# Date 2008-01-16 Time 04:15:16 PST -0800 (1200485716.25 s)
#phil __OFF__

Command line arguments: "../245.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 28436
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 245

-------------------------------------------------------------------------------
  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, 45.7567, 85.5261, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.27, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 45.7567, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.7893 1.95228
Completeness in resolution range: 0.964168
Completeness with d_max=infinity: 0.961187

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.7893
                             d_min =   1.9523

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, 45.7567, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.7893 1.95228
Completeness in resolution range: 0.964168
Completeness with d_max=infinity: 0.961187

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.7897 -  4.1774 [2132/2156]  1918   214  10.0%
  bin  2:  4.1774 -  3.3282 [2038/2058]  1836   202   9.9%
  bin  3:  3.3282 -  2.9111 [2032/2051]  1825   207  10.2%
  bin  4:  2.9111 -  2.6466 [2000/2030]  1803   197   9.8%
  bin  5:  2.6466 -  2.4578 [2010/2029]  1808   202  10.0%
  bin  6:  2.4578 -  2.3135 [1955/1980]  1761   194   9.9%
  bin  7:  2.3135 -  2.1980 [1982/2010]  1781   201  10.1%
  bin  8:  2.1980 -  2.1026 [1977/2013]  1781   196   9.9%
  bin  9:  2.1026 -  2.0219 [1927/1969]  1735   192  10.0%
  bin 10:  2.0219 -  1.9523 [1536/2021]  1382   154  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_245/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: 0.14 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:
        1.36 -     2.07: 24
        2.07 -     2.78: 626
        2.78 -     3.48: 4677
        3.48 -     4.19: 9587
        4.19 -     4.90: 14181
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.359 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  70 " - " O   HOH Z 302 "  1.545 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 302 " - " O   HOH Z  70 "  1.545 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.573 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 271 " - " O   HOH Z 342 "  1.628 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 29090 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_245/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_245/model_refine_001.geo

CPU time processing inputs: 9.23


============================ 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 45.75675 85.5261 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4640   r_free= 0.4609   ksol= 0.00   Bsol= 0.00   scale= 0.910    |
|                                                                             |
| 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:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.274749                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7897 -  4.6593 0.99   1389  153 0.3862 0.3907      6.5806      6.5918|
|  2:  4.6593 -  3.7176 0.99   1330  152 0.4088 0.3681      6.8058      6.7613|
|  3:  3.7176 -  3.2533 0.99   1303  140 0.4488 0.4224      6.7113      6.7536|
|  4:  3.2533 -  2.9585 0.99   1298  149 0.4515 0.4288      6.5367      6.5047|
|  5:  2.9585 -  2.7479 0.99   1292  145 0.4942 0.4829       6.372      6.3751|
|  6:  2.7479 -  2.5868 0.99   1298  139 0.4883 0.5168       6.279      6.2148|
|  7:  2.5868 -  2.4578 0.99   1280  144 0.4909 0.5105      6.2268      6.2038|
|  8:  2.4578 -  2.3513 0.98   1269  141 0.5095 0.5003      6.1893      6.1676|
|  9:  2.3513 -  2.2611 0.98   1256  140 0.4992 0.5005      6.1117      6.1767|
| 10:  2.2611 -  2.1833 1.00   1283  143 0.4918 0.5263      6.1014      6.1177|
| 11:  2.1833 -  2.1153 0.97   1256  138 0.5013 0.5150      6.0166      6.0524|
| 12:  2.1153 -  2.0550 0.98   1248  138 0.4784 0.4634      5.9661      5.9619|
| 13:  2.0550 -  2.0010 0.99   1291  140 0.4984 0.4859       5.871      5.8275|
| 14:  2.0010 -  1.9523 0.66    837   97 0.5223 0.4802      5.8645      5.7753|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7897 -  4.6593  1389   153  0.67  37.19   0.82     0.73      82723.47|
|  2:  4.6593 -  3.7176  1330   152  0.68  36.66   0.91     0.81     113425.53|
|  3:  3.7176 -  3.2533  1303   140  0.59  44.59   0.93     0.79     118232.75|
|  4:  3.2533 -  2.9585  1298   149  0.51  51.30   0.95     0.70     105767.98|
|  5:  2.9585 -  2.7479  1292   145  0.42  58.14   0.90     0.60      82070.21|
|  6:  2.7479 -  2.5868  1298   139  0.40  59.98   0.90     0.55      71329.05|
|  7:  2.5868 -  2.4578  1280   144  0.36  62.57   0.94     0.53      66587.11|
|  8:  2.4578 -  2.3513  1269   141  0.34  64.32   0.95     0.51      62423.25|
|  9:  2.3513 -  2.2611  1256   140  0.34  64.40   0.92     0.50      57369.92|
| 10:  2.2611 -  2.1833  1283   143  0.37  62.38   0.98     0.54      48140.94|
| 11:  2.1833 -  2.1153  1256   138  0.38  61.19   0.99     0.60      43684.89|
| 12:  2.1153 -  2.0550  1248   138  0.43  57.99   1.02     0.65      37131.52|
| 13:  2.0550 -  2.0010  1291   140  0.42  58.46   0.98     0.66      31822.33|
| 14:  2.0010 -  1.9523   837    97  0.46  55.06   0.99     0.66      24750.20|
|alpha:            min =        0.50 max =            0.81 mean =         0.63|
|beta:             min =    24750.20 max =       118232.75 mean =     69029.93|
|figures of merit: min =        0.00 max =            1.00 mean =         0.46|
|phase err.(work): min =        0.00 max =           89.99 mean =        55.11|
|phase err.(test): min =        0.00 max =           89.92 mean =        54.94|
|-----------------------------------------------------------------------------|

============================== 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 = 14.905331             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.755   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.240468              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.522   (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 |  1.359 -  1.713:        7 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.713 -  2.068:       17 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.068 -  2.422:       43 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.422 -  2.776:      583 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.776 -  3.130:     2229 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.130 -  3.484:     2448 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.484 -  3.838:     4566 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.838 -  4.192:     5021 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.192 -  4.546:     6382 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.546 -  4.900:     7799 |
|-----------------------------------------------------------------------------|
|-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 |        0.203 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.106    4.900  1.359 |       0.832 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.289)------------------------------------------|
|    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: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4640   r_free= 0.4609   ksol= 0.00   Bsol= 0.00   scale= 0.910    |
|                                                                             |
| 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:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.274749                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4546   r_free= 0.4491   ksol= 0.36   Bsol= 22.01   scale= 0.925   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.27,2.24,-1.17,0.00,-0.00,-0.00); trace/3= -0.40                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.268455                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.099525             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.572   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.248872              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.398   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4546      final r-factor (work) = 0.3597          |
| start r-factor (free) = 0.4491      final r-factor (free) = 0.3947          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 38.1163 = 12.10 * 0.50 * 6.2670 + 1.00 * 0.2026                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 37.4277 = 12.10 * 0.50 * 6.1628 + 1.00 * 0.1445                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3597      final r-factor (work) = 0.3321          |
| start r-factor (free) = 0.3947      final r-factor (free) = 0.4035          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.7028 = 1.25 * 1.00 * 6.1628 + 1.00 * 0.0063                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.6198 = 1.25 * 1.00 * 6.0805 + 1.00 * 0.0260                               |
|-----------------------------------------------------------------------------|
| number of iterations = 8       |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.289)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.81   16.93    None  None   None       |
|    all(noH): 2823   0      0.00    85.81   16.93    None  None   None       |
|    Sol.    : 438    0      1.25    63.77   35.92    None  None   None       |
|    Mac.    : 2385   0      0.00    85.81   13.44    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 -   8.581:  774   |   5:    42.907 -  51.488:   92        |
|      1:     8.581 -  17.163:  952   |   6:    51.488 -  60.069:   55        |
|      2:    17.163 -  25.744:  560   |   7:    60.069 -  68.650:    5        |
|      3:    25.744 -  34.325:  240   |   8:    68.650 -  77.232:    0        |
|      4:    34.325 -  42.907:  144   |   9:    77.232 -  85.813:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3321 r_free = 0.4035             target_work(ml) = 6.084         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3318 r_free = 0.4044             target_work(ml) = 6.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3318   r_free= 0.4044   ksol= 0.36   Bsol= 22.01   scale= 0.979   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.27,2.24,-1.17,0.00,-0.00,-0.00); trace/3= -0.40                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.083864                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3314   r_free= 0.4026   ksol= 0.35   Bsol= 57.33   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.41,1.32,-0.45,0.00,-0.00,-0.00); trace/3= -0.18                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.083686                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.773093              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.028  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.813591              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 106.606  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3314      final r-factor (work) = 0.2648          |
| start r-factor (free) = 0.4026      final r-factor (free) = 0.3295          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.8637 = 9.77 * 0.50 * 6.0818 + 1.00 * 0.1445                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.4410 = 9.77 * 0.50 * 6.0038 + 1.00 * 0.1029                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2648      final r-factor (work) = 0.2463          |
| start r-factor (free) = 0.3295      final r-factor (free) = 0.3251          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9012 = 0.81 * 1.00 * 6.0038 + 1.00 * 0.0166                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7886 = 0.81 * 1.00 * 5.8678 + 1.00 * 0.0146                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.289)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.17   17.76    None  None   None       |
|    all(noH): 2823   0      0.00    82.17   17.76    None  None   None       |
|    Sol.    : 438    0      2.94    82.17   38.49    None  None   None       |
|    Mac.    : 2385   0      0.00    78.57   13.95    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 -   8.217:  798   |   5:    41.087 -  49.304:  106        |
|      1:     8.217 -  16.435:  916   |   6:    49.304 -  57.521:   84        |
|      2:    16.435 -  24.652:  462   |   7:    57.521 -  65.739:   44        |
|      3:    24.652 -  32.869:  241   |   8:    65.739 -  73.956:   18        |
|      4:    32.869 -  41.087:  146   |   9:    73.956 -  82.173:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2463 r_free = 0.3251             target_work(ml) = 5.862         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2460 r_free = 0.3250             target_work(ml) = 5.861         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2460   r_free= 0.3250   ksol= 0.35   Bsol= 57.33   scale= 1.030   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.41,1.32,-0.45,0.00,-0.00,-0.00); trace/3= -0.18                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.861342                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2458   r_free= 0.3230   ksol= 0.34   Bsol= 51.05   scale= 1.028   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.01,0.11,0.04,0.00,0.00,0.00); trace/3= -0.28                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.857489                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.758732              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.614  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.240703              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 154.144  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2458      final r-factor (work) = 0.1938          |
| start r-factor (free) = 0.3230      final r-factor (free) = 0.2558          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.9963 = 5.76 * 0.50 * 5.8671 + 1.00 * 0.1029                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.6744 = 5.76 * 0.50 * 5.7641 + 1.00 * 0.0776                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1938      final r-factor (work) = 0.1760          |
| start r-factor (free) = 0.2558      final r-factor (free) = 0.2333          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4018 = 0.24 * 1.00 * 5.7641 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3527 = 0.24 * 1.00 * 5.5854 + 1.00 * 0.0083                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.289)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.43    78.01   16.84    None  None   None       |
|    all(noH): 2823   0      1.43    78.01   16.84    None  None   None       |
|    Sol.    : 438    0      5.65    77.14   39.15    None  None   None       |
|    Mac.    : 2385   0      1.43    78.01   12.74    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.435 -   9.092:  924   |   5:    39.723 -  47.381:  119        |
|      1:     9.092 -  16.750: 1055   |   6:    47.381 -  55.038:   85        |
|      2:    16.750 -  24.408:  300   |   7:    55.038 -  62.696:   50        |
|      3:    24.408 -  32.065:  150   |   8:    62.696 -  70.354:   14        |
|      4:    32.065 -  39.723:  115   |   9:    70.354 -  78.011:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1760 r_free = 0.2333             target_work(ml) = 5.539         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1755 r_free = 0.2321             target_work(ml) = 5.536         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1755   r_free= 0.2321   ksol= 0.34   Bsol= 51.05   scale= 1.045   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.01,0.11,0.04,0.00,0.00,0.00); trace/3= -0.28                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.536340                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1750   r_free= 0.2306   ksol= 0.32   Bsol= 36.93   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.87,-1.38,-0.54,-0.00,-0.00,-0.00); trace/3= -1.26                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.533052                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.052394              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.286  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.298685              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.588  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1750      final r-factor (work) = 0.1413          |
| start r-factor (free) = 0.2306      final r-factor (free) = 0.1892          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.6067 = 3.05 * 0.50 * 5.5884 + 1.00 * 0.0776                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.3667 = 3.05 * 0.50 * 5.4431 + 1.00 * 0.0595                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1413      final r-factor (work) = 0.1329          |
| start r-factor (free) = 0.1892      final r-factor (free) = 0.1828          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6340 = 0.30 * 1.00 * 5.4431 + 1.00 * 0.0083                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5933 = 0.30 * 1.00 * 5.3060 + 1.00 * 0.0085                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.289)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.81    80.11   16.76    None  None   None       |
|    all(noH): 2823   0      0.81    80.11   16.76    None  None   None       |
|    Sol.    : 438    0      3.99    78.31   40.77    None  None   None       |
|    Mac.    : 2385   0      0.81    80.11   12.35    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:     0.806 -   8.736:  852   |   5:    40.457 -  48.387:   93        |
|      1:     8.736 -  16.666: 1175   |   6:    48.387 -  56.318:   90        |
|      2:    16.666 -  24.597:  289   |   7:    56.318 -  64.248:   71        |
|      3:    24.597 -  32.527:  116   |   8:    64.248 -  72.178:   15        |
|      4:    32.527 -  40.457:  111   |   9:    72.178 -  80.108:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1329 r_free = 0.1828             target_work(ml) = 5.285         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1327 r_free = 0.1824             target_work(ml) = 5.284         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1327   r_free= 0.1824   ksol= 0.32   Bsol= 36.93   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.87,-1.38,-0.54,-0.00,-0.00,-0.00); trace/3= -1.26                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.283992                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1327   r_free= 0.1821   ksol= 0.32   Bsol= 36.93   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.04,-1.81,-0.66,-0.00,-0.00,-0.00); trace/3= -1.50                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.282656                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.310815              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 117.041  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.945178              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.911  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1327      final r-factor (work) = 0.1208          |
| start r-factor (free) = 0.1821      final r-factor (free) = 0.1688          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1898 = 2.31 * 0.50 * 5.3058 + 1.00 * 0.0595                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1148 = 2.31 * 0.50 * 5.2439 + 1.00 * 0.0560                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1208      final r-factor (work) = 0.1175          |
| start r-factor (free) = 0.1688      final r-factor (free) = 0.1680          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9649 = 0.95 * 1.00 * 5.2439 + 1.00 * 0.0085                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9150 = 0.95 * 1.00 * 5.1894 + 1.00 * 0.0101                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.289)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.73   17.06    None  None   None       |
|    all(noH): 2823   0      0.00    91.73   17.06    None  None   None       |
|    Sol.    : 438    0      4.61    91.73   42.94    None  None   None       |
|    Mac.    : 2385   0      0.00    88.89   12.30    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 -   9.173: 1004   |   5:    45.863 -  55.035:   87        |
|      1:     9.173 -  18.345: 1146   |   6:    55.035 -  64.208:   83        |
|      2:    18.345 -  27.518:  219   |   7:    64.208 -  73.380:   45        |
|      3:    27.518 -  36.690:  118   |   8:    73.380 -  82.553:   18        |
|      4:    36.690 -  45.863:   96   |   9:    82.553 -  91.725:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1175 r_free = 0.1680             target_work(ml) = 5.187         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1174 r_free = 0.1679             target_work(ml) = 5.187         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1174   r_free= 0.1679   ksol= 0.32   Bsol= 36.93   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.04,-1.81,-0.66,-0.00,-0.00,-0.00); trace/3= -1.50                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.186797                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7897 -  4.6593 0.99   1389  153 0.1023 0.1345       5.414      5.5874|
|  2:  4.6593 -  3.7176 0.99   1330  152 0.0883 0.1225      5.4844      5.7117|
|  3:  3.7176 -  3.2533 0.99   1303  140 0.1131 0.1540      5.5457      5.8835|
|  4:  3.2533 -  2.9585 0.99   1298  149 0.1301 0.1827      5.5233      5.6991|
|  5:  2.9585 -  2.7479 0.99   1292  145 0.1414 0.1907      5.3887      5.6187|
|  6:  2.7479 -  2.5868 0.99   1298  139 0.1247 0.1838      5.2422      5.4426|
|  7:  2.5868 -  2.4578 0.99   1280  144 0.1340 0.1720      5.1946      5.4158|
|  8:  2.4578 -  2.3513 0.98   1269  141 0.1258 0.1815      5.1219      5.3687|
|  9:  2.3513 -  2.2611 0.98   1256  140 0.1212 0.1743      5.0578      5.2795|
| 10:  2.2611 -  2.1833 1.00   1283  143 0.1151 0.1784      4.9975       5.224|
| 11:  2.1833 -  2.1153 0.97   1256  138 0.1172 0.1954      4.9821       5.352|
| 12:  2.1153 -  2.0550 0.98   1248  138 0.1181 0.1854      4.9346      5.2459|
| 13:  2.0550 -  2.0010 0.99   1291  140 0.1163 0.1978      4.8157       5.119|
| 14:  2.0010 -  1.9523 0.66    837   97 0.1036 0.1604      4.6844      4.8996|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7897 -  4.6593  1389   153  0.93   9.75   0.99     0.96       7764.74|
|  2:  4.6593 -  3.7176  1330   152  0.95   8.54   1.04     1.02      10214.49|
|  3:  3.7176 -  3.2533  1303   140  0.93  12.52   1.05     1.05      12227.98|
|  4:  3.2533 -  2.9585  1298   149  0.91  15.03   1.03     1.01      12076.50|
|  5:  2.9585 -  2.7479  1292   145  0.89  16.77   1.01     0.98       9347.17|
|  6:  2.7479 -  2.5868  1298   139  0.89  16.74   0.99     0.96       7595.10|
|  7:  2.5868 -  2.4578  1280   144  0.89  16.71   1.00     0.97       6554.99|
|  8:  2.4578 -  2.3513  1269   141  0.90  16.03   1.01     1.00       5766.22|
|  9:  2.3513 -  2.2611  1256   140  0.91  15.54   1.02     0.98       5221.04|
| 10:  2.2611 -  2.1833  1283   143  0.89  16.53   1.01     0.98       4845.94|
| 11:  2.1833 -  2.1153  1256   138  0.89  17.26   1.01     0.98       4882.27|
| 12:  2.1153 -  2.0550  1248   138  0.90  16.73   1.03     1.01       4526.27|
| 13:  2.0550 -  2.0010  1291   140  0.89  16.96   1.02     1.00       3568.55|
| 14:  2.0010 -  1.9523   837    97  0.92  14.06   1.01     0.97       2671.62|
|alpha:            min =        0.96 max =            1.05 mean =         0.99|
|beta:             min =     2671.62 max =        12227.98 mean =      7091.35|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.76 mean =        14.91|
|phase err.(test): min =        0.00 max =           88.37 mean =        14.59|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1174   r_free= 0.1679   ksol= 0.30   Bsol= 37.38   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.02,-1.85,-0.60,-0.00,-0.00,-0.00); trace/3= -1.49                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.186060                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1174   r_free= 0.1679   ksol= 0.30   Bsol= 37.38   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.02,-1.85,-0.60,-0.00,-0.00,-0.00); trace/3= -1.49                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.186060                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7897 -  4.6593 0.99   1389  153 0.1018 0.1339      5.4071       5.582|
|  2:  4.6593 -  3.7176 0.99   1330  152 0.0887 0.1229      5.4856      5.7151|
|  3:  3.7176 -  3.2533 0.99   1303  140 0.1134 0.1544      5.5476      5.8864|
|  4:  3.2533 -  2.9585 0.99   1298  149 0.1302 0.1827      5.5238      5.6991|
|  5:  2.9585 -  2.7479 0.99   1292  145 0.1414 0.1905      5.3882       5.618|
|  6:  2.7479 -  2.5868 0.99   1298  139 0.1247 0.1835      5.2413      5.4409|
|  7:  2.5868 -  2.4578 0.99   1280  144 0.1339 0.1720      5.1938      5.4153|
|  8:  2.4578 -  2.3513 0.98   1269  141 0.1257 0.1813      5.1212      5.3677|
|  9:  2.3513 -  2.2611 0.98   1256  140 0.1212 0.1742      5.0575      5.2788|
| 10:  2.2611 -  2.1833 1.00   1283  143 0.1150 0.1785       4.997      5.2245|
| 11:  2.1833 -  2.1153 0.97   1256  138 0.1171 0.1953      4.9818      5.3511|
| 12:  2.1153 -  2.0550 0.98   1248  138 0.1180 0.1853       4.934       5.246|
| 13:  2.0550 -  2.0010 0.99   1291  140 0.1163 0.1976      4.8149      5.1178|
| 14:  2.0010 -  1.9523 0.66    837   97 0.1035 0.1600       4.683      4.8975|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7897 -  4.6593  1389   153  0.94   9.66   0.99     0.96       7621.64|
|  2:  4.6593 -  3.7176  1330   152  0.95   8.51   1.04     1.02      10174.17|
|  3:  3.7176 -  3.2533  1303   140  0.92  12.56   1.05     1.05      12293.23|
|  4:  3.2533 -  2.9585  1298   149  0.91  15.04   1.03     1.01      12094.76|
|  5:  2.9585 -  2.7479  1292   145  0.89  16.74   1.01     0.98       9333.09|
|  6:  2.7479 -  2.5868  1298   139  0.89  16.72   0.99     0.97       7576.90|
|  7:  2.5868 -  2.4578  1280   144  0.89  16.69   1.00     0.97       6538.32|
|  8:  2.4578 -  2.3513  1269   141  0.90  16.01   1.01     1.00       5755.62|
|  9:  2.3513 -  2.2611  1256   140  0.91  15.54   1.02     0.98       5215.67|
| 10:  2.2611 -  2.1833  1283   143  0.89  16.52   1.01     0.98       4842.17|
| 11:  2.1833 -  2.1153  1256   138  0.89  17.25   1.01     0.98       4879.84|
| 12:  2.1153 -  2.0550  1248   138  0.90  16.72   1.03     1.01       4520.65|
| 13:  2.0550 -  2.0010  1291   140  0.89  16.94   1.02     1.00       3560.57|
| 14:  2.0010 -  1.9523   837    97  0.92  14.02   1.01     0.98       2661.30|
|alpha:            min =        0.96 max =            1.05 mean =         0.99|
|beta:             min =     2661.30 max =        12293.23 mean =      7076.56|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.78 mean =        14.89|
|phase err.(test): min =        0.00 max =           88.49 mean =        14.56|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.289)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.73   17.06    None  None   None       |
|    all(noH): 2823   0      0.00    91.73   17.06    None  None   None       |
|    Sol.    : 438    0      4.61    91.73   42.94    None  None   None       |
|    Mac.    : 2385   0      0.00    88.89   12.31    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   9.176: 1004   |   5:    45.866 -  55.038:   87        |
|      1:     9.176 -  18.348: 1146   |   6:    55.038 -  64.211:   83        |
|      2:    18.348 -  27.521:  219   |   7:    64.211 -  73.383:   45        |
|      3:    27.521 -  36.693:  118   |   8:    73.383 -  82.556:   18        |
|      4:    36.693 -  45.866:   96   |   9:    82.556 -  91.728:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 301         
Filter by distance & map next to the model:
   mapped sites are within: 0.603 - 4.249
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 296 from: 301
   mapped sites are within: 0.796 - 4.249

peak=    7.612 closest distance to " O   HOH Z 387 " =    2.179
peak=    7.090 closest distance to " O   HOH Z 431 " =    2.224
peak=    6.967 closest distance to " O   HOH Z 130 " =    1.265
peak=    6.064 closest distance to " NE2 GLN A  11 " =    1.327
peak=    6.027 closest distance to " O   HOH Z  65 " =    1.778
peak=    5.991 closest distance to " O   HOH Z 427 " =    1.430
peak=    5.936 closest distance to " O   HOH Z 142 " =    1.798
peak=    5.609 closest distance to " O   HOH Z 287 " =    2.041
peak=    5.526 closest distance to " O   HOH Z 222 " =    1.311
peak=    5.521 closest distance to " O   HOH Z 112 " =    1.631
peak=    5.517 closest distance to " O   HOH Z  63 " =    2.175
peak=    5.412 closest distance to " O   HOH Z   7 " =    1.825
peak=    5.367 closest distance to " O   HOH Z 417 " =    2.206
peak=    5.349 closest distance to " CG  PRO A  54 " =    1.298
peak=    5.330 closest distance to " O   HOH Z 236 " =    1.564
peak=    5.199 closest distance to " O   HOH Z  29 " =    1.307
peak=    5.186 closest distance to " CB  ARG A 275 " =    1.018
peak=    5.170 closest distance to " O   HOH Z 403 " =    1.532
peak=    5.102 closest distance to " O   HOH Z 390 " =    1.063
peak=    5.028 closest distance to " O   HOH Z  49 " =    1.402
peak=    4.994 closest distance to " O   HOH Z  78 " =    1.626
peak=    4.992 closest distance to " O   HOH Z 245 " =    1.250
peak=    4.987 closest distance to " CG  PRO A 213 " =    1.245
peak=    4.955 closest distance to " O   HOH Z 427 " =    1.741
peak=    4.878 closest distance to " O   HOH Z 375 " =    1.073
peak=    4.848 closest distance to " CB  PRO A  54 " =    1.035
peak=    4.829 closest distance to " O   HOH Z 124 " =    1.583
peak=    4.788 closest distance to " O   HOH Z 289 " =    1.177
peak=    4.707 closest distance to " O   HOH Z 414 " =    1.358
peak=    4.670 closest distance to " O   HOH Z  63 " =    1.908
peak=    4.670 closest distance to " O   HOH Z   9 " =    1.192
peak=    4.664 closest distance to " O   HOH Z 193 " =    1.764
peak=    4.649 closest distance to " NH2 ARG A  56 " =    2.042
peak=    4.632 closest distance to " O   HOH Z 145 " =    1.488
peak=    4.580 closest distance to " O   HOH Z 423 " =    1.801
peak=    4.578 closest distance to " O   HOH Z 272 " =    1.881
peak=    4.547 closest distance to " O   HOH Z 232 " =    2.225
peak=    4.518 closest distance to " CA  TYR A  30 " =    1.004
peak=    4.445 closest distance to " O   PRO A 198 " =    1.232
peak=    4.440 closest distance to " O   HOH Z 371 " =    2.008
peak=    4.434 closest distance to " O   HOH Z 214 " =    1.358
peak=    4.386 closest distance to " O   HOH Z 158 " =    1.368
peak=    4.374 closest distance to " O   HOH Z  61 " =    1.513
peak=    4.373 closest distance to " O   HOH Z 380 " =    1.916
peak=    4.366 closest distance to " O   HOH Z 217 " =    2.967
peak=    4.363 closest distance to " O   HOH Z  92 " =    1.286
peak=    4.327 closest distance to " CB  SER A   3 " =    1.233
peak=    4.269 closest distance to " O   HOH Z 298 " =    1.933
peak=    4.259 closest distance to " CB  ASN A 148 " =    1.367
peak=    4.249 closest distance to " O   HOH Z 416 " =    1.232
peak=    4.245 closest distance to " O   HOH Z 368 " =    3.560
peak=    4.243 closest distance to " CB  GLN A 183 " =    1.118
peak=    4.226 closest distance to " O   HOH Z 211 " =    1.073
peak=    4.223 closest distance to " O   HOH Z 392 " =    1.363
peak=    4.223 closest distance to " O   HOH Z 130 " =    2.425
peak=    4.196 closest distance to " O   HOH Z 385 " =    1.679
peak=    4.192 closest distance to " O   HOH Z 316 " =    2.931
peak=    4.164 closest distance to " CB  GLN A 223 " =    1.476
peak=    4.152 closest distance to " O   HOH Z 424 " =    1.177
peak=    4.134 closest distance to " O   HOH Z  28 " =    1.327
peak=    4.112 closest distance to " O   HOH Z 371 " =    2.274
peak=    4.064 closest distance to " O   HOH Z 139 " =    1.345
peak=    4.015 closest distance to " OG BSER A 164 " =    2.112
peak=    3.998 closest distance to " O   HOH Z 156 " =    3.168
peak=    3.977 closest distance to " O   SER A  87 " =    2.323
peak=    3.968 closest distance to " O   HOH Z 327 " =    1.797
peak=    3.959 closest distance to " O   HOH Z 425 " =    1.471
peak=    3.955 closest distance to " CG2 THR A 221 " =    1.313
peak=    3.952 closest distance to " O   HOH Z 402 " =    1.505
peak=    3.933 closest distance to " N   ALA A   1 " =    2.615
peak=    3.918 closest distance to " O   HOH Z 215 " =    1.521
peak=    3.913 closest distance to " CG  TRP A 179 " =    2.134
peak=    3.890 closest distance to " O   HOH Z   2 " =    1.984
peak=    3.884 closest distance to " O   HOH Z  24 " =    1.734
peak=    3.880 closest distance to " CB  GLU A 128 " =    1.043
peak=    3.876 closest distance to " O   ASP A 286 " =    2.574
peak=    3.864 closest distance to " O   HOH Z 213 " =    1.655
peak=    3.863 closest distance to " O   HOH Z 117 " =    1.261
peak=    3.847 closest distance to " CG  GLN A  11 " =    2.065
peak=    3.846 closest distance to " O   HOH Z 422 " =    2.493
peak=    3.840 closest distance to " O   HOH Z 378 " =    0.917
peak=    3.839 closest distance to " O   HOH Z 415 " =    1.135
peak=    3.838 closest distance to " O   HOH Z 365 " =    2.515
peak=    3.829 closest distance to " O   HOH Z  69 " =    2.385
peak=    3.817 closest distance to " CB  SER A  63 " =    1.407
peak=    3.796 closest distance to " O   HOH Z  88 " =    3.141
peak=    3.795 closest distance to " CG2 VAL A 257 " =    0.868
peak=    3.790 closest distance to " NZ  LYS A 117 " =    1.185
peak=    3.789 closest distance to " O   HOH Z 106 " =    2.455
peak=    3.787 closest distance to " O   HOH Z 234 " =    3.604
peak=    3.776 closest distance to " O   HOH Z 352 " =    1.723
peak=    3.775 closest distance to " OG BSER A  99 " =    2.283
peak=    3.773 closest distance to " O   HOH Z 302 " =    1.357
peak=    3.773 closest distance to " CB  GLU A 152 " =    1.221
peak=    3.765 closest distance to " O   HOH Z 166 " =    1.902
peak=    3.764 closest distance to " O   HOH Z   6 " =    2.070
peak=    3.753 closest distance to " CB  THR A 157 " =    1.071
peak=    3.753 closest distance to " O   HOH Z  61 " =    1.684
peak=    3.753 closest distance to " CG1BVAL A 121 " =    2.181
peak=    3.748 closest distance to " O   HOH Z 363 " =    1.070
peak=    3.747 closest distance to " CB  LEU A 300 " =    0.975
peak=    3.744 closest distance to " OG BSER A 212 " =    2.790
peak=    3.743 closest distance to " O   HOH Z 261 " =    1.890
peak=    3.739 closest distance to " O   HOH Z 359 " =    1.408
peak=    3.737 closest distance to " CB  SER A 276 " =    1.205
peak=    3.726 closest distance to " NH1AARG A 145 " =    1.172
peak=    3.721 closest distance to " OG  SER A  62 " =    2.916
peak=    3.720 closest distance to " CB  TRP A 266 " =    1.159
peak=    3.715 closest distance to " CG  PRO A  90 " =    1.119
peak=    3.694 closest distance to " O   HOH Z 412 " =    1.983
peak=    3.692 closest distance to " O   HOH Z 130 " =    2.106
peak=    3.691 closest distance to " O   HOH Z 413 " =    1.615
peak=    3.681 closest distance to " O   HOH Z 151 " =    1.680
peak=    3.674 closest distance to " O   HOH Z 368 " =    1.932
peak=    3.673 closest distance to " CG  PRO A 198 " =    1.273
peak=    3.672 closest distance to " O   HOH Z 385 " =    3.280
peak=    3.672 closest distance to " CA  ASN A 215 " =    1.146
peak=    3.672 closest distance to " O   HOH Z 329 " =    3.518
peak=    3.663 closest distance to " CB  GLU A 277 " =    3.381
peak=    3.649 closest distance to " NE2 GLN A  58 " =    3.855
peak=    3.645 closest distance to " N   ALA A   1 " =    1.285
peak=    3.643 closest distance to " O   HOH Z  59 " =    1.398
peak=    3.639 closest distance to " O   HOH Z 425 " =    2.059
peak=    3.634 closest distance to " O   HOH Z 244 " =    1.683
peak=    3.629 closest distance to " O   HOH Z  64 " =    2.010
peak=    3.626 closest distance to " CA  LEU A 282 " =    1.059
peak=    3.612 closest distance to " CA  ALA A 299 " =    0.958
peak=    3.608 closest distance to " NE1 TRP A 274 " =    1.042
peak=    3.603 closest distance to " O   HOH Z 434 " =    1.275
peak=    3.602 closest distance to " N   GLU A   2 " =    1.286
peak=    3.597 closest distance to " O   HOH Z 128 " =    2.053
peak=    3.597 closest distance to " O   HOH Z  93 " =    1.848
peak=    3.586 closest distance to " CA  PHE A 283 " =    1.298
peak=    3.586 closest distance to " O   HOH Z 389 " =    1.188
peak=    3.586 closest distance to " CB  SER A 216 " =    0.988
peak=    3.582 closest distance to " O   HOH Z 405 " =    1.443
peak=    3.581 closest distance to " O   HOH Z 158 " =    2.324
peak=    3.570 closest distance to " C   ALA A   1 " =    1.635
peak=    3.564 closest distance to " O   HOH Z  44 " =    1.699
peak=    3.562 closest distance to " OD2 ASP A 286 " =    2.495
peak=    3.558 closest distance to " CG2AVAL A 121 " =    2.492
peak=    3.558 closest distance to " CB  GLN A  89 " =    1.317
peak=    3.556 closest distance to " O   HOH Z  97 " =    1.891
peak=    3.554 closest distance to " N   HIS A  86 " =    1.853
peak=    3.536 closest distance to " O   HOH Z 258 " =    2.085
peak=    3.527 closest distance to " O   HOH Z 365 " =    1.523
peak=    3.525 closest distance to " O   HOH Z 227 " =    1.956
peak=    3.522 closest distance to " O   HOH Z  47 " =    1.546
peak=    3.521 closest distance to " O   HOH Z 212 " =    1.521
peak=    3.520 closest distance to " CB  ARG A 190 " =    1.806
peak=    3.515 closest distance to " O   HOH Z 394 " =    1.722
peak=    3.510 closest distance to " CD2 TRP A 179 " =    1.511
peak=    3.505 closest distance to " O   HOH Z 250 " =    1.446
peak=    3.493 closest distance to " O   HOH Z 152 " =    2.302
peak=    3.487 closest distance to " O   HOH Z 344 " =    3.042
peak=    3.480 closest distance to " O   HOH Z 419 " =    2.136
peak=    3.480 closest distance to " O   HOH Z 189 " =    2.811
peak=    3.478 closest distance to " CG1 ILE A 120 " =    1.469
peak=    3.470 closest distance to " O   HOH Z 411 " =    3.646
peak=    3.468 closest distance to " O   HOH Z 119 " =    4.249
peak=    3.467 closest distance to " NZ  LYS A 119 " =    2.641
peak=    3.464 closest distance to " CB  GLU A 277 " =    1.032
peak=    3.460 closest distance to " CB  TRP A 179 " =    1.281
peak=    3.459 closest distance to " O   HOH Z 293 " =    1.538
peak=    3.458 closest distance to " O   HOH Z   7 " =    3.235
peak=    3.457 closest distance to " CB  THR A  31 " =    1.531
peak=    3.454 closest distance to " O   HOH Z  73 " =    1.802
peak=    3.452 closest distance to " CB  VAL A 202 " =    1.626
peak=    3.431 closest distance to " O  BHOH Z  74 " =    1.295
peak=    3.430 closest distance to " O   HOH Z 419 " =    1.683
peak=    3.429 closest distance to " CE AMET A  47 " =    1.272
peak=    3.427 closest distance to " O   HOH Z 437 " =    2.018
peak=    3.426 closest distance to " NE2 GLN A 278 " =    3.534
peak=    3.423 closest distance to " CG  LEU A 167 " =    1.258
peak=    3.422 closest distance to " CA  MET A  40 " =    1.132
peak=    3.419 closest distance to " CB  SER A  26 " =    1.695
peak=    3.418 closest distance to " CB  MET A 105 " =    0.909
peak=    3.415 closest distance to " O   HOH Z  65 " =    1.310
peak=    3.415 closest distance to " CB  TYR A 116 " =    1.074
peak=    3.415 closest distance to " O   HOH Z 175 " =    1.968
peak=    3.415 closest distance to " CD1 ILE A 263 " =    1.311
peak=    3.413 closest distance to " CD  LYS A 166 " =    1.473
peak=    3.410 closest distance to " O   HOH Z 108 " =    2.002
peak=    3.410 closest distance to " CB  PHE A 130 " =    1.053
peak=    3.409 closest distance to " CE  LYS A  76 " =    0.852
peak=    3.409 closest distance to " O   HOH Z 116 " =    2.551
peak=    3.401 closest distance to " CZ2 TRP A 150 " =    1.151
peak=    3.401 closest distance to " O   HOH Z 423 " =    1.661
peak=    3.396 closest distance to " CE  LYS A 119 " =    1.186
peak=    3.393 closest distance to " CB  LYS A 290 " =    1.451
peak=    3.389 closest distance to " O   HOH Z  11 " =    1.344
peak=    3.389 closest distance to " CB  ASP A 200 " =    0.909
peak=    3.385 closest distance to " O   HOH Z 326 " =    1.818
peak=    3.384 closest distance to " O   HOH Z 155 " =    1.845
peak=    3.383 closest distance to " CA  ARG A 195 " =    1.560
peak=    3.381 closest distance to " CB  SER A  26 " =    1.392
peak=    3.380 closest distance to " CB  ARG A 138 " =    0.796
peak=    3.379 closest distance to " CB  VAL A 265 " =    1.371
peak=    3.370 closest distance to " O   HOH Z 291 " =    1.479
peak=    3.367 closest distance to " O   HOH Z 115 " =    1.350
peak=    3.360 closest distance to " O   HOH Z  44 " =    3.011
peak=    3.356 closest distance to " CA  ILE A 234 " =    1.003
peak=    3.352 closest distance to " CB  ALA A   1 " =    1.010
peak=    3.351 closest distance to " O   HOH Z 128 " =    2.038
peak=    3.347 closest distance to " O   HOH Z 358 " =    1.217
peak=    3.342 closest distance to " OD1 ASP A 286 " =    1.158
peak=    3.336 closest distance to " O   HOH Z 156 " =    2.539
peak=    3.333 closest distance to " CB  MET A 105 " =    1.073
peak=    3.331 closest distance to " NH1BARG A 145 " =    1.454
peak=    3.329 closest distance to " O   HOH Z  58 " =    1.580
peak=    3.324 closest distance to " O   HOH Z 117 " =    1.672
peak=    3.322 closest distance to " O   HOH Z 222 " =    1.958
peak=    3.317 closest distance to " C   PHE A 208 " =    1.088
peak=    3.314 closest distance to " O   HOH Z 290 " =    0.974
peak=    3.313 closest distance to " N   TYR A  15 " =    1.163
peak=    3.313 closest distance to " O   HOH Z 357 " =    1.770
peak=    3.312 closest distance to " O   HOH Z  50 " =    1.818
peak=    3.308 closest distance to " O   HOH Z 153 " =    3.567
peak=    3.307 closest distance to " N   SER A 271 " =    1.060
peak=    3.307 closest distance to " CG  LYS A 166 " =    1.325
peak=    3.300 closest distance to " O   HOH Z 207 " =    2.149
peak=    3.299 closest distance to " O   HOH Z 193 " =    1.839
peak=    3.299 closest distance to " O   HOH Z 424 " =    2.969
peak=    3.297 closest distance to " CA  ASN A 127 " =    1.087
peak=    3.291 closest distance to " CB  HIS A 108 " =    0.823
peak=    3.278 closest distance to " O   HOH Z 119 " =    1.528
peak=    3.277 closest distance to " O   HOH Z 158 " =    3.066
peak=    3.277 closest distance to " O   HOH Z 282 " =    1.569
peak=    3.274 closest distance to " O   HOH Z 215 " =    2.973
peak=    3.274 closest distance to " O   HOH Z 214 " =    1.845
peak=    3.274 closest distance to " N   GLN A 278 " =    1.082
peak=    3.272 closest distance to " CG  PRO A 243 " =    1.171
peak=    3.269 closest distance to " O   HOH Z  80 " =    1.959
peak=    3.267 closest distance to " NH1 ARG A  14 " =    1.021
peak=    3.264 closest distance to " O   HOH Z  32 " =    2.075
peak=    3.264 closest distance to " OD1 ASN A  69 " =    2.436
peak=    3.262 closest distance to " OG1 THR A 246 " =    1.241
peak=    3.259 closest distance to " O   HOH Z   1 " =    1.808
peak=    3.259 closest distance to " OG1 THR A 221 " =    1.297
peak=    3.258 closest distance to " O   HOH Z 426 " =    1.932
peak=    3.256 closest distance to " NZ  LYS A  76 " =    1.575
peak=    3.252 closest distance to " CB  ASN A 215 " =    1.043
peak=    3.251 closest distance to " O   HOH Z 233 " =    2.133
peak=    3.249 closest distance to " O   HOH Z 214 " =    3.105
peak=    3.247 closest distance to " O   HOH Z 288 " =    1.957
peak=    3.237 closest distance to " CB  LEU A 228 " =    1.107
peak=    3.237 closest distance to " O   ALA A 165 " =    1.324
peak=    3.234 closest distance to " CB  ALA A 114 " =    1.342
peak=    3.230 closest distance to " OE2 GLU A  53 " =    1.969
peak=    3.228 closest distance to " CB  LYS A 117 " =    1.128
peak=    3.225 closest distance to " O   HOH Z 112 " =    2.219
peak=    3.220 closest distance to " CB  ALA A 114 " =    1.213
peak=    3.216 closest distance to " O   HOH Z 185 " =    1.616
peak=    3.215 closest distance to " CG2 VAL A 232 " =    0.878
peak=    3.209 closest distance to " N   SER A 210 " =    1.289
peak=    3.202 closest distance to " CZ  PHE A  38 " =    1.196
peak=    3.201 closest distance to " OG  SER A  22 " =    2.674
peak=    3.198 closest distance to " O   HOH Z 383 " =    2.189
peak=    3.194 closest distance to " O  BHOH Z 338 " =    2.419
peak=    3.192 closest distance to " O   HOH Z  66 " =    2.081
peak=    3.190 closest distance to " O   HOH Z   9 " =    1.991
peak=    3.186 closest distance to " CG  LYS A  76 " =    1.621
peak=    3.182 closest distance to " CB  ALA A  84 " =    1.521
peak=    3.181 closest distance to " N   ASN A 127 " =    1.344
peak=    3.177 closest distance to " CG  GLN A  89 " =    1.375
peak=    3.175 closest distance to " O   HOH Z 426 " =    1.000
peak=    3.174 closest distance to " O   HOH Z 311 " =    2.453
peak=    3.170 closest distance to " O   HOH Z 386 " =    1.218
peak=    3.163 closest distance to " CG1 VAL A 174 " =    1.426
peak=    3.156 closest distance to " O   HOH Z  68 " =    1.738
peak=    3.155 closest distance to " CA  GLU A 152 " =    1.333
peak=    3.151 closest distance to " CA  MET A 105 " =    0.803
peak=    3.150 closest distance to " ND1 HIS A  81 " =    1.375
peak=    3.145 closest distance to " O   HOH Z  90 " =    2.093
peak=    3.136 closest distance to " CG  MET A 185 " =    1.491
peak=    3.134 closest distance to " CG1 VAL A 126 " =    1.146
peak=    3.130 closest distance to " O   HOH Z 128 " =    2.941
peak=    3.126 closest distance to " O   HOH Z 171 " =    2.382
peak=    3.123 closest distance to " O   HOH Z 172 " =    1.878
peak=    3.121 closest distance to " NE2 GLN A  73 " =    1.379
peak=    3.118 closest distance to " O   HOH Z  18 " =    1.721
peak=    3.118 closest distance to " CA  ALA A 160 " =    1.617
peak=    3.113 closest distance to " CB  ARG A  79 " =    1.213
peak=    3.112 closest distance to " CA  GLY A 241 " =    3.561
peak=    3.110 closest distance to " O   HOH Z 423 " =    1.663
peak=    3.108 closest distance to " O   HOH Z 173 " =    2.093
peak=    3.106 closest distance to " O   HOH Z  17 " =    1.952
peak=    3.095 closest distance to " OD1 ASN A 217 " =    1.642
peak=    3.091 closest distance to " NE AARG A 275 " =    1.700
peak=    3.085 closest distance to " O   HOH Z  57 " =    1.776
peak=    3.083 closest distance to " CZ AARG A 102 " =    1.936
peak=    3.081 closest distance to " CA  ALA A 160 " =    1.061
peak=    3.074 closest distance to " CB  ALA A  34 " =    1.179
peak=    3.070 closest distance to " CG2 VAL A 197 " =    1.115
peak=    3.069 closest distance to " O   HOH Z 303 " =    1.606
peak=    3.058 closest distance to " OG BSER A  99 " =    2.605

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 203         
Filter by distance & map next to the model:
   mapped sites are within: 0.803 - 4.836
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 203 from: 203
   mapped sites are within: 0.803 - 4.836

peak=   -4.509 closest distance to " O   HOH Z 385 " =    1.030
peak=   -4.212 closest distance to " O   PRO A 198 " =    1.212
peak=   -4.195 closest distance to " O   HOH Z  60 " =    1.863
peak=   -4.049 closest distance to " O   HOH Z 298 " =    1.044
peak=   -4.016 closest distance to " CD  ARG A  14 " =    3.188
peak=   -3.996 closest distance to " O   HOH Z 407 " =    3.151
peak=   -3.991 closest distance to " O   MET A  40 " =    2.776
peak=   -3.988 closest distance to " CD  ARG A 156 " =    1.908
peak=   -3.984 closest distance to " OD2 ASP A 191 " =    1.375
peak=   -3.971 closest distance to " O   SER A  22 " =    2.598
peak=   -3.968 closest distance to " OE1 GLU A 277 " =    1.983
peak=   -3.937 closest distance to " O   HOH Z 313 " =    1.286
peak=   -3.921 closest distance to " CZ  PHE A  59 " =    1.364
peak=   -3.915 closest distance to " O   HOH Z 185 " =    1.847
peak=   -3.904 closest distance to " CA  GLY A  98 " =    1.758
peak=   -3.895 closest distance to " N   GLN A  58 " =    1.689
peak=   -3.871 closest distance to " OG BSER A 134 " =    1.361
peak=   -3.862 closest distance to " CB  ALA A 291 " =    2.200
peak=   -3.862 closest distance to " O   HOH Z 416 " =    0.808
peak=   -3.848 closest distance to " O   HOH Z  37 " =    1.514
peak=   -3.843 closest distance to " O   HOH Z  13 " =    1.645
peak=   -3.841 closest distance to " O   PRO A 243 " =    2.446
peak=   -3.820 closest distance to " O   SER A  95 " =    1.248
peak=   -3.812 closest distance to " O   HOH Z  88 " =    1.725
peak=   -3.799 closest distance to " CZ2 TRP A 274 " =    0.915
peak=   -3.779 closest distance to " O   HOH Z 429 " =    1.954
peak=   -3.766 closest distance to " N   THR A 157 " =    1.522
peak=   -3.757 closest distance to " O   HOH Z  24 " =    1.123
peak=   -3.755 closest distance to " O   HOH Z 438 " =    0.842
peak=   -3.753 closest distance to " O   HOH Z  90 " =    2.322
peak=   -3.752 closest distance to " O   HOH Z 195 " =    1.842
peak=   -3.742 closest distance to " CB  PRO A 243 " =    2.552
peak=   -3.720 closest distance to " CD2 LEU A 237 " =    2.468
peak=   -3.706 closest distance to " CG  GLN A  58 " =    1.009
peak=   -3.700 closest distance to " CD2 TYR A 293 " =    1.705
peak=   -3.695 closest distance to " OE1 GLN A 183 " =    1.381
peak=   -3.690 closest distance to " OG  SER A  97 " =    2.125
peak=   -3.688 closest distance to " O   HOH Z 171 " =    2.905
peak=   -3.688 closest distance to " O   SER A 135 " =    1.555
peak=   -3.686 closest distance to " O   HOH Z 372 " =    2.575
peak=   -3.680 closest distance to " CE  LYS A  76 " =    2.984
peak=   -3.675 closest distance to " O   HOH Z 290 " =    1.140
peak=   -3.669 closest distance to " OD2 ASP A 171 " =    1.938
peak=   -3.669 closest distance to " CD1 LEU A 101 " =    2.250
peak=   -3.668 closest distance to " O   PRO A 198 " =    1.293
peak=   -3.655 closest distance to " O   HOH Z 236 " =    2.195
peak=   -3.654 closest distance to " C   HIS A 108 " =    1.212
peak=   -3.626 closest distance to " O   HOH Z 198 " =    1.853
peak=   -3.625 closest distance to " O   HOH Z  56 " =    1.788
peak=   -3.620 closest distance to " O   ILE A  49 " =    1.560
peak=   -3.609 closest distance to " CB  ALA A   7 " =    1.859
peak=   -3.609 closest distance to " N   ALA A   1 " =    1.340
peak=   -3.607 closest distance to " CA  GLY A 133 " =    1.842
peak=   -3.605 closest distance to " O   HOH Z 415 " =    1.153
peak=   -3.603 closest distance to " O   HOH Z  43 " =    1.901
peak=   -3.601 closest distance to " O   HOH Z  28 " =    1.985
peak=   -3.600 closest distance to " O   PHE A 218 " =    1.414
peak=   -3.598 closest distance to " CD  GLN A 223 " =    1.604
peak=   -3.588 closest distance to " N   GLN A  58 " =    1.236
peak=   -3.586 closest distance to " NE  ARG A  36 " =    1.900
peak=   -3.586 closest distance to " O   VAL A 189 " =    2.255
peak=   -3.586 closest distance to " N   VAL A  72 " =    1.621
peak=   -3.578 closest distance to " O   HOH Z 426 " =    2.056
peak=   -3.571 closest distance to " NH2 ARG A  79 " =    1.988
peak=   -3.565 closest distance to " CG  MET A 105 " =    0.892
peak=   -3.558 closest distance to " CE  LYS A  76 " =    2.842
peak=   -3.557 closest distance to " CB  TYR A  15 " =    2.180
peak=   -3.556 closest distance to " N   ALA A 248 " =    1.564
peak=   -3.555 closest distance to " O   HOH Z 351 " =    1.571
peak=   -3.550 closest distance to " O   HOH Z  39 " =    1.274
peak=   -3.546 closest distance to " CG2 ILE A  20 " =    2.736
peak=   -3.541 closest distance to " OG  SER A  87 " =    1.213
peak=   -3.532 closest distance to " O   HOH Z  65 " =    0.831
peak=   -3.511 closest distance to " O   HOH Z 425 " =    1.047
peak=   -3.508 closest distance to " O   HOH Z 412 " =    4.836
peak=   -3.506 closest distance to " O   HOH Z 388 " =    2.051
peak=   -3.505 closest distance to " CG  PHE A 283 " =    2.571
peak=   -3.502 closest distance to " O   HOH Z 131 " =    4.092
peak=   -3.499 closest distance to " O   PRO A  54 " =    1.435
peak=   -3.491 closest distance to " O   HOH Z  22 " =    2.673
peak=   -3.485 closest distance to " OE2 GLU A 152 " =    1.080
peak=   -3.476 closest distance to " O   HOH Z 211 " =    1.425
peak=   -3.461 closest distance to " C   ALA A 158 " =    1.481
peak=   -3.457 closest distance to " NH2 ARG A 219 " =    1.715
peak=   -3.452 closest distance to " C   ILE A 239 " =    1.970
peak=   -3.450 closest distance to " OE1 GLU A  44 " =    1.868
peak=   -3.449 closest distance to " CA  GLY A 203 " =    2.267
peak=   -3.439 closest distance to " CG  ASP A 231 " =    0.811
peak=   -3.428 closest distance to " O   THR A 235 " =    1.441
peak=   -3.428 closest distance to " O   HOH Z 143 " =    2.303
peak=   -3.422 closest distance to " O   VAL A  67 " =    2.750
peak=   -3.420 closest distance to " O   TYR A 186 " =    1.548
peak=   -3.417 closest distance to " ND2 ASN A 209 " =    1.864
peak=   -3.417 closest distance to " O   HOH Z 137 " =    1.415
peak=   -3.416 closest distance to " O   ALA A   1 " =    1.389
peak=   -3.416 closest distance to " CA  GLY A 241 " =    2.113
peak=   -3.413 closest distance to " OG  SER A   3 " =    1.522
peak=   -3.410 closest distance to " CB  ILE A  33 " =    2.798
peak=   -3.407 closest distance to " O   HOH Z 213 " =    1.207
peak=   -3.406 closest distance to " CG  LEU A  83 " =    2.085
peak=   -3.404 closest distance to " O   HOH Z 369 " =    2.288
peak=   -3.399 closest distance to " OD2 ASP A  27 " =    1.514
peak=   -3.399 closest distance to " NE2 GLN A  55 " =    0.913
peak=   -3.383 closest distance to " O   VAL A 125 " =    2.110
peak=   -3.383 closest distance to " O   ALA A 161 " =    1.841
peak=   -3.378 closest distance to " O   GLU A 152 " =    1.449
peak=   -3.377 closest distance to " OXT GLY A 302 " =    2.895
peak=   -3.361 closest distance to " OG  SER A 245 " =    1.297
peak=   -3.360 closest distance to " CB  PHE A 192 " =    1.726
peak=   -3.358 closest distance to " O   HOH Z 197 " =    3.097
peak=   -3.357 closest distance to " OG  SER A  63 " =    1.178
peak=   -3.350 closest distance to " N   ARG A 159 " =    1.874
peak=   -3.348 closest distance to " O   HOH Z 359 " =    1.619
peak=   -3.343 closest distance to " O   ALA A  10 " =    1.641
peak=   -3.338 closest distance to " CE3 TRP A 274 " =    2.368
peak=   -3.335 closest distance to " ND2 ASN A 252 " =    1.747
peak=   -3.329 closest distance to " CG  GLU A 152 " =    1.475
peak=   -3.327 closest distance to " O   ASN A 252 " =    1.098
peak=   -3.324 closest distance to " CG1 ILE A 263 " =    1.859
peak=   -3.316 closest distance to " O   ALA A 180 " =    1.064
peak=   -3.316 closest distance to " O   ILE A 120 " =    1.865
peak=   -3.310 closest distance to " O   HOH Z 102 " =    1.592
peak=   -3.309 closest distance to " CG2 THR A 178 " =    1.816
peak=   -3.305 closest distance to " O   HOH Z 283 " =    2.361
peak=   -3.304 closest distance to " OG  SER A 245 " =    1.814
peak=   -3.298 closest distance to " C   ASN A 285 " =    2.085
peak=   -3.298 closest distance to " O   HOH Z   4 " =    0.803
peak=   -3.297 closest distance to " NE1 TRP A 179 " =    1.256
peak=   -3.296 closest distance to " NH1 ARG A  56 " =    2.375
peak=   -3.294 closest distance to " O   HOH Z 393 " =    2.853
peak=   -3.292 closest distance to " C   ALA A 114 " =    1.948
peak=   -3.289 closest distance to " CG  GLN A 223 " =    1.346
peak=   -3.284 closest distance to " O   HOH Z 318 " =    1.519
peak=   -3.284 closest distance to " C   GLN A 205 " =    1.930
peak=   -3.284 closest distance to " CD  LYS A 166 " =    2.360
peak=   -3.282 closest distance to " OG ASER A 216 " =    1.120
peak=   -3.281 closest distance to " O   HOH Z 288 " =    1.417
peak=   -3.273 closest distance to " OE1 GLN A 223 " =    2.077
peak=   -3.273 closest distance to " CG  PHE A 225 " =    1.165
peak=   -3.270 closest distance to " CB  ASN A  39 " =    2.234
peak=   -3.269 closest distance to " O   HOH Z 250 " =    1.351
peak=   -3.267 closest distance to " O   HOH Z 166 " =    1.472
peak=   -3.267 closest distance to " O   HOH Z  52 " =    1.199
peak=   -3.266 closest distance to " CD  LYS A 289 " =    2.403
peak=   -3.262 closest distance to " O   HOH Z 266 " =    4.481
peak=   -3.260 closest distance to " N   VAL A 232 " =    2.140
peak=   -3.259 closest distance to " O   ARG A 145 " =    1.582
peak=   -3.258 closest distance to " CB  GLN A  55 " =    1.259
peak=   -3.258 closest distance to " O   HOH Z 428 " =    2.266
peak=   -3.258 closest distance to " OG  SER A  63 " =    1.428
peak=   -3.256 closest distance to " O   GLY A  80 " =    2.425
peak=   -3.255 closest distance to " O   ASP A 162 " =    2.054
peak=   -3.251 closest distance to " CB  CYS A 201 " =    2.044
peak=   -3.240 closest distance to " CE2 TYR A  30 " =    2.696
peak=   -3.232 closest distance to " CD  GLN A  88 " =    0.813
peak=   -3.227 closest distance to " O   HOH Z 231 " =    1.889
peak=   -3.226 closest distance to " O   HOH Z 414 " =    1.581
peak=   -3.225 closest distance to " O   HOH Z 265 " =    1.919
peak=   -3.224 closest distance to " CE2 PHE A 218 " =    2.358
peak=   -3.219 closest distance to " O   HOH Z 298 " =    2.359
peak=   -3.218 closest distance to " CG  PRO A 243 " =    1.446
peak=   -3.213 closest distance to " O   HOH Z 422 " =    0.836
peak=   -3.211 closest distance to " CG  GLN A  11 " =    2.048
peak=   -3.206 closest distance to " ND2 ASN A  39 " =    1.309
peak=   -3.203 closest distance to " N   ALA A   1 " =    1.085
peak=   -3.193 closest distance to " CE3 TRP A  70 " =    2.070
peak=   -3.193 closest distance to " CE2 TYR A 116 " =    2.981
peak=   -3.192 closest distance to " O   HOH Z 134 " =    3.507
peak=   -3.192 closest distance to " SD  MET A 188 " =    1.332
peak=   -3.186 closest distance to " O   HOH Z  93 " =    1.771
peak=   -3.186 closest distance to " ND2 ASN A  60 " =    1.407
peak=   -3.183 closest distance to " CZ3 TRP A 179 " =    2.612
peak=   -3.182 closest distance to " CG1 VAL A 174 " =    2.895
peak=   -3.177 closest distance to " O   VAL A 174 " =    2.165
peak=   -3.172 closest distance to " OH  TYR A 214 " =    1.298
peak=   -3.167 closest distance to " C   SER A 288 " =    0.984
peak=   -3.164 closest distance to " CZ3 TRP A 123 " =    1.611
peak=   -3.161 closest distance to " CG  ARG A 219 " =    2.728
peak=   -3.160 closest distance to " O   HOH Z 100 " =    1.378
peak=   -3.160 closest distance to " O   HOH Z 126 " =    1.942
peak=   -3.155 closest distance to " O   THR A 220 " =    1.719
peak=   -3.150 closest distance to " CG2BVAL A  72 " =    1.619
peak=   -3.148 closest distance to " O   TRP A  70 " =    1.353
peak=   -3.145 closest distance to " CG  ARG A  66 " =    2.099
peak=   -3.143 closest distance to " CB  ALA A  43 " =    2.135
peak=   -3.142 closest distance to " O   ASP A 191 " =    1.500
peak=   -3.138 closest distance to " CB  ALA A 100 " =    1.759
peak=   -3.132 closest distance to " O   HOH Z 359 " =    3.588
peak=   -3.132 closest distance to " O   HOH Z 348 " =    2.072
peak=   -3.130 closest distance to " CB  ALA A 131 " =    1.820
peak=   -3.127 closest distance to " O   HOH Z 200 " =    3.728
peak=   -3.121 closest distance to " O   HOH Z 337 " =    1.575
peak=   -3.118 closest distance to " CD  PRO A 198 " =    1.440
peak=   -3.109 closest distance to " CG  ARG A 219 " =    2.278
peak=   -3.109 closest distance to " CG2 ILE A  49 " =    2.689
peak=   -3.106 closest distance to " O   HOH Z 292 " =    1.701
peak=   -3.101 closest distance to " OG  SER A 206 " =    1.820
peak=   -3.083 closest distance to " CG  ARG A 259 " =    2.703
peak=   -3.068 closest distance to " O   HOH Z  88 " =    2.416
peak=   -3.064 closest distance to " O   ASN A 187 " =    1.316
peak=   -3.052 closest distance to " CZ  TYR A 169 " =    1.890
peak=   -3.025 closest distance to " OD2 ASP A 171 " =    1.387
peak=   -3.010 closest distance to " O   HOH Z 426 " =    1.647

================= 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    :  0.4640 0.4609   6.274749e+00   6.266344e+00
   1_bss:  0.4546 0.4491   6.268455e+00   6.251483e+00
   1_xyz:  0.3597 0.3947   6.122631e+00   6.184989e+00
   1_adp:  0.3321 0.4035   6.084350e+00   6.190404e+00
   1_occ:  0.3318 0.4044   6.083864e+00   6.190925e+00
   2_bss:  0.3314 0.4026   6.083686e+00   6.190251e+00
   2_xyz:  0.2648 0.3295   5.903672e+00   6.045345e+00
   2_adp:  0.2463 0.3251   5.861506e+00   6.035860e+00
   2_occ:  0.2460 0.3250   5.861342e+00   6.036014e+00
   3_bss:  0.2458 0.3230   5.857489e+00   6.032133e+00
   3_xyz:  0.1938 0.2558   5.630240e+00   5.833065e+00
   3_adp:  0.1760 0.2333   5.538916e+00   5.750943e+00
   3_occ:  0.1755 0.2321   5.536340e+00   5.747634e+00
   4_bss:  0.1750 0.2306   5.533052e+00   5.742113e+00
   4_xyz:  0.1413 0.1892   5.333373e+00   5.557446e+00
   4_adp:  0.1329 0.1828   5.284857e+00   5.519384e+00
   4_occ:  0.1327 0.1824   5.283992e+00   5.518034e+00
   5_bss:  0.1327 0.1821   5.282656e+00   5.516682e+00
   5_xyz:  0.1208 0.1688   5.202236e+00   5.441128e+00
   5_adp:  0.1175 0.1680   5.187401e+00   5.434630e+00
   5_occ:  0.1174 0.1679   5.186797e+00   5.433681e+00
   5_bss:  0.1174 0.1679   5.186060e+00   5.433187e+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:  0.356  22.008  -2.271   2.239  -1.167   0.000  -0.000  -0.000
   1_xyz:  0.356  22.008  -2.271   2.239  -1.167   0.000  -0.000  -0.000
   1_adp:  0.356  22.008  -2.271   2.239  -1.167   0.000  -0.000  -0.000
   1_occ:  0.356  22.008  -2.271   2.239  -1.167   0.000  -0.000  -0.000
   2_bss:  0.355  57.332  -1.405   1.320  -0.446   0.000  -0.000  -0.000
   2_xyz:  0.355  57.332  -1.405   1.320  -0.446   0.000  -0.000  -0.000
   2_adp:  0.355  57.332  -1.405   1.320  -0.446   0.000  -0.000  -0.000
   2_occ:  0.355  57.332  -1.405   1.320  -0.446   0.000  -0.000  -0.000
   3_bss:  0.340  51.047  -1.008   0.111   0.043   0.000   0.000   0.000
   3_xyz:  0.340  51.047  -1.008   0.111   0.043   0.000   0.000   0.000
   3_adp:  0.340  51.047  -1.008   0.111   0.043   0.000   0.000   0.000
   3_occ:  0.340  51.047  -1.008   0.111   0.043   0.000   0.000   0.000
   4_bss:  0.320  36.927  -1.869  -1.382  -0.544  -0.000  -0.000  -0.000
   4_xyz:  0.320  36.927  -1.869  -1.382  -0.544  -0.000  -0.000  -0.000
   4_adp:  0.320  36.927  -1.869  -1.382  -0.544  -0.000  -0.000  -0.000
   4_occ:  0.320  36.927  -1.869  -1.382  -0.544  -0.000  -0.000  -0.000
   5_bss:  0.316  36.927  -2.041  -1.813  -0.655  -0.000  -0.000  -0.000
   5_xyz:  0.316  36.927  -2.041  -1.813  -0.655  -0.000  -0.000  -0.000
   5_adp:  0.316  36.927  -2.041  -1.813  -0.655  -0.000  -0.000  -0.000
   5_occ:  0.316  36.927  -2.041  -1.813  -0.655  -0.000  -0.000  -0.000
   5_bss:  0.302  37.381  -2.016  -1.850  -0.603  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  55.089 0.4579  0.6310    69035.519
   1_bss:  53.915 0.4714  0.6401    64950.739
   1_xyz:  45.106 0.5811  0.7716    48103.651
   1_adp:  45.332 0.5782  0.7556    49132.667
   1_occ:  45.410 0.5772  0.7536    49318.365
   2_bss:  45.138 0.5804  0.7678    48891.158
   2_xyz:  34.837 0.7031  0.9122    30332.966
   2_adp:  34.009 0.7128  0.9143    29527.340
   2_occ:  34.043 0.7123  0.9135    29536.945
   3_bss:  33.773 0.7153  0.9136    29043.733
   3_xyz:  25.421 0.8069  0.9954    16931.341
   3_adp:  22.526 0.8374  1.0102    13931.950
   3_occ:  22.432 0.8383  1.0105    13792.199
   4_bss:  22.295 0.8393  0.9747    13542.714
   4_xyz:  17.699 0.8830  0.9982     9028.684
   4_adp:  16.706 0.8923  0.9967     8427.204
   4_occ:  16.685 0.8925  0.9966     8392.325
   5_bss:  16.651 0.8927  0.9882     8361.214
   5_xyz:  15.065 0.9062  0.9951     7162.314
   5_adp:  14.889 0.9079  0.9911     7107.050
   5_occ:  14.874 0.9080  0.9911     7091.814
   5_bss:  14.856 0.9082  0.9918     7077.010
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.106   2.0262e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.106   2.0262e-01
   1_xyz:   1.620  0.013  0.113 15.668  0.006  4.103   1.4451e-01
   1_adp:   1.620  0.013  0.113 15.668  0.006  4.103   1.4451e-01
   1_occ:   1.620  0.013  0.113 15.668  0.006  4.103   1.4451e-01
   2_bss:   1.620  0.013  0.113 15.668  0.006  4.103   1.4451e-01
   2_xyz:   1.379  0.010  0.099 15.300  0.006  4.105   1.0290e-01
   2_adp:   1.379  0.010  0.099 15.300  0.006  4.105   1.0290e-01
   2_occ:   1.379  0.010  0.099 15.300  0.006  4.105   1.0290e-01
   3_bss:   1.379  0.010  0.099 15.300  0.006  4.105   1.0290e-01
   3_xyz:   1.148  0.009  0.077 14.610  0.005  4.106   7.7611e-02
   3_adp:   1.148  0.009  0.077 14.610  0.005  4.106   7.7611e-02
   3_occ:   1.148  0.009  0.077 14.610  0.005  4.106   7.7611e-02
   4_bss:   1.148  0.009  0.077 14.610  0.005  4.106   7.7611e-02
   4_xyz:   1.018  0.006  0.070 14.417  0.004  4.113   5.9463e-02
   4_adp:   1.018  0.006  0.070 14.417  0.004  4.113   5.9463e-02
   4_occ:   1.018  0.006  0.070 14.417  0.004  4.113   5.9463e-02
   5_bss:   1.018  0.006  0.070 14.417  0.004  4.113   5.9463e-02
   5_xyz:   0.962  0.006  0.067 14.386  0.004  4.115   5.5962e-02
   5_adp:   0.962  0.006  0.067 14.386  0.004  4.115   5.5962e-02
   5_occ:   0.962  0.006  0.067 14.386  0.004  4.115   5.5962e-02
   5_bss:   0.962  0.006  0.067 14.386  0.004  4.115   5.5962e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.359   2.3755e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.359   2.3755e-01
   1_xyz:  10.145  0.078  0.509 79.409  0.035  1.865   1.1952e-01
   1_adp:  10.145  0.078  0.509 79.409  0.035  1.865   1.1952e-01
   1_occ:  10.145  0.078  0.509 79.409  0.035  1.865   1.1952e-01
   2_bss:  10.145  0.078  0.509 79.409  0.035  1.865   1.1952e-01
   2_xyz:   8.989  0.057  0.304 81.200  0.041  1.999   9.9084e-02
   2_adp:   8.989  0.057  0.304 81.200  0.041  1.999   9.9084e-02
   2_occ:   8.989  0.057  0.304 81.200  0.041  1.999   9.9084e-02
   3_bss:   8.989  0.057  0.304 81.200  0.041  1.999   9.9084e-02
   3_xyz:   7.759  0.051  0.235 77.382  0.027  2.239   9.1739e-02
   3_adp:   7.759  0.051  0.235 77.382  0.027  2.239   9.1739e-02
   3_occ:   7.759  0.051  0.235 77.382  0.027  2.239   9.1739e-02
   4_bss:   7.759  0.051  0.235 77.382  0.027  2.239   9.1739e-02
   4_xyz:   7.641  0.045  0.232 82.346  0.036  2.298   5.2761e-02
   4_adp:   7.641  0.045  0.232 82.346  0.036  2.298   5.2761e-02
   4_occ:   7.641  0.045  0.232 82.346  0.036  2.298   5.2761e-02
   5_bss:   7.641  0.045  0.232 82.346  0.036  2.298   5.2761e-02
   5_xyz:   7.489  0.045  0.210 82.504  0.033  2.293   4.2904e-02
   5_adp:   7.489  0.045  0.210 82.504  0.033  2.293   4.2904e-02
   5_occ:   7.489  0.045  0.210 82.504  0.033  2.293   4.2904e-02
   5_bss:   7.489  0.045  0.210 82.504  0.033  2.293   4.2904e-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:  85.81   0.00  16.93  85.81   0.00  13.44  63.77   1.25  35.92
   1_occ:  85.81   0.00  16.93  85.81   0.00  13.44  63.77   1.25  35.92
   2_bss:  85.81   0.00  16.93  85.81   0.00  13.44  63.77   1.25  35.92
   2_xyz:  85.81   0.00  16.93  85.81   0.00  13.44  63.77   1.25  35.92
   2_adp:  82.17   0.00  17.76  78.57   0.00  13.95  82.17   2.94  38.49
   2_occ:  82.17   0.00  17.76  78.57   0.00  13.95  82.17   2.94  38.49
   3_bss:  82.17   0.00  17.76  78.57   0.00  13.95  82.17   2.94  38.49
   3_xyz:  82.17   0.00  17.76  78.57   0.00  13.95  82.17   2.94  38.49
   3_adp:  78.01   1.43  16.84  78.01   1.43  12.74  77.14   5.65  39.15
   3_occ:  78.01   1.43  16.84  78.01   1.43  12.74  77.14   5.65  39.15
   4_bss:  78.01   1.43  16.84  78.01   1.43  12.74  77.14   5.65  39.15
   4_xyz:  78.01   1.43  16.84  78.01   1.43  12.74  77.14   5.65  39.15
   4_adp:  80.11   0.81  16.76  80.11   0.81  12.35  78.31   3.99  40.77
   4_occ:  80.11   0.81  16.76  80.11   0.81  12.35  78.31   3.99  40.77
   5_bss:  80.11   0.81  16.76  80.11   0.81  12.35  78.31   3.99  40.77
   5_xyz:  80.11   0.81  16.76  80.11   0.81  12.35  78.31   3.99  40.77
   5_adp:  91.73   0.00  17.06  88.89   0.00  12.30  91.73   4.61  42.94
   5_occ:  91.73   0.00  17.06  88.89   0.00  12.30  91.73   4.61  42.94
   5_bss:  91.73   0.00  17.06  88.89   0.00  12.31  91.73   4.61  42.94
------------------------------------------------------------------------
 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:    1.807    0.036    0.379
   1_adp:    1.807    0.036    0.379
   1_occ:    1.807    0.036    0.379
   2_bss:    1.807    0.036    0.379
   2_xyz:    1.539    0.042    0.582
   2_adp:    1.539    0.042    0.582
   2_occ:    1.539    0.042    0.582
   3_bss:    1.539    0.042    0.582
   3_xyz:    1.666    0.053    0.732
   3_adp:    1.666    0.053    0.732
   3_occ:    1.666    0.053    0.732
   4_bss:    1.666    0.053    0.732
   4_xyz:    1.658    0.069    0.801
   4_adp:    1.658    0.069    0.801
   4_occ:    1.658    0.069    0.801
   5_bss:    1.658    0.069    0.801
   5_xyz:    1.731    0.110    0.826
   5_adp:    1.731    0.110    0.826
   5_occ:    1.731    0.110    0.826
   5_bss:    1.731    0.110    0.826
------------------------------------------------------------------------

CPU time actual refinement: 350.63


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_245/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_245/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_245/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_245/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_245/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 350.49 
  Macro-tasks:
    bulk solvent and scale       = 45.79  
    individual site refinement   = 145.78 
    weights calculation          = 29.11  
    collect and process          = 6.15   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 226.93 
  Micro-tasks:
    mask                            = 2.37   
    f_calc                          = 111.27 
    alpha_beta                      = 8.49   
    target                          = 1.20   
    gradients_wrt_atomic_parameters = 120.99 
    fmodel                         = 7.67   
    r_factors                      = 0.23   
    phase_errors                   = 10.57  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 263.06 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.902 micro seconds
Total CPU time: 6.07 minutes
from_scatterers_fft:    660 calls, 110.92 s
gradients_fft:          605 calls, 107.24 s

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

# Date 2008-01-16 Time 04:21:19 PST -0800 (1200486079.84 s)
Start R-work = 0.4640, R-free = 0.4609 (no bulk solvent and anisotropic scale)
Final R-work = 0.1388, R-free = 0.1832 (no bulk solvent and anisotropic scale)

Start R-work = 0.4546, R-free = 0.4491
Final R-work = 0.1174, R-free = 0.1679