# Date 2008-01-16 Time 00:33:31 PST -0800 (1200472411.50 s)
#phil __OFF__

Command line arguments: "../63.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 12810
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 63

-------------------------------------------------------------------------------
  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.modify_start_model.adp.set_b_iso = 10

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (68.4938, 46.93, 87.6859, 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: 3.28, 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: (68.4938, 46.93, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8117 1.9509
Completeness in resolution range: 0.926106
Completeness with d_max=infinity: 0.923313

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8117
                             d_min =   1.9509

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: (68.4938, 46.93, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8117 1.9509
Completeness in resolution range: 0.926106
Completeness with d_max=infinity: 0.923313

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8121 -  4.1747 [2222/2250]  1997   225  10.1%
  bin  2:  4.1747 -  3.3259 [2128/2151]  1912   216  10.2%
  bin  3:  3.3259 -  2.9091 [2112/2134]  1910   202   9.6%
  bin  4:  2.9091 -  2.6448 [2090/2109]  1874   216  10.3%
  bin  5:  2.6448 -  2.4561 [2064/2093]  1852   212  10.3%
  bin  6:  2.4561 -  2.3119 [2051/2093]  1853   198   9.7%
  bin  7:  2.3119 -  2.1965 [2049/2085]  1847   202   9.9%
  bin  8:  2.1965 -  2.1011 [2064/2105]  1855   209  10.1%
  bin  9:  2.1011 -  2.0205 [2017/2063]  1825   192   9.5%
  bin 10:  2.0205 -  1.9509 [ 792/2069]   705    87  11.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_63/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.22 -     1.95: 15
        1.95 -     2.69: 150
        2.69 -     3.43: 4518
        3.43 -     4.16: 9453
        4.16 -     4.90: 14450
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.216 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.295 3.040 -x+1,y-1/2,-z+1/2
  " NH1 ARG A  24 " - " O   GLY A  91 "  1.301 3.120 -x+1,y+1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 176 "  1.335 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.544 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28581 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 =====================

Setting all isotropic ADP = 10.000: selected atoms: all (2823)
Shaking sites (RMS = 0.500): selected atoms: all (2823)

==================== 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/trial/run_63/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_63/model_refine_001.geo

CPU time processing inputs: 9.33


============================ 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 = 68.49375 46.93 87.68585 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
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4774   r_free= 0.4707   ksol= 0.00   Bsol= 0.00   scale= 0.798    |
|                                                                             |
| 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:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.279594                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8121 -  4.6563 0.99   1443  159 0.3855 0.3753      6.5846      6.6031|
|  2:  4.6563 -  3.7150 0.99   1396  155 0.3781 0.4250      6.7304      6.8281|
|  3:  3.7150 -  3.2511 0.99   1357  156 0.4488 0.4100       6.662      6.6539|
|  4:  3.2511 -  2.9564 0.99   1352  140 0.4728 0.4768      6.5069       6.495|
|  5:  2.9564 -  2.7460 0.99   1338  153 0.5001 0.5063      6.3516      6.3939|
|  6:  2.7460 -  2.5850 0.98   1333  149 0.5106 0.5227      6.2852       6.206|
|  7:  2.5850 -  2.4561 0.99   1326  159 0.5072 0.5070      6.2245      6.1581|
|  8:  2.4561 -  2.3496 0.99   1345  138 0.5224 0.4917      6.1672      6.1449|
|  9:  2.3496 -  2.2595 0.98   1330  145 0.5376 0.4928      6.1288       6.183|
| 10:  2.2595 -  2.1818 0.98   1307  142 0.5332 0.5251      6.0967      6.0846|
| 11:  2.1818 -  2.1138 0.98   1296  160 0.5304 0.4970      6.0174      6.0126|
| 12:  2.1138 -  2.0535 0.99   1342  140 0.5387 0.5038      5.9612      5.9388|
| 13:  2.0535 -  1.9996 0.86   1154  118 0.5355 0.5204      5.8809      5.8423|
| 14:  1.9996 -  1.9509 0.24    311   45 0.5349 0.5388      5.9307      5.7317|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8121 -  4.6563  1443   159  0.69  34.96   0.80     0.71      72734.08|
|  2:  4.6563 -  3.7150  1396   155  0.69  36.07   0.90     0.75     108302.18|
|  3:  3.7150 -  3.2511  1357   156  0.59  44.50   0.83     0.70     114290.50|
|  4:  3.2511 -  2.9564  1352   140  0.49  52.70   0.79     0.60     103239.25|
|  5:  2.9564 -  2.7460  1338   153  0.39  60.40   0.74     0.48      85578.23|
|  6:  2.7460 -  2.5850  1333   149  0.34  64.21   0.72     0.41      77198.32|
|  7:  2.5850 -  2.4561  1326   159  0.34  64.37   0.75     0.40      68404.21|
|  8:  2.4561 -  2.3496  1345   138  0.37  62.07   0.73     0.45      57709.67|
|  9:  2.3496 -  2.2595  1330   145  0.41  59.39   0.72     0.51      51461.88|
| 10:  2.2595 -  2.1818  1307   142  0.41  59.16   0.74     0.49      43508.74|
| 11:  2.1818 -  2.1138  1296   160  0.37  62.21   0.74     0.47      45095.07|
| 12:  2.1138 -  2.0535  1342   140  0.33  65.22   0.75     0.44      42150.98|
| 13:  2.0535 -  1.9996  1154   118  0.32  66.46   0.73     0.42      38251.54|
| 14:  1.9996 -  1.9509   311    45  0.37  62.52   0.78     0.39      28672.73|
|alpha:            min =        0.39 max =            0.75 mean =         0.53|
|beta:             min =    28672.73 max =       114290.50 mean =     69763.41|
|figures of merit: min =        0.00 max =            1.00 mean =         0.45|
|phase err.(work): min =        0.00 max =           89.97 mean =        56.06|
|phase err.(test): min =        0.00 max =           89.94 mean =        56.50|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.087522             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.963   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.094550              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.346   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.029 -  1.416:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.416 -  1.804:       19 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.804 -  2.191:      110 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.191 -  2.578:      540 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.578 -  2.965:     1347 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.965 -  3.352:     2487 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.352 -  3.739:     3980 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.739 -  4.126:     5220 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.126 -  4.513:     6837 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.513 -  4.900:     8071 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.376 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.088    4.900  1.029 |       3.100 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.640)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    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:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

                ----------Modify initial isotropic ADP----------               

Randomizing
|-ADP statistics (Wilson B = 11.640)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4841   r_free= 0.4738   ksol= 0.00   Bsol= 0.00   scale= 0.768    |
|                                                                             |
| 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:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.281074                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4689   r_free= 0.4650   ksol= 0.33   Bsol= 5.23   scale= 1.012    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.75,7.80,10.27,0.00,0.00,0.00); trace/3= 8.94                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.271312                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.122995             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.546   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.166986              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 75.017   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4689      final r-factor (work) = 0.3834          |
| start r-factor (free) = 0.4650      final r-factor (free) = 0.4015          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 91.4354 = 12.12 * 0.50 * 6.2788 + 1.00 * 53.3764                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 37.6467 = 12.12 * 0.50 * 6.1872 + 1.00 * 0.1427                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3834      final r-factor (work) = 0.3355          |
| start r-factor (free) = 0.4015      final r-factor (free) = 0.3835          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.2348 = 1.17 * 1.00 * 6.1872 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.1162 = 1.17 * 1.00 * 6.0839 + 1.00 * 0.0164                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.640)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    61.26   12.86    None  None   None       |
|    all(noH): 2823   0      0.00    61.26   12.86    None  None   None       |
|    Sol.    : 438    0      0.00    60.96   25.90    None  None   None       |
|    Mac.    : 2385   0      0.00    61.26   10.47    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 -   6.126:  981   |   5:    30.630 -  36.756:  100        |
|      1:     6.126 -  12.252:  686   |   6:    36.756 -  42.882:   77        |
|      2:    12.252 -  18.378:  435   |   7:    42.882 -  49.008:   31        |
|      3:    18.378 -  24.504:  290   |   8:    49.008 -  55.134:   22        |
|      4:    24.504 -  30.630:  190   |   9:    55.134 -  61.260:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3355 r_free = 0.3835             target_work(ml) = 6.060         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3354 r_free = 0.3839             target_work(ml) = 6.059         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3354   r_free= 0.3839   ksol= 0.33   Bsol= 5.23   scale= 1.116    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.75,7.80,10.27,0.00,0.00,0.00); trace/3= 8.94                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 6.059068                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3309   r_free= 0.3794   ksol= 0.32   Bsol= 33.54   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.52,3.60,6.14,0.00,0.00,0.00); trace/3= 4.75                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.49 A                  |
| x-ray target function (ml) for work reflections: 6.059419                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.735913              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.256   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.515961              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 124.980  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3309      final r-factor (work) = 0.2431          |
| start r-factor (free) = 0.3794      final r-factor (free) = 0.2924          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.5887 = 5.74 * 0.50 * 6.0831 + 1.00 * 0.1427                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.0993 = 5.74 * 0.50 * 5.9335 + 1.00 * 0.0821                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2431      final r-factor (work) = 0.2174          |
| start r-factor (free) = 0.2924      final r-factor (free) = 0.2718          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0883 = 0.52 * 1.00 * 5.9335 + 1.00 * 0.0268                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0153 = 0.52 * 1.00 * 5.7477 + 1.00 * 0.0497                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.640)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    72.26   13.27    None  None   None       |
|    all(noH): 2823   0      0.00    72.26   13.27    None  None   None       |
|    Sol.    : 438    0      1.28    72.26   33.64    None  None   None       |
|    Mac.    : 2385   0      0.00    71.43   9.53     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 -   7.226: 1260   |   5:    36.130 -  43.357:   95        |
|      1:     7.226 -  14.452:  709   |   6:    43.357 -  50.583:   79        |
|      2:    14.452 -  21.678:  335   |   7:    50.583 -  57.809:   41        |
|      3:    21.678 -  28.904:  150   |   8:    57.809 -  65.035:   20        |
|      4:    28.904 -  36.130:  123   |   9:    65.035 -  72.261:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2174 r_free = 0.2718             target_work(ml) = 5.713         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2172 r_free = 0.2719             target_work(ml) = 5.713         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2172   r_free= 0.2719   ksol= 0.32   Bsol= 33.54   scale= 1.055   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.52,3.60,6.14,0.00,0.00,0.00); trace/3= 4.75                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.712925                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2150   r_free= 0.2705   ksol= 0.31   Bsol= 42.92   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.17,2.58,4.26,0.00,0.00,0.00); trace/3= 3.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.710505                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.453221              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.107   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.153875              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.219   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2150      final r-factor (work) = 0.1526          |
| start r-factor (free) = 0.2705      final r-factor (free) = 0.1976          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.7635 = 5.45 * 0.50 * 5.7512 + 1.00 * 0.0821                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.2794 = 5.45 * 0.50 * 5.5759 + 1.00 * 0.0760                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1526      final r-factor (work) = 0.1361          |
| start r-factor (free) = 0.1976      final r-factor (free) = 0.1840          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.4635 = 1.15 * 1.00 * 5.5759 + 1.00 * 0.0296                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.1875 = 1.15 * 1.00 * 5.3470 + 1.00 * 0.0177                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.640)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.51   13.79    None  None   None       |
|    all(noH): 2823   0      0.00    87.51   13.79    None  None   None       |
|    Sol.    : 438    0      1.51    79.06   38.90    None  None   None       |
|    Mac.    : 2385   0      0.00    87.51   9.18     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 -   8.751: 1540   |   5:    43.755 -  52.506:   98        |
|      1:     8.751 -  17.502:  669   |   6:    52.506 -  61.258:   68        |
|      2:    17.502 -  26.253:  177   |   7:    61.258 -  70.009:   35        |
|      3:    26.253 -  35.004:  114   |   8:    70.009 -  78.760:   19        |
|      4:    35.004 -  43.755:  100   |   9:    78.760 -  87.511:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1361 r_free = 0.1840             target_work(ml) = 5.310         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1359 r_free = 0.1842             target_work(ml) = 5.309         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1359   r_free= 0.1842   ksol= 0.31   Bsol= 42.92   scale= 1.028   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.17,2.58,4.26,0.00,0.00,0.00); trace/3= 3.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.309443                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1354   r_free= 0.1847   ksol= 0.31   Bsol= 45.97   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.15,1.99,3.50,0.00,0.00,0.00); trace/3= 2.21                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.308435                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.932273              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 116.205  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.329334              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 99.154   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1354      final r-factor (work) = 0.1251          |
| start r-factor (free) = 0.1847      final r-factor (free) = 0.1726          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2479 = 1.93 * 0.50 * 5.3530 + 1.00 * 0.0762                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1565 = 1.93 * 0.50 * 5.2789 + 1.00 * 0.0564                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1251      final r-factor (work) = 0.1236          |
| start r-factor (free) = 0.1726      final r-factor (free) = 0.1687          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7542 = 0.33 * 1.00 * 5.2789 + 1.00 * 0.0157                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7380 = 0.33 * 1.00 * 5.2429 + 1.00 * 0.0113                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.640)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.53   13.30    None  None   None       |
|    all(noH): 2823   0      0.00    89.53   13.30    None  None   None       |
|    Sol.    : 438    0      2.29    78.40   37.17    None  None   None       |
|    Mac.    : 2385   0      0.00    89.53   8.92     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 -   8.953: 1633   |   5:    44.767 -  53.720:   90        |
|      1:     8.953 -  17.907:  615   |   6:    53.720 -  62.673:   53        |
|      2:    17.907 -  26.860:  164   |   7:    62.673 -  71.626:   25        |
|      3:    26.860 -  35.813:  126   |   8:    71.626 -  80.580:   13        |
|      4:    35.813 -  44.767:  102   |   9:    80.580 -  89.533:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1236 r_free = 0.1687             target_work(ml) = 5.230         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1234 r_free = 0.1686             target_work(ml) = 5.230         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1234   r_free= 0.1686   ksol= 0.31   Bsol= 45.97   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.15,1.99,3.50,0.00,0.00,0.00); trace/3= 2.21                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.229509                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1234   r_free= 0.1686   ksol= 0.32   Bsol= 45.97   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.15,1.99,3.50,0.00,0.00,0.00); trace/3= 2.21                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.229519                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.374946              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 133.821  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.570327              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 157.692  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1234      final r-factor (work) = 0.1162          |
| start r-factor (free) = 0.1686      final r-factor (free) = 0.1609          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2817 = 2.37 * 0.50 * 5.2425 + 1.00 * 0.0564                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2437 = 2.37 * 0.50 * 5.2028 + 1.00 * 0.0656                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1162      final r-factor (work) = 0.1148          |
| start r-factor (free) = 0.1609      final r-factor (free) = 0.1609          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9785 = 0.57 * 1.00 * 5.2028 + 1.00 * 0.0113                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9627 = 0.57 * 1.00 * 5.1742 + 1.00 * 0.0118                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.640)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.83   13.13    None  None   None       |
|    all(noH): 2823   0      0.00    91.83   13.13    None  None   None       |
|    Sol.    : 438    0      1.74    82.66   36.73    None  None   None       |
|    Mac.    : 2385   0      0.00    91.83   8.80     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.183: 1685   |   5:    45.913 -  55.096:   94        |
|      1:     9.183 -  18.365:  580   |   6:    55.096 -  64.278:   39        |
|      2:    18.365 -  27.548:  163   |   7:    64.278 -  73.461:   20        |
|      3:    27.548 -  36.730:  126   |   8:    73.461 -  82.643:   11        |
|      4:    36.730 -  45.913:  102   |   9:    82.643 -  91.826:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1148 r_free = 0.1609             target_work(ml) = 5.174         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1147 r_free = 0.1609             target_work(ml) = 5.174         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1147   r_free= 0.1609   ksol= 0.32   Bsol= 45.97   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.15,1.99,3.50,0.00,0.00,0.00); trace/3= 2.21                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.173806                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8121 -  4.6563 0.99   1443  159 0.1019 0.1364      5.4243      5.6054|
|  2:  4.6563 -  3.7150 0.99   1396  155 0.0854 0.1109      5.4415       5.643|
|  3:  3.7150 -  3.2511 0.99   1357  156 0.1080 0.1505      5.4826       5.797|
|  4:  3.2511 -  2.9564 0.99   1352  140 0.1254 0.1614      5.4505      5.6346|
|  5:  2.9564 -  2.7460 0.99   1338  153 0.1353 0.1544      5.3519      5.5077|
|  6:  2.7460 -  2.5850 0.98   1333  149 0.1275 0.2162      5.2317      5.5398|
|  7:  2.5850 -  2.4561 0.99   1326  159 0.1285 0.1645      5.1924      5.3433|
|  8:  2.4561 -  2.3496 0.99   1345  138 0.1186 0.1776      5.0819      5.3152|
|  9:  2.3496 -  2.2595 0.98   1330  145 0.1190 0.1888      5.0364      5.3785|
| 10:  2.2595 -  2.1818 0.98   1307  142 0.1164 0.1727      4.9641      5.1762|
| 11:  2.1818 -  2.1138 0.98   1296  160 0.1188 0.1864      4.9417      5.2854|
| 12:  2.1138 -  2.0535 0.99   1342  140 0.1182 0.1672      4.9067      5.1214|
| 13:  2.0535 -  1.9996 0.86   1154  118 0.1119 0.1711      4.7691       4.974|
| 14:  1.9996 -  1.9509 0.24    311   45 0.0967 0.1606      4.6538      4.8615|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8121 -  4.6563  1443   159  0.94   9.83   0.98     0.95       8141.49|
|  2:  4.6563 -  3.7150  1396   155  0.95   8.31   1.02     1.01       9369.83|
|  3:  3.7150 -  3.2511  1357   156  0.93  11.69   1.03     1.03      10616.61|
|  4:  3.2511 -  2.9564  1352   140  0.92  13.89   1.01     1.01      10245.89|
|  5:  2.9564 -  2.7460  1338   153  0.90  16.64   1.00     0.98       9121.35|
|  6:  2.7460 -  2.5850  1333   149  0.89  16.89   0.98     0.94       7251.98|
|  7:  2.5850 -  2.4561  1326   159  0.90  16.33   0.99     0.95       6570.44|
|  8:  2.4561 -  2.3496  1345   138  0.90  15.84   1.00     0.98       5569.82|
|  9:  2.3496 -  2.2595  1330   145  0.90  16.32   1.01     0.97       5172.86|
| 10:  2.2595 -  2.1818  1307   142  0.90  16.37   1.00     0.96       4542.38|
| 11:  2.1818 -  2.1138  1296   160  0.90  16.84   1.00     0.96       4497.50|
| 12:  2.1138 -  2.0535  1342   140  0.89  17.00   1.01     1.01       4286.35|
| 13:  2.0535 -  1.9996  1154   118  0.90  16.19   0.99     0.97       3278.91|
| 14:  1.9996 -  1.9509   311    45  0.93  12.48   0.99     0.96       2351.15|
|alpha:            min =        0.94 max =            1.03 mean =         0.98|
|beta:             min =     2351.15 max =        10616.61 mean =      6810.87|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.97 mean =        14.66|
|phase err.(test): min =        0.00 max =           89.64 mean =        14.24|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1147   r_free= 0.1609   ksol= 0.32   Bsol= 48.18   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.12,-0.20,1.32,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.173768                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1147   r_free= 0.1609   ksol= 0.32   Bsol= 48.18   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.12,-0.20,1.32,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.173768                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8121 -  4.6563 0.99   1443  159 0.1019 0.1364      5.4243      5.6052|
|  2:  4.6563 -  3.7150 0.99   1396  155 0.0854 0.1109      5.4413      5.6427|
|  3:  3.7150 -  3.2511 0.99   1357  156 0.1080 0.1504      5.4821      5.7963|
|  4:  3.2511 -  2.9564 0.99   1352  140 0.1254 0.1614      5.4504      5.6344|
|  5:  2.9564 -  2.7460 0.99   1338  153 0.1353 0.1545       5.352      5.5078|
|  6:  2.7460 -  2.5850 0.98   1333  149 0.1275 0.2163      5.2319      5.5398|
|  7:  2.5850 -  2.4561 0.99   1326  159 0.1285 0.1644      5.1922      5.3431|
|  8:  2.4561 -  2.3496 0.99   1345  138 0.1186 0.1776      5.0818      5.3149|
|  9:  2.3496 -  2.2595 0.98   1330  145 0.1190 0.1887      5.0363      5.3781|
| 10:  2.2595 -  2.1818 0.98   1307  142 0.1164 0.1728      4.9641      5.1766|
| 11:  2.1818 -  2.1138 0.98   1296  160 0.1188 0.1866      4.9419      5.2859|
| 12:  2.1138 -  2.0535 0.99   1342  140 0.1182 0.1672      4.9066      5.1212|
| 13:  2.0535 -  1.9996 0.86   1154  118 0.1119 0.1712      4.7694      4.9746|
| 14:  1.9996 -  1.9509 0.24    311   45 0.0967 0.1608      4.6535      4.8623|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8121 -  4.6563  1443   159  0.94   9.83   0.98     0.95       8140.93|
|  2:  4.6563 -  3.7150  1396   155  0.95   8.31   1.02     1.01       9363.65|
|  3:  3.7150 -  3.2511  1357   156  0.93  11.68   1.03     1.03      10603.03|
|  4:  3.2511 -  2.9564  1352   140  0.92  13.89   1.01     1.01      10242.44|
|  5:  2.9564 -  2.7460  1338   153  0.90  16.64   1.00     0.98       9120.77|
|  6:  2.7460 -  2.5850  1333   149  0.89  16.90   0.98     0.94       7254.08|
|  7:  2.5850 -  2.4561  1326   159  0.90  16.32   0.99     0.95       6567.27|
|  8:  2.4561 -  2.3496  1345   138  0.90  15.84   1.00     0.98       5567.51|
|  9:  2.3496 -  2.2595  1330   145  0.90  16.32   1.01     0.98       5169.62|
| 10:  2.2595 -  2.1818  1307   142  0.90  16.38   1.00     0.96       4543.43|
| 11:  2.1818 -  2.1138  1296   160  0.90  16.85   1.00     0.96       4500.51|
| 12:  2.1138 -  2.0535  1342   140  0.89  17.01   1.01     1.01       4288.73|
| 13:  2.0535 -  1.9996  1154   118  0.90  16.20   0.99     0.97       3283.42|
| 14:  1.9996 -  1.9509   311    45  0.93  12.48   0.99     0.96       2354.82|
|alpha:            min =        0.94 max =            1.03 mean =         0.98|
|beta:             min =     2354.82 max =        10603.03 mean =      6809.32|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.97 mean =        14.66|
|phase err.(test): min =        0.00 max =           89.64 mean =        14.24|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.640)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.22    94.04   15.35    None  None   None       |
|    all(noH): 2823   0      2.22    94.04   15.35    None  None   None       |
|    Sol.    : 438    0      3.95    84.88   38.94    None  None   None       |
|    Mac.    : 2385   0      2.22    94.04   11.01    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:     2.217 -  11.399: 1685   |   5:    48.130 -  57.312:   94        |
|      1:    11.399 -  20.582:  580   |   6:    57.312 -  66.495:   39        |
|      2:    20.582 -  29.764:  163   |   7:    66.495 -  75.677:   20        |
|      3:    29.764 -  38.947:  126   |   8:    75.677 -  84.860:   11        |
|      4:    38.947 -  48.130:  102   |   9:    84.860 -  94.043:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 299         
Filter by distance & map next to the model:
   mapped sites are within: 0.441 - 4.698
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 295 from: 299
   mapped sites are within: 0.716 - 4.698

peak=   11.132 closest distance to " CB  VAL A 230 " =    1.442
peak=    9.294 closest distance to " CG2 VAL A 296 " =    1.512
peak=    6.260 closest distance to " CG  LEU A   5 " =    1.196
peak=    5.646 closest distance to " CG  PRO A  54 " =    1.304
peak=    5.610 closest distance to " NE2 GLN A  11 " =    1.174
peak=    5.551 closest distance to " CG  LEU A 228 " =    1.175
peak=    5.519 closest distance to " O   HOH Z 188 " =    1.584
peak=    5.516 closest distance to " CD2 LEU A   5 " =    1.109
peak=    5.396 closest distance to " NH2 ARG A  56 " =    2.126
peak=    5.285 closest distance to " CB  ARG A 275 " =    0.952
peak=    5.210 closest distance to " CB  GLN A 223 " =    1.481
peak=    5.121 closest distance to " O   HOH Z 232 " =    2.334
peak=    4.941 closest distance to " O   HOH Z 248 " =    1.368
peak=    4.870 closest distance to " O   HOH Z 193 " =    1.818
peak=    4.816 closest distance to " O   HOH Z  43 " =    1.390
peak=    4.720 closest distance to " O   HOH Z 142 " =    1.680
peak=    4.661 closest distance to " O   SER A  87 " =    2.324
peak=    4.631 closest distance to " CB  GLN A 183 " =    1.313
peak=    4.614 closest distance to " O   HOH Z 403 " =    1.619
peak=    4.595 closest distance to " O   HOH Z 346 " =    1.580
peak=    4.594 closest distance to " O   HOH Z  85 " =    1.608
peak=    4.515 closest distance to " CB  VAL A 230 " =    1.170
peak=    4.510 closest distance to " O   HOH Z 209 " =    2.335
peak=    4.481 closest distance to " CB  PRO A  54 " =    0.971
peak=    4.417 closest distance to " O   HOH Z 272 " =    1.846
peak=    4.403 closest distance to " CB  SER A  63 " =    1.199
peak=    4.383 closest distance to " O   HOH Z 126 " =    1.891
peak=    4.323 closest distance to " O   HOH Z  61 " =    1.793
peak=    4.315 closest distance to " O   HOH Z   3 " =    1.884
peak=    4.312 closest distance to " O   HOH Z 238 " =    1.244
peak=    4.312 closest distance to " CZ  PHE A 218 " =    1.179
peak=    4.303 closest distance to " O   HOH Z 265 " =    2.107
peak=    4.299 closest distance to " O   HOH Z 287 " =    1.928
peak=    4.298 closest distance to " O   HOH Z  63 " =    1.963
peak=    4.294 closest distance to " O   HOH Z 402 " =    1.395
peak=    4.294 closest distance to " O   HOH Z 369 " =    2.601
peak=    4.265 closest distance to " CD2 TRP A 179 " =    1.355
peak=    4.263 closest distance to " O   HOH Z 124 " =    1.307
peak=    4.263 closest distance to " O   HOH Z  78 " =    1.662
peak=    4.243 closest distance to " CG  PRO A 213 " =    1.236
peak=    4.237 closest distance to " O   HOH Z 303 " =    2.127
peak=    4.188 closest distance to " O   HOH Z  44 " =    2.063
peak=    4.176 closest distance to " O   HOH Z  97 " =    1.579
peak=    4.171 closest distance to " CG  PRO A 243 " =    1.128
peak=    4.158 closest distance to " O   HOH Z 313 " =    1.967
peak=    4.155 closest distance to " O   HOH Z 126 " =    1.536
peak=    4.140 closest distance to " O   HOH Z  15 " =    2.148
peak=    4.123 closest distance to " CB  ALA A   9 " =    1.622
peak=    4.116 closest distance to " ND2 ASN A 187 " =    1.529
peak=    4.110 closest distance to " O   HOH Z 422 " =    2.438
peak=    4.093 closest distance to " CG  GLN A  58 " =    0.882
peak=    4.086 closest distance to " O   HOH Z 128 " =    2.298
peak=    4.077 closest distance to " O   HOH Z 368 " =    2.217
peak=    4.075 closest distance to " CB  ASN A 142 " =    1.149
peak=    4.070 closest distance to " O   HOH Z  59 " =    1.856
peak=    4.061 closest distance to " CB  ARG A  79 " =    1.418
peak=    4.058 closest distance to " O   HOH Z 188 " =    2.536
peak=    4.048 closest distance to " CD  ARG A 269 " =    1.034
peak=    4.048 closest distance to " CB  ASN A 148 " =    1.332
peak=    4.032 closest distance to " O   HOH Z 427 " =    2.935
peak=    4.020 closest distance to " CD2 LEU A 228 " =    1.292
peak=    4.009 closest distance to " CB  SER A  26 " =    1.837
peak=    4.007 closest distance to " CB  VAL A 265 " =    1.302
peak=    4.001 closest distance to " O   HOH Z 406 " =    1.446
peak=    3.980 closest distance to " CG2 ILE A 234 " =    1.089
peak=    3.979 closest distance to " C   PRO A 198 " =    1.515
peak=    3.966 closest distance to " CB  GLU A 277 " =    3.594
peak=    3.965 closest distance to " CA  ALA A  51 " =    0.966
peak=    3.964 closest distance to " O   HOH Z 130 " =    2.597
peak=    3.958 closest distance to " O   HOH Z 251 " =    1.580
peak=    3.958 closest distance to " O   HOH Z  43 " =    2.305
peak=    3.957 closest distance to " CA  ARG A  36 " =    1.045
peak=    3.955 closest distance to " CB  ARG A 190 " =    1.721
peak=    3.935 closest distance to " O   HOH Z  95 " =    1.207
peak=    3.931 closest distance to " O   HOH Z  80 " =    1.726
peak=    3.921 closest distance to " N   PHE A 130 " =    1.365
peak=    3.910 closest distance to " O   HOH Z 423 " =    1.866
peak=    3.888 closest distance to " CG  PRO A 198 " =    1.224
peak=    3.886 closest distance to " O   HOH Z 411 " =    4.002
peak=    3.881 closest distance to " O   HOH Z 234 " =    3.503
peak=    3.875 closest distance to " CB  TRP A 266 " =    1.160
peak=    3.874 closest distance to " CB  VAL A 202 " =    1.599
peak=    3.872 closest distance to " O   HOH Z 365 " =    2.642
peak=    3.863 closest distance to " O   HOH Z 327 " =    1.568
peak=    3.855 closest distance to " O   HOH Z 143 " =    1.470
peak=    3.848 closest distance to " CB  ASN A 110 " =    1.114
peak=    3.831 closest distance to " CG2 VAL A 257 " =    0.778
peak=    3.830 closest distance to " O   HOH Z 141 " =    1.677
peak=    3.820 closest distance to " CD  LYS A  76 " =    1.806
peak=    3.814 closest distance to " CB  VAL A 296 " =    0.973
peak=    3.799 closest distance to " O   HOH Z 261 " =    2.336
peak=    3.787 closest distance to " CD  LYS A 166 " =    1.354
peak=    3.787 closest distance to " CA  TYR A  30 " =    0.983
peak=    3.769 closest distance to " CB  THR A  52 " =    0.896
peak=    3.765 closest distance to " O   HOH Z 126 " =    1.673
peak=    3.765 closest distance to " O   HOH Z  78 " =    2.220
peak=    3.764 closest distance to " O   HOH Z 298 " =    1.697
peak=    3.761 closest distance to " N   ASN A  39 " =    1.253
peak=    3.746 closest distance to " CG  LEU A 167 " =    1.306
peak=    3.744 closest distance to " O  BHOH Z 338 " =    2.362
peak=    3.739 closest distance to " O   HOH Z 246 " =    1.254
peak=    3.733 closest distance to " O   HOH Z  19 " =    1.962
peak=    3.715 closest distance to " OE1 GLU A   2 " =    2.125
peak=    3.709 closest distance to " OG ASER A 258 " =    2.883
peak=    3.706 closest distance to " O   HOH Z 425 " =    1.948
peak=    3.705 closest distance to " O   HOH Z  97 " =    2.023
peak=    3.698 closest distance to " CB  ALA A 248 " =    1.350
peak=    3.696 closest distance to " CB  THR A  31 " =    1.578
peak=    3.689 closest distance to " O   HOH Z 371 " =    2.886
peak=    3.680 closest distance to " CB  GLU A 152 " =    1.177
peak=    3.676 closest distance to " NZ  LYS A 117 " =    2.770
peak=    3.668 closest distance to " O   HOH Z 352 " =    1.308
peak=    3.667 closest distance to " ND2 ASN A 249 " =    0.925
peak=    3.662 closest distance to " CB  ARG A  79 " =    0.917
peak=    3.660 closest distance to " O   HOH Z 337 " =    1.747
peak=    3.652 closest distance to " O   HOH Z 130 " =    2.193
peak=    3.645 closest distance to " O   HOH Z  88 " =    3.445
peak=    3.643 closest distance to " O   HOH Z 406 " =    1.807
peak=    3.642 closest distance to " CB  TYR A 169 " =    0.771
peak=    3.635 closest distance to " CG  GLN A  88 " =    1.082
peak=    3.631 closest distance to " O   HOH Z 359 " =    1.353
peak=    3.628 closest distance to " CG2 ILE A 120 " =    1.327
peak=    3.627 closest distance to " O   ASP A 124 " =    1.226
peak=    3.620 closest distance to " O   HOH Z  88 " =    2.568
peak=    3.619 closest distance to " CA  ALA A 129 " =    1.598
peak=    3.618 closest distance to " O   HOH Z  40 " =    1.824
peak=    3.615 closest distance to " CA  ASN A 215 " =    0.976
peak=    3.615 closest distance to " NH2BARG A 145 " =    2.247
peak=    3.614 closest distance to " O   HOH Z 214 " =    2.513
peak=    3.607 closest distance to " O   HOH Z 350 " =    1.910
peak=    3.604 closest distance to " O   HOH Z 345 " =    3.060
peak=    3.596 closest distance to " CB  SER A   3 " =    1.174
peak=    3.591 closest distance to " O   HOH Z 329 " =    4.023
peak=    3.577 closest distance to " O   HOH Z 173 " =    2.162
peak=    3.576 closest distance to " O   HOH Z 280 " =    3.024
peak=    3.573 closest distance to " N   ASP A 162 " =    1.182
peak=    3.573 closest distance to " O   HOH Z 258 " =    2.183
peak=    3.564 closest distance to " CB  SER A 212 " =    1.386
peak=    3.564 closest distance to " CZ  PHE A  38 " =    1.090
peak=    3.562 closest distance to " NH2AARG A 145 " =    1.066
peak=    3.560 closest distance to " O   GLY A  91 " =    1.608
peak=    3.559 closest distance to " O   HOH Z 337 " =    3.598
peak=    3.556 closest distance to " O   HOH Z 187 " =    2.203
peak=    3.556 closest distance to " CB  ASN A  39 " =    0.868
peak=    3.555 closest distance to " CD1AILE A 234 " =    0.849
peak=    3.547 closest distance to " CA  ASN A 127 " =    1.076
peak=    3.540 closest distance to " O   HOH Z 250 " =    1.329
peak=    3.535 closest distance to " CB  PHE A 204 " =    0.994
peak=    3.530 closest distance to " CG2AVAL A 121 " =    2.368
peak=    3.525 closest distance to " O   HOH Z 130 " =    2.540
peak=    3.508 closest distance to " O   HOH Z 132 " =    2.466
peak=    3.505 closest distance to " O   HOH Z 158 " =    3.016
peak=    3.504 closest distance to " CB BVAL A  41 " =    1.195
peak=    3.501 closest distance to " CE1 TYR A 186 " =    1.264
peak=    3.477 closest distance to " CG2 ILE A  20 " =    1.499
peak=    3.477 closest distance to " CA  ASP A 149 " =    1.136
peak=    3.474 closest distance to " O   HOH Z  10 " =    1.745
peak=    3.458 closest distance to " O   HOH Z 109 " =    1.274
peak=    3.451 closest distance to " O   HOH Z 392 " =    2.713
peak=    3.449 closest distance to " O   HOH Z 299 " =    4.101
peak=    3.448 closest distance to " O   HOH Z 118 " =    1.401
peak=    3.440 closest distance to " OE1 GLN A  73 " =    2.479
peak=    3.438 closest distance to " O   HOH Z 425 " =    1.305
peak=    3.432 closest distance to " CB  ASN A 187 " =    1.291
peak=    3.426 closest distance to " CG AARG A 275 " =    1.200
peak=    3.425 closest distance to " O   HOH Z 132 " =    2.855
peak=    3.425 closest distance to " CG  LYS A 119 " =    1.172
peak=    3.420 closest distance to " CD  LYS A 119 " =    1.834
peak=    3.417 closest distance to " O   HOH Z 357 " =    1.998
peak=    3.415 closest distance to " CB  GLN A  88 " =    1.235
peak=    3.408 closest distance to " N   SER A 135 " =    1.379
peak=    3.407 closest distance to " O   HOH Z  68 " =    2.233
peak=    3.405 closest distance to " N   ARG A 156 " =    1.341
peak=    3.404 closest distance to " CD2 TYR A 186 " =    1.101
peak=    3.402 closest distance to " O   HOH Z 128 " =    1.907
peak=    3.395 closest distance to " CB  ASP A 140 " =    1.119
peak=    3.394 closest distance to " CG  LYS A 289 " =    1.401
peak=    3.389 closest distance to " CD2 LEU A 297 " =    0.959
peak=    3.389 closest distance to " CG  GLU A  37 " =    0.907
peak=    3.384 closest distance to " O   HOH Z 385 " =    3.882
peak=    3.379 closest distance to " O   HOH Z  21 " =    1.892
peak=    3.378 closest distance to " CG  MET A 185 " =    1.152
peak=    3.374 closest distance to " O   HOH Z 344 " =    2.654
peak=    3.372 closest distance to " CB  SER A  62 " =    1.169
peak=    3.366 closest distance to " CB  GLU A  46 " =    1.002
peak=    3.365 closest distance to " CB  ALA A 295 " =    1.244
peak=    3.363 closest distance to " O   HOH Z 272 " =    2.148
peak=    3.357 closest distance to " O   HOH Z 388 " =    2.205
peak=    3.355 closest distance to " CB  TRP A 179 " =    1.337
peak=    3.354 closest distance to " OG1 THR A 264 " =    0.736
peak=    3.354 closest distance to " CB  HIS A 108 " =    0.862
peak=    3.353 closest distance to " O   HOH Z 421 " =    1.973
peak=    3.350 closest distance to " OG BSER A 164 " =    2.117
peak=    3.349 closest distance to " O   HOH Z 380 " =    2.008
peak=    3.348 closest distance to " CA  ARG A 195 " =    1.142
peak=    3.347 closest distance to " OG  SER A  62 " =    2.725
peak=    3.346 closest distance to " O   HOH Z  94 " =    2.066
peak=    3.344 closest distance to " CB  LYS A 117 " =    1.166
peak=    3.342 closest distance to " O   HOH Z   1 " =    1.792
peak=    3.341 closest distance to " O   HOH Z 371 " =    3.220
peak=    3.338 closest distance to " CG  ARG A  66 " =    2.484
peak=    3.334 closest distance to " O   HOH Z 172 " =    3.879
peak=    3.333 closest distance to " NH2BARG A 190 " =    1.688
peak=    3.332 closest distance to " CA  PHE A 283 " =    1.105
peak=    3.332 closest distance to " CA  TYR A 116 " =    1.497
peak=    3.316 closest distance to " O   THR A  31 " =    1.843
peak=    3.316 closest distance to " O   HOH Z 236 " =    1.526
peak=    3.316 closest distance to " O   HOH Z 112 " =    1.045
peak=    3.315 closest distance to " CG  MET A 185 " =    0.927
peak=    3.312 closest distance to " OG1 THR A 221 " =    1.377
peak=    3.312 closest distance to " CB  PRO A  90 " =    1.147
peak=    3.311 closest distance to " O   HOH Z 303 " =    1.607
peak=    3.308 closest distance to " O   HOH Z 435 " =    2.011
peak=    3.308 closest distance to " CB  ARG A 156 " =    1.149
peak=    3.307 closest distance to " CG1 ILE A  49 " =    1.400
peak=    3.306 closest distance to " CA  ASN A 217 " =    1.206
peak=    3.305 closest distance to " O   HOH Z 375 " =    0.998
peak=    3.304 closest distance to " CA  ILE A 234 " =    0.971
peak=    3.301 closest distance to " O   HOH Z 273 " =    3.022
peak=    3.299 closest distance to " O   HOH Z 410 " =    3.040
peak=    3.295 closest distance to " O   HOH Z  30 " =    1.358
peak=    3.293 closest distance to " O   HOH Z   1 " =    1.844
peak=    3.289 closest distance to " OD1 ASN A  69 " =    2.405
peak=    3.287 closest distance to " O   HOH Z 180 " =    2.154
peak=    3.286 closest distance to " O   SER A 164 " =    1.150
peak=    3.285 closest distance to " CA  SER A  32 " =    1.791
peak=    3.285 closest distance to " CA  ASP A 162 " =    1.030
peak=    3.285 closest distance to " CB  ALA A 114 " =    1.112
peak=    3.283 closest distance to " O   HOH Z 368 " =    4.698
peak=    3.281 closest distance to " CE  LYS A  76 " =    0.910
peak=    3.280 closest distance to " NE2 GLN A  77 " =    3.202
peak=    3.278 closest distance to " CA  LEU A 282 " =    1.285
peak=    3.276 closest distance to " CA  ALA A 158 " =    1.522
peak=    3.273 closest distance to " CA  SER A 146 " =    1.983
peak=    3.272 closest distance to " CA  VAL A  41 " =    0.897
peak=    3.270 closest distance to " O   ALA A   1 " =    1.797
peak=    3.268 closest distance to " O   THR A 220 " =    1.298
peak=    3.262 closest distance to " O   HOH Z 421 " =    3.156
peak=    3.260 closest distance to " CG2 THR A  18 " =    1.595
peak=    3.259 closest distance to " O   HOH Z 325 " =    2.148
peak=    3.255 closest distance to " CB  ALA A 104 " =    0.802
peak=    3.254 closest distance to " O   HOH Z 407 " =    2.582
peak=    3.249 closest distance to " CB  ARG A 139 " =    0.979
peak=    3.243 closest distance to " CG  GLN A  55 " =    2.370
peak=    3.235 closest distance to " O   HOH Z 148 " =    3.401
peak=    3.231 closest distance to " CB  THR A  52 " =    0.866
peak=    3.229 closest distance to " CA  LYS A 117 " =    1.173
peak=    3.210 closest distance to " CD1 ILE A 106 " =    1.118
peak=    3.208 closest distance to " O   HOH Z 361 " =    3.514
peak=    3.202 closest distance to " O   HOH Z 203 " =    1.555
peak=    3.198 closest distance to " CG1 ILE A  33 " =    1.264
peak=    3.198 closest distance to " CG2 ILE A 239 " =    0.737
peak=    3.196 closest distance to " O   HOH Z 389 " =    1.591
peak=    3.194 closest distance to " O   HOH Z 282 " =    1.947
peak=    3.194 closest distance to " CB  THR A 235 " =    1.236
peak=    3.192 closest distance to " O   HOH Z 419 " =    1.721
peak=    3.189 closest distance to " CA  GLY A 267 " =    0.949
peak=    3.186 closest distance to " O   HOH Z   9 " =    1.933
peak=    3.185 closest distance to " O   HOH Z 322 " =    1.987
peak=    3.185 closest distance to " O   HOH Z 102 " =    1.180
peak=    3.184 closest distance to " O   HOH Z 353 " =    2.621
peak=    3.181 closest distance to " O   HOH Z 361 " =    3.115
peak=    3.179 closest distance to " CB  TYR A  30 " =    1.082
peak=    3.175 closest distance to " CA  SER A  87 " =    0.963
peak=    3.171 closest distance to " CB  ASN A 215 " =    1.093
peak=    3.164 closest distance to " CZ3 TRP A  85 " =    0.934
peak=    3.162 closest distance to " CB  SER A  99 " =    1.340
peak=    3.161 closest distance to " O   HOH Z 213 " =    1.834
peak=    3.161 closest distance to " O   HOH Z 293 " =    1.959
peak=    3.159 closest distance to " O   HOH Z 301 " =    1.718
peak=    3.148 closest distance to " O   HOH Z 193 " =    1.574
peak=    3.147 closest distance to " OE1 GLN A 194 " =    1.529
peak=    3.146 closest distance to " NH1 ARG A  66 " =    1.322
peak=    3.139 closest distance to " CG2 THR A 220 " =    0.716
peak=    3.139 closest distance to " O   HOH Z 162 " =    2.999
peak=    3.136 closest distance to " N   ALA A 256 " =    0.967
peak=    3.135 closest distance to " CG1 ILE A 120 " =    1.123
peak=    3.131 closest distance to " O   HOH Z 200 " =    2.268
peak=    3.129 closest distance to " O   HOH Z 222 " =    2.236
peak=    3.111 closest distance to " CA  LYS A 290 " =    1.181
peak=    3.102 closest distance to " CG  ARG A 269 " =    1.498
peak=    3.095 closest distance to " O   HOH Z 355 " =    1.787
peak=    3.094 closest distance to " OG ASER A 212 " =    1.809
peak=    3.087 closest distance to " CZ2 TRP A 150 " =    1.089
peak=    3.084 closest distance to " CB  TRP A 179 " =    1.435
peak=    3.072 closest distance to " O   HOH Z 336 " =    1.640
peak=    3.070 closest distance to " CB  LYS A 290 " =    0.897
peak=    3.070 closest distance to " CD  ARG A 195 " =    0.849
peak=    3.069 closest distance to " CB  LEU A 300 " =    0.910
peak=    3.066 closest distance to " O   HOH Z 313 " =    1.487
peak=    3.060 closest distance to " CG1 VAL A 153 " =    0.859
peak=    3.057 closest distance to " O   THR A 182 " =    1.472
peak=    3.046 closest distance to " O   HOH Z 344 " =    1.579
peak=    3.043 closest distance to " CB  VAL A 296 " =    1.393
peak=    3.027 closest distance to " CB  SER A  62 " =    0.914

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 195         
Filter by distance & map next to the model:
   mapped sites are within: 0.588 - 5.693
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 191 from: 195
   mapped sites are within: 0.728 - 5.693

peak=   -4.864 closest distance to " CG2 VAL A 230 " =    0.728
peak=   -4.839 closest distance to " CG  GLN A  58 " =    1.009
peak=   -4.620 closest distance to " CD  ARG A  14 " =    3.184
peak=   -4.594 closest distance to " OG BSER A 134 " =    1.346
peak=   -4.325 closest distance to " O   VAL A  67 " =    2.509
peak=   -4.254 closest distance to " C   HIS A 108 " =    1.188
peak=   -4.217 closest distance to " CD  ARG A 156 " =    2.051
peak=   -4.194 closest distance to " O   HOH Z 193 " =    1.296
peak=   -4.142 closest distance to " CG  GLN A 223 " =    2.258
peak=   -4.126 closest distance to " O   PRO A 163 " =    2.073
peak=   -4.119 closest distance to " CD1 LEU A 101 " =    2.342
peak=   -4.105 closest distance to " O   HOH Z 266 " =    5.401
peak=   -4.090 closest distance to " O   HOH Z 394 " =    1.631
peak=   -4.043 closest distance to " O   HOH Z 290 " =    1.126
peak=   -4.018 closest distance to " O   HOH Z 211 " =    1.353
peak=   -3.979 closest distance to " CE  MET A 105 " =    2.412
peak=   -3.952 closest distance to " O   HOH Z 166 " =    1.958
peak=   -3.935 closest distance to " OXT GLY A 302 " =    2.838
peak=   -3.932 closest distance to " CG1 VAL A 112 " =    2.735
peak=   -3.930 closest distance to " CD2 TYR A 293 " =    1.938
peak=   -3.926 closest distance to " CG2 VAL A 296 " =    1.906
peak=   -3.919 closest distance to " CA  VAL A  67 " =    2.929
peak=   -3.903 closest distance to " CB  PHE A 192 " =    2.006
peak=   -3.895 closest distance to " N   ALA A 248 " =    1.660
peak=   -3.872 closest distance to " CA  GLY A 241 " =    2.421
peak=   -3.872 closest distance to " CE2 TYR A  30 " =    2.743
peak=   -3.871 closest distance to " CZ2 TRP A  92 " =    2.825
peak=   -3.870 closest distance to " NE2 GLN A  88 " =    1.171
peak=   -3.860 closest distance to " O   PHE A 218 " =    1.626
peak=   -3.835 closest distance to " O   HOH Z 351 " =    1.470
peak=   -3.827 closest distance to " CB  ALA A  43 " =    2.424
peak=   -3.796 closest distance to " NE2 GLN A  11 " =    1.888
peak=   -3.784 closest distance to " O   HOH Z 100 " =    0.996
peak=   -3.751 closest distance to " CB  ALA A 248 " =    2.309
peak=   -3.749 closest distance to " O   ALA A 227 " =    1.385
peak=   -3.729 closest distance to " O   HOH Z  11 " =    1.844
peak=   -3.729 closest distance to " O   HOH Z 216 " =    1.257
peak=   -3.724 closest distance to " CA  ASP A 298 " =    1.072
peak=   -3.718 closest distance to " CD2 PHE A 225 " =    1.136
peak=   -3.718 closest distance to " CD1 PHE A 130 " =    2.275
peak=   -3.709 closest distance to " CG1 VAL A 250 " =    2.674
peak=   -3.669 closest distance to " O   HOH Z 387 " =    2.497
peak=   -3.669 closest distance to " O   ASN A  45 " =    1.955
peak=   -3.657 closest distance to " O   PRO A 198 " =    1.232
peak=   -3.649 closest distance to " CE BMET A  47 " =    1.204
peak=   -3.622 closest distance to " C   SER A 206 " =    1.470
peak=   -3.597 closest distance to " NE2 GLN A  88 " =    1.914
peak=   -3.592 closest distance to " CB  ASP A 132 " =    2.275
peak=   -3.585 closest distance to " OE1 GLN A 183 " =    1.463
peak=   -3.581 closest distance to " O   ASN A 187 " =    1.555
peak=   -3.575 closest distance to " O   HOH Z 281 " =    2.888
peak=   -3.569 closest distance to " CD1 ILE A 199 " =    2.337
peak=   -3.569 closest distance to " CA  GLY A 133 " =    1.892
peak=   -3.564 closest distance to " CB  ASP A 132 " =    2.329
peak=   -3.564 closest distance to " O   HOH Z 131 " =    4.076
peak=   -3.559 closest distance to " OH  TYR A 172 " =    1.814
peak=   -3.541 closest distance to " CD1 LEU A 255 " =    2.690
peak=   -3.537 closest distance to " O   HOH Z 374 " =    1.819
peak=   -3.519 closest distance to " CB  ALA A 248 " =    2.058
peak=   -3.509 closest distance to " CE3 TRP A 150 " =    2.035
peak=   -3.497 closest distance to " OD2 ASP A 191 " =    1.350
peak=   -3.488 closest distance to " NH2AARG A 275 " =    4.871
peak=   -3.485 closest distance to " OG ASER A 134 " =    1.408
peak=   -3.482 closest distance to " CB  ALA A 161 " =    2.464
peak=   -3.481 closest distance to " CG2 THR A  18 " =    2.882
peak=   -3.478 closest distance to " O   HOH Z 114 " =    3.178
peak=   -3.473 closest distance to " ND2 ASN A 249 " =    2.264
peak=   -3.469 closest distance to " O   HOH Z 429 " =    1.831
peak=   -3.463 closest distance to " O   HOH Z 372 " =    2.157
peak=   -3.463 closest distance to " CG  PHE A 283 " =    2.589
peak=   -3.462 closest distance to " O   HOH Z 102 " =    1.748
peak=   -3.454 closest distance to " O   HOH Z 165 " =    1.974
peak=   -3.452 closest distance to " CB  SER A 210 " =    1.161
peak=   -3.451 closest distance to " O   HOH Z 407 " =    2.653
peak=   -3.446 closest distance to " ND2 ASN A  45 " =    1.191
peak=   -3.439 closest distance to " O   HOH Z 421 " =    3.192
peak=   -3.436 closest distance to " O   HOH Z 196 " =    2.273
peak=   -3.433 closest distance to " N   SER A 276 " =    1.351
peak=   -3.420 closest distance to " CZ3 TRP A 179 " =    1.325
peak=   -3.418 closest distance to " O   HOH Z 243 " =    2.075
peak=   -3.415 closest distance to " N   HIS A 115 " =    2.184
peak=   -3.415 closest distance to " O   HOH Z 371 " =    2.148
peak=   -3.409 closest distance to " CG  LEU A   5 " =    0.941
peak=   -3.406 closest distance to " OE2 GLU A 152 " =    1.399
peak=   -3.403 closest distance to " O   HOH Z 191 " =    5.571
peak=   -3.402 closest distance to " O   HOH Z 110 " =    1.588
peak=   -3.396 closest distance to " CA  GLY A 133 " =    2.231
peak=   -3.394 closest distance to " ND2 ASN A 187 " =    1.627
peak=   -3.394 closest distance to " OH  TYR A 169 " =    0.902
peak=   -3.392 closest distance to " CG  ASP A 231 " =    0.794
peak=   -3.391 closest distance to " O   HOH Z 252 " =    3.904
peak=   -3.389 closest distance to " OG  SER A  97 " =    2.290
peak=   -3.388 closest distance to " O   HOH Z 357 " =    2.096
peak=   -3.384 closest distance to " O   HOH Z 431 " =    1.974
peak=   -3.383 closest distance to " NH2 ARG A 159 " =    2.358
peak=   -3.381 closest distance to " O   HOH Z 301 " =    2.310
peak=   -3.380 closest distance to " O   HOH Z 134 " =    3.222
peak=   -3.379 closest distance to " O   SER A 210 " =    1.852
peak=   -3.376 closest distance to " O   ALA A 292 " =    1.855
peak=   -3.376 closest distance to " O   HOH Z 137 " =    1.527
peak=   -3.372 closest distance to " CG2 ILE A 263 " =    2.247
peak=   -3.370 closest distance to " O   HOH Z 423 " =    2.178
peak=   -3.368 closest distance to " CZ  ARG A  66 " =    1.127
peak=   -3.368 closest distance to " O   HOH Z 345 " =    1.801
peak=   -3.365 closest distance to " OG  SER A  87 " =    1.394
peak=   -3.364 closest distance to " OD1 ASN A 301 " =    1.967
peak=   -3.363 closest distance to " ND2 ASN A  39 " =    1.134
peak=   -3.359 closest distance to " O   HOH Z 185 " =    2.374
peak=   -3.354 closest distance to " O   HOH Z 203 " =    1.813
peak=   -3.353 closest distance to " O   HOH Z 116 " =    1.713
peak=   -3.353 closest distance to " CG  TRP A 266 " =    2.011
peak=   -3.352 closest distance to " O   HOH Z 107 " =    1.002
peak=   -3.332 closest distance to " CB  PRO A 163 " =    2.428
peak=   -3.328 closest distance to " N   GLY A 196 " =    1.759
peak=   -3.327 closest distance to " O   PRO A 198 " =    1.265
peak=   -3.322 closest distance to " O   SER A 273 " =    1.479
peak=   -3.322 closest distance to " O   TRP A  92 " =    1.983
peak=   -3.312 closest distance to " CB  ASP A 231 " =    2.416
peak=   -3.290 closest distance to " CA  GLY A  23 " =    1.780
peak=   -3.290 closest distance to " N   ASP A 286 " =    2.071
peak=   -3.287 closest distance to " O   HOH Z 218 " =    3.974
peak=   -3.287 closest distance to " CB  ALA A 291 " =    2.035
peak=   -3.280 closest distance to " CG2 THR A 178 " =    2.451
peak=   -3.277 closest distance to " NE  ARG A  66 " =    4.264
peak=   -3.276 closest distance to " O   HOH Z  11 " =    2.116
peak=   -3.276 closest distance to " OXT GLY A 302 " =    3.548
peak=   -3.275 closest distance to " O   HOH Z 154 " =    1.613
peak=   -3.272 closest distance to " CD1 PHE A  59 " =    1.985
peak=   -3.266 closest distance to " CZ  PHE A  38 " =    2.381
peak=   -3.265 closest distance to " CB  TYR A  15 " =    2.216
peak=   -3.265 closest distance to " CD2 PHE A  61 " =    2.168
peak=   -3.263 closest distance to " O   HOH Z 286 " =    1.882
peak=   -3.258 closest distance to " ND2 ASN A 252 " =    1.867
peak=   -3.257 closest distance to " O   SER A 146 " =    1.274
peak=   -3.257 closest distance to " CE3 TRP A 274 " =    2.208
peak=   -3.251 closest distance to " O   HOH Z 174 " =    3.828
peak=   -3.250 closest distance to " CB  ASN A  39 " =    2.288
peak=   -3.250 closest distance to " OD2 ASP A 171 " =    2.132
peak=   -3.250 closest distance to " O   HOH Z 352 " =    1.684
peak=   -3.245 closest distance to " CG1 VAL A  78 " =    2.519
peak=   -3.240 closest distance to " O   HOH Z   3 " =    1.997
peak=   -3.239 closest distance to " O   TRP A  70 " =    1.534
peak=   -3.237 closest distance to " OG  SER A   3 " =    1.462
peak=   -3.237 closest distance to " O   HOH Z 208 " =    2.065
peak=   -3.235 closest distance to " O   HOH Z 423 " =    2.522
peak=   -3.229 closest distance to " O   ASN A 252 " =    1.286
peak=   -3.224 closest distance to " O   HOH Z 265 " =    2.336
peak=   -3.224 closest distance to " O   GLY A  80 " =    2.565
peak=   -3.220 closest distance to " CA  LYS A 166 " =    2.070
peak=   -3.217 closest distance to " O   VAL A 174 " =    2.282
peak=   -3.216 closest distance to " O   VAL A 189 " =    2.527
peak=   -3.211 closest distance to " N   ALA A 226 " =    1.937
peak=   -3.206 closest distance to " C   GLN A 205 " =    1.834
peak=   -3.204 closest distance to " CB  SER A 245 " =    2.124
peak=   -3.203 closest distance to " O   HOH Z 111 " =    4.594
peak=   -3.198 closest distance to " O   HOH Z 136 " =    2.391
peak=   -3.194 closest distance to " O   SER A 276 " =    1.707
peak=   -3.190 closest distance to " CD2 LEU A 167 " =    1.802
peak=   -3.189 closest distance to " C   MET A 188 " =    1.465
peak=   -3.177 closest distance to " O   HOH Z 139 " =    3.262
peak=   -3.175 closest distance to " C   LEU A 143 " =    0.954
peak=   -3.172 closest distance to " O   HOH Z 179 " =    2.176
peak=   -3.166 closest distance to " O   HOH Z 236 " =    1.605
peak=   -3.165 closest distance to " O   HOH Z 111 " =    1.736
peak=   -3.161 closest distance to " OG BSER A 134 " =    1.648
peak=   -3.157 closest distance to " CE1 TYR A 247 " =    2.595
peak=   -3.157 closest distance to " CG2 VAL A 202 " =    2.635
peak=   -3.151 closest distance to " CZ  ARG A 259 " =    0.963
peak=   -3.148 closest distance to " O   HOH Z 313 " =    1.777
peak=   -3.148 closest distance to " N   THR A  52 " =    1.684
peak=   -3.143 closest distance to " CG  GLN A 103 " =    2.509
peak=   -3.136 closest distance to " O   HOH Z 389 " =    1.403
peak=   -3.136 closest distance to " N   PHE A  59 " =    2.073
peak=   -3.135 closest distance to " O   HOH Z 139 " =    5.024
peak=   -3.135 closest distance to " NH1AARG A 275 " =    1.986
peak=   -3.126 closest distance to " CG  LEU A 228 " =    1.027
peak=   -3.119 closest distance to " O   ASP A  27 " =    1.985
peak=   -3.119 closest distance to " CA  GLY A  98 " =    1.938
peak=   -3.119 closest distance to " NH2 ARG A  66 " =    5.693
peak=   -3.119 closest distance to " O   HOH Z  64 " =    2.769
peak=   -3.116 closest distance to " CB  HIS A  86 " =    1.146
peak=   -3.115 closest distance to " CB  GLN A  55 " =    1.350
peak=   -3.111 closest distance to " CZ  TYR A 169 " =    1.857
peak=   -3.107 closest distance to " NH2 ARG A  79 " =    2.052
peak=   -3.103 closest distance to " CD  PRO A 243 " =    1.987
peak=   -3.090 closest distance to " CD2 LEU A 237 " =    2.492
peak=   -3.084 closest distance to " CZ2 TRP A 274 " =    0.998
peak=   -3.082 closest distance to " O   HOH Z 113 " =    1.903
peak=   -3.072 closest distance to " CB  TYR A 172 " =    2.461
peak=   -3.072 closest distance to " O   HOH Z 256 " =    1.279
peak=   -3.060 closest distance to " CB  LEU A 300 " =    2.600

================= 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    :  0.4774 0.4707   6.279594e+00   6.272066e+00
   1_bss:  0.4689 0.4650   6.271312e+00   6.266370e+00
   1_xyz:  0.3834 0.4015   6.150820e+00   6.193636e+00
   1_adp:  0.3355 0.3835   6.059754e+00   6.155458e+00
   1_occ:  0.3354 0.3839   6.059068e+00   6.156679e+00
   2_bss:  0.3309 0.3794   6.059419e+00   6.157074e+00
   2_xyz:  0.2431 0.2924   5.801262e+00   5.959456e+00
   2_adp:  0.2174 0.2718   5.712959e+00   5.889975e+00
   2_occ:  0.2172 0.2719   5.712925e+00   5.890315e+00
   3_bss:  0.2150 0.2705   5.710505e+00   5.887238e+00
   3_xyz:  0.1526 0.1976   5.401408e+00   5.607365e+00
   3_adp:  0.1361 0.1840   5.310072e+00   5.538874e+00
   3_occ:  0.1359 0.1842   5.309443e+00   5.538839e+00
   4_bss:  0.1354 0.1847   5.308435e+00   5.536731e+00
   4_xyz:  0.1251 0.1726   5.247153e+00   5.476332e+00
   4_adp:  0.1236 0.1687   5.229994e+00   5.450152e+00
   4_occ:  0.1234 0.1686   5.229509e+00   5.450050e+00
   5_bss:  0.1234 0.1686   5.229519e+00   5.449942e+00
   5_xyz:  0.1162 0.1609   5.179514e+00   5.409622e+00
   5_adp:  0.1148 0.1609   5.174019e+00   5.407644e+00
   5_occ:  0.1147 0.1609   5.173806e+00   5.407643e+00
   5_bss:  0.1147 0.1609   5.173768e+00   5.407568e+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:  0.331   5.228   8.750   7.797  10.274   0.000   0.000   0.000
   1_xyz:  0.331   5.228   8.750   7.797  10.274   0.000   0.000   0.000
   1_adp:  0.331   5.228   8.750   7.797  10.274   0.000   0.000   0.000
   1_occ:  0.331   5.228   8.750   7.797  10.274   0.000   0.000   0.000
   2_bss:  0.321  33.537   4.521   3.599   6.145   0.000   0.000   0.000
   2_xyz:  0.321  33.537   4.521   3.599   6.145   0.000   0.000   0.000
   2_adp:  0.321  33.537   4.521   3.599   6.145   0.000   0.000   0.000
   2_occ:  0.321  33.537   4.521   3.599   6.145   0.000   0.000   0.000
   3_bss:  0.314  42.919   2.173   2.578   4.263   0.000   0.000   0.000
   3_xyz:  0.314  42.919   2.173   2.578   4.263   0.000   0.000   0.000
   3_adp:  0.314  42.919   2.173   2.578   4.263   0.000   0.000   0.000
   3_occ:  0.314  42.919   2.173   2.578   4.263   0.000   0.000   0.000
   4_bss:  0.311  45.967   1.147   1.989   3.499   0.000   0.000   0.000
   4_xyz:  0.311  45.967   1.147   1.989   3.499   0.000   0.000   0.000
   4_adp:  0.311  45.967   1.147   1.989   3.499   0.000   0.000   0.000
   4_occ:  0.311  45.967   1.147   1.989   3.499   0.000   0.000   0.000
   5_bss:  0.320  45.967   1.147   1.989   3.499   0.000   0.000   0.000
   5_xyz:  0.320  45.967   1.147   1.989   3.499   0.000   0.000   0.000
   5_adp:  0.320  45.967   1.147   1.989   3.499   0.000   0.000   0.000
   5_occ:  0.320  45.967   1.147   1.989   3.499   0.000   0.000   0.000
   5_bss:  0.320  48.184  -1.118  -0.200   1.318  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  56.103 0.4444  0.5258    69761.598
   1_bss:  56.160 0.4421  0.6853    67844.469
   1_xyz:  46.147 0.5674  0.8472    48163.301
   1_adp:  41.712 0.6221  0.9651    41975.641
   1_occ:  41.783 0.6213  0.9619    42084.715
   2_bss:  41.466 0.6253  0.8382    41973.405
   2_xyz:  30.302 0.7539  0.9716    22941.099
   2_adp:  27.185 0.7883  1.0094    19189.066
   2_occ:  27.215 0.7879  1.0090    19223.983
   3_bss:  27.051 0.7898  0.9482    19076.080
   3_xyz:  19.072 0.8702  1.0018    10112.730
   3_adp:  17.437 0.8855  1.0049     8852.261
   3_occ:  17.435 0.8855  1.0047     8836.662
   4_bss:  17.358 0.8862  0.9767     8786.530
   4_xyz:  16.024 0.8981  0.9803     7763.383
   4_adp:  15.503 0.9028  0.9788     7448.483
   4_occ:  15.505 0.9028  0.9787     7446.868
   5_bss:  15.506 0.9028  0.9788     7446.584
   5_xyz:  14.703 0.9092  0.9822     6847.639
   5_adp:  14.617 0.9102  0.9782     6815.871
   5_occ:  14.619 0.9101  0.9781     6810.455
   5_bss:  14.620 0.9101  0.9782     6808.903
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.088   5.3376e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.088   5.3376e+01
   1_xyz:   1.699  0.013  0.107 18.124  0.006  4.106   1.4273e-01
   1_adp:   1.699  0.013  0.107 18.124  0.006  4.106   1.4273e-01
   1_occ:   1.699  0.013  0.107 18.124  0.006  4.106   1.4273e-01
   2_bss:   1.699  0.013  0.107 18.124  0.006  4.106   1.4273e-01
   2_xyz:   1.157  0.009  0.082 16.131  0.005  4.111   8.2143e-02
   2_adp:   1.157  0.009  0.082 16.131  0.005  4.111   8.2143e-02
   2_occ:   1.157  0.009  0.082 16.131  0.005  4.111   8.2143e-02
   3_bss:   1.157  0.009  0.082 16.131  0.005  4.111   8.2143e-02
   3_xyz:   1.157  0.008  0.082 15.992  0.004  4.126   7.6024e-02
   3_adp:   1.157  0.008  0.082 15.992  0.004  4.126   7.6024e-02
   3_occ:   1.157  0.008  0.082 15.992  0.004  4.126   7.6024e-02
   4_bss:   1.157  0.008  0.082 15.992  0.004  4.126   7.6024e-02
   4_xyz:   0.959  0.006  0.073 15.471  0.004  4.117   5.6408e-02
   4_adp:   0.959  0.006  0.073 15.471  0.004  4.117   5.6408e-02
   4_occ:   0.959  0.006  0.073 15.471  0.004  4.117   5.6408e-02
   5_bss:   0.959  0.006  0.073 15.471  0.004  4.117   5.6408e-02
   5_xyz:   1.066  0.007  0.081 15.496  0.004  4.110   6.5576e-02
   5_adp:   1.066  0.007  0.081 15.496  0.004  4.110   6.5576e-02
   5_occ:   1.066  0.007  0.081 15.496  0.004  4.110   6.5576e-02
   5_bss:   1.066  0.007  0.081 15.496  0.004  4.110   6.5576e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.029   6.9095e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.029   6.9095e+00
   1_xyz:  14.929  0.163  0.475 86.071  0.036  2.138   1.0112e-01
   1_adp:  14.929  0.163  0.475 86.071  0.036  2.138   1.0112e-01
   1_occ:  14.929  0.163  0.475 86.071  0.036  2.138   1.0112e-01
   2_bss:  14.929  0.163  0.475 86.071  0.036  2.138   1.0112e-01
   2_xyz:   6.818  0.081  0.267 85.025  0.043  2.233   1.2007e-01
   2_adp:   6.818  0.081  0.267 85.025  0.043  2.233   1.2007e-01
   2_occ:   6.818  0.081  0.267 85.025  0.043  2.233   1.2007e-01
   3_bss:   6.818  0.081  0.267 85.025  0.043  2.233   1.2007e-01
   3_xyz:   8.345  0.053  0.450 84.727  0.040  2.264   5.9271e-02
   3_adp:   8.345  0.053  0.450 84.727  0.040  2.264   5.9271e-02
   3_occ:   8.345  0.053  0.450 84.727  0.040  2.264   5.9271e-02
   4_bss:   8.345  0.053  0.450 84.727  0.040  2.264   5.9271e-02
   4_xyz:   6.682  0.043  0.343 82.070  0.033  2.394   3.9135e-02
   4_adp:   6.682  0.043  0.343 82.070  0.033  2.394   3.9135e-02
   4_occ:   6.682  0.043  0.343 82.070  0.033  2.394   3.9135e-02
   5_bss:   6.682  0.043  0.343 82.070  0.033  2.394   3.9135e-02
   5_xyz:   6.928  0.045  0.395 83.462  0.037  2.322   4.1798e-02
   5_adp:   6.928  0.045  0.395 83.462  0.037  2.322   4.1798e-02
   5_occ:   6.928  0.045  0.395 83.462  0.037  2.322   4.1798e-02
   5_bss:   6.928  0.045  0.395 83.462  0.037  2.322   4.1798e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00
   1_bss:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_xyz:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_adp:  61.26   0.00  12.86  61.26   0.00  10.47  60.96   0.00  25.90
   1_occ:  61.26   0.00  12.86  61.26   0.00  10.47  60.96   0.00  25.90
   2_bss:  61.26   0.00  12.86  61.26   0.00  10.47  60.96   0.00  25.90
   2_xyz:  61.26   0.00  12.86  61.26   0.00  10.47  60.96   0.00  25.90
   2_adp:  72.26   0.00  13.27  71.43   0.00   9.53  72.26   1.28  33.64
   2_occ:  72.26   0.00  13.27  71.43   0.00   9.53  72.26   1.28  33.64
   3_bss:  72.26   0.00  13.27  71.43   0.00   9.53  72.26   1.28  33.64
   3_xyz:  72.26   0.00  13.27  71.43   0.00   9.53  72.26   1.28  33.64
   3_adp:  87.51   0.00  13.79  87.51   0.00   9.18  79.06   1.51  38.90
   3_occ:  87.51   0.00  13.79  87.51   0.00   9.18  79.06   1.51  38.90
   4_bss:  87.51   0.00  13.79  87.51   0.00   9.18  79.06   1.51  38.90
   4_xyz:  87.51   0.00  13.79  87.51   0.00   9.18  79.06   1.51  38.90
   4_adp:  89.53   0.00  13.30  89.53   0.00   8.92  78.40   2.29  37.17
   4_occ:  89.53   0.00  13.30  89.53   0.00   8.92  78.40   2.29  37.17
   5_bss:  89.53   0.00  13.30  89.53   0.00   8.92  78.40   2.29  37.17
   5_xyz:  89.53   0.00  13.30  89.53   0.00   8.92  78.40   2.29  37.17
   5_adp:  91.83   0.00  13.13  91.83   0.00   8.80  82.66   1.74  36.73
   5_occ:  91.83   0.00  13.13  91.83   0.00   8.80  82.66   1.74  36.73
   5_bss:  94.04   2.22  15.35  94.04   2.22  11.01  84.88   3.95  38.94
------------------------------------------------------------------------
 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:    1.298    0.041    0.415
   1_adp:    1.298    0.041    0.415
   1_occ:    1.298    0.041    0.415
   2_bss:    1.298    0.041    0.415
   2_xyz:    1.730    0.044    0.578
   2_adp:    1.730    0.044    0.578
   2_occ:    1.730    0.044    0.578
   3_bss:    1.730    0.044    0.578
   3_xyz:    1.737    0.044    0.665
   3_adp:    1.737    0.044    0.665
   3_occ:    1.737    0.044    0.665
   4_bss:    1.737    0.044    0.665
   4_xyz:    1.814    0.037    0.683
   4_adp:    1.814    0.037    0.683
   4_occ:    1.814    0.037    0.683
   5_bss:    1.814    0.037    0.683
   5_xyz:    1.875    0.059    0.700
   5_adp:    1.875    0.059    0.700
   5_occ:    1.875    0.059    0.700
   5_bss:    1.875    0.059    0.700
------------------------------------------------------------------------

CPU time actual refinement: 347.79


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_63/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/trial/run_63/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_63/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_63/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_63/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 347.64 
  Macro-tasks:
    bulk solvent and scale       = 40.64  
    individual site refinement   = 140.23 
    weights calculation          = 32.57  
    collect and process          = 6.55   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 220.09 
  Micro-tasks:
    mask                            = 1.85   
    f_calc                          = 109.66 
    alpha_beta                      = 8.29   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 119.53 
    fmodel                         = 7.29   
    r_factors                      = 0.35   
    phase_errors                   = 10.49  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 258.90 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.884 micro seconds
Total CPU time: 6.03 minutes
from_scatterers_fft:    673 calls, 109.26 s
gradients_fft:          618 calls, 106.12 s

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

# Date 2008-01-16 Time 00:39:34 PST -0800 (1200472774.16 s)
Start R-work = 0.4774, R-free = 0.4707 (no bulk solvent and anisotropic scale)
Final R-work = 0.1324, R-free = 0.1760 (no bulk solvent and anisotropic scale)

Start R-work = 0.4689, R-free = 0.4650
Final R-work = 0.1147, R-free = 0.1609