# Date 2008-01-16 Time 02:16:29 PST -0800 (1200478589.25 s)
#phil __OFF__

Command line arguments: "../765.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 27294
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 765

-------------------------------------------------------------------------------
  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, 46.4607, 86.822, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.28, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 46.4607, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0689 1.98258
Completeness in resolution range: 0.960528
Completeness with d_max=infinity: 0.95757

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0689
                             d_min =   1.9826

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, 46.4607, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0689 1.98258
Completeness in resolution range: 0.960528
Completeness with d_max=infinity: 0.95757

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0694 -  4.2426 [2145/2169]  1931   214  10.0%
  bin  2:  4.2426 -  3.3799 [2043/2063]  1838   205  10.0%
  bin  3:  3.3799 -  2.9564 [2041/2060]  1835   206  10.1%
  bin  4:  2.9564 -  2.6877 [2010/2040]  1812   198   9.9%
  bin  5:  2.6877 -  2.4960 [2006/2025]  1805   201  10.0%
  bin  6:  2.4960 -  2.3494 [1978/2003]  1779   199  10.1%
  bin  7:  2.3494 -  2.2322 [1985/2013]  1785   200  10.1%
  bin  8:  2.2322 -  2.1353 [1985/2021]  1790   195   9.8%
  bin  9:  2.1353 -  2.0533 [1955/1997]  1759   196  10.0%
  bin 10:  2.0533 -  1.9826 [1441/2003]  1296   145  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_765/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 17
        2.42 -     3.04: 2182
        3.04 -     3.66: 4690
        3.66 -     4.28: 9051
        4.28 -     4.90: 12321
  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
  " OG1 THR A  29 " - " O   HOH Z 245 "  2.305 3.040 x,y+1,z
  " O   HOH Z  70 " - " O   HOH Z 302 "  2.320 3.040 -x+1/2,-y+1,z+1/2
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  ... (remaining 28256 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_765/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_765/model_refine_001.geo

CPU time processing inputs: 9.17


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.60125 46.4607 86.82195 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: 1.98 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4376   r_free= 0.4228   ksol= 0.00   Bsol= 0.00   scale= 0.820    |
|                                                                             |
| 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:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.231261                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0694 -  4.7321 0.99   1394  155 0.3699 0.3501       6.539      6.4852|
|  2:  4.7321 -  3.7754 0.99   1336  150 0.3283 0.3173      6.6548      6.6253|
|  3:  3.7754 -  3.3039 0.99   1317  141 0.3689 0.3380      6.5481      6.5481|
|  4:  3.3039 -  3.0045 0.99   1297  150 0.4177 0.3767      6.4662      6.3885|
|  5:  3.0045 -  2.7906 0.99   1296  146 0.4593 0.4283      6.3187      6.3264|
|  6:  2.7906 -  2.6269 0.99   1303  134 0.4605 0.5206       6.236      6.1662|
|  7:  2.6269 -  2.4960 0.99   1278  148 0.4922 0.4782      6.2085      6.2175|
|  8:  2.4960 -  2.3878 0.98   1277  143 0.4939 0.4423      6.1568      6.1406|
|  9:  2.3878 -  2.2962 0.98   1265  140 0.4720 0.4950      6.0749      6.1057|
| 10:  2.2962 -  2.2172 1.00   1288  145 0.5023 0.4491      6.1032      6.0382|
| 11:  2.2172 -  2.1481 0.97   1266  138 0.5079 0.4778        6.02      6.0105|
| 12:  2.1481 -  2.0869 0.98   1252  141 0.5006 0.5119      5.9687      6.0021|
| 13:  2.0869 -  2.0320 0.99   1287  137 0.4981 0.4905      5.8673      5.8114|
| 14:  2.0320 -  1.9826 0.61    774   91 0.5174 0.5154      5.8633      5.7568|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0694 -  4.7321  1394   155  0.74  31.11   0.81     0.77      59376.91|
|  2:  4.7321 -  3.7754  1336   150  0.78  27.65   0.90     0.84      72067.19|
|  3:  3.7754 -  3.3039  1317   141  0.71  34.15   0.89     0.81      74644.24|
|  4:  3.3039 -  3.0045  1297   150  0.66  39.27   0.83     0.72      67800.41|
|  5:  3.0045 -  2.7906  1296   146  0.56  47.43   0.78     0.64      60833.35|
|  6:  2.7906 -  2.6269  1303   134  0.52  50.69   0.75     0.58      57246.30|
|  7:  2.6269 -  2.4960  1278   148  0.47  54.47   0.75     0.54      55489.66|
|  8:  2.4960 -  2.3878  1277   143  0.46  55.62   0.75     0.53      51295.29|
|  9:  2.3878 -  2.2962  1265   140  0.49  52.72   0.75     0.55      43826.33|
| 10:  2.2962 -  2.2172  1288   145  0.49  52.96   0.78     0.57      38459.72|
| 11:  2.2172 -  2.1481  1266   138  0.47  54.51   0.76     0.57      37289.13|
| 12:  2.1481 -  2.0869  1252   141  0.43  57.67   0.79     0.52      37327.77|
| 13:  2.0869 -  2.0320  1287   137  0.40  60.12   0.74     0.48      33363.56|
| 14:  2.0320 -  1.9826   774    91  0.45  56.53   0.74     0.47      25637.61|
|alpha:            min =        0.47 max =            0.84 mean =         0.62|
|beta:             min =    25637.61 max =        74644.24 mean =     52005.10|
|figures of merit: min =        0.00 max =            1.00 mean =         0.55|
|phase err.(work): min =        0.00 max =           89.97 mean =        47.74|
|phase err.(test): min =        0.00 max =           90.00 mean =        47.98|
|-----------------------------------------------------------------------------|

============================== 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 = 7.605982              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 75.595   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.696702              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.824   (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:      172 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      685 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1493 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2624 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3949 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5048 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6574 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7683 |
|-----------------------------------------------------------------------------|
|-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 |       53.826 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.090    4.900  1.196 |       1.704 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.906)------------------------------------------|
|    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 = 11.906)------------------------------------------|
|    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: 1.98 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4456   r_free= 0.4281   ksol= 0.00   Bsol= 0.00   scale= 0.788    |
|                                                                             |
| 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:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.237138                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4294   r_free= 0.4078   ksol= 0.34   Bsol= 9.52   scale= 1.030    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.63,9.38,8.84,0.00,0.00,0.00); trace/3= 8.62                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.226896                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.940342              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 77.535   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.669807              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.372   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4294      final r-factor (work) = 0.3222          |
| start r-factor (free) = 0.4078      final r-factor (free) = 0.3398          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 75.4849 = 6.94 * 0.50 * 6.2414 + 1.00 * 53.8260                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.2147 = 6.94 * 0.50 * 6.0796 + 1.00 * 0.1173                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3222      final r-factor (work) = 0.2602          |
| start r-factor (free) = 0.3398      final r-factor (free) = 0.3019          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0869 = 0.67 * 1.00 * 6.0796 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9694 = 0.67 * 1.00 * 5.9074 + 1.00 * 0.0126                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.906)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    67.61   11.13    None  None   None       |
|    all(noH): 2823   0      0.00    67.61   11.13    None  None   None       |
|    Sol.    : 438    0      0.00    67.61   27.38    None  None   None       |
|    Mac.    : 2385   0      0.00    60.78   8.15     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.761: 1289   |   5:    33.805 -  40.566:   81        |
|      1:     6.761 -  13.522:  759   |   6:    40.566 -  47.327:   56        |
|      2:    13.522 -  20.283:  311   |   7:    47.327 -  54.088:   16        |
|      3:    20.283 -  27.044:  181   |   8:    54.088 -  60.849:   11        |
|      4:    27.044 -  33.805:  117   |   9:    60.849 -  67.610:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2602 r_free = 0.3019             target_work(ml) = 5.853         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2596 r_free = 0.3019             target_work(ml) = 5.851         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2596   r_free= 0.3019   ksol= 0.34   Bsol= 9.52   scale= 1.107    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.63,9.38,8.84,0.00,0.00,0.00); trace/3= 8.62                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.851323                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2530   r_free= 0.2937   ksol= 0.34   Bsol= 40.49   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.02,4.87,5.25,0.00,0.00,0.00); trace/3= 4.72                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.846328                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.018387              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.143   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.310703              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 125.475  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2530      final r-factor (work) = 0.1764          |
| start r-factor (free) = 0.2937      final r-factor (free) = 0.2200          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.0440 = 3.02 * 0.50 * 5.9152 + 1.00 * 0.1168                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.6228 = 3.02 * 0.50 * 5.6727 + 1.00 * 0.0617                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1764      final r-factor (work) = 0.1601          |
| start r-factor (free) = 0.2200      final r-factor (free) = 0.2052          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7749 = 0.31 * 1.00 * 5.6727 + 1.00 * 0.0124                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7140 = 0.31 * 1.00 * 5.4728 + 1.00 * 0.0136                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.906)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    68.38   11.22    None  None   None       |
|    all(noH): 2823   0      0.00    68.38   11.22    None  None   None       |
|    Sol.    : 438    0      0.00    68.38   31.40    None  None   None       |
|    Mac.    : 2385   0      0.00    62.65   7.51     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.838: 1467   |   5:    34.189 -  41.027:  117        |
|      1:     6.838 -  13.676:  678   |   6:    41.027 -  47.864:   76        |
|      2:    13.676 -  20.513:  211   |   7:    47.864 -  54.702:   29        |
|      3:    20.513 -  27.351:  111   |   8:    54.702 -  61.540:    8        |
|      4:    27.351 -  34.189:  123   |   9:    61.540 -  68.378:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1601 r_free = 0.2052             target_work(ml) = 5.438         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1600 r_free = 0.2050             target_work(ml) = 5.438         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1600   r_free= 0.2050   ksol= 0.34   Bsol= 40.49   scale= 1.031   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.02,4.87,5.25,0.00,0.00,0.00); trace/3= 4.72                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.437923                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1595   r_free= 0.2042   ksol= 0.33   Bsol= 40.49   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.11,3.32,4.48,0.00,0.00,0.00); trace/3= 3.64                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.437881                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.180731              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.099  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.758726              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 100.466  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1595      final r-factor (work) = 0.1298          |
| start r-factor (free) = 0.2042      final r-factor (free) = 0.1731          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0356 = 2.18 * 0.50 * 5.4788 + 1.00 * 0.0617                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8828 = 2.18 * 0.50 * 5.3425 + 1.00 * 0.0574                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1298      final r-factor (work) = 0.1235          |
| start r-factor (free) = 0.1731      final r-factor (free) = 0.1691          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.4078 = 1.76 * 1.00 * 5.3425 + 1.00 * 0.0117                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.2249 = 1.76 * 1.00 * 5.2372 + 1.00 * 0.0142                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.906)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.13   12.13    None  None   None       |
|    all(noH): 2823   0      0.00    79.13   12.13    None  None   None       |
|    Sol.    : 438    0      0.46    78.34   36.01    None  None   None       |
|    Mac.    : 2385   0      0.00    79.13   7.75     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 -   7.913: 1629   |   5:    39.563 -  47.476:   84        |
|      1:     7.913 -  15.825:  589   |   6:    47.476 -  55.389:   78        |
|      2:    15.825 -  23.738:  168   |   7:    55.389 -  63.302:   37        |
|      3:    23.738 -  31.651:  104   |   8:    63.302 -  71.214:   20        |
|      4:    31.651 -  39.563:  106   |   9:    71.214 -  79.127:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1235 r_free = 0.1691             target_work(ml) = 5.225         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1235 r_free = 0.1692             target_work(ml) = 5.225         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1235   r_free= 0.1692   ksol= 0.33   Bsol= 40.49   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.11,3.32,4.48,0.00,0.00,0.00); trace/3= 3.64                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.224807                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1236   r_free= 0.1692   ksol= 0.32   Bsol= 40.49   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.99,3.03,4.36,0.00,0.00,0.00); trace/3= 3.46                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.224547                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.307378              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 130.081  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.200792              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.125  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1236      final r-factor (work) = 0.1126          |
| start r-factor (free) = 0.1692      final r-factor (free) = 0.1614          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.7168 = 3.31 * 0.50 * 5.2364 + 1.00 * 0.0574                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.6457 = 3.31 * 0.50 * 5.1852 + 1.00 * 0.0709                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1126      final r-factor (work) = 0.1127          |
| start r-factor (free) = 0.1614      final r-factor (free) = 0.1579          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0551 = 0.20 * 1.00 * 5.1852 + 1.00 * 0.0140                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0484 = 0.20 * 1.00 * 5.1662 + 1.00 * 0.0111                               |
|-----------------------------------------------------------------------------|
| number of iterations = 14      |    number of function evaluations = 17     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.906)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.73   11.57    None  None   None       |
|    all(noH): 2823   0      0.00    78.73   11.57    None  None   None       |
|    Sol.    : 438    0      1.37    75.17   33.81    None  None   None       |
|    Mac.    : 2385   0      0.00    78.73   7.49     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 -   7.873: 1698   |   5:    39.364 -  47.236:   78        |
|      1:     7.873 -  15.745:  553   |   6:    47.236 -  55.109:   67        |
|      2:    15.745 -  23.618:  154   |   7:    55.109 -  62.982:   30        |
|      3:    23.618 -  31.491:  121   |   8:    62.982 -  70.854:   19        |
|      4:    31.491 -  39.364:  100   |   9:    70.854 -  78.727:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1127 r_free = 0.1579             target_work(ml) = 5.152         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1126 r_free = 0.1578             target_work(ml) = 5.151         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1126   r_free= 0.1578   ksol= 0.32   Bsol= 40.49   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.99,3.03,4.36,0.00,0.00,0.00); trace/3= 3.46                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.151482                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1126   r_free= 0.1578   ksol= 0.32   Bsol= 40.49   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.99,3.03,4.36,0.00,0.00,0.00); trace/3= 3.46                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.151539                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.447647              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 149.126  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.281487              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 94.281   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1126      final r-factor (work) = 0.1150          |
| start r-factor (free) = 0.1578      final r-factor (free) = 0.1581          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8102 = 1.45 * 0.50 * 5.1661 + 1.00 * 0.0709                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.7902 = 1.45 * 0.50 * 5.1618 + 1.00 * 0.0540                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1150      final r-factor (work) = 0.1147          |
| start r-factor (free) = 0.1581      final r-factor (free) = 0.1587          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4642 = 0.28 * 1.00 * 5.1618 + 1.00 * 0.0112                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4696 = 0.28 * 1.00 * 5.1618 + 1.00 * 0.0167                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.906)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.23   11.38    None  None   None       |
|    all(noH): 2823   0      0.00    80.23   11.38    None  None   None       |
|    Sol.    : 438    0      1.31    69.69   32.87    None  None   None       |
|    Mac.    : 2385   0      0.00    80.23   7.43     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.023: 1715   |   5:    40.115 -  48.138:   78        |
|      1:     8.023 -  16.046:  543   |   6:    48.138 -  56.161:   60        |
|      2:    16.046 -  24.069:  159   |   7:    56.161 -  64.184:   17        |
|      3:    24.069 -  32.092:  116   |   8:    64.184 -  72.207:   11        |
|      4:    32.092 -  40.115:  122   |   9:    72.207 -  80.231:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1147 r_free = 0.1587             target_work(ml) = 5.164         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1146 r_free = 0.1587             target_work(ml) = 5.164         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1146   r_free= 0.1587   ksol= 0.32   Bsol= 40.49   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.99,3.03,4.36,0.00,0.00,0.00); trace/3= 3.46                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.164296                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0694 -  4.7321 0.99   1394  155 0.1006 0.1301      5.3921      5.5321|
|  2:  4.7321 -  3.7754 0.99   1336  150 0.0882 0.1140      5.4531      5.6277|
|  3:  3.7754 -  3.3039 0.99   1317  141 0.1081 0.1488      5.4881      5.8525|
|  4:  3.3039 -  3.0045 0.99   1297  150 0.1230 0.1718      5.4683      5.6253|
|  5:  3.0045 -  2.7906 0.99   1296  146 0.1362 0.1687      5.3531      5.5637|
|  6:  2.7906 -  2.6269 0.99   1303  134 0.1221 0.2001      5.2114      5.4817|
|  7:  2.6269 -  2.4960 0.99   1278  148 0.1319 0.1605       5.197      5.3727|
|  8:  2.4960 -  2.3878 0.98   1277  143 0.1221 0.1729      5.1031      5.3497|
|  9:  2.3878 -  2.2962 0.98   1265  140 0.1240 0.1830      5.0839      5.3245|
| 10:  2.2962 -  2.2172 1.00   1288  145 0.1147 0.1640      4.9653      5.2208|
| 11:  2.2172 -  2.1481 0.97   1266  138 0.1171 0.1817      4.9539      5.2868|
| 12:  2.1481 -  2.0869 0.98   1252  141 0.1137 0.1684       4.882      5.1729|
| 13:  2.0869 -  2.0320 0.99   1287  137 0.1169 0.1698      4.8053      5.0575|
| 14:  2.0320 -  1.9826 0.61    774   91 0.1075 0.1682      4.7067      4.8964|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0694 -  4.7321  1394   155  0.94   9.11   0.98     0.95       7152.59|
|  2:  4.7321 -  3.7754  1336   150  0.95   7.90   1.02     1.00       9046.89|
|  3:  3.7754 -  3.3039  1317   141  0.93  11.40   1.02     1.02      10449.53|
|  4:  3.3039 -  3.0045  1297   150  0.92  13.80   1.01     0.98      10543.64|
|  5:  3.0045 -  2.7906  1296   146  0.90  16.23   1.00     0.97       8685.10|
|  6:  2.7906 -  2.6269  1303   134  0.90  15.87   0.98     0.96       7041.47|
|  7:  2.6269 -  2.4960  1278   148  0.90  15.86   0.99     0.96       6384.74|
|  8:  2.4960 -  2.3878  1277   143  0.90  15.75   0.99     0.97       5566.63|
|  9:  2.3878 -  2.2962  1265   140  0.90  16.00   1.01     0.97       5454.13|
| 10:  2.2962 -  2.2172  1288   145  0.90  15.78   1.01     0.97       4451.20|
| 11:  2.2172 -  2.1481  1266   138  0.90  16.00   1.00     0.95       4250.36|
| 12:  2.1481 -  2.0869  1252   141  0.91  15.02   1.02     1.02       3897.77|
| 13:  2.0869 -  2.0320  1287   137  0.90  16.46   1.00     0.98       3447.20|
| 14:  2.0320 -  1.9826   774    91  0.91  14.90   0.99     0.96       2777.16|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2777.16 max =        10543.64 mean =      6504.44|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.22|
|phase err.(test): min =        0.00 max =           89.34 mean =        13.71|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1146   r_free= 0.1587   ksol= 0.32   Bsol= 43.95   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.47,-0.43,0.90,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.164296                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1146   r_free= 0.1587   ksol= 0.32   Bsol= 43.95   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.47,-0.43,0.90,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.164296                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0694 -  4.7321 0.99   1394  155 0.1006 0.1301      5.3921      5.5321|
|  2:  4.7321 -  3.7754 0.99   1336  150 0.0882 0.1140      5.4531      5.6277|
|  3:  3.7754 -  3.3039 0.99   1317  141 0.1081 0.1488      5.4881      5.8525|
|  4:  3.3039 -  3.0045 0.99   1297  150 0.1230 0.1718      5.4683      5.6253|
|  5:  3.0045 -  2.7906 0.99   1296  146 0.1362 0.1687      5.3531      5.5637|
|  6:  2.7906 -  2.6269 0.99   1303  134 0.1221 0.2001      5.2114      5.4817|
|  7:  2.6269 -  2.4960 0.99   1278  148 0.1319 0.1605       5.197      5.3727|
|  8:  2.4960 -  2.3878 0.98   1277  143 0.1221 0.1729      5.1031      5.3497|
|  9:  2.3878 -  2.2962 0.98   1265  140 0.1240 0.1830      5.0839      5.3245|
| 10:  2.2962 -  2.2172 1.00   1288  145 0.1147 0.1640      4.9653      5.2208|
| 11:  2.2172 -  2.1481 0.97   1266  138 0.1171 0.1817      4.9539      5.2868|
| 12:  2.1481 -  2.0869 0.98   1252  141 0.1137 0.1684       4.882      5.1729|
| 13:  2.0869 -  2.0320 0.99   1287  137 0.1169 0.1698      4.8053      5.0575|
| 14:  2.0320 -  1.9826 0.61    774   91 0.1075 0.1682      4.7067      4.8964|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0694 -  4.7321  1394   155  0.94   9.11   0.98     0.95       7152.59|
|  2:  4.7321 -  3.7754  1336   150  0.95   7.90   1.02     1.00       9046.89|
|  3:  3.7754 -  3.3039  1317   141  0.93  11.40   1.02     1.02      10449.53|
|  4:  3.3039 -  3.0045  1297   150  0.92  13.80   1.01     0.98      10543.64|
|  5:  3.0045 -  2.7906  1296   146  0.90  16.23   1.00     0.97       8685.10|
|  6:  2.7906 -  2.6269  1303   134  0.90  15.87   0.98     0.96       7041.47|
|  7:  2.6269 -  2.4960  1278   148  0.90  15.86   0.99     0.96       6384.74|
|  8:  2.4960 -  2.3878  1277   143  0.90  15.75   0.99     0.97       5566.63|
|  9:  2.3878 -  2.2962  1265   140  0.90  16.00   1.01     0.97       5454.13|
| 10:  2.2962 -  2.2172  1288   145  0.90  15.78   1.01     0.97       4451.20|
| 11:  2.2172 -  2.1481  1266   138  0.90  16.00   1.00     0.95       4250.36|
| 12:  2.1481 -  2.0869  1252   141  0.91  15.02   1.02     1.02       3897.77|
| 13:  2.0869 -  2.0320  1287   137  0.90  16.46   1.00     0.98       3447.20|
| 14:  2.0320 -  1.9826   774    91  0.91  14.90   0.99     0.96       2777.16|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2777.16 max =        10543.64 mean =      6504.44|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.22|
|phase err.(test): min =        0.00 max =           89.34 mean =        13.71|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.906)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.46    83.69   14.84    None  None   None       |
|    all(noH): 2823   0      3.46    83.69   14.84    None  None   None       |
|    Sol.    : 438    0      4.77    73.15   36.33    None  None   None       |
|    Mac.    : 2385   0      3.46    83.69   10.89    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:     3.461 -  11.484: 1715   |   5:    43.576 -  51.599:   78        |
|      1:    11.484 -  19.507:  543   |   6:    51.599 -  59.623:   60        |
|      2:    19.507 -  27.530:  159   |   7:    59.623 -  67.646:   17        |
|      3:    27.530 -  35.553:  116   |   8:    67.646 -  75.669:   11        |
|      4:    35.553 -  43.576:  122   |   9:    75.669 -  83.692:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 309         
Filter by distance & map next to the model:
   mapped sites are within: 0.331 - 4.734
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 304 from: 309
   mapped sites are within: 0.714 - 4.734

peak=   11.278 closest distance to " CB  VAL A 230 " =    1.482
peak=    7.785 closest distance to " CG2 VAL A 296 " =    1.155
peak=    6.115 closest distance to " CD2 LEU A   5 " =    1.293
peak=    6.098 closest distance to " CG  LEU A   5 " =    1.253
peak=    5.952 closest distance to " NH2 ARG A  56 " =    2.165
peak=    5.820 closest distance to " CG  PRO A  54 " =    1.382
peak=    5.474 closest distance to " NE2 GLN A  11 " =    1.188
peak=    5.461 closest distance to " O   HOH Z 142 " =    1.993
peak=    5.159 closest distance to " O   HOH Z 232 " =    2.291
peak=    5.098 closest distance to " CB  GLN A 223 " =    1.448
peak=    5.097 closest distance to " CB  PRO A  54 " =    1.038
peak=    5.079 closest distance to " CG  LEU A 228 " =    1.172
peak=    4.970 closest distance to " CB  VAL A 296 " =    1.114
peak=    4.913 closest distance to " CB  GLN A 183 " =    1.198
peak=    4.795 closest distance to " O   HOH Z   9 " =    1.455
peak=    4.782 closest distance to " CG  PRO A 198 " =    1.268
peak=    4.706 closest distance to " CB  ARG A 275 " =    0.925
peak=    4.633 closest distance to " CG  PRO A 213 " =    1.237
peak=    4.615 closest distance to " CB  SER A  63 " =    1.279
peak=    4.604 closest distance to " CB  ASN A 148 " =    1.327
peak=    4.597 closest distance to " CG  PRO A 243 " =    1.139
peak=    4.596 closest distance to " ND2 ASN A 187 " =    1.517
peak=    4.575 closest distance to " O   HOH Z 427 " =    2.846
peak=    4.574 closest distance to " O   HOH Z 126 " =    1.950
peak=    4.562 closest distance to " O   HOH Z 425 " =    1.501
peak=    4.522 closest distance to " O   HOH Z  55 " =    2.418
peak=    4.442 closest distance to " O   HOH Z 236 " =    2.100
peak=    4.432 closest distance to " O   HOH Z 209 " =    2.274
peak=    4.391 closest distance to " CB  SER A   3 " =    1.334
peak=    4.369 closest distance to " O   HOH Z 369 " =    2.084
peak=    4.369 closest distance to " CB  VAL A 230 " =    1.149
peak=    4.351 closest distance to " C   PRO A 198 " =    1.546
peak=    4.326 closest distance to " CB  TRP A 266 " =    1.000
peak=    4.318 closest distance to " CB  GLU A 152 " =    1.208
peak=    4.303 closest distance to " CB  VAL A 265 " =    1.328
peak=    4.283 closest distance to " CD2 LEU A 228 " =    1.162
peak=    4.279 closest distance to " O   HOH Z 272 " =    1.812
peak=    4.272 closest distance to " O   HOH Z 346 " =    1.611
peak=    4.218 closest distance to " CB BVAL A  41 " =    0.902
peak=    4.214 closest distance to " O   HOH Z 368 " =    2.003
peak=    4.212 closest distance to " O   HOH Z 298 " =    1.773
peak=    4.198 closest distance to " O   HOH Z  78 " =    1.645
peak=    4.191 closest distance to " O   HOH Z 316 " =    3.089
peak=    4.165 closest distance to " CB  GLU A 128 " =    1.013
peak=    4.132 closest distance to " CZ  PHE A 218 " =    1.098
peak=    4.124 closest distance to " CG  LEU A 167 " =    1.217
peak=    4.083 closest distance to " CB  ASN A  39 " =    0.878
peak=    4.079 closest distance to " O   HOH Z 234 " =    3.725
peak=    4.076 closest distance to " O   HOH Z  61 " =    1.622
peak=    4.073 closest distance to " O   SER A  87 " =    2.293
peak=    4.056 closest distance to " CB  ARG A  79 " =    1.462
peak=    4.050 closest distance to " CA  THR A 264 " =    0.782
peak=    4.049 closest distance to " CB  SER A 216 " =    0.835
peak=    4.019 closest distance to " N   PHE A 130 " =    1.218
peak=    4.011 closest distance to " CG2 VAL A 257 " =    0.919
peak=    3.995 closest distance to " CB  ASN A 142 " =    1.015
peak=    3.985 closest distance to " O   HOH Z 261 " =    1.995
peak=    3.981 closest distance to " O   HOH Z 303 " =    2.154
peak=    3.980 closest distance to " CA  TYR A  30 " =    0.996
peak=    3.960 closest distance to " O   HOH Z 193 " =    1.651
peak=    3.953 closest distance to " OG  SER A  97 " =    2.986
peak=    3.934 closest distance to " O   HOH Z  43 " =    1.920
peak=    3.910 closest distance to " O   HOH Z 389 " =    1.874
peak=    3.904 closest distance to " O   HOH Z 193 " =    1.824
peak=    3.864 closest distance to " OD1 ASN A  69 " =    2.604
peak=    3.862 closest distance to " NH2AARG A 190 " =    1.858
peak=    3.841 closest distance to " CA  ALA A  51 " =    0.983
peak=    3.836 closest distance to " O   HOH Z  30 " =    1.547
peak=    3.828 closest distance to " CB  ASN A 187 " =    1.138
peak=    3.808 closest distance to " O   HOH Z   2 " =    1.641
peak=    3.795 closest distance to " CG2AVAL A  72 " =    1.627
peak=    3.778 closest distance to " CD  ARG A 159 " =    0.740
peak=    3.772 closest distance to " CB  LEU A 143 " =    1.156
peak=    3.760 closest distance to " O   HOH Z 158 " =    3.212
peak=    3.758 closest distance to " CB  SER A 212 " =    1.293
peak=    3.758 closest distance to " NH1AARG A 145 " =    1.141
peak=    3.756 closest distance to " O   HOH Z 411 " =    3.683
peak=    3.755 closest distance to " O   HOH Z 203 " =    1.780
peak=    3.746 closest distance to " CB  VAL A 202 " =    1.573
peak=    3.742 closest distance to " O   HOH Z 126 " =    1.651
peak=    3.709 closest distance to " O   HOH Z 280 " =    2.994
peak=    3.706 closest distance to " CB  ARG A 190 " =    1.501
peak=    3.701 closest distance to " CA  SER A  87 " =    0.955
peak=    3.689 closest distance to " CB  MET A  40 " =    0.837
peak=    3.672 closest distance to " CB  TRP A 179 " =    1.461
peak=    3.665 closest distance to " OG BSER A 164 " =    2.193
peak=    3.662 closest distance to " CB  THR A 157 " =    1.149
peak=    3.655 closest distance to " CG1 VAL A 153 " =    0.919
peak=    3.654 closest distance to " CD1 LEU A 300 " =    1.137
peak=    3.654 closest distance to " N   ASN A  39 " =    1.160
peak=    3.650 closest distance to " O   HOH Z 250 " =    1.370
peak=    3.648 closest distance to " O   HOH Z  10 " =    1.729
peak=    3.646 closest distance to " CB  ALA A   9 " =    1.585
peak=    3.645 closest distance to " CA  ASN A 215 " =    1.126
peak=    3.632 closest distance to " O   HOH Z  68 " =    2.110
peak=    3.629 closest distance to " CD  LYS A 166 " =    1.341
peak=    3.614 closest distance to " O   HOH Z 214 " =    2.114
peak=    3.601 closest distance to " O   HOH Z 380 " =    1.689
peak=    3.598 closest distance to " O   HOH Z 368 " =    3.631
peak=    3.598 closest distance to " O   HOH Z 128 " =    2.101
peak=    3.597 closest distance to " O   HOH Z  21 " =    1.728
peak=    3.596 closest distance to " CE1 TYR A 186 " =    1.346
peak=    3.592 closest distance to " CB  HIS A 108 " =    0.822
peak=    3.592 closest distance to " CB  ALA A 291 " =    1.316
peak=    3.589 closest distance to " O   HOH Z 273 " =    2.778
peak=    3.588 closest distance to " ND1 HIS A  86 " =    1.696
peak=    3.587 closest distance to " CB  LEU A 228 " =    1.269
peak=    3.586 closest distance to " O   HOH Z   7 " =    1.419
peak=    3.584 closest distance to " CB  GLN A  88 " =    1.248
peak=    3.582 closest distance to " CB  ASP A 140 " =    0.857
peak=    3.581 closest distance to " O   HOH Z 263 " =    1.631
peak=    3.580 closest distance to " O   HOH Z 359 " =    3.993
peak=    3.578 closest distance to " O   HOH Z 145 " =    1.864
peak=    3.552 closest distance to " CE  LYS A  76 " =    0.882
peak=    3.544 closest distance to " O   HOH Z 409 " =    2.997
peak=    3.538 closest distance to " O   HOH Z 437 " =    1.872
peak=    3.536 closest distance to " O   HOH Z 419 " =    1.886
peak=    3.535 closest distance to " CG  GLN A  88 " =    1.070
peak=    3.530 closest distance to " CG  MET A 185 " =    1.213
peak=    3.529 closest distance to " O   HOH Z  88 " =    3.115
peak=    3.528 closest distance to " NZ  LYS A 117 " =    3.055
peak=    3.526 closest distance to " CB  SER A 210 " =    0.770
peak=    3.522 closest distance to " O   HOH Z  40 " =    2.492
peak=    3.518 closest distance to " O   HOH Z   1 " =    1.779
peak=    3.510 closest distance to " CD1 ILE A  33 " =    1.683
peak=    3.506 closest distance to " CB  GLU A 277 " =    3.589
peak=    3.504 closest distance to " CA  LYS A 117 " =    1.192
peak=    3.502 closest distance to " O   HOH Z 403 " =    1.645
peak=    3.490 closest distance to " O   HOH Z 435 " =    2.048
peak=    3.490 closest distance to " O   HOH Z 422 " =    2.644
peak=    3.488 closest distance to " O   HOH Z  63 " =    1.336
peak=    3.480 closest distance to " CA  ARG A  36 " =    1.105
peak=    3.479 closest distance to " N   SER A 135 " =    1.350
peak=    3.472 closest distance to " O   HOH Z 193 " =    1.891
peak=    3.468 closest distance to " O   HOH Z 180 " =    2.115
peak=    3.466 closest distance to " NE2 HIS A 207 " =    1.268
peak=    3.466 closest distance to " O   HOH Z 130 " =    2.086
peak=    3.463 closest distance to " O   HOH Z  59 " =    1.808
peak=    3.461 closest distance to " CB  SER A 273 " =    0.904
peak=    3.455 closest distance to " CB  ASN A 110 " =    1.055
peak=    3.454 closest distance to " CB  ALA A 104 " =    0.714
peak=    3.452 closest distance to " C   ALA A 299 " =    0.978
peak=    3.451 closest distance to " O   HOH Z 222 " =    2.445
peak=    3.450 closest distance to " OD2 ASP A 286 " =    2.794
peak=    3.448 closest distance to " CZ  PHE A 192 " =    0.911
peak=    3.445 closest distance to " O   HOH Z 291 " =    1.588
peak=    3.443 closest distance to " CB  ASN A 224 " =    1.011
peak=    3.440 closest distance to " ND2 ASN A 249 " =    0.878
peak=    3.440 closest distance to " O   HOH Z 344 " =    2.952
peak=    3.437 closest distance to " O   HOH Z  97 " =    2.019
peak=    3.435 closest distance to " O   HOH Z   3 " =    1.999
peak=    3.433 closest distance to " O   HOH Z  40 " =    1.923
peak=    3.431 closest distance to " CA  ARG A 195 " =    1.160
peak=    3.430 closest distance to " O   HOH Z 366 " =    2.888
peak=    3.429 closest distance to " O   HOH Z 172 " =    3.155
peak=    3.428 closest distance to " CD  ARG A 269 " =    0.998
peak=    3.426 closest distance to " CB  THR A  82 " =    1.347
peak=    3.426 closest distance to " O   HOH Z   1 " =    1.753
peak=    3.425 closest distance to " CB  GLU A  46 " =    0.953
peak=    3.422 closest distance to " N   GLN A 278 " =    1.147
peak=    3.422 closest distance to " CB  VAL A 250 " =    1.120
peak=    3.421 closest distance to " CA  PHE A 283 " =    1.185
peak=    3.420 closest distance to " CA  LEU A 282 " =    1.109
peak=    3.419 closest distance to " O   HOH Z 371 " =    2.817
peak=    3.416 closest distance to " O   HOH Z 260 " =    1.482
peak=    3.415 closest distance to " CG  MET A 185 " =    1.028
peak=    3.413 closest distance to " O   HOH Z 248 " =    1.586
peak=    3.411 closest distance to " CA  ALA A  21 " =    1.099
peak=    3.410 closest distance to " CD BLYS A 290 " =    1.084
peak=    3.405 closest distance to " CA  ALA A 233 " =    1.152
peak=    3.401 closest distance to " OE2 GLU A  53 " =    1.994
peak=    3.396 closest distance to " O   HOH Z 128 " =    1.846
peak=    3.395 closest distance to " CA  ILE A 234 " =    0.889
peak=    3.385 closest distance to " CG2 THR A 221 " =    0.991
peak=    3.376 closest distance to " CG BARG A 102 " =    1.873
peak=    3.373 closest distance to " CG1 ILE A  33 " =    1.322
peak=    3.372 closest distance to " N   ARG A 156 " =    1.318
peak=    3.371 closest distance to " CG1 VAL A 296 " =    1.216
peak=    3.368 closest distance to " O   HOH Z 197 " =    3.315
peak=    3.363 closest distance to " O   HOH Z 148 " =    3.438
peak=    3.361 closest distance to " O   HOH Z 305 " =    3.462
peak=    3.360 closest distance to " O   HOH Z 353 " =    2.548
peak=    3.356 closest distance to " CA  ALA A 154 " =    1.011
peak=    3.355 closest distance to " CA  ASP A 162 " =    0.988
peak=    3.350 closest distance to " O   HOH Z 145 " =    3.662
peak=    3.348 closest distance to " O   TYR A 116 " =    1.302
peak=    3.347 closest distance to " OG BSER A 134 " =    3.111
peak=    3.345 closest distance to " OE2 GLU A   2 " =    1.794
peak=    3.343 closest distance to " CE3 TRP A 150 " =    0.943
peak=    3.339 closest distance to " CB  LYS A 117 " =    1.240
peak=    3.336 closest distance to " CD1 LEU A 228 " =    2.084
peak=    3.332 closest distance to " O   HOH Z 290 " =    1.180
peak=    3.332 closest distance to " NH2BARG A 190 " =    1.541
peak=    3.322 closest distance to " CG1 ILE A 151 " =    1.065
peak=    3.320 closest distance to " O   HOH Z 128 " =    2.109
peak=    3.320 closest distance to " O   HOH Z 423 " =    1.572
peak=    3.316 closest distance to " CB  ILE A 120 " =    1.359
peak=    3.316 closest distance to " CA  LYS A 290 " =    1.246
peak=    3.314 closest distance to " O   HOH Z 371 " =    1.694
peak=    3.312 closest distance to " CB  ALA A 248 " =    1.425
peak=    3.299 closest distance to " CB  ALA A 137 " =    1.045
peak=    3.296 closest distance to " O   HOH Z 423 " =    2.629
peak=    3.294 closest distance to " CA  ALA A 291 " =    0.897
peak=    3.293 closest distance to " N   SER A 271 " =    0.980
peak=    3.290 closest distance to " CB  GLN A 278 " =    0.858
peak=    3.289 closest distance to " CG1 ILE A  49 " =    1.438
peak=    3.289 closest distance to " O   HOH Z 132 " =    2.507
peak=    3.288 closest distance to " CA  ARG A 102 " =    1.165
peak=    3.281 closest distance to " CB  ALA A  34 " =    1.019
peak=    3.277 closest distance to " CD2 TRP A 179 " =    1.315
peak=    3.276 closest distance to " CA  TYR A  30 " =    1.081
peak=    3.273 closest distance to " OG BSER A 212 " =    2.808
peak=    3.272 closest distance to " CG2 ILE A 120 " =    1.165
peak=    3.271 closest distance to " O   HOH Z 227 " =    2.038
peak=    3.271 closest distance to " NH1 ARG A 138 " =    1.107
peak=    3.270 closest distance to " CG  MET A 113 " =    1.210
peak=    3.262 closest distance to " O   HOH Z 285 " =    2.732
peak=    3.261 closest distance to " CA  THR A 221 " =    0.891
peak=    3.258 closest distance to " O   HOH Z 423 " =    1.689
peak=    3.255 closest distance to " CB  SER A  26 " =    1.690
peak=    3.255 closest distance to " CZ  PHE A  38 " =    1.150
peak=    3.254 closest distance to " O   HOH Z  97 " =    2.604
peak=    3.252 closest distance to " NZ  LYS A  48 " =    1.278
peak=    3.252 closest distance to " CD  ARG A  66 " =    2.610
peak=    3.251 closest distance to " O   HOH Z 105 " =    1.566
peak=    3.251 closest distance to " O   HOH Z 258 " =    2.240
peak=    3.250 closest distance to " NH2AARG A 275 " =    3.628
peak=    3.249 closest distance to " O   HOH Z   2 " =    1.511
peak=    3.246 closest distance to " O   HOH Z 109 " =    2.511
peak=    3.242 closest distance to " O   ASP A 124 " =    1.111
peak=    3.241 closest distance to " N   ASN A 127 " =    1.241
peak=    3.238 closest distance to " O   HOH Z 345 " =    3.460
peak=    3.236 closest distance to " CG2 VAL A 197 " =    1.090
peak=    3.235 closest distance to " CD1 LEU A 261 " =    1.253
peak=    3.234 closest distance to " NH2BARG A 145 " =    1.930
peak=    3.234 closest distance to " O   HOH Z  61 " =    1.542
peak=    3.227 closest distance to " CG2 ILE A  20 " =    1.571
peak=    3.226 closest distance to " O   HOH Z 133 " =    1.640
peak=    3.221 closest distance to " O   HOH Z 213 " =    2.336
peak=    3.219 closest distance to " O   HOH Z   9 " =    1.869
peak=    3.218 closest distance to " O   HOH Z 187 " =    2.318
peak=    3.216 closest distance to " CG  GLN A 278 " =    1.318
peak=    3.216 closest distance to " O   HOH Z 322 " =    2.053
peak=    3.211 closest distance to " CA  ALA A 158 " =    1.195
peak=    3.210 closest distance to " OG  SER A 206 " =    1.216
peak=    3.206 closest distance to " O   TRP A 274 " =    1.803
peak=    3.206 closest distance to " NE AARG A 275 " =    1.247
peak=    3.204 closest distance to " O   HOH Z  48 " =    1.587
peak=    3.203 closest distance to " CB  ASN A 215 " =    1.171
peak=    3.200 closest distance to " O   HOH Z 147 " =    1.766
peak=    3.196 closest distance to " CB  ARG A 139 " =    0.950
peak=    3.190 closest distance to " O   HOH Z 282 " =    1.932
peak=    3.186 closest distance to " O  BHOH Z 338 " =    2.472
peak=    3.183 closest distance to " O   MET A 105 " =    1.682
peak=    3.183 closest distance to " O   HOH Z 424 " =    2.577
peak=    3.180 closest distance to " CD2 LEU A 255 " =    1.656
peak=    3.180 closest distance to " O   HOH Z 126 " =    1.453
peak=    3.178 closest distance to " CD1 ILE A 106 " =    0.878
peak=    3.178 closest distance to " OG1 THR A 294 " =    2.429
peak=    3.178 closest distance to " O   HOH Z 329 " =    2.899
peak=    3.178 closest distance to " O   HOH Z 175 " =    2.066
peak=    3.176 closest distance to " CA  ILE A 106 " =    0.735
peak=    3.176 closest distance to " CB  PRO A 198 " =    0.941
peak=    3.173 closest distance to " O   HOH Z 153 " =    3.809
peak=    3.171 closest distance to " CB  SER A  62 " =    1.178
peak=    3.169 closest distance to " O   PRO A  90 " =    1.568
peak=    3.168 closest distance to " OG  SER A  62 " =    2.750
peak=    3.167 closest distance to " CD1 LEU A  96 " =    0.763
peak=    3.166 closest distance to " CA  VAL A  41 " =    0.782
peak=    3.163 closest distance to " O   ALA A 158 " =    1.421
peak=    3.162 closest distance to " CB  TRP A 150 " =    1.475
peak=    3.161 closest distance to " O   PHE A 192 " =    1.367
peak=    3.160 closest distance to " CB  ALA A 114 " =    1.172
peak=    3.159 closest distance to " CB  VAL A 268 " =    0.831
peak=    3.154 closest distance to " CD1 ILE A 263 " =    1.235
peak=    3.153 closest distance to " CB  ALA A 227 " =    0.999
peak=    3.152 closest distance to " CB  PRO A 243 " =    1.355
peak=    3.152 closest distance to " CB  THR A  31 " =    1.614
peak=    3.151 closest distance to " CG  ARG A 159 " =    0.962
peak=    3.148 closest distance to " ND1 HIS A  81 " =    1.731
peak=    3.145 closest distance to " O   HOH Z 294 " =    1.543
peak=    3.141 closest distance to " N   ALA A 256 " =    1.154
peak=    3.140 closest distance to " O   HOH Z 426 " =    1.843
peak=    3.134 closest distance to " CA  SER A 146 " =    1.684
peak=    3.133 closest distance to " CD  ARG A 195 " =    3.491
peak=    3.131 closest distance to " O   HOH Z 124 " =    1.878
peak=    3.131 closest distance to " CB  ALA A 242 " =    0.756
peak=    3.128 closest distance to " CZ3 TRP A 266 " =    1.138
peak=    3.126 closest distance to " O   HOH Z 173 " =    2.114
peak=    3.118 closest distance to " N   SER A  12 " =    1.573
peak=    3.110 closest distance to " CB  SER A 245 " =    3.250
peak=    3.100 closest distance to " O   HOH Z 329 " =    3.927
peak=    3.092 closest distance to " O   HOH Z 350 " =    1.567
peak=    3.089 closest distance to " O   HOH Z 425 " =    1.942
peak=    3.085 closest distance to " O   HOH Z 222 " =    2.345
peak=    3.082 closest distance to " C   GLN A  88 " =    1.412
peak=    3.074 closest distance to " O   HOH Z 154 " =    2.227
peak=    3.069 closest distance to " O   ALA A 292 " =    1.718
peak=    3.069 closest distance to " CB  ALA A   1 " =    4.734
peak=    3.057 closest distance to " O   HOH Z 325 " =    2.259
peak=    3.057 closest distance to " CB  ALA A 180 " =    1.208
peak=    3.032 closest distance to " O   HOH Z 251 " =    1.583
peak=    3.026 closest distance to " CB  ILE A  20 " =    1.439
peak=    3.023 closest distance to " CB  PHE A 204 " =    0.774

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 204         
Filter by distance & map next to the model:
   mapped sites are within: 0.559 - 5.412
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 202 from: 204
   mapped sites are within: 0.715 - 5.412

peak=   -5.370 closest distance to " CG2 VAL A 230 " =    0.715
peak=   -4.436 closest distance to " CB  PRO A 243 " =    2.643
peak=   -4.343 closest distance to " CD  ARG A  14 " =    3.226
peak=   -4.287 closest distance to " O   HOH Z 290 " =    1.098
peak=   -4.267 closest distance to " CD  ARG A 156 " =    2.038
peak=   -4.068 closest distance to " O   HOH Z 435 " =    2.891
peak=   -4.057 closest distance to " N   ALA A  43 " =    2.436
peak=   -4.050 closest distance to " O   HOH Z 266 " =    5.261
peak=   -4.044 closest distance to " CE2 TYR A  30 " =    2.743
peak=   -4.034 closest distance to " CG2 VAL A 296 " =    1.410
peak=   -3.973 closest distance to " O   PRO A 198 " =    1.152
peak=   -3.966 closest distance to " O   HOH Z 351 " =    1.490
peak=   -3.942 closest distance to " O   HOH Z 231 " =    1.740
peak=   -3.937 closest distance to " CB  ALA A  43 " =    2.548
peak=   -3.933 closest distance to " O   TYR A 247 " =    2.846
peak=   -3.925 closest distance to " CA  GLY A 241 " =    2.343
peak=   -3.921 closest distance to " O   HOH Z 140 " =    1.270
peak=   -3.914 closest distance to " CD  GLN A  58 " =    0.985
peak=   -3.914 closest distance to " CG  GLN A 223 " =    2.002
peak=   -3.903 closest distance to " CZ3 TRP A 179 " =    1.217
peak=   -3.893 closest distance to " O   HOH Z 185 " =    2.254
peak=   -3.863 closest distance to " CB  PHE A 192 " =    1.816
peak=   -3.860 closest distance to " OG BSER A 134 " =    1.238
peak=   -3.859 closest distance to " O   VAL A  67 " =    2.567
peak=   -3.856 closest distance to " O   GLY A 203 " =    2.443
peak=   -3.848 closest distance to " CG1 VAL A 112 " =    2.794
peak=   -3.843 closest distance to " CB  ALA A 161 " =    2.589
peak=   -3.818 closest distance to " CG1 VAL A 112 " =    2.618
peak=   -3.812 closest distance to " CB  ALA A 248 " =    2.080
peak=   -3.799 closest distance to " O   HOH Z  52 " =    1.431
peak=   -3.791 closest distance to " O   HOH Z 394 " =    1.499
peak=   -3.773 closest distance to " O   ARG A 145 " =    1.584
peak=   -3.740 closest distance to " C   HIS A 108 " =    1.253
peak=   -3.739 closest distance to " N   THR A 157 " =    1.473
peak=   -3.735 closest distance to " C   MET A 188 " =    1.469
peak=   -3.724 closest distance to " CB  ALA A 248 " =    2.439
peak=   -3.715 closest distance to " CG1 VAL A 296 " =    1.337
peak=   -3.698 closest distance to " NH2 ARG A  79 " =    1.975
peak=   -3.678 closest distance to " ND2 ASN A  45 " =    1.201
peak=   -3.661 closest distance to " O   HOH Z 114 " =    2.929
peak=   -3.655 closest distance to " O   HOH Z 166 " =    2.116
peak=   -3.651 closest distance to " C   ASP A 231 " =    2.616
peak=   -3.631 closest distance to " CB  PRO A 163 " =    2.504
peak=   -3.630 closest distance to " O   HOH Z 359 " =    3.317
peak=   -3.624 closest distance to " CA  GLY A 203 " =    2.443
peak=   -3.621 closest distance to " O   HOH Z 389 " =    2.051
peak=   -3.611 closest distance to " O   VAL A 189 " =    2.588
peak=   -3.609 closest distance to " O   HOH Z 231 " =    1.180
peak=   -3.592 closest distance to " CE BMET A  47 " =    1.600
peak=   -3.583 closest distance to " O   HOH Z  11 " =    1.934
peak=   -3.580 closest distance to " CG  ASP A 231 " =    0.760
peak=   -3.578 closest distance to " O   VAL A  67 " =    2.908
peak=   -3.573 closest distance to " C   ALA A 158 " =    1.397
peak=   -3.569 closest distance to " O   HOH Z 176 " =    0.787
peak=   -3.554 closest distance to " C   LEU A 222 " =    0.831
peak=   -3.548 closest distance to " O   HOH Z  51 " =    1.037
peak=   -3.545 closest distance to " O   HOH Z  60 " =    2.307
peak=   -3.545 closest distance to " CG  TRP A 266 " =    1.859
peak=   -3.542 closest distance to " CD2 LEU A   5 " =    1.061
peak=   -3.542 closest distance to " CB  VAL A 296 " =    1.155
peak=   -3.541 closest distance to " N   ALA A 226 " =    2.134
peak=   -3.538 closest distance to " O   HOH Z 166 " =    2.314
peak=   -3.528 closest distance to " CA  ASP A  27 " =    2.398
peak=   -3.524 closest distance to " ND2 ASN A 249 " =    2.425
peak=   -3.512 closest distance to " O   HOH Z 377 " =    0.756
peak=   -3.507 closest distance to " N   GLN A  58 " =    1.872
peak=   -3.501 closest distance to " O   SER A  22 " =    2.250
peak=   -3.498 closest distance to " CE2 PHE A 218 " =    2.506
peak=   -3.489 closest distance to " CD1 LEU A 101 " =    2.361
peak=   -3.489 closest distance to " O   HOH Z 103 " =    1.797
peak=   -3.484 closest distance to " O   HOH Z 134 " =    2.960
peak=   -3.482 closest distance to " CB  PRO A 280 " =    2.133
peak=   -3.477 closest distance to " CG  MET A 105 " =    0.954
peak=   -3.451 closest distance to " CD1 LEU A 101 " =    2.861
peak=   -3.448 closest distance to " CD1 LEU A 228 " =    2.278
peak=   -3.428 closest distance to " O   HOH Z 191 " =    5.412
peak=   -3.428 closest distance to " OG  SER A  87 " =    1.439
peak=   -3.428 closest distance to " O   HOH Z 313 " =    1.447
peak=   -3.427 closest distance to " O   PRO A 163 " =    2.010
peak=   -3.421 closest distance to " CA  GLY A 241 " =    3.082
peak=   -3.420 closest distance to " O   HOH Z 166 " =    1.529
peak=   -3.414 closest distance to " O   HOH Z 134 " =    3.666
peak=   -3.411 closest distance to " CB  ALA A 291 " =    2.316
peak=   -3.408 closest distance to " CE3 TRP A 150 " =    2.118
peak=   -3.404 closest distance to " O   HOH Z 198 " =    2.330
peak=   -3.402 closest distance to " O   GLY A  17 " =    1.337
peak=   -3.398 closest distance to " O   GLY A  80 " =    2.486
peak=   -3.395 closest distance to " OE1 GLN A  88 " =    1.129
peak=   -3.391 closest distance to " O   HOH Z  44 " =    2.239
peak=   -3.390 closest distance to " O   SER A 271 " =    2.224
peak=   -3.387 closest distance to " CD  LYS A 289 " =    2.491
peak=   -3.380 closest distance to " O   HOH Z 211 " =    1.388
peak=   -3.376 closest distance to " ND2 ASN A 187 " =    1.608
peak=   -3.373 closest distance to " O   HOH Z 417 " =    2.844
peak=   -3.369 closest distance to " CA  GLY A  98 " =    1.908
peak=   -3.368 closest distance to " O   HOH Z 359 " =    1.611
peak=   -3.368 closest distance to " O   HOH Z 350 " =    1.990
peak=   -3.365 closest distance to " O   HOH Z 423 " =    1.168
peak=   -3.365 closest distance to " CD1 LEU A   5 " =    2.663
peak=   -3.364 closest distance to " OG  SER A  97 " =    2.305
peak=   -3.363 closest distance to " CB  ALA A 291 " =    2.191
peak=   -3.360 closest distance to " CE1 TYR A 169 " =    2.499
peak=   -3.359 closest distance to " O   HOH Z   9 " =    1.561
peak=   -3.356 closest distance to " CB  ASN A  69 " =    1.310
peak=   -3.355 closest distance to " CG2 ILE A 263 " =    2.411
peak=   -3.355 closest distance to " O   HOH Z  65 " =    1.120
peak=   -3.351 closest distance to " OG  SER A  63 " =    1.143
peak=   -3.348 closest distance to " O   HOH Z 389 " =    1.377
peak=   -3.345 closest distance to " CB  VAL A 230 " =    1.077
peak=   -3.343 closest distance to " CE  MET A 105 " =    2.350
peak=   -3.339 closest distance to " CB  TRP A  85 " =    2.512
peak=   -3.337 closest distance to " O   HOH Z 309 " =    2.479
peak=   -3.336 closest distance to " CG  PHE A 283 " =    2.675
peak=   -3.328 closest distance to " NE2 GLN A 278 " =    1.963
peak=   -3.327 closest distance to " O   HOH Z  73 " =    2.207
peak=   -3.326 closest distance to " N   SER A 212 " =    1.924
peak=   -3.324 closest distance to " N   SER A   3 " =    1.941
peak=   -3.320 closest distance to " O   HOH Z 390 " =    2.378
peak=   -3.318 closest distance to " NZ  LYS A 119 " =    3.385
peak=   -3.315 closest distance to " NH2AARG A 275 " =    5.235
peak=   -3.313 closest distance to " CD  GLU A 277 " =    1.213
peak=   -3.311 closest distance to " CD  ARG A 139 " =    1.615
peak=   -3.311 closest distance to " OD1 ASN A 187 " =    1.628
peak=   -3.303 closest distance to " O   HOH Z 102 " =    1.675
peak=   -3.298 closest distance to " O   HOH Z 281 " =    2.695
peak=   -3.295 closest distance to " OXT GLY A 302 " =    2.965
peak=   -3.292 closest distance to " O   HOH Z 369 " =    2.250
peak=   -3.292 closest distance to " O   HOH Z 295 " =    1.552
peak=   -3.292 closest distance to " CB  ALA A 114 " =    2.465
peak=   -3.292 closest distance to " O   HOH Z 241 " =    1.311
peak=   -3.292 closest distance to " CZ2 TRP A 274 " =    0.941
peak=   -3.287 closest distance to " CD  PRO A 213 " =    2.050
peak=   -3.282 closest distance to " CZ  TYR A 169 " =    1.597
peak=   -3.274 closest distance to " O   HOH Z 407 " =    3.120
peak=   -3.271 closest distance to " CD2 LEU A 300 " =    2.785
peak=   -3.265 closest distance to " CG  GLU A 152 " =    0.718
peak=   -3.265 closest distance to " O   ALA A 161 " =    1.604
peak=   -3.262 closest distance to " O   HOH Z 437 " =    1.726
peak=   -3.261 closest distance to " OD2 ASP A 171 " =    2.192
peak=   -3.260 closest distance to " CA  SER A 135 " =    1.381
peak=   -3.256 closest distance to " OH  TYR A 172 " =    1.805
peak=   -3.255 closest distance to " OD1 ASN A 148 " =    1.416
peak=   -3.251 closest distance to " C   PHE A  59 " =    1.309
peak=   -3.249 closest distance to " O   HOH Z 275 " =    1.401
peak=   -3.248 closest distance to " CG2 THR A 157 " =    2.195
peak=   -3.247 closest distance to " CD1 TYR A 247 " =    2.855
peak=   -3.246 closest distance to " N   ALA A 248 " =    1.588
peak=   -3.245 closest distance to " CG1 VAL A 250 " =    2.761
peak=   -3.237 closest distance to " CH2 TRP A 179 " =    1.823
peak=   -3.232 closest distance to " C   ASN A 285 " =    2.350
peak=   -3.230 closest distance to " O   HOH Z 262 " =    2.791
peak=   -3.230 closest distance to " CG  GLN A 278 " =    2.194
peak=   -3.229 closest distance to " CG  LEU A 228 " =    0.954
peak=   -3.226 closest distance to " CD1 ILE A 199 " =    2.544
peak=   -3.226 closest distance to " CD2 TYR A 293 " =    2.005
peak=   -3.216 closest distance to " CG2 VAL A 202 " =    2.705
peak=   -3.214 closest distance to " CB  ASP A 132 " =    2.378
peak=   -3.214 closest distance to " CD  PRO A 243 " =    2.098
peak=   -3.210 closest distance to " CA  ASP A 298 " =    1.078
peak=   -3.206 closest distance to " O   SER A 135 " =    1.434
peak=   -3.206 closest distance to " O   HOH Z 426 " =    1.690
peak=   -3.203 closest distance to " N   ALA A 248 " =    2.533
peak=   -3.199 closest distance to " N   HIS A 115 " =    2.239
peak=   -3.199 closest distance to " O   ALA A  51 " =    1.452
peak=   -3.197 closest distance to " C   GLU A 236 " =    0.914
peak=   -3.197 closest distance to " O   PRO A 198 " =    1.327
peak=   -3.196 closest distance to " CG1 VAL A 197 " =    2.262
peak=   -3.195 closest distance to " OG  SER A 206 " =    1.714
peak=   -3.191 closest distance to " CD2 LEU A 300 " =    2.859
peak=   -3.187 closest distance to " O   MET A  40 " =    2.727
peak=   -3.182 closest distance to " CD1 PHE A  59 " =    1.951
peak=   -3.182 closest distance to " O   GLY A 211 " =    1.246
peak=   -3.178 closest distance to " O   HOH Z 371 " =    2.213
peak=   -3.173 closest distance to " O   HOH Z 346 " =    1.821
peak=   -3.172 closest distance to " O   GLY A 196 " =    1.290
peak=   -3.170 closest distance to " O   HOH Z  38 " =    1.788
peak=   -3.165 closest distance to " CD1 ILE A 239 " =    2.596
peak=   -3.161 closest distance to " ND2 ASN A 252 " =    1.873
peak=   -3.158 closest distance to " CB  ALA A   9 " =    2.596
peak=   -3.158 closest distance to " NH2 ARG A 159 " =    2.322
peak=   -3.156 closest distance to " ND2BASN A 224 " =    1.564
peak=   -3.148 closest distance to " N   SER A 276 " =    1.282
peak=   -3.139 closest distance to " ND2 ASN A  60 " =    1.786
peak=   -3.133 closest distance to " O   HOH Z  63 " =    1.868
peak=   -3.122 closest distance to " O   HOH Z 353 " =    2.038
peak=   -3.120 closest distance to " O   HOH Z 131 " =    4.124
peak=   -3.120 closest distance to " O   HOH Z  89 " =    2.999
peak=   -3.118 closest distance to " C   ASN A 187 " =    1.826
peak=   -3.114 closest distance to " OG BSER A 134 " =    1.746
peak=   -3.110 closest distance to " CG  ARG A 269 " =    2.500
peak=   -3.110 closest distance to " CG  PRO A 163 " =    2.561
peak=   -3.105 closest distance to " N   ALA A 248 " =    1.875
peak=   -3.097 closest distance to " N   THR A  52 " =    1.762
peak=   -3.096 closest distance to " O   TRP A  70 " =    1.391
peak=   -3.096 closest distance to " CB  TYR A 172 " =    2.425
peak=   -3.090 closest distance to " CB  TYR A  15 " =    2.167
peak=   -3.074 closest distance to " O   HOH Z  13 " =    1.877
peak=   -3.071 closest distance to " NH2 ARG A  79 " =    1.546
peak=   -3.063 closest distance to " CD  GLN A  88 " =    0.898
peak=   -3.058 closest distance to " NH2BARG A 275 " =    1.668
peak=   -3.055 closest distance to " CE  LYS A  76 " =    2.602
peak=   -3.031 closest distance to " O   HOH Z 198 " =    1.003

================= 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    :  0.4376 0.4228   6.231261e+00   6.204639e+00
   1_bss:  0.4294 0.4078   6.226896e+00   6.190472e+00
   1_xyz:  0.3222 0.3398   6.026263e+00   6.059221e+00
   1_adp:  0.2602 0.3019   5.852658e+00   5.959391e+00
   1_occ:  0.2596 0.3019   5.851323e+00   5.960061e+00
   2_bss:  0.2530 0.2937   5.846328e+00   5.951509e+00
   2_xyz:  0.1764 0.2200   5.524659e+00   5.694529e+00
   2_adp:  0.1601 0.2052   5.438312e+00   5.622458e+00
   2_occ:  0.1600 0.2050   5.437923e+00   5.622432e+00
   3_bss:  0.1595 0.2042   5.437881e+00   5.621143e+00
   3_xyz:  0.1298 0.1731   5.260947e+00   5.475346e+00
   3_adp:  0.1235 0.1691   5.225045e+00   5.450386e+00
   3_occ:  0.1235 0.1692   5.224807e+00   5.450043e+00
   4_bss:  0.1236 0.1692   5.224547e+00   5.449823e+00
   4_xyz:  0.1126 0.1614   5.162873e+00   5.412842e+00
   4_adp:  0.1127 0.1579   5.151856e+00   5.390850e+00
   4_occ:  0.1126 0.1578   5.151482e+00   5.390411e+00
   5_bss:  0.1126 0.1578   5.151539e+00   5.390450e+00
   5_xyz:  0.1150 0.1581   5.163648e+00   5.394534e+00
   5_adp:  0.1147 0.1587   5.164254e+00   5.399230e+00
   5_occ:  0.1146 0.1587   5.164296e+00   5.399430e+00
   5_bss:  0.1146 0.1587   5.164296e+00   5.399430e+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:  0.344   9.524   7.633   9.378   8.837   0.000   0.000   0.000
   1_xyz:  0.344   9.524   7.633   9.378   8.837   0.000   0.000   0.000
   1_adp:  0.344   9.524   7.633   9.378   8.837   0.000   0.000   0.000
   1_occ:  0.344   9.524   7.633   9.378   8.837   0.000   0.000   0.000
   2_bss:  0.342  40.489   4.022   4.875   5.250   0.000   0.000   0.000
   2_xyz:  0.342  40.489   4.022   4.875   5.250   0.000   0.000   0.000
   2_adp:  0.342  40.489   4.022   4.875   5.250   0.000   0.000   0.000
   2_occ:  0.342  40.489   4.022   4.875   5.250   0.000   0.000   0.000
   3_bss:  0.327  40.489   3.114   3.319   4.476   0.000   0.000   0.000
   3_xyz:  0.327  40.489   3.114   3.319   4.476   0.000   0.000   0.000
   3_adp:  0.327  40.489   3.114   3.319   4.476   0.000   0.000   0.000
   3_occ:  0.327  40.489   3.114   3.319   4.476   0.000   0.000   0.000
   4_bss:  0.316  40.489   2.994   3.031   4.359   0.000   0.000   0.000
   4_xyz:  0.316  40.489   2.994   3.031   4.359   0.000   0.000   0.000
   4_adp:  0.316  40.489   2.994   3.031   4.359   0.000   0.000   0.000
   4_occ:  0.316  40.489   2.994   3.031   4.359   0.000   0.000   0.000
   5_bss:  0.318  40.489   2.994   3.031   4.359   0.000   0.000   0.000
   5_xyz:  0.318  40.489   2.994   3.031   4.359   0.000   0.000   0.000
   5_adp:  0.318  40.489   2.994   3.031   4.359   0.000   0.000   0.000
   5_occ:  0.318  40.489   2.994   3.031   4.359   0.000   0.000   0.000
   5_bss:  0.318  43.950  -0.468  -0.430   0.898   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  47.763 0.5493  0.6192    52002.856
   1_bss:  47.583 0.5495  0.7972    49447.622
   1_xyz:  36.757 0.6800  0.9556    31771.445
   1_adp:  30.092 0.7574  1.0562    23477.295
   1_occ:  30.109 0.7572  1.0547    23459.157
   2_bss:  29.613 0.7624  0.9236    22779.806
   2_xyz:  21.218 0.8497  0.9939    12156.892
   2_adp:  19.158 0.8703  1.0032    10446.991
   2_occ:  19.161 0.8702  1.0030    10432.067
   3_bss:  19.090 0.8709  0.9646    10384.492
   3_xyz:  15.907 0.8989  0.9834     7601.770
   3_adp:  15.353 0.9039  0.9837     7257.361
   3_occ:  15.348 0.9040  0.9836     7250.985
   4_bss:  15.352 0.9039  0.9770     7254.372
   4_xyz:  14.580 0.9102  0.9795     6664.663
   4_adp:  14.064 0.9146  0.9804     6409.025
   4_occ:  14.055 0.9146  0.9804     6398.197
   5_bss:  14.056 0.9146  0.9804     6399.386
   5_xyz:  14.081 0.9146  0.9798     6448.057
   5_adp:  14.161 0.9140  0.9770     6503.372
   5_occ:  14.165 0.9140  0.9769     6504.499
   5_bss:  14.165 0.9140  0.9769     6504.499
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.090   5.3826e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.090   5.3826e+01
   1_xyz:   1.508  0.011  0.100 18.112  0.005  4.120   1.1731e-01
   1_adp:   1.508  0.011  0.100 18.112  0.005  4.120   1.1731e-01
   1_occ:   1.508  0.011  0.100 18.112  0.005  4.120   1.1731e-01
   2_bss:   1.508  0.011  0.100 18.112  0.005  4.120   1.1731e-01
   2_xyz:   0.976  0.007  0.072 16.229  0.004  4.121   6.1662e-02
   2_adp:   0.976  0.007  0.072 16.229  0.004  4.121   6.1662e-02
   2_occ:   0.976  0.007  0.072 16.229  0.004  4.121   6.1662e-02
   3_bss:   0.976  0.007  0.072 16.229  0.004  4.121   6.1662e-02
   3_xyz:   0.959  0.006  0.076 15.763  0.003  4.127   5.7446e-02
   3_adp:   0.959  0.006  0.076 15.763  0.003  4.127   5.7446e-02
   3_occ:   0.959  0.006  0.076 15.763  0.003  4.127   5.7446e-02
   4_bss:   0.959  0.006  0.076 15.763  0.003  4.127   5.7446e-02
   4_xyz:   1.066  0.009  0.087 15.773  0.004  4.110   7.0886e-02
   4_adp:   1.066  0.009  0.087 15.773  0.004  4.110   7.0886e-02
   4_occ:   1.066  0.009  0.087 15.773  0.004  4.110   7.0886e-02
   5_bss:   1.066  0.009  0.087 15.773  0.004  4.110   7.0886e-02
   5_xyz:   0.911  0.006  0.075 15.349  0.003  4.110   5.3987e-02
   5_adp:   0.911  0.006  0.075 15.349  0.003  4.110   5.3987e-02
   5_occ:   0.911  0.006  0.075 15.349  0.003  4.110   5.3987e-02
   5_bss:   0.911  0.006  0.075 15.349  0.003  4.110   5.3987e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9789e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9789e+00
   1_xyz:  11.727  0.146  0.419 88.616  0.031  2.256   8.5548e-02
   1_adp:  11.727  0.146  0.419 88.616  0.031  2.256   8.5548e-02
   1_occ:  11.727  0.146  0.419 88.616  0.031  2.256   8.5548e-02
   2_bss:  11.727  0.146  0.419 88.616  0.031  2.256   8.5548e-02
   2_xyz:   6.403  0.061  0.294 89.004  0.042  2.327   4.4689e-02
   2_adp:   6.403  0.061  0.294 89.004  0.042  2.327   4.4689e-02
   2_occ:   6.403  0.061  0.294 89.004  0.042  2.327   4.4689e-02
   3_bss:   6.403  0.061  0.294 89.004  0.042  2.327   4.4689e-02
   3_xyz:   7.365  0.055  0.410 82.652  0.027  2.312   3.5048e-02
   3_adp:   7.365  0.055  0.410 82.652  0.027  2.312   3.5048e-02
   3_occ:   7.365  0.055  0.410 82.652  0.027  2.312   3.5048e-02
   4_bss:   7.365  0.055  0.410 82.652  0.027  2.312   3.5048e-02
   4_xyz:   7.093  0.047  0.594 83.454  0.038  2.295   5.5859e-02
   4_adp:   7.093  0.047  0.594 83.454  0.038  2.295   5.5859e-02
   4_occ:   7.093  0.047  0.594 83.454  0.038  2.295   5.5859e-02
   5_bss:   7.093  0.047  0.594 83.454  0.038  2.295   5.5859e-02
   5_xyz:   7.027  0.041  0.443 83.335  0.036  2.356   3.3219e-02
   5_adp:   7.027  0.041  0.443 83.335  0.036  2.356   3.3219e-02
   5_occ:   7.027  0.041  0.443 83.335  0.036  2.356   3.3219e-02
   5_bss:   7.027  0.041  0.443 83.335  0.036  2.356   3.3219e-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:  67.61   0.00  11.13  60.78   0.00   8.15  67.61   0.00  27.38
   1_occ:  67.61   0.00  11.13  60.78   0.00   8.15  67.61   0.00  27.38
   2_bss:  67.61   0.00  11.13  60.78   0.00   8.15  67.61   0.00  27.38
   2_xyz:  67.61   0.00  11.13  60.78   0.00   8.15  67.61   0.00  27.38
   2_adp:  68.38   0.00  11.22  62.65   0.00   7.51  68.38   0.00  31.40
   2_occ:  68.38   0.00  11.22  62.65   0.00   7.51  68.38   0.00  31.40
   3_bss:  68.38   0.00  11.22  62.65   0.00   7.51  68.38   0.00  31.40
   3_xyz:  68.38   0.00  11.22  62.65   0.00   7.51  68.38   0.00  31.40
   3_adp:  79.13   0.00  12.13  79.13   0.00   7.75  78.34   0.46  36.01
   3_occ:  79.13   0.00  12.13  79.13   0.00   7.75  78.34   0.46  36.01
   4_bss:  79.13   0.00  12.13  79.13   0.00   7.75  78.34   0.46  36.01
   4_xyz:  79.13   0.00  12.13  79.13   0.00   7.75  78.34   0.46  36.01
   4_adp:  78.73   0.00  11.57  78.73   0.00   7.49  75.17   1.37  33.81
   4_occ:  78.73   0.00  11.57  78.73   0.00   7.49  75.17   1.37  33.81
   5_bss:  78.73   0.00  11.57  78.73   0.00   7.49  75.17   1.37  33.81
   5_xyz:  78.73   0.00  11.57  78.73   0.00   7.49  75.17   1.37  33.81
   5_adp:  80.23   0.00  11.38  80.23   0.00   7.43  69.69   1.31  32.87
   5_occ:  80.23   0.00  11.38  80.23   0.00   7.43  69.69   1.31  32.87
   5_bss:  83.69   3.46  14.84  83.69   3.46  10.89  73.15   4.77  36.33
------------------------------------------------------------------------
 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:    1.191    0.015    0.399
   1_adp:    1.191    0.015    0.399
   1_occ:    1.191    0.015    0.399
   2_bss:    1.191    0.015    0.399
   2_xyz:    1.371    0.041    0.502
   2_adp:    1.371    0.041    0.502
   2_occ:    1.371    0.041    0.502
   3_bss:    1.371    0.041    0.502
   3_xyz:    1.441    0.019    0.538
   3_adp:    1.441    0.019    0.538
   3_occ:    1.441    0.019    0.538
   4_bss:    1.441    0.019    0.538
   4_xyz:    1.567    0.026    0.562
   4_adp:    1.567    0.026    0.562
   4_occ:    1.567    0.026    0.562
   5_bss:    1.567    0.026    0.562
   5_xyz:    1.598    0.014    0.566
   5_adp:    1.598    0.014    0.566
   5_occ:    1.598    0.014    0.566
   5_bss:    1.598    0.014    0.566
------------------------------------------------------------------------

CPU time actual refinement: 331.25


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_765/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_765/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_765/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_765/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_765/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 331.10 
  Macro-tasks:
    bulk solvent and scale       = 38.73  
    individual site refinement   = 145.35 
    weights calculation          = 31.78  
    collect and process          = 6.50   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 222.47 
  Micro-tasks:
    mask                            = 1.77   
    f_calc                          = 101.24 
    alpha_beta                      = 7.93   
    target                          = 1.13   
    gradients_wrt_atomic_parameters = 114.61 
    fmodel                         = 7.21   
    r_factors                      = 0.19   
    phase_errors                   = 10.95  
    foms                           = 0.24   
    TOTAL for micro-tasks          = 245.27 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.559 micro seconds
Total CPU time: 5.74 minutes
from_scatterers_fft:    659 calls, 100.85 s
gradients_fft:          605 calls, 100.13 s

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

# Date 2008-01-16 Time 02:22:12 PST -0800 (1200478932.77 s)
Start R-work = 0.4376, R-free = 0.4228 (no bulk solvent and anisotropic scale)
Final R-work = 0.1324, R-free = 0.1762 (no bulk solvent and anisotropic scale)

Start R-work = 0.4294, R-free = 0.4078
Final R-work = 0.1146, R-free = 0.1587