# Date 2008-01-16 Time 01:46:46 PST -0800 (1200476806.30 s)
#phil __OFF__

Command line arguments: "../565.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 = 9136
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 565

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.8988, 47.3993, 85.9581, 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: 3.24, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 47.3993, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.919 1.99047
Completeness in resolution range: 0.971725
Completeness with d_max=infinity: 0.96865

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9190
                             d_min =   1.9905

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 47.3993, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.919 1.99047
Completeness in resolution range: 0.971725
Completeness with d_max=infinity: 0.96865

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9194 -  4.2582 [2114/2141]  1903   211  10.0%
  bin  2:  4.2582 -  3.3929 [2031/2047]  1827   204  10.0%
  bin  3:  3.3929 -  2.9679 [2012/2031]  1809   203  10.1%
  bin  4:  2.9679 -  2.6983 [1984/2014]  1792   192   9.7%
  bin  5:  2.6983 -  2.5059 [1967/1986]  1766   201  10.2%
  bin  6:  2.5059 -  2.3587 [1965/2001]  1770   195   9.9%
  bin  7:  2.3587 -  2.2410 [1959/1992]  1765   194   9.9%
  bin  8:  2.2410 -  2.1437 [1940/1975]  1742   198  10.2%
  bin  9:  2.1437 -  2.0614 [1941/1968]  1747   194  10.0%
  bin 10:  2.0614 -  1.9905 [1676/2004]  1509   167  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_565/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 20
        2.42 -     3.04: 2185
        3.04 -     3.66: 4692
        3.66 -     4.28: 8998
        4.28 -     4.90: 12382
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z  18 " - " O   HOH Z 102 "  2.257 3.040 -x+1,y+1/2,-z+1/2
  " OD2 ASP A 107 " - " OG BSER A 216 "  2.259 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.269 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28272 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_565/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_565/model_refine_001.geo

CPU time processing inputs: 9.06


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.89875 47.3993 85.95805 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4363   r_free= 0.4242   ksol= 0.00   Bsol= 0.00   scale= 0.822    |
|                                                                             |
| 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:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.229194                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9194 -  4.7489 0.99   1374  153 0.3613 0.3392      6.5133      6.4853|
|  2:  4.7489 -  3.7897 0.99   1322  146 0.3345 0.3576      6.6509      6.6916|
|  3:  3.7897 -  3.3167 0.99   1298  146 0.3748 0.3551      6.5758       6.574|
|  4:  3.3167 -  3.0162 0.99   1285  138 0.4142 0.3655       6.456       6.335|
|  5:  3.0162 -  2.8015 0.99   1275  143 0.4518 0.4726      6.3228      6.3635|
|  6:  2.8015 -  2.6373 0.99   1278  146 0.4573 0.5042      6.2411      6.2237|
|  7:  2.6373 -  2.5059 0.99   1265  139 0.4716 0.4377      6.2114      6.1055|
|  8:  2.5059 -  2.3972 0.98   1270  142 0.4781 0.4457      6.1633      6.1344|
|  9:  2.3972 -  2.3053 0.98   1260  139 0.4929 0.4999       6.092      6.1014|
| 10:  2.3053 -  2.2260 0.98   1248  136 0.4991 0.4827      6.1136      6.0717|
| 11:  2.2260 -  2.1566 1.00   1264  147 0.4952 0.4214      6.0219      6.0263|
| 12:  2.1566 -  2.0951 0.97   1254  128 0.5100 0.4928      5.9681      6.0104|
| 13:  2.0951 -  2.0401 0.98   1241  138 0.5021 0.5392      5.8902      5.8909|
| 14:  2.0401 -  1.9905 0.79    996  118 0.5141 0.4590      5.8375      5.7256|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9194 -  4.7489  1374   153  0.72  32.20   0.82     0.74      61681.54|
|  2:  4.7489 -  3.7897  1322   146  0.77  29.16   0.92     0.81      76163.08|
|  3:  3.7897 -  3.3167  1298   146  0.71  34.90   0.87     0.79      77913.42|
|  4:  3.3167 -  3.0162  1285   138  0.65  39.34   0.83     0.71      66514.68|
|  5:  3.0162 -  2.8015  1275   143  0.56  47.48   0.78     0.63      60685.39|
|  6:  2.8015 -  2.6373  1278   146  0.54  48.83   0.76     0.59      53947.41|
|  7:  2.6373 -  2.5059  1265   139  0.52  50.49   0.76     0.58      50928.08|
|  8:  2.5059 -  2.3972  1270   142  0.52  50.23   0.77     0.59      45043.55|
|  9:  2.3972 -  2.3053  1260   139  0.50  52.07   0.74     0.58      41654.55|
| 10:  2.3053 -  2.2260  1248   136  0.51  51.51   0.76     0.57      38650.64|
| 11:  2.2260 -  2.1566  1264   147  0.47  54.46   0.78     0.55      37501.09|
| 12:  2.1566 -  2.0951  1254   128  0.43  57.64   0.77     0.52      37046.70|
| 13:  2.0951 -  2.0401  1241   138  0.40  60.36   0.76     0.47      33525.63|
| 14:  2.0401 -  1.9905   996   118  0.39  60.85   0.74     0.43      27912.40|
|alpha:            min =        0.43 max =            0.81 mean =         0.62|
|beta:             min =    27912.40 max =        77913.42 mean =     51274.74|
|figures of merit: min =        0.00 max =            1.00 mean =         0.55|
|phase err.(work): min =        0.00 max =           90.00 mean =        47.41|
|phase err.(test): min =        0.00 max =           89.98 mean =        47.36|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.838095              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 75.447   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.676261              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.762   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       22 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      164 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      683 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1518 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2626 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3905 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5085 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6562 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7710 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.786 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.091    4.900  1.196 |       1.736 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.900)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 11.900)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4441   r_free= 0.4322   ksol= 0.00   Bsol= 0.00   scale= 0.790    |
|                                                                             |
| 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:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.234274                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4277   r_free= 0.4168   ksol= 0.34   Bsol= 17.12   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.15,9.87,7.98,0.00,0.00,0.00); trace/3= 8.33                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.221878                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.511381              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 77.192   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.681403              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.559   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4277      final r-factor (work) = 0.3191          |
| start r-factor (free) = 0.4168      final r-factor (free) = 0.3404          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 77.2363 = 7.51 * 0.50 * 6.2439 + 1.00 * 53.7860                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.9229 = 7.51 * 0.50 * 6.0716 + 1.00 * 0.1200                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3191      final r-factor (work) = 0.2558          |
| start r-factor (free) = 0.3404      final r-factor (free) = 0.2883          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1519 = 0.68 * 1.00 * 6.0716 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0301 = 0.68 * 1.00 * 5.8960 + 1.00 * 0.0126                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.900)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    64.82   10.81    None  None   None       |
|    all(noH): 2823   0      0.00    64.82   10.81    None  None   None       |
|    Sol.    : 438    0      0.00    64.82   27.49    None  None   None       |
|    Mac.    : 2385   0      0.00    64.26   7.75     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.482: 1379   |   5:    32.411 -  38.894:   97        |
|      1:     6.482 -  12.965:  688   |   6:    38.894 -  45.376:   64        |
|      2:    12.965 -  19.447:  272   |   7:    45.376 -  51.858:   41        |
|      3:    19.447 -  25.929:  156   |   8:    51.858 -  58.341:    7        |
|      4:    25.929 -  32.411:  110   |   9:    58.341 -  64.823:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2558 r_free = 0.2883             target_work(ml) = 5.833         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2553 r_free = 0.2881             target_work(ml) = 5.832         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2553   r_free= 0.2881   ksol= 0.34   Bsol= 17.12   scale= 1.088   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.15,9.87,7.98,0.00,0.00,0.00); trace/3= 8.33                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.831609                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2512   r_free= 0.2830   ksol= 0.33   Bsol= 40.66   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.89,6.04,5.16,0.00,0.00,0.00); trace/3= 5.03                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.830079                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.597551              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.529   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.351193              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 119.018  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2512      final r-factor (work) = 0.1769          |
| start r-factor (free) = 0.2830      final r-factor (free) = 0.2134          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7854 = 2.60 * 0.50 * 5.9025 + 1.00 * 0.1194                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.4079 = 2.60 * 0.50 * 5.6581 + 1.00 * 0.0593                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1769      final r-factor (work) = 0.1633          |
| start r-factor (free) = 0.2134      final r-factor (free) = 0.2013          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0011 = 0.35 * 1.00 * 5.6581 + 1.00 * 0.0140                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9392 = 0.35 * 1.00 * 5.4696 + 1.00 * 0.0183                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.900)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    71.18   11.30    None  None   None       |
|    all(noH): 2823   0      0.00    71.18   11.30    None  None   None       |
|    Sol.    : 438    0      1.19    63.80   31.84    None  None   None       |
|    Mac.    : 2385   0      0.00    71.18   7.53     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.118: 1529   |   5:    35.591 -  42.709:  110        |
|      1:     7.118 -  14.236:  649   |   6:    42.709 -  49.828:   73        |
|      2:    14.236 -  21.355:  195   |   7:    49.828 -  56.946:   38        |
|      3:    21.355 -  28.473:  109   |   8:    56.946 -  64.064:   13        |
|      4:    28.473 -  35.591:  102   |   9:    64.064 -  71.182:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1633 r_free = 0.2013             target_work(ml) = 5.445         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1632 r_free = 0.2012             target_work(ml) = 5.445         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1632   r_free= 0.2012   ksol= 0.33   Bsol= 40.66   scale= 1.032   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.89,6.04,5.16,0.00,0.00,0.00); trace/3= 5.03                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.444910                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1621   r_free= 0.2014   ksol= 0.32   Bsol= 40.66   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.83,4.20,4.25,0.00,0.00,0.00); trace/3= 3.76                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.445002                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.516436              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.268  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.240173              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 102.531  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1621      final r-factor (work) = 0.1241          |
| start r-factor (free) = 0.2014      final r-factor (free) = 0.1637          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.6877 = 3.52 * 0.50 * 5.4763 + 1.00 * 0.0593                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.4359 = 3.52 * 0.50 * 5.3274 + 1.00 * 0.0692                               |
|-----------------------------------------------------------------------------|
| 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) = 0.1192          |
| start r-factor (free) = 0.1637      final r-factor (free) = 0.1575          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2940 = 0.24 * 1.00 * 5.3274 + 1.00 * 0.0145                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2574 = 0.24 * 1.00 * 5.1937 + 1.00 * 0.0100                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.900)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    72.45   11.26    None  None   None       |
|    all(noH): 2823   0      0.00    72.45   11.26    None  None   None       |
|    Sol.    : 438    0      0.91    62.43   32.52    None  None   None       |
|    Mac.    : 2385   0      0.00    72.45   7.36     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.245: 1604   |   5:    36.226 -  43.471:   97        |
|      1:     7.245 -  14.490:  612   |   6:    43.471 -  50.716:   75        |
|      2:    14.490 -  21.735:  161   |   7:    50.716 -  57.961:   35        |
|      3:    21.735 -  28.981:  109   |   8:    57.961 -  65.206:   13        |
|      4:    28.981 -  36.226:  111   |   9:    65.206 -  72.451:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1192 r_free = 0.1575             target_work(ml) = 5.176         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1191 r_free = 0.1574             target_work(ml) = 5.175         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1191   r_free= 0.1574   ksol= 0.32   Bsol= 40.66   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.83,4.20,4.25,0.00,0.00,0.00); trace/3= 3.76                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.175417                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1195   r_free= 0.1576   ksol= 0.32   Bsol= 44.57   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.63,3.64,4.05,0.00,0.00,0.00); trace/3= 3.44                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.177561                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.407712              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 135.590  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.157052              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 119.578  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1195      final r-factor (work) = 0.1137          |
| start r-factor (free) = 0.1576      final r-factor (free) = 0.1555          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3236 = 2.41 * 0.50 * 5.1953 + 1.00 * 0.0692                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2746 = 2.41 * 0.50 * 5.1566 + 1.00 * 0.0667                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1137      final r-factor (work) = 0.1140          |
| start r-factor (free) = 0.1555      final r-factor (free) = 0.1549          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8202 = 0.16 * 1.00 * 5.1566 + 1.00 * 0.0104                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8181 = 0.16 * 1.00 * 5.1497 + 1.00 * 0.0093                               |
|-----------------------------------------------------------------------------|
| number of iterations = 19      |    number of function evaluations = 33     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.900)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    72.31   11.22    None  None   None       |
|    all(noH): 2823   0      0.00    72.31   11.22    None  None   None       |
|    Sol.    : 438    0      0.97    62.35   32.32    None  None   None       |
|    Mac.    : 2385   0      0.00    72.31   7.34     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.231: 1631   |   5:    36.156 -  43.387:   97        |
|      1:     7.231 -  14.462:  593   |   6:    43.387 -  50.618:   73        |
|      2:    14.462 -  21.693:  153   |   7:    50.618 -  57.849:   36        |
|      3:    21.693 -  28.925:  114   |   8:    57.849 -  65.080:   12        |
|      4:    28.925 -  36.156:  108   |   9:    65.080 -  72.311:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1140 r_free = 0.1549             target_work(ml) = 5.147         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1139 r_free = 0.1551             target_work(ml) = 5.147         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1139   r_free= 0.1551   ksol= 0.32   Bsol= 44.57   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.63,3.64,4.05,0.00,0.00,0.00); trace/3= 3.44                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.147281                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1139   r_free= 0.1550   ksol= 0.33   Bsol= 44.57   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.59,3.48,4.00,0.00,0.00,0.00); trace/3= 3.36                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.147202                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.081668              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 158.976  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.136397              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 134.195  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1139      final r-factor (work) = 0.1131          |
| start r-factor (free) = 0.1550      final r-factor (free) = 0.1541          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4261 = 2.08 * 0.50 * 5.1491 + 1.00 * 0.0667                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4189 = 2.08 * 0.50 * 5.1448 + 1.00 * 0.0639                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1131      final r-factor (work) = 0.1109          |
| start r-factor (free) = 0.1541      final r-factor (free) = 0.1558          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.0007 = 2.14 * 1.00 * 5.1448 + 1.00 * 0.0093                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.9796 = 2.14 * 1.00 * 5.1318 + 1.00 * 0.0160                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.900)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.98   11.64    None  None   None       |
|    all(noH): 2823   0      0.00    83.98   11.64    None  None   None       |
|    Sol.    : 438    0      0.92    72.13   34.33    None  None   None       |
|    Mac.    : 2385   0      0.00    83.98   7.47     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 -   8.398: 1756   |   5:    41.990 -  50.388:   87        |
|      1:     8.398 -  16.796:  508   |   6:    50.388 -  58.786:   62        |
|      2:    16.796 -  25.194:  156   |   7:    58.786 -  67.184:   20        |
|      3:    25.194 -  33.592:  109   |   8:    67.184 -  75.582:    9        |
|      4:    33.592 -  41.990:  111   |   9:    75.582 -  83.980:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1109 r_free = 0.1558             target_work(ml) = 5.141         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1108 r_free = 0.1558             target_work(ml) = 5.141         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1108   r_free= 0.1558   ksol= 0.33   Bsol= 44.57   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.59,3.48,4.00,0.00,0.00,0.00); trace/3= 3.36                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.140514                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9194 -  4.7489 0.99   1374  153 0.1003 0.1255      5.3861      5.5022|
|  2:  4.7489 -  3.7897 0.99   1322  146 0.0858 0.1114       5.439       5.637|
|  3:  3.7897 -  3.3167 0.99   1298  146 0.1049 0.1464      5.4714      5.8535|
|  4:  3.3167 -  3.0162 0.99   1285  138 0.1191 0.1489      5.4428      5.5905|
|  5:  3.0162 -  2.8015 0.99   1275  143 0.1288 0.1700      5.3218      5.5172|
|  6:  2.8015 -  2.6373 0.99   1278  146 0.1223 0.1825      5.2171        5.47|
|  7:  2.6373 -  2.5059 0.99   1265  139 0.1232 0.1622      5.1609      5.3499|
|  8:  2.5059 -  2.3972 0.98   1270  142 0.1159 0.1768      5.0834       5.377|
|  9:  2.3972 -  2.3053 0.98   1260  139 0.1152 0.1832      5.0252      5.2829|
| 10:  2.3053 -  2.2260 0.98   1248  136 0.1103 0.1692      4.9763      5.2271|
| 11:  2.2260 -  2.1566 1.00   1264  147 0.1118 0.1688      4.9257      5.2743|
| 12:  2.1566 -  2.0951 0.97   1254  128 0.1101 0.1666      4.8695      5.1549|
| 13:  2.0951 -  2.0401 0.98   1241  138 0.1130 0.1677      4.7957      5.0463|
| 14:  2.0401 -  1.9905 0.79    996  118 0.1045 0.1835      4.6961      4.9878|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9194 -  4.7489  1374   153  0.94   8.97   0.98     0.95       7088.67|
|  2:  4.7489 -  3.7897  1322   146  0.95   7.83   1.01     1.00       8884.80|
|  3:  3.7897 -  3.3167  1298   146  0.94  11.00   1.02     1.01      10257.95|
|  4:  3.3167 -  3.0162  1285   138  0.92  13.09   1.00     0.99       9971.15|
|  5:  3.0162 -  2.8015  1275   143  0.90  15.69   0.99     0.96       8240.43|
|  6:  2.8015 -  2.6373  1278   146  0.90  15.78   0.98     0.94       7015.46|
|  7:  2.6373 -  2.5059  1265   139  0.91  15.50   0.98     0.95       6205.99|
|  8:  2.5059 -  2.3972  1270   142  0.91  15.15   0.99     0.96       5485.13|
|  9:  2.3972 -  2.3053  1260   139  0.90  15.83   1.00     0.97       5057.49|
| 10:  2.3053 -  2.2260  1248   136  0.90  15.72   1.00     0.96       4605.41|
| 11:  2.2260 -  2.1566  1264   147  0.90  15.72   0.99     0.96       4232.75|
| 12:  2.1566 -  2.0951  1254   128  0.92  14.80   1.00     0.98       3852.50|
| 13:  2.0951 -  2.0401  1241   138  0.91  15.70   0.99     0.97       3380.97|
| 14:  2.0401 -  1.9905   996   118  0.91  15.61   0.97     0.93       2807.47|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     2807.47 max =        10257.95 mean =      6307.18|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.99 mean =        13.94|
|phase err.(test): min =        0.00 max =           89.17 mean =        13.52|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1108   r_free= 0.1557   ksol= 0.32   Bsol= 49.15   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.73,0.09,0.64,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.140391                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1108   r_free= 0.1557   ksol= 0.32   Bsol= 49.15   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.73,0.09,0.64,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.140391                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9194 -  4.7489 0.99   1374  153 0.1003 0.1258      5.3856      5.5026|
|  2:  4.7489 -  3.7897 0.99   1322  146 0.0860 0.1116      5.4405       5.639|
|  3:  3.7897 -  3.3167 0.99   1298  146 0.1050 0.1465      5.4722      5.8537|
|  4:  3.3167 -  3.0162 0.99   1285  138 0.1190 0.1488      5.4424      5.5901|
|  5:  3.0162 -  2.8015 0.99   1275  143 0.1287 0.1699      5.3209      5.5162|
|  6:  2.8015 -  2.6373 0.99   1278  146 0.1222 0.1824      5.2164      5.4693|
|  7:  2.6373 -  2.5059 0.99   1265  139 0.1232 0.1623      5.1606      5.3498|
|  8:  2.5059 -  2.3972 0.98   1270  142 0.1159 0.1767      5.0833      5.3769|
|  9:  2.3972 -  2.3053 0.98   1260  139 0.1152 0.1832      5.0251      5.2831|
| 10:  2.3053 -  2.2260 0.98   1248  136 0.1103 0.1693      4.9761       5.227|
| 11:  2.2260 -  2.1566 1.00   1264  147 0.1118 0.1687      4.9254       5.274|
| 12:  2.1566 -  2.0951 0.97   1254  128 0.1101 0.1665      4.8692      5.1544|
| 13:  2.0951 -  2.0401 0.98   1241  138 0.1130 0.1676      4.7954       5.046|
| 14:  2.0401 -  1.9905 0.79    996  118 0.1045 0.1835      4.6958      4.9873|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9194 -  4.7489  1374   153  0.94   8.98   0.98     0.95       7090.43|
|  2:  4.7489 -  3.7897  1322   146  0.95   7.84   1.02     1.00       8904.65|
|  3:  3.7897 -  3.3167  1298   146  0.94  11.02   1.02     1.02      10282.12|
|  4:  3.3167 -  3.0162  1285   138  0.92  13.08   1.01     0.99       9962.90|
|  5:  3.0162 -  2.8015  1275   143  0.90  15.68   1.00     0.96       8226.32|
|  6:  2.8015 -  2.6373  1278   146  0.90  15.77   0.98     0.95       7004.28|
|  7:  2.6373 -  2.5059  1265   139  0.91  15.50   0.99     0.96       6201.27|
|  8:  2.5059 -  2.3972  1270   142  0.91  15.15   0.99     0.97       5483.60|
|  9:  2.3972 -  2.3053  1260   139  0.90  15.83   1.01     0.97       5057.60|
| 10:  2.3053 -  2.2260  1248   136  0.90  15.72   1.01     0.97       4603.38|
| 11:  2.2260 -  2.1566  1264   147  0.90  15.71   1.00     0.96       4230.32|
| 12:  2.1566 -  2.0951  1254   128  0.92  14.80   1.01     0.99       3849.15|
| 13:  2.0951 -  2.0401  1241   138  0.91  15.70   1.00     0.98       3377.22|
| 14:  2.0401 -  1.9905   996   118  0.91  15.60   0.98     0.94       2803.73|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2803.73 max =        10282.12 mean =      6306.68|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.98 mean =        13.94|
|phase err.(test): min =        0.00 max =           89.13 mean =        13.51|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.900)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.52    87.50   15.16    None  None   None       |
|    all(noH): 2823   0      3.52    87.50   15.16    None  None   None       |
|    Sol.    : 438    0      4.44    75.65   37.85    None  None   None       |
|    Mac.    : 2385   0      3.52    87.50   10.99    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     3.518 -  11.916: 1756   |   5:    45.508 -  53.906:   87        |
|      1:    11.916 -  20.314:  508   |   6:    53.906 -  62.304:   62        |
|      2:    20.314 -  28.712:  156   |   7:    62.304 -  70.702:   20        |
|      3:    28.712 -  37.110:  109   |   8:    70.702 -  79.100:    9        |
|      4:    37.110 -  45.508:  111   |   9:    79.100 -  87.498:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 315         
Filter by distance & map next to the model:
   mapped sites are within: 0.334 - 4.827
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 308 from: 315
   mapped sites are within: 0.723 - 4.827

peak=   10.389 closest distance to " CG2 VAL A 230 " =    1.348
peak=    6.430 closest distance to " CG  LEU A   5 " =    1.147
peak=    6.359 closest distance to " CG2 VAL A 296 " =    1.084
peak=    5.759 closest distance to " NH2 ARG A  56 " =    2.296
peak=    5.732 closest distance to " CG  LEU A 228 " =    1.169
peak=    5.526 closest distance to " CB  VAL A 296 " =    1.094
peak=    5.457 closest distance to " CG  PRO A  54 " =    1.264
peak=    5.394 closest distance to " CB  VAL A 230 " =    1.182
peak=    5.361 closest distance to " CB  GLN A 223 " =    1.417
peak=    5.118 closest distance to " CB  ARG A 275 " =    0.901
peak=    4.871 closest distance to " CB  PRO A  54 " =    0.919
peak=    4.837 closest distance to " CB  SER A  63 " =    1.221
peak=    4.836 closest distance to " CD2 LEU A   5 " =    1.120
peak=    4.772 closest distance to " NE2 GLN A  11 " =    1.060
peak=    4.709 closest distance to " CB  GLN A 183 " =    1.334
peak=    4.686 closest distance to " O   HOH Z 126 " =    1.890
peak=    4.639 closest distance to " O   HOH Z 232 " =    2.360
peak=    4.565 closest distance to " CG  PRO A 213 " =    1.223
peak=    4.486 closest distance to " O   HOH Z 142 " =    1.591
peak=    4.424 closest distance to " CB  GLU A 152 " =    1.183
peak=    4.411 closest distance to " CA  TYR A  30 " =    0.915
peak=    4.409 closest distance to " C   PRO A 198 " =    1.478
peak=    4.404 closest distance to " CG  PRO A 243 " =    1.131
peak=    4.398 closest distance to " O   SER A  87 " =    2.273
peak=    4.389 closest distance to " O   HOH Z 209 " =    2.317
peak=    4.353 closest distance to " O   HOH Z  43 " =    2.148
peak=    4.342 closest distance to " O   HOH Z 193 " =    1.755
peak=    4.341 closest distance to " O   HOH Z 316 " =    2.974
peak=    4.331 closest distance to " O   HOH Z 298 " =    1.853
peak=    4.324 closest distance to " CG  PRO A 198 " =    1.189
peak=    4.317 closest distance to " O   HOH Z 402 " =    1.463
peak=    4.284 closest distance to " CB  SER A   3 " =    1.276
peak=    4.268 closest distance to " O   HOH Z 272 " =    1.910
peak=    4.217 closest distance to " O   HOH Z 369 " =    2.286
peak=    4.212 closest distance to " CZ  PHE A 218 " =    1.115
peak=    4.202 closest distance to " O   HOH Z 346 " =    1.591
peak=    4.200 closest distance to " O   HOH Z 423 " =    1.827
peak=    4.179 closest distance to " O   HOH Z 427 " =    2.938
peak=    4.170 closest distance to " O   HOH Z 236 " =    1.882
peak=    4.168 closest distance to " CB  ASN A 148 " =    1.363
peak=    4.153 closest distance to " O   HOH Z 234 " =    3.578
peak=    4.126 closest distance to " O   HOH Z 303 " =    2.120
peak=    4.124 closest distance to " CB  ARG A  79 " =    1.374
peak=    4.085 closest distance to " O   HOH Z  97 " =    1.960
peak=    4.080 closest distance to " O   HOH Z  59 " =    2.263
peak=    4.067 closest distance to " O   HOH Z 368 " =    2.289
peak=    4.055 closest distance to " O   HOH Z 203 " =    1.734
peak=    4.048 closest distance to " OD1 ASN A  69 " =    2.563
peak=    4.030 closest distance to " O   HOH Z 403 " =    1.706
peak=    4.029 closest distance to " O   HOH Z 189 " =    2.615
peak=    4.027 closest distance to " O   HOH Z  85 " =    1.330
peak=    4.004 closest distance to " O   HOH Z  80 " =    1.719
peak=    3.991 closest distance to " CB  GLU A 277 " =    3.590
peak=    3.987 closest distance to " CB  TRP A 179 " =    1.384
peak=    3.986 closest distance to " O   HOH Z 158 " =    3.095
peak=    3.982 closest distance to " CB BVAL A  41 " =    0.823
peak=    3.977 closest distance to " CD2 LEU A 228 " =    1.104
peak=    3.968 closest distance to " O   HOH Z  97 " =    2.476
peak=    3.967 closest distance to " O   HOH Z  61 " =    1.623
peak=    3.964 closest distance to " CG1BVAL A  72 " =    1.697
peak=    3.951 closest distance to " ND2 ASN A 187 " =    1.431
peak=    3.948 closest distance to " O   HOH Z 389 " =    1.919
peak=    3.946 closest distance to " O   HOH Z 124 " =    1.317
peak=    3.930 closest distance to " O   HOH Z 265 " =    2.424
peak=    3.926 closest distance to " O   HOH Z  54 " =    1.641
peak=    3.922 closest distance to " CB  VAL A 265 " =    1.259
peak=    3.912 closest distance to " CB  GLU A 128 " =    1.075
peak=    3.902 closest distance to " O   HOH Z  78 " =    1.649
peak=    3.902 closest distance to " CB  TRP A 266 " =    0.990
peak=    3.902 closest distance to " O   HOH Z 280 " =    2.920
peak=    3.896 closest distance to " CB  ARG A 139 " =    0.899
peak=    3.886 closest distance to " O   HOH Z 371 " =    3.314
peak=    3.867 closest distance to " CA  ALA A  21 " =    1.173
peak=    3.866 closest distance to " CB  ARG A 190 " =    1.656
peak=    3.862 closest distance to " OD2 ASP A 286 " =    2.797
peak=    3.841 closest distance to " O   HOH Z 197 " =    2.873
peak=    3.840 closest distance to " N   ASN A  39 " =    1.242
peak=    3.820 closest distance to " O   HOH Z 248 " =    1.626
peak=    3.818 closest distance to " O   HOH Z  40 " =    1.730
peak=    3.810 closest distance to " CA  ASN A 215 " =    1.225
peak=    3.801 closest distance to " O   HOH Z 344 " =    2.994
peak=    3.794 closest distance to " O   TRP A 274 " =    1.929
peak=    3.783 closest distance to " CB  VAL A 202 " =    1.505
peak=    3.771 closest distance to " NH2 ARG A 156 " =    1.132
peak=    3.771 closest distance to " CG1 VAL A 296 " =    1.224
peak=    3.766 closest distance to " O   HOH Z  63 " =    2.166
peak=    3.763 closest distance to " O   HOH Z 383 " =    1.959
peak=    3.753 closest distance to " O   HOH Z  15 " =    2.102
peak=    3.739 closest distance to " NZ  LYS A 117 " =    3.157
peak=    3.731 closest distance to " O   HOH Z 250 " =    1.350
peak=    3.726 closest distance to " O   HOH Z 417 " =    3.055
peak=    3.723 closest distance to " O   HOH Z 411 " =    3.834
peak=    3.719 closest distance to " O   HOH Z  48 " =    1.627
peak=    3.709 closest distance to " O   HOH Z 214 " =    2.396
peak=    3.706 closest distance to " OG BSER A 164 " =    2.187
peak=    3.698 closest distance to " CG  ARG A  66 " =    2.813
peak=    3.687 closest distance to " O   HOH Z 426 " =    1.520
peak=    3.680 closest distance to " OD2 ASP A 298 " =    3.828
peak=    3.678 closest distance to " CG1 ILE A  49 " =    1.475
peak=    3.677 closest distance to " CA  ALA A  51 " =    0.986
peak=    3.676 closest distance to " CB  ALA A 248 " =    1.407
peak=    3.675 closest distance to " O   ALA A 165 " =    1.456
peak=    3.674 closest distance to " CB  ASP A 140 " =    0.961
peak=    3.672 closest distance to " O   HOH Z  48 " =    1.508
peak=    3.664 closest distance to " O   HOH Z 245 " =    1.367
peak=    3.653 closest distance to " CB  ASN A  39 " =    0.828
peak=    3.649 closest distance to " O   HOH Z  66 " =    2.142
peak=    3.644 closest distance to " O   MET A 105 " =    1.833
peak=    3.642 closest distance to " CB  ARG A  79 " =    0.885
peak=    3.638 closest distance to " CD  LYS A 166 " =    1.321
peak=    3.636 closest distance to " CG1 VAL A 153 " =    0.959
peak=    3.635 closest distance to " CA  ASP A 140 " =    1.170
peak=    3.634 closest distance to " O   HOH Z 365 " =    2.992
peak=    3.632 closest distance to " O   HOH Z 263 " =    1.691
peak=    3.630 closest distance to " CA  ARG A 195 " =    1.208
peak=    3.622 closest distance to " O   HOH Z 345 " =    3.055
peak=    3.614 closest distance to " CE1 TYR A 186 " =    1.275
peak=    3.612 closest distance to " O   HOH Z 227 " =    1.557
peak=    3.610 closest distance to " CA  VAL A  41 " =    0.804
peak=    3.609 closest distance to " CA  LYS A 117 " =    1.283
peak=    3.607 closest distance to " CG1 ILE A  33 " =    1.269
peak=    3.606 closest distance to " O   HOH Z 128 " =    2.221
peak=    3.602 closest distance to " CD  ARG A 159 " =    0.733
peak=    3.577 closest distance to " CB  ALA A   9 " =    1.613
peak=    3.577 closest distance to " O   HOH Z 422 " =    2.669
peak=    3.570 closest distance to " CD2 TRP A 179 " =    1.371
peak=    3.558 closest distance to " CB  ASN A 142 " =    1.213
peak=    3.555 closest distance to " CD1 LEU A  96 " =    0.723
peak=    3.547 closest distance to " CA  ALA A 158 " =    1.293
peak=    3.543 closest distance to " O   HOH Z  21 " =    1.714
peak=    3.543 closest distance to " O   HOH Z 407 " =    2.627
peak=    3.543 closest distance to " CD  ARG A 269 " =    0.983
peak=    3.539 closest distance to " O   HOH Z 147 " =    1.778
peak=    3.536 closest distance to " CB  THR A  31 " =    1.584
peak=    3.536 closest distance to " O   HOH Z 357 " =    1.927
peak=    3.536 closest distance to " O   HOH Z 193 " =    2.083
peak=    3.535 closest distance to " CG2 ILE A  20 " =    1.446
peak=    3.522 closest distance to " O   HOH Z 435 " =    1.939
peak=    3.515 closest distance to " CA  ARG A  36 " =    1.000
peak=    3.502 closest distance to " CB  ALA A 291 " =    1.347
peak=    3.501 closest distance to " CG2 THR A 221 " =    1.208
peak=    3.495 closest distance to " O   HOH Z 134 " =    1.372
peak=    3.491 closest distance to " O   HOH Z 180 " =    2.167
peak=    3.488 closest distance to " O   HOH Z 261 " =    1.972
peak=    3.485 closest distance to " CB  SER A  26 " =    1.732
peak=    3.484 closest distance to " CB  THR A 157 " =    1.198
peak=    3.478 closest distance to " CG  GLN A  77 " =    2.243
peak=    3.478 closest distance to " CA  ASP A 191 " =    1.119
peak=    3.464 closest distance to " O   ASP A 124 " =    1.180
peak=    3.459 closest distance to " CG  MET A 185 " =    1.143
peak=    3.455 closest distance to " NZ  LYS A 166 " =    3.084
peak=    3.454 closest distance to " O   HOH Z 261 " =    2.213
peak=    3.453 closest distance to " O   HOH Z 247 " =    1.286
peak=    3.451 closest distance to " O   HOH Z  35 " =    2.328
peak=    3.451 closest distance to " O   HOH Z 128 " =    2.001
peak=    3.443 closest distance to " O   HOH Z 271 " =    2.585
peak=    3.441 closest distance to " O   GLN A 278 " =    1.295
peak=    3.440 closest distance to " O   HOH Z 273 " =    2.823
peak=    3.436 closest distance to " CE1 HIS A 108 " =    1.112
peak=    3.426 closest distance to " O   HOH Z 133 " =    2.620
peak=    3.424 closest distance to " O   HOH Z 250 " =    1.427
peak=    3.419 closest distance to " O   HOH Z 132 " =    2.611
peak=    3.418 closest distance to " O   HOH Z 403 " =    1.313
peak=    3.398 closest distance to " CA  THR A 221 " =    0.887
peak=    3.397 closest distance to " O   HOH Z  88 " =    2.965
peak=    3.387 closest distance to " OE1 GLU A   2 " =    2.130
peak=    3.386 closest distance to " N   ARG A 190 " =    1.054
peak=    3.380 closest distance to " CE  LYS A  76 " =    0.859
peak=    3.370 closest distance to " O   HOH Z 261 " =    1.762
peak=    3.363 closest distance to " CA  ASP A 162 " =    1.105
peak=    3.360 closest distance to " O   HOH Z 291 " =    1.522
peak=    3.359 closest distance to " O   HOH Z 209 " =    2.463
peak=    3.354 closest distance to " NE2 GLN A  77 " =    3.267
peak=    3.354 closest distance to " OE1 GLN A  11 " =    1.754
peak=    3.353 closest distance to " CD1 LEU A 300 " =    1.217
peak=    3.352 closest distance to " CB  LEU A 143 " =    1.160
peak=    3.351 closest distance to " CG2 ILE A 120 " =    1.123
peak=    3.346 closest distance to " O   HOH Z  49 " =    2.527
peak=    3.345 closest distance to " O   HOH Z 420 " =    2.074
peak=    3.345 closest distance to " CB  TRP A 150 " =    1.409
peak=    3.344 closest distance to " O   HOH Z 130 " =    2.336
peak=    3.342 closest distance to " CG2 ILE A 234 " =    2.063
peak=    3.338 closest distance to " N   VAL A 126 " =    1.398
peak=    3.337 closest distance to " O   HOH Z 298 " =    4.827
peak=    3.337 closest distance to " CG2 VAL A 257 " =    0.793
peak=    3.336 closest distance to " CB  ALA A 295 " =    1.209
peak=    3.334 closest distance to " O   HOH Z 421 " =    1.633
peak=    3.332 closest distance to " CA  VAL A 126 " =    0.969
peak=    3.325 closest distance to " CA  PHE A 283 " =    1.241
peak=    3.323 closest distance to " CD BLYS A 290 " =    1.038
peak=    3.322 closest distance to " O   HOH Z 423 " =    3.252
peak=    3.322 closest distance to " O   HOH Z 126 " =    1.595
peak=    3.320 closest distance to " CB  MET A  47 " =    1.168
peak=    3.320 closest distance to " O   HOH Z 425 " =    2.069
peak=    3.320 closest distance to " CG BARG A 102 " =    1.788
peak=    3.319 closest distance to " OG1 THR A 294 " =    2.312
peak=    3.318 closest distance to " O   HOH Z 227 " =    2.074
peak=    3.315 closest distance to " O   HOH Z 112 " =    1.622
peak=    3.314 closest distance to " CG  GLN A  58 " =    2.760
peak=    3.308 closest distance to " CG2 VAL A 197 " =    1.080
peak=    3.305 closest distance to " CB  HIS A 108 " =    0.853
peak=    3.305 closest distance to " CB  GLU A  46 " =    1.080
peak=    3.304 closest distance to " CA  ALA A 291 " =    0.879
peak=    3.304 closest distance to " CB  ILE A 120 " =    1.307
peak=    3.303 closest distance to " O   HOH Z 102 " =    1.280
peak=    3.298 closest distance to " O   HOH Z 437 " =    1.939
peak=    3.292 closest distance to " O   HOH Z 419 " =    1.633
peak=    3.290 closest distance to " OG  SER A  22 " =    2.716
peak=    3.289 closest distance to " NH2 ARG A  79 " =    1.332
peak=    3.289 closest distance to " O   HOH Z 171 " =    2.473
peak=    3.283 closest distance to " CA  ASN A 176 " =    1.132
peak=    3.280 closest distance to " N   SER A 135 " =    1.451
peak=    3.276 closest distance to " CG  LEU A 281 " =    1.034
peak=    3.276 closest distance to " CD1 ILE A 106 " =    0.986
peak=    3.274 closest distance to " O   HOH Z 411 " =    1.755
peak=    3.273 closest distance to " ND1 HIS A  81 " =    1.621
peak=    3.265 closest distance to " CA  THR A 264 " =    0.801
peak=    3.265 closest distance to " CA  LYS A 290 " =    1.221
peak=    3.264 closest distance to " O   HOH Z 368 " =    3.629
peak=    3.260 closest distance to " O   HOH Z 187 " =    2.297
peak=    3.256 closest distance to " CA  GLY A  80 " =    0.742
peak=    3.252 closest distance to " OD1 ASN A 217 " =    1.756
peak=    3.251 closest distance to " N   ASP A 162 " =    1.287
peak=    3.250 closest distance to " O   HOH Z 313 " =    1.755
peak=    3.248 closest distance to " OD1 ASP A 231 " =    1.893
peak=    3.243 closest distance to " O   HOH Z 332 " =    1.461
peak=    3.243 closest distance to " CG  GLN A  88 " =    0.998
peak=    3.243 closest distance to " O   ALA A 158 " =    1.305
peak=    3.241 closest distance to " CD2 TYR A  30 " =    0.877
peak=    3.235 closest distance to " O   HOH Z 406 " =    1.590
peak=    3.235 closest distance to " O   ASN A  74 " =    1.648
peak=    3.234 closest distance to " CB  SER A 273 " =    0.800
peak=    3.233 closest distance to " O   HOH Z 116 " =    1.728
peak=    3.233 closest distance to " OG BSER A 134 " =    2.912
peak=    3.232 closest distance to " CB  ALA A   1 " =    1.237
peak=    3.232 closest distance to " O   HOH Z 305 " =    3.579
peak=    3.231 closest distance to " O   HOH Z  66 " =    2.319
peak=    3.229 closest distance to " ND2 ASN A 110 " =    1.602
peak=    3.229 closest distance to " O   HOH Z 367 " =    3.442
peak=    3.227 closest distance to " O   HOH Z 329 " =    3.921
peak=    3.223 closest distance to " O   HOH Z  44 " =    1.784
peak=    3.223 closest distance to " CZ  PHE A  38 " =    1.302
peak=    3.219 closest distance to " CD1 LEU A 228 " =    1.850
peak=    3.215 closest distance to " CB  GLN A  88 " =    1.167
peak=    3.213 closest distance to " O   HOH Z 417 " =    2.179
peak=    3.212 closest distance to " CB  SER A 216 " =    0.744
peak=    3.210 closest distance to " N   SER A 288 " =    1.743
peak=    3.198 closest distance to " OG1 THR A 294 " =    1.677
peak=    3.198 closest distance to " CD1AILE A 234 " =    0.939
peak=    3.196 closest distance to " CA  GLY A 211 " =    1.326
peak=    3.195 closest distance to " O   HOH Z 336 " =    1.677
peak=    3.194 closest distance to " CZ3 TRP A  85 " =    0.939
peak=    3.194 closest distance to " CB  GLN A 205 " =    1.125
peak=    3.192 closest distance to " CA  ALA A 233 " =    1.367
peak=    3.191 closest distance to " CA  TYR A 116 " =    1.456
peak=    3.191 closest distance to " O   HOH Z 251 " =    1.397
peak=    3.191 closest distance to " O   HOH Z 185 " =    1.755
peak=    3.190 closest distance to " CB  LEU A 228 " =    1.276
peak=    3.190 closest distance to " NH2AARG A 275 " =    3.643
peak=    3.188 closest distance to " O   HOH Z  48 " =    1.293
peak=    3.185 closest distance to " CD2 HIS A  81 " =    1.023
peak=    3.180 closest distance to " NH1AARG A 145 " =    1.136
peak=    3.179 closest distance to " O   HOH Z 252 " =    1.758
peak=    3.177 closest distance to " O   HOH Z 189 " =    2.714
peak=    3.175 closest distance to " CB  ASN A 110 " =    1.198
peak=    3.172 closest distance to " O   HOH Z  10 " =    1.724
peak=    3.170 closest distance to " O   HOH Z  88 " =    2.549
peak=    3.170 closest distance to " O   HOH Z 374 " =    2.639
peak=    3.168 closest distance to " O   HOH Z 414 " =    1.736
peak=    3.166 closest distance to " O   HOH Z 380 " =    1.938
peak=    3.165 closest distance to " CA  ALA A  84 " =    1.369
peak=    3.163 closest distance to " CB  LEU A 255 " =    0.789
peak=    3.158 closest distance to " O   HOH Z 271 " =    1.486
peak=    3.155 closest distance to " C   ALA A 299 " =    0.935
peak=    3.153 closest distance to " OE2 GLU A  53 " =    2.017
peak=    3.142 closest distance to " O   HOH Z  85 " =    1.887
peak=    3.142 closest distance to " CA  ALA A 160 " =    0.848
peak=    3.141 closest distance to " O   HOH Z 148 " =    3.235
peak=    3.137 closest distance to " O   HOH Z 279 " =    2.128
peak=    3.135 closest distance to " CB  GLN A 278 " =    0.867
peak=    3.129 closest distance to " CD  PRO A 243 " =    1.272
peak=    3.128 closest distance to " O   HOH Z 361 " =    3.216
peak=    3.128 closest distance to " CG  MET A 185 " =    1.107
peak=    3.126 closest distance to " CD  LYS A 119 " =    1.855
peak=    3.121 closest distance to " O   HOH Z 260 " =    1.523
peak=    3.116 closest distance to " CD1 PHE A 204 " =    1.298
peak=    3.115 closest distance to " CB  SER A  62 " =    0.839
peak=    3.114 closest distance to " C   TYR A 214 " =    1.396
peak=    3.114 closest distance to " O   HOH Z  90 " =    3.373
peak=    3.106 closest distance to " CD1 ILE A  33 " =    1.618
peak=    3.103 closest distance to " CG  ARG A  66 " =    0.930
peak=    3.094 closest distance to " CG2AVAL A 121 " =    2.239
peak=    3.082 closest distance to " O   THR A 220 " =    1.285
peak=    3.080 closest distance to " O   HOH Z 193 " =    1.530
peak=    3.080 closest distance to " O   HOH Z 135 " =    1.823
peak=    3.078 closest distance to " O   HOH Z 280 " =    2.664
peak=    3.072 closest distance to " CB  ASN A 215 " =    1.175
peak=    3.069 closest distance to " O   ASP A 124 " =    1.765
peak=    3.067 closest distance to " O   SER A 164 " =    1.142
peak=    3.066 closest distance to " O   HOH Z 256 " =    2.380
peak=    3.064 closest distance to " O   HOH Z 387 " =    3.095
peak=    3.060 closest distance to " CA  SER A  87 " =    1.062
peak=    3.053 closest distance to " O   HOH Z 353 " =    2.741
peak=    3.044 closest distance to " CA  ILE A 106 " =    0.745
peak=    3.037 closest distance to " CB  ALA A 100 " =    1.185
peak=    3.034 closest distance to " O   HOH Z  40 " =    2.717
peak=    3.025 closest distance to " CG2 VAL A 202 " =    1.075
peak=    2.988 closest distance to " O   HOH Z 175 " =    2.162

                           ----------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: 0.829 - 5.549
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 215 from: 216
   mapped sites are within: 0.829 - 5.549

peak=   -5.275 closest distance to " CG2 VAL A 230 " =    0.831
peak=   -4.762 closest distance to " SG  CYS A 254 " =    3.287
peak=   -4.633 closest distance to " CD  ARG A 156 " =    2.028
peak=   -4.477 closest distance to " O   HOH Z 266 " =    4.862
peak=   -4.334 closest distance to " CA  SER A 164 " =    2.157
peak=   -4.275 closest distance to " CD  GLN A  58 " =    1.151
peak=   -4.214 closest distance to " C   HIS A 108 " =    1.184
peak=   -4.184 closest distance to " CG  GLN A 223 " =    2.138
peak=   -4.140 closest distance to " OG BSER A 134 " =    1.240
peak=   -4.136 closest distance to " CG2BVAL A  41 " =    2.666
peak=   -4.133 closest distance to " CG  ASP A 231 " =    0.829
peak=   -4.130 closest distance to " O   HOH Z 196 " =    2.131
peak=   -4.072 closest distance to " OXT GLY A 302 " =    2.818
peak=   -4.010 closest distance to " CB  PRO A 243 " =    2.634
peak=   -4.010 closest distance to " CB  ALA A 161 " =    2.525
peak=   -3.947 closest distance to " OG  SER A  97 " =    2.263
peak=   -3.934 closest distance to " O   HOH Z 166 " =    1.846
peak=   -3.930 closest distance to " O   HOH Z 231 " =    2.097
peak=   -3.921 closest distance to " O   HOH Z 114 " =    3.211
peak=   -3.908 closest distance to " CD1 LEU A 101 " =    2.419
peak=   -3.906 closest distance to " ND2 ASN A  45 " =    1.033
peak=   -3.884 closest distance to " CB  PHE A 192 " =    1.925
peak=   -3.859 closest distance to " CE2 TYR A  30 " =    2.738
peak=   -3.809 closest distance to " O   HOH Z  11 " =    1.887
peak=   -3.805 closest distance to " O   VAL A  67 " =    2.754
peak=   -3.779 closest distance to " O   HOH Z 351 " =    1.499
peak=   -3.775 closest distance to " ND2 ASN A 187 " =    1.693
peak=   -3.767 closest distance to " CE3 TRP A 150 " =    2.099
peak=   -3.757 closest distance to " CE2 PHE A 218 " =    2.682
peak=   -3.745 closest distance to " OD1 ASN A 187 " =    1.733
peak=   -3.744 closest distance to " CZ3 TRP A 179 " =    1.253
peak=   -3.737 closest distance to " CG1 VAL A 250 " =    2.732
peak=   -3.736 closest distance to " O   HOH Z  13 " =    1.592
peak=   -3.723 closest distance to " O   HOH Z 290 " =    1.215
peak=   -3.718 closest distance to " NE2 GLN A  88 " =    1.937
peak=   -3.714 closest distance to " CB  ALA A 248 " =    2.288
peak=   -3.702 closest distance to " N   THR A 235 " =    1.401
peak=   -3.673 closest distance to " O   HOH Z 407 " =    2.967
peak=   -3.671 closest distance to " O   HOH Z  37 " =    1.832
peak=   -3.669 closest distance to " CD  LYS A 289 " =    2.507
peak=   -3.637 closest distance to " N   ALA A 226 " =    1.987
peak=   -3.632 closest distance to " O   ALA A 256 " =    1.590
peak=   -3.627 closest distance to " CB  ALA A 248 " =    2.025
peak=   -3.626 closest distance to " O   HOH Z 166 " =    1.528
peak=   -3.622 closest distance to " CG1 VAL A 112 " =    2.764
peak=   -3.614 closest distance to " CD1 LEU A  25 " =    2.458
peak=   -3.610 closest distance to " OG ASER A 134 " =    1.192
peak=   -3.602 closest distance to " CZ  TYR A 169 " =    1.699
peak=   -3.577 closest distance to " CA  ASP A 298 " =    1.040
peak=   -3.571 closest distance to " O   HOH Z  52 " =    1.613
peak=   -3.565 closest distance to " C   ILE A 239 " =    2.115
peak=   -3.564 closest distance to " O   HOH Z 185 " =    2.390
peak=   -3.560 closest distance to " O   HOH Z 353 " =    2.130
peak=   -3.553 closest distance to " NH2AARG A 275 " =    5.021
peak=   -3.553 closest distance to " CG2 ILE A 263 " =    2.367
peak=   -3.553 closest distance to " N   GLN A  58 " =    1.503
peak=   -3.549 closest distance to " O   HOH Z 389 " =    1.825
peak=   -3.543 closest distance to " O   GLY A  75 " =    1.856
peak=   -3.539 closest distance to " NH2 ARG A  66 " =    1.652
peak=   -3.538 closest distance to " N   SER A 212 " =    2.018
peak=   -3.535 closest distance to " CG1 VAL A 296 " =    1.185
peak=   -3.533 closest distance to " CB  ASP A 171 " =    2.345
peak=   -3.533 closest distance to " CG2 VAL A 296 " =    1.202
peak=   -3.532 closest distance to " CD1 PHE A  59 " =    1.947
peak=   -3.529 closest distance to " O   HOH Z  44 " =    2.192
peak=   -3.529 closest distance to " O   HOH Z 165 " =    1.905
peak=   -3.523 closest distance to " O   HOH Z  19 " =    2.129
peak=   -3.521 closest distance to " C   ALA A 158 " =    1.223
peak=   -3.517 closest distance to " OD1 ASN A 148 " =    1.483
peak=   -3.510 closest distance to " CD2 LEU A 167 " =    1.696
peak=   -3.508 closest distance to " CG  GLU A 277 " =    1.097
peak=   -3.505 closest distance to " CB  PRO A 163 " =    2.567
peak=   -3.504 closest distance to " CB  ALA A 291 " =    2.342
peak=   -3.503 closest distance to " CB  ASN A  39 " =    2.212
peak=   -3.498 closest distance to " CD2 LEU A 300 " =    2.630
peak=   -3.497 closest distance to " O   HOH Z 292 " =    4.407
peak=   -3.496 closest distance to " O   HOH Z 283 " =    1.961
peak=   -3.485 closest distance to " CD  ARG A 139 " =    1.578
peak=   -3.467 closest distance to " O   HOH Z 193 " =    1.804
peak=   -3.450 closest distance to " OG  SER A  62 " =    1.683
peak=   -3.448 closest distance to " O   HOH Z  60 " =    2.252
peak=   -3.432 closest distance to " O   HOH Z 435 " =    2.742
peak=   -3.427 closest distance to " CB  ASP A 132 " =    2.308
peak=   -3.427 closest distance to " N   THR A 157 " =    1.530
peak=   -3.424 closest distance to " CD1 LEU A 101 " =    2.649
peak=   -3.420 closest distance to " O   HOH Z 234 " =    4.080
peak=   -3.409 closest distance to " CB  GLN A  11 " =    1.802
peak=   -3.408 closest distance to " O   HOH Z  17 " =    1.443
peak=   -3.405 closest distance to " CB  ALA A  43 " =    2.451
peak=   -3.396 closest distance to " O   VAL A 189 " =    2.601
peak=   -3.396 closest distance to " N   ALA A  43 " =    2.549
peak=   -3.386 closest distance to " NE2 GLN A 103 " =    1.761
peak=   -3.383 closest distance to " OG  SER A 206 " =    1.627
peak=   -3.382 closest distance to " C   THR A 279 " =    1.171
peak=   -3.373 closest distance to " CB  ALA A 291 " =    2.195
peak=   -3.373 closest distance to " O   ALA A 161 " =    1.696
peak=   -3.369 closest distance to " O   HOH Z 102 " =    1.618
peak=   -3.368 closest distance to " C   MET A 188 " =    1.458
peak=   -3.365 closest distance to " NH2 ARG A  79 " =    2.042
peak=   -3.364 closest distance to " CA  GLY A 203 " =    2.372
peak=   -3.359 closest distance to " OG1 THR A  82 " =    1.447
peak=   -3.357 closest distance to " C   SER A 206 " =    1.585
peak=   -3.350 closest distance to " CG  ARG A 269 " =    2.273
peak=   -3.348 closest distance to " O   SER A 271 " =    2.052
peak=   -3.346 closest distance to " O   SER A  95 " =    1.706
peak=   -3.338 closest distance to " CA  GLY A 133 " =    2.012
peak=   -3.335 closest distance to " C   ASP A 231 " =    2.591
peak=   -3.330 closest distance to " O   PRO A 198 " =    1.251
peak=   -3.328 closest distance to " N   ALA A 248 " =    1.737
peak=   -3.325 closest distance to " O   HOH Z 426 " =    1.697
peak=   -3.320 closest distance to " O   HOH Z  97 " =    1.262
peak=   -3.319 closest distance to " CE  MET A 105 " =    2.077
peak=   -3.315 closest distance to " O   PHE A 218 " =    1.754
peak=   -3.315 closest distance to " O   HOH Z   6 " =    1.771
peak=   -3.308 closest distance to " NH2 ARG A 159 " =    2.325
peak=   -3.306 closest distance to " O   ARG A  24 " =    2.046
peak=   -3.306 closest distance to " CG1 VAL A 230 " =    1.889
peak=   -3.305 closest distance to " CB  TYR A  15 " =    2.186
peak=   -3.303 closest distance to " CG  ARG A 219 " =    2.757
peak=   -3.296 closest distance to " O   HOH Z 311 " =    3.666
peak=   -3.294 closest distance to " CG1 VAL A 112 " =    2.627
peak=   -3.291 closest distance to " O   GLY A 196 " =    1.094
peak=   -3.286 closest distance to " O   HOH Z 431 " =    1.800
peak=   -3.286 closest distance to " CD  ARG A 195 " =    5.141
peak=   -3.279 closest distance to " OG  SER A  26 " =    1.331
peak=   -3.273 closest distance to " O   HOH Z  15 " =    1.520
peak=   -3.273 closest distance to " NE2 GLN A  88 " =    1.113
peak=   -3.272 closest distance to " O   LYS A 117 " =    1.632
peak=   -3.272 closest distance to " CD2 TYR A 293 " =    2.013
peak=   -3.269 closest distance to " O   LEU A 167 " =    1.503
peak=   -3.262 closest distance to " O   VAL A 125 " =    2.349
peak=   -3.261 closest distance to " O   HOH Z 198 " =    2.221
peak=   -3.259 closest distance to " ND2 ASN A  69 " =    1.792
peak=   -3.258 closest distance to " CZ  PHE A  59 " =    1.599
peak=   -3.258 closest distance to " O   HOH Z 423 " =    2.150
peak=   -3.251 closest distance to " O   HOH Z 126 " =    1.958
peak=   -3.250 closest distance to " O   HOH Z 123 " =    2.315
peak=   -3.247 closest distance to " O   HOH Z 222 " =    1.555
peak=   -3.242 closest distance to " OG BSER A 210 " =    2.141
peak=   -3.242 closest distance to " NE2 GLN A 194 " =    1.780
peak=   -3.239 closest distance to " O   HOH Z 369 " =    2.293
peak=   -3.239 closest distance to " O   GLY A  80 " =    2.451
peak=   -3.229 closest distance to " N   VAL A 230 " =    1.046
peak=   -3.227 closest distance to " CG  TRP A 266 " =    1.992
peak=   -3.225 closest distance to " O   HOH Z 252 " =    4.041
peak=   -3.222 closest distance to " O   ILE A 234 " =    1.193
peak=   -3.221 closest distance to " C   LEU A 143 " =    1.015
peak=   -3.217 closest distance to " CE BMET A  47 " =    1.879
peak=   -3.214 closest distance to " O   HOH Z 211 " =    1.744
peak=   -3.209 closest distance to " N   HIS A 115 " =    2.057
peak=   -3.207 closest distance to " O   HOH Z 131 " =    4.065
peak=   -3.207 closest distance to " CG  ASP A  50 " =    2.322
peak=   -3.206 closest distance to " O   HOH Z 262 " =    2.768
peak=   -3.203 closest distance to " O   HOH Z 191 " =    5.549
peak=   -3.202 closest distance to " O   GLY A  80 " =    2.550
peak=   -3.200 closest distance to " O   MET A  40 " =    2.682
peak=   -3.200 closest distance to " O   HOH Z  43 " =    1.769
peak=   -3.196 closest distance to " O   HOH Z 177 " =    1.695
peak=   -3.195 closest distance to " O   HOH Z  38 " =    1.652
peak=   -3.193 closest distance to " N   MET A 105 " =    2.642
peak=   -3.193 closest distance to " CE  LYS A 166 " =    3.051
peak=   -3.191 closest distance to " OG BSER A 134 " =    1.762
peak=   -3.190 closest distance to " O   ALA A  51 " =    1.451
peak=   -3.188 closest distance to " N   SER A 276 " =    1.386
peak=   -3.185 closest distance to " O   HOH Z 411 " =    3.679
peak=   -3.184 closest distance to " NE1 TRP A 266 " =    2.339
peak=   -3.182 closest distance to " O   ASP A 171 " =    1.999
peak=   -3.180 closest distance to " O   HOH Z 174 " =    4.341
peak=   -3.175 closest distance to " O   HOH Z 372 " =    2.241
peak=   -3.174 closest distance to " O   HOH Z 422 " =    1.621
peak=   -3.173 closest distance to " CG  PHE A 283 " =    2.752
peak=   -3.173 closest distance to " NH1 ARG A 195 " =    2.595
peak=   -3.171 closest distance to " CD1 LEU A 228 " =    2.140
peak=   -3.168 closest distance to " CG  GLU A  53 " =    1.522
peak=   -3.165 closest distance to " ND2 ASN A 252 " =    1.827
peak=   -3.164 closest distance to " O   VAL A 197 " =    1.354
peak=   -3.164 closest distance to " CD1 ILE A 199 " =    2.407
peak=   -3.164 closest distance to " O   ASN A  45 " =    1.902
peak=   -3.163 closest distance to " O   ALA A 160 " =    1.461
peak=   -3.163 closest distance to " O   HOH Z 313 " =    1.930
peak=   -3.158 closest distance to " C   GLN A  58 " =    2.278
peak=   -3.157 closest distance to " O   HOH Z 339 " =    1.788
peak=   -3.154 closest distance to " OXT GLY A 302 " =    3.403
peak=   -3.153 closest distance to " CD  ARG A 259 " =    2.476
peak=   -3.150 closest distance to " O   HOH Z 210 " =    1.097
peak=   -3.146 closest distance to " O   HOH Z  11 " =    2.088
peak=   -3.145 closest distance to " O   HOH Z 313 " =    1.132
peak=   -3.141 closest distance to " ND2 ASN A  60 " =    1.673
peak=   -3.130 closest distance to " O   PRO A 198 " =    1.351
peak=   -3.123 closest distance to " CB  ASP A 132 " =    2.371
peak=   -3.120 closest distance to " O   HOH Z 414 " =    1.985
peak=   -3.110 closest distance to " CG  GLU A   2 " =    1.817
peak=   -3.106 closest distance to " O   HOH Z  47 " =    1.558
peak=   -3.103 closest distance to " SG ACYS A 201 " =    2.227
peak=   -3.102 closest distance to " O   HOH Z 139 " =    3.134
peak=   -3.100 closest distance to " O   SER A 258 " =    1.903
peak=   -3.098 closest distance to " CD1 TYR A 247 " =    2.356
peak=   -3.093 closest distance to " CG1 VAL A 197 " =    2.203
peak=   -3.092 closest distance to " CD2 TYR A 247 " =    2.245
peak=   -3.092 closest distance to " C   ASP A 270 " =    1.276
peak=   -3.089 closest distance to " O   HOH Z 397 " =    1.151
peak=   -3.089 closest distance to " O   HOH Z 412 " =    4.882
peak=   -3.087 closest distance to " CG1 VAL A  78 " =    2.579
peak=   -3.087 closest distance to " O   HOH Z  10 " =    1.546
peak=   -3.083 closest distance to " CA  GLY A 241 " =    3.037
peak=   -3.064 closest distance to " O   HOH Z 110 " =    1.469
peak=   -3.064 closest distance to " CG  LEU A 228 " =    1.064
peak=   -3.062 closest distance to " CD  GLN A 223 " =    1.609
peak=   -3.047 closest distance to " O   HOH Z 128 " =    2.524
peak=   -3.042 closest distance to " O   HOH Z 350 " =    1.861
peak=   -3.037 closest distance to " NH2 ARG A  79 " =    1.535
peak=   -3.030 closest distance to " OD1 ASP A 200 " =    1.392
peak=   -3.027 closest distance to " C   LEU A 222 " =    0.895
peak=   -3.022 closest distance to " OD1 ASN A 301 " =    1.967
peak=   -3.002 closest distance to " O   HOH Z 414 " =    1.628

================= 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    :  0.4363 0.4242   6.229194e+00   6.206865e+00
   1_bss:  0.4277 0.4168   6.221878e+00   6.193401e+00
   1_xyz:  0.3191 0.3404   6.016208e+00   6.059162e+00
   1_adp:  0.2558 0.2883   5.832751e+00   5.934330e+00
   1_occ:  0.2553 0.2881   5.831609e+00   5.934446e+00
   2_bss:  0.2512 0.2830   5.830079e+00   5.926933e+00
   2_xyz:  0.1769 0.2134   5.515195e+00   5.674408e+00
   2_adp:  0.1633 0.2013   5.445175e+00   5.615902e+00
   2_occ:  0.1632 0.2012   5.444910e+00   5.616011e+00
   3_bss:  0.1621 0.2014   5.445002e+00   5.616402e+00
   3_xyz:  0.1241 0.1637   5.212415e+00   5.428746e+00
   3_adp:  0.1192 0.1575   5.176114e+00   5.395532e+00
   3_occ:  0.1191 0.1574   5.175417e+00   5.395031e+00
   4_bss:  0.1195 0.1576   5.177561e+00   5.395013e+00
   4_xyz:  0.1137 0.1555   5.148779e+00   5.382046e+00
   4_adp:  0.1140 0.1549   5.147291e+00   5.378469e+00
   4_occ:  0.1139 0.1551   5.147281e+00   5.378865e+00
   5_bss:  0.1139 0.1550   5.147202e+00   5.378828e+00
   5_xyz:  0.1131 0.1541   5.142542e+00   5.374732e+00
   5_adp:  0.1109 0.1558   5.140677e+00   5.385941e+00
   5_occ:  0.1108 0.1558   5.140514e+00   5.385895e+00
   5_bss:  0.1108 0.1557   5.140391e+00   5.385832e+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:  0.336  17.122   7.150   9.868   7.982   0.000   0.000   0.000
   1_xyz:  0.336  17.122   7.150   9.868   7.982   0.000   0.000   0.000
   1_adp:  0.336  17.122   7.150   9.868   7.982   0.000   0.000   0.000
   1_occ:  0.336  17.122   7.150   9.868   7.982   0.000   0.000   0.000
   2_bss:  0.327  40.659   3.888   6.037   5.155   0.000   0.000   0.000
   2_xyz:  0.327  40.659   3.888   6.037   5.155   0.000   0.000   0.000
   2_adp:  0.327  40.659   3.888   6.037   5.155   0.000   0.000   0.000
   2_occ:  0.327  40.659   3.888   6.037   5.155   0.000   0.000   0.000
   3_bss:  0.318  40.659   2.826   4.202   4.253   0.000   0.000   0.000
   3_xyz:  0.318  40.659   2.826   4.202   4.253   0.000   0.000   0.000
   3_adp:  0.318  40.659   2.826   4.202   4.253   0.000   0.000   0.000
   3_occ:  0.318  40.659   2.826   4.202   4.253   0.000   0.000   0.000
   4_bss:  0.324  44.568   2.634   3.641   4.046   0.000   0.000   0.000
   4_xyz:  0.324  44.568   2.634   3.641   4.046   0.000   0.000   0.000
   4_adp:  0.324  44.568   2.634   3.641   4.046   0.000   0.000   0.000
   4_occ:  0.324  44.568   2.634   3.641   4.046   0.000   0.000   0.000
   5_bss:  0.325  44.568   2.590   3.476   4.000   0.000   0.000   0.000
   5_xyz:  0.325  44.568   2.590   3.476   4.000   0.000   0.000   0.000
   5_adp:  0.325  44.568   2.590   3.476   4.000   0.000   0.000   0.000
   5_occ:  0.325  44.568   2.590   3.476   4.000   0.000   0.000   0.000
   5_bss:  0.322  49.151  -0.729   0.092   0.637   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  47.402 0.5544  0.6157    51270.409
   1_bss:  47.203 0.5547  0.7897    49022.424
   1_xyz:  36.853 0.6787  0.9439    31546.733
   1_adp:  29.259 0.7668  1.0405    21952.122
   1_occ:  29.253 0.7669  1.0398    21934.616
   2_bss:  28.946 0.7701  0.9270    21484.961
   2_xyz:  20.846 0.8532  0.9971    11673.801
   2_adp:  19.282 0.8686  1.0094    10322.858
   2_occ:  19.286 0.8685  1.0092    10325.692
   3_bss:  19.289 0.8687  0.9637    10365.152
   3_xyz:  15.004 0.9063  0.9856     6864.108
   3_adp:  14.228 0.9131  0.9882     6474.230
   3_occ:  14.216 0.9132  0.9881     6469.645
   4_bss:  14.210 0.9132  0.9765     6486.647
   4_xyz:  13.827 0.9167  0.9762     6286.482
   4_adp:  13.719 0.9176  0.9765     6248.020
   4_occ:  13.724 0.9176  0.9765     6255.488
   5_bss:  13.721 0.9176  0.9736     6255.370
   5_xyz:  13.629 0.9183  0.9738     6190.374
   5_adp:  13.904 0.9161  0.9683     6306.644
   5_occ:  13.901 0.9161  0.9682     6306.478
   5_bss:  13.899 0.9161  0.9740     6305.981
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.3786e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.3786e+01
   1_xyz:   1.547  0.012  0.104 17.776  0.006  4.122   1.1999e-01
   1_adp:   1.547  0.012  0.104 17.776  0.006  4.122   1.1999e-01
   1_occ:   1.547  0.012  0.104 17.776  0.006  4.122   1.1999e-01
   2_bss:   1.547  0.012  0.104 17.776  0.006  4.122   1.1999e-01
   2_xyz:   0.973  0.006  0.070 15.962  0.003  4.123   5.9266e-02
   2_adp:   0.973  0.006  0.070 15.962  0.003  4.123   5.9266e-02
   2_occ:   0.973  0.006  0.070 15.962  0.003  4.123   5.9266e-02
   3_bss:   0.973  0.006  0.070 15.962  0.003  4.123   5.9266e-02
   3_xyz:   1.078  0.008  0.087 15.747  0.004  4.133   6.9208e-02
   3_adp:   1.078  0.008  0.087 15.747  0.004  4.133   6.9208e-02
   3_occ:   1.078  0.008  0.087 15.747  0.004  4.133   6.9208e-02
   4_bss:   1.078  0.008  0.087 15.747  0.004  4.133   6.9208e-02
   4_xyz:   1.054  0.008  0.087 15.636  0.004  4.135   6.6729e-02
   4_adp:   1.054  0.008  0.087 15.636  0.004  4.135   6.6729e-02
   4_occ:   1.054  0.008  0.087 15.636  0.004  4.135   6.6729e-02
   5_bss:   1.054  0.008  0.087 15.636  0.004  4.135   6.6729e-02
   5_xyz:   1.025  0.008  0.084 15.410  0.004  4.112   6.3945e-02
   5_adp:   1.025  0.008  0.084 15.410  0.004  4.112   6.3945e-02
   5_occ:   1.025  0.008  0.084 15.410  0.004  4.112   6.3945e-02
   5_bss:   1.025  0.008  0.084 15.410  0.004  4.112   6.3945e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9734e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9734e+00
   1_xyz:  13.564  0.142  0.469 86.714  0.043  2.318   9.0804e-02
   1_adp:  13.564  0.142  0.469 86.714  0.043  2.318   9.0804e-02
   1_occ:  13.564  0.142  0.469 86.714  0.043  2.318   9.0804e-02
   2_bss:  13.564  0.142  0.469 86.714  0.043  2.318   9.0804e-02
   2_xyz:   6.829  0.072  0.231 81.858  0.028  2.268   5.0006e-02
   2_adp:   6.829  0.072  0.231 81.858  0.028  2.268   5.0006e-02
   2_occ:   6.829  0.072  0.231 81.858  0.028  2.268   5.0006e-02
   3_bss:   6.829  0.072  0.231 81.858  0.028  2.268   5.0006e-02
   3_xyz:   7.129  0.052  0.616 82.732  0.040  2.305   5.4223e-02
   3_adp:   7.129  0.052  0.616 82.732  0.040  2.305   5.4223e-02
   3_occ:   7.129  0.052  0.616 82.732  0.040  2.305   5.4223e-02
   4_bss:   7.129  0.052  0.616 82.732  0.040  2.305   5.4223e-02
   4_xyz:   7.444  0.049  0.637 82.323  0.039  2.336   4.6632e-02
   4_adp:   7.444  0.049  0.637 82.323  0.039  2.336   4.6632e-02
   4_occ:   7.444  0.049  0.637 82.323  0.039  2.336   4.6632e-02
   5_bss:   7.444  0.049  0.637 82.323  0.039  2.336   4.6632e-02
   5_xyz:   7.072  0.046  0.582 82.658  0.037  2.348   4.3040e-02
   5_adp:   7.072  0.046  0.582 82.658  0.037  2.348   4.3040e-02
   5_occ:   7.072  0.046  0.582 82.658  0.037  2.348   4.3040e-02
   5_bss:   7.072  0.046  0.582 82.658  0.037  2.348   4.3040e-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:  64.82   0.00  10.81  64.26   0.00   7.75  64.82   0.00  27.49
   1_occ:  64.82   0.00  10.81  64.26   0.00   7.75  64.82   0.00  27.49
   2_bss:  64.82   0.00  10.81  64.26   0.00   7.75  64.82   0.00  27.49
   2_xyz:  64.82   0.00  10.81  64.26   0.00   7.75  64.82   0.00  27.49
   2_adp:  71.18   0.00  11.30  71.18   0.00   7.53  63.80   1.19  31.84
   2_occ:  71.18   0.00  11.30  71.18   0.00   7.53  63.80   1.19  31.84
   3_bss:  71.18   0.00  11.30  71.18   0.00   7.53  63.80   1.19  31.84
   3_xyz:  71.18   0.00  11.30  71.18   0.00   7.53  63.80   1.19  31.84
   3_adp:  72.45   0.00  11.26  72.45   0.00   7.36  62.43   0.91  32.52
   3_occ:  72.45   0.00  11.26  72.45   0.00   7.36  62.43   0.91  32.52
   4_bss:  72.45   0.00  11.26  72.45   0.00   7.36  62.43   0.91  32.52
   4_xyz:  72.45   0.00  11.26  72.45   0.00   7.36  62.43   0.91  32.52
   4_adp:  72.31   0.00  11.22  72.31   0.00   7.34  62.35   0.97  32.32
   4_occ:  72.31   0.00  11.22  72.31   0.00   7.34  62.35   0.97  32.32
   5_bss:  72.31   0.00  11.22  72.31   0.00   7.34  62.35   0.97  32.32
   5_xyz:  72.31   0.00  11.22  72.31   0.00   7.34  62.35   0.97  32.32
   5_adp:  83.98   0.00  11.64  83.98   0.00   7.47  72.13   0.92  34.33
   5_occ:  83.98   0.00  11.64  83.98   0.00   7.47  72.13   0.92  34.33
   5_bss:  87.50   3.52  15.16  87.50   3.52  10.99  75.65   4.44  37.85
------------------------------------------------------------------------
 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:    1.174    0.014    0.405
   1_adp:    1.174    0.014    0.405
   1_occ:    1.174    0.014    0.405
   2_bss:    1.174    0.014    0.405
   2_xyz:    1.603    0.046    0.507
   2_adp:    1.603    0.046    0.507
   2_occ:    1.603    0.046    0.507
   3_bss:    1.603    0.046    0.507
   3_xyz:    1.513    0.051    0.555
   3_adp:    1.513    0.051    0.555
   3_occ:    1.513    0.051    0.555
   4_bss:    1.513    0.051    0.555
   4_xyz:    1.549    0.047    0.571
   4_adp:    1.549    0.047    0.571
   4_occ:    1.549    0.047    0.571
   5_bss:    1.549    0.047    0.571
   5_xyz:    1.573    0.043    0.581
   5_adp:    1.573    0.043    0.581
   5_occ:    1.573    0.043    0.581
   5_bss:    1.573    0.043    0.581
------------------------------------------------------------------------

CPU time actual refinement: 337.21


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_565/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_565/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_565/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_565/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_565/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 337.05 
  Macro-tasks:
    bulk solvent and scale       = 40.19  
    individual site refinement   = 141.12 
    weights calculation          = 31.81  
    collect and process          = 6.53   
    model show statistics        = 0.14   
    TOTAL for macro-tasks        = 219.79 
  Micro-tasks:
    mask                            = 1.73   
    f_calc                          = 103.77 
    alpha_beta                      = 8.35   
    target                          = 1.11   
    gradients_wrt_atomic_parameters = 115.88 
    fmodel                         = 7.38   
    r_factors                      = 0.24   
    phase_errors                   = 10.90  
    foms                           = 0.30   
    TOTAL for micro-tasks          = 249.66 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.638 micro seconds
Total CPU time: 5.84 minutes
from_scatterers_fft:    682 calls, 103.32 s
gradients_fft:          628 calls, 101.49 s

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

# Date 2008-01-16 Time 01:52:35 PST -0800 (1200477155.75 s)
Start R-work = 0.4363, R-free = 0.4242 (no bulk solvent and anisotropic scale)
Final R-work = 0.1279, R-free = 0.1714 (no bulk solvent and anisotropic scale)

Start R-work = 0.4277, R-free = 0.4168
Final R-work = 0.1108, R-free = 0.1557