# Date 2008-01-16 Time 02:10:34 PST -0800 (1200478234.22 s)
#phil __OFF__

Command line arguments: "../730.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 3155
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 730

-------------------------------------------------------------------------------
  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, 45.7567, 85.9581, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.37, per 1000 atoms: 1.19


================================== 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, 45.7567, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0278 1.95346
Completeness in resolution range: 0.943321
Completeness with d_max=infinity: 0.940603

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0278
                             d_min =   1.9535

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, 45.7567, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0278 1.95346
Completeness in resolution range: 0.943321
Completeness with d_max=infinity: 0.940603

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0283 -  4.1812 [2185/2212]  1965   220  10.1%
  bin  2:  4.1812 -  3.3307 [2096/2116]  1889   207   9.9%
  bin  3:  3.3307 -  2.9131 [2075/2094]  1866   209  10.1%
  bin  4:  2.9131 -  2.6484 [2046/2076]  1839   207  10.1%
  bin  5:  2.6484 -  2.4594 [2036/2055]  1841   195   9.6%
  bin  6:  2.4594 -  2.3150 [2025/2050]  1814   211  10.4%
  bin  7:  2.3150 -  2.1994 [2018/2046]  1818   200   9.9%
  bin  8:  2.1994 -  2.1039 [1999/2035]  1798   201  10.1%
  bin  9:  2.1039 -  2.0231 [2013/2055]  1818   195   9.7%
  bin 10:  2.0231 -  1.9535 [1096/2027]   982   114  10.4%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_730/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:
        1.68 -     2.32: 31
        2.32 -     2.97: 1803
        2.97 -     3.61: 4619
        3.61 -     4.26: 9298
        4.26 -     4.90: 12900
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.681 3.040 x,y+1,z
  " O   HOH Z 201 " - " O   HOH Z 349 "  1.693 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.742 3.040 x,y+1,z
  " O   HOH Z 204 " - " O   HOH Z 296 "  1.794 3.040 -x+1/2,-y+1,z+1/2
  " N   ASN A 148 " - " O   HOH Z 138 "  1.794 3.120 x,y-1,z
  ... (remaining 28646 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_730/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_730/model_refine_001.geo

CPU time processing inputs: 9.00


============================ 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 45.75675 85.95805 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4898   r_free= 0.4867   ksol= 0.00   Bsol= 0.00   scale= 0.789    |
|                                                                             |
| 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:   0.79 A                  |
| x-ray target function (ml) for work reflections: 6.296547                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0283 -  4.6642 0.99   1416  158 0.4289 0.4283      6.6365      6.6989|
|  2:  4.6642 -  3.7206 0.99   1355  152 0.4249 0.3770      6.8416      6.7743|
|  3:  3.7206 -  3.2557 0.99   1345  143 0.4443 0.4333      6.6957      6.6889|
|  4:  3.2557 -  2.9605 0.99   1333  155 0.4866 0.4800      6.5514      6.5152|
|  5:  2.9605 -  2.7497 0.99   1324  149 0.5160 0.5324      6.3771      6.3932|
|  6:  2.7497 -  2.5885 0.99   1306  143 0.5207 0.5369      6.2907      6.2183|
|  7:  2.5885 -  2.4594 0.99   1321  138 0.5157 0.4886       6.254      6.1885|
|  8:  2.4594 -  2.3528 0.98   1292  148 0.5335 0.5026      6.1765      6.1963|
|  9:  2.3528 -  2.2625 0.98   1286  151 0.5254 0.5428      6.1216       6.164|
| 10:  2.2625 -  2.1847 1.00   1311  143 0.5234 0.5327      6.1019      6.0774|
| 11:  2.1847 -  2.1166 0.98   1296  137 0.5011 0.4845      6.0389      6.0321|
| 12:  2.1166 -  2.0562 0.98   1287  145 0.5183 0.5836      5.9504      6.0253|
| 13:  2.0562 -  2.0022 0.98   1269  140 0.5472 0.5226      5.8813      5.8065|
| 14:  2.0022 -  1.9535 0.38    489   57 0.5599 0.4898      5.8925      5.8368|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0283 -  4.6642  1416   158  0.60  42.59   0.78     0.67     103144.15|
|  2:  4.6642 -  3.7206  1355   152  0.67  38.14   0.85     0.75     125263.58|
|  3:  3.7206 -  3.2557  1345   143  0.57  46.53   0.85     0.71     126241.86|
|  4:  3.2557 -  2.9605  1333   155  0.47  54.34   0.79     0.57     110893.26|
|  5:  2.9605 -  2.7497  1324   149  0.35  63.40   0.73     0.45      92080.86|
|  6:  2.7497 -  2.5885  1306   143  0.32  65.72   0.71     0.38      80574.08|
|  7:  2.5885 -  2.4594  1321   138  0.30  67.78   0.76     0.35      71630.22|
|  8:  2.4594 -  2.3528  1292   148  0.29  68.46   0.72     0.35      64403.06|
|  9:  2.3528 -  2.2625  1286   151  0.30  67.39   0.73     0.36      57437.54|
| 10:  2.2625 -  2.1847  1311   143  0.32  66.14   0.75     0.39      50815.52|
| 11:  2.1847 -  2.1166  1296   137  0.30  67.49   0.80     0.38      50023.78|
| 12:  2.1166 -  2.0562  1287   145  0.27  69.76   0.78     0.36      45816.33|
| 13:  2.0562 -  2.0022  1269   140  0.26  70.64   0.71     0.35      39785.12|
| 14:  2.0022 -  1.9535   489    57  0.37  62.74   0.74     0.41      28644.77|
|alpha:            min =        0.35 max =            0.75 mean =         0.47|
|beta:             min =    28644.77 max =       126241.86 mean =     77546.92|
|figures of merit: min =        0.00 max =            1.00 mean =         0.39|
|phase err.(work): min =        0.00 max =           89.99 mean =        60.45|
|phase err.(test): min =        0.00 max =           89.91 mean =        60.66|
|-----------------------------------------------------------------------------|

============================== 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 = 20.288277             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.662   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.622242              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.554   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       35 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      175 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      713 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1533 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2673 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3973 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5149 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6612 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7792 |
|-----------------------------------------------------------------------------|
|-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 |       53.260 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.088    4.900  1.196 |       2.341 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.585)------------------------------------------|
|    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 = 11.585)------------------------------------------|
|    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: 1.95 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4943   r_free= 0.4885   ksol= 0.00   Bsol= 0.00   scale= 0.760    |
|                                                                             |
| 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:   0.77 A                  |
| x-ray target function (ml) for work reflections: 6.297886                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4809   r_free= 0.4756   ksol= 0.39   Bsol= 20.00   scale= 0.969   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.41,9.65,6.78,0.00,0.00,0.00); trace/3= 7.61                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.78 A                  |
| x-ray target function (ml) for work reflections: 6.290667                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 16.932922             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.514   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.623082              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.117   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4809      final r-factor (work) = 0.4141          |
| start r-factor (free) = 0.4756      final r-factor (free) = 0.4453          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 106.5304 = 16.93 * 0.50 * 6.2919 + 1.00 * 53.2600                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 52.9332 = 16.93 * 0.50 * 6.2349 + 1.00 * 0.1455                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4141      final r-factor (work) = 0.3783          |
| start r-factor (free) = 0.4453      final r-factor (free) = 0.4414          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.1342 = 1.62 * 1.00 * 6.2349 + 1.00 * 0.0144                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.0547 = 1.62 * 1.00 * 6.1836 + 1.00 * 0.0183                              |
|-----------------------------------------------------------------------------|
| number of iterations = 15      |    number of function evaluations = 18     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.585)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    61.81   13.03    None  None   None       |
|    all(noH): 2823   0      0.00    61.81   13.03    None  None   None       |
|    Sol.    : 438    0      0.00    57.23   20.17    None  None   None       |
|    Mac.    : 2385   0      0.00    61.81   11.72    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.181:  749   |   5:    30.905 -  37.086:   95        |
|      1:     6.181 -  12.362:  800   |   6:    37.086 -  43.267:   39        |
|      2:    12.362 -  18.543:  562   |   7:    43.267 -  49.448:   17        |
|      3:    18.543 -  24.724:  372   |   8:    49.448 -  55.629:    5        |
|      4:    24.724 -  30.905:  179   |   9:    55.629 -  61.811:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3783 r_free = 0.4414             target_work(ml) = 6.178         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3781 r_free = 0.4416             target_work(ml) = 6.177         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3781   r_free= 0.4416   ksol= 0.39   Bsol= 20.00   scale= 1.073   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.41,9.65,6.78,0.00,0.00,0.00); trace/3= 7.61                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.177084                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3767   r_free= 0.4381   ksol= 0.37   Bsol= 39.92   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.41,5.71,3.98,0.00,0.00,0.00); trace/3= 4.37                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.177761                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.245453             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.125  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.902555              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.929  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3767      final r-factor (work) = 0.3309          |
| start r-factor (free) = 0.4381      final r-factor (free) = 0.4065          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 34.8939 = 11.25 * 0.50 * 6.1800 + 1.00 * 0.1455                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 34.5269 = 11.25 * 0.50 * 6.1239 + 1.00 * 0.0937                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3309      final r-factor (work) = 0.3153          |
| start r-factor (free) = 0.4065      final r-factor (free) = 0.3953          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.5499 = 0.90 * 1.00 * 6.1239 + 1.00 * 0.0227                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.4875 = 0.90 * 1.00 * 6.0653 + 1.00 * 0.0132                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.585)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    66.74   13.25    None  None   None       |
|    all(noH): 2823   0      0.00    66.74   13.25    None  None   None       |
|    Sol.    : 438    0      0.00    66.74   23.51    None  None   None       |
|    Mac.    : 2385   0      0.00    66.66   11.37    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 -   6.674:  897   |   5:    33.371 -  40.045:   97        |
|      1:     6.674 -  13.349:  791   |   6:    40.045 -  46.720:   40        |
|      2:    13.349 -  20.023:  518   |   7:    46.720 -  53.394:   14        |
|      3:    20.023 -  26.697:  315   |   8:    53.394 -  60.068:    3        |
|      4:    26.697 -  33.371:  142   |   9:    60.068 -  66.742:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3153 r_free = 0.3953             target_work(ml) = 6.052         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3151 r_free = 0.3948             target_work(ml) = 6.052         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3151   r_free= 0.3948   ksol= 0.37   Bsol= 39.92   scale= 1.028   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.41,5.71,3.98,0.00,0.00,0.00); trace/3= 4.37                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.051821                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3161   r_free= 0.3934   ksol= 0.34   Bsol= 39.92   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.11,4.08,3.67,0.00,0.00,0.00); trace/3= 3.62                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.052077                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.189129             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 113.822  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.981313              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 155.208  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3161      final r-factor (work) = 0.2565          |
| start r-factor (free) = 0.3934      final r-factor (free) = 0.3255          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.9959 = 10.19 * 0.50 * 6.0657 + 1.00 * 0.0937                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.5355 = 10.19 * 0.50 * 5.9736 + 1.00 * 0.1027                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2565      final r-factor (work) = 0.2300          |
| start r-factor (free) = 0.3255      final r-factor (free) = 0.3045          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.8752 = 0.98 * 1.00 * 5.9736 + 1.00 * 0.0132                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.7293 = 0.98 * 1.00 * 5.8228 + 1.00 * 0.0153                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.585)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.77   14.36    None  None   None       |
|    all(noH): 2823   0      0.00    89.77   14.36    None  None   None       |
|    Sol.    : 438    0      0.00    89.77   35.06    None  None   None       |
|    Mac.    : 2385   0      0.00    74.49   10.55    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 -   8.977: 1336   |   5:    44.883 -  53.859:   72        |
|      1:     8.977 -  17.953:  726   |   6:    53.859 -  62.836:   49        |
|      2:    17.953 -  26.930:  301   |   7:    62.836 -  71.812:   18        |
|      3:    26.930 -  35.906:  191   |   8:    71.812 -  80.789:    2        |
|      4:    35.906 -  44.883:  126   |   9:    80.789 -  89.765:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2300 r_free = 0.3045             target_work(ml) = 5.786         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2294 r_free = 0.3048             target_work(ml) = 5.785         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2294   r_free= 0.3048   ksol= 0.34   Bsol= 39.92   scale= 1.046   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.11,4.08,3.67,0.00,0.00,0.00); trace/3= 3.62                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.784977                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2281   r_free= 0.3024   ksol= 0.33   Bsol= 45.56   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.14,2.28,2.91,0.00,0.00,0.00); trace/3= 2.44                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.780495                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.737598              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.082  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.410823              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.118  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2281      final r-factor (work) = 0.1817          |
| start r-factor (free) = 0.3024      final r-factor (free) = 0.2416          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.8934 = 4.74 * 0.50 * 5.8218 + 1.00 * 0.1027                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.5470 = 4.74 * 0.50 * 5.6917 + 1.00 * 0.0645                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1817      final r-factor (work) = 0.1684          |
| start r-factor (free) = 0.2416      final r-factor (free) = 0.2268          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3537 = 0.41 * 1.00 * 5.6917 + 1.00 * 0.0154                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2870 = 0.41 * 1.00 * 5.5343 + 1.00 * 0.0134                               |
|-----------------------------------------------------------------------------|
| number of iterations = 8       |    number of function evaluations = 10     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.585)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.77   14.09    None  None   None       |
|    all(noH): 2823   0      0.00    88.77   14.09    None  None   None       |
|    Sol.    : 438    0      3.04    88.77   36.34    None  None   None       |
|    Mac.    : 2385   0      0.00    75.69   10.01    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 -   8.877: 1449   |   5:    44.386 -  53.263:   86        |
|      1:     8.877 -  17.754:  684   |   6:    53.263 -  62.140:   52        |
|      2:    17.754 -  26.631:  229   |   7:    62.140 -  71.017:   18        |
|      3:    26.631 -  35.509:  174   |   8:    71.017 -  79.894:    2        |
|      4:    35.509 -  44.386:  127   |   9:    79.894 -  88.771:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1684 r_free = 0.2268             target_work(ml) = 5.502         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1682 r_free = 0.2263             target_work(ml) = 5.500         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1682   r_free= 0.2263   ksol= 0.33   Bsol= 45.56   scale= 1.032   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.14,2.28,2.91,0.00,0.00,0.00); trace/3= 2.44                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.499981                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1680   r_free= 0.2265   ksol= 0.33   Bsol= 45.56   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.49,1.19,2.44,0.00,0.00,0.00); trace/3= 1.71                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.499139                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.439474              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 109.210  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.873737              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 94.521   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1680      final r-factor (work) = 0.1426          |
| start r-factor (free) = 0.2265      final r-factor (free) = 0.2003          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.5830 = 3.44 * 0.50 * 5.5349 + 1.00 * 0.0645                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.4107 = 3.44 * 0.50 * 5.4350 + 1.00 * 0.0640                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1426      final r-factor (work) = 0.1331          |
| start r-factor (free) = 0.2003      final r-factor (free) = 0.1883          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7619 = 0.87 * 1.00 * 5.4350 + 1.00 * 0.0132                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6937 = 0.87 * 1.00 * 5.3419 + 1.00 * 0.0263                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.585)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.06   14.37    None  None   None       |
|    all(noH): 2823   0      0.00    89.06   14.37    None  None   None       |
|    Sol.    : 438    0      2.76    88.82   40.48    None  None   None       |
|    Mac.    : 2385   0      0.00    89.06   9.58     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 -   8.906: 1527   |   5:    44.529 -  53.435:   95        |
|      1:     8.906 -  17.812:  677   |   6:    53.435 -  62.341:   69        |
|      2:    17.812 -  26.718:  171   |   7:    62.341 -  71.247:   36        |
|      3:    26.718 -  35.624:  129   |   8:    71.247 -  80.153:   22        |
|      4:    35.624 -  44.529:   91   |   9:    80.153 -  89.059:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1331 r_free = 0.1883             target_work(ml) = 5.308         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1327 r_free = 0.1879             target_work(ml) = 5.306         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1327   r_free= 0.1879   ksol= 0.33   Bsol= 45.56   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.49,1.19,2.44,0.00,0.00,0.00); trace/3= 1.71                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.305523                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0283 -  4.6642 0.99   1416  158 0.1031 0.1436      5.4519      5.6635|
|  2:  4.6642 -  3.7206 0.99   1355  152 0.0953 0.1296      5.5591      5.8093|
|  3:  3.7206 -  3.2557 0.99   1345  143 0.1265 0.1696       5.632      5.9416|
|  4:  3.2557 -  2.9605 0.99   1333  155 0.1524 0.2092      5.6434      5.7989|
|  5:  2.9605 -  2.7497 0.99   1324  149 0.1621 0.2226      5.5046      5.7615|
|  6:  2.7497 -  2.5885 0.99   1306  143 0.1417 0.2149       5.366      5.5692|
|  7:  2.5885 -  2.4594 0.99   1321  138 0.1488 0.2005      5.3232      5.5025|
|  8:  2.4594 -  2.3528 0.98   1292  148 0.1450 0.2189      5.2488       5.565|
|  9:  2.3528 -  2.2625 0.98   1286  151 0.1472 0.2134      5.2144       5.436|
| 10:  2.2625 -  2.1847 1.00   1311  143 0.1364 0.2041      5.1235      5.3729|
| 11:  2.1847 -  2.1166 0.98   1296  137 0.1311 0.2073      5.0922      5.4092|
| 12:  2.1166 -  2.0562 0.98   1287  145 0.1352 0.2065      5.0294      5.3131|
| 13:  2.0562 -  2.0022 0.98   1269  140 0.1405 0.1904      4.9187      5.1129|
| 14:  2.0022 -  1.9535 0.38    489   57 0.1208 0.1725       4.785      4.9999|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0283 -  4.6642  1416   158  0.93  10.98   0.98     0.96       9326.94|
|  2:  4.6642 -  3.7206  1355   152  0.94   9.99   1.03     1.01      12232.77|
|  3:  3.7206 -  3.2557  1345   143  0.91  14.51   1.05     1.04      14715.06|
|  4:  3.2557 -  2.9605  1333   155  0.88  18.00   1.03     0.99      15762.27|
|  5:  2.9605 -  2.7497  1324   149  0.86  20.03   1.00     0.96      12333.46|
|  6:  2.7497 -  2.5885  1306   143  0.86  20.45   0.99     0.95      10250.02|
|  7:  2.5885 -  2.4594  1321   138  0.87  19.57   1.00     0.97       8996.02|
|  8:  2.4594 -  2.3528  1292   148  0.86  20.04   1.00     0.95       7934.50|
|  9:  2.3528 -  2.2625  1286   151  0.87  19.91   1.01     0.96       7422.35|
| 10:  2.2625 -  2.1847  1311   143  0.86  20.10   1.01     0.96       6501.72|
| 11:  2.1847 -  2.1166  1296   137  0.87  19.68   1.01     0.95       6139.26|
| 12:  2.1166 -  2.0562  1287   145  0.87  19.79   1.02     1.01       5662.25|
| 13:  2.0562 -  2.0022  1269   140  0.87  19.73   1.01     0.98       4305.85|
| 14:  2.0022 -  1.9535   489    57  0.90  16.17   1.00     0.97       3129.37|
|alpha:            min =        0.95 max =            1.04 mean =         0.98|
|beta:             min =     3129.37 max =        15762.27 mean =      9231.05|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.88 mean =        17.78|
|phase err.(test): min =        0.00 max =           88.86 mean =        17.04|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1331   r_free= 0.1873   ksol= 0.32   Bsol= 45.70   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.17,-0.63,0.79,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.303681                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1331   r_free= 0.1873   ksol= 0.32   Bsol= 45.70   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.17,-0.63,0.79,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.303681                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0283 -  4.6642 0.99   1416  158 0.1035 0.1374      5.4291      5.6287|
|  2:  4.6642 -  3.7206 0.99   1355  152 0.0959 0.1305      5.5558      5.8216|
|  3:  3.7206 -  3.2557 0.99   1345  143 0.1272 0.1688      5.6359      5.9423|
|  4:  3.2557 -  2.9605 0.99   1333  155 0.1527 0.2094      5.6452      5.8021|
|  5:  2.9605 -  2.7497 0.99   1324  149 0.1625 0.2223      5.5063      5.7618|
|  6:  2.7497 -  2.5885 0.99   1306  143 0.1415 0.2149      5.3661      5.5706|
|  7:  2.5885 -  2.4594 0.99   1321  138 0.1487 0.2008      5.3225      5.5016|
|  8:  2.4594 -  2.3528 0.98   1292  148 0.1449 0.2182      5.2476      5.5622|
|  9:  2.3528 -  2.2625 0.98   1286  151 0.1470 0.2124      5.2131      5.4327|
| 10:  2.2625 -  2.1847 1.00   1311  143 0.1363 0.2047      5.1233      5.3761|
| 11:  2.1847 -  2.1166 0.98   1296  137 0.1309 0.2076      5.0927      5.4108|
| 12:  2.1166 -  2.0562 0.98   1287  145 0.1350 0.2064      5.0295      5.3136|
| 13:  2.0562 -  2.0022 0.98   1269  140 0.1405 0.1895      4.9179        5.11|
| 14:  2.0022 -  1.9535 0.38    489   57 0.1207 0.1717      4.7826      4.9984|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0283 -  4.6642  1416   158  0.93  10.48   0.98     0.96       8531.44|
|  2:  4.6642 -  3.7206  1355   152  0.94   9.82   1.03     1.01      11830.35|
|  3:  3.7206 -  3.2557  1345   143  0.91  14.53   1.05     1.04      14817.23|
|  4:  3.2557 -  2.9605  1333   155  0.88  18.05   1.02     0.99      15847.85|
|  5:  2.9605 -  2.7497  1324   149  0.86  20.07   1.00     0.96      12365.14|
|  6:  2.7497 -  2.5885  1306   143  0.86  20.48   0.99     0.94      10260.71|
|  7:  2.5885 -  2.4594  1321   138  0.87  19.54   1.00     0.97       8976.70|
|  8:  2.4594 -  2.3528  1292   148  0.87  20.00   0.99     0.95       7906.22|
|  9:  2.3528 -  2.2625  1286   151  0.87  19.86   1.01     0.95       7397.19|
| 10:  2.2625 -  2.1847  1311   143  0.86  20.11   1.00     0.95       6505.48|
| 11:  2.1847 -  2.1166  1296   137  0.87  19.72   1.01     0.95       6162.93|
| 12:  2.1166 -  2.0562  1287   145  0.87  19.81   1.02     1.01       5670.24|
| 13:  2.0562 -  2.0022  1269   140  0.87  19.71   1.01     0.98       4296.75|
| 14:  2.0022 -  1.9535   489    57  0.90  16.10   1.00     0.97       3107.93|
|alpha:            min =        0.94 max =            1.04 mean =         0.97|
|beta:             min =     3107.93 max =        15847.85 mean =      9149.66|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.93 mean =        17.73|
|phase err.(test): min =        0.00 max =           89.32 mean =        16.96|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.585)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.62    90.68   15.99    None  None   None       |
|    all(noH): 2823   0      1.62    90.68   15.99    None  None   None       |
|    Sol.    : 438    0      4.38    90.44   42.10    None  None   None       |
|    Mac.    : 2385   0      1.62    90.68   11.20    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:     1.621 -  10.527: 1527   |   5:    46.150 -  55.056:   95        |
|      1:    10.527 -  19.432:  677   |   6:    55.056 -  63.962:   69        |
|      2:    19.432 -  28.338:  171   |   7:    63.962 -  72.868:   36        |
|      3:    28.338 -  37.244:  129   |   8:    72.868 -  81.774:   22        |
|      4:    37.244 -  46.150:   91   |   9:    81.774 -  90.679:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 334         
Filter by distance & map next to the model:
   mapped sites are within: 0.448 - 5.505
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 327 from: 334
   mapped sites are within: 0.715 - 5.505

peak=    9.915 closest distance to " CB  VAL A 296 " =    1.429
peak=    7.962 closest distance to " CG2 VAL A 230 " =    1.333
peak=    7.373 closest distance to " O   HOH Z 130 " =    2.083
peak=    7.371 closest distance to " O   HOH Z 390 " =    1.177
peak=    6.893 closest distance to " CG  ARG A 138 " =    1.220
peak=    6.288 closest distance to " CD2 LEU A   5 " =    1.460
peak=    6.216 closest distance to " O   HOH Z 415 " =    1.348
peak=    6.124 closest distance to " O   HOH Z  65 " =    1.640
peak=    5.996 closest distance to " O   HOH Z 387 " =    1.539
peak=    5.935 closest distance to " O   HOH Z 350 " =    1.440
peak=    5.803 closest distance to " CD1AILE A 234 " =    1.096
peak=    5.773 closest distance to " O   HOH Z 424 " =    1.788
peak=    5.708 closest distance to " O   HOH Z   7 " =    2.181
peak=    5.674 closest distance to " O   HOH Z 268 " =    1.088
peak=    5.510 closest distance to " O   HOH Z   9 " =    1.865
peak=    5.421 closest distance to " NH2 ARG A  56 " =    2.033
peak=    5.379 closest distance to " NE2 GLN A  11 " =    1.264
peak=    5.353 closest distance to " O   HOH Z  46 " =    1.197
peak=    5.334 closest distance to " O   HOH Z 403 " =    1.555
peak=    5.324 closest distance to " O   HOH Z 124 " =    1.758
peak=    5.268 closest distance to " O   HOH Z 105 " =    1.229
peak=    5.259 closest distance to " O   HOH Z 222 " =    1.545
peak=    5.238 closest distance to " CB  PRO A  54 " =    1.116
peak=    5.073 closest distance to " O   HOH Z 417 " =    1.760
peak=    5.014 closest distance to " CB  VAL A 230 " =    1.209
peak=    4.974 closest distance to " O   HOH Z 289 " =    1.304
peak=    4.940 closest distance to " O   HOH Z 214 " =    1.400
peak=    4.910 closest distance to " O   HOH Z 375 " =    1.193
peak=    4.864 closest distance to " O   HOH Z 410 " =    1.509
peak=    4.830 closest distance to " O   HOH Z 363 " =    1.198
peak=    4.791 closest distance to " O   HOH Z 427 " =    1.239
peak=    4.716 closest distance to " O   HOH Z 142 " =    2.033
peak=    4.681 closest distance to " O   HOH Z  27 " =    1.128
peak=    4.675 closest distance to " OE1 GLU A   2 " =    1.930
peak=    4.667 closest distance to " O   HOH Z 418 " =    1.294
peak=    4.658 closest distance to " O   HOH Z 225 " =    1.726
peak=    4.606 closest distance to " O   HOH Z 112 " =    1.209
peak=    4.550 closest distance to " CG  LEU A   5 " =    1.180
peak=    4.515 closest distance to " O   HOH Z 126 " =    1.769
peak=    4.513 closest distance to " O   HOH Z 361 " =    1.697
peak=    4.513 closest distance to " O   PRO A 198 " =    1.365
peak=    4.503 closest distance to " O   HOH Z  63 " =    1.777
peak=    4.496 closest distance to " CE  MET A  93 " =    1.476
peak=    4.494 closest distance to " O   HOH Z 239 " =    1.505
peak=    4.480 closest distance to " O   HOH Z 316 " =    3.052
peak=    4.479 closest distance to " O   HOH Z 358 " =    1.334
peak=    4.443 closest distance to " O   HOH Z 427 " =    2.253
peak=    4.398 closest distance to " CB  SER A   3 " =    1.502
peak=    4.368 closest distance to " O   HOH Z 139 " =    2.000
peak=    4.349 closest distance to " O   HOH Z  30 " =    2.049
peak=    4.327 closest distance to " O   HOH Z  78 " =    1.880
peak=    4.323 closest distance to " O   HOH Z 127 " =    1.101
peak=    4.314 closest distance to " O   HOH Z 369 " =    2.213
peak=    4.308 closest distance to " O   HOH Z 250 " =    2.199
peak=    4.307 closest distance to " O   HOH Z  69 " =    2.350
peak=    4.306 closest distance to " O   HOH Z 357 " =    1.446
peak=    4.274 closest distance to " O   HOH Z 133 " =    1.649
peak=    4.272 closest distance to " O   HOH Z 380 " =    2.216
peak=    4.261 closest distance to " O   HOH Z 287 " =    1.767
peak=    4.261 closest distance to " O   HOH Z  28 " =    1.488
peak=    4.250 closest distance to " NH1 ARG A 138 " =    0.995
peak=    4.232 closest distance to " O   HOH Z 414 " =    1.653
peak=    4.226 closest distance to " NZ BLYS A 290 " =    1.027
peak=    4.204 closest distance to " CB  ARG A 275 " =    1.138
peak=    4.202 closest distance to " O   HOH Z 402 " =    1.487
peak=    4.186 closest distance to " O   HOH Z  59 " =    1.462
peak=    4.181 closest distance to " CG  LEU A 228 " =    1.052
peak=    4.168 closest distance to " O   HOH Z  48 " =    1.695
peak=    4.167 closest distance to " O   HOH Z  15 " =    0.988
peak=    4.154 closest distance to " O   HOH Z 400 " =    0.796
peak=    4.136 closest distance to " CA  ILE A 234 " =    1.061
peak=    4.123 closest distance to " O   HOH Z 232 " =    2.027
peak=    4.110 closest distance to " CG  PRO A  54 " =    1.284
peak=    4.098 closest distance to " OG BSER A 258 " =    0.988
peak=    4.092 closest distance to " O   HOH Z 384 " =    1.680
peak=    4.080 closest distance to " O   HOH Z 389 " =    1.466
peak=    4.078 closest distance to " O   HOH Z 423 " =    1.760
peak=    4.073 closest distance to " O   HOH Z 193 " =    1.623
peak=    4.071 closest distance to " O   HOH Z 416 " =    1.426
peak=    4.063 closest distance to " OE1 GLU A   2 " =    2.065
peak=    4.057 closest distance to " OG  SER A 276 " =    0.939
peak=    4.052 closest distance to " O   HOH Z 193 " =    1.833
peak=    4.047 closest distance to " O   HOH Z 132 " =    1.088
peak=    4.038 closest distance to " O   HOH Z 392 " =    1.629
peak=    4.035 closest distance to " O   HOH Z 298 " =    1.991
peak=    4.035 closest distance to " O   HOH Z 123 " =    1.170
peak=    4.027 closest distance to " O   HOH Z 293 " =    1.458
peak=    4.026 closest distance to " O   HOH Z 371 " =    3.034
peak=    4.022 closest distance to " O   HOH Z 130 " =    2.319
peak=    4.021 closest distance to " O   HOH Z 215 " =    1.448
peak=    4.016 closest distance to " CB  SER A 216 " =    1.079
peak=    4.001 closest distance to " CA  ASN A 127 " =    1.151
peak=    3.996 closest distance to " O   HOH Z 426 " =    1.100
peak=    3.986 closest distance to " CA  SER A  87 " =    0.916
peak=    3.969 closest distance to " NH2AARG A 145 " =    2.307
peak=    3.969 closest distance to " O   HOH Z 147 " =    1.481
peak=    3.959 closest distance to " CB  ASP A 124 " =    0.996
peak=    3.957 closest distance to " O   HOH Z   7 " =    3.067
peak=    3.947 closest distance to " CG  TRP A 179 " =    2.249
peak=    3.943 closest distance to " CG  PRO A 280 " =    0.910
peak=    3.935 closest distance to " CG  PRO A 198 " =    1.313
peak=    3.932 closest distance to " NE1 TRP A 274 " =    1.033
peak=    3.931 closest distance to " CB  GLN A 223 " =    1.368
peak=    3.929 closest distance to " O   HOH Z 233 " =    1.424
peak=    3.929 closest distance to " OG  SER A  62 " =    3.174
peak=    3.917 closest distance to " O   HOH Z 419 " =    2.200
peak=    3.906 closest distance to " CB  ASN A 148 " =    1.426
peak=    3.894 closest distance to " CG  PRO A 213 " =    1.271
peak=    3.877 closest distance to " NZ  LYS A 117 " =    1.198
peak=    3.847 closest distance to " O   HOH Z  91 " =    2.450
peak=    3.834 closest distance to " O   HOH Z  30 " =    1.322
peak=    3.834 closest distance to " CB  GLN A 183 " =    1.115
peak=    3.833 closest distance to " CB  GLU A 277 " =    3.615
peak=    3.831 closest distance to " O   HOH Z  61 " =    1.766
peak=    3.827 closest distance to " CG  LEU A 167 " =    1.357
peak=    3.827 closest distance to " O   GLY A 302 " =    2.362
peak=    3.826 closest distance to " CG2 ILE A 234 " =    0.843
peak=    3.820 closest distance to " O   HOH Z 344 " =    1.183
peak=    3.796 closest distance to " CB  GLU A 128 " =    1.048
peak=    3.793 closest distance to " CG2 THR A 220 " =    1.077
peak=    3.792 closest distance to " O   HOH Z 217 " =    2.565
peak=    3.773 closest distance to " CB  LEU A 300 " =    0.909
peak=    3.769 closest distance to " O   HOH Z   6 " =    2.087
peak=    3.763 closest distance to " O   HOH Z 356 " =    1.814
peak=    3.753 closest distance to " O   HOH Z 371 " =    1.877
peak=    3.734 closest distance to " O   HOH Z 405 " =    1.840
peak=    3.732 closest distance to " O   HOH Z 359 " =    1.369
peak=    3.731 closest distance to " CB  SER A  62 " =    1.231
peak=    3.710 closest distance to " CB  TRP A 266 " =    0.956
peak=    3.710 closest distance to " O   HOH Z 371 " =    2.164
peak=    3.701 closest distance to " N   GLN A 278 " =    1.063
peak=    3.701 closest distance to " CA  ALA A 295 " =    0.886
peak=    3.692 closest distance to " CG1 ILE A 120 " =    1.491
peak=    3.692 closest distance to " O   HOH Z 258 " =    2.175
peak=    3.686 closest distance to " O   HOH Z   1 " =    1.789
peak=    3.673 closest distance to " CD2 LEU A 228 " =    1.279
peak=    3.663 closest distance to " O   HOH Z  44 " =    2.684
peak=    3.660 closest distance to " O   HOH Z 176 " =    1.885
peak=    3.638 closest distance to " CB  TRP A 179 " =    1.455
peak=    3.638 closest distance to " OD1 ASP A 200 " =    1.513
peak=    3.622 closest distance to " NH2 ARG A 219 " =    1.818
peak=    3.610 closest distance to " CD2 LEU A 297 " =    0.883
peak=    3.608 closest distance to " CG  GLN A  11 " =    2.220
peak=    3.604 closest distance to " NE AARG A 275 " =    1.602
peak=    3.603 closest distance to " O   HOH Z 263 " =    1.468
peak=    3.597 closest distance to " NE2 GLN A  58 " =    3.729
peak=    3.596 closest distance to " CG2 THR A 178 " =    1.153
peak=    3.592 closest distance to " O   HOH Z 108 " =    1.935
peak=    3.592 closest distance to " O   HOH Z 143 " =    1.426
peak=    3.586 closest distance to " CB  VAL A 202 " =    1.629
peak=    3.580 closest distance to " N   TYR A  15 " =    1.026
peak=    3.579 closest distance to " CA  LEU A 282 " =    1.046
peak=    3.576 closest distance to " O   HOH Z 353 " =    1.769
peak=    3.572 closest distance to " O   HOH Z  65 " =    1.620
peak=    3.567 closest distance to " OG ASER A 134 " =    1.282
peak=    3.565 closest distance to " CG1BVAL A 121 " =    2.291
peak=    3.565 closest distance to " O   HOH Z 411 " =    3.278
peak=    3.555 closest distance to " CG1AVAL A 121 " =    0.925
peak=    3.554 closest distance to " O   HOH Z 375 " =    2.269
peak=    3.543 closest distance to " O   HOH Z 431 " =    0.935
peak=    3.537 closest distance to " O   HOH Z 217 " =    1.808
peak=    3.537 closest distance to " O   HOH Z 184 " =    1.641
peak=    3.536 closest distance to " CB  VAL A 265 " =    1.342
peak=    3.529 closest distance to " O   HOH Z  68 " =    1.972
peak=    3.526 closest distance to " O   HOH Z 278 " =    1.003
peak=    3.524 closest distance to " O   HOH Z 166 " =    1.525
peak=    3.523 closest distance to " CA  ALA A  21 " =    1.045
peak=    3.521 closest distance to " CB  ALA A 104 " =    0.971
peak=    3.519 closest distance to " CB  GLU A 277 " =    1.021
peak=    3.519 closest distance to " O   HOH Z 374 " =    1.130
peak=    3.512 closest distance to " O   HOH Z 368 " =    1.863
peak=    3.506 closest distance to " O   HOH Z 247 " =    1.229
peak=    3.505 closest distance to " O   HOH Z  22 " =    2.024
peak=    3.503 closest distance to " O   HOH Z 245 " =    1.400
peak=    3.502 closest distance to " NE2 GLN A  58 " =    5.505
peak=    3.500 closest distance to " O   HOH Z  57 " =    1.062
peak=    3.499 closest distance to " CG  GLN A  88 " =    1.089
peak=    3.495 closest distance to " O   HOH Z 353 " =    2.122
peak=    3.493 closest distance to " O   HOH Z 412 " =    1.821
peak=    3.486 closest distance to " N   GLY A 136 " =    1.145
peak=    3.480 closest distance to " CD BLYS A 290 " =    1.038
peak=    3.480 closest distance to " CA  TYR A  30 " =    1.079
peak=    3.472 closest distance to " O   HOH Z  61 " =    1.509
peak=    3.469 closest distance to " CG  LYS A  76 " =    1.579
peak=    3.468 closest distance to " O   HOH Z 213 " =    1.589
peak=    3.468 closest distance to " O   HOH Z 207 " =    2.462
peak=    3.468 closest distance to " O   HOH Z 406 " =    1.806
peak=    3.464 closest distance to " O   HOH Z 389 " =    1.471
peak=    3.463 closest distance to " NE AARG A 145 " =    1.247
peak=    3.461 closest distance to " O   HOH Z 186 " =    1.027
peak=    3.460 closest distance to " O   HOH Z  94 " =    2.412
peak=    3.459 closest distance to " O   HOH Z 422 " =    2.674
peak=    3.454 closest distance to " O   HOH Z  43 " =    1.209
peak=    3.453 closest distance to " O   HOH Z  50 " =    1.559
peak=    3.453 closest distance to " O   HOH Z  39 " =    1.272
peak=    3.452 closest distance to " CG  GLN A 278 " =    3.960
peak=    3.451 closest distance to " O   HOH Z 368 " =    3.267
peak=    3.449 closest distance to " CA  ALA A 158 " =    1.077
peak=    3.447 closest distance to " CG  PRO A 243 " =    1.079
peak=    3.440 closest distance to " O   HOH Z 423 " =    1.492
peak=    3.434 closest distance to " O   HOH Z 180 " =    2.150
peak=    3.432 closest distance to " CG2 THR A 221 " =    1.315
peak=    3.431 closest distance to " O   HOH Z 366 " =    2.832
peak=    3.430 closest distance to " CB  ASN A 285 " =    1.015
peak=    3.426 closest distance to " CB  GLU A 152 " =    1.407
peak=    3.423 closest distance to " CE3 TRP A 274 " =    1.353
peak=    3.420 closest distance to " NH1 ARG A  56 " =    1.248
peak=    3.415 closest distance to " CA  TRP A  92 " =    1.133
peak=    3.412 closest distance to " O   HOH Z  55 " =    2.222
peak=    3.400 closest distance to " O   HOH Z 128 " =    1.963
peak=    3.394 closest distance to " O   HOH Z 334 " =    2.819
peak=    3.390 closest distance to " NH1AARG A 145 " =    0.834
peak=    3.389 closest distance to " O   HOH Z 145 " =    2.621
peak=    3.385 closest distance to " CD1 ILE A  33 " =    1.771
peak=    3.382 closest distance to " CB  SER A  63 " =    1.280
peak=    3.380 closest distance to " OD1 ASN A 217 " =    1.567
peak=    3.377 closest distance to " O   HOH Z 158 " =    1.219
peak=    3.376 closest distance to " O   HOH Z 119 " =    1.453
peak=    3.375 closest distance to " O   VAL A  72 " =    0.869
peak=    3.368 closest distance to " CB  ASN A 142 " =    1.020
peak=    3.366 closest distance to " CB  ALA A  10 " =    1.036
peak=    3.365 closest distance to " O   HOH Z 234 " =    3.682
peak=    3.365 closest distance to " O   HOH Z 244 " =    1.474
peak=    3.364 closest distance to " CB  SER A 276 " =    1.226
peak=    3.359 closest distance to " O   HOH Z 172 " =    1.646
peak=    3.355 closest distance to " CA  GLY A 267 " =    1.374
peak=    3.354 closest distance to " CA  ALA A  51 " =    1.129
peak=    3.347 closest distance to " CB  LEU A 228 " =    1.343
peak=    3.346 closest distance to " OD2 ASP A 286 " =    2.497
peak=    3.343 closest distance to " O   HOH Z 158 " =    2.469
peak=    3.341 closest distance to " O   HOH Z 158 " =    2.851
peak=    3.341 closest distance to " O   ASN A 301 " =    2.051
peak=    3.340 closest distance to " O   HOH Z 214 " =    1.714
peak=    3.340 closest distance to " O   HOH Z 378 " =    1.024
peak=    3.336 closest distance to " O   ALA A 291 " =    1.546
peak=    3.336 closest distance to " CG  ARG A 159 " =    0.892
peak=    3.335 closest distance to " CD  ARG A 159 " =    0.773
peak=    3.334 closest distance to " O   HOH Z 390 " =    2.358
peak=    3.333 closest distance to " O   HOH Z 151 " =    1.582
peak=    3.332 closest distance to " CB  TYR A 169 " =    0.715
peak=    3.330 closest distance to " O   HOH Z  58 " =    1.731
peak=    3.323 closest distance to " CB  MET A  40 " =    0.791
peak=    3.323 closest distance to " O   ALA A 165 " =    1.259
peak=    3.321 closest distance to " O   HOH Z 239 " =    1.544
peak=    3.316 closest distance to " O   HOH Z 329 " =    3.869
peak=    3.315 closest distance to " CB  SER A 273 " =    0.968
peak=    3.312 closest distance to " O   HOH Z  88 " =    3.367
peak=    3.311 closest distance to " CA  ARG A 195 " =    1.340
peak=    3.310 closest distance to " OE1 GLN A 240 " =    1.738
peak=    3.306 closest distance to " NH1 ARG A  14 " =    0.982
peak=    3.302 closest distance to " O   HOH Z  76 " =    1.099
peak=    3.298 closest distance to " O   HOH Z 340 " =    1.914
peak=    3.297 closest distance to " O   HOH Z 167 " =    1.830
peak=    3.292 closest distance to " O   HOH Z 323 " =    1.681
peak=    3.291 closest distance to " CG  LYS A 119 " =    1.059
peak=    3.286 closest distance to " O   HOH Z 248 " =    1.963
peak=    3.285 closest distance to " O   HOH Z 381 " =    0.951
peak=    3.282 closest distance to " CB  ARG A 138 " =    1.122
peak=    3.282 closest distance to " OD1 ASP A  50 " =    0.931
peak=    3.282 closest distance to " CB  ASN A  39 " =    0.844
peak=    3.270 closest distance to " CB  PHE A 225 " =    1.499
peak=    3.266 closest distance to " NE2 GLN A  73 " =    1.423
peak=    3.263 closest distance to " O   HOH Z 328 " =    1.572
peak=    3.261 closest distance to " O   HOH Z 227 " =    1.675
peak=    3.259 closest distance to " N   GLU A   2 " =    1.340
peak=    3.256 closest distance to " O   HOH Z  49 " =    1.067
peak=    3.255 closest distance to " OG BSER A 212 " =    2.772
peak=    3.254 closest distance to " CB  THR A  31 " =    1.613
peak=    3.253 closest distance to " CB  ASP A 200 " =    0.908
peak=    3.253 closest distance to " O   HOH Z 117 " =    1.891
peak=    3.248 closest distance to " CD2 LEU A 300 " =    1.062
peak=    3.243 closest distance to " CA  ALA A 299 " =    0.927
peak=    3.226 closest distance to " O   HOH Z 222 " =    1.684
peak=    3.220 closest distance to " N   ALA A 299 " =    1.426
peak=    3.216 closest distance to " CA  ALA A 292 " =    0.863
peak=    3.216 closest distance to " OG BSER A 210 " =    1.122
peak=    3.215 closest distance to " OD1 ASN A 170 " =    1.217
peak=    3.214 closest distance to " O   HOH Z  26 " =    1.531
peak=    3.211 closest distance to " CA  PHE A 283 " =    1.428
peak=    3.211 closest distance to " N   ALA A   1 " =    1.313
peak=    3.211 closest distance to " O   HOH Z 334 " =    1.470
peak=    3.211 closest distance to " O   HOH Z 362 " =    1.662
peak=    3.201 closest distance to " O   HOH Z 272 " =    2.133
peak=    3.200 closest distance to " CG2 VAL A 257 " =    0.956
peak=    3.199 closest distance to " CB  ASP A 140 " =    1.029
peak=    3.196 closest distance to " O   HOH Z  10 " =    1.774
peak=    3.195 closest distance to " O   HOH Z 240 " =    2.061
peak=    3.194 closest distance to " O   HOH Z  47 " =    1.626
peak=    3.193 closest distance to " O   HOH Z 352 " =    1.494
peak=    3.184 closest distance to " O   HOH Z 175 " =    1.998
peak=    3.183 closest distance to " CD2 LEU A 167 " =    1.031
peak=    3.176 closest distance to " ND2BASN A 224 " =    0.825
peak=    3.173 closest distance to " O   HOH Z 434 " =    1.331
peak=    3.173 closest distance to " N   SER A  97 " =    0.819
peak=    3.172 closest distance to " O   HOH Z 153 " =    3.489
peak=    3.168 closest distance to " CB  PHE A 204 " =    0.816
peak=    3.168 closest distance to " CE  LYS A  48 " =    1.009
peak=    3.166 closest distance to " O   HOH Z 116 " =    1.199
peak=    3.166 closest distance to " CB  GLN A 223 " =    1.864
peak=    3.163 closest distance to " OG BSER A  99 " =    2.119
peak=    3.162 closest distance to " O   HOH Z 119 " =    4.050
peak=    3.157 closest distance to " OD2 ASP A  50 " =    1.120
peak=    3.156 closest distance to " O   HOH Z 425 " =    2.077
peak=    3.154 closest distance to " CZ3 TRP A 266 " =    1.160
peak=    3.152 closest distance to " O   HOH Z 393 " =    1.388
peak=    3.144 closest distance to " CG1 ILE A  33 " =    1.340
peak=    3.144 closest distance to " O   HOH Z 375 " =    2.175
peak=    3.137 closest distance to " O   HOH Z 148 " =    1.560
peak=    3.135 closest distance to " NH2BARG A 145 " =    1.462
peak=    3.125 closest distance to " CB  GLN A  89 " =    1.139
peak=    3.121 closest distance to " ND1 HIS A  81 " =    1.644
peak=    3.118 closest distance to " O   HOH Z 280 " =    1.737
peak=    3.117 closest distance to " CD1 LEU A 228 " =    1.665
peak=    3.116 closest distance to " NH2 ARG A 269 " =    1.035
peak=    3.112 closest distance to " OE1 GLU A  53 " =    1.515
peak=    3.106 closest distance to " O   HOH Z 272 " =    1.774
peak=    3.100 closest distance to " O   HOH Z 413 " =    1.615
peak=    3.096 closest distance to " O   HOH Z 189 " =    2.596
peak=    3.086 closest distance to " O   HOH Z 129 " =    1.008
peak=    3.081 closest distance to " O   HOH Z 166 " =    2.912
peak=    3.078 closest distance to " O   HOH Z 106 " =    2.541
peak=    3.067 closest distance to " O   HOH Z 367 " =    2.295
peak=    3.066 closest distance to " O   HOH Z 133 " =    2.286
peak=    3.065 closest distance to " O   HOH Z 291 " =    1.340
peak=    3.064 closest distance to " CE3 TRP A  85 " =    1.024
peak=    3.064 closest distance to " O   HOH Z 287 " =    1.941
peak=    3.061 closest distance to " CG2 VAL A 202 " =    1.437

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 200         
Filter by distance & map next to the model:
   mapped sites are within: 0.698 - 5.496
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 198 from: 200
   mapped sites are within: 0.702 - 5.496

peak=   -4.738 closest distance to " CG2 VAL A 230 " =    0.927
peak=   -4.518 closest distance to " CD  ARG A  14 " =    3.052
peak=   -4.518 closest distance to " OE1 GLU A 277 " =    2.416
peak=   -4.455 closest distance to " OG ASER A 134 " =    1.136
peak=   -4.450 closest distance to " O   PRO A 198 " =    1.146
peak=   -4.282 closest distance to " OG  SER A  97 " =    2.274
peak=   -4.188 closest distance to " CG  MET A 105 " =    0.891
peak=   -4.116 closest distance to " CB  ASP A  27 " =    2.465
peak=   -4.112 closest distance to " CA  GLY A 133 " =    2.027
peak=   -4.106 closest distance to " OG BSER A 134 " =    1.602
peak=   -4.042 closest distance to " O   HOH Z 350 " =    1.977
peak=   -4.022 closest distance to " O   HOH Z 385 " =    0.990
peak=   -3.994 closest distance to " O   HOH Z  76 " =    1.240
peak=   -3.980 closest distance to " CG1 VAL A 296 " =    0.747
peak=   -3.966 closest distance to " O   HOH Z  95 " =    1.185
peak=   -3.945 closest distance to " O   HOH Z 286 " =    1.743
peak=   -3.934 closest distance to " C   PHE A 155 " =    0.887
peak=   -3.919 closest distance to " OG  SER A  26 " =    0.985
peak=   -3.914 closest distance to " CG  PRO A 163 " =    2.421
peak=   -3.792 closest distance to " O   HOH Z 242 " =    1.587
peak=   -3.777 closest distance to " CA  GLY A  98 " =    1.844
peak=   -3.774 closest distance to " CB  PRO A 243 " =    2.499
peak=   -3.768 closest distance to " O   HOH Z 111 " =    0.956
peak=   -3.759 closest distance to " O   ALA A  51 " =    1.302
peak=   -3.757 closest distance to " CD1 TRP A 179 " =    1.183
peak=   -3.752 closest distance to " O   HOH Z 186 " =    1.378
peak=   -3.729 closest distance to " CD2 LEU A   5 " =    0.943
peak=   -3.728 closest distance to " O   HOH Z 359 " =    1.492
peak=   -3.716 closest distance to " O   TRP A 179 " =    1.843
peak=   -3.716 closest distance to " O   HOH Z 163 " =    1.607
peak=   -3.713 closest distance to " O   HOH Z 415 " =    0.953
peak=   -3.710 closest distance to " O   GLN A  11 " =    1.625
peak=   -3.703 closest distance to " O   GLY A  98 " =    1.975
peak=   -3.703 closest distance to " O   HOH Z  43 " =    1.897
peak=   -3.701 closest distance to " O   HOH Z 435 " =    2.167
peak=   -3.695 closest distance to " O   ARG A 145 " =    1.453
peak=   -3.684 closest distance to " CB  TYR A  15 " =    2.115
peak=   -3.678 closest distance to " OG1 THR A 157 " =    1.716
peak=   -3.674 closest distance to " CD  LYS A 289 " =    2.322
peak=   -3.666 closest distance to " O   HOH Z 198 " =    2.219
peak=   -3.666 closest distance to " O   HOH Z  61 " =    1.329
peak=   -3.665 closest distance to " O   HOH Z 431 " =    1.163
peak=   -3.659 closest distance to " NH2 ARG A  79 " =    1.985
peak=   -3.655 closest distance to " O   HOH Z 129 " =    4.579
peak=   -3.633 closest distance to " O   HOH Z 126 " =    1.659
peak=   -3.623 closest distance to " N   PRO A 163 " =    1.439
peak=   -3.607 closest distance to " C   ILE A 239 " =    2.021
peak=   -3.606 closest distance to " O   HOH Z  52 " =    0.970
peak=   -3.582 closest distance to " O   HOH Z 235 " =    1.050
peak=   -3.569 closest distance to " O   HOH Z 140 " =    1.324
peak=   -3.559 closest distance to " CB  ALA A 248 " =    1.967
peak=   -3.540 closest distance to " O   HOH Z 313 " =    1.157
peak=   -3.531 closest distance to " CB  ALA A 291 " =    2.064
peak=   -3.524 closest distance to " OG  SER A  63 " =    1.480
peak=   -3.518 closest distance to " O   SER A  22 " =    2.587
peak=   -3.510 closest distance to " O   HOH Z 111 " =    2.162
peak=   -3.507 closest distance to " O   HOH Z 420 " =    3.181
peak=   -3.501 closest distance to " O   HOH Z 298 " =    0.922
peak=   -3.500 closest distance to " N   GLN A  58 " =    1.198
peak=   -3.498 closest distance to " CB  ASN A  39 " =    2.230
peak=   -3.488 closest distance to " O   HOH Z  68 " =    1.297
peak=   -3.486 closest distance to " N   VAL A 125 " =    0.978
peak=   -3.483 closest distance to " CD  ARG A 138 " =    1.462
peak=   -3.483 closest distance to " O   HOH Z  88 " =    2.374
peak=   -3.481 closest distance to " O   HOH Z 413 " =    4.393
peak=   -3.478 closest distance to " O   HOH Z 352 " =    1.833
peak=   -3.478 closest distance to " O   HOH Z 407 " =    3.004
peak=   -3.477 closest distance to " CD  LYS A 166 " =    2.590
peak=   -3.472 closest distance to " O   ASN A 301 " =    1.426
peak=   -3.454 closest distance to " CA  ASN A 217 " =    1.956
peak=   -3.450 closest distance to " O   THR A  42 " =    2.521
peak=   -3.449 closest distance to " O   ASP A 191 " =    1.920
peak=   -3.448 closest distance to " N   ARG A 138 " =    1.629
peak=   -3.446 closest distance to " OG  SER A 206 " =    1.888
peak=   -3.445 closest distance to " O   HOH Z 393 " =    2.952
peak=   -3.442 closest distance to " O   HOH Z 151 " =    1.084
peak=   -3.436 closest distance to " O   TRP A  70 " =    1.568
peak=   -3.432 closest distance to " CG  ARG A 138 " =    0.974
peak=   -3.422 closest distance to " CD1 LEU A 222 " =    2.381
peak=   -3.420 closest distance to " O   HOH Z  77 " =    1.659
peak=   -3.414 closest distance to " O   THR A  18 " =    1.665
peak=   -3.414 closest distance to " O   HOH Z 416 " =    0.866
peak=   -3.411 closest distance to " OG  SER A  87 " =    1.400
peak=   -3.410 closest distance to " O   HOH Z 236 " =    1.846
peak=   -3.402 closest distance to " CB  PHE A 130 " =    1.193
peak=   -3.401 closest distance to " N   SER A 276 " =    1.144
peak=   -3.390 closest distance to " CB  VAL A 230 " =    0.936
peak=   -3.387 closest distance to " O   HOH Z 426 " =    1.954
peak=   -3.386 closest distance to " O   HOH Z 197 " =    3.254
peak=   -3.384 closest distance to " O   HOH Z 139 " =    2.005
peak=   -3.383 closest distance to " O   ILE A  49 " =    1.720
peak=   -3.381 closest distance to " O   HOH Z 143 " =    0.866
peak=   -3.380 closest distance to " O   HOH Z  56 " =    2.027
peak=   -3.376 closest distance to " O   HOH Z 369 " =    1.665
peak=   -3.374 closest distance to " O   HOH Z 426 " =    1.489
peak=   -3.370 closest distance to " N   HIS A 115 " =    2.114
peak=   -3.364 closest distance to " CG  TRP A 266 " =    1.729
peak=   -3.364 closest distance to " O   VAL A 174 " =    2.519
peak=   -3.364 closest distance to " CG  GLU A 277 " =    1.200
peak=   -3.362 closest distance to " C   GLN A 205 " =    1.995
peak=   -3.358 closest distance to " N   LYS A 166 " =    1.850
peak=   -3.349 closest distance to " OG1 THR A 264 " =    2.248
peak=   -3.338 closest distance to " O   HOH Z 389 " =    2.138
peak=   -3.338 closest distance to " O   HOH Z 285 " =    3.004
peak=   -3.331 closest distance to " O   HOH Z 376 " =    2.368
peak=   -3.330 closest distance to " C   ALA A 158 " =    1.487
peak=   -3.327 closest distance to " O   HOH Z 402 " =    1.417
peak=   -3.325 closest distance to " O   HOH Z 131 " =    3.851
peak=   -3.317 closest distance to " CG2 THR A  31 " =    2.332
peak=   -3.313 closest distance to " O   HOH Z   1 " =    3.750
peak=   -3.313 closest distance to " CE1 PHE A  59 " =    1.414
peak=   -3.305 closest distance to " O   HOH Z 389 " =    0.997
peak=   -3.298 closest distance to " N   ALA A   1 " =    1.100
peak=   -3.297 closest distance to " O   PRO A 243 " =    2.485
peak=   -3.297 closest distance to " OD2 ASP A 270 " =    1.324
peak=   -3.297 closest distance to " O   HOH Z  39 " =    1.237
peak=   -3.296 closest distance to " O   HOH Z 174 " =    2.966
peak=   -3.295 closest distance to " O   HOH Z 275 " =    1.859
peak=   -3.291 closest distance to " N   LEU A 282 " =    2.263
peak=   -3.286 closest distance to " O   HOH Z 189 " =    3.040
peak=   -3.279 closest distance to " OE2 GLU A 152 " =    2.162
peak=   -3.279 closest distance to " O   HOH Z 132 " =    0.901
peak=   -3.278 closest distance to " CD  GLN A  77 " =    1.317
peak=   -3.277 closest distance to " O   GLY A 211 " =    1.224
peak=   -3.265 closest distance to " CB  ALA A 227 " =    2.214
peak=   -3.265 closest distance to " CE2 TYR A  30 " =    2.702
peak=   -3.265 closest distance to " O   HOH Z  15 " =    0.877
peak=   -3.262 closest distance to " O   HOH Z 353 " =    1.254
peak=   -3.258 closest distance to " CG  ASP A 231 " =    0.702
peak=   -3.257 closest distance to " OG  SER A  63 " =    1.399
peak=   -3.256 closest distance to " O  BHOH Z  74 " =    2.582
peak=   -3.253 closest distance to " CG  ASP A  50 " =    0.977
peak=   -3.251 closest distance to " OD2 ASP A  50 " =    1.254
peak=   -3.250 closest distance to " O   HOH Z 185 " =    2.126
peak=   -3.246 closest distance to " N   VAL A  72 " =    1.881
peak=   -3.245 closest distance to " O   HOH Z 231 " =    1.812
peak=   -3.244 closest distance to " CD1 LEU A 297 " =    2.290
peak=   -3.244 closest distance to " O   HOH Z 102 " =    1.595
peak=   -3.243 closest distance to " OE1 GLN A  58 " =    5.427
peak=   -3.243 closest distance to " O   HOH Z 298 " =    2.557
peak=   -3.241 closest distance to " O   HOH Z 300 " =    1.147
peak=   -3.236 closest distance to " O   ASP A 270 " =    1.690
peak=   -3.236 closest distance to " CG2AVAL A  41 " =    2.733
peak=   -3.235 closest distance to " OE2 GLU A 152 " =    0.969
peak=   -3.230 closest distance to " O   HOH Z 275 " =    1.570
peak=   -3.229 closest distance to " CG BLYS A 290 " =    0.944
peak=   -3.220 closest distance to " CZ2 TRP A 274 " =    0.952
peak=   -3.219 closest distance to " O   HOH Z 218 " =    3.593
peak=   -3.215 closest distance to " CG1 ILE A 263 " =    2.000
peak=   -3.210 closest distance to " NE1 TRP A 177 " =    1.713
peak=   -3.209 closest distance to " OE1 GLN A 223 " =    2.286
peak=   -3.209 closest distance to " O   HOH Z 268 " =    0.941
peak=   -3.209 closest distance to " CG  PHE A  59 " =    1.778
peak=   -3.206 closest distance to " O   HOH Z 356 " =    4.021
peak=   -3.205 closest distance to " CG  LEU A 228 " =    1.014
peak=   -3.204 closest distance to " C   HIS A 108 " =    1.197
peak=   -3.198 closest distance to " CD1 LEU A   5 " =    2.467
peak=   -3.195 closest distance to " OG  SER A 245 " =    1.408
peak=   -3.193 closest distance to " C   ARG A  79 " =    2.551
peak=   -3.193 closest distance to " O   HOH Z 377 " =    1.176
peak=   -3.193 closest distance to " O   HOH Z  93 " =    2.335
peak=   -3.191 closest distance to " ND2BASN A 224 " =    1.466
peak=   -3.184 closest distance to " N   ASP A 270 " =    1.442
peak=   -3.181 closest distance to " O   ILE A 106 " =    2.086
peak=   -3.179 closest distance to " O   HOH Z 429 " =    1.504
peak=   -3.177 closest distance to " CD2 HIS A 115 " =    2.004
peak=   -3.177 closest distance to " CD2 TYR A 293 " =    1.846
peak=   -3.175 closest distance to " CB  ALA A  43 " =    2.299
peak=   -3.173 closest distance to " O   HOH Z 211 " =    1.284
peak=   -3.171 closest distance to " CG  ARG A 219 " =    2.434
peak=   -3.169 closest distance to " O   HOH Z  52 " =    1.765
peak=   -3.160 closest distance to " NE2 GLN A 223 " =    1.504
peak=   -3.150 closest distance to " C   VAL A 265 " =    0.968
peak=   -3.149 closest distance to " O   HOH Z 339 " =    1.718
peak=   -3.147 closest distance to " O   HOH Z  28 " =    1.507
peak=   -3.147 closest distance to " O   HOH Z 390 " =    2.278
peak=   -3.147 closest distance to " O   HOH Z 124 " =    4.192
peak=   -3.143 closest distance to " O   HOH Z 237 " =    2.357
peak=   -3.142 closest distance to " CA  GLY A  35 " =    1.864
peak=   -3.141 closest distance to " CD2 TRP A 150 " =    1.347
peak=   -3.137 closest distance to " CG  GLN A  88 " =    0.821
peak=   -3.125 closest distance to " O   HOH Z  40 " =    4.175
peak=   -3.125 closest distance to " N   GLN A  88 " =    1.651
peak=   -3.120 closest distance to " O   HOH Z 290 " =    1.225
peak=   -3.116 closest distance to " O   PRO A 163 " =    1.947
peak=   -3.116 closest distance to " NH2AARG A 275 " =    5.386
peak=   -3.110 closest distance to " CD  ARG A 156 " =    1.716
peak=   -3.109 closest distance to " O   HOH Z 368 " =    2.653
peak=   -3.106 closest distance to " O   HOH Z 385 " =    2.308
peak=   -3.095 closest distance to " O   HOH Z  60 " =    2.191
peak=   -3.093 closest distance to " CD2 LEU A 237 " =    2.233
peak=   -3.084 closest distance to " O   HOH Z 318 " =    1.624
peak=   -3.082 closest distance to " CG1 VAL A 296 " =    2.223
peak=   -3.076 closest distance to " O   GLY A  80 " =    2.523
peak=   -3.070 closest distance to " O   HOH Z 412 " =    5.496
peak=   -3.069 closest distance to " CD  ARG A 139 " =    1.677
peak=   -3.047 closest distance to " O   HOH Z 292 " =    1.593
peak=   -3.042 closest distance to " CB  ALA A 100 " =    2.055

================= 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    :  0.4898 0.4867   6.296547e+00   6.285274e+00
   1_bss:  0.4809 0.4756   6.290667e+00   6.276637e+00
   1_xyz:  0.4141 0.4453   6.219376e+00   6.249963e+00
   1_adp:  0.3783 0.4414   6.177648e+00   6.245930e+00
   1_occ:  0.3781 0.4416   6.177084e+00   6.246161e+00
   2_bss:  0.3767 0.4381   6.177761e+00   6.244537e+00
   2_xyz:  0.3309 0.4065   6.076296e+00   6.193351e+00
   2_adp:  0.3153 0.3953   6.052120e+00   6.176929e+00
   2_occ:  0.3151 0.3948   6.051821e+00   6.176613e+00
   3_bss:  0.3161 0.3934   6.052077e+00   6.175163e+00
   3_xyz:  0.2565 0.3255   5.871204e+00   6.032542e+00
   3_adp:  0.2300 0.3045   5.785506e+00   5.978153e+00
   3_occ:  0.2294 0.3048   5.784977e+00   5.978757e+00
   4_bss:  0.2281 0.3024   5.780495e+00   5.973101e+00
   4_xyz:  0.1817 0.2416   5.565619e+00   5.782272e+00
   4_adp:  0.1684 0.2268   5.501537e+00   5.726906e+00
   4_occ:  0.1682 0.2263   5.499981e+00   5.724789e+00
   5_bss:  0.1680 0.2265   5.499139e+00   5.725040e+00
   5_xyz:  0.1426 0.2003   5.369548e+00   5.610328e+00
   5_adp:  0.1331 0.1883   5.307574e+00   5.548214e+00
   5_occ:  0.1327 0.1879   5.305523e+00   5.546475e+00
   5_bss:  0.1331 0.1873   5.303681e+00   5.544662e+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:  0.393  20.000   6.407   9.647   6.778   0.000   0.000   0.000
   1_xyz:  0.393  20.000   6.407   9.647   6.778   0.000   0.000   0.000
   1_adp:  0.393  20.000   6.407   9.647   6.778   0.000   0.000   0.000
   1_occ:  0.393  20.000   6.407   9.647   6.778   0.000   0.000   0.000
   2_bss:  0.368  39.922   3.411   5.712   3.975   0.000   0.000   0.000
   2_xyz:  0.368  39.922   3.411   5.712   3.975   0.000   0.000   0.000
   2_adp:  0.368  39.922   3.411   5.712   3.975   0.000   0.000   0.000
   2_occ:  0.368  39.922   3.411   5.712   3.975   0.000   0.000   0.000
   3_bss:  0.336  39.923   3.107   4.079   3.672   0.000   0.000   0.000
   3_xyz:  0.336  39.923   3.107   4.079   3.672   0.000   0.000   0.000
   3_adp:  0.336  39.923   3.107   4.079   3.672   0.000   0.000   0.000
   3_occ:  0.336  39.923   3.107   4.079   3.672   0.000   0.000   0.000
   4_bss:  0.333  45.555   2.143   2.276   2.912   0.000   0.000   0.000
   4_xyz:  0.333  45.555   2.143   2.276   2.912   0.000   0.000   0.000
   4_adp:  0.333  45.555   2.143   2.276   2.912   0.000   0.000   0.000
   4_occ:  0.333  45.555   2.143   2.276   2.912   0.000   0.000   0.000
   5_bss:  0.330  45.555   1.487   1.189   2.440   0.000   0.000   0.000
   5_xyz:  0.330  45.555   1.487   1.189   2.440   0.000   0.000   0.000
   5_adp:  0.330  45.555   1.487   1.189   2.440   0.000   0.000   0.000
   5_occ:  0.330  45.555   1.487   1.189   2.440   0.000   0.000   0.000
   5_bss:  0.319  45.705  -0.166  -0.627   0.793  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  60.470 0.3884  0.4680    77544.942
   1_bss:  59.430 0.4011  0.6026    74922.511
   1_xyz:  54.140 0.4680  0.6884    64315.104
   1_adp:  53.432 0.4768  0.7453    63379.915
   1_occ:  53.420 0.4771  0.7452    63558.068
   2_bss:  53.100 0.4809  0.6731    62905.746
   2_xyz:  46.909 0.5574  0.7746    50010.368
   2_adp:  44.540 0.5874  0.8179    47120.347
   2_occ:  44.535 0.5874  0.8178    47088.141
   3_bss:  44.311 0.5899  0.7994    46585.165
   3_xyz:  34.511 0.7065  0.9338    29697.652
   3_adp:  31.262 0.7438  0.9648    25336.713
   3_occ:  31.289 0.7435  0.9640    25345.446
   4_bss:  31.048 0.7459  0.9263    24848.635
   4_xyz:  24.023 0.8208  0.9820    15126.534
   4_adp:  22.152 0.8402  0.9942    13344.379
   4_occ:  22.084 0.8408  0.9942    13250.636
   5_bss:  22.037 0.8412  0.9677    13217.434
   5_xyz:  19.189 0.8692  0.9799    10453.357
   5_adp:  17.751 0.8829  0.9768     9296.624
   5_occ:  17.706 0.8832  0.9765     9231.552
   5_bss:  17.651 0.8836  0.9735     9150.088
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.088   5.3260e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.088   5.3260e+01
   1_xyz:   1.699  0.013  0.106 18.314  0.007  4.105   1.4553e-01
   1_adp:   1.699  0.013  0.106 18.314  0.007  4.105   1.4553e-01
   1_occ:   1.699  0.013  0.106 18.314  0.007  4.105   1.4553e-01
   2_bss:   1.699  0.013  0.106 18.314  0.007  4.105   1.4553e-01
   2_xyz:   1.212  0.008  0.081 16.426  0.005  4.103   9.3731e-02
   2_adp:   1.212  0.008  0.081 16.426  0.005  4.103   9.3731e-02
   2_occ:   1.212  0.008  0.081 16.426  0.005  4.103   9.3731e-02
   3_bss:   1.212  0.008  0.081 16.426  0.005  4.103   9.3731e-02
   3_xyz:   1.322  0.009  0.093 16.760  0.005  4.104   1.0272e-01
   3_adp:   1.322  0.009  0.093 16.760  0.005  4.104   1.0272e-01
   3_occ:   1.322  0.009  0.093 16.760  0.005  4.104   1.0272e-01
   4_bss:   1.322  0.009  0.093 16.760  0.005  4.104   1.0272e-01
   4_xyz:   1.000  0.007  0.072 15.568  0.003  4.115   6.4464e-02
   4_adp:   1.000  0.007  0.072 15.568  0.003  4.115   6.4464e-02
   4_occ:   1.000  0.007  0.072 15.568  0.003  4.115   6.4464e-02
   5_bss:   1.000  0.007  0.072 15.568  0.003  4.115   6.4464e-02
   5_xyz:   1.036  0.006  0.075 15.527  0.003  4.106   6.3988e-02
   5_adp:   1.036  0.006  0.075 15.527  0.003  4.106   6.3988e-02
   5_occ:   1.036  0.006  0.075 15.527  0.003  4.106   6.3988e-02
   5_bss:   1.036  0.006  0.075 15.527  0.003  4.106   6.3988e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9007e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9007e+00
   1_xyz:  13.043  0.191  0.426 84.895  0.041  2.134   9.9915e-02
   1_adp:  13.043  0.191  0.426 84.895  0.041  2.134   9.9915e-02
   1_occ:  13.043  0.191  0.426 84.895  0.041  2.134   9.9915e-02
   2_bss:  13.043  0.191  0.426 84.895  0.041  2.134   9.9915e-02
   2_xyz:   8.338  0.093  0.341 81.788  0.055  1.982   5.5983e-02
   2_adp:   8.338  0.093  0.341 81.788  0.055  1.982   5.5983e-02
   2_occ:   8.338  0.093  0.341 81.788  0.055  1.982   5.5983e-02
   3_bss:   8.338  0.093  0.341 81.788  0.055  1.982   5.5983e-02
   3_xyz:   8.558  0.063  0.362 82.317  0.029  2.055   6.2980e-02
   3_adp:   8.558  0.063  0.362 82.317  0.029  2.055   6.2980e-02
   3_occ:   8.558  0.063  0.362 82.317  0.029  2.055   6.2980e-02
   4_bss:   8.558  0.063  0.362 82.317  0.029  2.055   6.2980e-02
   4_xyz:   7.109  0.043  0.267 77.001  0.025  2.260   5.3655e-02
   4_adp:   7.109  0.043  0.267 77.001  0.025  2.260   5.3655e-02
   4_occ:   7.109  0.043  0.267 77.001  0.025  2.260   5.3655e-02
   5_bss:   7.109  0.043  0.267 77.001  0.025  2.260   5.3655e-02
   5_xyz:   7.612  0.061  0.246 82.037  0.031  2.286   4.5022e-02
   5_adp:   7.612  0.061  0.246 82.037  0.031  2.286   4.5022e-02
   5_occ:   7.612  0.061  0.246 82.037  0.031  2.286   4.5022e-02
   5_bss:   7.612  0.061  0.246 82.037  0.031  2.286   4.5022e-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:  61.81   0.00  13.03  61.81   0.00  11.72  57.23   0.00  20.17
   1_occ:  61.81   0.00  13.03  61.81   0.00  11.72  57.23   0.00  20.17
   2_bss:  61.81   0.00  13.03  61.81   0.00  11.72  57.23   0.00  20.17
   2_xyz:  61.81   0.00  13.03  61.81   0.00  11.72  57.23   0.00  20.17
   2_adp:  66.74   0.00  13.25  66.66   0.00  11.37  66.74   0.00  23.51
   2_occ:  66.74   0.00  13.25  66.66   0.00  11.37  66.74   0.00  23.51
   3_bss:  66.74   0.00  13.25  66.66   0.00  11.37  66.74   0.00  23.51
   3_xyz:  66.74   0.00  13.25  66.66   0.00  11.37  66.74   0.00  23.51
   3_adp:  89.77   0.00  14.36  74.49   0.00  10.55  89.77   0.00  35.06
   3_occ:  89.77   0.00  14.36  74.49   0.00  10.55  89.77   0.00  35.06
   4_bss:  89.77   0.00  14.36  74.49   0.00  10.55  89.77   0.00  35.06
   4_xyz:  89.77   0.00  14.36  74.49   0.00  10.55  89.77   0.00  35.06
   4_adp:  88.77   0.00  14.09  75.69   0.00  10.01  88.77   3.04  36.34
   4_occ:  88.77   0.00  14.09  75.69   0.00  10.01  88.77   3.04  36.34
   5_bss:  88.77   0.00  14.09  75.69   0.00  10.01  88.77   3.04  36.34
   5_xyz:  88.77   0.00  14.09  75.69   0.00  10.01  88.77   3.04  36.34
   5_adp:  89.06   0.00  14.37  89.06   0.00   9.58  88.82   2.76  40.48
   5_occ:  89.06   0.00  14.37  89.06   0.00   9.58  88.82   2.76  40.48
   5_bss:  90.68   1.62  15.99  90.68   1.62  11.20  90.44   4.38  42.10
------------------------------------------------------------------------
 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:    1.248    0.024    0.412
   1_adp:    1.248    0.024    0.412
   1_occ:    1.248    0.024    0.412
   2_bss:    1.248    0.024    0.412
   2_xyz:    1.566    0.037    0.558
   2_adp:    1.566    0.037    0.558
   2_occ:    1.566    0.037    0.558
   3_bss:    1.566    0.037    0.558
   3_xyz:    1.853    0.029    0.735
   3_adp:    1.853    0.029    0.735
   3_occ:    1.853    0.029    0.735
   4_bss:    1.853    0.029    0.735
   4_xyz:    2.041    0.033    0.818
   4_adp:    2.041    0.033    0.818
   4_occ:    2.041    0.033    0.818
   5_bss:    2.041    0.033    0.818
   5_xyz:    2.130    0.045    0.863
   5_adp:    2.130    0.045    0.863
   5_occ:    2.130    0.045    0.863
   5_bss:    2.130    0.045    0.863
------------------------------------------------------------------------

CPU time actual refinement: 367.66


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_730/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_730/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_730/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_730/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_730/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 367.51 
  Macro-tasks:
    bulk solvent and scale       = 44.35  
    individual site refinement   = 155.93 
    weights calculation          = 33.30  
    collect and process          = 6.49   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 240.17 
  Micro-tasks:
    mask                            = 2.91   
    f_calc                          = 119.07 
    alpha_beta                      = 8.57   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 123.52 
    fmodel                         = 7.58   
    r_factors                      = 0.19   
    phase_errors                   = 10.84  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 274.12 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 5.163 micro seconds
Total CPU time: 6.35 minutes
from_scatterers_fft:    648 calls, 118.51 s
gradients_fft:          593 calls, 111.99 s

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

# Date 2008-01-16 Time 02:16:56 PST -0800 (1200478616.26 s)
Start R-work = 0.4898, R-free = 0.4867 (no bulk solvent and anisotropic scale)
Final R-work = 0.1484, R-free = 0.1999 (no bulk solvent and anisotropic scale)

Start R-work = 0.4809, R-free = 0.4756
Final R-work = 0.1331, R-free = 0.1873