# Date 2008-01-16 Time 02:17:29 PST -0800 (1200478649.94 s)
#phil __OFF__

Command line arguments: "../775.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 22887
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 775

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.6012, 46.6953, 86.39, 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: 2.78, per 1000 atoms: 0.98


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 46.6953, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0485 1.99157
Completeness in resolution range: 0.973512
Completeness with d_max=infinity: 0.970473

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0485
                             d_min =   1.9916

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 46.6953, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0485 1.99157
Completeness in resolution range: 0.973512
Completeness with d_max=infinity: 0.970473

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0489 -  4.2613 [2108/2132]  1898   210  10.0%
  bin  2:  4.2613 -  3.3951 [2034/2054]  1829   205  10.1%
  bin  3:  3.3951 -  2.9697 [2003/2022]  1802   201  10.0%
  bin  4:  2.9697 -  2.6999 [1986/2016]  1791   195   9.8%
  bin  5:  2.6999 -  2.5073 [1981/2000]  1783   198  10.0%
  bin  6:  2.5073 -  2.3601 [1959/1984]  1757   202  10.3%
  bin  7:  2.3601 -  2.2423 [1948/1976]  1755   193   9.9%
  bin  8:  2.2423 -  2.1449 [1955/1991]  1762   193   9.9%
  bin  9:  2.1449 -  2.0626 [1927/1969]  1735   192  10.0%
  bin 10:  2.0626 -  1.9916 [1688/1978]  1518   170  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_775/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: 0.11 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: 9
        2.42 -     3.04: 2201
        3.04 -     3.66: 4658
        3.66 -     4.28: 9061
        4.28 -     4.90: 12328
  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
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.362 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 341 " - " O   HOH Z 207 "  2.362 3.040 -x+1/2,-y+1,z-1/2
  ... (remaining 28252 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_775/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_775/model_refine_001.geo

CPU time processing inputs: 7.75


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.60125 46.69535 86.39 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 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4127   r_free= 0.3981   ksol= 0.00   Bsol= 0.00   scale= 0.834    |
|                                                                             |
| 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:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.196503                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0489 -  4.7527 0.99   1378  152 0.3567 0.3405      6.5026      6.4279|
|  2:  4.7527 -  3.7922 0.99   1314  147 0.3002 0.2974      6.5808      6.5718|
|  3:  3.7922 -  3.3187 0.99   1294  143 0.3432 0.3185      6.4926      6.5093|
|  4:  3.3187 -  3.0180 0.99   1278  146 0.3847 0.3326      6.4133      6.3008|
|  5:  3.0180 -  2.8031 0.99   1289  142 0.4291 0.4224      6.2771      6.3128|
|  6:  2.8031 -  2.6388 0.99   1275  139 0.4331 0.4914      6.2122      6.1705|
|  7:  2.6388 -  2.5073 0.99   1275  140 0.4673 0.4512      6.1858      6.2075|
|  8:  2.5073 -  2.3986 0.98   1246  142 0.4637 0.4283      6.1353      6.0925|
|  9:  2.3986 -  2.3066 0.98   1265  139 0.4457 0.4515      6.0562      6.0433|
| 10:  2.3066 -  2.2273 1.00   1253  143 0.4768 0.4478      6.0868       6.053|
| 11:  2.2273 -  2.1578 0.97   1253  133 0.4901 0.3975      6.0271      5.9282|
| 12:  2.1578 -  2.0963 0.98   1241  142 0.4640 0.4913        5.95      5.9852|
| 13:  2.0963 -  2.0413 0.99   1268  140 0.4853 0.4847      5.8717      5.8619|
| 14:  2.0413 -  1.9916 0.79   1001  111 0.4826 0.4538      5.8211      5.7191|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0489 -  4.7527  1378   152  0.75  30.05   0.81     0.78      54986.00|
|  2:  4.7527 -  3.7922  1314   147  0.81  25.71   0.92     0.85      62689.22|
|  3:  3.7922 -  3.3187  1294   143  0.75  31.00   0.89     0.83      63264.25|
|  4:  3.3187 -  3.0180  1278   146  0.70  35.37   0.85     0.75      57431.27|
|  5:  3.0180 -  2.8031  1289   142  0.60  43.70   0.79     0.67      53814.63|
|  6:  2.8031 -  2.6388  1275   139  0.57  46.83   0.78     0.62      51152.73|
|  7:  2.6388 -  2.5073  1275   140  0.53  49.47   0.76     0.60      48772.37|
|  8:  2.5073 -  2.3986  1246   142  0.53  49.43   0.78     0.60      44329.81|
|  9:  2.3986 -  2.3066  1265   139  0.56  47.02   0.76     0.62      37521.94|
| 10:  2.3066 -  2.2273  1253   143  0.57  46.76   0.79     0.63      32678.60|
| 11:  2.2273 -  2.1578  1253   133  0.55  48.02   0.77     0.63      31000.01|
| 12:  2.1578 -  2.0963  1241   142  0.51  51.64   0.81     0.60      32059.31|
| 13:  2.0963 -  2.0413  1268   140  0.48  54.11   0.77     0.56      29244.12|
| 14:  2.0413 -  1.9916  1001   111  0.52  50.73   0.75     0.54      22144.75|
|alpha:            min =        0.54 max =            0.85 mean =         0.67|
|beta:             min =    22144.75 max =        63264.25 mean =     44906.44|
|figures of merit: min =        0.00 max =            1.00 mean =         0.61|
|phase err.(work): min =        0.00 max =           90.00 mean =        43.27|
|phase err.(test): min =        0.00 max =           89.92 mean =        43.41|
|-----------------------------------------------------------------------------|

============================== 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 = 6.233840              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 72.554   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.516525              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.593   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       21 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      167 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      682 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1495 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2639 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3920 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5068 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6560 |
| 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 |       53.798 |
| 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 |       1.648 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.926)------------------------------------------|
|    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 = 11.926)------------------------------------------|
|    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 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4217   r_free= 0.4070   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:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.204801                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4042   r_free= 0.3856   ksol= 0.36   Bsol= 20.00   scale= 1.032   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.62,8.49,8.20,0.00,0.00,0.00); trace/3= 8.10                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.192961                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.938997              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 74.775   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.525103              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 75.998   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4042      final r-factor (work) = 0.2892          |
| start r-factor (free) = 0.3856      final r-factor (free) = 0.3089          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 72.2624 = 5.94 * 0.50 * 6.2180 + 1.00 * 53.7981                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.9530 = 5.94 * 0.50 * 6.0098 + 1.00 * 0.1069                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2892      final r-factor (work) = 0.2129          |
| start r-factor (free) = 0.3089      final r-factor (free) = 0.2437          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1705 = 0.53 * 1.00 * 6.0098 + 1.00 * 0.0148                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0427 = 0.53 * 1.00 * 5.7737 + 1.00 * 0.0109                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 34     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.926)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    55.87   10.18    None  None   None       |
|    all(noH): 2823   0      0.00    55.87   10.18    None  None   None       |
|    Sol.    : 438    0      0.00    55.87   28.04    None  None   None       |
|    Mac.    : 2385   0      0.00    55.51   6.90     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 -   5.587: 1316   |   5:    27.936 -  33.524:  100        |
|      1:     5.587 -  11.175:  733   |   6:    33.524 -  39.111:   89        |
|      2:    11.175 -  16.762:  235   |   7:    39.111 -  44.698:   54        |
|      3:    16.762 -  22.349:  131   |   8:    44.698 -  50.285:   23        |
|      4:    22.349 -  27.936:  125   |   9:    50.285 -  55.873:   17        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2129 r_free = 0.2437             target_work(ml) = 5.660         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2122 r_free = 0.2435             target_work(ml) = 5.659         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2122   r_free= 0.2435   ksol= 0.36   Bsol= 20.00   scale= 1.090   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.62,8.49,8.20,0.00,0.00,0.00); trace/3= 8.10                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.658603                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2058   r_free= 0.2368   ksol= 0.34   Bsol= 41.36   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.27,4.60,5.25,0.00,0.00,0.00); trace/3= 4.70                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.653047                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.560076              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 92.560   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.259797              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 118.116  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2058      final r-factor (work) = 0.1445          |
| start r-factor (free) = 0.2368      final r-factor (free) = 0.1817          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5183 = 2.56 * 0.50 * 5.7903 + 1.00 * 0.1065                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0743 = 2.56 * 0.50 * 5.4790 + 1.00 * 0.0609                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1445      final r-factor (work) = 0.1340          |
| start r-factor (free) = 0.1817      final r-factor (free) = 0.1738          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4341 = 0.26 * 1.00 * 5.4790 + 1.00 * 0.0107                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4741 = 0.26 * 1.00 * 5.2989 + 1.00 * 0.0975                               |
|-----------------------------------------------------------------------------|
| number of iterations = 12      |    number of function evaluations = 13     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.926)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    57.73   10.47    None  None   None       |
|    all(noH): 2823   0      0.00    57.73   10.47    None  None   None       |
|    Sol.    : 438    0      0.00    56.72   30.19    None  None   None       |
|    Mac.    : 2385   0      0.00    57.73   6.84     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:     0.000 -   5.773: 1413   |   5:    28.866 -  34.639:  103        |
|      1:     5.773 -  11.546:  655   |   6:    34.639 -  40.412:  107        |
|      2:    11.546 -  17.319:  236   |   7:    40.412 -  46.185:   66        |
|      3:    17.319 -  23.092:  108   |   8:    46.185 -  51.958:   25        |
|      4:    23.092 -  28.866:   96   |   9:    51.958 -  57.731:   14        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1340 r_free = 0.1738             target_work(ml) = 5.276         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1339 r_free = 0.1737             target_work(ml) = 5.276         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1339   r_free= 0.1737   ksol= 0.34   Bsol= 41.36   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.27,4.60,5.25,0.00,0.00,0.00); trace/3= 4.70                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.275864                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1340   r_free= 0.1736   ksol= 0.33   Bsol= 41.36   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.56,3.70,4.76,0.00,0.00,0.00); trace/3= 4.01                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.277015                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.656777              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 119.024  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.615523              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.983   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1340      final r-factor (work) = 0.1172          |
| start r-factor (free) = 0.1736      final r-factor (free) = 0.1601          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1048 = 2.66 * 0.50 * 5.3026 + 1.00 * 0.0609                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9933 = 2.66 * 0.50 * 5.2132 + 1.00 * 0.0682                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1172      final r-factor (work) = 0.1131          |
| start r-factor (free) = 0.1601      final r-factor (free) = 0.1584          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 18.8602 = 3.62 * 1.00 * 5.2132 + 1.00 * 0.0119                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 18.6548 = 3.62 * 1.00 * 5.1557 + 1.00 * 0.0142                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.926)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    75.09   11.33    None  None   None       |
|    all(noH): 2823   0      0.00    75.09   11.33    None  None   None       |
|    Sol.    : 438    0      0.17    75.09   34.36    None  None   None       |
|    Mac.    : 2385   0      0.00    74.89   7.11     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 -   7.509: 1679   |   5:    37.545 -  45.054:   87        |
|      1:     7.509 -  15.018:  539   |   6:    45.054 -  52.563:   77        |
|      2:    15.018 -  22.527:  164   |   7:    52.563 -  60.071:   42        |
|      3:    22.527 -  30.036:  105   |   8:    60.071 -  67.580:   23        |
|      4:    30.036 -  37.545:   98   |   9:    67.580 -  75.089:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1131 r_free = 0.1584             target_work(ml) = 5.152         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1130 r_free = 0.1583             target_work(ml) = 5.152         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1130   r_free= 0.1583   ksol= 0.33   Bsol= 41.36   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.56,3.70,4.76,0.00,0.00,0.00); trace/3= 4.01                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.151593                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1130   r_free= 0.1583   ksol= 0.32   Bsol= 41.36   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.52,3.63,4.76,0.00,0.00,0.00); trace/3= 3.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.151166                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.235170              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 141.794  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.148415              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 128.807  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1130      final r-factor (work) = 0.1111          |
| start r-factor (free) = 0.1583      final r-factor (free) = 0.1581          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8297 = 2.24 * 0.50 * 5.1552 + 1.00 * 0.0683                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8134 = 2.24 * 0.50 * 5.1454 + 1.00 * 0.0630                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1111      final r-factor (work) = 0.1132          |
| start r-factor (free) = 0.1581      final r-factor (free) = 0.1557          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7778 = 0.15 * 1.00 * 5.1454 + 1.00 * 0.0142                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7815 = 0.15 * 1.00 * 5.1549 + 1.00 * 0.0165                               |
|-----------------------------------------------------------------------------|
| number of iterations = 10      |    number of function evaluations = 11     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.926)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    74.00   10.90    None  None   None       |
|    all(noH): 2823   0      0.00    74.00   10.90    None  None   None       |
|    Sol.    : 438    0      0.96    69.69   32.52    None  None   None       |
|    Mac.    : 2385   0      0.00    74.00   6.94     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 -   7.400: 1714   |   5:    36.999 -  44.399:   85        |
|      1:     7.400 -  14.800:  539   |   6:    44.399 -  51.799:   71        |
|      2:    14.800 -  22.199:  145   |   7:    51.799 -  59.199:   37        |
|      3:    22.199 -  29.599:  108   |   8:    59.199 -  66.598:   19        |
|      4:    29.599 -  36.999:   99   |   9:    66.598 -  73.998:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1132 r_free = 0.1557             target_work(ml) = 5.144         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1132 r_free = 0.1556             target_work(ml) = 5.144         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1132   r_free= 0.1556   ksol= 0.32   Bsol= 41.36   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.52,3.63,4.76,0.00,0.00,0.00); trace/3= 3.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.143524                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1132   r_free= 0.1556   ksol= 0.32   Bsol= 41.36   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.52,3.63,4.76,0.00,0.00,0.00); trace/3= 3.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.143524                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.760944              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 157.185  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.380611              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.247   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1132      final r-factor (work) = 0.1102          |
| start r-factor (free) = 0.1556      final r-factor (free) = 0.1546          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1788 = 2.76 * 0.50 * 5.1546 + 1.00 * 0.0630                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1555 = 2.76 * 0.50 * 5.1311 + 1.00 * 0.0721                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1102      final r-factor (work) = 0.1092          |
| start r-factor (free) = 0.1546      final r-factor (free) = 0.1553          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9728 = 0.38 * 1.00 * 5.1311 + 1.00 * 0.0198                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9740 = 0.38 * 1.00 * 5.1221 + 1.00 * 0.0244                               |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.926)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    75.71   10.90    None  None   None       |
|    all(noH): 2823   0      0.00    75.71   10.90    None  None   None       |
|    Sol.    : 438    0      0.66    67.58   32.41    None  None   None       |
|    Mac.    : 2385   0      0.00    75.71   6.95     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 -   7.571: 1717   |   5:    37.856 -  45.427:   83        |
|      1:     7.571 -  15.142:  527   |   6:    45.427 -  52.998:   71        |
|      2:    15.142 -  22.713:  150   |   7:    52.998 -  60.569:   24        |
|      3:    22.713 -  30.284:  113   |   8:    60.569 -  68.140:   14        |
|      4:    30.284 -  37.856:  119   |   9:    68.140 -  75.711:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1092 r_free = 0.1553             target_work(ml) = 5.127         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1089 r_free = 0.1552             target_work(ml) = 5.126         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1089   r_free= 0.1552   ksol= 0.32   Bsol= 41.36   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.52,3.63,4.76,0.00,0.00,0.00); trace/3= 3.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.126017                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0489 -  4.7527 0.99   1378  152 0.0990 0.1295      5.3745      5.5075|
|  2:  4.7527 -  3.7922 0.99   1314  147 0.0852 0.1170      5.4398      5.6594|
|  3:  3.7922 -  3.3187 0.99   1294  143 0.1045 0.1495      5.4728      5.8389|
|  4:  3.3187 -  3.0180 0.99   1278  146 0.1172 0.1536      5.4363      5.5778|
|  5:  3.0180 -  2.8031 0.99   1289  142 0.1283 0.1718      5.3127      5.5686|
|  6:  2.8031 -  2.6388 0.99   1275  139 0.1144 0.1849      5.1842      5.4455|
|  7:  2.6388 -  2.5073 0.99   1275  140 0.1252 0.1497      5.1582      5.3239|
|  8:  2.5073 -  2.3986 0.98   1246  142 0.1126 0.1737      5.0495      5.3667|
|  9:  2.3986 -  2.3066 0.98   1265  139 0.1132 0.1698      5.0216      5.2535|
| 10:  2.3066 -  2.2273 1.00   1253  143 0.1065 0.1654      4.9339      5.2156|
| 11:  2.2273 -  2.1578 0.97   1253  133 0.1104 0.1710      4.9216      5.2177|
| 12:  2.1578 -  2.0963 0.98   1241  142 0.1076 0.1693      4.8464      5.2165|
| 13:  2.0963 -  2.0413 0.99   1268  140 0.1103 0.1686      4.7831      5.0506|
| 14:  2.0413 -  1.9916 0.79   1001  111 0.1036 0.1688      4.6766      4.9101|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0489 -  4.7527  1378   152  0.94   8.96   0.98     0.96       6952.55|
|  2:  4.7527 -  3.7922  1314   147  0.95   7.85   1.02     1.01       9133.27|
|  3:  3.7922 -  3.3187  1294   143  0.93  11.20   1.02     1.02      10400.87|
|  4:  3.3187 -  3.0180  1278   146  0.92  13.04   1.00     0.99       9989.86|
|  5:  3.0180 -  2.8031  1289   142  0.90  15.57   0.99     0.97       8145.48|
|  6:  2.8031 -  2.6388  1275   139  0.91  15.40   0.98     0.95       6828.68|
|  7:  2.6388 -  2.5073  1275   140  0.90  15.58   0.99     0.96       6084.61|
|  8:  2.5073 -  2.3986  1246   142  0.91  14.44   0.99     0.97       5014.05|
|  9:  2.3986 -  2.3066  1265   139  0.91  15.02   1.01     0.99       4928.78|
| 10:  2.3066 -  2.2273  1253   143  0.91  14.66   1.00     0.97       4126.68|
| 11:  2.2273 -  2.1578  1253   133  0.90  16.11   1.00     0.97       4252.33|
| 12:  2.1578 -  2.0963  1241   142  0.92  14.47   1.02     1.00       3683.92|
| 13:  2.0963 -  2.0413  1268   140  0.91  15.57   1.01     1.00       3305.67|
| 14:  2.0413 -  1.9916  1001   111  0.92  14.68   0.99     0.95       2647.20|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2647.20 max =        10400.87 mean =      6192.06|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.95 mean =        13.69|
|phase err.(test): min =        0.00 max =           87.24 mean =        13.25|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1091   r_free= 0.1550   ksol= 0.32   Bsol= 47.21   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.44,-0.34,0.79,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.126737                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1091   r_free= 0.1550   ksol= 0.32   Bsol= 47.21   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.44,-0.34,0.79,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.126737                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0489 -  4.7527 0.99   1378  152 0.0997 0.1282      5.3888      5.5108|
|  2:  4.7527 -  3.7922 0.99   1314  147 0.0860 0.1146      5.4432        5.64|
|  3:  3.7922 -  3.3187 0.99   1294  143 0.1046 0.1487      5.4695      5.8354|
|  4:  3.3187 -  3.0180 0.99   1278  146 0.1171 0.1539      5.4343       5.578|
|  5:  3.0180 -  2.8031 0.99   1289  142 0.1281 0.1701      5.3104      5.5583|
|  6:  2.8031 -  2.6388 0.99   1275  139 0.1144 0.1839      5.1822      5.4456|
|  7:  2.6388 -  2.5073 0.99   1275  140 0.1252 0.1498       5.158      5.3249|
|  8:  2.5073 -  2.3986 0.98   1246  142 0.1128 0.1742        5.05      5.3671|
|  9:  2.3986 -  2.3066 0.98   1265  139 0.1130 0.1700      5.0212       5.254|
| 10:  2.3066 -  2.2273 1.00   1253  143 0.1064 0.1651      4.9346      5.2159|
| 11:  2.2273 -  2.1578 0.97   1253  133 0.1104 0.1719      4.9218      5.2207|
| 12:  2.1578 -  2.0963 0.98   1241  142 0.1075 0.1692      4.8468      5.2167|
| 13:  2.0963 -  2.0413 0.99   1268  140 0.1101 0.1687      4.7829      5.0514|
| 14:  2.0413 -  1.9916 0.79   1001  111 0.1037 0.1683      4.6762      4.9091|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0489 -  4.7527  1378   152  0.94   9.02   0.98     0.95       7075.63|
|  2:  4.7527 -  3.7922  1314   147  0.95   7.83   1.02     1.00       9048.13|
|  3:  3.7922 -  3.3187  1294   143  0.94  11.07   1.02     1.02      10228.54|
|  4:  3.3187 -  3.0180  1278   146  0.92  12.98   1.00     0.99       9904.00|
|  5:  3.0180 -  2.8031  1289   142  0.90  15.51   0.99     0.97       8089.64|
|  6:  2.8031 -  2.6388  1275   139  0.91  15.35   0.98     0.96       6783.96|
|  7:  2.6388 -  2.5073  1275   140  0.91  15.55   0.99     0.96       6068.04|
|  8:  2.5073 -  2.3986  1246   142  0.91  14.47   0.99     0.97       5030.25|
|  9:  2.3986 -  2.3066  1265   139  0.91  15.03   1.01     0.98       4936.85|
| 10:  2.3066 -  2.2273  1253   143  0.91  14.68   1.00     0.97       4136.42|
| 11:  2.2273 -  2.1578  1253   133  0.90  16.14   1.00     0.97       4258.75|
| 12:  2.1578 -  2.0963  1241   142  0.92  14.52   1.02     1.00       3694.10|
| 13:  2.0963 -  2.0413  1268   140  0.91  15.58   1.01     1.00       3308.07|
| 14:  2.0413 -  1.9916  1001   111  0.92  14.67   0.99     0.95       2643.51|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2643.51 max =        10228.54 mean =      6171.50|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.91 mean =        13.68|
|phase err.(test): min =        0.00 max =           89.34 mean =        13.23|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.926)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.97    79.68   14.87    None  None   None       |
|    all(noH): 2823   0      3.97    79.68   14.87    None  None   None       |
|    Sol.    : 438    0      4.63    71.54   36.37    None  None   None       |
|    Mac.    : 2385   0      3.97    79.68   10.92    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:     3.969 -  11.540: 1717   |   5:    41.825 -  49.396:   83        |
|      1:    11.540 -  19.112:  527   |   6:    49.396 -  56.967:   71        |
|      2:    19.112 -  26.683:  150   |   7:    56.967 -  64.538:   24        |
|      3:    26.683 -  34.254:  113   |   8:    64.538 -  72.109:   14        |
|      4:    34.254 -  41.825:  119   |   9:    72.109 -  79.680:    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)= 299         
Filter by distance & map next to the model:
   mapped sites are within: 0.362 - 4.217
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 292 from: 299
   mapped sites are within: 0.707 - 4.217

peak=   10.899 closest distance to " CG2 VAL A 230 " =    1.408
peak=    6.334 closest distance to " NH2 ARG A  56 " =    2.253
peak=    6.212 closest distance to " CG  LEU A   5 " =    1.203
peak=    5.832 closest distance to " CG2 VAL A 296 " =    1.041
peak=    5.689 closest distance to " NE2 GLN A  11 " =    1.193
peak=    5.680 closest distance to " CG  LEU A 228 " =    1.155
peak=    5.527 closest distance to " CB  VAL A 296 " =    1.118
peak=    5.326 closest distance to " O   HOH Z 142 " =    1.784
peak=    5.248 closest distance to " CD2 LEU A   5 " =    1.154
peak=    5.164 closest distance to " CB  GLN A 183 " =    1.231
peak=    5.134 closest distance to " O   HOH Z 126 " =    1.911
peak=    5.111 closest distance to " CB  GLN A 223 " =    1.473
peak=    5.003 closest distance to " CB  VAL A 230 " =    1.196
peak=    4.998 closest distance to " O   HOH Z 232 " =    2.347
peak=    4.790 closest distance to " CB  SER A  63 " =    1.271
peak=    4.583 closest distance to " CB  GLU A 152 " =    1.234
peak=    4.570 closest distance to " O   HOH Z 209 " =    2.307
peak=    4.558 closest distance to " CB  ARG A 275 " =    0.882
peak=    4.543 closest distance to " C   PRO A 198 " =    1.464
peak=    4.530 closest distance to " O   HOH Z  61 " =    1.669
peak=    4.517 closest distance to " CG  PRO A 213 " =    1.194
peak=    4.493 closest distance to " O   HOH Z 427 " =    3.027
peak=    4.458 closest distance to " O   SER A  87 " =    2.331
peak=    4.415 closest distance to " O   HOH Z 369 " =    2.103
peak=    4.400 closest distance to " O   HOH Z 272 " =    1.900
peak=    4.396 closest distance to " CB  ARG A  79 " =    1.432
peak=    4.395 closest distance to " ND2 ASN A 187 " =    1.465
peak=    4.383 closest distance to " O   HOH Z 346 " =    1.654
peak=    4.330 closest distance to " O   HOH Z  43 " =    1.956
peak=    4.317 closest distance to " O   HOH Z 248 " =    1.618
peak=    4.288 closest distance to " O   HOH Z 298 " =    1.774
peak=    4.287 closest distance to " O   HOH Z 158 " =    3.191
peak=    4.282 closest distance to " OG ASER A 258 " =    3.052
peak=    4.278 closest distance to " O   HOH Z 368 " =    2.142
peak=    4.275 closest distance to " O   HOH Z 403 " =    1.650
peak=    4.273 closest distance to " O   HOH Z  66 " =    2.270
peak=    4.245 closest distance to " OD1 ASN A  69 " =    2.676
peak=    4.238 closest distance to " CB  SER A   3 " =    1.300
peak=    4.226 closest distance to " O   HOH Z  78 " =    1.848
peak=    4.199 closest distance to " CB  TRP A 266 " =    0.971
peak=    4.198 closest distance to " CB  VAL A 265 " =    1.359
peak=    4.198 closest distance to " O   HOH Z 261 " =    2.279
peak=    4.196 closest distance to " O   HOH Z 193 " =    1.831
peak=    4.177 closest distance to " O   HOH Z 236 " =    1.968
peak=    4.153 closest distance to " CD2 LEU A 228 " =    1.154
peak=    4.137 closest distance to " CB  ASN A 148 " =    1.405
peak=    4.052 closest distance to " O   HOH Z 303 " =    2.109
peak=    4.045 closest distance to " CD  ARG A  66 " =    2.657
peak=    4.040 closest distance to " O   HOH Z 203 " =    1.763
peak=    4.030 closest distance to " O   HOH Z 425 " =    1.383
peak=    4.026 closest distance to " O   HOH Z 189 " =    2.611
peak=    3.988 closest distance to " CG  PRO A 243 " =    1.106
peak=    3.976 closest distance to " CB  ALA A   9 " =    1.568
peak=    3.975 closest distance to " CA  TYR A  30 " =    0.970
peak=    3.967 closest distance to " O   HOH Z 265 " =    2.492
peak=    3.957 closest distance to " O   HOH Z 234 " =    3.625
peak=    3.915 closest distance to " CB  ASN A 187 " =    1.289
peak=    3.895 closest distance to " CB  ASP A 140 " =    0.854
peak=    3.880 closest distance to " O   HOH Z 423 " =    1.747
peak=    3.875 closest distance to " CZ  PHE A 218 " =    1.082
peak=    3.861 closest distance to " O   HOH Z  59 " =    1.959
peak=    3.824 closest distance to " O   HOH Z 263 " =    1.682
peak=    3.824 closest distance to " CB  LEU A 143 " =    1.138
peak=    3.815 closest distance to " O   HOH Z 197 " =    3.239
peak=    3.811 closest distance to " CG2 VAL A 257 " =    0.893
peak=    3.806 closest distance to " CB  GLU A 128 " =    1.001
peak=    3.775 closest distance to " CB  ASN A  39 " =    0.855
peak=    3.773 closest distance to " CB  GLU A 277 " =    3.576
peak=    3.768 closest distance to " N   PHE A 130 " =    1.269
peak=    3.760 closest distance to " O   HOH Z 147 " =    1.752
peak=    3.739 closest distance to " CB  ASN A 142 " =    1.046
peak=    3.732 closest distance to " O   HOH Z  21 " =    1.713
peak=    3.731 closest distance to " O   HOH Z  15 " =    2.129
peak=    3.726 closest distance to " CB  ARG A 139 " =    0.964
peak=    3.726 closest distance to " O   HOH Z 132 " =    2.682
peak=    3.720 closest distance to " O   HOH Z 291 " =    1.662
peak=    3.716 closest distance to " CA  ALA A  51 " =    0.974
peak=    3.708 closest distance to " CB  SER A 212 " =    1.164
peak=    3.700 closest distance to " CG1BVAL A  72 " =    1.623
peak=    3.698 closest distance to " O   HOH Z 411 " =    3.742
peak=    3.693 closest distance to " CG  PRO A 198 " =    1.238
peak=    3.686 closest distance to " NH1AARG A 145 " =    1.049
peak=    3.685 closest distance to " CB BVAL A  41 " =    1.260
peak=    3.678 closest distance to " CB  LEU A 228 " =    1.248
peak=    3.669 closest distance to " O   HOH Z 193 " =    1.714
peak=    3.669 closest distance to " O   HOH Z 344 " =    3.038
peak=    3.662 closest distance to " CD  LYS A 166 " =    1.281
peak=    3.659 closest distance to " O   HOH Z 313 " =    1.797
peak=    3.647 closest distance to " CA  ASN A 215 " =    1.160
peak=    3.644 closest distance to " N   ASN A  39 " =    1.188
peak=    3.639 closest distance to " CG1 VAL A 153 " =    0.945
peak=    3.629 closest distance to " O   HOH Z 280 " =    2.989
peak=    3.629 closest distance to " OG BSER A 164 " =    2.228
peak=    3.627 closest distance to " NH2 ARG A 156 " =    1.137
peak=    3.623 closest distance to " O   HOH Z 214 " =    2.070
peak=    3.623 closest distance to " CB  SER A 216 " =    0.818
peak=    3.603 closest distance to " O   HOH Z 180 " =    2.146
peak=    3.592 closest distance to " O   HOH Z  88 " =    3.121
peak=    3.589 closest distance to " O   HOH Z 128 " =    2.049
peak=    3.588 closest distance to " O   HOH Z 407 " =    2.256
peak=    3.584 closest distance to " O   HOH Z 145 " =    1.970
peak=    3.582 closest distance to " OD2 ASP A 286 " =    2.775
peak=    3.582 closest distance to " O   HOH Z 128 " =    2.218
peak=    3.581 closest distance to " O   HOH Z 371 " =    2.971
peak=    3.581 closest distance to " CB  VAL A 202 " =    1.576
peak=    3.576 closest distance to " CA  SER A  87 " =    0.925
peak=    3.565 closest distance to " CG2 ILE A  20 " =    1.587
peak=    3.562 closest distance to " CA  ALA A  21 " =    1.127
peak=    3.551 closest distance to " O   HOH Z  97 " =    1.986
peak=    3.550 closest distance to " O   HOH Z 417 " =    3.312
peak=    3.540 closest distance to " CA  ASP A 162 " =    1.013
peak=    3.539 closest distance to " CD BLYS A 290 " =    1.109
peak=    3.537 closest distance to " CA  THR A 264 " =    0.804
peak=    3.534 closest distance to " O   HOH Z 193 " =    1.957
peak=    3.533 closest distance to " CG2 THR A 221 " =    1.254
peak=    3.532 closest distance to " CB  ARG A 190 " =    1.623
peak=    3.531 closest distance to " CB  ALA A 291 " =    1.443
peak=    3.530 closest distance to " O   HOH Z 250 " =    1.373
peak=    3.523 closest distance to " O   TRP A 274 " =    1.879
peak=    3.517 closest distance to " CB  PRO A  54 " =    0.771
peak=    3.516 closest distance to " CD2 TRP A 179 " =    1.320
peak=    3.508 closest distance to " CB  THR A  82 " =    1.340
peak=    3.507 closest distance to " CA  ALA A 158 " =    1.252
peak=    3.506 closest distance to " O   GLN A 278 " =    1.292
peak=    3.505 closest distance to " CB  TRP A 179 " =    1.404
peak=    3.503 closest distance to " O   MET A 105 " =    1.798
peak=    3.503 closest distance to " O   HOH Z 305 " =    3.532
peak=    3.502 closest distance to " CG  GLN A  88 " =    1.114
peak=    3.501 closest distance to " O   HOH Z 419 " =    1.870
peak=    3.500 closest distance to " CD1 ILE A  33 " =    1.706
peak=    3.498 closest distance to " O   HOH Z  10 " =    1.766
peak=    3.496 closest distance to " CA  PHE A 283 " =    1.221
peak=    3.495 closest distance to " CA  LYS A 117 " =    1.187
peak=    3.485 closest distance to " O   HOH Z 437 " =    1.813
peak=    3.482 closest distance to " O   HOH Z 148 " =    3.301
peak=    3.477 closest distance to " O   HOH Z   1 " =    1.866
peak=    3.472 closest distance to " ND2 ASN A 249 " =    1.866
peak=    3.465 closest distance to " O   HOH Z 175 " =    2.173
peak=    3.464 closest distance to " CA  ARG A 195 " =    1.175
peak=    3.461 closest distance to " CG  LEU A 167 " =    1.210
peak=    3.457 closest distance to " CB  THR A  31 " =    1.602
peak=    3.456 closest distance to " CB  ASN A 224 " =    1.048
peak=    3.450 closest distance to " NH1 ARG A 138 " =    1.172
peak=    3.450 closest distance to " O   HOH Z 299 " =    4.217
peak=    3.448 closest distance to " CD  ARG A 159 " =    0.707
peak=    3.446 closest distance to " O   HOH Z 350 " =    1.615
peak=    3.446 closest distance to " CE  LYS A  76 " =    0.895
peak=    3.444 closest distance to " CB  GLU A  46 " =    1.007
peak=    3.441 closest distance to " O   HOH Z 145 " =    3.706
peak=    3.440 closest distance to " CB  THR A 157 " =    1.118
peak=    3.437 closest distance to " O  BHOH Z 338 " =    2.419
peak=    3.437 closest distance to " CB  ALA A  34 " =    0.761
peak=    3.434 closest distance to " O   HOH Z 366 " =    2.983
peak=    3.426 closest distance to " CG  MET A 185 " =    1.175
peak=    3.424 closest distance to " CA  GLY A 267 " =    0.739
peak=    3.417 closest distance to " CG BARG A 275 " =    1.443
peak=    3.416 closest distance to " O   HOH Z 402 " =    1.417
peak=    3.414 closest distance to " O   HOH Z 380 " =    1.690
peak=    3.413 closest distance to " O   HOH Z  19 " =    2.502
peak=    3.410 closest distance to " O   HOH Z 290 " =    1.077
peak=    3.409 closest distance to " CG1 VAL A 296 " =    1.186
peak=    3.407 closest distance to " CB  HIS A 108 " =    0.784
peak=    3.405 closest distance to " O   HOH Z 303 " =    1.763
peak=    3.401 closest distance to " CB  TRP A 150 " =    1.351
peak=    3.400 closest distance to " O   HOH Z 409 " =    3.102
peak=    3.400 closest distance to " CB  ALA A 248 " =    0.981
peak=    3.390 closest distance to " OG  SER A  22 " =    2.855
peak=    3.389 closest distance to " O   HOH Z   1 " =    1.746
peak=    3.386 closest distance to " CG1 ILE A  49 " =    1.351
peak=    3.380 closest distance to " O   HOH Z 133 " =    1.590
peak=    3.376 closest distance to " CB  ILE A  20 " =    1.435
peak=    3.375 closest distance to " CB  SER A 273 " =    0.850
peak=    3.375 closest distance to " N   VAL A 126 " =    1.327
peak=    3.368 closest distance to " CB  MET A  40 " =    0.833
peak=    3.368 closest distance to " ND2 ASN A 110 " =    1.693
peak=    3.367 closest distance to " CD1 LEU A 228 " =    1.990
peak=    3.367 closest distance to " O   HOH Z 245 " =    1.407
peak=    3.366 closest distance to " CA  ALA A 233 " =    1.067
peak=    3.364 closest distance to " O   HOH Z 286 " =    2.416
peak=    3.361 closest distance to " CA  TYR A 116 " =    1.368
peak=    3.359 closest distance to " O   HOH Z  66 " =    2.279
peak=    3.358 closest distance to " O   HOH Z 273 " =    2.697
peak=    3.353 closest distance to " O   HOH Z  44 " =    2.974
peak=    3.351 closest distance to " O   HOH Z 353 " =    2.615
peak=    3.351 closest distance to " O   HOH Z  30 " =    1.379
peak=    3.350 closest distance to " O   HOH Z  61 " =    1.582
peak=    3.347 closest distance to " O   HOH Z 406 " =    1.691
peak=    3.345 closest distance to " NZ  LYS A 117 " =    3.250
peak=    3.342 closest distance to " O   HOH Z 172 " =    3.371
peak=    3.341 closest distance to " CZ  PHE A 192 " =    0.965
peak=    3.332 closest distance to " CG1 ILE A 151 " =    1.058
peak=    3.331 closest distance to " CA  TYR A  30 " =    1.053
peak=    3.330 closest distance to " CA  ALA A 154 " =    0.995
peak=    3.327 closest distance to " CB  ILE A 120 " =    1.289
peak=    3.327 closest distance to " CA  VAL A 126 " =    0.811
peak=    3.326 closest distance to " O   HOH Z 426 " =    1.616
peak=    3.323 closest distance to " O   HOH Z 368 " =    3.535
peak=    3.314 closest distance to " O   HOH Z 126 " =    1.533
peak=    3.310 closest distance to " O   HOH Z 329 " =    3.906
peak=    3.305 closest distance to " OD1 ASN A 148 " =    1.733
peak=    3.303 closest distance to " NH2BARG A 190 " =    1.691
peak=    3.301 closest distance to " O   HOH Z   3 " =    1.888
peak=    3.300 closest distance to " CD1 LEU A   5 " =    1.381
peak=    3.298 closest distance to " CB  GLN A 205 " =    1.076
peak=    3.296 closest distance to " O   HOH Z 227 " =    2.161
peak=    3.294 closest distance to " ND1 HIS A  86 " =    1.643
peak=    3.293 closest distance to " CG1 ILE A  33 " =    1.253
peak=    3.291 closest distance to " CD1 ILE A 263 " =    1.259
peak=    3.288 closest distance to " O   HOH Z 128 " =    1.955
peak=    3.283 closest distance to " CB  GLN A  88 " =    1.209
peak=    3.282 closest distance to " CD1 LEU A 300 " =    1.267
peak=    3.279 closest distance to " O   HOH Z 234 " =    1.780
peak=    3.278 closest distance to " OG1 THR A 294 " =    1.702
peak=    3.277 closest distance to " CA  ALA A 291 " =    0.927
peak=    3.277 closest distance to " CB  SER A 245 " =    3.194
peak=    3.276 closest distance to " CE1 TYR A 186 " =    1.373
peak=    3.272 closest distance to " O   HOH Z 124 " =    1.329
peak=    3.268 closest distance to " O   HOH Z 133 " =    2.482
peak=    3.267 closest distance to " OE1 GLN A  11 " =    2.128
peak=    3.265 closest distance to " O   HOH Z 435 " =    1.947
peak=    3.262 closest distance to " N   SER A 135 " =    1.379
peak=    3.261 closest distance to " O   HOH Z 425 " =    2.069
peak=    3.257 closest distance to " O   HOH Z  97 " =    2.593
peak=    3.256 closest distance to " CA  VAL A  41 " =    0.820
peak=    3.255 closest distance to " O   HOH Z 171 " =    2.264
peak=    3.250 closest distance to " O   HOH Z 227 " =    1.693
peak=    3.247 closest distance to " N   ARG A 156 " =    1.280
peak=    3.246 closest distance to " O   HOH Z 189 " =    2.743
peak=    3.237 closest distance to " NE2 HIS A 207 " =    1.384
peak=    3.235 closest distance to " NZ  LYS A  76 " =    1.403
peak=    3.230 closest distance to " CG  GLN A 278 " =    1.247
peak=    3.229 closest distance to " O   HOH Z 313 " =    1.681
peak=    3.228 closest distance to " CA  ARG A  36 " =    1.082
peak=    3.226 closest distance to " CB  GLN A 278 " =    0.843
peak=    3.225 closest distance to " O   HOH Z 251 " =    1.523
peak=    3.224 closest distance to " O   HOH Z 422 " =    2.645
peak=    3.222 closest distance to " O   HOH Z 154 " =    2.138
peak=    3.222 closest distance to " O   HOH Z 359 " =    1.933
peak=    3.220 closest distance to " O   HOH Z 417 " =    2.017
peak=    3.218 closest distance to " O   HOH Z  40 " =    1.364
peak=    3.217 closest distance to " O   HOH Z 345 " =    3.408
peak=    3.217 closest distance to " CG2 ILE A 120 " =    1.254
peak=    3.217 closest distance to " OG BSER A 134 " =    3.005
peak=    3.215 closest distance to " N   ASP A 162 " =    1.330
peak=    3.210 closest distance to " CA  LEU A 282 " =    1.056
peak=    3.208 closest distance to " CB  LYS A 290 " =    0.935
peak=    3.204 closest distance to " CB  THR A 235 " =    1.112
peak=    3.199 closest distance to " O   HOH Z 359 " =    3.748
peak=    3.195 closest distance to " CA  ALA A  84 " =    1.438
peak=    3.195 closest distance to " O   HOH Z 295 " =    1.547
peak=    3.190 closest distance to " CA  THR A 221 " =    0.967
peak=    3.189 closest distance to " ND1 HIS A  81 " =    1.743
peak=    3.187 closest distance to " CD  LYS A 119 " =    1.566
peak=    3.185 closest distance to " CB  SER A  26 " =    1.614
peak=    3.180 closest distance to " N   GLN A 278 " =    1.156
peak=    3.173 closest distance to " O   HOH Z  44 " =    1.685
peak=    3.172 closest distance to " NH1 ARG A  66 " =    1.615
peak=    3.171 closest distance to " C   ALA A 299 " =    0.946
peak=    3.168 closest distance to " O   HOH Z 141 " =    1.625
peak=    3.165 closest distance to " CB  ASN A 110 " =    1.104
peak=    3.165 closest distance to " CG  GLN A  77 " =    2.160
peak=    3.158 closest distance to " CB  LYS A 117 " =    1.212
peak=    3.158 closest distance to " O   HOH Z  48 " =    1.637
peak=    3.147 closest distance to " O   HOH Z 285 " =    2.792
peak=    3.145 closest distance to " CB  LEU A 300 " =    0.862
peak=    3.144 closest distance to " CA  LYS A 290 " =    1.235
peak=    3.144 closest distance to " O   SER A 164 " =    1.226
peak=    3.142 closest distance to " CA  ASP A 140 " =    1.199
peak=    3.141 closest distance to " NZ  LYS A  48 " =    1.321
peak=    3.141 closest distance to " O   HOH Z 271 " =    2.027
peak=    3.139 closest distance to " CD2 LEU A 255 " =    1.596
peak=    3.138 closest distance to " O   HOH Z 423 " =    2.885
peak=    3.138 closest distance to " CG  ARG A 159 " =    0.948
peak=    3.135 closest distance to " O   HOH Z 383 " =    1.774
peak=    3.134 closest distance to " OE2 GLU A  53 " =    2.051
peak=    3.131 closest distance to " O   HOH Z 112 " =    1.612
peak=    3.124 closest distance to " CB  MET A  47 " =    1.203
peak=    3.122 closest distance to " O   HOH Z  85 " =    2.184
peak=    3.122 closest distance to " CA  ILE A 106 " =    0.742
peak=    3.120 closest distance to " CG  LYS A  76 " =    0.957
peak=    3.117 closest distance to " O   HOH Z 286 " =    2.470
peak=    3.110 closest distance to " O   HOH Z 156 " =    3.352
peak=    3.109 closest distance to " OG  SER A 206 " =    1.268
peak=    3.108 closest distance to " CB  MET A  40 " =    1.127
peak=    3.103 closest distance to " O   HOH Z 213 " =    2.019
peak=    3.100 closest distance to " CA  SER A 146 " =    1.747
peak=    3.087 closest distance to " CD  ARG A  79 " =    2.102
peak=    3.076 closest distance to " CA  MET A 105 " =    0.959
peak=    3.067 closest distance to " OG  SER A  62 " =    2.881
peak=    3.062 closest distance to " CD1 ILE A 106 " =    1.059
peak=    3.053 closest distance to " CB  GLU A 277 " =    3.757
peak=    3.050 closest distance to " O   HOH Z 258 " =    1.875

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 209         
Filter by distance & map next to the model:
   mapped sites are within: 0.570 - 5.443
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 206 from: 209
   mapped sites are within: 0.757 - 5.443

peak=   -5.476 closest distance to " CG2 VAL A 230 " =    0.770
peak=   -4.541 closest distance to " CB  PRO A 243 " =    2.628
peak=   -4.415 closest distance to " CD  ARG A 156 " =    2.017
peak=   -4.337 closest distance to " CG  GLN A 223 " =    1.964
peak=   -4.284 closest distance to " SG  CYS A 254 " =    3.314
peak=   -4.209 closest distance to " O   HOH Z 266 " =    5.098
peak=   -4.164 closest distance to " C   HIS A 108 " =    1.226
peak=   -4.118 closest distance to " O   HOH Z 290 " =    1.196
peak=   -4.116 closest distance to " O   ILE A 109 " =    2.574
peak=   -4.078 closest distance to " CG2 VAL A 296 " =    1.232
peak=   -4.023 closest distance to " CA  VAL A  67 " =    2.707
peak=   -4.007 closest distance to " OG BSER A 134 " =    1.217
peak=   -3.998 closest distance to " CB  ALA A 248 " =    2.082
peak=   -3.934 closest distance to " O   HOH Z 351 " =    1.504
peak=   -3.927 closest distance to " CD  GLN A  58 " =    1.049
peak=   -3.910 closest distance to " O   PRO A 163 " =    2.062
peak=   -3.869 closest distance to " CB  PHE A 192 " =    1.883
peak=   -3.850 closest distance to " CG2BVAL A  41 " =    2.621
peak=   -3.848 closest distance to " O   HOH Z 231 " =    1.966
peak=   -3.844 closest distance to " O   HOH Z 435 " =    2.857
peak=   -3.841 closest distance to " CG  ASP A 231 " =    0.757
peak=   -3.827 closest distance to " CG2 THR A   4 " =    1.917
peak=   -3.822 closest distance to " ND2 ASN A  45 " =    1.734
peak=   -3.808 closest distance to " O   HOH Z 196 " =    2.289
peak=   -3.802 closest distance to " CB  ALA A  43 " =    2.488
peak=   -3.752 closest distance to " O   HOH Z 185 " =    2.281
peak=   -3.735 closest distance to " CB  ALA A 291 " =    2.310
peak=   -3.715 closest distance to " O   HOH Z 211 " =    1.574
peak=   -3.710 closest distance to " O   HOH Z 166 " =    2.002
peak=   -3.697 closest distance to " CE2 TYR A  30 " =    2.780
peak=   -3.688 closest distance to " O   HOH Z 389 " =    2.067
peak=   -3.683 closest distance to " NH2 ARG A  79 " =    1.988
peak=   -3.680 closest distance to " CB  PRO A 163 " =    2.536
peak=   -3.673 closest distance to " O   VAL A 189 " =    2.596
peak=   -3.672 closest distance to " CZ3 TRP A 179 " =    1.220
peak=   -3.652 closest distance to " C   ALA A 158 " =    1.334
peak=   -3.647 closest distance to " CB  ALA A 291 " =    2.163
peak=   -3.644 closest distance to " N   GLN A  58 " =    1.757
peak=   -3.640 closest distance to " O   HOH Z 407 " =    3.066
peak=   -3.623 closest distance to " CG1 VAL A 296 " =    1.327
peak=   -3.617 closest distance to " CG  TRP A 266 " =    1.839
peak=   -3.611 closest distance to " CG2 THR A 178 " =    2.213
peak=   -3.611 closest distance to " CB  PRO A 280 " =    2.171
peak=   -3.609 closest distance to " O   HOH Z 114 " =    3.063
peak=   -3.608 closest distance to " CG1 VAL A 112 " =    2.635
peak=   -3.605 closest distance to " CD1 LEU A 228 " =    2.175
peak=   -3.599 closest distance to " CB  ALA A 248 " =    2.422
peak=   -3.594 closest distance to " NH2 ARG A 159 " =    2.399
peak=   -3.591 closest distance to " N   THR A 157 " =    1.473
peak=   -3.585 closest distance to " CG1 VAL A 112 " =    2.949
peak=   -3.577 closest distance to " NH2AARG A 275 " =    5.208
peak=   -3.572 closest distance to " CD2 LEU A 300 " =    2.730
peak=   -3.560 closest distance to " CD1 LEU A 101 " =    2.390
peak=   -3.558 closest distance to " CD  ARG A 139 " =    1.599
peak=   -3.554 closest distance to " O   PRO A 198 " =    1.236
peak=   -3.550 closest distance to " OXT GLY A 302 " =    2.919
peak=   -3.549 closest distance to " O   HOH Z 394 " =    1.519
peak=   -3.532 closest distance to " CB  ASP A 132 " =    2.265
peak=   -3.524 closest distance to " C   LEU A 222 " =    0.872
peak=   -3.521 closest distance to " N   ALA A 226 " =    2.070
peak=   -3.518 closest distance to " CE  MET A 105 " =    2.241
peak=   -3.513 closest distance to " O   SER A  22 " =    2.248
peak=   -3.512 closest distance to " CB  ASP A 132 " =    2.334
peak=   -3.502 closest distance to " CA  GLY A 241 " =    3.121
peak=   -3.492 closest distance to " C   MET A 188 " =    1.408
peak=   -3.486 closest distance to " CG1 VAL A 250 " =    2.757
peak=   -3.481 closest distance to " N   ASP A 171 " =    2.366
peak=   -3.465 closest distance to " O   ALA A 161 " =    1.627
peak=   -3.463 closest distance to " C   ASP A 231 " =    2.571
peak=   -3.462 closest distance to " O   HOH Z 313 " =    1.665
peak=   -3.460 closest distance to " CB  VAL A 296 " =    1.089
peak=   -3.457 closest distance to " CG  PHE A 283 " =    2.683
peak=   -3.452 closest distance to " O   HOH Z  13 " =    1.496
peak=   -3.451 closest distance to " O   HOH Z  38 " =    1.663
peak=   -3.444 closest distance to " OG  SER A  26 " =    1.147
peak=   -3.444 closest distance to " CE2 PHE A 218 " =    2.507
peak=   -3.439 closest distance to " O   GLY A  80 " =    2.552
peak=   -3.438 closest distance to " OG BSER A 134 " =    1.659
peak=   -3.437 closest distance to " O   HOH Z  63 " =    1.387
peak=   -3.437 closest distance to " NZ  LYS A 119 " =    3.501
peak=   -3.437 closest distance to " OG  SER A  97 " =    2.207
peak=   -3.437 closest distance to " CD1 LEU A 101 " =    2.600
peak=   -3.433 closest distance to " OD1 ASN A 187 " =    1.569
peak=   -3.433 closest distance to " O   HOH Z  73 " =    2.185
peak=   -3.431 closest distance to " OG  SER A  87 " =    1.408
peak=   -3.431 closest distance to " N   GLN A  77 " =    1.718
peak=   -3.428 closest distance to " OD1 ASN A 148 " =    1.473
peak=   -3.427 closest distance to " O   GLY A 196 " =    1.249
peak=   -3.425 closest distance to " NE2 GLN A  88 " =    1.858
peak=   -3.424 closest distance to " CG2 ILE A 263 " =    2.387
peak=   -3.417 closest distance to " CA  GLY A 203 " =    2.364
peak=   -3.417 closest distance to " N   ALA A  43 " =    2.420
peak=   -3.415 closest distance to " CE BMET A  47 " =    1.683
peak=   -3.410 closest distance to " O   HOH Z 102 " =    1.569
peak=   -3.408 closest distance to " O   HOH Z 353 " =    2.066
peak=   -3.406 closest distance to " CA  GLY A 241 " =    2.280
peak=   -3.404 closest distance to " ND2 ASN A 249 " =    2.397
peak=   -3.402 closest distance to " CD1 PHE A  59 " =    2.026
peak=   -3.393 closest distance to " OXT GLY A 302 " =    3.508
peak=   -3.393 closest distance to " CD  LYS A 289 " =    2.496
peak=   -3.392 closest distance to " O   HOH Z 198 " =    2.191
peak=   -3.388 closest distance to " N   ALA A 248 " =    1.780
peak=   -3.387 closest distance to " O   ARG A 145 " =    1.598
peak=   -3.386 closest distance to " CB  ASP A 171 " =    2.266
peak=   -3.384 closest distance to " CZ  PHE A  59 " =    1.502
peak=   -3.375 closest distance to " O   HOH Z 339 " =    1.823
peak=   -3.371 closest distance to " O   HOH Z  22 " =    2.450
peak=   -3.367 closest distance to " O   HOH Z 417 " =    3.051
peak=   -3.365 closest distance to " O   HOH Z 140 " =    1.615
peak=   -3.365 closest distance to " CG  LEU A 228 " =    0.969
peak=   -3.364 closest distance to " O   HOH Z  60 " =    2.048
peak=   -3.355 closest distance to " CA  ASP A 298 " =    1.089
peak=   -3.354 closest distance to " N   MET A 188 " =    1.860
peak=   -3.352 closest distance to " CD2 LEU A 237 " =    2.740
peak=   -3.351 closest distance to " N   PHE A  59 " =    2.065
peak=   -3.344 closest distance to " C   LEU A 143 " =    1.068
peak=   -3.339 closest distance to " CB  VAL A 230 " =    1.015
peak=   -3.333 closest distance to " O   HOH Z 426 " =    1.649
peak=   -3.331 closest distance to " OD2 ASP A  50 " =    2.333
peak=   -3.326 closest distance to " CE3 TRP A 150 " =    2.021
peak=   -3.324 closest distance to " CA  GLY A  98 " =    1.852
peak=   -3.322 closest distance to " CD1 LEU A 297 " =    2.410
peak=   -3.320 closest distance to " O   HOH Z 187 " =    1.606
peak=   -3.318 closest distance to " N   SER A 276 " =    1.306
peak=   -3.318 closest distance to " O   PRO A 198 " =    1.337
peak=   -3.316 closest distance to " NH2BARG A 275 " =    1.694
peak=   -3.316 closest distance to " O   LYS A 117 " =    1.754
peak=   -3.312 closest distance to " O   HOH Z 275 " =    1.430
peak=   -3.311 closest distance to " CB  TYR A  15 " =    2.180
peak=   -3.308 closest distance to " ND2 ASN A  60 " =    1.817
peak=   -3.307 closest distance to " SG BCYS A 201 " =    1.940
peak=   -3.296 closest distance to " NE2 GLN A 278 " =    1.974
peak=   -3.288 closest distance to " CG1 VAL A 230 " =    1.922
peak=   -3.284 closest distance to " CZ  TYR A 169 " =    1.554
peak=   -3.279 closest distance to " O   HOH Z 241 " =    1.338
peak=   -3.279 closest distance to " O   HOH Z  43 " =    1.846
peak=   -3.275 closest distance to " O   GLN A 240 " =    2.139
peak=   -3.268 closest distance to " O   ALA A  51 " =    1.354
peak=   -3.265 closest distance to " CA  ASP A  27 " =    2.541
peak=   -3.264 closest distance to " CD2 PHE A  61 " =    2.503
peak=   -3.259 closest distance to " O   MET A  40 " =    2.709
peak=   -3.256 closest distance to " CG1 VAL A 197 " =    2.222
peak=   -3.253 closest distance to " O   HOH Z 175 " =    4.261
peak=   -3.250 closest distance to " O   HOH Z 372 " =    2.327
peak=   -3.245 closest distance to " O   HOH Z 165 " =    1.913
peak=   -3.243 closest distance to " CB  ASN A  69 " =    1.213
peak=   -3.243 closest distance to " CD2 LEU A 167 " =    1.821
peak=   -3.241 closest distance to " O   HOH Z 388 " =    2.155
peak=   -3.240 closest distance to " O   HOH Z 134 " =    2.924
peak=   -3.239 closest distance to " O   HOH Z  52 " =    1.511
peak=   -3.238 closest distance to " O   ARG A  24 " =    2.032
peak=   -3.231 closest distance to " ND2 ASN A 187 " =    1.577
peak=   -3.227 closest distance to " OG  SER A  62 " =    1.629
peak=   -3.227 closest distance to " OG1 THR A 178 " =    1.293
peak=   -3.224 closest distance to " NH2 ARG A  79 " =    1.608
peak=   -3.224 closest distance to " C   PHE A  59 " =    1.362
peak=   -3.223 closest distance to " O   HOH Z 359 " =    3.197
peak=   -3.223 closest distance to " O   HOH Z 191 " =    5.443
peak=   -3.222 closest distance to " CZ  PHE A 192 " =    2.903
peak=   -3.219 closest distance to " CD1 ILE A 199 " =    2.520
peak=   -3.213 closest distance to " N   ALA A 248 " =    2.291
peak=   -3.202 closest distance to " O   HOH Z 350 " =    1.755
peak=   -3.201 closest distance to " CD  PRO A 213 " =    2.176
peak=   -3.199 closest distance to " O   HOH Z 152 " =    5.143
peak=   -3.196 closest distance to " NE2 GLN A 194 " =    1.853
peak=   -3.191 closest distance to " O   HOH Z 234 " =    4.119
peak=   -3.186 closest distance to " C   VAL A 174 " =    1.785
peak=   -3.185 closest distance to " CD2 LEU A 300 " =    3.236
peak=   -3.182 closest distance to " O   HOH Z 281 " =    3.189
peak=   -3.180 closest distance to " O   HOH Z  89 " =    2.913
peak=   -3.180 closest distance to " CG  GLU A 152 " =    1.184
peak=   -3.174 closest distance to " O   HOH Z 103 " =    1.836
peak=   -3.174 closest distance to " O   GLY A  17 " =    1.287
peak=   -3.171 closest distance to " O   HOH Z 313 " =    1.121
peak=   -3.169 closest distance to " OH  TYR A 214 " =    1.198
peak=   -3.169 closest distance to " CB  ASN A  39 " =    2.206
peak=   -3.165 closest distance to " ND2 ASN A  60 " =    1.445
peak=   -3.158 closest distance to " O   HOH Z  51 " =    1.235
peak=   -3.155 closest distance to " CD2 LEU A   5 " =    1.154
peak=   -3.154 closest distance to " O   HOH Z 222 " =    1.494
peak=   -3.153 closest distance to " NH1 ARG A 195 " =    2.529
peak=   -3.149 closest distance to " O   GLY A 211 " =    1.372
peak=   -3.148 closest distance to " CE1 PHE A 208 " =    2.478
peak=   -3.144 closest distance to " CG  GLU A 277 " =    1.227
peak=   -3.141 closest distance to " CE1 TYR A 169 " =    2.474
peak=   -3.125 closest distance to " CG2BVAL A  41 " =    1.712
peak=   -3.125 closest distance to " O   HOH Z  10 " =    1.476
peak=   -3.124 closest distance to " CD  GLN A  88 " =    0.889
peak=   -3.118 closest distance to " O   HOH Z 295 " =    1.592
peak=   -3.117 closest distance to " OG  SER A 206 " =    1.711
peak=   -3.114 closest distance to " O   HOH Z 281 " =    2.721
peak=   -3.108 closest distance to " CE  LYS A  76 " =    2.791
peak=   -3.107 closest distance to " O   HOH Z 311 " =    3.818
peak=   -3.104 closest distance to " O   HOH Z 423 " =    2.113
peak=   -3.094 closest distance to " N   ASP A 286 " =    2.360
peak=   -3.086 closest distance to " CB  TRP A 177 " =    2.351
peak=   -3.084 closest distance to " O   HOH Z 123 " =    2.528
peak=   -3.079 closest distance to " CD2 TYR A 247 " =    2.372
peak=   -3.076 closest distance to " O   HOH Z 436 " =    1.642
peak=   -3.076 closest distance to " O   HOH Z 359 " =    1.613
peak=   -3.075 closest distance to " O   HOH Z 193 " =    2.020
peak=   -3.075 closest distance to " O   HOH Z  77 " =    1.783
peak=   -3.060 closest distance to " CG2 VAL A 189 " =    1.962
peak=   -3.043 closest distance to " NH1 ARG A  36 " =    2.017
peak=   -3.034 closest distance to " O   HOH Z 298 " =    2.700
peak=   -3.025 closest distance to " OD1 ASN A 301 " =    1.949

================= 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    :  0.4127 0.3981   6.196503e+00   6.167215e+00
   1_bss:  0.4042 0.3856   6.192961e+00   6.153358e+00
   1_xyz:  0.2892 0.3089   5.938262e+00   5.987478e+00
   1_adp:  0.2129 0.2437   5.659921e+00   5.786318e+00
   1_occ:  0.2122 0.2435   5.658603e+00   5.787950e+00
   2_bss:  0.2058 0.2368   5.653047e+00   5.779783e+00
   2_xyz:  0.1445 0.1817   5.336058e+00   5.521633e+00
   2_adp:  0.1340 0.1738   5.276461e+00   5.475796e+00
   2_occ:  0.1339 0.1737   5.275864e+00   5.475280e+00
   3_bss:  0.1340 0.1736   5.277015e+00   5.476044e+00
   3_xyz:  0.1172 0.1601   5.173562e+00   5.404859e+00
   3_adp:  0.1131 0.1584   5.151680e+00   5.395913e+00
   3_occ:  0.1130 0.1583   5.151593e+00   5.395915e+00
   4_bss:  0.1130 0.1583   5.151166e+00   5.395579e+00
   4_xyz:  0.1111 0.1581   5.144201e+00   5.394799e+00
   4_adp:  0.1132 0.1557   5.144182e+00   5.379151e+00
   4_occ:  0.1132 0.1556   5.143524e+00   5.378443e+00
   5_bss:  0.1132 0.1556   5.143524e+00   5.378443e+00
   5_xyz:  0.1102 0.1546   5.127389e+00   5.372149e+00
   5_adp:  0.1092 0.1553   5.127435e+00   5.379290e+00
   5_occ:  0.1089 0.1552   5.126017e+00   5.378432e+00
   5_bss:  0.1091 0.1550   5.126737e+00   5.376633e+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:  0.355  20.000   7.621   8.485   8.197   0.000   0.000   0.000
   1_xyz:  0.355  20.000   7.621   8.485   8.197   0.000   0.000   0.000
   1_adp:  0.355  20.000   7.621   8.485   8.197   0.000   0.000   0.000
   1_occ:  0.355  20.000   7.621   8.485   8.197   0.000   0.000   0.000
   2_bss:  0.340  41.360   4.268   4.596   5.250   0.000   0.000   0.000
   2_xyz:  0.340  41.360   4.268   4.596   5.250   0.000   0.000   0.000
   2_adp:  0.340  41.360   4.268   4.596   5.250   0.000   0.000   0.000
   2_occ:  0.340  41.360   4.268   4.596   5.250   0.000   0.000   0.000
   3_bss:  0.326  41.360   3.560   3.701   4.762   0.000   0.000   0.000
   3_xyz:  0.326  41.360   3.560   3.701   4.762   0.000   0.000   0.000
   3_adp:  0.326  41.360   3.560   3.701   4.762   0.000   0.000   0.000
   3_occ:  0.326  41.360   3.560   3.701   4.762   0.000   0.000   0.000
   4_bss:  0.319  41.360   3.525   3.626   4.758   0.000   0.000   0.000
   4_xyz:  0.319  41.360   3.525   3.626   4.758   0.000   0.000   0.000
   4_adp:  0.319  41.360   3.525   3.626   4.758   0.000   0.000   0.000
   4_occ:  0.319  41.360   3.525   3.626   4.758   0.000   0.000   0.000
   5_bss:  0.319  41.360   3.525   3.626   4.758   0.000   0.000   0.000
   5_xyz:  0.319  41.360   3.525   3.626   4.758   0.000   0.000   0.000
   5_adp:  0.319  41.360   3.525   3.626   4.758   0.000   0.000   0.000
   5_occ:  0.319  41.360   3.525   3.626   4.758   0.000   0.000   0.000
   5_bss:  0.322  47.214  -0.444  -0.344   0.788   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  43.287 0.6051  0.6668    44907.684
   1_bss:  43.307 0.6025  0.8452    42585.298
   1_xyz:  32.542 0.7290  0.9920    25697.277
   1_adp:  23.287 0.8307  1.0787    14959.746
   1_occ:  23.331 0.8302  1.0774    14974.061
   2_bss:  23.006 0.8333  0.9548    14576.160
   2_xyz:  16.793 0.8913  0.9956     8205.277
   2_adp:  15.672 0.9015  1.0026     7548.759
   2_occ:  15.660 0.9016  1.0026     7536.121
   3_bss:  15.672 0.9015  0.9766     7558.694
   3_xyz:  14.274 0.9127  0.9821     6537.203
   3_adp:  14.099 0.9143  0.9804     6401.856
   3_occ:  14.098 0.9143  0.9803     6400.264
   4_bss:  14.091 0.9143  0.9789     6392.438
   4_xyz:  14.018 0.9151  0.9783     6389.228
   4_adp:  13.649 0.9181  0.9801     6204.447
   4_occ:  13.638 0.9182  0.9802     6194.756
   5_bss:  13.638 0.9182  0.9802     6194.756
   5_xyz:  13.509 0.9192  0.9808     6126.337
   5_adp:  13.663 0.9180  0.9786     6201.578
   5_occ:  13.646 0.9181  0.9785     6192.323
   5_bss:  13.632 0.9182  0.9779     6171.755
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.3798e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.3798e+01
   1_xyz:   1.421  0.010  0.097 17.898  0.005  4.121   1.0687e-01
   1_adp:   1.421  0.010  0.097 17.898  0.005  4.121   1.0687e-01
   1_occ:   1.421  0.010  0.097 17.898  0.005  4.121   1.0687e-01
   2_bss:   1.421  0.010  0.097 17.898  0.005  4.121   1.0687e-01
   2_xyz:   0.970  0.006  0.074 16.345  0.004  4.121   6.0870e-02
   2_adp:   0.970  0.006  0.074 16.345  0.004  4.121   6.0870e-02
   2_occ:   0.970  0.006  0.074 16.345  0.004  4.121   6.0870e-02
   3_bss:   0.970  0.006  0.074 16.345  0.004  4.121   6.0870e-02
   3_xyz:   1.048  0.008  0.086 16.057  0.004  4.129   6.8161e-02
   3_adp:   1.048  0.008  0.086 16.057  0.004  4.129   6.8161e-02
   3_occ:   1.048  0.008  0.086 16.057  0.004  4.129   6.8161e-02
   4_bss:   1.048  0.008  0.086 16.057  0.004  4.129   6.8161e-02
   4_xyz:   0.994  0.007  0.083 15.869  0.004  4.116   6.2980e-02
   4_adp:   0.994  0.007  0.083 15.869  0.004  4.116   6.2980e-02
   4_occ:   0.994  0.007  0.083 15.869  0.004  4.116   6.2980e-02
   5_bss:   0.994  0.007  0.083 15.869  0.004  4.116   6.2980e-02
   5_xyz:   1.077  0.009  0.090 15.957  0.004  4.118   7.2094e-02
   5_adp:   1.077  0.009  0.090 15.957  0.004  4.118   7.2094e-02
   5_occ:   1.077  0.009  0.090 15.957  0.004  4.118   7.2094e-02
   5_bss:   1.077  0.009  0.090 15.957  0.004  4.118   7.2094e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9756e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9756e+00
   1_xyz:  11.263  0.126  0.431 88.242  0.032  2.280   7.8111e-02
   1_adp:  11.263  0.126  0.431 88.242  0.032  2.280   7.8111e-02
   1_occ:  11.263  0.126  0.431 88.242  0.032  2.280   7.8111e-02
   2_bss:  11.263  0.126  0.431 88.242  0.032  2.280   7.8111e-02
   2_xyz:   7.160  0.053  0.401 83.918  0.039  2.284   4.1586e-02
   2_adp:   7.160  0.053  0.401 83.918  0.039  2.284   4.1586e-02
   2_occ:   7.160  0.053  0.401 83.918  0.039  2.284   4.1586e-02
   3_bss:   7.160  0.053  0.401 83.918  0.039  2.284   4.1586e-02
   3_xyz:   6.817  0.041  0.582 83.562  0.038  2.277   4.9840e-02
   3_adp:   6.817  0.041  0.582 83.562  0.038  2.277   4.9840e-02
   3_occ:   6.817  0.041  0.582 83.562  0.038  2.277   4.9840e-02
   4_bss:   6.817  0.041  0.582 83.562  0.038  2.277   4.9840e-02
   4_xyz:   7.123  0.039  0.567 83.451  0.038  2.344   4.2520e-02
   4_adp:   7.123  0.039  0.567 83.451  0.038  2.344   4.2520e-02
   4_occ:   7.123  0.039  0.567 83.451  0.038  2.344   4.2520e-02
   5_bss:   7.123  0.039  0.567 83.451  0.038  2.344   4.2520e-02
   5_xyz:   6.827  0.045  0.669 83.491  0.040  2.258   5.2710e-02
   5_adp:   6.827  0.045  0.669 83.491  0.040  2.258   5.2710e-02
   5_occ:   6.827  0.045  0.669 83.491  0.040  2.258   5.2710e-02
   5_bss:   6.827  0.045  0.669 83.491  0.040  2.258   5.2710e-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:  55.87   0.00  10.18  55.51   0.00   6.90  55.87   0.00  28.04
   1_occ:  55.87   0.00  10.18  55.51   0.00   6.90  55.87   0.00  28.04
   2_bss:  55.87   0.00  10.18  55.51   0.00   6.90  55.87   0.00  28.04
   2_xyz:  55.87   0.00  10.18  55.51   0.00   6.90  55.87   0.00  28.04
   2_adp:  57.73   0.00  10.47  57.73   0.00   6.84  56.72   0.00  30.19
   2_occ:  57.73   0.00  10.47  57.73   0.00   6.84  56.72   0.00  30.19
   3_bss:  57.73   0.00  10.47  57.73   0.00   6.84  56.72   0.00  30.19
   3_xyz:  57.73   0.00  10.47  57.73   0.00   6.84  56.72   0.00  30.19
   3_adp:  75.09   0.00  11.33  74.89   0.00   7.11  75.09   0.17  34.36
   3_occ:  75.09   0.00  11.33  74.89   0.00   7.11  75.09   0.17  34.36
   4_bss:  75.09   0.00  11.33  74.89   0.00   7.11  75.09   0.17  34.36
   4_xyz:  75.09   0.00  11.33  74.89   0.00   7.11  75.09   0.17  34.36
   4_adp:  74.00   0.00  10.90  74.00   0.00   6.94  69.69   0.96  32.52
   4_occ:  74.00   0.00  10.90  74.00   0.00   6.94  69.69   0.96  32.52
   5_bss:  74.00   0.00  10.90  74.00   0.00   6.94  69.69   0.96  32.52
   5_xyz:  74.00   0.00  10.90  74.00   0.00   6.94  69.69   0.96  32.52
   5_adp:  75.71   0.00  10.90  75.71   0.00   6.95  67.58   0.66  32.41
   5_occ:  75.71   0.00  10.90  75.71   0.00   6.95  67.58   0.66  32.41
   5_bss:  79.68   3.97  14.87  79.68   3.97  10.92  71.54   4.63  36.37
------------------------------------------------------------------------
 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:    1.149    0.024    0.396
   1_adp:    1.149    0.024    0.396
   1_occ:    1.149    0.024    0.396
   2_bss:    1.149    0.024    0.396
   2_xyz:    1.326    0.017    0.465
   2_adp:    1.326    0.017    0.465
   2_occ:    1.326    0.017    0.465
   3_bss:    1.326    0.017    0.465
   3_xyz:    1.380    0.038    0.494
   3_adp:    1.380    0.038    0.494
   3_occ:    1.380    0.038    0.494
   4_bss:    1.380    0.038    0.494
   4_xyz:    1.486    0.035    0.500
   4_adp:    1.486    0.035    0.500
   4_occ:    1.486    0.035    0.500
   5_bss:    1.486    0.035    0.500
   5_xyz:    1.525    0.036    0.506
   5_adp:    1.525    0.036    0.506
   5_occ:    1.525    0.036    0.506
   5_bss:    1.525    0.036    0.506
------------------------------------------------------------------------

CPU time actual refinement: 274.07


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_775/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_775/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_775/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_775/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_775/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 273.94 
  Macro-tasks:
    bulk solvent and scale       = 34.21  
    individual site refinement   = 113.56 
    weights calculation          = 26.58  
    collect and process          = 5.37   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 179.81 
  Micro-tasks:
    mask                            = 1.48   
    f_calc                          = 83.13  
    alpha_beta                      = 6.82   
    target                          = 0.95   
    gradients_wrt_atomic_parameters = 93.81  
    fmodel                         = 6.01   
    r_factors                      = 0.17   
    phase_errors                   = 8.90   
    foms                           = 0.15   
    TOTAL for micro-tasks          = 201.42 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 3.832 micro seconds
Total CPU time: 4.76 minutes
from_scatterers_fft:    658 calls, 82.93 s
gradients_fft:          603 calls, 82.11 s

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

# Date 2008-01-16 Time 02:22:14 PST -0800 (1200478934.56 s)
Start R-work = 0.4127, R-free = 0.3981 (no bulk solvent and anisotropic scale)
Final R-work = 0.1267, R-free = 0.1715 (no bulk solvent and anisotropic scale)

Start R-work = 0.4042, R-free = 0.3856
Final R-work = 0.1091, R-free = 0.1550