# Date 2008-01-16 Time 02:57:24 PST -0800 (1200481044.15 s)
#phil __OFF__

Command line arguments: "../1042.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 21608
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1042

-------------------------------------------------------------------------------
  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: (71.3037, 47.1647, 87.6859, 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: 3.28, per 1000 atoms: 1.16


================================== 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: (71.3037, 47.1647, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2189 2.01224
Completeness in resolution range: 0.969752
Completeness with d_max=infinity: 0.966737

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2189
                             d_min =   2.0122

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: (71.3037, 47.1647, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2189 2.01224
Completeness in resolution range: 0.969752
Completeness with d_max=infinity: 0.966737

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2193 -  4.3056 [2118/2142]  1905   213  10.1%
  bin  2:  4.3056 -  3.4303 [2036/2056]  1833   203  10.0%
  bin  3:  3.4303 -  3.0005 [2014/2033]  1814   200   9.9%
  bin  4:  3.0005 -  2.7279 [1998/2028]  1798   200  10.0%
  bin  5:  2.7279 -  2.5333 [1988/2007]  1788   200  10.1%
  bin  6:  2.5333 -  2.3846 [1957/1982]  1759   198  10.1%
  bin  7:  2.3846 -  2.2655 [1954/1982]  1761   193   9.9%
  bin  8:  2.2655 -  2.1672 [1965/2001]  1770   195   9.9%
  bin  9:  2.1672 -  2.0840 [1942/1984]  1749   193   9.9%
  bin 10:  2.0840 -  2.0122 [1617/1985]  1453   164  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1042/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:
        1.81 -     2.42: 10
        2.42 -     3.04: 2165
        3.04 -     3.66: 4570
        3.66 -     4.28: 8859
        4.28 -     4.90: 12212
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.877 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z  42 " - " O   HOH Z 183 "  2.285 3.040 -x+1,y+1/2,-z+1/2
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  ... (remaining 27811 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_1042/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1042/model_refine_001.geo

CPU time processing inputs: 9.07


============================ 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 = 71.30375 47.16465 87.68585 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.01 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4578   r_free= 0.4479   ksol= 0.00   Bsol= 0.00   scale= 0.796    |
|                                                                             |
| 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:   0.64 A                  |
| x-ray target function (ml) for work reflections: 6.257010                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2193 -  4.8022 0.99   1380  153 0.3773 0.3438      6.5681      6.4477|
|  2:  4.8022 -  3.8316 0.99   1325  149 0.3590 0.3863      6.7173      6.8058|
|  3:  3.8316 -  3.3532 0.99   1298  142 0.4098 0.3824      6.6316      6.6114|
|  4:  3.3532 -  3.0493 0.99   1287  145 0.4424 0.3898      6.5015      6.3833|
|  5:  3.0493 -  2.8322 0.99   1281  143 0.4769 0.4632      6.3467      6.3918|
|  6:  2.8322 -  2.6662 0.99   1295  140 0.4867 0.5378      6.2734      6.1874|
|  7:  2.6662 -  2.5333 0.99   1272  144 0.5064 0.4877      6.2287      6.2334|
|  8:  2.5333 -  2.4235 0.98   1257  137 0.5126 0.4576      6.1744      6.1104|
|  9:  2.4235 -  2.3305 0.98   1263  142 0.4937 0.5479      6.1024      6.1622|
| 10:  2.3305 -  2.2504 1.00   1262  143 0.5148 0.4968      6.1152      6.0968|
| 11:  2.2504 -  2.1802 0.97   1264  136 0.4991 0.4844      6.0257      6.0607|
| 12:  2.1802 -  2.1181 0.98   1236  140 0.5076 0.5062      5.9834       5.982|
| 13:  2.1181 -  2.0624 0.99   1281  142 0.5189 0.4754      5.9006      5.8279|
| 14:  2.0624 -  2.0122 0.74    929  103 0.5250 0.4905      5.8534      5.7571|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2193 -  4.8022  1380   153  0.74  30.84   0.80     0.76      58298.74|
|  2:  4.8022 -  3.8316  1325   149  0.76  30.24   0.89     0.80      83144.12|
|  3:  3.8316 -  3.3532  1298   142  0.68  37.40   0.84     0.76      88726.99|
|  4:  3.3532 -  3.0493  1287   145  0.59  44.39   0.81     0.66      81163.32|
|  5:  3.0493 -  2.8322  1281   143  0.50  51.69   0.75     0.57      69767.43|
|  6:  2.8322 -  2.6662  1295   140  0.46  55.02   0.74     0.51      64418.90|
|  7:  2.6662 -  2.5333  1272   144  0.42  58.21   0.72     0.47      60209.95|
|  8:  2.5333 -  2.4235  1257   137  0.40  59.59   0.73     0.46      55610.99|
|  9:  2.4235 -  2.3305  1263   142  0.41  58.99   0.72     0.46      50693.00|
| 10:  2.3305 -  2.2504  1262   143  0.42  58.68   0.75     0.48      44997.81|
| 11:  2.2504 -  2.1802  1264   136  0.42  58.64   0.75     0.49      41579.50|
| 12:  2.1802 -  2.1181  1236   140  0.42  58.27   0.74     0.50      37836.83|
| 13:  2.1181 -  2.0624  1281   142  0.42  58.58   0.72     0.49      32494.16|
| 14:  2.0624 -  2.0122   929   103  0.47  54.59   0.70     0.49      24613.07|
|alpha:            min =        0.46 max =            0.80 mean =         0.57|
|beta:             min =    24613.07 max =        88726.99 mean =     57524.31|
|figures of merit: min =        0.00 max =            1.00 mean =         0.51|
|phase err.(work): min =        0.00 max =           89.98 mean =        50.78|
|phase err.(test): min =        0.00 max =           89.97 mean =        50.82|
|-----------------------------------------------------------------------------|

============================== 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 = 10.407655             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.214   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.890716              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.568   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       21 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      160 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      676 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1473 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2578 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3833 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5001 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6464 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7615 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       54.474 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.093    4.900  1.196 |       1.618 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.319)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 12.319)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4639   r_free= 0.4488   ksol= 0.00   Bsol= 0.00   scale= 0.767    |
|                                                                             |
| 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:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.259629                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4497   r_free= 0.4329   ksol= 0.33   Bsol= 46.05   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.85,7.27,9.95,0.00,0.00,0.00); trace/3= 8.36                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.250945                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.606980              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.335   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.837065              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.963   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4497      final r-factor (work) = 0.3458          |
| start r-factor (free) = 0.4329      final r-factor (free) = 0.3709          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 84.5522 = 9.61 * 0.50 * 6.2617 + 1.00 * 54.4742                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.5349 = 9.61 * 0.50 * 6.1200 + 1.00 * 0.1378                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3458      final r-factor (work) = 0.2946          |
| start r-factor (free) = 0.3709      final r-factor (free) = 0.3358          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.1372 = 0.84 * 1.00 * 6.1200 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.0283 = 0.84 * 1.00 * 5.9908 + 1.00 * 0.0137                               |
|-----------------------------------------------------------------------------|
| number of iterations = 19      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.319)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.94   11.15    None  None   None       |
|    all(noH): 2823   0      0.00    76.94   11.15    None  None   None       |
|    Sol.    : 438    0      0.00    76.94   27.36    None  None   None       |
|    Mac.    : 2385   0      0.00    61.14   8.17     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.695: 1406   |   5:    38.472 -  46.167:   60        |
|      1:     7.695 -  15.389:  768   |   6:    46.167 -  53.861:   33        |
|      2:    15.389 -  23.083:  269   |   7:    53.861 -  61.556:   11        |
|      3:    23.083 -  30.778:  159   |   8:    61.556 -  69.250:    3        |
|      4:    30.778 -  38.472:  113   |   9:    69.250 -  76.944:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2946 r_free = 0.3358             target_work(ml) = 5.951         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2940 r_free = 0.3370             target_work(ml) = 5.950         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2940   r_free= 0.3370   ksol= 0.33   Bsol= 46.05   scale= 1.066   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.85,7.27,9.95,0.00,0.00,0.00); trace/3= 8.36                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.950068                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2917   r_free= 0.3335   ksol= 0.31   Bsol= 49.94   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.94,4.58,6.75,0.00,0.00,0.00); trace/3= 5.42                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 5.951035                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.866737              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.097   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.421135              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 127.286  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2917      final r-factor (work) = 0.1928          |
| start r-factor (free) = 0.3335      final r-factor (free) = 0.2387          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.7010 = 5.87 * 0.50 * 5.9874 + 1.00 * 0.1378                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.0565 = 5.87 * 0.50 * 5.7871 + 1.00 * 0.0808                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1928      final r-factor (work) = 0.1722          |
| start r-factor (free) = 0.2387      final r-factor (free) = 0.2201          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4709 = 0.42 * 1.00 * 5.7871 + 1.00 * 0.0338                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4689 = 0.42 * 1.00 * 5.5379 + 1.00 * 0.1367                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.319)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.31   11.25    None  None   None       |
|    all(noH): 2823   0      0.00    80.31   11.25    None  None   None       |
|    Sol.    : 438    0      0.00    76.35   31.01    None  None   None       |
|    Mac.    : 2385   0      0.00    80.31   7.62     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 -   8.031: 1606   |   5:    40.153 -  48.184:   80        |
|      1:     8.031 -  16.061:  614   |   6:    48.184 -  56.214:   33        |
|      2:    16.061 -  24.092:  191   |   7:    56.214 -  64.245:    6        |
|      3:    24.092 -  32.123:  153   |   8:    64.245 -  72.276:    1        |
|      4:    32.123 -  40.153:  137   |   9:    72.276 -  80.306:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1722 r_free = 0.2201             target_work(ml) = 5.499         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1720 r_free = 0.2202             target_work(ml) = 5.498         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1720   r_free= 0.2202   ksol= 0.31   Bsol= 49.94   scale= 1.029   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.94,4.58,6.75,0.00,0.00,0.00); trace/3= 5.42                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.498454                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1708   r_free= 0.2189   ksol= 0.34   Bsol= 65.77   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.52,3.49,4.93,0.00,0.00,0.00); trace/3= 3.98                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.499610                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.293769              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.487   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.861049              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.671   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1708      final r-factor (work) = 0.1347          |
| start r-factor (free) = 0.2189      final r-factor (free) = 0.1812          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.9906 = 4.29 * 0.50 * 5.5473 + 1.00 * 0.0813                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.6772 = 4.29 * 0.50 * 5.4011 + 1.00 * 0.0817                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1347      final r-factor (work) = 0.1253          |
| start r-factor (free) = 0.1812      final r-factor (free) = 0.1743          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 15.4676 = 2.86 * 1.00 * 5.4011 + 1.00 * 0.0149                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 15.0766 = 2.86 * 1.00 * 5.2628 + 1.00 * 0.0195                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.319)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.32   12.39    None  None   None       |
|    all(noH): 2823   0      0.00    81.32   12.39    None  None   None       |
|    Sol.    : 438    0      0.00    81.32   37.39    None  None   None       |
|    Mac.    : 2385   0      0.00    78.48   7.79     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 -   8.132: 1656   |   5:    40.659 -  48.791:   78        |
|      1:     8.132 -  16.264:  572   |   6:    48.791 -  56.923:   86        |
|      2:    16.264 -  24.395:  164   |   7:    56.923 -  65.054:   51        |
|      3:    24.395 -  32.527:  111   |   8:    65.054 -  73.186:   14        |
|      4:    32.527 -  40.659:   78   |   9:    73.186 -  81.318:   13        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1253 r_free = 0.1743             target_work(ml) = 5.245         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1252 r_free = 0.1743             target_work(ml) = 5.244         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1252   r_free= 0.1743   ksol= 0.34   Bsol= 65.77   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.52,3.49,4.93,0.00,0.00,0.00); trace/3= 3.98                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.244282                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1253   r_free= 0.1741   ksol= 0.34   Bsol= 65.77   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.15,3.19,4.54,0.00,0.00,0.00); trace/3= 3.63                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.243509                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.856387              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 117.203  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.311773              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 98.858   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1253      final r-factor (work) = 0.1156          |
| start r-factor (free) = 0.1741      final r-factor (free) = 0.1669          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.2300 = 3.86 * 0.50 * 5.2628 + 1.00 * 0.0822                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.1411 = 3.86 * 0.50 * 5.2125 + 1.00 * 0.0904                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1156      final r-factor (work) = 0.1152          |
| start r-factor (free) = 0.1669      final r-factor (free) = 0.1635          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6413 = 0.31 * 1.00 * 5.2125 + 1.00 * 0.0161                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6334 = 0.31 * 1.00 * 5.1896 + 1.00 * 0.0154                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.319)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.28   11.86    None  None   None       |
|    all(noH): 2823   0      0.00    80.28   11.86    None  None   None       |
|    Sol.    : 438    0      0.49    80.28   35.33    None  None   None       |
|    Mac.    : 2385   0      0.00    78.27   7.55     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 -   8.028: 1692   |   5:    40.139 -  48.167:   82        |
|      1:     8.028 -  16.056:  559   |   6:    48.167 -  56.195:   78        |
|      2:    16.056 -  24.084:  155   |   7:    56.195 -  64.223:   35        |
|      3:    24.084 -  32.111:  104   |   8:    64.223 -  72.250:   10        |
|      4:    32.111 -  40.139:   96   |   9:    72.250 -  80.278:   12        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1152 r_free = 0.1635             target_work(ml) = 5.178         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1151 r_free = 0.1634             target_work(ml) = 5.177         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1151   r_free= 0.1634   ksol= 0.34   Bsol= 65.77   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.15,3.19,4.54,0.00,0.00,0.00); trace/3= 3.63                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.177227                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1151   r_free= 0.1634   ksol= 0.34   Bsol= 65.77   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.15,3.19,4.54,0.00,0.00,0.00); trace/3= 3.63                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.177227                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.778723              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 159.554  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.564823              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 95.638   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1151      final r-factor (work) = 0.1190          |
| start r-factor (free) = 0.1634      final r-factor (free) = 0.1658          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7058 = 1.78 * 0.50 * 5.1892 + 1.00 * 0.0907                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.6839 = 1.78 * 0.50 * 5.1935 + 1.00 * 0.0650                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1190      final r-factor (work) = 0.1186          |
| start r-factor (free) = 0.1658      final r-factor (free) = 0.1662          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9492 = 0.56 * 1.00 * 5.1935 + 1.00 * 0.0158                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9754 = 0.56 * 1.00 * 5.1985 + 1.00 * 0.0392                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.319)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.82   11.84    None  None   None       |
|    all(noH): 2823   0      0.00    81.82   11.84    None  None   None       |
|    Sol.    : 438    0      0.58    81.82   35.21    None  None   None       |
|    Mac.    : 2385   0      0.00    79.74   7.55     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 -   8.182: 1707   |   5:    40.909 -  49.090:   82        |
|      1:     8.182 -  16.363:  544   |   6:    49.090 -  57.272:   73        |
|      2:    16.363 -  24.545:  156   |   7:    57.272 -  65.454:   30        |
|      3:    24.545 -  32.727:  109   |   8:    65.454 -  73.635:   11        |
|      4:    32.727 -  40.909:  102   |   9:    73.635 -  81.817:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1186 r_free = 0.1662             target_work(ml) = 5.202         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1184 r_free = 0.1664             target_work(ml) = 5.201         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1184   r_free= 0.1664   ksol= 0.34   Bsol= 65.77   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.15,3.19,4.54,0.00,0.00,0.00); trace/3= 3.63                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.200839                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2193 -  4.8022 0.99   1380  153 0.1035 0.1390      5.4273      5.5729|
|  2:  4.8022 -  3.8316 0.99   1325  149 0.0891 0.1161      5.4765      5.6659|
|  3:  3.8316 -  3.3532 0.99   1298  142 0.1091 0.1498      5.5074      5.8466|
|  4:  3.3532 -  3.0493 0.99   1287  145 0.1254 0.1638      5.4849      5.6391|
|  5:  3.0493 -  2.8322 0.99   1281  143 0.1403 0.1799      5.3875      5.6049|
|  6:  2.8322 -  2.6662 0.99   1295  140 0.1277 0.2184      5.2754      5.5746|
|  7:  2.6662 -  2.5333 0.99   1272  144 0.1377 0.1668      5.2412      5.3931|
|  8:  2.5333 -  2.4235 0.98   1257  137 0.1271 0.1827      5.1511       5.415|
|  9:  2.4235 -  2.3305 0.98   1263  142 0.1255 0.1841      5.1113      5.3472|
| 10:  2.3305 -  2.2504 1.00   1262  143 0.1241 0.1785      5.0414      5.2878|
| 11:  2.2504 -  2.1802 0.97   1264  136 0.1233 0.1865      5.0011      5.2777|
| 12:  2.1802 -  2.1181 0.98   1236  140 0.1201 0.1860      4.9334      5.2668|
| 13:  2.1181 -  2.0624 0.99   1281  142 0.1215 0.1841      4.8542      5.1161|
| 14:  2.0624 -  2.0122 0.74    929  103 0.1129 0.1833      4.7441      4.9962|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2193 -  4.8022  1380   153  0.94   9.60   0.97     0.94       7953.35|
|  2:  4.8022 -  3.8316  1325   149  0.95   8.37   1.00     0.98       9671.41|
|  3:  3.8316 -  3.3532  1298   142  0.93  11.53   1.01     1.01      10984.08|
|  4:  3.3532 -  3.0493  1287   145  0.92  13.96   1.00     0.98      10806.55|
|  5:  3.0493 -  2.8322  1281   143  0.89  16.65   0.99     0.96       9287.94|
|  6:  2.8322 -  2.6662  1295   140  0.89  17.03   0.98     0.95       8156.08|
|  7:  2.6662 -  2.5333  1272   144  0.89  16.97   0.98     0.96       7176.72|
|  8:  2.5333 -  2.4235  1257   137  0.90  16.53   0.98     0.96       6218.12|
|  9:  2.4235 -  2.3305  1263   142  0.90  16.54   0.99     0.95       5861.00|
| 10:  2.3305 -  2.2504  1262   143  0.89  16.62   0.99     0.95       5001.20|
| 11:  2.2504 -  2.1802  1264   136  0.89  17.19   0.98     0.94       4803.70|
| 12:  2.1802 -  2.1181  1236   140  0.91  15.95   1.00     0.98       4325.46|
| 13:  2.1181 -  2.0624  1281   142  0.89  17.31   0.98     0.96       3813.04|
| 14:  2.0624 -  2.0122   929   103  0.91  15.63   0.96     0.92       2976.24|
|alpha:            min =        0.92 max =            1.01 mean =         0.96|
|beta:             min =     2976.24 max =        10984.08 mean =      7041.53|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.97 mean =        14.92|
|phase err.(test): min =        0.00 max =           88.17 mean =        14.39|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1184   r_free= 0.1663   ksol= 0.32   Bsol= 61.82   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.47,-0.44,0.91,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.200584                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1184   r_free= 0.1663   ksol= 0.32   Bsol= 61.82   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.47,-0.44,0.91,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.200584                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2193 -  4.8022 0.99   1380  153 0.1030 0.1387      5.4201      5.5676|
|  2:  4.8022 -  3.8316 0.99   1325  149 0.0888 0.1155      5.4728      5.6617|
|  3:  3.8316 -  3.3532 0.99   1298  142 0.1089 0.1497       5.506      5.8461|
|  4:  3.3532 -  3.0493 0.99   1287  145 0.1255 0.1640      5.4863      5.6401|
|  5:  3.0493 -  2.8322 0.99   1281  143 0.1406 0.1802      5.3897      5.6075|
|  6:  2.8322 -  2.6662 0.99   1295  140 0.1280 0.2188      5.2774      5.5763|
|  7:  2.6662 -  2.5333 0.99   1272  144 0.1378 0.1670      5.2426      5.3945|
|  8:  2.5333 -  2.4235 0.98   1257  137 0.1273 0.1827      5.1519      5.4156|
|  9:  2.4235 -  2.3305 0.98   1263  142 0.1255 0.1841      5.1117      5.3471|
| 10:  2.3305 -  2.2504 1.00   1262  143 0.1242 0.1786      5.0418      5.2886|
| 11:  2.2504 -  2.1802 0.97   1264  136 0.1233 0.1865      5.0014      5.2778|
| 12:  2.1802 -  2.1181 0.98   1236  140 0.1201 0.1861      4.9335      5.2673|
| 13:  2.1181 -  2.0624 0.99   1281  142 0.1215 0.1842      4.8545      5.1165|
| 14:  2.0624 -  2.0122 0.74    929  103 0.1129 0.1834      4.7443      4.9964|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2193 -  4.8022  1380   153  0.94   9.54   0.96     0.94       7830.82|
|  2:  4.8022 -  3.8316  1325   149  0.95   8.29   1.00     0.98       9585.83|
|  3:  3.8316 -  3.3532  1298   142  0.93  11.50   1.01     1.01      10944.36|
|  4:  3.3532 -  3.0493  1287   145  0.92  13.98   1.00     0.98      10829.87|
|  5:  3.0493 -  2.8322  1281   143  0.89  16.68   0.99     0.96       9327.93|
|  6:  2.8322 -  2.6662  1295   140  0.89  17.07   0.98     0.95       8192.99|
|  7:  2.6662 -  2.5333  1272   144  0.89  17.02   0.98     0.96       7199.96|
|  8:  2.5333 -  2.4235  1257   137  0.90  16.55   0.98     0.96       6228.64|
|  9:  2.4235 -  2.3305  1263   142  0.90  16.54   0.99     0.95       5866.20|
| 10:  2.3305 -  2.2504  1262   143  0.89  16.62   0.99     0.95       5003.48|
| 11:  2.2504 -  2.1802  1264   136  0.89  17.20   0.98     0.94       4807.13|
| 12:  2.1802 -  2.1181  1236   140  0.91  15.95   1.00     0.98       4328.83|
| 13:  2.1181 -  2.0624  1281   142  0.89  17.32   0.98     0.96       3816.65|
| 14:  2.0624 -  2.0122   929   103  0.91  15.64   0.96     0.92       2978.43|
|alpha:            min =        0.92 max =            1.01 mean =         0.96|
|beta:             min =     2978.43 max =        10944.36 mean =      7033.72|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.92|
|phase err.(test): min =        0.00 max =           88.32 mean =        14.39|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.319)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.63    85.44   15.47    None  None   None       |
|    all(noH): 2823   0      3.63    85.44   15.47    None  None   None       |
|    Sol.    : 438    0      4.20    85.44   38.83    None  None   None       |
|    Mac.    : 2385   0      3.63    83.37   11.18    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     3.627 -  11.809: 1707   |   5:    44.536 -  52.717:   82        |
|      1:    11.809 -  19.990:  544   |   6:    52.717 -  60.899:   73        |
|      2:    19.990 -  28.172:  156   |   7:    60.899 -  69.081:   30        |
|      3:    28.172 -  36.354:  109   |   8:    69.081 -  77.262:   11        |
|      4:    36.354 -  44.536:  102   |   9:    77.262 -  85.444:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 345         
Filter by distance & map next to the model:
   mapped sites are within: 0.319 - 4.836
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 334 from: 345
   mapped sites are within: 0.724 - 4.836

peak=   10.026 closest distance to " CG2 VAL A 230 " =    1.388
peak=    5.957 closest distance to " NH2 ARG A  56 " =    2.266
peak=    5.928 closest distance to " CG  LEU A   5 " =    1.225
peak=    5.771 closest distance to " CB  GLN A 223 " =    1.440
peak=    5.557 closest distance to " CG2 VAL A 296 " =    1.015
peak=    5.485 closest distance to " CG  LEU A 228 " =    1.163
peak=    5.209 closest distance to " CD2 LEU A   5 " =    1.144
peak=    5.002 closest distance to " O   HOH Z 232 " =    2.275
peak=    4.987 closest distance to " CB  VAL A 296 " =    1.096
peak=    4.894 closest distance to " CZ  PHE A 218 " =    1.087
peak=    4.875 closest distance to " CG  PRO A 198 " =    1.274
peak=    4.808 closest distance to " CG1 VAL A 296 " =    1.195
peak=    4.799 closest distance to " CB  GLN A 183 " =    1.274
peak=    4.655 closest distance to " NE2 GLN A  11 " =    1.106
peak=    4.599 closest distance to " CB  VAL A 230 " =    1.230
peak=    4.541 closest distance to " CG  PRO A 213 " =    1.207
peak=    4.518 closest distance to " CB  SER A  63 " =    1.311
peak=    4.488 closest distance to " O   HOH Z 265 " =    2.188
peak=    4.483 closest distance to " O   HOH Z 369 " =    2.123
peak=    4.439 closest distance to " CB  ASP A 124 " =    0.807
peak=    4.388 closest distance to " CG  PRO A 243 " =    1.122
peak=    4.364 closest distance to " O   PRO A 198 " =    1.574
peak=    4.351 closest distance to " CB  GLU A 128 " =    1.065
peak=    4.324 closest distance to " O   HOH Z 298 " =    1.900
peak=    4.278 closest distance to " CB  ARG A 190 " =    1.605
peak=    4.256 closest distance to " O   HOH Z 368 " =    2.254
peak=    4.239 closest distance to " O   HOH Z 427 " =    3.135
peak=    4.238 closest distance to " CB  ASN A 148 " =    1.373
peak=    4.225 closest distance to " CB  TRP A 266 " =    1.000
peak=    4.204 closest distance to " CG  MET A 185 " =    1.235
peak=    4.184 closest distance to " CA  TYR A  30 " =    1.002
peak=    4.149 closest distance to " O   HOH Z 303 " =    2.136
peak=    4.147 closest distance to " CA  ALA A  51 " =    0.963
peak=    4.122 closest distance to " O   HOH Z 126 " =    2.030
peak=    4.104 closest distance to " CB  ARG A  79 " =    1.489
peak=    4.084 closest distance to " CB  ASN A 142 " =    1.045
peak=    4.079 closest distance to " O   HOH Z 425 " =    1.466
peak=    4.067 closest distance to " CD2 LEU A 228 " =    1.319
peak=    4.058 closest distance to " CB  ASP A 140 " =    0.952
peak=    4.055 closest distance to " O   HOH Z 142 " =    1.651
peak=    4.042 closest distance to " O   HOH Z 411 " =    3.793
peak=    4.040 closest distance to " O   HOH Z  78 " =    1.692
peak=    4.036 closest distance to " O   HOH Z 236 " =    2.021
peak=    4.022 closest distance to " ND2 ASN A 187 " =    1.465
peak=    4.019 closest distance to " O   HOH Z 126 " =    1.564
peak=    4.019 closest distance to " CB  ARG A 275 " =    0.925
peak=    4.012 closest distance to " O   HOH Z 234 " =    3.773
peak=    3.992 closest distance to " O   SER A  87 " =    2.330
peak=    3.957 closest distance to " CB  VAL A 202 " =    1.641
peak=    3.951 closest distance to " O   HOH Z 188 " =    3.044
peak=    3.951 closest distance to " O   HOH Z  43 " =    2.000
peak=    3.939 closest distance to " CA  ALA A 295 " =    1.102
peak=    3.938 closest distance to " O   HOH Z 261 " =    1.910
peak=    3.936 closest distance to " NH1AARG A 145 " =    1.282
peak=    3.930 closest distance to " CD  LYS A 166 " =    1.304
peak=    3.921 closest distance to " CB  VAL A 265 " =    1.282
peak=    3.916 closest distance to " CD  ARG A 269 " =    0.971
peak=    3.908 closest distance to " CZ  PHE A 192 " =    0.957
peak=    3.900 closest distance to " CA  ARG A 195 " =    1.217
peak=    3.893 closest distance to " ND2 ASN A 249 " =    1.890
peak=    3.859 closest distance to " O   HOH Z 158 " =    3.163
peak=    3.857 closest distance to " CB  GLU A 152 " =    1.196
peak=    3.853 closest distance to " CB  GLU A  46 " =    0.941
peak=    3.850 closest distance to " CD  ARG A 159 " =    0.761
peak=    3.832 closest distance to " OD1 ASN A  69 " =    2.571
peak=    3.828 closest distance to " CB  GLU A 277 " =    3.732
peak=    3.827 closest distance to " O   HOH Z 184 " =    1.480
peak=    3.825 closest distance to " CB  ALA A 104 " =    0.802
peak=    3.823 closest distance to " O   HOH Z 316 " =    3.157
peak=    3.819 closest distance to " CB  ASN A  39 " =    0.901
peak=    3.815 closest distance to " O   HOH Z 346 " =    1.616
peak=    3.813 closest distance to " CG2 VAL A 257 " =    0.901
peak=    3.812 closest distance to " CD ALYS A 290 " =    1.043
peak=    3.798 closest distance to " O   HOH Z 423 " =    1.747
peak=    3.797 closest distance to " O   HOH Z 359 " =    1.528
peak=    3.794 closest distance to " N   ASN A  39 " =    1.248
peak=    3.790 closest distance to " O   HOH Z 214 " =    2.245
peak=    3.790 closest distance to " CD1 LEU A  96 " =    0.735
peak=    3.785 closest distance to " O   HOH Z 171 " =    3.923
peak=    3.759 closest distance to " O   HOH Z 285 " =    2.505
peak=    3.754 closest distance to " O   HOH Z  19 " =    2.380
peak=    3.741 closest distance to " O   ASP A 124 " =    1.089
peak=    3.740 closest distance to " CA  SER A  87 " =    0.978
peak=    3.739 closest distance to " CZ  PHE A  38 " =    1.175
peak=    3.739 closest distance to " CZ3 TRP A 266 " =    1.134
peak=    3.734 closest distance to " CB  ALA A   9 " =    1.615
peak=    3.734 closest distance to " CB  PRO A  54 " =    0.817
peak=    3.733 closest distance to " CG1 VAL A 153 " =    1.000
peak=    3.725 closest distance to " O   HOH Z  21 " =    1.774
peak=    3.724 closest distance to " N   PHE A 130 " =    1.223
peak=    3.723 closest distance to " CB  THR A  82 " =    1.377
peak=    3.722 closest distance to " CA  ARG A  36 " =    1.163
peak=    3.717 closest distance to " CA  THR A 264 " =    0.734
peak=    3.712 closest distance to " O   HOH Z  61 " =    1.691
peak=    3.712 closest distance to " CG2 THR A 221 " =    1.061
peak=    3.704 closest distance to " O   HOH Z 403 " =    1.635
peak=    3.704 closest distance to " O   HOH Z 193 " =    2.127
peak=    3.698 closest distance to " CB  LEU A 143 " =    1.224
peak=    3.693 closest distance to " O   HOH Z 272 " =    1.894
peak=    3.686 closest distance to " O   HOH Z 290 " =    1.140
peak=    3.682 closest distance to " CB  ALA A 291 " =    1.232
peak=    3.677 closest distance to " NE2 HIS A 207 " =    1.200
peak=    3.664 closest distance to " O   HOH Z 280 " =    2.969
peak=    3.654 closest distance to " CG1 ILE A 151 " =    1.115
peak=    3.651 closest distance to " O   MET A 105 " =    1.789
peak=    3.641 closest distance to " O   HOH Z 155 " =    3.458
peak=    3.635 closest distance to " CG  LEU A 167 " =    1.182
peak=    3.635 closest distance to " O   HOH Z 313 " =    1.756
peak=    3.635 closest distance to " CG1 ILE A  49 " =    1.534
peak=    3.630 closest distance to " O   HOH Z  44 " =    2.106
peak=    3.630 closest distance to " O   HOH Z  80 " =    1.801
peak=    3.627 closest distance to " OG BSER A 164 " =    2.212
peak=    3.625 closest distance to " CE  LYS A  76 " =    0.858
peak=    3.624 closest distance to " CB  ASN A 187 " =    1.139
peak=    3.624 closest distance to " CB  LEU A 228 " =    1.205
peak=    3.624 closest distance to " CB AVAL A  41 " =    1.282
peak=    3.612 closest distance to " O  BHOH Z  74 " =    1.283
peak=    3.606 closest distance to " CB  SER A   3 " =    1.395
peak=    3.601 closest distance to " O   HOH Z 422 " =    2.706
peak=    3.601 closest distance to " CD  ARG A  66 " =    2.443
peak=    3.598 closest distance to " CD1 LEU A 300 " =    1.171
peak=    3.586 closest distance to " O   HOH Z 227 " =    1.752
peak=    3.585 closest distance to " O   HOH Z 402 " =    1.478
peak=    3.583 closest distance to " CB  LEU A  83 " =    0.780
peak=    3.582 closest distance to " CA  MET A 105 " =    0.989
peak=    3.577 closest distance to " CB  GLN A  89 " =    1.200
peak=    3.573 closest distance to " CB  MET A  40 " =    0.800
peak=    3.568 closest distance to " N   SER A 135 " =    1.470
peak=    3.564 closest distance to " CA  ALA A  21 " =    1.144
peak=    3.562 closest distance to " CA  VAL A 125 " =    1.214
peak=    3.561 closest distance to " O  BHOH Z 338 " =    2.374
peak=    3.554 closest distance to " CA  TYR A  30 " =    1.079
peak=    3.554 closest distance to " O   HOH Z 368 " =    3.560
peak=    3.552 closest distance to " CB  ARG A  79 " =    0.940
peak=    3.551 closest distance to " CD1 LEU A   5 " =    1.340
peak=    3.551 closest distance to " O   HOH Z 406 " =    1.543
peak=    3.550 closest distance to " CA  ASN A 215 " =    1.192
peak=    3.547 closest distance to " CG1 ILE A  33 " =    1.306
peak=    3.543 closest distance to " CB  SER A 210 " =    0.867
peak=    3.533 closest distance to " CE1 TYR A 186 " =    1.282
peak=    3.515 closest distance to " CB  SER A 212 " =    1.276
peak=    3.513 closest distance to " O   HOH Z 180 " =    2.157
peak=    3.510 closest distance to " CB  LYS A 117 " =    1.215
peak=    3.507 closest distance to " O   HOH Z 248 " =    1.647
peak=    3.506 closest distance to " O   HOH Z   9 " =    2.033
peak=    3.505 closest distance to " O   HOH Z 102 " =    1.333
peak=    3.500 closest distance to " O   HOH Z 353 " =    2.602
peak=    3.494 closest distance to " O   HOH Z  48 " =    1.668
peak=    3.494 closest distance to " O   HOH Z  78 " =    2.247
peak=    3.491 closest distance to " O   HOH Z 291 " =    1.616
peak=    3.478 closest distance to " CD1 ILE A 199 " =    0.849
peak=    3.477 closest distance to " CB  ASN A 110 " =    1.165
peak=    3.473 closest distance to " O   PRO A 213 " =    1.558
peak=    3.470 closest distance to " CG  PHE A 204 " =    0.940
peak=    3.462 closest distance to " O   HOH Z 273 " =    2.877
peak=    3.459 closest distance to " CG  MET A 185 " =    1.009
peak=    3.457 closest distance to " CA  LYS A 117 " =    1.253
peak=    3.452 closest distance to " O   HOH Z 238 " =    2.331
peak=    3.445 closest distance to " CB  SER A 216 " =    0.838
peak=    3.443 closest distance to " CB  ALA A 242 " =    0.809
peak=    3.439 closest distance to " O   HOH Z 247 " =    1.422
peak=    3.437 closest distance to " O   HOH Z  88 " =    3.200
peak=    3.436 closest distance to " CB  ILE A 120 " =    1.344
peak=    3.434 closest distance to " CG  ARG A 269 " =    1.770
peak=    3.433 closest distance to " CA  VAL A  41 " =    0.815
peak=    3.429 closest distance to " O   ALA A 165 " =    1.499
peak=    3.427 closest distance to " CA  ALA A 291 " =    0.904
peak=    3.425 closest distance to " CG  GLU A  37 " =    0.856
peak=    3.411 closest distance to " O   HOH Z  68 " =    2.029
peak=    3.409 closest distance to " ND2 ASN A 249 " =    0.856
peak=    3.408 closest distance to " CA  ALA A 158 " =    1.200
peak=    3.400 closest distance to " CB  TRP A 179 " =    1.499
peak=    3.398 closest distance to " CB  MET A  47 " =    0.997
peak=    3.396 closest distance to " O   HOH Z 437 " =    1.524
peak=    3.393 closest distance to " CB  ALA A  34 " =    0.934
peak=    3.392 closest distance to " CB  SER A 273 " =    0.926
peak=    3.391 closest distance to " O   HOH Z 213 " =    1.918
peak=    3.391 closest distance to " CA  ALA A 154 " =    1.004
peak=    3.391 closest distance to " CA  GLY A 211 " =    1.373
peak=    3.391 closest distance to " CB  PRO A 243 " =    1.411
peak=    3.390 closest distance to " CA  LEU A 282 " =    1.023
peak=    3.388 closest distance to " O   HOH Z 403 " =    1.433
peak=    3.381 closest distance to " CB  THR A  31 " =    1.627
peak=    3.381 closest distance to " CD2 LEU A   5 " =    0.724
peak=    3.380 closest distance to " CG2AVAL A  72 " =    1.827
peak=    3.376 closest distance to " CB  TRP A 150 " =    1.394
peak=    3.370 closest distance to " CG2 ILE A 263 " =    0.974
peak=    3.370 closest distance to " NH2 ARG A 156 " =    1.049
peak=    3.368 closest distance to " O   GLN A  88 " =    1.635
peak=    3.366 closest distance to " O   HOH Z 172 " =    3.741
peak=    3.366 closest distance to " O   HOH Z 109 " =    2.735
peak=    3.364 closest distance to " CZ3 TRP A 274 " =    4.650
peak=    3.364 closest distance to " ND1 HIS A  81 " =    1.687
peak=    3.363 closest distance to " CA  MET A  40 " =    1.214
peak=    3.362 closest distance to " CD2 TRP A 179 " =    1.314
peak=    3.361 closest distance to " O   HOH Z 128 " =    2.196
peak=    3.358 closest distance to " O   HOH Z 193 " =    1.721
peak=    3.353 closest distance to " O   HOH Z 166 " =    3.758
peak=    3.353 closest distance to " O   HOH Z  10 " =    1.791
peak=    3.352 closest distance to " C   ALA A 299 " =    0.940
peak=    3.350 closest distance to " CG  GLN A  88 " =    1.082
peak=    3.350 closest distance to " CA  LYS A 181 " =    1.085
peak=    3.348 closest distance to " CB  HIS A 108 " =    0.807
peak=    3.347 closest distance to " CA  THR A 221 " =    0.923
peak=    3.343 closest distance to " O   THR A 220 " =    1.196
peak=    3.343 closest distance to " CB  GLN A 103 " =    1.076
peak=    3.340 closest distance to " CG BARG A 102 " =    1.864
peak=    3.337 closest distance to " O   HOH Z 313 " =    1.688
peak=    3.337 closest distance to " CG BARG A 275 " =    1.498
peak=    3.337 closest distance to " N   VAL A 126 " =    1.312
peak=    3.336 closest distance to " O   HOH Z 215 " =    2.955
peak=    3.328 closest distance to " NZ  LYS A 117 " =    3.235
peak=    3.323 closest distance to " O   TYR A 116 " =    1.311
peak=    3.320 closest distance to " O   PHE A  61 " =    1.372
peak=    3.319 closest distance to " O   HOH Z 147 " =    1.771
peak=    3.319 closest distance to " O   HOH Z 112 " =    1.634
peak=    3.317 closest distance to " CA  ILE A 106 " =    0.754
peak=    3.313 closest distance to " O   HOH Z  20 " =    1.635
peak=    3.306 closest distance to " CB  PRO A  90 " =    1.284
peak=    3.305 closest distance to " O   ASN A  74 " =    1.518
peak=    3.303 closest distance to " CB  ALA A 248 " =    1.143
peak=    3.303 closest distance to " O   HOH Z 141 " =    1.740
peak=    3.302 closest distance to " CG  ARG A 138 " =    1.141
peak=    3.300 closest distance to " O   HOH Z   9 " =    1.301
peak=    3.295 closest distance to " O   GLN A 278 " =    1.370
peak=    3.294 closest distance to " CA  ASN A 217 " =    1.325
peak=    3.293 closest distance to " CA  GLU A 152 " =    0.906
peak=    3.292 closest distance to " O   ALA A 158 " =    1.430
peak=    3.291 closest distance to " O   HOH Z 294 " =    1.559
peak=    3.291 closest distance to " O   HOH Z  63 " =    1.859
peak=    3.290 closest distance to " O   TRP A 274 " =    1.810
peak=    3.278 closest distance to " CA  TYR A 116 " =    1.495
peak=    3.276 closest distance to " CZ3 TRP A  85 " =    1.053
peak=    3.276 closest distance to " CB  ALA A 227 " =    1.046
peak=    3.276 closest distance to " O   HOH Z 365 " =    2.983
peak=    3.275 closest distance to " O   HOH Z 130 " =    2.245
peak=    3.269 closest distance to " O   HOH Z 325 " =    2.333
peak=    3.267 closest distance to " CB  ALA A 114 " =    1.137
peak=    3.267 closest distance to " O   HOH Z 371 " =    3.003
peak=    3.263 closest distance to " CB  ALA A 248 " =    1.360
peak=    3.260 closest distance to " O   HOH Z 145 " =    1.821
peak=    3.256 closest distance to " CB  ARG A 145 " =    0.815
peak=    3.255 closest distance to " CE2 TYR A  30 " =    0.818
peak=    3.253 closest distance to " CB  ASN A 173 " =    1.052
peak=    3.251 closest distance to " NZ  LYS A  48 " =    1.390
peak=    3.251 closest distance to " CA  ASN A 127 " =    1.064
peak=    3.250 closest distance to " CB  TYR A 116 " =    0.873
peak=    3.249 closest distance to " CE3 TRP A 150 " =    1.071
peak=    3.246 closest distance to " O   HOH Z 193 " =    1.958
peak=    3.245 closest distance to " O   HOH Z 327 " =    2.300
peak=    3.245 closest distance to " OG  SER A 276 " =    1.319
peak=    3.244 closest distance to " O   GLU A   2 " =    1.545
peak=    3.244 closest distance to " NH1 ARG A 138 " =    1.137
peak=    3.238 closest distance to " CG2 THR A 220 " =    0.888
peak=    3.237 closest distance to " CB  GLN A  88 " =    1.246
peak=    3.235 closest distance to " CB  VAL A 268 " =    0.852
peak=    3.235 closest distance to " O   HOH Z 187 " =    2.362
peak=    3.234 closest distance to " O   HOH Z 435 " =    2.024
peak=    3.232 closest distance to " CA  LYS A 290 " =    1.185
peak=    3.229 closest distance to " O   HOH Z 197 " =    2.883
peak=    3.227 closest distance to " O   HOH Z 258 " =    2.094
peak=    3.226 closest distance to " CH2 TRP A  70 " =    1.032
peak=    3.222 closest distance to " CB  TYR A 247 " =    1.014
peak=    3.221 closest distance to " O   THR A 251 " =    1.219
peak=    3.218 closest distance to " O   HOH Z  97 " =    2.156
peak=    3.217 closest distance to " O   HOH Z 201 " =    2.939
peak=    3.215 closest distance to " CA  ALA A 160 " =    0.980
peak=    3.210 closest distance to " CA  ARG A 102 " =    1.240
peak=    3.210 closest distance to " CA  ASP A 191 " =    0.824
peak=    3.209 closest distance to " OG  SER A  22 " =    2.852
peak=    3.202 closest distance to " O   HOH Z 384 " =    3.133
peak=    3.200 closest distance to " O   HOH Z 185 " =    1.982
peak=    3.195 closest distance to " O   HOH Z  40 " =    1.681
peak=    3.191 closest distance to " CB  ALA A  43 " =    0.886
peak=    3.189 closest distance to " O   HOH Z 359 " =    4.270
peak=    3.188 closest distance to " CD  ARG A 219 " =    1.090
peak=    3.187 closest distance to " NE  ARG A  79 " =    1.198
peak=    3.186 closest distance to " OG  SER A  62 " =    2.973
peak=    3.182 closest distance to " O   HOH Z 261 " =    1.577
peak=    3.179 closest distance to " O   HOH Z 128 " =    2.245
peak=    3.176 closest distance to " CA  GLN A  88 " =    1.417
peak=    3.168 closest distance to " CG  ARG A 159 " =    0.989
peak=    3.167 closest distance to " CB  THR A 157 " =    1.103
peak=    3.167 closest distance to " CB  LEU A  96 " =    1.312
peak=    3.166 closest distance to " O   HOH Z 203 " =    1.801
peak=    3.166 closest distance to " N   TYR A  15 " =    0.808
peak=    3.165 closest distance to " O   HOH Z   4 " =    1.764
peak=    3.163 closest distance to " CG ALYS A 290 " =    1.083
peak=    3.161 closest distance to " O   HOH Z 134 " =    2.713
peak=    3.161 closest distance to " N   ALA A 256 " =    1.143
peak=    3.160 closest distance to " O   HOH Z 163 " =    1.605
peak=    3.159 closest distance to " CB  ALA A 137 " =    1.096
peak=    3.157 closest distance to " O   HOH Z 245 " =    1.330
peak=    3.157 closest distance to " O   HOH Z 350 " =    1.660
peak=    3.157 closest distance to " NH1 ARG A  14 " =    0.930
peak=    3.156 closest distance to " OH  TYR A 214 " =    1.259
peak=    3.153 closest distance to " N   ASN A 127 " =    1.202
peak=    3.151 closest distance to " O   HOH Z 133 " =    2.513
peak=    3.147 closest distance to " CB  LEU A 300 " =    0.851
peak=    3.144 closest distance to " CA  ASP A 162 " =    0.969
peak=    3.142 closest distance to " CA  ARG A 139 " =    1.084
peak=    3.140 closest distance to " N   GLY A  98 " =    1.136
peak=    3.140 closest distance to " O   HOH Z 188 " =    1.915
peak=    3.138 closest distance to " CA  VAL A 112 " =    1.116
peak=    3.135 closest distance to " O   HOH Z 302 " =    1.976
peak=    3.134 closest distance to " CB  ASN A 215 " =    1.228
peak=    3.132 closest distance to " O   HOH Z 305 " =    3.675
peak=    3.131 closest distance to " NH2AARG A 145 " =    1.305
peak=    3.130 closest distance to " OG BSER A 134 " =    2.890
peak=    3.129 closest distance to " O   THR A 182 " =    1.361
peak=    3.126 closest distance to " O   HOH Z 162 " =    4.094
peak=    3.126 closest distance to " CA  ALA A 233 " =    1.577
peak=    3.123 closest distance to " NH2AARG A 275 " =    3.496
peak=    3.122 closest distance to " CG2 ILE A 120 " =    1.003
peak=    3.115 closest distance to " OE2 GLU A  53 " =    1.931
peak=    3.113 closest distance to " O   HOH Z 215 " =    1.434
peak=    3.111 closest distance to " O   HOH Z 295 " =    1.505
peak=    3.108 closest distance to " O   HOH Z 391 " =    3.014
peak=    3.099 closest distance to " O   HOH Z  59 " =    2.209
peak=    3.092 closest distance to " CB  ALA A   1 " =    4.836
peak=    3.091 closest distance to " CD1 LEU A 281 " =    1.076
peak=    3.086 closest distance to " CE2 PHE A  16 " =    0.937
peak=    3.082 closest distance to " CD1 ILE A 106 " =    0.941
peak=    3.081 closest distance to " O   HOH Z 329 " =    4.110
peak=    3.070 closest distance to " O   ALA A 292 " =    1.737
peak=    3.067 closest distance to " N   GLN A 278 " =    1.125
peak=    3.064 closest distance to " OE2 GLU A   2 " =    1.917
peak=    3.064 closest distance to " O   ASN A 209 " =    1.337
peak=    3.059 closest distance to " CB  VAL A 257 " =    0.739
peak=    3.058 closest distance to " OD1 ASN A 217 " =    1.617
peak=    3.035 closest distance to " N   ASP A 162 " =    1.255
peak=    3.027 closest distance to " O   GLY A  91 " =    1.198
peak=    3.013 closest distance to " CG1 ILE A  20 " =    1.266
peak=    3.008 closest distance to " N   GLY A 133 " =    3.774

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 218         
Filter by distance & map next to the model:
   mapped sites are within: 0.618 - 5.524
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 217 from: 218
   mapped sites are within: 0.738 - 5.524

peak=   -5.165 closest distance to " CG2 VAL A 230 " =    0.803
peak=   -4.672 closest distance to " CG1 VAL A 296 " =    1.150
peak=   -4.560 closest distance to " CG1 VAL A 112 " =    2.664
peak=   -4.442 closest distance to " CD  GLN A  58 " =    0.957
peak=   -4.307 closest distance to " CB  PRO A 243 " =    2.707
peak=   -4.302 closest distance to " CD  ARG A  14 " =    3.285
peak=   -4.289 closest distance to " CD  ARG A 156 " =    2.085
peak=   -4.209 closest distance to " O   HOH Z 211 " =    1.129
peak=   -4.100 closest distance to " O   HOH Z  73 " =    2.266
peak=   -4.068 closest distance to " OE1 GLN A 223 " =    2.145
peak=   -4.024 closest distance to " O   HOH Z 411 " =    5.524
peak=   -3.996 closest distance to " O   HOH Z 166 " =    1.903
peak=   -3.966 closest distance to " O   HOH Z 196 " =    2.300
peak=   -3.947 closest distance to " CG2 ILE A  49 " =    2.819
peak=   -3.915 closest distance to " O   ILE A 109 " =    2.594
peak=   -3.902 closest distance to " CZ3 TRP A 179 " =    1.169
peak=   -3.895 closest distance to " O   VAL A  67 " =    2.725
peak=   -3.881 closest distance to " CG1 VAL A 250 " =    2.783
peak=   -3.869 closest distance to " O   HOH Z 351 " =    1.538
peak=   -3.855 closest distance to " O   HOH Z 231 " =    2.109
peak=   -3.854 closest distance to " O   HOH Z 394 " =    1.605
peak=   -3.839 closest distance to " CA  GLY A 241 " =    3.174
peak=   -3.818 closest distance to " NH2AARG A 275 " =    5.369
peak=   -3.803 closest distance to " CE2 TYR A  30 " =    2.733
peak=   -3.803 closest distance to " CA  ASP A 298 " =    1.050
peak=   -3.795 closest distance to " OG  SER A  97 " =    2.351
peak=   -3.780 closest distance to " N   ALA A  43 " =    2.497
peak=   -3.763 closest distance to " CG  ARG A 269 " =    2.445
peak=   -3.760 closest distance to " OE1 GLN A  88 " =    0.955
peak=   -3.756 closest distance to " C   HIS A 108 " =    1.123
peak=   -3.737 closest distance to " CG1 VAL A 112 " =    2.920
peak=   -3.734 closest distance to " CG  HIS A  86 " =    1.124
peak=   -3.733 closest distance to " O   HOH Z  52 " =    1.614
peak=   -3.720 closest distance to " C   ALA A 158 " =    1.346
peak=   -3.704 closest distance to " O   HOH Z 290 " =    1.294
peak=   -3.695 closest distance to " O   VAL A 189 " =    2.603
peak=   -3.693 closest distance to " O   SER A 271 " =    2.262
peak=   -3.691 closest distance to " CG  ASP A 231 " =    0.777
peak=   -3.686 closest distance to " CA  GLY A 241 " =    2.342
peak=   -3.679 closest distance to " O   HOH Z  10 " =    1.553
peak=   -3.671 closest distance to " O   HOH Z  37 " =    1.947
peak=   -3.668 closest distance to " O   HOH Z 216 " =    1.325
peak=   -3.651 closest distance to " CE3 TRP A 150 " =    2.181
peak=   -3.644 closest distance to " N   THR A  18 " =    1.316
peak=   -3.636 closest distance to " OD1 ASN A 148 " =    1.395
peak=   -3.636 closest distance to " CB  PHE A 192 " =    2.008
peak=   -3.625 closest distance to " O   VAL A  67 " =    2.709
peak=   -3.601 closest distance to " O   HOH Z 177 " =    1.817
peak=   -3.595 closest distance to " O   HOH Z  38 " =    1.465
peak=   -3.594 closest distance to " O   HOH Z 435 " =    2.796
peak=   -3.592 closest distance to " CD2 TYR A 293 " =    1.975
peak=   -3.566 closest distance to " CD1 LEU A   5 " =    2.576
peak=   -3.553 closest distance to " O   HOH Z 185 " =    2.444
peak=   -3.547 closest distance to " O   HOH Z  11 " =    1.795
peak=   -3.534 closest distance to " O   GLY A 203 " =    2.344
peak=   -3.530 closest distance to " CE BMET A  47 " =    1.824
peak=   -3.528 closest distance to " O   PRO A 198 " =    1.229
peak=   -3.523 closest distance to " N   ALA A 226 " =    2.221
peak=   -3.523 closest distance to " CG  GLU A 277 " =    1.216
peak=   -3.516 closest distance to " CB  VAL A 230 " =    1.088
peak=   -3.515 closest distance to " O   HOH Z 241 " =    1.253
peak=   -3.514 closest distance to " CD2 PHE A  61 " =    2.595
peak=   -3.513 closest distance to " NE2 GLN A 194 " =    1.894
peak=   -3.501 closest distance to " O   GLY A 211 " =    1.397
peak=   -3.485 closest distance to " OG BSER A 134 " =    1.343
peak=   -3.485 closest distance to " CB  ALA A 248 " =    2.402
peak=   -3.476 closest distance to " O   ASP A  27 " =    2.074
peak=   -3.474 closest distance to " OXT GLY A 302 " =    3.058
peak=   -3.474 closest distance to " C   MET A 188 " =    1.352
peak=   -3.467 closest distance to " O   HOH Z 176 " =    0.738
peak=   -3.463 closest distance to " O   HOH Z  44 " =    2.261
peak=   -3.460 closest distance to " CG2 VAL A 296 " =    1.282
peak=   -3.449 closest distance to " C   LEU A 143 " =    1.083
peak=   -3.449 closest distance to " CB  ALA A 248 " =    2.160
peak=   -3.446 closest distance to " NH2 ARG A  79 " =    1.547
peak=   -3.441 closest distance to " CA  GLY A 203 " =    2.500
peak=   -3.439 closest distance to " O   HOH Z 113 " =    2.410
peak=   -3.433 closest distance to " CG1 VAL A 265 " =    2.443
peak=   -3.431 closest distance to " CB  ALA A  43 " =    2.659
peak=   -3.430 closest distance to " CG  MET A 105 " =    0.995
peak=   -3.427 closest distance to " O   HOH Z 106 " =    1.918
peak=   -3.427 closest distance to " CD1 TRP A 274 " =    0.963
peak=   -3.427 closest distance to " CD2 LEU A 167 " =    1.810
peak=   -3.419 closest distance to " O   HOH Z 275 " =    1.544
peak=   -3.415 closest distance to " NE2 GLN A  88 " =    2.130
peak=   -3.414 closest distance to " O   HOH Z 426 " =    1.664
peak=   -3.413 closest distance to " OG  SER A  87 " =    1.610
peak=   -3.410 closest distance to " ND2 ASN A  45 " =    1.131
peak=   -3.402 closest distance to " CD1 LEU A 228 " =    2.407
peak=   -3.399 closest distance to " CD1 LEU A 101 " =    2.488
peak=   -3.395 closest distance to " N   THR A  52 " =    1.595
peak=   -3.393 closest distance to " O   HOH Z 128 " =    2.625
peak=   -3.390 closest distance to " O   HOH Z 389 " =    1.998
peak=   -3.386 closest distance to " O   HOH Z 407 " =    3.213
peak=   -3.382 closest distance to " CG1 VAL A  67 " =    2.817
peak=   -3.382 closest distance to " O   GLY A 196 " =    1.285
peak=   -3.375 closest distance to " CG  TRP A 266 " =    1.847
peak=   -3.372 closest distance to " CD  GLN A 223 " =    1.246
peak=   -3.371 closest distance to " O   HOH Z 222 " =    1.612
peak=   -3.367 closest distance to " O   TYR A 247 " =    2.921
peak=   -3.367 closest distance to " CD  PRO A 213 " =    2.180
peak=   -3.366 closest distance to " N   SER A   3 " =    2.091
peak=   -3.363 closest distance to " CG  LEU A 101 " =    2.418
peak=   -3.362 closest distance to " CE  MET A 105 " =    2.399
peak=   -3.359 closest distance to " OD2 ASP A  50 " =    2.365
peak=   -3.356 closest distance to " C   LEU A 222 " =    0.938
peak=   -3.354 closest distance to " O   PRO A 163 " =    2.225
peak=   -3.354 closest distance to " O   HOH Z 133 " =    1.300
peak=   -3.353 closest distance to " O   GLY A  80 " =    2.605
peak=   -3.348 closest distance to " N   THR A 157 " =    1.568
peak=   -3.342 closest distance to " C   PHE A  59 " =    1.285
peak=   -3.340 closest distance to " O   HOH Z 231 " =    1.412
peak=   -3.335 closest distance to " CE3 TRP A  70 " =    1.755
peak=   -3.333 closest distance to " O   HOH Z 232 " =    1.765
peak=   -3.330 closest distance to " ND2 ASN A  60 " =    1.407
peak=   -3.321 closest distance to " O   HOH Z 114 " =    3.041
peak=   -3.320 closest distance to " CA  ASN A 127 " =    1.096
peak=   -3.313 closest distance to " OG  SER A 206 " =    1.811
peak=   -3.311 closest distance to " O   HOH Z 359 " =    2.970
peak=   -3.311 closest distance to " CG1 VAL A 125 " =    1.945
peak=   -3.306 closest distance to " O   HOH Z 377 " =    1.936
peak=   -3.299 closest distance to " ND2 ASN A  45 " =    1.415
peak=   -3.297 closest distance to " O   LEU A 101 " =    2.888
peak=   -3.297 closest distance to " O   HOH Z 251 " =    4.939
peak=   -3.293 closest distance to " O   HOH Z  60 " =    2.009
peak=   -3.292 closest distance to " O   HOH Z 350 " =    1.975
peak=   -3.292 closest distance to " O   HOH Z   9 " =    1.606
peak=   -3.291 closest distance to " CA  GLY A  98 " =    2.094
peak=   -3.285 closest distance to " CB  PRO A 163 " =    2.542
peak=   -3.284 closest distance to " CG  LEU A   5 " =    1.563
peak=   -3.280 closest distance to " OD1 ASN A 249 " =    2.423
peak=   -3.273 closest distance to " CD2 LEU A 300 " =    2.765
peak=   -3.259 closest distance to " O   HOH Z 353 " =    2.066
peak=   -3.255 closest distance to " O   HOH Z 102 " =    1.624
peak=   -3.252 closest distance to " O   MET A  40 " =    2.810
peak=   -3.244 closest distance to " C   ASN A 285 " =    2.446
peak=   -3.240 closest distance to " O   HOH Z 252 " =    3.806
peak=   -3.236 closest distance to " O   ALA A   7 " =    1.485
peak=   -3.234 closest distance to " CD1 PHE A  59 " =    1.994
peak=   -3.233 closest distance to " O   HOH Z 166 " =    1.783
peak=   -3.231 closest distance to " O   HOH Z 136 " =    2.367
peak=   -3.230 closest distance to " O   HOH Z 123 " =    2.504
peak=   -3.229 closest distance to " O   HOH Z 234 " =    4.484
peak=   -3.228 closest distance to " CE  LYS A  76 " =    2.553
peak=   -3.228 closest distance to " O   HOH Z 285 " =    1.819
peak=   -3.226 closest distance to " CG2BVAL A  41 " =    1.803
peak=   -3.222 closest distance to " CA  GLY A 133 " =    2.330
peak=   -3.219 closest distance to " NH2 ARG A  66 " =    2.156
peak=   -3.219 closest distance to " N   ALA A 248 " =    1.865
peak=   -3.218 closest distance to " O   GLY A  80 " =    2.315
peak=   -3.217 closest distance to " O   HOH Z 262 " =    2.847
peak=   -3.217 closest distance to " CG2 VAL A 112 " =    2.559
peak=   -3.214 closest distance to " CG  ARG A 259 " =    2.471
peak=   -3.201 closest distance to " OD2 ASP A 171 " =    1.872
peak=   -3.199 closest distance to " CB  ALA A  10 " =    2.272
peak=   -3.195 closest distance to " O   HOH Z 174 " =    2.537
peak=   -3.193 closest distance to " OG1 THR A  82 " =    1.457
peak=   -3.191 closest distance to " O   HOH Z 431 " =    1.866
peak=   -3.188 closest distance to " CB  ASP A 132 " =    2.338
peak=   -3.188 closest distance to " CD1 ILE A 239 " =    2.112
peak=   -3.187 closest distance to " O   HOH Z  44 " =    1.107
peak=   -3.182 closest distance to " O   TYR A  30 " =    2.473
peak=   -3.181 closest distance to " O   HOH Z 290 " =    0.809
peak=   -3.179 closest distance to " O   HOH Z 390 " =    2.267
peak=   -3.179 closest distance to " CB  TRP A  85 " =    2.576
peak=   -3.178 closest distance to " CA  ALA A 248 " =    2.550
peak=   -3.178 closest distance to " NE2 GLN A  88 " =    1.033
peak=   -3.178 closest distance to " CB  VAL A 296 " =    1.321
peak=   -3.177 closest distance to " CD1 ILE A 151 " =    2.448
peak=   -3.176 closest distance to " O   HOH Z  19 " =    2.241
peak=   -3.174 closest distance to " CG2 THR A 178 " =    2.220
peak=   -3.172 closest distance to " NE2 GLN A 103 " =    1.842
peak=   -3.170 closest distance to " N   SER A 276 " =    1.403
peak=   -3.166 closest distance to " CA  SER A 135 " =    1.312
peak=   -3.166 closest distance to " O   HOH Z 265 " =    2.445
peak=   -3.163 closest distance to " O   HOH Z  13 " =    1.525
peak=   -3.163 closest distance to " O   HOH Z 377 " =    1.368
peak=   -3.161 closest distance to " CD1 TYR A 247 " =    2.302
peak=   -3.158 closest distance to " O   HOH Z 393 " =    1.390
peak=   -3.158 closest distance to " C   ASN A 187 " =    1.871
peak=   -3.157 closest distance to " CG  PRO A 163 " =    2.421
peak=   -3.154 closest distance to " ND2 ASN A  69 " =    1.893
peak=   -3.146 closest distance to " CB  ASN A  69 " =    1.356
peak=   -3.145 closest distance to " C   ALA A 165 " =    1.968
peak=   -3.144 closest distance to " NH2 ARG A  79 " =    2.101
peak=   -3.142 closest distance to " OH  TYR A 247 " =    1.834
peak=   -3.141 closest distance to " CG1 VAL A 197 " =    2.290
peak=   -3.140 closest distance to " O   HOH Z   6 " =    1.584
peak=   -3.140 closest distance to " CG2 VAL A 230 " =    2.675
peak=   -3.139 closest distance to " NH2 ARG A  36 " =    2.363
peak=   -3.135 closest distance to " CG2 VAL A 189 " =    2.095
peak=   -3.134 closest distance to " O   HOH Z  43 " =    1.720
peak=   -3.133 closest distance to " CB  GLN A  11 " =    1.587
peak=   -3.131 closest distance to " O   HOH Z 191 " =    3.345
peak=   -3.126 closest distance to " O   HOH Z  17 " =    1.558
peak=   -3.120 closest distance to " CB  ALA A 291 " =    2.311
peak=   -3.119 closest distance to " CD  GLN A  88 " =    0.861
peak=   -3.113 closest distance to " OG  SER A  63 " =    1.199
peak=   -3.108 closest distance to " ND2 ASN A 187 " =    1.639
peak=   -3.103 closest distance to " C   GLY A  13 " =    0.938
peak=   -3.098 closest distance to " CB  ASN A 252 " =    1.564
peak=   -3.081 closest distance to " OD1 ASN A 173 " =    1.332
peak=   -3.077 closest distance to " CD1 ILE A 199 " =    2.655
peak=   -3.077 closest distance to " O   HOH Z 317 " =    2.195
peak=   -3.073 closest distance to " O   HOH Z 396 " =    2.133
peak=   -3.070 closest distance to " CG1 VAL A 112 " =    2.872
peak=   -3.064 closest distance to " C   ASP A 270 " =    1.177
peak=   -3.061 closest distance to " CD  PRO A 243 " =    2.058
peak=   -3.055 closest distance to " O   HOH Z 265 " =    1.887
peak=   -3.052 closest distance to " O   HOH Z 200 " =    4.436
peak=   -3.050 closest distance to " O   HOH Z 184 " =    1.592
peak=   -3.042 closest distance to " CD2 TYR A 247 " =    2.299
peak=   -3.042 closest distance to " NE2 GLN A 194 " =    1.991
peak=   -3.041 closest distance to " CA  ARG A 139 " =    1.039
peak=   -3.026 closest distance to " O   HOH Z 326 " =    5.036
peak=   -3.024 closest distance to " CG  ARG A 269 " =    2.060
peak=   -3.021 closest distance to " O   HOH Z 111 " =    2.463

================= 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    :  0.4578 0.4479   6.257010e+00   6.232317e+00
   1_bss:  0.4497 0.4329   6.250945e+00   6.222299e+00
   1_xyz:  0.3458 0.3709   6.078544e+00   6.120815e+00
   1_adp:  0.2946 0.3358   5.950976e+00   6.050004e+00
   1_occ:  0.2940 0.3370   5.950068e+00   6.051786e+00
   2_bss:  0.2917 0.3335   5.951035e+00   6.050169e+00
   2_xyz:  0.1928 0.2387   5.594229e+00   5.765457e+00
   2_adp:  0.1722 0.2201   5.499161e+00   5.690234e+00
   2_occ:  0.1720 0.2202   5.498454e+00   5.690057e+00
   3_bss:  0.1708 0.2189   5.499610e+00   5.690596e+00
   3_xyz:  0.1347 0.1812   5.294650e+00   5.518262e+00
   3_adp:  0.1253 0.1743   5.244558e+00   5.484338e+00
   3_occ:  0.1252 0.1743   5.244282e+00   5.484168e+00
   4_bss:  0.1253 0.1741   5.243509e+00   5.482808e+00
   4_xyz:  0.1156 0.1669   5.189142e+00   5.443267e+00
   4_adp:  0.1152 0.1635   5.177870e+00   5.423801e+00
   4_occ:  0.1151 0.1634   5.177227e+00   5.423354e+00
   5_bss:  0.1151 0.1634   5.177227e+00   5.423354e+00
   5_xyz:  0.1190 0.1658   5.200973e+00   5.436342e+00
   5_adp:  0.1186 0.1662   5.201900e+00   5.440670e+00
   5_occ:  0.1184 0.1664   5.200839e+00   5.439938e+00
   5_bss:  0.1184 0.1663   5.200584e+00   5.439827e+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:  0.328  46.053   7.853   7.272   9.954   0.000   0.000   0.000
   1_xyz:  0.328  46.053   7.853   7.272   9.954   0.000   0.000   0.000
   1_adp:  0.328  46.053   7.853   7.272   9.954   0.000   0.000   0.000
   1_occ:  0.328  46.053   7.853   7.272   9.954   0.000   0.000   0.000
   2_bss:  0.313  49.937   4.937   4.583   6.747   0.000   0.000   0.000
   2_xyz:  0.313  49.937   4.937   4.583   6.747   0.000   0.000   0.000
   2_adp:  0.313  49.937   4.937   4.583   6.747   0.000   0.000   0.000
   2_occ:  0.313  49.937   4.937   4.583   6.747   0.000   0.000   0.000
   3_bss:  0.336  65.769   3.521   3.491   4.929   0.000   0.000   0.000
   3_xyz:  0.336  65.769   3.521   3.491   4.929   0.000   0.000   0.000
   3_adp:  0.336  65.769   3.521   3.491   4.929   0.000   0.000   0.000
   3_occ:  0.336  65.769   3.521   3.491   4.929   0.000   0.000   0.000
   4_bss:  0.336  65.769   3.152   3.190   4.539   0.000   0.000   0.000
   4_xyz:  0.336  65.769   3.152   3.190   4.539   0.000   0.000   0.000
   4_adp:  0.336  65.769   3.152   3.190   4.539   0.000   0.000   0.000
   4_occ:  0.336  65.769   3.152   3.190   4.539   0.000   0.000   0.000
   5_bss:  0.336  65.769   3.152   3.190   4.539   0.000   0.000   0.000
   5_xyz:  0.336  65.769   3.152   3.190   4.539   0.000   0.000   0.000
   5_adp:  0.336  65.769   3.152   3.190   4.539   0.000   0.000   0.000
   5_occ:  0.336  65.769   3.152   3.190   4.539   0.000   0.000   0.000
   5_bss:  0.322  61.825  -0.475  -0.437   0.912   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  50.779 0.5116  0.5685    57524.545
   1_bss:  49.953 0.5212  0.7456    55579.205
   1_xyz:  41.325 0.6258  0.8650    38484.390
   1_adp:  35.681 0.6936  0.9541    30766.768
   1_occ:  35.756 0.6926  0.9519    30872.687
   2_bss:  35.632 0.6939  0.8592    30697.378
   2_xyz:  23.577 0.8258  0.9885    14520.720
   2_adp:  21.030 0.8521  1.0033    12257.512
   2_occ:  21.034 0.8520  1.0030    12248.470
   3_bss:  21.048 0.8520  0.9522    12312.580
   3_xyz:  16.764 0.8917  0.9756     8386.725
   3_adp:  15.972 0.8987  0.9756     7755.541
   3_occ:  15.969 0.8988  0.9755     7753.243
   4_bss:  15.947 0.8989  0.9629     7722.852
   4_xyz:  15.013 0.9070  0.9666     7066.662
   4_adp:  14.576 0.9108  0.9655     6822.993
   4_occ:  14.565 0.9108  0.9655     6816.183
   5_bss:  14.565 0.9108  0.9655     6816.183
   5_xyz:  14.773 0.9094  0.9638     6995.852
   5_adp:  14.875 0.9086  0.9599     7048.241
   5_occ:  14.865 0.9086  0.9597     7041.520
   5_bss:  14.866 0.9086  0.9596     7033.712
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.093   5.4474e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.093   5.4474e+01
   1_xyz:   1.667  0.013  0.108 18.077  0.006  4.113   1.3777e-01
   1_adp:   1.667  0.013  0.108 18.077  0.006  4.113   1.3777e-01
   1_occ:   1.667  0.013  0.108 18.077  0.006  4.113   1.3777e-01
   2_bss:   1.667  0.013  0.108 18.077  0.006  4.113   1.3777e-01
   2_xyz:   1.138  0.009  0.078 16.704  0.005  4.136   8.0776e-02
   2_adp:   1.138  0.009  0.078 16.704  0.005  4.136   8.0776e-02
   2_occ:   1.138  0.009  0.078 16.704  0.005  4.136   8.0776e-02
   3_bss:   1.138  0.009  0.078 16.704  0.005  4.136   8.0776e-02
   3_xyz:   1.160  0.010  0.088 16.202  0.004  4.137   8.1747e-02
   3_adp:   1.160  0.010  0.088 16.202  0.004  4.137   8.1747e-02
   3_occ:   1.160  0.010  0.088 16.202  0.004  4.137   8.1747e-02
   4_bss:   1.160  0.010  0.088 16.202  0.004  4.137   8.1747e-02
   4_xyz:   1.203  0.012  0.095 16.090  0.004  4.132   9.0424e-02
   4_adp:   1.203  0.012  0.095 16.090  0.004  4.132   9.0424e-02
   4_occ:   1.203  0.012  0.095 16.090  0.004  4.132   9.0424e-02
   5_bss:   1.203  0.012  0.095 16.090  0.004  4.132   9.0424e-02
   5_xyz:   1.013  0.009  0.080 15.662  0.004  4.127   6.4981e-02
   5_adp:   1.013  0.009  0.080 15.662  0.004  4.127   6.4981e-02
   5_occ:   1.013  0.009  0.080 15.662  0.004  4.127   6.4981e-02
   5_bss:   1.013  0.009  0.080 15.662  0.004  4.127   6.4981e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0635e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0635e+00
   1_xyz:  13.942  0.159  0.437 85.298  0.037  2.301   1.0494e-01
   1_adp:  13.942  0.159  0.437 85.298  0.037  2.301   1.0494e-01
   1_occ:  13.942  0.159  0.437 85.298  0.037  2.301   1.0494e-01
   2_bss:  13.942  0.159  0.437 85.298  0.037  2.301   1.0494e-01
   2_xyz:   7.211  0.093  0.252 87.042  0.036  2.308   1.0826e-01
   2_adp:   7.211  0.093  0.252 87.042  0.036  2.308   1.0826e-01
   2_occ:   7.211  0.093  0.252 87.042  0.036  2.308   1.0826e-01
   3_bss:   7.211  0.093  0.252 87.042  0.036  2.308   1.0826e-01
   3_xyz:   7.403  0.065  0.452 83.389  0.041  2.365   7.9787e-02
   3_adp:   7.403  0.065  0.452 83.389  0.041  2.365   7.9787e-02
   3_occ:   7.403  0.065  0.452 83.389  0.041  2.365   7.9787e-02
   4_bss:   7.403  0.065  0.452 83.389  0.041  2.365   7.9787e-02
   4_xyz:   7.798  0.053  0.576 82.777  0.042  2.319   6.2548e-02
   4_adp:   7.798  0.053  0.576 82.777  0.042  2.319   6.2548e-02
   4_occ:   7.798  0.053  0.576 82.777  0.042  2.319   6.2548e-02
   5_bss:   7.798  0.053  0.576 82.777  0.042  2.319   6.2548e-02
   5_xyz:   7.904  0.048  0.391 81.718  0.039  2.402   3.8588e-02
   5_adp:   7.904  0.048  0.391 81.718  0.039  2.402   3.8588e-02
   5_occ:   7.904  0.048  0.391 81.718  0.039  2.402   3.8588e-02
   5_bss:   7.904  0.048  0.391 81.718  0.039  2.402   3.8588e-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:  76.94   0.00  11.15  61.14   0.00   8.17  76.94   0.00  27.36
   1_occ:  76.94   0.00  11.15  61.14   0.00   8.17  76.94   0.00  27.36
   2_bss:  76.94   0.00  11.15  61.14   0.00   8.17  76.94   0.00  27.36
   2_xyz:  76.94   0.00  11.15  61.14   0.00   8.17  76.94   0.00  27.36
   2_adp:  80.31   0.00  11.25  80.31   0.00   7.62  76.35   0.00  31.01
   2_occ:  80.31   0.00  11.25  80.31   0.00   7.62  76.35   0.00  31.01
   3_bss:  80.31   0.00  11.25  80.31   0.00   7.62  76.35   0.00  31.01
   3_xyz:  80.31   0.00  11.25  80.31   0.00   7.62  76.35   0.00  31.01
   3_adp:  81.32   0.00  12.39  78.48   0.00   7.79  81.32   0.00  37.39
   3_occ:  81.32   0.00  12.39  78.48   0.00   7.79  81.32   0.00  37.39
   4_bss:  81.32   0.00  12.39  78.48   0.00   7.79  81.32   0.00  37.39
   4_xyz:  81.32   0.00  12.39  78.48   0.00   7.79  81.32   0.00  37.39
   4_adp:  80.28   0.00  11.86  78.27   0.00   7.55  80.28   0.49  35.33
   4_occ:  80.28   0.00  11.86  78.27   0.00   7.55  80.28   0.49  35.33
   5_bss:  80.28   0.00  11.86  78.27   0.00   7.55  80.28   0.49  35.33
   5_xyz:  80.28   0.00  11.86  78.27   0.00   7.55  80.28   0.49  35.33
   5_adp:  81.82   0.00  11.84  79.74   0.00   7.55  81.82   0.58  35.21
   5_occ:  81.82   0.00  11.84  79.74   0.00   7.55  81.82   0.58  35.21
   5_bss:  85.44   3.63  15.47  83.37   3.63  11.18  85.44   4.20  38.83
------------------------------------------------------------------------
 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:    1.255    0.027    0.413
   1_adp:    1.255    0.027    0.413
   1_occ:    1.255    0.027    0.413
   2_bss:    1.255    0.027    0.413
   2_xyz:    1.577    0.026    0.563
   2_adp:    1.577    0.026    0.563
   2_occ:    1.577    0.026    0.563
   3_bss:    1.577    0.026    0.563
   3_xyz:    1.530    0.048    0.605
   3_adp:    1.530    0.048    0.605
   3_occ:    1.530    0.048    0.605
   4_bss:    1.530    0.048    0.605
   4_xyz:    1.550    0.015    0.627
   4_adp:    1.550    0.015    0.627
   4_occ:    1.550    0.015    0.627
   5_bss:    1.550    0.015    0.627
   5_xyz:    1.629    0.025    0.631
   5_adp:    1.629    0.025    0.631
   5_occ:    1.629    0.025    0.631
   5_bss:    1.629    0.025    0.631
------------------------------------------------------------------------

CPU time actual refinement: 330.22


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1042/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_1042/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1042/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1042/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1042/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 330.06 
  Macro-tasks:
    bulk solvent and scale       = 36.97  
    individual site refinement   = 140.97 
    weights calculation          = 33.11  
    collect and process          = 6.69   
    model show statistics        = 0.14   
    TOTAL for macro-tasks        = 217.88 
  Micro-tasks:
    mask                            = 1.76   
    f_calc                          = 100.47 
    alpha_beta                      = 8.34   
    target                          = 1.21   
    gradients_wrt_atomic_parameters = 113.34 
    fmodel                         = 6.99   
    r_factors                      = 0.18   
    phase_errors                   = 10.93  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 243.50 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.593 micro seconds
Total CPU time: 5.72 minutes
from_scatterers_fft:    662 calls, 100.11 s
gradients_fft:          607 calls,  99.46 s

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

# Date 2008-01-16 Time 03:03:07 PST -0800 (1200481387.04 s)
Start R-work = 0.4578, R-free = 0.4479 (no bulk solvent and anisotropic scale)
Final R-work = 0.1350, R-free = 0.1815 (no bulk solvent and anisotropic scale)

Start R-work = 0.4497, R-free = 0.4329
Final R-work = 0.1184, R-free = 0.1663