# Date 2008-01-16 Time 03:09:57 PST -0800 (1200481797.46 s)
#phil __OFF__

Command line arguments: "../1132.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 11798
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1132

-------------------------------------------------------------------------------
  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: (71.655, 46.4607, 88.5498, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.655, 46.4607, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.3141 1.98373
Completeness in resolution range: 0.93055
Completeness with d_max=infinity: 0.927861

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.3141
                             d_min =   1.9837

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.655, 46.4607, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.3141 1.98373
Completeness in resolution range: 0.93055
Completeness with d_max=infinity: 0.927861

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.3145 -  4.2463 [2212/2238]  1991   221  10.0%
  bin  2:  4.2463 -  3.3823 [2132/2152]  1918   214  10.0%
  bin  3:  3.3823 -  2.9583 [2088/2107]  1882   206   9.9%
  bin  4:  2.9583 -  2.6894 [2076/2106]  1861   215  10.4%
  bin  5:  2.6894 -  2.4975 [2068/2087]  1870   198   9.6%
  bin  6:  2.4975 -  2.3508 [2077/2102]  1865   212  10.2%
  bin  7:  2.3508 -  2.2335 [2021/2049]  1813   208  10.3%
  bin  8:  2.2335 -  2.1365 [2047/2083]  1841   206  10.1%
  bin  9:  2.1365 -  2.0545 [2028/2070]  1837   191   9.4%
  bin 10:  2.0545 -  1.9837 [ 840/2057]   752    88  10.5%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1132/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 19
        2.42 -     3.04: 2169
        3.04 -     3.66: 4629
        3.66 -     4.28: 8874
        4.28 -     4.90: 12172
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 324 " - " O   HOH Z 374 "  2.206 3.040 -x,y-1/2,-z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z  50 " - " O   HOH Z  95 "  2.247 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  95 " - " O   HOH Z  50 "  2.247 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 27858 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_1132/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1132/model_refine_001.geo

CPU time processing inputs: 9.28


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.655 46.4607 88.54975 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: 1.98 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5026   r_free= 0.4939   ksol= 0.00   Bsol= 0.00   scale= 0.765    |
|                                                                             |
| 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:   0.82 A                  |
| x-ray target function (ml) for work reflections: 6.301474                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3145 -  4.7369 0.99   1434  158 0.4212 0.3975      6.6456      6.5918|
|  2:  4.7369 -  3.7784 0.99   1386  155 0.4297 0.4512      6.8458      6.8968|
|  3:  3.7784 -  3.3062 0.99   1356  147 0.4746 0.4392      6.6951      6.6601|
|  4:  3.3062 -  3.0064 0.99   1344  154 0.5054 0.4614      6.5528      6.5006|
|  5:  3.0064 -  2.7923 0.99   1334  152 0.5309 0.5062      6.3821      6.3865|
|  6:  2.7923 -  2.6286 0.99   1346  146 0.5298 0.5468      6.2749       6.228|
|  7:  2.6286 -  2.4975 0.99   1322  142 0.5507 0.4999      6.2506      6.1825|
|  8:  2.4975 -  2.3892 0.98   1315  155 0.5515 0.5494      6.1839      6.1887|
|  9:  2.3892 -  2.2976 0.98   1311  145 0.5350 0.5923      6.1302      6.2122|
| 10:  2.2976 -  2.2185 1.00   1333  145 0.5414 0.5312      6.0929      6.0878|
| 11:  2.2185 -  2.1494 0.98   1306  143 0.5268 0.5214      6.0373      6.0298|
| 12:  2.1494 -  2.0881 0.98   1308  142 0.5398 0.5222      5.9372       5.956|
| 13:  2.0881 -  2.0332 0.93   1228  139 0.5371 0.5033       5.888      5.8136|
| 14:  2.0332 -  1.9837 0.23    307   36 0.5258 0.5209      5.8528      5.8511|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.3145 -  4.7369  1434   158  0.68  35.82   0.77     0.72      78656.72|
|  2:  4.7369 -  3.7784  1386   155  0.68  37.01   0.85     0.75     119517.89|
|  3:  3.7784 -  3.3062  1356   147  0.55  47.53   0.81     0.68     126959.67|
|  4:  3.3062 -  3.0064  1344   154  0.46  54.95   0.75     0.57     112734.64|
|  5:  3.0064 -  2.7923  1334   152  0.37  61.71   0.71     0.46      88778.93|
|  6:  2.7923 -  2.6286  1346   146  0.32  65.93   0.69     0.37      78177.12|
|  7:  2.6286 -  2.4975  1322   142  0.28  69.02   0.71     0.32      72173.20|
|  8:  2.4975 -  2.3892  1315   155  0.24  72.12   0.70     0.29      66763.11|
|  9:  2.3892 -  2.2976  1311   145  0.24  71.86   0.70     0.29      62608.33|
| 10:  2.2976 -  2.2185  1333   145  0.24  72.40   0.71     0.28      55591.21|
| 11:  2.2185 -  2.1494  1306   143  0.23  72.58   0.77     0.30      52466.04|
| 12:  2.1494 -  2.0881  1308   142  0.25  71.49   0.71     0.32      46338.96|
| 13:  2.0881 -  2.0332  1228   139  0.26  70.58   0.69     0.34      40120.36|
| 14:  2.0332 -  1.9837   307    36  0.33  65.42   0.72     0.36      31871.89|
|alpha:            min =        0.28 max =            0.75 mean =         0.44|
|beta:             min =    31871.89 max =       126959.67 mean =     76764.00|
|figures of merit: min =        0.00 max =            1.00 mean =         0.37|
|phase err.(work): min =        0.00 max =           89.98 mean =        61.48|
|phase err.(test): min =        0.00 max =           89.97 mean =        61.47|
|-----------------------------------------------------------------------------|

============================== 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 = 19.713796             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.093   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.812807              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.522   (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 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       23 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      168 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      678 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1483 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2601 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3861 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     4999 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6474 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7577 |
|-----------------------------------------------------------------------------|
|-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 |       54.414 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.090    4.900  1.196 |       1.706 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.246)------------------------------------------|
|    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 = 12.246)------------------------------------------|
|    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: 1.98 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5065   r_free= 0.4976   ksol= 0.00   Bsol= 0.00   scale= 0.738    |
|                                                                             |
| 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:   0.82 A                  |
| x-ray target function (ml) for work reflections: 6.302431                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4951   r_free= 0.4842   ksol= 0.32   Bsol= 35.49   scale= 0.955   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.90,6.73,10.72,0.00,0.00,0.00); trace/3= 8.45                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.82 A                  |
| x-ray target function (ml) for work reflections: 6.297987                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 16.936804             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.866   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.597225              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.186   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4951      final r-factor (work) = 0.4256          |
| start r-factor (free) = 0.4842      final r-factor (free) = 0.4455          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 107.7239 = 16.94 * 0.50 * 6.2952 + 1.00 * 54.4139                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 52.9508 = 16.94 * 0.50 * 6.2341 + 1.00 * 0.1576                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4256      final r-factor (work) = 0.3792          |
| start r-factor (free) = 0.4455      final r-factor (free) = 0.4338          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.9718 = 1.60 * 1.00 * 6.2341 + 1.00 * 0.0145                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.8702 = 1.60 * 1.00 * 6.1657 + 1.00 * 0.0223                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.246)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.58   16.66    None  None   None       |
|    all(noH): 2823   0      0.00    91.58   16.66    None  None   None       |
|    Sol.    : 438    0      0.00    91.58   28.94    None  None   None       |
|    Mac.    : 2385   0      0.00    79.63   14.40    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 -   9.158: 1107   |   5:    45.789 -  54.947:   70        |
|      1:     9.158 -  18.316:  721   |   6:    54.947 -  64.104:   48        |
|      2:    18.316 -  27.473:  458   |   7:    64.104 -  73.262:   25        |
|      3:    27.473 -  36.631:  245   |   8:    73.262 -  82.420:    9        |
|      4:    36.631 -  45.789:  137   |   9:    82.420 -  91.578:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3792 r_free = 0.4338             target_work(ml) = 6.152         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3784 r_free = 0.4343             target_work(ml) = 6.151         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3784   r_free= 0.4343   ksol= 0.32   Bsol= 35.49   scale= 1.105   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.90,6.73,10.72,0.00,0.00,0.00); trace/3= 8.45                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.151329                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3768   r_free= 0.4317   ksol= 0.31   Bsol= 41.80   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.64,3.61,7.14,0.00,0.00,0.00); trace/3= 5.13                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.152411                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.387322              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.305   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.560711              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.441  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3768      final r-factor (work) = 0.3077          |
| start r-factor (free) = 0.4317      final r-factor (free) = 0.3705          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.9120 = 7.39 * 0.50 * 6.1604 + 1.00 * 0.1576                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.5203 = 7.39 * 0.50 * 6.0709 + 1.00 * 0.0965                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3077      final r-factor (work) = 0.2896          |
| start r-factor (free) = 0.3705      final r-factor (free) = 0.3529          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4264 = 0.56 * 1.00 * 6.0709 + 1.00 * 0.0224                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3642 = 0.56 * 1.00 * 5.9724 + 1.00 * 0.0154                               |
|-----------------------------------------------------------------------------|
| number of iterations = 13      |    number of function evaluations = 18     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.246)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.82   15.96    None  None   None       |
|    all(noH): 2823   0      0.00    92.82   15.96    None  None   None       |
|    Sol.    : 438    0      0.00    92.82   32.55    None  None   None       |
|    Mac.    : 2385   0      0.00    80.35   12.91    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 -   9.282: 1166   |   5:    46.411 -  55.693:   50        |
|      1:     9.282 -  18.564:  754   |   6:    55.693 -  64.975:   48        |
|      2:    18.564 -  27.847:  439   |   7:    64.975 -  74.257:   15        |
|      3:    27.847 -  37.129:  221   |   8:    74.257 -  83.540:    7        |
|      4:    37.129 -  46.411:  121   |   9:    83.540 -  92.822:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2896 r_free = 0.3529             target_work(ml) = 5.953         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2894 r_free = 0.3526             target_work(ml) = 5.952         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2894   r_free= 0.3526   ksol= 0.31   Bsol= 41.80   scale= 1.068   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.64,3.61,7.14,0.00,0.00,0.00); trace/3= 5.13                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.44 A                  |
| x-ray target function (ml) for work reflections: 5.952421                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2883   r_free= 0.3516   ksol= 0.32   Bsol= 56.98   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.30,1.61,4.66,0.00,0.00,0.00); trace/3= 2.86                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.45 A                  |
| x-ray target function (ml) for work reflections: 5.953654                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.272700              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 93.566   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.702665              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 126.053  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2883      final r-factor (work) = 0.2274          |
| start r-factor (free) = 0.3516      final r-factor (free) = 0.2911          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.8559 = 4.27 * 0.50 * 5.9725 + 1.00 * 0.0965                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.5948 = 4.27 * 0.50 * 5.8617 + 1.00 * 0.0721                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2274      final r-factor (work) = 0.2036          |
| start r-factor (free) = 0.2911      final r-factor (free) = 0.2666          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1348 = 0.70 * 1.00 * 5.8617 + 1.00 * 0.0159                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0311 = 0.70 * 1.00 * 5.7159 + 1.00 * 0.0148                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.246)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.69   15.79    None  None   None       |
|    all(noH): 2823   0      0.00    90.69   15.79    None  None   None       |
|    Sol.    : 438    0      0.00    90.69   40.03    None  None   None       |
|    Mac.    : 2385   0      0.00    86.65   11.33    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 -   9.069: 1273   |   5:    45.346 -  54.415:  116        |
|      1:     9.069 -  18.138:  792   |   6:    54.415 -  63.484:   58        |
|      2:    18.138 -  27.208:  284   |   7:    63.484 -  72.554:   35        |
|      3:    27.208 -  36.277:  148   |   8:    72.554 -  81.623:   10        |
|      4:    36.277 -  45.346:   98   |   9:    81.623 -  90.692:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2036 r_free = 0.2666             target_work(ml) = 5.678         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2034 r_free = 0.2667             target_work(ml) = 5.678         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2034   r_free= 0.2667   ksol= 0.32   Bsol= 56.98   scale= 1.030   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.30,1.61,4.66,0.00,0.00,0.00); trace/3= 2.86                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.677922                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2034   r_free= 0.2662   ksol= 0.33   Bsol= 70.50   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.33,0.78,3.29,0.00,0.00,0.00); trace/3= 1.80                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.678728                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.539395              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.877  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.312843              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 150.077  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2034      final r-factor (work) = 0.1705          |
| start r-factor (free) = 0.2662      final r-factor (free) = 0.2307          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3324 = 2.54 * 0.50 * 5.7182 + 1.00 * 0.0721                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1742 = 2.54 * 0.50 * 5.6047 + 1.00 * 0.0579                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1705      final r-factor (work) = 0.1640          |
| start r-factor (free) = 0.2307      final r-factor (free) = 0.2209          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7681 = 0.31 * 1.00 * 5.6047 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7374 = 0.31 * 1.00 * 5.5093 + 1.00 * 0.0139                               |
|-----------------------------------------------------------------------------|
| number of iterations = 11      |    number of function evaluations = 20     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.246)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.26   15.24    None  None   None       |
|    all(noH): 2823   0      0.00    89.26   15.24    None  None   None       |
|    Sol.    : 438    0      2.17    89.26   40.03    None  None   None       |
|    Mac.    : 2385   0      0.00    84.56   10.69    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 -   8.926: 1345   |   5:    44.628 -  53.554:  105        |
|      1:     8.926 -  17.851:  790   |   6:    53.554 -  62.479:   65        |
|      2:    17.851 -  26.777:  241   |   7:    62.479 -  71.405:   32        |
|      3:    26.777 -  35.702:  123   |   8:    71.405 -  80.330:   14        |
|      4:    35.702 -  44.628:   99   |   9:    80.330 -  89.256:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1640 r_free = 0.2209             target_work(ml) = 5.484         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1640 r_free = 0.2208             target_work(ml) = 5.483         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1640   r_free= 0.2208   ksol= 0.33   Bsol= 70.50   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.33,0.78,3.29,0.00,0.00,0.00); trace/3= 1.80                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.483068                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1641   r_free= 0.2206   ksol= 0.33   Bsol= 70.50   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.77,0.32,2.55,0.00,0.00,0.00); trace/3= 1.21                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.483595                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.792841              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.060  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.874122              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 97.489   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1641      final r-factor (work) = 0.1368          |
| start r-factor (free) = 0.2206      final r-factor (free) = 0.1878          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.2645 = 4.79 * 0.50 * 5.5108 + 1.00 * 0.0583                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.0549 = 4.79 * 0.50 * 5.4118 + 1.00 * 0.0858                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1368      final r-factor (work) = 0.1301          |
| start r-factor (free) = 0.1878      final r-factor (free) = 0.1830          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7432 = 0.87 * 1.00 * 5.4118 + 1.00 * 0.0126                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6507 = 0.87 * 1.00 * 5.3046 + 1.00 * 0.0138                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.246)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    105.13  15.45    None  None   None       |
|    all(noH): 2823   0      0.00    105.13  15.45    None  None   None       |
|    Sol.    : 438    0      3.19    105.13  42.41    None  None   None       |
|    Mac.    : 2385   0      0.00    81.06   10.50    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.513: 1598   |   5:    52.567 -  63.080:   90        |
|      1:    10.513 -  21.027:  673   |   6:    63.080 -  73.594:   44        |
|      2:    21.027 -  31.540:  167   |   7:    73.594 -  84.107:   28        |
|      3:    31.540 -  42.054:  113   |   8:    84.107 -  94.621:    7        |
|      4:    42.054 -  52.567:  102   |   9:    94.621 - 105.134:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1301 r_free = 0.1830             target_work(ml) = 5.288         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1301 r_free = 0.1830             target_work(ml) = 5.287         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1301   r_free= 0.1830   ksol= 0.33   Bsol= 70.50   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.77,0.32,2.55,0.00,0.00,0.00); trace/3= 1.21                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.287296                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3145 -  4.7369 0.99   1434  158 0.0971 0.1386      5.3932      5.5995|
|  2:  4.7369 -  3.7784 0.99   1386  155 0.0894 0.1182      5.4852      5.6902|
|  3:  3.7784 -  3.3062 0.99   1356  147 0.1233 0.1743      5.5897      5.9267|
|  4:  3.3062 -  3.0064 0.99   1344  154 0.1427 0.1984      5.5857      5.7762|
|  5:  3.0064 -  2.7923 0.99   1334  152 0.1615 0.2005       5.499      5.6934|
|  6:  2.7923 -  2.6286 0.99   1346  146 0.1527 0.2427      5.3749      5.6582|
|  7:  2.6286 -  2.4975 0.99   1322  142 0.1489 0.1807      5.3132      5.4409|
|  8:  2.4975 -  2.3892 0.98   1315  155 0.1451 0.1981      5.2364      5.4733|
|  9:  2.3892 -  2.2976 0.98   1311  145 0.1452 0.2279      5.1996      5.4807|
| 10:  2.2976 -  2.2185 1.00   1333  145 0.1371 0.1826      5.1043       5.262|
| 11:  2.2185 -  2.1494 0.98   1306  143 0.1346 0.2201      5.0808      5.4633|
| 12:  2.1494 -  2.0881 0.98   1308  142 0.1345 0.1980      4.9965       5.245|
| 13:  2.0881 -  2.0332 0.93   1228  139 0.1309 0.1872      4.9159      5.1238|
| 14:  2.0332 -  1.9837 0.23    307   36 0.1221 0.1905      4.8316      5.0639|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.3145 -  4.7369  1434   158  0.94   9.50   0.97     0.94       7737.01|
|  2:  4.7369 -  3.7784  1386   155  0.95   8.85   1.01     1.00      10244.30|
|  3:  3.7784 -  3.3062  1356   147  0.92  13.35   1.03     1.03      12923.20|
|  4:  3.3062 -  3.0064  1344   154  0.89  16.85   1.01     0.99      13800.16|
|  5:  3.0064 -  2.7923  1334   152  0.87  19.62   1.00     0.98      11929.10|
|  6:  2.7923 -  2.6286  1346   146  0.86  20.33   0.98     0.94      10010.93|
|  7:  2.6286 -  2.4975  1322   142  0.87  19.11   0.99     0.95       8763.92|
|  8:  2.4975 -  2.3892  1315   155  0.87  19.62   0.99     0.96       7605.20|
|  9:  2.3892 -  2.2976  1311   145  0.87  19.48   0.99     0.94       7049.20|
| 10:  2.2976 -  2.2185  1333   145  0.87  19.14   1.00     0.95       5970.45|
| 11:  2.2185 -  2.1494  1306   143  0.87  19.37   0.99     0.93       5838.18|
| 12:  2.1494 -  2.0881  1308   142  0.88  18.79   1.00     0.99       5137.75|
| 13:  2.0881 -  2.0332  1228   139  0.86  20.34   0.99     0.96       4609.05|
| 14:  2.0332 -  1.9837   307    36  0.89  17.36   0.97     0.93       3727.42|
|alpha:            min =        0.93 max =            1.03 mean =         0.97|
|beta:             min =     3727.42 max =        13800.16 mean =      8547.30|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.76 mean =        17.16|
|phase err.(test): min =        0.00 max =           89.71 mean =        16.43|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1304   r_free= 0.1829   ksol= 0.33   Bsol= 71.61   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.38,-0.86,1.24,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.287711                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1304   r_free= 0.1829   ksol= 0.33   Bsol= 71.61   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.38,-0.86,1.24,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.287711                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3145 -  4.7369 0.99   1434  158 0.0989 0.1326      5.3926      5.5835|
|  2:  4.7369 -  3.7784 0.99   1386  155 0.0900 0.1199      5.4886      5.6988|
|  3:  3.7784 -  3.3062 0.99   1356  147 0.1236 0.1739       5.593      5.9248|
|  4:  3.3062 -  3.0064 0.99   1344  154 0.1430 0.1991      5.5868      5.7786|
|  5:  3.0064 -  2.7923 0.99   1334  152 0.1615 0.2002      5.4995      5.6946|
|  6:  2.7923 -  2.6286 0.99   1346  146 0.1527 0.2428       5.375      5.6573|
|  7:  2.6286 -  2.4975 0.99   1322  142 0.1490 0.1805      5.3133      5.4405|
|  8:  2.4975 -  2.3892 0.98   1315  155 0.1450 0.1982       5.236      5.4736|
|  9:  2.3892 -  2.2976 0.98   1311  145 0.1450 0.2280      5.1991      5.4817|
| 10:  2.2976 -  2.2185 1.00   1333  145 0.1371 0.1822      5.1041      5.2604|
| 11:  2.2185 -  2.1494 0.98   1306  143 0.1345 0.2194      5.0798      5.4615|
| 12:  2.1494 -  2.0881 0.98   1308  142 0.1345 0.1982      4.9959      5.2455|
| 13:  2.0881 -  2.0332 0.93   1228  139 0.1309 0.1873      4.9159      5.1237|
| 14:  2.0332 -  1.9837 0.23    307   36 0.1221 0.1902      4.8317      5.0631|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.3145 -  4.7369  1434   158  0.94   9.36   0.96     0.94       7437.17|
|  2:  4.7369 -  3.7784  1386   155  0.95   8.75   1.01     0.99      10157.19|
|  3:  3.7784 -  3.3062  1356   147  0.92  13.49   1.03     1.03      13065.05|
|  4:  3.3062 -  3.0064  1344   154  0.89  16.87   1.01     0.98      13821.21|
|  5:  3.0064 -  2.7923  1334   152  0.87  19.64   1.00     0.98      11977.39|
|  6:  2.7923 -  2.6286  1346   146  0.86  20.32   0.97     0.93      10006.86|
|  7:  2.6286 -  2.4975  1322   142  0.87  19.11   0.99     0.95       8764.89|
|  8:  2.4975 -  2.3892  1315   155  0.87  19.61   0.99     0.95       7603.19|
|  9:  2.3892 -  2.2976  1311   145  0.87  19.48   0.99     0.94       7056.52|
| 10:  2.2976 -  2.2185  1333   145  0.87  19.12   0.99     0.95       5963.09|
| 11:  2.2185 -  2.1494  1306   143  0.87  19.33   0.99     0.93       5823.37|
| 12:  2.1494 -  2.0881  1308   142  0.88  18.76   0.99     0.99       5125.52|
| 13:  2.0881 -  2.0332  1228   139  0.86  20.33   0.98     0.96       4606.02|
| 14:  2.0332 -  1.9837   307    36  0.89  17.37   0.96     0.93       3727.90|
|alpha:            min =        0.93 max =            1.03 mean =         0.96|
|beta:             min =     3727.90 max =        13821.21 mean =      8529.62|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.81 mean =        17.14|
|phase err.(test): min =        0.00 max =           89.57 mean =        16.38|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.246)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.10    106.24  16.55    None  None   None       |
|    all(noH): 2823   0      1.10    106.24  16.55    None  None   None       |
|    Sol.    : 438    0      4.29    106.24  43.52    None  None   None       |
|    Mac.    : 2385   0      1.10    82.17   11.60    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.101 -  11.615: 1598   |   5:    53.668 -  64.182:   90        |
|      1:    11.615 -  22.128:  673   |   6:    64.182 -  74.695:   44        |
|      2:    22.128 -  32.641:  167   |   7:    74.695 -  85.208:   28        |
|      3:    32.641 -  43.155:  113   |   8:    85.208 -  95.722:    7        |
|      4:    43.155 -  53.668:  102   |   9:    95.722 - 106.235:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 328         
Filter by distance & map next to the model:
   mapped sites are within: 0.491 - 5.219
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 322 from: 328
   mapped sites are within: 0.714 - 5.219

peak=    9.420 closest distance to " CB  VAL A 230 " =    1.438
peak=    8.607 closest distance to " O   HOH Z 103 " =    1.133
peak=    6.928 closest distance to " CG2 VAL A 296 " =    1.328
peak=    6.884 closest distance to " CD2 LEU A   5 " =    1.310
peak=    6.733 closest distance to " O   HOH Z  70 " =    1.238
peak=    6.320 closest distance to " CG  ARG A 138 " =    1.252
peak=    5.473 closest distance to " O   HOH Z 102 " =    1.308
peak=    5.434 closest distance to " NE2 GLN A  11 " =    1.099
peak=    5.336 closest distance to " O   HOH Z 222 " =    1.422
peak=    5.176 closest distance to " O   HOH Z 127 " =    1.288
peak=    5.032 closest distance to " O   HOH Z   7 " =    1.654
peak=    4.980 closest distance to " CG  PRO A  54 " =    1.418
peak=    4.979 closest distance to " CB  GLN A 223 " =    1.555
peak=    4.951 closest distance to " CB  ASN A 148 " =    1.477
peak=    4.914 closest distance to " NH1 ARG A 138 " =    1.116
peak=    4.875 closest distance to " OE1 GLN A  73 " =    2.243
peak=    4.874 closest distance to " CD1AILE A 234 " =    1.097
peak=    4.869 closest distance to " O   HOH Z 427 " =    2.764
peak=    4.848 closest distance to " CB  VAL A 230 " =    1.285
peak=    4.760 closest distance to " O   HOH Z 232 " =    2.177
peak=    4.634 closest distance to " O   HOH Z 130 " =    1.039
peak=    4.633 closest distance to " O   HOH Z 369 " =    2.015
peak=    4.555 closest distance to " O   HOH Z 298 " =    2.199
peak=    4.542 closest distance to " CG  LEU A 228 " =    1.167
peak=    4.528 closest distance to " O   HOH Z   9 " =    2.132
peak=    4.439 closest distance to " NH2 ARG A  56 " =    1.074
peak=    4.423 closest distance to " OE1 GLN A  55 " =    1.143
peak=    4.423 closest distance to " CB  PRO A  54 " =    1.037
peak=    4.347 closest distance to " CB  ASP A 124 " =    0.829
peak=    4.289 closest distance to " O   HOH Z 406 " =    1.635
peak=    4.288 closest distance to " CB  SER A  63 " =    1.335
peak=    4.277 closest distance to " CB  GLN A 183 " =    1.214
peak=    4.277 closest distance to " CZ3 TRP A 266 " =    1.195
peak=    4.272 closest distance to " O   HOH Z 287 " =    2.199
peak=    4.250 closest distance to " O   HOH Z 148 " =    1.476
peak=    4.230 closest distance to " O   HOH Z 183 " =    1.695
peak=    4.229 closest distance to " O   HOH Z 423 " =    1.770
peak=    4.221 closest distance to " O   HOH Z 117 " =    1.103
peak=    4.219 closest distance to " O   HOH Z  69 " =    1.039
peak=    4.218 closest distance to " CG  ASN A  60 " =    1.116
peak=    4.208 closest distance to " CD2 LEU A 228 " =    1.229
peak=    4.174 closest distance to " NH2AARG A 190 " =    1.907
peak=    4.173 closest distance to " NH1AARG A 145 " =    1.215
peak=    4.143 closest distance to " NH1 ARG A  56 " =    1.187
peak=    4.130 closest distance to " CZ  PHE A 218 " =    1.117
peak=    4.114 closest distance to " O   HOH Z 182 " =    1.279
peak=    4.112 closest distance to " O   HOH Z 207 " =    1.338
peak=    4.097 closest distance to " CG  LEU A 167 " =    1.287
peak=    4.081 closest distance to " O   SER A  87 " =    2.397
peak=    4.068 closest distance to " O   HOH Z 273 " =    1.258
peak=    4.041 closest distance to " CB  SER A 216 " =    1.110
peak=    4.034 closest distance to " O   HOH Z 246 " =    1.167
peak=    4.024 closest distance to " O   HOH Z 411 " =    3.005
peak=    4.022 closest distance to " CD  ARG A 159 " =    0.774
peak=    4.014 closest distance to " OE1 GLN A  55 " =    1.373
peak=    4.004 closest distance to " CD  ARG A 138 " =    1.092
peak=    3.999 closest distance to " O   HOH Z 255 " =    1.037
peak=    3.995 closest distance to " CE  LYS A  76 " =    0.925
peak=    3.994 closest distance to " CB  VAL A 202 " =    1.540
peak=    3.982 closest distance to " O   HOH Z 186 " =    1.220
peak=    3.979 closest distance to " CA  VAL A 125 " =    1.189
peak=    3.968 closest distance to " CG  LEU A   5 " =    1.401
peak=    3.958 closest distance to " CG2 ILE A 234 " =    0.943
peak=    3.958 closest distance to " O   HOH Z 111 " =    1.709
peak=    3.933 closest distance to " O   HOH Z 425 " =    1.648
peak=    3.919 closest distance to " O   TYR A 116 " =    1.235
peak=    3.919 closest distance to " CA  ALA A  51 " =    1.069
peak=    3.919 closest distance to " CB  MET A  40 " =    0.849
peak=    3.917 closest distance to " O   HOH Z 112 " =    1.023
peak=    3.905 closest distance to " CB  VAL A 265 " =    1.310
peak=    3.887 closest distance to " CA  ASN A 127 " =    1.139
peak=    3.878 closest distance to " CB  GLU A 277 " =    3.741
peak=    3.868 closest distance to " O   HOH Z 353 " =    2.599
peak=    3.857 closest distance to " CG  LYS A  76 " =    1.738
peak=    3.836 closest distance to " O   HOH Z  53 " =    2.477
peak=    3.820 closest distance to " CG  PRO A 243 " =    1.097
peak=    3.819 closest distance to " O   HOH Z 180 " =    2.210
peak=    3.818 closest distance to " CB  TYR A 169 " =    0.933
peak=    3.815 closest distance to " O   HOH Z 380 " =    1.641
peak=    3.814 closest distance to " CB  ASN A 142 " =    0.932
peak=    3.808 closest distance to " O   HOH Z 251 " =    1.804
peak=    3.798 closest distance to " O   HOH Z 193 " =    1.948
peak=    3.796 closest distance to " CA  LEU A 282 " =    1.155
peak=    3.792 closest distance to " CA  ASP A 124 " =    0.811
peak=    3.789 closest distance to " O   HOH Z 145 " =    1.665
peak=    3.788 closest distance to " CD1 ILE A  33 " =    2.034
peak=    3.787 closest distance to " CE3 TRP A 274 " =    1.350
peak=    3.771 closest distance to " CB  LEU A 237 " =    0.914
peak=    3.764 closest distance to " CG2 THR A 221 " =    1.199
peak=    3.761 closest distance to " O   HOH Z 258 " =    1.767
peak=    3.761 closest distance to " OE2 GLU A   2 " =    2.258
peak=    3.728 closest distance to " O   HOH Z 410 " =    1.596
peak=    3.726 closest distance to " CG BARG A 275 " =    1.339
peak=    3.718 closest distance to " O   HOH Z 148 " =    3.828
peak=    3.702 closest distance to " CD1 LEU A 300 " =    1.123
peak=    3.696 closest distance to " ND2 ASN A 187 " =    1.745
peak=    3.696 closest distance to " O   HOH Z 126 " =    2.129
peak=    3.694 closest distance to " CA  GLY A 267 " =    1.208
peak=    3.684 closest distance to " CA  ARG A 195 " =    1.375
peak=    3.683 closest distance to " O   HOH Z  68 " =    2.088
peak=    3.682 closest distance to " CB  THR A  52 " =    1.029
peak=    3.679 closest distance to " CG  GLU A  37 " =    1.130
peak=    3.679 closest distance to " CA  ARG A  36 " =    1.161
peak=    3.675 closest distance to " CD1 LEU A   5 " =    1.399
peak=    3.671 closest distance to " CB  ASN A  39 " =    0.994
peak=    3.666 closest distance to " O   ASP A 200 " =    1.739
peak=    3.660 closest distance to " NH2AARG A 145 " =    1.118
peak=    3.656 closest distance to " O   HOH Z  49 " =    1.113
peak=    3.656 closest distance to " O   HOH Z  61 " =    1.564
peak=    3.654 closest distance to " CE3 TRP A  85 " =    1.081
peak=    3.651 closest distance to " CG  GLN A  89 " =    1.615
peak=    3.650 closest distance to " O   HOH Z 184 " =    1.604
peak=    3.644 closest distance to " O   HOH Z 193 " =    1.743
peak=    3.639 closest distance to " O   HOH Z 332 " =    1.593
peak=    3.634 closest distance to " N   ALA A 256 " =    1.072
peak=    3.631 closest distance to " O   HOH Z 145 " =    2.233
peak=    3.628 closest distance to " ND2BASN A 224 " =    0.869
peak=    3.626 closest distance to " CD  ARG A 195 " =    3.557
peak=    3.622 closest distance to " CA  TYR A  30 " =    1.057
peak=    3.620 closest distance to " O   HOH Z 290 " =    1.358
peak=    3.585 closest distance to " CD  GLN A 240 " =    1.652
peak=    3.584 closest distance to " N   PHE A 130 " =    1.363
peak=    3.582 closest distance to " O   HOH Z 265 " =    1.865
peak=    3.577 closest distance to " NE2 HIS A 207 " =    1.083
peak=    3.577 closest distance to " O   HOH Z 359 " =    1.522
peak=    3.573 closest distance to " CG1 VAL A 296 " =    1.230
peak=    3.572 closest distance to " CB  ARG A 138 " =    1.364
peak=    3.568 closest distance to " O   HOH Z 303 " =    2.222
peak=    3.561 closest distance to " CB  ASN A 110 " =    1.166
peak=    3.555 closest distance to " CD2 TRP A 179 " =    1.352
peak=    3.547 closest distance to " CB  ARG A 275 " =    1.098
peak=    3.542 closest distance to " O   HOH Z  88 " =    3.804
peak=    3.539 closest distance to " C   GLN A  73 " =    1.087
peak=    3.529 closest distance to " CG  PRO A 213 " =    1.313
peak=    3.526 closest distance to " O   HOH Z  63 " =    1.150
peak=    3.526 closest distance to " CG  GLN A  58 " =    1.287
peak=    3.524 closest distance to " O   PRO A 198 " =    1.553
peak=    3.523 closest distance to " CB  SER A  62 " =    0.885
peak=    3.522 closest distance to " CG2 VAL A 257 " =    0.954
peak=    3.515 closest distance to " C   PRO A  54 " =    0.807
peak=    3.512 closest distance to " OG1 THR A 264 " =    0.821
peak=    3.512 closest distance to " O   HOH Z 167 " =    1.671
peak=    3.512 closest distance to " O   HOH Z 368 " =    2.305
peak=    3.511 closest distance to " ND1 HIS A  81 " =    2.152
peak=    3.510 closest distance to " CB  SER A   3 " =    1.730
peak=    3.504 closest distance to " O   HOH Z 156 " =    2.901
peak=    3.500 closest distance to " CA  GLY A 196 " =    0.958
peak=    3.488 closest distance to " CA  ILE A 234 " =    1.114
peak=    3.486 closest distance to " O   HOH Z 214 " =    2.287
peak=    3.486 closest distance to " NE1 TRP A 274 " =    0.964
peak=    3.484 closest distance to " CD  ARG A  66 " =    2.292
peak=    3.478 closest distance to " CB  ALA A  10 " =    1.023
peak=    3.473 closest distance to " N   TYR A  15 " =    1.127
peak=    3.467 closest distance to " O   HOH Z 126 " =    1.754
peak=    3.463 closest distance to " CB  GLU A 128 " =    1.055
peak=    3.461 closest distance to " CB  ASN A  60 " =    0.856
peak=    3.461 closest distance to " O   HOH Z 392 " =    1.267
peak=    3.458 closest distance to " CA  PRO A  54 " =    1.360
peak=    3.455 closest distance to " CA  ARG A 102 " =    1.090
peak=    3.445 closest distance to " CB  TRP A 179 " =    1.442
peak=    3.437 closest distance to " CD1BILE A 234 " =    1.156
peak=    3.434 closest distance to " CA  ARG A 139 " =    1.157
peak=    3.431 closest distance to " O   HOH Z 427 " =    1.423
peak=    3.428 closest distance to " O   HOH Z  65 " =    1.237
peak=    3.426 closest distance to " CZ3 TRP A 177 " =    1.143
peak=    3.426 closest distance to " CB  GLU A 152 " =    1.111
peak=    3.424 closest distance to " CA  TYR A 116 " =    1.432
peak=    3.420 closest distance to " O   HOH Z  97 " =    1.478
peak=    3.417 closest distance to " O   HOH Z 411 " =    1.453
peak=    3.413 closest distance to " CD BLYS A 290 " =    1.063
peak=    3.412 closest distance to " O   HOH Z 188 " =    2.970
peak=    3.408 closest distance to " CA  ALA A 129 " =    1.325
peak=    3.406 closest distance to " O   HOH Z 361 " =    1.331
peak=    3.402 closest distance to " CZ3 TRP A  92 " =    1.395
peak=    3.398 closest distance to " O   HOH Z 316 " =    3.106
peak=    3.398 closest distance to " NZ  LYS A 119 " =    2.929
peak=    3.397 closest distance to " CA  ASN A  74 " =    1.299
peak=    3.397 closest distance to " CG1 ILE A 151 " =    1.244
peak=    3.396 closest distance to " CE1 TYR A 186 " =    1.245
peak=    3.395 closest distance to " O   HOH Z 437 " =    1.443
peak=    3.395 closest distance to " O   THR A 182 " =    1.481
peak=    3.394 closest distance to " CG2 ILE A  20 " =    1.568
peak=    3.392 closest distance to " O   HOH Z  30 " =    1.838
peak=    3.391 closest distance to " CA  ALA A 184 " =    1.203
peak=    3.386 closest distance to " O   ASN A 209 " =    1.572
peak=    3.386 closest distance to " O   HOH Z  88 " =    3.201
peak=    3.384 closest distance to " OD1 ASP A  65 " =    1.669
peak=    3.384 closest distance to " O   HOH Z 421 " =    2.343
peak=    3.379 closest distance to " CG  PRO A 198 " =    1.285
peak=    3.379 closest distance to " O   HOH Z 185 " =    1.880
peak=    3.377 closest distance to " CB  ASP A 107 " =    1.160
peak=    3.374 closest distance to " O   HOH Z 154 " =    1.965
peak=    3.373 closest distance to " CB  TRP A 266 " =    0.993
peak=    3.373 closest distance to " CB  ALA A   1 " =    4.828
peak=    3.373 closest distance to " O   HOH Z 368 " =    4.339
peak=    3.369 closest distance to " O   HOH Z  71 " =    1.273
peak=    3.363 closest distance to " N   CYS A 260 " =    1.044
peak=    3.362 closest distance to " O   HOH Z  70 " =    2.825
peak=    3.360 closest distance to " O   HOH Z 258 " =    1.175
peak=    3.358 closest distance to " OG  SER A  62 " =    2.719
peak=    3.355 closest distance to " O   HOH Z 346 " =    1.623
peak=    3.352 closest distance to " CZ  PHE A  38 " =    1.253
peak=    3.351 closest distance to " O   HOH Z 357 " =    2.503
peak=    3.351 closest distance to " CD  ARG A 269 " =    0.864
peak=    3.350 closest distance to " O   HOH Z 197 " =    1.830
peak=    3.349 closest distance to " O   HOH Z 203 " =    1.806
peak=    3.349 closest distance to " O   HOH Z 298 " =    2.468
peak=    3.340 closest distance to " O   HOH Z 218 " =    1.722
peak=    3.340 closest distance to " O   HOH Z  10 " =    1.749
peak=    3.338 closest distance to " OG  SER A 135 " =    1.287
peak=    3.335 closest distance to " O   HOH Z 119 " =    1.714
peak=    3.331 closest distance to " O   HOH Z 248 " =    1.091
peak=    3.324 closest distance to " O   HOH Z   4 " =    1.684
peak=    3.324 closest distance to " CB  GLN A  88 " =    1.417
peak=    3.324 closest distance to " CB  ARG A  79 " =    1.218
peak=    3.324 closest distance to " CA  ASP A 162 " =    0.907
peak=    3.323 closest distance to " O   HOH Z  85 " =    1.926
peak=    3.322 closest distance to " O   HOH Z 245 " =    1.259
peak=    3.318 closest distance to " CB  TRP A 150 " =    1.238
peak=    3.318 closest distance to " CB  ALA A 104 " =    0.714
peak=    3.316 closest distance to " O   HOH Z 280 " =    3.084
peak=    3.312 closest distance to " O   HOH Z  57 " =    1.467
peak=    3.311 closest distance to " O   HOH Z   2 " =    1.571
peak=    3.306 closest distance to " CA  MET A 105 " =    0.894
peak=    3.306 closest distance to " NH1 ARG A  14 " =    1.033
peak=    3.306 closest distance to " CD1 ILE A 199 " =    1.016
peak=    3.304 closest distance to " CG  GLN A 144 " =    0.909
peak=    3.300 closest distance to " O   HOH Z 122 " =    1.908
peak=    3.298 closest distance to " O   HOH Z  43 " =    1.166
peak=    3.292 closest distance to " O   HOH Z 172 " =    5.219
peak=    3.288 closest distance to " CA  GLN A  94 " =    0.753
peak=    3.287 closest distance to " CA  ALA A 160 " =    1.138
peak=    3.285 closest distance to " O   HOH Z  77 " =    1.337
peak=    3.281 closest distance to " O   THR A 251 " =    1.213
peak=    3.280 closest distance to " O   HOH Z 234 " =    3.966
peak=    3.278 closest distance to " CA  ARG A 156 " =    1.146
peak=    3.273 closest distance to " CA  ASN A 284 " =    0.999
peak=    3.271 closest distance to " O   MET A 105 " =    1.768
peak=    3.271 closest distance to " O   HOH Z 218 " =    1.597
peak=    3.267 closest distance to " CA  ILE A 263 " =    0.992
peak=    3.261 closest distance to " CB  ALA A  34 " =    1.456
peak=    3.260 closest distance to " O   HOH Z  80 " =    1.669
peak=    3.259 closest distance to " CG1 VAL A 153 " =    0.909
peak=    3.258 closest distance to " CB  ARG A 156 " =    1.390
peak=    3.252 closest distance to " O   HOH Z 303 " =    2.826
peak=    3.251 closest distance to " CB  GLU A 236 " =    1.311
peak=    3.249 closest distance to " O   PRO A 198 " =    1.321
peak=    3.244 closest distance to " O   HOH Z 158 " =    3.010
peak=    3.244 closest distance to " OE1 GLN A 278 " =    1.123
peak=    3.237 closest distance to " O   HOH Z  28 " =    1.415
peak=    3.236 closest distance to " O   HOH Z 124 " =    1.997
peak=    3.236 closest distance to " NZ  LYS A 117 " =    2.875
peak=    3.229 closest distance to " CB  ALA A 114 " =    1.679
peak=    3.229 closest distance to " O   HOH Z 148 " =    2.349
peak=    3.226 closest distance to " O   HOH Z 422 " =    2.724
peak=    3.225 closest distance to " CG2BVAL A  41 " =    1.093
peak=    3.222 closest distance to " O   HOH Z 273 " =    2.662
peak=    3.215 closest distance to " N   ASP A 162 " =    1.223
peak=    3.213 closest distance to " CG  ARG A 269 " =    1.794
peak=    3.213 closest distance to " O   HOH Z 153 " =    3.900
peak=    3.213 closest distance to " CD  LYS A 166 " =    1.364
peak=    3.200 closest distance to " CA  ILE A 106 " =    0.853
peak=    3.199 closest distance to " CH2 TRP A  92 " =    2.280
peak=    3.199 closest distance to " O   HOH Z 110 " =    1.681
peak=    3.198 closest distance to " O   HOH Z 143 " =    1.367
peak=    3.197 closest distance to " O   HOH Z 128 " =    2.164
peak=    3.196 closest distance to " O   HOH Z 334 " =    1.613
peak=    3.196 closest distance to " O   HOH Z  78 " =    1.685
peak=    3.196 closest distance to " CG  LYS A 119 " =    1.101
peak=    3.194 closest distance to " NE2 GLN A  58 " =    4.544
peak=    3.194 closest distance to " N   SER A 271 " =    1.000
peak=    3.192 closest distance to " O   HOH Z 116 " =    0.884
peak=    3.188 closest distance to " O   HOH Z 385 " =    3.741
peak=    3.188 closest distance to " O   HOH Z 172 " =    2.908
peak=    3.185 closest distance to " O   THR A 294 " =    1.148
peak=    3.184 closest distance to " N   GLY A 262 " =    1.173
peak=    3.182 closest distance to " O   HOH Z 342 " =    0.905
peak=    3.177 closest distance to " CB  THR A 235 " =    1.440
peak=    3.175 closest distance to " O   HOH Z 132 " =    2.624
peak=    3.175 closest distance to " O   HOH Z 327 " =    1.490
peak=    3.174 closest distance to " N   SER A 135 " =    1.306
peak=    3.171 closest distance to " CB  GLU A 175 " =    0.957
peak=    3.165 closest distance to " OG  SER A  28 " =    1.491
peak=    3.164 closest distance to " O   HOH Z 211 " =    1.635
peak=    3.160 closest distance to " CB  ARG A 259 " =    1.867
peak=    3.157 closest distance to " CG  MET A 113 " =    1.574
peak=    3.157 closest distance to " N   GLU A 152 " =    1.523
peak=    3.156 closest distance to " O   HOH Z 173 " =    1.817
peak=    3.154 closest distance to " N   TYR A 172 " =    1.099
peak=    3.152 closest distance to " O   HOH Z 174 " =    1.149
peak=    3.151 closest distance to " CB  ALA A  43 " =    1.079
peak=    3.150 closest distance to " O   HOH Z 343 " =    2.893
peak=    3.149 closest distance to " CB  ILE A 120 " =    1.167
peak=    3.145 closest distance to " O   HOH Z 238 " =    1.435
peak=    3.132 closest distance to " O   HOH Z 171 " =    3.076
peak=    3.132 closest distance to " O   HOH Z 329 " =    4.277
peak=    3.132 closest distance to " CG  PRO A  90 " =    1.510
peak=    3.131 closest distance to " O   TRP A  70 " =    1.642
peak=    3.129 closest distance to " O   HOH Z 435 " =    2.472
peak=    3.129 closest distance to " O   PHE A  61 " =    1.511
peak=    3.124 closest distance to " O   HOH Z 116 " =    1.964
peak=    3.122 closest distance to " CE1 HIS A 115 " =    1.070
peak=    3.122 closest distance to " CG  ARG A 159 " =    0.890
peak=    3.119 closest distance to " O   HOH Z 216 " =    3.595
peak=    3.116 closest distance to " O   HOH Z 189 " =    3.906
peak=    3.112 closest distance to " N   ALA A   7 " =    1.258
peak=    3.111 closest distance to " CD2 LEU A 167 " =    1.422
peak=    3.111 closest distance to " CB  ARG A 102 " =    0.924
peak=    3.109 closest distance to " O   HOH Z  59 " =    1.911
peak=    3.106 closest distance to " CB  GLN A  89 " =    1.092
peak=    3.103 closest distance to " O   HOH Z 272 " =    1.797
peak=    3.100 closest distance to " O   HOH Z 434 " =    2.662
peak=    3.098 closest distance to " O   HOH Z 238 " =    3.064
peak=    3.089 closest distance to " OD1 ASN A 217 " =    1.515
peak=    3.087 closest distance to " CA  VAL A 112 " =    1.193
peak=    3.075 closest distance to " O   HOH Z 285 " =    2.085
peak=    3.072 closest distance to " CD  ARG A 195 " =    0.962
peak=    3.058 closest distance to " O   PHE A 192 " =    1.320
peak=    3.034 closest distance to " CA  ALA A 154 " =    1.104
peak=    3.020 closest distance to " O   HOH Z 417 " =    2.914
peak=    3.017 closest distance to " O   HOH Z 281 " =    2.622
peak=    3.007 closest distance to " O   HOH Z 357 " =    2.118

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 232         
Filter by distance & map next to the model:
   mapped sites are within: 0.352 - 5.524
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 229 from: 232
   mapped sites are within: 0.728 - 5.524

peak=   -4.924 closest distance to " CD  ARG A 138 " =    1.302
peak=   -4.802 closest distance to " CG2 VAL A 230 " =    0.895
peak=   -4.514 closest distance to " O   PRO A 198 " =    1.372
peak=   -4.428 closest distance to " OE1 GLN A  88 " =    0.986
peak=   -4.371 closest distance to " CZ2 TRP A  92 " =    2.849
peak=   -4.355 closest distance to " CB  VAL A 230 " =    0.980
peak=   -4.342 closest distance to " CD  ARG A  14 " =    3.183
peak=   -4.271 closest distance to " CD  GLN A  55 " =    1.078
peak=   -4.240 closest distance to " CA  ASP A  27 " =    2.566
peak=   -4.184 closest distance to " CG  ARG A 219 " =    2.446
peak=   -4.178 closest distance to " CG  ARG A 259 " =    2.486
peak=   -4.109 closest distance to " CG  GLN A  88 " =    0.836
peak=   -4.074 closest distance to " O   HOH Z 103 " =    0.945
peak=   -4.064 closest distance to " O   PRO A 163 " =    2.005
peak=   -4.040 closest distance to " O   HOH Z  52 " =    0.889
peak=   -3.994 closest distance to " OE1 GLN A  88 " =    1.078
peak=   -3.972 closest distance to " OG  SER A  97 " =    2.203
peak=   -3.952 closest distance to " O   HOH Z 111 " =    1.595
peak=   -3.901 closest distance to " O   HOH Z 407 " =    3.052
peak=   -3.893 closest distance to " CD1 LEU A 101 " =    2.362
peak=   -3.862 closest distance to " CB  PRO A 163 " =    2.369
peak=   -3.850 closest distance to " O   HOH Z 102 " =    1.322
peak=   -3.845 closest distance to " O   HOH Z  39 " =    0.876
peak=   -3.810 closest distance to " CG2 VAL A 296 " =    1.194
peak=   -3.806 closest distance to " O   SER A 276 " =    1.661
peak=   -3.800 closest distance to " CD  LYS A 289 " =    2.305
peak=   -3.799 closest distance to " CB  ALA A  43 " =    2.718
peak=   -3.746 closest distance to " O   HOH Z 275 " =    1.883
peak=   -3.745 closest distance to " O   HOH Z 364 " =    2.836
peak=   -3.740 closest distance to " O   HOH Z  44 " =    0.923
peak=   -3.731 closest distance to " O   HOH Z 103 " =    0.728
peak=   -3.729 closest distance to " CB  PRO A 243 " =    2.645
peak=   -3.712 closest distance to " CB  TRP A  85 " =    2.476
peak=   -3.707 closest distance to " CA  ASN A 110 " =    1.028
peak=   -3.706 closest distance to " NZ  LYS A 166 " =    1.129
peak=   -3.693 closest distance to " CD  ARG A 156 " =    2.002
peak=   -3.693 closest distance to " CD1 TYR A 247 " =    2.685
peak=   -3.691 closest distance to " OD1 ASN A  60 " =    0.832
peak=   -3.689 closest distance to " OG BSER A 134 " =    1.564
peak=   -3.684 closest distance to " OG  SER A  28 " =    2.062
peak=   -3.671 closest distance to " CB  HIS A  86 " =    1.159
peak=   -3.671 closest distance to " O   HOH Z  69 " =    1.928
peak=   -3.669 closest distance to " CB  ALA A 161 " =    2.718
peak=   -3.660 closest distance to " CD2 HIS A 207 " =    2.125
peak=   -3.654 closest distance to " O   HOH Z 144 " =    1.320
peak=   -3.651 closest distance to " O   HOH Z 389 " =    1.561
peak=   -3.647 closest distance to " O   HOH Z  37 " =    2.182
peak=   -3.639 closest distance to " OE1 GLN A 278 " =    1.191
peak=   -3.638 closest distance to " O   HOH Z  70 " =    1.974
peak=   -3.637 closest distance to " O   HOH Z 100 " =    0.951
peak=   -3.630 closest distance to " OG  SER A 141 " =    1.770
peak=   -3.630 closest distance to " O   HOH Z 359 " =    3.156
peak=   -3.617 closest distance to " O   HOH Z 216 " =    1.191
peak=   -3.605 closest distance to " CG2AVAL A  41 " =    2.809
peak=   -3.602 closest distance to " CE2 TRP A  70 " =    2.472
peak=   -3.598 closest distance to " O   HOH Z 255 " =    1.072
peak=   -3.592 closest distance to " O   HOH Z 166 " =    1.638
peak=   -3.573 closest distance to " O   HOH Z 231 " =    1.999
peak=   -3.558 closest distance to " O   HOH Z 193 " =    1.209
peak=   -3.556 closest distance to " CB  ALA A 129 " =    2.642
peak=   -3.555 closest distance to " CA  GLY A 241 " =    3.023
peak=   -3.555 closest distance to " O   HOH Z 115 " =    1.318
peak=   -3.547 closest distance to " O   HOH Z 377 " =    1.812
peak=   -3.542 closest distance to " CG2 THR A  52 " =    2.859
peak=   -3.538 closest distance to " ND2 ASN A  69 " =    1.700
peak=   -3.537 closest distance to " CD2 LEU A   5 " =    0.925
peak=   -3.536 closest distance to " OG  SER A  87 " =    1.384
peak=   -3.536 closest distance to " C   ALA A 158 " =    1.351
peak=   -3.535 closest distance to " CG  MET A 105 " =    0.998
peak=   -3.535 closest distance to " CG2BVAL A  72 " =    2.247
peak=   -3.534 closest distance to " CB  ALA A   9 " =    2.682
peak=   -3.532 closest distance to " CG  TRP A 266 " =    1.691
peak=   -3.532 closest distance to " O   HOH Z 133 " =    1.818
peak=   -3.529 closest distance to " NH2AARG A 275 " =    5.524
peak=   -3.524 closest distance to " CG2 VAL A 112 " =    2.673
peak=   -3.518 closest distance to " O   HOH Z 394 " =    1.655
peak=   -3.513 closest distance to " O   HOH Z 207 " =    1.239
peak=   -3.510 closest distance to " O   HOH Z 389 " =    2.440
peak=   -3.505 closest distance to " CA  GLY A 133 " =    2.304
peak=   -3.504 closest distance to " O   HOH Z 183 " =    1.471
peak=   -3.504 closest distance to " OD1 ASP A 171 " =    1.552
peak=   -3.499 closest distance to " O   HOH Z  32 " =    1.679
peak=   -3.494 closest distance to " CD2 LEU A 237 " =    2.453
peak=   -3.493 closest distance to " O   HOH Z 145 " =    1.324
peak=   -3.480 closest distance to " CG1 VAL A  78 " =    2.888
peak=   -3.478 closest distance to " O   HOH Z   9 " =    1.515
peak=   -3.474 closest distance to " O   HOH Z 118 " =    1.777
peak=   -3.470 closest distance to " CG2BVAL A  41 " =    2.211
peak=   -3.460 closest distance to " CD1 LEU A   5 " =    2.479
peak=   -3.453 closest distance to " CB  GLN A  55 " =    1.309
peak=   -3.453 closest distance to " O   HOH Z  63 " =    1.877
peak=   -3.452 closest distance to " O   HOH Z 198 " =    2.128
peak=   -3.451 closest distance to " O   HOH Z  11 " =    1.750
peak=   -3.443 closest distance to " CG1 VAL A 250 " =    2.599
peak=   -3.443 closest distance to " O   HOH Z 231 " =    0.729
peak=   -3.420 closest distance to " O   GLY A 203 " =    2.563
peak=   -3.407 closest distance to " C   LEU A 222 " =    1.210
peak=   -3.406 closest distance to " O   PHE A 218 " =    1.573
peak=   -3.405 closest distance to " O   HOH Z 177 " =    2.697
peak=   -3.405 closest distance to " O   HOH Z 118 " =    1.144
peak=   -3.402 closest distance to " O   HOH Z 149 " =    2.102
peak=   -3.401 closest distance to " O   HOH Z 112 " =    0.974
peak=   -3.399 closest distance to " C   ASN A 285 " =    2.480
peak=   -3.396 closest distance to " CG1BVAL A  72 " =    2.368
peak=   -3.394 closest distance to " O   HOH Z 350 " =    1.836
peak=   -3.393 closest distance to " O   HOH Z 368 " =    1.430
peak=   -3.392 closest distance to " O   ASP A  27 " =    1.793
peak=   -3.388 closest distance to " CE1 TYR A 169 " =    2.634
peak=   -3.387 closest distance to " CE2 TYR A  30 " =    2.642
peak=   -3.387 closest distance to " CG1 VAL A 296 " =    1.509
peak=   -3.385 closest distance to " O   HOH Z 351 " =    1.499
peak=   -3.382 closest distance to " CE3 TRP A 150 " =    2.434
peak=   -3.376 closest distance to " O   HOH Z 286 " =    1.637
peak=   -3.373 closest distance to " OE1 GLN A  89 " =    1.663
peak=   -3.372 closest distance to " CG2 VAL A 202 " =    2.810
peak=   -3.362 closest distance to " CB  ASP A 200 " =    2.613
peak=   -3.362 closest distance to " O   HOH Z 426 " =    1.698
peak=   -3.361 closest distance to " CG1 VAL A  78 " =    2.404
peak=   -3.360 closest distance to " O   SER A 271 " =    2.078
peak=   -3.360 closest distance to " CA  ARG A  56 " =    1.010
peak=   -3.360 closest distance to " CZ  TYR A 169 " =    1.840
peak=   -3.357 closest distance to " O   HOH Z  60 " =    1.224
peak=   -3.355 closest distance to " CE BMET A  47 " =    1.348
peak=   -3.348 closest distance to " CB  ALA A 161 " =    1.667
peak=   -3.348 closest distance to " CD2 TYR A 293 " =    1.991
peak=   -3.344 closest distance to " OD1 ASN A 173 " =    1.117
peak=   -3.342 closest distance to " ND2 ASN A 285 " =    2.161
peak=   -3.342 closest distance to " CA  GLY A 241 " =    2.452
peak=   -3.341 closest distance to " O   HOH Z 434 " =    1.746
peak=   -3.338 closest distance to " O   HOH Z 435 " =    2.264
peak=   -3.337 closest distance to " CG  GLU A 277 " =    1.316
peak=   -3.334 closest distance to " OG BSER A 134 " =    1.874
peak=   -3.334 closest distance to " CB  ALA A 227 " =    2.396
peak=   -3.332 closest distance to " OG  SER A  62 " =    4.351
peak=   -3.332 closest distance to " CG  ARG A 269 " =    2.330
peak=   -3.331 closest distance to " O   HOH Z 201 " =    1.710
peak=   -3.321 closest distance to " O   HOH Z  68 " =    1.390
peak=   -3.316 closest distance to " O   PRO A 243 " =    2.449
peak=   -3.311 closest distance to " C   ASN A 176 " =    1.355
peak=   -3.305 closest distance to " CG  LEU A   5 " =    0.982
peak=   -3.304 closest distance to " CG AMET A  47 " =    1.050
peak=   -3.301 closest distance to " O   GLY A  80 " =    2.601
peak=   -3.301 closest distance to " CG1 VAL A 125 " =    2.392
peak=   -3.300 closest distance to " CA  GLY A  98 " =    1.985
peak=   -3.300 closest distance to " CG  ARG A 138 " =    0.868
peak=   -3.299 closest distance to " CD1 LEU A 255 " =    3.045
peak=   -3.297 closest distance to " N   ASP A 132 " =    2.083
peak=   -3.297 closest distance to " NE2 GLN A 240 " =    1.381
peak=   -3.293 closest distance to " O   HOH Z 100 " =    0.897
peak=   -3.293 closest distance to " CB  ASP A 132 " =    2.419
peak=   -3.289 closest distance to " CA  SER A  62 " =    2.710
peak=   -3.281 closest distance to " O   HOH Z 368 " =    1.721
peak=   -3.279 closest distance to " CD2 LEU A 143 " =    2.491
peak=   -3.277 closest distance to " CA  ASP A 298 " =    1.093
peak=   -3.276 closest distance to " O   HOH Z  10 " =    1.536
peak=   -3.263 closest distance to " ND2 ASN A  60 " =    4.024
peak=   -3.260 closest distance to " O   ARG A  56 " =    4.444
peak=   -3.254 closest distance to " N   ASP A 270 " =    1.512
peak=   -3.254 closest distance to " O   HOH Z 166 " =    2.163
peak=   -3.253 closest distance to " OD2 ASP A  50 " =    1.757
peak=   -3.252 closest distance to " NE2 HIS A  86 " =    2.244
peak=   -3.248 closest distance to " O   HOH Z 128 " =    2.599
peak=   -3.247 closest distance to " C   HIS A 108 " =    1.205
peak=   -3.246 closest distance to " CE3 TRP A  70 " =    1.722
peak=   -3.243 closest distance to " N   THR A 157 " =    1.532
peak=   -3.242 closest distance to " CB  PRO A  54 " =    2.518
peak=   -3.242 closest distance to " O   HOH Z 219 " =    4.518
peak=   -3.242 closest distance to " CD1 ILE A 151 " =    1.888
peak=   -3.235 closest distance to " O   HOH Z 238 " =    0.948
peak=   -3.235 closest distance to " O   HOH Z 385 " =    1.998
peak=   -3.234 closest distance to " O   HOH Z 244 " =    1.903
peak=   -3.233 closest distance to " CB  ALA A 291 " =    2.122
peak=   -3.232 closest distance to " C   GLU A   2 " =    1.884
peak=   -3.231 closest distance to " CA  GLY A  91 " =    2.215
peak=   -3.230 closest distance to " CG2 ILE A  20 " =    2.753
peak=   -3.226 closest distance to " O   HOH Z 155 " =    1.106
peak=   -3.225 closest distance to " O   HOH Z 139 " =    1.014
peak=   -3.222 closest distance to " ND2 ASN A 173 " =    1.920
peak=   -3.218 closest distance to " O   HOH Z 412 " =    4.586
peak=   -3.218 closest distance to " O   HOH Z 118 " =    1.064
peak=   -3.218 closest distance to " O   HOH Z 236 " =    1.364
peak=   -3.217 closest distance to " NE2 GLN A 223 " =    1.502
peak=   -3.216 closest distance to " N   SER A 212 " =    1.985
peak=   -3.215 closest distance to " CB  PHE A 130 " =    1.221
peak=   -3.214 closest distance to " O   HOH Z 292 " =    1.577
peak=   -3.210 closest distance to " O   HOH Z 410 " =    2.161
peak=   -3.200 closest distance to " CD  GLN A  58 " =    1.130
peak=   -3.197 closest distance to " CB  ALA A 100 " =    2.141
peak=   -3.193 closest distance to " O   HOH Z 275 " =    1.628
peak=   -3.189 closest distance to " O   HOH Z 341 " =    1.040
peak=   -3.188 closest distance to " O   HOH Z 252 " =    3.750
peak=   -3.184 closest distance to " C   ASN A 148 " =    1.701
peak=   -3.183 closest distance to " CD1 ILE A 199 " =    2.528
peak=   -3.178 closest distance to " O   TYR A  30 " =    2.514
peak=   -3.177 closest distance to " O   HOH Z 251 " =    4.682
peak=   -3.174 closest distance to " CD  PRO A 243 " =    1.989
peak=   -3.170 closest distance to " OE1 GLN A 223 " =    2.234
peak=   -3.163 closest distance to " O   ALA A  84 " =    1.686
peak=   -3.161 closest distance to " O   ASP A 253 " =    1.768
peak=   -3.161 closest distance to " CG  PRO A 213 " =    1.978
peak=   -3.160 closest distance to " O   LYS A 117 " =    1.938
peak=   -3.152 closest distance to " O   HOH Z 131 " =    3.964
peak=   -3.151 closest distance to " O   HOH Z 281 " =    2.782
peak=   -3.151 closest distance to " CD2 TRP A  85 " =    1.179
peak=   -3.148 closest distance to " NH2 ARG A  79 " =    2.127
peak=   -3.145 closest distance to " O   HOH Z 241 " =    1.477
peak=   -3.140 closest distance to " CE1 PHE A  16 " =    2.686
peak=   -3.135 closest distance to " OD1 ASP A 107 " =    1.088
peak=   -3.131 closest distance to " OG  SER A 245 " =    1.491
peak=   -3.129 closest distance to " NE2 GLN A  11 " =    1.666
peak=   -3.126 closest distance to " O   HOH Z  77 " =    1.596
peak=   -3.119 closest distance to " O   HOH Z 257 " =    1.539
peak=   -3.118 closest distance to " CE2 PHE A 218 " =    2.535
peak=   -3.116 closest distance to " CD  GLN A  77 " =    1.117
peak=   -3.112 closest distance to " CA  GLY A 133 " =    2.064
peak=   -3.112 closest distance to " CG  LEU A 282 " =    2.607
peak=   -3.095 closest distance to " O   HOH Z 171 " =    0.962
peak=   -3.092 closest distance to " OH  TYR A 172 " =    1.735
peak=   -3.083 closest distance to " O   HOH Z 313 " =    1.641
peak=   -3.078 closest distance to " C   PHE A  59 " =    1.058
peak=   -3.074 closest distance to " O   SER A  22 " =    2.761
peak=   -3.074 closest distance to " NH2 ARG A  56 " =    0.900
peak=   -3.069 closest distance to " CG  GLN A  88 " =    1.358
peak=   -3.058 closest distance to " O   HOH Z 116 " =    4.008
peak=   -3.049 closest distance to " O   HOH Z  69 " =    1.698
peak=   -3.048 closest distance to " O   HOH Z 387 " =    1.142
peak=   -3.045 closest distance to " O   HOH Z 250 " =    1.681
peak=   -3.032 closest distance to " CD2 PHE A  16 " =    2.382
peak=   -3.025 closest distance to " NZ  LYS A 166 " =    1.212

================= 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    :  0.5026 0.4939   6.301474e+00   6.287949e+00
   1_bss:  0.4951 0.4842   6.297987e+00   6.283214e+00
   1_xyz:  0.4256 0.4455   6.216123e+00   6.237402e+00
   1_adp:  0.3792 0.4338   6.151516e+00   6.224290e+00
   1_occ:  0.3784 0.4343   6.151329e+00   6.225560e+00
   2_bss:  0.3768 0.4317   6.152411e+00   6.224875e+00
   2_xyz:  0.3077 0.3705   5.992668e+00   6.121000e+00
   2_adp:  0.2896 0.3529   5.952920e+00   6.088316e+00
   2_occ:  0.2894 0.3526   5.952421e+00   6.087693e+00
   3_bss:  0.2883 0.3516   5.953654e+00   6.088467e+00
   3_xyz:  0.2274 0.2911   5.760727e+00   5.941934e+00
   3_adp:  0.2036 0.2666   5.678198e+00   5.874044e+00
   3_occ:  0.2034 0.2667   5.677922e+00   5.873925e+00
   4_bss:  0.2034 0.2662   5.678728e+00   5.873801e+00
   4_xyz:  0.1705 0.2307   5.523476e+00   5.741603e+00
   4_adp:  0.1640 0.2209   5.483731e+00   5.693961e+00
   4_occ:  0.1640 0.2208   5.483068e+00   5.693023e+00
   5_bss:  0.1641 0.2206   5.483595e+00   5.692688e+00
   5_xyz:  0.1368 0.1878   5.327265e+00   5.555737e+00
   5_adp:  0.1301 0.1830   5.287637e+00   5.522605e+00
   5_occ:  0.1301 0.1830   5.287296e+00   5.522295e+00
   5_bss:  0.1304 0.1829   5.287711e+00   5.521583e+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:  0.322  35.485   7.897   6.734  10.723   0.000   0.000   0.000
   1_xyz:  0.322  35.485   7.897   6.734  10.723   0.000   0.000   0.000
   1_adp:  0.322  35.485   7.897   6.734  10.723   0.000   0.000   0.000
   1_occ:  0.322  35.485   7.897   6.734  10.723   0.000   0.000   0.000
   2_bss:  0.311  41.796   4.639   3.606   7.142   0.000   0.000   0.000
   2_xyz:  0.311  41.796   4.639   3.606   7.142   0.000   0.000   0.000
   2_adp:  0.311  41.796   4.639   3.606   7.142   0.000   0.000   0.000
   2_occ:  0.311  41.796   4.639   3.606   7.142   0.000   0.000   0.000
   3_bss:  0.315  56.980   2.302   1.614   4.663   0.000   0.000   0.000
   3_xyz:  0.315  56.980   2.302   1.614   4.663   0.000   0.000   0.000
   3_adp:  0.315  56.980   2.302   1.614   4.663   0.000   0.000   0.000
   3_occ:  0.315  56.980   2.302   1.614   4.663   0.000   0.000   0.000
   4_bss:  0.330  70.504   1.327   0.776   3.290   0.000   0.000   0.000
   4_xyz:  0.330  70.504   1.327   0.776   3.290   0.000   0.000   0.000
   4_adp:  0.330  70.504   1.327   0.776   3.290   0.000   0.000   0.000
   4_occ:  0.330  70.504   1.327   0.776   3.290   0.000   0.000   0.000
   5_bss:  0.332  70.504   0.770   0.319   2.550   0.000   0.000   0.000
   5_xyz:  0.332  70.504   0.770   0.319   2.550   0.000   0.000   0.000
   5_adp:  0.332  70.504   0.770   0.319   2.550   0.000   0.000   0.000
   5_occ:  0.332  70.504   0.770   0.319   2.550   0.000   0.000   0.000
   5_bss:  0.325  71.605  -0.376  -0.862   1.237   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  61.478 0.3741  0.4412    76766.422
   1_bss:  60.944 0.3806  0.5731    75777.272
   1_xyz:  52.796 0.4843  0.7110    59684.070
   1_adp:  50.054 0.5192  0.8350    56482.764
   1_occ:  50.240 0.5169  0.8298    56812.872
   2_bss:  50.101 0.5184  0.7435    56509.139
   2_xyz:  40.682 0.6331  0.8862    38411.166
   2_adp:  37.947 0.6664  0.9284    34714.628
   2_occ:  37.939 0.6664  0.9278    34637.942
   3_bss:  37.891 0.6671  0.8594    34689.783
   3_xyz:  30.000 0.7569  0.9503    22650.484
   3_adp:  27.007 0.7901  0.9642    18975.732
   3_occ:  27.030 0.7898  0.9631    18960.832
   4_bss:  27.008 0.7901  0.9289    18974.084
   4_xyz:  22.752 0.8340  0.9636    13870.338
   4_adp:  21.289 0.8492  0.9678    12642.083
   4_occ:  21.269 0.8494  0.9679    12610.777
   5_bss:  21.243 0.8496  0.9487    12598.846
   5_xyz:  17.811 0.8820  0.9691     9156.892
   5_adp:  17.093 0.8885  0.9664     8557.187
   5_occ:  17.083 0.8886  0.9663     8548.129
   5_bss:  17.067 0.8887  0.9622     8530.459
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.090   5.4414e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.090   5.4414e+01
   1_xyz:   1.797  0.015  0.113 18.450  0.007  4.108   1.5761e-01
   1_adp:   1.797  0.015  0.113 18.450  0.007  4.108   1.5761e-01
   1_occ:   1.797  0.015  0.113 18.450  0.007  4.108   1.5761e-01
   2_bss:   1.797  0.015  0.113 18.450  0.007  4.108   1.5761e-01
   2_xyz:   1.198  0.009  0.083 16.550  0.005  4.109   9.6450e-02
   2_adp:   1.198  0.009  0.083 16.550  0.005  4.109   9.6450e-02
   2_occ:   1.198  0.009  0.083 16.550  0.005  4.109   9.6450e-02
   3_bss:   1.198  0.009  0.083 16.550  0.005  4.109   9.6450e-02
   3_xyz:   1.124  0.008  0.083 15.872  0.004  4.128   7.2058e-02
   3_adp:   1.124  0.008  0.083 15.872  0.004  4.128   7.2058e-02
   3_occ:   1.124  0.008  0.083 15.872  0.004  4.128   7.2058e-02
   4_bss:   1.124  0.008  0.083 15.872  0.004  4.128   7.2058e-02
   4_xyz:   0.938  0.007  0.069 15.485  0.003  4.138   5.7928e-02
   4_adp:   0.938  0.007  0.069 15.485  0.003  4.138   5.7928e-02
   4_occ:   0.938  0.007  0.069 15.485  0.003  4.138   5.7928e-02
   5_bss:   0.938  0.007  0.069 15.485  0.003  4.138   5.7928e-02
   5_xyz:   1.186  0.011  0.090 15.662  0.004  4.132   8.5849e-02
   5_adp:   1.186  0.011  0.090 15.662  0.004  4.132   8.5849e-02
   5_occ:   1.186  0.011  0.090 15.662  0.004  4.132   8.5849e-02
   5_bss:   1.186  0.011  0.090 15.662  0.004  4.132   8.5849e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0551e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0551e+00
   1_xyz:  14.869  0.183  0.459 86.087  0.045  2.196   1.1236e-01
   1_adp:  14.869  0.183  0.459 86.087  0.045  2.196   1.1236e-01
   1_occ:  14.869  0.183  0.459 86.087  0.045  2.196   1.1236e-01
   2_bss:  14.869  0.183  0.459 86.087  0.045  2.196   1.1236e-01
   2_xyz:   6.866  0.060  0.293 81.931  0.048  2.220   2.0282e-01
   2_adp:   6.866  0.060  0.293 81.931  0.048  2.220   2.0282e-01
   2_occ:   6.866  0.060  0.293 81.931  0.048  2.220   2.0282e-01
   3_bss:   6.866  0.060  0.293 81.931  0.048  2.220   2.0282e-01
   3_xyz:   8.437  0.063  0.329 82.431  0.033  2.338   6.4052e-02
   3_adp:   8.437  0.063  0.329 82.431  0.033  2.338   6.4052e-02
   3_occ:   8.437  0.063  0.329 82.431  0.033  2.338   6.4052e-02
   4_bss:   8.437  0.063  0.329 82.431  0.033  2.338   6.4052e-02
   4_xyz:   7.887  0.046  0.234 83.077  0.040  2.335   7.0550e-02
   4_adp:   7.887  0.046  0.234 83.077  0.040  2.335   7.0550e-02
   4_occ:   7.887  0.046  0.234 83.077  0.040  2.335   7.0550e-02
   5_bss:   7.887  0.046  0.234 83.077  0.040  2.335   7.0550e-02
   5_xyz:   8.835  0.088  0.456 84.186  0.037  2.288   8.1029e-02
   5_adp:   8.835  0.088  0.456 84.186  0.037  2.288   8.1029e-02
   5_occ:   8.835  0.088  0.456 84.186  0.037  2.288   8.1029e-02
   5_bss:   8.835  0.088  0.456 84.186  0.037  2.288   8.1029e-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:  91.58   0.00  16.66  79.63   0.00  14.40  91.58   0.00  28.94
   1_occ:  91.58   0.00  16.66  79.63   0.00  14.40  91.58   0.00  28.94
   2_bss:  91.58   0.00  16.66  79.63   0.00  14.40  91.58   0.00  28.94
   2_xyz:  91.58   0.00  16.66  79.63   0.00  14.40  91.58   0.00  28.94
   2_adp:  92.82   0.00  15.96  80.35   0.00  12.91  92.82   0.00  32.55
   2_occ:  92.82   0.00  15.96  80.35   0.00  12.91  92.82   0.00  32.55
   3_bss:  92.82   0.00  15.96  80.35   0.00  12.91  92.82   0.00  32.55
   3_xyz:  92.82   0.00  15.96  80.35   0.00  12.91  92.82   0.00  32.55
   3_adp:  90.69   0.00  15.79  86.65   0.00  11.33  90.69   0.00  40.03
   3_occ:  90.69   0.00  15.79  86.65   0.00  11.33  90.69   0.00  40.03
   4_bss:  90.69   0.00  15.79  86.65   0.00  11.33  90.69   0.00  40.03
   4_xyz:  90.69   0.00  15.79  86.65   0.00  11.33  90.69   0.00  40.03
   4_adp:  89.26   0.00  15.24  84.56   0.00  10.69  89.26   2.17  40.03
   4_occ:  89.26   0.00  15.24  84.56   0.00  10.69  89.26   2.17  40.03
   5_bss:  89.26   0.00  15.24  84.56   0.00  10.69  89.26   2.17  40.03
   5_xyz:  89.26   0.00  15.24  84.56   0.00  10.69  89.26   2.17  40.03
   5_adp: 105.13   0.00  15.45  81.06   0.00  10.50 105.13   3.19  42.41
   5_occ: 105.13   0.00  15.45  81.06   0.00  10.50 105.13   3.19  42.41
   5_bss: 106.24   1.10  16.55  82.17   1.10  11.60 106.24   4.29  43.52
------------------------------------------------------------------------
 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:    1.260    0.022    0.416
   1_adp:    1.260    0.022    0.416
   1_occ:    1.260    0.022    0.416
   2_bss:    1.260    0.022    0.416
   2_xyz:    1.722    0.030    0.575
   2_adp:    1.722    0.030    0.575
   2_occ:    1.722    0.030    0.575
   3_bss:    1.722    0.030    0.575
   3_xyz:    1.604    0.061    0.678
   3_adp:    1.604    0.061    0.678
   3_occ:    1.604    0.061    0.678
   4_bss:    1.604    0.061    0.678
   4_xyz:    1.762    0.030    0.751
   4_adp:    1.762    0.030    0.751
   4_occ:    1.762    0.030    0.751
   5_bss:    1.762    0.030    0.751
   5_xyz:    1.834    0.047    0.799
   5_adp:    1.834    0.047    0.799
   5_occ:    1.834    0.047    0.799
   5_bss:    1.834    0.047    0.799
------------------------------------------------------------------------

CPU time actual refinement: 359.77


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1132/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_1132/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1132/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1132/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1132/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 359.62 
  Macro-tasks:
    bulk solvent and scale       = 36.15  
    individual site refinement   = 154.73 
    weights calculation          = 32.86  
    collect and process          = 6.36   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 230.21 
  Micro-tasks:
    mask                            = 3.14   
    f_calc                          = 117.56 
    alpha_beta                      = 8.39   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 127.71 
    fmodel                         = 6.68   
    r_factors                      = 0.19   
    phase_errors                   = 10.12  
    foms                           = 0.30   
    TOTAL for micro-tasks          = 275.25 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 5.041 micro seconds
Total CPU time: 6.22 minutes
from_scatterers_fft:    654 calls, 117.24 s
gradients_fft:          600 calls, 114.08 s

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

# Date 2008-01-16 Time 03:16:09 PST -0800 (1200482169.62 s)
Start R-work = 0.5026, R-free = 0.4939 (no bulk solvent and anisotropic scale)
Final R-work = 0.1466, R-free = 0.2003 (no bulk solvent and anisotropic scale)

Start R-work = 0.4951, R-free = 0.4842
Final R-work = 0.1304, R-free = 0.1829