# Date 2008-01-16 Time 01:44:26 PST -0800 (1200476666.40 s)
#phil __OFF__

Command line arguments: "../535.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 3494
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 535

-------------------------------------------------------------------------------
  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: (69.8988, 46.6953, 87.2539, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.29, per 1000 atoms: 1.17


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 46.6953, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.979 1.99025
Completeness in resolution range: 0.971918
Completeness with d_max=infinity: 0.968889

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9790
                             d_min =   1.9903

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 46.6953, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.979 1.99025
Completeness in resolution range: 0.971918
Completeness with d_max=infinity: 0.968889

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9794 -  4.2581 [2124/2148]  1909   215  10.1%
  bin  2:  4.2581 -  3.3927 [2032/2052]  1833   199   9.8%
  bin  3:  3.3927 -  2.9676 [2010/2029]  1809   201  10.0%
  bin  4:  2.9676 -  2.6980 [1968/1998]  1767   201  10.2%
  bin  5:  2.6980 -  2.5056 [1992/2011]  1793   199  10.0%
  bin  6:  2.5056 -  2.3585 [1967/1992]  1772   195   9.9%
  bin  7:  2.3585 -  2.2408 [1946/1974]  1751   195  10.0%
  bin  8:  2.2408 -  2.1435 [1960/1996]  1765   195   9.9%
  bin  9:  2.1435 -  2.0612 [1929/1971]  1734   195  10.1%
  bin 10:  2.0612 -  1.9903 [1661/1984]  1497   164   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_535/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: 2192
        3.04 -     3.66: 4677
        3.66 -     4.28: 9042
        4.28 -     4.90: 12362
  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
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.873 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 183 "  2.042 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  2.165 3.040 -x+1,y+1/2,-z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  ... (remaining 28287 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_535/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_535/model_refine_001.geo

CPU time processing inputs: 9.18


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.89875 46.69535 87.2539 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  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: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4287   r_free= 0.4121   ksol= 0.00   Bsol= 0.00   scale= 0.825    |
|                                                                             |
| 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:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.220458                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9794 -  4.7490 0.99   1382  152 0.3593 0.3355      6.5167      6.4429|
|  2:  4.7490 -  3.7895 0.99   1312  151 0.3150 0.3239      6.6061      6.6634|
|  3:  3.7895 -  3.3164 0.99   1299  141 0.3665 0.3323      6.5434      6.5165|
|  4:  3.3164 -  3.0159 0.99   1296  141 0.4092 0.3846        6.45      6.3758|
|  5:  3.0159 -  2.8012 0.99   1269  144 0.4392 0.4563      6.3056      6.3203|
|  6:  2.8012 -  2.6370 0.99   1286  144 0.4474 0.5036      6.2242      6.1981|
|  7:  2.6370 -  2.5056 0.99   1267  142 0.4721 0.4684      6.2017      6.1655|
|  8:  2.5056 -  2.3970 0.98   1271  137 0.4814 0.4386      6.1551      6.1445|
|  9:  2.3970 -  2.3051 0.98   1248  142 0.4769 0.4621      6.0776      6.0946|
| 10:  2.3051 -  2.2258 1.00   1275  139 0.5051 0.4230      6.1239      6.0036|
| 11:  2.2258 -  2.1564 0.97   1248  138 0.4927 0.4455      6.0269      5.9927|
| 12:  2.1564 -  2.0949 0.98   1252  139 0.5046 0.4554      5.9719      5.9777|
| 13:  2.0949 -  2.0399 0.99   1250  139 0.4877 0.4822      5.8803      5.8408|
| 14:  2.0399 -  1.9903 0.77    975  110 0.5026 0.4686      5.8523      5.7263|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9794 -  4.7490  1382   152  0.75  30.26   0.81     0.77      56481.81|
|  2:  4.7490 -  3.7895  1312   151  0.78  27.60   0.92     0.83      69696.83|
|  3:  3.7895 -  3.3164  1299   141  0.72  33.35   0.89     0.81      73063.63|
|  4:  3.3164 -  3.0159  1296   141  0.65  39.31   0.83     0.71      67335.82|
|  5:  3.0159 -  2.8012  1269   144  0.56  47.41   0.79     0.63      61845.59|
|  6:  2.8012 -  2.6370  1286   144  0.52  50.47   0.76     0.58      57517.68|
|  7:  2.6370 -  2.5056  1267   142  0.49  52.66   0.76     0.56      53616.62|
|  8:  2.5056 -  2.3970  1271   137  0.50  52.15   0.76     0.57      47303.63|
|  9:  2.3970 -  2.3051  1248   142  0.54  49.30   0.75     0.61      40172.20|
| 10:  2.3051 -  2.2258  1275   139  0.55  48.66   0.78     0.62      34720.05|
| 11:  2.2258 -  2.1564  1248   138  0.54  48.94   0.76     0.62      32341.71|
| 12:  2.1564 -  2.0949  1252   139  0.50  52.31   0.79     0.60      32072.67|
| 13:  2.0949 -  2.0399  1250   139  0.48  53.60   0.76     0.56      28867.99|
| 14:  2.0399 -  1.9903   975   110  0.50  52.26   0.75     0.53      23369.04|
|alpha:            min =        0.53 max =            0.83 mean =         0.65|
|beta:             min =    23369.04 max =        73063.63 mean =     49119.24|
|figures of merit: min =        0.00 max =            1.00 mean =         0.58|
|phase err.(work): min =        0.00 max =           89.99 mean =        45.29|
|phase err.(test): min =        0.00 max =           89.87 mean =        45.44|
|-----------------------------------------------------------------------------|

============================== 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 = 6.779067              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 75.083   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.581089              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.142   (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:       25 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      171 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      681 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1493 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2637 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3921 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5081 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6567 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7739 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.728 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.092    4.900  1.196 |       1.723 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.883)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 11.883)------------------------------------------|
|    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: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4389   r_free= 0.4185   ksol= 0.00   Bsol= 0.00   scale= 0.793    |
|                                                                             |
| 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:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.227465                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4212   r_free= 0.4016   ksol= 0.34   Bsol= 15.74   scale= 1.030   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.24,8.35,9.72,0.00,0.00,0.00); trace/3= 8.44                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.214938                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.205944              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 76.966   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.539574              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 75.158   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4212      final r-factor (work) = 0.3079          |
| start r-factor (free) = 0.4016      final r-factor (free) = 0.3254          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 73.0779 = 6.21 * 0.50 * 6.2360 + 1.00 * 53.7278                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.8795 = 6.21 * 0.50 * 6.0475 + 1.00 * 0.1143                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3079      final r-factor (work) = 0.2411          |
| start r-factor (free) = 0.3254      final r-factor (free) = 0.2755          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2778 = 0.54 * 1.00 * 6.0475 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1638 = 0.54 * 1.00 * 5.8430 + 1.00 * 0.0110                               |
|-----------------------------------------------------------------------------|
| number of iterations = 19      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.883)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    51.98   10.43    None  None   None       |
|    all(noH): 2823   0      0.00    51.98   10.43    None  None   None       |
|    Sol.    : 438    0      0.00    51.98   27.17    None  None   None       |
|    Mac.    : 2385   0      0.00    49.60   7.35     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   5.198: 1123   |   5:    25.989 -  31.186:  104        |
|      1:     5.198 -  10.395:  771   |   6:    31.186 -  36.384:  100        |
|      2:    10.395 -  15.593:  334   |   7:    36.384 -  41.582:   55        |
|      3:    15.593 -  20.791:  168   |   8:    41.582 -  46.779:   37        |
|      4:    20.791 -  25.989:  114   |   9:    46.779 -  51.977:   17        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2411 r_free = 0.2755             target_work(ml) = 5.771         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2405 r_free = 0.2753             target_work(ml) = 5.770         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2405   r_free= 0.2753   ksol= 0.34   Bsol= 15.74   scale= 1.098   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.24,8.35,9.72,0.00,0.00,0.00); trace/3= 8.44                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.769531                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2343   r_free= 0.2687   ksol= 0.33   Bsol= 39.93   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.70,4.20,6.05,0.00,0.00,0.00); trace/3= 4.65                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.766663                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.542490              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.501   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.300581              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 124.113  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2343      final r-factor (work) = 0.1604          |
| start r-factor (free) = 0.2687      final r-factor (free) = 0.1982          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5648 = 2.54 * 0.50 * 5.8611 + 1.00 * 0.1139                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1607 = 2.54 * 0.50 * 5.5877 + 1.00 * 0.0574                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1604      final r-factor (work) = 0.1473          |
| start r-factor (free) = 0.1982      final r-factor (free) = 0.1884          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6904 = 0.30 * 1.00 * 5.5877 + 1.00 * 0.0109                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6298 = 0.30 * 1.00 * 5.3795 + 1.00 * 0.0128                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.883)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    55.14   10.73    None  None   None       |
|    all(noH): 2823   0      0.00    55.14   10.73    None  None   None       |
|    Sol.    : 438    0      0.63    55.14   30.12    None  None   None       |
|    Mac.    : 2385   0      0.00    53.15   7.16     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 -   5.515: 1267   |   5:    27.572 -  33.087:   97        |
|      1:     5.515 -  11.029:  736   |   6:    33.087 -  38.601:  120        |
|      2:    11.029 -  16.543:  261   |   7:    38.601 -  44.116:   70        |
|      3:    16.543 -  22.058:  127   |   8:    44.116 -  49.630:   38        |
|      4:    22.058 -  27.572:   94   |   9:    49.630 -  55.145:   13        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1473 r_free = 0.1884             target_work(ml) = 5.355         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1472 r_free = 0.1884             target_work(ml) = 5.355         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1472   r_free= 0.1884   ksol= 0.33   Bsol= 39.93   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.70,4.20,6.05,0.00,0.00,0.00); trace/3= 4.65                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.355107                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1468   r_free= 0.1884   ksol= 0.32   Bsol= 39.93   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.00,3.45,4.99,0.00,0.00,0.00); trace/3= 3.81                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.355839                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.566705              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 109.127  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.541018              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 100.891  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1468      final r-factor (work) = 0.1202          |
| start r-factor (free) = 0.1884      final r-factor (free) = 0.1645          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.6581 = 3.57 * 0.50 * 5.3835 + 1.00 * 0.0574                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.4594 = 3.57 * 0.50 * 5.2645 + 1.00 * 0.0709                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1202      final r-factor (work) = 0.1145          |
| start r-factor (free) = 0.1645      final r-factor (free) = 0.1609          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 18.6547 = 3.54 * 1.00 * 5.2645 + 1.00 * 0.0129                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 18.3394 = 3.54 * 1.00 * 5.1747 + 1.00 * 0.0155                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.883)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    75.85   11.59    None  None   None       |
|    all(noH): 2823   0      0.00    75.85   11.59    None  None   None       |
|    Sol.    : 438    0      0.27    68.92   34.82    None  None   None       |
|    Mac.    : 2385   0      0.00    75.85   7.33     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 -   7.586: 1658   |   5:    37.927 -  45.513:   88        |
|      1:     7.586 -  15.171:  555   |   6:    45.513 -  53.098:   75        |
|      2:    15.171 -  22.757:  166   |   7:    53.098 -  60.684:   56        |
|      3:    22.757 -  30.342:  100   |   8:    60.684 -  68.269:   14        |
|      4:    30.342 -  37.927:  105   |   9:    68.269 -  75.855:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1145 r_free = 0.1609             target_work(ml) = 5.164         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1144 r_free = 0.1608             target_work(ml) = 5.164         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1144   r_free= 0.1608   ksol= 0.32   Bsol= 39.93   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.00,3.45,4.99,0.00,0.00,0.00); trace/3= 3.81                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.164169                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1145   r_free= 0.1605   ksol= 0.32   Bsol= 39.93   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.00,3.45,4.99,0.00,0.00,0.00); trace/3= 3.81                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.164157                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.490911              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 127.682  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.287189              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 101.714  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1145      final r-factor (work) = 0.1115          |
| start r-factor (free) = 0.1605      final r-factor (free) = 0.1584          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5156 = 2.49 * 0.50 * 5.1746 + 1.00 * 0.0709                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4835 = 2.49 * 0.50 * 5.1545 + 1.00 * 0.0638                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1115      final r-factor (work) = 0.1120          |
| start r-factor (free) = 0.1584      final r-factor (free) = 0.1567          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5054 = 0.29 * 1.00 * 5.1545 + 1.00 * 0.0251                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5449 = 0.29 * 1.00 * 5.1504 + 1.00 * 0.0658                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.883)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.33   11.05    None  None   None       |
|    all(noH): 2823   0      0.00    76.33   11.05    None  None   None       |
|    Sol.    : 438    0      0.95    67.31   32.50    None  None   None       |
|    Mac.    : 2385   0      0.00    76.33   7.11     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.633: 1698   |   5:    38.163 -  45.795:   83        |
|      1:     7.633 -  15.265:  546   |   6:    45.795 -  53.428:   70        |
|      2:    15.265 -  22.898:  149   |   7:    53.428 -  61.060:   26        |
|      3:    22.898 -  30.530:  113   |   8:    61.060 -  68.693:   14        |
|      4:    30.530 -  38.163:  122   |   9:    68.693 -  76.325:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1120 r_free = 0.1567             target_work(ml) = 5.144         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1119 r_free = 0.1567             target_work(ml) = 5.143         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1119   r_free= 0.1567   ksol= 0.32   Bsol= 39.93   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.00,3.45,4.99,0.00,0.00,0.00); trace/3= 3.81                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.143330                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1119   r_free= 0.1567   ksol= 0.32   Bsol= 39.93   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.00,3.45,4.99,0.00,0.00,0.00); trace/3= 3.81                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.143330                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.483507              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 158.021  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.459306              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.743   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1119      final r-factor (work) = 0.1136          |
| start r-factor (free) = 0.1567      final r-factor (free) = 0.1570          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8839 = 1.48 * 0.50 * 5.1499 + 1.00 * 0.0639                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8745 = 1.48 * 0.50 * 5.1504 + 1.00 * 0.0542                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1136      final r-factor (work) = 0.1132          |
| start r-factor (free) = 0.1570      final r-factor (free) = 0.1572          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3822 = 0.46 * 1.00 * 5.1504 + 1.00 * 0.0166                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3776 = 0.46 * 1.00 * 5.1508 + 1.00 * 0.0118                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.883)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.14   11.05    None  None   None       |
|    all(noH): 2823   0      0.00    78.14   11.05    None  None   None       |
|    Sol.    : 438    0      0.77    67.34   32.64    None  None   None       |
|    Mac.    : 2385   0      0.00    78.14   7.09     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.814: 1739   |   5:    39.069 -  46.882:   85        |
|      1:     7.814 -  15.628:  508   |   6:    46.882 -  54.696:   65        |
|      2:    15.628 -  23.441:  154   |   7:    54.696 -  62.510:   24        |
|      3:    23.441 -  31.255:  116   |   8:    62.510 -  70.324:   10        |
|      4:    31.255 -  39.069:  120   |   9:    70.324 -  78.137:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1132 r_free = 0.1572             target_work(ml) = 5.153         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1131 r_free = 0.1572             target_work(ml) = 5.153         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1131   r_free= 0.1572   ksol= 0.32   Bsol= 39.93   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.00,3.45,4.99,0.00,0.00,0.00); trace/3= 3.81                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.153103                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9794 -  4.7490 0.99   1382  152 0.1012 0.1289      5.3977      5.5191|
|  2:  4.7490 -  3.7895 0.99   1312  151 0.0867 0.1115      5.4476      5.6417|
|  3:  3.7895 -  3.3164 0.99   1299  141 0.1056 0.1459      5.4794      5.8236|
|  4:  3.3164 -  3.0159 0.99   1296  141 0.1207 0.1597      5.4495      5.5934|
|  5:  3.0159 -  2.8012 0.99   1269  144 0.1332 0.1738      5.3375      5.5624|
|  6:  2.8012 -  2.6370 0.99   1286  144 0.1220 0.2002      5.2173      5.5212|
|  7:  2.6370 -  2.5056 0.99   1267  142 0.1284 0.1581      5.1834      5.3419|
|  8:  2.5056 -  2.3970 0.98   1271  137 0.1198 0.1669      5.0971      5.3386|
|  9:  2.3970 -  2.3051 0.98   1248  142 0.1183 0.1851      5.0495      5.3052|
| 10:  2.3051 -  2.2258 1.00   1275  139 0.1153 0.1665      4.9769      5.2366|
| 11:  2.2258 -  2.1564 0.97   1248  138 0.1156 0.1680      4.9543      5.2084|
| 12:  2.1564 -  2.0949 0.98   1252  139 0.1167 0.1704      4.8846      5.2571|
| 13:  2.0949 -  2.0399 0.99   1250  139 0.1133 0.1727       4.809      5.0524|
| 14:  2.0399 -  1.9903 0.77    975  110 0.1038 0.1746      4.6939      4.9476|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9794 -  4.7490  1382   152  0.94   9.23   0.98     0.95       7229.11|
|  2:  4.7490 -  3.7895  1312   151  0.95   7.86   1.01     1.00       9033.02|
|  3:  3.7895 -  3.3164  1299   141  0.94  10.98   1.03     1.02      10269.94|
|  4:  3.3164 -  3.0159  1296   141  0.92  13.13   1.00     0.99      10109.88|
|  5:  3.0159 -  2.8012  1269   144  0.90  15.55   1.00     0.97       8318.31|
|  6:  2.8012 -  2.6370  1286   144  0.90  16.07   0.98     0.95       7150.96|
|  7:  2.6370 -  2.5056  1267   142  0.90  15.75   0.98     0.95       6245.43|
|  8:  2.5056 -  2.3970  1271   137  0.91  14.99   0.99     0.97       5427.67|
|  9:  2.3970 -  2.3051  1248   142  0.91  15.54   1.01     0.98       5241.30|
| 10:  2.3051 -  2.2258  1275   139  0.90  15.81   1.00     0.96       4410.20|
| 11:  2.2258 -  2.1564  1248   138  0.90  16.16   1.00     0.97       4519.64|
| 12:  2.1564 -  2.0949  1252   139  0.91  15.76   1.01     1.00       3928.75|
| 13:  2.0949 -  2.0399  1250   139  0.91  15.77   1.00     0.98       3435.32|
| 14:  2.0399 -  1.9903   975   110  0.92  14.61   0.98     0.95       2714.08|
|alpha:            min =        0.95 max =            1.02 mean =         0.97|
|beta:             min =     2714.08 max =        10269.94 mean =      6381.87|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.96 mean =        14.02|
|phase err.(test): min =        0.00 max =           89.74 mean =        13.62|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1131   r_free= 0.1572   ksol= 0.32   Bsol= 43.74   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.81,-0.36,1.18,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.153103                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1131   r_free= 0.1572   ksol= 0.32   Bsol= 43.74   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.81,-0.36,1.18,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.153103                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9794 -  4.7490 0.99   1382  152 0.1012 0.1289      5.3977      5.5191|
|  2:  4.7490 -  3.7895 0.99   1312  151 0.0867 0.1115      5.4476      5.6417|
|  3:  3.7895 -  3.3164 0.99   1299  141 0.1056 0.1459      5.4794      5.8236|
|  4:  3.3164 -  3.0159 0.99   1296  141 0.1207 0.1597      5.4495      5.5934|
|  5:  3.0159 -  2.8012 0.99   1269  144 0.1332 0.1738      5.3375      5.5624|
|  6:  2.8012 -  2.6370 0.99   1286  144 0.1220 0.2002      5.2173      5.5212|
|  7:  2.6370 -  2.5056 0.99   1267  142 0.1284 0.1581      5.1834      5.3419|
|  8:  2.5056 -  2.3970 0.98   1271  137 0.1198 0.1669      5.0971      5.3386|
|  9:  2.3970 -  2.3051 0.98   1248  142 0.1183 0.1851      5.0495      5.3052|
| 10:  2.3051 -  2.2258 1.00   1275  139 0.1153 0.1665      4.9769      5.2366|
| 11:  2.2258 -  2.1564 0.97   1248  138 0.1156 0.1680      4.9543      5.2084|
| 12:  2.1564 -  2.0949 0.98   1252  139 0.1167 0.1704      4.8846      5.2571|
| 13:  2.0949 -  2.0399 0.99   1250  139 0.1133 0.1727       4.809      5.0524|
| 14:  2.0399 -  1.9903 0.77    975  110 0.1038 0.1746      4.6939      4.9476|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9794 -  4.7490  1382   152  0.94   9.23   0.98     0.95       7229.11|
|  2:  4.7490 -  3.7895  1312   151  0.95   7.86   1.01     1.00       9033.02|
|  3:  3.7895 -  3.3164  1299   141  0.94  10.98   1.03     1.02      10269.94|
|  4:  3.3164 -  3.0159  1296   141  0.92  13.13   1.00     0.99      10109.88|
|  5:  3.0159 -  2.8012  1269   144  0.90  15.55   1.00     0.97       8318.31|
|  6:  2.8012 -  2.6370  1286   144  0.90  16.07   0.98     0.95       7150.96|
|  7:  2.6370 -  2.5056  1267   142  0.90  15.75   0.98     0.95       6245.43|
|  8:  2.5056 -  2.3970  1271   137  0.91  14.99   0.99     0.97       5427.67|
|  9:  2.3970 -  2.3051  1248   142  0.91  15.54   1.01     0.98       5241.30|
| 10:  2.3051 -  2.2258  1275   139  0.90  15.81   1.00     0.96       4410.20|
| 11:  2.2258 -  2.1564  1248   138  0.90  16.16   1.00     0.97       4519.64|
| 12:  2.1564 -  2.0949  1252   139  0.91  15.76   1.01     1.00       3928.75|
| 13:  2.0949 -  2.0399  1250   139  0.91  15.77   1.00     0.98       3435.32|
| 14:  2.0399 -  1.9903   975   110  0.92  14.61   0.98     0.95       2714.08|
|alpha:            min =        0.95 max =            1.02 mean =         0.97|
|beta:             min =     2714.08 max =        10269.94 mean =      6381.87|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.96 mean =        14.02|
|phase err.(test): min =        0.00 max =           89.74 mean =        13.62|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.883)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.81    81.95   14.86    None  None   None       |
|    all(noH): 2823   0      3.81    81.95   14.86    None  None   None       |
|    Sol.    : 438    0      4.59    71.15   36.46    None  None   None       |
|    Mac.    : 2385   0      3.81    81.95   10.90    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:     3.814 -  11.627: 1739   |   5:    42.882 -  50.696:   85        |
|      1:    11.627 -  19.441:  508   |   6:    50.696 -  58.510:   65        |
|      2:    19.441 -  27.255:  154   |   7:    58.510 -  66.323:   24        |
|      3:    27.255 -  35.069:  116   |   8:    66.323 -  74.137:   10        |
|      4:    35.069 -  42.882:  120   |   9:    74.137 -  81.951:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 318         
Filter by distance & map next to the model:
   mapped sites are within: 0.299 - 4.119
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 309 from: 318
   mapped sites are within: 0.705 - 4.119

peak=   11.356 closest distance to " CB  VAL A 230 " =    1.478
peak=    8.012 closest distance to " CG2 VAL A 296 " =    1.197
peak=    6.477 closest distance to " CG  LEU A   5 " =    1.246
peak=    6.185 closest distance to " NH2 ARG A  56 " =    2.167
peak=    5.829 closest distance to " CG  PRO A  54 " =    1.360
peak=    5.794 closest distance to " CD2 LEU A   5 " =    1.188
peak=    5.441 closest distance to " O   HOH Z 142 " =    1.900
peak=    5.418 closest distance to " NE2 GLN A  11 " =    1.179
peak=    5.286 closest distance to " CB  GLN A 223 " =    1.468
peak=    5.281 closest distance to " CG  LEU A 228 " =    1.172
peak=    5.199 closest distance to " CB  PRO A  54 " =    1.021
peak=    5.068 closest distance to " CB  ARG A 275 " =    0.946
peak=    4.915 closest distance to " CB  GLN A 183 " =    1.240
peak=    4.817 closest distance to " CB  VAL A 296 " =    1.052
peak=    4.647 closest distance to " CG  PRO A 198 " =    1.263
peak=    4.612 closest distance to " ND2 ASN A 187 " =    1.595
peak=    4.582 closest distance to " CG  PRO A 213 " =    1.250
peak=    4.568 closest distance to " CZ  PHE A 218 " =    1.137
peak=    4.560 closest distance to " CG  PRO A 243 " =    1.115
peak=    4.518 closest distance to " O   HOH Z 346 " =    1.604
peak=    4.515 closest distance to " O   HOH Z 232 " =    2.334
peak=    4.491 closest distance to " CB  VAL A 230 " =    1.145
peak=    4.487 closest distance to " CB  VAL A 265 " =    1.315
peak=    4.486 closest distance to " O   HOH Z 209 " =    2.276
peak=    4.462 closest distance to " O   HOH Z 126 " =    1.874
peak=    4.393 closest distance to " O   HOH Z   9 " =    1.292
peak=    4.393 closest distance to " CB  SER A  63 " =    1.239
peak=    4.388 closest distance to " O   HOH Z  61 " =    1.683
peak=    4.374 closest distance to " CB  ARG A  79 " =    1.399
peak=    4.336 closest distance to " O   HOH Z 272 " =    1.823
peak=    4.322 closest distance to " O   HOH Z 265 " =    2.331
peak=    4.317 closest distance to " O   SER A  87 " =    2.254
peak=    4.303 closest distance to " CB  ASN A 148 " =    1.347
peak=    4.302 closest distance to " O   HOH Z 427 " =    3.013
peak=    4.228 closest distance to " C   PRO A 198 " =    1.516
peak=    4.198 closest distance to " O   HOH Z  43 " =    2.016
peak=    4.182 closest distance to " O   HOH Z 369 " =    2.086
peak=    4.176 closest distance to " CB  TRP A 266 " =    1.036
peak=    4.152 closest distance to " OG  SER A  97 " =    2.908
peak=    4.120 closest distance to " CD2 LEU A 228 " =    1.068
peak=    4.099 closest distance to " CB  GLU A 152 " =    1.222
peak=    4.084 closest distance to " CA  TYR A  30 " =    0.977
peak=    4.073 closest distance to " CB  ASN A  39 " =    0.934
peak=    4.073 closest distance to " O   HOH Z 313 " =    1.868
peak=    4.055 closest distance to " CB  ASN A 142 " =    1.083
peak=    4.042 closest distance to " O   HOH Z 303 " =    2.104
peak=    4.041 closest distance to " CG2 VAL A 257 " =    0.874
peak=    4.041 closest distance to " O   HOH Z 158 " =    3.216
peak=    4.027 closest distance to " O   HOH Z 298 " =    1.751
peak=    4.020 closest distance to " O   HOH Z 423 " =    1.769
peak=    3.999 closest distance to " O   HOH Z 234 " =    3.729
peak=    3.995 closest distance to " O   HOH Z 402 " =    1.391
peak=    3.985 closest distance to " O   HOH Z 248 " =    1.566
peak=    3.985 closest distance to " CB  SER A   3 " =    1.244
peak=    3.985 closest distance to " O   HOH Z 236 " =    2.120
peak=    3.984 closest distance to " O   HOH Z 126 " =    1.893
peak=    3.983 closest distance to " O   HOH Z  78 " =    1.665
peak=    3.970 closest distance to " O   HOH Z 193 " =    1.784
peak=    3.954 closest distance to " CB  VAL A 202 " =    1.615
peak=    3.949 closest distance to " CB  GLU A 128 " =    0.964
peak=    3.948 closest distance to " OG ASER A 258 " =    3.080
peak=    3.948 closest distance to " N   ASN A  39 " =    1.121
peak=    3.893 closest distance to " O   HOH Z 411 " =    3.854
peak=    3.885 closest distance to " CB  ALA A   9 " =    1.589
peak=    3.880 closest distance to " CB  ARG A  79 " =    0.908
peak=    3.875 closest distance to " O   HOH Z 368 " =    2.072
peak=    3.871 closest distance to " CB  ASN A 187 " =    1.272
peak=    3.867 closest distance to " CB  ASP A 124 " =    0.705
peak=    3.860 closest distance to " CG1BVAL A  72 " =    1.581
peak=    3.858 closest distance to " CA  ASN A 215 " =    1.041
peak=    3.842 closest distance to " CB  ARG A 190 " =    1.625
peak=    3.839 closest distance to " N   PHE A 130 " =    1.225
peak=    3.814 closest distance to " CG  LEU A 167 " =    1.221
peak=    3.807 closest distance to " CG1 VAL A 153 " =    0.963
peak=    3.795 closest distance to " O   HOH Z 261 " =    1.856
peak=    3.783 closest distance to " CB BVAL A  41 " =    1.110
peak=    3.781 closest distance to " CB  ASP A 140 " =    0.958
peak=    3.775 closest distance to " OD1 ASN A  69 " =    2.582
peak=    3.764 closest distance to " O   HOH Z 261 " =    1.694
peak=    3.761 closest distance to " O   HOH Z  59 " =    1.868
peak=    3.755 closest distance to " CE  LYS A  76 " =    0.853
peak=    3.736 closest distance to " O   HOH Z 214 " =    2.159
peak=    3.735 closest distance to " CG  MET A 185 " =    1.224
peak=    3.725 closest distance to " CB  SER A  26 " =    1.712
peak=    3.725 closest distance to " CB  ASN A 110 " =    1.047
peak=    3.709 closest distance to " CA  ARG A  36 " =    1.028
peak=    3.703 closest distance to " O   HOH Z  66 " =    2.217
peak=    3.699 closest distance to " O   HOH Z 371 " =    2.900
peak=    3.685 closest distance to " O   HOH Z 251 " =    1.521
peak=    3.679 closest distance to " O   HOH Z 389 " =    1.778
peak=    3.679 closest distance to " CA  PHE A 283 " =    1.201
peak=    3.669 closest distance to " OG BSER A 164 " =    2.164
peak=    3.668 closest distance to " O   HOH Z 203 " =    1.656
peak=    3.666 closest distance to " CB  GLU A 277 " =    3.611
peak=    3.664 closest distance to " O   HOH Z 353 " =    2.499
peak=    3.659 closest distance to " CA  SER A  87 " =    1.009
peak=    3.659 closest distance to " O   HOH Z 145 " =    2.134
peak=    3.653 closest distance to " O   HOH Z 126 " =    1.535
peak=    3.650 closest distance to " NH1AARG A 145 " =    1.089
peak=    3.649 closest distance to " CA  ALA A  51 " =    0.956
peak=    3.649 closest distance to " CA  THR A 264 " =    0.769
peak=    3.646 closest distance to " O   HOH Z 425 " =    1.391
peak=    3.646 closest distance to " CG1 ILE A  49 " =    1.482
peak=    3.630 closest distance to " CD  LYS A 166 " =    1.284
peak=    3.627 closest distance to " CB  ALA A 248 " =    1.422
peak=    3.623 closest distance to " CB  GLU A  46 " =    0.948
peak=    3.613 closest distance to " O   HOH Z  10 " =    1.740
peak=    3.607 closest distance to " CB  THR A  31 " =    1.480
peak=    3.595 closest distance to " CA  ALA A  21 " =    1.126
peak=    3.595 closest distance to " CB  TRP A 179 " =    1.398
peak=    3.593 closest distance to " O   HOH Z 128 " =    2.129
peak=    3.584 closest distance to " CB  ALA A 291 " =    1.333
peak=    3.580 closest distance to " CD  ARG A 269 " =    0.979
peak=    3.573 closest distance to " O   HOH Z 280 " =    3.028
peak=    3.573 closest distance to " O   HOH Z 273 " =    2.791
peak=    3.569 closest distance to " O   HOH Z  97 " =    2.437
peak=    3.560 closest distance to " O   HOH Z  97 " =    1.993
peak=    3.553 closest distance to " O   HOH Z   3 " =    1.940
peak=    3.550 closest distance to " CA  VAL A  41 " =    0.725
peak=    3.544 closest distance to " O   HOH Z  40 " =    1.531
peak=    3.542 closest distance to " O   HOH Z  21 " =    1.771
peak=    3.541 closest distance to " O   HOH Z 147 " =    1.777
peak=    3.526 closest distance to " NZ  LYS A 117 " =    3.243
peak=    3.525 closest distance to " CG2 ILE A 120 " =    1.139
peak=    3.525 closest distance to " CB  SER A 212 " =    1.262
peak=    3.523 closest distance to " CB  GLN A  88 " =    1.177
peak=    3.521 closest distance to " CA  ASP A 162 " =    0.999
peak=    3.515 closest distance to " O   HOH Z 257 " =    2.312
peak=    3.515 closest distance to " CB  HIS A 108 " =    0.828
peak=    3.513 closest distance to " ND2 ASN A 249 " =    0.870
peak=    3.509 closest distance to " CA  ARG A 195 " =    1.158
peak=    3.505 closest distance to " NZ  LYS A  48 " =    1.198
peak=    3.500 closest distance to " CD2 TRP A 179 " =    1.367
peak=    3.500 closest distance to " O   HOH Z   9 " =    1.994
peak=    3.495 closest distance to " O   HOH Z 172 " =    3.266
peak=    3.494 closest distance to " CG1 VAL A 296 " =    1.226
peak=    3.491 closest distance to " CB  THR A 157 " =    1.154
peak=    3.491 closest distance to " O   HOH Z 250 " =    1.353
peak=    3.489 closest distance to " O   HOH Z 148 " =    3.454
peak=    3.485 closest distance to " CB  SER A 216 " =    0.758
peak=    3.481 closest distance to " CB  SER A 273 " =    0.892
peak=    3.478 closest distance to " CB  LEU A 143 " =    1.185
peak=    3.470 closest distance to " CZ  PHE A  38 " =    1.151
peak=    3.468 closest distance to " CE1 TYR A 186 " =    1.336
peak=    3.457 closest distance to " O   HOH Z 291 " =    1.561
peak=    3.455 closest distance to " O   HOH Z 403 " =    1.622
peak=    3.452 closest distance to " CB  LYS A 117 " =    1.265
peak=    3.451 closest distance to " CD1 LEU A 261 " =    1.194
peak=    3.447 closest distance to " O   HOH Z 403 " =    1.491
peak=    3.447 closest distance to " N   SER A 135 " =    1.336
peak=    3.432 closest distance to " O   HOH Z 285 " =    2.643
peak=    3.431 closest distance to " O  BHOH Z 338 " =    2.407
peak=    3.431 closest distance to " CG  GLN A  88 " =    1.055
peak=    3.424 closest distance to " O   HOH Z   1 " =    1.765
peak=    3.421 closest distance to " O   ASP A 124 " =    1.076
peak=    3.421 closest distance to " CD1 LEU A  96 " =    0.726
peak=    3.420 closest distance to " CG  ARG A  66 " =    2.691
peak=    3.415 closest distance to " O   HOH Z  92 " =    2.410
peak=    3.411 closest distance to " CZ3 TRP A 266 " =    1.140
peak=    3.408 closest distance to " O   HOH Z 299 " =    4.119
peak=    3.402 closest distance to " CB  GLN A 278 " =    0.931
peak=    3.401 closest distance to " O   HOH Z 128 " =    2.099
peak=    3.401 closest distance to " O   TRP A 274 " =    1.773
peak=    3.389 closest distance to " N   ARG A 156 " =    1.327
peak=    3.387 closest distance to " O   HOH Z 425 " =    2.078
peak=    3.385 closest distance to " CA  ALA A 291 " =    0.855
peak=    3.385 closest distance to " NE2 GLN A  77 " =    3.168
peak=    3.378 closest distance to " CA  TYR A 116 " =    1.400
peak=    3.373 closest distance to " O   HOH Z 407 " =    2.377
peak=    3.373 closest distance to " CD1 ILE A 263 " =    1.258
peak=    3.372 closest distance to " O   GLN A 278 " =    1.313
peak=    3.369 closest distance to " CB  MET A  40 " =    0.795
peak=    3.368 closest distance to " CA  TYR A  30 " =    1.084
peak=    3.367 closest distance to " O   HOH Z 419 " =    1.908
peak=    3.365 closest distance to " CB  PRO A  90 " =    1.120
peak=    3.358 closest distance to " O   HOH Z 132 " =    2.505
peak=    3.357 closest distance to " CG  MET A 185 " =    1.014
peak=    3.354 closest distance to " CA  ALA A 233 " =    1.206
peak=    3.353 closest distance to " CD1 ILE A 106 " =    0.992
peak=    3.352 closest distance to " CB  ARG A 139 " =    0.888
peak=    3.349 closest distance to " O   HOH Z 368 " =    3.530
peak=    3.348 closest distance to " CB  ALA A 242 " =    0.783
peak=    3.347 closest distance to " CA  LYS A 117 " =    1.199
peak=    3.346 closest distance to " CD1 ILE A  33 " =    1.755
peak=    3.344 closest distance to " O   HOH Z 421 " =    1.922
peak=    3.343 closest distance to " O   HOH Z 344 " =    2.975
peak=    3.342 closest distance to " CD1 LEU A 300 " =    1.279
peak=    3.342 closest distance to " O   HOH Z 193 " =    1.862
peak=    3.341 closest distance to " O   HOH Z 422 " =    2.632
peak=    3.341 closest distance to " CG2 ILE A  20 " =    1.500
peak=    3.339 closest distance to " O   ASN A  74 " =    1.491
peak=    3.337 closest distance to " CD BLYS A 290 " =    1.106
peak=    3.332 closest distance to " CG  LEU A 281 " =    1.061
peak=    3.330 closest distance to " O   HOH Z 180 " =    2.141
peak=    3.330 closest distance to " O   HOH Z 329 " =    4.026
peak=    3.326 closest distance to " N   GLY A 133 " =    3.722
peak=    3.326 closest distance to " CB  ASN A 173 " =    1.048
peak=    3.323 closest distance to " CB  TRP A 150 " =    1.427
peak=    3.319 closest distance to " CG1 ILE A 120 " =    1.052
peak=    3.313 closest distance to " O   HOH Z  48 " =    1.582
peak=    3.313 closest distance to " O   ALA A   1 " =    1.747
peak=    3.312 closest distance to " O   HOH Z 128 " =    2.045
peak=    3.311 closest distance to " CB  ALA A 114 " =    1.128
peak=    3.308 closest distance to " O   HOH Z 392 " =    3.130
peak=    3.304 closest distance to " CG  MET A 113 " =    1.037
peak=    3.299 closest distance to " O   HOH Z 337 " =    3.514
peak=    3.296 closest distance to " OD2 ASP A 286 " =    2.731
peak=    3.291 closest distance to " CB  GLN A  89 " =    1.266
peak=    3.291 closest distance to " CA  ALA A 154 " =    0.994
peak=    3.283 closest distance to " O   HOH Z 109 " =    2.530
peak=    3.280 closest distance to " CG AARG A 275 " =    1.216
peak=    3.280 closest distance to " C   ALA A 299 " =    0.918
peak=    3.278 closest distance to " O   HOH Z 290 " =    1.135
peak=    3.276 closest distance to " O   HOH Z  88 " =    2.843
peak=    3.275 closest distance to " N   GLN A 278 " =    1.223
peak=    3.272 closest distance to " CB  LEU A 228 " =    1.270
peak=    3.268 closest distance to " O   HOH Z 359 " =    3.850
peak=    3.264 closest distance to " CD2 LEU A 297 " =    0.936
peak=    3.260 closest distance to " O   HOH Z 437 " =    1.790
peak=    3.259 closest distance to " O   HOH Z 336 " =    1.739
peak=    3.256 closest distance to " O   HOH Z 417 " =    3.240
peak=    3.254 closest distance to " O   HOH Z 234 " =    1.832
peak=    3.253 closest distance to " CA  ASP A 191 " =    1.100
peak=    3.252 closest distance to " CB  ASN A 215 " =    1.144
peak=    3.246 closest distance to " O   HOH Z 350 " =    1.594
peak=    3.243 closest distance to " O   HOH Z 435 " =    1.998
peak=    3.242 closest distance to " O   HOH Z 406 " =    1.579
peak=    3.237 closest distance to " CA  PHE A  59 " =    0.963
peak=    3.237 closest distance to " O   HOH Z 305 " =    3.628
peak=    3.234 closest distance to " CA  ILE A 234 " =    0.881
peak=    3.232 closest distance to " O   LYS A 290 " =    2.400
peak=    3.226 closest distance to " O   HOH Z 366 " =    2.935
peak=    3.222 closest distance to " CB  SER A 210 " =    0.817
peak=    3.220 closest distance to " OE1 GLU A   2 " =    1.920
peak=    3.216 closest distance to " CB  VAL A 268 " =    0.847
peak=    3.216 closest distance to " O   PHE A 192 " =    1.401
peak=    3.214 closest distance to " CG1 ILE A  33 " =    1.299
peak=    3.213 closest distance to " O   HOH Z 245 " =    1.360
peak=    3.212 closest distance to " O   HOH Z 187 " =    2.309
peak=    3.211 closest distance to " N   ASP A 162 " =    1.267
peak=    3.209 closest distance to " O   HOH Z 371 " =    1.617
peak=    3.206 closest distance to " CD1 LEU A 228 " =    2.053
peak=    3.201 closest distance to " OE2 GLU A   2 " =    1.792
peak=    3.199 closest distance to " NH2 ARG A 156 " =    1.093
peak=    3.196 closest distance to " O   HOH Z 263 " =    1.658
peak=    3.196 closest distance to " O   HOH Z 380 " =    1.842
peak=    3.194 closest distance to " O   HOH Z 345 " =    3.335
peak=    3.194 closest distance to " O   HOH Z   1 " =    1.782
peak=    3.192 closest distance to " CA  SER A 146 " =    1.740
peak=    3.191 closest distance to " O   HOH Z 227 " =    2.110
peak=    3.190 closest distance to " CE1 HIS A 108 " =    1.164
peak=    3.188 closest distance to " O   HOH Z 359 " =    1.329
peak=    3.188 closest distance to " NH2BARG A 145 " =    2.000
peak=    3.188 closest distance to " CB  PRO A 198 " =    1.046
peak=    3.187 closest distance to " CB  ILE A  20 " =    1.454
peak=    3.187 closest distance to " OG BSER A 134 " =    3.019
peak=    3.186 closest distance to " CA  LEU A 282 " =    1.178
peak=    3.182 closest distance to " CA  THR A 221 " =    0.983
peak=    3.180 closest distance to " O   HOH Z 294 " =    1.546
peak=    3.177 closest distance to " O   HOH Z  88 " =    2.717
peak=    3.173 closest distance to " CB  LYS A 290 " =    0.921
peak=    3.172 closest distance to " CG BARG A 102 " =    1.780
peak=    3.172 closest distance to " CB  ASN A 224 " =    1.025
peak=    3.171 closest distance to " CA  ILE A 106 " =    0.737
peak=    3.171 closest distance to " CE3 TRP A 150 " =    0.966
peak=    3.169 closest distance to " CA  ALA A 158 " =    1.310
peak=    3.168 closest distance to " CB  ALA A 180 " =    1.243
peak=    3.166 closest distance to " O   HOH Z 141 " =    1.712
peak=    3.165 closest distance to " CB  THR A  52 " =    0.923
peak=    3.160 closest distance to " O   HOH Z 130 " =    2.117
peak=    3.160 closest distance to " O   HOH Z  44 " =    1.689
peak=    3.155 closest distance to " CB  GLN A 205 " =    1.099
peak=    3.154 closest distance to " CA  ARG A 159 " =    1.226
peak=    3.153 closest distance to " ND1 HIS A  86 " =    1.661
peak=    3.150 closest distance to " CG2 THR A 221 " =    1.120
peak=    3.150 closest distance to " O   HOH Z  85 " =    2.196
peak=    3.149 closest distance to " O   HOH Z  30 " =    1.393
peak=    3.149 closest distance to " CB  PHE A 204 " =    0.770
peak=    3.149 closest distance to " CA  LYS A 290 " =    1.149
peak=    3.149 closest distance to " O   HOH Z 424 " =    1.491
peak=    3.144 closest distance to " CB  SER A  62 " =    1.241
peak=    3.129 closest distance to " OG1 THR A 279 " =    1.406
peak=    3.128 closest distance to " O   HOH Z 193 " =    1.653
peak=    3.124 closest distance to " O   HOH Z 213 " =    2.168
peak=    3.124 closest distance to " O   ALA A 292 " =    1.662
peak=    3.121 closest distance to " CD  ARG A  66 " =    2.581
peak=    3.116 closest distance to " O   HOH Z 357 " =    1.942
peak=    3.113 closest distance to " CA  MET A 105 " =    0.967
peak=    3.112 closest distance to " O   ARG A  56 " =    2.881
peak=    3.104 closest distance to " O   HOH Z  66 " =    2.126
peak=    3.100 closest distance to " NE2 HIS A 207 " =    1.231
peak=    3.100 closest distance to " O   HOH Z 325 " =    2.176
peak=    3.092 closest distance to " CG  ARG A 159 " =    0.959
peak=    3.089 closest distance to " CA  ARG A 102 " =    1.143
peak=    3.088 closest distance to " CG  LYS A  76 " =    0.923
peak=    3.086 closest distance to " O   MET A 105 " =    1.859
peak=    3.084 closest distance to " CB  PRO A 243 " =    1.562
peak=    3.084 closest distance to " CB  TYR A 116 " =    0.798
peak=    3.082 closest distance to " O   THR A 220 " =    1.306
peak=    3.080 closest distance to " CG  GLN A  77 " =    2.157
peak=    3.076 closest distance to " O   HOH Z 124 " =    1.204
peak=    3.072 closest distance to " O   SER A 164 " =    1.300
peak=    3.069 closest distance to " OE2 GLU A  53 " =    1.983
peak=    3.067 closest distance to " CB  LEU A 300 " =    0.878
peak=    3.065 closest distance to " CB  VAL A 257 " =    0.721
peak=    3.055 closest distance to " O   HOH Z 417 " =    2.206
peak=    3.032 closest distance to " O   HOH Z 116 " =    1.713
peak=    3.029 closest distance to " O   HOH Z 423 " =    2.884
peak=    3.028 closest distance to " O   HOH Z 172 " =    3.648

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 189         
Filter by distance & map next to the model:
   mapped sites are within: 0.732 - 5.443
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 188 from: 189
   mapped sites are within: 0.732 - 5.443

peak=   -5.274 closest distance to " CG2 VAL A 230 " =    0.732
peak=   -4.474 closest distance to " CB  PHE A 192 " =    1.947
peak=   -4.470 closest distance to " SG  CYS A 254 " =    3.340
peak=   -4.427 closest distance to " OG BSER A 134 " =    1.258
peak=   -4.394 closest distance to " CD  GLN A  58 " =    1.062
peak=   -4.332 closest distance to " CD  ARG A 156 " =    2.038
peak=   -4.307 closest distance to " CB  PRO A 243 " =    2.711
peak=   -4.268 closest distance to " O   HOH Z 266 " =    5.316
peak=   -4.168 closest distance to " O   HOH Z 290 " =    1.153
peak=   -4.160 closest distance to " CG2 VAL A 296 " =    1.447
peak=   -4.122 closest distance to " CE2 TYR A  30 " =    2.745
peak=   -4.107 closest distance to " C   HIS A 108 " =    1.207
peak=   -4.026 closest distance to " O   HOH Z 231 " =    2.072
peak=   -4.018 closest distance to " CG  GLN A 223 " =    2.097
peak=   -4.001 closest distance to " O   HOH Z 351 " =    1.492
peak=   -3.979 closest distance to " O   HOH Z 185 " =    2.395
peak=   -3.977 closest distance to " O   VAL A  67 " =    2.611
peak=   -3.962 closest distance to " CA  VAL A  67 " =    2.921
peak=   -3.961 closest distance to " O   HOH Z 114 " =    3.015
peak=   -3.909 closest distance to " CB  ALA A  43 " =    2.506
peak=   -3.906 closest distance to " ND2 ASN A  45 " =    1.481
peak=   -3.905 closest distance to " CB  ALA A 248 " =    2.145
peak=   -3.901 closest distance to " CD1 LEU A 255 " =    2.894
peak=   -3.863 closest distance to " CG1 VAL A 112 " =    2.838
peak=   -3.850 closest distance to " O   HOH Z 166 " =    1.986
peak=   -3.840 closest distance to " CG2 VAL A 296 " =    0.957
peak=   -3.813 closest distance to " CB  ALA A 248 " =    2.389
peak=   -3.808 closest distance to " O   PRO A 198 " =    1.170
peak=   -3.790 closest distance to " CB  ALA A 161 " =    2.543
peak=   -3.783 closest distance to " CE  MET A 105 " =    2.249
peak=   -3.775 closest distance to " CZ3 TRP A 179 " =    1.226
peak=   -3.771 closest distance to " CG  ASP A 231 " =    0.792
peak=   -3.745 closest distance to " O   HOH Z 196 " =    2.232
peak=   -3.744 closest distance to " OXT GLY A 302 " =    2.857
peak=   -3.744 closest distance to " N   THR A 157 " =    1.462
peak=   -3.741 closest distance to " O   HOH Z 394 " =    1.509
peak=   -3.686 closest distance to " ND2 ASN A 187 " =    1.490
peak=   -3.683 closest distance to " OD2 ASP A 171 " =    2.268
peak=   -3.658 closest distance to " O   PRO A 163 " =    2.114
peak=   -3.656 closest distance to " N   ALA A  43 " =    2.534
peak=   -3.649 closest distance to " O   TYR A 247 " =    2.814
peak=   -3.632 closest distance to " N   ALA A 226 " =    2.078
peak=   -3.624 closest distance to " CE BMET A  47 " =    1.435
peak=   -3.622 closest distance to " ND2 ASN A 249 " =    2.517
peak=   -3.597 closest distance to " O   HOH Z  11 " =    1.876
peak=   -3.597 closest distance to " OG  SER A  97 " =    2.322
peak=   -3.595 closest distance to " C   MET A 188 " =    1.402
peak=   -3.590 closest distance to " O   HOH Z 211 " =    1.565
peak=   -3.587 closest distance to " O   HOH Z  44 " =    2.270
peak=   -3.587 closest distance to " CB  PRO A 280 " =    2.121
peak=   -3.565 closest distance to " NE  ARG A 156 " =    1.913
peak=   -3.558 closest distance to " CB  ALA A 291 " =    2.230
peak=   -3.548 closest distance to " CA  ASP A 298 " =    1.113
peak=   -3.545 closest distance to " CA  GLY A 241 " =    3.107
peak=   -3.527 closest distance to " O   HOH Z 102 " =    1.690
peak=   -3.517 closest distance to " N   ALA A 248 " =    1.770
peak=   -3.509 closest distance to " O   HOH Z 389 " =    2.087
peak=   -3.482 closest distance to " CG2 ILE A 263 " =    2.360
peak=   -3.477 closest distance to " CG  TRP A 266 " =    1.891
peak=   -3.472 closest distance to " OD1 ASN A 148 " =    1.400
peak=   -3.465 closest distance to " CE3 TRP A 150 " =    2.069
peak=   -3.465 closest distance to " CA  GLY A 241 " =    2.369
peak=   -3.462 closest distance to " CB  ASN A  39 " =    2.264
peak=   -3.458 closest distance to " O   HOH Z 140 " =    1.483
peak=   -3.457 closest distance to " CG  PHE A 283 " =    2.763
peak=   -3.440 closest distance to " O   HOH Z  13 " =    1.798
peak=   -3.435 closest distance to " O   HOH Z 103 " =    1.810
peak=   -3.434 closest distance to " CG1 VAL A 250 " =    2.766
peak=   -3.433 closest distance to " NH2AARG A 275 " =    5.130
peak=   -3.430 closest distance to " O   VAL A 189 " =    2.592
peak=   -3.426 closest distance to " CB  ALA A 291 " =    2.253
peak=   -3.420 closest distance to " N   THR A  52 " =    1.686
peak=   -3.419 closest distance to " OD1 ASN A 187 " =    1.703
peak=   -3.418 closest distance to " CZ2 TRP A  92 " =    2.810
peak=   -3.410 closest distance to " O   HOH Z 243 " =    1.902
peak=   -3.403 closest distance to " CD  ARG A 139 " =    1.606
peak=   -3.401 closest distance to " O   HOH Z 313 " =    1.634
peak=   -3.395 closest distance to " O   MET A  40 " =    2.766
peak=   -3.383 closest distance to " O   HOH Z 407 " =    3.008
peak=   -3.377 closest distance to " O   HOH Z  15 " =    1.529
peak=   -3.371 closest distance to " O   HOH Z 191 " =    5.443
peak=   -3.367 closest distance to " O   HOH Z 313 " =    1.168
peak=   -3.366 closest distance to " C   LEU A 222 " =    0.828
peak=   -3.364 closest distance to " O   HOH Z 198 " =    2.021
peak=   -3.364 closest distance to " O   ALA A 161 " =    1.722
peak=   -3.358 closest distance to " O   SER A 271 " =    2.201
peak=   -3.353 closest distance to " N   ASP A 171 " =    2.338
peak=   -3.352 closest distance to " CA  ASN A 127 " =    1.302
peak=   -3.347 closest distance to " CA  GLY A  98 " =    1.875
peak=   -3.342 closest distance to " O   ARG A 145 " =    1.660
peak=   -3.337 closest distance to " NH2 ARG A  79 " =    1.518
peak=   -3.330 closest distance to " C   GLY A  17 " =    1.279
peak=   -3.330 closest distance to " CG1 VAL A 197 " =    2.281
peak=   -3.328 closest distance to " CB  PRO A 163 " =    2.524
peak=   -3.327 closest distance to " CG1 VAL A 112 " =    2.640
peak=   -3.325 closest distance to " CG1 VAL A 125 " =    1.981
peak=   -3.319 closest distance to " CD1 PHE A  59 " =    1.967
peak=   -3.318 closest distance to " CZ  PHE A 192 " =    2.798
peak=   -3.317 closest distance to " CB  ASP A 132 " =    2.409
peak=   -3.315 closest distance to " CD1 ILE A 239 " =    2.279
peak=   -3.313 closest distance to " O   SER A 210 " =    1.972
peak=   -3.312 closest distance to " N   HIS A 115 " =    2.160
peak=   -3.309 closest distance to " O   SER A  22 " =    2.340
peak=   -3.308 closest distance to " OG  SER A 206 " =    1.644
peak=   -3.304 closest distance to " C   LEU A 143 " =    1.027
peak=   -3.303 closest distance to " CA  GLY A 203 " =    2.464
peak=   -3.303 closest distance to " N   GLN A  58 " =    1.915
peak=   -3.302 closest distance to " CZ  TYR A 169 " =    1.691
peak=   -3.300 closest distance to " CD2 TYR A 293 " =    2.028
peak=   -3.300 closest distance to " O   PRO A 198 " =    1.345
peak=   -3.299 closest distance to " O   ARG A  24 " =    2.060
peak=   -3.290 closest distance to " CD  LYS A 289 " =    2.491
peak=   -3.285 closest distance to " CG1 VAL A  67 " =    3.057
peak=   -3.281 closest distance to " O   GLY A  80 " =    2.492
peak=   -3.280 closest distance to " O   ALA A  10 " =    1.791
peak=   -3.275 closest distance to " O   HOH Z  73 " =    2.291
peak=   -3.273 closest distance to " NH2 ARG A  79 " =    2.050
peak=   -3.273 closest distance to " CE2 PHE A 218 " =    2.526
peak=   -3.273 closest distance to " CB  GLN A  11 " =    1.819
peak=   -3.271 closest distance to " NE2 GLN A  88 " =    1.926
peak=   -3.270 closest distance to " O   GLY A 196 " =    1.225
peak=   -3.270 closest distance to " OD1 ASN A 249 " =    2.305
peak=   -3.270 closest distance to " NE2 GLN A 278 " =    1.866
peak=   -3.269 closest distance to " NE2 GLN A 194 " =    1.784
peak=   -3.268 closest distance to " C   PHE A  59 " =    1.355
peak=   -3.265 closest distance to " CB  ASP A 132 " =    2.341
peak=   -3.252 closest distance to " NE2 GLN A  88 " =    1.121
peak=   -3.252 closest distance to " CB  VAL A 296 " =    1.048
peak=   -3.247 closest distance to " CB  TRP A  85 " =    2.612
peak=   -3.245 closest distance to " ND2 ASN A 252 " =    1.924
peak=   -3.245 closest distance to " CG1 VAL A 296 " =    1.350
peak=   -3.242 closest distance to " CB  ALA A  10 " =    2.316
peak=   -3.240 closest distance to " CB  ASN A  69 " =    1.239
peak=   -3.239 closest distance to " OH  TYR A 247 " =    2.053
peak=   -3.239 closest distance to " CZ  PHE A  59 " =    1.505
peak=   -3.236 closest distance to " N   VAL A 230 " =    1.172
peak=   -3.234 closest distance to " OG  SER A  63 " =    1.160
peak=   -3.231 closest distance to " CD1 LEU A 101 " =    2.286
peak=   -3.222 closest distance to " O   HOH Z 210 " =    1.131
peak=   -3.216 closest distance to " O   HOH Z  43 " =    1.831
peak=   -3.214 closest distance to " CD  PRO A 243 " =    2.068
peak=   -3.213 closest distance to " O   ALA A  51 " =    1.379
peak=   -3.211 closest distance to " O   HOH Z  60 " =    2.062
peak=   -3.208 closest distance to " O   HOH Z 134 " =    3.190
peak=   -3.206 closest distance to " O   SER A 135 " =    1.439
peak=   -3.206 closest distance to " N   ALA A 248 " =    2.174
peak=   -3.201 closest distance to " N   THR A 235 " =    1.244
peak=   -3.200 closest distance to " CG1BVAL A  72 " =    2.396
peak=   -3.197 closest distance to " O   HOH Z 389 " =    1.438
peak=   -3.195 closest distance to " C   ALA A 158 " =    1.387
peak=   -3.193 closest distance to " O   HOH Z  38 " =    1.711
peak=   -3.190 closest distance to " O   HOH Z 256 " =    1.270
peak=   -3.188 closest distance to " CE1 TYR A 247 " =    2.792
peak=   -3.186 closest distance to " OE1 GLN A  88 " =    1.070
peak=   -3.177 closest distance to " CG  GLU A 277 " =    1.193
peak=   -3.172 closest distance to " CA  VAL A 296 " =    0.984
peak=   -3.171 closest distance to " CG  LEU A 228 " =    1.013
peak=   -3.168 closest distance to " O   HOH Z  52 " =    1.555
peak=   -3.167 closest distance to " O   ILE A 106 " =    2.030
peak=   -3.165 closest distance to " OD2 ASP A  50 " =    2.225
peak=   -3.158 closest distance to " CD2 LEU A 300 " =    2.835
peak=   -3.157 closest distance to " CG  ARG A 269 " =    2.974
peak=   -3.155 closest distance to " O   HOH Z 281 " =    2.706
peak=   -3.151 closest distance to " O   HOH Z 149 " =    2.223
peak=   -3.150 closest distance to " CD2 LEU A   5 " =    1.209
peak=   -3.149 closest distance to " O   HOH Z  63 " =    1.673
peak=   -3.146 closest distance to " O   HOH Z 295 " =    1.581
peak=   -3.128 closest distance to " O   ALA A 248 " =    1.795
peak=   -3.126 closest distance to " CA  PRO A 243 " =    2.261
peak=   -3.126 closest distance to " CG1 VAL A 112 " =    2.774
peak=   -3.123 closest distance to " CD  PRO A 213 " =    2.077
peak=   -3.123 closest distance to " CE  LYS A  76 " =    2.642
peak=   -3.122 closest distance to " O   HOH Z 128 " =    2.494
peak=   -3.119 closest distance to " N   SER A 276 " =    1.264
peak=   -3.111 closest distance to " CA  GLY A 133 " =    1.961
peak=   -3.108 closest distance to " CG2 VAL A 202 " =    2.707
peak=   -3.108 closest distance to " OD2 ASP A 191 " =    1.326
peak=   -3.108 closest distance to " O   HOH Z 175 " =    4.231
peak=   -3.102 closest distance to " O   HOH Z  10 " =    1.436
peak=   -3.101 closest distance to " OE2 GLU A 152 " =    1.249
peak=   -3.087 closest distance to " O   HOH Z 371 " =    2.100
peak=   -3.082 closest distance to " O   TRP A  70 " =    1.426
peak=   -3.078 closest distance to " O   HOH Z 216 " =    1.507
peak=   -3.076 closest distance to " O   HOH Z 166 " =    1.575
peak=   -3.075 closest distance to " OG  SER A  62 " =    1.644
peak=   -3.075 closest distance to " O   HOH Z 139 " =    3.144
peak=   -3.073 closest distance to " O   HOH Z 346 " =    1.787
peak=   -3.046 closest distance to " C   ASP A 270 " =    1.379

================= 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    :  0.4287 0.4121   6.220458e+00   6.188290e+00
   1_bss:  0.4212 0.4016   6.214938e+00   6.173341e+00
   1_xyz:  0.3079 0.3254   5.986337e+00   6.018342e+00
   1_adp:  0.2411 0.2755   5.771115e+00   5.883492e+00
   1_occ:  0.2405 0.2753   5.769531e+00   5.884342e+00
   2_bss:  0.2343 0.2687   5.766663e+00   5.877515e+00
   2_xyz:  0.1604 0.1982   5.425717e+00   5.595096e+00
   2_adp:  0.1473 0.1884   5.355269e+00   5.543297e+00
   2_occ:  0.1472 0.1884   5.355107e+00   5.543800e+00
   3_bss:  0.1468 0.1884   5.355839e+00   5.544264e+00
   3_xyz:  0.1202 0.1645   5.198365e+00   5.429724e+00
   3_adp:  0.1145 0.1609   5.164486e+00   5.409087e+00
   3_occ:  0.1144 0.1608   5.164169e+00   5.408768e+00
   4_bss:  0.1145 0.1605   5.164157e+00   5.407189e+00
   4_xyz:  0.1115 0.1584   5.147184e+00   5.396929e+00
   4_adp:  0.1120 0.1567   5.144105e+00   5.386149e+00
   4_occ:  0.1119 0.1567   5.143330e+00   5.385594e+00
   5_bss:  0.1119 0.1567   5.143330e+00   5.385594e+00
   5_xyz:  0.1136 0.1570   5.153120e+00   5.389853e+00
   5_adp:  0.1132 0.1572   5.153066e+00   5.392254e+00
   5_occ:  0.1131 0.1572   5.153103e+00   5.392468e+00
   5_bss:  0.1131 0.1572   5.153103e+00   5.392468e+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:  0.342  15.735   7.243   8.346   9.718   0.000   0.000   0.000
   1_xyz:  0.342  15.735   7.243   8.346   9.718   0.000   0.000   0.000
   1_adp:  0.342  15.735   7.243   8.346   9.718   0.000   0.000   0.000
   1_occ:  0.342  15.735   7.243   8.346   9.718   0.000   0.000   0.000
   2_bss:  0.331  39.931   3.705   4.201   6.049   0.000   0.000   0.000
   2_xyz:  0.331  39.931   3.705   4.201   6.049   0.000   0.000   0.000
   2_adp:  0.331  39.931   3.705   4.201   6.049   0.000   0.000   0.000
   2_occ:  0.331  39.931   3.705   4.201   6.049   0.000   0.000   0.000
   3_bss:  0.322  39.931   3.003   3.449   4.989   0.000   0.000   0.000
   3_xyz:  0.322  39.931   3.003   3.449   4.989   0.000   0.000   0.000
   3_adp:  0.322  39.931   3.003   3.449   4.989   0.000   0.000   0.000
   3_occ:  0.322  39.931   3.003   3.449   4.989   0.000   0.000   0.000
   4_bss:  0.322  39.931   3.003   3.449   4.989   0.000   0.000   0.000
   4_xyz:  0.322  39.931   3.003   3.449   4.989   0.000   0.000   0.000
   4_adp:  0.322  39.931   3.003   3.449   4.989   0.000   0.000   0.000
   4_occ:  0.322  39.931   3.003   3.449   4.989   0.000   0.000   0.000
   5_bss:  0.322  39.931   3.003   3.449   4.989   0.000   0.000   0.000
   5_xyz:  0.322  39.931   3.003   3.449   4.989   0.000   0.000   0.000
   5_adp:  0.322  39.931   3.003   3.449   4.989   0.000   0.000   0.000
   5_occ:  0.322  39.931   3.003   3.449   4.989   0.000   0.000   0.000
   5_bss:  0.322  43.744  -0.811  -0.364   1.175   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  45.306 0.5805  0.6462    49119.170
   1_bss:  45.052 0.5816  0.8346    46291.142
   1_xyz:  34.204 0.7099  0.9810    27938.576
   1_adp:  27.056 0.7906  1.0598    19098.972
   1_occ:  27.070 0.7904  1.0585    19102.492
   2_bss:  26.713 0.7942  0.9271    18679.225
   2_xyz:  18.647 0.8744  0.9936     9717.838
   2_adp:  17.235 0.8879  1.0029     8783.091
   2_occ:  17.256 0.8877  1.0027     8778.073
   3_bss:  17.245 0.8878  0.9720     8793.470
   3_xyz:  14.892 0.9074  0.9814     6886.771
   3_adp:  14.461 0.9111  0.9788     6586.736
   3_occ:  14.455 0.9112  0.9788     6580.557
   4_bss:  14.444 0.9112  0.9782     6563.797
   4_xyz:  14.081 0.9146  0.9792     6436.914
   4_adp:  13.847 0.9166  0.9775     6318.714
   4_occ:  13.837 0.9167  0.9774     6311.531
   5_bss:  13.837 0.9167  0.9774     6311.531
   5_xyz:  13.913 0.9161  0.9768     6355.981
   5_adp:  13.977 0.9156  0.9744     6379.748
   5_occ:  13.981 0.9156  0.9743     6381.640
   5_bss:  13.981 0.9156  0.9743     6381.640
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.3728e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.3728e+01
   1_xyz:   1.500  0.011  0.100 17.823  0.006  4.121   1.1428e-01
   1_adp:   1.500  0.011  0.100 17.823  0.006  4.121   1.1428e-01
   1_occ:   1.500  0.011  0.100 17.823  0.006  4.121   1.1428e-01
   2_bss:   1.500  0.011  0.100 17.823  0.006  4.121   1.1428e-01
   2_xyz:   0.945  0.006  0.074 15.961  0.003  4.121   5.7382e-02
   2_adp:   0.945  0.006  0.074 15.961  0.003  4.121   5.7382e-02
   2_occ:   0.945  0.006  0.074 15.961  0.003  4.121   5.7382e-02
   3_bss:   0.945  0.006  0.074 15.961  0.003  4.121   5.7382e-02
   3_xyz:   1.084  0.009  0.086 15.803  0.004  4.131   7.0889e-02
   3_adp:   1.084  0.009  0.086 15.803  0.004  4.131   7.0889e-02
   3_occ:   1.084  0.009  0.086 15.803  0.004  4.131   7.0889e-02
   4_bss:   1.084  0.009  0.086 15.803  0.004  4.131   7.0889e-02
   4_xyz:   1.018  0.008  0.083 15.570  0.004  4.133   6.3768e-02
   4_adp:   1.018  0.008  0.083 15.570  0.004  4.133   6.3768e-02
   4_occ:   1.018  0.008  0.083 15.570  0.004  4.133   6.3768e-02
   5_bss:   1.018  0.008  0.083 15.570  0.004  4.133   6.3768e-02
   5_xyz:   0.923  0.006  0.075 15.278  0.003  4.116   5.4162e-02
   5_adp:   0.923  0.006  0.075 15.278  0.003  4.116   5.4162e-02
   5_occ:   0.923  0.006  0.075 15.278  0.003  4.116   5.4162e-02
   5_bss:   0.923  0.006  0.075 15.278  0.003  4.116   5.4162e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9659e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9659e+00
   1_xyz:  12.245  0.136  0.406 89.684  0.033  2.219   8.3956e-02
   1_adp:  12.245  0.136  0.406 89.684  0.033  2.219   8.3956e-02
   1_occ:  12.245  0.136  0.406 89.684  0.033  2.219   8.3956e-02
   2_bss:  12.245  0.136  0.406 89.684  0.033  2.219   8.3956e-02
   2_xyz:   6.151  0.041  0.338 87.051  0.038  2.325   4.4906e-02
   2_adp:   6.151  0.041  0.338 87.051  0.038  2.325   4.4906e-02
   2_occ:   6.151  0.041  0.338 87.051  0.038  2.325   4.4906e-02
   3_bss:   6.151  0.041  0.338 87.051  0.038  2.325   4.4906e-02
   3_xyz:   6.509  0.046  0.570 83.731  0.038  2.231   6.6954e-02
   3_adp:   6.509  0.046  0.570 83.731  0.038  2.231   6.6954e-02
   3_occ:   6.509  0.046  0.570 83.731  0.038  2.231   6.6954e-02
   4_bss:   6.509  0.046  0.570 83.731  0.038  2.231   6.6954e-02
   4_xyz:   6.448  0.044  0.527 83.039  0.039  2.353   4.5162e-02
   4_adp:   6.448  0.044  0.527 83.039  0.039  2.353   4.5162e-02
   4_occ:   6.448  0.044  0.527 83.039  0.039  2.353   4.5162e-02
   5_bss:   6.448  0.044  0.527 83.039  0.039  2.353   4.5162e-02
   5_xyz:   6.201  0.043  0.443 82.891  0.036  2.349   3.1728e-02
   5_adp:   6.201  0.043  0.443 82.891  0.036  2.349   3.1728e-02
   5_occ:   6.201  0.043  0.443 82.891  0.036  2.349   3.1728e-02
   5_bss:   6.201  0.043  0.443 82.891  0.036  2.349   3.1728e-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:  51.98   0.00  10.43  49.60   0.00   7.35  51.98   0.00  27.17
   1_occ:  51.98   0.00  10.43  49.60   0.00   7.35  51.98   0.00  27.17
   2_bss:  51.98   0.00  10.43  49.60   0.00   7.35  51.98   0.00  27.17
   2_xyz:  51.98   0.00  10.43  49.60   0.00   7.35  51.98   0.00  27.17
   2_adp:  55.14   0.00  10.73  53.15   0.00   7.16  55.14   0.63  30.12
   2_occ:  55.14   0.00  10.73  53.15   0.00   7.16  55.14   0.63  30.12
   3_bss:  55.14   0.00  10.73  53.15   0.00   7.16  55.14   0.63  30.12
   3_xyz:  55.14   0.00  10.73  53.15   0.00   7.16  55.14   0.63  30.12
   3_adp:  75.85   0.00  11.59  75.85   0.00   7.33  68.92   0.27  34.82
   3_occ:  75.85   0.00  11.59  75.85   0.00   7.33  68.92   0.27  34.82
   4_bss:  75.85   0.00  11.59  75.85   0.00   7.33  68.92   0.27  34.82
   4_xyz:  75.85   0.00  11.59  75.85   0.00   7.33  68.92   0.27  34.82
   4_adp:  76.33   0.00  11.05  76.33   0.00   7.11  67.31   0.95  32.50
   4_occ:  76.33   0.00  11.05  76.33   0.00   7.11  67.31   0.95  32.50
   5_bss:  76.33   0.00  11.05  76.33   0.00   7.11  67.31   0.95  32.50
   5_xyz:  76.33   0.00  11.05  76.33   0.00   7.11  67.31   0.95  32.50
   5_adp:  78.14   0.00  11.05  78.14   0.00   7.09  67.34   0.77  32.64
   5_occ:  78.14   0.00  11.05  78.14   0.00   7.09  67.34   0.77  32.64
   5_bss:  81.95   3.81  14.86  81.95   3.81  10.90  71.15   4.59  36.46
------------------------------------------------------------------------
 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:    1.210    0.020    0.399
   1_adp:    1.210    0.020    0.399
   1_occ:    1.210    0.020    0.399
   2_bss:    1.210    0.020    0.399
   2_xyz:    1.478    0.017    0.489
   2_adp:    1.478    0.017    0.489
   2_occ:    1.478    0.017    0.489
   3_bss:    1.478    0.017    0.489
   3_xyz:    1.456    0.041    0.524
   3_adp:    1.456    0.041    0.524
   3_occ:    1.456    0.041    0.524
   4_bss:    1.456    0.041    0.524
   4_xyz:    1.566    0.041    0.535
   4_adp:    1.566    0.041    0.535
   4_occ:    1.566    0.041    0.535
   5_bss:    1.566    0.041    0.535
   5_xyz:    1.657    0.024    0.540
   5_adp:    1.657    0.024    0.540
   5_occ:    1.657    0.024    0.540
   5_bss:    1.657    0.024    0.540
------------------------------------------------------------------------

CPU time actual refinement: 342.19


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_535/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_535/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_535/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_535/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_535/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 342.04 
  Macro-tasks:
    bulk solvent and scale       = 40.72  
    individual site refinement   = 148.34 
    weights calculation          = 32.38  
    collect and process          = 6.56   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 228.11 
  Micro-tasks:
    mask                            = 1.81   
    f_calc                          = 105.19 
    alpha_beta                      = 7.88   
    target                          = 1.13   
    gradients_wrt_atomic_parameters = 118.66 
    fmodel                         = 7.32   
    r_factors                      = 0.22   
    phase_errors                   = 11.03  
    foms                           = 0.26   
    TOTAL for micro-tasks          = 253.50 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.662 micro seconds
Total CPU time: 5.93 minutes
from_scatterers_fft:    683 calls, 104.69 s
gradients_fft:          628 calls, 103.77 s

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

# Date 2008-01-16 Time 01:50:22 PST -0800 (1200477022.78 s)
Start R-work = 0.4287, R-free = 0.4121 (no bulk solvent and anisotropic scale)
Final R-work = 0.1313, R-free = 0.1747 (no bulk solvent and anisotropic scale)

Start R-work = 0.4212, R-free = 0.4016
Final R-work = 0.1131, R-free = 0.1572