# Date 2008-01-16 Time 01:45:58 PST -0800 (1200476758.53 s)
#phil __OFF__

Command line arguments: "../553.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 32632
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 553

-------------------------------------------------------------------------------
  PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography
  User: phzwart
-------------------------------------------------------------------------------

              phenix.refine: Macromolecular Structure Refinement

-------------------------------------------------------------------------------
Phenix developers include:
  Paul Adams, Pavel Afonine, Vicent Chen, Ian Davis, Kreshna Gopal,
  Ralf Grosse-Kunstleve, Li-Wei Hung, Robert Immormino, Tom Ioerger,
  Airlie McCoy, Erik McKee, Nigel Moriarty, Reetal Pai, Randy Read,
  Jane Richardson, David Richardson, Tod Romo, Jim Sacchettini,
  Nicholas Sauter, Jacob Smith, Laurent Storoni, Tom Terwilliger,
  Peter Zwart
Phenix home page:
  http://www.phenix-online.org/
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Phenix components are copyrighted by:
  - Lawrence Berkeley National Laboratory
  - Los Alamos National Laboratory
  - University of Cambridge
  - Duke University
  - Texas Agricultural Experiment Station &
    Texas Engineering Experiment Station
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Major third-party components of Phenix include:
    Python, wxwidgets, wxPython, Boost, SCons, Clipper,
    CCP4 Monomer Library, CCP4 I/O libraries, PyCifRW, FFTPACK, L-BFGS
  Enter phenix.acknowledgments for details.
-------------------------------------------------------------------------------

Processing inputs. This may take a minute or two.

Command line parameter definitions:
  refinement.modify_start_model.adp.set_b_iso = 10

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.8988, 47.1647, 85.5261, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.30, per 1000 atoms: 1.17


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 47.1647, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8986 1.98115
Completeness in resolution range: 0.967693
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 =  14.8986
                             d_min =   1.9811

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 47.1647, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8986 1.98115
Completeness in resolution range: 0.967693
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: 14.8990 -  4.2386 [2122/2149]  1910   212  10.0%
  bin  2:  4.2386 -  3.3772 [2035/2051]  1831   204  10.0%
  bin  3:  3.3772 -  2.9540 [2020/2039]  1817   203  10.0%
  bin  4:  2.9540 -  2.6857 [1996/2026]  1798   198   9.9%
  bin  5:  2.6857 -  2.4941 [1978/1997]  1780   198  10.0%
  bin  6:  2.4941 -  2.3477 [1966/2002]  1774   192   9.8%
  bin  7:  2.3477 -  2.2305 [1975/2008]  1771   204  10.3%
  bin  8:  2.2305 -  2.1337 [1948/1982]  1752   196  10.1%
  bin  9:  2.1337 -  2.0518 [1947/1975]  1756   191   9.8%
  bin 10:  2.0518 -  1.9811 [1602/2014]  1441   161  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_553/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: 0.15 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 19
        2.42 -     3.04: 2207
        3.04 -     3.66: 4717
        3.66 -     4.28: 9052
        4.28 -     4.90: 12417
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  52 " - " O   HOH Z 183 "  2.109 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  2.142 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  2.151 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  ... (remaining 28407 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_553/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_553/model_refine_001.geo

CPU time processing inputs: 9.42


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.89875 47.16465 85.5261 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4265   r_free= 0.4178   ksol= 0.00   Bsol= 0.00   scale= 0.830    |
|                                                                             |
| 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:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.216872                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8990 -  4.7272 0.99   1376  154 0.3586 0.3431      6.5042      6.4757|
|  2:  4.7272 -  3.7721 0.99   1334  145 0.3272 0.3250       6.625      6.6391|
|  3:  3.7721 -  3.3012 0.99   1300  148 0.3627 0.3544      6.5462      6.5746|
|  4:  3.3012 -  3.0021 0.99   1294  143 0.3990 0.3764      6.4294      6.3486|
|  5:  3.0021 -  2.7884 0.99   1285  139 0.4345 0.4712      6.3018      6.3471|
|  6:  2.7884 -  2.6250 0.99   1279  145 0.4473 0.5099      6.2235      6.2204|
|  7:  2.6250 -  2.4941 0.99   1268  141 0.4721 0.4279      6.2099      6.1019|
|  8:  2.4941 -  2.3860 0.98   1275  140 0.4742 0.4429      6.1503      6.1248|
|  9:  2.3860 -  2.2945 0.98   1277  144 0.4807 0.4837      6.0825       6.101|
| 10:  2.2945 -  2.2156 0.98   1233  133 0.4816 0.4778      6.0988      6.0545|
| 11:  2.2156 -  2.1465 1.00   1275  148 0.4871 0.4275       6.019      5.9932|
| 12:  2.1465 -  2.0853 0.97   1251  130 0.4967 0.4756      5.9701      6.0146|
| 13:  2.0853 -  2.0306 0.98   1240  142 0.4959 0.5408      5.8694      5.8732|
| 14:  2.0306 -  1.9811 0.73    943  107 0.5087 0.4509      5.8374      5.7317|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8990 -  4.7272  1376   154  0.73  31.45   0.82     0.75      59339.95|
|  2:  4.7272 -  3.7721  1334   145  0.78  28.43   0.92     0.82      72717.35|
|  3:  3.7721 -  3.3012  1300   148  0.71  34.27   0.88     0.80      74947.02|
|  4:  3.3012 -  3.0021  1294   143  0.65  39.35   0.84     0.72      66689.70|
|  5:  3.0021 -  2.7884  1285   139  0.56  47.27   0.78     0.63      60898.88|
|  6:  2.7884 -  2.6250  1279   145  0.54  49.00   0.77     0.60      54249.68|
|  7:  2.6250 -  2.4941  1268   141  0.53  49.85   0.76     0.59      50104.84|
|  8:  2.4941 -  2.3860  1275   140  0.53  49.56   0.77     0.60      44167.50|
|  9:  2.3860 -  2.2945  1277   144  0.53  49.78   0.76     0.61      39354.87|
| 10:  2.2945 -  2.2156  1233   133  0.55  48.67   0.78     0.61      35529.47|
| 11:  2.2156 -  2.1465  1275   148  0.52  51.00   0.78     0.60      34018.38|
| 12:  2.1465 -  2.0853  1251   130  0.47  54.94   0.78     0.56      35125.05|
| 13:  2.0853 -  2.0306  1240   142  0.43  58.11   0.77     0.51      31644.84|
| 14:  2.0306 -  1.9811   943   107  0.46  55.63   0.75     0.50      24904.10|
|alpha:            min =        0.50 max =            0.82 mean =         0.64|
|beta:             min =    24904.10 max =        74947.02 mean =     49573.13|
|figures of merit: min =        0.00 max =            1.00 mean =         0.57|
|phase err.(work): min =        0.00 max =           89.99 mean =        45.85|
|phase err.(test): min =        0.00 max =           89.93 mean =        45.86|
|-----------------------------------------------------------------------------|

============================== 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 = 7.345583              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 74.608   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.597953              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.172   (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:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       23 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      160 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      696 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1520 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2649 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3931 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5094 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6615 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7730 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.572 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.091    4.900  1.196 |       1.753 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.791)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 11.791)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4353   r_free= 0.4261   ksol= 0.00   Bsol= 0.00   scale= 0.798    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.223323                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4177   r_free= 0.4095   ksol= 0.34   Bsol= 14.49   scale= 1.028   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.32,8.68,8.49,0.00,0.00,0.00); trace/3= 8.16                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.212366                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.801418              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 76.615   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.613454              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.417   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4177      final r-factor (work) = 0.3079          |
| start r-factor (free) = 0.4095      final r-factor (free) = 0.3328          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 74.7674 = 6.80 * 0.50 * 6.2325 + 1.00 * 53.5724                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.6898 = 6.80 * 0.50 * 6.0498 + 1.00 * 0.1163                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3079      final r-factor (work) = 0.2418          |
| start r-factor (free) = 0.3328      final r-factor (free) = 0.2770          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7260 = 0.61 * 1.00 * 6.0498 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6038 = 0.61 * 1.00 * 5.8562 + 1.00 * 0.0112                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.791)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    62.29   10.53    None  None   None       |
|    all(noH): 2823   0      0.00    62.29   10.53    None  None   None       |
|    Sol.    : 438    0      0.00    58.12   27.80    None  None   None       |
|    Mac.    : 2385   0      0.00    62.29   7.36     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.229: 1400   |   5:    31.144 -  37.372:   99        |
|      1:     6.229 -  12.458:  695   |   6:    37.372 -  43.601:   74        |
|      2:    12.458 -  18.686:  237   |   7:    43.601 -  49.830:   35        |
|      3:    18.686 -  24.915:  139   |   8:    49.830 -  56.059:   17        |
|      4:    24.915 -  31.144:  120   |   9:    56.059 -  62.287:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2418 r_free = 0.2770             target_work(ml) = 5.774         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2412 r_free = 0.2769             target_work(ml) = 5.773         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2412   r_free= 0.2769   ksol= 0.34   Bsol= 14.49   scale= 1.091   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.32,8.68,8.49,0.00,0.00,0.00); trace/3= 8.16                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.773116                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2361   r_free= 0.2705   ksol= 0.33   Bsol= 35.57   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.95,4.97,5.56,0.00,0.00,0.00); trace/3= 4.83                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.771590                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.949940              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.335   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.306326              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 117.879  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2361      final r-factor (work) = 0.1493          |
| start r-factor (free) = 0.2705      final r-factor (free) = 0.1867          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.6349 = 4.95 * 0.50 * 5.8664 + 1.00 * 0.1157                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.8540 = 4.95 * 0.50 * 5.5707 + 1.00 * 0.0667                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1493      final r-factor (work) = 0.1339          |
| start r-factor (free) = 0.1867      final r-factor (free) = 0.1732          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7175 = 0.31 * 1.00 * 5.5707 + 1.00 * 0.0111                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6352 = 0.31 * 1.00 * 5.3052 + 1.00 * 0.0101                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.791)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    68.05   11.08    None  None   None       |
|    all(noH): 2823   0      0.00    68.05   11.08    None  None   None       |
|    Sol.    : 438    0      1.20    59.58   31.86    None  None   None       |
|    Mac.    : 2385   0      0.00    68.05   7.27     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.805: 1538   |   5:    34.027 -  40.832:  110        |
|      1:     6.805 -  13.611:  644   |   6:    40.832 -  47.638:   89        |
|      2:    13.611 -  20.416:  175   |   7:    47.638 -  54.443:   46        |
|      3:    20.416 -  27.222:  103   |   8:    54.443 -  61.249:   13        |
|      4:    27.222 -  34.027:  100   |   9:    61.249 -  68.054:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1339 r_free = 0.1732             target_work(ml) = 5.267         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1338 r_free = 0.1731             target_work(ml) = 5.267         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1338   r_free= 0.1731   ksol= 0.33   Bsol= 35.57   scale= 1.035   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.95,4.97,5.56,0.00,0.00,0.00); trace/3= 4.83                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.266752                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1329   r_free= 0.1719   ksol= 0.32   Bsol= 35.57   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.98,3.79,4.29,0.00,0.00,0.00); trace/3= 3.69                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.266262                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.533460              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 113.019  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.267578              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.396  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1329      final r-factor (work) = 0.1207          |
| start r-factor (free) = 0.1719      final r-factor (free) = 0.1576          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.1436 = 1.53 * 0.50 * 5.3174 + 1.00 * 0.0666                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.0590 = 1.53 * 0.50 * 5.2236 + 1.00 * 0.0539                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1207      final r-factor (work) = 0.1184          |
| start r-factor (free) = 0.1576      final r-factor (free) = 0.1561          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4077 = 0.27 * 1.00 * 5.2236 + 1.00 * 0.0100                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3955 = 0.27 * 1.00 * 5.1772 + 1.00 * 0.0102                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.791)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    70.29   11.16    None  None   None       |
|    all(noH): 2823   0      0.00    70.29   11.16    None  None   None       |
|    Sol.    : 438    0      0.78    61.93   32.38    None  None   None       |
|    Mac.    : 2385   0      0.00    70.29   7.27     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 -   7.029: 1603   |   5:    35.147 -  42.177:  109        |
|      1:     7.029 -  14.059:  597   |   6:    42.177 -  49.206:   76        |
|      2:    14.059 -  21.088:  167   |   7:    49.206 -  56.235:   42        |
|      3:    21.088 -  28.118:  108   |   8:    56.235 -  63.265:   11        |
|      4:    28.118 -  35.147:  104   |   9:    63.265 -  70.294:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1184 r_free = 0.1561             target_work(ml) = 5.172         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1183 r_free = 0.1561             target_work(ml) = 5.172         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1183   r_free= 0.1561   ksol= 0.32   Bsol= 35.57   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.98,3.79,4.29,0.00,0.00,0.00); trace/3= 3.69                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.171845                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1183   r_free= 0.1560   ksol= 0.32   Bsol= 35.57   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.78,3.50,4.04,0.00,0.00,0.00); trace/3= 3.44                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.171745                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.856519              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 140.124  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.401092              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 156.890  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1183      final r-factor (work) = 0.1126          |
| start r-factor (free) = 0.1560      final r-factor (free) = 0.1545          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8596 = 1.86 * 0.50 * 5.1771 + 1.00 * 0.0539                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8399 = 1.86 * 0.50 * 5.1488 + 1.00 * 0.0604                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1126      final r-factor (work) = 0.1117          |
| start r-factor (free) = 0.1545      final r-factor (free) = 0.1549          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0753 = 0.40 * 1.00 * 5.1488 + 1.00 * 0.0101                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0705 = 0.40 * 1.00 * 5.1349 + 1.00 * 0.0109                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.791)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    72.75   11.20    None  None   None       |
|    all(noH): 2823   0      0.00    72.75   11.20    None  None   None       |
|    Sol.    : 438    0      0.88    63.17   32.58    None  None   None       |
|    Mac.    : 2385   0      0.00    72.75   7.28     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 -   7.275: 1637   |   5:    36.376 -  43.651:  104        |
|      1:     7.275 -  14.550:  580   |   6:    43.651 -  50.926:   72        |
|      2:    14.550 -  21.825:  158   |   7:    50.926 -  58.201:   37        |
|      3:    21.825 -  29.100:  112   |   8:    58.201 -  65.476:    8        |
|      4:    29.100 -  36.376:  109   |   9:    65.476 -  72.751:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1117 r_free = 0.1549             target_work(ml) = 5.137         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1117 r_free = 0.1550             target_work(ml) = 5.138         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1117   r_free= 0.1550   ksol= 0.32   Bsol= 35.57   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.78,3.50,4.04,0.00,0.00,0.00); trace/3= 3.44                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.137794                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1117   r_free= 0.1550   ksol= 0.32   Bsol= 39.03   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.83,3.49,4.06,0.00,0.00,0.00); trace/3= 3.46                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.137335                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.701541              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 155.245  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.547574              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 151.632  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1117      final r-factor (work) = 0.1083          |
| start r-factor (free) = 0.1550      final r-factor (free) = 0.1541          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9964 = 2.70 * 0.50 * 5.1348 + 1.00 * 0.0605                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9914 = 2.70 * 0.50 * 5.1245 + 1.00 * 0.0694                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1083      final r-factor (work) = 0.1081          |
| start r-factor (free) = 0.1541      final r-factor (free) = 0.1546          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8170 = 0.55 * 1.00 * 5.1245 + 1.00 * 0.0110                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8157 = 0.55 * 1.00 * 5.1213 + 1.00 * 0.0114                               |
|-----------------------------------------------------------------------------|
| number of iterations = 8       |    number of function evaluations = 9      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.791)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    73.18   11.16    None  None   None       |
|    all(noH): 2823   0      0.00    73.18   11.16    None  None   None       |
|    Sol.    : 438    0      1.03    63.20   32.62    None  None   None       |
|    Mac.    : 2385   0      0.00    73.18   7.21     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 -   7.318: 1649   |   5:    36.591 -  43.909:  100        |
|      1:     7.318 -  14.636:  565   |   6:    43.909 -  51.227:   74        |
|      2:    14.636 -  21.955:  164   |   7:    51.227 -  58.545:   35        |
|      3:    21.955 -  29.273:  112   |   8:    58.545 -  65.864:    8        |
|      4:    29.273 -  36.591:  110   |   9:    65.864 -  73.182:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1081 r_free = 0.1546             target_work(ml) = 5.124         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1081 r_free = 0.1546             target_work(ml) = 5.124         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1081   r_free= 0.1546   ksol= 0.32   Bsol= 39.03   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.83,3.49,4.06,0.00,0.00,0.00); trace/3= 3.46                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.123513                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8990 -  4.7272 0.99   1376  154 0.1001 0.1272      5.3822      5.5187|
|  2:  4.7272 -  3.7721 0.99   1334  145 0.0845 0.1124       5.428      5.6348|
|  3:  3.7721 -  3.3012 0.99   1300  148 0.1019 0.1499      5.4518      5.8496|
|  4:  3.3012 -  3.0021 0.99   1294  143 0.1181 0.1477      5.4332      5.5716|
|  5:  3.0021 -  2.7884 0.99   1285  139 0.1252 0.1656      5.2958      5.5054|
|  6:  2.7884 -  2.6250 0.99   1279  145 0.1168 0.1831      5.1891      5.4576|
|  7:  2.6250 -  2.4941 0.99   1268  141 0.1188 0.1581      5.1347      5.3346|
|  8:  2.4941 -  2.3860 0.98   1275  140 0.1131 0.1773      5.0634      5.3752|
|  9:  2.3860 -  2.2945 0.98   1277  144 0.1135 0.1765      5.0119      5.3099|
| 10:  2.2945 -  2.2156 0.98   1233  133 0.1053 0.1640      4.9448      5.1533|
| 11:  2.2156 -  2.1465 1.00   1275  148 0.1092 0.1680      4.9054      5.2583|
| 12:  2.1465 -  2.0853 0.97   1251  130 0.1043 0.1682       4.845      5.1403|
| 13:  2.0853 -  2.0306 0.98   1240  142 0.1106 0.1670       4.779      5.0381|
| 14:  2.0306 -  1.9811 0.73    943  107 0.1034 0.1775      4.6825      4.9557|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8990 -  4.7272  1376   154  0.94   8.96   0.98     0.96       7088.42|
|  2:  4.7272 -  3.7721  1334   145  0.95   7.80   1.02     1.00       8906.87|
|  3:  3.7721 -  3.3012  1300   148  0.94  10.94   1.03     1.02      10099.27|
|  4:  3.3012 -  3.0021  1294   143  0.92  13.11   1.00     0.99       9967.38|
|  5:  3.0021 -  2.7884  1285   139  0.90  15.35   0.99     0.96       7878.89|
|  6:  2.7884 -  2.6250  1279   145  0.90  15.53   0.98     0.95       6803.49|
|  7:  2.6250 -  2.4941  1268   141  0.91  15.13   0.99     0.96       5938.09|
|  8:  2.4941 -  2.3860  1275   140  0.91  14.92   0.99     0.97       5333.01|
|  9:  2.3860 -  2.2945  1277   144  0.91  15.42   1.00     0.98       4895.69|
| 10:  2.2945 -  2.2156  1233   133  0.91  15.25   1.00     0.97       4378.50|
| 11:  2.2156 -  2.1465  1275   148  0.90  15.72   1.00     0.96       4135.31|
| 12:  2.1465 -  2.0853  1251   130  0.92  14.39   1.01     0.99       3731.84|
| 13:  2.0853 -  2.0306  1240   142  0.90  15.77   1.01     1.00       3320.25|
| 14:  2.0306 -  1.9811   943   107  0.91  15.13   0.99     0.95       2704.66|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2704.66 max =        10099.27 mean =      6186.98|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           90.00 mean =        13.73|
|phase err.(test): min =        0.00 max =           89.61 mean =        13.31|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1081   r_free= 0.1546   ksol= 0.32   Bsol= 42.57   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.63,0.02,0.61,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.124609                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1081   r_free= 0.1546   ksol= 0.32   Bsol= 42.57   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.63,0.02,0.61,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.124609                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8990 -  4.7272 0.99   1376  154 0.0992 0.1292      5.3853      5.5265|
|  2:  4.7272 -  3.7721 0.99   1334  145 0.0856 0.1121      5.4367      5.6388|
|  3:  3.7721 -  3.3012 0.99   1300  148 0.1014 0.1494       5.451      5.8365|
|  4:  3.3012 -  3.0021 0.99   1294  143 0.1186 0.1475      5.4335      5.5726|
|  5:  3.0021 -  2.7884 0.99   1285  139 0.1252 0.1653      5.2952      5.5048|
|  6:  2.7884 -  2.6250 0.99   1279  145 0.1168 0.1828      5.1888      5.4594|
|  7:  2.6250 -  2.4941 0.99   1268  141 0.1188 0.1589       5.135      5.3357|
|  8:  2.4941 -  2.3860 0.98   1275  140 0.1133 0.1768      5.0636      5.3731|
|  9:  2.3860 -  2.2945 0.98   1277  144 0.1133 0.1764      5.0115      5.3106|
| 10:  2.2945 -  2.2156 0.98   1233  133 0.1053 0.1645      4.9455      5.1547|
| 11:  2.2156 -  2.1465 1.00   1275  148 0.1090 0.1678      4.9059      5.2605|
| 12:  2.1465 -  2.0853 0.97   1251  130 0.1041 0.1688      4.8464      5.1436|
| 13:  2.0853 -  2.0306 0.98   1240  142 0.1107 0.1675      4.7801      5.0397|
| 14:  2.0306 -  1.9811 0.73    943  107 0.1034 0.1776       4.683      4.9562|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8990 -  4.7272  1376   154  0.94   9.19   0.98     0.96       7308.59|
|  2:  4.7272 -  3.7721  1334   145  0.95   7.97   1.02     1.00       9021.95|
|  3:  3.7721 -  3.3012  1300   148  0.94  10.92   1.03     1.02      10113.47|
|  4:  3.3012 -  3.0021  1294   143  0.92  13.06   1.01     0.99       9873.79|
|  5:  3.0021 -  2.7884  1285   139  0.90  15.34   0.99     0.96       7850.93|
|  6:  2.7884 -  2.6250  1279   145  0.90  15.53   0.98     0.95       6803.16|
|  7:  2.6250 -  2.4941  1268   141  0.91  15.11   0.99     0.96       5938.76|
|  8:  2.4941 -  2.3860  1275   140  0.91  14.91   1.00     0.97       5329.29|
|  9:  2.3860 -  2.2945  1277   144  0.91  15.42   1.01     0.98       4891.96|
| 10:  2.2945 -  2.2156  1233   133  0.91  15.27   1.01     0.98       4386.20|
| 11:  2.2156 -  2.1465  1275   148  0.90  15.76   1.00     0.97       4152.36|
| 12:  2.1465 -  2.0853  1251   130  0.92  14.43   1.01     0.99       3750.69|
| 13:  2.0853 -  2.0306  1240   142  0.90  15.79   1.01     1.00       3330.24|
| 14:  2.0306 -  1.9811   943   107  0.91  15.14   0.99     0.96       2706.53|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2706.53 max =        10113.47 mean =      6208.41|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.96 mean =        13.76|
|phase err.(test): min =        0.00 max =           88.83 mean =        13.32|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.791)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.54    76.72   14.70    None  None   None       |
|    all(noH): 2823   0      3.54    76.72   14.70    None  None   None       |
|    Sol.    : 438    0      4.57    66.74   36.16    None  None   None       |
|    Mac.    : 2385   0      3.54    76.72   10.75    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:     3.540 -  10.858: 1649   |   5:    40.131 -  47.449:  100        |
|      1:    10.858 -  18.176:  565   |   6:    47.449 -  54.767:   74        |
|      2:    18.176 -  25.495:  164   |   7:    54.767 -  62.085:   35        |
|      3:    25.495 -  32.813:  112   |   8:    62.085 -  69.404:    8        |
|      4:    32.813 -  40.131:  110   |   9:    69.404 -  76.722:    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)= 313         
Filter by distance & map next to the model:
   mapped sites are within: 0.344 - 5.967
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 309 from: 313
   mapped sites are within: 0.709 - 5.967

peak=   10.406 closest distance to " CG2 VAL A 230 " =    1.381
peak=    6.322 closest distance to " CG  LEU A   5 " =    1.204
peak=    6.270 closest distance to " CG2 VAL A 296 " =    1.065
peak=    6.076 closest distance to " NH2 ARG A  56 " =    2.253
peak=    5.797 closest distance to " CG  LEU A 228 " =    1.198
peak=    5.776 closest distance to " CB  VAL A 296 " =    1.101
peak=    5.311 closest distance to " CG  PRO A  54 " =    1.214
peak=    5.238 closest distance to " CB  VAL A 230 " =    1.200
peak=    5.146 closest distance to " O   HOH Z 126 " =    1.888
peak=    5.108 closest distance to " CB  GLN A 223 " =    1.452
peak=    5.104 closest distance to " NE2 GLN A  11 " =    1.107
peak=    5.101 closest distance to " CD2 LEU A   5 " =    1.157
peak=    5.064 closest distance to " CB  SER A  63 " =    1.244
peak=    5.005 closest distance to " CB  ARG A 275 " =    0.896
peak=    4.976 closest distance to " CB  GLN A 183 " =    1.301
peak=    4.966 closest distance to " O   HOH Z 209 " =    2.361
peak=    4.917 closest distance to " O   HOH Z 142 " =    1.665
peak=    4.901 closest distance to " O   HOH Z 272 " =    1.910
peak=    4.621 closest distance to " O   HOH Z 193 " =    1.775
peak=    4.548 closest distance to " CB  GLU A 152 " =    1.148
peak=    4.545 closest distance to " O   HOH Z  66 " =    2.276
peak=    4.518 closest distance to " C   PRO A 198 " =    1.477
peak=    4.479 closest distance to " O   SER A  87 " =    2.204
peak=    4.477 closest distance to " CG  PRO A 213 " =    1.216
peak=    4.473 closest distance to " O   HOH Z 298 " =    1.793
peak=    4.414 closest distance to " O   HOH Z 124 " =    1.397
peak=    4.358 closest distance to " O   HOH Z 368 " =    2.203
peak=    4.353 closest distance to " O   HOH Z 369 " =    2.076
peak=    4.351 closest distance to " CB  SER A   3 " =    1.278
peak=    4.342 closest distance to " O   HOH Z 316 " =    2.980
peak=    4.328 closest distance to " O   HOH Z  59 " =    2.182
peak=    4.310 closest distance to " ND2 ASN A 187 " =    1.493
peak=    4.303 closest distance to " CB  PRO A  54 " =    0.883
peak=    4.294 closest distance to " O   HOH Z  43 " =    2.073
peak=    4.289 closest distance to " O   HOH Z  63 " =    2.206
peak=    4.271 closest distance to " O   HOH Z 423 " =    1.832
peak=    4.244 closest distance to " OD1 ASN A  69 " =    2.544
peak=    4.236 closest distance to " CB  ARG A  79 " =    1.401
peak=    4.235 closest distance to " O   HOH Z 234 " =    3.533
peak=    4.222 closest distance to " O   HOH Z 427 " =    2.952
peak=    4.217 closest distance to " O   HOH Z 236 " =    1.886
peak=    4.212 closest distance to " O   HOH Z 303 " =    2.062
peak=    4.207 closest distance to " O   HOH Z  78 " =    1.762
peak=    4.205 closest distance to " O   HOH Z  40 " =    1.557
peak=    4.200 closest distance to " O   HOH Z 232 " =    2.358
peak=    4.116 closest distance to " O   HOH Z 203 " =    1.754
peak=    4.104 closest distance to " O   HOH Z 346 " =    1.573
peak=    4.088 closest distance to " O   HOH Z 407 " =    2.526
peak=    4.082 closest distance to " O   HOH Z  61 " =    1.617
peak=    4.056 closest distance to " O   HOH Z 402 " =    1.459
peak=    4.048 closest distance to " CB  ARG A 139 " =    0.918
peak=    4.020 closest distance to " O   HOH Z  54 " =    1.600
peak=    3.997 closest distance to " O   HOH Z 403 " =    1.673
peak=    3.979 closest distance to " CG  PRO A 243 " =    1.141
peak=    3.978 closest distance to " O   HOH Z 158 " =    3.107
peak=    3.976 closest distance to " CA  TYR A  30 " =    0.950
peak=    3.966 closest distance to " CB  GLU A 128 " =    1.062
peak=    3.959 closest distance to " O   HOH Z 189 " =    2.501
peak=    3.958 closest distance to " CB  TRP A 179 " =    1.337
peak=    3.953 closest distance to " CB  GLU A 277 " =    3.544
peak=    3.952 closest distance to " O   HOH Z  85 " =    1.383
peak=    3.949 closest distance to " O   HOH Z  15 " =    2.125
peak=    3.936 closest distance to " O   HOH Z  97 " =    1.914
peak=    3.934 closest distance to " O   HOH Z 371 " =    3.258
peak=    3.929 closest distance to " CG1BVAL A  72 " =    1.586
peak=    3.919 closest distance to " CG  ARG A  66 " =    2.780
peak=    3.909 closest distance to " O   HOH Z 197 " =    2.955
peak=    3.905 closest distance to " CB  ARG A 190 " =    1.675
peak=    3.872 closest distance to " CD2 LEU A 228 " =    1.144
peak=    3.871 closest distance to " CB  ASN A 148 " =    1.346
peak=    3.869 closest distance to " OD2 ASP A 286 " =    2.783
peak=    3.867 closest distance to " O   HOH Z  80 " =    1.696
peak=    3.860 closest distance to " O   HOH Z  97 " =    2.536
peak=    3.856 closest distance to " CB  VAL A 265 " =    1.290
peak=    3.853 closest distance to " O   HOH Z 345 " =    3.085
peak=    3.830 closest distance to " O   HOH Z 280 " =    2.949
peak=    3.813 closest distance to " O   HOH Z 245 " =    1.420
peak=    3.808 closest distance to " O   HOH Z 263 " =    1.595
peak=    3.808 closest distance to " O   HOH Z  66 " =    2.289
peak=    3.793 closest distance to " CA  ALA A  21 " =    1.128
peak=    3.792 closest distance to " O   TRP A 274 " =    1.908
peak=    3.787 closest distance to " O   HOH Z 417 " =    3.107
peak=    3.776 closest distance to " O   HOH Z 261 " =    2.184
peak=    3.771 closest distance to " CZ  PHE A 218 " =    1.101
peak=    3.765 closest distance to " O   HOH Z 411 " =    3.734
peak=    3.765 closest distance to " O   HOH Z  48 " =    1.490
peak=    3.764 closest distance to " CB  VAL A 202 " =    1.534
peak=    3.763 closest distance to " O   HOH Z 128 " =    2.093
peak=    3.762 closest distance to " O   HOH Z 248 " =    1.643
peak=    3.760 closest distance to " CD BLYS A 290 " =    1.131
peak=    3.755 closest distance to " CD2 TRP A 179 " =    1.409
peak=    3.741 closest distance to " O   HOH Z 214 " =    2.136
peak=    3.719 closest distance to " OE1 GLU A   2 " =    2.188
peak=    3.717 closest distance to " O   HOH Z 273 " =    2.666
peak=    3.712 closest distance to " O   HOH Z 344 " =    2.945
peak=    3.695 closest distance to " CB  TRP A 266 " =    0.982
peak=    3.693 closest distance to " CB  ASN A  39 " =    0.884
peak=    3.693 closest distance to " O   HOH Z 261 " =    2.208
peak=    3.682 closest distance to " CA  LYS A 117 " =    1.271
peak=    3.679 closest distance to " CB  ALA A   9 " =    1.614
peak=    3.676 closest distance to " CB  ASP A 140 " =    0.909
peak=    3.675 closest distance to " O   HOH Z 128 " =    2.104
peak=    3.669 closest distance to " O   HOH Z 291 " =    1.565
peak=    3.651 closest distance to " CG  PRO A 198 " =    1.142
peak=    3.642 closest distance to " O   HOH Z 366 " =    2.996
peak=    3.640 closest distance to " CB  SER A  26 " =    1.628
peak=    3.639 closest distance to " O   HOH Z 426 " =    1.536
peak=    3.639 closest distance to " O   HOH Z 250 " =    1.344
peak=    3.631 closest distance to " CG1 ILE A  33 " =    1.292
peak=    3.631 closest distance to " CA  ALA A  51 " =    0.939
peak=    3.622 closest distance to " O   HOH Z 389 " =    1.880
peak=    3.615 closest distance to " NH2 ARG A 156 " =    1.107
peak=    3.612 closest distance to " O   HOH Z 227 " =    1.613
peak=    3.610 closest distance to " O   HOH Z 329 " =    3.868
peak=    3.608 closest distance to " CB  ALA A 291 " =    1.376
peak=    3.607 closest distance to " O   HOH Z 422 " =    2.712
peak=    3.598 closest distance to " CB  ALA A 248 " =    1.397
peak=    3.592 closest distance to " CE1 TYR A 186 " =    1.293
peak=    3.592 closest distance to " CG2 ILE A  20 " =    1.454
peak=    3.585 closest distance to " CG  GLN A  77 " =    2.147
peak=    3.574 closest distance to " CD  LYS A 166 " =    1.317
peak=    3.556 closest distance to " CA  ASP A 140 " =    1.185
peak=    3.549 closest distance to " O   HOH Z 299 " =    4.275
peak=    3.549 closest distance to " N   ASN A  39 " =    1.214
peak=    3.543 closest distance to " CG1 ILE A  49 " =    1.419
peak=    3.541 closest distance to " OG BSER A 164 " =    2.175
peak=    3.539 closest distance to " CB  THR A  31 " =    1.671
peak=    3.533 closest distance to " O   HOH Z 261 " =    1.599
peak=    3.532 closest distance to " O   HOH Z 322 " =    2.070
peak=    3.528 closest distance to " O   HOH Z  21 " =    1.675
peak=    3.523 closest distance to " CG2 THR A 221 " =    1.193
peak=    3.519 closest distance to " NZ  LYS A 117 " =    3.246
peak=    3.506 closest distance to " O   HOH Z 147 " =    1.765
peak=    3.505 closest distance to " CB BVAL A  41 " =    1.092
peak=    3.500 closest distance to " CA  ASN A 215 " =    1.237
peak=    3.500 closest distance to " O   HOH Z 112 " =    1.624
peak=    3.497 closest distance to " CD  LYS A 119 " =    1.743
peak=    3.493 closest distance to " O   MET A 105 " =    1.831
peak=    3.483 closest distance to " O   HOH Z 250 " =    1.455
peak=    3.480 closest distance to " CB  GLN A  88 " =    1.166
peak=    3.473 closest distance to " O   HOH Z 193 " =    1.971
peak=    3.468 closest distance to " CB  ASN A 142 " =    1.104
peak=    3.463 closest distance to " O   HOH Z 417 " =    2.131
peak=    3.462 closest distance to " O   HOH Z 383 " =    2.047
peak=    3.462 closest distance to " ND2 ASN A 110 " =    1.657
peak=    3.461 closest distance to " CA  VAL A  41 " =    0.807
peak=    3.461 closest distance to " CG  MET A 185 " =    1.123
peak=    3.460 closest distance to " CG  GLN A  58 " =    2.811
peak=    3.452 closest distance to " O   ASP A 124 " =    1.162
peak=    3.451 closest distance to " N   SER A 135 " =    1.434
peak=    3.450 closest distance to " O   HOH Z 359 " =    1.824
peak=    3.443 closest distance to " CA  PHE A 283 " =    1.246
peak=    3.441 closest distance to " CA  ASN A 176 " =    1.066
peak=    3.439 closest distance to " O   HOH Z  88 " =    2.991
peak=    3.437 closest distance to " O   HOH Z 286 " =    2.236
peak=    3.435 closest distance to " CG  MET A 185 " =    1.130
peak=    3.420 closest distance to " CA  ALA A 158 " =    1.239
peak=    3.419 closest distance to " O   HOH Z 337 " =    3.644
peak=    3.415 closest distance to " O   HOH Z 420 " =    1.993
peak=    3.413 closest distance to " CA  THR A 264 " =    0.766
peak=    3.408 closest distance to " CD1 LEU A 300 " =    1.259
peak=    3.403 closest distance to " CG2 ILE A 120 " =    1.252
peak=    3.402 closest distance to " OG1 THR A 294 " =    2.347
peak=    3.397 closest distance to " O   HOH Z  48 " =    1.575
peak=    3.391 closest distance to " NH2 ARG A  79 " =    1.351
peak=    3.385 closest distance to " O   HOH Z 227 " =    2.089
peak=    3.384 closest distance to " CD  ARG A 159 " =    0.731
peak=    3.383 closest distance to " O   HOH Z 134 " =    1.373
peak=    3.380 closest distance to " CG1 VAL A 296 " =    1.203
peak=    3.379 closest distance to " O   HOH Z 421 " =    1.656
peak=    3.379 closest distance to " O   HOH Z   9 " =    2.141
peak=    3.376 closest distance to " NZ  LYS A 166 " =    3.046
peak=    3.375 closest distance to " CA  ASP A 162 " =    1.091
peak=    3.375 closest distance to " CG1 VAL A 153 " =    0.974
peak=    3.374 closest distance to " CB  HIS A 108 " =    0.837
peak=    3.371 closest distance to " CA  ARG A 195 " =    1.190
peak=    3.370 closest distance to " O   HOH Z 166 " =    3.741
peak=    3.367 closest distance to " O   HOH Z 258 " =    2.335
peak=    3.366 closest distance to " CB  TRP A 150 " =    1.389
peak=    3.364 closest distance to " CB  GLN A 205 " =    1.126
peak=    3.358 closest distance to " CB  LEU A 143 " =    1.124
peak=    3.355 closest distance to " O   HOH Z 303 " =    1.660
peak=    3.353 closest distance to " CA  VAL A 126 " =    0.856
peak=    3.347 closest distance to " O   HOH Z 132 " =    2.661
peak=    3.340 closest distance to " CD  ARG A 269 " =    0.966
peak=    3.339 closest distance to " O   HOH Z 148 " =    3.200
peak=    3.329 closest distance to " CA  THR A 221 " =    0.911
peak=    3.326 closest distance to " CA  ALA A 291 " =    0.944
peak=    3.321 closest distance to " O   HOH Z 313 " =    1.757
peak=    3.321 closest distance to " CD2 HIS A  81 " =    1.121
peak=    3.319 closest distance to " CB  THR A 157 " =    1.176
peak=    3.319 closest distance to " CA  ASP A 191 " =    0.946
peak=    3.315 closest distance to " O   HOH Z  44 " =    1.755
peak=    3.313 closest distance to " NH2BARG A 145 " =    1.984
peak=    3.313 closest distance to " CB  ALA A 248 " =    0.980
peak=    3.310 closest distance to " O   HOH Z 135 " =    1.723
peak=    3.310 closest distance to " O   HOH Z 419 " =    1.616
peak=    3.308 closest distance to " CB  GLN A 278 " =    0.851
peak=    3.306 closest distance to " O   HOH Z 180 " =    2.119
peak=    3.304 closest distance to " O   HOH Z 199 " =    1.599
peak=    3.303 closest distance to " O   HOH Z  61 " =    1.567
peak=    3.299 closest distance to " O   HOH Z 295 " =    1.534
peak=    3.299 closest distance to " CA  ALA A  84 " =    1.465
peak=    3.294 closest distance to " O   THR A  31 " =    1.551
peak=    3.292 closest distance to " CG  LEU A 167 " =    1.167
peak=    3.291 closest distance to " O   HOH Z  40 " =    2.617
peak=    3.288 closest distance to " CD1 ILE A 106 " =    1.029
peak=    3.288 closest distance to " O   HOH Z 406 " =    1.763
peak=    3.287 closest distance to " CG BARG A 102 " =    1.758
peak=    3.283 closest distance to " CB  ILE A  20 " =    1.463
peak=    3.283 closest distance to " OD1 ASP A 231 " =    1.900
peak=    3.282 closest distance to " O   HOH Z 155 " =    3.278
peak=    3.279 closest distance to " O   HOH Z  19 " =    2.012
peak=    3.277 closest distance to " O   HOH Z 189 " =    2.656
peak=    3.276 closest distance to " N   VAL A 126 " =    1.356
peak=    3.276 closest distance to " O   HOH Z 172 " =    3.847
peak=    3.275 closest distance to " CB  GLU A  46 " =    1.070
peak=    3.273 closest distance to " O   HOH Z  49 " =    2.352
peak=    3.273 closest distance to " O   HOH Z  88 " =    2.428
peak=    3.270 closest distance to " O   HOH Z 406 " =    1.609
peak=    3.263 closest distance to " CA  ALA A 233 " =    1.236
peak=    3.262 closest distance to " O   HOH Z 368 " =    3.568
peak=    3.251 closest distance to " O   HOH Z 414 " =    1.935
peak=    3.250 closest distance to " CB  SER A 212 " =    1.192
peak=    3.247 closest distance to " O   HOH Z 265 " =    2.367
peak=    3.244 closest distance to " O   HOH Z 286 " =    2.460
peak=    3.241 closest distance to " CD2 TYR A  30 " =    0.892
peak=    3.241 closest distance to " CA  ALA A 295 " =    0.994
peak=    3.235 closest distance to " CB  ALA A   1 " =    1.181
peak=    3.235 closest distance to " O   HOH Z 367 " =    3.427
peak=    3.229 closest distance to " CA  LEU A 282 " =    1.077
peak=    3.229 closest distance to " NZ  LYS A  48 " =    1.331
peak=    3.225 closest distance to " O   HOH Z 234 " =    1.794
peak=    3.224 closest distance to " O   HOH Z 251 " =    1.633
peak=    3.223 closest distance to " O   HOH Z 133 " =    2.593
peak=    3.217 closest distance to " CA  ILE A 106 " =    0.770
peak=    3.217 closest distance to " CA  TYR A 116 " =    1.379
peak=    3.216 closest distance to " O   ALA A 158 " =    1.366
peak=    3.216 closest distance to " O   HOH Z 437 " =    1.972
peak=    3.215 closest distance to " O   HOH Z 435 " =    1.876
peak=    3.213 closest distance to " OG  SER A  22 " =    2.734
peak=    3.212 closest distance to " CD1 ILE A  33 " =    1.584
peak=    3.210 closest distance to " O   HOH Z  83 " =    1.604
peak=    3.210 closest distance to " CB  ILE A 120 " =    1.344
peak=    3.207 closest distance to " O   HOH Z 128 " =    1.941
peak=    3.207 closest distance to " CG2 VAL A 257 " =    0.826
peak=    3.205 closest distance to " CZ3 TRP A  85 " =    0.918
peak=    3.202 closest distance to " O   HOH Z 423 " =    3.166
peak=    3.202 closest distance to " O   HOH Z 380 " =    1.998
peak=    3.201 closest distance to " CA  THR A  52 " =    1.017
peak=    3.199 closest distance to " CB  LEU A   5 " =    1.253
peak=    3.198 closest distance to " O   HOH Z 173 " =    2.266
peak=    3.198 closest distance to " CA  ARG A  36 " =    1.013
peak=    3.197 closest distance to " CB  LEU A 228 " =    1.324
peak=    3.192 closest distance to " O   HOH Z 175 " =    2.100
peak=    3.187 closest distance to " ND1 HIS A  81 " =    1.626
peak=    3.180 closest distance to " O   HOH Z 411 " =    1.777
peak=    3.179 closest distance to " CB  TYR A 169 " =    1.185
peak=    3.176 closest distance to " N   ASP A 162 " =    1.323
peak=    3.175 closest distance to " O   HOH Z 305 " =    3.577
peak=    3.173 closest distance to " CG2 ILE A 234 " =    2.049
peak=    3.172 closest distance to " O   HOH Z 171 " =    2.461
peak=    3.171 closest distance to " C   TYR A 214 " =    1.438
peak=    3.170 closest distance to " CG  LYS A  76 " =    1.010
peak=    3.169 closest distance to " O   HOH Z  10 " =    1.794
peak=    3.169 closest distance to " O   GLN A 278 " =    1.161
peak=    3.168 closest distance to " CB  ASN A 215 " =    1.171
peak=    3.167 closest distance to " O   HOH Z 357 " =    1.811
peak=    3.165 closest distance to " CG2 THR A 294 " =    1.607
peak=    3.165 closest distance to " CG  GLN A  89 " =    1.522
peak=    3.159 closest distance to " CB  ALA A 295 " =    1.269
peak=    3.157 closest distance to " O   HOH Z 146 " =    1.518
peak=    3.154 closest distance to " O   HOH Z 193 " =    1.534
peak=    3.154 closest distance to " CB  ASN A 110 " =    1.159
peak=    3.144 closest distance to " O   HOH Z 126 " =    1.596
peak=    3.141 closest distance to " CD2 LEU A 255 " =    1.475
peak=    3.140 closest distance to " O   HOH Z   1 " =    2.076
peak=    3.136 closest distance to " OE2 GLU A  53 " =    2.009
peak=    3.135 closest distance to " O   HOH Z 425 " =    2.064
peak=    3.135 closest distance to " CD  ARG A 195 " =    3.541
peak=    3.132 closest distance to " O   HOH Z 341 " =    1.852
peak=    3.126 closest distance to " O   HOH Z 359 " =    3.724
peak=    3.126 closest distance to " CG  GLU A 277 " =    2.176
peak=    3.122 closest distance to " NE2 GLN A  58 " =    5.967
peak=    3.121 closest distance to " CA  SER A 146 " =    1.793
peak=    3.119 closest distance to " CB  LYS A 290 " =    1.038
peak=    3.119 closest distance to " NH2BARG A 190 " =    1.764
peak=    3.112 closest distance to " O   HOH Z 403 " =    1.349
peak=    3.108 closest distance to " N   ARG A 156 " =    1.360
peak=    3.107 closest distance to " CB  ASN A 224 " =    1.052
peak=    3.104 closest distance to " O   HOH Z 336 " =    1.699
peak=    3.103 closest distance to " O   HOH Z 353 " =    2.719
peak=    3.100 closest distance to " O   HOH Z 281 " =    4.664
peak=    3.096 closest distance to " O   HOH Z 427 " =    3.130
peak=    3.089 closest distance to " CB  SER A 216 " =    0.709
peak=    3.085 closest distance to " O   HOH Z 116 " =    1.760
peak=    3.083 closest distance to " CZ2 TRP A 274 " =    1.579
peak=    3.081 closest distance to " O   HOH Z 151 " =    1.785
peak=    3.079 closest distance to " O   HOH Z 250 " =    1.741
peak=    3.074 closest distance to " O   HOH Z 368 " =    2.645
peak=    3.073 closest distance to " CB  LEU A 255 " =    0.778
peak=    3.073 closest distance to " CA  LYS A 290 " =    1.226
peak=    3.070 closest distance to " O   HOH Z  85 " =    2.073
peak=    3.068 closest distance to " O   HOH Z 409 " =    3.530
peak=    3.059 closest distance to " CB  ALA A 100 " =    1.188
peak=    3.056 closest distance to " OG ASER A  99 " =    1.535
peak=    3.041 closest distance to " O   SER A 164 " =    1.173
peak=    3.040 closest distance to " O   HOH Z 271 " =    2.306
peak=    3.010 closest distance to " O   HOH Z  32 " =    1.795

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 200         
Filter by distance & map next to the model:
   mapped sites are within: 0.558 - 5.423
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 197 from: 200
   mapped sites are within: 0.767 - 5.423

peak=   -5.737 closest distance to " CG2 VAL A 230 " =    0.767
peak=   -4.863 closest distance to " SG  CYS A 254 " =    3.211
peak=   -4.589 closest distance to " CD  ARG A 156 " =    2.024
peak=   -4.567 closest distance to " O   HOH Z 266 " =    4.748
peak=   -4.366 closest distance to " CG  GLN A 223 " =    2.145
peak=   -4.263 closest distance to " O   PRO A 163 " =    2.177
peak=   -4.248 closest distance to " C   HIS A 108 " =    1.214
peak=   -4.228 closest distance to " CB  PRO A 243 " =    2.617
peak=   -4.218 closest distance to " CB  ALA A 161 " =    2.581
peak=   -4.147 closest distance to " O   HOH Z 290 " =    1.123
peak=   -4.073 closest distance to " CG2BVAL A  41 " =    2.580
peak=   -4.069 closest distance to " CD2 LEU A 300 " =    2.805
peak=   -4.001 closest distance to " OG BSER A 134 " =    1.187
peak=   -3.999 closest distance to " OXT GLY A 302 " =    2.789
peak=   -3.993 closest distance to " O   HOH Z 196 " =    2.047
peak=   -3.956 closest distance to " CE2 TYR A  30 " =    2.758
peak=   -3.950 closest distance to " O   VAL A  67 " =    2.743
peak=   -3.945 closest distance to " CG2 VAL A 296 " =    1.276
peak=   -3.937 closest distance to " O   HOH Z 351 " =    1.487
peak=   -3.858 closest distance to " O   HOH Z 166 " =    1.877
peak=   -3.852 closest distance to " NH2AARG A 275 " =    5.067
peak=   -3.847 closest distance to " CG1 VAL A 112 " =    2.685
peak=   -3.833 closest distance to " CZ3 TRP A 179 " =    1.268
peak=   -3.832 closest distance to " N   GLN A  58 " =    1.681
peak=   -3.814 closest distance to " CD  GLN A  58 " =    1.142
peak=   -3.778 closest distance to " O   HOH Z  11 " =    1.890
peak=   -3.771 closest distance to " NE2 GLN A  88 " =    1.946
peak=   -3.766 closest distance to " O   HOH Z 114 " =    3.106
peak=   -3.752 closest distance to " CD  ARG A 139 " =    1.645
peak=   -3.737 closest distance to " CB  ALA A 248 " =    2.053
peak=   -3.736 closest distance to " CD1 LEU A 101 " =    2.404
peak=   -3.722 closest distance to " O   HOH Z 103 " =    1.854
peak=   -3.711 closest distance to " OG  SER A  97 " =    2.257
peak=   -3.707 closest distance to " CB  PHE A 192 " =    1.923
peak=   -3.705 closest distance to " ND2 ASN A  45 " =    1.034
peak=   -3.701 closest distance to " CG  ASP A 231 " =    0.815
peak=   -3.678 closest distance to " ND2 ASN A 187 " =    1.511
peak=   -3.658 closest distance to " CD1 PHE A  59 " =    1.917
peak=   -3.651 closest distance to " CZ  TYR A 169 " =    1.718
peak=   -3.642 closest distance to " O   HOH Z 211 " =    1.680
peak=   -3.633 closest distance to " O   HOH Z 231 " =    2.136
peak=   -3.630 closest distance to " N   ALA A 226 " =    2.040
peak=   -3.623 closest distance to " N   HIS A 115 " =    2.095
peak=   -3.614 closest distance to " O   HOH Z  63 " =    1.272
peak=   -3.607 closest distance to " CA  ASP A 298 " =    1.039
peak=   -3.601 closest distance to " CG  PHE A 283 " =    2.807
peak=   -3.598 closest distance to " O   HOH Z  52 " =    1.420
peak=   -3.595 closest distance to " O   HOH Z 435 " =    2.766
peak=   -3.593 closest distance to " CG1 VAL A 250 " =    2.768
peak=   -3.587 closest distance to " CB  ALA A 291 " =    2.235
peak=   -3.587 closest distance to " O   HOH Z 165 " =    1.949
peak=   -3.586 closest distance to " O   HOH Z  13 " =    1.474
peak=   -3.580 closest distance to " CB  PRO A 163 " =    2.541
peak=   -3.564 closest distance to " C   ALA A 158 " =    1.240
peak=   -3.559 closest distance to " CB  PRO A 280 " =    2.148
peak=   -3.541 closest distance to " N   THR A 157 " =    1.515
peak=   -3.541 closest distance to " OD2 ASP A 171 " =    2.262
peak=   -3.538 closest distance to " CD  LYS A 289 " =    2.495
peak=   -3.538 closest distance to " O   PRO A 198 " =    1.263
peak=   -3.533 closest distance to " O   HOH Z 234 " =    3.988
peak=   -3.532 closest distance to " O   HOH Z 126 " =    1.929
peak=   -3.532 closest distance to " CB  ASP A 132 " =    2.347
peak=   -3.532 closest distance to " O   HOH Z  47 " =    1.503
peak=   -3.514 closest distance to " CG  ARG A 269 " =    2.288
peak=   -3.510 closest distance to " O   HOH Z 389 " =    1.881
peak=   -3.510 closest distance to " CB  ASP A 132 " =    2.272
peak=   -3.504 closest distance to " C   MET A 188 " =    1.504
peak=   -3.497 closest distance to " OG BSER A 134 " =    1.704
peak=   -3.493 closest distance to " O   HOH Z 185 " =    2.400
peak=   -3.491 closest distance to " CB  ALA A 248 " =    2.350
peak=   -3.488 closest distance to " CG1 VAL A 112 " =    2.589
peak=   -3.483 closest distance to " CD1 LEU A 228 " =    2.151
peak=   -3.481 closest distance to " NH2 ARG A  79 " =    1.960
peak=   -3.475 closest distance to " O   HOH Z  11 " =    2.154
peak=   -3.472 closest distance to " O   ALA A 161 " =    1.690
peak=   -3.469 closest distance to " O   HOH Z  43 " =    1.783
peak=   -3.465 closest distance to " O   HOH Z 283 " =    1.922
peak=   -3.464 closest distance to " O   HOH Z 198 " =    2.342
peak=   -3.461 closest distance to " O   HOH Z 311 " =    3.642
peak=   -3.454 closest distance to " O   HOH Z 407 " =    2.988
peak=   -3.451 closest distance to " O   MET A  40 " =    2.643
peak=   -3.450 closest distance to " O   HOH Z 339 " =    1.845
peak=   -3.449 closest distance to " CG  LEU A 228 " =    0.965
peak=   -3.442 closest distance to " OG ASER A 134 " =    1.305
peak=   -3.442 closest distance to " N   PHE A  59 " =    2.237
peak=   -3.435 closest distance to " O   HOH Z 193 " =    1.760
peak=   -3.432 closest distance to " CG1 VAL A 296 " =    1.292
peak=   -3.428 closest distance to " O   GLY A 196 " =    1.124
peak=   -3.427 closest distance to " CE3 TRP A 150 " =    2.009
peak=   -3.426 closest distance to " O   HOH Z 394 " =    1.576
peak=   -3.424 closest distance to " CB  ASN A  69 " =    1.131
peak=   -3.423 closest distance to " O   HOH Z  19 " =    2.167
peak=   -3.423 closest distance to " O   HOH Z 102 " =    1.627
peak=   -3.421 closest distance to " CG2 ILE A 263 " =    2.301
peak=   -3.414 closest distance to " OXT GLY A 302 " =    3.397
peak=   -3.413 closest distance to " CB  ALA A 291 " =    2.173
peak=   -3.410 closest distance to " OD1 ASN A  39 " =    2.160
peak=   -3.410 closest distance to " N   THR A 235 " =    1.346
peak=   -3.400 closest distance to " N   ALA A 248 " =    1.735
peak=   -3.398 closest distance to " O   HOH Z 353 " =    2.103
peak=   -3.389 closest distance to " O   HOH Z  44 " =    2.133
peak=   -3.389 closest distance to " N   SER A 276 " =    1.333
peak=   -3.378 closest distance to " CB  GLN A  11 " =    1.855
peak=   -3.372 closest distance to " CG  GLU A 277 " =    1.156
peak=   -3.369 closest distance to " O   HOH Z 372 " =    2.247
peak=   -3.366 closest distance to " CB  ASN A  39 " =    2.189
peak=   -3.366 closest distance to " CE  MET A 105 " =    2.020
peak=   -3.362 closest distance to " C   SER A 206 " =    1.546
peak=   -3.362 closest distance to " O   HOH Z  17 " =    1.586
peak=   -3.360 closest distance to " CG1 VAL A 230 " =    1.825
peak=   -3.360 closest distance to " O   VAL A 125 " =    2.289
peak=   -3.354 closest distance to " N   ALA A  43 " =    2.559
peak=   -3.347 closest distance to " OG  SER A  62 " =    1.642
peak=   -3.343 closest distance to " O   VAL A 189 " =    2.605
peak=   -3.335 closest distance to " CD  ARG A 195 " =    5.157
peak=   -3.326 closest distance to " OD1 ASN A 187 " =    1.673
peak=   -3.321 closest distance to " O   HOH Z 313 " =    1.748
peak=   -3.318 closest distance to " OD1 ASN A 301 " =    2.040
peak=   -3.316 closest distance to " OG  SER A  26 " =    1.206
peak=   -3.315 closest distance to " O   SER A  95 " =    1.571
peak=   -3.312 closest distance to " CG2 THR A 221 " =    2.065
peak=   -3.310 closest distance to " NZ  LYS A 119 " =    3.552
peak=   -3.310 closest distance to " CZ  PHE A  59 " =    1.552
peak=   -3.310 closest distance to " O   GLY A  75 " =    1.835
peak=   -3.308 closest distance to " CG  ASP A  50 " =    2.336
peak=   -3.299 closest distance to " CG  TRP A 266 " =    1.916
peak=   -3.293 closest distance to " CE2 PHE A 218 " =    2.573
peak=   -3.291 closest distance to " O   ALA A  51 " =    1.323
peak=   -3.284 closest distance to " O   HOH Z 191 " =    5.423
peak=   -3.283 closest distance to " O   HOH Z 198 " =    1.357
peak=   -3.279 closest distance to " CA  GLY A 133 " =    1.995
peak=   -3.268 closest distance to " CD1 LEU A 101 " =    2.625
peak=   -3.266 closest distance to " NH1 ARG A 195 " =    2.572
peak=   -3.265 closest distance to " O   HOH Z 369 " =    2.264
peak=   -3.264 closest distance to " O   LYS A 117 " =    1.612
peak=   -3.263 closest distance to " OG1 THR A  82 " =    1.466
peak=   -3.260 closest distance to " O   SER A 210 " =    1.970
peak=   -3.258 closest distance to " O   HOH Z 426 " =    1.703
peak=   -3.255 closest distance to " CD1 LEU A  25 " =    2.431
peak=   -3.254 closest distance to " CA  GLY A  98 " =    1.887
peak=   -3.253 closest distance to " O   HOH Z 244 " =    2.036
peak=   -3.249 closest distance to " O   HOH Z 222 " =    1.428
peak=   -3.246 closest distance to " C   ASN A 285 " =    2.375
peak=   -3.239 closest distance to " OG  SER A  87 " =    1.416
peak=   -3.239 closest distance to " O   HOH Z  10 " =    1.454
peak=   -3.238 closest distance to " C   ASP A 231 " =    2.635
peak=   -3.238 closest distance to " O   HOH Z 411 " =    3.792
peak=   -3.238 closest distance to " O   HOH Z 262 " =    2.734
peak=   -3.238 closest distance to " C   GLN A 205 " =    1.916
peak=   -3.230 closest distance to " NE2 GLN A 194 " =    1.741
peak=   -3.218 closest distance to " NE2 GLN A 103 " =    1.691
peak=   -3.217 closest distance to " OD1 ASN A 148 " =    1.508
peak=   -3.216 closest distance to " OG  SER A 206 " =    1.677
peak=   -3.213 closest distance to " CA  GLY A 133 " =    2.256
peak=   -3.210 closest distance to " O   HOH Z  22 " =    2.454
peak=   -3.205 closest distance to " ND2 ASN A 249 " =    2.357
peak=   -3.204 closest distance to " O   PRO A 198 " =    1.291
peak=   -3.204 closest distance to " O   HOH Z 422 " =    1.592
peak=   -3.198 closest distance to " O   SER A  22 " =    2.250
peak=   -3.196 closest distance to " NH2 ARG A  66 " =    1.726
peak=   -3.195 closest distance to " CB  ALA A  51 " =    1.860
peak=   -3.194 closest distance to " CG  GLU A  53 " =    1.578
peak=   -3.193 closest distance to " CD1 TYR A 247 " =    2.433
peak=   -3.190 closest distance to " O   HOH Z  60 " =    2.129
peak=   -3.186 closest distance to " N   ASP A 171 " =    2.297
peak=   -3.177 closest distance to " O   HOH Z 175 " =    4.364
peak=   -3.177 closest distance to " CG  ARG A 219 " =    2.715
peak=   -3.174 closest distance to " O   PHE A 218 " =    1.704
peak=   -3.171 closest distance to " CG  MET A 105 " =    0.900
peak=   -3.168 closest distance to " OE1 GLN A  77 " =    1.709
peak=   -3.164 closest distance to " O   HOH Z 389 " =    4.759
peak=   -3.162 closest distance to " CD  GLN A  88 " =    0.914
peak=   -3.157 closest distance to " CG  GLU A   2 " =    1.832
peak=   -3.155 closest distance to " CG1 VAL A 112 " =    2.840
peak=   -3.155 closest distance to " O   GLY A  80 " =    2.325
peak=   -3.152 closest distance to " O   ALA A  10 " =    1.801
peak=   -3.146 closest distance to " CG1 VAL A 197 " =    2.174
peak=   -3.140 closest distance to " O   LEU A 167 " =    1.486
peak=   -3.135 closest distance to " CE BMET A  47 " =    1.776
peak=   -3.134 closest distance to " CD2 LEU A 237 " =    2.631
peak=   -3.134 closest distance to " O   HOH Z  38 " =    1.654
peak=   -3.126 closest distance to " N   GLN A  77 " =    1.552
peak=   -3.126 closest distance to " O   HOH Z 414 " =    1.503
peak=   -3.118 closest distance to " O   HOH Z  90 " =    1.851
peak=   -3.114 closest distance to " NH2 ARG A  79 " =    1.600
peak=   -3.104 closest distance to " NE2 GLN A  58 " =    1.213
peak=   -3.098 closest distance to " O   TRP A  92 " =    1.812
peak=   -3.098 closest distance to " N   MET A 105 " =    2.636
peak=   -3.092 closest distance to " CE  LYS A 166 " =    3.051
peak=   -3.089 closest distance to " O   HOH Z 313 " =    1.083
peak=   -3.079 closest distance to " ND2 ASN A  60 " =    1.469
peak=   -3.077 closest distance to " CA  GLY A 241 " =    3.002
peak=   -3.072 closest distance to " CD2 TYR A 247 " =    2.374
peak=   -3.071 closest distance to " O   HOH Z 210 " =    1.122
peak=   -3.030 closest distance to " CE1 HIS A  81 " =    1.467
peak=   -3.024 closest distance to " O   HOH Z 298 " =    2.517
peak=   -3.015 closest distance to " CG  PHE A 283 " =    2.645

================= 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    :  0.4265 0.4178   6.216872e+00   6.198491e+00
   1_bss:  0.4177 0.4095   6.212366e+00   6.182188e+00
   1_xyz:  0.3079 0.3328   5.988674e+00   6.038917e+00
   1_adp:  0.2418 0.2770   5.774433e+00   5.886179e+00
   1_occ:  0.2412 0.2769   5.773116e+00   5.885678e+00
   2_bss:  0.2361 0.2705   5.771590e+00   5.879699e+00
   2_xyz:  0.1493 0.1867   5.363764e+00   5.550340e+00
   2_adp:  0.1339 0.1732   5.267445e+00   5.472117e+00
   2_occ:  0.1338 0.1731   5.266752e+00   5.471592e+00
   3_bss:  0.1329 0.1719   5.266262e+00   5.469674e+00
   3_xyz:  0.1207 0.1576   5.186541e+00   5.397972e+00
   3_adp:  0.1184 0.1561   5.172257e+00   5.387539e+00
   3_occ:  0.1183 0.1561   5.171845e+00   5.387296e+00
   4_bss:  0.1183 0.1560   5.171745e+00   5.387228e+00
   4_xyz:  0.1126 0.1545   5.139242e+00   5.372785e+00
   4_adp:  0.1117 0.1549   5.137443e+00   5.376107e+00
   4_occ:  0.1117 0.1550   5.137794e+00   5.376734e+00
   5_bss:  0.1117 0.1550   5.137335e+00   5.376337e+00
   5_xyz:  0.1083 0.1541   5.123058e+00   5.373809e+00
   5_adp:  0.1081 0.1546   5.123530e+00   5.376552e+00
   5_occ:  0.1081 0.1546   5.123513e+00   5.376647e+00
   5_bss:  0.1081 0.1546   5.124609e+00   5.377343e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.342  14.493   7.323   8.679   8.493   0.000   0.000   0.000
   1_xyz:  0.342  14.493   7.323   8.679   8.493   0.000   0.000   0.000
   1_adp:  0.342  14.493   7.323   8.679   8.493   0.000   0.000   0.000
   1_occ:  0.342  14.493   7.323   8.679   8.493   0.000   0.000   0.000
   2_bss:  0.332  35.572   3.950   4.974   5.559   0.000   0.000   0.000
   2_xyz:  0.332  35.572   3.950   4.974   5.559   0.000   0.000   0.000
   2_adp:  0.332  35.572   3.950   4.974   5.559   0.000   0.000   0.000
   2_occ:  0.332  35.572   3.950   4.974   5.559   0.000   0.000   0.000
   3_bss:  0.321  35.572   2.984   3.785   4.288   0.000   0.000   0.000
   3_xyz:  0.321  35.572   2.984   3.785   4.288   0.000   0.000   0.000
   3_adp:  0.321  35.572   2.984   3.785   4.288   0.000   0.000   0.000
   3_occ:  0.321  35.572   2.984   3.785   4.288   0.000   0.000   0.000
   4_bss:  0.321  35.572   2.782   3.502   4.037   0.000   0.000   0.000
   4_xyz:  0.321  35.572   2.782   3.502   4.037   0.000   0.000   0.000
   4_adp:  0.321  35.572   2.782   3.502   4.037   0.000   0.000   0.000
   4_occ:  0.321  35.572   2.782   3.502   4.037   0.000   0.000   0.000
   5_bss:  0.321  39.031   2.832   3.486   4.064   0.000   0.000   0.000
   5_xyz:  0.321  39.031   2.832   3.486   4.064   0.000   0.000   0.000
   5_adp:  0.321  39.031   2.832   3.486   4.064   0.000   0.000   0.000
   5_occ:  0.321  39.031   2.832   3.486   4.064   0.000   0.000   0.000
   5_bss:  0.321  42.571  -0.626   0.019   0.607   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  45.851 0.5739  0.6413    49569.482
   1_bss:  45.967 0.5697  0.8116    47131.903
   1_xyz:  35.664 0.6923  0.9621    29767.414
   1_adp:  27.321 0.7875  1.0614    19212.093
   1_occ:  27.289 0.7879  1.0611    19156.033
   2_bss:  27.054 0.7903  0.9436    18878.871
   2_xyz:  17.556 0.8842  1.0148     8770.857
   2_adp:  15.812 0.8999  1.0263     7592.200
   2_occ:  15.801 0.9000  1.0261     7576.231
   3_bss:  15.783 0.9000  0.9835     7539.985
   3_xyz:  14.185 0.9137  0.9879     6446.802
   3_adp:  13.931 0.9159  0.9893     6343.252
   3_occ:  13.921 0.9160  0.9893     6342.729
   4_bss:  13.919 0.9160  0.9805     6341.819
   4_xyz:  13.607 0.9184  0.9803     6144.611
   4_adp:  13.668 0.9180  0.9784     6174.165
   4_occ:  13.678 0.9179  0.9782     6181.782
   5_bss:  13.667 0.9180  0.9791     6179.265
   5_xyz:  13.623 0.9184  0.9791     6156.955
   5_adp:  13.687 0.9179  0.9764     6184.635
   5_occ:  13.688 0.9178  0.9763     6186.666
   5_bss:  13.718 0.9176  0.9787     6208.097
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.3572e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.3572e+01
   1_xyz:   1.515  0.011  0.102 17.742  0.006  4.121   1.1630e-01
   1_adp:   1.515  0.011  0.102 17.742  0.006  4.121   1.1630e-01
   1_occ:   1.515  0.011  0.102 17.742  0.006  4.121   1.1630e-01
   2_bss:   1.515  0.011  0.102 17.742  0.006  4.121   1.1630e-01
   2_xyz:   1.055  0.007  0.080 15.970  0.004  4.122   6.6692e-02
   2_adp:   1.055  0.007  0.080 15.970  0.004  4.122   6.6692e-02
   2_occ:   1.055  0.007  0.080 15.970  0.004  4.122   6.6692e-02
   3_bss:   1.055  0.007  0.080 15.970  0.004  4.122   6.6692e-02
   3_xyz:   0.920  0.005  0.075 15.586  0.003  4.116   5.3918e-02
   3_adp:   0.920  0.005  0.075 15.586  0.003  4.116   5.3918e-02
   3_occ:   0.920  0.005  0.075 15.586  0.003  4.116   5.3918e-02
   4_bss:   0.920  0.005  0.075 15.586  0.003  4.116   5.3918e-02
   4_xyz:   1.003  0.006  0.081 15.508  0.004  4.118   6.0443e-02
   4_adp:   1.003  0.006  0.081 15.508  0.004  4.118   6.0443e-02
   4_occ:   1.003  0.006  0.081 15.508  0.004  4.118   6.0443e-02
   5_bss:   1.003  0.006  0.081 15.508  0.004  4.118   6.0443e-02
   5_xyz:   1.079  0.008  0.089 15.603  0.004  4.118   6.9354e-02
   5_adp:   1.079  0.008  0.089 15.603  0.004  4.118   6.9354e-02
   5_occ:   1.079  0.008  0.089 15.603  0.004  4.118   6.9354e-02
   5_bss:   1.079  0.008  0.089 15.603  0.004  4.118   6.9354e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9456e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9456e+00
   1_xyz:  13.046  0.139  0.449 87.439  0.045  2.260   8.7275e-02
   1_adp:  13.046  0.139  0.449 87.439  0.045  2.260   8.7275e-02
   1_occ:  13.046  0.139  0.449 87.439  0.045  2.260   8.7275e-02
   2_bss:  13.046  0.139  0.449 87.439  0.045  2.260   8.7275e-02
   2_xyz:   6.746  0.039  0.457 81.708  0.035  2.300   5.4169e-02
   2_adp:   6.746  0.039  0.457 81.708  0.035  2.300   5.4169e-02
   2_occ:   6.746  0.039  0.457 81.708  0.035  2.300   5.4169e-02
   3_bss:   6.746  0.039  0.457 81.708  0.035  2.300   5.4169e-02
   3_xyz:   6.234  0.041  0.500 82.428  0.036  2.403   3.1509e-02
   3_adp:   6.234  0.041  0.500 82.428  0.036  2.403   3.1509e-02
   3_occ:   6.234  0.041  0.500 82.428  0.036  2.403   3.1509e-02
   4_bss:   6.234  0.041  0.500 82.428  0.036  2.403   3.1509e-02
   4_xyz:   7.070  0.040  0.576 83.204  0.037  2.337   3.8930e-02
   4_adp:   7.070  0.040  0.576 83.204  0.037  2.337   3.8930e-02
   4_occ:   7.070  0.040  0.576 83.204  0.037  2.337   3.8930e-02
   5_bss:   7.070  0.040  0.576 83.204  0.037  2.337   3.8930e-02
   5_xyz:   7.209  0.049  0.689 82.179  0.038  2.296   5.2247e-02
   5_adp:   7.209  0.049  0.689 82.179  0.038  2.296   5.2247e-02
   5_occ:   7.209  0.049  0.689 82.179  0.038  2.296   5.2247e-02
   5_bss:   7.209  0.049  0.689 82.179  0.038  2.296   5.2247e-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:  62.29   0.00  10.53  62.29   0.00   7.36  58.12   0.00  27.80
   1_occ:  62.29   0.00  10.53  62.29   0.00   7.36  58.12   0.00  27.80
   2_bss:  62.29   0.00  10.53  62.29   0.00   7.36  58.12   0.00  27.80
   2_xyz:  62.29   0.00  10.53  62.29   0.00   7.36  58.12   0.00  27.80
   2_adp:  68.05   0.00  11.08  68.05   0.00   7.27  59.58   1.20  31.86
   2_occ:  68.05   0.00  11.08  68.05   0.00   7.27  59.58   1.20  31.86
   3_bss:  68.05   0.00  11.08  68.05   0.00   7.27  59.58   1.20  31.86
   3_xyz:  68.05   0.00  11.08  68.05   0.00   7.27  59.58   1.20  31.86
   3_adp:  70.29   0.00  11.16  70.29   0.00   7.27  61.93   0.78  32.38
   3_occ:  70.29   0.00  11.16  70.29   0.00   7.27  61.93   0.78  32.38
   4_bss:  70.29   0.00  11.16  70.29   0.00   7.27  61.93   0.78  32.38
   4_xyz:  70.29   0.00  11.16  70.29   0.00   7.27  61.93   0.78  32.38
   4_adp:  72.75   0.00  11.20  72.75   0.00   7.28  63.17   0.88  32.58
   4_occ:  72.75   0.00  11.20  72.75   0.00   7.28  63.17   0.88  32.58
   5_bss:  72.75   0.00  11.20  72.75   0.00   7.28  63.17   0.88  32.58
   5_xyz:  72.75   0.00  11.20  72.75   0.00   7.28  63.17   0.88  32.58
   5_adp:  73.18   0.00  11.16  73.18   0.00   7.21  63.20   1.03  32.62
   5_occ:  73.18   0.00  11.16  73.18   0.00   7.21  63.20   1.03  32.62
   5_bss:  76.72   3.54  14.70  76.72   3.54  10.75  66.74   4.57  36.16
------------------------------------------------------------------------
 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:    1.177    0.022    0.403
   1_adp:    1.177    0.022    0.403
   1_occ:    1.177    0.022    0.403
   2_bss:    1.177    0.022    0.403
   2_xyz:    1.381    0.022    0.508
   2_adp:    1.381    0.022    0.508
   2_occ:    1.381    0.022    0.508
   3_bss:    1.381    0.022    0.508
   3_xyz:    1.458    0.025    0.525
   3_adp:    1.458    0.025    0.525
   3_occ:    1.458    0.025    0.525
   4_bss:    1.458    0.025    0.525
   4_xyz:    1.493    0.019    0.541
   4_adp:    1.493    0.019    0.541
   4_occ:    1.493    0.019    0.541
   5_bss:    1.493    0.019    0.541
   5_xyz:    1.485    0.016    0.549
   5_adp:    1.485    0.016    0.549
   5_occ:    1.485    0.016    0.549
   5_bss:    1.485    0.016    0.549
------------------------------------------------------------------------

CPU time actual refinement: 323.64


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_553/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_553/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_553/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_553/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_553/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 323.49 
  Macro-tasks:
    bulk solvent and scale       = 40.39  
    individual site refinement   = 133.17 
    weights calculation          = 33.05  
    collect and process          = 6.56   
    model show statistics        = 0.14   
    TOTAL for macro-tasks        = 213.31 
  Micro-tasks:
    mask                            = 1.74   
    f_calc                          = 97.61  
    alpha_beta                      = 8.22   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 108.86 
    fmodel                         = 7.32   
    r_factors                      = 0.27   
    phase_errors                   = 10.55  
    foms                           = 0.23   
    TOTAL for micro-tasks          = 235.95 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.526 micro seconds
Total CPU time: 5.62 minutes
from_scatterers_fft:    649 calls, 97.13 s
gradients_fft:          593 calls, 95.07 s

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

# Date 2008-01-16 Time 01:51:34 PST -0800 (1200477094.63 s)
Start R-work = 0.4265, R-free = 0.4178 (no bulk solvent and anisotropic scale)
Final R-work = 0.1257, R-free = 0.1704 (no bulk solvent and anisotropic scale)

Start R-work = 0.4177, R-free = 0.4095
Final R-work = 0.1081, R-free = 0.1546