# Date 2008-01-16 Time 02:25:47 PST -0800 (1200479147.34 s)
#phil __OFF__

Command line arguments: "../823.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 30779
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 823

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.6012, 47.6339, 88.1178, 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: 3.34, per 1000 atoms: 1.18


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 47.6339, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1289 2.01064
Completeness in resolution range: 0.963125
Completeness with d_max=infinity: 0.960104

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1289
                             d_min =   2.0106

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 47.6339, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1289 2.01064
Completeness in resolution range: 0.963125
Completeness with d_max=infinity: 0.960104

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1294 -  4.3017 [2145/2172]  1929   216  10.1%
  bin  2:  4.3017 -  3.4275 [2038/2054]  1837   201   9.9%
  bin  3:  3.4275 -  2.9980 [2036/2055]  1831   205  10.1%
  bin  4:  2.9980 -  2.7257 [1999/2029]  1797   202  10.1%
  bin  5:  2.7257 -  2.5313 [1996/2015]  1795   201  10.1%
  bin  6:  2.5313 -  2.3826 [1984/2009]  1790   194   9.8%
  bin  7:  2.3826 -  2.2637 [1971/2004]  1777   194   9.8%
  bin  8:  2.2637 -  2.1655 [1974/2005]  1774   200  10.1%
  bin  9:  2.1655 -  2.0823 [1937/1979]  1741   196  10.1%
  bin 10:  2.0823 -  2.0106 [1509/2017]  1359   150   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_823/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:
        1.73 -     2.37: 13
        2.37 -     3.00: 1882
        3.00 -     3.63: 4498
        3.63 -     4.27: 8910
        4.27 -     4.90: 12455
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.735 3.040 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  50 " - " O   HOH Z  95 "  1.931 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  95 " - " O   HOH Z  50 "  1.931 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.002 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 27753 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_823/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_823/model_refine_001.geo

CPU time processing inputs: 9.12


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.60125 47.63395 88.1178 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.01 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4889   r_free= 0.4792   ksol= 0.00   Bsol= 0.00   scale= 0.774    |
|                                                                             |
| 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:   0.78 A                  |
| x-ray target function (ml) for work reflections: 6.286864                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1294 -  4.7976 0.99   1390  153 0.3940 0.3741       6.596      6.5324|
|  2:  4.7976 -  3.8283 0.99   1326  151 0.4104 0.4630       6.808      6.9508|
|  3:  3.8283 -  3.3504 0.99   1317  146 0.4555 0.4274      6.6966      6.6532|
|  4:  3.3504 -  3.0468 0.99   1296  137 0.4794 0.4189      6.5496      6.4502|
|  5:  3.0468 -  2.8299 0.99   1293  145 0.5167 0.4827      6.3876       6.396|
|  6:  2.8299 -  2.6640 0.99   1284  148 0.5161 0.5561      6.2874      6.2307|
|  7:  2.6640 -  2.5313 0.99   1283  145 0.5200 0.4559      6.2499       6.154|
|  8:  2.5313 -  2.4215 0.98   1288  135 0.5244 0.4483      6.1973      6.1527|
|  9:  2.4215 -  2.3287 0.98   1260  146 0.5198 0.6248      6.1085      6.1943|
| 10:  2.3287 -  2.2486 0.99   1265  140 0.5546 0.4738      6.1378      6.1024|
| 11:  2.2486 -  2.1785 0.99   1272  141 0.5227 0.5384      6.0293      6.0866|
| 12:  2.1785 -  2.1164 0.97   1260  138 0.5454 0.5485      5.9784      6.0384|
| 13:  2.1164 -  2.0608 0.99   1269  139 0.5412 0.5224      5.9023      5.8233|
| 14:  2.0608 -  2.0106 0.65    827   95 0.5551 0.5428      5.8619      5.7745|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1294 -  4.7976  1390   153  0.70  34.29   0.79     0.72      70363.83|
|  2:  4.7976 -  3.8283  1326   151  0.70  35.59   0.86     0.74     108829.45|
|  3:  3.8283 -  3.3504  1317   146  0.59  44.45   0.80     0.69     115050.12|
|  4:  3.3504 -  3.0468  1296   137  0.51  51.17   0.78     0.58     100219.76|
|  5:  3.0468 -  2.8299  1293   145  0.43  57.32   0.73     0.50      79608.93|
|  6:  2.8299 -  2.6640  1284   148  0.41  59.34   0.70     0.46      70500.63|
|  7:  2.6640 -  2.5313  1283   145  0.40  60.03   0.72     0.45      63146.10|
|  8:  2.5313 -  2.4215  1288   135  0.39  60.87   0.73     0.45      57468.58|
|  9:  2.4215 -  2.3287  1260   146  0.35  63.69   0.69     0.41      55403.62|
| 10:  2.3287 -  2.2486  1265   140  0.32  65.99   0.71     0.38      51964.35|
| 11:  2.2486 -  2.1785  1272   141  0.30  67.82   0.73     0.36      49461.55|
| 12:  2.1785 -  2.1164  1260   138  0.29  68.51   0.73     0.35      44437.20|
| 13:  2.1164 -  2.0608  1269   139  0.25  71.47   0.70     0.30      39803.92|
| 14:  2.0608 -  2.0106   827    95  0.17  77.06   0.70     0.19      34525.36|
|alpha:            min =        0.19 max =            0.74 mean =         0.48|
|beta:             min =    34525.36 max =       115050.12 mean =     68379.22|
|figures of merit: min =        0.00 max =            1.00 mean =         0.42|
|phase err.(work): min =        0.00 max =           90.00 mean =        57.64|
|phase err.(test): min =        0.00 max =           89.93 mean =        57.84|
|-----------------------------------------------------------------------------|

============================== 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 = 14.965189             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.342   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.462552              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.213   (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:       27 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      160 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      672 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1476 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2568 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3824 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     4971 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6459 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7614 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       54.559 |
| 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 |       1.723 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.339)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 12.339)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4944   r_free= 0.4805   ksol= 0.00   Bsol= 0.00   scale= 0.746    |
|                                                                             |
| 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:   0.76 A                  |
| x-ray target function (ml) for work reflections: 6.288583                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4813   r_free= 0.4682   ksol= 0.30   Bsol= 20.00   scale= 0.974   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.21,9.60,10.70,0.00,0.00,0.00); trace/3= 8.84                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.76 A                  |
| x-ray target function (ml) for work reflections: 6.280110                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.313021             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.275   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.304123              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.823   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4813      final r-factor (work) = 0.3996          |
| start r-factor (free) = 0.4682      final r-factor (free) = 0.4201          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 96.4097 = 13.31 * 0.50 * 6.2872 + 1.00 * 54.5590                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 41.4110 = 13.31 * 0.50 * 6.1991 + 1.00 * 0.1467                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3996      final r-factor (work) = 0.3559          |
| start r-factor (free) = 0.4201      final r-factor (free) = 0.4079          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.0988 = 1.30 * 1.00 * 6.1991 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.9973 = 1.30 * 1.00 * 6.1166 + 1.00 * 0.0205                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.339)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    110.49  14.29    None  None   None       |
|    all(noH): 2823   0      0.00    110.49  14.29    None  None   None       |
|    Sol.    : 438    0      0.00    110.49  28.02    None  None   None       |
|    Mac.    : 2385   0      0.00    70.98   11.76    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.049: 1467   |   5:    55.246 -  66.295:   27        |
|      1:    11.049 -  22.098:  757   |   6:    66.295 -  77.344:   11        |
|      2:    22.098 -  33.148:  352   |   7:    77.344 -  88.393:    5        |
|      3:    33.148 -  44.197:  131   |   8:    88.393 -  99.442:    1        |
|      4:    44.197 -  55.246:   70   |   9:    99.442 - 110.492:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3559 r_free = 0.4079             target_work(ml) = 6.100         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3552 r_free = 0.4081             target_work(ml) = 6.099         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3552   r_free= 0.4081   ksol= 0.30   Bsol= 20.00   scale= 1.091   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.21,9.60,10.70,0.00,0.00,0.00); trace/3= 8.84                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.099102                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3531   r_free= 0.4037   ksol= 0.32   Bsol= 51.25   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.04,5.96,6.75,0.00,0.00,0.00); trace/3= 5.25                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.100790                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.967993              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.618   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.493123              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 121.804  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3531      final r-factor (work) = 0.2746          |
| start r-factor (free) = 0.4037      final r-factor (free) = 0.3284          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.3808 = 5.97 * 0.50 * 6.1106 + 1.00 * 0.1467                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.9701 = 5.97 * 0.50 * 5.9907 + 1.00 * 0.0938                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2746      final r-factor (work) = 0.2525          |
| start r-factor (free) = 0.3284      final r-factor (free) = 0.3045          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9807 = 0.49 * 1.00 * 5.9907 + 1.00 * 0.0265                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9106 = 0.49 * 1.00 * 5.8611 + 1.00 * 0.0203                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.339)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    111.26  13.27    None  None   None       |
|    all(noH): 2823   0      0.00    111.26  13.27    None  None   None       |
|    Sol.    : 438    0      0.00    111.26  32.36    None  None   None       |
|    Mac.    : 2385   0      0.00    65.99   9.76     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.126: 1690   |   5:    55.629 -  66.755:   32        |
|      1:    11.126 -  22.252:  638   |   6:    66.755 -  77.881:    9        |
|      2:    22.252 -  33.378:  252   |   7:    77.881 -  89.007:    3        |
|      3:    33.378 -  44.503:  126   |   8:    89.007 - 100.133:    0        |
|      4:    44.503 -  55.629:   72   |   9:   100.133 - 111.258:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2525 r_free = 0.3045             target_work(ml) = 5.835         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2522 r_free = 0.3049             target_work(ml) = 5.834         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2522   r_free= 0.3049   ksol= 0.32   Bsol= 51.25   scale= 1.037   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.04,5.96,6.75,0.00,0.00,0.00); trace/3= 5.25                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.834417                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2514   r_free= 0.3048   ksol= 0.30   Bsol= 51.25   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.05,3.76,4.47,0.00,0.00,0.00); trace/3= 3.42                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.835133                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.205379              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 93.976   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.142791              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 93.492   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2514      final r-factor (work) = 0.1746          |
| start r-factor (free) = 0.3048      final r-factor (free) = 0.2176          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.2861 = 6.21 * 0.50 * 5.8634 + 1.00 * 0.0938                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.7644 = 6.21 * 0.50 * 5.6976 + 1.00 * 0.0864                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1746      final r-factor (work) = 0.1549          |
| start r-factor (free) = 0.2176      final r-factor (free) = 0.2029          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.5248 = 1.14 * 1.00 * 5.6976 + 1.00 * 0.0136                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.2666 = 1.14 * 1.00 * 5.4494 + 1.00 * 0.0391                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.339)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    102.56  14.17    None  None   None       |
|    all(noH): 2823   0      0.00    102.56  14.17    None  None   None       |
|    Sol.    : 438    0      1.24    102.56  39.88    None  None   None       |
|    Mac.    : 2385   0      0.00    97.83   9.45     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 -  10.256: 1704   |   5:    51.278 -  61.534:   85        |
|      1:    10.256 -  20.511:  572   |   6:    61.534 -  71.789:   58        |
|      2:    20.511 -  30.767:  171   |   7:    71.789 -  82.045:   18        |
|      3:    30.767 -  41.022:  104   |   8:    82.045 -  92.300:    4        |
|      4:    41.022 -  51.278:  104   |   9:    92.300 - 102.556:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1549 r_free = 0.2029             target_work(ml) = 5.414         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1547 r_free = 0.2029             target_work(ml) = 5.414         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1547   r_free= 0.2029   ksol= 0.30   Bsol= 51.25   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.05,3.76,4.47,0.00,0.00,0.00); trace/3= 3.42                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.414158                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1545   r_free= 0.2033   ksol= 0.32   Bsol= 72.68   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.64,2.71,3.74,0.00,0.00,0.00); trace/3= 2.70                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.413847                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.960243              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.669  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.619305              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 94.376   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1545      final r-factor (work) = 0.1388          |
| start r-factor (free) = 0.2033      final r-factor (free) = 0.1861          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4303 = 1.96 * 0.50 * 5.4522 + 1.00 * 0.0864                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3242 = 1.96 * 0.50 * 5.3712 + 1.00 * 0.0597                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1388      final r-factor (work) = 0.1355          |
| start r-factor (free) = 0.1861      final r-factor (free) = 0.1835          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3509 = 0.62 * 1.00 * 5.3712 + 1.00 * 0.0245                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3265 = 0.62 * 1.00 * 5.3187 + 1.00 * 0.0326                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.339)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.72   13.84    None  None   None       |
|    all(noH): 2823   0      0.00    98.72   13.84    None  None   None       |
|    Sol.    : 438    0      1.06    98.72   39.91    None  None   None       |
|    Mac.    : 2385   0      0.00    87.96   9.05     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.872: 1705   |   5:    49.360 -  59.232:   75        |
|      1:     9.872 -  19.744:  578   |   6:    59.232 -  69.104:   61        |
|      2:    19.744 -  29.616:  150   |   7:    69.104 -  78.976:   29        |
|      3:    29.616 -  39.488:  111   |   8:    78.976 -  88.848:    5        |
|      4:    39.488 -  49.360:  106   |   9:    88.848 -  98.720:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1355 r_free = 0.1835             target_work(ml) = 5.311         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1353 r_free = 0.1834             target_work(ml) = 5.311         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1353   r_free= 0.1834   ksol= 0.32   Bsol= 72.68   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.64,2.71,3.74,0.00,0.00,0.00); trace/3= 2.70                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.310697                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1352   r_free= 0.1832   ksol= 0.33   Bsol= 72.68   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.69,2.49,3.66,0.00,0.00,0.00); trace/3= 2.61                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.310287                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.735146              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 121.134  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.286875              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 95.983   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1352      final r-factor (work) = 0.1241          |
| start r-factor (free) = 0.1832      final r-factor (free) = 0.1723          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3320 = 2.74 * 0.50 * 5.3176 + 1.00 * 0.0597                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.2849 = 2.74 * 0.50 * 5.2734 + 1.00 * 0.0732                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1241      final r-factor (work) = 0.1239          |
| start r-factor (free) = 0.1723      final r-factor (free) = 0.1692          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5329 = 0.29 * 1.00 * 5.2734 + 1.00 * 0.0201                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5161 = 0.29 * 1.00 * 5.2380 + 1.00 * 0.0135                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.339)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.51   13.09    None  None   None       |
|    all(noH): 2823   0      0.00    93.51   13.09    None  None   None       |
|    Sol.    : 438    0      1.45    93.51   37.59    None  None   None       |
|    Mac.    : 2385   0      0.00    85.55   8.59     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.351: 1711   |   5:    46.757 -  56.108:   79        |
|      1:     9.351 -  18.703:  574   |   6:    56.108 -  65.459:   52        |
|      2:    18.703 -  28.054:  157   |   7:    65.459 -  74.810:   24        |
|      3:    28.054 -  37.405:  118   |   8:    74.810 -  84.162:   10        |
|      4:    37.405 -  46.757:   94   |   9:    84.162 -  93.513:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1239 r_free = 0.1692             target_work(ml) = 5.228         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1238 r_free = 0.1691             target_work(ml) = 5.228         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1238   r_free= 0.1691   ksol= 0.33   Bsol= 72.68   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.69,2.49,3.66,0.00,0.00,0.00); trace/3= 2.61                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.227779                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1294 -  4.7976 0.99   1390  153 0.1047 0.1367      5.4391      5.5627|
|  2:  4.7976 -  3.8283 0.99   1326  151 0.0879 0.1128      5.4693      5.6836|
|  3:  3.8283 -  3.3504 0.99   1317  146 0.1128 0.1581       5.529       5.892|
|  4:  3.3504 -  3.0468 0.99   1296  137 0.1289 0.1651      5.5073      5.6543|
|  5:  3.0468 -  2.8299 0.99   1293  145 0.1525 0.1834      5.4448      5.5923|
|  6:  2.8299 -  2.6640 0.99   1284  148 0.1397 0.2285      5.3213      5.6333|
|  7:  2.6640 -  2.5313 0.99   1283  145 0.1446 0.1752      5.2827      5.4245|
|  8:  2.5313 -  2.4215 0.98   1288  135 0.1339 0.1829      5.1921        5.42|
|  9:  2.4215 -  2.3287 0.98   1260  146 0.1353 0.1959       5.126       5.357|
| 10:  2.3287 -  2.2486 0.99   1265  140 0.1308 0.1699      5.0766       5.263|
| 11:  2.2486 -  2.1785 0.99   1272  141 0.1300 0.2104      5.0213      5.3528|
| 12:  2.1785 -  2.1164 0.97   1260  138 0.1271 0.1762      4.9583      5.2504|
| 13:  2.1164 -  2.0608 0.99   1269  139 0.1249 0.1839      4.8589      5.0611|
| 14:  2.0608 -  2.0106 0.65    827   95 0.1186 0.1770      4.7341      4.9862|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1294 -  4.7976  1390   153  0.94   9.68   0.96     0.93       8143.07|
|  2:  4.7976 -  3.8283  1326   151  0.95   8.67   1.00     0.98       9710.70|
|  3:  3.8283 -  3.3504  1317   146  0.93  11.80   1.01     1.01      11302.60|
|  4:  3.3504 -  3.0468  1296   137  0.92  14.19   1.00     0.98      11134.02|
|  5:  3.0468 -  2.8299  1293   145  0.88  17.95   0.99     0.97      10199.87|
|  6:  2.8299 -  2.6640  1284   148  0.88  18.21   0.97     0.94       8749.92|
|  7:  2.6640 -  2.5313  1283   145  0.89  17.59   0.98     0.94       7667.12|
|  8:  2.5313 -  2.4215  1288   135  0.89  17.01   0.98     0.95       6556.13|
|  9:  2.4215 -  2.3287  1260   146  0.89  17.26   0.99     0.95       5927.69|
| 10:  2.3287 -  2.2486  1265   140  0.88  17.71   0.98     0.94       5366.22|
| 11:  2.2486 -  2.1785  1272   141  0.89  17.81   0.98     0.93       5048.71|
| 12:  2.1785 -  2.1164  1260   138  0.90  16.99   0.99     0.98       4565.77|
| 13:  2.1164 -  2.0608  1269   139  0.90  16.45   0.97     0.95       3651.20|
| 14:  2.0608 -  2.0106   827    95  0.91  15.37   0.95     0.91       2702.08|
|alpha:            min =        0.91 max =            1.01 mean =         0.96|
|beta:             min =     2702.08 max =        11302.60 mean =      7346.28|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           90.00 mean =        15.41|
|phase err.(test): min =        0.00 max =           89.06 mean =        14.74|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1238   r_free= 0.1687   ksol= 0.32   Bsol= 68.46   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.85,-0.19,1.05,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.226561                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1238   r_free= 0.1687   ksol= 0.32   Bsol= 68.46   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.85,-0.19,1.05,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.226561                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1294 -  4.7976 0.99   1390  153 0.1040 0.1324      5.4244      5.5393|
|  2:  4.7976 -  3.8283 0.99   1326  151 0.0882 0.1112      5.4653      5.6722|
|  3:  3.8283 -  3.3504 0.99   1317  146 0.1126 0.1568      5.5268      5.8885|
|  4:  3.3504 -  3.0468 0.99   1296  137 0.1293 0.1658       5.509      5.6601|
|  5:  3.0468 -  2.8299 0.99   1293  145 0.1527 0.1835      5.4469      5.5931|
|  6:  2.8299 -  2.6640 0.99   1284  148 0.1398 0.2284      5.3218      5.6329|
|  7:  2.6640 -  2.5313 0.99   1283  145 0.1446 0.1757      5.2835      5.4256|
|  8:  2.5313 -  2.4215 0.98   1288  135 0.1340 0.1833      5.1926      5.4211|
|  9:  2.4215 -  2.3287 0.98   1260  146 0.1352 0.1957      5.1262      5.3564|
| 10:  2.3287 -  2.2486 0.99   1265  140 0.1308 0.1701      5.0767      5.2646|
| 11:  2.2486 -  2.1785 0.99   1272  141 0.1300 0.2103      5.0216      5.3526|
| 12:  2.1785 -  2.1164 0.97   1260  138 0.1271 0.1762      4.9584      5.2503|
| 13:  2.1164 -  2.0608 0.99   1269  139 0.1249 0.1837      4.8584      5.0609|
| 14:  2.0608 -  2.0106 0.65    827   95 0.1187 0.1767      4.7337      4.9851|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1294 -  4.7976  1390   153  0.94   9.61   0.96     0.93       7829.67|
|  2:  4.7976 -  3.8283  1326   151  0.95   8.53   1.00     0.98       9441.06|
|  3:  3.8283 -  3.3504  1317   146  0.93  11.68   1.01     1.01      11161.29|
|  4:  3.3504 -  3.0468  1296   137  0.92  14.20   1.00     0.98      11126.75|
|  5:  3.0468 -  2.8299  1293   145  0.88  17.96   0.99     0.97      10230.92|
|  6:  2.8299 -  2.6640  1284   148  0.88  18.21   0.97     0.94       8748.06|
|  7:  2.6640 -  2.5313  1283   145  0.89  17.61   0.98     0.95       7688.38|
|  8:  2.5313 -  2.4215  1288   135  0.89  17.02   0.98     0.95       6561.59|
|  9:  2.4215 -  2.3287  1260   146  0.89  17.27   1.00     0.95       5938.88|
| 10:  2.3287 -  2.2486  1265   140  0.88  17.70   0.99     0.94       5368.58|
| 11:  2.2486 -  2.1785  1272   141  0.89  17.81   0.98     0.93       5053.72|
| 12:  2.1785 -  2.1164  1260   138  0.90  16.99   1.00     0.99       4568.51|
| 13:  2.1164 -  2.0608  1269   139  0.90  16.44   0.97     0.96       3647.03|
| 14:  2.0608 -  2.0106   827    95  0.91  15.36   0.95     0.91       2694.96|
|alpha:            min =        0.91 max =            1.01 mean =         0.96|
|beta:             min =     2694.96 max =        11161.29 mean =      7295.18|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           90.00 mean =        15.39|
|phase err.(test): min =        0.00 max =           89.01 mean =        14.72|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.339)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.67    96.18   15.76    None  None   None       |
|    all(noH): 2823   0      2.67    96.18   15.76    None  None   None       |
|    Sol.    : 438    0      4.11    96.18   40.25    None  None   None       |
|    Mac.    : 2385   0      2.67    88.22   11.26    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:     2.667 -  12.018: 1711   |   5:    49.423 -  58.774:   79        |
|      1:    12.018 -  21.369:  574   |   6:    58.774 -  68.126:   52        |
|      2:    21.369 -  30.721:  157   |   7:    68.126 -  77.477:   24        |
|      3:    30.721 -  40.072:  118   |   8:    77.477 -  86.828:   10        |
|      4:    40.072 -  49.423:   94   |   9:    86.828 -  96.180:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 339         
Filter by distance & map next to the model:
   mapped sites are within: 0.306 - 5.603
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 334 from: 339
   mapped sites are within: 0.726 - 5.603

peak=    9.953 closest distance to " CB  VAL A 230 " =    1.431
peak=    6.027 closest distance to " O   HOH Z 210 " =    1.337
peak=    5.746 closest distance to " NH2 ARG A  56 " =    2.205
peak=    5.630 closest distance to " CG  LEU A   5 " =    1.286
peak=    5.445 closest distance to " CB  GLN A 223 " =    1.486
peak=    5.029 closest distance to " CB  VAL A 296 " =    1.115
peak=    5.019 closest distance to " CB  SER A  63 " =    1.190
peak=    4.995 closest distance to " CG  LEU A 228 " =    1.294
peak=    4.950 closest distance to " CD1AILE A 234 " =    1.172
peak=    4.722 closest distance to " CG  PRO A  54 " =    1.355
peak=    4.710 closest distance to " CG  PRO A 280 " =    0.884
peak=    4.678 closest distance to " CB  GLN A 183 " =    1.232
peak=    4.669 closest distance to " O   HOH Z 403 " =    1.778
peak=    4.669 closest distance to " O   HOH Z 128 " =    1.519
peak=    4.655 closest distance to " CD2 LEU A   5 " =    1.134
peak=    4.652 closest distance to " O   HOH Z 248 " =    1.491
peak=    4.605 closest distance to " CG1 VAL A 296 " =    1.183
peak=    4.598 closest distance to " CD2 LEU A 228 " =    1.256
peak=    4.590 closest distance to " O   HOH Z  49 " =    1.479
peak=    4.510 closest distance to " CG  PRO A 198 " =    1.380
peak=    4.506 closest distance to " CG2 VAL A 296 " =    1.018
peak=    4.420 closest distance to " O   HOH Z 265 " =    2.026
peak=    4.406 closest distance to " O   HOH Z 214 " =    1.442
peak=    4.404 closest distance to " CB  ARG A 275 " =    0.926
peak=    4.373 closest distance to " O   HOH Z 126 " =    1.657
peak=    4.364 closest distance to " O   HOH Z 425 " =    1.600
peak=    4.337 closest distance to " CD  LYS A 166 " =    1.404
peak=    4.328 closest distance to " CB  PRO A  54 " =    0.946
peak=    4.312 closest distance to " CA  VAL A 230 " =    1.226
peak=    4.311 closest distance to " CA  ALA A  51 " =    1.021
peak=    4.275 closest distance to " O   HOH Z 251 " =    1.645
peak=    4.274 closest distance to " CA  TYR A  30 " =    0.985
peak=    4.269 closest distance to " O   HOH Z 411 " =    3.836
peak=    4.262 closest distance to " CB  ARG A 190 " =    1.659
peak=    4.261 closest distance to " O   PRO A 198 " =    1.546
peak=    4.246 closest distance to " CZ  PHE A 218 " =    1.146
peak=    4.232 closest distance to " O   HOH Z 369 " =    1.983
peak=    4.223 closest distance to " CD  ARG A  66 " =    2.581
peak=    4.209 closest distance to " O   HOH Z 365 " =    2.439
peak=    4.209 closest distance to " CG  PRO A 243 " =    1.194
peak=    4.199 closest distance to " CB  ASP A 124 " =    0.740
peak=    4.178 closest distance to " CD2 TRP A 179 " =    1.283
peak=    4.174 closest distance to " NE2 GLN A  11 " =    1.118
peak=    4.165 closest distance to " O   HOH Z  63 " =    1.970
peak=    4.143 closest distance to " CB  GLU A 277 " =    3.786
peak=    4.135 closest distance to " CB  TRP A 266 " =    0.989
peak=    4.130 closest distance to " O   HOH Z 234 " =    3.704
peak=    4.118 closest distance to " O   SER A  87 " =    2.340
peak=    4.105 closest distance to " O   HOH Z 232 " =    2.210
peak=    4.086 closest distance to " CA  ALA A 295 " =    1.024
peak=    4.086 closest distance to " O   HOH Z   4 " =    1.679
peak=    4.064 closest distance to " CA  ILE A 106 " =    0.785
peak=    4.052 closest distance to " O   HOH Z 130 " =    1.161
peak=    4.047 closest distance to " O   HOH Z 142 " =    1.667
peak=    4.030 closest distance to " O   HOH Z  76 " =    1.270
peak=    3.998 closest distance to " O   HOH Z 199 " =    1.624
peak=    3.996 closest distance to " CB  ARG A  79 " =    1.473
peak=    3.990 closest distance to " O   HOH Z 431 " =    1.192
peak=    3.984 closest distance to " CG AARG A 275 " =    1.254
peak=    3.975 closest distance to " CZ3 TRP A 266 " =    1.143
peak=    3.954 closest distance to " CB  ASN A 142 " =    1.179
peak=    3.942 closest distance to " CB  VAL A 202 " =    1.473
peak=    3.927 closest distance to " OG  SER A 245 " =    1.637
peak=    3.921 closest distance to " CB  GLU A 128 " =    1.071
peak=    3.912 closest distance to " CB  ASN A  39 " =    0.848
peak=    3.904 closest distance to " CG  PRO A 213 " =    1.246
peak=    3.897 closest distance to " CB  TRP A 179 " =    1.325
peak=    3.893 closest distance to " O   HOH Z  40 " =    1.870
peak=    3.890 closest distance to " OG BSER A 164 " =    2.139
peak=    3.871 closest distance to " O   HOH Z 359 " =    1.687
peak=    3.866 closest distance to " O   HOH Z 188 " =    3.067
peak=    3.865 closest distance to " CB  TYR A 169 " =    0.784
peak=    3.864 closest distance to " CA  ARG A 195 " =    1.175
peak=    3.859 closest distance to " O   HOH Z  56 " =    1.789
peak=    3.857 closest distance to " CB  GLU A 152 " =    1.135
peak=    3.845 closest distance to " CB  ASN A 148 " =    1.353
peak=    3.837 closest distance to " O   HOH Z 422 " =    2.674
peak=    3.831 closest distance to " O   HOH Z 346 " =    1.535
peak=    3.826 closest distance to " O   ASP A 124 " =    1.214
peak=    3.820 closest distance to " O   HOH Z 402 " =    1.517
peak=    3.815 closest distance to " O   HOH Z 285 " =    2.228
peak=    3.812 closest distance to " O   HOH Z  48 " =    1.776
peak=    3.808 closest distance to " N   ASN A  39 " =    1.227
peak=    3.787 closest distance to " O   HOH Z 423 " =    1.794
peak=    3.785 closest distance to " OG  SER A 276 " =    1.470
peak=    3.783 closest distance to " CB  GLU A  46 " =    0.951
peak=    3.782 closest distance to " CB  GLN A  88 " =    1.218
peak=    3.779 closest distance to " O   HOH Z 287 " =    1.921
peak=    3.764 closest distance to " O   HOH Z 131 " =    2.361
peak=    3.757 closest distance to " CB  LEU A  83 " =    0.732
peak=    3.754 closest distance to " O   HOH Z 316 " =    3.200
peak=    3.753 closest distance to " O   HOH Z 146 " =    1.649
peak=    3.751 closest distance to " CG2 THR A 221 " =    1.057
peak=    3.749 closest distance to " NH1AARG A 145 " =    1.253
peak=    3.744 closest distance to " O   HOH Z 261 " =    2.184
peak=    3.740 closest distance to " O   HOH Z 272 " =    1.984
peak=    3.740 closest distance to " ND2 ASN A 187 " =    1.621
peak=    3.740 closest distance to " CB BVAL A  41 " =    1.080
peak=    3.737 closest distance to " O   HOH Z  44 " =    2.017
peak=    3.732 closest distance to " CD1 LEU A  96 " =    0.793
peak=    3.732 closest distance to " O   HOH Z 247 " =    1.492
peak=    3.717 closest distance to " CA  SER A  87 " =    0.977
peak=    3.713 closest distance to " O   HOH Z 280 " =    2.940
peak=    3.712 closest distance to " O   HOH Z 394 " =    1.490
peak=    3.711 closest distance to " CG1 VAL A 153 " =    0.971
peak=    3.708 closest distance to " CZ3 TRP A  85 " =    0.924
peak=    3.703 closest distance to " O   HOH Z  43 " =    2.010
peak=    3.695 closest distance to " CD1 LEU A   5 " =    1.375
peak=    3.693 closest distance to " CG  MET A 185 " =    1.233
peak=    3.689 closest distance to " O   HOH Z 155 " =    3.393
peak=    3.683 closest distance to " CB  ASP A 140 " =    0.947
peak=    3.675 closest distance to " CA  ALA A  21 " =    1.159
peak=    3.651 closest distance to " O   HOH Z 313 " =    1.720
peak=    3.646 closest distance to " O   HOH Z 368 " =    1.920
peak=    3.646 closest distance to " CB  SER A  26 " =    1.774
peak=    3.644 closest distance to " O   HOH Z 427 " =    3.046
peak=    3.643 closest distance to " CB  ALA A   9 " =    1.666
peak=    3.641 closest distance to " O   ASP A 200 " =    1.684
peak=    3.638 closest distance to " O   HOH Z 298 " =    1.790
peak=    3.632 closest distance to " CA  ASP A 191 " =    0.983
peak=    3.632 closest distance to " O   HOH Z 126 " =    1.959
peak=    3.629 closest distance to " CZ3 TRP A 274 " =    4.451
peak=    3.623 closest distance to " CA  TYR A 116 " =    1.373
peak=    3.623 closest distance to " O  BHOH Z 338 " =    2.232
peak=    3.622 closest distance to " NH2 ARG A 156 " =    1.114
peak=    3.621 closest distance to " CB  TRP A 150 " =    1.520
peak=    3.616 closest distance to " CA  GLY A 267 " =    0.891
peak=    3.613 closest distance to " O   HOH Z 303 " =    2.305
peak=    3.600 closest distance to " O   HOH Z 433 " =    1.568
peak=    3.594 closest distance to " O   HOH Z 437 " =    1.697
peak=    3.593 closest distance to " O   HOH Z 420 " =    5.603
peak=    3.588 closest distance to " CD  PRO A  54 " =    0.997
peak=    3.577 closest distance to " CB  SER A  62 " =    0.889
peak=    3.568 closest distance to " O   HOH Z 154 " =    1.510
peak=    3.566 closest distance to " O   ALA A 165 " =    1.381
peak=    3.563 closest distance to " O   HOH Z  78 " =    1.683
peak=    3.560 closest distance to " O   HOH Z 141 " =    1.648
peak=    3.558 closest distance to " O   HOH Z  80 " =    1.896
peak=    3.558 closest distance to " CB  LEU A 143 " =    1.214
peak=    3.556 closest distance to " CA  PRO A  54 " =    1.386
peak=    3.554 closest distance to " OD2 ASP A 298 " =    3.843
peak=    3.553 closest distance to " CD  ARG A 269 " =    0.984
peak=    3.546 closest distance to " O   HOH Z 213 " =    1.768
peak=    3.543 closest distance to " OE1 GLU A   2 " =    1.638
peak=    3.541 closest distance to " O   HOH Z 102 " =    1.311
peak=    3.537 closest distance to " CD  ARG A 159 " =    0.783
peak=    3.537 closest distance to " O   HOH Z 353 " =    2.535
peak=    3.532 closest distance to " CB  ASN A 187 " =    1.091
peak=    3.530 closest distance to " CA  ALA A 160 " =    1.046
peak=    3.530 closest distance to " CB  GLN A  89 " =    1.117
peak=    3.529 closest distance to " CD1 LEU A 300 " =    1.093
peak=    3.527 closest distance to " O   HOH Z 273 " =    2.862
peak=    3.525 closest distance to " CB  PRO A 198 " =    1.033
peak=    3.525 closest distance to " CA  ASP A 162 " =    1.018
peak=    3.523 closest distance to " CG2 ILE A 234 " =    1.103
peak=    3.522 closest distance to " CE1 TYR A 186 " =    1.243
peak=    3.522 closest distance to " CE3 TRP A  85 " =    1.048
peak=    3.520 closest distance to " O   HOH Z 393 " =    3.754
peak=    3.517 closest distance to " O   HOH Z 203 " =    1.749
peak=    3.515 closest distance to " O   HOH Z 193 " =    1.820
peak=    3.512 closest distance to " O   HOH Z 383 " =    1.912
peak=    3.507 closest distance to " O   PRO A 213 " =    1.441
peak=    3.506 closest distance to " O   HOH Z 193 " =    1.898
peak=    3.503 closest distance to " O   HOH Z  63 " =    1.205
peak=    3.500 closest distance to " CG  PHE A 204 " =    0.997
peak=    3.498 closest distance to " OD1 ASN A  69 " =    2.430
peak=    3.494 closest distance to " CA  MET A 105 " =    0.959
peak=    3.483 closest distance to " CE  LYS A  76 " =    0.875
peak=    3.481 closest distance to " CB  SER A   3 " =    1.410
peak=    3.479 closest distance to " N   SER A 164 " =    0.940
peak=    3.474 closest distance to " CZ  PHE A 192 " =    1.067
peak=    3.471 closest distance to " O   HOH Z 406 " =    1.522
peak=    3.467 closest distance to " O   HOH Z 313 " =    1.685
peak=    3.465 closest distance to " CB  SER A 141 " =    1.146
peak=    3.463 closest distance to " CG1 ILE A  33 " =    1.253
peak=    3.462 closest distance to " CZ3 TRP A  92 " =    1.409
peak=    3.456 closest distance to " CG2AVAL A 121 " =    2.087
peak=    3.454 closest distance to " CG  LEU A 167 " =    1.092
peak=    3.453 closest distance to " ND2 ASN A 249 " =    1.922
peak=    3.445 closest distance to " CB  ALA A 248 " =    1.378
peak=    3.441 closest distance to " O   HOH Z 151 " =    1.708
peak=    3.440 closest distance to " CD  LYS A 119 " =    1.930
peak=    3.434 closest distance to " CB  VAL A 265 " =    1.280
peak=    3.432 closest distance to " CA  ALA A 291 " =    0.843
peak=    3.432 closest distance to " O   HOH Z 368 " =    3.379
peak=    3.432 closest distance to " O   HOH Z 327 " =    2.288
peak=    3.431 closest distance to " CG  GLU A  37 " =    0.970
peak=    3.430 closest distance to " O   ASN A 209 " =    1.258
peak=    3.420 closest distance to " CA  ARG A  36 " =    1.100
peak=    3.417 closest distance to " CG1 ILE A 120 " =    1.053
peak=    3.416 closest distance to " CB  MET A  40 " =    0.925
peak=    3.415 closest distance to " CB  ARG A  79 " =    0.937
peak=    3.415 closest distance to " CG1 ILE A  49 " =    1.608
peak=    3.414 closest distance to " O   HOH Z 258 " =    2.085
peak=    3.413 closest distance to " CB  ASP A 107 " =    1.177
peak=    3.411 closest distance to " CA  LEU A 282 " =    1.100
peak=    3.408 closest distance to " O   HOH Z   3 " =    2.011
peak=    3.408 closest distance to " O   HOH Z 417 " =    3.098
peak=    3.403 closest distance to " CA  VAL A  41 " =    0.726
peak=    3.396 closest distance to " CB  PRO A  90 " =    1.222
peak=    3.394 closest distance to " OE1 GLN A  11 " =    1.948
peak=    3.393 closest distance to " O   THR A 182 " =    1.421
peak=    3.390 closest distance to " O   HOH Z  21 " =    1.748
peak=    3.389 closest distance to " N   ARG A 190 " =    1.035
peak=    3.388 closest distance to " O   HOH Z 407 " =    2.548
peak=    3.385 closest distance to " CB  ALA A 100 " =    1.335
peak=    3.383 closest distance to " NH2AARG A 145 " =    1.101
peak=    3.379 closest distance to " CD1 ILE A 199 " =    1.037
peak=    3.379 closest distance to " CB  ALA A 291 " =    1.166
peak=    3.379 closest distance to " CG  ARG A 138 " =    1.263
peak=    3.372 closest distance to " O   HOH Z  59 " =    2.134
peak=    3.367 closest distance to " O   HOH Z 120 " =    2.743
peak=    3.364 closest distance to " CB  SER A 273 " =    0.997
peak=    3.364 closest distance to " N   CYS A 260 " =    0.835
peak=    3.364 closest distance to " CG  MET A 188 " =    0.853
peak=    3.362 closest distance to " O   HOH Z  19 " =    1.862
peak=    3.360 closest distance to " CB  THR A  52 " =    1.065
peak=    3.350 closest distance to " CA  VAL A 125 " =    1.211
peak=    3.343 closest distance to " O   PRO A  90 " =    1.470
peak=    3.342 closest distance to " NZ  LYS A  48 " =    1.295
peak=    3.342 closest distance to " CD  ARG A  66 " =    2.260
peak=    3.338 closest distance to " CB  ASN A 285 " =    0.953
peak=    3.335 closest distance to " CB  PRO A 243 " =    1.487
peak=    3.333 closest distance to " N   PHE A 130 " =    1.234
peak=    3.332 closest distance to " CA  ALA A 100 " =    0.996
peak=    3.327 closest distance to " O   LEU A 228 " =    1.914
peak=    3.325 closest distance to " CD1 LEU A 101 " =    1.101
peak=    3.323 closest distance to " CD2 TYR A 186 " =    0.999
peak=    3.321 closest distance to " CE3 TRP A 150 " =    1.066
peak=    3.318 closest distance to " O   HOH Z 158 " =    3.016
peak=    3.315 closest distance to " CB  MET A  47 " =    1.063
peak=    3.314 closest distance to " O   HOH Z 337 " =    1.833
peak=    3.313 closest distance to " O   HOH Z 343 " =    2.739
peak=    3.313 closest distance to " NH1 ARG A  14 " =    1.032
peak=    3.312 closest distance to " O   HOH Z  83 " =    1.539
peak=    3.311 closest distance to " CE1 HIS A 115 " =    1.031
peak=    3.310 closest distance to " O   HOH Z 299 " =    4.367
peak=    3.309 closest distance to " O   HOH Z 391 " =    2.941
peak=    3.309 closest distance to " CB  ARG A 219 " =    1.409
peak=    3.306 closest distance to " CD1 ILE A  33 " =    1.744
peak=    3.304 closest distance to " CZ  PHE A  38 " =    1.166
peak=    3.301 closest distance to " CB  SER A 288 " =    1.437
peak=    3.295 closest distance to " O   HOH Z 174 " =    2.286
peak=    3.294 closest distance to " CB  GLN A 103 " =    0.900
peak=    3.292 closest distance to " CB  ASN A 215 " =    1.227
peak=    3.291 closest distance to " CG  GLN A  77 " =    0.890
peak=    3.290 closest distance to " O   THR A 220 " =    1.280
peak=    3.289 closest distance to " CA  LYS A 117 " =    1.234
peak=    3.289 closest distance to " O   HOH Z 184 " =    1.524
peak=    3.289 closest distance to " CA  GLU A 152 " =    0.948
peak=    3.287 closest distance to " O   HOH Z 132 " =    2.786
peak=    3.284 closest distance to " O   HOH Z 197 " =    1.800
peak=    3.281 closest distance to " O   ASN A  74 " =    1.938
peak=    3.281 closest distance to " O   HOH Z 116 " =    1.808
peak=    3.280 closest distance to " CA  ASN A 217 " =    1.246
peak=    3.280 closest distance to " CG2AVAL A  72 " =    1.800
peak=    3.278 closest distance to " O   HOH Z 238 " =    0.920
peak=    3.277 closest distance to " O   HOH Z 357 " =    2.583
peak=    3.272 closest distance to " O   HOH Z 134 " =    1.348
peak=    3.268 closest distance to " O   HOH Z 148 " =    3.233
peak=    3.265 closest distance to " CA  ALA A 154 " =    1.058
peak=    3.259 closest distance to " O  BHOH Z  74 " =    1.310
peak=    3.253 closest distance to " O   HOH Z 371 " =    2.554
peak=    3.247 closest distance to " CB  ALA A 104 " =    0.765
peak=    3.247 closest distance to " CB  ALA A 248 " =    1.118
peak=    3.239 closest distance to " CG  GLN A  58 " =    2.945
peak=    3.236 closest distance to " O   HOH Z  47 " =    2.790
peak=    3.236 closest distance to " O   HOH Z   9 " =    2.000
peak=    3.235 closest distance to " OG1 THR A 294 " =    2.396
peak=    3.235 closest distance to " CB  VAL A 257 " =    0.765
peak=    3.235 closest distance to " CG  MET A 185 " =    0.900
peak=    3.233 closest distance to " O   ASP A 124 " =    1.790
peak=    3.229 closest distance to " O   HOH Z 146 " =    2.106
peak=    3.227 closest distance to " CB  ASN A 187 " =    1.495
peak=    3.226 closest distance to " CG1 ILE A  20 " =    1.275
peak=    3.225 closest distance to " OD1 ASN A 217 " =    1.587
peak=    3.224 closest distance to " O   HOH Z 133 " =    2.466
peak=    3.224 closest distance to " O   GLU A   2 " =    1.541
peak=    3.222 closest distance to " O   HOH Z 368 " =    4.148
peak=    3.221 closest distance to " O   ASN A 284 " =    1.820
peak=    3.212 closest distance to " CA  THR A 264 " =    0.761
peak=    3.209 closest distance to " O   HOH Z 193 " =    1.899
peak=    3.206 closest distance to " O   HOH Z 365 " =    2.825
peak=    3.205 closest distance to " CD  ARG A 195 " =    1.004
peak=    3.204 closest distance to " CB  ALA A 242 " =    0.806
peak=    3.201 closest distance to " O   HOH Z 147 " =    1.744
peak=    3.198 closest distance to " O   HOH Z 329 " =    3.176
peak=    3.197 closest distance to " O   HOH Z  88 " =    3.267
peak=    3.196 closest distance to " CG2 VAL A 197 " =    1.095
peak=    3.194 closest distance to " O   HOH Z 124 " =    1.133
peak=    3.191 closest distance to " CA  ASP A 140 " =    1.307
peak=    3.191 closest distance to " O   HOH Z  61 " =    1.563
peak=    3.189 closest distance to " O   HOH Z 166 " =    1.627
peak=    3.179 closest distance to " N   VAL A 126 " =    1.583
peak=    3.173 closest distance to " CB  THR A  31 " =    1.427
peak=    3.172 closest distance to " CE1 HIS A 108 " =    1.221
peak=    3.171 closest distance to " O   HOH Z 117 " =    1.853
peak=    3.164 closest distance to " O   ALA A 158 " =    1.248
peak=    3.162 closest distance to " CA  ASN A 127 " =    1.077
peak=    3.159 closest distance to " O   HOH Z 156 " =    2.602
peak=    3.157 closest distance to " CB  PHE A 283 " =    0.786
peak=    3.156 closest distance to " O   HOH Z 344 " =    2.977
peak=    3.156 closest distance to " O   HOH Z 329 " =    4.184
peak=    3.150 closest distance to " CD ALYS A 290 " =    1.072
peak=    3.150 closest distance to " O   HOH Z 393 " =    3.256
peak=    3.148 closest distance to " OG BSER A 134 " =    2.761
peak=    3.144 closest distance to " O   HOH Z 271 " =    2.445
peak=    3.142 closest distance to " CG2 ILE A 120 " =    1.140
peak=    3.142 closest distance to " O   HOH Z 148 " =    2.039
peak=    3.139 closest distance to " O   HOH Z 109 " =    2.596
peak=    3.139 closest distance to " O   HOH Z 163 " =    1.615
peak=    3.133 closest distance to " ND2 ASN A 249 " =    0.887
peak=    3.132 closest distance to " CG2 ILE A  20 " =    1.300
peak=    3.131 closest distance to " CA  GLY A 241 " =    0.910
peak=    3.127 closest distance to " CB  LEU A 300 " =    0.946
peak=    3.126 closest distance to " CE  LYS A 119 " =    1.131
peak=    3.113 closest distance to " O   HOH Z 145 " =    2.172
peak=    3.111 closest distance to " OE1 GLN A  55 " =    1.425
peak=    3.107 closest distance to " NZ  LYS A 117 " =    1.392
peak=    3.103 closest distance to " O   GLY A  91 " =    1.251
peak=    3.103 closest distance to " OD1 ASN A 148 " =    1.646
peak=    3.101 closest distance to " O   HOH Z 261 " =    1.249
peak=    3.096 closest distance to " CA  GLU A  46 " =    0.743
peak=    3.096 closest distance to " CA  GLY A  35 " =    1.028
peak=    3.092 closest distance to " O   PHE A 192 " =    1.427
peak=    3.082 closest distance to " CB  SER A  97 " =    1.241
peak=    3.072 closest distance to " O   MET A 105 " =    1.717
peak=    3.067 closest distance to " CA  GLY A 211 " =    1.361
peak=    3.064 closest distance to " O   HOH Z  90 " =    3.449
peak=    3.060 closest distance to " O   HOH Z 201 " =    2.947
peak=    3.058 closest distance to " CB  ALA A  43 " =    0.960
peak=    3.054 closest distance to " O   HOH Z 263 " =    1.652
peak=    3.045 closest distance to " O   HOH Z 124 " =    1.813
peak=    3.007 closest distance to " CB  SER A  62 " =    1.245

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 216         
Filter by distance & map next to the model:
   mapped sites are within: 0.654 - 5.648
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 214 from: 216
   mapped sites are within: 0.738 - 5.648

peak=   -5.606 closest distance to " CG2 VAL A 230 " =    0.738
peak=   -4.446 closest distance to " O   HOH Z 166 " =    1.513
peak=   -4.391 closest distance to " CD  GLN A  58 " =    0.965
peak=   -4.281 closest distance to " CG1 VAL A 250 " =    2.712
peak=   -4.274 closest distance to " O   HOH Z  10 " =    1.650
peak=   -4.249 closest distance to " CG2BVAL A  41 " =    2.776
peak=   -4.220 closest distance to " O   HOH Z 411 " =    5.579
peak=   -4.209 closest distance to " O   HOH Z 211 " =    1.042
peak=   -4.182 closest distance to " CG1 VAL A 296 " =    1.114
peak=   -4.100 closest distance to " CG  ARG A 269 " =    2.324
peak=   -4.091 closest distance to " CG1 VAL A 112 " =    2.687
peak=   -4.075 closest distance to " CE2 TYR A  30 " =    2.735
peak=   -4.070 closest distance to " O   HOH Z 351 " =    1.629
peak=   -4.067 closest distance to " O   HOH Z 193 " =    1.303
peak=   -4.066 closest distance to " O   HOH Z 196 " =    2.588
peak=   -4.063 closest distance to " CD  ARG A  14 " =    3.283
peak=   -4.025 closest distance to " CD1 PHE A  59 " =    2.026
peak=   -4.007 closest distance to " CG2 ILE A  49 " =    2.889
peak=   -3.987 closest distance to " CB  PRO A 243 " =    2.744
peak=   -3.985 closest distance to " CD  ARG A 156 " =    2.072
peak=   -3.976 closest distance to " O   SER A 271 " =    2.150
peak=   -3.950 closest distance to " O   PRO A 198 " =    1.225
peak=   -3.940 closest distance to " CA  ASP A 298 " =    1.108
peak=   -3.925 closest distance to " CD2 TYR A 293 " =    1.947
peak=   -3.870 closest distance to " CE2 PHE A  61 " =    2.644
peak=   -3.855 closest distance to " O   HOH Z 394 " =    1.584
peak=   -3.854 closest distance to " O   HOH Z  37 " =    2.112
peak=   -3.851 closest distance to " CB  ALA A 161 " =    2.591
peak=   -3.832 closest distance to " CH2 TRP A 179 " =    1.180
peak=   -3.820 closest distance to " OD1 ASN A 148 " =    1.385
peak=   -3.819 closest distance to " CE3 TRP A  70 " =    1.863
peak=   -3.788 closest distance to " CD1 LEU A 101 " =    2.416
peak=   -3.766 closest distance to " CG  GLN A 103 " =    2.513
peak=   -3.760 closest distance to " O   HOH Z 200 " =    1.534
peak=   -3.739 closest distance to " O   HOH Z  73 " =    2.472
peak=   -3.732 closest distance to " CG2 VAL A 189 " =    2.095
peak=   -3.731 closest distance to " O   PRO A 163 " =    2.215
peak=   -3.724 closest distance to " O   HOH Z 438 " =    3.042
peak=   -3.716 closest distance to " CE3 TRP A 150 " =    2.382
peak=   -3.715 closest distance to " O   HOH Z 210 " =    0.773
peak=   -3.669 closest distance to " O   HOH Z 290 " =    1.062
peak=   -3.669 closest distance to " O   HOH Z 216 " =    1.021
peak=   -3.663 closest distance to " CG1 VAL A 112 " =    2.710
peak=   -3.651 closest distance to " CB  ALA A 248 " =    2.277
peak=   -3.625 closest distance to " O   HOH Z  52 " =    1.783
peak=   -3.616 closest distance to " CD  GLN A  73 " =    0.771
peak=   -3.604 closest distance to " O   HOH Z 133 " =    0.970
peak=   -3.600 closest distance to " OE1 GLN A  88 " =    0.953
peak=   -3.598 closest distance to " O   HOH Z 285 " =    1.955
peak=   -3.598 closest distance to " O   HOH Z 149 " =    2.119
peak=   -3.597 closest distance to " CG  MET A 105 " =    0.947
peak=   -3.592 closest distance to " CG2 VAL A 202 " =    2.778
peak=   -3.578 closest distance to " CD  PRO A 243 " =    1.932
peak=   -3.572 closest distance to " O   HOH Z 150 " =    1.746
peak=   -3.571 closest distance to " CA  VAL A  67 " =    2.931
peak=   -3.566 closest distance to " CA  TYR A  68 " =    2.904
peak=   -3.562 closest distance to " O   SER A 210 " =    1.742
peak=   -3.560 closest distance to " C   HIS A 108 " =    1.197
peak=   -3.551 closest distance to " O   HOH Z 185 " =    2.500
peak=   -3.542 closest distance to " O   HOH Z 340 " =    1.380
peak=   -3.531 closest distance to " N   ALA A 226 " =    2.058
peak=   -3.519 closest distance to " C   SER A 206 " =    1.393
peak=   -3.514 closest distance to " CG  GLU A 277 " =    1.286
peak=   -3.512 closest distance to " CA  GLY A 241 " =    3.225
peak=   -3.510 closest distance to " CD2 PHE A  61 " =    2.087
peak=   -3.509 closest distance to " O   TYR A 186 " =    1.857
peak=   -3.500 closest distance to " CD  GLN A  88 " =    0.919
peak=   -3.496 closest distance to " CG2BVAL A  41 " =    1.766
peak=   -3.491 closest distance to " CG  GLU A  53 " =    1.593
peak=   -3.489 closest distance to " ND2BASN A 224 " =    1.915
peak=   -3.488 closest distance to " CB  ALA A 248 " =    2.150
peak=   -3.488 closest distance to " CZ  ARG A 259 " =    0.875
peak=   -3.485 closest distance to " OG BSER A 134 " =    1.402
peak=   -3.485 closest distance to " CD  GLN A 223 " =    1.224
peak=   -3.485 closest distance to " O   HOH Z 407 " =    3.115
peak=   -3.480 closest distance to " CG  LEU A   5 " =    0.895
peak=   -3.475 closest distance to " CG  PRO A 243 " =    1.650
peak=   -3.473 closest distance to " CA  LYS A 166 " =    2.143
peak=   -3.471 closest distance to " OE2 GLU A 277 " =    2.834
peak=   -3.468 closest distance to " OD1 ASN A 173 " =    1.430
peak=   -3.462 closest distance to " CZ  TYR A 169 " =    1.754
peak=   -3.450 closest distance to " O   HOH Z 128 " =    2.637
peak=   -3.447 closest distance to " O   HOH Z 136 " =    2.644
peak=   -3.440 closest distance to " CB  ALA A  10 " =    2.235
peak=   -3.439 closest distance to " CG  GLN A  58 " =    1.265
peak=   -3.439 closest distance to " O   HOH Z  13 " =    1.793
peak=   -3.436 closest distance to " O   HOH Z 166 " =    1.532
peak=   -3.431 closest distance to " O   HOH Z 231 " =    2.263
peak=   -3.431 closest distance to " O   HOH Z 396 " =    2.209
peak=   -3.427 closest distance to " O   HOH Z 251 " =    4.855
peak=   -3.418 closest distance to " CG  ASP A 231 " =    0.819
peak=   -3.417 closest distance to " O   HOH Z  93 " =    2.307
peak=   -3.417 closest distance to " NE  ARG A  66 " =    4.232
peak=   -3.408 closest distance to " C   ALA A 158 " =    1.405
peak=   -3.408 closest distance to " CE2 TRP A  70 " =    2.153
peak=   -3.404 closest distance to " NE2 GLN A 194 " =    1.954
peak=   -3.400 closest distance to " CD  LYS A 289 " =    2.374
peak=   -3.394 closest distance to " O   HOH Z 177 " =    1.961
peak=   -3.391 closest distance to " O   HOH Z 431 " =    2.349
peak=   -3.384 closest distance to " NH2 ARG A  36 " =    2.512
peak=   -3.382 closest distance to " CA  GLY A 241 " =    2.339
peak=   -3.380 closest distance to " O   SER A 276 " =    1.701
peak=   -3.378 closest distance to " C   ASN A 285 " =    2.402
peak=   -3.377 closest distance to " O   GLY A  17 " =    1.243
peak=   -3.360 closest distance to " CG1BVAL A  72 " =    2.539
peak=   -3.359 closest distance to " N   ALA A  43 " =    2.693
peak=   -3.354 closest distance to " CE  LYS A  76 " =    2.647
peak=   -3.352 closest distance to " O   ALA A 299 " =    2.329
peak=   -3.352 closest distance to " CG2 ILE A 263 " =    2.308
peak=   -3.350 closest distance to " CG2 THR A 178 " =    2.464
peak=   -3.349 closest distance to " O   HOH Z 377 " =    1.959
peak=   -3.344 closest distance to " C   LEU A 143 " =    1.094
peak=   -3.342 closest distance to " NH2 ARG A 159 " =    2.393
peak=   -3.341 closest distance to " O   HOH Z 174 " =    3.877
peak=   -3.340 closest distance to " O   HOH Z 411 " =    1.715
peak=   -3.335 closest distance to " CD2 PHE A 192 " =    2.109
peak=   -3.334 closest distance to " OD1 ASP A 171 " =    1.628
peak=   -3.332 closest distance to " O   HOH Z 107 " =    0.942
peak=   -3.330 closest distance to " OG BSER A 210 " =    1.485
peak=   -3.330 closest distance to " O   ALA A 227 " =    1.482
peak=   -3.330 closest distance to " OG  SER A  97 " =    2.328
peak=   -3.316 closest distance to " O   GLY A  80 " =    2.668
peak=   -3.314 closest distance to " OG  SER A  63 " =    1.136
peak=   -3.313 closest distance to " O   HOH Z 227 " =    1.208
peak=   -3.310 closest distance to " O   HOH Z  60 " =    1.814
peak=   -3.309 closest distance to " O   HOH Z 348 " =    2.323
peak=   -3.306 closest distance to " CD2 LEU A 300 " =    2.597
peak=   -3.301 closest distance to " O   HOH Z 114 " =    3.183
peak=   -3.301 closest distance to " O   GLY A 203 " =    2.415
peak=   -3.299 closest distance to " O   HOH Z 110 " =    1.590
peak=   -3.295 closest distance to " O   HOH Z 234 " =    4.417
peak=   -3.294 closest distance to " CB  VAL A 230 " =    1.118
peak=   -3.294 closest distance to " CD2 LEU A 167 " =    1.818
peak=   -3.292 closest distance to " CA  GLY A 133 " =    2.375
peak=   -3.292 closest distance to " O   HOH Z  11 " =    1.946
peak=   -3.291 closest distance to " O   GLN A  94 " =    2.345
peak=   -3.289 closest distance to " O   ASP A  27 " =    2.105
peak=   -3.288 closest distance to " CH2 TRP A 150 " =    1.084
peak=   -3.286 closest distance to " OE1 GLN A 223 " =    2.148
peak=   -3.282 closest distance to " O   HOH Z 359 " =    2.861
peak=   -3.281 closest distance to " O   HOH Z 236 " =    1.581
peak=   -3.278 closest distance to " N   PHE A  59 " =    2.076
peak=   -3.276 closest distance to " CG  TRP A 266 " =    1.781
peak=   -3.274 closest distance to " CZ  PHE A  38 " =    2.595
peak=   -3.271 closest distance to " O   HOH Z 191 " =    5.648
peak=   -3.269 closest distance to " CE BMET A  47 " =    1.782
peak=   -3.267 closest distance to " CG2 THR A 221 " =    2.390
peak=   -3.264 closest distance to " SG  CYS A 260 " =    2.416
peak=   -3.261 closest distance to " CG  ARG A 219 " =    2.784
peak=   -3.258 closest distance to " C   LYS A  76 " =    1.607
peak=   -3.257 closest distance to " O   HOH Z 377 " =    1.135
peak=   -3.253 closest distance to " CB  HIS A  86 " =    1.205
peak=   -3.251 closest distance to " CD1 ILE A 151 " =    2.502
peak=   -3.249 closest distance to " O   HOH Z 111 " =    1.562
peak=   -3.246 closest distance to " O   HOH Z 435 " =    2.532
peak=   -3.244 closest distance to " ND2 ASN A  45 " =    2.156
peak=   -3.242 closest distance to " NE2 GLN A  11 " =    1.547
peak=   -3.241 closest distance to " CG1 VAL A 197 " =    2.318
peak=   -3.241 closest distance to " CB  TRP A  85 " =    2.615
peak=   -3.230 closest distance to " CG  LEU A   5 " =    1.469
peak=   -3.224 closest distance to " O   HOH Z 252 " =    3.709
peak=   -3.224 closest distance to " C   MET A 188 " =    1.349
peak=   -3.221 closest distance to " O   HOH Z 171 " =    2.261
peak=   -3.219 closest distance to " ND2 ASN A  45 " =    1.167
peak=   -3.214 closest distance to " NH2 ARG A  79 " =    1.641
peak=   -3.212 closest distance to " O   HOH Z 275 " =    1.627
peak=   -3.205 closest distance to " CB  ALA A 114 " =    2.509
peak=   -3.192 closest distance to " O   SER A  95 " =    2.012
peak=   -3.192 closest distance to " CD2 PHE A 225 " =    1.183
peak=   -3.188 closest distance to " O   HOH Z 115 " =    1.736
peak=   -3.187 closest distance to " CG  LEU A  83 " =    2.082
peak=   -3.186 closest distance to " O   HOH Z 198 " =    1.985
peak=   -3.184 closest distance to " C   ASP A 270 " =    1.322
peak=   -3.183 closest distance to " NE  ARG A  79 " =    1.220
peak=   -3.183 closest distance to " O   HOH Z  78 " =    1.870
peak=   -3.180 closest distance to " O   HOH Z 259 " =    1.910
peak=   -3.175 closest distance to " CG1BVAL A  72 " =    5.577
peak=   -3.174 closest distance to " CG2 VAL A 296 " =    1.094
peak=   -3.169 closest distance to " OG  SER A  22 " =    2.193
peak=   -3.168 closest distance to " NE2 GLN A 103 " =    1.827
peak=   -3.167 closest distance to " O   HOH Z 231 " =    1.781
peak=   -3.166 closest distance to " O   HOH Z 154 " =    1.339
peak=   -3.165 closest distance to " O   HOH Z 105 " =    2.092
peak=   -3.159 closest distance to " C   ALA A 165 " =    1.908
peak=   -3.157 closest distance to " O   HOH Z  17 " =    1.472
peak=   -3.155 closest distance to " N   SER A 276 " =    1.513
peak=   -3.154 closest distance to " CG  ASP A 298 " =    0.962
peak=   -3.153 closest distance to " CZ  PHE A 283 " =    2.109
peak=   -3.150 closest distance to " SD  MET A  40 " =    2.040
peak=   -3.149 closest distance to " O   GLY A  75 " =    2.125
peak=   -3.149 closest distance to " O   HOH Z 429 " =    1.524
peak=   -3.148 closest distance to " O   HOH Z 208 " =    1.526
peak=   -3.147 closest distance to " O   HOH Z  30 " =    1.356
peak=   -3.143 closest distance to " CB  PRO A 163 " =    2.551
peak=   -3.140 closest distance to " O   HOH Z 238 " =    0.988
peak=   -3.137 closest distance to " O   HOH Z   6 " =    1.724
peak=   -3.135 closest distance to " O   HOH Z 222 " =    1.842
peak=   -3.135 closest distance to " NH2AARG A 275 " =    5.166
peak=   -3.133 closest distance to " O   HOH Z 423 " =    2.284
peak=   -3.133 closest distance to " CE3 TRP A 274 " =    2.569
peak=   -3.131 closest distance to " O   HOH Z 136 " =    0.973
peak=   -3.128 closest distance to " OH  TYR A 247 " =    1.877
peak=   -3.121 closest distance to " O   HOH Z  44 " =    0.817
peak=   -3.118 closest distance to " C   VAL A 265 " =    0.893
peak=   -3.105 closest distance to " CA  VAL A 197 " =    0.963
peak=   -3.102 closest distance to " O   HOH Z 113 " =    2.436
peak=   -3.101 closest distance to " O   HOH Z 205 " =    0.905
peak=   -3.096 closest distance to " OD2 ASP A 272 " =    1.591
peak=   -3.079 closest distance to " CZ  TYR A  68 " =    1.193
peak=   -3.065 closest distance to " CD  GLN A 223 " =    0.865
peak=   -3.057 closest distance to " O   HOH Z  38 " =    1.219
peak=   -3.049 closest distance to " CA  SER A  62 " =    2.558
peak=   -3.032 closest distance to " CB  ALA A  51 " =    1.968
peak=   -3.026 closest distance to " OG  SER A 141 " =    1.728

================= 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    :  0.4889 0.4792   6.286864e+00   6.270956e+00
   1_bss:  0.4813 0.4682   6.280110e+00   6.264787e+00
   1_xyz:  0.3996 0.4201   6.176236e+00   6.198815e+00
   1_adp:  0.3559 0.4079   6.099708e+00   6.173520e+00
   1_occ:  0.3552 0.4081   6.099102e+00   6.174343e+00
   2_bss:  0.3531 0.4037   6.100790e+00   6.173714e+00
   2_xyz:  0.2746 0.3284   5.897793e+00   6.029105e+00
   2_adp:  0.2525 0.3045   5.834752e+00   5.975192e+00
   2_occ:  0.2522 0.3049   5.834417e+00   5.975689e+00
   3_bss:  0.2514 0.3048   5.835133e+00   5.975207e+00
   3_xyz:  0.1746 0.2176   5.506927e+00   5.697383e+00
   3_adp:  0.1549 0.2029   5.414408e+00   5.629724e+00
   3_occ:  0.1547 0.2029   5.414158e+00   5.630203e+00
   4_bss:  0.1545 0.2033   5.413847e+00   5.629185e+00
   4_xyz:  0.1388 0.1861   5.329125e+00   5.545725e+00
   4_adp:  0.1355 0.1835   5.311068e+00   5.528003e+00
   4_occ:  0.1353 0.1834   5.310697e+00   5.528456e+00
   5_bss:  0.1352 0.1832   5.310287e+00   5.528072e+00
   5_xyz:  0.1241 0.1723   5.237610e+00   5.469155e+00
   5_adp:  0.1239 0.1692   5.228381e+00   5.453567e+00
   5_occ:  0.1238 0.1691   5.227779e+00   5.453036e+00
   5_bss:  0.1238 0.1687   5.226561e+00   5.450621e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.300  20.000   6.215   9.604  10.702   0.000   0.000   0.000
   1_xyz:  0.300  20.000   6.215   9.604  10.702   0.000   0.000   0.000
   1_adp:  0.300  20.000   6.215   9.604  10.702   0.000   0.000   0.000
   1_occ:  0.300  20.000   6.215   9.604  10.702   0.000   0.000   0.000
   2_bss:  0.316  51.245   3.044   5.964   6.751   0.000   0.000   0.000
   2_xyz:  0.316  51.245   3.044   5.964   6.751   0.000   0.000   0.000
   2_adp:  0.316  51.245   3.044   5.964   6.751   0.000   0.000   0.000
   2_occ:  0.316  51.245   3.044   5.964   6.751   0.000   0.000   0.000
   3_bss:  0.303  51.245   2.045   3.759   4.466   0.000   0.000   0.000
   3_xyz:  0.303  51.245   2.045   3.759   4.466   0.000   0.000   0.000
   3_adp:  0.303  51.245   2.045   3.759   4.466   0.000   0.000   0.000
   3_occ:  0.303  51.245   2.045   3.759   4.466   0.000   0.000   0.000
   4_bss:  0.315  72.684   1.638   2.715   3.744   0.000   0.000   0.000
   4_xyz:  0.315  72.684   1.638   2.715   3.744   0.000   0.000   0.000
   4_adp:  0.315  72.684   1.638   2.715   3.744   0.000   0.000   0.000
   4_occ:  0.315  72.684   1.638   2.715   3.744   0.000   0.000   0.000
   5_bss:  0.329  72.684   1.692   2.490   3.655   0.000   0.000   0.000
   5_xyz:  0.329  72.684   1.692   2.490   3.655   0.000   0.000   0.000
   5_adp:  0.329  72.684   1.692   2.490   3.655   0.000   0.000   0.000
   5_occ:  0.329  72.684   1.692   2.490   3.655   0.000   0.000   0.000
   5_bss:  0.325  68.456  -0.853  -0.194   1.048  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  57.659 0.4237  0.4791    68376.476
   1_bss:  56.713 0.4353  0.6385    67254.725
   1_xyz:  48.006 0.5440  0.7757    49938.538
   1_adp:  45.053 0.5810  0.8793    46022.101
   1_occ:  45.096 0.5805  0.8777    46129.237
   2_bss:  44.931 0.5825  0.7806    45976.918
   2_xyz:  35.148 0.6991  0.9229    29544.566
   2_adp:  31.895 0.7371  0.9462    25415.795
   2_occ:  31.918 0.7368  0.9456    25429.907
   3_bss:  31.802 0.7382  0.8883    25359.471
   3_xyz:  21.643 0.8451  0.9769    12407.935
   3_adp:  19.571 0.8656  0.9802    10674.244
   3_occ:  19.583 0.8655  0.9800    10678.202
   4_bss:  19.520 0.8662  0.9555    10646.362
   4_xyz:  17.582 0.8843  0.9611     8888.752
   4_adp:  17.082 0.8892  0.9530     8601.729
   4_occ:  17.106 0.8890  0.9526     8610.954
   5_bss:  17.089 0.8891  0.9502     8598.235
   5_xyz:  15.780 0.9003  0.9591     7554.853
   5_adp:  15.360 0.9041  0.9551     7354.698
   5_occ:  15.345 0.9042  0.9551     7345.775
   5_bss:  15.325 0.9043  0.9569     7294.657
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.093   5.4559e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.093   5.4559e+01
   1_xyz:   1.732  0.014  0.109 18.164  0.007  4.112   1.4673e-01
   1_adp:   1.732  0.014  0.109 18.164  0.007  4.112   1.4673e-01
   1_occ:   1.732  0.014  0.109 18.164  0.007  4.112   1.4673e-01
   2_bss:   1.732  0.014  0.109 18.164  0.007  4.112   1.4673e-01
   2_xyz:   1.301  0.010  0.080 16.123  0.005  4.113   9.3784e-02
   2_adp:   1.301  0.010  0.080 16.123  0.005  4.113   9.3784e-02
   2_occ:   1.301  0.010  0.080 16.123  0.005  4.113   9.3784e-02
   3_bss:   1.301  0.010  0.080 16.123  0.005  4.113   9.3784e-02
   3_xyz:   1.241  0.010  0.088 16.135  0.004  4.141   8.6429e-02
   3_adp:   1.241  0.010  0.088 16.135  0.004  4.141   8.6429e-02
   3_occ:   1.241  0.010  0.088 16.135  0.004  4.141   8.6429e-02
   4_bss:   1.241  0.010  0.088 16.135  0.004  4.141   8.6429e-02
   4_xyz:   0.974  0.007  0.074 15.304  0.003  4.117   5.9737e-02
   4_adp:   0.974  0.007  0.074 15.304  0.003  4.117   5.9737e-02
   4_occ:   0.974  0.007  0.074 15.304  0.003  4.117   5.9737e-02
   5_bss:   0.974  0.007  0.074 15.304  0.003  4.117   5.9737e-02
   5_xyz:   1.103  0.010  0.086 15.421  0.004  4.124   7.3215e-02
   5_adp:   1.103  0.010  0.086 15.421  0.004  4.124   7.3215e-02
   5_occ:   1.103  0.010  0.086 15.421  0.004  4.124   7.3215e-02
   5_bss:   1.103  0.010  0.086 15.421  0.004  4.124   7.3215e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0736e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0736e+00
   1_xyz:  14.911  0.175  0.462 89.719  0.041  2.267   1.0905e-01
   1_adp:  14.911  0.175  0.462 89.719  0.041  2.267   1.0905e-01
   1_occ:  14.911  0.175  0.462 89.719  0.041  2.267   1.0905e-01
   2_bss:  14.911  0.175  0.462 89.719  0.041  2.267   1.0905e-01
   2_xyz:  10.284  0.093  0.305 86.016  0.035  2.040   1.4847e-01
   2_adp:  10.284  0.093  0.305 86.016  0.035  2.040   1.4847e-01
   2_occ:  10.284  0.093  0.305 86.016  0.035  2.040   1.4847e-01
   3_bss:  10.284  0.093  0.305 86.016  0.035  2.040   1.4847e-01
   3_xyz:  10.073  0.055  0.336 88.596  0.038  2.286   7.1046e-02
   3_adp:  10.073  0.055  0.336 88.596  0.038  2.286   7.1046e-02
   3_occ:  10.073  0.055  0.336 88.596  0.038  2.286   7.1046e-02
   4_bss:  10.073  0.055  0.336 88.596  0.038  2.286   7.1046e-02
   4_xyz:   7.119  0.051  0.315 88.442  0.034  2.360   4.7072e-02
   4_adp:   7.119  0.051  0.315 88.442  0.034  2.360   4.7072e-02
   4_occ:   7.119  0.051  0.315 88.442  0.034  2.360   4.7072e-02
   5_bss:   7.119  0.051  0.315 88.442  0.034  2.360   4.7072e-02
   5_xyz:   7.689  0.050  0.470 87.444  0.033  2.384   4.7523e-02
   5_adp:   7.689  0.050  0.470 87.444  0.033  2.384   4.7523e-02
   5_occ:   7.689  0.050  0.470 87.444  0.033  2.384   4.7523e-02
   5_bss:   7.689  0.050  0.470 87.444  0.033  2.384   4.7523e-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: 110.49   0.00  14.29  70.98   0.00  11.76 110.49   0.00  28.02
   1_occ: 110.49   0.00  14.29  70.98   0.00  11.76 110.49   0.00  28.02
   2_bss: 110.49   0.00  14.29  70.98   0.00  11.76 110.49   0.00  28.02
   2_xyz: 110.49   0.00  14.29  70.98   0.00  11.76 110.49   0.00  28.02
   2_adp: 111.26   0.00  13.27  65.99   0.00   9.76 111.26   0.00  32.36
   2_occ: 111.26   0.00  13.27  65.99   0.00   9.76 111.26   0.00  32.36
   3_bss: 111.26   0.00  13.27  65.99   0.00   9.76 111.26   0.00  32.36
   3_xyz: 111.26   0.00  13.27  65.99   0.00   9.76 111.26   0.00  32.36
   3_adp: 102.56   0.00  14.17  97.83   0.00   9.45 102.56   1.24  39.88
   3_occ: 102.56   0.00  14.17  97.83   0.00   9.45 102.56   1.24  39.88
   4_bss: 102.56   0.00  14.17  97.83   0.00   9.45 102.56   1.24  39.88
   4_xyz: 102.56   0.00  14.17  97.83   0.00   9.45 102.56   1.24  39.88
   4_adp:  98.72   0.00  13.84  87.96   0.00   9.05  98.72   1.06  39.91
   4_occ:  98.72   0.00  13.84  87.96   0.00   9.05  98.72   1.06  39.91
   5_bss:  98.72   0.00  13.84  87.96   0.00   9.05  98.72   1.06  39.91
   5_xyz:  98.72   0.00  13.84  87.96   0.00   9.05  98.72   1.06  39.91
   5_adp:  93.51   0.00  13.09  85.55   0.00   8.59  93.51   1.45  37.59
   5_occ:  93.51   0.00  13.09  85.55   0.00   8.59  93.51   1.45  37.59
   5_bss:  96.18   2.67  15.76  88.22   2.67  11.26  96.18   4.11  40.25
------------------------------------------------------------------------
 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:    1.264    0.019    0.413
   1_adp:    1.264    0.019    0.413
   1_occ:    1.264    0.019    0.413
   2_bss:    1.264    0.019    0.413
   2_xyz:    1.951    0.016    0.591
   2_adp:    1.951    0.016    0.591
   2_occ:    1.951    0.016    0.591
   3_bss:    1.951    0.016    0.591
   3_xyz:    1.830    0.056    0.697
   3_adp:    1.830    0.056    0.697
   3_occ:    1.830    0.056    0.697
   4_bss:    1.830    0.056    0.697
   4_xyz:    2.098    0.042    0.735
   4_adp:    2.098    0.042    0.735
   4_occ:    2.098    0.042    0.735
   5_bss:    2.098    0.042    0.735
   5_xyz:    2.142    0.049    0.756
   5_adp:    2.142    0.049    0.756
   5_occ:    2.142    0.049    0.756
   5_bss:    2.142    0.049    0.756
------------------------------------------------------------------------

CPU time actual refinement: 328.64


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_823/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_823/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_823/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_823/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_823/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 328.49 
  Macro-tasks:
    bulk solvent and scale       = 39.80  
    individual site refinement   = 131.99 
    weights calculation          = 31.81  
    collect and process          = 6.61   
    model show statistics        = 0.14   
    TOTAL for macro-tasks        = 210.35 
  Micro-tasks:
    mask                            = 2.33   
    f_calc                          = 100.49 
    alpha_beta                      = 8.82   
    target                          = 1.21   
    gradients_wrt_atomic_parameters = 110.36 
    fmodel                         = 7.39   
    r_factors                      = 0.37   
    phase_errors                   = 10.61  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 241.85 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.701 micro seconds
Total CPU time: 5.70 minutes
from_scatterers_fft:    638 calls, 100.08 s
gradients_fft:          583 calls,  97.78 s

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

# Date 2008-01-16 Time 02:31:28 PST -0800 (1200479488.44 s)
Start R-work = 0.4889, R-free = 0.4792 (no bulk solvent and anisotropic scale)
Final R-work = 0.1400, R-free = 0.1836 (no bulk solvent and anisotropic scale)

Start R-work = 0.4813, R-free = 0.4682
Final R-work = 0.1238, R-free = 0.1687