# Date 2008-01-16 Time 03:33:14 PST -0800 (1200483194.33 s)
#phil __OFF__

Command line arguments: "../1282.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 13614
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1282

-------------------------------------------------------------------------------
  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: (72.0062, 47.1647, 86.822, 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: 2.78, per 1000 atoms: 0.98


================================== 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: (72.0062, 47.1647, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2858 2.01038
Completeness in resolution range: 0.967597
Completeness with d_max=infinity: 0.964643

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2858
                             d_min =   2.0104

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: (72.0062, 47.1647, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2858 2.01038
Completeness in resolution range: 0.967597
Completeness with d_max=infinity: 0.964643

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2862 -  4.3021 [2122/2147]  1912   210   9.9%
  bin  2:  4.3021 -  3.4273 [2043/2063]  1838   205  10.0%
  bin  3:  3.4273 -  2.9978 [2019/2038]  1814   205  10.2%
  bin  4:  2.9978 -  2.7254 [1995/2025]  1800   195   9.8%
  bin  5:  2.7254 -  2.5310 [1988/2007]  1793   195   9.8%
  bin  6:  2.5310 -  2.3824 [1988/2013]  1784   204  10.3%
  bin  7:  2.3824 -  2.2634 [1939/1967]  1743   196  10.1%
  bin  8:  2.2634 -  2.1652 [1976/2012]  1777   199  10.1%
  bin  9:  2.1652 -  2.0821 [1951/1993]  1756   195  10.0%
  bin 10:  2.0821 -  2.0104 [1568/1980]  1413   155   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1282/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: 0.12 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:
        1.54 -     2.22: 3
        2.22 -     2.89: 1266
        2.89 -     3.56: 4381
        3.56 -     4.23: 9066
        4.23 -     4.90: 13158
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.544 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 208 " - " O   HOH Z 342 "  2.082 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z 107 " - " O   HOH Z 340 "  2.219 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 27869 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_1282/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1282/model_refine_001.geo

CPU time processing inputs: 8.02


============================ 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 = 72.00625 47.16465 86.82195 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: 2.01 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4614   r_free= 0.4485   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:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.263720                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2862 -  4.7985 0.99   1385  153 0.3802 0.3547      6.5686        6.45|
|  2:  4.7985 -  3.8284 0.99   1329  148 0.3682 0.3913      6.7476      6.7867|
|  3:  3.8284 -  3.3503 0.99   1297  142 0.4099 0.3787      6.6237       6.651|
|  4:  3.3503 -  3.0466 0.99   1299  153 0.4422 0.3944       6.508      6.4214|
|  5:  3.0466 -  2.8297 0.99   1287  138 0.4812 0.5019      6.3541      6.3979|
|  6:  2.8297 -  2.6638 0.99   1282  141 0.4850 0.4895      6.2683      6.2205|
|  7:  2.6638 -  2.5310 0.99   1278  135 0.5145 0.5070      6.2386      6.2593|
|  8:  2.5310 -  2.4213 0.98   1265  151 0.5191 0.4756       6.177       6.144|
|  9:  2.4213 -  2.3284 0.98   1245  138 0.4947 0.5224      6.1132      6.1462|
| 10:  2.3284 -  2.2483 1.00   1291  140 0.5125 0.4685      6.1066      6.0982|
| 11:  2.2483 -  2.1782 0.97   1252  137 0.5121 0.4802       6.047      6.0303|
| 12:  2.1782 -  2.1161 0.98   1250  142 0.5209 0.5455      5.9816      6.0491|
| 13:  2.1161 -  2.0605 1.00   1265  136 0.5240 0.4929      5.9034      5.8467|
| 14:  2.0605 -  2.0104 0.71    905  105 0.5202 0.4442      5.8659      5.7054|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2862 -  4.7985  1385   153  0.73  31.83   0.79     0.76      62312.06|
|  2:  4.7985 -  3.8284  1329   148  0.75  31.27   0.89     0.79      87395.47|
|  3:  3.8284 -  3.3503  1297   142  0.66  38.99   0.83     0.74      94825.17|
|  4:  3.3503 -  3.0466  1299   153  0.57  46.07   0.81     0.65      87775.31|
|  5:  3.0466 -  2.8297  1287   138  0.47  54.45   0.73     0.55      75965.19|
|  6:  2.8297 -  2.6638  1282   141  0.42  57.96   0.75     0.49      69014.42|
|  7:  2.6638 -  2.5310  1278   135  0.39  60.68   0.71     0.43      63649.06|
|  8:  2.5310 -  2.4213  1265   151  0.37  62.27   0.72     0.43      58364.06|
|  9:  2.4213 -  2.3284  1245   138  0.40  60.31   0.73     0.44      51081.87|
| 10:  2.3284 -  2.2483  1291   140  0.41  59.31   0.74     0.46      45577.34|
| 11:  2.2483 -  2.1782  1252   137  0.40  60.09   0.75     0.46      42111.81|
| 12:  2.1782 -  2.1161  1250   142  0.39  60.84   0.75     0.46      39679.17|
| 13:  2.1161 -  2.0605  1265   136  0.41  58.99   0.71     0.49      33187.14|
| 14:  2.0605 -  2.0104   905   105  0.51  51.69   0.71     0.55      22962.62|
|alpha:            min =        0.43 max =            0.79 mean =         0.55|
|beta:             min =    22962.62 max =        94825.17 mean =     60601.25|
|figures of merit: min =        0.00 max =            1.00 mean =         0.49|
|phase err.(work): min =        0.00 max =           90.00 mean =        52.25|
|phase err.(test): min =        0.00 max =           89.98 mean =        51.93|
|-----------------------------------------------------------------------------|

============================== 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 = 11.553339             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 77.899   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.886247              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.786   (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:       21 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      160 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      675 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1479 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2593 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3853 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     4974 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6491 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7611 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       54.418 |
| 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 |       1.611 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.323)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 12.323)------------------------------------------|
|    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: 2.01 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4676   r_free= 0.4525   ksol= 0.00   Bsol= 0.00   scale= 0.765    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.265035                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4541   r_free= 0.4362   ksol= 0.30   Bsol= 20.00   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (10.37,7.65,7.92,0.00,0.00,0.00); trace/3= 8.65                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.257412                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.517265             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.235   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.868036              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.243   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4541      final r-factor (work) = 0.3536          |
| start r-factor (free) = 0.4362      final r-factor (free) = 0.3805          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 87.3740 = 10.52 * 0.50 * 6.2670 + 1.00 * 54.4181                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 32.4124 = 10.52 * 0.50 * 6.1374 + 1.00 * 0.1381                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3536      final r-factor (work) = 0.3059          |
| start r-factor (free) = 0.3805      final r-factor (free) = 0.3469          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.3419 = 0.87 * 1.00 * 6.1374 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.2480 = 0.87 * 1.00 * 6.0303 + 1.00 * 0.0135                               |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.323)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    73.32   11.11    None  None   None       |
|    all(noH): 2823   0      0.00    73.32   11.11    None  None   None       |
|    Sol.    : 438    0      0.00    73.32   25.93    None  None   None       |
|    Mac.    : 2385   0      0.00    61.54   8.39     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 -   7.332: 1409   |   5:    36.661 -  43.993:   61        |
|      1:     7.332 -  14.664:  689   |   6:    43.993 -  51.325:   45        |
|      2:    14.664 -  21.997:  338   |   7:    51.325 -  58.657:   14        |
|      3:    21.997 -  29.329:  154   |   8:    58.657 -  65.990:    5        |
|      4:    29.329 -  36.661:  105   |   9:    65.990 -  73.322:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3059 r_free = 0.3469             target_work(ml) = 5.997         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3053 r_free = 0.3476             target_work(ml) = 5.996         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3053   r_free= 0.3476   ksol= 0.30   Bsol= 20.00   scale= 1.066   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (10.37,7.65,7.92,0.00,0.00,0.00); trace/3= 8.65                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.46 A                  |
| x-ray target function (ml) for work reflections: 5.996189                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3030   r_free= 0.3443   ksol= 0.33   Bsol= 50.00   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.21,4.88,5.49,0.00,0.00,0.00); trace/3= 5.86                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 5.996719                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.085893              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.154   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.474877              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 125.596  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3030      final r-factor (work) = 0.2214          |
| start r-factor (free) = 0.3443      final r-factor (free) = 0.2760          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.4632 = 5.09 * 0.50 * 6.0265 + 1.00 * 0.1381                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.9855 = 5.09 * 0.50 * 5.8640 + 1.00 * 0.0736                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2214      final r-factor (work) = 0.2059          |
| start r-factor (free) = 0.2760      final r-factor (free) = 0.2593          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8223 = 0.47 * 1.00 * 5.8640 + 1.00 * 0.0376                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8961 = 0.47 * 1.00 * 5.6941 + 1.00 * 0.1921                               |
|-----------------------------------------------------------------------------|
| number of iterations = 8       |    number of function evaluations = 13     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.323)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.08   11.40    None  None   None       |
|    all(noH): 2823   0      0.00    79.08   11.40    None  None   None       |
|    Sol.    : 438    0      0.00    73.63   28.52    None  None   None       |
|    Mac.    : 2385   0      0.00    79.08   8.25     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 -   7.908: 1471   |   5:    39.541 -  47.450:   61        |
|      1:     7.908 -  15.817:  714   |   6:    47.450 -  55.358:   37        |
|      2:    15.817 -  23.725:  254   |   7:    55.358 -  63.266:   12        |
|      3:    23.725 -  31.633:  175   |   8:    63.266 -  71.175:    2        |
|      4:    31.633 -  39.541:   95   |   9:    71.175 -  79.083:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2059 r_free = 0.2593             target_work(ml) = 5.666         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2055 r_free = 0.2591             target_work(ml) = 5.666         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2055   r_free= 0.2591   ksol= 0.33   Bsol= 50.00   scale= 1.039   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.21,4.88,5.49,0.00,0.00,0.00); trace/3= 5.86                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.665743                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2042   r_free= 0.2567   ksol= 0.33   Bsol= 50.00   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.39,3.53,4.35,0.00,0.00,0.00); trace/3= 4.09                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.665252                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.377265              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.917  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 5.086375              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.615   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2042      final r-factor (work) = 0.1590          |
| start r-factor (free) = 0.2567      final r-factor (free) = 0.2072          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.6954 = 3.38 * 0.50 * 5.6980 + 1.00 * 0.0736                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.4580 = 3.38 * 0.50 * 5.5574 + 1.00 * 0.0736                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1590      final r-factor (work) = 0.1407          |
| start r-factor (free) = 0.2072      final r-factor (free) = 0.1923          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 28.2835 = 5.09 * 1.00 * 5.5574 + 1.00 * 0.0166                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 27.3803 = 5.09 * 1.00 * 5.3796 + 1.00 * 0.0175                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.323)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.01   13.02    None  None   None       |
|    all(noH): 2823   0      0.00    90.01   13.02    None  None   None       |
|    Sol.    : 438    0      0.00    90.01   38.54    None  None   None       |
|    Mac.    : 2385   0      0.00    83.50   8.33     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.001: 1673   |   5:    45.006 -  54.007:   82        |
|      1:     9.001 -  18.002:  572   |   6:    54.007 -  63.008:   73        |
|      2:    18.002 -  27.004:  176   |   7:    63.008 -  72.009:   30        |
|      3:    27.004 -  36.005:   98   |   8:    72.009 -  81.011:   19        |
|      4:    36.005 -  45.006:   96   |   9:    81.011 -  90.012:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1407 r_free = 0.1923             target_work(ml) = 5.347         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1405 r_free = 0.1924             target_work(ml) = 5.347         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1405   r_free= 0.1924   ksol= 0.33   Bsol= 50.00   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.39,3.53,4.35,0.00,0.00,0.00); trace/3= 4.09                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.347051                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1405   r_free= 0.1921   ksol= 0.33   Bsol= 67.58   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.32,2.84,3.81,0.00,0.00,0.00); trace/3= 3.32                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.345959                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.637180              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.818  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.131710              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 119.868  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1405      final r-factor (work) = 0.1243          |
| start r-factor (free) = 0.1921      final r-factor (free) = 0.1786          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.8640 = 3.64 * 0.50 * 5.3835 + 1.00 * 0.0736                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.7135 = 3.64 * 0.50 * 5.2958 + 1.00 * 0.0825                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1243      final r-factor (work) = 0.1209          |
| start r-factor (free) = 0.1786      final r-factor (free) = 0.1737          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.3067 = 2.13 * 1.00 * 5.2958 + 1.00 * 0.0175                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.1861 = 2.13 * 1.00 * 5.2397 + 1.00 * 0.0166                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.323)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.23   12.92    None  None   None       |
|    all(noH): 2823   0      0.00    99.23   12.92    None  None   None       |
|    Sol.    : 438    0      0.68    99.23   38.75    None  None   None       |
|    Mac.    : 2385   0      0.00    91.60   8.18     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.924: 1810   |   5:    49.617 -  59.541:   85        |
|      1:     9.924 -  19.847:  492   |   6:    59.541 -  69.464:   49        |
|      2:    19.847 -  29.771:  153   |   7:    69.464 -  79.388:   20        |
|      3:    29.771 -  39.694:  111   |   8:    79.388 -  89.311:    9        |
|      4:    39.694 -  49.617:   90   |   9:    89.311 -  99.235:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1209 r_free = 0.1737             target_work(ml) = 5.225         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1208 r_free = 0.1737             target_work(ml) = 5.225         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1208   r_free= 0.1737   ksol= 0.33   Bsol= 67.58   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.32,2.84,3.81,0.00,0.00,0.00); trace/3= 3.32                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.225379                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1208   r_free= 0.1737   ksol= 0.33   Bsol= 65.14   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.27,2.94,3.94,0.00,0.00,0.00); trace/3= 3.38                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.225422                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.894338              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 142.427  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.209093              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.629  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1208      final r-factor (work) = 0.1180          |
| start r-factor (free) = 0.1737      final r-factor (free) = 0.1704          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6652 = 2.89 * 0.50 * 5.2397 + 1.00 * 0.0825                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6254 = 2.89 * 0.50 * 5.2164 + 1.00 * 0.0764                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1180      final r-factor (work) = 0.1194          |
| start r-factor (free) = 0.1704      final r-factor (free) = 0.1669          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1072 = 0.21 * 1.00 * 5.2164 + 1.00 * 0.0165                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1163 = 0.21 * 1.00 * 5.2140 + 1.00 * 0.0261                               |
|-----------------------------------------------------------------------------|
| number of iterations = 15      |    number of function evaluations = 16     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.323)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.01   12.18    None  None   None       |
|    all(noH): 2823   0      0.00    90.01   12.18    None  None   None       |
|    Sol.    : 438    0      1.40    90.01   35.58    None  None   None       |
|    Mac.    : 2385   0      0.00    87.81   7.89     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.001: 1773   |   5:    45.006 -  54.007:   90        |
|      1:     9.001 -  18.003:  529   |   6:    54.007 -  63.009:   41        |
|      2:    18.003 -  27.004:  152   |   7:    63.009 -  72.010:   24        |
|      3:    27.004 -  36.005:  118   |   8:    72.010 -  81.011:    8        |
|      4:    36.005 -  45.006:   82   |   9:    81.011 -  90.012:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1194 r_free = 0.1669             target_work(ml) = 5.201         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1192 r_free = 0.1668             target_work(ml) = 5.201         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1192   r_free= 0.1668   ksol= 0.33   Bsol= 65.14   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.27,2.94,3.94,0.00,0.00,0.00); trace/3= 3.38                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.200959                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2862 -  4.7985 0.99   1385  153 0.1022 0.1383      5.4039      5.5578|
|  2:  4.7985 -  3.8284 0.99   1329  148 0.0882 0.1146      5.4673      5.6687|
|  3:  3.8284 -  3.3503 0.99   1297  142 0.1087 0.1585      5.5035       5.893|
|  4:  3.3503 -  3.0466 0.99   1299  153 0.1273 0.1603      5.5028      5.6263|
|  5:  3.0466 -  2.8297 0.99   1287  138 0.1434 0.1958      5.3923      5.6595|
|  6:  2.8297 -  2.6638 0.99   1282  141 0.1318 0.1911        5.29      5.4974|
|  7:  2.6638 -  2.5310 0.99   1278  135 0.1369 0.1784      5.2382      5.4465|
|  8:  2.5310 -  2.4213 0.98   1265  151 0.1278 0.1738      5.1373      5.3691|
|  9:  2.4213 -  2.3284 0.98   1245  138 0.1255 0.1908        5.11      5.3651|
| 10:  2.3284 -  2.2483 1.00   1291  140 0.1263 0.1940      5.0413      5.3487|
| 11:  2.2483 -  2.1782 0.97   1252  137 0.1257 0.1809       5.024      5.2711|
| 12:  2.1782 -  2.1161 0.98   1250  142 0.1183 0.1848      4.9303      5.2307|
| 13:  2.1161 -  2.0605 1.00   1265  136 0.1281 0.1798      4.8549      5.1246|
| 14:  2.0605 -  2.0104 0.71    905  105 0.1193 0.1721      4.7258      4.9358|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2862 -  4.7985  1385   153  0.94   9.26   0.97     0.95       7574.57|
|  2:  4.7985 -  3.8284  1329   148  0.95   8.42   1.00     0.98       9780.38|
|  3:  3.8284 -  3.3503  1297   142  0.93  11.83   1.02     1.01      11177.53|
|  4:  3.3503 -  3.0466  1299   153  0.91  14.43   1.00     0.98      11320.28|
|  5:  3.0466 -  2.8297  1287   138  0.89  17.05   0.99     0.97       9307.31|
|  6:  2.8297 -  2.6638  1282   141  0.89  16.99   0.98     0.96       8197.20|
|  7:  2.6638 -  2.5310  1278   135  0.90  16.64   0.99     0.97       6974.16|
|  8:  2.5310 -  2.4213  1265   151  0.90  16.38   0.98     0.96       5984.16|
|  9:  2.4213 -  2.3284  1245   138  0.90  16.68   1.00     0.96       5816.89|
| 10:  2.3284 -  2.2483  1291   140  0.90  16.47   0.99     0.95       4890.26|
| 11:  2.2483 -  2.1782  1252   137  0.89  17.33   0.99     0.94       4917.42|
| 12:  2.1782 -  2.1161  1250   142  0.91  15.46   1.00     1.00       4314.12|
| 13:  2.1161 -  2.0605  1265   136  0.89  17.27   0.99     0.98       3681.91|
| 14:  2.0605 -  2.0104   905   105  0.91  15.38   0.97     0.95       2724.18|
|alpha:            min =        0.94 max =            1.01 mean =         0.97|
|beta:             min =     2724.18 max =        11320.28 mean =      7027.17|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.83 mean =        14.90|
|phase err.(test): min =        0.00 max =           89.93 mean =        14.22|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1195   r_free= 0.1666   ksol= 0.33   Bsol= 68.32   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.18,-0.42,0.60,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.201709                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1195   r_free= 0.1666   ksol= 0.33   Bsol= 68.32   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.18,-0.42,0.60,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.201709                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2862 -  4.7985 0.99   1385  153 0.1033 0.1349      5.4069      5.5501|
|  2:  4.7985 -  3.8284 0.99   1329  148 0.0884 0.1143      5.4705      5.6658|
|  3:  3.8284 -  3.3503 0.99   1297  142 0.1088 0.1590      5.5042       5.894|
|  4:  3.3503 -  3.0466 0.99   1299  153 0.1273 0.1618      5.5042       5.634|
|  5:  3.0466 -  2.8297 0.99   1287  138 0.1436 0.1963      5.3935      5.6604|
|  6:  2.8297 -  2.6638 0.99   1282  141 0.1317 0.1905      5.2898      5.4964|
|  7:  2.6638 -  2.5310 0.99   1278  135 0.1369 0.1780      5.2375      5.4456|
|  8:  2.5310 -  2.4213 0.98   1265  151 0.1278 0.1741      5.1375      5.3705|
|  9:  2.4213 -  2.3284 0.98   1245  138 0.1256 0.1908      5.1099      5.3651|
| 10:  2.3284 -  2.2483 1.00   1291  140 0.1263 0.1941      5.0415      5.3489|
| 11:  2.2483 -  2.1782 0.97   1252  137 0.1256 0.1811      5.0238       5.271|
| 12:  2.1782 -  2.1161 0.98   1250  142 0.1183 0.1846      4.9309      5.2307|
| 13:  2.1161 -  2.0605 1.00   1265  136 0.1280 0.1802      4.8551      5.1257|
| 14:  2.0605 -  2.0104 0.71    905  105 0.1193 0.1723      4.7263      4.9363|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2862 -  4.7985  1385   153  0.94   9.55   0.96     0.94       7585.66|
|  2:  4.7985 -  3.8284  1329   148  0.95   8.46   0.99     0.98       9780.51|
|  3:  3.8284 -  3.3503  1297   142  0.93  11.85   1.01     1.01      11198.04|
|  4:  3.3503 -  3.0466  1299   153  0.91  14.46   1.00     0.97      11374.05|
|  5:  3.0466 -  2.8297  1287   138  0.89  17.09   0.99     0.96       9345.31|
|  6:  2.8297 -  2.6638  1282   141  0.89  17.00   0.98     0.95       8201.46|
|  7:  2.6638 -  2.5310  1278   135  0.90  16.63   0.99     0.96       6968.90|
|  8:  2.5310 -  2.4213  1265   151  0.90  16.38   0.97     0.95       5989.06|
|  9:  2.4213 -  2.3284  1245   138  0.90  16.68   0.99     0.95       5813.82|
| 10:  2.3284 -  2.2483  1291   140  0.90  16.48   0.99     0.94       4894.96|
| 11:  2.2483 -  2.1782  1252   137  0.89  17.34   0.98     0.93       4920.02|
| 12:  2.1782 -  2.1161  1250   142  0.91  15.47   0.99     0.99       4320.91|
| 13:  2.1161 -  2.0605  1265   136  0.89  17.28   0.98     0.97       3686.05|
| 14:  2.0605 -  2.0104   905   105  0.91  15.39   0.96     0.94       2728.65|
|alpha:            min =        0.93 max =            1.01 mean =         0.96|
|beta:             min =     2728.65 max =        11374.05 mean =      7037.90|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.97 mean =        14.93|
|phase err.(test): min =        0.00 max =           89.09 mean =        14.28|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.323)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.18    93.19   15.36    None  None   None       |
|    all(noH): 2823   0      3.18    93.19   15.36    None  None   None       |
|    Sol.    : 438    0      4.58    93.19   38.76    None  None   None       |
|    Mac.    : 2385   0      3.18    90.99   11.07    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:     3.182 -  12.183: 1773   |   5:    48.188 -  57.189:   90        |
|      1:    12.183 -  21.184:  529   |   6:    57.189 -  66.190:   41        |
|      2:    21.184 -  30.186:  152   |   7:    66.190 -  75.192:   24        |
|      3:    30.186 -  39.187:  118   |   8:    75.192 -  84.193:    8        |
|      4:    39.187 -  48.188:   82   |   9:    84.193 -  93.194:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 337         
Filter by distance & map next to the model:
   mapped sites are within: 0.330 - 4.867
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 327 from: 337
   mapped sites are within: 0.706 - 4.867

peak=    9.947 closest distance to " CG2 VAL A 230 " =    1.446
peak=    7.386 closest distance to " CG2 VAL A 296 " =    1.178
peak=    6.010 closest distance to " CG  LEU A   5 " =    1.266
peak=    5.504 closest distance to " CB  GLN A 223 " =    1.437
peak=    5.433 closest distance to " CD2 LEU A   5 " =    1.176
peak=    5.367 closest distance to " O   HOH Z 111 " =    1.901
peak=    5.195 closest distance to " CG  LEU A 228 " =    1.215
peak=    5.017 closest distance to " CB  SER A  63 " =    1.296
peak=    4.936 closest distance to " O   HOH Z 232 " =    2.209
peak=    4.892 closest distance to " CB  VAL A 230 " =    1.301
peak=    4.672 closest distance to " O   HOH Z 369 " =    2.017
peak=    4.621 closest distance to " CB  GLN A 183 " =    1.229
peak=    4.548 closest distance to " CG  PRO A 243 " =    1.130
peak=    4.534 closest distance to " O   HOH Z 368 " =    2.253
peak=    4.491 closest distance to " CB  ASP A 124 " =    0.746
peak=    4.460 closest distance to " CZ  PHE A 218 " =    1.067
peak=    4.458 closest distance to " CB  TRP A 266 " =    0.925
peak=    4.452 closest distance to " O   HOH Z 236 " =    1.943
peak=    4.447 closest distance to " NH1AARG A 145 " =    1.236
peak=    4.426 closest distance to " O   HOH Z 298 " =    1.959
peak=    4.420 closest distance to " O   HOH Z 265 " =    2.330
peak=    4.403 closest distance to " CG  PRO A 213 " =    1.237
peak=    4.397 closest distance to " CG2 THR A 221 " =    0.997
peak=    4.361 closest distance to " O   PRO A 198 " =    1.572
peak=    4.351 closest distance to " O   HOH Z 303 " =    2.162
peak=    4.331 closest distance to " O   HOH Z 184 " =    1.641
peak=    4.326 closest distance to " O   HOH Z 425 " =    1.542
peak=    4.319 closest distance to " CB  GLU A 128 " =    1.093
peak=    4.289 closest distance to " NE2 GLN A  11 " =    1.107
peak=    4.261 closest distance to " CD1 LEU A 300 " =    1.201
peak=    4.242 closest distance to " O   HOH Z 102 " =    1.446
peak=    4.209 closest distance to " O   HOH Z 410 " =    1.335
peak=    4.194 closest distance to " O   HOH Z 112 " =    1.576
peak=    4.188 closest distance to " ND2 ASN A 187 " =    1.541
peak=    4.181 closest distance to " O   HOH Z 234 " =    3.793
peak=    4.172 closest distance to " CB  ASN A 148 " =    1.359
peak=    4.153 closest distance to " CG  PRO A 198 " =    1.291
peak=    4.152 closest distance to " O   HOH Z 403 " =    1.725
peak=    4.127 closest distance to " O   HOH Z 272 " =    1.923
peak=    4.122 closest distance to " O   HOH Z 316 " =    3.143
peak=    4.080 closest distance to " O   HOH Z 261 " =    1.905
peak=    4.068 closest distance to " CB  GLU A 152 " =    1.187
peak=    4.050 closest distance to " CB  ASP A 140 " =    0.829
peak=    4.042 closest distance to " O   HOH Z 183 " =    1.250
peak=    4.040 closest distance to " CZ  PHE A 192 " =    0.970
peak=    4.037 closest distance to " O   HOH Z 247 " =    1.411
peak=    4.032 closest distance to " NH2 ARG A 156 " =    1.137
peak=    4.021 closest distance to " O   HOH Z 427 " =    3.244
peak=    4.012 closest distance to " NH1 ARG A  56 " =    1.037
peak=    3.998 closest distance to " CB  ASN A 187 " =    1.001
peak=    3.995 closest distance to " CB  GLU A 277 " =    3.704
peak=    3.987 closest distance to " O   HOH Z  88 " =    3.462
peak=    3.986 closest distance to " CD2 LEU A 228 " =    1.204
peak=    3.985 closest distance to " CB  VAL A 202 " =    1.567
peak=    3.983 closest distance to " O   HOH Z 126 " =    1.591
peak=    3.979 closest distance to " O   HOH Z 193 " =    2.188
peak=    3.967 closest distance to " O   HOH Z 411 " =    3.593
peak=    3.957 closest distance to " CG  ARG A 138 " =    1.181
peak=    3.941 closest distance to " CD  ARG A  66 " =    2.363
peak=    3.935 closest distance to " CB  ARG A  79 " =    1.509
peak=    3.904 closest distance to " CB  LEU A 143 " =    1.175
peak=    3.894 closest distance to " OD1 ASN A  69 " =    2.574
peak=    3.886 closest distance to " O   HOH Z  15 " =    1.814
peak=    3.880 closest distance to " CB  SER A 216 " =    0.863
peak=    3.869 closest distance to " CB  LEU A 228 " =    1.180
peak=    3.862 closest distance to " CB  ALA A   9 " =    1.601
peak=    3.854 closest distance to " O   HOH Z 346 " =    1.532
peak=    3.849 closest distance to " CA  ALA A 295 " =    1.104
peak=    3.842 closest distance to " CD1 LEU A   5 " =    1.312
peak=    3.842 closest distance to " O   HOH Z 437 " =    1.795
peak=    3.824 closest distance to " O   HOH Z  63 " =    1.939
peak=    3.824 closest distance to " CB  SER A   3 " =    1.467
peak=    3.822 closest distance to " O   HOH Z  80 " =    1.819
peak=    3.814 closest distance to " CB  ALA A 104 " =    0.801
peak=    3.813 closest distance to " O   HOH Z 214 " =    2.042
peak=    3.811 closest distance to " O   HOH Z 290 " =    1.311
peak=    3.811 closest distance to " CD  ARG A 159 " =    0.769
peak=    3.807 closest distance to " O   SER A  87 " =    2.290
peak=    3.804 closest distance to " O   HOH Z  68 " =    1.663
peak=    3.803 closest distance to " CB  ARG A 275 " =    0.891
peak=    3.788 closest distance to " CG1 ILE A  33 " =    1.303
peak=    3.785 closest distance to " CG1 VAL A 153 " =    0.973
peak=    3.778 closest distance to " CB  GLU A  46 " =    0.972
peak=    3.778 closest distance to " CG BARG A 275 " =    1.511
peak=    3.771 closest distance to " O   HOH Z  57 " =    1.500
peak=    3.770 closest distance to " O   HOH Z 126 " =    1.966
peak=    3.768 closest distance to " CB  VAL A 296 " =    1.172
peak=    3.754 closest distance to " CD2 LEU A 255 " =    1.602
peak=    3.751 closest distance to " O   HOH Z 163 " =    1.778
peak=    3.751 closest distance to " CA  MET A  40 " =    1.146
peak=    3.744 closest distance to " CD ALYS A 290 " =    1.067
peak=    3.743 closest distance to " CA  LEU A 282 " =    0.990
peak=    3.725 closest distance to " CB  ALA A  34 " =    0.778
peak=    3.704 closest distance to " O   HOH Z 132 " =    2.551
peak=    3.701 closest distance to " CB  ASN A  39 " =    0.876
peak=    3.700 closest distance to " O   HOH Z 158 " =    3.020
peak=    3.690 closest distance to " O   HOH Z  78 " =    1.747
peak=    3.683 closest distance to " CB  VAL A 265 " =    1.330
peak=    3.678 closest distance to " O   HOH Z 193 " =    1.722
peak=    3.668 closest distance to " O   HOH Z 188 " =    3.026
peak=    3.666 closest distance to " CB  ASN A 142 " =    0.956
peak=    3.663 closest distance to " O   HOH Z 213 " =    1.970
peak=    3.663 closest distance to " CB  ARG A 190 " =    1.641
peak=    3.659 closest distance to " CB  PRO A  54 " =    0.759
peak=    3.649 closest distance to " ND2 ASN A 249 " =    1.946
peak=    3.648 closest distance to " O   HOH Z 201 " =    3.135
peak=    3.644 closest distance to " CD  LYS A 166 " =    1.267
peak=    3.643 closest distance to " OD1 ASN A 217 " =    1.627
peak=    3.643 closest distance to " CB  TRP A 150 " =    1.390
peak=    3.631 closest distance to " O   ASP A 124 " =    1.157
peak=    3.630 closest distance to " O   HOH Z  98 " =    1.989
peak=    3.627 closest distance to " CB  ALA A 242 " =    0.766
peak=    3.627 closest distance to " CA  ALA A  51 " =    0.982
peak=    3.627 closest distance to " CB  SER A 212 " =    1.245
peak=    3.625 closest distance to " CA  SER A  87 " =    0.895
peak=    3.620 closest distance to " O   HOH Z 128 " =    2.287
peak=    3.618 closest distance to " O   HOH Z 133 " =    2.362
peak=    3.609 closest distance to " CA  ALA A  21 " =    1.210
peak=    3.609 closest distance to " O   HOH Z  78 " =    2.170
peak=    3.606 closest distance to " ND1 HIS A  81 " =    1.702
peak=    3.595 closest distance to " CB  ILE A 120 " =    1.322
peak=    3.590 closest distance to " N   SER A 135 " =    1.394
peak=    3.586 closest distance to " CB  SER A 141 " =    1.001
peak=    3.577 closest distance to " CG1BVAL A  72 " =    1.381
peak=    3.568 closest distance to " O   MET A 105 " =    1.777
peak=    3.563 closest distance to " CG AARG A 275 " =    1.274
peak=    3.560 closest distance to " CG  LEU A 167 " =    1.190
peak=    3.560 closest distance to " O   HOH Z  68 " =    1.972
peak=    3.559 closest distance to " N   PHE A 130 " =    1.241
peak=    3.559 closest distance to " CG  MET A 185 " =    1.334
peak=    3.553 closest distance to " OE1 GLN A  11 " =    1.913
peak=    3.552 closest distance to " O   HOH Z 258 " =    2.186
peak=    3.544 closest distance to " OG  SER A 276 " =    1.470
peak=    3.544 closest distance to " CA  THR A 221 " =    0.883
peak=    3.542 closest distance to " O   ALA A 158 " =    1.370
peak=    3.537 closest distance to " O   HOH Z  97 " =    2.030
peak=    3.531 closest distance to " O   HOH Z 185 " =    2.321
peak=    3.517 closest distance to " N   ASN A  39 " =    1.272
peak=    3.514 closest distance to " CA  TYR A  30 " =    0.972
peak=    3.514 closest distance to " O   HOH Z 174 " =    1.183
peak=    3.509 closest distance to " O   HOH Z 280 " =    2.957
peak=    3.507 closest distance to " O   GLN A 278 " =    1.236
peak=    3.506 closest distance to " CB  LEU A  83 " =    0.792
peak=    3.496 closest distance to " CD  ARG A 269 " =    0.955
peak=    3.492 closest distance to " O   HOH Z 135 " =    2.028
peak=    3.492 closest distance to " O   HOH Z 134 " =    1.437
peak=    3.492 closest distance to " NE2 HIS A 207 " =    1.203
peak=    3.490 closest distance to " O   HOH Z  21 " =    1.706
peak=    3.490 closest distance to " O   HOH Z 197 " =    2.798
peak=    3.486 closest distance to " CA  ALA A 158 " =    1.097
peak=    3.483 closest distance to " O   HOH Z 171 " =    3.978
peak=    3.473 closest distance to " CB  THR A  82 " =    1.402
peak=    3.473 closest distance to " O   HOH Z 180 " =    2.055
peak=    3.473 closest distance to " CB  ALA A   1 " =    4.778
peak=    3.469 closest distance to " O   HOH Z   4 " =    1.832
peak=    3.467 closest distance to " O   HOH Z 353 " =    2.740
peak=    3.465 closest distance to " OD2 ASP A 286 " =    2.960
peak=    3.464 closest distance to " CA  ASP A 162 " =    0.930
peak=    3.459 closest distance to " CB  MET A  47 " =    1.042
peak=    3.458 closest distance to " CA  ASP A 191 " =    0.770
peak=    3.453 closest distance to " O   HOH Z 423 " =    1.731
peak=    3.453 closest distance to " O   HOH Z 285 " =    2.936
peak=    3.442 closest distance to " CB  ALA A 291 " =    1.259
peak=    3.442 closest distance to " O   HOH Z 250 " =    1.359
peak=    3.431 closest distance to " O   HOH Z 128 " =    2.253
peak=    3.430 closest distance to " C   TYR A 214 " =    1.572
peak=    3.425 closest distance to " O   TYR A 116 " =    1.203
peak=    3.418 closest distance to " O   HOH Z 295 " =    1.532
peak=    3.417 closest distance to " O   HOH Z 350 " =    1.778
peak=    3.417 closest distance to " O   HOH Z 144 " =    1.584
peak=    3.414 closest distance to " NZ  LYS A 117 " =    3.242
peak=    3.410 closest distance to " O   HOH Z 313 " =    1.806
peak=    3.409 closest distance to " NZ  LYS A  48 " =    1.396
peak=    3.402 closest distance to " CB  ALA A 248 " =    1.357
peak=    3.390 closest distance to " O   HOH Z 156 " =    2.883
peak=    3.389 closest distance to " O   HOH Z  53 " =    2.589
peak=    3.384 closest distance to " CB  ALA A 248 " =    1.173
peak=    3.383 closest distance to " O   HOH Z 216 " =    3.038
peak=    3.382 closest distance to " CA  ILE A  33 " =    1.665
peak=    3.382 closest distance to " O   HOH Z 273 " =    2.731
peak=    3.379 closest distance to " CB  ALA A 161 " =    0.907
peak=    3.379 closest distance to " O   HOH Z 271 " =    2.826
peak=    3.378 closest distance to " O   HOH Z 133 " =    1.769
peak=    3.377 closest distance to " CB  GLN A  89 " =    1.176
peak=    3.373 closest distance to " NH2 ARG A  79 " =    1.338
peak=    3.365 closest distance to " CZ3 TRP A  85 " =    1.136
peak=    3.363 closest distance to " O   HOH Z 175 " =    2.298
peak=    3.362 closest distance to " O   TRP A 274 " =    1.822
peak=    3.357 closest distance to " CD1 TRP A 266 " =    1.027
peak=    3.357 closest distance to " CA  LYS A 181 " =    1.039
peak=    3.356 closest distance to " CB  ALA A 100 " =    1.410
peak=    3.356 closest distance to " O   HOH Z  43 " =    1.806
peak=    3.354 closest distance to " OG  SER A  22 " =    2.918
peak=    3.352 closest distance to " O   HOH Z 227 " =    1.784
peak=    3.350 closest distance to " CA  ASN A 127 " =    0.976
peak=    3.344 closest distance to " CD2 TRP A 179 " =    1.297
peak=    3.343 closest distance to " CG1 ILE A  49 " =    1.597
peak=    3.340 closest distance to " CA  VAL A 112 " =    1.096
peak=    3.339 closest distance to " O   HOH Z 368 " =    3.582
peak=    3.338 closest distance to " O   HOH Z  30 " =    1.261
peak=    3.337 closest distance to " CG  GLU A  37 " =    0.884
peak=    3.334 closest distance to " O   HOH Z 134 " =    2.519
peak=    3.333 closest distance to " CB  LYS A 117 " =    1.173
peak=    3.328 closest distance to " CA  GLN A  88 " =    1.586
peak=    3.324 closest distance to " O   HOH Z 339 " =    2.282
peak=    3.324 closest distance to " CG2 ILE A 234 " =    0.936
peak=    3.319 closest distance to " CG BARG A 102 " =    1.815
peak=    3.318 closest distance to " O   ASN A 209 " =    1.353
peak=    3.316 closest distance to " CA  ILE A 106 " =    0.795
peak=    3.315 closest distance to " CA  THR A 264 " =    0.706
peak=    3.313 closest distance to " OD1 ASP A 231 " =    1.865
peak=    3.312 closest distance to " CB  THR A  31 " =    1.586
peak=    3.309 closest distance to " CB  GLN A  88 " =    1.256
peak=    3.309 closest distance to " N   TYR A  15 " =    0.711
peak=    3.304 closest distance to " CB  PHE A  16 " =    1.148
peak=    3.301 closest distance to " O   HOH Z 422 " =    2.635
peak=    3.296 closest distance to " O   HOH Z  10 " =    1.874
peak=    3.291 closest distance to " CA  ARG A 195 " =    1.274
peak=    3.286 closest distance to " CA  LYS A 117 " =    1.193
peak=    3.284 closest distance to " O   HOH Z 291 " =    1.626
peak=    3.273 closest distance to " CA  TRP A  92 " =    0.980
peak=    3.272 closest distance to " O   HOH Z 392 " =    1.843
peak=    3.272 closest distance to " CZ3 TRP A 274 " =    4.867
peak=    3.269 closest distance to " O   HOH Z 148 " =    2.040
peak=    3.269 closest distance to " O   HOH Z 294 " =    1.578
peak=    3.269 closest distance to " O   HOH Z  44 " =    2.089
peak=    3.268 closest distance to " CA  ALA A 154 " =    1.017
peak=    3.264 closest distance to " CB  VAL A 268 " =    0.846
peak=    3.261 closest distance to " O   HOH Z 193 " =    2.116
peak=    3.261 closest distance to " O   HOH Z 124 " =    1.866
peak=    3.258 closest distance to " CG1 VAL A 174 " =    1.059
peak=    3.258 closest distance to " NE AARG A 275 " =    1.383
peak=    3.255 closest distance to " CD1 ILE A  33 " =    1.688
peak=    3.254 closest distance to " CA  ASN A 215 " =    1.212
peak=    3.254 closest distance to " O   HOH Z 302 " =    1.895
peak=    3.254 closest distance to " CE2 TYR A 186 " =    0.978
peak=    3.251 closest distance to " O   HOH Z 116 " =    1.873
peak=    3.251 closest distance to " CA  TYR A 116 " =    1.503
peak=    3.250 closest distance to " ND1 HIS A  86 " =    1.597
peak=    3.249 closest distance to " OD2 ASP A 200 " =    1.258
peak=    3.247 closest distance to " O   HOH Z 371 " =    3.057
peak=    3.247 closest distance to " O   HOH Z 383 " =    2.138
peak=    3.247 closest distance to " O   HOH Z 197 " =    1.877
peak=    3.245 closest distance to " CA  ALA A 299 " =    0.950
peak=    3.242 closest distance to " O   HOH Z  48 " =    1.776
peak=    3.242 closest distance to " O   HOH Z 173 " =    1.674
peak=    3.241 closest distance to " CA  GLU A  46 " =    0.793
peak=    3.240 closest distance to " CB  LEU A 237 " =    0.852
peak=    3.240 closest distance to " O   HOH Z 172 " =    3.838
peak=    3.232 closest distance to " CA  ALA A 184 " =    1.084
peak=    3.231 closest distance to " CG2 THR A  42 " =    0.723
peak=    3.231 closest distance to " CA  ASP A 140 " =    1.339
peak=    3.231 closest distance to " CG  ARG A 269 " =    1.756
peak=    3.227 closest distance to " CG1 ILE A 120 " =    1.111
peak=    3.227 closest distance to " NH1 ARG A  14 " =    0.949
peak=    3.224 closest distance to " CA  LYS A 290 " =    1.345
peak=    3.224 closest distance to " OG BSER A 164 " =    2.246
peak=    3.223 closest distance to " O   HOH Z 413 " =    1.899
peak=    3.220 closest distance to " CB  SER A 210 " =    0.867
peak=    3.219 closest distance to " CB  TRP A 179 " =    1.419
peak=    3.219 closest distance to " CD  GLU A 152 " =    0.910
peak=    3.214 closest distance to " O   HOH Z 109 " =    2.699
peak=    3.214 closest distance to " CA  ALA A 160 " =    1.009
peak=    3.212 closest distance to " CE1 TYR A 186 " =    1.258
peak=    3.206 closest distance to " O   HOH Z 406 " =    1.541
peak=    3.205 closest distance to " O   HOH Z  61 " =    1.657
peak=    3.203 closest distance to " O   HOH Z 141 " =    1.653
peak=    3.197 closest distance to " O   HOH Z 147 " =    1.696
peak=    3.197 closest distance to " O   HOH Z 313 " =    1.801
peak=    3.196 closest distance to " CD  ARG A 219 " =    1.034
peak=    3.195 closest distance to " O   HOH Z  49 " =    3.256
peak=    3.195 closest distance to " CG  GLN A  88 " =    1.073
peak=    3.194 closest distance to " O   HOH Z 263 " =    1.562
peak=    3.189 closest distance to " CA  GLU A 152 " =    0.894
peak=    3.188 closest distance to " NE  ARG A  79 " =    1.144
peak=    3.187 closest distance to " CB  SER A  62 " =    1.199
peak=    3.187 closest distance to " O   HOH Z 175 " =    3.711
peak=    3.187 closest distance to " O   HOH Z  61 " =    1.666
peak=    3.182 closest distance to " O   HOH Z 301 " =    1.850
peak=    3.182 closest distance to " O   HOH Z 326 " =    2.204
peak=    3.179 closest distance to " CB  GLN A 103 " =    0.997
peak=    3.178 closest distance to " N   ARG A 190 " =    1.019
peak=    3.177 closest distance to " O   HOH Z  85 " =    2.016
peak=    3.177 closest distance to " NH1BARG A 275 " =    1.252
peak=    3.175 closest distance to " CG  LEU A  25 " =    1.844
peak=    3.173 closest distance to " CD1 ILE A 106 " =    0.888
peak=    3.172 closest distance to " CE  MET A 113 " =    1.764
peak=    3.169 closest distance to " O   HOH Z 203 " =    1.856
peak=    3.168 closest distance to " O   HOH Z 409 " =    3.053
peak=    3.164 closest distance to " CA  VAL A  41 " =    0.896
peak=    3.163 closest distance to " O   HOH Z 417 " =    2.025
peak=    3.162 closest distance to " O   HOH Z 355 " =    1.788
peak=    3.160 closest distance to " N   ASN A 127 " =    1.256
peak=    3.157 closest distance to " OE1 GLN A 278 " =    0.939
peak=    3.156 closest distance to " CA  ARG A  36 " =    1.221
peak=    3.149 closest distance to " CB  MET A  40 " =    0.763
peak=    3.149 closest distance to " O   HOH Z 435 " =    1.973
peak=    3.143 closest distance to " O  BHOH Z 338 " =    2.500
peak=    3.140 closest distance to " O   HOH Z 153 " =    1.866
peak=    3.139 closest distance to " CD1 LEU A  96 " =    0.750
peak=    3.134 closest distance to " O   HOH Z 345 " =    3.495
peak=    3.133 closest distance to " O   HOH Z 391 " =    3.021
peak=    3.128 closest distance to " CB  PRO A 243 " =    1.216
peak=    3.125 closest distance to " CG ALYS A 290 " =    1.124
peak=    3.124 closest distance to " CB  ASP A 140 " =    0.712
peak=    3.121 closest distance to " CB  LYS A 193 " =    1.100
peak=    3.119 closest distance to " CA  GLY A 211 " =    1.276
peak=    3.116 closest distance to " OG  SER A  28 " =    1.545
peak=    3.114 closest distance to " O   HOH Z 327 " =    1.904
peak=    3.114 closest distance to " O   HOH Z  89 " =    1.923
peak=    3.111 closest distance to " CZ3 TRP A  92 " =    1.479
peak=    3.108 closest distance to " CG  GLN A  89 " =    1.441
peak=    3.107 closest distance to " O   HOH Z 148 " =    3.237
peak=    3.103 closest distance to " CA  MET A 105 " =    0.923
peak=    3.100 closest distance to " O   HOH Z 344 " =    3.095
peak=    3.098 closest distance to " CB  TYR A 116 " =    0.990
peak=    3.092 closest distance to " O   HOH Z 254 " =    1.528
peak=    3.087 closest distance to " CB  ALA A 227 " =    1.015
peak=    3.086 closest distance to " O   HOH Z  58 " =    1.492
peak=    3.069 closest distance to " O   ALA A 292 " =    1.762
peak=    3.068 closest distance to " CB  LEU A 261 " =    0.722
peak=    3.067 closest distance to " CG  MET A 185 " =    1.032
peak=    3.060 closest distance to " O   HOH Z  64 " =    2.841
peak=    3.048 closest distance to " CB  ALA A 114 " =    1.233
peak=    3.045 closest distance to " CG  ARG A 159 " =    0.952
peak=    3.027 closest distance to " CB  ARG A 138 " =    0.993
peak=    3.025 closest distance to " CD1AILE A 234 " =    0.915

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 198         
Filter by distance & map next to the model:
   mapped sites are within: 0.718 - 5.509
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 197 from: 198
   mapped sites are within: 0.718 - 5.509

peak=   -5.649 closest distance to " CG2 VAL A 230 " =    0.754
peak=   -4.230 closest distance to " O   HOH Z 231 " =    1.732
peak=   -4.166 closest distance to " O   VAL A  67 " =    2.688
peak=   -4.116 closest distance to " CG1 VAL A 112 " =    2.596
peak=   -4.099 closest distance to " CG1 VAL A 296 " =    1.445
peak=   -4.067 closest distance to " O   HOH Z 211 " =    1.327
peak=   -4.057 closest distance to " C   ALA A 158 " =    1.323
peak=   -4.050 closest distance to " O   ILE A 109 " =    2.677
peak=   -4.027 closest distance to " OE1 GLN A  88 " =    0.939
peak=   -3.992 closest distance to " OE1 GLN A 223 " =    2.201
peak=   -3.983 closest distance to " CD  ARG A 156 " =    2.023
peak=   -3.979 closest distance to " O   HOH Z 166 " =    1.932
peak=   -3.954 closest distance to " O   HOH Z 411 " =    5.262
peak=   -3.950 closest distance to " O   HOH Z 231 " =    1.126
peak=   -3.936 closest distance to " CB  PRO A 243 " =    2.690
peak=   -3.912 closest distance to " CA  GLY A 241 " =    2.284
peak=   -3.908 closest distance to " CG1 VAL A 250 " =    2.758
peak=   -3.883 closest distance to " OG  SER A  87 " =    1.625
peak=   -3.826 closest distance to " O   HOH Z 377 " =    1.580
peak=   -3.820 closest distance to " OG  SER A  97 " =    2.280
peak=   -3.810 closest distance to " CG  LEU A 101 " =    2.484
peak=   -3.806 closest distance to " O   HOH Z  73 " =    2.114
peak=   -3.802 closest distance to " CD1 LEU A 228 " =    2.495
peak=   -3.779 closest distance to " CE2 TYR A  30 " =    2.835
peak=   -3.778 closest distance to " O   HOH Z  38 " =    1.172
peak=   -3.777 closest distance to " O   HOH Z 290 " =    1.437
peak=   -3.747 closest distance to " CG  MET A 105 " =    0.973
peak=   -3.732 closest distance to " NH2AARG A 275 " =    5.509
peak=   -3.730 closest distance to " C   ASN A 285 " =    2.577
peak=   -3.720 closest distance to " CG  ASP A 231 " =    0.764
peak=   -3.715 closest distance to " O   HOH Z 394 " =    1.557
peak=   -3.707 closest distance to " O   GLY A 211 " =    1.450
peak=   -3.697 closest distance to " CG2 VAL A 296 " =    0.895
peak=   -3.695 closest distance to " CG  TRP A 266 " =    1.789
peak=   -3.687 closest distance to " O   GLY A  80 " =    2.547
peak=   -3.687 closest distance to " CA  GLY A 241 " =    3.118
peak=   -3.682 closest distance to " O   HOH Z  10 " =    1.497
peak=   -3.681 closest distance to " CD1 LEU A   5 " =    2.567
peak=   -3.675 closest distance to " O   PRO A 163 " =    2.138
peak=   -3.671 closest distance to " CZ2 TRP A  92 " =    2.877
peak=   -3.660 closest distance to " CD1 PHE A  59 " =    1.933
peak=   -3.652 closest distance to " CA  ASP A 298 " =    1.063
peak=   -3.648 closest distance to " ND2 ASN A  60 " =    1.463
peak=   -3.634 closest distance to " O   VAL A 189 " =    2.612
peak=   -3.625 closest distance to " CG  TYR A 186 " =    2.297
peak=   -3.624 closest distance to " O   HOH Z 196 " =    2.332
peak=   -3.616 closest distance to " O   HOH Z  19 " =    2.364
peak=   -3.613 closest distance to " O   SER A 271 " =    2.311
peak=   -3.601 closest distance to " CD2 LEU A 167 " =    1.777
peak=   -3.597 closest distance to " O   PRO A 198 " =    1.293
peak=   -3.593 closest distance to " N   ALA A 226 " =    2.194
peak=   -3.588 closest distance to " CE3 TRP A  70 " =    1.802
peak=   -3.586 closest distance to " NH2 ARG A  79 " =    2.018
peak=   -3.582 closest distance to " CD1 TYR A 247 " =    2.369
peak=   -3.573 closest distance to " O   HOH Z  43 " =    1.643
peak=   -3.561 closest distance to " CD  ARG A  14 " =    3.293
peak=   -3.560 closest distance to " O   HOH Z 177 " =    1.580
peak=   -3.558 closest distance to " O   HOH Z 389 " =    1.989
peak=   -3.553 closest distance to " N   ALA A  43 " =    2.649
peak=   -3.545 closest distance to " O   HOH Z  52 " =    1.785
peak=   -3.542 closest distance to " CD1 ILE A 151 " =    2.438
peak=   -3.541 closest distance to " O   HOH Z 185 " =    2.378
peak=   -3.534 closest distance to " O   HOH Z  13 " =    1.490
peak=   -3.522 closest distance to " O   HOH Z 184 " =    1.440
peak=   -3.519 closest distance to " O   HOH Z 435 " =    2.662
peak=   -3.515 closest distance to " OG ASER A 134 " =    1.512
peak=   -3.512 closest distance to " O   HOH Z 241 " =    1.217
peak=   -3.510 closest distance to " O   HOH Z 351 " =    1.519
peak=   -3.507 closest distance to " O   HOH Z  94 " =    2.253
peak=   -3.505 closest distance to " CG2 VAL A 112 " =    2.632
peak=   -3.504 closest distance to " OXT GLY A 302 " =    3.110
peak=   -3.493 closest distance to " CZ3 TRP A 179 " =    1.108
peak=   -3.492 closest distance to " OG BSER A 134 " =    1.956
peak=   -3.488 closest distance to " CD1 LEU A 101 " =    2.696
peak=   -3.484 closest distance to " O   HOH Z 377 " =    1.280
peak=   -3.484 closest distance to " N   ALA A 248 " =    2.461
peak=   -3.484 closest distance to " CD  GLN A  58 " =    1.016
peak=   -3.484 closest distance to " O   HOH Z 222 " =    1.224
peak=   -3.481 closest distance to " OD2 ASP A  50 " =    2.253
peak=   -3.480 closest distance to " O   HOH Z  11 " =    1.905
peak=   -3.477 closest distance to " O   HOH Z 183 " =    1.318
peak=   -3.476 closest distance to " NE2 GLN A  88 " =    0.920
peak=   -3.470 closest distance to " OG BSER A 134 " =    1.327
peak=   -3.470 closest distance to " O   LEU A 101 " =    2.922
peak=   -3.461 closest distance to " OD1 ASN A 148 " =    1.516
peak=   -3.457 closest distance to " CG2 ILE A 263 " =    2.450
peak=   -3.456 closest distance to " N   THR A  18 " =    1.265
peak=   -3.455 closest distance to " O   HOH Z 111 " =    2.118
peak=   -3.452 closest distance to " O   HOH Z 113 " =    1.755
peak=   -3.451 closest distance to " CD2 TYR A 293 " =    1.996
peak=   -3.440 closest distance to " ND2 ASN A  45 " =    2.214
peak=   -3.439 closest distance to " OH  TYR A 172 " =    1.637
peak=   -3.437 closest distance to " CD2 PHE A  61 " =    1.868
peak=   -3.435 closest distance to " CD2 LEU A 300 " =    2.753
peak=   -3.427 closest distance to " OG  SER A  26 " =    1.354
peak=   -3.424 closest distance to " C   HIS A 108 " =    1.195
peak=   -3.422 closest distance to " CB  PRO A 163 " =    2.512
peak=   -3.418 closest distance to " O   HOH Z 275 " =    1.572
peak=   -3.416 closest distance to " NH2 ARG A  66 " =    1.987
peak=   -3.413 closest distance to " CB  VAL A 230 " =    1.021
peak=   -3.406 closest distance to " O   HOH Z 407 " =    3.426
peak=   -3.400 closest distance to " O   HOH Z 216 " =    1.628
peak=   -3.398 closest distance to " CB  TRP A  85 " =    2.575
peak=   -3.395 closest distance to " O   HOH Z 353 " =    2.207
peak=   -3.378 closest distance to " O   HOH Z 103 " =    1.917
peak=   -3.377 closest distance to " O   HOH Z 236 " =    1.260
peak=   -3.377 closest distance to " O   HOH Z 426 " =    1.683
peak=   -3.376 closest distance to " OG  SER A 206 " =    1.813
peak=   -3.372 closest distance to " O   HOH Z 114 " =    1.685
peak=   -3.368 closest distance to " O   HOH Z  17 " =    1.428
peak=   -3.354 closest distance to " CD  LYS A 289 " =    2.420
peak=   -3.353 closest distance to " C   ASN A 187 " =    1.782
peak=   -3.351 closest distance to " CE BMET A  47 " =    1.910
peak=   -3.349 closest distance to " CG1 VAL A 197 " =    2.359
peak=   -3.348 closest distance to " CG1 VAL A 112 " =    2.899
peak=   -3.347 closest distance to " N   THR A 157 " =    1.608
peak=   -3.342 closest distance to " CA  ASN A 127 " =    1.134
peak=   -3.341 closest distance to " CD  GLN A  88 " =    0.824
peak=   -3.332 closest distance to " CD1 ILE A  33 " =    2.377
peak=   -3.325 closest distance to " N   SER A 212 " =    1.857
peak=   -3.325 closest distance to " O   HOH Z 359 " =    3.121
peak=   -3.324 closest distance to " CG  GLU A 277 " =    1.314
peak=   -3.309 closest distance to " O   ASP A  27 " =    1.923
peak=   -3.306 closest distance to " O   HOH Z 396 " =    1.937
peak=   -3.304 closest distance to " CD  GLN A 223 " =    0.718
peak=   -3.300 closest distance to " NE2 GLN A 103 " =    1.764
peak=   -3.298 closest distance to " N   LYS A 166 " =    2.024
peak=   -3.298 closest distance to " O   HOH Z  60 " =    2.243
peak=   -3.294 closest distance to " O   LEU A 167 " =    1.487
peak=   -3.292 closest distance to " ND2 ASN A  45 " =    1.147
peak=   -3.289 closest distance to " NH2 ARG A  79 " =    1.559
peak=   -3.285 closest distance to " CZ2 TRP A 274 " =    1.013
peak=   -3.284 closest distance to " CE  LYS A  76 " =    2.644
peak=   -3.283 closest distance to " O   HOH Z  44 " =    2.180
peak=   -3.281 closest distance to " O   HOH Z 234 " =    4.572
peak=   -3.281 closest distance to " O   HOH Z 198 " =    1.546
peak=   -3.279 closest distance to " OD1 ASN A 249 " =    2.201
peak=   -3.277 closest distance to " O   HOH Z 186 " =    0.953
peak=   -3.271 closest distance to " O   HOH Z  92 " =    1.318
peak=   -3.263 closest distance to " O   HOH Z 118 " =    3.276
peak=   -3.261 closest distance to " CG2 VAL A 189 " =    2.083
peak=   -3.260 closest distance to " C   LEU A 222 " =    0.828
peak=   -3.258 closest distance to " O   HOH Z 102 " =    1.601
peak=   -3.254 closest distance to " O   VAL A 125 " =    2.265
peak=   -3.252 closest distance to " O   HOH Z 166 " =    1.755
peak=   -3.251 closest distance to " N   SER A   3 " =    2.194
peak=   -3.227 closest distance to " C   GLY A  13 " =    0.912
peak=   -3.220 closest distance to " CE1 TYR A 169 " =    2.611
peak=   -3.220 closest distance to " N   PHE A  59 " =    2.176
peak=   -3.219 closest distance to " OD1 ASN A 173 " =    1.224
peak=   -3.219 closest distance to " CG  PRO A 163 " =    2.379
peak=   -3.219 closest distance to " CE3 TRP A 150 " =    2.243
peak=   -3.203 closest distance to " O   HOH Z 252 " =    3.883
peak=   -3.199 closest distance to " O   HOH Z 105 " =    2.177
peak=   -3.199 closest distance to " CG1 VAL A  67 " =    2.842
peak=   -3.198 closest distance to " O   HOH Z 136 " =    0.943
peak=   -3.197 closest distance to " O   GLY A 203 " =    2.353
peak=   -3.193 closest distance to " O   SER A 276 " =    1.703
peak=   -3.188 closest distance to " SG  CYS A 168 " =    1.229
peak=   -3.176 closest distance to " O   HOH Z 357 " =    2.170
peak=   -3.172 closest distance to " CD1 TRP A 179 " =    0.917
peak=   -3.172 closest distance to " CD  ARG A 139 " =    1.722
peak=   -3.169 closest distance to " O   HOH Z 128 " =    2.609
peak=   -3.165 closest distance to " CB  ALA A 114 " =    2.469
peak=   -3.163 closest distance to " CB  ALA A  43 " =    2.599
peak=   -3.162 closest distance to " O   ALA A   7 " =    1.454
peak=   -3.160 closest distance to " N   SER A 276 " =    1.447
peak=   -3.155 closest distance to " CD  PRO A 213 " =    2.197
peak=   -3.155 closest distance to " CA  GLY A 133 " =    2.273
peak=   -3.144 closest distance to " CB  ASP A 286 " =    2.197
peak=   -3.143 closest distance to " ND2 ASN A  60 " =    1.886
peak=   -3.141 closest distance to " O   HOH Z  60 " =    2.027
peak=   -3.138 closest distance to " CB  ALA A 291 " =    2.185
peak=   -3.136 closest distance to " CG  ARG A 269 " =    2.310
peak=   -3.135 closest distance to " CD1 TYR A 247 " =    2.879
peak=   -3.133 closest distance to " O   HOH Z 371 " =    1.586
peak=   -3.133 closest distance to " OG1 THR A 246 " =    1.447
peak=   -3.132 closest distance to " CB  VAL A 296 " =    0.978
peak=   -3.132 closest distance to " OG1 THR A  82 " =    1.678
peak=   -3.131 closest distance to " O   HOH Z 106 " =    1.985
peak=   -3.128 closest distance to " CB  PHE A 130 " =    1.290
peak=   -3.127 closest distance to " CB  ALA A 291 " =    2.261
peak=   -3.118 closest distance to " C   VAL A 174 " =    1.810
peak=   -3.113 closest distance to " C   LEU A 143 " =    1.201
peak=   -3.110 closest distance to " O   HOH Z 128 " =    4.258
peak=   -3.101 closest distance to " OD1 ASP A 171 " =    1.642
peak=   -3.096 closest distance to " O   HOH Z 410 " =    1.676
peak=   -3.091 closest distance to " O   HOH Z 109 " =    0.899
peak=   -3.080 closest distance to " CD1 ILE A 199 " =    2.659
peak=   -3.080 closest distance to " C   PHE A  59 " =    1.218
peak=   -3.074 closest distance to " CG  GLU A   2 " =    1.836
peak=   -3.068 closest distance to " O   HOH Z 150 " =    2.072
peak=   -3.057 closest distance to " NH2 ARG A  66 " =    1.431
peak=   -3.046 closest distance to " O   HOH Z 313 " =    1.050
peak=   -3.040 closest distance to " C   MET A 188 " =    1.501
peak=   -3.037 closest distance to " CG2 THR A 235 " =    1.925
peak=   -3.034 closest distance to " O   HOH Z 308 " =    1.717

================= 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    :  0.4614 0.4485   6.263720e+00   6.244100e+00
   1_bss:  0.4541 0.4362   6.257412e+00   6.233315e+00
   1_xyz:  0.3536 0.3805   6.102817e+00   6.149455e+00
   1_adp:  0.3059 0.3469   5.997157e+00   6.094689e+00
   1_occ:  0.3053 0.3476   5.996189e+00   6.095643e+00
   2_bss:  0.3030 0.3443   5.996719e+00   6.095128e+00
   2_xyz:  0.2214 0.2760   5.728938e+00   5.891993e+00
   2_adp:  0.2059 0.2593   5.666283e+00   5.839404e+00
   2_occ:  0.2055 0.2591   5.665743e+00   5.838874e+00
   3_bss:  0.2042 0.2567   5.665252e+00   5.837087e+00
   3_xyz:  0.1590 0.2072   5.436232e+00   5.638809e+00
   3_adp:  0.1407 0.1923   5.347307e+00   5.577628e+00
   3_occ:  0.1405 0.1924   5.347051e+00   5.577581e+00
   4_bss:  0.1405 0.1921   5.345959e+00   5.575520e+00
   4_xyz:  0.1243 0.1786   5.249443e+00   5.500989e+00
   4_adp:  0.1209 0.1737   5.225489e+00   5.476938e+00
   4_occ:  0.1208 0.1737   5.225379e+00   5.476769e+00
   5_bss:  0.1208 0.1737   5.225422e+00   5.476880e+00
   5_xyz:  0.1180 0.1704   5.205892e+00   5.459173e+00
   5_adp:  0.1194 0.1669   5.201475e+00   5.441021e+00
   5_occ:  0.1192 0.1668   5.200959e+00   5.440748e+00
   5_bss:  0.1195 0.1666   5.201709e+00   5.440739e+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:  0.300  20.001  10.369   7.654   7.924   0.000   0.000   0.000
   1_xyz:  0.300  20.001  10.369   7.654   7.924   0.000   0.000   0.000
   1_adp:  0.300  20.001  10.369   7.654   7.924   0.000   0.000   0.000
   1_occ:  0.300  20.001  10.369   7.654   7.924   0.000   0.000   0.000
   2_bss:  0.327  50.000   7.209   4.883   5.495   0.000   0.000   0.000
   2_xyz:  0.327  50.000   7.209   4.883   5.495   0.000   0.000   0.000
   2_adp:  0.327  50.000   7.209   4.883   5.495   0.000   0.000   0.000
   2_occ:  0.327  50.000   7.209   4.883   5.495   0.000   0.000   0.000
   3_bss:  0.328  50.000   4.389   3.525   4.354   0.000   0.000   0.000
   3_xyz:  0.328  50.000   4.389   3.525   4.354   0.000   0.000   0.000
   3_adp:  0.328  50.000   4.389   3.525   4.354   0.000   0.000   0.000
   3_occ:  0.328  50.000   4.389   3.525   4.354   0.000   0.000   0.000
   4_bss:  0.333  67.582   3.318   2.838   3.807   0.000   0.000   0.000
   4_xyz:  0.333  67.582   3.318   2.838   3.807   0.000   0.000   0.000
   4_adp:  0.333  67.582   3.318   2.838   3.807   0.000   0.000   0.000
   4_occ:  0.333  67.582   3.318   2.838   3.807   0.000   0.000   0.000
   5_bss:  0.326  65.143   3.274   2.939   3.938   0.000   0.000   0.000
   5_xyz:  0.326  65.143   3.274   2.939   3.938   0.000   0.000   0.000
   5_adp:  0.326  65.143   3.274   2.939   3.938   0.000   0.000   0.000
   5_occ:  0.326  65.143   3.274   2.939   3.938   0.000   0.000   0.000
   5_bss:  0.327  68.325  -0.185  -0.420   0.604   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  52.215 0.4936  0.5518    60602.446
   1_bss:  51.648 0.4995  0.7217    58354.865
   1_xyz:  43.859 0.5946  0.8344    42566.092
   1_adp:  38.530 0.6597  0.9248    35135.147
   1_occ:  38.599 0.6588  0.9228    35208.278
   2_bss:  38.502 0.6600  0.8402    35094.370
   2_xyz:  28.074 0.7784  0.9680    20080.985
   2_adp:  25.662 0.8050  1.0012    17618.524
   2_occ:  25.657 0.8050  1.0008    17600.467
   3_bss:  25.567 0.8060  0.9397    17502.897
   3_xyz:  19.629 0.8653  0.9808    10922.828
   3_adp:  18.143 0.8792  0.9837     9424.797
   3_occ:  18.140 0.8792  0.9836     9426.430
   4_bss:  18.089 0.8796  0.9571     9369.638
   4_xyz:  16.302 0.8957  0.9659     7949.787
   4_adp:  15.717 0.9010  0.9645     7577.718
   4_occ:  15.714 0.9010  0.9645     7575.888
   5_bss:  15.721 0.9010  0.9665     7578.789
   5_xyz:  15.307 0.9046  0.9678     7270.356
   5_adp:  14.836 0.9086  0.9689     7039.643
   5_occ:  14.830 0.9087  0.9688     7027.438
   5_bss:  14.867 0.9083  0.9614     7038.178
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.4418e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.4418e+01
   1_xyz:   1.663  0.013  0.108 18.144  0.006  4.113   1.3807e-01
   1_adp:   1.663  0.013  0.108 18.144  0.006  4.113   1.3807e-01
   1_occ:   1.663  0.013  0.108 18.144  0.006  4.113   1.3807e-01
   2_bss:   1.663  0.013  0.108 18.144  0.006  4.113   1.3807e-01
   2_xyz:   1.064  0.008  0.076 16.575  0.005  4.133   7.3619e-02
   2_adp:   1.064  0.008  0.076 16.575  0.005  4.133   7.3619e-02
   2_occ:   1.064  0.008  0.076 16.575  0.005  4.133   7.3619e-02
   3_bss:   1.064  0.008  0.076 16.575  0.005  4.133   7.3619e-02
   3_xyz:   1.094  0.008  0.081 16.156  0.004  4.116   7.3592e-02
   3_adp:   1.094  0.008  0.081 16.156  0.004  4.116   7.3592e-02
   3_occ:   1.094  0.008  0.081 16.156  0.004  4.116   7.3592e-02
   4_bss:   1.094  0.008  0.081 16.156  0.004  4.116   7.3592e-02
   4_xyz:   1.157  0.011  0.089 16.200  0.004  4.126   8.2488e-02
   4_adp:   1.157  0.011  0.089 16.200  0.004  4.126   8.2488e-02
   4_occ:   1.157  0.011  0.089 16.200  0.004  4.126   8.2488e-02
   5_bss:   1.157  0.011  0.089 16.200  0.004  4.126   8.2488e-02
   5_xyz:   1.113  0.010  0.087 15.778  0.004  4.129   7.6375e-02
   5_adp:   1.113  0.010  0.087 15.778  0.004  4.129   7.6375e-02
   5_occ:   1.113  0.010  0.087 15.778  0.004  4.129   7.6375e-02
   5_bss:   1.113  0.010  0.087 15.778  0.004  4.129   7.6375e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0563e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0563e+00
   1_xyz:  13.726  0.159  0.436 85.664  0.037  2.183   1.0374e-01
   1_adp:  13.726  0.159  0.436 85.664  0.037  2.183   1.0374e-01
   1_occ:  13.726  0.159  0.436 85.664  0.037  2.183   1.0374e-01
   2_bss:  13.726  0.159  0.436 85.664  0.037  2.183   1.0374e-01
   2_xyz:   7.177  0.059  0.269 83.704  0.038  2.293   7.2922e-02
   2_adp:   7.177  0.059  0.269 83.704  0.038  2.293   7.2922e-02
   2_occ:   7.177  0.059  0.269 83.704  0.038  2.293   7.2922e-02
   3_bss:   7.177  0.059  0.269 83.704  0.038  2.293   7.2922e-02
   3_xyz:   8.340  0.069  0.390 85.201  0.044  2.347   7.6533e-02
   3_adp:   8.340  0.069  0.390 85.201  0.044  2.347   7.6533e-02
   3_occ:   8.340  0.069  0.390 85.201  0.044  2.347   7.6533e-02
   4_bss:   8.340  0.069  0.390 85.201  0.044  2.347   7.6533e-02
   4_xyz:   9.872  0.070  0.483 83.579  0.041  2.330   5.6201e-02
   4_adp:   9.872  0.070  0.483 83.579  0.041  2.330   5.6201e-02
   4_occ:   9.872  0.070  0.483 83.579  0.041  2.330   5.6201e-02
   5_bss:   9.872  0.070  0.483 83.579  0.041  2.330   5.6201e-02
   5_xyz:   8.582  0.046  0.527 82.763  0.041  2.335   4.9514e-02
   5_adp:   8.582  0.046  0.527 82.763  0.041  2.335   4.9514e-02
   5_occ:   8.582  0.046  0.527 82.763  0.041  2.335   4.9514e-02
   5_bss:   8.582  0.046  0.527 82.763  0.041  2.335   4.9514e-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:  73.32   0.00  11.11  61.54   0.00   8.39  73.32   0.00  25.93
   1_occ:  73.32   0.00  11.11  61.54   0.00   8.39  73.32   0.00  25.93
   2_bss:  73.32   0.00  11.11  61.54   0.00   8.39  73.32   0.00  25.93
   2_xyz:  73.32   0.00  11.11  61.54   0.00   8.39  73.32   0.00  25.93
   2_adp:  79.08   0.00  11.40  79.08   0.00   8.25  73.63   0.00  28.52
   2_occ:  79.08   0.00  11.40  79.08   0.00   8.25  73.63   0.00  28.52
   3_bss:  79.08   0.00  11.40  79.08   0.00   8.25  73.63   0.00  28.52
   3_xyz:  79.08   0.00  11.40  79.08   0.00   8.25  73.63   0.00  28.52
   3_adp:  90.01   0.00  13.02  83.50   0.00   8.33  90.01   0.00  38.54
   3_occ:  90.01   0.00  13.02  83.50   0.00   8.33  90.01   0.00  38.54
   4_bss:  90.01   0.00  13.02  83.50   0.00   8.33  90.01   0.00  38.54
   4_xyz:  90.01   0.00  13.02  83.50   0.00   8.33  90.01   0.00  38.54
   4_adp:  99.23   0.00  12.92  91.60   0.00   8.18  99.23   0.68  38.75
   4_occ:  99.23   0.00  12.92  91.60   0.00   8.18  99.23   0.68  38.75
   5_bss:  99.23   0.00  12.92  91.60   0.00   8.18  99.23   0.68  38.75
   5_xyz:  99.23   0.00  12.92  91.60   0.00   8.18  99.23   0.68  38.75
   5_adp:  90.01   0.00  12.18  87.81   0.00   7.89  90.01   1.40  35.58
   5_occ:  90.01   0.00  12.18  87.81   0.00   7.89  90.01   1.40  35.58
   5_bss:  93.19   3.18  15.36  90.99   3.18  11.07  93.19   4.58  38.76
------------------------------------------------------------------------
 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:    1.222    0.016    0.412
   1_adp:    1.222    0.016    0.412
   1_occ:    1.222    0.016    0.412
   2_bss:    1.222    0.016    0.412
   2_xyz:    1.545    0.037    0.550
   2_adp:    1.545    0.037    0.550
   2_occ:    1.545    0.037    0.550
   3_bss:    1.545    0.037    0.550
   3_xyz:    1.509    0.082    0.620
   3_adp:    1.509    0.082    0.620
   3_occ:    1.509    0.082    0.620
   4_bss:    1.509    0.082    0.620
   4_xyz:    1.549    0.043    0.653
   4_adp:    1.549    0.043    0.653
   4_occ:    1.549    0.043    0.653
   5_bss:    1.549    0.043    0.653
   5_xyz:    1.633    0.042    0.663
   5_adp:    1.633    0.042    0.663
   5_occ:    1.633    0.042    0.663
   5_bss:    1.633    0.042    0.663
------------------------------------------------------------------------

CPU time actual refinement: 278.62


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1282/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_1282/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1282/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1282/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1282/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 278.49 
  Macro-tasks:
    bulk solvent and scale       = 35.29  
    individual site refinement   = 115.48 
    weights calculation          = 26.97  
    collect and process          = 5.57   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 183.43 
  Micro-tasks:
    mask                            = 1.96   
    f_calc                          = 83.33  
    alpha_beta                      = 7.23   
    target                          = 1.02   
    gradients_wrt_atomic_parameters = 93.84  
    fmodel                         = 6.25   
    r_factors                      = 0.26   
    phase_errors                   = 8.87   
    foms                           = 0.19   
    TOTAL for micro-tasks          = 202.95 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 3.888 micro seconds
Total CPU time: 4.84 minutes
from_scatterers_fft:    658 calls, 83.13 s
gradients_fft:          603 calls, 81.93 s

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

# Date 2008-01-16 Time 03:38:03 PST -0800 (1200483483.39 s)
Start R-work = 0.4614, R-free = 0.4485 (no bulk solvent and anisotropic scale)
Final R-work = 0.1352, R-free = 0.1819 (no bulk solvent and anisotropic scale)

Start R-work = 0.4541, R-free = 0.4362
Final R-work = 0.1195, R-free = 0.1666