -3.137 closest distance to " CB  PRO A  54 " =    2.396
peak=   -3.131 closest distance to " O   HOH Z 241 " =    1.401
peak=   -3.131 closest distance to " O   ALA A  10 " =    1.641
peak=   -3.131 closest distance to " N   ASP A 171 " =    2.313
peak=   -3.128 closest distance to " O   HOH Z 175 " =    4.297
peak=   -3.127 closest distance to " O   HOH Z 281 " =    2.754
peak=   -3.123 closest distance to " O   HOH Z 253 " =    3.925
peak=   -3.122 closest distance to " OD2 ASP A 191 " =    1.469
peak=   -3.121 closest distance to " C   GLY A  13 " =    1.058
peak=   -3.120 closest distance to " O   HOH Z 123 " =    2.463
peak=   -3.118 closest distance to " OE1 GLN A  88 " =    1.247
peak=   -3.116 closest distance to " O   HOH Z 417 " =    2.718
peak=   -3.114 closest distance to " O   HOH Z 292 " =    1.615
peak=   -3.110 closest distance to " OD1AASN A 224 " =    1.813
peak=   -3.103 closest distance to " C   MET A 188 " =    1.454
peak=   -3.088 closest distance to " CD1 TRP A 179 " =    1.026
peak=   -3.045 closest distance to " OH  TYR A 247 " =    1.773
peak=   -3.045 closest distance to " SG ACYS A 201 " =    1.939
peak=   -3.043 closest distance to " O   HOH Z 283 " =    5.631
peak=   -3.003 closest distance to " CD1 LEU A 228 " =    2.059

================= 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    :  0.3677 0.3658   6.145707e+00   6.137920e+00
   1_bss:  0.3550 0.3567   6.129243e+00   6.118168e+00
   1_xyz:  0.1955 0.2206   5.594126e+00   5.696119e+00
   1_adp:  0.1779 0.2301   5.542466e+00   5.737463e+00
   1_occ:  0.1776 0.2299   5.541155e+00   5.736302e+00
   2_bss:  0.1748 0.2261   5.525825e+00   5.719032e+00
   2_xyz:  0.1337 0.1823   5.297553e+00   5.528124e+00
   2_adp:  0.1288 0.1707   5.248872e+00   5.463171e+00
   2_occ:  0.1286 0.1708   5.248477e+00   5.463553e+00
   3_bss:  0.1286 0.1702   5.245386e+00   5.460275e+00
   3_xyz:  0.1137 0.1570   5.146082e+00   5.381069e+00
   3_adp:  0.1105 0.1546   5.126707e+00   5.368830e+00
   3_occ:  0.1104 0.1546   5.126722e+00   5.369064e+00
   4_bss:  0.1104 0.1545   5.126260e+00   5.368668e+00
   4_xyz:  0.1087 0.1540   5.119176e+00   5.367922e+00
   4_adp:  0.1079 0.1542   5.118418e+00   5.371420e+00
   4_occ:  0.1079 0.1543   5.118559e+00   5.371785e+00
   5_bss:  0.1078 0.1543   5.118543e+00   5.371774e+00
   5_xyz:  0.1068 0.1546   5.113419e+00   5.372225e+00
   5_adp:  0.1068 0.1544   5.112055e+00   5.370992e+00
   5_occ:  0.1068 0.1543   5.112050e+00   5.371081e+00
   5_bss:  0.1068 0.1538   5.110691e+00   5.367015e+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:  0.335  41.102  -1.506   2.082  -1.591   0.000  -0.000  -0.000
   1_xyz:  0.335  41.102  -1.506   2.082  -1.591   0.000  -0.000  -0.000
   1_adp:  0.335  41.102  -1.506   2.082  -1.591   0.000  -0.000  -0.000
   1_occ:  0.335  41.102  -1.506   2.082  -1.591   0.000  -0.000  -0.000
   2_bss:  0.329  49.453  -2.223  -1.474  -1.686  -0.000  -0.000  -0.000
   2_xyz:  0.329  49.453  -2.223  -1.474  -1.686  -0.000  -0.000  -0.000
   2_adp:  0.329  49.453  -2.223  -1.474  -1.686  -0.000  -0.000  -0.000
   2_occ:  0.329  49.453  -2.223  -1.474  -1.686  -0.000  -0.000  -0.000
   3_bss:  0.326  49.453  -2.415  -2.384  -1.539  -0.000  -0.000  -0.000
   3_xyz:  0.326  49.453  -2.415  -2.384  -1.539  -0.000  -0.000  -0.000
   3_adp:  0.326  49.453  -2.415  -2.384  -1.539  -0.000  -0.000  -0.000
   3_occ:  0.326  49.453  -2.415  -2.384  -1.539  -0.000  -0.000  -0.000
   4_bss:  0.326  49.453  -2.385  -2.585  -1.479  -0.000  -0.000  -0.000
   4_xyz:  0.326  49.453  -2.385  -2.585  -1.479  -0.000  -0.000  -0.000
   4_adp:  0.326  49.453  -2.385  -2.585  -1.479  -0.000  -0.000  -0.000
   4_occ:  0.326  49.453  -2.385  -2.585  -1.479  -0.000  -0.000  -0.000
   5_bss:  0.326  49.453  -2.188  -2.487  -1.270  -0.000  -0.000  -0.000
   5_xyz:  0.326  49.453  -2.188  -2.487  -1.270  -0.000  -0.000  -0.000
   5_adp:  0.326  49.453  -2.188  -2.487  -1.270  -0.000  -0.000  -0.000
   5_occ:  0.326  49.453  -2.188  -2.487  -1.270  -0.000  -0.000  -0.000
   5_bss:  0.322  49.427  -2.043  -2.381  -1.119  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  40.060 0.6445  0.8360    40726.277
   1_bss:  39.161 0.6533  0.8382    37904.118
   1_xyz:  21.096 0.8526  1.0114    12537.534
   1_adp:  22.290 0.8400  1.0008    13476.007
   1_occ:  22.274 0.8401  1.0004    13420.466
   2_bss:  21.669 0.8459  0.9566    12821.793
   2_xyz:  17.015 0.8890  0.9846     8360.947
   2_adp:  15.466 0.9032  0.9903     7475.722
   2_occ:  15.476 0.9031  0.9901     7478.087
   3_bss:  15.377 0.9038  0.9792     7407.924
   3_xyz:  13.819 0.9162  0.9844     6254.130
   3_adp:  13.559 0.9185  0.9810     6097.312
   3_occ:  13.565 0.9184  0.9809     6098.292
   4_bss:  13.556 0.9185  0.9798     6094.654
   4_xyz:  13.498 0.9192  0.9790     6103.311
   4_adp:  13.568 0.9187  0.9734     6130.634
   4_occ:  13.574 0.9186  0.9733     6133.930
   5_bss:  13.576 0.9186  0.9793     6134.872
   5_xyz:  13.550 0.9187  0.9797     6136.631
   5_adp:  13.514 0.9191  0.9743     6111.333
   5_occ:  13.516 0.9190  0.9743     6110.944
   5_bss:  13.475 0.9192  0.9783     6035.302
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.110   1.6441e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.110   1.6441e-01
   1_xyz:   1.362  0.013  0.091 15.289  0.007  4.111   1.1925e-01
   1_adp:   1.362  0.013  0.091 15.289  0.007  4.111   1.1925e-01
   1_occ:   1.362  0.013  0.091 15.289  0.007  4.111   1.1925e-01
   2_bss:   1.362  0.013  0.091 15.289  0.007  4.111   1.1925e-01
   2_xyz:   0.970  0.006  0.072 14.655  0.004  4.115   5.5965e-02
   2_adp:   0.970  0.006  0.072 14.655  0.004  4.115   5.5965e-02
   2_occ:   0.970  0.006  0.072 14.655  0.004  4.115   5.5965e-02
   3_bss:   0.970  0.006  0.072 14.655  0.004  4.115   5.5965e-02
   3_xyz:   1.033  0.008  0.079 14.959  0.004  4.118   6.5539e-02
   3_adp:   1.033  0.008  0.079 14.959  0.004  4.118   6.5539e-02
   3_occ:   1.033  0.008  0.079 14.959  0.004  4.118   6.5539e-02
   4_bss:   1.033  0.008  0.079 14.959  0.004  4.118   6.5539e-02
   4_xyz:   1.006  0.007  0.076 14.832  0.004  4.118   6.1667e-02
   4_adp:   1.006  0.007  0.076 14.832  0.004  4.118   6.1667e-02
   4_occ:   1.006  0.007  0.076 14.832  0.004  4.118   6.1667e-02
   5_bss:   1.006  0.007  0.076 14.832  0.004  4.118   6.1667e-02
   5_xyz:   1.024  0.008  0.077 14.852  0.004  4.119   6.3808e-02
   5_adp:   1.024  0.008  0.077 14.852  0.004  4.119   6.3808e-02
   5_occ:   1.024  0.008  0.077 14.852  0.004  4.119   6.3808e-02
   5_bss:   1.024  0.008  0.077 14.852  0.004  4.119   6.3808e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4020e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4020e-01
   1_xyz:   9.206  0.115  0.405 85.210  0.062  2.181   2.8743e-01
   1_adp:   9.206  0.115  0.405 85.210  0.062  2.181   2.8743e-01
   1_occ:   9.206  0.115  0.405 85.210  0.062  2.181   2.8743e-01
   2_bss:   9.206  0.115  0.405 85.210  0.062  2.181   2.8743e-01
   2_xyz:   7.586  0.047  0.220 83.073  0.037  2.324   4.2942e-02
   2_adp:   7.586  0.047  0.220 83.073  0.037  2.324   4.2942e-02
   2_occ:   7.586  0.047  0.220 83.073  0.037  2.324   4.2942e-02
   3_bss:   7.586  0.047  0.220 83.073  0.037  2.324   4.2942e-02
   3_xyz:   7.667  0.042  0.245 85.794  0.032  2.252   5.7147e-02
   3_adp:   7.667  0.042  0.245 85.794  0.032  2.252   5.7147e-02
   3_occ:   7.667  0.042  0.245 85.794  0.032  2.252   5.7147e-02
   4_bss:   7.667  0.042  0.245 85.794  0.032  2.252   5.7147e-02
   4_xyz:   7.341  0.037  0.230 84.856  0.040  2.308   4.6889e-02
   4_adp:   7.341  0.037  0.230 84.856  0.040  2.308   4.6889e-02
   4_occ:   7.341  0.037  0.230 84.856  0.040  2.308   4.6889e-02
   5_bss:   7.341  0.037  0.230 84.856  0.040  2.308   4.6889e-02
   5_xyz:   7.283  0.035  0.247 85.018  0.033  2.268   4.9346e-02
   5_adp:   7.283  0.035  0.247 85.018  0.033  2.268   4.9346e-02
   5_occ:   7.283  0.035  0.247 85.018  0.033  2.268   4.9346e-02
   5_bss:   7.283  0.035  0.247 85.018  0.033  2.268   4.9346e-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:  85.67   0.00  17.44  74.15   0.00  13.11  85.67   6.30  40.97
   1_occ:  85.67   0.00  17.44  74.15   0.00  13.11  85.67   6.30  40.97
   2_bss:  85.67   0.00  17.44  74.15   0.00  13.11  85.67   6.30  40.97
   2_xyz:  85.67   0.00  17.44  74.15   0.00  13.11  85.67   6.30  40.97
   2_adp:  74.99   1.93  16.70  74.99   1.93  12.86  74.81   6.85  37.65
   2_occ:  74.99   1.93  16.70  74.99   1.93  12.86  74.81   6.85  37.65
   3_bss:  74.99   1.93  16.70  74.99   1.93  12.86  74.81   6.85  37.65
   3_xyz:  74.99   1.93  16.70  74.99   1.93  12.86  74.81   6.85  37.65
   3_adp:  80.01   1.03  16.81  80.01   1.03  12.83  76.74   6.81  38.49
   3_occ:  80.01   1.03  16.81  80.01   1.03  12.83  76.74   6.81  38.49
   4_bss:  80.01   1.03  16.81  80.01   1.03  12.83  76.74   6.81  38.49
   4_xyz:  80.01   1.03  16.81  80.01   1.03  12.83  76.74   6.81  38.49
   4_adp:  82.43   0.86  16.75  82.43   0.86  12.74  78.72   6.58  38.60
   4_occ:  82.43   0.86  16.75  82.43   0.86  12.74  78.72   6.58  38.60
   5_bss:  82.43   0.86  16.75  82.43   0.86  12.74  78.72   6.58  38.60
   5_xyz:  82.43   0.86  16.75  82.43   0.86  12.74  78.72   6.58  38.60
   5_adp:  84.16   0.77  16.56  84.16   0.77  12.59  80.68   6.54  38.19
   5_occ:  84.16   0.77  16.56  84.16   0.77  12.59  80.68   6.54  38.19
   5_bss:  84.13   0.74  16.54  84.13   0.74  12.57  80.66   6.51  38.16
------------------------------------------------------------------------
 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:    1.131    0.025    0.420
   1_adp:    1.131    0.025    0.420
   1_occ:    1.131    0.025    0.420
   2_bss:    1.131    0.025    0.420
   2_xyz:    0.967    0.025    0.454
   2_adp:    0.967    0.025    0.454
   2_occ:    0.967    0.025    0.454
   3_bss:    0.967    0.025    0.454
   3_xyz:    0.965    0.023    0.501
   3_adp:    0.965    0.023    0.501
   3_occ:    0.965    0.023    0.501
   4_bss:    0.965    0.023    0.501
   4_xyz:    1.164    0.062    0.512
   4_adp:    1.164    0.062    0.512
   4_occ:    1.164    0.062    0.512
   5_bss:    1.164    0.062    0.512
   5_xyz:    1.282    0.058    0.520
   5_adp:    1.282    0.058    0.520
   5_occ:    1.282    0.058    0.520
   5_bss:    1.282    0.058    0.520
------------------------------------------------------------------------

CPU time actual refinement: 265.65


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_873/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_873/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_873/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_873/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_873/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 265.52 
  Macro-tasks:
    bulk solvent and scale       = 30.63  
    individual site refinement   = 110.13 
    weights calculation          = 24.19  
    collect and process          = 5.43   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 170.47 
  Micro-tasks:
    mask                            = 1.47   
    f_calc                          = 83.87  
    alpha_beta                      = 6.88   
    target                          = 0.98   
    gradients_wrt_atomic_parameters = 92.04  
    fmodel                         = 5.50   
    r_factors                      = 0.05   
    phase_errors                   = 9.02   
    foms                           = 0.22   
    TOTAL for micro-tasks          = 200.03 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 3.760 micro seconds
Total CPU time: 4.62 minutes
from_scatterers_fft:    645 calls, 83.64 s
gradients_fft:          590 calls, 80.41 s

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

# Date 2008-01-16 Time 05:51:18 PST -0800 (1200491478.92 s)
Start R-work = 0.3677, R-free = 0.3658 (no bulk solvent and anisotropic scale)
Final R-work = 0.1309, R-free = 0.1744 (no bulk solvent and anisotropic scale)

Start R-work = 0.3550, R-free = 0.3567
Final R-work = 0.1068, R-free = 0.1538