# Date 2008-01-16 Time 01:46:14 PST -0800 (1200476774.26 s)
#phil __OFF__

Command line arguments: "../556.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 18323
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 556

-------------------------------------------------------------------------------
  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, 86.822, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.26, per 1000 atoms: 1.15


================================== 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, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9592 1.99059
Completeness in resolution range: 0.968123
Completeness with d_max=infinity: 0.96507

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9592
                             d_min =   1.9906

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, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9592 1.99059
Completeness in resolution range: 0.968123
Completeness with d_max=infinity: 0.96507

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9596 -  4.2587 [2131/2158]  1917   214  10.0%
  bin  2:  4.2587 -  3.3932 [2036/2052]  1833   203  10.0%
  bin  3:  3.3932 -  2.9681 [2027/2046]  1825   202  10.0%
  bin  4:  2.9681 -  2.6985 [1987/2017]  1784   203  10.2%
  bin  5:  2.6985 -  2.5060 [1988/2007]  1792   196   9.9%
  bin  6:  2.5060 -  2.3589 [1976/2001]  1781   195   9.9%
  bin  7:  2.3589 -  2.2411 [1969/2003]  1774   195   9.9%
  bin  8:  2.2411 -  2.1439 [1941/1971]  1743   198  10.2%
  bin  9:  2.1439 -  2.0616 [1945/1987]  1751   194  10.0%
  bin 10:  2.0616 -  1.9906 [1589/1992]  1430   159  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_556/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: 13
        2.42 -     3.04: 2197
        3.04 -     3.66: 4635
        3.66 -     4.28: 9017
        4.28 -     4.90: 12329
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " OE1 GLN A  55 " - " O   HOH Z 403 "  2.150 3.040 -x+1,y-1/2,-z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z  42 " - " O   HOH Z 183 "  2.231 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  2.311 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28186 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_556/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_556/model_refine_001.geo

CPU time processing inputs: 9.20


============================ 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 86.82195 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4175   r_free= 0.4024   ksol= 0.00   Bsol= 0.00   scale= 0.829    |
|                                                                             |
| 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:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.205086                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9596 -  4.7496 0.99   1383  153 0.3493 0.3272      6.4934      6.4329|
|  2:  4.7496 -  3.7901 0.99   1319  150 0.3066 0.3229      6.5816      6.6514|
|  3:  3.7901 -  3.3170 0.99   1313  144 0.3578 0.3294      6.5217      6.4976|
|  4:  3.3170 -  3.0164 0.99   1294  139 0.3912 0.3570      6.4178      6.3132|
|  5:  3.0164 -  2.8017 0.99   1282  143 0.4320 0.4389      6.2921      6.3313|
|  6:  2.8017 -  2.6375 0.99   1279  145 0.4380 0.5015      6.2172      6.1806|
|  7:  2.6375 -  2.5060 0.99   1281  144 0.4567 0.4399      6.1862      6.1287|
|  8:  2.5060 -  2.3974 0.98   1280  139 0.4735 0.4282      6.1394       6.097|
|  9:  2.3974 -  2.3054 0.98   1246  140 0.4702 0.4699      6.0727      6.0681|
| 10:  2.3054 -  2.2262 0.99   1267  139 0.4834 0.4337      6.1093      5.9832|
| 11:  2.2262 -  2.1568 0.99   1267  143 0.4784 0.3989       6.002      5.9732|
| 12:  2.1568 -  2.0953 0.97   1244  134 0.4931 0.4760       5.955      6.0008|
| 13:  2.0953 -  2.0403 0.99   1281  143 0.4782 0.4957      5.8687      5.8455|
| 14:  2.0403 -  1.9906 0.72    894  103 0.4979 0.4379      5.8476      5.7064|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9596 -  4.7496  1383   153  0.75  30.05   0.82     0.76      55136.02|
|  2:  4.7496 -  3.7901  1319   150  0.79  26.85   0.92     0.83      66484.23|
|  3:  3.7901 -  3.3170  1313   144  0.74  32.24   0.88     0.81      67675.55|
|  4:  3.3170 -  3.0164  1294   139  0.69  36.70   0.84     0.73      59636.91|
|  5:  3.0164 -  2.8017  1282   143  0.59  44.73   0.79     0.66      55398.25|
|  6:  2.8017 -  2.6375  1279   145  0.57  46.80   0.77     0.62      51518.03|
|  7:  2.6375 -  2.5060  1281   144  0.53  49.26   0.77     0.60      48432.58|
|  8:  2.5060 -  2.3974  1280   139  0.54  48.76   0.78     0.61      41954.27|
|  9:  2.3974 -  2.3054  1246   140  0.57  46.42   0.74     0.64      36281.56|
| 10:  2.3054 -  2.2262  1267   139  0.58  45.55   0.78     0.65      32452.61|
| 11:  2.2262 -  2.1568  1267   143  0.55  48.05   0.77     0.64      31384.96|
| 12:  2.1568 -  2.0953  1244   134  0.50  52.09   0.79     0.60      31759.53|
| 13:  2.0953 -  2.0403  1281   143  0.49  53.04   0.76     0.56      28339.96|
| 14:  2.0403 -  1.9906   894   103  0.52  50.53   0.74     0.55      22047.10|
|alpha:            min =        0.55 max =            0.83 mean =         0.67|
|beta:             min =    22047.10 max =        67675.55 mean =     45617.76|
|figures of merit: min =        0.00 max =            1.00 mean =         0.61|
|phase err.(work): min =        0.00 max =           90.00 mean =        43.33|
|phase err.(test): min =        0.00 max =           89.76 mean =        43.54|
|-----------------------------------------------------------------------------|

============================== 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 = 6.373992              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 73.138   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.523409              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.366   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       22 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      163 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      687 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1491 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2622 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3914 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5033 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6575 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7735 |
|-----------------------------------------------------------------------------|
|-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 |       53.835 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.093    4.900  1.196 |       1.683 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.956)------------------------------------------|
|    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 = 11.956)------------------------------------------|
|    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 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4267   r_free= 0.4052   ksol= 0.00   Bsol= 0.00   scale= 0.798    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.214762                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4099   r_free= 0.3879   ksol= 0.34   Bsol= 20.01   scale= 1.030   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.26,8.62,8.83,0.00,0.00,0.00); trace/3= 8.24                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.200584                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.024291              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 75.104   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.494138              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 74.623   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4099      final r-factor (work) = 0.2925          |
| start r-factor (free) = 0.3879      final r-factor (free) = 0.3112          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 72.5889 = 6.02 * 0.50 * 6.2260 + 1.00 * 53.8352                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.2175 = 6.02 * 0.50 * 6.0115 + 1.00 * 0.1099                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2925      final r-factor (work) = 0.2208          |
| start r-factor (free) = 0.3112      final r-factor (free) = 0.2500          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9853 = 0.49 * 1.00 * 6.0115 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8691 = 0.49 * 1.00 * 5.7850 + 1.00 * 0.0105                               |
|-----------------------------------------------------------------------------|
| number of iterations = 19      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.956)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    49.36   9.99     None  None   None       |
|    all(noH): 2823   0      0.00    49.36   9.99     None  None   None       |
|    Sol.    : 438    0      0.00    49.14   26.46    None  None   None       |
|    Mac.    : 2385   0      0.00    49.36   6.96     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 -   4.936: 1123   |   5:    24.682 -  29.618:   98        |
|      1:     4.936 -   9.873:  791   |   6:    29.618 -  34.554:  101        |
|      2:     9.873 -  14.809:  318   |   7:    34.554 -  39.490:   82        |
|      3:    14.809 -  19.745:  155   |   8:    39.490 -  44.427:   36        |
|      4:    19.745 -  24.682:   99   |   9:    44.427 -  49.363:   20        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2208 r_free = 0.2500             target_work(ml) = 5.687         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2201 r_free = 0.2502             target_work(ml) = 5.685         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2201   r_free= 0.2502   ksol= 0.34   Bsol= 20.01   scale= 1.089   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.26,8.62,8.83,0.00,0.00,0.00); trace/3= 8.24                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.684939                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2140   r_free= 0.2454   ksol= 0.33   Bsol= 39.93   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.56,4.82,5.36,0.00,0.00,0.00); trace/3= 4.58                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.683931                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.694639              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.270   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.247468              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 115.806  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2140      final r-factor (work) = 0.1488          |
| start r-factor (free) = 0.2454      final r-factor (free) = 0.1815          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9378 = 2.69 * 0.50 * 5.8102 + 1.00 * 0.1095                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.4799 = 2.69 * 0.50 * 5.5065 + 1.00 * 0.0609                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1488      final r-factor (work) = 0.1369          |
| start r-factor (free) = 0.1815      final r-factor (free) = 0.1709          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3781 = 0.25 * 1.00 * 5.5065 + 1.00 * 0.0155                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3521 = 0.25 * 1.00 * 5.3108 + 1.00 * 0.0378                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.956)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    71.26   10.53    None  None   None       |
|    all(noH): 2823   0      0.00    71.26   10.53    None  None   None       |
|    Sol.    : 438    0      0.71    53.69   30.32    None  None   None       |
|    Mac.    : 2385   0      0.00    71.26   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 -   7.126: 1639   |   5:    35.630 -  42.756:  124        |
|      1:     7.126 -  14.252:  578   |   6:    42.756 -  49.882:   65        |
|      2:    14.252 -  21.378:  170   |   7:    49.882 -  57.007:   11        |
|      3:    21.378 -  28.504:  118   |   8:    57.007 -  64.133:    0        |
|      4:    28.504 -  35.630:  117   |   9:    64.133 -  71.259:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1369 r_free = 0.1709             target_work(ml) = 5.285         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1368 r_free = 0.1709             target_work(ml) = 5.285         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1368   r_free= 0.1709   ksol= 0.33   Bsol= 39.93   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.56,4.82,5.36,0.00,0.00,0.00); trace/3= 4.58                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.284619                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1365   r_free= 0.1717   ksol= 0.32   Bsol= 39.93   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.04,3.95,4.78,0.00,0.00,0.00); trace/3= 3.92                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.285443                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.623226              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 115.686  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.584128              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 93.530   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1365      final r-factor (work) = 0.1158          |
| start r-factor (free) = 0.1717      final r-factor (free) = 0.1565          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.6849 = 3.62 * 0.50 * 5.3124 + 1.00 * 0.0609                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.5130 = 3.62 * 0.50 * 5.2080 + 1.00 * 0.0781                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1158      final r-factor (work) = 0.1116          |
| start r-factor (free) = 0.1565      final r-factor (free) = 0.1546          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0571 = 0.58 * 1.00 * 5.2080 + 1.00 * 0.0150                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0176 = 0.58 * 1.00 * 5.1438 + 1.00 * 0.0130                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.956)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    72.24   11.09    None  None   None       |
|    all(noH): 2823   0      0.00    72.24   11.09    None  None   None       |
|    Sol.    : 438    0      0.06    66.90   33.13    None  None   None       |
|    Mac.    : 2385   0      0.00    72.24   7.04     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 -   7.224: 1662   |   5:    36.118 -  43.341:   82        |
|      1:     7.224 -  14.447:  547   |   6:    43.341 -  50.565:   71        |
|      2:    14.447 -  21.671:  168   |   7:    50.565 -  57.789:   53        |
|      3:    21.671 -  28.894:  101   |   8:    57.789 -  65.012:   18        |
|      4:    28.894 -  36.118:  116   |   9:    65.012 -  72.236:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1116 r_free = 0.1546             target_work(ml) = 5.139         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1115 r_free = 0.1546             target_work(ml) = 5.138         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1115   r_free= 0.1546   ksol= 0.32   Bsol= 39.93   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.04,3.95,4.78,0.00,0.00,0.00); trace/3= 3.92                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.138227                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1115   r_free= 0.1546   ksol= 0.32   Bsol= 39.93   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.09,3.82,4.78,0.00,0.00,0.00); trace/3= 3.90                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.137926                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.463226              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 148.811  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.280675              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 100.963  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1115      final r-factor (work) = 0.1085          |
| start r-factor (free) = 0.1546      final r-factor (free) = 0.1548          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.9843 = 3.46 * 0.50 * 5.1433 + 1.00 * 0.0781                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.9580 = 3.46 * 0.50 * 5.1270 + 1.00 * 0.0800                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1085      final r-factor (work) = 0.1091          |
| start r-factor (free) = 0.1548      final r-factor (free) = 0.1550          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4518 = 0.28 * 1.00 * 5.1270 + 1.00 * 0.0127                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4560 = 0.28 * 1.00 * 5.1275 + 1.00 * 0.0169                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.956)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    73.28   10.79    None  None   None       |
|    all(noH): 2823   0      0.00    73.28   10.79    None  None   None       |
|    Sol.    : 438    0      0.65    65.81   31.82    None  None   None       |
|    Mac.    : 2385   0      0.00    73.28   6.93     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 -   7.328: 1692   |   5:    36.639 -  43.967:   83        |
|      1:     7.328 -  14.656:  538   |   6:    43.967 -  51.295:   70        |
|      2:    14.656 -  21.983:  158   |   7:    51.295 -  58.622:   33        |
|      3:    21.983 -  29.311:  108   |   8:    58.622 -  65.950:   13        |
|      4:    29.311 -  36.639:  125   |   9:    65.950 -  73.278:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1091 r_free = 0.1550             target_work(ml) = 5.128         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1089 r_free = 0.1551             target_work(ml) = 5.127         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1089   r_free= 0.1551   ksol= 0.32   Bsol= 39.93   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.09,3.82,4.78,0.00,0.00,0.00); trace/3= 3.90                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.127270                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1090   r_free= 0.1550   ksol= 0.32   Bsol= 39.93   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.12,3.81,4.81,0.00,0.00,0.00); trace/3= 3.91                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.127751                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.817467              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 165.570  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.518013              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 101.541  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1090      final r-factor (work) = 0.1120          |
| start r-factor (free) = 0.1550      final r-factor (free) = 0.1561          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7396 = 1.82 * 0.50 * 5.1275 + 1.00 * 0.0800                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7323 = 1.82 * 0.50 * 5.1401 + 1.00 * 0.0613                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1120      final r-factor (work) = 0.1114          |
| start r-factor (free) = 0.1561      final r-factor (free) = 0.1562          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6938 = 0.52 * 1.00 * 5.1401 + 1.00 * 0.0311                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6773 = 0.52 * 1.00 * 5.1424 + 1.00 * 0.0135                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.956)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.37   10.96    None  None   None       |
|    all(noH): 2823   0      0.00    77.37   10.96    None  None   None       |
|    Sol.    : 438    0      0.59    66.32   32.61    None  None   None       |
|    Mac.    : 2385   0      0.00    77.37   6.98     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 -   7.737: 1734   |   5:    38.685 -  46.422:  100        |
|      1:     7.737 -  15.474:  509   |   6:    46.422 -  54.159:   63        |
|      2:    15.474 -  23.211:  156   |   7:    54.159 -  61.896:   20        |
|      3:    23.211 -  30.948:  109   |   8:    61.896 -  69.633:   11        |
|      4:    30.948 -  38.685:  118   |   9:    69.633 -  77.370:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1114 r_free = 0.1562             target_work(ml) = 5.146         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1114 r_free = 0.1562             target_work(ml) = 5.145         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1114   r_free= 0.1562   ksol= 0.32   Bsol= 39.93   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.12,3.81,4.81,0.00,0.00,0.00); trace/3= 3.91                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.145434                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9596 -  4.7496 0.99   1383  153 0.1004 0.1272      5.3919      5.5077|
|  2:  4.7496 -  3.7901 0.99   1319  150 0.0856 0.1100      5.4367      5.6399|
|  3:  3.7901 -  3.3170 0.99   1313  144 0.1046 0.1478       5.467      5.8318|
|  4:  3.3170 -  3.0164 0.99   1294  139 0.1184 0.1483       5.432      5.5632|
|  5:  3.0164 -  2.8017 0.99   1282  143 0.1319 0.1676      5.3229      5.5295|
|  6:  2.8017 -  2.6375 0.99   1279  145 0.1188 0.1913      5.2042      5.4797|
|  7:  2.6375 -  2.5060 0.99   1281  144 0.1245 0.1641      5.1724      5.3624|
|  8:  2.5060 -  2.3974 0.98   1280  139 0.1166 0.1757      5.0886      5.3748|
|  9:  2.3974 -  2.3054 0.98   1246  140 0.1185 0.1911      5.0442      5.3283|
| 10:  2.3054 -  2.2262 0.99   1267  139 0.1119 0.1585      4.9839      5.1853|
| 11:  2.2262 -  2.1568 0.99   1267  143 0.1153 0.1756      4.9413      5.2601|
| 12:  2.1568 -  2.0953 0.97   1244  134 0.1133 0.1665      4.8779      5.2022|
| 13:  2.0953 -  2.0403 0.99   1281  143 0.1122 0.1664      4.7943      5.0292|
| 14:  2.0403 -  1.9906 0.72    894  103 0.1036 0.1874      4.6864      4.9935|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9596 -  4.7496  1383   153  0.94   9.17   0.98     0.95       7229.98|
|  2:  4.7496 -  3.7901  1319   150  0.95   7.83   1.01     1.00       8829.39|
|  3:  3.7901 -  3.3170  1313   144  0.94  10.83   1.02     1.02      10018.69|
|  4:  3.3170 -  3.0164  1294   139  0.93  12.91   1.00     0.99       9763.54|
|  5:  3.0164 -  2.8017  1282   143  0.90  15.61   0.99     0.96       8110.94|
|  6:  2.8017 -  2.6375  1279   145  0.90  15.76   0.98     0.95       6995.46|
|  7:  2.6375 -  2.5060  1281   144  0.91  15.54   0.98     0.95       6273.24|
|  8:  2.5060 -  2.3974  1280   139  0.91  15.13   0.99     0.97       5500.03|
|  9:  2.3974 -  2.3054  1246   140  0.91  15.91   1.01     0.98       5268.49|
| 10:  2.3054 -  2.2262  1267   139  0.90  16.05   1.00     0.95       4597.24|
| 11:  2.2262 -  2.1568  1267   143  0.90  16.14   1.00     0.96       4391.34|
| 12:  2.1568 -  2.0953  1244   134  0.91  15.46   1.01     1.00       3941.46|
| 13:  2.0953 -  2.0403  1281   143  0.91  15.67   1.00     0.98       3365.49|
| 14:  2.0403 -  1.9906   894   103  0.91  14.85   0.98     0.93       2671.90|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2671.90 max =        10018.69 mean =      6319.41|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.99 mean =        13.99|
|phase err.(test): min =        0.00 max =           88.59 mean =        13.53|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1113   r_free= 0.1561   ksol= 0.32   Bsol= 46.51   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.78,-0.13,0.91,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.145196                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1113   r_free= 0.1561   ksol= 0.32   Bsol= 46.51   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.78,-0.13,0.91,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.145196                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9596 -  4.7496 0.99   1383  153 0.1005 0.1274       5.393      5.5088|
|  2:  4.7496 -  3.7901 0.99   1319  150 0.0858 0.1103      5.4386      5.6425|
|  3:  3.7901 -  3.3170 0.99   1313  144 0.1048 0.1478      5.4679      5.8319|
|  4:  3.3170 -  3.0164 0.99   1294  139 0.1183 0.1481      5.4312      5.5623|
|  5:  3.0164 -  2.8017 0.99   1282  143 0.1319 0.1674      5.3214       5.528|
|  6:  2.8017 -  2.6375 0.99   1279  145 0.1186 0.1909      5.2029       5.478|
|  7:  2.6375 -  2.5060 0.99   1281  144 0.1244 0.1641      5.1714      5.3618|
|  8:  2.5060 -  2.3974 0.98   1280  139 0.1165 0.1756       5.088      5.3744|
|  9:  2.3974 -  2.3054 0.98   1246  140 0.1185 0.1911      5.0438      5.3283|
| 10:  2.3054 -  2.2262 0.99   1267  139 0.1119 0.1585      4.9836      5.1849|
| 11:  2.2262 -  2.1568 0.99   1267  143 0.1152 0.1755      4.9409      5.2596|
| 12:  2.1568 -  2.0953 0.97   1244  134 0.1133 0.1664      4.8775      5.2018|
| 13:  2.0953 -  2.0403 0.99   1281  143 0.1122 0.1663      4.7939      5.0288|
| 14:  2.0403 -  1.9906 0.72    894  103 0.1036 0.1872      4.6857      4.9925|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9596 -  4.7496  1383   153  0.94   9.19   0.98     0.95       7252.49|
|  2:  4.7496 -  3.7901  1319   150  0.95   7.85   1.01     1.00       8859.02|
|  3:  3.7901 -  3.3170  1313   144  0.94  10.84   1.02     1.02      10042.65|
|  4:  3.3170 -  3.0164  1294   139  0.93  12.90   1.00     0.99       9746.77|
|  5:  3.0164 -  2.8017  1282   143  0.90  15.59   0.99     0.96       8086.49|
|  6:  2.8017 -  2.6375  1279   145  0.90  15.73   0.98     0.95       6975.88|
|  7:  2.6375 -  2.5060  1281   144  0.91  15.52   0.98     0.95       6258.84|
|  8:  2.5060 -  2.3974  1280   139  0.91  15.12   0.99     0.97       5492.76|
|  9:  2.3974 -  2.3054  1246   140  0.91  15.90   1.01     0.98       5264.10|
| 10:  2.3054 -  2.2262  1267   139  0.90  16.05   1.00     0.95       4594.55|
| 11:  2.2262 -  2.1568  1267   143  0.90  16.13   1.00     0.96       4387.29|
| 12:  2.1568 -  2.0953  1244   134  0.91  15.44   1.01     1.00       3936.89|
| 13:  2.0953 -  2.0403  1281   143  0.91  15.66   1.00     0.98       3360.33|
| 14:  2.0403 -  1.9906   894   103  0.91  14.83   0.98     0.94       2666.26|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2666.26 max =        10042.65 mean =      6317.39|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.98 mean =        13.98|
|phase err.(test): min =        0.00 max =           88.53 mean =        13.53|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.956)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.92    81.29   14.88    None  None   None       |
|    all(noH): 2823   0      3.92    81.29   14.88    None  None   None       |
|    Sol.    : 438    0      4.51    70.24   36.53    None  None   None       |
|    Mac.    : 2385   0      3.92    81.29   10.90    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     3.920 -  11.657: 1734   |   5:    42.605 -  50.342:  100        |
|      1:    11.657 -  19.394:  509   |   6:    50.342 -  58.079:   63        |
|      2:    19.394 -  27.131:  156   |   7:    58.079 -  65.816:   20        |
|      3:    27.131 -  34.868:  109   |   8:    65.816 -  73.553:   11        |
|      4:    34.868 -  42.605:  118   |   9:    73.553 -  81.290:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 313         
Filter by distance & map next to the model:
   mapped sites are within: 0.267 - 4.266
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 303 from: 313
   mapped sites are within: 0.710 - 4.266

peak=    9.716 closest distance to " CG2 VAL A 230 " =    1.221
peak=    6.552 closest distance to " CG  LEU A   5 " =    1.213
peak=    6.393 closest distance to " CG2 VAL A 296 " =    1.082
peak=    6.033 closest distance to " NH2 ARG A  56 " =    2.247
peak=    5.818 closest distance to " CG  LEU A 228 " =    1.169
peak=    5.704 closest distance to " CG  PRO A  54 " =    1.287
peak=    5.627 closest distance to " CB  VAL A 296 " =    1.126
peak=    5.606 closest distance to " CB  VAL A 230 " =    1.195
peak=    5.348 closest distance to " CD2 LEU A   5 " =    1.178
peak=    5.313 closest distance to " CB  GLN A 223 " =    1.433
peak=    5.292 closest distance to " CB  ARG A 275 " =    0.950
peak=    5.006 closest distance to " CB  PRO A  54 " =    0.949
peak=    4.908 closest distance to " O   HOH Z 126 " =    1.858
peak=    4.863 closest distance to " NE2 GLN A  11 " =    1.093
peak=    4.838 closest distance to " O   HOH Z 142 " =    1.673
peak=    4.768 closest distance to " CB  GLN A 183 " =    1.281
peak=    4.680 closest distance to " O   HOH Z 209 " =    2.276
peak=    4.648 closest distance to " CB  SER A  63 " =    1.264
peak=    4.622 closest distance to " O   HOH Z 272 " =    1.873
peak=    4.507 closest distance to " CG  PRO A 213 " =    1.201
peak=    4.506 closest distance to " CZ  PHE A 218 " =    1.134
peak=    4.497 closest distance to " C   PRO A 198 " =    1.503
peak=    4.457 closest distance to " CG  PRO A 243 " =    1.092
peak=    4.387 closest distance to " CB  ARG A  79 " =    1.435
peak=    4.355 closest distance to " CG  PRO A 198 " =    1.229
peak=    4.337 closest distance to " O   HOH Z  61 " =    1.645
peak=    4.331 closest distance to " O   HOH Z  43 " =    2.048
peak=    4.328 closest distance to " CA  TYR A  30 " =    0.940
peak=    4.319 closest distance to " O   HOH Z 232 " =    2.389
peak=    4.312 closest distance to " O   HOH Z 369 " =    2.253
peak=    4.305 closest distance to " CB  GLU A 152 " =    1.183
peak=    4.301 closest distance to " O   HOH Z 423 " =    1.821
peak=    4.299 closest distance to " O   HOH Z 346 " =    1.659
peak=    4.282 closest distance to " O   SER A  87 " =    2.248
peak=    4.274 closest distance to " O   HOH Z 427 " =    2.989
peak=    4.225 closest distance to " O   HOH Z 316 " =    3.103
peak=    4.219 closest distance to " O   HOH Z 402 " =    1.439
peak=    4.177 closest distance to " O   HOH Z 234 " =    3.618
peak=    4.170 closest distance to " O   HOH Z 236 " =    1.962
peak=    4.159 closest distance to " O   HOH Z 368 " =    2.202
peak=    4.150 closest distance to " CB  ASN A 148 " =    1.404
peak=    4.130 closest distance to " CB  VAL A 265 " =    1.276
peak=    4.128 closest distance to " O   HOH Z 298 " =    1.777
peak=    4.107 closest distance to " ND2 ASN A 187 " =    1.493
peak=    4.094 closest distance to " O   HOH Z 248 " =    1.619
peak=    4.093 closest distance to " O   HOH Z 126 " =    2.110
peak=    4.072 closest distance to " O   HOH Z 265 " =    2.284
peak=    4.072 closest distance to " O   HOH Z 193 " =    1.765
peak=    4.026 closest distance to " CB  ARG A 190 " =    1.656
peak=    4.026 closest distance to " O   HOH Z  78 " =    1.650
peak=    4.021 closest distance to " O   HOH Z 189 " =    2.724
peak=    4.021 closest distance to " O   HOH Z 158 " =    3.197
peak=    4.019 closest distance to " CB  SER A   3 " =    1.242
peak=    4.006 closest distance to " O   HOH Z  66 " =    2.299
peak=    3.996 closest distance to " O   HOH Z 214 " =    2.159
peak=    3.990 closest distance to " O   HOH Z 203 " =    1.675
peak=    3.975 closest distance to " CB  GLU A 277 " =    3.601
peak=    3.972 closest distance to " OD1 ASN A  69 " =    2.572
peak=    3.967 closest distance to " O   HOH Z 261 " =    1.789
peak=    3.965 closest distance to " CB  GLU A 128 " =    1.026
peak=    3.941 closest distance to " CD2 LEU A 228 " =    1.150
peak=    3.928 closest distance to " O   HOH Z 147 " =    1.802
peak=    3.922 closest distance to " O   HOH Z 303 " =    2.087
peak=    3.901 closest distance to " O   HOH Z  40 " =    1.693
peak=    3.861 closest distance to " CG1BVAL A  72 " =    1.638
peak=    3.856 closest distance to " CB  TRP A 266 " =    0.974
peak=    3.851 closest distance to " CB  VAL A 202 " =    1.507
peak=    3.850 closest distance to " O   HOH Z 261 " =    2.267
peak=    3.849 closest distance to " O   HOH Z  59 " =    2.139
peak=    3.844 closest distance to " CB  TRP A 179 " =    1.429
peak=    3.824 closest distance to " CG1 VAL A 296 " =    1.177
peak=    3.822 closest distance to " CB  ASP A 140 " =    1.024
peak=    3.807 closest distance to " CG1 ILE A  49 " =    1.511
peak=    3.802 closest distance to " O   HOH Z 280 " =    2.941
peak=    3.801 closest distance to " CB  ASN A  39 " =    0.899
peak=    3.790 closest distance to " O   HOH Z 403 " =    1.640
peak=    3.767 closest distance to " CA  ARG A  36 " =    1.039
peak=    3.761 closest distance to " O   HOH Z 250 " =    1.364
peak=    3.758 closest distance to " CG  MET A 185 " =    1.197
peak=    3.757 closest distance to " CA  ASN A 215 " =    1.137
peak=    3.752 closest distance to " CE1 TYR A 186 " =    1.390
peak=    3.745 closest distance to " O   HOH Z  15 " =    2.145
peak=    3.738 closest distance to " N   ASN A  39 " =    1.198
peak=    3.738 closest distance to " CG  ARG A  66 " =    2.524
peak=    3.736 closest distance to " ND2 ASN A 249 " =    1.920
peak=    3.731 closest distance to " CB  THR A  31 " =    1.521
peak=    3.725 closest distance to " CB  ARG A  79 " =    0.902
peak=    3.724 closest distance to " CG2 VAL A 257 " =    0.835
peak=    3.723 closest distance to " O   HOH Z  97 " =    1.996
peak=    3.719 closest distance to " O   TRP A 274 " =    1.835
peak=    3.708 closest distance to " CD  ARG A 269 " =    0.988
peak=    3.704 closest distance to " CB  ASN A 142 " =    1.138
peak=    3.694 closest distance to " CA  ALA A  51 " =    0.920
peak=    3.687 closest distance to " O   HOH Z  97 " =    2.444
peak=    3.683 closest distance to " CA  THR A 264 " =    0.760
peak=    3.683 closest distance to " O   HOH Z 417 " =    3.097
peak=    3.679 closest distance to " CD2 TRP A 179 " =    1.393
peak=    3.658 closest distance to " CA  ARG A 195 " =    1.238
peak=    3.658 closest distance to " CA  ALA A  21 " =    1.100
peak=    3.654 closest distance to " O   HOH Z 128 " =    2.167
peak=    3.648 closest distance to " O   HOH Z 245 " =    1.407
peak=    3.646 closest distance to " CD  LYS A 166 " =    1.314
peak=    3.645 closest distance to " O   HOH Z 411 " =    3.804
peak=    3.643 closest distance to " CG1 ILE A  33 " =    1.305
peak=    3.639 closest distance to " O   HOH Z 344 " =    3.015
peak=    3.637 closest distance to " O   HOH Z 371 " =    3.151
peak=    3.629 closest distance to " OG BSER A 164 " =    2.183
peak=    3.624 closest distance to " O   HOH Z 128 " =    2.071
peak=    3.622 closest distance to " O   HOH Z  21 " =    1.778
peak=    3.618 closest distance to " O   HOH Z 273 " =    2.760
peak=    3.612 closest distance to " O   HOH Z 313 " =    1.750
peak=    3.610 closest distance to " O   HOH Z 261 " =    1.920
peak=    3.610 closest distance to " O   HOH Z 126 " =    1.617
peak=    3.609 closest distance to " O   HOH Z  19 " =    2.239
peak=    3.603 closest distance to " CB AVAL A  41 " =    1.050
peak=    3.594 closest distance to " CB  SER A  26 " =    1.760
peak=    3.590 closest distance to " CB  ALA A   9 " =    1.582
peak=    3.589 closest distance to " NH2 ARG A 156 " =    1.104
peak=    3.587 closest distance to " CA  LYS A 117 " =    1.257
peak=    3.585 closest distance to " O   HOH Z 172 " =    3.633
peak=    3.581 closest distance to " O   HOH Z 197 " =    2.999
peak=    3.569 closest distance to " O   HOH Z  80 " =    1.711
peak=    3.564 closest distance to " CA  PHE A 283 " =    1.213
peak=    3.560 closest distance to " CD  ARG A 159 " =    0.722
peak=    3.554 closest distance to " CB  ALA A 248 " =    1.472
peak=    3.549 closest distance to " O   HOH Z 407 " =    2.449
peak=    3.537 closest distance to " O   HOH Z 112 " =    1.656
peak=    3.531 closest distance to " CE  LYS A  76 " =    0.865
peak=    3.528 closest distance to " O   HOH Z 193 " =    1.991
peak=    3.523 closest distance to " O   HOH Z 422 " =    2.636
peak=    3.516 closest distance to " CB  GLU A  46 " =    1.022
peak=    3.516 closest distance to " CG  LEU A 167 " =    1.207
peak=    3.515 closest distance to " O   HOH Z 291 " =    1.573
peak=    3.505 closest distance to " CB  ASN A 110 " =    1.099
peak=    3.501 closest distance to " O   HOH Z 285 " =    2.818
peak=    3.495 closest distance to " O   HOH Z 180 " =    2.164
peak=    3.494 closest distance to " CZ  PHE A  38 " =    1.183
peak=    3.492 closest distance to " CB  GLN A 278 " =    0.838
peak=    3.492 closest distance to " CG1 VAL A 153 " =    0.967
peak=    3.478 closest distance to " NH1AARG A 145 " =    1.128
peak=    3.475 closest distance to " O   MET A 105 " =    1.829
peak=    3.471 closest distance to " O   HOH Z  54 " =    1.586
peak=    3.467 closest distance to " CB  GLN A 205 " =    1.097
peak=    3.461 closest distance to " CD BLYS A 290 " =    1.048
peak=    3.461 closest distance to " CB  SER A 212 " =    1.147
peak=    3.461 closest distance to " CB  ARG A 139 " =    0.908
peak=    3.457 closest distance to " CB  ALA A 291 " =    1.295
peak=    3.445 closest distance to " NE2 GLN A  77 " =    3.303
peak=    3.442 closest distance to " N   PHE A 130 " =    1.214
peak=    3.442 closest distance to " O   HOH Z 305 " =    3.691
peak=    3.433 closest distance to " N   SER A 135 " =    1.374
peak=    3.430 closest distance to " O   HOH Z 383 " =    1.875
peak=    3.428 closest distance to " CA  VAL A  41 " =    0.808
peak=    3.426 closest distance to " OE1 GLU A   2 " =    2.083
peak=    3.418 closest distance to " NZ  LYS A 117 " =    3.261
peak=    3.415 closest distance to " CA  SER A  87 " =    1.016
peak=    3.415 closest distance to " OD2 ASP A 286 " =    2.798
peak=    3.414 closest distance to " CB  ASN A 215 " =    1.168
peak=    3.413 closest distance to " CB  HIS A 108 " =    0.839
peak=    3.412 closest distance to " NZ  LYS A  76 " =    1.560
peak=    3.408 closest distance to " O   HOH Z 421 " =    1.729
peak=    3.404 closest distance to " O   HOH Z 263 " =    1.691
peak=    3.404 closest distance to " CB  THR A 157 " =    1.199
peak=    3.399 closest distance to " CA  ALA A 158 " =    1.272
peak=    3.397 closest distance to " O   HOH Z 435 " =    1.974
peak=    3.396 closest distance to " O   HOH Z 417 " =    2.255
peak=    3.394 closest distance to " OG1 THR A 294 " =    2.387
peak=    3.394 closest distance to " O   HOH Z 353 " =    2.667
peak=    3.387 closest distance to " NH1BARG A 190 " =    2.063
peak=    3.387 closest distance to " O   HOH Z 365 " =    2.918
peak=    3.384 closest distance to " CG AARG A 275 " =    1.223
peak=    3.381 closest distance to " CD  ARG A  66 " =    2.657
peak=    3.378 closest distance to " O   ASP A 124 " =    1.140
peak=    3.374 closest distance to " O   HOH Z  66 " =    2.280
peak=    3.371 closest distance to " CD1 LEU A 300 " =    1.242
peak=    3.369 closest distance to " CB  ALA A 242 " =    0.882
peak=    3.367 closest distance to " O   HOH Z 368 " =    3.573
peak=    3.358 closest distance to " CG2 ILE A  20 " =    1.480
peak=    3.351 closest distance to " O   HOH Z 171 " =    3.842
peak=    3.349 closest distance to " CA  ALA A 291 " =    0.846
peak=    3.349 closest distance to " CG  MET A 185 " =    1.049
peak=    3.347 closest distance to " O   HOH Z 148 " =    3.305
peak=    3.347 closest distance to " O   HOH Z 187 " =    2.318
peak=    3.346 closest distance to " O   HOH Z   9 " =    2.071
peak=    3.344 closest distance to " CB  LEU A 228 " =    1.284
peak=    3.334 closest distance to " CA  LEU A 282 " =    1.048
peak=    3.333 closest distance to " CB  TRP A 150 " =    1.429
peak=    3.332 closest distance to " O   HOH Z 102 " =    1.295
peak=    3.332 closest distance to " O   HOH Z 345 " =    3.213
peak=    3.331 closest distance to " CA  ASN A 127 " =    1.030
peak=    3.330 closest distance to " CB  MET A  47 " =    1.091
peak=    3.329 closest distance to " CA  LYS A 181 " =    1.097
peak=    3.329 closest distance to " CA  ASP A 162 " =    1.041
peak=    3.327 closest distance to " O   HOH Z 403 " =    1.411
peak=    3.326 closest distance to " CA  ASN A 217 " =    1.191
peak=    3.325 closest distance to " O   HOH Z  40 " =    2.065
peak=    3.322 closest distance to " N   ASP A 162 " =    1.263
peak=    3.321 closest distance to " O   HOH Z 337 " =    3.534
peak=    3.320 closest distance to " O   HOH Z 380 " =    1.895
peak=    3.318 closest distance to " O   HOH Z 251 " =    1.466
peak=    3.318 closest distance to " CB  GLN A  89 " =    1.199
peak=    3.317 closest distance to " N   VAL A 126 " =    1.452
peak=    3.314 closest distance to " CB  ALA A 104 " =    0.710
peak=    3.312 closest distance to " ND1 HIS A  81 " =    1.686
peak=    3.310 closest distance to " CG2 ILE A 120 " =    1.161
peak=    3.308 closest distance to " CB  GLN A  88 " =    1.155
peak=    3.308 closest distance to " CG2 THR A 221 " =    1.242
peak=    3.306 closest distance to " CA  ASP A 140 " =    1.228
peak=    3.306 closest distance to " O   HOH Z 426 " =    1.612
peak=    3.305 closest distance to " O   HOH Z  85 " =    1.294
peak=    3.301 closest distance to " O   HOH Z 216 " =    2.807
peak=    3.296 closest distance to " O   HOH Z 234 " =    1.844
peak=    3.295 closest distance to " CD  LYS A 119 " =    1.542
peak=    3.293 closest distance to " CB  THR A  52 " =    0.956
peak=    3.290 closest distance to " NZ  LYS A  48 " =    1.246
peak=    3.289 closest distance to " O   HOH Z   1 " =    2.087
peak=    3.284 closest distance to " CA  ASN A 176 " =    1.097
peak=    3.284 closest distance to " CG1 VAL A 230 " =    1.046
peak=    3.279 closest distance to " CA  VAL A 125 " =    1.149
peak=    3.277 closest distance to " O   HOH Z  88 " =    2.492
peak=    3.276 closest distance to " O   HOH Z 299 " =    4.266
peak=    3.274 closest distance to " CB  MET A  40 " =    0.815
peak=    3.272 closest distance to " CE1 HIS A 108 " =    1.136
peak=    3.272 closest distance to " CA  ALA A 295 " =    1.042
peak=    3.269 closest distance to " CA  ILE A 106 " =    0.733
peak=    3.265 closest distance to " O   HOH Z  48 " =    1.562
peak=    3.260 closest distance to " O   HOH Z 359 " =    1.383
peak=    3.260 closest distance to " O   HOH Z  49 " =    2.352
peak=    3.256 closest distance to " O   HOH Z 171 " =    2.342
peak=    3.255 closest distance to " CD2 LEU A 297 " =    0.914
peak=    3.254 closest distance to " CB  PHE A 204 " =    0.825
peak=    3.253 closest distance to " CA  THR A 221 " =    0.938
peak=    3.251 closest distance to " O  BHOH Z 338 " =    2.475
peak=    3.249 closest distance to " O   HOH Z 185 " =    1.729
peak=    3.249 closest distance to " CA  ASP A 191 " =    1.094
peak=    3.249 closest distance to " O   HOH Z 258 " =    2.182
peak=    3.248 closest distance to " CG  GLN A 205 " =    0.929
peak=    3.246 closest distance to " O   HOH Z  44 " =    1.698
peak=    3.245 closest distance to " CA  ALA A 154 " =    0.960
peak=    3.245 closest distance to " CD  LYS A  76 " =    1.911
peak=    3.244 closest distance to " CB  SER A 273 " =    0.879
peak=    3.240 closest distance to " CA  ALA A 233 " =    1.371
peak=    3.240 closest distance to " N   SER A  12 " =    1.590
peak=    3.236 closest distance to " O   HOH Z 141 " =    1.551
peak=    3.235 closest distance to " CA  TYR A 116 " =    1.403
peak=    3.231 closest distance to " O   HOH Z  88 " =    2.982
peak=    3.228 closest distance to " CG  GLN A  88 " =    1.024
peak=    3.225 closest distance to " CG1 ILE A 151 " =    1.050
peak=    3.224 closest distance to " O   HOH Z  10 " =    1.750
peak=    3.219 closest distance to " CG  GLN A  77 " =    2.060
peak=    3.217 closest distance to " NH2 ARG A  79 " =    1.313
peak=    3.214 closest distance to " O   ARG A  56 " =    2.855
peak=    3.214 closest distance to " CD1 ILE A 106 " =    1.016
peak=    3.212 closest distance to " CB  ILE A 120 " =    1.319
peak=    3.212 closest distance to " CA  ALA A  84 " =    1.338
peak=    3.210 closest distance to " CB  GLU A 277 " =    3.728
peak=    3.206 closest distance to " ND2 ASN A 249 " =    0.892
peak=    3.204 closest distance to " NE2 HIS A 207 " =    1.246
peak=    3.202 closest distance to " CB  ALA A  34 " =    0.927
peak=    3.200 closest distance to " O   HOH Z 329 " =    4.001
peak=    3.198 closest distance to " O   SER A 164 " =    1.219
peak=    3.197 closest distance to " CD1 LEU A 261 " =    1.189
peak=    3.195 closest distance to " O   HOH Z 313 " =    1.709
peak=    3.193 closest distance to " O   HOH Z 286 " =    2.319
peak=    3.190 closest distance to " O   HOH Z 256 " =    2.415
peak=    3.188 closest distance to " O   HOH Z   4 " =    1.813
peak=    3.187 closest distance to " O   HOH Z 133 " =    2.554
peak=    3.186 closest distance to " O   HOH Z 302 " =    2.022
peak=    3.181 closest distance to " O   HOH Z 425 " =    1.990
peak=    3.178 closest distance to " CZ3 TRP A  85 " =    0.920
peak=    3.177 closest distance to " O   HOH Z 325 " =    2.203
peak=    3.176 closest distance to " CB  ALA A 114 " =    1.162
peak=    3.176 closest distance to " O   HOH Z 227 " =    2.024
peak=    3.175 closest distance to " CA  PHE A  59 " =    0.999
peak=    3.174 closest distance to " CA  SER A 146 " =    1.743
peak=    3.170 closest distance to " OG  SER A  22 " =    2.716
peak=    3.169 closest distance to " N   ARG A 156 " =    1.384
peak=    3.165 closest distance to " CA  GLY A 267 " =    0.792
peak=    3.159 closest distance to " CA  MET A 105 " =    0.996
peak=    3.155 closest distance to " O   HOH Z 406 " =    1.526
peak=    3.148 closest distance to " O   HOH Z 437 " =    1.882
peak=    3.138 closest distance to " CB  PRO A 243 " =    1.571
peak=    3.138 closest distance to " O   GLN A 278 " =    1.505
peak=    3.135 closest distance to " CG2 VAL A 197 " =    1.055
peak=    3.120 closest distance to " ND2 ASN A 110 " =    1.611
peak=    3.117 closest distance to " CB  GLN A 103 " =    0.966
peak=    3.116 closest distance to " CB  ALA A 248 " =    0.962
peak=    3.115 closest distance to " CB  ASN A 224 " =    1.000
peak=    3.109 closest distance to " O   HOH Z 336 " =    1.683
peak=    3.101 closest distance to " O   HOH Z 193 " =    1.584
peak=    3.097 closest distance to " O   HOH Z 294 " =    1.567
peak=    3.096 closest distance to " CA  ILE A 234 " =    0.796
peak=    3.092 closest distance to " O   HOH Z  62 " =    2.267
peak=    3.076 closest distance to " O   HOH Z 357 " =    1.909
peak=    3.069 closest distance to " O   HOH Z  90 " =    3.308
peak=    3.066 closest distance to " O   ALA A   1 " =    1.717
peak=    3.064 closest distance to " CH2 TRP A 266 " =    1.093
peak=    3.051 closest distance to " CB  TYR A 116 " =    0.822
peak=    3.044 closest distance to " CB  SER A 216 " =    0.795
peak=    3.040 closest distance to " CB  ILE A  20 " =    1.422
peak=    3.029 closest distance to " O   ALA A 292 " =    1.733
peak=    3.026 closest distance to " O   HOH Z 271 " =    2.277
peak=    3.017 closest distance to " CB  TYR A 169 " =    1.205

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 190         
Filter by distance & map next to the model:
   mapped sites are within: 0.749 - 5.518
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 189 from: 190
   mapped sites are within: 0.749 - 5.518

peak=   -5.328 closest distance to " CG2 VAL A 230 " =    0.888
peak=   -4.697 closest distance to " SG  CYS A 254 " =    3.295
peak=   -4.486 closest distance to " CD  GLN A  58 " =    1.064
peak=   -4.477 closest distance to " CD  ARG A 156 " =    2.018
peak=   -4.422 closest distance to " CB  PRO A 243 " =    2.657
peak=   -4.245 closest distance to " O   HOH Z 266 " =    5.206
peak=   -4.228 closest distance to " CG  GLN A 223 " =    2.117
peak=   -4.184 closest distance to " C   HIS A 108 " =    1.182
peak=   -4.176 closest distance to " O   HOH Z 196 " =    2.077
peak=   -4.065 closest distance to " O   HOH Z 351 " =    1.527
peak=   -4.054 closest distance to " O   ILE A 109 " =    2.560
peak=   -4.036 closest distance to " CG2BVAL A  41 " =    2.724
peak=   -4.013 closest distance to " O   HOH Z 290 " =    1.179
peak=   -3.999 closest distance to " O   HOH Z 114 " =    3.076
peak=   -3.981 closest distance to " OG BSER A 134 " =    1.221
peak=   -3.966 closest distance to " O   HOH Z 231 " =    2.139
peak=   -3.949 closest distance to " CG1 VAL A 112 " =    2.771
peak=   -3.944 closest distance to " CE2 TYR A  30 " =    2.750
peak=   -3.939 closest distance to " CA  ASP A 298 " =    1.083
peak=   -3.935 closest distance to " OXT GLY A 302 " =    2.740
peak=   -3.906 closest distance to " O   HOH Z 166 " =    1.973
peak=   -3.880 closest distance to " CZ3 TRP A 179 " =    1.220
peak=   -3.869 closest distance to " CB  PHE A 192 " =    1.982
peak=   -3.851 closest distance to " ND2 ASN A  45 " =    1.107
peak=   -3.828 closest distance to " CA  VAL A  67 " =    2.916
peak=   -3.825 closest distance to " O   PRO A 163 " =    2.171
peak=   -3.819 closest distance to " CG2 VAL A 296 " =    1.269
peak=   -3.812 closest distance to " CG  ASP A 231 " =    0.797
peak=   -3.798 closest distance to " O   HOH Z 185 " =    2.420
peak=   -3.731 closest distance to " O   HOH Z 435 " =    2.782
peak=   -3.718 closest distance to " ND2 ASN A 187 " =    1.559
peak=   -3.713 closest distance to " OG  SER A  97 " =    2.329
peak=   -3.685 closest distance to " CE3 TRP A 150 " =    2.142
peak=   -3.655 closest distance to " N   ALA A 226 " =    2.074
peak=   -3.654 closest distance to " O   HOH Z 102 " =    1.635
peak=   -3.650 closest distance to " O   HOH Z 394 " =    1.564
peak=   -3.646 closest distance to " CB  ALA A 248 " =    2.339
peak=   -3.641 closest distance to " O   PRO A 198 " =    1.212
peak=   -3.639 closest distance to " CB  ASP A 132 " =    2.316
peak=   -3.635 closest distance to " CE  MET A 105 " =    2.150
peak=   -3.634 closest distance to " NE2 GLN A  88 " =    1.850
peak=   -3.633 closest distance to " CG2 ILE A 263 " =    2.340
peak=   -3.602 closest distance to " ND2 ASN A  45 " =    1.644
peak=   -3.590 closest distance to " CB  ASP A 171 " =    2.321
peak=   -3.587 closest distance to " O   HOH Z  11 " =    1.845
peak=   -3.586 closest distance to " CG1 VAL A 250 " =    2.742
peak=   -3.581 closest distance to " CB  ALA A 291 " =    2.282
peak=   -3.575 closest distance to " O   HOH Z 211 " =    1.693
peak=   -3.557 closest distance to " N   ALA A  43 " =    2.549
peak=   -3.556 closest distance to " N   VAL A 230 " =    1.059
peak=   -3.554 closest distance to " CG  GLU A 277 " =    1.108
peak=   -3.551 closest distance to " OD1 ASN A 148 " =    1.460
peak=   -3.550 closest distance to " CB  VAL A 230 " =    1.053
peak=   -3.549 closest distance to " C   MET A 188 " =    1.402
peak=   -3.534 closest distance to " CD1 LEU A 101 " =    2.379
peak=   -3.528 closest distance to " O   HOH Z 389 " =    1.924
peak=   -3.526 closest distance to " CG1 VAL A 112 " =    2.903
peak=   -3.520 closest distance to " O   HOH Z  13 " =    1.646
peak=   -3.515 closest distance to " CD1 PHE A  59 " =    1.939
peak=   -3.515 closest distance to " O   HOH Z  44 " =    2.259
peak=   -3.512 closest distance to " O   HOH Z  37 " =    1.834
peak=   -3.512 closest distance to " CG  TRP A 266 " =    1.899
peak=   -3.502 closest distance to " CG1 VAL A 296 " =    1.240
peak=   -3.490 closest distance to " CB  PRO A 163 " =    2.551
peak=   -3.489 closest distance to " CA  GLY A 241 " =    3.108
peak=   -3.475 closest distance to " N   THR A 157 " =    1.472
peak=   -3.471 closest distance to " O   HOH Z 429 " =    2.039
peak=   -3.469 closest distance to " NH2 ARG A  79 " =    2.045
peak=   -3.462 closest distance to " CB  ALA A  43 " =    2.533
peak=   -3.458 closest distance to " C   LEU A 143 " =    1.005
peak=   -3.458 closest distance to " N   GLN A  58 " =    1.634
peak=   -3.456 closest distance to " CE2 PHE A 218 " =    2.613
peak=   -3.456 closest distance to " C   ILE A 239 " =    2.057
peak=   -3.446 closest distance to " CD  LYS A 289 " =    2.515
peak=   -3.441 closest distance to " CD1 LEU A 101 " =    2.829
peak=   -3.433 closest distance to " CD  ARG A 139 " =    1.638
peak=   -3.427 closest distance to " CZ  TYR A 169 " =    1.718
peak=   -3.420 closest distance to " CB  ASN A  39 " =    2.261
peak=   -3.417 closest distance to " N   ALA A 248 " =    1.813
peak=   -3.413 closest distance to " O   HOH Z 165 " =    1.875
peak=   -3.411 closest distance to " NE2 GLN A 278 " =    1.951
peak=   -3.399 closest distance to " CD2 LEU A 300 " =    2.703
peak=   -3.399 closest distance to " NH2 ARG A  79 " =    1.569
peak=   -3.396 closest distance to " CG1 VAL A 112 " =    2.615
peak=   -3.394 closest distance to " O   VAL A 189 " =    2.619
peak=   -3.391 closest distance to " CD2 TYR A 293 " =    2.034
peak=   -3.387 closest distance to " O   HOH Z 256 " =    1.280
peak=   -3.385 closest distance to " N   THR A 235 " =    1.347
peak=   -3.384 closest distance to " O   ALA A  10 " =    1.774
peak=   -3.383 closest distance to " CB  ALA A 291 " =    2.191
peak=   -3.381 closest distance to " O   HOH Z 198 " =    2.201
peak=   -3.377 closest distance to " NH2AARG A 275 " =    5.098
peak=   -3.376 closest distance to " NE2 GLN A 103 " =    1.770
peak=   -3.370 closest distance to " O   HOH Z  52 " =    1.548
peak=   -3.368 closest distance to " CG  ARG A 269 " =    2.367
peak=   -3.368 closest distance to " CB  ASN A  69 " =    1.175
peak=   -3.365 closest distance to " OD2 ASP A  50 " =    2.273
peak=   -3.364 closest distance to " O   HOH Z 313 " =    1.092
peak=   -3.363 closest distance to " CG1 VAL A 230 " =    1.931
peak=   -3.362 closest distance to " CD2 LEU A 167 " =    1.815
peak=   -3.349 closest distance to " C   ALA A 158 " =    1.287
peak=   -3.341 closest distance to " CG  PHE A 283 " =    2.777
peak=   -3.341 closest distance to " O   HOH Z 313 " =    1.687
peak=   -3.338 closest distance to " O   HOH Z 369 " =    2.266
peak=   -3.337 closest distance to " O   HOH Z  63 " =    1.352
peak=   -3.337 closest distance to " NE2 GLN A 194 " =    1.829
peak=   -3.337 closest distance to " CA  GLY A 203 " =    2.417
peak=   -3.334 closest distance to " O   SER A 210 " =    1.975
peak=   -3.329 closest distance to " OD1 ASN A 187 " =    1.726
peak=   -3.328 closest distance to " ND2 ASN A 249 " =    2.404
peak=   -3.327 closest distance to " CB  VAL A 296 " =    1.146
peak=   -3.326 closest distance to " O   HOH Z 222 " =    1.520
peak=   -3.326 closest distance to " O   HOH Z 311 " =    3.716
peak=   -3.324 closest distance to " CD2 TYR A 247 " =    2.300
peak=   -3.323 closest distance to " O   HOH Z  73 " =    2.242
peak=   -3.320 closest distance to " O   HOH Z 407 " =    2.960
peak=   -3.318 closest distance to " CD1 LEU A  25 " =    2.498
peak=   -3.317 closest distance to " O   MET A  40 " =    2.779
peak=   -3.313 closest distance to " O   HOH Z 262 " =    2.856
peak=   -3.310 closest distance to " O   SER A  95 " =    1.656
peak=   -3.306 closest distance to " CG1 VAL A  67 " =    3.095
peak=   -3.305 closest distance to " O   HOH Z 134 " =    2.989
peak=   -3.294 closest distance to " O   GLY A 196 " =    1.144
peak=   -3.294 closest distance to " CD1 LEU A 228 " =    2.189
peak=   -3.292 closest distance to " CD  PRO A 243 " =    2.097
peak=   -3.290 closest distance to " CB  ASP A 132 " =    2.382
peak=   -3.283 closest distance to " O   HOH Z  10 " =    1.491
peak=   -3.282 closest distance to " O   HOH Z  15 " =    1.576
peak=   -3.278 closest distance to " OG ASER A 134 " =    1.324
peak=   -3.274 closest distance to " O   HOH Z 191 " =    5.518
peak=   -3.272 closest distance to " OG BSER A 134 " =    1.820
peak=   -3.261 closest distance to " O   HOH Z 359 " =    3.105
peak=   -3.258 closest distance to " O   SER A 271 " =    2.137
peak=   -3.255 closest distance to " O   LEU A 167 " =    1.474
peak=   -3.252 closest distance to " N   THR A  52 " =    1.660
peak=   -3.251 closest distance to " CD1 ILE A 239 " =    2.158
peak=   -3.247 closest distance to " ND2 ASN A 252 " =    1.822
peak=   -3.244 closest distance to " O   HOH Z  19 " =    2.312
peak=   -3.244 closest distance to " CZ  PHE A 155 " =    1.142
peak=   -3.242 closest distance to " C   ASP A 231 " =    2.506
peak=   -3.241 closest distance to " O   ALA A 161 " =    1.705
peak=   -3.240 closest distance to " O   ARG A  24 " =    2.035
peak=   -3.239 closest distance to " N   MET A 188 " =    1.934
peak=   -3.233 closest distance to " O   HOH Z   6 " =    1.618
peak=   -3.231 closest distance to " O   HOH Z  60 " =    2.060
peak=   -3.226 closest distance to " CG1 VAL A 197 " =    2.182
peak=   -3.224 closest distance to " C   ASP A 270 " =    1.234
peak=   -3.220 closest distance to " C   SER A 206 " =    1.498
peak=   -3.216 closest distance to " O   HOH Z  88 " =    4.528
peak=   -3.216 closest distance to " CD1 ILE A 199 " =    2.462
peak=   -3.214 closest distance to " O   LYS A 117 " =    1.666
peak=   -3.209 closest distance to " O   HOH Z 353 " =    2.182
peak=   -3.208 closest distance to " O   HOH Z 339 " =    1.810
peak=   -3.205 closest distance to " N   PHE A  59 " =    2.145
peak=   -3.198 closest distance to " CD  GLN A 223 " =    0.749
peak=   -3.194 closest distance to " CD2 PHE A  61 " =    2.511
peak=   -3.193 closest distance to " N   ASP A 171 " =    2.313
peak=   -3.188 closest distance to " O   HOH Z 326 " =    5.167
peak=   -3.181 closest distance to " O   HOH Z 139 " =    3.120
peak=   -3.178 closest distance to " O   HOH Z 298 " =    2.669
peak=   -3.176 closest distance to " O   HOH Z  47 " =    1.627
peak=   -3.172 closest distance to " O   HOH Z 426 " =    1.650
peak=   -3.169 closest distance to " OG  SER A  62 " =    1.659
peak=   -3.158 closest distance to " O   HOH Z 200 " =    4.585
peak=   -3.157 closest distance to " O   GLY A  80 " =    2.545
peak=   -3.155 closest distance to " O   HOH Z 177 " =    1.732
peak=   -3.145 closest distance to " O   HOH Z 234 " =    4.062
peak=   -3.136 closest distance to " O   HOH Z 174 " =    4.242
peak=   -3.136 closest distance to " OXT GLY A 302 " =    3.514
peak=   -3.134 closest distance to " CB  GLN A  11 " =    1.809
peak=   -3.133 closest distance to " OG  SER A 206 " =    1.675
peak=   -3.132 closest distance to " O   HOH Z 131 " =    4.081
peak=   -3.130 closest distance to " CA  GLY A 133 " =    1.976
peak=   -3.127 closest distance to " O   HOH Z 193 " =    1.789
peak=   -3.125 closest distance to " O   HOH Z 422 " =    1.620
peak=   -3.123 closest distance to " CB  TRP A  85 " =    2.521
peak=   -3.103 closest distance to " CE1 TYR A 247 " =    2.684
peak=   -3.101 closest distance to " O   HOH Z 166 " =    1.546
peak=   -3.093 closest distance to " O   HOH Z 285 " =    1.682
peak=   -3.089 closest distance to " O   ALA A  51 " =    1.403
peak=   -3.089 closest distance to " O   HOH Z 210 " =    1.187
peak=   -3.088 closest distance to " O   HOH Z 350 " =    1.930
peak=   -3.082 closest distance to " CB  LEU A  83 " =    2.317
peak=   -3.075 closest distance to " CA  SER A  62 " =    2.620
peak=   -3.073 closest distance to " N   SER A   3 " =    1.976
peak=   -3.056 closest distance to " O   HOH Z 423 " =    2.153
peak=   -3.034 closest distance to " CG1 VAL A 296 " =    1.337
peak=   -3.031 closest distance to " O   HOH Z 244 " =    2.010
peak=   -3.003 closest distance to " NH2 ARG A  79 " =    1.913

================= 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    :  0.4175 0.4024   6.205086e+00   6.171455e+00
   1_bss:  0.4099 0.3879   6.200584e+00   6.153731e+00
   1_xyz:  0.2925 0.3112   5.945047e+00   5.984556e+00
   1_adp:  0.2208 0.2500   5.686574e+00   5.795623e+00
   1_occ:  0.2201 0.2502   5.684939e+00   5.796566e+00
   2_bss:  0.2140 0.2454   5.683931e+00   5.791397e+00
   2_xyz:  0.1488 0.1815   5.355066e+00   5.524273e+00
   2_adp:  0.1369 0.1709   5.285015e+00   5.467350e+00
   2_occ:  0.1368 0.1709   5.284619e+00   5.467561e+00
   3_bss:  0.1365 0.1717   5.285443e+00   5.468402e+00
   3_xyz:  0.1158 0.1565   5.160149e+00   5.387792e+00
   3_adp:  0.1116 0.1546   5.138506e+00   5.376720e+00
   3_occ:  0.1115 0.1546   5.138227e+00   5.376660e+00
   4_bss:  0.1115 0.1546   5.137926e+00   5.376459e+00
   4_xyz:  0.1085 0.1548   5.125238e+00   5.375301e+00
   4_adp:  0.1091 0.1550   5.127691e+00   5.376210e+00
   4_occ:  0.1089 0.1551   5.127270e+00   5.376399e+00
   5_bss:  0.1090 0.1550   5.127751e+00   5.375034e+00
   5_xyz:  0.1120 0.1561   5.145901e+00   5.384471e+00
   5_adp:  0.1114 0.1562   5.145643e+00   5.388583e+00
   5_occ:  0.1114 0.1562   5.145434e+00   5.388362e+00
   5_bss:  0.1113 0.1561   5.145196e+00   5.388097e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.342  20.010   7.260   8.625   8.831   0.000   0.000   0.000
   1_xyz:  0.342  20.010   7.260   8.625   8.831   0.000   0.000   0.000
   1_adp:  0.342  20.010   7.260   8.625   8.831   0.000   0.000   0.000
   1_occ:  0.342  20.010   7.260   8.625   8.831   0.000   0.000   0.000
   2_bss:  0.333  39.927   3.557   4.819   5.358   0.000   0.000   0.000
   2_xyz:  0.333  39.927   3.557   4.819   5.358   0.000   0.000   0.000
   2_adp:  0.333  39.927   3.557   4.819   5.358   0.000   0.000   0.000
   2_occ:  0.333  39.927   3.557   4.819   5.358   0.000   0.000   0.000
   3_bss:  0.321  39.927   3.041   3.952   4.779   0.000   0.000   0.000
   3_xyz:  0.321  39.927   3.041   3.952   4.779   0.000   0.000   0.000
   3_adp:  0.321  39.927   3.041   3.952   4.779   0.000   0.000   0.000
   3_occ:  0.321  39.927   3.041   3.952   4.779   0.000   0.000   0.000
   4_bss:  0.317  39.927   3.087   3.821   4.779   0.000   0.000   0.000
   4_xyz:  0.317  39.927   3.087   3.821   4.779   0.000   0.000   0.000
   4_adp:  0.317  39.927   3.087   3.821   4.779   0.000   0.000   0.000
   4_occ:  0.317  39.927   3.087   3.821   4.779   0.000   0.000   0.000
   5_bss:  0.317  39.927   3.115   3.808   4.815   0.000   0.000   0.000
   5_xyz:  0.317  39.927   3.115   3.808   4.815   0.000   0.000   0.000
   5_adp:  0.317  39.927   3.115   3.808   4.815   0.000   0.000   0.000
   5_occ:  0.317  39.927   3.115   3.808   4.815   0.000   0.000   0.000
   5_bss:  0.320  46.510  -0.780  -0.129   0.909   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  43.347 0.6049  0.6658    45614.377
   1_bss:  42.544 0.6128  0.8653    42692.182
   1_xyz:  32.630 0.7276  0.9931    25579.778
   1_adp:  24.251 0.8200  1.0710    15504.406
   1_occ:  24.261 0.8199  1.0701    15529.609
   2_bss:  24.077 0.8218  0.9395    15338.831
   2_xyz:  17.154 0.8879  0.9876     8399.003
   2_adp:  15.811 0.8999  0.9968     7518.997
   2_occ:  15.811 0.8999  0.9967     7517.236
   3_bss:  15.818 0.8998  0.9723     7540.184
   3_xyz:  14.068 0.9144  0.9780     6350.125
   3_adp:  13.816 0.9166  0.9774     6206.892
   3_occ:  13.812 0.9166  0.9773     6206.557
   4_bss:  13.807 0.9166  0.9765     6203.535
   4_xyz:  13.692 0.9177  0.9768     6189.988
   4_adp:  13.671 0.9180  0.9746     6196.522
   4_occ:  13.667 0.9180  0.9745     6198.093
   5_bss:  13.680 0.9179  0.9747     6179.764
   5_xyz:  13.845 0.9166  0.9737     6289.088
   5_adp:  13.944 0.9158  0.9719     6320.546
   5_occ:  13.941 0.9158  0.9718     6318.488
   5_bss:  13.934 0.9159  0.9722     6316.475
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.093   5.3835e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.093   5.3835e+01
   1_xyz:   1.461  0.011  0.100 17.710  0.006  4.124   1.0990e-01
   1_adp:   1.461  0.011  0.100 17.710  0.006  4.124   1.0990e-01
   1_occ:   1.461  0.011  0.100 17.710  0.006  4.124   1.0990e-01
   2_bss:   1.461  0.011  0.100 17.710  0.006  4.124   1.0990e-01
   2_xyz:   0.989  0.007  0.074 15.926  0.004  4.125   6.0895e-02
   2_adp:   0.989  0.007  0.074 15.926  0.004  4.125   6.0895e-02
   2_occ:   0.989  0.007  0.074 15.926  0.004  4.125   6.0895e-02
   3_bss:   0.989  0.007  0.074 15.926  0.004  4.125   6.0895e-02
   3_xyz:   1.140  0.010  0.095 15.902  0.004  4.135   7.8067e-02
   3_adp:   1.140  0.010  0.095 15.902  0.004  4.135   7.8067e-02
   3_occ:   1.140  0.010  0.095 15.902  0.004  4.135   7.8067e-02
   4_bss:   1.140  0.010  0.095 15.902  0.004  4.135   7.8067e-02
   4_xyz:   1.146  0.010  0.097 15.852  0.004  4.138   7.9982e-02
   4_adp:   1.146  0.010  0.097 15.852  0.004  4.138   7.9982e-02
   4_occ:   1.146  0.010  0.097 15.852  0.004  4.138   7.9982e-02
   5_bss:   1.146  0.010  0.097 15.852  0.004  4.138   7.9982e-02
   5_xyz:   0.996  0.007  0.083 15.481  0.004  4.138   6.1341e-02
   5_adp:   0.996  0.007  0.083 15.481  0.004  4.138   6.1341e-02
   5_occ:   0.996  0.007  0.083 15.481  0.004  4.138   6.1341e-02
   5_bss:   0.996  0.007  0.083 15.481  0.004  4.138   6.1341e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9802e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9802e+00
   1_xyz:  12.020  0.127  0.396 87.372  0.036  2.268   8.1969e-02
   1_adp:  12.020  0.127  0.396 87.372  0.036  2.268   8.1969e-02
   1_occ:  12.020  0.127  0.396 87.372  0.036  2.268   8.1969e-02
   2_bss:  12.020  0.127  0.396 87.372  0.036  2.268   8.1969e-02
   2_xyz:   6.464  0.059  0.411 82.375  0.032  2.332   4.4810e-02
   2_adp:   6.464  0.059  0.411 82.375  0.032  2.332   4.4810e-02
   2_occ:   6.464  0.059  0.411 82.375  0.032  2.332   4.4810e-02
   3_bss:   6.464  0.059  0.411 82.375  0.032  2.332   4.4810e-02
   3_xyz:   7.417  0.053  0.720 83.914  0.040  2.338   6.0989e-02
   3_adp:   7.417  0.053  0.720 83.914  0.040  2.338   6.0989e-02
   3_occ:   7.417  0.053  0.720 83.914  0.040  2.338   6.0989e-02
   4_bss:   7.417  0.053  0.720 83.914  0.040  2.338   6.0989e-02
   4_xyz:   7.639  0.057  0.726 81.937  0.041  2.311   6.2596e-02
   4_adp:   7.639  0.057  0.726 81.937  0.041  2.311   6.2596e-02
   4_occ:   7.639  0.057  0.726 81.937  0.041  2.311   6.2596e-02
   5_bss:   7.639  0.057  0.726 81.937  0.041  2.311   6.2596e-02
   5_xyz:   6.843  0.047  0.558 82.898  0.038  2.353   3.9297e-02
   5_adp:   6.843  0.047  0.558 82.898  0.038  2.353   3.9297e-02
   5_occ:   6.843  0.047  0.558 82.898  0.038  2.353   3.9297e-02
   5_bss:   6.843  0.047  0.558 82.898  0.038  2.353   3.9297e-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:  49.36   0.00   9.99  49.36   0.00   6.96  49.14   0.00  26.46
   1_occ:  49.36   0.00   9.99  49.36   0.00   6.96  49.14   0.00  26.46
   2_bss:  49.36   0.00   9.99  49.36   0.00   6.96  49.14   0.00  26.46
   2_xyz:  49.36   0.00   9.99  49.36   0.00   6.96  49.14   0.00  26.46
   2_adp:  71.26   0.00  10.53  71.26   0.00   6.89  53.69   0.71  30.32
   2_occ:  71.26   0.00  10.53  71.26   0.00   6.89  53.69   0.71  30.32
   3_bss:  71.26   0.00  10.53  71.26   0.00   6.89  53.69   0.71  30.32
   3_xyz:  71.26   0.00  10.53  71.26   0.00   6.89  53.69   0.71  30.32
   3_adp:  72.24   0.00  11.09  72.24   0.00   7.04  66.90   0.06  33.13
   3_occ:  72.24   0.00  11.09  72.24   0.00   7.04  66.90   0.06  33.13
   4_bss:  72.24   0.00  11.09  72.24   0.00   7.04  66.90   0.06  33.13
   4_xyz:  72.24   0.00  11.09  72.24   0.00   7.04  66.90   0.06  33.13
   4_adp:  73.28   0.00  10.79  73.28   0.00   6.93  65.81   0.65  31.82
   4_occ:  73.28   0.00  10.79  73.28   0.00   6.93  65.81   0.65  31.82
   5_bss:  73.28   0.00  10.79  73.28   0.00   6.93  65.81   0.65  31.82
   5_xyz:  73.28   0.00  10.79  73.28   0.00   6.93  65.81   0.65  31.82
   5_adp:  77.37   0.00  10.96  77.37   0.00   6.98  66.32   0.59  32.61
   5_occ:  77.37   0.00  10.96  77.37   0.00   6.98  66.32   0.59  32.61
   5_bss:  81.29   3.92  14.88  81.29   3.92  10.90  70.24   4.51  36.53
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.186    0.013    0.399
   1_adp:    1.186    0.013    0.399
   1_occ:    1.186    0.013    0.399
   2_bss:    1.186    0.013    0.399
   2_xyz:    1.488    0.021    0.477
   2_adp:    1.488    0.021    0.477
   2_occ:    1.488    0.021    0.477
   3_bss:    1.488    0.021    0.477
   3_xyz:    1.345    0.047    0.508
   3_adp:    1.345    0.047    0.508
   3_occ:    1.345    0.047    0.508
   4_bss:    1.345    0.047    0.508
   4_xyz:    1.324    0.030    0.516
   4_adp:    1.324    0.030    0.516
   4_occ:    1.324    0.030    0.516
   5_bss:    1.324    0.030    0.516
   5_xyz:    1.406    0.045    0.522
   5_adp:    1.406    0.045    0.522
   5_occ:    1.406    0.045    0.522
   5_bss:    1.406    0.045    0.522
------------------------------------------------------------------------

CPU time actual refinement: 341.95


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_556/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_556/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_556/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_556/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_556/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 341.80 
  Macro-tasks:
    bulk solvent and scale       = 40.55  
    individual site refinement   = 151.76 
    weights calculation          = 31.94  
    collect and process          = 6.57   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 230.94 
  Micro-tasks:
    mask                            = 1.80   
    f_calc                          = 105.01 
    alpha_beta                      = 8.12   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 119.08 
    fmodel                         = 7.62   
    r_factors                      = 0.19   
    phase_errors                   = 11.05  
    foms                           = 0.24   
    TOTAL for micro-tasks          = 254.29 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.611 micro seconds
Total CPU time: 5.92 minutes
from_scatterers_fft:    687 calls, 104.68 s
gradients_fft:          631 calls, 103.76 s

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

# Date 2008-01-16 Time 01:52:09 PST -0800 (1200477129.01 s)
Start R-work = 0.4175, R-free = 0.4024 (no bulk solvent and anisotropic scale)
Final R-work = 0.1292, R-free = 0.1724 (no bulk solvent and anisotropic scale)

Start R-work = 0.4099, R-free = 0.3879
Final R-work = 0.1113, R-free = 0.1561