# Date 2008-01-16 Time 02:13:47 PST -0800 (1200478427.34 s)
#phil __OFF__

Command line arguments: "../740.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 = 24685
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 740

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.6012, 45.9914, 85.5261, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 45.9914, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.007 1.96275
Completeness in resolution range: 0.956261
Completeness with d_max=infinity: 0.953422

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0070
                             d_min =   1.9628

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 45.9914, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.007 1.96275
Completeness in resolution range: 0.956261
Completeness with d_max=infinity: 0.953422

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0074 -  4.2006 [2148/2174]  1935   213   9.9%
  bin  2:  4.2006 -  3.3463 [2067/2087]  1858   209  10.1%
  bin  3:  3.3463 -  2.9269 [2044/2063]  1842   202   9.9%
  bin  4:  2.9269 -  2.6609 [2027/2057]  1822   205  10.1%
  bin  5:  2.6609 -  2.4711 [2016/2035]  1820   196   9.7%
  bin  6:  2.4711 -  2.3259 [1988/2013]  1779   209  10.5%
  bin  7:  2.3259 -  2.2098 [2000/2028]  1803   197   9.8%
  bin  8:  2.2098 -  2.1139 [1974/2010]  1777   197  10.0%
  bin  9:  2.1139 -  2.0327 [1965/2007]  1767   198  10.1%
  bin 10:  2.0327 -  1.9628 [1360/2011]  1227   133   9.8%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_740/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: 0.13 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:
        1.80 -     2.42: 35
        2.42 -     3.04: 2234
        3.04 -     3.66: 4760
        3.66 -     4.28: 9166
        4.28 -     4.90: 12439
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 204 " - " O   HOH Z 296 "  1.803 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.883 3.040 x,y+1,z
  " O   HOH Z 201 " - " O   HOH Z 349 "  1.926 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.941 3.040 x,y+1,z
  ... (remaining 28629 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_740/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_740/model_refine_001.geo

CPU time processing inputs: 9.11


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.60125 45.9914 85.5261 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: 1.96 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4825   r_free= 0.4743   ksol= 0.00   Bsol= 0.00   scale= 0.797    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.76 A                  |
| x-ray target function (ml) for work reflections: 6.285310                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0074 -  4.6855 0.99   1396  157 0.4130 0.4140      6.6053      6.6655|
|  2:  4.6855 -  3.7380 0.99   1344  148 0.4085 0.3754      6.8114      6.7303|
|  3:  3.7380 -  3.2710 0.99   1327  144 0.4348 0.4095      6.6768       6.718|
|  4:  3.2710 -  2.9745 0.99   1312  153 0.4705 0.4577        6.55      6.4743|
|  5:  2.9745 -  2.7627 0.99   1298  143 0.5113 0.5271      6.3708      6.4062|
|  6:  2.7627 -  2.6007 0.99   1303  141 0.5053 0.5349      6.2843      6.2188|
|  7:  2.6007 -  2.4711 0.99   1297  139 0.5182 0.4597      6.2564      6.2129|
|  8:  2.4711 -  2.3639 0.98   1257  146 0.5323 0.4525      6.1778      6.1532|
|  9:  2.3639 -  2.2732 0.98   1273  148 0.5150 0.5391      6.1223      6.1773|
| 10:  2.2732 -  2.1951 1.00   1295  141 0.5199 0.5473      6.1103      6.1005|
| 11:  2.1951 -  2.1266 0.98   1295  137 0.5093 0.5045      6.0365      6.0378|
| 12:  2.1266 -  2.0660 0.98   1247  144 0.5108 0.5614      5.9714      6.0206|
| 13:  2.0660 -  2.0117 0.99   1278  138 0.5464 0.5492      5.8865      5.8202|
| 14:  2.0117 -  1.9628 0.55    708   80 0.5630 0.4811      5.8617      5.8232|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0074 -  4.6855  1396   157  0.64  39.61   0.79     0.70      90398.60|
|  2:  4.6855 -  3.7380  1344   148  0.69  36.00   0.87     0.78     113376.63|
|  3:  3.7380 -  3.2710  1327   144  0.59  44.40   0.85     0.73     117046.71|
|  4:  3.2710 -  2.9745  1312   153  0.51  51.23   0.80     0.61     104655.33|
|  5:  2.9745 -  2.7627  1298   143  0.39  60.69   0.74     0.48      87122.48|
|  6:  2.7627 -  2.6007  1303   141  0.38  61.49   0.73     0.44      75059.37|
|  7:  2.6007 -  2.4711  1297   139  0.36  63.08   0.75     0.42      66517.18|
|  8:  2.4711 -  2.3639  1257   146  0.35  63.83   0.72     0.42      60133.90|
|  9:  2.3639 -  2.2732  1273   148  0.35  63.39   0.73     0.41      53867.80|
| 10:  2.2732 -  2.1951  1295   141  0.35  63.76   0.76     0.42      48865.69|
| 11:  2.1951 -  2.1266  1295   137  0.31  66.93   0.78     0.38      48860.44|
| 12:  2.1266 -  2.0660  1247   144  0.27  69.91   0.78     0.34      46950.04|
| 13:  2.0660 -  2.0117  1278   138  0.23  73.08   0.73     0.30      41135.25|
| 14:  2.0117 -  1.9628   708    80  0.29  68.27   0.70     0.32      30305.05|
|alpha:            min =        0.30 max =            0.78 mean =         0.49|
|beta:             min =    30305.05 max =       117046.71 mean =     72130.14|
|figures of merit: min =        0.00 max =            1.00 mean =         0.41|
|phase err.(work): min =        0.00 max =           89.98 mean =        58.40|
|phase err.(test): min =        0.00 max =           89.88 mean =        58.61|
|-----------------------------------------------------------------------------|

============================== 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 = 17.017458             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.887   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.519022              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.200   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       35 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      170 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      702 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1546 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2664 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3976 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5136 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6614 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7823 |
|-----------------------------------------------------------------------------|
|-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 |       53.227 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.089    4.900  1.196 |       2.043 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.607)------------------------------------------|
|    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 = 11.607)------------------------------------------|
|    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: 1.96 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4880   r_free= 0.4763   ksol= 0.00   Bsol= 0.00   scale= 0.766    |
|                                                                             |
| 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:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.287338                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4731   r_free= 0.4602   ksol= 0.36   Bsol= 0.00   scale= 0.997    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.24,10.31,7.89,0.00,0.00,0.00); trace/3= 8.48                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.76 A                  |
| x-ray target function (ml) for work reflections: 6.278847                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.832414             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.882   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.362640              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.259   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4731      final r-factor (work) = 0.3975          |
| start r-factor (free) = 0.4602      final r-factor (free) = 0.4239          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 96.6766 = 13.83 * 0.50 * 6.2824 + 1.00 * 53.2265                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 43.0669 = 13.83 * 0.50 * 6.2063 + 1.00 * 0.1427                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3975      final r-factor (work) = 0.3558          |
| start r-factor (free) = 0.4239      final r-factor (free) = 0.4104          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.4713 = 1.36 * 1.00 * 6.2063 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.3762 = 1.36 * 1.00 * 6.1338 + 1.00 * 0.0181                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.607)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.09   13.75    None  None   None       |
|    all(noH): 2823   0      0.00    88.09   13.75    None  None   None       |
|    Sol.    : 438    0      0.00    85.06   24.59    None  None   None       |
|    Mac.    : 2385   0      0.00    88.09   11.76    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.809: 1207   |   5:    44.044 -  52.853:   46        |
|      1:     8.809 -  17.618:  785   |   6:    52.853 -  61.661:   20        |
|      2:    17.618 -  26.426:  453   |   7:    61.661 -  70.470:    4        |
|      3:    26.426 -  35.235:  201   |   8:    70.470 -  79.279:    2        |
|      4:    35.235 -  44.044:  102   |   9:    79.279 -  88.088:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3558 r_free = 0.4104             target_work(ml) = 6.119         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3556 r_free = 0.4106             target_work(ml) = 6.118         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3556   r_free= 0.4106   ksol= 0.36   Bsol= 0.00   scale= 1.110    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.24,10.31,7.89,0.00,0.00,0.00); trace/3= 8.48                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.118443                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3522   r_free= 0.4055   ksol= 0.35   Bsol= 35.12   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.78,5.88,4.73,0.00,0.00,0.00); trace/3= 4.80                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.118481                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.765318              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.728   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.657240              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.472  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3522      final r-factor (work) = 0.2911          |
| start r-factor (free) = 0.4055      final r-factor (free) = 0.3476          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.8128 = 5.77 * 0.50 * 6.1298 + 1.00 * 0.1427                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.4877 = 5.77 * 0.50 * 6.0383 + 1.00 * 0.0812                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2911      final r-factor (work) = 0.2731          |
| start r-factor (free) = 0.3476      final r-factor (free) = 0.3363          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9870 = 0.66 * 1.00 * 6.0383 + 1.00 * 0.0184                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9169 = 0.66 * 1.00 * 5.9390 + 1.00 * 0.0136                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.607)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.59   14.02    None  None   None       |
|    all(noH): 2823   0      0.00    91.59   14.02    None  None   None       |
|    Sol.    : 438    0      0.00    90.34   29.92    None  None   None       |
|    Mac.    : 2385   0      0.00    91.59   11.10    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.159: 1283   |   5:    45.796 -  54.955:   49        |
|      1:     9.159 -  18.318:  786   |   6:    54.955 -  64.115:   17        |
|      2:    18.318 -  27.478:  388   |   7:    64.115 -  73.274:    7        |
|      3:    27.478 -  36.637:  184   |   8:    73.274 -  82.433:    1        |
|      4:    36.637 -  45.796:  105   |   9:    82.433 -  91.592:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2731 r_free = 0.3363             target_work(ml) = 5.921         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2728 r_free = 0.3365             target_work(ml) = 5.921         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2728   r_free= 0.3365   ksol= 0.35   Bsol= 35.12   scale= 1.066   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.78,5.88,4.73,0.00,0.00,0.00); trace/3= 4.80                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.921323                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2717   r_free= 0.3339   ksol= 0.34   Bsol= 43.12   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.41,3.24,3.17,0.00,0.00,0.00); trace/3= 2.94                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.921118                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.531212              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.966   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.824656              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.328  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2717      final r-factor (work) = 0.2065          |
| start r-factor (free) = 0.3339      final r-factor (free) = 0.2631          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.5356 = 4.53 * 0.50 * 5.9386 + 1.00 * 0.0811                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.2284 = 4.53 * 0.50 * 5.8028 + 1.00 * 0.0817                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2065      final r-factor (work) = 0.1840          |
| start r-factor (free) = 0.2631      final r-factor (free) = 0.2443          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7987 = 0.82 * 1.00 * 5.8028 + 1.00 * 0.0134                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6458 = 0.82 * 1.00 * 5.6168 + 1.00 * 0.0139                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.607)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.69   14.32    None  None   None       |
|    all(noH): 2823   0      0.00    96.69   14.32    None  None   None       |
|    Sol.    : 438    0      1.41    92.92   37.50    None  None   None       |
|    Mac.    : 2385   0      0.00    96.69   10.06    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.669: 1538   |   5:    48.343 -  58.012:   91        |
|      1:     9.669 -  19.337:  647   |   6:    58.012 -  67.680:   37        |
|      2:    19.337 -  29.006:  217   |   7:    67.680 -  77.349:    5        |
|      3:    29.006 -  38.674:  154   |   8:    77.349 -  87.017:    2        |
|      4:    38.674 -  48.343:  129   |   9:    87.017 -  96.686:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1840 r_free = 0.2443             target_work(ml) = 5.580         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1838 r_free = 0.2437             target_work(ml) = 5.579         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1838   r_free= 0.2437   ksol= 0.34   Bsol= 43.12   scale= 1.042   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.41,3.24,3.17,0.00,0.00,0.00); trace/3= 2.94                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.579379                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1836   r_free= 0.2422   ksol= 0.33   Bsol= 47.85   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.64,1.78,2.53,0.00,0.00,0.00); trace/3= 1.99                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.576646                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.462186              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.179   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.839586              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.685  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1836      final r-factor (work) = 0.1499          |
| start r-factor (free) = 0.2422      final r-factor (free) = 0.2057          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9999 = 2.46 * 0.50 * 5.6196 + 1.00 * 0.0817                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8106 = 2.46 * 0.50 * 5.4885 + 1.00 * 0.0538                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1499      final r-factor (work) = 0.1420          |
| start r-factor (free) = 0.2057      final r-factor (free) = 0.1972          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6218 = 0.84 * 1.00 * 5.4885 + 1.00 * 0.0138                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5413 = 0.84 * 1.00 * 5.3815 + 1.00 * 0.0231                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.607)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    102.86  14.37    None  None   None       |
|    all(noH): 2823   0      0.00    102.86  14.37    None  None   None       |
|    Sol.    : 438    0      2.43    96.06   40.06    None  None   None       |
|    Mac.    : 2385   0      0.00    102.86  9.65     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.287: 1688   |   5:    51.432 -  61.719:   91        |
|      1:    10.287 -  20.573:  583   |   6:    61.719 -  72.005:   37        |
|      2:    20.573 -  30.859:  165   |   7:    72.005 -  82.292:   14        |
|      3:    30.859 -  41.146:  122   |   8:    82.292 -  92.578:    5        |
|      4:    41.146 -  51.432:  116   |   9:    92.578 - 102.865:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1420 r_free = 0.1972             target_work(ml) = 5.359         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1419 r_free = 0.1969             target_work(ml) = 5.358         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1419   r_free= 0.1969   ksol= 0.33   Bsol= 47.85   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.64,1.78,2.53,0.00,0.00,0.00); trace/3= 1.99                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.358284                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1422   r_free= 0.1972   ksol= 0.32   Bsol= 46.20   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.52,1.27,2.40,0.00,0.00,0.00); trace/3= 1.73                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.357972                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.273403              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 115.612  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.666487              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 94.040   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1422      final r-factor (work) = 0.1255          |
| start r-factor (free) = 0.1972      final r-factor (free) = 0.1777          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1711 = 2.27 * 0.50 * 5.3816 + 1.00 * 0.0538                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0922 = 2.27 * 0.50 * 5.3090 + 1.00 * 0.0574                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1255      final r-factor (work) = 0.1224          |
| start r-factor (free) = 0.1777      final r-factor (free) = 0.1719          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5554 = 0.67 * 1.00 * 5.3090 + 1.00 * 0.0170                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5186 = 0.67 * 1.00 * 5.2415 + 1.00 * 0.0252                               |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 18     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.607)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.84  14.04    None  None   None       |
|    all(noH): 2823   0      0.00    104.84  14.04    None  None   None       |
|    Sol.    : 438    0      2.71    96.65   39.47    None  None   None       |
|    Mac.    : 2385   0      0.00    104.84  9.37     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.484: 1778   |   5:    52.418 -  62.902:   80        |
|      1:    10.484 -  20.967:  532   |   6:    62.902 -  73.385:   37        |
|      2:    20.967 -  31.451:  145   |   7:    73.385 -  83.869:   11        |
|      3:    31.451 -  41.934:  119   |   8:    83.869 -  94.352:    6        |
|      4:    41.934 -  52.418:  113   |   9:    94.352 - 104.836:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1224 r_free = 0.1719             target_work(ml) = 5.225         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1221 r_free = 0.1718             target_work(ml) = 5.223         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1221   r_free= 0.1718   ksol= 0.32   Bsol= 46.20   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.52,1.27,2.40,0.00,0.00,0.00); trace/3= 1.73                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.223326                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0074 -  4.6855 0.99   1396  157 0.0997 0.1316      5.4003      5.5897|
|  2:  4.6855 -  3.7380 0.99   1344  148 0.0905 0.1261      5.4902      5.7081|
|  3:  3.7380 -  3.2710 0.99   1327  144 0.1163 0.1504      5.5567      5.8824|
|  4:  3.2710 -  2.9745 0.99   1312  153 0.1340 0.1919      5.5555       5.717|
|  5:  2.9745 -  2.7627 0.99   1298  143 0.1481 0.1991      5.4138      5.6595|
|  6:  2.7627 -  2.6007 0.99   1303  141 0.1299 0.1820      5.2785      5.4922|
|  7:  2.6007 -  2.4711 0.99   1297  139 0.1398 0.1859      5.2507      5.4594|
|  8:  2.4711 -  2.3639 0.98   1257  146 0.1337 0.1910      5.1617      5.4206|
|  9:  2.3639 -  2.2732 0.98   1273  148 0.1285 0.1942      5.1162      5.3969|
| 10:  2.2732 -  2.1951 1.00   1295  141 0.1256 0.1876      5.0498      5.2694|
| 11:  2.1951 -  2.1266 0.98   1295  137 0.1279 0.1979      5.0423      5.3459|
| 12:  2.1266 -  2.0660 0.98   1247  144 0.1214 0.1833      4.9599      5.2426|
| 13:  2.0660 -  2.0117 0.99   1278  138 0.1246 0.1927      4.8481      5.1235|
| 14:  2.0117 -  1.9628 0.55    708   80 0.1122 0.1573      4.7183      4.9218|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0074 -  4.6855  1396   157  0.93   9.88   0.98     0.96       7984.42|
|  2:  4.6855 -  3.7380  1344   148  0.95   8.85   1.03     1.01      10288.49|
|  3:  3.7380 -  3.2710  1327   144  0.92  12.96   1.05     1.03      12411.40|
|  4:  3.2710 -  2.9745  1312   153  0.90  15.84   1.02     1.00      12881.61|
|  5:  2.9745 -  2.7627  1298   143  0.89  17.64   1.00     0.97       9819.54|
|  6:  2.7627 -  2.6007  1303   141  0.89  17.50   0.99     0.96       8239.19|
|  7:  2.6007 -  2.4711  1297   139  0.89  17.43   1.00     0.97       7363.82|
|  8:  2.4711 -  2.3639  1257   146  0.89  17.37   0.99     0.97       6315.92|
|  9:  2.3639 -  2.2732  1273   148  0.89  17.16   1.01     0.98       6051.11|
| 10:  2.2732 -  2.1951  1295   141  0.89  17.62   1.00     0.96       5322.58|
| 11:  2.1951 -  2.1266  1295   137  0.88  18.04   1.01     0.96       5336.22|
| 12:  2.1266 -  2.0660  1247   144  0.89  17.19   1.02     1.01       4786.30|
| 13:  2.0660 -  2.0117  1278   138  0.89  17.75   1.01     0.99       3766.82|
| 14:  2.0117 -  1.9628   708    80  0.91  15.56   1.00     0.97       2880.65|
|alpha:            min =        0.96 max =            1.03 mean =         0.98|
|beta:             min =     2880.65 max =        12881.61 mean =      7580.50|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           90.00 mean =        15.71|
|phase err.(test): min =        0.00 max =           88.67 mean =        15.09|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1221   r_free= 0.1718   ksol= 0.32   Bsol= 47.98   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.19,-0.49,0.68,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.223338                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1221   r_free= 0.1718   ksol= 0.32   Bsol= 47.98   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.19,-0.49,0.68,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.223338                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0074 -  4.6855 0.99   1396  157 0.0997 0.1316      5.4007      5.5902|
|  2:  4.6855 -  3.7380 0.99   1344  148 0.0905 0.1261      5.4904      5.7081|
|  3:  3.7380 -  3.2710 0.99   1327  144 0.1163 0.1504      5.5568      5.8825|
|  4:  3.2710 -  2.9745 0.99   1312  153 0.1340 0.1919      5.5555      5.7171|
|  5:  2.9745 -  2.7627 0.99   1298  143 0.1481 0.1991      5.4137      5.6593|
|  6:  2.7627 -  2.6007 0.99   1303  141 0.1299 0.1819      5.2783       5.492|
|  7:  2.6007 -  2.4711 0.99   1297  139 0.1398 0.1859      5.2506      5.4596|
|  8:  2.4711 -  2.3639 0.98   1257  146 0.1337 0.1910      5.1617      5.4205|
|  9:  2.3639 -  2.2732 0.98   1273  148 0.1285 0.1941      5.1161      5.3966|
| 10:  2.2732 -  2.1951 1.00   1295  141 0.1256 0.1876      5.0499        5.27|
| 11:  2.1951 -  2.1266 0.98   1295  137 0.1279 0.1979      5.0424      5.3461|
| 12:  2.1266 -  2.0660 0.98   1247  144 0.1214 0.1832      4.9598      5.2426|
| 13:  2.0660 -  2.0117 0.99   1278  138 0.1246 0.1926       4.848       5.123|
| 14:  2.0117 -  1.9628 0.55    708   80 0.1121 0.1570      4.7179      4.9213|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0074 -  4.6855  1396   157  0.93   9.88   0.98     0.96       7989.79|
|  2:  4.6855 -  3.7380  1344   148  0.95   8.85   1.03     1.01      10293.60|
|  3:  3.7380 -  3.2710  1327   144  0.92  12.96   1.05     1.03      12416.17|
|  4:  3.2710 -  2.9745  1312   153  0.90  15.84   1.02     1.00      12881.30|
|  5:  2.9745 -  2.7627  1298   143  0.89  17.64   1.00     0.97       9815.45|
|  6:  2.7627 -  2.6007  1303   141  0.89  17.50   0.99     0.96       8237.69|
|  7:  2.6007 -  2.4711  1297   139  0.89  17.43   1.00     0.97       7362.37|
|  8:  2.4711 -  2.3639  1257   146  0.89  17.37   0.99     0.97       6316.36|
|  9:  2.3639 -  2.2732  1273   148  0.89  17.16   1.01     0.98       6051.42|
| 10:  2.2732 -  2.1951  1295   141  0.89  17.62   1.00     0.96       5324.76|
| 11:  2.1951 -  2.1266  1295   137  0.88  18.05   1.01     0.96       5338.19|
| 12:  2.1266 -  2.0660  1247   144  0.89  17.19   1.02     1.02       4786.04|
| 13:  2.0660 -  2.0117  1278   138  0.89  17.75   1.01     0.99       3765.30|
| 14:  2.0117 -  1.9628   708    80  0.91  15.55   1.00     0.98       2877.53|
|alpha:            min =        0.96 max =            1.03 mean =         0.98|
|beta:             min =     2877.53 max =        12881.30 mean =      7581.24|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           90.00 mean =        15.71|
|phase err.(test): min =        0.00 max =           88.67 mean =        15.10|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.607)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.78    106.61  15.82    None  None   None       |
|    all(noH): 2823   0      1.78    106.61  15.82    None  None   None       |
|    Sol.    : 438    0      4.49    98.43   41.25    None  None   None       |
|    Mac.    : 2385   0      1.78    106.61  11.15    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.779 -  12.262: 1778   |   5:    54.196 -  64.680:   80        |
|      1:    12.262 -  22.746:  532   |   6:    64.680 -  75.164:   37        |
|      2:    22.746 -  33.229:  145   |   7:    75.164 -  85.647:   11        |
|      3:    33.229 -  43.713:  119   |   8:    85.647 -  96.131:    6        |
|      4:    43.713 -  54.196:  113   |   9:    96.131 - 106.614:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 328         
Filter by distance & map next to the model:
   mapped sites are within: 0.249 - 5.497
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 325 from: 328
   mapped sites are within: 0.733 - 5.497

peak=    9.545 closest distance to " CB  VAL A 230 " =    1.433
peak=    9.461 closest distance to " CG2 VAL A 296 " =    1.519
peak=    7.942 closest distance to " O   HOH Z 130 " =    1.638
peak=    7.391 closest distance to " CG  ARG A 138 " =    1.155
peak=    6.726 closest distance to " CD2 LEU A   5 " =    1.324
peak=    6.255 closest distance to " O   HOH Z  65 " =    1.391
peak=    5.822 closest distance to " NE2 GLN A  11 " =    1.198
peak=    5.813 closest distance to " CD1AILE A 234 " =    1.070
peak=    5.653 closest distance to " O   HOH Z 385 " =    1.029
peak=    5.524 closest distance to " O   HOH Z 424 " =    1.291
peak=    5.235 closest distance to " NH2 ARG A  56 " =    2.075
peak=    5.120 closest distance to " O   HOH Z 124 " =    1.691
peak=    5.096 closest distance to " CG  LEU A   5 " =    1.239
peak=    5.090 closest distance to " O   HOH Z 427 " =    1.242
peak=    5.089 closest distance to " O   HOH Z   7 " =    1.666
peak=    5.075 closest distance to " CB  PRO A  54 " =    1.079
peak=    5.051 closest distance to " O   HOH Z   9 " =    1.554
peak=    4.988 closest distance to " O   PRO A 198 " =    1.363
peak=    4.982 closest distance to " O   HOH Z 144 " =    1.964
peak=    4.973 closest distance to " CB  VAL A 230 " =    1.202
peak=    4.919 closest distance to " O   HOH Z 127 " =    1.090
peak=    4.832 closest distance to " CD2 LEU A 228 " =    1.192
peak=    4.800 closest distance to " O   HOH Z 222 " =    1.233
peak=    4.789 closest distance to " CG  PRO A  54 " =    1.343
peak=    4.742 closest distance to " O   HOH Z 214 " =    1.350
peak=    4.722 closest distance to " NH1 ARG A 138 " =    0.980
peak=    4.678 closest distance to " O   HOH Z 425 " =    1.655
peak=    4.668 closest distance to " O   HOH Z  63 " =    1.627
peak=    4.649 closest distance to " O   HOH Z 126 " =    1.972
peak=    4.634 closest distance to " CG  PRO A 213 " =    1.274
peak=    4.611 closest distance to " O   HOH Z 232 " =    2.141
peak=    4.576 closest distance to " CB  ASN A 148 " =    1.331
peak=    4.557 closest distance to " CB  GLN A 183 " =    1.200
peak=    4.557 closest distance to " CB  SER A   3 " =    1.376
peak=    4.488 closest distance to " O   HOH Z 369 " =    2.053
peak=    4.484 closest distance to " O   HOH Z 139 " =    1.450
peak=    4.483 closest distance to " CG  PRO A 198 " =    1.273
peak=    4.469 closest distance to " O   HOH Z 427 " =    2.287
peak=    4.467 closest distance to " CB  ARG A 275 " =    0.962
peak=    4.450 closest distance to " O   HOH Z 193 " =    1.720
peak=    4.449 closest distance to " O   HOH Z 225 " =    1.588
peak=    4.448 closest distance to " O   HOH Z 316 " =    2.920
peak=    4.406 closest distance to " CG  LEU A 228 " =    1.158
peak=    4.390 closest distance to " O   HOH Z 403 " =    1.370
peak=    4.379 closest distance to " CB  SER A  63 " =    1.324
peak=    4.373 closest distance to " O   HOH Z   2 " =    1.883
peak=    4.357 closest distance to " O   HOH Z 287 " =    1.849
peak=    4.341 closest distance to " CB  SER A 216 " =    0.985
peak=    4.335 closest distance to " O   HOH Z 410 " =    1.518
peak=    4.332 closest distance to " O   HOH Z  91 " =    2.399
peak=    4.332 closest distance to " O   HOH Z  78 " =    1.662
peak=    4.317 closest distance to " CD  ARG A 138 " =    0.982
peak=    4.313 closest distance to " O   HOH Z 298 " =    1.980
peak=    4.300 closest distance to " O   HOH Z 132 " =    1.134
peak=    4.219 closest distance to " O   HOH Z 236 " =    1.737
peak=    4.215 closest distance to " O   HOH Z 414 " =    1.338
peak=    4.205 closest distance to " O   HOH Z 418 " =    1.037
peak=    4.178 closest distance to " O   HOH Z 375 " =    0.962
peak=    4.166 closest distance to " O   HOH Z 193 " =    1.702
peak=    4.157 closest distance to " CG  LEU A 167 " =    1.199
peak=    4.146 closest distance to " OG  SER A  62 " =    3.156
peak=    4.142 closest distance to " O   HOH Z 417 " =    1.379
peak=    4.095 closest distance to " O   HOH Z 380 " =    1.859
peak=    4.086 closest distance to " O   HOH Z 371 " =    2.789
peak=    4.069 closest distance to " O   HOH Z 145 " =    1.979
peak=    4.052 closest distance to " O   HOH Z 147 " =    1.431
peak=    4.051 closest distance to " O   HOH Z 390 " =    1.144
peak=    4.049 closest distance to " O   HOH Z 217 " =    3.102
peak=    4.048 closest distance to " O   HOH Z 419 " =    1.921
peak=    4.045 closest distance to " O   HOH Z 344 " =    1.199
peak=    4.039 closest distance to " O   HOH Z 117 " =    1.850
peak=    3.999 closest distance to " O   HOH Z  30 " =    1.897
peak=    3.987 closest distance to " CB  GLN A 223 " =    1.448
peak=    3.964 closest distance to " CD2 TRP A 179 " =    2.263
peak=    3.953 closest distance to " O   HOH Z 389 " =    1.789
peak=    3.928 closest distance to " O   HOH Z 234 " =    3.432
peak=    3.925 closest distance to " CB  GLU A 128 " =    1.023
peak=    3.923 closest distance to " O   HOH Z  59 " =    1.582
peak=    3.915 closest distance to " CB  TRP A 266 " =    1.040
peak=    3.912 closest distance to " O   HOH Z 126 " =    1.550
peak=    3.911 closest distance to " O   HOH Z   1 " =    1.864
peak=    3.908 closest distance to " O   HOH Z 422 " =    2.437
peak=    3.907 closest distance to " O   HOH Z  61 " =    1.596
peak=    3.906 closest distance to " O   HOH Z 361 " =    1.507
peak=    3.879 closest distance to " CB  TRP A 179 " =    1.383
peak=    3.879 closest distance to " O   HOH Z 112 " =    1.009
peak=    3.876 closest distance to " CB  VAL A 265 " =    1.289
peak=    3.875 closest distance to " O   HOH Z 263 " =    1.524
peak=    3.870 closest distance to " CB  TYR A 169 " =    0.792
peak=    3.863 closest distance to " NE1 TRP A 274 " =    0.956
peak=    3.859 closest distance to " CA  PHE A 283 " =    1.361
peak=    3.858 closest distance to " N   GLN A 278 " =    1.010
peak=    3.849 closest distance to " O   HOH Z 207 " =    2.262
peak=    3.829 closest distance to " CG  GLN A  11 " =    2.240
peak=    3.806 closest distance to " CB  VAL A 202 " =    1.677
peak=    3.804 closest distance to " CB  GLU A 277 " =    3.570
peak=    3.802 closest distance to " O   HOH Z 384 " =    1.391
peak=    3.795 closest distance to " CA  ASN A 127 " =    1.090
peak=    3.793 closest distance to " O   HOH Z 184 " =    1.393
peak=    3.790 closest distance to " CB  MET A  40 " =    0.900
peak=    3.786 closest distance to " CG2 THR A 221 " =    1.241
peak=    3.768 closest distance to " NH1AARG A 145 " =    0.968
peak=    3.765 closest distance to " O   HOH Z 392 " =    1.380
peak=    3.764 closest distance to " O   HOH Z 222 " =    1.969
peak=    3.761 closest distance to " OD2 ASP A 286 " =    2.519
peak=    3.757 closest distance to " O   HOH Z 272 " =    1.867
peak=    3.756 closest distance to " CB  ASP A 124 " =    0.828
peak=    3.743 closest distance to " O   HOH Z 359 " =    1.358
peak=    3.735 closest distance to " O   HOH Z 405 " =    1.553
peak=    3.730 closest distance to " CG  GLN A  88 " =    1.124
peak=    3.716 closest distance to " O   HOH Z 258 " =    2.152
peak=    3.710 closest distance to " CA  ILE A 234 " =    0.971
peak=    3.699 closest distance to " O   HOH Z  68 " =    2.131
peak=    3.683 closest distance to " O   HOH Z 119 " =    1.446
peak=    3.682 closest distance to " O   HOH Z  55 " =    1.804
peak=    3.682 closest distance to " CB  SER A 276 " =    1.127
peak=    3.680 closest distance to " OE2 GLU A   2 " =    1.981
peak=    3.677 closest distance to " O   HOH Z 181 " =    2.321
peak=    3.673 closest distance to " CD  GLN A 240 " =    1.633
peak=    3.657 closest distance to " O   HOH Z  32 " =    2.423
peak=    3.650 closest distance to " CB BVAL A  41 " =    1.350
peak=    3.648 closest distance to " CE  MET A  93 " =    1.450
peak=    3.647 closest distance to " OD1 ASN A 217 " =    1.711
peak=    3.645 closest distance to " N   ALA A   1 " =    1.069
peak=    3.642 closest distance to " O   HOH Z 411 " =    3.370
peak=    3.640 closest distance to " CG2 VAL A 257 " =    0.948
peak=    3.639 closest distance to " O   HOH Z 133 " =    1.478
peak=    3.627 closest distance to " NH1 ARG A  14 " =    0.982
peak=    3.625 closest distance to " CB  ILE A 234 " =    0.923
peak=    3.621 closest distance to " O   HOH Z 368 " =    1.897
peak=    3.621 closest distance to " O   HOH Z 423 " =    1.608
peak=    3.615 closest distance to " CB  LYS A 117 " =    1.197
peak=    3.614 closest distance to " NZ BLYS A 290 " =    0.967
peak=    3.614 closest distance to " CD BLYS A 290 " =    1.063
peak=    3.611 closest distance to " O   HOH Z  48 " =    1.615
peak=    3.606 closest distance to " NE2 GLN A  58 " =    3.369
peak=    3.600 closest distance to " O   HOH Z 193 " =    1.849
peak=    3.600 closest distance to " CA  LEU A 101 " =    1.615
peak=    3.598 closest distance to " CG  PRO A 280 " =    0.896
peak=    3.594 closest distance to " O   HOH Z 358 " =    1.392
peak=    3.594 closest distance to " N   GLU A   2 " =    1.333
peak=    3.593 closest distance to " O   HOH Z 233 " =    1.555
peak=    3.587 closest distance to " CG1 ILE A 120 " =    1.376
peak=    3.585 closest distance to " CG  LYS A  76 " =    1.501
peak=    3.579 closest distance to " O   HOH Z 305 " =    3.304
peak=    3.570 closest distance to " O   HOH Z 278 " =    0.876
peak=    3.568 closest distance to " ND1 HIS A  86 " =    1.820
peak=    3.566 closest distance to " N   PHE A 130 " =    1.220
peak=    3.566 closest distance to " O   ASN A 301 " =    2.288
peak=    3.555 closest distance to " CG  GLN A  89 " =    1.363
peak=    3.552 closest distance to " CA  ALA A 158 " =    1.085
peak=    3.545 closest distance to " CA  GLY A 267 " =    1.116
peak=    3.540 closest distance to " O   ALA A 165 " =    1.268
peak=    3.539 closest distance to " NE AARG A 275 " =    1.403
peak=    3.537 closest distance to " O   HOH Z  59 " =    2.202
peak=    3.534 closest distance to " O   HOH Z 189 " =    2.534
peak=    3.519 closest distance to " N   TYR A  15 " =    0.977
peak=    3.517 closest distance to " CA  ASN A  74 " =    1.201
peak=    3.512 closest distance to " CB  LEU A 237 " =    0.925
peak=    3.511 closest distance to " O   HOH Z 290 " =    0.995
peak=    3.509 closest distance to " O   HOH Z 108 " =    1.959
peak=    3.509 closest distance to " N   SER A 271 " =    1.047
peak=    3.507 closest distance to " O   HOH Z 146 " =    1.669
peak=    3.504 closest distance to " CE3 TRP A 274 " =    2.288
peak=    3.491 closest distance to " O   HOH Z 303 " =    1.697
peak=    3.490 closest distance to " CD  ARG A 269 " =    0.971
peak=    3.486 closest distance to " O   HOH Z 143 " =    1.035
peak=    3.486 closest distance to " O   HOH Z 425 " =    1.987
peak=    3.484 closest distance to " O   HOH Z 352 " =    1.547
peak=    3.481 closest distance to " O   HOH Z  88 " =    3.601
peak=    3.476 closest distance to " CB  ASN A  39 " =    0.903
peak=    3.474 closest distance to " OG  SER A  62 " =    2.732
peak=    3.471 closest distance to " CA  LEU A 282 " =    1.132
peak=    3.469 closest distance to " O   HOH Z 158 " =    2.739
peak=    3.466 closest distance to " O   HOH Z 371 " =    1.802
peak=    3.464 closest distance to " O   HOH Z  22 " =    1.994
peak=    3.462 closest distance to " CD  ARG A 159 " =    0.733
peak=    3.454 closest distance to " O   HOH Z 385 " =    3.249
peak=    3.443 closest distance to " C   ASN A 209 " =    1.670
peak=    3.428 closest distance to " CB  GLU A 152 " =    1.395
peak=    3.427 closest distance to " O   HOH Z 171 " =    2.709
peak=    3.421 closest distance to " O   HOH Z 343 " =    3.317
peak=    3.420 closest distance to " O   HOH Z 227 " =    1.603
peak=    3.419 closest distance to " O   HOH Z 244 " =    1.612
peak=    3.418 closest distance to " NZ  LYS A 117 " =    1.110
peak=    3.415 closest distance to " O   HOH Z  58 " =    1.789
peak=    3.411 closest distance to " O   HOH Z 148 " =    1.553
peak=    3.411 closest distance to " CA  SER A  87 " =    0.973
peak=    3.407 closest distance to " CA  ALA A  51 " =    1.082
peak=    3.404 closest distance to " C   ALA A 299 " =    0.976
peak=    3.401 closest distance to " OG BSER A 212 " =    2.769
peak=    3.399 closest distance to " CA  ALA A 248 " =    1.248
peak=    3.396 closest distance to " OD1 ASN A  69 " =    2.743
peak=    3.390 closest distance to " O   HOH Z  44 " =    2.788
peak=    3.387 closest distance to " CG BARG A 102 " =    1.863
peak=    3.385 closest distance to " O   HOH Z 402 " =    1.495
peak=    3.384 closest distance to " O   HOH Z 134 " =    1.550
peak=    3.383 closest distance to " O   HOH Z 424 " =    2.590
peak=    3.383 closest distance to " O   HOH Z  78 " =    1.906
peak=    3.382 closest distance to " O   HOH Z 130 " =    2.245
peak=    3.381 closest distance to " O   HOH Z 293 " =    1.476
peak=    3.380 closest distance to " O   HOH Z 334 " =    2.960
peak=    3.377 closest distance to " CD  PRO A 243 " =    1.612
peak=    3.375 closest distance to " O   HOH Z 122 " =    1.912
peak=    3.374 closest distance to " CG  ARG A 159 " =    0.931
peak=    3.372 closest distance to " O   HOH Z 214 " =    1.849
peak=    3.366 closest distance to " O   HOH Z  40 " =    2.289
peak=    3.365 closest distance to " O   HOH Z 334 " =    1.563
peak=    3.363 closest distance to " OD1BASN A 224 " =    2.401
peak=    3.357 closest distance to " ND1 HIS A  81 " =    1.608
peak=    3.353 closest distance to " O   HOH Z 132 " =    2.257
peak=    3.352 closest distance to " OE1 GLU A   2 " =    2.038
peak=    3.345 closest distance to " CD1 ILE A  33 " =    1.784
peak=    3.345 closest distance to " O   HOH Z 250 " =    1.330
peak=    3.344 closest distance to " CA  THR A 221 " =    0.903
peak=    3.343 closest distance to " O   HOH Z 357 " =    2.307
peak=    3.337 closest distance to " CB  LEU A 228 " =    1.284
peak=    3.337 closest distance to " CB  PHE A 225 " =    1.439
peak=    3.334 closest distance to " O   GLY A 302 " =    2.072
peak=    3.333 closest distance to " O   HOH Z 207 " =    1.843
peak=    3.332 closest distance to " O   HOH Z 384 " =    1.568
peak=    3.331 closest distance to " O   HOH Z  64 " =    2.210
peak=    3.327 closest distance to " O   HOH Z  64 " =    2.129
peak=    3.324 closest distance to " O   MET A 105 " =    1.675
peak=    3.322 closest distance to " OG BSER A  99 " =    2.128
peak=    3.321 closest distance to " O   HOH Z  20 " =    2.512
peak=    3.313 closest distance to " O   HOH Z  49 " =    1.454
peak=    3.312 closest distance to " OG BSER A 134 " =    2.965
peak=    3.302 closest distance to " CA  ASN A 215 " =    1.142
peak=    3.302 closest distance to " O   HOH Z 260 " =    1.060
peak=    3.300 closest distance to " CG2 ILE A 234 " =    0.843
peak=    3.296 closest distance to " O   HOH Z 357 " =    1.384
peak=    3.292 closest distance to " O   HOH Z 175 " =    2.065
peak=    3.291 closest distance to " O   HOH Z   6 " =    1.639
peak=    3.286 closest distance to " CB  ALA A   1 " =    0.858
peak=    3.286 closest distance to " O   HOH Z 353 " =    2.460
peak=    3.286 closest distance to " O   HOH Z 153 " =    3.622
peak=    3.284 closest distance to " O   HOH Z 145 " =    1.948
peak=    3.280 closest distance to " CG1 VAL A 153 " =    0.836
peak=    3.280 closest distance to " O   HOH Z  39 " =    1.186
peak=    3.269 closest distance to " O   HOH Z  69 " =    2.454
peak=    3.269 closest distance to " O   HOH Z 247 " =    1.189
peak=    3.268 closest distance to " ND2 ASN A 249 " =    0.837
peak=    3.268 closest distance to " O   HOH Z 133 " =    2.468
peak=    3.267 closest distance to " O   HOH Z 209 " =    2.316
peak=    3.266 closest distance to " O   HOH Z 128 " =    1.983
peak=    3.265 closest distance to " CG1AVAL A 121 " =    0.948
peak=    3.263 closest distance to " NE AARG A 145 " =    1.228
peak=    3.262 closest distance to " CB  LEU A 300 " =    0.899
peak=    3.261 closest distance to " O   HOH Z 368 " =    3.581
peak=    3.252 closest distance to " NH2BARG A 145 " =    2.078
peak=    3.251 closest distance to " NZ  LYS A  48 " =    1.956
peak=    3.249 closest distance to " O   HOH Z 426 " =    1.077
peak=    3.246 closest distance to " O   HOH Z 108 " =    1.335
peak=    3.246 closest distance to " O   HOH Z 172 " =    2.893
peak=    3.243 closest distance to " O   HOH Z 329 " =    3.699
peak=    3.243 closest distance to " N   VAL A 126 " =    1.173
peak=    3.243 closest distance to " CB  VAL A 296 " =    1.116
peak=    3.237 closest distance to " O   ASN A 217 " =    1.116
peak=    3.236 closest distance to " CE1 TYR A 186 " =    1.232
peak=    3.235 closest distance to " CB  SER A  62 " =    1.120
peak=    3.233 closest distance to " O   HOH Z 346 " =    1.612
peak=    3.233 closest distance to " CG1 ILE A  33 " =    1.379
peak=    3.233 closest distance to " O   HOH Z 276 " =    1.338
peak=    3.232 closest distance to " O   ALA A 158 " =    1.437
peak=    3.232 closest distance to " O   HOH Z 356 " =    1.332
peak=    3.230 closest distance to " CG  LYS A 119 " =    1.102
peak=    3.225 closest distance to " O   HOH Z 166 " =    1.362
peak=    3.224 closest distance to " O   HOH Z 128 " =    2.125
peak=    3.219 closest distance to " O   HOH Z 109 " =    2.373
peak=    3.219 closest distance to " O   HOH Z   9 " =    1.773
peak=    3.218 closest distance to " CB  THR A 157 " =    1.039
peak=    3.216 closest distance to " CB  VAL A 250 " =    1.012
peak=    3.214 closest distance to " C   LYS A 290 " =    1.412
peak=    3.203 closest distance to " CA  TYR A  30 " =    0.962
peak=    3.200 closest distance to " CB  LEU A 143 " =    0.949
peak=    3.195 closest distance to " O   HOH Z  44 " =    1.971
peak=    3.193 closest distance to " O   HOH Z 326 " =    1.320
peak=    3.191 closest distance to " O   HOH Z  28 " =    1.488
peak=    3.190 closest distance to " CG1 ILE A 151 " =    1.051
peak=    3.189 closest distance to " O   HOH Z 220 " =    1.349
peak=    3.188 closest distance to " O   HOH Z 362 " =    2.155
peak=    3.187 closest distance to " CB  TYR A  30 " =    1.921
peak=    3.186 closest distance to " O   HOH Z 406 " =    1.569
peak=    3.184 closest distance to " CA  ARG A 102 " =    1.105
peak=    3.182 closest distance to " CA  ALA A 180 " =    1.324
peak=    3.176 closest distance to " CE3 TRP A 150 " =    1.011
peak=    3.175 closest distance to " O   HOH Z  51 " =    1.260
peak=    3.174 closest distance to " O   HOH Z 110 " =    1.832
peak=    3.172 closest distance to " NH2BARG A 190 " =    1.506
peak=    3.169 closest distance to " N   GLY A 196 " =    1.091
peak=    3.164 closest distance to " OD1 ASN A  45 " =    1.316
peak=    3.164 closest distance to " CB  ARG A 139 " =    1.027
peak=    3.162 closest distance to " CD1 LEU A 281 " =    1.035
peak=    3.158 closest distance to " CB  ALA A 291 " =    1.438
peak=    3.158 closest distance to " O   HOH Z 154 " =    2.276
peak=    3.156 closest distance to " O   HOH Z 327 " =    1.566
peak=    3.156 closest distance to " O   HOH Z 213 " =    2.123
peak=    3.155 closest distance to " NH1BARG A 275 " =    1.472
peak=    3.153 closest distance to " O   HOH Z 350 " =    1.423
peak=    3.152 closest distance to " O   HOH Z 281 " =    1.933
peak=    3.149 closest distance to " CB  SER A 210 " =    0.876
peak=    3.148 closest distance to " O   HOH Z 129 " =    0.880
peak=    3.146 closest distance to " CG1BVAL A  72 " =    0.865
peak=    3.136 closest distance to " CE  MET A  40 " =    1.020
peak=    3.133 closest distance to " CB  ASN A 187 " =    1.059
peak=    3.132 closest distance to " O   HOH Z  48 " =    1.568
peak=    3.118 closest distance to " CA  ARG A  36 " =    1.111
peak=    3.106 closest distance to " O   HOH Z 302 " =    1.548
peak=    3.106 closest distance to " CB  PHE A 204 " =    0.838
peak=    3.102 closest distance to " CD1 LEU A 300 " =    1.206
peak=    3.091 closest distance to " O   HOH Z  59 " =    1.870
peak=    3.085 closest distance to " NE2 GLN A  58 " =    5.497
peak=    3.079 closest distance to " O   HOH Z 392 " =    1.928
peak=    3.076 closest distance to " CD  LYS A 166 " =    1.355
peak=    3.072 closest distance to " O   HOH Z 217 " =    1.504
peak=    3.067 closest distance to " ND2 ASN A 187 " =    1.689
peak=    3.066 closest distance to " O   HOH Z 323 " =    1.708
peak=    3.063 closest distance to " O   HOH Z 280 " =    2.707
peak=    3.058 closest distance to " CA  GLY A 136 " =    1.146
peak=    3.058 closest distance to " CB  ALA A 104 " =    0.768
peak=    3.047 closest distance to " O   HOH Z  88 " =    3.071
peak=    3.044 closest distance to " O   HOH Z 135 " =    1.921
peak=    3.033 closest distance to " O   HOH Z 373 " =    1.452
peak=    3.024 closest distance to " O   HOH Z 366 " =    2.995

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 198         
Filter by distance & map next to the model:
   mapped sites are within: 0.690 - 5.944
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 196 from: 198
   mapped sites are within: 0.763 - 5.944

peak=   -5.103 closest distance to " CG2 VAL A 230 " =    0.836
peak=   -4.666 closest distance to " CD  ARG A 138 " =    1.224
peak=   -4.334 closest distance to " CA  GLY A 133 " =    1.968
peak=   -4.284 closest distance to " O   PRO A 198 " =    1.120
peak=   -4.245 closest distance to " O   HOH Z 385 " =    1.025
peak=   -4.196 closest distance to " O   HOH Z  43 " =    1.757
peak=   -4.143 closest distance to " OG BSER A 134 " =    1.440
peak=   -4.087 closest distance to " OE1 GLU A 277 " =    2.346
peak=   -4.083 closest distance to " O   HOH Z 298 " =    0.906
peak=   -4.073 closest distance to " CD  ARG A  14 " =    3.017
peak=   -4.045 closest distance to " CA  GLY A  98 " =    1.868
peak=   -4.032 closest distance to " CD  ARG A 156 " =    1.856
peak=   -4.014 closest distance to " OG ASER A 134 " =    1.122
peak=   -3.958 closest distance to " O   HOH Z 266 " =    4.647
peak=   -3.926 closest distance to " CG  ARG A 138 " =    0.933
peak=   -3.924 closest distance to " CG  PRO A 163 " =    2.564
peak=   -3.912 closest distance to " CB  PRO A 243 " =    2.600
peak=   -3.902 closest distance to " NH2 ARG A  79 " =    1.978
peak=   -3.875 closest distance to " CD1 LEU A 101 " =    2.283
peak=   -3.873 closest distance to " O   HOH Z 412 " =    5.944
peak=   -3.858 closest distance to " NH1 ARG A  56 " =    2.412
peak=   -3.847 closest distance to " O   HOH Z 407 " =    3.120
peak=   -3.846 closest distance to " O   HOH Z 350 " =    1.778
peak=   -3.824 closest distance to " CB  ASN A  39 " =    2.145
peak=   -3.816 closest distance to " O   HOH Z 185 " =    2.107
peak=   -3.804 closest distance to " O   HOH Z 231 " =    1.770
peak=   -3.801 closest distance to " O   HOH Z  13 " =    1.646
peak=   -3.793 closest distance to " CE2 TYR A  30 " =    2.744
peak=   -3.765 closest distance to " OG  SER A  87 " =    1.328
peak=   -3.759 closest distance to " O   HOH Z 103 " =    1.407
peak=   -3.753 closest distance to " O   HOH Z 290 " =    1.164
peak=   -3.752 closest distance to " CB  TYR A  15 " =    2.101
peak=   -3.749 closest distance to " O   HOH Z 198 " =    2.404
peak=   -3.735 closest distance to " O   HOH Z 377 " =    1.832
peak=   -3.732 closest distance to " O   HOH Z  76 " =    1.259
peak=   -3.726 closest distance to " O   HOH Z 211 " =    1.303
peak=   -3.707 closest distance to " CD1 LEU A 255 " =    2.909
peak=   -3.704 closest distance to " O   HOH Z 359 " =    1.644
peak=   -3.702 closest distance to " O   PRO A 243 " =    2.440
peak=   -3.688 closest distance to " OG  SER A 245 " =    1.262
peak=   -3.687 closest distance to " CD2 LEU A   5 " =    0.941
peak=   -3.679 closest distance to " O   HOH Z  71 " =    1.135
peak=   -3.672 closest distance to " O   HOH Z 166 " =    1.678
peak=   -3.667 closest distance to " O   HOH Z 388 " =    2.195
peak=   -3.660 closest distance to " CG  ASN A 301 " =    1.888
peak=   -3.647 closest distance to " O   ILE A  49 " =    1.706
peak=   -3.646 closest distance to " CE2 TYR A 116 " =    2.954
peak=   -3.633 closest distance to " CD  LYS A 289 " =    2.419
peak=   -3.628 closest distance to " O   HOH Z  11 " =    1.993
peak=   -3.624 closest distance to " CG  MET A 105 " =    0.958
peak=   -3.623 closest distance to " CA  ASP A  27 " =    2.337
peak=   -3.618 closest distance to " C   HIS A 108 " =    1.192
peak=   -3.618 closest distance to " CE2 PHE A 218 " =    2.495
peak=   -3.616 closest distance to " O   HOH Z 111 " =    0.934
peak=   -3.610 closest distance to " O   HOH Z 207 " =    1.855
peak=   -3.590 closest distance to " O   HOH Z 231 " =    0.800
peak=   -3.581 closest distance to " O   HOH Z 415 " =    1.043
peak=   -3.565 closest distance to " CG2 VAL A 296 " =    1.993
peak=   -3.558 closest distance to " O   HOH Z 435 " =    2.034
peak=   -3.541 closest distance to " N   ALA A   1 " =    1.155
peak=   -3.526 closest distance to " CB  ALA A 248 " =    2.020
peak=   -3.519 closest distance to " C   ASN A 285 " =    2.105
peak=   -3.516 closest distance to " OE1 GLN A  88 " =    1.082
peak=   -3.516 closest distance to " O   HOH Z 414 " =    1.890
peak=   -3.512 closest distance to " N   SER A 276 " =    1.154
peak=   -3.512 closest distance to " O   VAL A 197 " =    1.577
peak=   -3.509 closest distance to " OG  SER A  26 " =    1.050
peak=   -3.509 closest distance to " N   PRO A 163 " =    1.557
peak=   -3.509 closest distance to " O   HOH Z 131 " =    3.909
peak=   -3.498 closest distance to " O   SER A  22 " =    2.564
peak=   -3.491 closest distance to " O   TYR A  30 " =    2.839
peak=   -3.489 closest distance to " O   HOH Z  47 " =    1.556
peak=   -3.489 closest distance to " O   HOH Z 143 " =    1.026
peak=   -3.483 closest distance to " O   ALA A   1 " =    1.203
peak=   -3.480 closest distance to " O   VAL A  67 " =    2.803
peak=   -3.480 closest distance to " O   GLY A  80 " =    2.416
peak=   -3.467 closest distance to " O   HOH Z 385 " =    1.991
peak=   -3.465 closest distance to " C   ARG A 269 " =    1.405
peak=   -3.450 closest distance to " O   HOH Z 426 " =    1.607
peak=   -3.446 closest distance to " CB  ASP A 132 " =    2.378
peak=   -3.445 closest distance to " O   SER A 135 " =    1.581
peak=   -3.443 closest distance to " CA  GLY A  35 " =    1.964
peak=   -3.434 closest distance to " CB  VAL A 230 " =    0.988
peak=   -3.434 closest distance to " CG  TRP A 266 " =    1.716
peak=   -3.432 closest distance to " O   HOH Z  51 " =    0.793
peak=   -3.419 closest distance to " N   THR A 157 " =    1.473
peak=   -3.418 closest distance to " O   ASN A 301 " =    1.317
peak=   -3.417 closest distance to " O   HOH Z 427 " =    1.726
peak=   -3.416 closest distance to " C   LEU A 143 " =    1.354
peak=   -3.402 closest distance to " O   HOH Z 111 " =    4.398
peak=   -3.395 closest distance to " CG2 THR A 178 " =    2.076
peak=   -3.393 closest distance to " C   ALA A 158 " =    1.278
peak=   -3.389 closest distance to " N   GLN A  58 " =    1.258
peak=   -3.377 closest distance to " O   GLN A  11 " =    1.574
peak=   -3.368 closest distance to " CD1 PHE A  59 " =    2.026
peak=   -3.364 closest distance to " CD  GLN A 223 " =    2.335
peak=   -3.364 closest distance to " O   HOH Z 125 " =    3.133
peak=   -3.362 closest distance to " CG  ASP A 231 " =    0.763
peak=   -3.362 closest distance to " CB  ALA A   7 " =    2.059
peak=   -3.362 closest distance to " CZ2 TRP A 274 " =    0.934
peak=   -3.360 closest distance to " OG  SER A 206 " =    1.710
peak=   -3.346 closest distance to " O   HOH Z 140 " =    1.264
peak=   -3.340 closest distance to " CG  PHE A 283 " =    2.497
peak=   -3.339 closest distance to " O   HOH Z 350 " =    2.546
peak=   -3.337 closest distance to " O   GLY A 211 " =    1.140
peak=   -3.330 closest distance to " O   HOH Z 365 " =    1.373
peak=   -3.328 closest distance to " CD  LYS A 166 " =    2.475
peak=   -3.325 closest distance to " O   VAL A  67 " =    2.685
peak=   -3.324 closest distance to " O   ALA A  51 " =    1.401
peak=   -3.318 closest distance to " O   HOH Z  65 " =    1.012
peak=   -3.318 closest distance to " O   HOH Z 275 " =    1.675
peak=   -3.314 closest distance to " N   MET A 188 " =    1.941
peak=   -3.314 closest distance to " O   PRO A 163 " =    1.934
peak=   -3.313 closest distance to " O   HOH Z   9 " =    1.623
peak=   -3.313 closest distance to " O   HOH Z 414 " =    2.006
peak=   -3.313 closest distance to " O   HOH Z 134 " =    2.722
peak=   -3.311 closest distance to " N   VAL A 125 " =    1.055
peak=   -3.310 closest distance to " CB  ALA A  43 " =    2.232
peak=   -3.308 closest distance to " O   HOH Z  90 " =    2.833
peak=   -3.307 closest distance to " O   SER A 216 " =    1.904
peak=   -3.304 closest distance to " CA  VAL A 296 " =    0.977
peak=   -3.304 closest distance to " N   LEU A 282 " =    2.223
peak=   -3.303 closest distance to " O   HOH Z 191 " =    5.342
peak=   -3.300 closest distance to " CB  ALA A 227 " =    2.312
peak=   -3.293 closest distance to " O   HOH Z 389 " =    1.899
peak=   -3.291 closest distance to " ND2 ASN A 187 " =    1.636
peak=   -3.289 closest distance to " NE2 GLN A  94 " =    1.595
peak=   -3.289 closest distance to " O   HOH Z  93 " =    2.275
peak=   -3.286 closest distance to " O   HOH Z 364 " =    1.571
peak=   -3.286 closest distance to " CB  PRO A 163 " =    2.402
peak=   -3.278 closest distance to " O   HOH Z  60 " =    1.854
peak=   -3.278 closest distance to " CG1 VAL A 197 " =    2.380
peak=   -3.275 closest distance to " CG  GLU A 152 " =    2.403
peak=   -3.269 closest distance to " OG  SER A  97 " =    2.136
peak=   -3.265 closest distance to " CZ  PHE A  59 " =    1.508
peak=   -3.265 closest distance to " O   HOH Z 351 " =    1.554
peak=   -3.265 closest distance to " NH2AARG A 275 " =    5.436
peak=   -3.264 closest distance to " CB  ALA A   9 " =    2.418
peak=   -3.256 closest distance to " N   HIS A 115 " =    2.076
peak=   -3.249 closest distance to " CD1 ILE A 151 " =    2.444
peak=   -3.245 closest distance to " OE1 GLN A  73 " =    2.456
peak=   -3.240 closest distance to " O   HOH Z 208 " =    2.120
peak=   -3.236 closest distance to " N   ALA A 248 " =    1.617
peak=   -3.232 closest distance to " O   HOH Z 216 " =    3.173
peak=   -3.231 closest distance to " O   HOH Z 377 " =    0.880
peak=   -3.228 closest distance to " O   HOH Z 359 " =    3.440
peak=   -3.226 closest distance to " O   HOH Z  40 " =    4.169
peak=   -3.224 closest distance to " N   PHE A  59 " =    2.093
peak=   -3.222 closest distance to " O   HOH Z 189 " =    2.765
peak=   -3.222 closest distance to " NE2 GLN A 223 " =    1.604
peak=   -3.218 closest distance to " O   HOH Z 352 " =    2.160
peak=   -3.216 closest distance to " O   HOH Z  39 " =    1.222
peak=   -3.214 closest distance to " O   HOH Z 137 " =    1.526
peak=   -3.210 closest distance to " O   HOH Z 102 " =    1.676
peak=   -3.206 closest distance to " O   GLY A  57 " =    1.364
peak=   -3.199 closest distance to " NH2 ARG A 219 " =    1.838
peak=   -3.197 closest distance to " O   ASP A 270 " =    1.652
peak=   -3.195 closest distance to " O   HOH Z 368 " =    2.464
peak=   -3.187 closest distance to " CD2 TRP A 150 " =    1.153
peak=   -3.180 closest distance to " CG2 THR A  31 " =    2.388
peak=   -3.176 closest distance to " N   ASP A 171 " =    2.596
peak=   -3.176 closest distance to " N   VAL A  72 " =    1.734
peak=   -3.163 closest distance to " N   THR A 235 " =    1.175
peak=   -3.158 closest distance to " CB  SER A 134 " =    1.861
peak=   -3.157 closest distance to " O   HOH Z  65 " =    1.237
peak=   -3.157 closest distance to " O   HOH Z 235 " =    1.141
peak=   -3.157 closest distance to " O   HOH Z 438 " =    0.785
peak=   -3.153 closest distance to " CD  GLN A  58 " =    0.986
peak=   -3.152 closest distance to " O   HOH Z 285 " =    2.838
peak=   -3.149 closest distance to " CG1BVAL A  72 " =    2.080
peak=   -3.148 closest distance to " C   VAL A 265 " =    0.789
peak=   -3.143 closest distance to " O   HOH Z 197 " =    3.211
peak=   -3.139 closest distance to " CG2 ILE A 151 " =    2.406
peak=   -3.136 closest distance to " CG  ARG A 259 " =    2.905
peak=   -3.135 closest distance to " CD2 LEU A 237 " =    2.238
peak=   -3.134 closest distance to " CZ  PHE A  16 " =    1.779
peak=   -3.132 closest distance to " CB  PHE A 130 " =    1.209
peak=   -3.128 closest distance to " O   ALA A 161 " =    1.847
peak=   -3.127 closest distance to " O   HOH Z  24 " =    1.180
peak=   -3.126 closest distance to " O   HOH Z  28 " =    1.715
peak=   -3.126 closest distance to " OE2 GLU A 152 " =    1.007
peak=   -3.123 closest distance to " O   HOH Z 292 " =    1.568
peak=   -3.121 closest distance to " O   GLN A 194 " =    1.421
peak=   -3.112 closest distance to " N   ALA A  43 " =    2.592
peak=   -3.107 closest distance to " O   HOH Z 414 " =    2.078
peak=   -3.094 closest distance to " CB  CYS A 201 " =    2.048
peak=   -3.091 closest distance to " O   HOH Z 168 " =    1.539
peak=   -3.080 closest distance to " CG  GLU A   2 " =    1.959
peak=   -3.071 closest distance to " CB  ALA A   1 " =    1.466
peak=   -3.064 closest distance to " CG1 ILE A 263 " =    2.062
peak=   -3.053 closest distance to " CZ2 TRP A  92 " =    2.720
peak=   -3.045 closest distance to " CG1 VAL A 296 " =    2.327
peak=   -3.041 closest distance to " O   HOH Z 389 " =    1.320
peak=   -3.037 closest distance to " OG1 THR A 178 " =    1.143
peak=   -3.022 closest distance to " CB  ASN A 301 " =    2.065
peak=   -3.022 closest distance to " CG  HIS A 108 " =    0.903

================= 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    :  0.4825 0.4743   6.285310e+00   6.275141e+00
   1_bss:  0.4731 0.4602   6.278847e+00   6.265430e+00
   1_xyz:  0.3975 0.4239   6.182692e+00   6.216461e+00
   1_adp:  0.3558 0.4104   6.119202e+00   6.203834e+00
   1_occ:  0.3556 0.4106   6.118443e+00   6.203642e+00
   2_bss:  0.3522 0.4055   6.118481e+00   6.201032e+00
   2_xyz:  0.2911 0.3476   5.964877e+00   6.088735e+00
   2_adp:  0.2731 0.3363   5.921223e+00   6.058185e+00
   2_occ:  0.2728 0.3365   5.921323e+00   6.059028e+00
   3_bss:  0.2717 0.3339   5.921118e+00   6.058356e+00
   3_xyz:  0.2065 0.2631   5.673926e+00   5.854270e+00
   3_adp:  0.1840 0.2443   5.580476e+00   5.789568e+00
   3_occ:  0.1838 0.2437   5.579379e+00   5.788500e+00
   4_bss:  0.1836 0.2422   5.576646e+00   5.784557e+00
   4_xyz:  0.1499 0.2057   5.404358e+00   5.638277e+00
   4_adp:  0.1420 0.1972   5.359078e+00   5.595402e+00
   4_occ:  0.1419 0.1969   5.358284e+00   5.594175e+00
   5_bss:  0.1422 0.1972   5.357972e+00   5.593872e+00
   5_xyz:  0.1255 0.1777   5.251113e+00   5.497063e+00
   5_adp:  0.1224 0.1719   5.224989e+00   5.467461e+00
   5_occ:  0.1221 0.1718   5.223326e+00   5.466037e+00
   5_bss:  0.1221 0.1718   5.223338e+00   5.466048e+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:  0.356   0.000   7.236  10.314   7.894   0.000   0.000   0.000
   1_xyz:  0.356   0.000   7.236  10.314   7.894   0.000   0.000   0.000
   1_adp:  0.356   0.000   7.236  10.314   7.894   0.000   0.000   0.000
   1_occ:  0.356   0.000   7.236  10.314   7.894   0.000   0.000   0.000
   2_bss:  0.353  35.123   3.781   5.881   4.734   0.000   0.000   0.000
   2_xyz:  0.353  35.123   3.781   5.881   4.734   0.000   0.000   0.000
   2_adp:  0.353  35.123   3.781   5.881   4.734   0.000   0.000   0.000
   2_occ:  0.353  35.123   3.781   5.881   4.734   0.000   0.000   0.000
   3_bss:  0.342  43.125   2.413   3.239   3.172   0.000   0.000   0.000
   3_xyz:  0.342  43.125   2.413   3.239   3.172   0.000   0.000   0.000
   3_adp:  0.342  43.125   2.413   3.239   3.172   0.000   0.000   0.000
   3_occ:  0.342  43.125   2.413   3.239   3.172   0.000   0.000   0.000
   4_bss:  0.333  47.845   1.642   1.782   2.533   0.000   0.000   0.000
   4_xyz:  0.333  47.845   1.642   1.782   2.533   0.000   0.000   0.000
   4_adp:  0.333  47.845   1.642   1.782   2.533   0.000   0.000   0.000
   4_occ:  0.333  47.845   1.642   1.782   2.533   0.000   0.000   0.000
   5_bss:  0.322  46.198   1.520   1.267   2.396   0.000   0.000   0.000
   5_xyz:  0.322  46.198   1.520   1.267   2.396   0.000   0.000   0.000
   5_adp:  0.322  46.198   1.520   1.267   2.396   0.000   0.000   0.000
   5_occ:  0.322  46.198   1.520   1.267   2.396   0.000   0.000   0.000
   5_bss:  0.322  47.976  -0.189  -0.493   0.681  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  58.421 0.4144  0.4918    72131.263
   1_bss:  57.536 0.4246  0.6390    68888.532
   1_xyz:  50.039 0.5188  0.7664    54577.814
   1_adp:  47.138 0.5557  0.8740    51343.118
   1_occ:  47.163 0.5554  0.8730    51380.151
   2_bss:  46.741 0.5604  0.7799    50765.666
   2_xyz:  37.636 0.6698  0.9121    34587.226
   2_adp:  35.136 0.6999  0.9587    31508.627
   2_occ:  35.213 0.6990  0.9572    31597.472
   3_bss:  35.053 0.7008  0.8973    31397.583
   3_xyz:  26.180 0.7987  0.9850    17767.451
   3_adp:  23.643 0.8257  0.9967    15115.030
   3_occ:  23.615 0.8260  0.9963    15050.752
   4_bss:  23.458 0.8273  0.9637    14840.854
   4_xyz:  19.726 0.8638  0.9851    10707.545
   4_adp:  18.575 0.8753  0.9825     9886.966
   4_occ:  18.549 0.8755  0.9824     9854.656
   5_bss:  18.533 0.8756  0.9729     9831.457
   5_xyz:  16.399 0.8947  0.9838     8017.615
   5_adp:  15.681 0.9012  0.9808     7614.001
   5_occ:  15.648 0.9015  0.9807     7581.134
   5_bss:  15.649 0.9015  0.9826     7581.869
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.089   5.3227e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.089   5.3227e+01
   1_xyz:   1.701  0.013  0.106 18.272  0.007  4.108   1.4272e-01
   1_adp:   1.701  0.013  0.106 18.272  0.007  4.108   1.4272e-01
   1_occ:   1.701  0.013  0.106 18.272  0.007  4.108   1.4272e-01
   2_bss:   1.701  0.013  0.106 18.272  0.007  4.108   1.4272e-01
   2_xyz:   1.156  0.009  0.075 15.960  0.005  4.120   8.1248e-02
   2_adp:   1.156  0.009  0.075 15.960  0.005  4.120   8.1248e-02
   2_occ:   1.156  0.009  0.075 15.960  0.005  4.120   8.1248e-02
   3_bss:   1.156  0.009  0.075 15.960  0.005  4.120   8.1248e-02
   3_xyz:   1.160  0.009  0.082 15.833  0.004  4.115   8.1660e-02
   3_adp:   1.160  0.009  0.082 15.833  0.004  4.115   8.1660e-02
   3_occ:   1.160  0.009  0.082 15.833  0.004  4.115   8.1660e-02
   4_bss:   1.160  0.009  0.082 15.833  0.004  4.115   8.1660e-02
   4_xyz:   0.894  0.005  0.066 15.295  0.003  4.106   5.3772e-02
   4_adp:   0.894  0.005  0.066 15.295  0.003  4.106   5.3772e-02
   4_occ:   0.894  0.005  0.066 15.295  0.003  4.106   5.3772e-02
   5_bss:   0.894  0.005  0.066 15.295  0.003  4.106   5.3772e-02
   5_xyz:   0.964  0.006  0.073 15.346  0.003  4.109   5.7434e-02
   5_adp:   0.964  0.006  0.073 15.346  0.003  4.109   5.7434e-02
   5_occ:   0.964  0.006  0.073 15.346  0.003  4.109   5.7434e-02
   5_bss:   0.964  0.006  0.073 15.346  0.003  4.109   5.7434e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.8986e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.8986e+00
   1_xyz:  13.529  0.169  0.455 89.420  0.038  2.188   1.0046e-01
   1_adp:  13.529  0.169  0.455 89.420  0.038  2.188   1.0046e-01
   1_occ:  13.529  0.169  0.455 89.420  0.038  2.188   1.0046e-01
   2_bss:  13.529  0.169  0.455 89.420  0.038  2.188   1.0046e-01
   2_xyz:   7.019  0.090  0.304 88.300  0.042  2.231   6.9124e-02
   2_adp:   7.019  0.090  0.304 88.300  0.042  2.231   6.9124e-02
   2_occ:   7.019  0.090  0.304 88.300  0.042  2.231   6.9124e-02
   3_bss:   7.019  0.090  0.304 88.300  0.042  2.231   6.9124e-02
   3_xyz:   7.417  0.053  0.362 86.087  0.038  2.243   1.3994e-01
   3_adp:   7.417  0.053  0.362 86.087  0.038  2.243   1.3994e-01
   3_occ:   7.417  0.053  0.362 86.087  0.038  2.243   1.3994e-01
   4_bss:   7.417  0.053  0.362 86.087  0.038  2.243   1.3994e-01
   4_xyz:   6.335  0.057  0.254 80.981  0.040  2.342   4.0344e-02
   4_adp:   6.335  0.057  0.254 80.981  0.040  2.342   4.0344e-02
   4_occ:   6.335  0.057  0.254 80.981  0.040  2.342   4.0344e-02
   5_bss:   6.335  0.057  0.254 80.981  0.040  2.342   4.0344e-02
   5_xyz:   7.353  0.055  0.311 83.807  0.029  2.330   4.3411e-02
   5_adp:   7.353  0.055  0.311 83.807  0.029  2.330   4.3411e-02
   5_occ:   7.353  0.055  0.311 83.807  0.029  2.330   4.3411e-02
   5_bss:   7.353  0.055  0.311 83.807  0.029  2.330   4.3411e-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:  88.09   0.00  13.75  88.09   0.00  11.76  85.06   0.00  24.59
   1_occ:  88.09   0.00  13.75  88.09   0.00  11.76  85.06   0.00  24.59
   2_bss:  88.09   0.00  13.75  88.09   0.00  11.76  85.06   0.00  24.59
   2_xyz:  88.09   0.00  13.75  88.09   0.00  11.76  85.06   0.00  24.59
   2_adp:  91.59   0.00  14.02  91.59   0.00  11.10  90.34   0.00  29.92
   2_occ:  91.59   0.00  14.02  91.59   0.00  11.10  90.34   0.00  29.92
   3_bss:  91.59   0.00  14.02  91.59   0.00  11.10  90.34   0.00  29.92
   3_xyz:  91.59   0.00  14.02  91.59   0.00  11.10  90.34   0.00  29.92
   3_adp:  96.69   0.00  14.32  96.69   0.00  10.06  92.92   1.41  37.50
   3_occ:  96.69   0.00  14.32  96.69   0.00  10.06  92.92   1.41  37.50
   4_bss:  96.69   0.00  14.32  96.69   0.00  10.06  92.92   1.41  37.50
   4_xyz:  96.69   0.00  14.32  96.69   0.00  10.06  92.92   1.41  37.50
   4_adp: 102.86   0.00  14.37 102.86   0.00   9.65  96.06   2.43  40.06
   4_occ: 102.86   0.00  14.37 102.86   0.00   9.65  96.06   2.43  40.06
   5_bss: 102.86   0.00  14.37 102.86   0.00   9.65  96.06   2.43  40.06
   5_xyz: 102.86   0.00  14.37 102.86   0.00   9.65  96.06   2.43  40.06
   5_adp: 104.84   0.00  14.04 104.84   0.00   9.37  96.65   2.71  39.47
   5_occ: 104.84   0.00  14.04 104.84   0.00   9.37  96.65   2.71  39.47
   5_bss: 106.61   1.78  15.82 106.61   1.78  11.15  98.43   4.49  41.25
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.235    0.013    0.412
   1_adp:    1.235    0.013    0.412
   1_occ:    1.235    0.013    0.412
   2_bss:    1.235    0.013    0.412
   2_xyz:    1.556    0.032    0.550
   2_adp:    1.556    0.032    0.550
   2_occ:    1.556    0.032    0.550
   3_bss:    1.556    0.032    0.550
   3_xyz:    1.599    0.047    0.671
   3_adp:    1.599    0.047    0.671
   3_occ:    1.599    0.047    0.671
   4_bss:    1.599    0.047    0.671
   4_xyz:    1.907    0.035    0.729
   4_adp:    1.907    0.035    0.729
   4_occ:    1.907    0.035    0.729
   5_bss:    1.907    0.035    0.729
   5_xyz:    2.013    0.075    0.769
   5_adp:    2.013    0.075    0.769
   5_occ:    2.013    0.075    0.769
   5_bss:    2.013    0.075    0.769
------------------------------------------------------------------------

CPU time actual refinement: 338.51


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_740/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_740/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_740/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_740/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_740/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 338.36 
  Macro-tasks:
    bulk solvent and scale       = 42.19  
    individual site refinement   = 136.68 
    weights calculation          = 32.85  
    collect and process          = 6.61   
    model show statistics        = 0.15   
    TOTAL for macro-tasks        = 218.48 
  Micro-tasks:
    mask                            = 2.40   
    f_calc                          = 104.76 
    alpha_beta                      = 8.36   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 113.89 
    fmodel                         = 7.01   
    r_factors                      = 0.28   
    phase_errors                   = 10.57  
    foms                           = 0.20   
    TOTAL for micro-tasks          = 248.62 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.813 micro seconds
Total CPU time: 5.87 minutes
from_scatterers_fft:    637 calls, 104.37 s
gradients_fft:          582 calls, 101.19 s

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

# Date 2008-01-16 Time 02:19:38 PST -0800 (1200478778.74 s)
Start R-work = 0.4825, R-free = 0.4743 (no bulk solvent and anisotropic scale)
Final R-work = 0.1380, R-free = 0.1862 (no bulk solvent and anisotropic scale)

Start R-work = 0.4731, R-free = 0.4602
Final R-work = 0.1221, R-free = 0.1718