# Date 2008-01-16 Time 01:46:11 PST -0800 (1200476771.69 s)
#phil __OFF__

Command line arguments: "../554.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 8033
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 554

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.8988, 47.1647, 85.9581, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.29, per 1000 atoms: 1.17


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 47.1647, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.919 1.99046
Completeness in resolution range: 0.976813
Completeness with d_max=infinity: 0.973705

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 47.1647, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.919 1.99046
Completeness in resolution range: 0.976813
Completeness with d_max=infinity: 0.973705

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9194 -  4.2582 [2104/2131]  1894   210  10.0%
  bin  2:  4.2582 -  3.3929 [2026/2042]  1823   203  10.0%
  bin  3:  3.3929 -  2.9679 [1993/2012]  1792   201  10.1%
  bin  4:  2.9679 -  2.6983 [1975/2005]  1782   193   9.8%
  bin  5:  2.6983 -  2.5058 [1963/1982]  1764   199  10.1%
  bin  6:  2.5058 -  2.3587 [1955/1980]  1757   198  10.1%
  bin  7:  2.3587 -  2.2410 [1953/1987]  1765   188   9.6%
  bin  8:  2.2410 -  2.1437 [1937/1968]  1740   197  10.2%
  bin  9:  2.1437 -  2.0614 [1923/1964]  1728   195  10.1%
  bin 10:  2.0614 -  1.9905 [1760/1983]  1585   175   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_554/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 15
        2.42 -     3.04: 2209
        3.04 -     3.66: 4680
        3.66 -     4.28: 9044
        4.28 -     4.90: 12391
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z  52 " - " O   HOH Z 183 "  2.219 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  2.294 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  2.337 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28334 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_554/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_554/model_refine_001.geo

CPU time processing inputs: 9.17


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.89875 47.16465 85.95805 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4167   r_free= 0.4053   ksol= 0.00   Bsol= 0.00   scale= 0.833    |
|                                                                             |
| 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:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.203957                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9194 -  4.7489 0.99   1373  153 0.3527 0.3337      6.4917      6.4523|
|  2:  4.7489 -  3.7897 0.99   1308  146 0.3125 0.3196      6.5897      6.6162|
|  3:  3.7897 -  3.3166 0.99   1294  143 0.3483 0.3368      6.5176        6.53|
|  4:  3.3166 -  3.0161 0.99   1286  139 0.3921 0.3527      6.4235      6.3114|
|  5:  3.0161 -  2.8015 0.99   1262  142 0.4201 0.4468      6.2838      6.3199|
|  6:  2.8015 -  2.6373 0.99   1273  144 0.4367 0.5024      6.2136      6.2381|
|  7:  2.6373 -  2.5058 0.99   1259  139 0.4623 0.4153      6.1957      6.0901|
|  8:  2.5058 -  2.3972 0.98   1258  142 0.4631 0.4407      6.1388      6.1193|
|  9:  2.3972 -  2.3053 0.98   1252  137 0.4697 0.4881      6.0834      6.0873|
| 10:  2.3053 -  2.2260 0.99   1248  137 0.4806 0.4476      6.1056      6.0266|
| 11:  2.2260 -  2.1566 0.99   1260  144 0.4708 0.3959      6.0158       5.964|
| 12:  2.1566 -  2.0951 0.97   1243  131 0.4905 0.4535      5.9719      6.0018|
| 13:  2.0951 -  2.0401 0.99   1236  139 0.4859 0.5345      5.8764      5.8927|
| 14:  2.0401 -  1.9905 0.85   1078  123 0.4985 0.4424      5.8289      5.7134|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9194 -  4.7489  1373   153  0.74  30.95   0.82     0.76      57625.26|
|  2:  4.7489 -  3.7897  1308   146  0.79  27.23   0.93     0.83      67459.42|
|  3:  3.7897 -  3.3166  1294   143  0.74  32.25   0.89     0.81      68025.07|
|  4:  3.3166 -  3.0161  1286   139  0.69  36.75   0.85     0.74      59975.53|
|  5:  3.0161 -  2.8015  1262   142  0.59  44.68   0.79     0.65      55872.22|
|  6:  2.8015 -  2.6373  1273   144  0.56  46.95   0.77     0.62      51160.39|
|  7:  2.6373 -  2.5058  1259   139  0.54  48.56   0.76     0.61      47859.85|
|  8:  2.5058 -  2.3972  1258   142  0.55  47.96   0.78     0.62      42252.93|
|  9:  2.3972 -  2.3053  1252   137  0.57  46.69   0.76     0.63      36164.76|
| 10:  2.3053 -  2.2260  1248   137  0.59  44.85   0.78     0.66      31570.05|
| 11:  2.2260 -  2.1566  1260   144  0.58  45.47   0.78     0.66      29312.99|
| 12:  2.1566 -  2.0951  1243   131  0.52  50.55   0.78     0.61      31280.34|
| 13:  2.0951 -  2.0401  1236   139  0.47  54.67   0.79     0.54      29207.98|
| 14:  2.0401 -  1.9905  1078   123  0.48  54.25   0.74     0.52      24268.06|
|alpha:            min =        0.52 max =            0.83 mean =         0.66|
|beta:             min =    24268.06 max =        68025.07 mean =     45621.82|
|figures of merit: min =        0.00 max =            1.00 mean =         0.60|
|phase err.(work): min =        0.00 max =           89.96 mean =        43.41|
|phase err.(test): min =        0.00 max =           89.94 mean =        43.46|
|-----------------------------------------------------------------------------|

============================== 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 = 6.592815              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 73.264   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.524650              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.244   (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:        3 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       24 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      159 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      681 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1526 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2636 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3915 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5077 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6613 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7713 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.682 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.091    4.900  1.196 |       1.713 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.851)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 11.851)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4257   r_free= 0.4130   ksol= 0.00   Bsol= 0.00   scale= 0.801    |
|                                                                             |
| 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:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.211230                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4083   r_free= 0.3964   ksol= 0.34   Bsol= 18.74   scale= 1.029   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.29,8.68,8.10,0.00,0.00,0.00); trace/3= 8.02                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.199097                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.255843              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 75.111   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.532721              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.442   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4083      final r-factor (work) = 0.2930          |
| start r-factor (free) = 0.3964      final r-factor (free) = 0.3155          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 73.1543 = 6.26 * 0.50 * 6.2253 + 1.00 * 53.6820                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.9311 = 6.26 * 0.50 * 6.0170 + 1.00 * 0.1103                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2930      final r-factor (work) = 0.2202          |
| start r-factor (free) = 0.3155      final r-factor (free) = 0.2502          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2201 = 0.53 * 1.00 * 6.0170 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0985 = 0.53 * 1.00 * 5.7961 + 1.00 * 0.0108                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.851)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    61.04   10.20    None  None   None       |
|    all(noH): 2823   0      0.00    61.04   10.20    None  None   None       |
|    Sol.    : 438    0      0.00    56.12   27.56    None  None   None       |
|    Mac.    : 2385   0      0.00    61.04   7.01     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.104: 1431   |   5:    30.522 -  36.626:  100        |
|      1:     6.104 -  12.209:  690   |   6:    36.626 -  42.730:   82        |
|      2:    12.209 -  18.313:  214   |   7:    42.730 -  48.834:   32        |
|      3:    18.313 -  24.417:  134   |   8:    48.834 -  54.939:   20        |
|      4:    24.417 -  30.522:  114   |   9:    54.939 -  61.043:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2202 r_free = 0.2502             target_work(ml) = 5.687         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2196 r_free = 0.2501             target_work(ml) = 5.686         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2196   r_free= 0.2501   ksol= 0.34   Bsol= 18.74   scale= 1.086   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.29,8.68,8.10,0.00,0.00,0.00); trace/3= 8.02                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.686051                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2144   r_free= 0.2443   ksol= 0.33   Bsol= 39.30   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.02,5.03,5.31,0.00,0.00,0.00); trace/3= 4.79                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.683438                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.005696              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 93.637   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.263846              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 114.675  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2144      final r-factor (work) = 0.1530          |
| start r-factor (free) = 0.2443      final r-factor (free) = 0.1850          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9366 = 2.01 * 0.50 * 5.8103 + 1.00 * 0.1098                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5835 = 2.01 * 0.50 * 5.5123 + 1.00 * 0.0555                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1530      final r-factor (work) = 0.1423          |
| start r-factor (free) = 0.1850      final r-factor (free) = 0.1761          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4674 = 0.26 * 1.00 * 5.5123 + 1.00 * 0.0130                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4305 = 0.26 * 1.00 * 5.3358 + 1.00 * 0.0227                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.851)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    71.07   10.76    None  None   None       |
|    all(noH): 2823   0      0.00    71.07   10.76    None  None   None       |
|    Sol.    : 438    0      0.84    56.04   30.97    None  None   None       |
|    Mac.    : 2385   0      0.00    71.07   7.05     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.107: 1625   |   5:    35.536 -  42.643:  134        |
|      1:     7.107 -  14.214:  593   |   6:    42.643 -  49.750:   58        |
|      2:    14.214 -  21.322:  164   |   7:    49.750 -  56.857:   26        |
|      3:    21.322 -  28.429:   98   |   8:    56.857 -  63.964:    5        |
|      4:    28.429 -  35.536:  118   |   9:    63.964 -  71.072:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1423 r_free = 0.1761             target_work(ml) = 5.316         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1422 r_free = 0.1762             target_work(ml) = 5.316         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1422   r_free= 0.1762   ksol= 0.33   Bsol= 39.30   scale= 1.025   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.02,5.03,5.31,0.00,0.00,0.00); trace/3= 4.79                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.315672                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1419   r_free= 0.1764   ksol= 0.33   Bsol= 39.30   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.06,3.92,4.49,0.00,0.00,0.00); trace/3= 3.82                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.316604                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.471745              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 113.252  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.316716              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 98.188   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1419      final r-factor (work) = 0.1226          |
| start r-factor (free) = 0.1764      final r-factor (free) = 0.1584          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.9867 = 1.47 * 0.50 * 5.3423 + 1.00 * 0.0555                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.9135 = 1.47 * 0.50 * 5.2454 + 1.00 * 0.0536                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1226      final r-factor (work) = 0.1193          |
| start r-factor (free) = 0.1584      final r-factor (free) = 0.1560          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6893 = 0.32 * 1.00 * 5.2454 + 1.00 * 0.0280                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6519 = 0.32 * 1.00 * 5.1813 + 1.00 * 0.0109                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.851)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    71.76   11.04    None  None   None       |
|    all(noH): 2823   0      0.00    71.76   11.04    None  None   None       |
|    Sol.    : 438    0      0.96    60.61   32.58    None  None   None       |
|    Mac.    : 2385   0      0.00    71.76   7.08     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 -   7.176: 1649   |   5:    35.880 -  43.057:  102        |
|      1:     7.176 -  14.352:  568   |   6:    43.057 -  50.233:   75        |
|      2:    14.352 -  21.528:  154   |   7:    50.233 -  57.409:   43        |
|      3:    21.528 -  28.704:  110   |   8:    57.409 -  64.585:   10        |
|      4:    28.704 -  35.880:  106   |   9:    64.585 -  71.761:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1193 r_free = 0.1560             target_work(ml) = 5.173         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1192 r_free = 0.1560             target_work(ml) = 5.173         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1192   r_free= 0.1560   ksol= 0.33   Bsol= 39.30   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.06,3.92,4.49,0.00,0.00,0.00); trace/3= 3.82                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.173095                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1192   r_free= 0.1560   ksol= 0.33   Bsol= 39.30   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.06,3.92,4.49,0.00,0.00,0.00); trace/3= 3.82                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.173095                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.405991              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 135.484  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.243394              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 152.968  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1192      final r-factor (work) = 0.1151          |
| start r-factor (free) = 0.1560      final r-factor (free) = 0.1552          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.6959 = 1.41 * 0.50 * 5.1811 + 1.00 * 0.0536                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.6791 = 1.41 * 0.50 * 5.1569 + 1.00 * 0.0539                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1151      final r-factor (work) = 0.1150          |
| start r-factor (free) = 0.1552      final r-factor (free) = 0.1549          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2661 = 0.24 * 1.00 * 5.1569 + 1.00 * 0.0109                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2648 = 0.24 * 1.00 * 5.1522 + 1.00 * 0.0108                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.851)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    73.18   10.88    None  None   None       |
|    all(noH): 2823   0      0.00    73.18   10.88    None  None   None       |
|    Sol.    : 438    0      0.80    62.02   31.87    None  None   None       |
|    Mac.    : 2385   0      0.00    73.18   7.02     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 -   7.318: 1674   |   5:    36.588 -  43.906:   94        |
|      1:     7.318 -  14.635:  559   |   6:    43.906 -  51.224:   71        |
|      2:    14.635 -  21.953:  150   |   7:    51.224 -  58.541:   31        |
|      3:    21.953 -  29.271:  117   |   8:    58.541 -  65.859:    6        |
|      4:    29.271 -  36.588:  115   |   9:    65.859 -  73.177:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1150 r_free = 0.1549             target_work(ml) = 5.151         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1150 r_free = 0.1548             target_work(ml) = 5.151         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1150   r_free= 0.1548   ksol= 0.33   Bsol= 39.30   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.06,3.92,4.49,0.00,0.00,0.00); trace/3= 3.82                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.151311                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1152   r_free= 0.1551   ksol= 0.33   Bsol= 39.30   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.97,3.69,4.36,0.00,0.00,0.00); trace/3= 3.67                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.153828                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.882892              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 154.939  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.467827              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 97.014   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1152      final r-factor (work) = 0.1112          |
| start r-factor (free) = 0.1551      final r-factor (free) = 0.1540          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9049 = 1.88 * 0.50 * 5.1528 + 1.00 * 0.0539                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8978 = 1.88 * 0.50 * 5.1373 + 1.00 * 0.0613                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1112      final r-factor (work) = 0.1106          |
| start r-factor (free) = 0.1540      final r-factor (free) = 0.1550          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4144 = 0.47 * 1.00 * 5.1373 + 1.00 * 0.0110                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4288 = 0.47 * 1.00 * 5.1285 + 1.00 * 0.0296                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.851)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.22   11.01    None  None   None       |
|    all(noH): 2823   0      0.00    78.22   11.01    None  None   None       |
|    Sol.    : 438    0      0.69    64.77   32.40    None  None   None       |
|    Mac.    : 2385   0      0.00    78.22   7.08     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 -   7.822: 1734   |   5:    39.109 -  46.930:  100        |
|      1:     7.822 -  15.644:  525   |   6:    46.930 -  54.752:   62        |
|      2:    15.644 -  23.465:  144   |   7:    54.752 -  62.574:   20        |
|      3:    23.465 -  31.287:  117   |   8:    62.574 -  70.396:    5        |
|      4:    31.287 -  39.109:  111   |   9:    70.396 -  78.217:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1106 r_free = 0.1550             target_work(ml) = 5.135         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1104 r_free = 0.1550             target_work(ml) = 5.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1104   r_free= 0.1550   ksol= 0.33   Bsol= 39.30   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.97,3.69,4.36,0.00,0.00,0.00); trace/3= 3.67                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.133428                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9194 -  4.7489 0.99   1373  153 0.1010 0.1268      5.3932      5.5115|
|  2:  4.7489 -  3.7897 0.99   1308  146 0.0866 0.1116      5.4418      5.6377|
|  3:  3.7897 -  3.3166 0.99   1294  143 0.1046 0.1473      5.4676      5.8419|
|  4:  3.3166 -  3.0161 0.99   1286  139 0.1176 0.1499      5.4335      5.5858|
|  5:  3.0161 -  2.8015 0.99   1262  142 0.1274 0.1702      5.3124      5.5153|
|  6:  2.8015 -  2.6373 0.99   1273  144 0.1205 0.1738      5.2095      5.4362|
|  7:  2.6373 -  2.5058 0.99   1259  139 0.1241 0.1676      5.1654      5.3891|
|  8:  2.5058 -  2.3972 0.98   1258  142 0.1157 0.1777      5.0832      5.3824|
|  9:  2.3972 -  2.3053 0.98   1252  137 0.1156 0.1688      5.0279      5.2531|
| 10:  2.3053 -  2.2260 0.99   1248  137 0.1091 0.1792      4.9678      5.2455|
| 11:  2.2260 -  2.1566 0.99   1260  144 0.1113 0.1662      4.9159       5.248|
| 12:  2.1566 -  2.0951 0.97   1243  131 0.1101 0.1624      4.8695      5.1733|
| 13:  2.0951 -  2.0401 0.99   1236  139 0.1104 0.1663      4.7867      5.0423|
| 14:  2.0401 -  1.9905 0.85   1078  123 0.1044 0.1770      4.6614      4.9607|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9194 -  4.7489  1373   153  0.94   9.06   0.98     0.96       7206.06|
|  2:  4.7489 -  3.7897  1308   146  0.95   7.90   1.02     1.00       8925.95|
|  3:  3.7897 -  3.3166  1294   143  0.94  10.93   1.02     1.02      10200.33|
|  4:  3.3166 -  3.0161  1286   139  0.93  12.81   1.00     0.99       9779.92|
|  5:  3.0161 -  2.8015  1262   142  0.90  15.32   0.99     0.96       8032.36|
|  6:  2.8015 -  2.6373  1273   144  0.90  15.67   0.98     0.94       6896.87|
|  7:  2.6373 -  2.5058  1259   139  0.91  15.54   0.98     0.96       6192.54|
|  8:  2.5058 -  2.3972  1258   142  0.91  14.86   0.99     0.97       5447.41|
|  9:  2.3972 -  2.3053  1252   137  0.91  15.50   1.00     0.97       5000.97|
| 10:  2.3053 -  2.2260  1248   137  0.90  15.51   1.00     0.97       4499.23|
| 11:  2.2260 -  2.1566  1260   144  0.90  15.75   1.00     0.97       4195.15|
| 12:  2.1566 -  2.0951  1243   131  0.92  14.73   1.00     0.99       3835.50|
| 13:  2.0951 -  2.0401  1236   139  0.91  15.07   1.00     0.99       3277.32|
| 14:  2.0401 -  1.9905  1078   123  0.91  14.65   0.98     0.95       2515.92|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2515.92 max =        10200.33 mean =      6216.88|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.85 mean =        13.74|
|phase err.(test): min =        0.00 max =           89.92 mean =        13.33|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1104   r_free= 0.1550   ksol= 0.32   Bsol= 43.05   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.68,-0.01,0.70,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.133157                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1104   r_free= 0.1550   ksol= 0.32   Bsol= 43.05   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.68,-0.01,0.70,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.133157                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9194 -  4.7489 0.99   1373  153 0.1009 0.1270      5.3908      5.5091|
|  2:  4.7489 -  3.7897 0.99   1308  146 0.0867 0.1117      5.4424      5.6391|
|  3:  3.7897 -  3.3166 0.99   1294  143 0.1046 0.1474      5.4683      5.8422|
|  4:  3.3166 -  3.0161 0.99   1286  139 0.1176 0.1499      5.4333      5.5856|
|  5:  3.0161 -  2.8015 0.99   1262  142 0.1274 0.1701      5.3119      5.5148|
|  6:  2.8015 -  2.6373 0.99   1273  144 0.1205 0.1737      5.2091      5.4356|
|  7:  2.6373 -  2.5058 0.99   1259  139 0.1241 0.1677      5.1652      5.3892|
|  8:  2.5058 -  2.3972 0.98   1258  142 0.1157 0.1777      5.0832      5.3823|
|  9:  2.3972 -  2.3053 0.98   1252  137 0.1156 0.1687      5.0278      5.2532|
| 10:  2.3053 -  2.2260 0.99   1248  137 0.1091 0.1792      4.9677      5.2455|
| 11:  2.2260 -  2.1566 0.99   1260  144 0.1113 0.1662      4.9157      5.2478|
| 12:  2.1566 -  2.0951 0.97   1243  131 0.1101 0.1623      4.8694      5.1731|
| 13:  2.0951 -  2.0401 0.99   1236  139 0.1104 0.1662      4.7865      5.0423|
| 14:  2.0401 -  1.9905 0.85   1078  123 0.1044 0.1769       4.661      4.9602|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9194 -  4.7489  1373   153  0.94   9.03   0.98     0.96       7158.49|
|  2:  4.7489 -  3.7897  1308   146  0.95   7.89   1.02     1.00       8915.99|
|  3:  3.7897 -  3.3166  1294   143  0.94  10.94   1.02     1.02      10216.74|
|  4:  3.3166 -  3.0161  1286   139  0.93  12.81   1.01     0.99       9775.49|
|  5:  3.0161 -  2.8015  1262   142  0.90  15.31   0.99     0.96       8024.30|
|  6:  2.8015 -  2.6373  1273   144  0.90  15.66   0.98     0.94       6890.46|
|  7:  2.6373 -  2.5058  1259   139  0.91  15.54   0.99     0.96       6189.83|
|  8:  2.5058 -  2.3972  1258   142  0.91  14.86   0.99     0.97       5446.85|
|  9:  2.3972 -  2.3053  1252   137  0.91  15.50   1.01     0.98       5001.23|
| 10:  2.3053 -  2.2260  1248   137  0.90  15.51   1.00     0.97       4497.90|
| 11:  2.2260 -  2.1566  1260   144  0.90  15.75   1.00     0.97       4193.33|
| 12:  2.1566 -  2.0951  1243   131  0.92  14.73   1.01     0.99       3834.24|
| 13:  2.0951 -  2.0401  1236   139  0.91  15.07   1.01     1.00       3274.87|
| 14:  2.0401 -  1.9905  1078   123  0.91  14.63   0.99     0.95       2512.58|
|alpha:            min =        0.94 max =            1.02 mean =         0.98|
|beta:             min =     2512.58 max =        10216.74 mean =      6211.38|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.90 mean =        13.74|
|phase err.(test): min =        0.00 max =           89.95 mean =        13.32|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.851)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.76    81.97   14.76    None  None   None       |
|    all(noH): 2823   0      3.76    81.97   14.76    None  None   None       |
|    Sol.    : 438    0      4.44    68.53   36.15    None  None   None       |
|    Mac.    : 2385   0      3.76    81.97   10.84    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:     3.756 -  11.578: 1734   |   5:    42.865 -  50.686:  100        |
|      1:    11.578 -  19.399:  525   |   6:    50.686 -  58.508:   62        |
|      2:    19.399 -  27.221:  144   |   7:    58.508 -  66.330:   20        |
|      3:    27.221 -  35.043:  117   |   8:    66.330 -  74.152:    5        |
|      4:    35.043 -  42.865:  111   |   9:    74.152 -  81.973:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 318         
Filter by distance & map next to the model:
   mapped sites are within: 0.287 - 4.791
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 312 from: 318
   mapped sites are within: 0.704 - 4.791

peak=   11.028 closest distance to " CG2 VAL A 230 " =    1.472
peak=    7.433 closest distance to " CG2 VAL A 296 " =    1.178
peak=    6.162 closest distance to " CG  LEU A   5 " =    1.220
peak=    5.665 closest distance to " CG  LEU A 228 " =    1.189
peak=    5.477 closest distance to " CG  PRO A  54 " =    1.280
peak=    5.408 closest distance to " CD2 LEU A   5 " =    1.153
peak=    5.340 closest distance to " NH2 ARG A  56 " =    2.174
peak=    5.273 closest distance to " CB  GLN A 223 " =    1.409
peak=    5.123 closest distance to " CB  VAL A 296 " =    1.081
peak=    5.065 closest distance to " CB  ARG A 275 " =    0.910
peak=    5.015 closest distance to " O   HOH Z 126 " =    1.965
peak=    4.908 closest distance to " NE2 GLN A  11 " =    1.071
peak=    4.891 closest distance to " O   HOH Z 232 " =    2.373
peak=    4.885 closest distance to " CB  GLN A 183 " =    1.306
peak=    4.853 closest distance to " O   HOH Z 142 " =    1.660
peak=    4.852 closest distance to " CB  VAL A 230 " =    1.173
peak=    4.844 closest distance to " CB  SER A  63 " =    1.242
peak=    4.831 closest distance to " CB  PRO A  54 " =    0.933
peak=    4.744 closest distance to " O   HOH Z 272 " =    1.909
peak=    4.648 closest distance to " O   HOH Z 209 " =    2.328
peak=    4.627 closest distance to " CG  PRO A 213 " =    1.250
peak=    4.467 closest distance to " CB  TYR A 169 " =    0.704
peak=    4.465 closest distance to " C   PRO A 198 " =    1.500
peak=    4.454 closest distance to " O   HOH Z 298 " =    1.824
peak=    4.449 closest distance to " O   HOH Z 193 " =    1.745
peak=    4.413 closest distance to " O   SER A  87 " =    2.208
peak=    4.385 closest distance to " CB  GLU A 152 " =    1.169
peak=    4.366 closest distance to " O   HOH Z 402 " =    1.472
peak=    4.318 closest distance to " O   HOH Z 236 " =    1.928
peak=    4.314 closest distance to " CB  SER A   3 " =    1.267
peak=    4.307 closest distance to " O   HOH Z 369 " =    2.144
peak=    4.281 closest distance to " CG  PRO A 243 " =    1.132
peak=    4.280 closest distance to " OG ASER A 258 " =    3.082
peak=    4.257 closest distance to " O   HOH Z 427 " =    2.974
peak=    4.244 closest distance to " O   HOH Z 423 " =    1.809
peak=    4.230 closest distance to " CB  ASN A 148 " =    1.411
peak=    4.216 closest distance to " O   HOH Z  61 " =    1.633
peak=    4.215 closest distance to " O   HOH Z 346 " =    1.584
peak=    4.213 closest distance to " O   HOH Z  78 " =    1.680
peak=    4.211 closest distance to " O   HOH Z 303 " =    2.090
peak=    4.200 closest distance to " CG  PRO A 198 " =    1.176
peak=    4.194 closest distance to " O   HOH Z 234 " =    3.605
peak=    4.183 closest distance to " O   HOH Z 203 " =    1.688
peak=    4.172 closest distance to " O   HOH Z  43 " =    2.111
peak=    4.170 closest distance to " ND2 ASN A 187 " =    1.503
peak=    4.156 closest distance to " CB  ARG A  79 " =    1.423
peak=    4.116 closest distance to " OD1 ASN A  69 " =    2.581
peak=    4.084 closest distance to " CD2 LEU A 228 " =    1.158
peak=    4.070 closest distance to " CA  TYR A  30 " =    0.927
peak=    4.044 closest distance to " O   HOH Z 158 " =    3.107
peak=    4.041 closest distance to " O   HOH Z  97 " =    1.967
peak=    4.034 closest distance to " CB  GLU A 128 " =    1.027
peak=    4.014 closest distance to " O   HOH Z 368 " =    2.180
peak=    4.012 closest distance to " O   HOH Z 403 " =    1.701
peak=    4.008 closest distance to " CB  TRP A 266 " =    0.937
peak=    3.993 closest distance to " CZ  PHE A 218 " =    1.103
peak=    3.992 closest distance to " CG1BVAL A  72 " =    1.676
peak=    3.987 closest distance to " O   HOH Z 189 " =    2.597
peak=    3.985 closest distance to " CB  GLU A 277 " =    3.558
peak=    3.970 closest distance to " CB  VAL A 265 " =    1.273
peak=    3.952 closest distance to " O   HOH Z  66 " =    2.236
peak=    3.950 closest distance to " O   HOH Z  40 " =    1.541
peak=    3.945 closest distance to " CB  ARG A 139 " =    0.946
peak=    3.939 closest distance to " O   HOH Z 214 " =    2.252
peak=    3.930 closest distance to " CB  ASN A  39 " =    0.840
peak=    3.925 closest distance to " O   HOH Z 250 " =    1.358
peak=    3.921 closest distance to " O   HOH Z 248 " =    1.629
peak=    3.918 closest distance to " O   HOH Z 197 " =    2.975
peak=    3.910 closest distance to " CB  TRP A 179 " =    1.361
peak=    3.895 closest distance to " O   HOH Z  54 " =    2.374
peak=    3.882 closest distance to " N   ASN A  39 " =    1.190
peak=    3.865 closest distance to " O   HOH Z 389 " =    1.896
peak=    3.859 closest distance to " O   HOH Z 128 " =    2.020
peak=    3.855 closest distance to " O   HOH Z  97 " =    2.466
peak=    3.855 closest distance to " O   HOH Z  59 " =    2.146
peak=    3.828 closest distance to " O   HOH Z  15 " =    2.072
peak=    3.826 closest distance to " CA  ALA A  21 " =    1.130
peak=    3.825 closest distance to " O   HOH Z 124 " =    1.358
peak=    3.814 closest distance to " O   HOH Z 280 " =    2.931
peak=    3.781 closest distance to " CB  ARG A 190 " =    1.627
peak=    3.781 closest distance to " O   TRP A 274 " =    1.886
peak=    3.767 closest distance to " O   HOH Z 371 " =    3.234
peak=    3.762 closest distance to " CB  VAL A 202 " =    1.536
peak=    3.740 closest distance to " CG  ARG A  66 " =    2.791
peak=    3.727 closest distance to " O   HOH Z  85 " =    1.345
peak=    3.723 closest distance to " CB  ASP A 140 " =    0.913
peak=    3.711 closest distance to " O   HOH Z 263 " =    1.658
peak=    3.710 closest distance to " O   HOH Z  63 " =    2.058
peak=    3.706 closest distance to " CG1 ILE A  33 " =    1.330
peak=    3.705 closest distance to " CA  VAL A  41 " =    0.803
peak=    3.700 closest distance to " O   HOH Z 407 " =    2.519
peak=    3.690 closest distance to " CB  ASN A 142 " =    1.116
peak=    3.672 closest distance to " CB  SER A  26 " =    1.671
peak=    3.671 closest distance to " O   HOH Z  54 " =    1.580
peak=    3.670 closest distance to " O   HOH Z 147 " =    1.738
peak=    3.663 closest distance to " CD2 TRP A 179 " =    1.400
peak=    3.661 closest distance to " O   HOH Z  80 " =    1.701
peak=    3.660 closest distance to " CD BLYS A 290 " =    1.113
peak=    3.660 closest distance to " CB  ALA A 248 " =    1.481
peak=    3.655 closest distance to " CA  ALA A  51 " =    0.916
peak=    3.639 closest distance to " CG2 ILE A  20 " =    1.424
peak=    3.631 closest distance to " O   HOH Z 273 " =    2.697
peak=    3.630 closest distance to " O   HOH Z  78 " =    2.131
peak=    3.623 closest distance to " O   HOH Z 411 " =    3.809
peak=    3.613 closest distance to " O   HOH Z 344 " =    2.976
peak=    3.610 closest distance to " O   HOH Z 422 " =    2.683
peak=    3.601 closest distance to " O   HOH Z 365 " =    2.963
peak=    3.601 closest distance to " CB  THR A  31 " =    1.572
peak=    3.592 closest distance to " CG1 ILE A  49 " =    1.464
peak=    3.592 closest distance to " O   HOH Z  88 " =    2.883
peak=    3.592 closest distance to " O   HOH Z 245 " =    1.385
peak=    3.580 closest distance to " CG  GLN A  77 " =    2.170
peak=    3.578 closest distance to " CB  ALA A   9 " =    1.569
peak=    3.576 closest distance to " CA  THR A 264 " =    0.777
peak=    3.572 closest distance to " O   HOH Z 417 " =    3.139
peak=    3.571 closest distance to " CE1 TYR A 186 " =    1.312
peak=    3.562 closest distance to " CB  ALA A 291 " =    1.378
peak=    3.562 closest distance to " CA  LYS A 117 " =    1.274
peak=    3.559 closest distance to " NH2 ARG A 156 " =    1.082
peak=    3.559 closest distance to " CD  LYS A 166 " =    1.328
peak=    3.556 closest distance to " O   MET A 105 " =    1.869
peak=    3.552 closest distance to " O   HOH Z 193 " =    1.966
peak=    3.547 closest distance to " CD  ARG A 159 " =    0.744
peak=    3.544 closest distance to " O   ASP A 124 " =    1.241
peak=    3.542 closest distance to " O   HOH Z 261 " =    2.217
peak=    3.538 closest distance to " CB  THR A 157 " =    1.159
peak=    3.532 closest distance to " O   HOH Z 102 " =    1.251
peak=    3.529 closest distance to " O   HOH Z 261 " =    2.072
peak=    3.527 closest distance to " CD  ARG A 269 " =    0.983
peak=    3.527 closest distance to " CA  ASN A 215 " =    1.156
peak=    3.516 closest distance to " OG1 THR A 294 " =    2.338
peak=    3.509 closest distance to " CB  ARG A  79 " =    0.885
peak=    3.503 closest distance to " O   HOH Z  48 " =    1.570
peak=    3.500 closest distance to " O   HOH Z 345 " =    3.097
peak=    3.497 closest distance to " OD2 ASP A 286 " =    2.798
peak=    3.494 closest distance to " CA  ARG A  36 " =    1.031
peak=    3.490 closest distance to " O   HOH Z 112 " =    1.654
peak=    3.487 closest distance to " O   HOH Z 128 " =    2.121
peak=    3.486 closest distance to " CA  ALA A 158 " =    1.261
peak=    3.485 closest distance to " CA  ARG A 195 " =    1.162
peak=    3.479 closest distance to " CG2 ILE A 234 " =    0.881
peak=    3.476 closest distance to " O   HOH Z  19 " =    2.059
peak=    3.473 closest distance to " CD1 ILE A 106 " =    1.017
peak=    3.473 closest distance to " CA  ASP A 162 " =    1.052
peak=    3.472 closest distance to " OE1 GLU A   2 " =    2.186
peak=    3.467 closest distance to " CG1 VAL A 153 " =    0.967
peak=    3.464 closest distance to " NZ  LYS A 117 " =    3.179
peak=    3.458 closest distance to " NH1BARG A 190 " =    2.060
peak=    3.454 closest distance to " CA  PHE A 283 " =    1.200
peak=    3.447 closest distance to " O   HOH Z 148 " =    3.235
peak=    3.447 closest distance to " CD1 LEU A 300 " =    1.236
peak=    3.442 closest distance to " CB  SER A 212 " =    1.185
peak=    3.442 closest distance to " NZ  LYS A 166 " =    3.056
peak=    3.439 closest distance to " CA  ASP A 140 " =    1.213
peak=    3.437 closest distance to " CG2 ILE A 120 " =    1.250
peak=    3.431 closest distance to " CB  HIS A 108 " =    0.784
peak=    3.429 closest distance to " CB  GLN A 205 " =    1.166
peak=    3.429 closest distance to " CE  LYS A  76 " =    0.884
peak=    3.426 closest distance to " O   HOH Z 145 " =    3.725
peak=    3.423 closest distance to " N   ARG A 190 " =    1.002
peak=    3.420 closest distance to " O   HOH Z 180 " =    2.131
peak=    3.420 closest distance to " OG BSER A 164 " =    2.227
peak=    3.419 closest distance to " O   HOH Z 172 " =    3.872
peak=    3.419 closest distance to " CB BVAL A  41 " =    1.178
peak=    3.408 closest distance to " CB  GLU A  46 " =    1.055
peak=    3.405 closest distance to " CD1 ILE A  33 " =    1.624
peak=    3.404 closest distance to " CB  GLN A 278 " =    0.863
peak=    3.402 closest distance to " O   HOH Z 261 " =    1.682
peak=    3.401 closest distance to " NH2 ARG A  79 " =    1.343
peak=    3.390 closest distance to " CA  ASP A 191 " =    1.051
peak=    3.390 closest distance to " CG2 VAL A 257 " =    0.832
peak=    3.385 closest distance to " N   ASP A 162 " =    1.338
peak=    3.384 closest distance to " CG  MET A 185 " =    1.053
peak=    3.382 closest distance to " O   HOH Z 134 " =    1.360
peak=    3.381 closest distance to " CB  TRP A 150 " =    1.425
peak=    3.380 closest distance to " O   HOH Z 421 " =    1.718
peak=    3.380 closest distance to " O   HOH Z 313 " =    1.788
peak=    3.374 closest distance to " O   HOH Z 383 " =    2.005
peak=    3.374 closest distance to " O   HOH Z  21 " =    1.713
peak=    3.373 closest distance to " CA  THR A 221 " =    0.907
peak=    3.371 closest distance to " ND2 ASN A 110 " =    1.666
peak=    3.371 closest distance to " O   HOH Z 227 " =    1.540
peak=    3.367 closest distance to " N   SER A 135 " =    1.373
peak=    3.367 closest distance to " CB  MET A  47 " =    1.219
peak=    3.364 closest distance to " O   ALA A 165 " =    1.437
peak=    3.364 closest distance to " CB  LEU A 143 " =    1.152
peak=    3.362 closest distance to " O   HOH Z 425 " =    1.987
peak=    3.362 closest distance to " O   HOH Z 299 " =    4.331
peak=    3.360 closest distance to " O   HOH Z 187 " =    2.320
peak=    3.354 closest distance to " CB  ALA A 295 " =    1.268
peak=    3.341 closest distance to " N   VAL A 126 " =    1.357
peak=    3.341 closest distance to " O   HOH Z 286 " =    2.311
peak=    3.340 closest distance to " O   HOH Z 329 " =    3.890
peak=    3.337 closest distance to " CA  ALA A  84 " =    1.370
peak=    3.334 closest distance to " O   HOH Z 337 " =    3.633
peak=    3.328 closest distance to " O   HOH Z 132 " =    2.680
peak=    3.327 closest distance to " CB  LYS A 290 " =    1.012
peak=    3.325 closest distance to " O   HOH Z 435 " =    1.966
peak=    3.325 closest distance to " O   HOH Z  48 " =    1.458
peak=    3.321 closest distance to " O   HOH Z 313 " =    1.747
peak=    3.320 closest distance to " O   HOH Z  66 " =    2.238
peak=    3.319 closest distance to " CB  LEU A 228 " =    1.291
peak=    3.318 closest distance to " N   ARG A 156 " =    1.399
peak=    3.317 closest distance to " O   HOH Z 291 " =    1.606
peak=    3.312 closest distance to " CB  ASN A 110 " =    1.137
peak=    3.311 closest distance to " O   HOH Z 426 " =    1.574
peak=    3.306 closest distance to " O   HOH Z 406 " =    1.584
peak=    3.302 closest distance to " CG AARG A 275 " =    1.225
peak=    3.302 closest distance to " O   HOH Z 305 " =    3.607
peak=    3.301 closest distance to " CD1 LEU A 228 " =    1.892
peak=    3.300 closest distance to " OG  SER A  22 " =    2.715
peak=    3.297 closest distance to " CA  ALA A 291 " =    0.916
peak=    3.297 closest distance to " CG BARG A 102 " =    1.768
peak=    3.294 closest distance to " CE1 HIS A 108 " =    1.131
peak=    3.292 closest distance to " NH1 ARG A 138 " =    1.144
peak=    3.289 closest distance to " CD  LYS A 119 " =    1.809
peak=    3.283 closest distance to " CA  LYS A 290 " =    1.227
peak=    3.282 closest distance to " O   HOH Z 250 " =    1.364
peak=    3.281 closest distance to " NE2 GLN A  77 " =    3.263
peak=    3.278 closest distance to " NZ  LYS A  76 " =    1.485
peak=    3.277 closest distance to " CB  ALA A 248 " =    1.035
peak=    3.276 closest distance to " O   HOH Z  44 " =    1.725
peak=    3.276 closest distance to " CA  ALA A 233 " =    1.283
peak=    3.273 closest distance to " O   HOH Z 193 " =    1.565
peak=    3.273 closest distance to " NH1AARG A 145 " =    1.115
peak=    3.272 closest distance to " O   HOH Z 417 " =    2.169
peak=    3.269 closest distance to " CB  ILE A 120 " =    1.328
peak=    3.267 closest distance to " CB  ASN A 215 " =    1.172
peak=    3.266 closest distance to " O   GLN A 278 " =    1.326
peak=    3.265 closest distance to " O   HOH Z 368 " =    3.651
peak=    3.248 closest distance to " O   HOH Z 189 " =    2.654
peak=    3.244 closest distance to " CA  VAL A 126 " =    0.934
peak=    3.240 closest distance to " CG1 VAL A 296 " =    1.225
peak=    3.240 closest distance to " CB  PHE A 204 " =    0.821
peak=    3.239 closest distance to " O   HOH Z 171 " =    2.383
peak=    3.238 closest distance to " O   HOH Z 251 " =    1.710
peak=    3.234 closest distance to " O   HOH Z  49 " =    2.432
peak=    3.234 closest distance to " O   HOH Z 419 " =    1.604
peak=    3.232 closest distance to " CA  LEU A 282 " =    1.092
peak=    3.231 closest distance to " CG  LEU A 167 " =    1.182
peak=    3.231 closest distance to " CZ2 TRP A 274 " =    1.536
peak=    3.230 closest distance to " O   HOH Z 271 " =    2.565
peak=    3.228 closest distance to " O   HOH Z 425 " =    1.310
peak=    3.224 closest distance to " O   HOH Z  62 " =    2.296
peak=    3.224 closest distance to " O   HOH Z  10 " =    1.775
peak=    3.222 closest distance to " CG  MET A 185 " =    1.115
peak=    3.220 closest distance to " O   HOH Z 359 " =    1.798
peak=    3.218 closest distance to " O   HOH Z 123 " =    2.204
peak=    3.217 closest distance to " CZ3 TRP A  85 " =    0.950
peak=    3.215 closest distance to " O   ALA A 158 " =    1.357
peak=    3.211 closest distance to " O   HOH Z 437 " =    1.935
peak=    3.208 closest distance to " N   ASN A 127 " =    1.216
peak=    3.206 closest distance to " OG1 THR A 294 " =    1.693
peak=    3.203 closest distance to " CG  GLN A  88 " =    0.984
peak=    3.200 closest distance to " O   HOH Z 135 " =    1.797
peak=    3.197 closest distance to " CG2 THR A 221 " =    1.181
peak=    3.194 closest distance to " CA  ILE A 106 " =    0.740
peak=    3.190 closest distance to " O   HOH Z 420 " =    1.914
peak=    3.189 closest distance to " O   HOH Z 209 " =    2.420
peak=    3.186 closest distance to " O  BHOH Z 338 " =    2.420
peak=    3.185 closest distance to " O   HOH Z   9 " =    2.117
peak=    3.185 closest distance to " O   HOH Z 286 " =    2.492
peak=    3.183 closest distance to " O   HOH Z 234 " =    1.837
peak=    3.178 closest distance to " O   GLY A  91 " =    1.494
peak=    3.178 closest distance to " CA  TYR A 116 " =    1.415
peak=    3.169 closest distance to " O   HOH Z 403 " =    1.330
peak=    3.168 closest distance to " CB  MET A  40 " =    0.780
peak=    3.164 closest distance to " OD1 ASP A 231 " =    1.909
peak=    3.163 closest distance to " CD  ARG A  79 " =    2.017
peak=    3.162 closest distance to " O   HOH Z   1 " =    2.128
peak=    3.159 closest distance to " CG2 VAL A 197 " =    1.069
peak=    3.159 closest distance to " CA  GLY A  80 " =    0.739
peak=    3.154 closest distance to " CB  ILE A  20 " =    1.441
peak=    3.153 closest distance to " N   PHE A 130 " =    1.305
peak=    3.152 closest distance to " OD1 ASN A 217 " =    1.718
peak=    3.152 closest distance to " CB  ALA A 114 " =    1.318
peak=    3.150 closest distance to " CD2 TYR A  30 " =    0.920
peak=    3.149 closest distance to " CG2 ILE A 234 " =    2.098
peak=    3.147 closest distance to " O   HOH Z 251 " =    1.444
peak=    3.146 closest distance to " NH2BARG A 145 " =    1.946
peak=    3.146 closest distance to " C   ALA A 299 " =    0.925
peak=    3.139 closest distance to " O   HOH Z 357 " =    1.856
peak=    3.136 closest distance to " CB  ALA A 100 " =    1.190
peak=    3.136 closest distance to " O   HOH Z 380 " =    1.949
peak=    3.133 closest distance to " CA  ASN A 176 " =    1.092
peak=    3.133 closest distance to " O   SER A 164 " =    1.067
peak=    3.132 closest distance to " CA  SER A 146 " =    1.751
peak=    3.132 closest distance to " O   HOH Z  50 " =    2.127
peak=    3.130 closest distance to " CD2 HIS A  81 " =    1.076
peak=    3.122 closest distance to " CB  SER A 216 " =    0.723
peak=    3.121 closest distance to " O   HOH Z 367 " =    3.468
peak=    3.121 closest distance to " O   HOH Z  40 " =    2.644
peak=    3.118 closest distance to " O   HOH Z  85 " =    2.144
peak=    3.114 closest distance to " O   ALA A   1 " =    1.745
peak=    3.113 closest distance to " CG  LEU A 281 " =    1.079
peak=    3.112 closest distance to " OD1BASN A 224 " =    2.331
peak=    3.108 closest distance to " CD2 LEU A 300 " =    1.044
peak=    3.103 closest distance to " O   HOH Z 298 " =    4.791
peak=    3.103 closest distance to " O   HOH Z 409 " =    3.572
peak=    3.101 closest distance to " O   HOH Z 353 " =    2.695
peak=    3.079 closest distance to " ND1 HIS A  81 " =    1.671
peak=    3.076 closest distance to " CD  LYS A  76 " =    1.886
peak=    3.074 closest distance to " O   HOH Z 256 " =    2.384
peak=    3.069 closest distance to " CD2 LEU A   5 " =    0.718
peak=    3.069 closest distance to " CG  GLN A  89 " =    1.518
peak=    3.065 closest distance to " O   HOH Z  46 " =    1.485
peak=    3.061 closest distance to " CA  SER A  87 " =    1.050
peak=    3.060 closest distance to " O   HOH Z 116 " =    1.741
peak=    3.045 closest distance to " O   HOH Z  19 " =    2.120
peak=    3.042 closest distance to " CG2 VAL A 202 " =    1.123
peak=    3.018 closest distance to " O   ASP A 124 " =    1.755
peak=    3.008 closest distance to " O   HOH Z  90 " =    3.278

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 196         
Filter by distance & map next to the model:
   mapped sites are within: 0.587 - 5.457
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 194 from: 196
   mapped sites are within: 0.776 - 5.457

peak=   -5.494 closest distance to " CG2 VAL A 230 " =    0.776
peak=   -4.676 closest distance to " SG  CYS A 254 " =    3.250
peak=   -4.621 closest distance to " CD  ARG A 156 " =    2.011
peak=   -4.452 closest distance to " O   HOH Z 266 " =    4.954
peak=   -4.223 closest distance to " O   HOH Z 290 " =    1.102
peak=   -4.193 closest distance to " C   HIS A 108 " =    1.185
peak=   -4.161 closest distance to " OG BSER A 134 " =    1.091
peak=   -4.120 closest distance to " CG  GLN A 223 " =    2.045
peak=   -4.091 closest distance to " CB  ALA A 161 " =    2.600
peak=   -4.090 closest distance to " CD  GLN A  58 " =    1.102
peak=   -4.061 closest distance to " CB  PRO A 243 " =    2.643
peak=   -3.999 closest distance to " CG2 VAL A 296 " =    1.196
peak=   -3.989 closest distance to " O   PRO A 163 " =    2.095
peak=   -3.986 closest distance to " O   HOH Z 196 " =    2.062
peak=   -3.979 closest distance to " OXT GLY A 302 " =    2.819
peak=   -3.967 closest distance to " CE2 TYR A  30 " =    2.783
peak=   -3.962 closest distance to " O   HOH Z 231 " =    2.049
peak=   -3.960 closest distance to " CA  VAL A  67 " =    2.721
peak=   -3.956 closest distance to " CG2BVAL A  41 " =    2.624
peak=   -3.942 closest distance to " O   HOH Z 114 " =    3.130
peak=   -3.932 closest distance to " NE2 GLN A  88 " =    1.977
peak=   -3.929 closest distance to " N   ALA A 226 " =    2.000
peak=   -3.917 closest distance to " O   HOH Z 351 " =    1.521
peak=   -3.874 closest distance to " ND2 ASN A 187 " =    1.597
peak=   -3.862 closest distance to " ND2 ASN A  45 " =    1.162
peak=   -3.836 closest distance to " CB  PHE A 192 " =    1.928
peak=   -3.819 closest distance to " CG  ASP A 231 " =    0.798
peak=   -3.814 closest distance to " O   HOH Z 166 " =    1.985
peak=   -3.792 closest distance to " N   GLN A  58 " =    1.677
peak=   -3.739 closest distance to " CD2 LEU A 300 " =    2.738
peak=   -3.731 closest distance to " O   HOH Z 394 " =    1.498
peak=   -3.724 closest distance to " OG  SER A   3 " =    1.718
peak=   -3.719 closest distance to " OG  SER A  97 " =    2.224
peak=   -3.715 closest distance to " CD1 LEU A 101 " =    2.410
peak=   -3.686 closest distance to " CG1 VAL A 112 " =    2.765
peak=   -3.686 closest distance to " CB  ALA A 248 " =    2.140
peak=   -3.674 closest distance to " CZ3 TRP A 179 " =    1.272
peak=   -3.666 closest distance to " OD2 ASP A 171 " =    2.352
peak=   -3.635 closest distance to " O   HOH Z  11 " =    1.868
peak=   -3.635 closest distance to " CZ  TYR A 169 " =    1.704
peak=   -3.630 closest distance to " O   HOH Z 389 " =    1.821
peak=   -3.622 closest distance to " O   HOH Z 211 " =    1.684
peak=   -3.597 closest distance to " CE3 TRP A 150 " =    2.119
peak=   -3.595 closest distance to " O   HOH Z 185 " =    2.365
peak=   -3.592 closest distance to " CD  ARG A 139 " =    1.637
peak=   -3.589 closest distance to " C   ALA A 158 " =    1.233
peak=   -3.586 closest distance to " CG1 VAL A 230 " =    1.849
peak=   -3.571 closest distance to " CE  MET A 105 " =    2.106
peak=   -3.570 closest distance to " CB  PRO A 163 " =    2.535
peak=   -3.569 closest distance to " O   HOH Z 166 " =    1.452
peak=   -3.569 closest distance to " CG  ASP A  50 " =    2.344
peak=   -3.559 closest distance to " O   HOH Z 165 " =    1.876
peak=   -3.558 closest distance to " N   THR A 157 " =    1.527
peak=   -3.550 closest distance to " CG  GLU A 277 " =    1.101
peak=   -3.550 closest distance to " NH2AARG A 275 " =    5.058
peak=   -3.547 closest distance to " O   SER A 210 " =    2.011
peak=   -3.539 closest distance to " C   MET A 188 " =    1.472
peak=   -3.534 closest distance to " NH2 ARG A  79 " =    1.987
peak=   -3.525 closest distance to " OG ASER A 134 " =    1.266
peak=   -3.523 closest distance to " O   HOH Z  13 " =    1.520
peak=   -3.518 closest distance to " CE2 PHE A 218 " =    2.622
peak=   -3.513 closest distance to " CB  ALA A 291 " =    2.249
peak=   -3.513 closest distance to " CG1 VAL A 250 " =    2.757
peak=   -3.511 closest distance to " O   HOH Z 435 " =    2.763
peak=   -3.509 closest distance to " CB  ALA A 248 " =    2.330
peak=   -3.506 closest distance to " O   HOH Z  44 " =    2.171
peak=   -3.505 closest distance to " CD1 PHE A  59 " =    1.971
peak=   -3.505 closest distance to " CD1 LEU A 101 " =    2.881
peak=   -3.494 closest distance to " N   THR A 235 " =    1.354
peak=   -3.493 closest distance to " O   HOH Z  19 " =    2.225
peak=   -3.492 closest distance to " CB  ASN A  69 " =    1.145
peak=   -3.484 closest distance to " C   ILE A 239 " =    2.116
peak=   -3.481 closest distance to " CA  ASP A 298 " =    1.058
peak=   -3.467 closest distance to " CG2 ILE A 263 " =    2.327
peak=   -3.463 closest distance to " CG  ARG A 269 " =    2.289
peak=   -3.448 closest distance to " CB  ALA A 291 " =    2.155
peak=   -3.439 closest distance to " CG  PHE A 283 " =    2.785
peak=   -3.433 closest distance to " NH2 ARG A  66 " =    1.737
peak=   -3.422 closest distance to " O   HOH Z 407 " =    3.001
peak=   -3.415 closest distance to " O   HOH Z  37 " =    1.813
peak=   -3.415 closest distance to " O   HOH Z  60 " =    1.841
peak=   -3.414 closest distance to " C   ASP A 231 " =    2.552
peak=   -3.413 closest distance to " O   HOH Z  47 " =    1.604
peak=   -3.412 closest distance to " O   VAL A 189 " =    2.607
peak=   -3.410 closest distance to " O   SER A  95 " =    1.643
peak=   -3.409 closest distance to " CD  LYS A 289 " =    2.525
peak=   -3.405 closest distance to " O   HOH Z 426 " =    1.576
peak=   -3.400 closest distance to " O   HOH Z 353 " =    2.074
peak=   -3.398 closest distance to " CG  TRP A 266 " =    1.908
peak=   -3.396 closest distance to " O   HOH Z  10 " =    1.439
peak=   -3.392 closest distance to " O   HOH Z 311 " =    3.667
peak=   -3.389 closest distance to " O   HOH Z 193 " =    1.936
peak=   -3.384 closest distance to " CG  LEU A 228 " =    1.009
peak=   -3.377 closest distance to " OD1 ASN A 148 " =    1.483
peak=   -3.376 closest distance to " O   HOH Z  17 " =    1.525
peak=   -3.373 closest distance to " CB  ASP A 132 " =    2.306
peak=   -3.369 closest distance to " C   GLN A  58 " =    2.254
peak=   -3.364 closest distance to " CB  ASN A  39 " =    2.196
peak=   -3.361 closest distance to " O   HOH Z 198 " =    2.263
peak=   -3.356 closest distance to " CD2 LEU A 167 " =    1.752
peak=   -3.356 closest distance to " NZ  LYS A 119 " =    3.493
peak=   -3.356 closest distance to " NE2 GLN A  88 " =    1.003
peak=   -3.355 closest distance to " CD1 ILE A 199 " =    2.444
peak=   -3.353 closest distance to " O   HOH Z  63 " =    1.171
peak=   -3.352 closest distance to " O   HOH Z 102 " =    1.633
peak=   -3.350 closest distance to " O   ALA A  51 " =    1.384
peak=   -3.346 closest distance to " N   MET A 188 " =    1.893
peak=   -3.344 closest distance to " O   GLY A 196 " =    1.106
peak=   -3.342 closest distance to " CG1 VAL A 112 " =    2.645
peak=   -3.342 closest distance to " O   SER A 271 " =    2.000
peak=   -3.328 closest distance to " O   HOH Z  52 " =    1.540
peak=   -3.327 closest distance to " O   HOH Z 234 " =    4.052
peak=   -3.326 closest distance to " OG BSER A 134 " =    1.753
peak=   -3.310 closest distance to " O   HOH Z 411 " =    3.832
peak=   -3.309 closest distance to " O   HOH Z 339 " =    1.802
peak=   -3.303 closest distance to " O   HOH Z 134 " =    2.748
peak=   -3.300 closest distance to " CE BMET A  47 " =    1.773
peak=   -3.296 closest distance to " N   ALA A  43 " =    2.614
peak=   -3.292 closest distance to " O   PRO A 198 " =    1.292
peak=   -3.292 closest distance to " CD1 LEU A  25 " =    2.498
peak=   -3.292 closest distance to " CD1 TYR A 247 " =    2.576
peak=   -3.291 closest distance to " OXT GLY A 302 " =    3.413
peak=   -3.289 closest distance to " O   GLY A  75 " =    1.799
peak=   -3.287 closest distance to " O   HOH Z 372 " =    2.295
peak=   -3.283 closest distance to " NE2 GLN A 103 " =    1.770
peak=   -3.282 closest distance to " CB  GLN A  11 " =    1.777
peak=   -3.281 closest distance to " O   HOH Z 292 " =    4.434
peak=   -3.270 closest distance to " O   PRO A 198 " =    1.232
peak=   -3.267 closest distance to " O   ALA A 161 " =    1.675
peak=   -3.256 closest distance to " OG  SER A  62 " =    1.622
peak=   -3.249 closest distance to " O   HOH Z 191 " =    5.457
peak=   -3.246 closest distance to " CD1 LEU A 228 " =    2.138
peak=   -3.246 closest distance to " O   GLY A  80 " =    2.445
peak=   -3.245 closest distance to " O   MET A  40 " =    2.706
peak=   -3.244 closest distance to " O   LEU A 167 " =    1.514
peak=   -3.238 closest distance to " O   HOH Z 295 " =    1.471
peak=   -3.235 closest distance to " O   HOH Z  43 " =    1.832
peak=   -3.233 closest distance to " CB  ASP A 132 " =    2.375
peak=   -3.232 closest distance to " OD1 ASN A  39 " =    2.173
peak=   -3.219 closest distance to " OG  SER A  26 " =    1.245
peak=   -3.215 closest distance to " O   HOH Z 389 " =    4.730
peak=   -3.209 closest distance to " N   HIS A 115 " =    2.059
peak=   -3.209 closest distance to " O   HOH Z 283 " =    2.092
peak=   -3.208 closest distance to " CG1 VAL A 112 " =    2.895
peak=   -3.207 closest distance to " N   ALA A 248 " =    1.712
peak=   -3.207 closest distance to " O   HOH Z  38 " =    1.655
peak=   -3.204 closest distance to " CG  GLU A  53 " =    1.611
peak=   -3.201 closest distance to " CA  GLY A 241 " =    3.023
peak=   -3.198 closest distance to " O   HOH Z 313 " =    1.113
peak=   -3.198 closest distance to " O   LYS A 117 " =    1.647
peak=   -3.196 closest distance to " CG1 VAL A 197 " =    2.222
peak=   -3.193 closest distance to " O   ALA A  10 " =    1.809
peak=   -3.186 closest distance to " O   HOH Z 111 " =    2.420
peak=   -3.182 closest distance to " C   THR A 279 " =    1.173
peak=   -3.178 closest distance to " O   HOH Z   6 " =    1.720
peak=   -3.175 closest distance to " OG1 THR A  82 " =    1.422
peak=   -3.164 closest distance to " NE2 GLN A 278 " =    2.042
peak=   -3.160 closest distance to " OG  SER A 206 " =    1.634
peak=   -3.158 closest distance to " O   HOH Z 384 " =    3.381
peak=   -3.157 closest distance to " O   HOH Z 139 " =    3.143
peak=   -3.156 closest distance to " O   SER A  22 " =    2.176
peak=   -3.156 closest distance to " O   HOH Z 350 " =    1.664
peak=   -3.155 closest distance to " O   HOH Z 123 " =    2.378
peak=   -3.154 closest distance to " O   GLN A 240 " =    2.137
peak=   -3.152 closest distance to " N   SER A   3 " =    2.059
peak=   -3.148 closest distance to " O   VAL A 125 " =    2.314
peak=   -3.147 closest distance to " N   VAL A 230 " =    1.173
peak=   -3.143 closest distance to " O   HOH Z 131 " =    4.089
peak=   -3.139 closest distance to " O   GLY A  80 " =    2.521
peak=   -3.136 closest distance to " O   HOH Z 313 " =    1.681
peak=   -3.134 closest distance to " CA  GLY A 133 " =    2.261
peak=   -3.133 closest distance to " O   HOH Z 310 " =    1.748
peak=   -3.132 closest distance to " NE2 GLN A 194 " =    1.758
peak=   -3.130 closest distance to " CD2 LEU A 237 " =    2.631
peak=   -3.128 closest distance to " NH2 ARG A  79 " =    1.591
peak=   -3.124 closest distance to " O   HOH Z 175 " =    4.311
peak=   -3.120 closest distance to " C   ASP A 270 " =    1.287
peak=   -3.105 closest distance to " CG  GLU A   2 " =    1.845
peak=   -3.104 closest distance to " N   LYS A 289 " =    1.594
peak=   -3.100 closest distance to " O   HOH Z 222 " =    1.496
peak=   -3.099 closest distance to " CG1 VAL A 296 " =    1.327
peak=   -3.097 closest distance to " CA  GLY A 133 " =    1.932
peak=   -3.096 closest distance to " CE1 HIS A  81 " =    1.298
peak=   -3.094 closest distance to " O   HOH Z 149 " =    2.074
peak=   -3.089 closest distance to " O   HOH Z 385 " =    2.212
peak=   -3.074 closest distance to " O   HOH Z 244 " =    2.006
peak=   -3.071 closest distance to " O   HOH Z 113 " =    2.430
peak=   -3.067 closest distance to " O   HOH Z 128 " =    2.595
peak=   -3.054 closest distance to " O   SER A 276 " =    1.672
peak=   -3.051 closest distance to " OD1 ASP A 200 " =    1.374
peak=   -3.050 closest distance to " CD2 TYR A 293 " =    2.094
peak=   -3.041 closest distance to " CB  ASP A 286 " =    2.246
peak=   -3.012 closest distance to " CD  GLN A  88 " =    0.789
peak=   -3.006 closest distance to " CD2 TYR A 247 " =    2.303

================= 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    :  0.4167 0.4053   6.203957e+00   6.177583e+00
   1_bss:  0.4083 0.3964   6.199097e+00   6.160838e+00
   1_xyz:  0.2930 0.3155   5.948999e+00   6.000193e+00
   1_adp:  0.2202 0.2502   5.687433e+00   5.802660e+00
   1_occ:  0.2196 0.2501   5.686051e+00   5.802651e+00
   2_bss:  0.2144 0.2443   5.683438e+00   5.794494e+00
   2_xyz:  0.1530 0.1850   5.377878e+00   5.541624e+00
   2_adp:  0.1423 0.1761   5.316015e+00   5.494662e+00
   2_occ:  0.1422 0.1762   5.315672e+00   5.494577e+00
   3_bss:  0.1419 0.1764   5.316604e+00   5.495375e+00
   3_xyz:  0.1226 0.1584   5.195004e+00   5.402701e+00
   3_adp:  0.1193 0.1560   5.173279e+00   5.385979e+00
   3_occ:  0.1192 0.1560   5.173095e+00   5.386140e+00
   4_bss:  0.1192 0.1560   5.173095e+00   5.386140e+00
   4_xyz:  0.1151 0.1552   5.152375e+00   5.380193e+00
   4_adp:  0.1150 0.1549   5.151412e+00   5.378650e+00
   4_occ:  0.1150 0.1548   5.151311e+00   5.378689e+00
   5_bss:  0.1152 0.1551   5.153828e+00   5.380465e+00
   5_xyz:  0.1112 0.1540   5.132306e+00   5.373222e+00
   5_adp:  0.1106 0.1550   5.134612e+00   5.381214e+00
   5_occ:  0.1104 0.1550   5.133428e+00   5.380473e+00
   5_bss:  0.1104 0.1550   5.133157e+00   5.380253e+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:  0.341  18.737   7.287   8.677   8.100   0.000   0.000   0.000
   1_xyz:  0.341  18.737   7.287   8.677   8.100   0.000   0.000   0.000
   1_adp:  0.341  18.737   7.287   8.677   8.100   0.000   0.000   0.000
   1_occ:  0.341  18.737   7.287   8.677   8.100   0.000   0.000   0.000
   2_bss:  0.334  39.298   4.023   5.029   5.312   0.000   0.000   0.000
   2_xyz:  0.334  39.298   4.023   5.029   5.312   0.000   0.000   0.000
   2_adp:  0.334  39.298   4.023   5.029   5.312   0.000   0.000   0.000
   2_occ:  0.334  39.298   4.023   5.029   5.312   0.000   0.000   0.000
   3_bss:  0.326  39.298   3.061   3.917   4.485   0.000   0.000   0.000
   3_xyz:  0.326  39.298   3.061   3.917   4.485   0.000   0.000   0.000
   3_adp:  0.326  39.298   3.061   3.917   4.485   0.000   0.000   0.000
   3_occ:  0.326  39.298   3.061   3.917   4.485   0.000   0.000   0.000
   4_bss:  0.326  39.298   3.061   3.917   4.485   0.000   0.000   0.000
   4_xyz:  0.326  39.298   3.061   3.917   4.485   0.000   0.000   0.000
   4_adp:  0.326  39.298   3.061   3.917   4.485   0.000   0.000   0.000
   4_occ:  0.326  39.298   3.061   3.917   4.485   0.000   0.000   0.000
   5_bss:  0.326  39.298   2.965   3.685   4.364   0.000   0.000   0.000
   5_xyz:  0.326  39.298   2.965   3.685   4.364   0.000   0.000   0.000
   5_adp:  0.326  39.298   2.965   3.685   4.364   0.000   0.000   0.000
   5_occ:  0.326  39.298   2.965   3.685   4.364   0.000   0.000   0.000
   5_bss:  0.321  43.054  -0.681  -0.015   0.696  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  43.416 0.6042  0.6649    45619.443
   1_bss:  43.492 0.6007  0.8423    43368.117
   1_xyz:  33.521 0.7173  0.9791    26771.059
   1_adp:  24.171 0.8212  1.0717    15586.931
   1_occ:  24.162 0.8213  1.0714    15574.462
   2_bss:  23.875 0.8240  0.9552    15209.966
   2_xyz:  17.346 0.8862  0.9997     8645.056
   2_adp:  16.212 0.8968  1.0093     7881.109
   2_occ:  16.213 0.8967  1.0092     7877.782
   3_bss:  16.240 0.8965  0.9732     7908.500
   3_xyz:  14.241 0.9132  0.9806     6477.371
   3_adp:  13.869 0.9164  0.9822     6292.296
   3_occ:  13.867 0.9164  0.9822     6294.256
   4_bss:  13.867 0.9164  0.9822     6294.256
   4_xyz:  13.678 0.9179  0.9824     6198.133
   4_adp:  13.631 0.9184  0.9814     6180.199
   4_occ:  13.630 0.9184  0.9813     6181.533
   5_bss:  13.683 0.9180  0.9754     6231.249
   5_xyz:  13.537 0.9190  0.9761     6138.055
   5_adp:  13.720 0.9176  0.9731     6222.182
   5_occ:  13.702 0.9178  0.9730     6216.171
   5_bss:  13.695 0.9178  0.9761     6210.660
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.3682e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.3682e+01
   1_xyz:   1.464  0.011  0.100 17.668  0.006  4.122   1.1027e-01
   1_adp:   1.464  0.011  0.100 17.668  0.006  4.122   1.1027e-01
   1_occ:   1.464  0.011  0.100 17.668  0.006  4.122   1.1027e-01
   2_bss:   1.464  0.011  0.100 17.668  0.006  4.122   1.1027e-01
   2_xyz:   0.930  0.006  0.071 15.914  0.003  4.121   5.5454e-02
   2_adp:   0.930  0.006  0.071 15.914  0.003  4.121   5.5454e-02
   2_occ:   0.930  0.006  0.071 15.914  0.003  4.121   5.5454e-02
   3_bss:   0.930  0.006  0.071 15.914  0.003  4.121   5.5454e-02
   3_xyz:   0.927  0.005  0.075 15.445  0.003  4.126   5.3557e-02
   3_adp:   0.927  0.005  0.075 15.445  0.003  4.126   5.3557e-02
   3_occ:   0.927  0.005  0.075 15.445  0.003  4.126   5.3557e-02
   4_bss:   0.927  0.005  0.075 15.445  0.003  4.126   5.3557e-02
   4_xyz:   0.919  0.006  0.076 15.414  0.003  4.117   5.3875e-02
   4_adp:   0.919  0.006  0.076 15.414  0.003  4.117   5.3875e-02
   4_occ:   0.919  0.006  0.076 15.414  0.003  4.117   5.3875e-02
   5_bss:   0.919  0.006  0.076 15.414  0.003  4.117   5.3875e-02
   5_xyz:   1.006  0.007  0.082 15.379  0.004  4.119   6.1296e-02
   5_adp:   1.006  0.007  0.082 15.379  0.004  4.119   6.1296e-02
   5_occ:   1.006  0.007  0.082 15.379  0.004  4.119   6.1296e-02
   5_bss:   1.006  0.007  0.082 15.379  0.004  4.119   6.1296e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9601e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9601e+00
   1_xyz:  12.243  0.128  0.424 86.757  0.042  2.260   8.2636e-02
   1_adp:  12.243  0.128  0.424 86.757  0.042  2.260   8.2636e-02
   1_occ:  12.243  0.128  0.424 86.757  0.042  2.260   8.2636e-02
   2_bss:  12.243  0.128  0.424 86.757  0.042  2.260   8.2636e-02
   2_xyz:   6.543  0.056  0.349 81.469  0.029  2.384   3.7336e-02
   2_adp:   6.543  0.056  0.349 81.469  0.029  2.384   3.7336e-02
   2_occ:   6.543  0.056  0.349 81.469  0.029  2.384   3.7336e-02
   3_bss:   6.543  0.056  0.349 81.469  0.029  2.384   3.7336e-02
   3_xyz:   6.196  0.039  0.496 82.490  0.037  2.396   3.1083e-02
   3_adp:   6.196  0.039  0.496 82.490  0.037  2.396   3.1083e-02
   3_occ:   6.196  0.039  0.496 82.490  0.037  2.396   3.1083e-02
   4_bss:   6.196  0.039  0.496 82.490  0.037  2.396   3.1083e-02
   4_xyz:   6.582  0.038  0.482 82.898  0.034  2.381   3.0898e-02
   4_adp:   6.582  0.038  0.482 82.898  0.034  2.381   3.0898e-02
   4_occ:   6.582  0.038  0.482 82.898  0.034  2.381   3.0898e-02
   5_bss:   6.582  0.038  0.482 82.898  0.034  2.381   3.0898e-02
   5_xyz:   6.957  0.044  0.574 82.869  0.037  2.325   3.9419e-02
   5_adp:   6.957  0.044  0.574 82.869  0.037  2.325   3.9419e-02
   5_occ:   6.957  0.044  0.574 82.869  0.037  2.325   3.9419e-02
   5_bss:   6.957  0.044  0.574 82.869  0.037  2.325   3.9419e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00
   1_bss:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_xyz:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_adp:  61.04   0.00  10.20  61.04   0.00   7.01  56.12   0.00  27.56
   1_occ:  61.04   0.00  10.20  61.04   0.00   7.01  56.12   0.00  27.56
   2_bss:  61.04   0.00  10.20  61.04   0.00   7.01  56.12   0.00  27.56
   2_xyz:  61.04   0.00  10.20  61.04   0.00   7.01  56.12   0.00  27.56
   2_adp:  71.07   0.00  10.76  71.07   0.00   7.05  56.04   0.84  30.97
   2_occ:  71.07   0.00  10.76  71.07   0.00   7.05  56.04   0.84  30.97
   3_bss:  71.07   0.00  10.76  71.07   0.00   7.05  56.04   0.84  30.97
   3_xyz:  71.07   0.00  10.76  71.07   0.00   7.05  56.04   0.84  30.97
   3_adp:  71.76   0.00  11.04  71.76   0.00   7.08  60.61   0.96  32.58
   3_occ:  71.76   0.00  11.04  71.76   0.00   7.08  60.61   0.96  32.58
   4_bss:  71.76   0.00  11.04  71.76   0.00   7.08  60.61   0.96  32.58
   4_xyz:  71.76   0.00  11.04  71.76   0.00   7.08  60.61   0.96  32.58
   4_adp:  73.18   0.00  10.88  73.18   0.00   7.02  62.02   0.80  31.87
   4_occ:  73.18   0.00  10.88  73.18   0.00   7.02  62.02   0.80  31.87
   5_bss:  73.18   0.00  10.88  73.18   0.00   7.02  62.02   0.80  31.87
   5_xyz:  73.18   0.00  10.88  73.18   0.00   7.02  62.02   0.80  31.87
   5_adp:  78.22   0.00  11.01  78.22   0.00   7.08  64.77   0.69  32.40
   5_occ:  78.22   0.00  11.01  78.22   0.00   7.08  64.77   0.69  32.40
   5_bss:  81.97   3.76  14.76  81.97   3.76  10.84  68.53   4.44  36.15
------------------------------------------------------------------------
 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:    1.161    0.018    0.400
   1_adp:    1.161    0.018    0.400
   1_occ:    1.161    0.018    0.400
   2_bss:    1.161    0.018    0.400
   2_xyz:    1.508    0.034    0.473
   2_adp:    1.508    0.034    0.473
   2_occ:    1.508    0.034    0.473
   3_bss:    1.508    0.034    0.473
   3_xyz:    1.511    0.045    0.498
   3_adp:    1.511    0.045    0.498
   3_occ:    1.511    0.045    0.498
   4_bss:    1.511    0.045    0.498
   4_xyz:    1.589    0.050    0.511
   4_adp:    1.589    0.050    0.511
   4_occ:    1.589    0.050    0.511
   5_bss:    1.589    0.050    0.511
   5_xyz:    1.598    0.026    0.521
   5_adp:    1.598    0.026    0.521
   5_occ:    1.598    0.026    0.521
   5_bss:    1.598    0.026    0.521
------------------------------------------------------------------------

CPU time actual refinement: 329.47


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_554/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_554/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_554/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_554/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_554/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 329.32 
  Macro-tasks:
    bulk solvent and scale       = 40.79  
    individual site refinement   = 139.14 
    weights calculation          = 32.16  
    collect and process          = 6.56   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 218.78 
  Micro-tasks:
    mask                            = 1.77   
    f_calc                          = 100.09 
    alpha_beta                      = 8.07   
    target                          = 1.13   
    gradients_wrt_atomic_parameters = 112.44 
    fmodel                         = 7.24   
    r_factors                      = 0.20   
    phase_errors                   = 10.96  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 242.18 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.571 micro seconds
Total CPU time: 5.72 minutes
from_scatterers_fft:    655 calls, 99.70 s
gradients_fft:          599 calls, 98.33 s

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

# Date 2008-01-16 Time 01:51:55 PST -0800 (1200477115.49 s)
Start R-work = 0.4167, R-free = 0.4053 (no bulk solvent and anisotropic scale)
Final R-work = 0.1282, R-free = 0.1708 (no bulk solvent and anisotropic scale)

Start R-work = 0.4083, R-free = 0.3964
Final R-work = 0.1104, R-free = 0.1550