# Date 2008-01-16 Time 01:46:14 PST -0800 (1200476774.43 s)
#phil __OFF__

Command line arguments: "../555.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 = 8397
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 555

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.8988, 47.1647, 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: (69.8988, 47.1647, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9392 1.99055
Completeness in resolution range: 0.972207
Completeness with d_max=infinity: 0.969129

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9392
                             d_min =   1.9905

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 47.1647, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9392 1.99055
Completeness in resolution range: 0.972207
Completeness with d_max=infinity: 0.969129

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9396 -  4.2585 [2117/2144]  1904   213  10.1%
  bin  2:  4.2585 -  3.3931 [2028/2044]  1826   202  10.0%
  bin  3:  3.3931 -  2.9680 [2014/2033]  1812   202  10.0%
  bin  4:  2.9680 -  2.6984 [1987/2017]  1789   198  10.0%
  bin  5:  2.6984 -  2.5060 [1973/1992]  1777   196   9.9%
  bin  6:  2.5060 -  2.3588 [1963/1988]  1765   198  10.1%
  bin  7:  2.3588 -  2.2411 [1954/1988]  1763   191   9.8%
  bin  8:  2.2411 -  2.1438 [1945/1976]  1748   197  10.1%
  bin  9:  2.1438 -  2.0615 [1939/1980]  1743   196  10.1%
  bin 10:  2.0615 -  1.9905 [1669/1987]  1503   166   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_555/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: 12
        2.42 -     3.04: 2203
        3.04 -     3.66: 4635
        3.66 -     4.28: 9060
        4.28 -     4.90: 12356
  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
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z  18 " - " O   HOH Z 102 "  2.318 3.040 -x+1,y+1/2,-z+1/2
  " OE1 GLN A  55 " - " O   HOH Z 403 "  2.323 3.040 -x+1,y-1/2,-z+1/2
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  ... (remaining 28261 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_555/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_555/model_refine_001.geo

CPU time processing inputs: 9.16


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.89875 47.16465 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: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4133   r_free= 0.3994   ksol= 0.00   Bsol= 0.00   scale= 0.834    |
|                                                                             |
| 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:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.198896                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9396 -  4.7493 0.99   1379  153 0.3497 0.3285      6.4889      6.4396|
|  2:  4.7493 -  3.7899 0.99   1310  148 0.3033 0.3167      6.5741      6.6106|
|  3:  3.7899 -  3.3168 0.99   1302  143 0.3463 0.3298      6.5074      6.5066|
|  4:  3.3168 -  3.0163 0.99   1294  139 0.3873 0.3454      6.4132      6.2996|
|  5:  3.0163 -  2.8016 0.99   1274  143 0.4246 0.4385      6.2833      6.3445|
|  6:  2.8016 -  2.6374 0.99   1274  145 0.4300 0.4860      6.2049       6.183|
|  7:  2.6374 -  2.5060 0.99   1275  140 0.4583 0.4318      6.1876      6.1168|
|  8:  2.5060 -  2.3973 0.98   1262  140 0.4665 0.4398      6.1392      6.1032|
|  9:  2.3973 -  2.3054 0.98   1251  142 0.4657 0.4785      6.0739      6.0631|
| 10:  2.3054 -  2.2261 0.99   1264  137 0.4823 0.4356      6.1025      5.9949|
| 11:  2.2261 -  2.1567 0.99   1255  143 0.4717 0.3911      6.0079      5.9536|
| 12:  2.1567 -  2.0952 0.97   1246  134 0.4852 0.4562      5.9554      6.0119|
| 13:  2.0952 -  2.0402 0.99   1265  140 0.4780 0.5126      5.8709      5.8589|
| 14:  2.0402 -  1.9905 0.78    979  112 0.4919 0.4356      5.8315       5.712|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9396 -  4.7493  1379   153  0.74  30.45   0.82     0.76      56141.26|
|  2:  4.7493 -  3.7899  1310   148  0.80  26.60   0.93     0.83      65143.96|
|  3:  3.7899 -  3.3168  1302   143  0.74  31.48   0.89     0.81      65274.07|
|  4:  3.3168 -  3.0163  1294   139  0.70  35.71   0.85     0.74      57101.98|
|  5:  3.0163 -  2.8016  1274   143  0.60  43.87   0.79     0.66      53843.36|
|  6:  2.8016 -  2.6374  1274   145  0.57  46.22   0.77     0.63      50150.97|
|  7:  2.6374 -  2.5060  1275   140  0.55  48.27   0.77     0.61      47147.12|
|  8:  2.5060 -  2.3973  1262   140  0.56  47.78   0.79     0.63      41429.95|
|  9:  2.3973 -  2.3054  1251   142  0.58  46.04   0.75     0.64      35550.04|
| 10:  2.3054 -  2.2261  1264   137  0.60  44.65   0.78     0.67      31553.95|
| 11:  2.2261 -  2.1567  1255   143  0.58  46.03   0.78     0.66      29756.11|
| 12:  2.1567 -  2.0952  1246   134  0.52  50.78   0.79     0.61      30950.88|
| 13:  2.0952 -  2.0402  1265   140  0.49  53.05   0.78     0.56      28175.51|
| 14:  2.0402 -  1.9905   979   112  0.51  51.81   0.75     0.54      22570.11|
|alpha:            min =        0.54 max =            0.83 mean =         0.67|
|beta:             min =    22570.11 max =        65274.07 mean =     44499.39|
|figures of merit: min =        0.00 max =            1.00 mean =         0.61|
|phase err.(work): min =        0.00 max =           89.98 mean =        42.74|
|phase err.(test): min =        0.00 max =           89.88 mean =        42.85|
|-----------------------------------------------------------------------------|

============================== Outliers rejection =============================

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 0
total                    = 0

====================== Target weights (before refinement) =====================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.299011              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 72.637   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.505084              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.751   (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:        3 |
| 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:      688 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1510 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2616 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3920 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5053 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6607 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7723 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.748 |
| 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 |       1.691 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.905)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 11.905)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4222   r_free= 0.4060   ksol= 0.00   Bsol= 0.00   scale= 0.802    |
|                                                                             |
| 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:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.208124                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4052   r_free= 0.3882   ksol= 0.35   Bsol= 20.00   scale= 1.032   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.34,8.73,8.26,0.00,0.00,0.00); trace/3= 8.11                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.194736                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.997924              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 74.662   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.498197              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 75.294   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4052      final r-factor (work) = 0.2878          |
| start r-factor (free) = 0.3882      final r-factor (free) = 0.3073          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 72.4090 = 6.00 * 0.50 * 6.2224 + 1.00 * 53.7482                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.1107 = 6.00 * 0.50 * 6.0030 + 1.00 * 0.1078                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2878      final r-factor (work) = 0.2132          |
| start r-factor (free) = 0.3073      final r-factor (free) = 0.2407          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0054 = 0.50 * 1.00 * 6.0030 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8857 = 0.50 * 1.00 * 5.7712 + 1.00 * 0.0104                               |
|-----------------------------------------------------------------------------|
| number of iterations = 14      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.905)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    49.52   9.79     None  None   None       |
|    all(noH): 2823   0      0.00    49.52   9.79     None  None   None       |
|    Sol.    : 438    0      0.00    49.52   26.36    None  None   None       |
|    Mac.    : 2385   0      0.00    45.55   6.74     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 -   4.952: 1180   |   5:    24.760 -  29.712:  102        |
|      1:     4.952 -   9.904:  770   |   6:    29.712 -  34.664:  105        |
|      2:     9.904 -  14.856:  294   |   7:    34.664 -  39.616:   87        |
|      3:    14.856 -  19.808:  156   |   8:    39.616 -  44.568:   30        |
|      4:    19.808 -  24.760:   88   |   9:    44.568 -  49.520:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2132 r_free = 0.2407             target_work(ml) = 5.657         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2126 r_free = 0.2406             target_work(ml) = 5.655         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2126   r_free= 0.2406   ksol= 0.35   Bsol= 20.00   scale= 1.086   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.34,8.73,8.26,0.00,0.00,0.00); trace/3= 8.11                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.654959                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2070   r_free= 0.2354   ksol= 0.33   Bsol= 38.27   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.95,5.02,5.28,0.00,0.00,0.00); trace/3= 4.75                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.652885                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.172516              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 93.672   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.242626              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 114.319  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2070      final r-factor (work) = 0.1487          |
| start r-factor (free) = 0.2354      final r-factor (free) = 0.1799          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3994 = 2.17 * 0.50 * 5.7924 + 1.00 * 0.1073                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0139 = 2.17 * 0.50 * 5.4836 + 1.00 * 0.0574                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1487      final r-factor (work) = 0.1378          |
| start r-factor (free) = 0.1799      final r-factor (free) = 0.1713          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3439 = 0.24 * 1.00 * 5.4836 + 1.00 * 0.0134                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3152 = 0.24 * 1.00 * 5.3102 + 1.00 * 0.0268                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.905)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    66.34   10.40    None  None   None       |
|    all(noH): 2823   0      0.00    66.34   10.40    None  None   None       |
|    Sol.    : 438    0      0.00    52.17   30.17    None  None   None       |
|    Mac.    : 2385   0      0.00    66.34   6.77     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.634: 1566   |   5:    33.169 -  39.803:  126        |
|      1:     6.634 -  13.268:  624   |   6:    39.803 -  46.436:   92        |
|      2:    13.268 -  19.901:  176   |   7:    46.436 -  53.070:   32        |
|      3:    19.901 -  26.535:  101   |   8:    53.070 -  59.704:    2        |
|      4:    26.535 -  33.169:  103   |   9:    59.704 -  66.338:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1378 r_free = 0.1713             target_work(ml) = 5.288         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1376 r_free = 0.1714             target_work(ml) = 5.288         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1376   r_free= 0.1714   ksol= 0.33   Bsol= 38.27   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.95,5.02,5.28,0.00,0.00,0.00); trace/3= 4.75                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.288026                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1373   r_free= 0.1714   ksol= 0.33   Bsol= 43.61   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.18,4.03,4.69,0.00,0.00,0.00); trace/3= 3.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.287504                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.222585              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 115.759  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.407170              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 95.686   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1373      final r-factor (work) = 0.1187          |
| start r-factor (free) = 0.1714      final r-factor (free) = 0.1561          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9618 = 2.22 * 0.50 * 5.3131 + 1.00 * 0.0574                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8605 = 2.22 * 0.50 * 5.2171 + 1.00 * 0.0627                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1187      final r-factor (work) = 0.1148          |
| start r-factor (free) = 0.1561      final r-factor (free) = 0.1542          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1433 = 0.41 * 1.00 * 5.2171 + 1.00 * 0.0190                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1114 = 0.41 * 1.00 * 5.1577 + 1.00 * 0.0114                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.905)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    68.63   10.86    None  None   None       |
|    all(noH): 2823   0      0.00    68.63   10.86    None  None   None       |
|    Sol.    : 438    0      0.55    63.31   32.47    None  None   None       |
|    Mac.    : 2385   0      0.00    68.63   6.89     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.863: 1631   |   5:    34.313 -  41.176:   86        |
|      1:     6.863 -  13.725:  566   |   6:    41.176 -  48.039:   88        |
|      2:    13.725 -  20.588:  168   |   7:    48.039 -  54.901:   56        |
|      3:    20.588 -  27.451:  104   |   8:    54.901 -  61.764:   20        |
|      4:    27.451 -  34.313:   99   |   9:    61.764 -  68.627:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1148 r_free = 0.1542             target_work(ml) = 5.152         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1147 r_free = 0.1543             target_work(ml) = 5.152         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1147   r_free= 0.1543   ksol= 0.33   Bsol= 43.61   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.18,4.03,4.69,0.00,0.00,0.00); trace/3= 3.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.151868                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1147   r_free= 0.1543   ksol= 0.33   Bsol= 43.61   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.18,4.03,4.69,0.00,0.00,0.00); trace/3= 3.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.151868                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.943996              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 135.532  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.218576              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 145.607  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1147      final r-factor (work) = 0.1123          |
| start r-factor (free) = 0.1543      final r-factor (free) = 0.1545          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0759 = 1.94 * 0.50 * 5.1574 + 1.00 * 0.0629                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0593 = 1.94 * 0.50 * 5.1427 + 1.00 * 0.0606                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1123      final r-factor (work) = 0.1128          |
| start r-factor (free) = 0.1545      final r-factor (free) = 0.1544          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1354 = 0.22 * 1.00 * 5.1427 + 1.00 * 0.0114                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1351 = 0.22 * 1.00 * 5.1447 + 1.00 * 0.0106                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.905)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    68.94   10.60    None  None   None       |
|    all(noH): 2823   0      0.00    68.94   10.60    None  None   None       |
|    Sol.    : 438    0      0.70    63.19   31.33    None  None   None       |
|    Mac.    : 2385   0      0.00    68.94   6.79     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.894: 1644   |   5:    34.470 -  41.364:   86        |
|      1:     6.894 -  13.788:  561   |   6:    41.364 -  48.258:   72        |
|      2:    13.788 -  20.682:  171   |   7:    48.258 -  55.153:   47        |
|      3:    20.682 -  27.576:  107   |   8:    55.153 -  62.047:   13        |
|      4:    27.576 -  34.470:  116   |   9:    62.047 -  68.941:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1128 r_free = 0.1544             target_work(ml) = 5.144         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1127 r_free = 0.1545             target_work(ml) = 5.144         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1127   r_free= 0.1545   ksol= 0.33   Bsol= 43.61   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.18,4.03,4.69,0.00,0.00,0.00); trace/3= 3.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.143901                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1127   r_free= 0.1545   ksol= 0.33   Bsol= 42.94   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.14,3.87,4.68,0.00,0.00,0.00); trace/3= 3.90                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.143655                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.713924              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 163.700  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.578928              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 96.621   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1127      final r-factor (work) = 0.1126          |
| start r-factor (free) = 0.1545      final r-factor (free) = 0.1548          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4690 = 1.71 * 0.50 * 5.1442 + 1.00 * 0.0606                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4656 = 1.71 * 0.50 * 5.1430 + 1.00 * 0.0583                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1126      final r-factor (work) = 0.1120          |
| start r-factor (free) = 0.1548      final r-factor (free) = 0.1557          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9880 = 0.58 * 1.00 * 5.1430 + 1.00 * 0.0106                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0038 = 0.58 * 1.00 * 5.1400 + 1.00 * 0.0281                               |
|-----------------------------------------------------------------------------|
| number of iterations = 9       |    number of function evaluations = 11     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.905)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.59   10.66    None  None   None       |
|    all(noH): 2823   0      0.00    76.59   10.66    None  None   None       |
|    Sol.    : 438    0      0.45    63.61   31.67    None  None   None       |
|    Mac.    : 2385   0      0.00    76.59   6.81     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 -   7.660: 1736   |   5:    38.297 -  45.957:   96        |
|      1:     7.660 -  15.319:  518   |   6:    45.957 -  53.616:   62        |
|      2:    15.319 -  22.978:  148   |   7:    53.616 -  61.276:   19        |
|      3:    22.978 -  30.638:  122   |   8:    61.276 -  68.935:    6        |
|      4:    30.638 -  38.297:  113   |   9:    68.935 -  76.595:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1120 r_free = 0.1557             target_work(ml) = 5.145         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1118 r_free = 0.1556             target_work(ml) = 5.144         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1118   r_free= 0.1556   ksol= 0.33   Bsol= 42.94   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.14,3.87,4.68,0.00,0.00,0.00); trace/3= 3.90                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.143866                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9396 -  4.7493 0.99   1379  153 0.1016 0.1271      5.3925       5.509|
|  2:  4.7493 -  3.7899 0.99   1310  148 0.0870 0.1130      5.4497       5.643|
|  3:  3.7899 -  3.3168 0.99   1302  143 0.1061 0.1478      5.4765       5.844|
|  4:  3.3168 -  3.0163 0.99   1294  139 0.1189 0.1480       5.439      5.5819|
|  5:  3.0163 -  2.8016 0.99   1274  143 0.1311 0.1661      5.3287      5.5344|
|  6:  2.8016 -  2.6374 0.99   1274  145 0.1214 0.1860      5.2098      5.4597|
|  7:  2.6374 -  2.5060 0.99   1275  140 0.1244 0.1616      5.1652      5.3513|
|  8:  2.5060 -  2.3973 0.98   1262  140 0.1177 0.1793      5.0928      5.3869|
|  9:  2.3973 -  2.3054 0.98   1251  142 0.1175 0.1846      5.0368      5.2973|
| 10:  2.3054 -  2.2261 0.99   1264  137 0.1114 0.1622      4.9751      5.1881|
| 11:  2.2261 -  2.1567 0.99   1255  143 0.1128 0.1731       4.926      5.2497|
| 12:  2.1567 -  2.0952 0.97   1246  134 0.1115 0.1614      4.8698      5.1795|
| 13:  2.0952 -  2.0402 0.99   1265  140 0.1138 0.1694      4.8005      5.0512|
| 14:  2.0402 -  1.9905 0.78    979  112 0.1066 0.1836        4.69      4.9783|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9396 -  4.7493  1379   153  0.94   9.02   0.98     0.96       7144.44|
|  2:  4.7493 -  3.7899  1310   148  0.95   7.81   1.01     1.00       8929.74|
|  3:  3.7899 -  3.3168  1302   143  0.94  11.01   1.02     1.01      10273.58|
|  4:  3.3168 -  3.0163  1294   139  0.93  12.94   1.00     0.98       9897.46|
|  5:  3.0163 -  2.8016  1274   143  0.90  15.69   0.99     0.96       8290.87|
|  6:  2.8016 -  2.6374  1274   145  0.90  15.64   0.98     0.94       6882.12|
|  7:  2.6374 -  2.5060  1275   140  0.91  15.41   0.98     0.96       6118.96|
|  8:  2.5060 -  2.3973  1262   140  0.91  14.98   0.99     0.96       5484.35|
|  9:  2.3973 -  2.3054  1251   142  0.91  15.73   1.00     0.97       5078.26|
| 10:  2.3054 -  2.2261  1264   137  0.90  15.81   1.00     0.96       4556.31|
| 11:  2.2261 -  2.1567  1255   143  0.90  15.75   1.00     0.96       4245.92|
| 12:  2.1567 -  2.0952  1246   134  0.91  15.07   1.00     0.99       3850.10|
| 13:  2.0952 -  2.0402  1265   140  0.91  15.51   1.00     0.99       3354.47|
| 14:  2.0402 -  1.9905   979   112  0.91  14.99   0.98     0.93       2657.15|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     2657.15 max =        10273.58 mean =      6288.69|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.96 mean =        13.88|
|phase err.(test): min =        0.00 max =           89.36 mean =        13.44|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1120   r_free= 0.1558   ksol= 0.32   Bsol= 46.90   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.74,-0.05,0.80,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.145982                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1120   r_free= 0.1558   ksol= 0.32   Bsol= 46.90   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.74,-0.05,0.80,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.145982                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9396 -  4.7493 0.99   1379  153 0.1022 0.1297      5.4111      5.5244|
|  2:  4.7493 -  3.7899 0.99   1310  148 0.0884 0.1129      5.4609      5.6454|
|  3:  3.7899 -  3.3168 0.99   1302  143 0.1059 0.1467      5.4761      5.8344|
|  4:  3.3168 -  3.0163 0.99   1294  139 0.1191 0.1476      5.4387      5.5781|
|  5:  3.0163 -  2.8016 0.99   1274  143 0.1311 0.1657       5.327      5.5325|
|  6:  2.8016 -  2.6374 0.99   1274  145 0.1213 0.1859      5.2087      5.4592|
|  7:  2.6374 -  2.5060 0.99   1275  140 0.1244 0.1624      5.1648      5.3521|
|  8:  2.5060 -  2.3973 0.98   1262  140 0.1178 0.1790      5.0935      5.3869|
|  9:  2.3973 -  2.3054 0.98   1251  142 0.1174 0.1844       5.037      5.2986|
| 10:  2.3054 -  2.2261 0.99   1264  137 0.1113 0.1622      4.9757      5.1894|
| 11:  2.2261 -  2.1567 0.99   1255  143 0.1127 0.1733      4.9266       5.252|
| 12:  2.1567 -  2.0952 0.97   1246  134 0.1114 0.1615        4.87      5.1798|
| 13:  2.0952 -  2.0402 0.99   1265  140 0.1137 0.1697      4.8004      5.0505|
| 14:  2.0402 -  1.9905 0.78    979  112 0.1066 0.1834      4.6892       4.978|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9396 -  4.7493  1379   153  0.94   9.38   0.98     0.95       7488.21|
|  2:  4.7493 -  3.7899  1310   148  0.95   8.00   1.01     1.00       9119.73|
|  3:  3.7899 -  3.3168  1302   143  0.94  10.99   1.02     1.02      10263.20|
|  4:  3.3168 -  3.0163  1294   139  0.93  12.89   1.00     0.99       9793.24|
|  5:  3.0163 -  2.8016  1274   143  0.90  15.61   0.99     0.96       8225.45|
|  6:  2.8016 -  2.6374  1274   145  0.90  15.60   0.98     0.94       6860.10|
|  7:  2.6374 -  2.5060  1275   140  0.91  15.39   0.99     0.96       6111.73|
|  8:  2.5060 -  2.3973  1262   140  0.91  14.98   0.99     0.96       5492.80|
|  9:  2.3973 -  2.3054  1251   142  0.91  15.74   1.00     0.97       5084.86|
| 10:  2.3054 -  2.2261  1264   137  0.90  15.85   1.00     0.97       4571.18|
| 11:  2.2261 -  2.1567  1255   143  0.90  15.77   1.00     0.97       4255.75|
| 12:  2.1567 -  2.0952  1246   134  0.91  15.08   1.01     0.99       3856.69|
| 13:  2.0952 -  2.0402  1265   140  0.91  15.50   1.00     0.99       3352.89|
| 14:  2.0402 -  1.9905   979   112  0.91  14.97   0.98     0.94       2650.61|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2650.61 max =        10263.20 mean =      6317.27|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           90.00 mean =        13.91|
|phase err.(test): min =        0.00 max =           89.19 mean =        13.50|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.905)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.96    80.55   14.62    None  None   None       |
|    all(noH): 2823   0      3.96    80.55   14.62    None  None   None       |
|    Sol.    : 438    0      4.41    67.56   35.62    None  None   None       |
|    Mac.    : 2385   0      3.96    80.55   10.76    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:     3.956 -  11.616: 1736   |   5:    42.254 -  49.913:   96        |
|      1:    11.616 -  19.275:  518   |   6:    49.913 -  57.573:   62        |
|      2:    19.275 -  26.935:  148   |   7:    57.573 -  65.232:   19        |
|      3:    26.935 -  34.594:  122   |   8:    65.232 -  72.892:    6        |
|      4:    34.594 -  42.254:  113   |   9:    72.892 -  80.551:    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)= 302         
Filter by distance & map next to the model:
   mapped sites are within: 0.280 - 4.335
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 297 from: 302
   mapped sites are within: 0.720 - 4.335

peak=   10.707 closest distance to " CG2 VAL A 230 " =    1.454
peak=    7.231 closest distance to " CG2 VAL A 296 " =    1.146
peak=    6.091 closest distance to " NH2 ARG A  56 " =    2.231
peak=    6.039 closest distance to " CG  LEU A   5 " =    1.250
peak=    5.815 closest distance to " CD2 LEU A   5 " =    1.182
peak=    5.743 closest distance to " CG  LEU A 228 " =    1.185
peak=    5.584 closest distance to " CG  PRO A  54 " =    1.306
peak=    5.515 closest distance to " CB  GLN A 223 " =    1.429
peak=    5.216 closest distance to " CB  ARG A 275 " =    0.921
peak=    5.061 closest distance to " CB  VAL A 230 " =    1.214
peak=    5.004 closest distance to " CB  VAL A 296 " =    1.092
peak=    5.000 closest distance to " O   HOH Z 232 " =    2.383
peak=    4.995 closest distance to " O   HOH Z 126 " =    1.901
peak=    4.949 closest distance to " CB  PRO A  54 " =    0.958
peak=    4.836 closest distance to " NE2 GLN A  11 " =    1.125
peak=    4.771 closest distance to " CG  PRO A 213 " =    1.259
peak=    4.766 closest distance to " CB  SER A  63 " =    1.246
peak=    4.727 closest distance to " O   HOH Z 209 " =    2.269
peak=    4.683 closest distance to " CB  GLN A 183 " =    1.306
peak=    4.614 closest distance to " CG  PRO A 243 " =    1.138
peak=    4.601 closest distance to " CG  PRO A 198 " =    1.203
peak=    4.572 closest distance to " O   HOH Z 272 " =    1.908
peak=    4.494 closest distance to " O   HOH Z 142 " =    1.653
peak=    4.437 closest distance to " C   PRO A 198 " =    1.502
peak=    4.385 closest distance to " CB  GLU A 152 " =    1.165
peak=    4.355 closest distance to " O   SER A  87 " =    2.280
peak=    4.350 closest distance to " O   HOH Z 368 " =    2.207
peak=    4.324 closest distance to " O   HOH Z 346 " =    1.623
peak=    4.320 closest distance to " ND2 ASN A 187 " =    1.516
peak=    4.308 closest distance to " O   HOH Z 402 " =    1.482
peak=    4.290 closest distance to " O   HOH Z  43 " =    2.080
peak=    4.285 closest distance to " O   HOH Z  63 " =    2.158
peak=    4.277 closest distance to " O   HOH Z 193 " =    1.785
peak=    4.270 closest distance to " CB  SER A   3 " =    1.272
peak=    4.269 closest distance to " O   HOH Z 298 " =    1.784
peak=    4.257 closest distance to " O   HOH Z  61 " =    1.643
peak=    4.202 closest distance to " O   HOH Z 423 " =    1.819
peak=    4.201 closest distance to " CZ  PHE A 218 " =    1.105
peak=    4.200 closest distance to " O   HOH Z 234 " =    3.610
peak=    4.190 closest distance to " O   HOH Z 369 " =    2.140
peak=    4.172 closest distance to " O   HOH Z  40 " =    1.614
peak=    4.172 closest distance to " O   HOH Z 189 " =    2.597
peak=    4.164 closest distance to " O   HOH Z  66 " =    2.296
peak=    4.135 closest distance to " CA  TYR A  30 " =    0.930
peak=    4.134 closest distance to " O   HOH Z 248 " =    1.625
peak=    4.121 closest distance to " CB  ARG A  79 " =    1.390
peak=    4.110 closest distance to " CD2 LEU A 228 " =    1.153
peak=    4.106 closest distance to " O   HOH Z 427 " =    2.998
peak=    4.097 closest distance to " O   HOH Z 316 " =    3.070
peak=    4.088 closest distance to " CB  GLU A 128 " =    1.027
peak=    4.074 closest distance to " CB  VAL A 265 " =    1.296
peak=    4.073 closest distance to " CB  ASN A 148 " =    1.402
peak=    4.053 closest distance to " CG1BVAL A  72 " =    1.644
peak=    4.028 closest distance to " O   HOH Z  78 " =    1.654
peak=    4.005 closest distance to " O   HOH Z 236 " =    1.934
peak=    4.004 closest distance to " O   HOH Z 203 " =    1.747
peak=    3.995 closest distance to " O   HOH Z 403 " =    1.699
peak=    3.991 closest distance to " O   HOH Z 214 " =    2.144
peak=    3.979 closest distance to " O   HOH Z 303 " =    2.069
peak=    3.966 closest distance to " CB  GLU A 277 " =    3.581
peak=    3.954 closest distance to " OD1 ASN A  69 " =    2.596
peak=    3.919 closest distance to " O   HOH Z  59 " =    2.161
peak=    3.918 closest distance to " O   HOH Z 158 " =    3.128
peak=    3.913 closest distance to " O   HOH Z 250 " =    1.364
peak=    3.901 closest distance to " CB  TRP A 179 " =    1.373
peak=    3.898 closest distance to " O   TRP A 274 " =    1.882
peak=    3.872 closest distance to " CD2 TRP A 179 " =    1.358
peak=    3.870 closest distance to " CA  ALA A  51 " =    0.952
peak=    3.857 closest distance to " O   HOH Z 280 " =    2.910
peak=    3.838 closest distance to " CB  TRP A 266 " =    0.974
peak=    3.837 closest distance to " O   HOH Z  15 " =    2.155
peak=    3.816 closest distance to " CB  ALA A 248 " =    1.416
peak=    3.808 closest distance to " CA  ASN A 215 " =    1.166
peak=    3.801 closest distance to " O   HOH Z  97 " =    2.434
peak=    3.798 closest distance to " N   ASN A  39 " =    1.176
peak=    3.798 closest distance to " CB  ARG A 190 " =    1.646
peak=    3.787 closest distance to " O   HOH Z 261 " =    1.707
peak=    3.785 closest distance to " O   HOH Z  97 " =    1.963
peak=    3.758 closest distance to " CG  ARG A  66 " =    2.740
peak=    3.753 closest distance to " O   HOH Z  54 " =    1.581
peak=    3.737 closest distance to " CB  ASN A 142 " =    1.111
peak=    3.736 closest distance to " CA  ARG A  36 " =    1.026
peak=    3.734 closest distance to " CA  VAL A  41 " =    0.793
peak=    3.730 closest distance to " O   HOH Z 407 " =    2.463
peak=    3.725 closest distance to " CB  VAL A 202 " =    1.524
peak=    3.720 closest distance to " CB  ASP A 140 " =    0.933
peak=    3.719 closest distance to " O   HOH Z 417 " =    3.109
peak=    3.703 closest distance to " O   HOH Z 371 " =    3.160
peak=    3.701 closest distance to " O   HOH Z 344 " =    2.992
peak=    3.699 closest distance to " CG1 ILE A  49 " =    1.454
peak=    3.693 closest distance to " O   HOH Z 411 " =    3.813
peak=    3.691 closest distance to " CB  ALA A   9 " =    1.594
peak=    3.685 closest distance to " O   HOH Z 147 " =    1.780
peak=    3.679 closest distance to " O   HOH Z 265 " =    2.370
peak=    3.670 closest distance to " CG2 ILE A  20 " =    1.427
peak=    3.670 closest distance to " CB  ASN A  39 " =    0.881
peak=    3.669 closest distance to " O   HOH Z 261 " =    2.245
peak=    3.663 closest distance to " O   HOH Z 313 " =    1.770
peak=    3.660 closest distance to " CB  ARG A  79 " =    0.893
peak=    3.655 closest distance to " O   HOH Z 291 " =    1.616
peak=    3.652 closest distance to " CD  ARG A 269 " =    0.987
peak=    3.649 closest distance to " CE1 TYR A 186 " =    1.351
peak=    3.647 closest distance to " NH2 ARG A 156 " =    1.120
peak=    3.644 closest distance to " O   HOH Z 389 " =    1.902
peak=    3.643 closest distance to " O   HOH Z 261 " =    2.008
peak=    3.637 closest distance to " CA  ARG A 195 " =    1.224
peak=    3.634 closest distance to " CB  ARG A 139 " =    0.894
peak=    3.627 closest distance to " O   HOH Z 273 " =    2.789
peak=    3.626 closest distance to " O   HOH Z 128 " =    2.119
peak=    3.620 closest distance to " CA  ALA A  21 " =    1.109
peak=    3.616 closest distance to " O   HOH Z  21 " =    1.779
peak=    3.615 closest distance to " CB  THR A  31 " =    1.542
peak=    3.612 closest distance to " CB  SER A  26 " =    1.685
peak=    3.604 closest distance to " O   HOH Z  85 " =    1.329
peak=    3.604 closest distance to " O   HOH Z 197 " =    3.032
peak=    3.585 closest distance to " CB  GLU A  46 " =    1.027
peak=    3.577 closest distance to " O   ASP A 124 " =    1.157
peak=    3.576 closest distance to " CB BVAL A  41 " =    1.118
peak=    3.575 closest distance to " O   HOH Z 128 " =    2.063
peak=    3.573 closest distance to " CD  LYS A 166 " =    1.298
peak=    3.572 closest distance to " O   HOH Z 383 " =    1.872
peak=    3.565 closest distance to " CG2 VAL A 257 " =    0.866
peak=    3.561 closest distance to " O   HOH Z 263 " =    1.695
peak=    3.558 closest distance to " O   HOH Z 124 " =    1.321
peak=    3.554 closest distance to " CA  LYS A 117 " =    1.281
peak=    3.549 closest distance to " O   HOH Z 148 " =    3.263
peak=    3.545 closest distance to " CG1 ILE A  33 " =    1.304
peak=    3.540 closest distance to " O   HOH Z  48 " =    1.601
peak=    3.538 closest distance to " NH1BARG A 190 " =    2.043
peak=    3.538 closest distance to " CB  ALA A 291 " =    1.344
peak=    3.537 closest distance to " CA  ASP A 162 " =    1.061
peak=    3.536 closest distance to " CD  ARG A 159 " =    0.720
peak=    3.530 closest distance to " CG1 VAL A 296 " =    1.195
peak=    3.522 closest distance to " CG1 VAL A 153 " =    0.979
peak=    3.522 closest distance to " CA  ASP A 140 " =    1.210
peak=    3.520 closest distance to " CG2 ILE A 120 " =    1.211
peak=    3.514 closest distance to " CB  TRP A 150 " =    1.414
peak=    3.502 closest distance to " CA  PHE A 283 " =    1.206
peak=    3.494 closest distance to " O   HOH Z 285 " =    2.897
peak=    3.494 closest distance to " O   HOH Z  80 " =    1.709
peak=    3.492 closest distance to " O   HOH Z 365 " =    2.981
peak=    3.491 closest distance to " N   SER A 135 " =    1.428
peak=    3.486 closest distance to " O   HOH Z  66 " =    2.261
peak=    3.481 closest distance to " CA  THR A 264 " =    0.782
peak=    3.478 closest distance to " CB  GLN A 205 " =    1.136
peak=    3.478 closest distance to " O   HOH Z 245 " =    1.402
peak=    3.476 closest distance to " OG1 THR A 294 " =    2.387
peak=    3.472 closest distance to " O   HOH Z 345 " =    3.114
peak=    3.466 closest distance to " O   HOH Z 426 " =    1.561
peak=    3.460 closest distance to " CB  ASN A 110 " =    1.150
peak=    3.450 closest distance to " O   HOH Z 435 " =    1.929
peak=    3.440 closest distance to " CA  ASP A 191 " =    1.059
peak=    3.434 closest distance to " O   MET A 105 " =    1.844
peak=    3.431 closest distance to " O   HOH Z 417 " =    2.281
peak=    3.428 closest distance to " O   HOH Z 193 " =    1.975
peak=    3.425 closest distance to " NZ  LYS A  76 " =    1.535
peak=    3.414 closest distance to " CB  GLN A 278 " =    0.861
peak=    3.412 closest distance to " CB  HIS A 108 " =    0.793
peak=    3.410 closest distance to " OE1 GLU A   2 " =    2.194
peak=    3.408 closest distance to " O   HOH Z 421 " =    1.688
peak=    3.407 closest distance to " O   HOH Z 305 " =    3.650
peak=    3.407 closest distance to " O   HOH Z 227 " =    1.594
peak=    3.402 closest distance to " O   HOH Z 422 " =    2.655
peak=    3.400 closest distance to " CG  GLN A  77 " =    2.128
peak=    3.398 closest distance to " O   HOH Z 172 " =    3.727
peak=    3.394 closest distance to " CE  LYS A  76 " =    0.894
peak=    3.394 closest distance to " CG  MET A 185 " =    1.130
peak=    3.393 closest distance to " CB  SER A 212 " =    1.218
peak=    3.390 closest distance to " CB  LEU A 143 " =    1.129
peak=    3.387 closest distance to " O   HOH Z  49 " =    2.377
peak=    3.387 closest distance to " CD1 LEU A 300 " =    1.300
peak=    3.386 closest distance to " O   HOH Z 329 " =    3.941
peak=    3.385 closest distance to " CD BLYS A 290 " =    1.103
peak=    3.383 closest distance to " O   HOH Z 180 " =    2.160
peak=    3.377 closest distance to " O   HOH Z  19 " =    2.177
peak=    3.376 closest distance to " OD2 ASP A 286 " =    2.817
peak=    3.371 closest distance to " N   ARG A 190 " =    0.979
peak=    3.368 closest distance to " CA  ALA A  84 " =    1.367
peak=    3.366 closest distance to " NE2 GLN A  77 " =    3.326
peak=    3.356 closest distance to " CB  PRO A 198 " =    1.046
peak=    3.355 closest distance to " O   HOH Z 337 " =    3.590
peak=    3.354 closest distance to " ND2 ASN A 110 " =    1.605
peak=    3.350 closest distance to " O   HOH Z 368 " =    3.521
peak=    3.350 closest distance to " O   ALA A 165 " =    1.463
peak=    3.349 closest distance to " O   HOH Z 380 " =    1.881
peak=    3.349 closest distance to " O   HOH Z  88 " =    2.950
peak=    3.346 closest distance to " NZ  LYS A 117 " =    3.183
peak=    3.344 closest distance to " CA  SER A  87 " =    1.031
peak=    3.344 closest distance to " CA  ILE A 106 " =    0.744
peak=    3.342 closest distance to " CG  MET A 185 " =    1.049
peak=    3.341 closest distance to " CG  LEU A 167 " =    1.186
peak=    3.340 closest distance to " O   HOH Z   9 " =    2.131
peak=    3.340 closest distance to " O   HOH Z 171 " =    2.419
peak=    3.338 closest distance to " O   HOH Z 112 " =    1.642
peak=    3.335 closest distance to " N   VAL A 126 " =    1.461
peak=    3.335 closest distance to " OG BSER A 164 " =    2.231
peak=    3.328 closest distance to " CB  THR A 157 " =    1.192
peak=    3.313 closest distance to " N   ASP A 162 " =    1.330
peak=    3.311 closest distance to " CB  GLN A  89 " =    1.209
peak=    3.309 closest distance to " CB  MET A  47 " =    1.126
peak=    3.306 closest distance to " CB  ILE A 120 " =    1.280
peak=    3.306 closest distance to " CZ3 TRP A  85 " =    0.919
peak=    3.305 closest distance to " O   HOH Z   4 " =    1.823
peak=    3.302 closest distance to " CD  LYS A 119 " =    1.575
peak=    3.294 closest distance to " CD2 LEU A 297 " =    0.904
peak=    3.287 closest distance to " O   HOH Z 258 " =    2.277
peak=    3.284 closest distance to " O   HOH Z 187 " =    2.297
peak=    3.278 closest distance to " NH1AARG A 145 " =    1.164
peak=    3.278 closest distance to " CB  ALA A 104 " =    0.727
peak=    3.275 closest distance to " CB  GLN A  88 " =    1.148
peak=    3.274 closest distance to " CA  VAL A 126 " =    0.869
peak=    3.274 closest distance to " O   GLN A 278 " =    1.304
peak=    3.273 closest distance to " CD  ARG A  66 " =    2.684
peak=    3.271 closest distance to " CG2 THR A 294 " =    1.723
peak=    3.271 closest distance to " N   ARG A 156 " =    1.379
peak=    3.268 closest distance to " CA  ALA A 158 " =    1.282
peak=    3.262 closest distance to " CA  THR A 221 " =    0.897
peak=    3.260 closest distance to " O   HOH Z 299 " =    4.335
peak=    3.256 closest distance to " O   HOH Z 251 " =    1.461
peak=    3.255 closest distance to " CD1 ILE A 106 " =    0.988
peak=    3.254 closest distance to " CE1 HIS A 108 " =    1.151
peak=    3.253 closest distance to " O   SER A 164 " =    1.105
peak=    3.252 closest distance to " CA  TYR A 116 " =    1.372
peak=    3.252 closest distance to " O   HOH Z 246 " =    1.342
peak=    3.252 closest distance to " CA  GLY A 211 " =    1.276
peak=    3.244 closest distance to " NH2 ARG A  79 " =    1.394
peak=    3.243 closest distance to " CG BARG A 102 " =    1.773
peak=    3.241 closest distance to " O   HOH Z  62 " =    2.266
peak=    3.239 closest distance to " O   HOH Z 227 " =    2.040
peak=    3.237 closest distance to " O   HOH Z 250 " =    1.738
peak=    3.237 closest distance to " CB  ALA A 248 " =    1.040
peak=    3.234 closest distance to " CA  GLY A  80 " =    0.796
peak=    3.233 closest distance to " O  BHOH Z 338 " =    2.431
peak=    3.231 closest distance to " CB  PHE A 204 " =    0.820
peak=    3.228 closest distance to " CB  LYS A 290 " =    0.940
peak=    3.222 closest distance to " N   PHE A 130 " =    1.276
peak=    3.219 closest distance to " O   HOH Z 286 " =    2.297
peak=    3.218 closest distance to " CG2 THR A 221 " =    1.215
peak=    3.217 closest distance to " CA  ASN A 217 " =    1.230
peak=    3.217 closest distance to " O   ARG A  56 " =    2.860
peak=    3.216 closest distance to " O   HOH Z 437 " =    1.977
peak=    3.215 closest distance to " CB  ALA A 114 " =    1.225
peak=    3.215 closest distance to " O   HOH Z 406 " =    1.645
peak=    3.213 closest distance to " O   GLY A  91 " =    1.411
peak=    3.213 closest distance to " CA  ALA A 154 " =    0.929
peak=    3.210 closest distance to " CA  LEU A 282 " =    1.064
peak=    3.209 closest distance to " CB  SER A 273 " =    0.837
peak=    3.207 closest distance to " CB  LEU A 228 " =    1.282
peak=    3.205 closest distance to " CB  GLN A 103 " =    0.930
peak=    3.204 closest distance to " O   HOH Z  88 " =    2.500
peak=    3.203 closest distance to " CZ  PHE A  38 " =    1.221
peak=    3.202 closest distance to " CD2 HIS A  81 " =    1.042
peak=    3.201 closest distance to " CA  ALA A 233 " =    1.280
peak=    3.192 closest distance to " O   HOH Z 353 " =    2.680
peak=    3.191 closest distance to " CA  LYS A 290 " =    1.173
peak=    3.191 closest distance to " CB  THR A  52 " =    1.025
peak=    3.181 closest distance to " ND1 HIS A  81 " =    1.718
peak=    3.175 closest distance to " CB  ASN A 224 " =    1.030
peak=    3.174 closest distance to " CG2 ILE A 234 " =    2.091
peak=    3.172 closest distance to " CB  ALA A 242 " =    0.823
peak=    3.172 closest distance to " O   HOH Z  10 " =    1.735
peak=    3.172 closest distance to " O   HOH Z 271 " =    2.510
peak=    3.168 closest distance to " CG  GLN A 205 " =    0.904
peak=    3.168 closest distance to " CA  ALA A 291 " =    0.906
peak=    3.167 closest distance to " O   HOH Z 425 " =    2.027
peak=    3.167 closest distance to " CG  MET A 188 " =    0.798
peak=    3.161 closest distance to " CD1 ILE A  33 " =    1.656
peak=    3.161 closest distance to " O   HOH Z 173 " =    2.335
peak=    3.157 closest distance to " CB  ASN A 215 " =    1.195
peak=    3.156 closest distance to " O   HOH Z 133 " =    2.427
peak=    3.155 closest distance to " CD1 ILE A 199 " =    0.812
peak=    3.151 closest distance to " CB  ALA A  34 " =    0.899
peak=    3.151 closest distance to " O   HOH Z 102 " =    1.263
peak=    3.149 closest distance to " CD1 LEU A 228 " =    1.894
peak=    3.147 closest distance to " O   HOH Z 193 " =    1.599
peak=    3.144 closest distance to " O   HOH Z 420 " =    1.881
peak=    3.140 closest distance to " O   HOH Z 135 " =    1.754
peak=    3.133 closest distance to " CB  SER A 216 " =    0.772
peak=    3.130 closest distance to " CA  SER A 146 " =    1.743
peak=    3.129 closest distance to " O   HOH Z   1 " =    2.067
peak=    3.125 closest distance to " CG  LEU A 281 " =    1.064
peak=    3.124 closest distance to " CD1 LEU A 261 " =    1.156
peak=    3.117 closest distance to " N   ASN A 127 " =    1.192
peak=    3.112 closest distance to " CA  ASN A 176 " =    1.040
peak=    3.103 closest distance to " O   HOH Z 303 " =    1.641
peak=    3.101 closest distance to " CB  PRO A 243 " =    1.484
peak=    3.078 closest distance to " CD  LYS A  76 " =    1.942
peak=    3.076 closest distance to " CD  ARG A  36 " =    0.963
peak=    3.075 closest distance to " C   ALA A 299 " =    0.920
peak=    3.068 closest distance to " CD2 TYR A  30 " =    0.907
peak=    3.066 closest distance to " CA  MET A 105 " =    0.990
peak=    3.054 closest distance to " CB  GLU A 277 " =    3.726
peak=    3.049 closest distance to " ND2 ASN A 249 " =    0.871
peak=    3.047 closest distance to " CA  ILE A 234 " =    0.777
peak=    3.035 closest distance to " CG  LEU A   5 " =    0.767
peak=    3.034 closest distance to " O   HOH Z 367 " =    3.554
peak=    3.032 closest distance to " O   HOH Z  90 " =    3.294

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 186         
Filter by distance & map next to the model:
   mapped sites are within: 0.634 - 5.436
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 183 from: 186
   mapped sites are within: 0.727 - 5.436

peak=   -5.867 closest distance to " CG2 VAL A 230 " =    0.727
peak=   -4.561 closest distance to " SG  CYS A 254 " =    3.262
peak=   -4.555 closest distance to " CD  GLN A  58 " =    1.026
peak=   -4.543 closest distance to " CD  ARG A 156 " =    2.046
peak=   -4.257 closest distance to " O   HOH Z 290 " =    1.098
peak=   -4.233 closest distance to " O   HOH Z 266 " =    5.065
peak=   -4.210 closest distance to " CG  GLN A 223 " =    2.070
peak=   -4.205 closest distance to " C   HIS A 108 " =    1.203
peak=   -4.158 closest distance to " CB  PRO A 243 " =    2.637
peak=   -4.061 closest distance to " O   HOH Z 351 " =    1.501
peak=   -4.037 closest distance to " O   PRO A 163 " =    2.179
peak=   -4.014 closest distance to " CG2 VAL A 296 " =    1.223
peak=   -4.008 closest distance to " O   HOH Z 114 " =    3.111
peak=   -3.990 closest distance to " CB  PHE A 192 " =    1.932
peak=   -3.976 closest distance to " O   ILE A 109 " =    2.612
peak=   -3.974 closest distance to " OG BSER A 134 " =    1.211
peak=   -3.959 closest distance to " CA  VAL A  67 " =    2.792
peak=   -3.955 closest distance to " O   HOH Z 196 " =    2.093
peak=   -3.931 closest distance to " N   ALA A 226 " =    2.058
peak=   -3.911 closest distance to " CG2BVAL A  41 " =    2.692
peak=   -3.883 closest distance to " CE2 TYR A  30 " =    2.741
peak=   -3.871 closest distance to " ND2 ASN A 187 " =    1.474
peak=   -3.869 closest distance to " O   HOH Z 166 " =    1.867
peak=   -3.851 closest distance to " ND2 ASN A  45 " =    1.061
peak=   -3.816 closest distance to " CZ3 TRP A 179 " =    1.244
peak=   -3.809 closest distance to " OXT GLY A 302 " =    2.773
peak=   -3.800 closest distance to " CG1 VAL A 112 " =    2.762
peak=   -3.791 closest distance to " OG  SER A  97 " =    2.244
peak=   -3.786 closest distance to " O   HOH Z 231 " =    2.109
peak=   -3.773 closest distance to " CG  ASP A 231 " =    0.829
peak=   -3.731 closest distance to " CB  ALA A 248 " =    2.131
peak=   -3.701 closest distance to " CA  ASP A 298 " =    1.052
peak=   -3.692 closest distance to " NE2 GLN A  88 " =    1.862
peak=   -3.689 closest distance to " CD2 LEU A 300 " =    2.689
peak=   -3.689 closest distance to " O   HOH Z 211 " =    1.684
peak=   -3.670 closest distance to " O   HOH Z 185 " =    2.407
peak=   -3.664 closest distance to " CE3 TRP A 150 " =    2.115
peak=   -3.663 closest distance to " NH2AARG A 275 " =    5.066
peak=   -3.659 closest distance to " N   GLN A  58 " =    1.716
peak=   -3.649 closest distance to " CB  ALA A 248 " =    2.372
peak=   -3.644 closest distance to " O   HOH Z 435 " =    2.785
peak=   -3.642 closest distance to " CD1 LEU A 101 " =    2.407
peak=   -3.619 closest distance to " CE  MET A 105 " =    2.142
peak=   -3.608 closest distance to " CB  PRO A 163 " =    2.545
peak=   -3.605 closest distance to " CB  ASP A 171 " =    2.324
peak=   -3.603 closest distance to " O   HOH Z  11 " =    1.862
peak=   -3.591 closest distance to " CG  GLU A 277 " =    1.142
peak=   -3.586 closest distance to " C   MET A 188 " =    1.450
peak=   -3.582 closest distance to " ND2 ASN A  45 " =    1.537
peak=   -3.579 closest distance to " O   HOH Z 165 " =    1.857
peak=   -3.578 closest distance to " CD  ARG A 139 " =    1.597
peak=   -3.548 closest distance to " O   PRO A 198 " =    1.214
peak=   -3.545 closest distance to " O   HOH Z  63 " =    1.296
peak=   -3.542 closest distance to " O   HOH Z  19 " =    2.266
peak=   -3.540 closest distance to " O   HOH Z  37 " =    1.841
peak=   -3.528 closest distance to " CG2 ILE A 263 " =    2.363
peak=   -3.523 closest distance to " OD2 ASP A  50 " =    2.252
peak=   -3.518 closest distance to " CE2 PHE A 218 " =    2.611
peak=   -3.510 closest distance to " NH2 ARG A  79 " =    2.001
peak=   -3.500 closest distance to " O   HOH Z 389 " =    1.922
peak=   -3.479 closest distance to " CB  ALA A  43 " =    2.460
peak=   -3.475 closest distance to " CG1 VAL A 250 " =    2.778
peak=   -3.475 closest distance to " CG1 VAL A 296 " =    1.254
peak=   -3.465 closest distance to " O   HOH Z  10 " =    1.514
peak=   -3.460 closest distance to " CG  ARG A 269 " =    2.344
peak=   -3.456 closest distance to " CB  ALA A 291 " =    2.250
peak=   -3.455 closest distance to " OG ASER A 134 " =    1.299
peak=   -3.453 closest distance to " CG1 VAL A 230 " =    1.869
peak=   -3.451 closest distance to " O   HOH Z  13 " =    1.546
peak=   -3.447 closest distance to " CZ  TYR A 169 " =    1.748
peak=   -3.445 closest distance to " O   HOH Z 394 " =    1.599
peak=   -3.442 closest distance to " CD1 LEU A 101 " =    2.887
peak=   -3.440 closest distance to " CB  ASN A  69 " =    1.148
peak=   -3.436 closest distance to " OG  SER A   3 " =    1.711
peak=   -3.432 closest distance to " CB  ASP A 132 " =    2.304
peak=   -3.426 closest distance to " N   ALA A  43 " =    2.533
peak=   -3.425 closest distance to " O   HOH Z  52 " =    1.515
peak=   -3.417 closest distance to " CG  PHE A 283 " =    2.763
peak=   -3.410 closest distance to " O   HOH Z 407 " =    3.007
peak=   -3.404 closest distance to " O   HOH Z  44 " =    2.220
peak=   -3.397 closest distance to " N   THR A 157 " =    1.462
peak=   -3.397 closest distance to " N   PHE A  59 " =    2.256
peak=   -3.396 closest distance to " CD  LYS A 289 " =    2.558
peak=   -3.396 closest distance to " OD1 ASN A 148 " =    1.462
peak=   -3.392 closest distance to " O   HOH Z 377 " =    2.149
peak=   -3.390 closest distance to " CG1 VAL A 112 " =    2.588
peak=   -3.387 closest distance to " CB  ASP A 132 " =    2.375
peak=   -3.379 closest distance to " NE2 GLN A 103 " =    1.736
peak=   -3.376 closest distance to " CG  TRP A 266 " =    1.922
peak=   -3.360 closest distance to " C   ASP A 231 " =    2.528
peak=   -3.348 closest distance to " NE2 GLN A 194 " =    1.819
peak=   -3.347 closest distance to " CD1 LEU A  25 " =    2.450
peak=   -3.344 closest distance to " N   THR A  52 " =    1.657
peak=   -3.342 closest distance to " O   VAL A 189 " =    2.642
peak=   -3.341 closest distance to " O   HOH Z 102 " =    1.669
peak=   -3.339 closest distance to " CA  GLY A 241 " =    3.061
peak=   -3.336 closest distance to " O   ALA A  10 " =    1.757
peak=   -3.334 closest distance to " O   HOH Z 313 " =    1.639
peak=   -3.332 closest distance to " O   HOH Z 113 " =    2.420
peak=   -3.330 closest distance to " CB  ASN A  39 " =    2.245
peak=   -3.329 closest distance to " CB  ALA A 291 " =    2.197
peak=   -3.326 closest distance to " CG1 VAL A 197 " =    2.203
peak=   -3.322 closest distance to " O   ALA A 161 " =    1.683
peak=   -3.322 closest distance to " NE2 GLN A  88 " =    0.988
peak=   -3.319 closest distance to " CD1 PHE A  59 " =    1.953
peak=   -3.318 closest distance to " O   SER A 271 " =    2.127
peak=   -3.316 closest distance to " CD1 LEU A 228 " =    2.170
peak=   -3.314 closest distance to " O   GLY A 196 " =    1.156
peak=   -3.314 closest distance to " N   ALA A 248 " =    1.819
peak=   -3.308 closest distance to " OXT GLY A 302 " =    3.410
peak=   -3.307 closest distance to " O   HOH Z 139 " =    5.192
peak=   -3.305 closest distance to " C   ALA A 158 " =    1.267
peak=   -3.304 closest distance to " OG BSER A 134 " =    1.789
peak=   -3.304 closest distance to " O   HOH Z  43 " =    1.798
peak=   -3.303 closest distance to " O   HOH Z 222 " =    1.512
peak=   -3.302 closest distance to " C   ASP A 270 " =    1.254
peak=   -3.299 closest distance to " O   HOH Z  22 " =    2.448
peak=   -3.297 closest distance to " CD1 TYR A 247 " =    2.743
peak=   -3.295 closest distance to " N   SER A 212 " =    2.015
peak=   -3.284 closest distance to " N   VAL A 230 " =    1.100
peak=   -3.282 closest distance to " O   HOH Z 353 " =    2.128
peak=   -3.279 closest distance to " C   SER A 206 " =    1.544
peak=   -3.277 closest distance to " NE2 GLN A 278 " =    1.946
peak=   -3.276 closest distance to " O   HOH Z 234 " =    4.045
peak=   -3.273 closest distance to " O   HOH Z  47 " =    1.575
peak=   -3.268 closest distance to " CB  TYR A  15 " =    2.185
peak=   -3.267 closest distance to " O   HOH Z 311 " =    3.734
peak=   -3.262 closest distance to " O   HOH Z  60 " =    1.926
peak=   -3.260 closest distance to " CB  GLN A  11 " =    1.754
peak=   -3.259 closest distance to " O   SER A  95 " =    1.683
peak=   -3.253 closest distance to " NH2 ARG A  79 " =    1.572
peak=   -3.252 closest distance to " O   MET A  40 " =    2.717
peak=   -3.246 closest distance to " N   MET A 188 " =    1.878
peak=   -3.246 closest distance to " C   LEU A 143 " =    1.036
peak=   -3.240 closest distance to " O   HOH Z 134 " =    2.888
peak=   -3.239 closest distance to " O   HOH Z 191 " =    5.436
peak=   -3.236 closest distance to " OG  SER A 206 " =    1.684
peak=   -3.233 closest distance to " CG1 VAL A 112 " =    2.861
peak=   -3.231 closest distance to " CB  ALA A  10 " =    2.258
peak=   -3.230 closest distance to " O   HOH Z 339 " =    1.767
peak=   -3.230 closest distance to " O   GLN A 240 " =    2.138
peak=   -3.228 closest distance to " O   LEU A 167 " =    1.507
peak=   -3.222 closest distance to " O   HOH Z 298 " =    2.582
peak=   -3.220 closest distance to " CA  GLY A 203 " =    2.431
peak=   -3.219 closest distance to " O   HOH Z 198 " =    2.216
peak=   -3.219 closest distance to " CG  LEU A 228 " =    0.970
peak=   -3.218 closest distance to " O   HOH Z 193 " =    1.858
peak=   -3.216 closest distance to " O   HOH Z 283 " =    2.258
peak=   -3.208 closest distance to " CD2 TYR A 293 " =    2.039
peak=   -3.196 closest distance to " C   ASN A 285 " =    2.308
peak=   -3.196 closest distance to " N   ASP A 171 " =    2.277
peak=   -3.196 closest distance to " O   HOH Z 372 " =    2.246
peak=   -3.194 closest distance to " O   HOH Z 426 " =    1.679
peak=   -3.192 closest distance to " CE BMET A  47 " =    1.772
peak=   -3.186 closest distance to " CB  VAL A 296 " =    1.168
peak=   -3.180 closest distance to " C   THR A 279 " =    1.199
peak=   -3.175 closest distance to " CD2 PHE A  61 " =    2.488
peak=   -3.170 closest distance to " CA  SER A  62 " =    2.582
peak=   -3.169 closest distance to " OG  SER A  62 " =    1.617
peak=   -3.167 closest distance to " O   HOH Z 357 " =    1.929
peak=   -3.165 closest distance to " O   HOH Z 350 " =    1.953
peak=   -3.162 closest distance to " CA  GLY A 241 " =    2.336
peak=   -3.161 closest distance to " O   HOH Z 313 " =    1.155
peak=   -3.160 closest distance to " O   ALA A  51 " =    1.425
peak=   -3.158 closest distance to " O   HOH Z 262 " =    2.849
peak=   -3.139 closest distance to " O   HOH Z 175 " =    4.290
peak=   -3.138 closest distance to " CA  GLY A 133 " =    1.981
peak=   -3.124 closest distance to " O   ARG A  24 " =    1.997
peak=   -3.122 closest distance to " CB  LEU A  83 " =    2.325
peak=   -3.120 closest distance to " CG  GLU A  53 " =    1.587
peak=   -3.112 closest distance to " O   GLY A  80 " =    2.352
peak=   -3.102 closest distance to " OG  SER A  26 " =    1.219
peak=   -3.102 closest distance to " O   HOH Z   6 " =    1.649
peak=   -3.101 closest distance to " O   SER A  22 " =    2.231
peak=   -3.097 closest distance to " CD1 ILE A 239 " =    2.215
peak=   -3.083 closest distance to " O   HOH Z 149 " =    2.111
peak=   -3.074 closest distance to " CD1 ILE A 151 " =    2.316
peak=   -3.050 closest distance to " C   LEU A 222 " =    0.907
peak=   -3.046 closest distance to " O   HOH Z 389 " =    4.727
peak=   -3.046 closest distance to " O   HOH Z  90 " =    1.830
peak=   -3.041 closest distance to " O   HOH Z 397 " =    1.162
peak=   -3.025 closest distance to " O   HOH Z 244 " =    2.018
peak=   -3.016 closest distance to " O   PRO A 198 " =    1.299

================= 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    :  0.4133 0.3994   6.198896e+00   6.168202e+00
   1_bss:  0.4052 0.3882   6.194736e+00   6.151043e+00
   1_xyz:  0.2878 0.3073   5.933311e+00   5.981265e+00
   1_adp:  0.2132 0.2407   5.656557e+00   5.770492e+00
   1_occ:  0.2126 0.2406   5.654959e+00   5.770935e+00
   2_bss:  0.2070 0.2354   5.652885e+00   5.763841e+00
   2_xyz:  0.1487 0.1799   5.352219e+00   5.518340e+00
   2_adp:  0.1378 0.1713   5.288308e+00   5.467232e+00
   2_occ:  0.1376 0.1714   5.288026e+00   5.467392e+00
   3_bss:  0.1373 0.1714   5.287504e+00   5.466009e+00
   3_xyz:  0.1187 0.1561   5.173162e+00   5.388300e+00
   3_adp:  0.1148 0.1542   5.152047e+00   5.376248e+00
   3_occ:  0.1147 0.1543   5.151868e+00   5.376385e+00
   4_bss:  0.1147 0.1543   5.151868e+00   5.376385e+00
   4_xyz:  0.1123 0.1545   5.142341e+00   5.377769e+00
   4_adp:  0.1128 0.1544   5.143780e+00   5.376692e+00
   4_occ:  0.1127 0.1545   5.143901e+00   5.377127e+00
   5_bss:  0.1127 0.1545   5.143655e+00   5.376948e+00
   5_xyz:  0.1126 0.1548   5.143732e+00   5.378795e+00
   5_adp:  0.1120 0.1557   5.144535e+00   5.384851e+00
   5_occ:  0.1118 0.1556   5.143866e+00   5.384648e+00
   5_bss:  0.1120 0.1558   5.145982e+00   5.385252e+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:  0.345  20.005   7.340   8.732   8.257   0.000   0.000   0.000
   1_xyz:  0.345  20.005   7.340   8.732   8.257   0.000   0.000   0.000
   1_adp:  0.345  20.005   7.340   8.732   8.257   0.000   0.000   0.000
   1_occ:  0.345  20.005   7.340   8.732   8.257   0.000   0.000   0.000
   2_bss:  0.334  38.269   3.954   5.020   5.280   0.000   0.000   0.000
   2_xyz:  0.334  38.269   3.954   5.020   5.280   0.000   0.000   0.000
   2_adp:  0.334  38.269   3.954   5.020   5.280   0.000   0.000   0.000
   2_occ:  0.334  38.269   3.954   5.020   5.280   0.000   0.000   0.000
   3_bss:  0.330  43.608   3.177   4.030   4.693   0.000   0.000   0.000
   3_xyz:  0.330  43.608   3.177   4.030   4.693   0.000   0.000   0.000
   3_adp:  0.330  43.608   3.177   4.030   4.693   0.000   0.000   0.000
   3_occ:  0.330  43.608   3.177   4.030   4.693   0.000   0.000   0.000
   4_bss:  0.330  43.608   3.177   4.030   4.693   0.000   0.000   0.000
   4_xyz:  0.330  43.608   3.177   4.030   4.693   0.000   0.000   0.000
   4_adp:  0.330  43.608   3.177   4.030   4.693   0.000   0.000   0.000
   4_occ:  0.330  43.608   3.177   4.030   4.693   0.000   0.000   0.000
   5_bss:  0.325  42.944   3.144   3.865   4.678   0.000   0.000   0.000
   5_xyz:  0.325  42.944   3.144   3.865   4.678   0.000   0.000   0.000
   5_adp:  0.325  42.944   3.144   3.865   4.678   0.000   0.000   0.000
   5_occ:  0.325  42.944   3.144   3.865   4.678   0.000   0.000   0.000
   5_bss:  0.321  46.900  -0.742  -0.054   0.796  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  42.754 0.6122  0.6715    44496.648
   1_bss:  42.360 0.6147  0.8621    41864.201
   1_xyz:  32.501 0.7290  0.9927    25359.898
   1_adp:  23.269 0.8303  1.0745    14539.099
   1_occ:  23.263 0.8304  1.0739    14538.474
   2_bss:  23.018 0.8328  0.9523    14231.945
   2_xyz:  16.936 0.8900  0.9927     8292.910
   2_adp:  15.760 0.9005  1.0013     7512.151
   2_occ:  15.765 0.9004  1.0012     7512.201
   3_bss:  15.732 0.9007  0.9724     7489.544
   3_xyz:  14.057 0.9145  0.9780     6343.544
   3_adp:  13.781 0.9169  0.9782     6188.118
   3_occ:  13.780 0.9169  0.9781     6190.172
   4_bss:  13.780 0.9169  0.9781     6190.172
   4_xyz:  13.715 0.9176  0.9779     6200.883
   4_adp:  13.661 0.9181  0.9769     6193.984
   4_occ:  13.668 0.9181  0.9767     6200.002
   5_bss:  13.662 0.9181  0.9743     6195.789
   5_xyz:  13.697 0.9178  0.9741     6222.589
   5_adp:  13.847 0.9166  0.9709     6291.307
   5_occ:  13.836 0.9167  0.9707     6287.855
   5_bss:  13.870 0.9164  0.9722     6316.470
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.3748e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.3748e+01
   1_xyz:   1.442  0.011  0.099 17.674  0.006  4.122   1.0784e-01
   1_adp:   1.442  0.011  0.099 17.674  0.006  4.122   1.0784e-01
   1_occ:   1.442  0.011  0.099 17.674  0.006  4.122   1.0784e-01
   2_bss:   1.442  0.011  0.099 17.674  0.006  4.122   1.0784e-01
   2_xyz:   0.954  0.006  0.073 15.935  0.003  4.124   5.7372e-02
   2_adp:   0.954  0.006  0.073 15.935  0.003  4.124   5.7372e-02
   2_occ:   0.954  0.006  0.073 15.935  0.003  4.124   5.7372e-02
   3_bss:   0.954  0.006  0.073 15.935  0.003  4.124   5.7372e-02
   3_xyz:   1.019  0.007  0.084 15.667  0.004  4.131   6.2709e-02
   3_adp:   1.019  0.007  0.084 15.667  0.004  4.131   6.2709e-02
   3_occ:   1.019  0.007  0.084 15.667  0.004  4.131   6.2709e-02
   4_bss:   1.019  0.007  0.084 15.667  0.004  4.131   6.2709e-02
   4_xyz:   0.989  0.007  0.082 15.431  0.004  4.119   6.0633e-02
   4_adp:   0.989  0.007  0.082 15.431  0.004  4.119   6.0633e-02
   4_occ:   0.989  0.007  0.082 15.431  0.004  4.119   6.0633e-02
   5_bss:   0.989  0.007  0.082 15.431  0.004  4.119   6.0633e-02
   5_xyz:   0.971  0.007  0.080 15.270  0.003  4.120   5.8269e-02
   5_adp:   0.971  0.007  0.080 15.270  0.003  4.120   5.8269e-02
   5_occ:   0.971  0.007  0.080 15.270  0.003  4.120   5.8269e-02
   5_bss:   0.971  0.007  0.080 15.270  0.003  4.120   5.8269e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9688e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9688e+00
   1_xyz:  11.838  0.125  0.402 86.891  0.038  2.264   8.0418e-02
   1_adp:  11.838  0.125  0.402 86.891  0.038  2.264   8.0418e-02
   1_occ:  11.838  0.125  0.402 86.891  0.038  2.264   8.0418e-02
   2_bss:  11.838  0.125  0.402 86.891  0.038  2.264   8.0418e-02
   2_xyz:   6.845  0.056  0.389 81.857  0.029  2.357   3.9445e-02
   2_adp:   6.845  0.056  0.389 81.857  0.029  2.357   3.9445e-02
   2_occ:   6.845  0.056  0.389 81.857  0.029  2.357   3.9445e-02
   3_bss:   6.845  0.056  0.389 81.857  0.029  2.357   3.9445e-02
   3_xyz:   6.753  0.047  0.595 83.501  0.037  2.370   4.8889e-02
   3_adp:   6.753  0.047  0.595 83.501  0.037  2.370   4.8889e-02
   3_occ:   6.753  0.047  0.595 83.501  0.037  2.370   4.8889e-02
   4_bss:   6.753  0.047  0.595 83.501  0.037  2.370   4.8889e-02
   4_xyz:   7.017  0.044  0.565 82.429  0.039  2.365   3.8808e-02
   4_adp:   7.017  0.044  0.565 82.429  0.039  2.365   3.8808e-02
   4_occ:   7.017  0.044  0.565 82.429  0.039  2.365   3.8808e-02
   5_bss:   7.017  0.044  0.565 82.429  0.039  2.365   3.8808e-02
   5_xyz:   6.727  0.043  0.539 83.028  0.036  2.353   3.6510e-02
   5_adp:   6.727  0.043  0.539 83.028  0.036  2.353   3.6510e-02
   5_occ:   6.727  0.043  0.539 83.028  0.036  2.353   3.6510e-02
   5_bss:   6.727  0.043  0.539 83.028  0.036  2.353   3.6510e-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:  49.52   0.00   9.79  45.55   0.00   6.74  49.52   0.00  26.36
   1_occ:  49.52   0.00   9.79  45.55   0.00   6.74  49.52   0.00  26.36
   2_bss:  49.52   0.00   9.79  45.55   0.00   6.74  49.52   0.00  26.36
   2_xyz:  49.52   0.00   9.79  45.55   0.00   6.74  49.52   0.00  26.36
   2_adp:  66.34   0.00  10.40  66.34   0.00   6.77  52.17   0.00  30.17
   2_occ:  66.34   0.00  10.40  66.34   0.00   6.77  52.17   0.00  30.17
   3_bss:  66.34   0.00  10.40  66.34   0.00   6.77  52.17   0.00  30.17
   3_xyz:  66.34   0.00  10.40  66.34   0.00   6.77  52.17   0.00  30.17
   3_adp:  68.63   0.00  10.86  68.63   0.00   6.89  63.31   0.55  32.47
   3_occ:  68.63   0.00  10.86  68.63   0.00   6.89  63.31   0.55  32.47
   4_bss:  68.63   0.00  10.86  68.63   0.00   6.89  63.31   0.55  32.47
   4_xyz:  68.63   0.00  10.86  68.63   0.00   6.89  63.31   0.55  32.47
   4_adp:  68.94   0.00  10.60  68.94   0.00   6.79  63.19   0.70  31.33
   4_occ:  68.94   0.00  10.60  68.94   0.00   6.79  63.19   0.70  31.33
   5_bss:  68.94   0.00  10.60  68.94   0.00   6.79  63.19   0.70  31.33
   5_xyz:  68.94   0.00  10.60  68.94   0.00   6.79  63.19   0.70  31.33
   5_adp:  76.59   0.00  10.66  76.59   0.00   6.81  63.61   0.45  31.67
   5_occ:  76.59   0.00  10.66  76.59   0.00   6.81  63.61   0.45  31.67
   5_bss:  80.55   3.96  14.62  80.55   3.96  10.76  67.56   4.41  35.62
------------------------------------------------------------------------
 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:    1.168    0.011    0.398
   1_adp:    1.168    0.011    0.398
   1_occ:    1.168    0.011    0.398
   2_bss:    1.168    0.011    0.398
   2_xyz:    1.496    0.024    0.470
   2_adp:    1.496    0.024    0.470
   2_occ:    1.496    0.024    0.470
   3_bss:    1.496    0.024    0.470
   3_xyz:    1.436    0.045    0.497
   3_adp:    1.436    0.045    0.497
   3_occ:    1.436    0.045    0.497
   4_bss:    1.436    0.045    0.497
   4_xyz:    1.524    0.038    0.506
   4_adp:    1.524    0.038    0.506
   4_occ:    1.524    0.038    0.506
   5_bss:    1.524    0.038    0.506
   5_xyz:    1.566    0.032    0.513
   5_adp:    1.566    0.032    0.513
   5_occ:    1.566    0.032    0.513
   5_bss:    1.566    0.032    0.513
------------------------------------------------------------------------

CPU time actual refinement: 322.30


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_555/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_555/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_555/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_555/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_555/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 322.15 
  Macro-tasks:
    bulk solvent and scale       = 40.62  
    individual site refinement   = 135.72 
    weights calculation          = 31.67  
    collect and process          = 6.53   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 214.64 
  Micro-tasks:
    mask                            = 1.70   
    f_calc                          = 96.60  
    alpha_beta                      = 7.92   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 109.44 
    fmodel                         = 7.11   
    r_factors                      = 0.17   
    phase_errors                   = 11.01  
    foms                           = 0.26   
    TOTAL for micro-tasks          = 235.36 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.471 micro seconds
Total CPU time: 5.59 minutes
from_scatterers_fft:    656 calls, 96.38 s
gradients_fft:          602 calls, 95.19 s

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

# Date 2008-01-16 Time 01:51:48 PST -0800 (1200477108.90 s)
Start R-work = 0.4133, R-free = 0.3994 (no bulk solvent and anisotropic scale)
Final R-work = 0.1296, R-free = 0.1718 (no bulk solvent and anisotropic scale)

Start R-work = 0.4052, R-free = 0.3882
Final R-work = 0.1120, R-free = 0.1558