# Date 2008-01-16 Time 02:22:18 PST -0800 (1200478938.28 s)
#phil __OFF__

Command line arguments: "../808.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 30341
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 808

-------------------------------------------------------------------------------
  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: (70.6012, 47.3993, 86.39, 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: 3.27, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 47.3993, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0485 2.00109
Completeness in resolution range: 0.972883
Completeness with d_max=infinity: 0.9698

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0485
                             d_min =   2.0011

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: (70.6012, 47.3993, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0485 2.00109
Completeness in resolution range: 0.972883
Completeness with d_max=infinity: 0.9698

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0489 -  4.2812 [2113/2140]  1902   211  10.0%
  bin  2:  4.2812 -  3.4111 [2029/2045]  1826   203  10.0%
  bin  3:  3.4111 -  2.9838 [2005/2024]  1802   203  10.1%
  bin  4:  2.9838 -  2.7127 [1990/2020]  1795   195   9.8%
  bin  5:  2.7127 -  2.5192 [1961/1980]  1762   199  10.1%
  bin  6:  2.5192 -  2.3713 [1961/1986]  1767   194   9.9%
  bin  7:  2.3713 -  2.2530 [1967/1999]  1771   196  10.0%
  bin  8:  2.2530 -  2.1552 [1935/1967]  1740   195  10.1%
  bin  9:  2.1552 -  2.0724 [1941/1983]  1746   195  10.0%
  bin 10:  2.0724 -  2.0011 [1687/1991]  1519   168  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_808/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 9
        2.42 -     3.04: 2171
        3.04 -     3.66: 4635
        3.66 -     4.28: 8940
        4.28 -     4.90: 12307
  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 207 " - " O   HOH Z 341 "  1.939 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z 206 " - " O   HOH Z 342 "  2.288 3.040 -x+1/2,-y+1,z+1/2
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  ... (remaining 28057 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_808/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_808/model_refine_001.geo

CPU time processing inputs: 9.11


============================ 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 = 70.60125 47.3993 86.39 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4323   r_free= 0.4163   ksol= 0.00   Bsol= 0.00   scale= 0.819    |
|                                                                             |
| 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: 6.224725                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0489 -  4.7747 0.99   1374  153 0.3607 0.3337      6.5167       6.437|
|  2:  4.7747 -  3.8101 0.99   1320  145 0.3257 0.3498      6.6342       6.705|
|  3:  3.8101 -  3.3345 0.99   1300  145 0.3713 0.3565      6.5677      6.5551|
|  4:  3.3345 -  3.0323 0.99   1286  144 0.4119 0.3565      6.4593      6.3222|
|  5:  3.0323 -  2.8165 0.99   1272  140 0.4500 0.4317      6.3145      6.3357|
|  6:  2.8165 -  2.6514 0.99   1278  143 0.4594 0.5036      6.2405      6.2202|
|  7:  2.6514 -  2.5192 0.99   1257  141 0.4696 0.4418      6.2019      6.1166|
|  8:  2.5192 -  2.4100 0.98   1268  140 0.4770 0.4164      6.1568        6.11|
|  9:  2.4100 -  2.3176 0.98   1270  138 0.4800 0.5016      6.0889      6.1238|
| 10:  2.3176 -  2.2379 0.98   1232  137 0.4992 0.4742      6.1165      6.0602|
| 11:  2.2379 -  2.1681 0.99   1270  147 0.4926 0.4407      6.0119      6.0364|
| 12:  2.1681 -  2.1063 0.97   1248  129 0.5008 0.4637      5.9766      5.9822|
| 13:  2.1063 -  2.0510 0.99   1234  142 0.4961 0.5198      5.8773      5.8857|
| 14:  2.0510 -  2.0011 0.80   1021  115 0.5073 0.4580      5.8384      5.7329|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0489 -  4.7747  1374   153  0.74  30.60   0.81     0.76      56738.37|
|  2:  4.7747 -  3.8101  1320   145  0.78  28.15   0.91     0.81      71785.90|
|  3:  3.8101 -  3.3345  1300   145  0.72  33.81   0.86     0.79      74033.77|
|  4:  3.3345 -  3.0323  1286   144  0.66  38.81   0.83     0.71      64590.47|
|  5:  3.0323 -  2.8165  1272   140  0.57  46.13   0.77     0.63      58143.01|
|  6:  2.8165 -  2.6514  1278   143  0.55  48.18   0.76     0.60      53365.67|
|  7:  2.6514 -  2.5192  1257   141  0.53  49.81   0.76     0.58      49995.29|
|  8:  2.5192 -  2.4100  1268   140  0.52  50.64   0.77     0.59      45767.96|
|  9:  2.4100 -  2.3176  1270   138  0.52  50.84   0.74     0.58      40829.06|
| 10:  2.3176 -  2.2379  1232   137  0.52  50.39   0.76     0.58      37668.00|
| 11:  2.2379 -  2.1681  1270   147  0.49  53.30   0.77     0.56      35464.94|
| 12:  2.1681 -  2.1063  1248   129  0.46  55.78   0.77     0.53      35320.66|
| 13:  2.1063 -  2.0510  1234   142  0.43  57.68   0.75     0.50      31709.78|
| 14:  2.0510 -  2.0011  1021   115  0.46  55.84   0.73     0.50      25953.38|
|alpha:            min =        0.50 max =            0.81 mean =         0.63|
|beta:             min =    25953.38 max =        74033.77 mean =     49238.18|
|figures of merit: min =        0.00 max =            1.00 mean =         0.57|
|phase err.(work): min =        0.00 max =           90.00 mean =        46.07|
|phase err.(test): min =        0.00 max =           89.70 mean =        46.07|
|-----------------------------------------------------------------------------|

============================== 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 = 7.754027              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 74.758   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.636762              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.109   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       23 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      159 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      680 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1489 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2600 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3871 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5032 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6551 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7655 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       54.109 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.092    4.900  1.196 |       1.647 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.097)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 12.097)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4396   r_free= 0.4208   ksol= 0.00   Bsol= 0.00   scale= 0.788    |
|                                                                             |
| 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: 6.230298                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4242   r_free= 0.4042   ksol= 0.33   Bsol= 19.18   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.33,9.85,8.05,0.00,0.00,0.00); trace/3= 8.41                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.219321                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.309295              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 76.716   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.632445              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.069   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4242      final r-factor (work) = 0.3118          |
| start r-factor (free) = 0.4042      final r-factor (free) = 0.3360          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 76.9148 = 7.31 * 0.50 * 6.2402 + 1.00 * 54.1090                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.2442 = 7.31 * 0.50 * 6.0541 + 1.00 * 0.1187                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3118      final r-factor (work) = 0.2478          |
| start r-factor (free) = 0.3360      final r-factor (free) = 0.2803          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8436 = 0.63 * 1.00 * 6.0541 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7301 = 0.63 * 1.00 * 5.8785 + 1.00 * 0.0122                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.097)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    75.57   10.46    None  None   None       |
|    all(noH): 2823   0      0.00    75.57   10.46    None  None   None       |
|    Sol.    : 438    0      0.00    75.57   27.05    None  None   None       |
|    Mac.    : 2385   0      0.00    62.15   7.42     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 -   7.557: 1583   |   5:    37.784 -  45.340:   85        |
|      1:     7.557 -  15.113:  637   |   6:    45.340 -  52.897:   35        |
|      2:    15.113 -  22.670:  219   |   7:    52.897 -  60.454:    8        |
|      3:    22.670 -  30.227:  153   |   8:    60.454 -  68.010:    3        |
|      4:    30.227 -  37.784:   99   |   9:    68.010 -  75.567:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2478 r_free = 0.2803             target_work(ml) = 5.808         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2472 r_free = 0.2804             target_work(ml) = 5.807         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2472   r_free= 0.2804   ksol= 0.33   Bsol= 19.18   scale= 1.081   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.33,9.85,8.05,0.00,0.00,0.00); trace/3= 8.41                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.806694                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2428   r_free= 0.2748   ksol= 0.33   Bsol= 48.20   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.01,5.99,5.07,0.00,0.00,0.00); trace/3= 5.02                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.804917                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.881137              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.045   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.343148              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 115.218  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2428      final r-factor (work) = 0.1715          |
| start r-factor (free) = 0.2748      final r-factor (free) = 0.2071          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.5969 = 2.88 * 0.50 * 5.8856 + 1.00 * 0.1184                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.1782 = 2.88 * 0.50 * 5.6339 + 1.00 * 0.0622                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1715      final r-factor (work) = 0.1575          |
| start r-factor (free) = 0.2071      final r-factor (free) = 0.1955          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9501 = 0.34 * 1.00 * 5.6339 + 1.00 * 0.0169                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9040 = 0.34 * 1.00 * 5.4438 + 1.00 * 0.0359                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.097)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    70.57   11.11    None  None   None       |
|    all(noH): 2823   0      0.00    70.57   11.11    None  None   None       |
|    Sol.    : 438    0      0.00    69.78   32.10    None  None   None       |
|    Mac.    : 2385   0      0.00    70.57   7.25     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.057: 1573   |   5:    35.283 -  42.340:   93        |
|      1:     7.057 -  14.113:  623   |   6:    42.340 -  49.396:   86        |
|      2:    14.113 -  21.170:  176   |   7:    49.396 -  56.453:   43        |
|      3:    21.170 -  28.227:  113   |   8:    56.453 -  63.510:   11        |
|      4:    28.227 -  35.283:   98   |   9:    63.510 -  70.566:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1575 r_free = 0.1955             target_work(ml) = 5.420         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1573 r_free = 0.1956             target_work(ml) = 5.420         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1573   r_free= 0.1956   ksol= 0.33   Bsol= 48.20   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.01,5.99,5.07,0.00,0.00,0.00); trace/3= 5.02                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.419619                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1567   r_free= 0.1953   ksol= 0.32   Bsol= 48.20   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.18,4.29,4.46,0.00,0.00,0.00); trace/3= 3.98                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.419538                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.687029              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 109.083  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.646546              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 94.249   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1567      final r-factor (work) = 0.1236          |
| start r-factor (free) = 0.1953      final r-factor (free) = 0.1637          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.1043 = 3.69 * 0.50 * 5.4472 + 1.00 * 0.0622                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.8680 = 3.69 * 0.50 * 5.3136 + 1.00 * 0.0723                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1236      final r-factor (work) = 0.1182          |
| start r-factor (free) = 0.1637      final r-factor (free) = 0.1601          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4507 = 0.65 * 1.00 * 5.3136 + 1.00 * 0.0152                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3694 = 0.65 * 1.00 * 5.1916 + 1.00 * 0.0128                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.097)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.53   11.48    None  None   None       |
|    all(noH): 2823   0      0.00    77.53   11.48    None  None   None       |
|    Sol.    : 438    0      0.55    69.97   34.23    None  None   None       |
|    Mac.    : 2385   0      0.00    77.53   7.30     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 -   7.753: 1687   |   5:    38.767 -  46.521:   89        |
|      1:     7.753 -  15.507:  547   |   6:    46.521 -  54.274:   83        |
|      2:    15.507 -  23.260:  157   |   7:    54.274 -  62.027:   33        |
|      3:    23.260 -  31.014:  108   |   8:    62.027 -  69.781:   10        |
|      4:    31.014 -  38.767:  104   |   9:    69.781 -  77.534:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1182 r_free = 0.1601             target_work(ml) = 5.181         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1181 r_free = 0.1601             target_work(ml) = 5.181         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1181   r_free= 0.1601   ksol= 0.32   Bsol= 48.20   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.18,4.29,4.46,0.00,0.00,0.00); trace/3= 3.98                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.180965                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1184   r_free= 0.1607   ksol= 0.32   Bsol= 49.44   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.07,3.79,4.32,0.00,0.00,0.00); trace/3= 3.73                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.182673                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.503217              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 139.911  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.218488              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 116.533  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1184      final r-factor (work) = 0.1182          |
| start r-factor (free) = 0.1607      final r-factor (free) = 0.1608          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.9751 = 1.50 * 0.50 * 5.1919 + 1.00 * 0.0728                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.9524 = 1.50 * 0.50 * 5.1849 + 1.00 * 0.0554                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1182      final r-factor (work) = 0.1192          |
| start r-factor (free) = 0.1608      final r-factor (free) = 0.1600          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1474 = 0.22 * 1.00 * 5.1849 + 1.00 * 0.0146                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3467 = 0.22 * 1.00 * 5.1921 + 1.00 * 0.2123                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.097)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    75.80   11.03    None  None   None       |
|    all(noH): 2823   0      0.00    75.80   11.03    None  None   None       |
|    Sol.    : 438    0      0.79    69.48   32.16    None  None   None       |
|    Mac.    : 2385   0      0.00    75.80   7.15     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 -   7.580: 1696   |   5:    37.902 -  45.483:   89        |
|      1:     7.580 -  15.161:  547   |   6:    45.483 -  53.063:   66        |
|      2:    15.161 -  22.741:  154   |   7:    53.063 -  60.643:   23        |
|      3:    22.741 -  30.322:  117   |   8:    60.643 -  68.224:   10        |
|      4:    30.322 -  37.902:  116   |   9:    68.224 -  75.804:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1192 r_free = 0.1600             target_work(ml) = 5.188         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1190 r_free = 0.1599             target_work(ml) = 5.187         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1190   r_free= 0.1599   ksol= 0.32   Bsol= 49.44   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.07,3.79,4.32,0.00,0.00,0.00); trace/3= 3.73                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.187271                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1190   r_free= 0.1599   ksol= 0.32   Bsol= 49.44   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.07,3.79,4.32,0.00,0.00,0.00); trace/3= 3.73                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.187286                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.418053              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 119.743  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 12.709990             wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.945   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1190      final r-factor (work) = 0.1132          |
| start r-factor (free) = 0.1599      final r-factor (free) = 0.1565          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3319 = 2.42 * 0.50 * 5.1913 + 1.00 * 0.0554                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3133 = 2.42 * 0.50 * 5.1634 + 1.00 * 0.0707                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1132      final r-factor (work) = 0.1116          |
| start r-factor (free) = 0.1565      final r-factor (free) = 0.1579          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 65.6427 = 12.71 * 1.00 * 5.1634 + 1.00 * 0.0165                             |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 65.3727 = 12.71 * 1.00 * 5.1422 + 1.00 * 0.0149                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.097)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.07   11.65    None  None   None       |
|    all(noH): 2823   0      0.00    92.07   11.65    None  None   None       |
|    Sol.    : 438    0      0.64    80.07   35.17    None  None   None       |
|    Mac.    : 2385   0      0.00    92.07   7.33     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.207: 1852   |   5:    46.033 -  55.240:   84        |
|      1:     9.207 -  18.413:  451   |   6:    55.240 -  64.446:   50        |
|      2:    18.413 -  27.620:  151   |   7:    64.446 -  73.653:   16        |
|      3:    27.620 -  36.827:  112   |   8:    73.653 -  82.860:    4        |
|      4:    36.827 -  46.033:  100   |   9:    82.860 -  92.066:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1116 r_free = 0.1579             target_work(ml) = 5.150         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1116 r_free = 0.1579             target_work(ml) = 5.150         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1116   r_free= 0.1579   ksol= 0.32   Bsol= 49.44   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.07,3.79,4.32,0.00,0.00,0.00); trace/3= 3.73                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.150172                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0489 -  4.7747 0.99   1374  153 0.0991 0.1292      5.3846      5.5131|
|  2:  4.7747 -  3.8101 0.99   1320  145 0.0848 0.1093      5.4309      5.6179|
|  3:  3.8101 -  3.3345 0.99   1300  145 0.1034 0.1465      5.4665       5.847|
|  4:  3.3345 -  3.0323 0.99   1286  144 0.1198 0.1544      5.4509      5.6057|
|  5:  3.0323 -  2.8165 0.99   1272  140 0.1320 0.1730      5.3401      5.5325|
|  6:  2.8165 -  2.6514 0.99   1278  143 0.1225 0.1844      5.2302      5.4682|
|  7:  2.6514 -  2.5192 0.99   1257  141 0.1269 0.1762      5.1821      5.4274|
|  8:  2.5192 -  2.4100 0.98   1268  140 0.1177 0.1752      5.0942      5.3855|
|  9:  2.4100 -  2.3176 0.98   1270  138 0.1188 0.1777      5.0535         5.3|
| 10:  2.3176 -  2.2379 0.98   1232  137 0.1107 0.1804      4.9911      5.2526|
| 11:  2.2379 -  2.1681 0.99   1270  147 0.1154 0.1710      4.9543      5.2643|
| 12:  2.1681 -  2.1063 0.97   1248  129 0.1127 0.1711       4.893       5.209|
| 13:  2.1063 -  2.0510 0.99   1234  142 0.1131 0.1640      4.8017      5.0496|
| 14:  2.0510 -  2.0011 0.80   1021  115 0.1054 0.1858      4.6751        4.99|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0489 -  4.7747  1374   153  0.94   9.13   0.97     0.95       7321.37|
|  2:  4.7747 -  3.8101  1320   145  0.95   7.89   1.01     0.99       8894.94|
|  3:  3.8101 -  3.3345  1300   145  0.94  10.95   1.02     1.01      10224.05|
|  4:  3.3345 -  3.0323  1286   144  0.92  13.45   1.00     0.98      10233.21|
|  5:  3.0323 -  2.8165  1272   140  0.90  16.09   0.99     0.96       8554.67|
|  6:  2.8165 -  2.6514  1278   143  0.90  16.07   0.98     0.95       7352.74|
|  7:  2.6514 -  2.5192  1257   141  0.90  15.97   0.98     0.96       6469.25|
|  8:  2.5192 -  2.4100  1268   140  0.91  15.32   0.99     0.96       5641.24|
|  9:  2.4100 -  2.3176  1270   138  0.90  16.02   1.00     0.96       5284.46|
| 10:  2.3176 -  2.2379  1232   137  0.90  15.82   0.99     0.95       4728.53|
| 11:  2.2379 -  2.1681  1270   147  0.90  16.49   0.99     0.94       4477.60|
| 12:  2.1681 -  2.1063  1248   129  0.91  15.31   1.00     0.98       4053.54|
| 13:  2.1063 -  2.0510  1234   142  0.90  15.86   0.99     0.98       3439.54|
| 14:  2.0510 -  2.0011  1021   115  0.91  14.88   0.97     0.93       2589.37|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     2589.37 max =        10233.21 mean =      6465.44|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.86 mean =        14.16|
|phase err.(test): min =        0.00 max =           89.53 mean =        13.69|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1116   r_free= 0.1579   ksol= 0.32   Bsol= 53.27   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.60,-0.02,0.62,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.149978                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1116   r_free= 0.1579   ksol= 0.32   Bsol= 53.27   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.60,-0.02,0.62,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.149978                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0489 -  4.7747 0.99   1374  153 0.0990 0.1292      5.3836      5.5129|
|  2:  4.7747 -  3.8101 0.99   1320  145 0.0849 0.1095      5.4318      5.6193|
|  3:  3.8101 -  3.3345 0.99   1300  145 0.1034 0.1466      5.4672      5.8475|
|  4:  3.3345 -  3.0323 0.99   1286  144 0.1198 0.1543      5.4507      5.6055|
|  5:  3.0323 -  2.8165 0.99   1272  140 0.1320 0.1730      5.3396      5.5319|
|  6:  2.8165 -  2.6514 0.99   1278  143 0.1224 0.1841      5.2296      5.4669|
|  7:  2.6514 -  2.5192 0.99   1257  141 0.1269 0.1765      5.1819      5.4277|
|  8:  2.5192 -  2.4100 0.98   1268  140 0.1177 0.1751      5.0941      5.3855|
|  9:  2.4100 -  2.3176 0.98   1270  138 0.1187 0.1775      5.0533         5.3|
| 10:  2.3176 -  2.2379 0.98   1232  137 0.1107 0.1805       4.991       5.253|
| 11:  2.2379 -  2.1681 0.99   1270  147 0.1154 0.1710      4.9541      5.2642|
| 12:  2.1681 -  2.1063 0.97   1248  129 0.1126 0.1713      4.8929      5.2087|
| 13:  2.1063 -  2.0510 0.99   1234  142 0.1132 0.1640      4.8013      5.0497|
| 14:  2.0510 -  2.0011 0.80   1021  115 0.1054 0.1854      4.6741      4.9887|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0489 -  4.7747  1374   153  0.94   9.14   0.97     0.95       7315.19|
|  2:  4.7747 -  3.8101  1320   145  0.95   7.90   1.01     0.99       8907.09|
|  3:  3.8101 -  3.3345  1300   145  0.94  10.97   1.02     1.02      10245.78|
|  4:  3.3345 -  3.0323  1286   144  0.92  13.45   1.00     0.99      10228.71|
|  5:  3.0323 -  2.8165  1272   140  0.90  16.07   0.99     0.96       8541.78|
|  6:  2.8165 -  2.6514  1278   143  0.90  16.06   0.98     0.95       7342.54|
|  7:  2.6514 -  2.5192  1257   141  0.90  15.96   0.99     0.96       6465.36|
|  8:  2.5192 -  2.4100  1268   140  0.91  15.32   0.99     0.96       5638.18|
|  9:  2.4100 -  2.3176  1270   138  0.90  16.02   1.00     0.97       5286.99|
| 10:  2.3176 -  2.2379  1232   137  0.90  15.82   1.00     0.96       4727.89|
| 11:  2.2379 -  2.1681  1270   147  0.90  16.49   0.99     0.95       4477.97|
| 12:  2.1681 -  2.1063  1248   129  0.91  15.31   1.00     0.98       4053.91|
| 13:  2.1063 -  2.0510  1234   142  0.90  15.85   1.00     0.98       3434.31|
| 14:  2.0510 -  2.0011  1021   115  0.91  14.85   0.98     0.93       2580.45|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2580.45 max =        10245.78 mean =      6464.28|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.16|
|phase err.(test): min =        0.00 max =           89.54 mean =        13.68|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.097)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.82    95.89   15.47    None  None   None       |
|    all(noH): 2823   0      3.82    95.89   15.47    None  None   None       |
|    Sol.    : 438    0      4.46    83.89   38.99    None  None   None       |
|    Mac.    : 2385   0      3.82    95.89   11.15    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:     3.824 -  13.030: 1852   |   5:    49.857 -  59.064:   84        |
|      1:    13.030 -  22.237:  451   |   6:    59.064 -  68.270:   50        |
|      2:    22.237 -  31.444:  151   |   7:    68.270 -  77.477:   16        |
|      3:    31.444 -  40.650:  112   |   8:    77.477 -  86.684:    4        |
|      4:    40.650 -  49.857:  100   |   9:    86.684 -  95.890:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 313         
Filter by distance & map next to the model:
   mapped sites are within: 0.324 - 5.852
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 302 from: 313
   mapped sites are within: 0.744 - 5.852

peak=   10.096 closest distance to " CG2 VAL A 230 " =    1.301
peak=    6.593 closest distance to " CG2 VAL A 296 " =    1.102
peak=    6.285 closest distance to " CG  LEU A   5 " =    1.128
peak=    6.198 closest distance to " NH2 ARG A  56 " =    2.301
peak=    5.908 closest distance to " CG  LEU A 228 " =    1.158
peak=    5.483 closest distance to " CB  GLN A 223 " =    1.422
peak=    5.399 closest distance to " CB  VAL A 230 " =    1.194
peak=    5.377 closest distance to " CG  PRO A  54 " =    1.244
peak=    5.252 closest distance to " CB  VAL A 296 " =    1.000
peak=    4.919 closest distance to " CB  GLN A 183 " =    1.322
peak=    4.885 closest distance to " CB  PRO A  54 " =    0.901
peak=    4.885 closest distance to " CB  SER A  63 " =    1.267
peak=    4.882 closest distance to " NE2 GLN A  11 " =    1.058
peak=    4.832 closest distance to " CD2 LEU A   5 " =    1.099
peak=    4.818 closest distance to " O   HOH Z 232 " =    2.373
peak=    4.689 closest distance to " CB  ARG A 275 " =    0.889
peak=    4.489 closest distance to " CG  PRO A 213 " =    1.187
peak=    4.468 closest distance to " O   HOH Z 126 " =    2.000
peak=    4.455 closest distance to " CA  TYR A  30 " =    0.963
peak=    4.383 closest distance to " O   HOH Z 369 " =    2.232
peak=    4.363 closest distance to " C   PRO A 198 " =    1.507
peak=    4.336 closest distance to " O   HOH Z  43 " =    2.044
peak=    4.315 closest distance to " O   HOH Z 298 " =    1.896
peak=    4.278 closest distance to " O   HOH Z 423 " =    1.808
peak=    4.250 closest distance to " O   HOH Z 427 " =    3.072
peak=    4.246 closest distance to " CB  ASN A 148 " =    1.373
peak=    4.232 closest distance to " O   HOH Z 316 " =    3.081
peak=    4.228 closest distance to " O   HOH Z 303 " =    2.090
peak=    4.221 closest distance to " O   HOH Z 272 " =    1.940
peak=    4.219 closest distance to " CG  PRO A 198 " =    1.165
peak=    4.206 closest distance to " O   HOH Z  44 " =    2.271
peak=    4.179 closest distance to " CB  ARG A 190 " =    1.638
peak=    4.178 closest distance to " O   SER A  87 " =    2.322
peak=    4.176 closest distance to " OD1 ASN A  69 " =    2.601
peak=    4.166 closest distance to " O   HOH Z 142 " =    1.479
peak=    4.163 closest distance to " O   HOH Z  63 " =    2.016
peak=    4.158 closest distance to " O   HOH Z 403 " =    1.674
peak=    4.143 closest distance to " CZ  PHE A 218 " =    1.099
peak=    4.134 closest distance to " O   HOH Z 368 " =    2.349
peak=    4.123 closest distance to " O   HOH Z 193 " =    1.805
peak=    4.120 closest distance to " O   HOH Z  61 " =    1.607
peak=    4.117 closest distance to " O   HOH Z 203 " =    1.780
peak=    4.083 closest distance to " CB  GLU A 277 " =    3.669
peak=    4.079 closest distance to " O   HOH Z 280 " =    2.915
peak=    4.075 closest distance to " O   HOH Z  97 " =    2.010
peak=    4.065 closest distance to " O   HOH Z 158 " =    3.120
peak=    4.064 closest distance to " O   HOH Z 236 " =    1.908
peak=    4.061 closest distance to " CB  GLU A 152 " =    1.186
peak=    4.052 closest distance to " O   HOH Z 234 " =    3.679
peak=    4.047 closest distance to " O   HOH Z 265 " =    2.305
peak=    4.044 closest distance to " CG  PRO A 243 " =    1.147
peak=    4.037 closest distance to " O   HOH Z  78 " =    1.657
peak=    4.031 closest distance to " O   HOH Z 402 " =    1.490
peak=    4.030 closest distance to " CB  TRP A 266 " =    0.978
peak=    4.030 closest distance to " O   HOH Z 346 " =    1.562
peak=    4.005 closest distance to " CB  GLU A 128 " =    1.120
peak=    3.976 closest distance to " O   HOH Z 189 " =    2.747
peak=    3.960 closest distance to " CD2 LEU A 228 " =    1.082
peak=    3.946 closest distance to " CB  SER A   3 " =    1.244
peak=    3.928 closest distance to " O   HOH Z  40 " =    1.719
peak=    3.917 closest distance to " CB  ARG A  79 " =    1.421
peak=    3.892 closest distance to " CA  ALA A  51 " =    0.960
peak=    3.856 closest distance to " O   HOH Z  48 " =    1.697
peak=    3.853 closest distance to " CA  TYR A  30 " =    1.047
peak=    3.840 closest distance to " OG BSER A 164 " =    2.174
peak=    3.836 closest distance to " CB  VAL A 265 " =    1.298
peak=    3.836 closest distance to " CB  TRP A 179 " =    1.455
peak=    3.834 closest distance to " CB  VAL A 202 " =    1.556
peak=    3.825 closest distance to " ND2 ASN A 249 " =    1.909
peak=    3.818 closest distance to " O   HOH Z 422 " =    2.685
peak=    3.817 closest distance to " O   HOH Z  80 " =    1.747
peak=    3.815 closest distance to " O   HOH Z  15 " =    2.128
peak=    3.813 closest distance to " CG1BVAL A  72 " =    1.736
peak=    3.810 closest distance to " O   HOH Z 411 " =    3.737
peak=    3.792 closest distance to " CG  ARG A  66 " =    2.721
peak=    3.788 closest distance to " C   ILE A 106 " =    1.882
peak=    3.787 closest distance to " O   HOH Z 214 " =    2.298
peak=    3.779 closest distance to " O   HOH Z 197 " =    2.831
peak=    3.766 closest distance to " O   HOH Z 147 " =    1.786
peak=    3.741 closest distance to " CG1 ILE A  33 " =    1.233
peak=    3.730 closest distance to " CB  ASP A 140 " =    1.020
peak=    3.720 closest distance to " CD  LYS A 166 " =    1.304
peak=    3.711 closest distance to " O   HOH Z 371 " =    3.239
peak=    3.704 closest distance to " CG2 THR A 221 " =    1.202
peak=    3.701 closest distance to " O   ALA A 165 " =    1.412
peak=    3.699 closest distance to " NH2 ARG A 156 " =    1.107
peak=    3.699 closest distance to " CB  ARG A 139 " =    0.868
peak=    3.698 closest distance to " CB BVAL A  41 " =    1.037
peak=    3.693 closest distance to " O   HOH Z 250 " =    1.331
peak=    3.690 closest distance to " O   HOH Z 285 " =    3.048
peak=    3.679 closest distance to " O   HOH Z 112 " =    1.667
peak=    3.678 closest distance to " CD BLYS A 290 " =    1.020
peak=    3.666 closest distance to " O   HOH Z  66 " =    2.202
peak=    3.666 closest distance to " CB  ASN A 187 " =    1.374
peak=    3.665 closest distance to " O   HOH Z 248 " =    1.629
peak=    3.662 closest distance to " CA  ALA A  21 " =    1.181
peak=    3.660 closest distance to " ND2 ASN A 187 " =    1.424
peak=    3.659 closest distance to " CA  ASN A 215 " =    1.219
peak=    3.656 closest distance to " CE1 TYR A 186 " =    1.288
peak=    3.652 closest distance to " CA  THR A 264 " =    0.744
peak=    3.650 closest distance to " CB  ALA A   9 " =    1.604
peak=    3.649 closest distance to " CB  ASN A 142 " =    1.219
peak=    3.648 closest distance to " O   HOH Z 134 " =    1.402
peak=    3.642 closest distance to " O   HOH Z 247 " =    1.336
peak=    3.639 closest distance to " CG  MET A 185 " =    1.197
peak=    3.637 closest distance to " O   HOH Z 102 " =    1.319
peak=    3.636 closest distance to " O   HOH Z 126 " =    1.621
peak=    3.633 closest distance to " O   HOH Z  97 " =    2.492
peak=    3.632 closest distance to " CA  ALA A 158 " =    1.259
peak=    3.627 closest distance to " CG1 ILE A  49 " =    1.522
peak=    3.616 closest distance to " N   VAL A 126 " =    1.429
peak=    3.608 closest distance to " O   ASP A 124 " =    1.102
peak=    3.607 closest distance to " CB  THR A 157 " =    1.201
peak=    3.606 closest distance to " CA  LYS A 117 " =    1.286
peak=    3.598 closest distance to " CD  ARG A 159 " =    0.772
peak=    3.590 closest distance to " CB  THR A  31 " =    1.635
peak=    3.577 closest distance to " CG1 VAL A 153 " =    0.984
peak=    3.576 closest distance to " CB  ASN A  39 " =    0.853
peak=    3.571 closest distance to " ND1 HIS A  81 " =    1.670
peak=    3.566 closest distance to " O   HOH Z 425 " =    1.297
peak=    3.565 closest distance to " O   HOH Z 383 " =    2.044
peak=    3.559 closest distance to " O   HOH Z 172 " =    3.866
peak=    3.555 closest distance to " O   HOH Z 344 " =    3.041
peak=    3.555 closest distance to " CA  ARG A  36 " =    1.053
peak=    3.551 closest distance to " O   HOH Z  19 " =    1.939
peak=    3.550 closest distance to " O   HOH Z 227 " =    1.728
peak=    3.550 closest distance to " O   HOH Z 261 " =    1.903
peak=    3.550 closest distance to " O   HOH Z 425 " =    2.025
peak=    3.550 closest distance to " N   ASN A  39 " =    1.297
peak=    3.549 closest distance to " O   HOH Z 180 " =    2.126
peak=    3.540 closest distance to " CA  THR A 221 " =    0.927
peak=    3.535 closest distance to " CD  ARG A 269 " =    0.951
peak=    3.533 closest distance to " NH1AARG A 145 " =    1.156
peak=    3.529 closest distance to " O   HOH Z 426 " =    1.545
peak=    3.528 closest distance to " OG1 THR A 294 " =    2.358
peak=    3.528 closest distance to " O   HOH Z 245 " =    1.335
peak=    3.522 closest distance to " O   HOH Z 263 " =    1.663
peak=    3.521 closest distance to " CE  LYS A  76 " =    0.850
peak=    3.521 closest distance to " O   HOH Z 128 " =    2.085
peak=    3.520 closest distance to " O   HOH Z  88 " =    3.119
peak=    3.514 closest distance to " CA  ARG A 195 " =    1.216
peak=    3.511 closest distance to " O   HOH Z 437 " =    1.849
peak=    3.510 closest distance to " CB  LEU A 143 " =    1.194
peak=    3.509 closest distance to " CD1 LEU A 300 " =    1.196
peak=    3.506 closest distance to " CB  ALA A 291 " =    1.395
peak=    3.502 closest distance to " O   TRP A 274 " =    1.888
peak=    3.501 closest distance to " O   GLN A 278 " =    1.265
peak=    3.501 closest distance to " O   HOH Z 365 " =    2.988
peak=    3.500 closest distance to " O   HOH Z  48 " =    1.421
peak=    3.498 closest distance to " CB  ALA A 248 " =    1.471
peak=    3.497 closest distance to " O   HOH Z 193 " =    2.129
peak=    3.495 closest distance to " O   HOH Z  48 " =    1.389
peak=    3.493 closest distance to " O   HOH Z  20 " =    1.503
peak=    3.490 closest distance to " O   HOH Z 133 " =    1.613
peak=    3.488 closest distance to " CB  GLU A  46 " =    1.031
peak=    3.483 closest distance to " CA  VAL A 125 " =    1.246
peak=    3.481 closest distance to " O   HOH Z  59 " =    2.398
peak=    3.475 closest distance to " CA  LEU A 282 " =    1.069
peak=    3.471 closest distance to " CA  ALA A 291 " =    0.895
peak=    3.460 closest distance to " CB  LEU A 228 " =    1.313
peak=    3.448 closest distance to " CB  ASN A 110 " =    1.255
peak=    3.448 closest distance to " O   HOH Z 128 " =    2.260
peak=    3.442 closest distance to " NE2 GLN A  77 " =    3.293
peak=    3.431 closest distance to " O   HOH Z  54 " =    1.537
peak=    3.430 closest distance to " O   HOH Z 313 " =    1.742
peak=    3.426 closest distance to " CB  MET A  40 " =    0.794
peak=    3.425 closest distance to " N   ASP A 162 " =    1.320
peak=    3.424 closest distance to " O   HOH Z 193 " =    1.615
peak=    3.424 closest distance to " CG  MET A 185 " =    1.097
peak=    3.422 closest distance to " O   HOH Z 420 " =    2.077
peak=    3.415 closest distance to " O   HOH Z 290 " =    0.927
peak=    3.412 closest distance to " CB  ARG A  79 " =    0.902
peak=    3.407 closest distance to " CB  TRP A 150 " =    1.355
peak=    3.406 closest distance to " O   HOH Z 417 " =    3.145
peak=    3.404 closest distance to " O   HOH Z 163 " =    1.469
peak=    3.404 closest distance to " OD2 ASP A 286 " =    2.865
peak=    3.402 closest distance to " NZ  LYS A 117 " =    3.193
peak=    3.402 closest distance to " CA  ALA A 295 " =    1.097
peak=    3.398 closest distance to " O   HOH Z 271 " =    2.646
peak=    3.397 closest distance to " CD2 TRP A 179 " =    1.388
peak=    3.395 closest distance to " CB  THR A  82 " =    1.383
peak=    3.392 closest distance to " CA  ASP A 191 " =    0.906
peak=    3.388 closest distance to " NH2 ARG A  79 " =    1.314
peak=    3.388 closest distance to " O   HOH Z 238 " =    2.324
peak=    3.385 closest distance to " O   HOH Z 435 " =    2.001
peak=    3.371 closest distance to " O   HOH Z  21 " =    1.692
peak=    3.369 closest distance to " O   HOH Z 329 " =    3.952
peak=    3.368 closest distance to " O   HOH Z 171 " =    2.357
peak=    3.367 closest distance to " CB  SER A  26 " =    1.762
peak=    3.364 closest distance to " CZ  PHE A 192 " =    0.975
peak=    3.362 closest distance to " CG2 VAL A 257 " =    0.818
peak=    3.362 closest distance to " CB  ALA A 100 " =    1.272
peak=    3.360 closest distance to " O   HOH Z 132 " =    2.657
peak=    3.360 closest distance to " CB  HIS A 108 " =    0.789
peak=    3.354 closest distance to " O   HOH Z 133 " =    2.370
peak=    3.352 closest distance to " O   HOH Z 359 " =    3.848
peak=    3.352 closest distance to " O   HOH Z 273 " =    2.801
peak=    3.351 closest distance to " CA  VAL A  41 " =    0.839
peak=    3.342 closest distance to " O   HOH Z 368 " =    3.628
peak=    3.342 closest distance to " O   HOH Z 299 " =    4.393
peak=    3.341 closest distance to " OG  SER A  22 " =    2.800
peak=    3.341 closest distance to " O  BHOH Z 338 " =    2.374
peak=    3.335 closest distance to " O   HOH Z 145 " =    2.187
peak=    3.324 closest distance to " CD  ARG A  66 " =    2.665
peak=    3.322 closest distance to " CB  MET A  47 " =    1.100
peak=    3.319 closest distance to " CA  ASP A 140 " =    1.172
peak=    3.318 closest distance to " O   ALA A 158 " =    1.378
peak=    3.311 closest distance to " CD1 ILE A 106 " =    0.949
peak=    3.309 closest distance to " O   HOH Z 407 " =    2.517
peak=    3.302 closest distance to " CB  GLN A  89 " =    1.168
peak=    3.299 closest distance to " O   HOH Z 421 " =    1.802
peak=    3.299 closest distance to " CA  TYR A 116 " =    1.441
peak=    3.287 closest distance to " NZ  LYS A  48 " =    1.370
peak=    3.285 closest distance to " CB  ALA A 248 " =    1.000
peak=    3.285 closest distance to " CG2 VAL A 197 " =    1.066
peak=    3.283 closest distance to " CA  LYS A 181 " =    1.045
peak=    3.283 closest distance to " CD1 LEU A   5 " =    1.361
peak=    3.282 closest distance to " CB  SER A 273 " =    0.811
peak=    3.281 closest distance to " CG  GLN A  58 " =    2.829
peak=    3.280 closest distance to " CZ3 TRP A  85 " =    0.932
peak=    3.280 closest distance to " CZ  PHE A  38 " =    1.251
peak=    3.279 closest distance to " CG2 ILE A  20 " =    1.331
peak=    3.278 closest distance to " CB  GLN A  88 " =    1.203
peak=    3.278 closest distance to " O   HOH Z 130 " =    2.248
peak=    3.278 closest distance to " O   HOH Z 327 " =    1.760
peak=    3.276 closest distance to " CA  GLY A 211 " =    1.314
peak=    3.270 closest distance to " CD1 ILE A  33 " =    1.641
peak=    3.268 closest distance to " CB  GLN A 205 " =    1.089
peak=    3.265 closest distance to " OE1 GLN A  11 " =    1.792
peak=    3.264 closest distance to " O   HOH Z 305 " =    3.611
peak=    3.263 closest distance to " CA  ALA A 160 " =    0.845
peak=    3.260 closest distance to " OD1 ASP A 231 " =    1.903
peak=    3.258 closest distance to " O   HOH Z 403 " =    1.403
peak=    3.256 closest distance to " CB  LYS A 117 " =    1.145
peak=    3.255 closest distance to " O   HOH Z 291 " =    1.532
peak=    3.250 closest distance to " CG  GLN A  88 " =    1.061
peak=    3.249 closest distance to " OD1 ASN A 217 " =    1.675
peak=    3.248 closest distance to " O   HOH Z 250 " =    1.374
peak=    3.244 closest distance to " O   HOH Z 353 " =    2.737
peak=    3.243 closest distance to " O   HOH Z 189 " =    2.818
peak=    3.241 closest distance to " CB  THR A  52 " =    0.953
peak=    3.235 closest distance to " CB  VAL A 268 " =    0.842
peak=    3.232 closest distance to " CB  SER A 212 " =    1.150
peak=    3.232 closest distance to " CA  ASP A 162 " =    1.155
peak=    3.228 closest distance to " O   HOH Z  35 " =    2.501
peak=    3.225 closest distance to " CD1 LEU A 228 " =    1.818
peak=    3.222 closest distance to " CG  LEU A 167 " =    1.175
peak=    3.218 closest distance to " O   ASN A  74 " =    1.593
peak=    3.216 closest distance to " O   HOH Z 345 " =    3.220
peak=    3.216 closest distance to " O   HOH Z 420 " =    5.852
peak=    3.215 closest distance to " NE  ARG A  79 " =    1.189
peak=    3.214 closest distance to " O   HOH Z 251 " =    1.423
peak=    3.210 closest distance to " C   TYR A 214 " =    1.480
peak=    3.207 closest distance to " CG2 THR A 220 " =    0.861
peak=    3.206 closest distance to " O   HOH Z 417 " =    2.254
peak=    3.204 closest distance to " CA  ILE A 106 " =    0.768
peak=    3.204 closest distance to " O   HOH Z 423 " =    3.116
peak=    3.202 closest distance to " CG BARG A 102 " =    1.840
peak=    3.201 closest distance to " CA  MET A 105 " =    1.040
peak=    3.201 closest distance to " O   HOH Z 261 " =    1.567
peak=    3.200 closest distance to " CG  GLN A  77 " =    2.200
peak=    3.198 closest distance to " O   THR A  31 " =    1.586
peak=    3.194 closest distance to " O   HOH Z  10 " =    1.762
peak=    3.187 closest distance to " O   HOH Z 116 " =    1.801
peak=    3.186 closest distance to " O   HOH Z 391 " =    3.005
peak=    3.184 closest distance to " CA  ASN A 176 " =    1.162
peak=    3.184 closest distance to " O   HOH Z 187 " =    2.316
peak=    3.180 closest distance to " O   HOH Z 135 " =    1.947
peak=    3.179 closest distance to " O   HOH Z 295 " =    1.530
peak=    3.172 closest distance to " O   HOH Z 148 " =    3.268
peak=    3.171 closest distance to " N   PHE A 130 " =    1.285
peak=    3.168 closest distance to " CA  SER A 146 " =    1.710
peak=    3.166 closest distance to " O   HOH Z 201 " =    3.092
peak=    3.165 closest distance to " CB  ASN A 215 " =    1.182
peak=    3.154 closest distance to " OG1 THR A 294 " =    1.688
peak=    3.150 closest distance to " O   HOH Z 298 " =    4.855
peak=    3.150 closest distance to " CB  GLN A 103 " =    1.057
peak=    3.147 closest distance to " CE1 HIS A 108 " =    1.122
peak=    3.146 closest distance to " NE2 HIS A 207 " =    1.370
peak=    3.144 closest distance to " O   HOH Z 260 " =    1.530
peak=    3.142 closest distance to " CB  ILE A 120 " =    1.383
peak=    3.140 closest distance to " N   ASN A 127 " =    1.206
peak=    3.137 closest distance to " CG BARG A 275 " =    1.372
peak=    3.134 closest distance to " O   HOH Z 325 " =    2.213
peak=    3.128 closest distance to " CB  SER A 216 " =    0.824
peak=    3.128 closest distance to " O   HOH Z 258 " =    1.593
peak=    3.127 closest distance to " CA  ALA A 233 " =    1.529
peak=    3.121 closest distance to " O   HOH Z   1 " =    2.311
peak=    3.118 closest distance to " O   HOH Z 145 " =    2.668
peak=    3.117 closest distance to " ND2 ASN A 301 " =    1.829
peak=    3.111 closest distance to " CG  MET A 188 " =    0.952
peak=    3.110 closest distance to " O   HOH Z 357 " =    1.985
peak=    3.108 closest distance to " O   HOH Z 359 " =    1.303
peak=    3.101 closest distance to " CE  LYS A  48 " =    1.094
peak=    3.091 closest distance to " CA  LYS A 290 " =    1.186
peak=    3.086 closest distance to " CD  LYS A  76 " =    2.054
peak=    3.078 closest distance to " OH  TYR A 214 " =    1.200
peak=    3.076 closest distance to " O   HOH Z 430 " =    3.998
peak=    3.062 closest distance to " O   HOH Z 256 " =    2.307
peak=    3.048 closest distance to " CG2 VAL A 202 " =    1.094
peak=    3.037 closest distance to " CB  ARG A 138 " =    0.955
peak=    3.037 closest distance to " O   HOH Z 302 " =    1.961

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 201         
Filter by distance & map next to the model:
   mapped sites are within: 0.797 - 5.565
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 200 from: 201
   mapped sites are within: 0.797 - 5.565

peak=   -5.172 closest distance to " CG2 VAL A 230 " =    0.832
peak=   -4.605 closest distance to " CD  ARG A 156 " =    2.007
peak=   -4.569 closest distance to " O   HOH Z 266 " =    5.047
peak=   -4.461 closest distance to " SG  CYS A 254 " =    3.403
peak=   -4.183 closest distance to " CD  GLN A  58 " =    1.090
peak=   -4.174 closest distance to " C   HIS A 108 " =    1.148
peak=   -4.174 closest distance to " CB  PRO A 243 " =    2.675
peak=   -4.168 closest distance to " CB  ALA A 161 " =    2.606
peak=   -4.158 closest distance to " OE1 GLN A 223 " =    2.134
peak=   -4.130 closest distance to " O   HOH Z 196 " =    2.229
peak=   -4.035 closest distance to " OXT GLY A 302 " =    2.933
peak=   -4.008 closest distance to " OG  SER A  97 " =    2.286
peak=   -3.982 closest distance to " OG BSER A 134 " =    1.208
peak=   -3.982 closest distance to " O   VAL A  67 " =    2.757
peak=   -3.981 closest distance to " O   HOH Z 231 " =    2.108
peak=   -3.943 closest distance to " CG2BVAL A  41 " =    2.634
peak=   -3.926 closest distance to " CE2 TYR A  30 " =    2.743
peak=   -3.916 closest distance to " CG1 VAL A 250 " =    2.750
peak=   -3.915 closest distance to " CB  PHE A 192 " =    1.823
peak=   -3.914 closest distance to " O   PRO A 163 " =    2.105
peak=   -3.905 closest distance to " CG  ASP A 231 " =    0.797
peak=   -3.853 closest distance to " O   HOH Z 166 " =    1.870
peak=   -3.849 closest distance to " O   HOH Z 114 " =    3.162
peak=   -3.778 closest distance to " O   HOH Z  37 " =    1.898
peak=   -3.772 closest distance to " O   HOH Z  52 " =    1.639
peak=   -3.771 closest distance to " NE2 GLN A  88 " =    1.993
peak=   -3.759 closest distance to " N   ALA A 226 " =    2.070
peak=   -3.712 closest distance to " O   HOH Z  11 " =    1.890
peak=   -3.704 closest distance to " CD2 LEU A 167 " =    1.684
peak=   -3.704 closest distance to " O   SER A 271 " =    2.021
peak=   -3.700 closest distance to " CA  ASP A 298 " =    1.020
peak=   -3.694 closest distance to " CG1 VAL A 112 " =    2.797
peak=   -3.661 closest distance to " CD1 LEU A 101 " =    2.464
peak=   -3.660 closest distance to " C   ALA A 158 " =    1.257
peak=   -3.660 closest distance to " CD2 LEU A 300 " =    2.724
peak=   -3.656 closest distance to " O   HOH Z 394 " =    1.584
peak=   -3.651 closest distance to " ND2 ASN A 187 " =    1.679
peak=   -3.649 closest distance to " CD1 PHE A  59 " =    1.961
peak=   -3.648 closest distance to " O   HOH Z  13 " =    1.617
peak=   -3.648 closest distance to " NH2AARG A 275 " =    5.145
peak=   -3.644 closest distance to " CG2 VAL A 296 " =    1.166
peak=   -3.638 closest distance to " OD1 ASN A 187 " =    1.618
peak=   -3.637 closest distance to " CE3 TRP A 150 " =    2.197
peak=   -3.634 closest distance to " O   HOH Z 283 " =    2.158
peak=   -3.633 closest distance to " ND2 ASN A  45 " =    1.079
peak=   -3.633 closest distance to " OG ASER A 134 " =    1.228
peak=   -3.632 closest distance to " CE2 PHE A 218 " =    2.611
peak=   -3.632 closest distance to " CZ3 TRP A 179 " =    1.207
peak=   -3.629 closest distance to " CG1 VAL A 112 " =    2.600
peak=   -3.627 closest distance to " O   HOH Z 426 " =    1.657
peak=   -3.617 closest distance to " O   HOH Z 292 " =    4.472
peak=   -3.596 closest distance to " OD1 ASN A 148 " =    1.490
peak=   -3.594 closest distance to " O   HOH Z 290 " =    1.253
peak=   -3.582 closest distance to " O   HOH Z  19 " =    2.183
peak=   -3.575 closest distance to " O   HOH Z 351 " =    1.546
peak=   -3.565 closest distance to " NH2 ARG A  66 " =    1.653
peak=   -3.556 closest distance to " CB  ASP A 171 " =    2.313
peak=   -3.554 closest distance to " ND2 ASN A  45 " =    1.480
peak=   -3.549 closest distance to " O   HOH Z 128 " =    2.634
peak=   -3.542 closest distance to " O   HOH Z  60 " =    1.992
peak=   -3.538 closest distance to " C   ASN A 187 " =    1.901
peak=   -3.538 closest distance to " CB  ALA A 248 " =    2.075
peak=   -3.533 closest distance to " NE2 GLN A 103 " =    1.762
peak=   -3.521 closest distance to " CB  PRO A 163 " =    2.565
peak=   -3.518 closest distance to " CG  ARG A 269 " =    2.357
peak=   -3.492 closest distance to " N   ALA A  43 " =    2.700
peak=   -3.491 closest distance to " O   HOH Z 389 " =    1.870
peak=   -3.485 closest distance to " N   GLN A  58 " =    1.647
peak=   -3.478 closest distance to " O   HOH Z 166 " =    1.602
peak=   -3.475 closest distance to " CG2 ILE A 263 " =    2.416
peak=   -3.469 closest distance to " O   HOH Z  43 " =    1.675
peak=   -3.468 closest distance to " CE  MET A 105 " =    2.219
peak=   -3.466 closest distance to " CG  GLU A 277 " =    1.132
peak=   -3.462 closest distance to " N   THR A 235 " =    1.349
peak=   -3.461 closest distance to " O   HOH Z 407 " =    3.087
peak=   -3.459 closest distance to " CB  ASP A 132 " =    2.330
peak=   -3.458 closest distance to " O   HOH Z 377 " =    2.152
peak=   -3.454 closest distance to " O   HOH Z 311 " =    3.759
peak=   -3.452 closest distance to " CB  ALA A 248 " =    2.319
peak=   -3.448 closest distance to " O   HOH Z 165 " =    1.889
peak=   -3.447 closest distance to " O   HOH Z 353 " =    2.141
peak=   -3.439 closest distance to " O   HOH Z 350 " =    1.741
peak=   -3.437 closest distance to " O   HOH Z  10 " =    1.522
peak=   -3.436 closest distance to " O   HOH Z 234 " =    4.228
peak=   -3.433 closest distance to " CG  TRP A 266 " =    1.903
peak=   -3.433 closest distance to " CB  ALA A 291 " =    2.205
peak=   -3.427 closest distance to " O   HOH Z  44 " =    2.143
peak=   -3.426 closest distance to " CD  LYS A 289 " =    2.462
peak=   -3.425 closest distance to " O   HOH Z  17 " =    1.424
peak=   -3.419 closest distance to " CE BMET A  47 " =    1.964
peak=   -3.416 closest distance to " CA  GLY A 241 " =    3.109
peak=   -3.412 closest distance to " C   LEU A 143 " =    1.012
peak=   -3.411 closest distance to " O   HOH Z 198 " =    2.364
peak=   -3.411 closest distance to " O   HOH Z 435 " =    2.686
peak=   -3.399 closest distance to " O   HOH Z 102 " =    1.635
peak=   -3.398 closest distance to " O   HOH Z  38 " =    1.559
peak=   -3.395 closest distance to " OG  SER A  62 " =    1.733
peak=   -3.390 closest distance to " CB  ALA A  43 " =    2.552
peak=   -3.389 closest distance to " O   HOH Z 185 " =    2.390
peak=   -3.389 closest distance to " CD  ARG A 139 " =    1.611
peak=   -3.387 closest distance to " O   VAL A 189 " =    2.609
peak=   -3.385 closest distance to " O   HOH Z   6 " =    1.759
peak=   -3.379 closest distance to " NH2 ARG A  79 " =    2.028
peak=   -3.376 closest distance to " O   ILE A 234 " =    1.205
peak=   -3.375 closest distance to " OG BSER A 134 " =    1.818
peak=   -3.375 closest distance to " C   SER A 206 " =    1.503
peak=   -3.366 closest distance to " O   GLY A  75 " =    1.972
peak=   -3.364 closest distance to " O   HOH Z 123 " =    2.439
peak=   -3.361 closest distance to " O   ARG A  24 " =    2.101
peak=   -3.358 closest distance to " OG  SER A  87 " =    1.493
peak=   -3.356 closest distance to " CZ  TYR A 169 " =    1.701
peak=   -3.344 closest distance to " OD2 ASP A  50 " =    2.334
peak=   -3.341 closest distance to " CD  PRO A 213 " =    2.175
peak=   -3.335 closest distance to " NH1 ARG A 195 " =    2.629
peak=   -3.332 closest distance to " N   SER A   3 " =    2.103
peak=   -3.332 closest distance to " OG  SER A  26 " =    1.349
peak=   -3.313 closest distance to " O   HOH Z 252 " =    3.998
peak=   -3.311 closest distance to " O   HOH Z 431 " =    1.848
peak=   -3.306 closest distance to " O   SER A 210 " =    1.990
peak=   -3.306 closest distance to " CD1 LEU A 101 " =    2.641
peak=   -3.301 closest distance to " CA  GLY A 133 " =    2.306
peak=   -3.299 closest distance to " CD1 LEU A 228 " =    2.272
peak=   -3.299 closest distance to " O   HOH Z 193 " =    1.885
peak=   -3.299 closest distance to " CB  ALA A 291 " =    2.353
peak=   -3.297 closest distance to " C   ASN A 285 " =    2.396
peak=   -3.292 closest distance to " C   MET A 188 " =    1.467
peak=   -3.291 closest distance to " CA  GLY A 203 " =    2.399
peak=   -3.290 closest distance to " CD1 LEU A  25 " =    2.458
peak=   -3.289 closest distance to " O   HOH Z  47 " =    1.671
peak=   -3.289 closest distance to " CG1 VAL A 296 " =    1.370
peak=   -3.286 closest distance to " CG  GLU A  53 " =    1.551
peak=   -3.283 closest distance to " NE2 GLN A 194 " =    1.799
peak=   -3.282 closest distance to " O   HOH Z 177 " =    1.716
peak=   -3.275 closest distance to " O   HOH Z 222 " =    1.569
peak=   -3.272 closest distance to " O   HOH Z 243 " =    2.049
peak=   -3.269 closest distance to " CG1 VAL A 230 " =    1.934
peak=   -3.264 closest distance to " NH2 ARG A 159 " =    2.341
peak=   -3.259 closest distance to " O   PRO A 198 " =    1.273
peak=   -3.259 closest distance to " O   HOH Z 369 " =    2.297
peak=   -3.258 closest distance to " N   ASP A 171 " =    2.359
peak=   -3.253 closest distance to " O   HOH Z 241 " =    1.377
peak=   -3.253 closest distance to " O   HOH Z 189 " =    1.842
peak=   -3.252 closest distance to " ND2 ASN A  69 " =    1.832
peak=   -3.249 closest distance to " CB  ASN A  39 " =    2.248
peak=   -3.249 closest distance to " N   ASN A  60 " =    1.267
peak=   -3.245 closest distance to " CD2 PHE A  61 " =    2.486
peak=   -3.240 closest distance to " O   HOH Z 191 " =    5.565
peak=   -3.240 closest distance to " CD2 TYR A 247 " =    2.270
peak=   -3.238 closest distance to " O   LEU A 167 " =    1.527
peak=   -3.231 closest distance to " N   MET A 105 " =    2.671
peak=   -3.231 closest distance to " O   LYS A 117 " =    1.673
peak=   -3.229 closest distance to " CG  PHE A 283 " =    2.815
peak=   -3.227 closest distance to " CB  GLN A  11 " =    1.810
peak=   -3.219 closest distance to " CA  ASN A 127 " =    1.100
peak=   -3.215 closest distance to " O   HOH Z 211 " =    1.674
peak=   -3.212 closest distance to " CG2 VAL A 189 " =    2.044
peak=   -3.211 closest distance to " CG1 VAL A 197 " =    2.259
peak=   -3.208 closest distance to " CG  PRO A 163 " =    2.485
peak=   -3.207 closest distance to " CG1 VAL A 112 " =    2.920
peak=   -3.203 closest distance to " O   HOH Z 313 " =    1.173
peak=   -3.203 closest distance to " NE2 GLN A  88 " =    0.988
peak=   -3.195 closest distance to " CD2 TYR A 293 " =    2.087
peak=   -3.192 closest distance to " O   HOH Z 377 " =    1.743
peak=   -3.191 closest distance to " O   HOH Z 149 " =    2.157
peak=   -3.188 closest distance to " O   HOH Z 111 " =    2.105
peak=   -3.187 closest distance to " CB  LEU A  83 " =    2.334
peak=   -3.186 closest distance to " O   HOH Z 113 " =    2.094
peak=   -3.184 closest distance to " ND2 ASN A  60 " =    1.754
peak=   -3.179 closest distance to " O   HOH Z 174 " =    2.305
peak=   -3.173 closest distance to " CD  GLN A 223 " =    1.593
peak=   -3.169 closest distance to " CD  ARG A 259 " =    2.510
peak=   -3.161 closest distance to " O   HOH Z 198 " =    1.510
peak=   -3.157 closest distance to " O   HOH Z 285 " =    1.598
peak=   -3.156 closest distance to " O   ASN A 301 " =    1.497
peak=   -3.148 closest distance to " CB  TYR A  15 " =    2.204
peak=   -3.139 closest distance to " O   PRO A 198 " =    1.387
peak=   -3.132 closest distance to " O   HOH Z 372 " =    2.292
peak=   -3.131 closest distance to " N   SER A 276 " =    1.407
peak=   -3.128 closest distance to " CD1 ILE A 199 " =    2.487
peak=   -3.127 closest distance to " O   ALA A 161 " =    1.692
peak=   -3.126 closest distance to " CG  GLU A   2 " =    1.843
peak=   -3.126 closest distance to " CA  ALA A 248 " =    2.633
peak=   -3.119 closest distance to " CD  ARG A 195 " =    5.124
peak=   -3.111 closest distance to " O   HOH Z 139 " =    3.075
peak=   -3.109 closest distance to " CZ2 TRP A  92 " =    2.779
peak=   -3.100 closest distance to " O   HOH Z  90 " =    1.616
peak=   -3.098 closest distance to " O   HOH Z 423 " =    2.125
peak=   -3.096 closest distance to " CG  LEU A 228 " =    1.084
peak=   -3.096 closest distance to " CE1 HIS A  81 " =    1.436
peak=   -3.096 closest distance to " O   HOH Z 262 " =    2.813
peak=   -3.091 closest distance to " CG1 VAL A  67 " =    3.113
peak=   -3.086 closest distance to " O   ASP A 270 " =    1.602
peak=   -3.080 closest distance to " O   VAL A 197 " =    1.419
peak=   -3.059 closest distance to " C   LEU A 222 " =    0.926
peak=   -3.052 closest distance to " O   HOH Z 298 " =    2.667
peak=   -3.052 closest distance to " O   HOH Z 353 " =    2.082
peak=   -3.049 closest distance to " C   ASP A 270 " =    1.224
peak=   -3.047 closest distance to " O   ALA A  51 " =    1.400
peak=   -3.029 closest distance to " CA  SER A  62 " =    2.446
peak=   -3.025 closest distance to " OD1 ASP A 200 " =    1.431

================= 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    :  0.4323 0.4163   6.224725e+00   6.197925e+00
   1_bss:  0.4242 0.4042   6.219321e+00   6.182789e+00
   1_xyz:  0.3118 0.3360   6.000458e+00   6.048218e+00
   1_adp:  0.2478 0.2803   5.807954e+00   5.915943e+00
   1_occ:  0.2472 0.2804   5.806694e+00   5.916444e+00
   2_bss:  0.2428 0.2748   5.804917e+00   5.910338e+00
   2_xyz:  0.1715 0.2071   5.490054e+00   5.657354e+00
   2_adp:  0.1575 0.1955   5.419637e+00   5.598682e+00
   2_occ:  0.1573 0.1956   5.419619e+00   5.599417e+00
   3_bss:  0.1567 0.1953   5.419538e+00   5.598644e+00
   3_xyz:  0.1236 0.1637   5.212734e+00   5.432830e+00
   3_adp:  0.1182 0.1601   5.181130e+00   5.413008e+00
   3_occ:  0.1181 0.1601   5.180965e+00   5.413001e+00
   4_bss:  0.1184 0.1607   5.182673e+00   5.413986e+00
   4_xyz:  0.1182 0.1608   5.187119e+00   5.415099e+00
   4_adp:  0.1192 0.1600   5.188325e+00   5.409797e+00
   4_occ:  0.1190 0.1599   5.187271e+00   5.409096e+00
   5_bss:  0.1190 0.1599   5.187286e+00   5.409102e+00
   5_xyz:  0.1132 0.1565   5.150717e+00   5.389651e+00
   5_adp:  0.1116 0.1579   5.150258e+00   5.399006e+00
   5_occ:  0.1116 0.1579   5.150172e+00   5.398975e+00
   5_bss:  0.1116 0.1579   5.149978e+00   5.398899e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.331  19.176   7.334   9.846   8.054   0.000   0.000   0.000
   1_xyz:  0.331  19.176   7.334   9.846   8.054   0.000   0.000   0.000
   1_adp:  0.331  19.176   7.334   9.846   8.054   0.000   0.000   0.000
   1_occ:  0.331  19.176   7.334   9.846   8.054   0.000   0.000   0.000
   2_bss:  0.331  48.201   4.010   5.987   5.066   0.000   0.000   0.000
   2_xyz:  0.331  48.201   4.010   5.987   5.066   0.000   0.000   0.000
   2_adp:  0.331  48.201   4.010   5.987   5.066   0.000   0.000   0.000
   2_occ:  0.331  48.201   4.010   5.987   5.066   0.000   0.000   0.000
   3_bss:  0.321  48.201   3.180   4.292   4.462   0.000   0.000   0.000
   3_xyz:  0.321  48.201   3.180   4.292   4.462   0.000   0.000   0.000
   3_adp:  0.321  48.201   3.180   4.292   4.462   0.000   0.000   0.000
   3_occ:  0.321  48.201   3.180   4.292   4.462   0.000   0.000   0.000
   4_bss:  0.323  49.441   3.072   3.794   4.321   0.000   0.000   0.000
   4_xyz:  0.323  49.441   3.072   3.794   4.321   0.000   0.000   0.000
   4_adp:  0.323  49.441   3.072   3.794   4.321   0.000   0.000   0.000
   4_occ:  0.323  49.441   3.072   3.794   4.321   0.000   0.000   0.000
   5_bss:  0.324  49.441   3.072   3.794   4.321   0.000   0.000   0.000
   5_xyz:  0.324  49.441   3.072   3.794   4.321   0.000   0.000   0.000
   5_adp:  0.324  49.441   3.072   3.794   4.321   0.000   0.000   0.000
   5_occ:  0.324  49.441   3.072   3.794   4.321   0.000   0.000   0.000
   5_bss:  0.320  53.265  -0.603  -0.020   0.623  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  46.074 0.5709  0.6287    49235.546
   1_bss:  45.486 0.5764  0.8165    46783.187
   1_xyz:  36.397 0.6841  0.9425    30850.471
   1_adp:  28.372 0.7766  1.0348    20774.266
   1_occ:  28.397 0.7762  1.0339    20791.744
   2_bss:  28.098 0.7794  0.9188    20405.132
   2_xyz:  20.222 0.8595  0.9857    11168.216
   2_adp:  18.716 0.8742  0.9974     9910.144
   2_occ:  18.728 0.8741  0.9970     9925.175
   3_bss:  18.692 0.8745  0.9604     9928.248
   3_xyz:  14.957 0.9069  0.9795     6875.650
   3_adp:  14.482 0.9111  0.9807     6641.297
   3_occ:  14.480 0.9111  0.9807     6644.003
   4_bss:  14.507 0.9109  0.9715     6682.056
   4_xyz:  14.430 0.9120  0.9699     6683.375
   4_adp:  14.280 0.9133  0.9685     6633.307
   4_occ:  14.263 0.9135  0.9684     6629.657
   5_bss:  14.263 0.9135  0.9684     6629.883
   5_xyz:  13.889 0.9162  0.9706     6365.689
   5_adp:  14.115 0.9144  0.9656     6464.225
   5_occ:  14.114 0.9144  0.9655     6465.213
   5_bss:  14.111 0.9144  0.9689     6464.053
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.4109e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.4109e+01
   1_xyz:   1.532  0.012  0.102 17.773  0.006  4.125   1.1870e-01
   1_adp:   1.532  0.012  0.102 17.773  0.006  4.125   1.1870e-01
   1_occ:   1.532  0.012  0.102 17.773  0.006  4.125   1.1870e-01
   2_bss:   1.532  0.012  0.102 17.773  0.006  4.125   1.1870e-01
   2_xyz:   0.998  0.007  0.071 16.062  0.004  4.127   6.2236e-02
   2_adp:   0.998  0.007  0.071 16.062  0.004  4.127   6.2236e-02
   2_occ:   0.998  0.007  0.071 16.062  0.004  4.127   6.2236e-02
   3_bss:   0.998  0.007  0.071 16.062  0.004  4.127   6.2236e-02
   3_xyz:   1.098  0.009  0.088 15.847  0.004  4.139   7.2321e-02
   3_adp:   1.098  0.009  0.088 15.847  0.004  4.139   7.2321e-02
   3_occ:   1.098  0.009  0.088 15.847  0.004  4.139   7.2321e-02
   4_bss:   1.098  0.009  0.088 15.847  0.004  4.139   7.2321e-02
   4_xyz:   0.934  0.006  0.076 15.377  0.003  4.125   5.5427e-02
   4_adp:   0.934  0.006  0.076 15.377  0.003  4.125   5.5427e-02
   4_occ:   0.934  0.006  0.076 15.377  0.003  4.125   5.5427e-02
   5_bss:   0.934  0.006  0.076 15.377  0.003  4.125   5.5427e-02
   5_xyz:   1.092  0.009  0.089 15.538  0.004  4.129   7.0690e-02
   5_adp:   1.092  0.009  0.089 15.538  0.004  4.129   7.0690e-02
   5_occ:   1.092  0.009  0.089 15.538  0.004  4.129   7.0690e-02
   5_bss:   1.092  0.009  0.089 15.538  0.004  4.129   7.0690e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0160e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0160e+00
   1_xyz:  13.129  0.139  0.449 89.063  0.040  2.313   9.0484e-02
   1_adp:  13.129  0.139  0.449 89.063  0.040  2.313   9.0484e-02
   1_occ:  13.129  0.139  0.449 89.063  0.040  2.313   9.0484e-02
   2_bss:  13.129  0.139  0.449 89.063  0.040  2.313   9.0484e-02
   2_xyz:   6.927  0.075  0.237 81.662  0.027  2.284   4.9294e-02
   2_adp:   6.927  0.075  0.237 81.662  0.027  2.284   4.9294e-02
   2_occ:   6.927  0.075  0.237 81.662  0.027  2.284   4.9294e-02
   3_bss:   6.927  0.075  0.237 81.662  0.027  2.284   4.9294e-02
   3_xyz:   7.188  0.053  0.614 84.501  0.042  2.330   5.1691e-02
   3_adp:   7.188  0.053  0.614 84.501  0.042  2.330   5.1691e-02
   3_occ:   7.188  0.053  0.614 84.501  0.042  2.330   5.1691e-02
   4_bss:   7.188  0.053  0.614 84.501  0.042  2.330   5.1691e-02
   4_xyz:   7.234  0.041  0.470 81.481  0.039  2.394   5.2870e-02
   4_adp:   7.234  0.041  0.470 81.481  0.039  2.394   5.2870e-02
   4_occ:   7.234  0.041  0.470 81.481  0.039  2.394   5.2870e-02
   5_bss:   7.234  0.041  0.470 81.481  0.039  2.394   5.2870e-02
   5_xyz:   7.787  0.046  0.636 82.909  0.040  2.318   4.6802e-02
   5_adp:   7.787  0.046  0.636 82.909  0.040  2.318   4.6802e-02
   5_occ:   7.787  0.046  0.636 82.909  0.040  2.318   4.6802e-02
   5_bss:   7.787  0.046  0.636 82.909  0.040  2.318   4.6802e-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:  75.57   0.00  10.46  62.15   0.00   7.42  75.57   0.00  27.05
   1_occ:  75.57   0.00  10.46  62.15   0.00   7.42  75.57   0.00  27.05
   2_bss:  75.57   0.00  10.46  62.15   0.00   7.42  75.57   0.00  27.05
   2_xyz:  75.57   0.00  10.46  62.15   0.00   7.42  75.57   0.00  27.05
   2_adp:  70.57   0.00  11.11  70.57   0.00   7.25  69.78   0.00  32.10
   2_occ:  70.57   0.00  11.11  70.57   0.00   7.25  69.78   0.00  32.10
   3_bss:  70.57   0.00  11.11  70.57   0.00   7.25  69.78   0.00  32.10
   3_xyz:  70.57   0.00  11.11  70.57   0.00   7.25  69.78   0.00  32.10
   3_adp:  77.53   0.00  11.48  77.53   0.00   7.30  69.97   0.55  34.23
   3_occ:  77.53   0.00  11.48  77.53   0.00   7.30  69.97   0.55  34.23
   4_bss:  77.53   0.00  11.48  77.53   0.00   7.30  69.97   0.55  34.23
   4_xyz:  77.53   0.00  11.48  77.53   0.00   7.30  69.97   0.55  34.23
   4_adp:  75.80   0.00  11.03  75.80   0.00   7.15  69.48   0.79  32.16
   4_occ:  75.80   0.00  11.03  75.80   0.00   7.15  69.48   0.79  32.16
   5_bss:  75.80   0.00  11.03  75.80   0.00   7.15  69.48   0.79  32.16
   5_xyz:  75.80   0.00  11.03  75.80   0.00   7.15  69.48   0.79  32.16
   5_adp:  92.07   0.00  11.65  92.07   0.00   7.33  80.07   0.64  35.17
   5_occ:  92.07   0.00  11.65  92.07   0.00   7.33  80.07   0.64  35.17
   5_bss:  95.89   3.82  15.47  95.89   3.82  11.15  83.89   4.46  38.99
------------------------------------------------------------------------
 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:    1.186    0.009    0.405
   1_adp:    1.186    0.009    0.405
   1_occ:    1.186    0.009    0.405
   2_bss:    1.186    0.009    0.405
   2_xyz:    1.544    0.010    0.501
   2_adp:    1.544    0.010    0.501
   2_occ:    1.544    0.010    0.501
   3_bss:    1.544    0.010    0.501
   3_xyz:    1.439    0.051    0.548
   3_adp:    1.439    0.051    0.548
   3_occ:    1.439    0.051    0.548
   4_bss:    1.439    0.051    0.548
   4_xyz:    1.598    0.024    0.559
   4_adp:    1.598    0.024    0.559
   4_occ:    1.598    0.024    0.559
   5_bss:    1.598    0.024    0.559
   5_xyz:    1.547    0.033    0.569
   5_adp:    1.547    0.033    0.569
   5_occ:    1.547    0.033    0.569
   5_bss:    1.547    0.033    0.569
------------------------------------------------------------------------

CPU time actual refinement: 331.96


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_808/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_808/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_808/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_808/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_808/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 331.81 
  Macro-tasks:
    bulk solvent and scale       = 43.17  
    individual site refinement   = 138.75 
    weights calculation          = 32.09  
    collect and process          = 6.64   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 220.77 
  Micro-tasks:
    mask                            = 1.71   
    f_calc                          = 100.66 
    alpha_beta                      = 7.90   
    target                          = 1.13   
    gradients_wrt_atomic_parameters = 112.23 
    fmodel                         = 7.30   
    r_factors                      = 0.19   
    phase_errors                   = 11.14  
    foms                           = 0.32   
    TOTAL for micro-tasks          = 242.58 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.607 micro seconds
Total CPU time: 5.75 minutes
from_scatterers_fft:    656 calls, 100.26 s
gradients_fft:          600 calls,  98.32 s

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

# Date 2008-01-16 Time 02:28:03 PST -0800 (1200479283.58 s)
Start R-work = 0.4323, R-free = 0.4163 (no bulk solvent and anisotropic scale)
Final R-work = 0.1283, R-free = 0.1732 (no bulk solvent and anisotropic scale)

Start R-work = 0.4242, R-free = 0.4042
Final R-work = 0.1116, R-free = 0.1579