# Date 2008-01-16 Time 04:31:25 PST -0800 (1200486685.36 s)
#phil __OFF__

Command line arguments: "../348.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 25223
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 348

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.1963, 47.8686, 87.2539, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 47.8686, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9854 1.97081
Completeness in resolution range: 0.930152
Completeness with d_max=infinity: 0.927334

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9854
                             d_min =   1.9708

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 47.8686, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9854 1.97081
Completeness in resolution range: 0.930152
Completeness with d_max=infinity: 0.927334

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9858 -  4.2174 [2212/2240]  1988   224  10.1%
  bin  2:  4.2174 -  3.3599 [2115/2138]  1904   211  10.0%
  bin  3:  3.3599 -  2.9388 [2092/2117]  1883   209  10.0%
  bin  4:  2.9388 -  2.6718 [2082/2098]  1874   208  10.0%
  bin  5:  2.6718 -  2.4812 [2038/2082]  1832   206  10.1%
  bin  6:  2.4812 -  2.3355 [2063/2091]  1861   202   9.8%
  bin  7:  2.3355 -  2.2189 [2036/2072]  1833   203  10.0%
  bin  8:  2.2189 -  2.1226 [2038/2080]  1833   205  10.1%
  bin  9:  2.1226 -  2.0411 [2018/2064]  1823   195   9.7%
  bin 10:  2.0411 -  1.9708 [ 895/2078]   799    96  10.7%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_348/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.15 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.50 -     2.18: 12
        2.18 -     2.86: 1160
        2.86 -     3.54: 4421
        3.54 -     4.22: 9134
        4.22 -     4.90: 13432
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.504 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  81 " - " O   HOH Z 186 "  1.611 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.706 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  70 " - " O   HOH Z 296 "  1.791 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  ... (remaining 28154 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_348/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_348/model_refine_001.geo

CPU time processing inputs: 9.07


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.19625 47.8686 87.2539 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 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4373   r_free= 0.4254   ksol= 0.00   Bsol= 0.00   scale= 0.907    |
|                                                                             |
| 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:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.245977                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9858 -  4.7040 0.99   1438  159 0.3433 0.3679      6.5063      6.5385|
|  2:  4.7040 -  3.7530 0.99   1383  155 0.3727 0.3693       6.752      6.7461|
|  3:  3.7530 -  3.2843 0.99   1348  149 0.4085 0.3781      6.6158      6.5638|
|  4:  3.2843 -  2.9866 0.99   1350  144 0.4250 0.3900      6.4515      6.3984|
|  5:  2.9866 -  2.7740 0.98   1333  151 0.4663 0.4156      6.3281      6.3252|
|  6:  2.7740 -  2.6114 0.99   1336  149 0.4653 0.4807      6.2425      6.1298|
|  7:  2.6114 -  2.4812 0.98   1293  151 0.4661 0.4281      6.1889      6.1005|
|  8:  2.4812 -  2.3736 0.99   1334  138 0.4849 0.4500      6.1541      6.1218|
|  9:  2.3736 -  2.2826 0.99   1327  152 0.4827 0.4606      6.0883      6.1426|
| 10:  2.2826 -  2.2041 0.98   1322  142 0.4925 0.4627      6.0782      6.0429|
| 11:  2.2041 -  2.1353 0.97   1294  147 0.5012 0.4870      6.0126      6.0041|
| 12:  2.1353 -  2.0745 0.99   1298  151 0.4898 0.5071       5.928      5.9813|
| 13:  2.0745 -  2.0200 0.91   1227  128 0.5043 0.5519      5.8542      5.8363|
| 14:  2.0200 -  1.9708 0.26    347   43 0.4627 0.4499      5.8649      5.7087|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9858 -  4.7040  1438   159  0.71  33.55   0.84     0.73      67027.09|
|  2:  4.7040 -  3.7530  1383   155  0.74  31.35   0.93     0.83      86179.07|
|  3:  3.7530 -  3.2843  1348   149  0.68  37.54   0.91     0.84      87180.68|
|  4:  3.2843 -  2.9866  1350   144  0.61  42.91   0.92     0.79      74157.67|
|  5:  2.9866 -  2.7740  1333   151  0.54  48.49   0.90     0.73      61095.54|
|  6:  2.7740 -  2.6114  1336   149  0.53  49.76   0.91     0.70      52295.35|
|  7:  2.6114 -  2.4812  1293   151  0.52  50.42   0.93     0.69      48361.13|
|  8:  2.4812 -  2.3736  1334   138  0.51  51.26   0.92     0.69      43987.82|
|  9:  2.3736 -  2.2826  1327   152  0.50  52.04   0.92     0.71      42687.29|
| 10:  2.2826 -  2.2041  1322   142  0.48  53.94   0.94     0.68      39571.49|
| 11:  2.2041 -  2.1353  1294   147  0.43  57.59   0.94     0.66      40937.60|
| 12:  2.1353 -  2.0745  1298   151  0.37  62.30   0.93     0.58      40646.10|
| 13:  2.0745 -  2.0200  1227   128  0.32  66.09   0.92     0.52      37269.96|
| 14:  2.0200 -  1.9708   347    43  0.36  63.00   1.00     0.46      28976.71|
|alpha:            min =        0.46 max =            0.84 mean =         0.70|
|beta:             min =    28976.71 max =        87180.68 mean =     55371.37|
|figures of merit: min =        0.00 max =            1.00 mean =         0.53|
|phase err.(work): min =        0.00 max =           89.99 mean =        48.98|
|phase err.(test): min =        0.00 max =           89.93 mean =        49.14|
|-----------------------------------------------------------------------------|

============================== 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 = 13.474504             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 91.218   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.428828              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.804   (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 |  1.504 -  1.844:        5 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.844 -  2.183:        7 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.183 -  2.523:       31 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.523 -  2.862:     1129 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.862 -  3.202:     1929 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.202 -  3.542:     2492 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.542 -  3.881:     4617 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.881 -  4.221:     4517 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.221 -  4.560:     6101 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.560 -  4.900:     7331 |
|-----------------------------------------------------------------------------|
|-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 |        0.174 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.112    4.900  1.504 |       0.336 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.973)------------------------------------------|
|    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 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4373   r_free= 0.4254   ksol= 0.00   Bsol= 0.00   scale= 0.907    |
|                                                                             |
| 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:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.245977                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4287   r_free= 0.4145   ksol= 0.29   Bsol= 27.32   scale= 0.946   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.93,4.20,-0.07,0.00,-0.00,-0.00); trace/3= 0.74                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.236783                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.958873             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.808   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.795667              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.587   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4287      final r-factor (work) = 0.2756          |
| start r-factor (free) = 0.4145      final r-factor (free) = 0.3011          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 37.4643 = 11.96 * 0.50 * 6.2364 + 1.00 * 0.1739                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 36.2093 = 11.96 * 0.50 * 6.0348 + 1.00 * 0.1245                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2756      final r-factor (work) = 0.2493          |
| start r-factor (free) = 0.3011      final r-factor (free) = 0.3159          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8077 = 0.80 * 1.00 * 6.0348 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6545 = 0.80 * 1.00 * 5.8324 + 1.00 * 0.0139                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.973)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.39   17.77    None  None   None       |
|    all(noH): 2823   0      0.00    85.39   17.77    None  None   None       |
|    Sol.    : 438    0      3.51    85.39   39.34    None  None   None       |
|    Mac.    : 2385   0      0.00    76.42   13.81    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 -   8.539:  780   |   5:    42.695 -  51.234:  102        |
|      1:     8.539 -  17.078: 1043   |   6:    51.234 -  59.772:   81        |
|      2:    17.078 -  25.617:  422   |   7:    59.772 -  68.311:   35        |
|      3:    25.617 -  34.156:  199   |   8:    68.311 -  76.850:   17        |
|      4:    34.156 -  42.695:  137   |   9:    76.850 -  85.389:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2493 r_free = 0.3159             target_work(ml) = 5.847         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2491 r_free = 0.3163             target_work(ml) = 5.847         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2491   r_free= 0.3163   ksol= 0.29   Bsol= 27.32   scale= 1.026   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.93,4.20,-0.07,0.00,-0.00,-0.00); trace/3= 0.74                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.847349                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2456   r_free= 0.3133   ksol= 0.32   Bsol= 62.67   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.47,0.85,-0.55,0.00,-0.00,-0.00); trace/3= -0.72                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.841053                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.364387              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.903  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.436382              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 146.231  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2456      final r-factor (work) = 0.1853          |
| start r-factor (free) = 0.3133      final r-factor (free) = 0.2291          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.8553 = 4.36 * 0.50 * 5.8339 + 1.00 * 0.1245                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.5858 = 4.36 * 0.50 * 5.7370 + 1.00 * 0.0666                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1853      final r-factor (work) = 0.1702          |
| start r-factor (free) = 0.2291      final r-factor (free) = 0.2115          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5173 = 0.44 * 1.00 * 5.7370 + 1.00 * 0.0138                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4253 = 0.44 * 1.00 * 5.5326 + 1.00 * 0.0110                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.973)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.42   17.74    None  None   None       |
|    all(noH): 2823   0      0.00    86.42   17.74    None  None   None       |
|    Sol.    : 438    0      5.63    84.12   41.55    None  None   None       |
|    Mac.    : 2385   0      0.00    86.42   13.37    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 -   8.642:  791   |   5:    43.211 -  51.853:  106        |
|      1:     8.642 -  17.284: 1178   |   6:    51.853 -  60.495:   85        |
|      2:    17.284 -  25.927:  322   |   7:    60.495 -  69.138:   41        |
|      3:    25.927 -  34.569:  148   |   8:    69.138 -  77.780:   26        |
|      4:    34.569 -  43.211:  116   |   9:    77.780 -  86.422:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1702 r_free = 0.2115             target_work(ml) = 5.501         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1700 r_free = 0.2116             target_work(ml) = 5.501         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1700   r_free= 0.2116   ksol= 0.32   Bsol= 62.67   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.47,0.85,-0.55,0.00,-0.00,-0.00); trace/3= -0.72                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.501053                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1698   r_free= 0.2108   ksol= 0.33   Bsol= 62.67   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.66,-0.38,-0.61,-0.00,-0.00,-0.00); trace/3= -1.22                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.499658                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.115805              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 110.373  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.233349              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 151.986  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1698      final r-factor (work) = 0.1401          |
| start r-factor (free) = 0.2108      final r-factor (free) = 0.1834          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9203 = 2.12 * 0.50 * 5.5333 + 1.00 * 0.0666                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7800 = 2.12 * 0.50 * 5.4105 + 1.00 * 0.0562                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1401      final r-factor (work) = 0.1345          |
| start r-factor (free) = 0.1834      final r-factor (free) = 0.1764          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2736 = 0.23 * 1.00 * 5.4105 + 1.00 * 0.0110                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2490 = 0.23 * 1.00 * 5.3123 + 1.00 * 0.0093                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.973)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.47    84.57   17.30    None  None   None       |
|    all(noH): 2823   0      1.47    84.57   17.30    None  None   None       |
|    Sol.    : 438    0      5.76    84.01   41.01    None  None   None       |
|    Mac.    : 2385   0      1.47    84.57   12.94    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:     1.467 -   9.777: 1018   |   5:    43.016 -  51.326:   95        |
|      1:     9.777 -  18.087: 1051   |   6:    51.326 -  59.636:   82        |
|      2:    18.087 -  26.397:  269   |   7:    59.636 -  67.946:   41        |
|      3:    26.397 -  34.706:  123   |   8:    67.946 -  76.256:   27        |
|      4:    34.706 -  43.016:  108   |   9:    76.256 -  84.566:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1345 r_free = 0.1764             target_work(ml) = 5.293         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1344 r_free = 0.1765             target_work(ml) = 5.293         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1344   r_free= 0.1765   ksol= 0.33   Bsol= 62.67   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.66,-0.38,-0.61,-0.00,-0.00,-0.00); trace/3= -1.22                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.292939                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1347   r_free= 0.1766   ksol= 0.33   Bsol= 63.67   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.84,-1.11,-0.75,-0.00,-0.00,-0.00); trace/3= -1.57                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.293809                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.914304              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 120.412  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.312254              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 143.512  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1347      final r-factor (work) = 0.1232          |
| start r-factor (free) = 0.1766      final r-factor (free) = 0.1650          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1424 = 1.91 * 0.50 * 5.3138 + 1.00 * 0.0562                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0862 = 1.91 * 0.50 * 5.2527 + 1.00 * 0.0586                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1232      final r-factor (work) = 0.1206          |
| start r-factor (free) = 0.1650      final r-factor (free) = 0.1656          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.9021 = 1.31 * 1.00 * 5.2527 + 1.00 * 0.0092                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.8453 = 1.31 * 1.00 * 5.2077 + 1.00 * 0.0114                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.973)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.18   17.47    None  None   None       |
|    all(noH): 2823   0      0.00    98.18   17.47    None  None   None       |
|    Sol.    : 438    0      0.00    89.66   42.91    None  None   None       |
|    Mac.    : 2385   0      0.16    98.18   12.80    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.818: 1080   |   5:    49.090 -  58.908:   89        |
|      1:     9.818 -  19.636: 1100   |   6:    58.908 -  68.726:   73        |
|      2:    19.636 -  29.454:  202   |   7:    68.726 -  78.544:   36        |
|      3:    29.454 -  39.272:  124   |   8:    78.544 -  88.362:    9        |
|      4:    39.272 -  49.090:  105   |   9:    88.362 -  98.180:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1206 r_free = 0.1656             target_work(ml) = 5.208         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1205 r_free = 0.1657             target_work(ml) = 5.208         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1205   r_free= 0.1657   ksol= 0.33   Bsol= 63.67   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.84,-1.11,-0.75,-0.00,-0.00,-0.00); trace/3= -1.57                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.208194                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1204   r_free= 0.1656   ksol= 0.33   Bsol= 63.67   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.60,-1.10,-0.53,-0.00,-0.00,-0.00); trace/3= -1.41                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.208309                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.688481              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 140.666  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.180582              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 120.032  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1204      final r-factor (work) = 0.1181          |
| start r-factor (free) = 0.1656      final r-factor (free) = 0.1647          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4553 = 1.69 * 0.50 * 5.2079 + 1.00 * 0.0586                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4447 = 1.69 * 0.50 * 5.2006 + 1.00 * 0.0542                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1181      final r-factor (work) = 0.1176          |
| start r-factor (free) = 0.1647      final r-factor (free) = 0.1649          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.1510 = 1.18 * 1.00 * 5.2006 + 1.00 * 0.0113                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.1441 = 1.18 * 1.00 * 5.1945 + 1.00 * 0.0116                               |
|-----------------------------------------------------------------------------|
| number of iterations = 19      |    number of function evaluations = 20     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.973)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    102.99  17.21    None  None   None       |
|    all(noH): 2823   0      0.00    102.99  17.21    None  None   None       |
|    Sol.    : 438    0      0.00    94.73   42.43    None  None   None       |
|    Mac.    : 2385   0      0.00    102.99  12.58    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.299: 1219   |   5:    51.494 -  61.793:   79        |
|      1:    10.299 -  20.598:  999   |   6:    61.793 -  72.091:   61        |
|      2:    20.598 -  30.896:  194   |   7:    72.091 -  82.390:   30        |
|      3:    30.896 -  41.195:  123   |   8:    82.390 -  92.689:    3        |
|      4:    41.195 -  51.494:  110   |   9:    92.689 - 102.987:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1176 r_free = 0.1649             target_work(ml) = 5.196         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1175 r_free = 0.1650             target_work(ml) = 5.196         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1175   r_free= 0.1650   ksol= 0.33   Bsol= 63.67   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.60,-1.10,-0.53,-0.00,-0.00,-0.00); trace/3= -1.41                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.195693                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9858 -  4.7040 0.99   1438  159 0.0967 0.1271       5.378      5.5446|
|  2:  4.7040 -  3.7530 0.99   1383  155 0.0837 0.1025      5.4129      5.5979|
|  3:  3.7530 -  3.2843 0.99   1348  149 0.1090 0.1535      5.4778       5.847|
|  4:  3.2843 -  2.9866 0.99   1350  144 0.1317 0.1767      5.4945      5.6702|
|  5:  2.9866 -  2.7740 0.98   1333  151 0.1415 0.1757      5.3868      5.5517|
|  6:  2.7740 -  2.6114 0.99   1336  149 0.1370 0.2237      5.2922      5.5606|
|  7:  2.6114 -  2.4812 0.98   1293  151 0.1333 0.1695      5.2244      5.3841|
|  8:  2.4812 -  2.3736 0.99   1334  138 0.1245 0.1753      5.1489      5.3318|
|  9:  2.3736 -  2.2826 0.99   1327  152 0.1237 0.1991      5.0765      5.4007|
| 10:  2.2826 -  2.2041 0.98   1322  142 0.1198 0.1785       5.003      5.2135|
| 11:  2.2041 -  2.1353 0.97   1294  147 0.1219 0.1879       4.959      5.2571|
| 12:  2.1353 -  2.0745 0.99   1298  151 0.1183 0.1699      4.8969      5.1471|
| 13:  2.0745 -  2.0200 0.91   1227  128 0.1205 0.1977      4.8322      5.1126|
| 14:  2.0200 -  1.9708 0.26    347   43 0.1074 0.1717      4.7587      4.9616|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9858 -  4.7040  1438   159  0.94   9.09   0.97     0.94       7189.50|
|  2:  4.7040 -  3.7530  1383   155  0.95   7.89   1.01     0.99       8656.58|
|  3:  3.7530 -  3.2843  1348   149  0.94  11.26   1.02     1.02      10299.95|
|  4:  3.2843 -  2.9866  1350   144  0.91  14.74   1.01     0.99      11090.46|
|  5:  2.9866 -  2.7740  1333   151  0.89  17.08   0.99     0.97       9483.21|
|  6:  2.7740 -  2.6114  1336   149  0.88  17.97   0.97     0.95       8264.02|
|  7:  2.6114 -  2.4812  1293   151  0.90  16.78   0.98     0.95       7041.22|
|  8:  2.4812 -  2.3736  1334   138  0.89  17.04   0.99     0.95       6425.22|
|  9:  2.3736 -  2.2826  1327   152  0.90  16.77   0.98     0.93       5460.12|
| 10:  2.2826 -  2.2041  1322   142  0.89  16.85   0.98     0.94       4913.10|
| 11:  2.2041 -  2.1353  1294   147  0.90  16.71   0.97     0.93       4470.22|
| 12:  2.1353 -  2.0745  1298   151  0.90  16.47   0.99     0.98       4143.13|
| 13:  2.0745 -  2.0200  1227   128  0.89  17.45   0.97     0.95       3720.94|
| 14:  2.0200 -  1.9708   347    43  0.90  16.37   0.95     0.90       3134.06|
|alpha:            min =        0.90 max =            1.02 mean =         0.96|
|beta:             min =     3134.06 max =        11090.46 mean =      6981.31|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.97 mean =        15.02|
|phase err.(test): min =        0.00 max =           89.89 mean =        14.57|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1174   r_free= 0.1649   ksol= 0.32   Bsol= 63.67   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.34,-0.95,-0.29,-0.00,-0.00,-0.00); trace/3= -1.19                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.195878                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1174   r_free= 0.1649   ksol= 0.32   Bsol= 63.67   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.34,-0.95,-0.29,-0.00,-0.00,-0.00); trace/3= -1.19                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.195878                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9858 -  4.7040 0.99   1438  159 0.0967 0.1273      5.3788      5.5464|
|  2:  4.7040 -  3.7530 0.99   1383  155 0.0838 0.1026      5.4138      5.5982|
|  3:  3.7530 -  3.2843 0.99   1348  149 0.1090 0.1536      5.4781      5.8472|
|  4:  3.2843 -  2.9866 0.99   1350  144 0.1317 0.1768      5.4945      5.6702|
|  5:  2.9866 -  2.7740 0.98   1333  151 0.1415 0.1756      5.3865       5.551|
|  6:  2.7740 -  2.6114 0.99   1336  149 0.1369 0.2236      5.2918      5.5602|
|  7:  2.6114 -  2.4812 0.98   1293  151 0.1333 0.1697      5.2244      5.3843|
|  8:  2.4812 -  2.3736 0.99   1334  138 0.1245 0.1753      5.1491      5.3317|
|  9:  2.3736 -  2.2826 0.99   1327  152 0.1236 0.1992      5.0769      5.4013|
| 10:  2.2826 -  2.2041 0.98   1322  142 0.1198 0.1786      5.0032      5.2142|
| 11:  2.2041 -  2.1353 0.97   1294  147 0.1219 0.1879      4.9593      5.2569|
| 12:  2.1353 -  2.0745 0.99   1298  151 0.1183 0.1699      4.8969      5.1472|
| 13:  2.0745 -  2.0200 0.91   1227  128 0.1206 0.1974      4.8321       5.111|
| 14:  2.0200 -  1.9708 0.26    347   43 0.1073 0.1718      4.7591      4.9622|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9858 -  4.7040  1438   159  0.94   9.09   0.97     0.94       7199.59|
|  2:  4.7040 -  3.7530  1383   155  0.95   7.90   1.01     0.99       8667.69|
|  3:  3.7530 -  3.2843  1348   149  0.94  11.27   1.03     1.02      10310.64|
|  4:  3.2843 -  2.9866  1350   144  0.91  14.75   1.01     1.00      11091.12|
|  5:  2.9866 -  2.7740  1333   151  0.89  17.07   1.00     0.98       9474.60|
|  6:  2.7740 -  2.6114  1336   149  0.88  17.96   0.98     0.95       8255.67|
|  7:  2.6114 -  2.4812  1293   151  0.90  16.78   0.99     0.96       7037.70|
|  8:  2.4812 -  2.3736  1334   138  0.89  17.05   1.00     0.96       6426.98|
|  9:  2.3736 -  2.2826  1327   152  0.90  16.78   0.99     0.94       5464.24|
| 10:  2.2826 -  2.2041  1322   142  0.89  16.86   0.99     0.95       4914.94|
| 11:  2.2041 -  2.1353  1294   147  0.90  16.72   0.98     0.94       4471.12|
| 12:  2.1353 -  2.0745  1298   151  0.90  16.47   1.00     0.99       4143.31|
| 13:  2.0745 -  2.0200  1227   128  0.89  17.44   0.98     0.96       3717.91|
| 14:  2.0200 -  1.9708   347    43  0.90  16.37   0.97     0.91       3131.15|
|alpha:            min =        0.91 max =            1.02 mean =         0.97|
|beta:             min =     3131.15 max =        11091.12 mean =      6982.72|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.97 mean =        15.03|
|phase err.(test): min =        0.00 max =           89.89 mean =        14.57|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.973)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    102.99  17.22    None  None   None       |
|    all(noH): 2823   0      0.00    102.99  17.22    None  None   None       |
|    Sol.    : 438    0      0.00    94.74   42.44    None  None   None       |
|    Mac.    : 2385   0      0.00    102.99  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:     0.003 -  10.302: 1219   |   5:    51.497 -  61.795:   79        |
|      1:    10.302 -  20.601:  999   |   6:    61.795 -  72.094:   61        |
|      2:    20.601 -  30.899:  194   |   7:    72.094 -  82.393:   30        |
|      3:    30.899 -  41.198:  123   |   8:    82.393 -  92.692:    3        |
|      4:    41.198 -  51.497:  110   |   9:    92.692 - 102.990:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 322         
Filter by distance & map next to the model:
   mapped sites are within: 0.623 - 5.438
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 318 from: 322
   mapped sites are within: 0.714 - 5.438

peak=    5.782 closest distance to " O   HOH Z 210 " =    1.146
peak=    5.555 closest distance to " O   HOH Z 113 " =    2.218
peak=    5.196 closest distance to " CG  PRO A  54 " =    1.348
peak=    5.164 closest distance to " CB  GLN A 223 " =    1.360
peak=    5.121 closest distance to " CG  PRO A  90 " =    1.226
peak=    5.058 closest distance to " O   HOH Z 403 " =    1.893
peak=    4.870 closest distance to " CA  TYR A  30 " =    0.910
peak=    4.835 closest distance to " CG  PRO A 280 " =    0.817
peak=    4.833 closest distance to " CG  PRO A 198 " =    1.172
peak=    4.790 closest distance to " CB  ARG A 275 " =    0.920
peak=    4.790 closest distance to " O   GLY A  23 " =    2.443
peak=    4.705 closest distance to " CB  ARG A 190 " =    1.807
peak=    4.644 closest distance to " CG  PRO A 213 " =    1.261
peak=    4.590 closest distance to " O   PRO A 198 " =    1.523
peak=    4.560 closest distance to " O   HOH Z 232 " =    2.309
peak=    4.531 closest distance to " O   HOH Z  49 " =    1.125
peak=    4.479 closest distance to " CB  SER A  63 " =    1.116
peak=    4.473 closest distance to " CA  ARG A  36 " =    1.042
peak=    4.431 closest distance to " CB  GLN A 183 " =    1.285
peak=    4.409 closest distance to " O   HOH Z 402 " =    1.524
peak=    4.384 closest distance to " O   HOH Z 369 " =    2.368
peak=    4.372 closest distance to " CB  PRO A  54 " =    1.000
peak=    4.350 closest distance to " O   HOH Z 130 " =    2.699
peak=    4.335 closest distance to " O   HOH Z 234 " =    3.710
peak=    4.302 closest distance to " CD2 TRP A 179 " =    1.365
peak=    4.285 closest distance to " O   HOH Z 298 " =    1.823
peak=    4.240 closest distance to " CB  GLU A 152 " =    1.093
peak=    4.238 closest distance to " O   HOH Z 102 " =    1.361
peak=    4.229 closest distance to " O   HOH Z 423 " =    1.844
peak=    4.184 closest distance to " O   HOH Z 209 " =    2.340
peak=    4.161 closest distance to " O   HOH Z 189 " =    2.696
peak=    4.152 closest distance to " O   HOH Z 433 " =    1.555
peak=    4.144 closest distance to " CB  GLU A 128 " =    1.193
peak=    4.123 closest distance to " CB  GLU A 277 " =    3.716
peak=    4.122 closest distance to " O   HOH Z  97 " =    2.013
peak=    4.112 closest distance to " O   HOH Z 203 " =    1.773
peak=    4.075 closest distance to " CA  ALA A  51 " =    0.993
peak=    4.056 closest distance to " CD  ARG A 269 " =    1.000
peak=    4.033 closest distance to " CG  PRO A 243 " =    1.112
peak=    4.026 closest distance to " NH2BARG A 145 " =    2.164
peak=    4.010 closest distance to " CB  TRP A 179 " =    1.297
peak=    4.000 closest distance to " O   HOH Z 346 " =    1.629
peak=    3.967 closest distance to " O   HOH Z 261 " =    2.202
peak=    3.964 closest distance to " CA  ARG A 195 " =    1.209
peak=    3.960 closest distance to " O   HOH Z 316 " =    2.994
peak=    3.959 closest distance to " O   HOH Z 389 " =    1.974
peak=    3.953 closest distance to " O   SER A  87 " =    2.265
peak=    3.952 closest distance to " N   ASN A  39 " =    1.236
peak=    3.947 closest distance to " NZ  LYS A 117 " =    3.005
peak=    3.942 closest distance to " O   HOH Z  80 " =    1.900
peak=    3.941 closest distance to " O   HOH Z  44 " =    2.071
peak=    3.935 closest distance to " CZ  PHE A 218 " =    1.066
peak=    3.929 closest distance to " CG2BVAL A  41 " =    0.869
peak=    3.917 closest distance to " CD2 LEU A 297 " =    0.871
peak=    3.916 closest distance to " O   HOH Z 134 " =    1.583
peak=    3.915 closest distance to " O   HOH Z  59 " =    2.293
peak=    3.902 closest distance to " NE2 GLN A  77 " =    3.223
peak=    3.893 closest distance to " O   HOH Z  63 " =    1.922
peak=    3.883 closest distance to " CB  SER A 141 " =    1.053
peak=    3.879 closest distance to " O   HOH Z  40 " =    1.933
peak=    3.863 closest distance to " CZ3 TRP A 266 " =    1.083
peak=    3.861 closest distance to " O   HOH Z  20 " =    1.306
peak=    3.861 closest distance to " O   HOH Z 128 " =    1.949
peak=    3.852 closest distance to " O   HOH Z 345 " =    1.737
peak=    3.844 closest distance to " O   HOH Z 258 " =    2.159
peak=    3.844 closest distance to " CB  ASN A 148 " =    1.400
peak=    3.838 closest distance to " CZ  PHE A  38 " =    1.247
peak=    3.830 closest distance to " O   HOH Z 412 " =    3.708
peak=    3.830 closest distance to " CB  ARG A  79 " =    1.375
peak=    3.826 closest distance to " O   HOH Z 368 " =    2.080
peak=    3.823 closest distance to " O   HOH Z 185 " =    1.758
peak=    3.818 closest distance to " O   HOH Z 126 " =    1.569
peak=    3.806 closest distance to " CG1 ILE A  33 " =    1.242
peak=    3.782 closest distance to " CA  ASN A 176 " =    1.500
peak=    3.777 closest distance to " O   HOH Z 406 " =    1.544
peak=    3.776 closest distance to " O   HOH Z 193 " =    1.656
peak=    3.773 closest distance to " CB  SER A  62 " =    0.908
peak=    3.769 closest distance to " CA  ALA A 160 " =    0.891
peak=    3.768 closest distance to " O   HOH Z 265 " =    1.947
peak=    3.768 closest distance to " ND2 ASN A 249 " =    0.918
peak=    3.765 closest distance to " O   HOH Z  15 " =    2.223
peak=    3.763 closest distance to " O   HOH Z 361 " =    3.238
peak=    3.761 closest distance to " CB  ALA A 248 " =    1.282
peak=    3.750 closest distance to " O   HOH Z 247 " =    1.464
peak=    3.726 closest distance to " CD  LYS A 166 " =    1.388
peak=    3.719 closest distance to " O   HOH Z 173 " =    2.194
peak=    3.719 closest distance to " CD  LYS A  76 " =    2.031
peak=    3.714 closest distance to " O   HOH Z 126 " =    2.038
peak=    3.711 closest distance to " O   HOH Z 357 " =    2.113
peak=    3.709 closest distance to " O   HOH Z 365 " =    2.587
peak=    3.706 closest distance to " O   HOH Z 132 " =    2.524
peak=    3.704 closest distance to " CG2 ILE A 120 " =    1.211
peak=    3.704 closest distance to " NZ  LYS A  48 " =    1.156
peak=    3.692 closest distance to " CB  VAL A 202 " =    1.500
peak=    3.688 closest distance to " O   HOH Z 403 " =    1.495
peak=    3.687 closest distance to " CB  ASN A  39 " =    0.865
peak=    3.678 closest distance to " O   HOH Z 142 " =    1.494
peak=    3.678 closest distance to " CG1BVAL A  72 " =    1.846
peak=    3.675 closest distance to " O   HOH Z 291 " =    1.460
peak=    3.671 closest distance to " CG  GLN A  11 " =    1.308
peak=    3.669 closest distance to " ND2 ASN A 187 " =    1.604
peak=    3.667 closest distance to " CB  ASN A 285 " =    0.999
peak=    3.664 closest distance to " OH  TYR A 116 " =    1.172
peak=    3.663 closest distance to " CB  SER A  26 " =    1.772
peak=    3.653 closest distance to " O   HOH Z 284 " =    2.903
peak=    3.648 closest distance to " O  BHOH Z  74 " =    1.196
peak=    3.641 closest distance to " N   HIS A 108 " =    1.770
peak=    3.640 closest distance to " NH2 ARG A 156 " =    1.182
peak=    3.629 closest distance to " O   HOH Z  85 " =    1.371
peak=    3.626 closest distance to " CB  TYR A 169 " =    0.720
peak=    3.625 closest distance to " O   HOH Z 359 " =    1.582
peak=    3.625 closest distance to " O   HOH Z 227 " =    1.703
peak=    3.612 closest distance to " CB  TRP A 266 " =    1.068
peak=    3.608 closest distance to " N   CYS A 260 " =    0.835
peak=    3.604 closest distance to " O   HOH Z 417 " =    2.898
peak=    3.600 closest distance to " O   HOH Z 250 " =    1.370
peak=    3.592 closest distance to " O   HOH Z 279 " =    2.150
peak=    3.587 closest distance to " O   HOH Z  61 " =    1.509
peak=    3.584 closest distance to " CB  SER A   3 " =    1.215
peak=    3.583 closest distance to " O   HOH Z 154 " =    1.462
peak=    3.581 closest distance to " CB  ASN A 142 " =    1.210
peak=    3.580 closest distance to " CD  ARG A 159 " =    0.824
peak=    3.579 closest distance to " CA  ALA A 295 " =    1.067
peak=    3.574 closest distance to " O   HOH Z 214 " =    2.640
peak=    3.568 closest distance to " NH1AARG A 145 " =    1.331
peak=    3.564 closest distance to " O   HOH Z 132 " =    2.785
peak=    3.554 closest distance to " CB  ARG A  79 " =    0.927
peak=    3.548 closest distance to " O   HOH Z 336 " =    1.860
peak=    3.547 closest distance to " NE2 GLN A  11 " =    1.086
peak=    3.547 closest distance to " OG BSER A 164 " =    2.293
peak=    3.546 closest distance to " CA  ASP A 162 " =    1.142
peak=    3.546 closest distance to " CA  ALA A 248 " =    1.214
peak=    3.539 closest distance to " O   ASP A 124 " =    1.758
peak=    3.538 closest distance to " CB  THR A  52 " =    0.790
peak=    3.533 closest distance to " O   HOH Z 383 " =    2.130
peak=    3.532 closest distance to " O   ASN A  74 " =    1.689
peak=    3.525 closest distance to " O   HOH Z 426 " =    1.400
peak=    3.523 closest distance to " CG  GLU A  37 " =    0.923
peak=    3.521 closest distance to " CB  LEU A 228 " =    1.122
peak=    3.519 closest distance to " O   HOH Z 393 " =    3.291
peak=    3.515 closest distance to " O   HOH Z 425 " =    1.300
peak=    3.514 closest distance to " O   THR A 220 " =    1.083
peak=    3.511 closest distance to " O   HOH Z 124 " =    2.031
peak=    3.502 closest distance to " OG BSER A 134 " =    2.806
peak=    3.495 closest distance to " O   HOH Z 128 " =    2.393
peak=    3.494 closest distance to " O   HOH Z  35 " =    2.222
peak=    3.494 closest distance to " O   TYR A 116 " =    1.448
peak=    3.494 closest distance to " O   HOH Z 214 " =    1.346
peak=    3.492 closest distance to " CA  ALA A  21 " =    1.280
peak=    3.492 closest distance to " O   HOH Z 303 " =    2.203
peak=    3.486 closest distance to " NH2AARG A 145 " =    2.365
peak=    3.486 closest distance to " O   HOH Z 163 " =    1.551
peak=    3.482 closest distance to " CD1 LEU A  96 " =    0.744
peak=    3.481 closest distance to " O   HOH Z 287 " =    1.787
peak=    3.479 closest distance to " O   HOH Z 421 " =    2.098
peak=    3.479 closest distance to " O   HOH Z 427 " =    2.978
peak=    3.476 closest distance to " CA  GLU A 152 " =    0.863
peak=    3.473 closest distance to " O   HOH Z  39 " =    1.059
peak=    3.472 closest distance to " O   HOH Z  21 " =    1.849
peak=    3.469 closest distance to " O   HOH Z 285 " =    2.892
peak=    3.465 closest distance to " CD  LYS A 119 " =    1.763
peak=    3.464 closest distance to " CB  ASP A 124 " =    0.714
peak=    3.459 closest distance to " O   HOH Z 248 " =    1.411
peak=    3.449 closest distance to " O   ALA A 165 " =    1.377
peak=    3.447 closest distance to " CG  MET A 185 " =    1.159
peak=    3.444 closest distance to " CB  MET A  40 " =    1.015
peak=    3.440 closest distance to " O   HOH Z 371 " =    3.023
peak=    3.438 closest distance to " O   HOH Z 245 " =    1.359
peak=    3.427 closest distance to " O   HOH Z 380 " =    1.718
peak=    3.421 closest distance to " O   HOH Z 353 " =    2.845
peak=    3.412 closest distance to " O   HOH Z 128 " =    1.711
peak=    3.409 closest distance to " CB  GLU A  46 " =    1.060
peak=    3.408 closest distance to " CE  LYS A 119 " =    1.122
peak=    3.404 closest distance to " O   HOH Z  68 " =    1.888
peak=    3.404 closest distance to " O   HOH Z 427 " =    3.122
peak=    3.399 closest distance to " O   HOH Z  78 " =    1.716
peak=    3.398 closest distance to " CB  PHE A  16 " =    1.017
peak=    3.397 closest distance to " CA  VAL A 125 " =    1.340
peak=    3.392 closest distance to " CA  SER A  87 " =    1.043
peak=    3.391 closest distance to " O   HOH Z 299 " =    4.437
peak=    3.382 closest distance to " CG2 ILE A  20 " =    1.421
peak=    3.380 closest distance to " O   HOH Z 251 " =    1.564
peak=    3.377 closest distance to " CG  LEU A 167 " =    1.080
peak=    3.374 closest distance to " CG2 THR A 221 " =    1.064
peak=    3.374 closest distance to " O   HOH Z 272 " =    1.887
peak=    3.373 closest distance to " O   HOH Z 345 " =    2.802
peak=    3.370 closest distance to " CB  LEU A  83 " =    0.799
peak=    3.369 closest distance to " CG AARG A 275 " =    1.183
peak=    3.367 closest distance to " CA  TYR A 116 " =    1.392
peak=    3.364 closest distance to " O   HOH Z  97 " =    2.220
peak=    3.363 closest distance to " O   HOH Z 124 " =    1.206
peak=    3.363 closest distance to " CE  LYS A  76 " =    0.820
peak=    3.362 closest distance to " CB  ARG A 269 " =    0.811
peak=    3.362 closest distance to " CG2 VAL A 197 " =    1.089
peak=    3.362 closest distance to " CB  ALA A 291 " =    1.237
peak=    3.357 closest distance to " O   HOH Z 271 " =    2.554
peak=    3.356 closest distance to " O   HOH Z 422 " =    2.620
peak=    3.355 closest distance to " CA  GLY A 241 " =    1.000
peak=    3.351 closest distance to " CA  ASP A 191 " =    1.200
peak=    3.350 closest distance to " O   THR A 251 " =    1.180
peak=    3.349 closest distance to " CB  THR A  31 " =    1.549
peak=    3.347 closest distance to " N   TYR A 116 " =    1.589
peak=    3.340 closest distance to " O   HOH Z 325 " =    2.066
peak=    3.340 closest distance to " O   HOH Z 193 " =    1.997
peak=    3.331 closest distance to " CB  PRO A 198 " =    1.099
peak=    3.329 closest distance to " CA  LYS A 117 " =    1.245
peak=    3.327 closest distance to " CA  ALA A 100 " =    1.088
peak=    3.321 closest distance to " O   HOH Z 313 " =    1.788
peak=    3.321 closest distance to " CA  ILE A 106 " =    0.814
peak=    3.318 closest distance to " O   HOH Z 313 " =    1.681
peak=    3.316 closest distance to " O   HOH Z 156 " =    2.615
peak=    3.316 closest distance to " O   HOH Z 327 " =    1.647
peak=    3.315 closest distance to " CA  ASP A 191 " =    0.917
peak=    3.311 closest distance to " CB  HIS A 108 " =    0.798
peak=    3.307 closest distance to " CB  ALA A 114 " =    0.780
peak=    3.306 closest distance to " O   HOH Z 298 " =    2.354
peak=    3.306 closest distance to " O   HOH Z 158 " =    3.021
peak=    3.306 closest distance to " CB  TYR A 247 " =    0.954
peak=    3.303 closest distance to " CE1 TYR A 186 " =    1.270
peak=    3.297 closest distance to " CZ3 TRP A  85 " =    0.901
peak=    3.296 closest distance to " CA  ASN A 127 " =    1.184
peak=    3.295 closest distance to " CB  ASN A 215 " =    1.190
peak=    3.289 closest distance to " O   ALA A 158 " =    1.132
peak=    3.288 closest distance to " CB  PRO A 243 " =    1.348
peak=    3.286 closest distance to " O   HOH Z  19 " =    1.424
peak=    3.274 closest distance to " CG1 VAL A 153 " =    1.056
peak=    3.268 closest distance to " OE1 GLU A   2 " =    1.860
peak=    3.265 closest distance to " OG  SER A 276 " =    1.436
peak=    3.264 closest distance to " O   HOH Z 361 " =    2.556
peak=    3.259 closest distance to " CG2 THR A  29 " =    1.331
peak=    3.258 closest distance to " O   TRP A 274 " =    1.789
peak=    3.256 closest distance to " OG BSER A 258 " =    3.272
peak=    3.252 closest distance to " O   HOH Z 147 " =    1.797
peak=    3.250 closest distance to " CD  GLN A 194 " =    1.639
peak=    3.244 closest distance to " CB  PRO A  90 " =    0.970
peak=    3.243 closest distance to " O   HOH Z 130 " =    2.299
peak=    3.238 closest distance to " O   HOH Z 130 " =    2.548
peak=    3.236 closest distance to " O   GLY A  91 " =    1.242
peak=    3.234 closest distance to " O   HOH Z 240 " =    2.776
peak=    3.233 closest distance to " CD  ARG A 195 " =    0.933
peak=    3.230 closest distance to " O   HOH Z 219 " =    5.155
peak=    3.228 closest distance to " O   THR A 182 " =    1.425
peak=    3.224 closest distance to " CG  ARG A  66 " =    0.968
peak=    3.222 closest distance to " OG  SER A  22 " =    2.698
peak=    3.220 closest distance to " OE1 GLN A  58 " =    3.347
peak=    3.215 closest distance to " CD  PRO A  54 " =    1.036
peak=    3.215 closest distance to " CD1 ILE A 199 " =    1.251
peak=    3.214 closest distance to " CB  VAL A 265 " =    1.174
peak=    3.214 closest distance to " O   HOH Z 344 " =    3.155
peak=    3.213 closest distance to " CG  ARG A 219 " =    1.233
peak=    3.210 closest distance to " O   HOH Z  63 " =    2.100
peak=    3.208 closest distance to " CB  MET A  47 " =    1.019
peak=    3.207 closest distance to " CA  VAL A  41 " =    0.928
peak=    3.205 closest distance to " O   HOH Z  63 " =    2.286
peak=    3.203 closest distance to " O   HOH Z 394 " =    1.485
peak=    3.203 closest distance to " CD1 LEU A 300 " =    1.151
peak=    3.199 closest distance to " NH1 ARG A  14 " =    1.251
peak=    3.199 closest distance to " O  BHOH Z 338 " =    2.128
peak=    3.194 closest distance to " OD2 ASP A 298 " =    3.788
peak=    3.190 closest distance to " O   HOH Z 176 " =    1.461
peak=    3.187 closest distance to " CG2 VAL A 257 " =    0.780
peak=    3.187 closest distance to " O   HOH Z 109 " =    1.864
peak=    3.186 closest distance to " O   HOH Z 282 " =    2.034
peak=    3.186 closest distance to " CA  THR A  42 " =    0.973
peak=    3.185 closest distance to " O   HOH Z  48 " =    1.663
peak=    3.183 closest distance to " OE1 GLN A  11 " =    1.959
peak=    3.181 closest distance to " O   HOH Z 298 " =    4.189
peak=    3.180 closest distance to " OG  SER A  62 " =    2.786
peak=    3.179 closest distance to " CA  ALA A 299 " =    0.918
peak=    3.178 closest distance to " N   ARG A 156 " =    1.539
peak=    3.175 closest distance to " O   HOH Z 435 " =    3.024
peak=    3.173 closest distance to " ND2 ASN A 110 " =    1.511
peak=    3.172 closest distance to " O   HOH Z  47 " =    2.176
peak=    3.166 closest distance to " O   HOH Z  88 " =    3.250
peak=    3.163 closest distance to " O   HOH Z 414 " =    1.661
peak=    3.160 closest distance to " CB  GLN A  88 " =    1.131
peak=    3.158 closest distance to " OD1 ASN A  69 " =    2.419
peak=    3.155 closest distance to " O   HOH Z 293 " =    1.934
peak=    3.154 closest distance to " N   ILE A  33 " =    1.049
peak=    3.152 closest distance to " O   HOH Z 162 " =    1.789
peak=    3.151 closest distance to " CD  ARG A 139 " =    1.257
peak=    3.147 closest distance to " OG BSER A 212 " =    2.607
peak=    3.144 closest distance to " CG  GLN A  58 " =    0.813
peak=    3.143 closest distance to " CB  PHE A 204 " =    0.793
peak=    3.141 closest distance to " OE1 GLN A 223 " =    2.315
peak=    3.140 closest distance to " CB  ASP A 140 " =    0.986
peak=    3.140 closest distance to " O   HOH Z 285 " =    1.388
peak=    3.139 closest distance to " O   HOH Z  78 " =    1.900
peak=    3.136 closest distance to " CB  MET A 105 " =    1.027
peak=    3.136 closest distance to " CE1 TYR A  30 " =    0.910
peak=    3.136 closest distance to " O   HOH Z 402 " =    2.951
peak=    3.135 closest distance to " CB  TYR A 169 " =    0.903
peak=    3.133 closest distance to " NH1 ARG A 269 " =    0.738
peak=    3.130 closest distance to " O   HOH Z   1 " =    2.668
peak=    3.129 closest distance to " O   HOH Z 374 " =    2.677
peak=    3.126 closest distance to " O   HOH Z 196 " =    1.279
peak=    3.125 closest distance to " N   TRP A 150 " =    1.110
peak=    3.123 closest distance to " ND2 ASN A 217 " =    1.060
peak=    3.122 closest distance to " O   HOH Z 141 " =    1.696
peak=    3.120 closest distance to " O   HOH Z 371 " =    1.354
peak=    3.117 closest distance to " CA  LEU A  83 " =    1.267
peak=    3.101 closest distance to " CA  SER A  32 " =    1.650
peak=    3.100 closest distance to " O   HOH Z 392 " =    2.301
peak=    3.098 closest distance to " CG  MET A 185 " =    0.947
peak=    3.096 closest distance to " O   HOH Z 301 " =    1.929
peak=    3.095 closest distance to " CB  PHE A 204 " =    0.859
peak=    3.089 closest distance to " N   THR A  52 " =    1.076
peak=    3.085 closest distance to " OG  SER A 245 " =    1.545
peak=    3.083 closest distance to " CA  GLU A  46 " =    0.913
peak=    3.082 closest distance to " N   ALA A 256 " =    1.098
peak=    3.081 closest distance to " N   VAL A 265 " =    1.262
peak=    3.078 closest distance to " CA  MET A 105 " =    1.090
peak=    3.074 closest distance to " CA  LYS A 290 " =    1.036
peak=    3.056 closest distance to " CA  GLN A  11 " =    1.017
peak=    3.048 closest distance to " O   HOH Z 305 " =    3.732
peak=    3.038 closest distance to " O   HOH Z 420 " =    5.438
peak=    3.018 closest distance to " CB  ASN A 148 " =    2.004
peak=    3.011 closest distance to " ND2 ASN A 301 " =    1.720

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 221         
Filter by distance & map next to the model:
   mapped sites are within: 0.889 - 5.991
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 219 from: 221
   mapped sites are within: 0.889 - 5.991

peak=   -4.586 closest distance to " O   HOH Z 266 " =    5.208
peak=   -4.373 closest distance to " C   HIS A 108 " =    1.045
peak=   -4.323 closest distance to " CD  GLN A  58 " =    1.025
peak=   -4.275 closest distance to " CD  ARG A  14 " =    3.424
peak=   -4.189 closest distance to " OXT GLY A 302 " =    2.920
peak=   -4.135 closest distance to " O   PRO A 198 " =    1.341
peak=   -4.084 closest distance to " O   HOH Z 166 " =    1.759
peak=   -4.079 closest distance to " CA  ASP A 298 " =    1.041
peak=   -4.069 closest distance to " CG2 ILE A  49 " =    2.714
peak=   -4.040 closest distance to " CD  ARG A 156 " =    2.069
peak=   -4.021 closest distance to " CD1 LEU A 101 " =    2.433
peak=   -4.018 closest distance to " O   HOH Z 165 " =    1.886
peak=   -3.958 closest distance to " CD2 LEU A 237 " =    2.427
peak=   -3.904 closest distance to " O   HOH Z  10 " =    1.620
peak=   -3.889 closest distance to " CB  PHE A 208 " =    2.338
peak=   -3.881 closest distance to " CD1 LEU A  25 " =    2.443
peak=   -3.849 closest distance to " O   HOH Z 377 " =    1.976
peak=   -3.840 closest distance to " O   ALA A  34 " =    2.330
peak=   -3.831 closest distance to " CZ  TYR A 169 " =    1.888
peak=   -3.825 closest distance to " CG2 ILE A  20 " =    2.967
peak=   -3.825 closest distance to " CD  GLN A 223 " =    1.362
peak=   -3.821 closest distance to " OG BSER A 134 " =    1.330
peak=   -3.781 closest distance to " O   HOH Z  13 " =    1.853
peak=   -3.778 closest distance to " O   PHE A 218 " =    1.476
peak=   -3.767 closest distance to " O   PRO A 163 " =    2.088
peak=   -3.760 closest distance to " O   VAL A  67 " =    2.802
peak=   -3.754 closest distance to " O   SER A 210 " =    1.755
peak=   -3.753 closest distance to " CE3 TRP A 150 " =    2.239
peak=   -3.742 closest distance to " CB  ALA A 184 " =    2.326
peak=   -3.738 closest distance to " OG  SER A  97 " =    2.225
peak=   -3.735 closest distance to " CB  PHE A 192 " =    2.037
peak=   -3.710 closest distance to " ND2BASN A 224 " =    1.856
peak=   -3.707 closest distance to " CB  PRO A 243 " =    2.697
peak=   -3.690 closest distance to " CD2 TYR A 293 " =    1.830
peak=   -3.678 closest distance to " O   HOH Z 196 " =    2.161
peak=   -3.667 closest distance to " C   THR A 279 " =    1.164
peak=   -3.665 closest distance to " CG  GLU A  53 " =    1.418
peak=   -3.663 closest distance to " CD2 PHE A  61 " =    2.146
peak=   -3.660 closest distance to " O   HOH Z 171 " =    2.375
peak=   -3.652 closest distance to " CA  GLY A 241 " =    2.346
peak=   -3.650 closest distance to " CH2 TRP A 150 " =    1.154
peak=   -3.647 closest distance to " CG  PRO A 243 " =    1.647
peak=   -3.643 closest distance to " NE2 GLN A  88 " =    1.789
peak=   -3.642 closest distance to " CG  ASP A 132 " =    2.334
peak=   -3.628 closest distance to " CB  ALA A  10 " =    2.212
peak=   -3.626 closest distance to " CG  GLN A  58 " =    1.196
peak=   -3.625 closest distance to " OE1 GLN A 223 " =    2.279
peak=   -3.619 closest distance to " NE2 GLN A 223 " =    1.269
peak=   -3.618 closest distance to " N   ALA A  43 " =    2.764
peak=   -3.612 closest distance to " CB  ALA A 161 " =    2.577
peak=   -3.609 closest distance to " ND2 ASN A 187 " =    1.618
peak=   -3.606 closest distance to " O   TRP A  92 " =    1.910
peak=   -3.606 closest distance to " CD1 PHE A  59 " =    2.019
peak=   -3.602 closest distance to " CH2 TRP A 179 " =    1.291
peak=   -3.590 closest distance to " CE2 TYR A  30 " =    2.711
peak=   -3.586 closest distance to " O   HOH Z 210 " =    0.889
peak=   -3.578 closest distance to " O   HOH Z 374 " =    1.915
peak=   -3.562 closest distance to " O   HOH Z 198 " =    1.782
peak=   -3.559 closest distance to " ND2 ASN A  69 " =    1.705
peak=   -3.559 closest distance to " O   HOH Z 102 " =    1.656
peak=   -3.553 closest distance to " CG1 VAL A 112 " =    2.629
peak=   -3.545 closest distance to " CG1AVAL A  41 " =    2.581
peak=   -3.533 closest distance to " O   HOH Z 418 " =    1.305
peak=   -3.527 closest distance to " O   HOH Z 372 " =    2.401
peak=   -3.526 closest distance to " CD  LYS A 289 " =    2.379
peak=   -3.522 closest distance to " ND2 ASN A  45 " =    1.167
peak=   -3.519 closest distance to " OD1 ASN A 148 " =    1.448
peak=   -3.516 closest distance to " O   HOH Z 283 " =    2.218
peak=   -3.514 closest distance to " NE  ARG A  66 " =    4.444
peak=   -3.512 closest distance to " O   HOH Z 214 " =    2.645
peak=   -3.506 closest distance to " CG  GLN A  11 " =    1.657
peak=   -3.503 closest distance to " O   HOH Z 290 " =    1.019
peak=   -3.502 closest distance to " O   ALA A   1 " =    1.984
peak=   -3.500 closest distance to " CG2 VAL A 189 " =    2.236
peak=   -3.500 closest distance to " O   HOH Z 301 " =    2.370
peak=   -3.498 closest distance to " C   ASN A 285 " =    2.223
peak=   -3.492 closest distance to " O   HOH Z  71 " =    2.011
peak=   -3.484 closest distance to " CB  SER A 210 " =    1.152
peak=   -3.480 closest distance to " O   HOH Z 394 " =    1.678
peak=   -3.470 closest distance to " O   HOH Z 351 " =    1.511
peak=   -3.463 closest distance to " O   HOH Z 366 " =    1.686
peak=   -3.462 closest distance to " O   HOH Z 197 " =    1.967
peak=   -3.461 closest distance to " C   SER A 206 " =    1.496
peak=   -3.461 closest distance to " ND2 ASN A 249 " =    2.225
peak=   -3.454 closest distance to " N   SER A 276 " =    1.484
peak=   -3.451 closest distance to " O   HOH Z 196 " =    1.774
peak=   -3.449 closest distance to " O   HOH Z  56 " =    1.247
peak=   -3.440 closest distance to " O   HOH Z 234 " =    4.087
peak=   -3.431 closest distance to " O   HOH Z 423 " =    2.397
peak=   -3.431 closest distance to " O   HOH Z 135 " =    1.453
peak=   -3.428 closest distance to " CD  ARG A  79 " =    1.221
peak=   -3.426 closest distance to " OD1 ASP A 191 " =    1.405
peak=   -3.423 closest distance to " O   HOH Z 185 " =    2.500
peak=   -3.414 closest distance to " O   HOH Z 154 " =    1.639
peak=   -3.411 closest distance to " CE BMET A  47 " =    1.552
peak=   -3.409 closest distance to " N   THR A  52 " =    1.723
peak=   -3.405 closest distance to " OD2 ASP A 171 " =    2.454
peak=   -3.404 closest distance to " CD  ARG A 195 " =    5.120
peak=   -3.404 closest distance to " CA  GLY A 203 " =    2.378
peak=   -3.402 closest distance to " O   HOH Z 422 " =    1.417
peak=   -3.400 closest distance to " CA  GLY A 241 " =    3.186
peak=   -3.392 closest distance to " O   HOH Z 384 " =    1.939
peak=   -3.390 closest distance to " CB  ALA A 291 " =    2.434
peak=   -3.379 closest distance to " CZ3 TRP A 274 " =    2.409
peak=   -3.375 closest distance to " O   HOH Z 264 " =    1.815
peak=   -3.374 closest distance to " CA  TYR A  68 " =    3.052
peak=   -3.373 closest distance to " O   HOH Z  88 " =    4.564
peak=   -3.368 closest distance to " CB  ALA A  43 " =    2.538
peak=   -3.368 closest distance to " CD  ARG A 139 " =    1.571
peak=   -3.368 closest distance to " O   GLN A  11 " =    1.253
peak=   -3.366 closest distance to " OD1 ASN A 301 " =    1.987
peak=   -3.366 closest distance to " CG1 VAL A  78 " =    2.546
peak=   -3.365 closest distance to " CG  GLN A 103 " =    2.509
peak=   -3.359 closest distance to " O   HOH Z  52 " =    1.727
peak=   -3.357 closest distance to " O   HOH Z 150 " =    1.126
peak=   -3.347 closest distance to " O   HOH Z  19 " =    2.363
peak=   -3.347 closest distance to " CZ  PHE A  38 " =    2.326
peak=   -3.346 closest distance to " CA  VAL A 197 " =    0.990
peak=   -3.344 closest distance to " O   HOH Z 174 " =    3.639
peak=   -3.335 closest distance to " O   HOH Z 252 " =    3.894
peak=   -3.332 closest distance to " CA  GLY A 133 " =    2.349
peak=   -3.332 closest distance to " O   SER A 271 " =    2.013
peak=   -3.331 closest distance to " OH  TYR A 172 " =    1.902
peak=   -3.327 closest distance to " CG1 VAL A 112 " =    2.767
peak=   -3.325 closest distance to " CG1 VAL A  78 " =    2.574
peak=   -3.324 closest distance to " CZ  ARG A  66 " =    1.173
peak=   -3.323 closest distance to " O   GLY A  80 " =    2.568
peak=   -3.317 closest distance to " O   SER A 273 " =    1.427
peak=   -3.316 closest distance to " NH2 ARG A  66 " =    5.991
peak=   -3.315 closest distance to " O   HOH Z 150 " =    2.008
peak=   -3.314 closest distance to " CA  GLY A 133 " =    2.021
peak=   -3.313 closest distance to " CB  TRP A  85 " =    2.434
peak=   -3.313 closest distance to " CD2 HIS A 207 " =    2.369
peak=   -3.311 closest distance to " CD2 TYR A 247 " =    2.382
peak=   -3.308 closest distance to " CD1 ILE A 151 " =    2.396
peak=   -3.307 closest distance to " CG  LEU A  83 " =    2.091
peak=   -3.302 closest distance to " O   HOH Z 287 " =    2.072
peak=   -3.298 closest distance to " O   VAL A 174 " =    2.162
peak=   -3.292 closest distance to " NH1 ARG A 195 " =    2.339
peak=   -3.286 closest distance to " CB  ALA A 248 " =    2.227
peak=   -3.284 closest distance to " O   HOH Z 114 " =    3.379
peak=   -3.282 closest distance to " OD2 ASP A 171 " =    1.745
peak=   -3.274 closest distance to " O   ALA A  10 " =    1.808
peak=   -3.274 closest distance to " CD1 ILE A 106 " =    2.187
peak=   -3.269 closest distance to " O   ALA A  34 " =    2.122
peak=   -3.269 closest distance to " O   HOH Z 145 " =    2.605
peak=   -3.267 closest distance to " O   HOH Z  37 " =    1.860
peak=   -3.267 closest distance to " N   GLY A  17 " =    1.771
peak=   -3.267 closest distance to " OG BSER A 210 " =    1.388
peak=   -3.265 closest distance to " ND2 ASN A  45 " =    2.002
peak=   -3.264 closest distance to " O   VAL A 189 " =    2.607
peak=   -3.259 closest distance to " N   ALA A 226 " =    1.928
peak=   -3.256 closest distance to " OD1 ASP A 171 " =    1.504
peak=   -3.255 closest distance to " O   HOH Z 392 " =    1.446
peak=   -3.250 closest distance to " CA  GLY A 241 " =    2.890
peak=   -3.249 closest distance to " O   HOH Z  15 " =    1.559
peak=   -3.249 closest distance to " O   HOH Z 285 " =    1.178
peak=   -3.243 closest distance to " O   HOH Z 252 " =    3.664
peak=   -3.242 closest distance to " O   TRP A  70 " =    1.541
peak=   -3.241 closest distance to " NH2 ARG A  79 " =    2.258
peak=   -3.239 closest distance to " O   HOH Z 177 " =    1.714
peak=   -3.237 closest distance to " O   HOH Z 111 " =    2.203
peak=   -3.237 closest distance to " O   SER A 276 " =    1.737
peak=   -3.234 closest distance to " O   HOH Z 377 " =    1.894
peak=   -3.234 closest distance to " OE2 GLU A   2 " =    1.716
peak=   -3.226 closest distance to " O   HOH Z  78 " =    1.833
peak=   -3.223 closest distance to " NH2 ARG A  79 " =    1.622
peak=   -3.221 closest distance to " O   HOH Z 106 " =    2.010
peak=   -3.218 closest distance to " OD2 ASP A 191 " =    1.656
peak=   -3.217 closest distance to " CB  ARG A 219 " =    2.315
peak=   -3.215 closest distance to " NH2 ARG A  66 " =    1.988
peak=   -3.214 closest distance to " CD2 PHE A 225 " =    1.293
peak=   -3.208 closest distance to " NE2 GLN A  88 " =    1.052
peak=   -3.203 closest distance to " O   HOH Z 128 " =    2.541
peak=   -3.195 closest distance to " NE2 GLN A 103 " =    1.787
peak=   -3.191 closest distance to " OE1 GLN A 183 " =    1.476
peak=   -3.190 closest distance to " O  BHOH Z 338 " =    1.133
peak=   -3.190 closest distance to " OD1 ASN A 187 " =    1.758
peak=   -3.185 closest distance to " O   HOH Z 434 " =    2.450
peak=   -3.183 closest distance to " O   HOH Z 357 " =    2.148
peak=   -3.178 closest distance to " O   GLU A 152 " =    1.433
peak=   -3.176 closest distance to " CG  ARG A 269 " =    2.285
peak=   -3.176 closest distance to " O   HOH Z 240 " =    3.962
peak=   -3.175 closest distance to " NE2 GLN A  94 " =    1.806
peak=   -3.173 closest distance to " O   HOH Z 407 " =    3.058
peak=   -3.172 closest distance to " O   HOH Z 150 " =    2.035
peak=   -3.168 closest distance to " OG1 THR A 157 " =    2.943
peak=   -3.166 closest distance to " O   SER A   3 " =    1.128
peak=   -3.165 closest distance to " O   HOH Z 166 " =    1.567
peak=   -3.164 closest distance to " N   ALA A 248 " =    1.771
peak=   -3.158 closest distance to " O   HOH Z 396 " =    1.762
peak=   -3.154 closest distance to " CB  ALA A   9 " =    2.559
peak=   -3.154 closest distance to " O   GLY A 196 " =    1.017
peak=   -3.154 closest distance to " O   HOH Z 200 " =    1.347
peak=   -3.152 closest distance to " CD  GLU A 236 " =    1.098
peak=   -3.149 closest distance to " CB  PHE A  16 " =    2.453
peak=   -3.148 closest distance to " NH2 ARG A  66 " =    5.448
peak=   -3.144 closest distance to " CB  PRO A 213 " =    1.805
peak=   -3.144 closest distance to " OD1 ASN A  39 " =    2.264
peak=   -3.138 closest distance to " SD  MET A 105 " =    2.527
peak=   -3.135 closest distance to " C   GLN A 144 " =    0.891
peak=   -3.134 closest distance to " CG2 ILE A 263 " =    2.039
peak=   -3.131 closest distance to " CD1 TRP A 179 " =    1.118
peak=   -3.127 closest distance to " O   HOH Z   6 " =    2.076
peak=   -3.125 closest distance to " O   ASN A 187 " =    1.608
peak=   -3.122 closest distance to " CB  SER A 146 " =    2.147
peak=   -3.121 closest distance to " O   HOH Z 265 " =    2.417
peak=   -3.104 closest distance to " O   HOH Z  41 " =    2.089
peak=   -3.099 closest distance to " CE1 TYR A 247 " =    2.703
peak=   -3.093 closest distance to " O   HOH Z  38 " =    1.542
peak=   -3.089 closest distance to " O   HOH Z 157 " =    3.561
peak=   -3.089 closest distance to " O   HOH Z  11 " =    1.755
peak=   -3.079 closest distance to " C   ALA A 158 " =    1.435
peak=   -3.078 closest distance to " CB  ASP A 286 " =    1.868
peak=   -3.073 closest distance to " O   HOH Z 174 " =    2.200
peak=   -3.049 closest distance to " O   HOH Z 171 " =    1.804
peak=   -3.048 closest distance to " CG2BVAL A  41 " =    1.566
peak=   -3.045 closest distance to " O   HOH Z 198 " =    1.621
peak=   -3.035 closest distance to " O   PRO A 198 " =    1.337

================= 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    :  0.4373 0.4254   6.245977e+00   6.222134e+00
   1_bss:  0.4287 0.4145   6.236783e+00   6.209910e+00
   1_xyz:  0.2756 0.3011   5.893992e+00   5.969824e+00
   1_adp:  0.2493 0.3159   5.847348e+00   6.001992e+00
   1_occ:  0.2491 0.3163   5.847349e+00   6.002416e+00
   2_bss:  0.2456 0.3133   5.841053e+00   5.996315e+00
   2_xyz:  0.1853 0.2291   5.571542e+00   5.746500e+00
   2_adp:  0.1702 0.2115   5.501455e+00   5.682035e+00
   2_occ:  0.1700 0.2116   5.501053e+00   5.681881e+00
   3_bss:  0.1698 0.2108   5.499658e+00   5.679781e+00
   3_xyz:  0.1401 0.1834   5.330186e+00   5.537175e+00
   3_adp:  0.1345 0.1764   5.293055e+00   5.496609e+00
   3_occ:  0.1344 0.1765   5.292939e+00   5.496681e+00
   4_bss:  0.1347 0.1766   5.293809e+00   5.495506e+00
   4_xyz:  0.1232 0.1650   5.219197e+00   5.432048e+00
   4_adp:  0.1206 0.1656   5.208182e+00   5.430438e+00
   4_occ:  0.1205 0.1657   5.208194e+00   5.430655e+00
   5_bss:  0.1204 0.1656   5.208309e+00   5.430751e+00
   5_xyz:  0.1181 0.1647   5.197638e+00   5.426354e+00
   5_adp:  0.1176 0.1649   5.195875e+00   5.426914e+00
   5_occ:  0.1175 0.1650   5.195693e+00   5.427063e+00
   5_bss:  0.1174 0.1649   5.195878e+00   5.427162e+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:  0.286  27.318  -1.925   4.201  -0.070   0.000  -0.000  -0.000
   1_xyz:  0.286  27.318  -1.925   4.201  -0.070   0.000  -0.000  -0.000
   1_adp:  0.286  27.318  -1.925   4.201  -0.070   0.000  -0.000  -0.000
   1_occ:  0.286  27.318  -1.925   4.201  -0.070   0.000  -0.000  -0.000
   2_bss:  0.324  62.671  -2.472   0.854  -0.547   0.000  -0.000  -0.000
   2_xyz:  0.324  62.671  -2.472   0.854  -0.547   0.000  -0.000  -0.000
   2_adp:  0.324  62.671  -2.472   0.854  -0.547   0.000  -0.000  -0.000
   2_occ:  0.324  62.671  -2.472   0.854  -0.547   0.000  -0.000  -0.000
   3_bss:  0.327  62.671  -2.655  -0.380  -0.614  -0.000  -0.000  -0.000
   3_xyz:  0.327  62.671  -2.655  -0.380  -0.614  -0.000  -0.000  -0.000
   3_adp:  0.327  62.671  -2.655  -0.380  -0.614  -0.000  -0.000  -0.000
   3_occ:  0.327  62.671  -2.655  -0.380  -0.614  -0.000  -0.000  -0.000
   4_bss:  0.328  63.666  -2.844  -1.112  -0.750  -0.000  -0.000  -0.000
   4_xyz:  0.328  63.666  -2.844  -1.112  -0.750  -0.000  -0.000  -0.000
   4_adp:  0.328  63.666  -2.844  -1.112  -0.750  -0.000  -0.000  -0.000
   4_occ:  0.328  63.666  -2.844  -1.112  -0.750  -0.000  -0.000  -0.000
   5_bss:  0.326  63.666  -2.600  -1.100  -0.532  -0.000  -0.000  -0.000
   5_xyz:  0.326  63.666  -2.600  -1.100  -0.532  -0.000  -0.000  -0.000
   5_adp:  0.326  63.666  -2.600  -1.100  -0.532  -0.000  -0.000  -0.000
   5_occ:  0.326  63.666  -2.600  -1.100  -0.532  -0.000  -0.000  -0.000
   5_bss:  0.324  63.669  -2.345  -0.946  -0.286  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  48.996 0.5343  0.7011    55365.297
   1_bss:  47.979 0.5454  0.7345    52120.607
   1_xyz:  31.867 0.7374  0.9424    24909.575
   1_adp:  33.485 0.7181  0.9205    27013.601
   1_occ:  33.541 0.7174  0.9194    27078.691
   2_bss:  33.018 0.7233  0.8843    26386.673
   2_xyz:  23.167 0.8292  0.9699    13680.149
   2_adp:  21.032 0.8516  0.9744    11881.518
   2_occ:  21.028 0.8517  0.9743    11879.943
   3_bss:  20.920 0.8526  0.9587    11765.737
   3_xyz:  17.392 0.8856  0.9788     8568.149
   3_adp:  16.478 0.8942  0.9781     8049.212
   3_occ:  16.482 0.8942  0.9779     8052.780
   4_bss:  16.453 0.8944  0.9662     8026.570
   4_xyz:  15.200 0.9050  0.9700     7072.761
   4_adp:  15.125 0.9058  0.9616     7061.481
   4_occ:  15.129 0.9058  0.9614     7061.292
   5_bss:  15.131 0.9058  0.9669     7062.407
   5_xyz:  14.970 0.9073  0.9685     6980.158
   5_adp:  14.978 0.9072  0.9598     6980.602
   5_occ:  14.979 0.9073  0.9597     6980.022
   5_bss:  14.983 0.9072  0.9672     6981.432
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.112   1.7389e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.112   1.7389e-01
   1_xyz:   1.557  0.012  0.095 15.795  0.006  4.113   1.2453e-01
   1_adp:   1.557  0.012  0.095 15.795  0.006  4.113   1.2453e-01
   1_occ:   1.557  0.012  0.095 15.795  0.006  4.113   1.2453e-01
   2_bss:   1.557  0.012  0.095 15.795  0.006  4.113   1.2453e-01
   2_xyz:   1.109  0.007  0.075 14.630  0.005  4.111   6.6634e-02
   2_adp:   1.109  0.007  0.075 14.630  0.005  4.111   6.6634e-02
   2_occ:   1.109  0.007  0.075 14.630  0.005  4.111   6.6634e-02
   3_bss:   1.109  0.007  0.075 14.630  0.005  4.111   6.6634e-02
   3_xyz:   0.991  0.007  0.068 14.266  0.003  4.118   5.6213e-02
   3_adp:   0.991  0.007  0.068 14.266  0.003  4.118   5.6213e-02
   3_occ:   0.991  0.007  0.068 14.266  0.003  4.118   5.6213e-02
   4_bss:   0.991  0.007  0.068 14.266  0.003  4.118   5.6213e-02
   4_xyz:   1.011  0.007  0.074 14.331  0.004  4.113   5.8586e-02
   4_adp:   1.011  0.007  0.074 14.331  0.004  4.113   5.8586e-02
   4_occ:   1.011  0.007  0.074 14.331  0.004  4.113   5.8586e-02
   5_bss:   1.011  0.007  0.074 14.331  0.004  4.113   5.8586e-02
   5_xyz:   0.959  0.007  0.072 14.214  0.003  4.114   5.4163e-02
   5_adp:   0.959  0.007  0.072 14.214  0.003  4.114   5.4163e-02
   5_occ:   0.959  0.007  0.072 14.214  0.003  4.114   5.4163e-02
   5_bss:   0.959  0.007  0.072 14.214  0.003  4.114   5.4163e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.504   2.4236e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.504   2.4236e-01
   1_xyz:   9.650  0.106  0.354 86.007  0.028  2.057   9.2545e-02
   1_adp:   9.650  0.106  0.354 86.007  0.028  2.057   9.2545e-02
   1_occ:   9.650  0.106  0.354 86.007  0.028  2.057   9.2545e-02
   2_bss:   9.650  0.106  0.354 86.007  0.028  2.057   9.2545e-02
   2_xyz:   7.423  0.040  0.224 82.161  0.063  2.329   4.6556e-02
   2_adp:   7.423  0.040  0.224 82.161  0.063  2.329   4.6556e-02
   2_occ:   7.423  0.040  0.224 82.161  0.063  2.329   4.6556e-02
   3_bss:   7.423  0.040  0.224 82.161  0.063  2.329   4.6556e-02
   3_xyz:   6.990  0.050  0.209 79.963  0.021  2.357   3.8752e-02
   3_adp:   6.990  0.050  0.209 79.963  0.021  2.357   3.8752e-02
   3_occ:   6.990  0.050  0.209 79.963  0.021  2.357   3.8752e-02
   4_bss:   6.990  0.050  0.209 79.963  0.021  2.357   3.8752e-02
   4_xyz:   7.572  0.039  0.248 82.953  0.028  2.340   4.0612e-02
   4_adp:   7.572  0.039  0.248 82.953  0.028  2.340   4.0612e-02
   4_occ:   7.572  0.039  0.248 82.953  0.028  2.340   4.0612e-02
   5_bss:   7.572  0.039  0.248 82.953  0.028  2.340   4.0612e-02
   5_xyz:   7.373  0.044  0.233 79.951  0.025  2.395   3.3929e-02
   5_adp:   7.373  0.044  0.233 79.951  0.025  2.395   3.3929e-02
   5_occ:   7.373  0.044  0.233 79.951  0.025  2.395   3.3929e-02
   5_bss:   7.373  0.044  0.233 79.951  0.025  2.395   3.3929e-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:  85.39   0.00  17.77  76.42   0.00  13.81  85.39   3.51  39.34
   1_occ:  85.39   0.00  17.77  76.42   0.00  13.81  85.39   3.51  39.34
   2_bss:  85.39   0.00  17.77  76.42   0.00  13.81  85.39   3.51  39.34
   2_xyz:  85.39   0.00  17.77  76.42   0.00  13.81  85.39   3.51  39.34
   2_adp:  86.42   0.00  17.74  86.42   0.00  13.37  84.12   5.63  41.55
   2_occ:  86.42   0.00  17.74  86.42   0.00  13.37  84.12   5.63  41.55
   3_bss:  86.42   0.00  17.74  86.42   0.00  13.37  84.12   5.63  41.55
   3_xyz:  86.42   0.00  17.74  86.42   0.00  13.37  84.12   5.63  41.55
   3_adp:  84.57   1.47  17.30  84.57   1.47  12.94  84.01   5.76  41.01
   3_occ:  84.57   1.47  17.30  84.57   1.47  12.94  84.01   5.76  41.01
   4_bss:  84.57   1.47  17.30  84.57   1.47  12.94  84.01   5.76  41.01
   4_xyz:  84.57   1.47  17.30  84.57   1.47  12.94  84.01   5.76  41.01
   4_adp:  98.18   0.00  17.47  98.18   0.16  12.80  89.66   0.00  42.91
   4_occ:  98.18   0.00  17.47  98.18   0.16  12.80  89.66   0.00  42.91
   5_bss:  98.18   0.00  17.47  98.18   0.16  12.80  89.66   0.00  42.91
   5_xyz:  98.18   0.00  17.47  98.18   0.16  12.80  89.66   0.00  42.91
   5_adp: 102.99   0.00  17.21 102.99   0.00  12.58  94.73   0.00  42.43
   5_occ: 102.99   0.00  17.21 102.99   0.00  12.58  94.73   0.00  42.43
   5_bss: 102.99   0.00  17.22 102.99   0.00  12.59  94.74   0.00  42.44
------------------------------------------------------------------------
 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:    1.572    0.013    0.494
   1_adp:    1.572    0.013    0.494
   1_occ:    1.572    0.013    0.494
   2_bss:    1.572    0.013    0.494
   2_xyz:    1.428    0.043    0.565
   2_adp:    1.428    0.043    0.565
   2_occ:    1.428    0.043    0.565
   3_bss:    1.428    0.043    0.565
   3_xyz:    1.309    0.033    0.656
   3_adp:    1.309    0.033    0.656
   3_occ:    1.309    0.033    0.656
   4_bss:    1.309    0.033    0.656
   4_xyz:    1.338    0.048    0.682
   4_adp:    1.338    0.048    0.682
   4_occ:    1.338    0.048    0.682
   5_bss:    1.338    0.048    0.682
   5_xyz:    1.333    0.091    0.700
   5_adp:    1.333    0.091    0.700
   5_occ:    1.333    0.091    0.700
   5_bss:    1.333    0.091    0.700
------------------------------------------------------------------------

CPU time actual refinement: 322.65


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_348/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_348/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_348/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_348/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_348/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 322.51 
  Macro-tasks:
    bulk solvent and scale       = 37.44  
    individual site refinement   = 133.55 
    weights calculation          = 28.84  
    collect and process          = 6.53   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 206.45 
  Micro-tasks:
    mask                            = 1.78   
    f_calc                          = 102.85 
    alpha_beta                      = 8.25   
    target                          = 1.13   
    gradients_wrt_atomic_parameters = 111.46 
    fmodel                         = 6.34   
    r_factors                      = 0.18   
    phase_errors                   = 10.98  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 243.25 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.619 micro seconds
Total CPU time: 5.60 minutes
from_scatterers_fft:    625 calls, 102.57 s
gradients_fft:          570 calls,  98.39 s

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

# Date 2008-01-16 Time 04:37:00 PST -0800 (1200487020.27 s)
Start R-work = 0.4373, R-free = 0.4254 (no bulk solvent and anisotropic scale)
Final R-work = 0.1378, R-free = 0.1801 (no bulk solvent and anisotropic scale)

Start R-work = 0.4287, R-free = 0.4145
Final R-work = 0.1174, R-free = 0.1649