# Date 2008-01-16 Time 02:03:55 PST -0800 (1200477835.38 s)
#phil __OFF__

Command line arguments: "../677.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 772
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 677

-------------------------------------------------------------------------------
  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: (70.25, 47.1647, 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: 3.22, per 1000 atoms: 1.14


================================== 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: (70.25, 47.1647, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0142 2.00053
Completeness in resolution range: 0.977154
Completeness with d_max=infinity: 0.974044

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0142
                             d_min =   2.0005

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: (70.25, 47.1647, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0142 2.00053
Completeness in resolution range: 0.977154
Completeness with d_max=infinity: 0.974044

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0146 -  4.2799 [2105/2129]  1894   211  10.0%
  bin  2:  4.2799 -  3.4101 [2028/2047]  1826   202  10.0%
  bin  3:  3.4101 -  2.9829 [1994/2013]  1795   199  10.0%
  bin  4:  2.9829 -  2.7119 [1972/2002]  1774   198  10.0%
  bin  5:  2.7119 -  2.5185 [1976/1995]  1780   196   9.9%
  bin  6:  2.5185 -  2.3706 [1946/1971]  1747   199  10.2%
  bin  7:  2.3706 -  2.2523 [1949/1977]  1757   192   9.9%
  bin  8:  2.2523 -  2.1546 [1953/1989]  1758   195  10.0%
  bin  9:  2.1546 -  2.0719 [1904/1946]  1711   193  10.1%
  bin 10:  2.0719 -  2.0005 [1762/1978]  1588   174   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_677/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: 9
        2.42 -     3.04: 2193
        3.04 -     3.66: 4613
        3.66 -     4.28: 8992
        4.28 -     4.90: 12329
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.214 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z  42 " - " O   HOH Z 183 "  2.259 3.040 -x+1,y+1/2,-z+1/2
  " OE1 GLN A  55 " - " O   HOH Z 403 "  2.308 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28131 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_677/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_677/model_refine_001.geo

CPU time processing inputs: 8.71


============================ 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 = 70.25 47.16465 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: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4141   r_free= 0.3985   ksol= 0.00   Bsol= 0.00   scale= 0.829    |
|                                                                             |
| 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:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.199990                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0146 -  4.7731 0.99   1375  153 0.3504 0.3253      6.4963       6.411|
|  2:  4.7731 -  3.8089 0.99   1306  146 0.3011 0.3123      6.5727      6.6298|
|  3:  3.8089 -  3.3335 0.99   1293  143 0.3529 0.3321      6.5203      6.5046|
|  4:  3.3335 -  3.0314 0.99   1284  139 0.3907 0.3464      6.4202      6.3084|
|  5:  3.0314 -  2.8157 0.99   1268  144 0.4220 0.4232      6.2825      6.3234|
|  6:  2.8157 -  2.6506 0.99   1276  141 0.4326 0.4817      6.2064      6.1735|
|  7:  2.6506 -  2.5185 0.99   1267  140 0.4591 0.4536      6.1904      6.1265|
|  8:  2.5185 -  2.4094 0.98   1249  139 0.4687 0.4137      6.1406       6.098|
|  9:  2.4094 -  2.3170 0.98   1253  143 0.4645 0.4709      6.0763      6.0737|
| 10:  2.3170 -  2.2373 0.99   1245  136 0.4864 0.4392      6.1039      6.0079|
| 11:  2.2373 -  2.1675 0.98   1256  137 0.4702 0.4100      6.0049      5.9536|
| 12:  2.1675 -  2.1057 0.97   1238  142 0.4814 0.4630      5.9608      6.0129|
| 13:  2.1057 -  2.0504 1.00   1251  136 0.4786 0.4968      5.8717      5.8617|
| 14:  2.0504 -  2.0005 0.85   1069  120 0.4896 0.4389      5.8342      5.7069|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0146 -  4.7731  1375   153  0.75  29.41   0.82     0.77      52803.80|
|  2:  4.7731 -  3.8089  1306   146  0.80  26.13   0.92     0.83      63822.24|
|  3:  3.8089 -  3.3335  1293   143  0.75  31.32   0.88     0.81      65296.10|
|  4:  3.3335 -  3.0314  1284   139  0.69  35.91   0.85     0.73      57485.07|
|  5:  3.0314 -  2.8157  1268   144  0.60  43.56   0.79     0.66      53639.24|
|  6:  2.8157 -  2.6506  1276   141  0.58  45.72   0.77     0.63      49783.39|
|  7:  2.6506 -  2.5185  1267   140  0.55  48.17   0.77     0.61      47220.79|
|  8:  2.5185 -  2.4094  1249   139  0.55  48.16   0.78     0.62      41818.83|
|  9:  2.4094 -  2.3170  1253   143  0.57  46.53   0.75     0.63      36378.65|
| 10:  2.3170 -  2.2373  1245   136  0.58  45.97   0.77     0.65      32678.93|
| 11:  2.2373 -  2.1675  1256   137  0.56  47.36   0.78     0.64      31083.82|
| 12:  2.1675 -  2.1057  1238   142  0.51  51.27   0.79     0.60      31465.50|
| 13:  2.1057 -  2.0504  1251   136  0.50  52.39   0.77     0.57      27929.38|
| 14:  2.0504 -  2.0005  1069   120  0.54  49.14   0.74     0.57      21372.72|
|alpha:            min =        0.57 max =            0.83 mean =         0.67|
|beta:             min =    21372.72 max =        65296.10 mean =     44233.96|
|figures of merit: min =        0.00 max =            1.00 mean =         0.61|
|phase err.(work): min =        0.00 max =           90.00 mean =        42.68|
|phase err.(test): min =        0.00 max =           89.85 mean =        42.86|
|-----------------------------------------------------------------------------|

============================== Outliers rejection =============================

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 0
total                    = 0

====================== Target weights (before refinement) =====================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.281322              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 72.712   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.503543              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.431   (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:       22 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      161 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      683 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1476 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2623 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3900 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5022 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6567 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7684 |
|-----------------------------------------------------------------------------|
|-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 |       53.990 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.093    4.900  1.196 |       1.642 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.028)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 12.028)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4233   r_free= 0.3999   ksol= 0.00   Bsol= 0.00   scale= 0.798    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.210633                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4067   r_free= 0.3819   ksol= 0.34   Bsol= 20.04   scale= 1.029   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.21,8.60,8.82,0.00,0.00,0.00); trace/3= 8.21                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.197401                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.951315              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 74.679   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.485479              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 74.987   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4067      final r-factor (work) = 0.2874          |
| start r-factor (free) = 0.3819      final r-factor (free) = 0.3066          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 72.5072 = 5.95 * 0.50 * 6.2229 + 1.00 * 53.9899                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.9588 = 5.95 * 0.50 * 5.9986 + 1.00 * 0.1090                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2874      final r-factor (work) = 0.2137          |
| start r-factor (free) = 0.3066      final r-factor (free) = 0.2424          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9270 = 0.49 * 1.00 * 5.9986 + 1.00 * 0.0148                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8103 = 0.49 * 1.00 * 5.7675 + 1.00 * 0.0104                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.028)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    57.66   10.09    None  None   None       |
|    all(noH): 2823   0      0.00    57.66   10.09    None  None   None       |
|    Sol.    : 438    0      0.00    57.66   27.43    None  None   None       |
|    Mac.    : 2385   0      0.00    54.05   6.90     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   5.766: 1342   |   5:    28.830 -  34.596:  110        |
|      1:     5.766 -  11.532:  721   |   6:    34.596 -  40.362:   74        |
|      2:    11.532 -  17.298:  266   |   7:    40.362 -  46.128:   55        |
|      3:    17.298 -  23.064:  117   |   8:    46.128 -  51.894:   23        |
|      4:    23.064 -  28.830:  110   |   9:    51.894 -  57.660:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2137 r_free = 0.2424             target_work(ml) = 5.658         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2129 r_free = 0.2426             target_work(ml) = 5.656         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2129   r_free= 0.2426   ksol= 0.34   Bsol= 20.04   scale= 1.085   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.21,8.60,8.82,0.00,0.00,0.00); trace/3= 8.21                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.656441                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2070   r_free= 0.2372   ksol= 0.33   Bsol= 47.00   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.60,4.83,5.35,0.00,0.00,0.00); trace/3= 4.59                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.653641                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.262938              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.092   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.246094              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 117.284  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2070      final r-factor (work) = 0.1482          |
| start r-factor (free) = 0.2372      final r-factor (free) = 0.1795          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6611 = 2.26 * 0.50 * 5.7911 + 1.00 * 0.1086                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2658 = 2.26 * 0.50 * 5.4851 + 1.00 * 0.0596                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1482      final r-factor (work) = 0.1382          |
| start r-factor (free) = 0.1795      final r-factor (free) = 0.1715          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3601 = 0.25 * 1.00 * 5.4851 + 1.00 * 0.0103                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3178 = 0.25 * 1.00 * 5.3153 + 1.00 * 0.0098                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.028)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    57.71   10.40    None  None   None       |
|    all(noH): 2823   0      0.00    57.71   10.40    None  None   None       |
|    Sol.    : 438    0      0.00    57.71   29.85    None  None   None       |
|    Mac.    : 2385   0      0.00    56.09   6.83     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   5.772: 1407   |   5:    28.857 -  34.629:   94        |
|      1:     5.772 -  11.543:  672   |   6:    34.629 -  40.400:   99        |
|      2:    11.543 -  17.314:  222   |   7:    40.400 -  46.172:   70        |
|      3:    17.314 -  23.086:  112   |   8:    46.172 -  51.943:   31        |
|      4:    23.086 -  28.857:  108   |   9:    51.943 -  57.715:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1382 r_free = 0.1715             target_work(ml) = 5.294         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1382 r_free = 0.1715             target_work(ml) = 5.293         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1382   r_free= 0.1715   ksol= 0.33   Bsol= 47.00   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.60,4.83,5.35,0.00,0.00,0.00); trace/3= 4.59                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.293121                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1383   r_free= 0.1723   ksol= 0.33   Bsol= 47.00   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.19,3.99,4.83,0.00,0.00,0.00); trace/3= 4.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.295098                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.350767              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 118.479  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.428743              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.525  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1383      final r-factor (work) = 0.1174          |
| start r-factor (free) = 0.1723      final r-factor (free) = 0.1569          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.9672 = 3.35 * 0.50 * 5.3168 + 1.00 * 0.0596                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.8150 = 3.35 * 0.50 * 5.2160 + 1.00 * 0.0763                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1174      final r-factor (work) = 0.1127          |
| start r-factor (free) = 0.1569      final r-factor (free) = 0.1556          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.6779 = 2.43 * 1.00 * 5.2160 + 1.00 * 0.0097                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.5190 = 2.43 * 1.00 * 5.1481 + 1.00 * 0.0155                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.028)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    74.78   11.27    None  None   None       |
|    all(noH): 2823   0      0.00    74.78   11.27    None  None   None       |
|    Sol.    : 438    0      0.00    73.10   34.30    None  None   None       |
|    Mac.    : 2385   0      0.00    74.78   7.04     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 -   7.479: 1700   |   5:    37.392 -  44.871:   77        |
|      1:     7.479 -  14.957:  522   |   6:    44.871 -  52.349:   74        |
|      2:    14.957 -  22.435:  158   |   7:    52.349 -  59.828:   51        |
|      3:    22.435 -  29.914:  107   |   8:    59.828 -  67.306:   19        |
|      4:    29.914 -  37.392:  107   |   9:    67.306 -  74.784:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1127 r_free = 0.1556             target_work(ml) = 5.146         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1126 r_free = 0.1556             target_work(ml) = 5.145         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1126   r_free= 0.1556   ksol= 0.33   Bsol= 47.00   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.19,3.99,4.83,0.00,0.00,0.00); trace/3= 4.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.145385                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1126   r_free= 0.1556   ksol= 0.33   Bsol= 50.11   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.33,3.95,4.89,0.00,0.00,0.00); trace/3= 4.06                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.144966                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.698032              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 147.118  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.306527              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 107.297  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1126      final r-factor (work) = 0.1140          |
| start r-factor (free) = 0.1556      final r-factor (free) = 0.1572          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4470 = 1.70 * 0.50 * 5.1480 + 1.00 * 0.0763                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4328 = 1.70 * 0.50 * 5.1524 + 1.00 * 0.0583                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1140      final r-factor (work) = 0.1147          |
| start r-factor (free) = 0.1572      final r-factor (free) = 0.1565          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5961 = 0.31 * 1.00 * 5.1524 + 1.00 * 0.0167                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6056 = 0.31 * 1.00 * 5.1615 + 1.00 * 0.0235                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.028)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    75.64   10.96    None  None   None       |
|    all(noH): 2823   0      0.00    75.64   10.96    None  None   None       |
|    Sol.    : 438    0      0.60    68.90   32.82    None  None   None       |
|    Mac.    : 2385   0      0.00    75.64   6.94     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.564: 1716   |   5:    37.819 -  45.383:   86        |
|      1:     7.564 -  15.128:  533   |   6:    45.383 -  52.947:   66        |
|      2:    15.128 -  22.692:  147   |   7:    52.947 -  60.511:   41        |
|      3:    22.692 -  30.256:  103   |   8:    60.511 -  68.075:   12        |
|      4:    30.256 -  37.819:  114   |   9:    68.075 -  75.639:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1147 r_free = 0.1565             target_work(ml) = 5.159         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1146 r_free = 0.1565             target_work(ml) = 5.158         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1146   r_free= 0.1565   ksol= 0.33   Bsol= 50.11   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.33,3.95,4.89,0.00,0.00,0.00); trace/3= 4.06                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.157678                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1146   r_free= 0.1565   ksol= 0.33   Bsol= 50.11   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.33,3.95,4.89,0.00,0.00,0.00); trace/3= 4.06                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.157714                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.992804              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 154.893  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.547505              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 97.474   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1146      final r-factor (work) = 0.1121          |
| start r-factor (free) = 0.1565      final r-factor (free) = 0.1555          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2005 = 1.99 * 0.50 * 5.1607 + 1.00 * 0.0583                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1928 = 1.99 * 0.50 * 5.1472 + 1.00 * 0.0641                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1121      final r-factor (work) = 0.1114          |
| start r-factor (free) = 0.1555      final r-factor (free) = 0.1563          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.9961 = 1.55 * 1.00 * 5.1472 + 1.00 * 0.0308                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.9672 = 1.55 * 1.00 * 5.1391 + 1.00 * 0.0144                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.028)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.49   11.15    None  None   None       |
|    all(noH): 2823   0      0.00    82.49   11.15    None  None   None       |
|    Sol.    : 438    0      0.20    75.30   33.83    None  None   None       |
|    Mac.    : 2385   0      0.00    82.49   6.99     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 -   8.249: 1788   |   5:    41.244 -  49.493:   85        |
|      1:     8.249 -  16.498:  475   |   6:    49.493 -  57.741:   63        |
|      2:    16.498 -  24.746:  153   |   7:    57.741 -  65.990:   19        |
|      3:    24.746 -  32.995:  103   |   8:    65.990 -  74.239:   11        |
|      4:    32.995 -  41.244:  121   |   9:    74.239 -  82.488:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1114 r_free = 0.1563             target_work(ml) = 5.144         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1114 r_free = 0.1563             target_work(ml) = 5.144         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1114   r_free= 0.1563   ksol= 0.33   Bsol= 50.11   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.33,3.95,4.89,0.00,0.00,0.00); trace/3= 4.06                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.143893                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0146 -  4.7731 0.99   1375  153 0.1015 0.1296      5.3968      5.5158|
|  2:  4.7731 -  3.8089 0.99   1306  146 0.0847 0.1112      5.4343      5.6292|
|  3:  3.8089 -  3.3335 0.99   1293  143 0.1039 0.1462      5.4682      5.8498|
|  4:  3.3335 -  3.0314 0.99   1284  139 0.1191 0.1487      5.4434       5.579|
|  5:  3.0314 -  2.8157 0.99   1268  144 0.1299 0.1682      5.3299      5.5417|
|  6:  2.8157 -  2.6506 0.99   1276  141 0.1208 0.1906      5.2117       5.493|
|  7:  2.6506 -  2.5185 0.99   1267  140 0.1249 0.1642       5.168      5.3473|
|  8:  2.5185 -  2.4094 0.98   1249  139 0.1167 0.1728      5.0903      5.3847|
|  9:  2.4094 -  2.3170 0.98   1253  143 0.1173 0.1825      5.0484      5.2955|
| 10:  2.3170 -  2.2373 0.99   1245  136 0.1131 0.1740      4.9847      5.2435|
| 11:  2.2373 -  2.1675 0.98   1256  137 0.1123 0.1669      4.9368      5.2178|
| 12:  2.1675 -  2.1057 0.97   1238  142 0.1125 0.1687      4.8846      5.2276|
| 13:  2.1057 -  2.0504 1.00   1251  136 0.1134 0.1689      4.8035       5.052|
| 14:  2.0504 -  2.0005 0.85   1069  120 0.1062 0.1808      4.6835      4.9812|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0146 -  4.7731  1375   153  0.94   9.17   0.98     0.96       7347.35|
|  2:  4.7731 -  3.8089  1306   146  0.95   7.79   1.01     1.00       8914.46|
|  3:  3.8089 -  3.3335  1293   143  0.94  10.83   1.02     1.02      10147.29|
|  4:  3.3335 -  3.0314  1284   139  0.92  13.03   1.00     0.99       9958.08|
|  5:  3.0314 -  2.8157  1268   144  0.90  15.64   0.99     0.96       8335.71|
|  6:  2.8157 -  2.6506  1276   141  0.90  15.82   0.98     0.96       7088.61|
|  7:  2.6506 -  2.5185  1267   140  0.91  15.50   0.99     0.96       6204.72|
|  8:  2.5185 -  2.4094  1249   139  0.91  14.88   0.99     0.96       5460.45|
|  9:  2.4094 -  2.3170  1253   143  0.90  15.93   1.01     0.98       5283.47|
| 10:  2.3170 -  2.2373  1245   136  0.90  16.12   1.00     0.95       4601.60|
| 11:  2.2373 -  2.1675  1256   137  0.90  15.81   0.99     0.96       4365.48|
| 12:  2.1675 -  2.1057  1238   142  0.91  15.21   1.01     1.00       3945.61|
| 13:  2.1057 -  2.0504  1251   136  0.91  15.39   1.00     0.97       3367.89|
| 14:  2.0504 -  2.0005  1069   120  0.91  15.04   0.97     0.93       2635.65|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2635.65 max =        10147.29 mean =      6335.53|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.99 mean =        13.94|
|phase err.(test): min =        0.00 max =           88.25 mean =        13.45|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1114   r_free= 0.1562   ksol= 0.33   Bsol= 54.18   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.70,-0.14,0.84,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.144134                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1114   r_free= 0.1562   ksol= 0.33   Bsol= 54.18   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.70,-0.14,0.84,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.144134                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0146 -  4.7731 0.99   1375  153 0.1020 0.1288      5.4076      5.5164|
|  2:  4.7731 -  3.8089 0.99   1306  146 0.0852 0.1096      5.4372      5.6147|
|  3:  3.8089 -  3.3335 0.99   1293  143 0.1040 0.1454      5.4651       5.844|
|  4:  3.3335 -  3.0314 0.99   1284  139 0.1190 0.1489      5.4403      5.5788|
|  5:  3.0314 -  2.8157 0.99   1268  144 0.1299 0.1669      5.3273      5.5342|
|  6:  2.8157 -  2.6506 0.99   1276  141 0.1207 0.1899      5.2102      5.4939|
|  7:  2.6506 -  2.5185 0.99   1267  140 0.1245 0.1644      5.1672      5.3466|
|  8:  2.5185 -  2.4094 0.98   1249  139 0.1165 0.1732      5.0901      5.3854|
|  9:  2.4094 -  2.3170 0.98   1253  143 0.1172 0.1823      5.0481      5.2956|
| 10:  2.3170 -  2.2373 0.99   1245  136 0.1130 0.1743      4.9849      5.2448|
| 11:  2.2373 -  2.1675 0.98   1256  137 0.1121 0.1673      4.9371      5.2202|
| 12:  2.1675 -  2.1057 0.97   1238  142 0.1125 0.1689       4.885      5.2273|
| 13:  2.1057 -  2.0504 1.00   1251  136 0.1133 0.1693      4.8033      5.0523|
| 14:  2.0504 -  2.0005 0.85   1069  120 0.1062 0.1808      4.6832       4.981|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0146 -  4.7731  1375   153  0.94   9.49   0.97     0.95       7465.00|
|  2:  4.7731 -  3.8089  1306   146  0.95   7.83   1.01     0.99       8888.55|
|  3:  3.8089 -  3.3335  1293   143  0.94  10.79   1.02     1.02      10016.36|
|  4:  3.3335 -  3.0314  1284   139  0.93  12.94   1.00     0.99       9815.29|
|  5:  3.0314 -  2.8157  1268   144  0.90  15.56   0.99     0.97       8263.19|
|  6:  2.8157 -  2.6506  1276   141  0.90  15.77   0.98     0.96       7049.34|
|  7:  2.6506 -  2.5185  1267   140  0.91  15.48   0.99     0.96       6201.15|
|  8:  2.5185 -  2.4094  1249   139  0.91  14.88   0.99     0.96       5465.12|
|  9:  2.4094 -  2.3170  1253   143  0.90  15.93   1.01     0.98       5287.67|
| 10:  2.3170 -  2.2373  1245   136  0.90  16.14   1.00     0.96       4608.63|
| 11:  2.2373 -  2.1675  1256   137  0.90  15.82   0.99     0.96       4372.97|
| 12:  2.1675 -  2.1057  1238   142  0.91  15.24   1.01     1.00       3954.65|
| 13:  2.1057 -  2.0504  1251   136  0.91  15.39   1.00     0.98       3369.38|
| 14:  2.0504 -  2.0005  1069   120  0.91  15.03   0.97     0.93       2633.91|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2633.91 max =        10016.36 mean =      6316.76|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.98 mean =        13.95|
|phase err.(test): min =        0.00 max =           88.67 mean =        13.46|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.028)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      4.07    86.56   15.23    None  None   None       |
|    all(noH): 2823   0      4.07    86.56   15.23    None  None   None       |
|    Sol.    : 438    0      4.27    79.37   37.90    None  None   None       |
|    Mac.    : 2385   0      4.07    86.56   11.06    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:     4.071 -  12.320: 1788   |   5:    45.315 -  53.563:   85        |
|      1:    12.320 -  20.568:  475   |   6:    53.563 -  61.812:   63        |
|      2:    20.568 -  28.817:  153   |   7:    61.812 -  70.061:   19        |
|      3:    28.817 -  37.066:  103   |   8:    70.061 -  78.310:   11        |
|      4:    37.066 -  45.315:  121   |   9:    78.310 -  86.558:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 303         
Filter by distance & map next to the model:
   mapped sites are within: 0.257 - 4.881
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 292 from: 303
   mapped sites are within: 0.720 - 4.881

peak=   10.344 closest distance to " CG2 VAL A 230 " =    1.345
peak=    6.715 closest distance to " CG2 VAL A 296 " =    1.099
peak=    6.272 closest distance to " CG  LEU A   5 " =    1.176
peak=    6.057 closest distance to " NH2 ARG A  56 " =    2.277
peak=    5.972 closest distance to " CG  LEU A 228 " =    1.177
peak=    5.595 closest distance to " CG  PRO A  54 " =    1.277
peak=    5.541 closest distance to " CD2 LEU A   5 " =    1.163
peak=    5.516 closest distance to " CB  GLN A 223 " =    1.447
peak=    5.187 closest distance to " CB  VAL A 230 " =    1.203
peak=    5.140 closest distance to " CB  VAL A 296 " =    1.096
peak=    5.024 closest distance to " CB  PRO A  54 " =    0.948
peak=    5.019 closest distance to " CB  GLN A 183 " =    1.316
peak=    4.982 closest distance to " NE2 GLN A  11 " =    1.096
peak=    4.872 closest distance to " CB  ARG A 275 " =    0.905
peak=    4.771 closest distance to " CB  SER A  63 " =    1.264
peak=    4.702 closest distance to " O   HOH Z 126 " =    1.931
peak=    4.561 closest distance to " O   HOH Z 142 " =    1.650
peak=    4.549 closest distance to " CG  PRO A 213 " =    1.197
peak=    4.470 closest distance to " CG  PRO A 198 " =    1.191
peak=    4.466 closest distance to " O   HOH Z 232 " =    2.385
peak=    4.438 closest distance to " C   PRO A 198 " =    1.518
peak=    4.418 closest distance to " O   HOH Z 248 " =    1.601
peak=    4.411 closest distance to " CG  PRO A 243 " =    1.118
peak=    4.377 closest distance to " O   SER A  87 " =    2.312
peak=    4.366 closest distance to " O   HOH Z 369 " =    2.261
peak=    4.354 closest distance to " O   HOH Z 368 " =    2.250
peak=    4.307 closest distance to " O   HOH Z  61 " =    1.661
peak=    4.287 closest distance to " O   HOH Z 189 " =    2.751
peak=    4.280 closest distance to " O   HOH Z 298 " =    1.832
peak=    4.271 closest distance to " O   HOH Z 272 " =    1.906
peak=    4.268 closest distance to " O   HOH Z  44 " =    2.277
peak=    4.248 closest distance to " O   HOH Z 427 " =    3.015
peak=    4.242 closest distance to " O   HOH Z 346 " =    1.619
peak=    4.225 closest distance to " CA  TYR A  30 " =    0.932
peak=    4.220 closest distance to " CZ  PHE A 218 " =    1.121
peak=    4.187 closest distance to " ND2 ASN A 187 " =    1.455
peak=    4.181 closest distance to " O   HOH Z  78 " =    1.688
peak=    4.167 closest distance to " CB  ARG A  79 " =    1.427
peak=    4.165 closest distance to " O   HOH Z  63 " =    2.101
peak=    4.157 closest distance to " O   HOH Z 402 " =    1.455
peak=    4.142 closest distance to " O   HOH Z 316 " =    3.097
peak=    4.122 closest distance to " CB  GLU A 152 " =    1.211
peak=    4.104 closest distance to " O   HOH Z  43 " =    2.038
peak=    4.097 closest distance to " O   HOH Z 193 " =    1.741
peak=    4.097 closest distance to " CB  ARG A 190 " =    1.618
peak=    4.089 closest distance to " O   HOH Z 423 " =    1.800
peak=    4.087 closest distance to " CB  GLU A 128 " =    1.042
peak=    4.075 closest distance to " O   HOH Z 203 " =    1.722
peak=    4.048 closest distance to " O   HOH Z  40 " =    1.656
peak=    4.029 closest distance to " OD1 ASN A  69 " =    2.616
peak=    4.023 closest distance to " O   HOH Z 214 " =    2.168
peak=    4.021 closest distance to " O   HOH Z 265 " =    2.350
peak=    4.007 closest distance to " CB  ASN A 148 " =    1.370
peak=    3.996 closest distance to " CB  VAL A 265 " =    1.326
peak=    3.995 closest distance to " CB  GLU A 277 " =    3.638
peak=    3.988 closest distance to " O   HOH Z 234 " =    3.659
peak=    3.985 closest distance to " O   HOH Z 303 " =    2.062
peak=    3.969 closest distance to " CB  TRP A 266 " =    0.961
peak=    3.962 closest distance to " CB  SER A   3 " =    1.251
peak=    3.952 closest distance to " CB  ASP A 140 " =    1.007
peak=    3.948 closest distance to " CD2 LEU A 228 " =    1.086
peak=    3.944 closest distance to " O   HOH Z 236 " =    1.927
peak=    3.939 closest distance to " O   HOH Z  66 " =    2.322
peak=    3.936 closest distance to " O   HOH Z 261 " =    1.702
peak=    3.927 closest distance to " O   HOH Z 158 " =    3.149
peak=    3.911 closest distance to " O   HOH Z  59 " =    2.187
peak=    3.899 closest distance to " O   HOH Z 280 " =    2.940
peak=    3.885 closest distance to " O   HOH Z  15 " =    2.146
peak=    3.870 closest distance to " O   HOH Z 411 " =    3.751
peak=    3.855 closest distance to " CB  VAL A 202 " =    1.546
peak=    3.840 closest distance to " NH2 ARG A 156 " =    1.128
peak=    3.839 closest distance to " CG1BVAL A  72 " =    1.731
peak=    3.800 closest distance to " O   HOH Z 147 " =    1.801
peak=    3.787 closest distance to " CG  ARG A  66 " =    2.655
peak=    3.786 closest distance to " O   HOH Z 403 " =    1.601
peak=    3.780 closest distance to " CB  TRP A 179 " =    1.409
peak=    3.778 closest distance to " CB  ASN A 142 " =    1.196
peak=    3.760 closest distance to " O   HOH Z 261 " =    1.899
peak=    3.755 closest distance to " CA  ARG A 195 " =    1.177
peak=    3.753 closest distance to " CD  LYS A 166 " =    1.317
peak=    3.748 closest distance to " O   HOH Z 250 " =    1.324
peak=    3.738 closest distance to " O   HOH Z 313 " =    1.774
peak=    3.724 closest distance to " CD2 TRP A 179 " =    1.377
peak=    3.711 closest distance to " CB AVAL A  41 " =    1.087
peak=    3.709 closest distance to " O   HOH Z  80 " =    1.672
peak=    3.704 closest distance to " CG1 VAL A 153 " =    0.971
peak=    3.699 closest distance to " O   HOH Z  97 " =    1.995
peak=    3.694 closest distance to " CB  ALA A   9 " =    1.578
peak=    3.690 closest distance to " N   ASN A  39 " =    1.261
peak=    3.687 closest distance to " CG2 VAL A 257 " =    0.854
peak=    3.678 closest distance to " CE1 TYR A 186 " =    1.346
peak=    3.648 closest distance to " O   HOH Z 128 " =    2.164
peak=    3.646 closest distance to " CA  ALA A  51 " =    0.929
peak=    3.642 closest distance to " CB  ARG A  79 " =    0.902
peak=    3.642 closest distance to " CG1 ILE A  49 " =    1.508
peak=    3.631 closest distance to " O   HOH Z 422 " =    2.656
peak=    3.625 closest distance to " O   HOH Z 285 " =    2.828
peak=    3.615 closest distance to " O   HOH Z  19 " =    2.282
peak=    3.614 closest distance to " CB  ARG A 139 " =    0.873
peak=    3.614 closest distance to " CD BLYS A 290 " =    0.998
peak=    3.613 closest distance to " NH1AARG A 145 " =    1.172
peak=    3.609 closest distance to " CA  ARG A  36 " =    1.058
peak=    3.608 closest distance to " O   HOH Z  48 " =    1.631
peak=    3.607 closest distance to " O   HOH Z 407 " =    2.465
peak=    3.606 closest distance to " CA  ALA A  21 " =    1.126
peak=    3.605 closest distance to " CB  ASN A  39 " =    0.904
peak=    3.605 closest distance to " O   TRP A 274 " =    1.853
peak=    3.604 closest distance to " CD  ARG A 269 " =    0.971
peak=    3.601 closest distance to " CA  PHE A 283 " =    1.233
peak=    3.594 closest distance to " CA  ASN A 215 " =    1.177
peak=    3.586 closest distance to " CB  ALA A 248 " =    1.487
peak=    3.586 closest distance to " O   HOH Z 371 " =    3.086
peak=    3.585 closest distance to " O   HOH Z  21 " =    1.738
peak=    3.575 closest distance to " CB  THR A  31 " =    1.590
peak=    3.571 closest distance to " ND2 ASN A 249 " =    1.883
peak=    3.571 closest distance to " CA  VAL A 125 " =    1.239
peak=    3.560 closest distance to " O   HOH Z 197 " =    3.079
peak=    3.559 closest distance to " CG  MET A 185 " =    1.180
peak=    3.557 closest distance to " CD2 LEU A   5 " =    0.734
peak=    3.557 closest distance to " O   HOH Z 102 " =    1.268
peak=    3.557 closest distance to " OG BSER A 164 " =    2.248
peak=    3.556 closest distance to " CB  GLU A  46 " =    1.036
peak=    3.554 closest distance to " O   HOH Z 180 " =    2.167
peak=    3.547 closest distance to " O   HOH Z 172 " =    3.701
peak=    3.543 closest distance to " OG1 THR A 294 " =    2.396
peak=    3.539 closest distance to " O   HOH Z 291 " =    1.624
peak=    3.537 closest distance to " O   HOH Z 365 " =    2.970
peak=    3.533 closest distance to " CE  LYS A  76 " =    0.868
peak=    3.530 closest distance to " O   MET A 105 " =    1.872
peak=    3.526 closest distance to " O   HOH Z 305 " =    3.705
peak=    3.521 closest distance to " O   HOH Z 126 " =    1.611
peak=    3.519 closest distance to " O   HOH Z 263 " =    1.695
peak=    3.510 closest distance to " CG1 ILE A  33 " =    1.279
peak=    3.509 closest distance to " CA  LYS A 117 " =    1.254
peak=    3.506 closest distance to " CB  SER A  26 " =    1.778
peak=    3.506 closest distance to " O   HOH Z 193 " =    2.053
peak=    3.503 closest distance to " O   HOH Z 251 " =    1.508
peak=    3.503 closest distance to " CG  MET A 185 " =    1.049
peak=    3.495 closest distance to " CD  ARG A 159 " =    0.720
peak=    3.493 closest distance to " O   HOH Z 273 " =    2.799
peak=    3.488 closest distance to " O   HOH Z 290 " =    1.004
peak=    3.487 closest distance to " O   HOH Z 128 " =    2.110
peak=    3.486 closest distance to " NZ  LYS A 117 " =    3.196
peak=    3.484 closest distance to " O   ASN A  74 " =    1.584
peak=    3.479 closest distance to " CB  ALA A 291 " =    1.359
peak=    3.475 closest distance to " CB  GLN A 205 " =    1.085
peak=    3.474 closest distance to " CB  THR A 157 " =    1.184
peak=    3.473 closest distance to " O   HOH Z 344 " =    3.046
peak=    3.472 closest distance to " CD1 LEU A 300 " =    1.298
peak=    3.462 closest distance to " NE2 GLN A  77 " =    3.284
peak=    3.462 closest distance to " O  BHOH Z 338 " =    2.431
peak=    3.448 closest distance to " O   HOH Z 368 " =    3.552
peak=    3.448 closest distance to " CG  LEU A 167 " =    1.183
peak=    3.446 closest distance to " CB  TRP A 150 " =    1.402
peak=    3.444 closest distance to " CG2 THR A 221 " =    1.230
peak=    3.444 closest distance to " O   HOH Z 417 " =    3.093
peak=    3.443 closest distance to " CB  THR A  52 " =    0.911
peak=    3.437 closest distance to " O   HOH Z  97 " =    2.481
peak=    3.436 closest distance to " O   HOH Z 145 " =    2.248
peak=    3.433 closest distance to " CA  THR A 264 " =    0.752
peak=    3.432 closest distance to " O   HOH Z 426 " =    1.572
peak=    3.429 closest distance to " CB  LEU A 143 " =    1.188
peak=    3.427 closest distance to " O   HOH Z 299 " =    4.367
peak=    3.424 closest distance to " O   HOH Z  66 " =    2.292
peak=    3.422 closest distance to " O   ASP A 124 " =    1.121
peak=    3.421 closest distance to " CB  SER A 212 " =    1.164
peak=    3.420 closest distance to " O   HOH Z 245 " =    1.364
peak=    3.419 closest distance to " O   HOH Z 146 " =    2.438
peak=    3.417 closest distance to " CA  ALA A 291 " =    0.876
peak=    3.409 closest distance to " N   VAL A 126 " =    1.436
peak=    3.401 closest distance to " CG1 VAL A 296 " =    1.191
peak=    3.400 closest distance to " CA  ALA A 158 " =    1.261
peak=    3.398 closest distance to " O   HOH Z 327 " =    1.822
peak=    3.398 closest distance to " O   HOH Z 437 " =    1.824
peak=    3.397 closest distance to " O   HOH Z 421 " =    1.807
peak=    3.394 closest distance to " O   HOH Z 247 " =    1.317
peak=    3.389 closest distance to " CA  ASP A 140 " =    1.225
peak=    3.385 closest distance to " CA  VAL A  41 " =    0.810
peak=    3.385 closest distance to " CA  ASP A 191 " =    1.115
peak=    3.381 closest distance to " O   GLN A 278 " =    1.265
peak=    3.381 closest distance to " N   SER A 135 " =    1.448
peak=    3.375 closest distance to " CA  LEU A 282 " =    1.064
peak=    3.371 closest distance to " CB  HIS A 108 " =    0.788
peak=    3.365 closest distance to " CB  ASN A 110 " =    1.159
peak=    3.365 closest distance to " CB  LEU A 228 " =    1.283
peak=    3.363 closest distance to " O   HOH Z 171 " =    2.351
peak=    3.358 closest distance to " CB  MET A  40 " =    0.809
peak=    3.357 closest distance to " O   ARG A  56 " =    2.858
peak=    3.356 closest distance to " CD  ARG A  66 " =    2.637
peak=    3.355 closest distance to " CA  THR A 221 " =    0.900
peak=    3.353 closest distance to " CA  MET A  40 " =    1.099
peak=    3.340 closest distance to " O   HOH Z 271 " =    2.489
peak=    3.337 closest distance to " O   HOH Z 193 " =    1.640
peak=    3.335 closest distance to " O   HOH Z 353 " =    2.705
peak=    3.332 closest distance to " CA  TYR A 116 " =    1.375
peak=    3.332 closest distance to " CG2 ILE A  20 " =    1.422
peak=    3.331 closest distance to " O   HOH Z 383 " =    1.968
peak=    3.331 closest distance to " CD2 LEU A 297 " =    0.929
peak=    3.330 closest distance to " N   ASP A 162 " =    1.307
peak=    3.329 closest distance to " O   HOH Z 133 " =    2.386
peak=    3.328 closest distance to " O   HOH Z 148 " =    3.296
peak=    3.316 closest distance to " O   HOH Z 380 " =    1.914
peak=    3.310 closest distance to " O   HOH Z 417 " =    2.192
peak=    3.309 closest distance to " CZ3 TRP A  85 " =    0.910
peak=    3.309 closest distance to " O   HOH Z 435 " =    1.983
peak=    3.308 closest distance to " O   HOH Z 329 " =    4.007
peak=    3.306 closest distance to " CA  ASP A 162 " =    1.085
peak=    3.303 closest distance to " O   ALA A 165 " =    1.466
peak=    3.303 closest distance to " O   HOH Z 134 " =    1.256
peak=    3.297 closest distance to " CB  GLN A  88 " =    1.162
peak=    3.284 closest distance to " O   HOH Z 187 " =    2.291
peak=    3.278 closest distance to " CB  GLN A  89 " =    1.222
peak=    3.278 closest distance to " OE1 GLN A  11 " =    1.804
peak=    3.278 closest distance to " CB  SER A 273 " =    0.839
peak=    3.274 closest distance to " O   HOH Z 166 " =    3.767
peak=    3.274 closest distance to " O   HOH Z  88 " =    3.101
peak=    3.270 closest distance to " CD  LYS A 119 " =    1.620
peak=    3.264 closest distance to " CD  ARG A  66 " =    2.155
peak=    3.261 closest distance to " O   HOH Z 406 " =    1.491
peak=    3.257 closest distance to " CA  ILE A 106 " =    0.734
peak=    3.257 closest distance to " CA  MET A 105 " =    1.003
peak=    3.255 closest distance to " O   HOH Z 403 " =    1.395
peak=    3.253 closest distance to " N   PHE A 130 " =    1.274
peak=    3.253 closest distance to " CG2AVAL A 121 " =    2.374
peak=    3.251 closest distance to " OG  SER A  22 " =    2.778
peak=    3.249 closest distance to " CB  LYS A 117 " =    1.195
peak=    3.248 closest distance to " CA  SER A 146 " =    1.734
peak=    3.246 closest distance to " OE1 GLU A   2 " =    2.029
peak=    3.246 closest distance to " CB  MET A  47 " =    1.063
peak=    3.241 closest distance to " CA  ALA A 154 " =    0.968
peak=    3.239 closest distance to " CZ  PHE A  38 " =    1.176
peak=    3.228 closest distance to " CZ  PHE A 192 " =    0.981
peak=    3.227 closest distance to " ND1 HIS A  81 " =    1.686
peak=    3.224 closest distance to " CA  SER A  87 " =    1.037
peak=    3.218 closest distance to " O   HOH Z 234 " =    1.814
peak=    3.213 closest distance to " O   HOH Z   4 " =    1.771
peak=    3.213 closest distance to " CB  ASN A 224 " =    0.992
peak=    3.207 closest distance to " NH2 ARG A  79 " =    1.372
peak=    3.205 closest distance to " O   HOH Z 132 " =    2.547
peak=    3.205 closest distance to " O   HOH Z 425 " =    1.300
peak=    3.201 closest distance to " CA  ASN A 127 " =    1.033
peak=    3.198 closest distance to " NE2 HIS A 207 " =    1.343
peak=    3.192 closest distance to " CG  GLN A  77 " =    2.154
peak=    3.192 closest distance to " CG2 ILE A 120 " =    1.242
peak=    3.190 closest distance to " CA  GLY A 211 " =    1.335
peak=    3.189 closest distance to " O   HOH Z  49 " =    2.488
peak=    3.185 closest distance to " O   SER A 164 " =    1.127
peak=    3.182 closest distance to " CG BARG A 102 " =    1.779
peak=    3.181 closest distance to " CD  LYS A  76 " =    1.899
peak=    3.176 closest distance to " CB  ASN A 215 " =    1.132
peak=    3.175 closest distance to " ND2 ASN A 249 " =    0.854
peak=    3.174 closest distance to " O   HOH Z   1 " =    2.071
peak=    3.174 closest distance to " O   HOH Z 216 " =    2.874
peak=    3.171 closest distance to " O   HOH Z 345 " =    3.264
peak=    3.171 closest distance to " CA  ASN A 217 " =    1.201
peak=    3.167 closest distance to " CA  ALA A 233 " =    1.409
peak=    3.165 closest distance to " OE2 GLU A  53 " =    1.983
peak=    3.165 closest distance to " N   ASN A 127 " =    1.239
peak=    3.164 closest distance to " CD1 LEU A 228 " =    1.889
peak=    3.164 closest distance to " CB  ALA A 248 " =    1.006
peak=    3.163 closest distance to " O   HOH Z 171 " =    3.808
peak=    3.162 closest distance to " CB  SER A 216 " =    0.819
peak=    3.159 closest distance to " CD1 ILE A  33 " =    1.656
peak=    3.157 closest distance to " O   HOH Z 298 " =    4.881
peak=    3.157 closest distance to " CB  GLN A 278 " =    0.849
peak=    3.153 closest distance to " O   HOH Z 420 " =    1.933
peak=    3.152 closest distance to " O   HOH Z 425 " =    2.039
peak=    3.148 closest distance to " O   HOH Z 325 " =    2.161
peak=    3.147 closest distance to " CA  ALA A  84 " =    1.382
peak=    3.143 closest distance to " CB  GLN A 103 " =    0.967
peak=    3.141 closest distance to " CG2 ILE A 234 " =    0.861
peak=    3.140 closest distance to " CE1 HIS A 108 " =    1.152
peak=    3.138 closest distance to " CG2 VAL A 197 " =    1.069
peak=    3.137 closest distance to " CB  VAL A 268 " =    0.821
peak=    3.133 closest distance to " O   HOH Z 124 " =    1.222
peak=    3.120 closest distance to " CG  GLN A 205 " =    0.874
peak=    3.120 closest distance to " O   HOH Z  88 " =    2.606
peak=    3.109 closest distance to " O   HOH Z 141 " =    1.547
peak=    3.096 closest distance to " O   HOH Z 256 " =    2.448
peak=    3.091 closest distance to " CB  ILE A  20 " =    1.470
peak=    3.088 closest distance to " CA  ILE A 234 " =    0.803
peak=    3.087 closest distance to " O   HOH Z  85 " =    1.347
peak=    3.071 closest distance to " CA  LYS A 290 " =    1.128
peak=    3.069 closest distance to " CA  ASN A 176 " =    1.117
peak=    3.065 closest distance to " O   HOH Z 301 " =    1.893
peak=    3.064 closest distance to " CB  ILE A 120 " =    1.324
peak=    3.053 closest distance to " N   GLY A 133 " =    3.705
peak=    3.049 closest distance to " O   HOH Z 213 " =    1.853
peak=    3.034 closest distance to " CH2 TRP A 266 " =    1.103
peak=    3.032 closest distance to " O   HOH Z 430 " =    3.977
peak=    3.021 closest distance to " O   ALA A 158 " =    1.354
peak=    3.013 closest distance to " CB  TYR A 116 " =    0.785

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 192         
Filter by distance & map next to the model:
   mapped sites are within: 0.816 - 5.473
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 191 from: 192
   mapped sites are within: 0.816 - 5.473

peak=   -5.168 closest distance to " CG2 VAL A 230 " =    0.820
peak=   -4.597 closest distance to " SG  CYS A 254 " =    3.356
peak=   -4.569 closest distance to " CD  ARG A 156 " =    2.031
peak=   -4.408 closest distance to " CD  GLN A  58 " =    1.081
peak=   -4.400 closest distance to " O   HOH Z 266 " =    5.204
peak=   -4.311 closest distance to " CB  PRO A 243 " =    2.643
peak=   -4.175 closest distance to " CG  GLN A 223 " =    2.145
peak=   -4.123 closest distance to " O   HOH Z 196 " =    2.130
peak=   -4.099 closest distance to " C   HIS A 108 " =    1.176
peak=   -4.084 closest distance to " O   ILE A 109 " =    2.620
peak=   -4.076 closest distance to " O   VAL A  67 " =    2.827
peak=   -4.059 closest distance to " OG BSER A 134 " =    1.196
peak=   -4.058 closest distance to " O   HOH Z 166 " =    1.909
peak=   -4.050 closest distance to " CG2BVAL A  41 " =    2.719
peak=   -4.045 closest distance to " CB  PHE A 192 " =    1.987
peak=   -4.001 closest distance to " O   HOH Z 114 " =    3.085
peak=   -3.996 closest distance to " O   HOH Z 231 " =    2.118
peak=   -3.985 closest distance to " CE2 TYR A  30 " =    2.720
peak=   -3.942 closest distance to " CG1 VAL A 112 " =    2.801
peak=   -3.941 closest distance to " O   HOH Z 351 " =    1.502
peak=   -3.926 closest distance to " OXT GLY A 302 " =    2.842
peak=   -3.897 closest distance to " CA  ASP A 298 " =    1.048
peak=   -3.878 closest distance to " CG2 VAL A 296 " =    1.236
peak=   -3.877 closest distance to " CG1 VAL A 250 " =    2.734
peak=   -3.874 closest distance to " O   PRO A 163 " =    2.156
peak=   -3.865 closest distance to " OG  SER A  97 " =    2.253
peak=   -3.838 closest distance to " NE2 GLN A  88 " =    1.923
peak=   -3.746 closest distance to " ND2 ASN A  45 " =    1.209
peak=   -3.726 closest distance to " ND2 ASN A 187 " =    1.597
peak=   -3.725 closest distance to " O   HOH Z 290 " =    1.223
peak=   -3.678 closest distance to " CZ3 TRP A 179 " =    1.209
peak=   -3.673 closest distance to " N   ALA A 226 " =    2.089
peak=   -3.657 closest distance to " CG  ASP A 231 " =    0.816
peak=   -3.648 closest distance to " CB  ALA A 248 " =    2.345
peak=   -3.643 closest distance to " O   HOH Z  11 " =    1.868
peak=   -3.623 closest distance to " CE  MET A 105 " =    2.180
peak=   -3.616 closest distance to " O   HOH Z 211 " =    1.635
peak=   -3.608 closest distance to " N   ALA A  43 " =    2.634
peak=   -3.600 closest distance to " O   HOH Z 389 " =    1.989
peak=   -3.597 closest distance to " NH2AARG A 275 " =    5.123
peak=   -3.595 closest distance to " O   HOH Z 377 " =    2.132
peak=   -3.593 closest distance to " O   HOH Z 435 " =    2.766
peak=   -3.593 closest distance to " O   HOH Z 113 " =    2.409
peak=   -3.586 closest distance to " O   HOH Z  44 " =    2.233
peak=   -3.584 closest distance to " CG2 ILE A 263 " =    2.367
peak=   -3.580 closest distance to " O   HOH Z  37 " =    1.863
peak=   -3.580 closest distance to " CE3 TRP A 150 " =    2.231
peak=   -3.577 closest distance to " CD2 LEU A 300 " =    2.713
peak=   -3.575 closest distance to " OD1 ASN A 148 " =    1.446
peak=   -3.560 closest distance to " O   HOH Z 102 " =    1.645
peak=   -3.558 closest distance to " CB  ALA A 291 " =    2.266
peak=   -3.548 closest distance to " CA  GLY A 241 " =    3.107
peak=   -3.545 closest distance to " CB  ALA A 248 " =    2.121
peak=   -3.544 closest distance to " CG  GLU A 277 " =    1.143
peak=   -3.538 closest distance to " O   HOH Z 185 " =    2.395
peak=   -3.531 closest distance to " O   HOH Z 394 " =    1.573
peak=   -3.526 closest distance to " CD1 LEU A 101 " =    2.396
peak=   -3.526 closest distance to " CG  TRP A 266 " =    1.890
peak=   -3.525 closest distance to " ND2 ASN A  45 " =    1.596
peak=   -3.518 closest distance to " NH2 ARG A  79 " =    2.056
peak=   -3.515 closest distance to " NE2 GLN A 103 " =    1.743
peak=   -3.507 closest distance to " CG1 VAL A 112 " =    2.660
peak=   -3.504 closest distance to " O   HOH Z  73 " =    2.219
peak=   -3.501 closest distance to " O   PRO A 198 " =    1.242
peak=   -3.494 closest distance to " CB  ASP A 132 " =    2.335
peak=   -3.488 closest distance to " O   HOH Z 165 " =    1.887
peak=   -3.482 closest distance to " CB  ALA A  43 " =    2.566
peak=   -3.480 closest distance to " O   HOH Z 292 " =    4.583
peak=   -3.478 closest distance to " C   ALA A 158 " =    1.259
peak=   -3.474 closest distance to " CD  LYS A 289 " =    2.477
peak=   -3.473 closest distance to " O   HOH Z 350 " =    1.957
peak=   -3.471 closest distance to " CB  ASP A 171 " =    2.301
peak=   -3.461 closest distance to " CZ  TYR A 169 " =    1.717
peak=   -3.460 closest distance to " CG  ARG A 269 " =    2.395
peak=   -3.456 closest distance to " O   HOH Z  13 " =    1.574
peak=   -3.450 closest distance to " O   SER A 271 " =    2.104
peak=   -3.447 closest distance to " CD1 PHE A  59 " =    1.977
peak=   -3.446 closest distance to " O   ALA A  10 " =    1.729
peak=   -3.436 closest distance to " O   HOH Z 198 " =    2.187
peak=   -3.432 closest distance to " C   MET A 188 " =    1.457
peak=   -3.427 closest distance to " C   LEU A 143 " =    1.050
peak=   -3.424 closest distance to " N   GLN A  58 " =    1.515
peak=   -3.417 closest distance to " OD1 ASN A 187 " =    1.672
peak=   -3.412 closest distance to " O   HOH Z  63 " =    1.255
peak=   -3.412 closest distance to " O   HOH Z  19 " =    2.300
peak=   -3.410 closest distance to " O   HOH Z  60 " =    1.965
peak=   -3.393 closest distance to " O   HOH Z 311 " =    3.775
peak=   -3.389 closest distance to " CB  PRO A 163 " =    2.543
peak=   -3.386 closest distance to " CD1 LEU A 101 " =    2.871
peak=   -3.382 closest distance to " OD2 ASP A  50 " =    2.291
peak=   -3.380 closest distance to " O   HOH Z 265 " =    2.240
peak=   -3.377 closest distance to " CE BMET A  47 " =    1.790
peak=   -3.376 closest distance to " O   VAL A 189 " =    2.612
peak=   -3.374 closest distance to " O   HOH Z  10 " =    1.481
peak=   -3.366 closest distance to " CD1 TYR A 247 " =    2.585
peak=   -3.365 closest distance to " CG1 VAL A 296 " =    1.343
peak=   -3.356 closest distance to " CD2 TYR A 293 " =    2.037
peak=   -3.355 closest distance to " OXT GLY A 302 " =    3.442
peak=   -3.351 closest distance to " CD1 LEU A 228 " =    2.218
peak=   -3.342 closest distance to " O   HOH Z 426 " =    1.684
peak=   -3.341 closest distance to " CB  ALA A 291 " =    2.196
peak=   -3.339 closest distance to " CE2 PHE A 218 " =    2.551
peak=   -3.335 closest distance to " NH2 ARG A  79 " =    1.588
peak=   -3.325 closest distance to " N   THR A 157 " =    1.516
peak=   -3.325 closest distance to " N   ASP A 171 " =    2.299
peak=   -3.322 closest distance to " CD  ARG A 139 " =    1.634
peak=   -3.317 closest distance to " C   ASN A 285 " =    2.356
peak=   -3.316 closest distance to " O   HOH Z 353 " =    2.108
peak=   -3.314 closest distance to " C   ASN A 187 " =    1.871
peak=   -3.311 closest distance to " CB  ASN A  39 " =    2.303
peak=   -3.308 closest distance to " CD2 PHE A  61 " =    2.566
peak=   -3.307 closest distance to " NE2 GLN A 278 " =    1.905
peak=   -3.306 closest distance to " O   HOH Z 313 " =    1.719
peak=   -3.302 closest distance to " O   HOH Z 191 " =    5.473
peak=   -3.299 closest distance to " O   SER A 210 " =    1.935
peak=   -3.298 closest distance to " O   HOH Z  43 " =    1.791
peak=   -3.296 closest distance to " N   ASN A  60 " =    1.309
peak=   -3.293 closest distance to " N   ALA A 248 " =    1.753
peak=   -3.293 closest distance to " O   HOH Z 359 " =    3.091
peak=   -3.292 closest distance to " O   HOH Z  47 " =    1.606
peak=   -3.287 closest distance to " CG1 VAL A 230 " =    1.953
peak=   -3.285 closest distance to " CD2 LEU A 167 " =    1.754
peak=   -3.285 closest distance to " NE2 GLN A 194 " =    1.801
peak=   -3.282 closest distance to " O   HOH Z 222 " =    1.513
peak=   -3.280 closest distance to " CB  ASN A  69 " =    1.164
peak=   -3.277 closest distance to " CA  GLY A 203 " =    2.463
peak=   -3.276 closest distance to " CG  PHE A 283 " =    2.761
peak=   -3.271 closest distance to " O   HOH Z  38 " =    1.588
peak=   -3.270 closest distance to " OG BSER A 134 " =    1.779
peak=   -3.269 closest distance to " O   HOH Z 134 " =    2.907
peak=   -3.268 closest distance to " O   LEU A 167 " =    1.481
peak=   -3.263 closest distance to " O   HOH Z  52 " =    1.571
peak=   -3.263 closest distance to " CB  GLN A  11 " =    1.814
peak=   -3.261 closest distance to " O   HOH Z 243 " =    1.926
peak=   -3.259 closest distance to " O   HOH Z 407 " =    3.046
peak=   -3.252 closest distance to " O   LYS A 117 " =    1.697
peak=   -3.249 closest distance to " CA  GLY A 133 " =    2.320
peak=   -3.243 closest distance to " O   MET A  40 " =    2.750
peak=   -3.242 closest distance to " CA  SER A  62 " =    2.643
peak=   -3.242 closest distance to " CG1 VAL A 197 " =    2.257
peak=   -3.240 closest distance to " CD  PRO A 243 " =    2.131
peak=   -3.237 closest distance to " N   SER A 276 " =    1.344
peak=   -3.234 closest distance to " CD2 TYR A 247 " =    2.308
peak=   -3.232 closest distance to " O   HOH Z 139 " =    3.149
peak=   -3.224 closest distance to " CB  ALA A  10 " =    2.228
peak=   -3.222 closest distance to " O   HOH Z 326 " =    5.139
peak=   -3.222 closest distance to " O   ARG A  24 " =    2.065
peak=   -3.220 closest distance to " CD1 LEU A  25 " =    2.447
peak=   -3.215 closest distance to " O   HOH Z 313 " =    1.131
peak=   -3.209 closest distance to " SD BMET A  47 " =    1.017
peak=   -3.206 closest distance to " O   HOH Z  90 " =    1.698
peak=   -3.202 closest distance to " OG ASER A 134 " =    1.290
peak=   -3.200 closest distance to " O   HOH Z 193 " =    1.756
peak=   -3.200 closest distance to " OG  SER A  62 " =    1.729
peak=   -3.193 closest distance to " ND2 ASN A 252 " =    1.863
peak=   -3.191 closest distance to " O   SER A 276 " =    1.699
peak=   -3.185 closest distance to " CD  GLN A 223 " =    1.522
peak=   -3.180 closest distance to " CG1 VAL A 112 " =    2.765
peak=   -3.178 closest distance to " O   PHE A 218 " =    1.684
peak=   -3.174 closest distance to " CB  ASP A 132 " =    2.373
peak=   -3.172 closest distance to " O   ALA A 161 " =    1.728
peak=   -3.161 closest distance to " O   HOH Z 298 " =    2.649
peak=   -3.160 closest distance to " CD2 LEU A 237 " =    2.864
peak=   -3.148 closest distance to " O   ALA A  51 " =    1.423
peak=   -3.148 closest distance to " O   HOH Z 177 " =    1.701
peak=   -3.146 closest distance to " C   ASP A 231 " =    2.460
peak=   -3.142 closest distance to " O   HOH Z 123 " =    2.539
peak=   -3.140 closest distance to " CD1 ILE A 151 " =    2.350
peak=   -3.140 closest distance to " O   HOH Z 339 " =    1.778
peak=   -3.139 closest distance to " CG2 VAL A 189 " =    2.021
peak=   -3.132 closest distance to " CA  GLY A  98 " =    1.932
peak=   -3.130 closest distance to " O   HOH Z 234 " =    4.146
peak=   -3.130 closest distance to " CB  TYR A  15 " =    2.190
peak=   -3.127 closest distance to " O   HOH Z   6 " =    1.639
peak=   -3.125 closest distance to " CZ  PHE A 192 " =    2.843
peak=   -3.125 closest distance to " CD  PRO A 213 " =    2.110
peak=   -3.122 closest distance to " C   GLY A  17 " =    1.295
peak=   -3.109 closest distance to " C   LEU A 222 " =    0.896
peak=   -3.104 closest distance to " C   ASP A 270 " =    1.280
peak=   -3.098 closest distance to " CB  LEU A  83 " =    2.329
peak=   -3.096 closest distance to " OG  SER A  26 " =    1.311
peak=   -3.096 closest distance to " CB  TYR A 172 " =    2.454
peak=   -3.088 closest distance to " O   HOH Z  17 " =    1.491
peak=   -3.087 closest distance to " O   HOH Z 357 " =    1.992
peak=   -3.087 closest distance to " O   PRO A 198 " =    1.356
peak=   -3.083 closest distance to " CE1 HIS A  81 " =    1.441
peak=   -3.080 closest distance to " N   ALA A 248 " =    2.453
peak=   -3.071 closest distance to " O   HOH Z 149 " =    2.167
peak=   -3.070 closest distance to " N   SER A   3 " =    2.020
peak=   -3.045 closest distance to " O   HOH Z 175 " =    4.222
peak=   -3.010 closest distance to " O   HOH Z 389 " =    4.853

================= 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    :  0.4141 0.3985   6.199990e+00   6.166067e+00
   1_bss:  0.4067 0.3819   6.197401e+00   6.147525e+00
   1_xyz:  0.2874 0.3066   5.932706e+00   5.976477e+00
   1_adp:  0.2137 0.2424   5.658139e+00   5.773340e+00
   1_occ:  0.2129 0.2426   5.656441e+00   5.774681e+00
   2_bss:  0.2070 0.2372   5.653641e+00   5.766911e+00
   2_xyz:  0.1482 0.1795   5.352257e+00   5.522906e+00
   2_adp:  0.1382 0.1715   5.293513e+00   5.473757e+00
   2_occ:  0.1382 0.1715   5.293121e+00   5.473748e+00
   3_bss:  0.1383 0.1723   5.295098e+00   5.475307e+00
   3_xyz:  0.1174 0.1569   5.167742e+00   5.392262e+00
   3_adp:  0.1127 0.1556   5.145698e+00   5.384895e+00
   3_occ:  0.1126 0.1556   5.145385e+00   5.384732e+00
   4_bss:  0.1126 0.1556   5.144966e+00   5.384402e+00
   4_xyz:  0.1140 0.1572   5.158182e+00   5.394885e+00
   4_adp:  0.1147 0.1565   5.158559e+00   5.390580e+00
   4_occ:  0.1146 0.1565   5.157678e+00   5.390092e+00
   5_bss:  0.1146 0.1565   5.157714e+00   5.390122e+00
   5_xyz:  0.1121 0.1555   5.143209e+00   5.384108e+00
   5_adp:  0.1114 0.1563   5.143838e+00   5.390080e+00
   5_occ:  0.1114 0.1563   5.143893e+00   5.390360e+00
   5_bss:  0.1114 0.1562   5.144134e+00   5.388668e+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:  0.338  20.041   7.211   8.597   8.819   0.000   0.000   0.000
   1_xyz:  0.338  20.041   7.211   8.597   8.819   0.000   0.000   0.000
   1_adp:  0.338  20.041   7.211   8.597   8.819   0.000   0.000   0.000
   1_occ:  0.338  20.041   7.211   8.597   8.819   0.000   0.000   0.000
   2_bss:  0.327  46.998   3.598   4.830   5.350   0.000   0.000   0.000
   2_xyz:  0.327  46.998   3.598   4.830   5.350   0.000   0.000   0.000
   2_adp:  0.327  46.998   3.598   4.830   5.350   0.000   0.000   0.000
   2_occ:  0.327  46.998   3.598   4.830   5.350   0.000   0.000   0.000
   3_bss:  0.327  46.998   3.194   3.995   4.826   0.000   0.000   0.000
   3_xyz:  0.327  46.998   3.194   3.995   4.826   0.000   0.000   0.000
   3_adp:  0.327  46.998   3.194   3.995   4.826   0.000   0.000   0.000
   3_occ:  0.327  46.998   3.194   3.995   4.826   0.000   0.000   0.000
   4_bss:  0.325  50.111   3.332   3.948   4.887   0.000   0.000   0.000
   4_xyz:  0.325  50.111   3.332   3.948   4.887   0.000   0.000   0.000
   4_adp:  0.325  50.111   3.332   3.948   4.887   0.000   0.000   0.000
   4_occ:  0.325  50.111   3.332   3.948   4.887   0.000   0.000   0.000
   5_bss:  0.327  50.111   3.332   3.948   4.887   0.000   0.000   0.000
   5_xyz:  0.327  50.111   3.332   3.948   4.887   0.000   0.000   0.000
   5_adp:  0.327  50.111   3.332   3.948   4.887   0.000   0.000   0.000
   5_occ:  0.327  50.111   3.332   3.948   4.887   0.000   0.000   0.000
   5_bss:  0.327  54.181  -0.698  -0.140   0.838   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  42.702 0.6127  0.6694    44232.629
   1_bss:  41.630 0.6241  0.8729    41204.714
   1_xyz:  32.252 0.7319  0.9909    25026.048
   1_adp:  23.333 0.8297  1.0701    14555.313
   1_occ:  23.365 0.8293  1.0692    14584.574
   2_bss:  23.120 0.8317  0.9401    14292.592
   2_xyz:  16.969 0.8898  0.9824     8321.544
   2_adp:  15.796 0.9003  0.9908     7592.518
   2_occ:  15.792 0.9004  0.9909     7591.198
   3_bss:  15.819 0.9002  0.9694     7638.157
   3_xyz:  14.047 0.9146  0.9756     6388.968
   3_adp:  13.882 0.9161  0.9735     6264.626
   3_occ:  13.876 0.9162  0.9735     6263.407
   4_bss:  13.867 0.9163  0.9754     6260.771
   4_xyz:  13.990 0.9156  0.9743     6402.734
   4_adp:  13.877 0.9165  0.9739     6351.460
   4_occ:  13.864 0.9166  0.9738     6346.885
   5_bss:  13.864 0.9166  0.9738     6347.585
   5_xyz:  13.758 0.9174  0.9744     6273.128
   5_adp:  13.888 0.9163  0.9712     6330.768
   5_occ:  13.893 0.9163  0.9711     6335.075
   5_bss:  13.904 0.9161  0.9708     6316.331
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.093   5.3990e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.093   5.3990e+01
   1_xyz:   1.451  0.011  0.099 17.719  0.006  4.125   1.0896e-01
   1_adp:   1.451  0.011  0.099 17.719  0.006  4.125   1.0896e-01
   1_occ:   1.451  0.011  0.099 17.719  0.006  4.125   1.0896e-01
   2_bss:   1.451  0.011  0.099 17.719  0.006  4.125   1.0896e-01
   2_xyz:   0.971  0.007  0.073 16.089  0.004  4.125   5.9593e-02
   2_adp:   0.971  0.007  0.073 16.089  0.004  4.125   5.9593e-02
   2_occ:   0.971  0.007  0.073 16.089  0.004  4.125   5.9593e-02
   3_bss:   0.971  0.007  0.073 16.089  0.004  4.125   5.9593e-02
   3_xyz:   1.127  0.010  0.093 15.900  0.004  4.137   7.6290e-02
   3_adp:   1.127  0.010  0.093 15.900  0.004  4.137   7.6290e-02
   3_occ:   1.127  0.010  0.093 15.900  0.004  4.137   7.6290e-02
   4_bss:   1.127  0.010  0.093 15.900  0.004  4.137   7.6290e-02
   4_xyz:   0.961  0.007  0.079 15.447  0.004  4.136   5.8350e-02
   4_adp:   0.961  0.007  0.079 15.447  0.004  4.136   5.8350e-02
   4_occ:   0.961  0.007  0.079 15.447  0.004  4.136   5.8350e-02
   5_bss:   0.961  0.007  0.079 15.447  0.004  4.136   5.8350e-02
   5_xyz:   1.025  0.008  0.085 15.433  0.004  4.139   6.4112e-02
   5_adp:   1.025  0.008  0.085 15.433  0.004  4.139   6.4112e-02
   5_occ:   1.025  0.008  0.085 15.433  0.004  4.139   6.4112e-02
   5_bss:   1.025  0.008  0.085 15.433  0.004  4.139   6.4112e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0005e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0005e+00
   1_xyz:  11.696  0.125  0.394 87.652  0.036  2.271   8.1358e-02
   1_adp:  11.696  0.125  0.394 87.652  0.036  2.271   8.1358e-02
   1_occ:  11.696  0.125  0.394 87.652  0.036  2.271   8.1358e-02
   2_bss:  11.696  0.125  0.394 87.652  0.036  2.271   8.1358e-02
   2_xyz:   7.506  0.055  0.368 81.880  0.033  2.346   3.9707e-02
   2_adp:   7.506  0.055  0.368 81.880  0.033  2.346   3.9707e-02
   2_occ:   7.506  0.055  0.368 81.880  0.033  2.346   3.9707e-02
   3_bss:   7.506  0.055  0.368 81.880  0.033  2.346   3.9707e-02
   3_xyz:   7.488  0.052  0.698 84.350  0.042  2.317   5.6940e-02
   3_adp:   7.488  0.052  0.698 84.350  0.042  2.317   5.6940e-02
   3_occ:   7.488  0.052  0.698 84.350  0.042  2.317   5.6940e-02
   4_bss:   7.488  0.052  0.698 84.350  0.042  2.317   5.6940e-02
   4_xyz:   6.746  0.044  0.510 82.262  0.039  2.388   3.7817e-02
   4_adp:   6.746  0.044  0.510 82.262  0.039  2.388   3.7817e-02
   4_occ:   6.746  0.044  0.510 82.262  0.039  2.388   3.7817e-02
   5_bss:   6.746  0.044  0.510 82.262  0.039  2.388   3.7817e-02
   5_xyz:   6.982  0.047  0.593 83.105  0.039  2.338   4.0568e-02
   5_adp:   6.982  0.047  0.593 83.105  0.039  2.338   4.0568e-02
   5_occ:   6.982  0.047  0.593 83.105  0.039  2.338   4.0568e-02
   5_bss:   6.982  0.047  0.593 83.105  0.039  2.338   4.0568e-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:  57.66   0.00  10.09  54.05   0.00   6.90  57.66   0.00  27.43
   1_occ:  57.66   0.00  10.09  54.05   0.00   6.90  57.66   0.00  27.43
   2_bss:  57.66   0.00  10.09  54.05   0.00   6.90  57.66   0.00  27.43
   2_xyz:  57.66   0.00  10.09  54.05   0.00   6.90  57.66   0.00  27.43
   2_adp:  57.71   0.00  10.40  56.09   0.00   6.83  57.71   0.00  29.85
   2_occ:  57.71   0.00  10.40  56.09   0.00   6.83  57.71   0.00  29.85
   3_bss:  57.71   0.00  10.40  56.09   0.00   6.83  57.71   0.00  29.85
   3_xyz:  57.71   0.00  10.40  56.09   0.00   6.83  57.71   0.00  29.85
   3_adp:  74.78   0.00  11.27  74.78   0.00   7.04  73.10   0.00  34.30
   3_occ:  74.78   0.00  11.27  74.78   0.00   7.04  73.10   0.00  34.30
   4_bss:  74.78   0.00  11.27  74.78   0.00   7.04  73.10   0.00  34.30
   4_xyz:  74.78   0.00  11.27  74.78   0.00   7.04  73.10   0.00  34.30
   4_adp:  75.64   0.00  10.96  75.64   0.00   6.94  68.90   0.60  32.82
   4_occ:  75.64   0.00  10.96  75.64   0.00   6.94  68.90   0.60  32.82
   5_bss:  75.64   0.00  10.96  75.64   0.00   6.94  68.90   0.60  32.82
   5_xyz:  75.64   0.00  10.96  75.64   0.00   6.94  68.90   0.60  32.82
   5_adp:  82.49   0.00  11.15  82.49   0.00   6.99  75.30   0.20  33.83
   5_occ:  82.49   0.00  11.15  82.49   0.00   6.99  75.30   0.20  33.83
   5_bss:  86.56   4.07  15.23  86.56   4.07  11.06  79.37   4.27  37.90
------------------------------------------------------------------------
 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:    1.179    0.021    0.399
   1_adp:    1.179    0.021    0.399
   1_occ:    1.179    0.021    0.399
   2_bss:    1.179    0.021    0.399
   2_xyz:    1.496    0.035    0.467
   2_adp:    1.496    0.035    0.467
   2_occ:    1.496    0.035    0.467
   3_bss:    1.496    0.035    0.467
   3_xyz:    1.370    0.041    0.497
   3_adp:    1.370    0.041    0.497
   3_occ:    1.370    0.041    0.497
   4_bss:    1.370    0.041    0.497
   4_xyz:    1.500    0.058    0.504
   4_adp:    1.500    0.058    0.504
   4_occ:    1.500    0.058    0.504
   5_bss:    1.500    0.058    0.504
   5_xyz:    1.502    0.067    0.511
   5_adp:    1.502    0.067    0.511
   5_occ:    1.502    0.067    0.511
   5_bss:    1.502    0.067    0.511
------------------------------------------------------------------------

CPU time actual refinement: 316.88


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_677/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_677/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_677/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_677/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_677/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 316.73 
  Macro-tasks:
    bulk solvent and scale       = 42.69  
    individual site refinement   = 125.39 
    weights calculation          = 31.35  
    collect and process          = 6.62   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 206.15 
  Micro-tasks:
    mask                            = 1.61   
    f_calc                          = 96.78  
    alpha_beta                      = 8.43   
    target                          = 1.25   
    gradients_wrt_atomic_parameters = 102.17 
    fmodel                         = 7.04   
    r_factors                      = 0.30   
    phase_errors                   = 11.90  
    foms                           = 0.23   
    TOTAL for micro-tasks          = 229.71 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.509 micro seconds
Total CPU time: 5.50 minutes
from_scatterers_fft:    629 calls, 96.33 s
gradients_fft:          573 calls, 91.11 s

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

# Date 2008-01-16 Time 02:09:25 PST -0800 (1200478165.44 s)
Start R-work = 0.4141, R-free = 0.3985 (no bulk solvent and anisotropic scale)
Final R-work = 0.1285, R-free = 0.1720 (no bulk solvent and anisotropic scale)

Start R-work = 0.4067, R-free = 0.3819
Final R-work = 0.1114, R-free = 0.1562