# Date 2008-01-16 Time 02:20:21 PST -0800 (1200478821.71 s)
#phil __OFF__

Command line arguments: "../787.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 22809
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 787

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.6012, 46.93, 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: 3.26, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 46.93, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0689 2.00158
Completeness in resolution range: 0.978227
Completeness with d_max=infinity: 0.975159

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0689
                             d_min =   2.0016

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 46.93, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0689 2.00158
Completeness in resolution range: 0.978227
Completeness with d_max=infinity: 0.975159

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0694 -  4.2824 [2102/2126]  1892   210  10.0%
  bin  2:  4.2824 -  3.4120 [2026/2046]  1822   204  10.1%
  bin  3:  3.4120 -  2.9845 [1993/2012]  1795   198   9.9%
  bin  4:  2.9845 -  2.7134 [1962/1992]  1764   198  10.1%
  bin  5:  2.7134 -  2.5199 [1978/1997]  1783   195   9.9%
  bin  6:  2.5199 -  2.3719 [1957/1982]  1758   199  10.2%
  bin  7:  2.3719 -  2.2535 [1941/1969]  1748   193   9.9%
  bin  8:  2.2535 -  2.1557 [1932/1968]  1739   193  10.0%
  bin  9:  2.1557 -  2.0729 [1914/1956]  1723   191  10.0%
  bin 10:  2.0729 -  2.0016 [1784/1977]  1606   178  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_787/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 8
        2.42 -     3.04: 2191
        3.04 -     3.66: 4607
        3.66 -     4.28: 9019
        4.28 -     4.90: 12290
  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 "  2.209 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  " O   HOH Z  42 " - " O   HOH Z 183 "  2.348 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28110 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_787/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_787/model_refine_001.geo

CPU time processing inputs: 9.16


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.60125 46.93 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 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4094   r_free= 0.3944   ksol= 0.00   Bsol= 0.00   scale= 0.832    |
|                                                                             |
| 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:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.191290                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0694 -  4.7761 0.99   1374  152 0.3518 0.3265      6.5015      6.3972|
|  2:  4.7761 -  3.8111 0.99   1303  146 0.2943 0.2905      6.5609      6.5852|
|  3:  3.8111 -  3.3353 0.99   1287  144 0.3420 0.3204      6.4885      6.4905|
|  4:  3.3353 -  3.0331 0.99   1284  142 0.3843 0.3280      6.4114      6.2892|
|  5:  3.0331 -  2.8172 0.99   1267  139 0.4194 0.4265      6.2747      6.3175|
|  6:  2.8172 -  2.6520 0.99   1272  143 0.4333 0.4738      6.2039      6.1639|
|  7:  2.6520 -  2.5199 0.99   1269  139 0.4633 0.4694      6.1823      6.1562|
|  8:  2.5199 -  2.4106 0.98   1248  141 0.4611 0.4299      6.1361      6.1269|
|  9:  2.4106 -  2.3182 0.98   1255  138 0.4482 0.4623      6.0582      6.0496|
| 10:  2.3182 -  2.2384 1.00   1237  141 0.4750 0.4404      6.0867      6.0203|
| 11:  2.2384 -  2.1687 0.97   1254  135 0.4777 0.4142      6.0107      5.9619|
| 12:  2.1687 -  2.1068 0.98   1244  140 0.4692 0.4548      5.9502      5.9784|
| 13:  2.1068 -  2.0515 0.99   1244  136 0.4758 0.4837      5.8651      5.8825|
| 14:  2.0515 -  2.0016 0.86   1092  123 0.4773 0.4246      5.8381      5.6773|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0694 -  4.7761  1374   152  0.76  28.91   0.81     0.78      51270.99|
|  2:  4.7761 -  3.8111  1303   146  0.81  25.30   0.92     0.84      60196.65|
|  3:  3.8111 -  3.3353  1287   144  0.76  30.43   0.89     0.82      61508.36|
|  4:  3.3353 -  3.0331  1284   142  0.70  35.05   0.85     0.75      56284.01|
|  5:  3.0331 -  2.8172  1267   139  0.61  42.69   0.79     0.68      52587.73|
|  6:  2.8172 -  2.6520  1272   143  0.57  46.13   0.77     0.63      50076.60|
|  7:  2.6520 -  2.5199  1269   139  0.54  48.85   0.76     0.60      47731.24|
|  8:  2.5199 -  2.4106  1248   141  0.54  49.10   0.78     0.61      43679.62|
|  9:  2.4106 -  2.3182  1255   138  0.56  47.31   0.76     0.62      37637.07|
| 10:  2.3182 -  2.2384  1237   141  0.57  46.54   0.78     0.64      33121.08|
| 11:  2.2384 -  2.1687  1254   135  0.55  48.05   0.78     0.62      31138.22|
| 12:  2.1687 -  2.1068  1244   140  0.52  50.91   0.80     0.61      31083.20|
| 13:  2.1068 -  2.0515  1244   136  0.51  51.37   0.77     0.58      27345.37|
| 14:  2.0515 -  2.0016  1092   123  0.58  46.45   0.75     0.59      19867.93|
|alpha:            min =        0.58 max =            0.84 mean =         0.67|
|beta:             min =    19867.93 max =        61508.36 mean =     43525.54|
|figures of merit: min =        0.00 max =            1.00 mean =         0.62|
|phase err.(work): min =        0.00 max =           89.95 mean =        42.43|
|phase err.(test): min =        0.00 max =           89.96 mean =        42.56|
|-----------------------------------------------------------------------------|

============================== 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 = 6.019579              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 72.242   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.487222              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.116   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       21 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      163 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      681 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1484 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2603 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3920 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5027 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6525 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7711 |
|-----------------------------------------------------------------------------|
|-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 |       53.993 |
| 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 |       1.625 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.037)------------------------------------------|
|    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 = 12.037)------------------------------------------|
|    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 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4188   r_free= 0.4002   ksol= 0.00   Bsol= 0.00   scale= 0.800    |
|                                                                             |
| 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:   0.50 A                  |
| x-ray target function (ml) for work reflections: 6.201369                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4016   r_free= 0.3791   ksol= 0.34   Bsol= 18.52   scale= 1.032   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.60,8.12,8.88,0.00,0.00,0.00); trace/3= 8.20                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.50 A                  |
| x-ray target function (ml) for work reflections: 6.188430                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.721123              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 74.318   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.490240              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 75.465   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4016      final r-factor (work) = 0.2831          |
| start r-factor (free) = 0.3791      final r-factor (free) = 0.3013          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 71.7768 = 5.72 * 0.50 * 6.2168 + 1.00 * 53.9933                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.2437 = 5.72 * 0.50 * 5.9910 + 1.00 * 0.1060                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2831      final r-factor (work) = 0.2048          |
| start r-factor (free) = 0.3013      final r-factor (free) = 0.2325          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9518 = 0.49 * 1.00 * 5.9910 + 1.00 * 0.0148                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8272 = 0.49 * 1.00 * 5.7452 + 1.00 * 0.0106                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.037)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    55.46   10.04    None  None   None       |
|    all(noH): 2823   0      0.00    55.46   10.04    None  None   None       |
|    Sol.    : 438    0      0.00    55.23   27.89    None  None   None       |
|    Mac.    : 2385   0      0.00    55.46   6.77     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 -   5.546: 1334   |   5:    27.730 -  33.275:   99        |
|      1:     5.546 -  11.092:  726   |   6:    33.275 -  38.821:  110        |
|      2:    11.092 -  16.638:  255   |   7:    38.821 -  44.367:   40        |
|      3:    16.638 -  22.184:  115   |   8:    44.367 -  49.913:   34        |
|      4:    22.184 -  27.730:   98   |   9:    49.913 -  55.459:   12        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2048 r_free = 0.2325             target_work(ml) = 5.619         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2039 r_free = 0.2325             target_work(ml) = 5.618         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2039   r_free= 0.2325   ksol= 0.34   Bsol= 18.52   scale= 1.087   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.60,8.12,8.88,0.00,0.00,0.00); trace/3= 8.20                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.617631                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1973   r_free= 0.2254   ksol= 0.34   Bsol= 50.00   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.08,4.34,5.46,0.00,0.00,0.00); trace/3= 4.63                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.612769                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.851495              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 93.012   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.236719              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 114.521  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1973      final r-factor (work) = 0.1463          |
| start r-factor (free) = 0.2254      final r-factor (free) = 0.1803          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4454 = 1.85 * 0.50 * 5.7681 + 1.00 * 0.1057                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1097 = 1.85 * 0.50 * 5.4576 + 1.00 * 0.0574                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1463      final r-factor (work) = 0.1373          |
| start r-factor (free) = 0.1803      final r-factor (free) = 0.1728          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3025 = 0.24 * 1.00 * 5.4576 + 1.00 * 0.0106                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4802 = 0.24 * 1.00 * 5.3115 + 1.00 * 0.2229                               |
|-----------------------------------------------------------------------------|
| number of iterations = 14      |    number of function evaluations = 15     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.037)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    57.00   10.38    None  None   None       |
|    all(noH): 2823   0      0.00    57.00   10.38    None  None   None       |
|    Sol.    : 438    0      0.00    56.34   29.95    None  None   None       |
|    Mac.    : 2385   0      0.00    57.00   6.79     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   5.700: 1393   |   5:    28.500 -  34.200:   92        |
|      1:     5.700 -  11.400:  672   |   6:    34.200 -  39.900:  108        |
|      2:    11.400 -  17.100:  240   |   7:    39.900 -  45.600:   67        |
|      3:    17.100 -  22.800:  102   |   8:    45.600 -  51.300:   32        |
|      4:    22.800 -  28.500:  103   |   9:    51.300 -  57.000:   14        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1373 r_free = 0.1728             target_work(ml) = 5.292         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1373 r_free = 0.1729             target_work(ml) = 5.292         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1373   r_free= 0.1729   ksol= 0.34   Bsol= 50.00   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.08,4.34,5.46,0.00,0.00,0.00); trace/3= 4.63                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.291873                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1372   r_free= 0.1730   ksol= 0.34   Bsol= 50.00   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.50,3.76,4.92,0.00,0.00,0.00); trace/3= 4.06                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.293050                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.755837              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 122.989  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 9.512811              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.794   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1372      final r-factor (work) = 0.1219          |
| start r-factor (free) = 0.1730      final r-factor (free) = 0.1616          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7212 = 1.76 * 0.50 * 5.3123 + 1.00 * 0.0574                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.6557 = 1.76 * 0.50 * 5.2334 + 1.00 * 0.0612                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1219      final r-factor (work) = 0.1175          |
| start r-factor (free) = 0.1616      final r-factor (free) = 0.1608          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 49.7996 = 9.51 * 1.00 * 5.2334 + 1.00 * 0.0151                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 49.3028 = 9.51 * 1.00 * 5.1811 + 1.00 * 0.0162                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.037)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.04   11.44    None  None   None       |
|    all(noH): 2823   0      0.00    77.04   11.44    None  None   None       |
|    Sol.    : 438    0      0.00    76.40   35.01    None  None   None       |
|    Mac.    : 2385   0      0.00    77.04   7.11     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.704: 1697   |   5:    38.520 -  46.224:   78        |
|      1:     7.704 -  15.408:  535   |   6:    46.224 -  53.928:   75        |
|      2:    15.408 -  23.112:  152   |   7:    53.928 -  61.632:   54        |
|      3:    23.112 -  30.816:  107   |   8:    61.632 -  69.336:   19        |
|      4:    30.816 -  38.520:   99   |   9:    69.336 -  77.040:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1175 r_free = 0.1608             target_work(ml) = 5.180         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1174 r_free = 0.1609             target_work(ml) = 5.180         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1174   r_free= 0.1609   ksol= 0.34   Bsol= 50.00   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.50,3.76,4.92,0.00,0.00,0.00); trace/3= 4.06                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.180313                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1174   r_free= 0.1609   ksol= 0.33   Bsol= 50.00   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.50,3.76,4.92,0.00,0.00,0.00); trace/3= 4.06                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.179402                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.823406              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 141.856  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.260919              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 98.471   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1174      final r-factor (work) = 0.1140          |
| start r-factor (free) = 0.1609      final r-factor (free) = 0.1596          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7841 = 1.82 * 0.50 * 5.1803 + 1.00 * 0.0612                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7694 = 1.82 * 0.50 * 5.1666 + 1.00 * 0.0590                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1140      final r-factor (work) = 0.1147          |
| start r-factor (free) = 0.1596      final r-factor (free) = 0.1574          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3640 = 0.26 * 1.00 * 5.1666 + 1.00 * 0.0159                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3796 = 0.26 * 1.00 * 5.1679 + 1.00 * 0.0312                               |
|-----------------------------------------------------------------------------|
| number of iterations = 9       |    number of function evaluations = 11     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.037)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.06   11.28    None  None   None       |
|    all(noH): 2823   0      0.00    77.06   11.28    None  None   None       |
|    Sol.    : 438    0      0.58    74.42   34.20    None  None   None       |
|    Mac.    : 2385   0      0.00    77.06   7.07     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 -   7.706: 1744   |   5:    38.530 -  46.236:   77        |
|      1:     7.706 -  15.412:  503   |   6:    46.236 -  53.942:   78        |
|      2:    15.412 -  23.118:  148   |   7:    53.942 -  61.649:   43        |
|      3:    23.118 -  30.824:  105   |   8:    61.649 -  69.355:   19        |
|      4:    30.824 -  38.530:  100   |   9:    69.355 -  77.061:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1147 r_free = 0.1574             target_work(ml) = 5.158         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1146 r_free = 0.1572             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 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1146   r_free= 0.1572   ksol= 0.33   Bsol= 50.00   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.50,3.76,4.92,0.00,0.00,0.00); trace/3= 4.06                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.157838                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1146   r_free= 0.1572   ksol= 0.33   Bsol= 50.00   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.50,3.76,4.92,0.00,0.00,0.00); trace/3= 4.06                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.157838                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.631309              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 155.534  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.553558              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.331   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1146      final r-factor (work) = 0.1138          |
| start r-factor (free) = 0.1572      final r-factor (free) = 0.1572          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.2737 = 1.63 * 0.50 * 5.1673 + 1.00 * 0.0590                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.2622 = 1.63 * 0.50 * 5.1548 + 1.00 * 0.0577                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1138      final r-factor (work) = 0.1133          |
| start r-factor (free) = 0.1572      final r-factor (free) = 0.1576          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9845 = 0.55 * 1.00 * 5.1548 + 1.00 * 0.1310                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8651 = 0.55 * 1.00 * 5.1517 + 1.00 * 0.0133                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.037)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.91   11.23    None  None   None       |
|    all(noH): 2823   0      0.00    77.91   11.23    None  None   None       |
|    Sol.    : 438    0      0.52    73.90   33.96    None  None   None       |
|    Mac.    : 2385   0      0.00    77.91   7.06     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:     0.000 -   7.791: 1736   |   5:    38.954 -  46.744:   80        |
|      1:     7.791 -  15.581:  507   |   6:    46.744 -  54.535:   73        |
|      2:    15.581 -  23.372:  155   |   7:    54.535 -  62.326:   40        |
|      3:    23.372 -  31.163:  108   |   8:    62.326 -  70.116:   18        |
|      4:    31.163 -  38.954:  102   |   9:    70.116 -  77.907:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1133 r_free = 0.1576             target_work(ml) = 5.154         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1133 r_free = 0.1576             target_work(ml) = 5.154         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1133   r_free= 0.1576   ksol= 0.33   Bsol= 50.00   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.50,3.76,4.92,0.00,0.00,0.00); trace/3= 4.06                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.154173                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0694 -  4.7761 0.99   1374  152 0.1021 0.1333      5.3991      5.5228|
|  2:  4.7761 -  3.8111 0.99   1303  146 0.0875 0.1153      5.4562      5.6537|
|  3:  3.8111 -  3.3353 0.99   1287  144 0.1062 0.1488      5.4902      5.8392|
|  4:  3.3353 -  3.0331 0.99   1284  142 0.1203 0.1564      5.4614      5.6102|
|  5:  3.0331 -  2.8172 0.99   1267  139 0.1320 0.1709      5.3389      5.5494|
|  6:  2.8172 -  2.6520 0.99   1272  143 0.1212 0.1907       5.214      5.4884|
|  7:  2.6520 -  2.5199 0.99   1269  139 0.1298 0.1570      5.1803      5.3239|
|  8:  2.5199 -  2.4106 0.98   1248  141 0.1197 0.1746      5.0998      5.4033|
|  9:  2.4106 -  2.3182 0.98   1255  138 0.1187 0.1769      5.0579       5.263|
| 10:  2.3182 -  2.2384 1.00   1237  141 0.1144 0.1705      4.9814      5.2658|
| 11:  2.2384 -  2.1687 0.97   1254  135 0.1167 0.1631      4.9476      5.1952|
| 12:  2.1687 -  2.1068 0.98   1244  140 0.1159 0.1796      4.8919      5.2652|
| 13:  2.1068 -  2.0515 0.99   1244  136 0.1155 0.1623      4.8203      5.0436|
| 14:  2.0515 -  2.0016 0.86   1092  123 0.1071 0.1846      4.6987      4.9889|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0694 -  4.7761  1374   152  0.94   9.17   0.98     0.95       7289.38|
|  2:  4.7761 -  3.8111  1303   146  0.95   8.02   1.01     1.00       9187.94|
|  3:  3.8111 -  3.3353  1287   144  0.93  11.20   1.02     1.01      10590.72|
|  4:  3.3353 -  3.0331  1284   142  0.92  13.25   1.01     0.99      10358.56|
|  5:  3.0331 -  2.8172  1267   139  0.90  15.65   1.00     0.97       8433.54|
|  6:  2.8172 -  2.6520  1272   143  0.90  15.76   0.99     0.96       7043.07|
|  7:  2.6520 -  2.5199  1269   139  0.91  15.56   0.99     0.96       6175.52|
|  8:  2.5199 -  2.4106  1248   141  0.91  15.00   0.99     0.97       5463.63|
|  9:  2.4106 -  2.3182  1255   138  0.91  15.67   1.01     0.98       5247.97|
| 10:  2.3182 -  2.2384  1237   141  0.91  15.28   1.00     0.96       4404.28|
| 11:  2.2384 -  2.1687  1254   135  0.90  16.04   1.00     0.96       4340.01|
| 12:  2.1687 -  2.1068  1244   140  0.91  15.23   1.01     0.99       3911.92|
| 13:  2.1068 -  2.0515  1244   136  0.90  15.87   1.00     0.99       3495.17|
| 14:  2.0515 -  2.0016  1092   123  0.91  15.01   0.98     0.94       2709.61|
|alpha:            min =        0.94 max =            1.01 mean =         0.97|
|beta:             min =     2709.61 max =        10590.72 mean =      6402.02|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           90.00 mean =        13.99|
|phase err.(test): min =        0.00 max =           88.88 mean =        13.56|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1135   r_free= 0.1574   ksol= 0.32   Bsol= 52.41   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.56,-0.30,0.86,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.155300                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1135   r_free= 0.1574   ksol= 0.32   Bsol= 52.41   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.56,-0.30,0.86,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.155300                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0694 -  4.7761 0.99   1374  152 0.1029 0.1297      5.4134       5.521|
|  2:  4.7761 -  3.8111 0.99   1303  146 0.0879 0.1138      5.4584      5.6434|
|  3:  3.8111 -  3.3353 0.99   1287  144 0.1064 0.1485      5.4875      5.8406|
|  4:  3.3353 -  3.0331 0.99   1284  142 0.1200 0.1566        5.46      5.6079|
|  5:  3.0331 -  2.8172 0.99   1267  139 0.1323 0.1700      5.3385      5.5453|
|  6:  2.8172 -  2.6520 0.99   1272  143 0.1213 0.1903       5.214      5.4901|
|  7:  2.6520 -  2.5199 0.99   1269  139 0.1297 0.1574      5.1807      5.3263|
|  8:  2.5199 -  2.4106 0.98   1248  141 0.1197 0.1753      5.1004      5.4031|
|  9:  2.4106 -  2.3182 0.98   1255  138 0.1186 0.1769      5.0579      5.2637|
| 10:  2.3182 -  2.2384 1.00   1237  141 0.1143 0.1707      4.9821      5.2665|
| 11:  2.2384 -  2.1687 0.97   1254  135 0.1167 0.1636      4.9482      5.1975|
| 12:  2.1687 -  2.1068 0.98   1244  140 0.1157 0.1798      4.8922      5.2652|
| 13:  2.1068 -  2.0515 0.99   1244  136 0.1153 0.1629      4.8202      5.0442|
| 14:  2.0515 -  2.0016 0.86   1092  123 0.1072 0.1847       4.699      4.9889|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0694 -  4.7761  1374   152  0.94   9.42   0.97     0.95       7360.93|
|  2:  4.7761 -  3.8111  1303   146  0.95   8.03   1.01     1.00       9154.93|
|  3:  3.8111 -  3.3353  1287   144  0.93  11.14   1.02     1.01      10454.60|
|  4:  3.3353 -  3.0331  1284   142  0.92  13.22   1.01     0.99      10306.46|
|  5:  3.0331 -  2.8172  1267   139  0.90  15.61   1.00     0.97       8386.53|
|  6:  2.8172 -  2.6520  1272   143  0.90  15.76   0.99     0.96       7044.90|
|  7:  2.6520 -  2.5199  1269   139  0.90  15.60   0.99     0.96       6188.67|
|  8:  2.5199 -  2.4106  1248   141  0.91  15.04   0.99     0.97       5480.61|
|  9:  2.4106 -  2.3182  1255   138  0.91  15.66   1.01     0.97       5250.97|
| 10:  2.3182 -  2.2384  1237   141  0.91  15.31   1.00     0.96       4413.75|
| 11:  2.2384 -  2.1687  1254   135  0.90  16.06   1.00     0.96       4350.08|
| 12:  2.1687 -  2.1068  1244   140  0.91  15.26   1.01     0.99       3919.69|
| 13:  2.1068 -  2.0515  1244   136  0.90  15.87   1.00     0.98       3497.48|
| 14:  2.0515 -  2.0016  1092   123  0.91  15.02   0.98     0.94       2711.33|
|alpha:            min =        0.94 max =            1.01 mean =         0.97|
|beta:             min =     2711.33 max =        10454.60 mean =      6392.74|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.89 mean =        14.01|
|phase err.(test): min =        0.00 max =           88.71 mean =        13.58|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.037)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      4.06    81.97   15.30    None  None   None       |
|    all(noH): 2823   0      4.06    81.97   15.30    None  None   None       |
|    Sol.    : 438    0      4.58    77.96   38.02    None  None   None       |
|    Mac.    : 2385   0      4.06    81.97   11.12    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:     4.061 -  11.852: 1736   |   5:    43.014 -  50.805:   80        |
|      1:    11.852 -  19.642:  507   |   6:    50.805 -  58.596:   73        |
|      2:    19.642 -  27.433:  155   |   7:    58.596 -  66.386:   40        |
|      3:    27.433 -  35.224:  108   |   8:    66.386 -  74.177:   18        |
|      4:    35.224 -  43.014:  102   |   9:    74.177 -  81.968:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 313         
Filter by distance & map next to the model:
   mapped sites are within: 0.074 - 4.210
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 301 from: 313
   mapped sites are within: 0.710 - 4.210

peak=   11.083 closest distance to " CB  VAL A 230 " =    1.467
peak=    7.700 closest distance to " CG2 VAL A 296 " =    1.180
peak=    6.226 closest distance to " NH2 ARG A  56 " =    2.254
peak=    6.075 closest distance to " CG  LEU A   5 " =    1.194
peak=    5.943 closest distance to " CD2 LEU A   5 " =    1.208
peak=    5.762 closest distance to " CB  GLN A 223 " =    1.444
peak=    5.569 closest distance to " CG  LEU A 228 " =    1.190
peak=    5.089 closest distance to " O   HOH Z 232 " =    2.335
peak=    5.024 closest distance to " NE2 GLN A  11 " =    1.136
peak=    4.939 closest distance to " CB  GLN A 183 " =    1.256
peak=    4.882 closest distance to " O   HOH Z 142 " =    1.730
peak=    4.831 closest distance to " CG  PRO A 213 " =    1.244
peak=    4.768 closest distance to " CB  SER A  63 " =    1.266
peak=    4.750 closest distance to " CB  ARG A 275 " =    0.901
peak=    4.644 closest distance to " CG  PRO A 243 " =    1.127
peak=    4.644 closest distance to " CB  VAL A 230 " =    1.195
peak=    4.599 closest distance to " CG  PRO A 198 " =    1.252
peak=    4.560 closest distance to " O   HOH Z 126 " =    1.943
peak=    4.545 closest distance to " O   HOH Z 427 " =    3.018
peak=    4.526 closest distance to " CB  VAL A 296 " =    1.053
peak=    4.519 closest distance to " C   PRO A 198 " =    1.533
peak=    4.474 closest distance to " O   HOH Z 298 " =    1.817
peak=    4.462 closest distance to " O   HOH Z 272 " =    1.924
peak=    4.432 closest distance to " O   HOH Z 369 " =    2.137
peak=    4.380 closest distance to " CZ  PHE A 218 " =    1.081
peak=    4.346 closest distance to " ND2 ASN A 187 " =    1.497
peak=    4.341 closest distance to " O   HOH Z 368 " =    2.199
peak=    4.319 closest distance to " O   HOH Z  78 " =    1.779
peak=    4.260 closest distance to " O   HOH Z  43 " =    1.995
peak=    4.259 closest distance to " CB  ASN A 148 " =    1.425
peak=    4.257 closest distance to " O   HOH Z 316 " =    3.108
peak=    4.221 closest distance to " O   HOH Z 209 " =    2.292
peak=    4.209 closest distance to " O   HOH Z 261 " =    2.023
peak=    4.206 closest distance to " O   HOH Z  61 " =    1.683
peak=    4.197 closest distance to " CB  TRP A 266 " =    0.993
peak=    4.186 closest distance to " O   SER A  87 " =    2.343
peak=    4.155 closest distance to " CB  ARG A  79 " =    1.445
peak=    4.154 closest distance to " O   HOH Z  68 " =    2.261
peak=    4.144 closest distance to " O   HOH Z 346 " =    1.632
peak=    4.132 closest distance to " CA  TYR A  30 " =    0.947
peak=    4.127 closest distance to " CB  VAL A 265 " =    1.294
peak=    4.123 closest distance to " CD2 LEU A 228 " =    1.143
peak=    4.112 closest distance to " CB  GLU A 152 " =    1.203
peak=    4.108 closest distance to " O   HOH Z 189 " =    2.868
peak=    4.100 closest distance to " O   HOH Z 303 " =    2.061
peak=    4.087 closest distance to " CB  ASP A 124 " =    0.710
peak=    4.085 closest distance to " O   HOH Z 236 " =    2.020
peak=    4.077 closest distance to " CB  GLU A 128 " =    1.019
peak=    4.058 closest distance to " CB  SER A   3 " =    1.309
peak=    4.053 closest distance to " O   HOH Z  54 " =    2.384
peak=    4.015 closest distance to " O   HOH Z 423 " =    1.701
peak=    3.988 closest distance to " OD1 ASN A  69 " =    2.628
peak=    3.982 closest distance to " O   HOH Z  63 " =    1.980
peak=    3.976 closest distance to " O   HOH Z 248 " =    1.616
peak=    3.969 closest distance to " CB  PRO A  54 " =    0.830
peak=    3.949 closest distance to " O   HOH Z 234 " =    3.704
peak=    3.942 closest distance to " CG2 VAL A 257 " =    0.888
peak=    3.922 closest distance to " CB  ASN A 187 " =    1.338
peak=    3.912 closest distance to " CB  ARG A 190 " =    1.639
peak=    3.904 closest distance to " CB  LEU A 143 " =    1.173
peak=    3.896 closest distance to " CB  ASP A 140 " =    0.892
peak=    3.893 closest distance to " O   HOH Z 403 " =    1.638
peak=    3.889 closest distance to " CB  ASN A  39 " =    0.929
peak=    3.880 closest distance to " O   HOH Z 425 " =    1.380
peak=    3.872 closest distance to " CA  ARG A 195 " =    1.197
peak=    3.872 closest distance to " O   HOH Z 203 " =    1.789
peak=    3.863 closest distance to " O   HOH Z 411 " =    3.731
peak=    3.858 closest distance to " CB  VAL A 202 " =    1.584
peak=    3.839 closest distance to " O   HOH Z 158 " =    3.191
peak=    3.827 closest distance to " CA  ALA A  51 " =    0.943
peak=    3.826 closest distance to " N   ASN A  39 " =    1.199
peak=    3.806 closest distance to " CB  GLU A 277 " =    3.640
peak=    3.784 closest distance to " CD  ARG A  66 " =    2.723
peak=    3.782 closest distance to " CA  SER A  87 " =    0.988
peak=    3.780 closest distance to " O   HOH Z 214 " =    2.128
peak=    3.770 closest distance to " CB  ASN A 142 " =    1.079
peak=    3.758 closest distance to " NH2 ARG A 156 " =    1.114
peak=    3.748 closest distance to " CD  LYS A 166 " =    1.293
peak=    3.747 closest distance to " CG1 VAL A 153 " =    0.953
peak=    3.743 closest distance to " O   HOH Z 402 " =    1.458
peak=    3.743 closest distance to " O   HOH Z 280 " =    2.983
peak=    3.741 closest distance to " CB  GLU A  46 " =    0.967
peak=    3.729 closest distance to " CB  ALA A 291 " =    1.340
peak=    3.720 closest distance to " O   HOH Z  15 " =    2.164
peak=    3.718 closest distance to " CG  LEU A 167 " =    1.188
peak=    3.717 closest distance to " CB  ALA A   9 " =    1.594
peak=    3.715 closest distance to " CD  ARG A 269 " =    1.001
peak=    3.713 closest distance to " CB BVAL A  41 " =    1.127
peak=    3.710 closest distance to " ND2 ASN A 249 " =    1.922
peak=    3.710 closest distance to " CG1BVAL A  72 " =    1.681
peak=    3.707 closest distance to " NH1AARG A 145 " =    1.163
peak=    3.702 closest distance to " CD BLYS A 290 " =    1.025
peak=    3.696 closest distance to " O   HOH Z 313 " =    1.793
peak=    3.682 closest distance to " O   HOH Z 193 " =    1.828
peak=    3.660 closest distance to " O   MET A 105 " =    1.859
peak=    3.655 closest distance to " O   HOH Z 290 " =    1.062
peak=    3.653 closest distance to " O   TRP A 274 " =    1.877
peak=    3.651 closest distance to " O   HOH Z 291 " =    1.677
peak=    3.643 closest distance to " N   PHE A 130 " =    1.233
peak=    3.642 closest distance to " O   HOH Z  40 " =    1.674
peak=    3.634 closest distance to " O   HOH Z 261 " =    1.514
peak=    3.631 closest distance to " CB  SER A 216 " =    0.819
peak=    3.609 closest distance to " CD2 TRP A 179 " =    1.340
peak=    3.598 closest distance to " CD1 ILE A  33 " =    1.679
peak=    3.594 closest distance to " O   HOH Z 147 " =    1.720
peak=    3.592 closest distance to " CB  SER A 212 " =    1.239
peak=    3.591 closest distance to " O   HOH Z  40 " =    2.545
peak=    3.588 closest distance to " O   HOH Z  97 " =    2.469
peak=    3.583 closest distance to " CD  ARG A 159 " =    0.725
peak=    3.578 closest distance to " O   HOH Z  21 " =    1.721
peak=    3.575 closest distance to " CB  ARG A  79 " =    0.900
peak=    3.574 closest distance to " CA  ALA A  21 " =    1.142
peak=    3.572 closest distance to " CB  TRP A 179 " =    1.435
peak=    3.571 closest distance to " O   HOH Z 128 " =    2.149
peak=    3.565 closest distance to " CA  ARG A  36 " =    1.078
peak=    3.558 closest distance to " CA  THR A 264 " =    0.791
peak=    3.556 closest distance to " CB  LEU A 228 " =    1.211
peak=    3.551 closest distance to " CB  ALA A 248 " =    1.379
peak=    3.543 closest distance to " O   HOH Z 422 " =    2.647
peak=    3.535 closest distance to " CD1 LEU A 300 " =    1.253
peak=    3.533 closest distance to " CA  PHE A 283 " =    1.154
peak=    3.532 closest distance to " O   HOH Z  19 " =    2.398
peak=    3.530 closest distance to " CA  LEU A 282 " =    1.046
peak=    3.522 closest distance to " CA  ASN A 215 " =    1.173
peak=    3.520 closest distance to " N   SER A 135 " =    1.405
peak=    3.517 closest distance to " CA  ALA A 158 " =    1.217
peak=    3.513 closest distance to " O   HOH Z 305 " =    3.630
peak=    3.512 closest distance to " CE  LYS A  76 " =    0.885
peak=    3.511 closest distance to " CB  ARG A 139 " =    0.866
peak=    3.507 closest distance to " CB  SER A 273 " =    0.887
peak=    3.507 closest distance to " O   HOH Z 145 " =    2.048
peak=    3.505 closest distance to " CB  THR A  31 " =    1.625
peak=    3.504 closest distance to " O   HOH Z 371 " =    3.016
peak=    3.504 closest distance to " O   HOH Z  80 " =    1.654
peak=    3.502 closest distance to " CG1 ILE A  49 " =    1.497
peak=    3.495 closest distance to " CB  THR A  82 " =    1.340
peak=    3.494 closest distance to " O   HOH Z 437 " =    1.807
peak=    3.494 closest distance to " CG  MET A 185 " =    1.168
peak=    3.494 closest distance to " O   HOH Z 251 " =    1.560
peak=    3.492 closest distance to " O   HOH Z 180 " =    2.156
peak=    3.488 closest distance to " CB  MET A  40 " =    0.800
peak=    3.486 closest distance to " O   HOH Z 365 " =    3.020
peak=    3.482 closest distance to " O   ASP A 124 " =    0.948
peak=    3.481 closest distance to " O   HOH Z 172 " =    3.519
peak=    3.478 closest distance to " CA  TYR A  30 " =    1.071
peak=    3.477 closest distance to " CA  VAL A  41 " =    0.784
peak=    3.477 closest distance to " CZ  PHE A 192 " =    0.983
peak=    3.475 closest distance to " CE1 TYR A 186 " =    1.355
peak=    3.472 closest distance to " O   HOH Z 344 " =    3.049
peak=    3.471 closest distance to " O  BHOH Z 338 " =    2.437
peak=    3.470 closest distance to " CA  ALA A 154 " =    0.963
peak=    3.467 closest distance to " O   HOH Z 353 " =    2.619
peak=    3.467 closest distance to " O   HOH Z  97 " =    2.079
peak=    3.461 closest distance to " O   HOH Z 227 " =    1.682
peak=    3.458 closest distance to " CG1 VAL A 296 " =    1.238
peak=    3.456 closest distance to " O   HOH Z 197 " =    3.205
peak=    3.453 closest distance to " O   HOH Z 435 " =    1.994
peak=    3.450 closest distance to " NE2 GLN A  77 " =    3.308
peak=    3.448 closest distance to " O   HOH Z 263 " =    1.677
peak=    3.447 closest distance to " CA  MET A 105 " =    0.975
peak=    3.441 closest distance to " O   HOH Z 368 " =    3.540
peak=    3.440 closest distance to " O   HOH Z  59 " =    2.133
peak=    3.430 closest distance to " O   HOH Z 133 " =    2.409
peak=    3.430 closest distance to " CB  LYS A 117 " =    1.243
peak=    3.423 closest distance to " N   ARG A 156 " =    1.359
peak=    3.419 closest distance to " O   HOH Z 132 " =    2.564
peak=    3.412 closest distance to " CB  HIS A 108 " =    0.818
peak=    3.411 closest distance to " O   HOH Z 193 " =    2.027
peak=    3.411 closest distance to " O   GLN A 278 " =    1.340
peak=    3.407 closest distance to " CA  ALA A 291 " =    0.878
peak=    3.397 closest distance to " CG  LEU A   5 " =    0.748
peak=    3.392 closest distance to " O   HOH Z  88 " =    3.151
peak=    3.392 closest distance to " O   HOH Z 273 " =    2.754
peak=    3.391 closest distance to " CA  ASP A 162 " =    1.030
peak=    3.389 closest distance to " O   HOH Z 126 " =    1.566
peak=    3.387 closest distance to " O   HOH Z 193 " =    1.716
peak=    3.385 closest distance to " OG BSER A 164 " =    2.253
peak=    3.378 closest distance to " O   HOH Z 258 " =    2.242
peak=    3.372 closest distance to " O   HOH Z 250 " =    1.359
peak=    3.368 closest distance to " CA  LYS A 117 " =    1.198
peak=    3.362 closest distance to " O   HOH Z 128 " =    2.161
peak=    3.352 closest distance to " O   HOH Z 407 " =    2.474
peak=    3.348 closest distance to " O   HOH Z 299 " =    4.210
peak=    3.347 closest distance to " CG2 THR A 221 " =    1.141
peak=    3.345 closest distance to " NZ  LYS A 117 " =    3.261
peak=    3.344 closest distance to " CZ  PHE A  38 " =    1.162
peak=    3.341 closest distance to " O  BHOH Z  74 " =    1.267
peak=    3.336 closest distance to " CB  THR A 157 " =    1.150
peak=    3.335 closest distance to " CG BARG A 102 " =    1.803
peak=    3.334 closest distance to " CD1 LEU A 228 " =    2.024
peak=    3.329 closest distance to " N   ARG A 190 " =    1.061
peak=    3.323 closest distance to " CG2 ILE A  20 " =    1.466
peak=    3.321 closest distance to " O   HOH Z 417 " =    2.042
peak=    3.320 closest distance to " CB  MET A  47 " =    1.055
peak=    3.320 closest distance to " N   VAL A 126 " =    1.412
peak=    3.318 closest distance to " CB  GLN A  89 " =    1.201
peak=    3.318 closest distance to " O   HOH Z 187 " =    2.330
peak=    3.314 closest distance to " CB  ASN A 110 " =    1.162
peak=    3.313 closest distance to " O   HOH Z  66 " =    2.204
peak=    3.312 closest distance to " CG2 ILE A 120 " =    1.260
peak=    3.311 closest distance to " CG  MET A 185 " =    1.029
peak=    3.311 closest distance to " CB  TRP A 150 " =    1.420
peak=    3.309 closest distance to " O   ASN A  74 " =    1.531
peak=    3.308 closest distance to " CB  GLN A  88 " =    1.213
peak=    3.308 closest distance to " N   GLN A 278 " =    1.141
peak=    3.304 closest distance to " CA  ALA A 295 " =    1.105
peak=    3.303 closest distance to " CA  MET A  40 " =    1.078
peak=    3.302 closest distance to " O   HOH Z 350 " =    1.614
peak=    3.296 closest distance to " O   HOH Z 145 " =    3.785
peak=    3.296 closest distance to " O   HOH Z  48 " =    1.607
peak=    3.294 closest distance to " CB  ALA A 248 " =    1.082
peak=    3.293 closest distance to " CB  ALA A 104 " =    0.752
peak=    3.290 closest distance to " CA  ILE A 234 " =    0.906
peak=    3.286 closest distance to " O   HOH Z 383 " =    1.876
peak=    3.285 closest distance to " CB  GLN A 103 " =    0.962
peak=    3.285 closest distance to " CB  ALA A 242 " =    0.792
peak=    3.284 closest distance to " O   ALA A 158 " =    1.399
peak=    3.280 closest distance to " ND1 HIS A  81 " =    1.679
peak=    3.280 closest distance to " CD1 LEU A 261 " =    1.214
peak=    3.276 closest distance to " ND2 ASN A 249 " =    0.862
peak=    3.273 closest distance to " O   HOH Z 285 " =    2.749
peak=    3.269 closest distance to " O   ALA A 165 " =    1.470
peak=    3.264 closest distance to " CA  THR A 221 " =    0.877
peak=    3.264 closest distance to " CA  VAL A 125 " =    1.131
peak=    3.263 closest distance to " O   HOH Z 213 " =    1.989
peak=    3.258 closest distance to " CA  TYR A 116 " =    1.459
peak=    3.256 closest distance to " O   HOH Z 227 " =    2.099
peak=    3.255 closest distance to " OG  SER A  22 " =    2.808
peak=    3.254 closest distance to " CA  LYS A 290 " =    1.236
peak=    3.252 closest distance to " CB  GLN A 205 " =    1.077
peak=    3.250 closest distance to " CB  SER A  26 " =    1.758
peak=    3.250 closest distance to " CG2 THR A 220 " =    0.888
peak=    3.247 closest distance to " C   TYR A 214 " =    1.568
peak=    3.245 closest distance to " O   HOH Z   1 " =    1.707
peak=    3.243 closest distance to " CG1 ILE A  33 " =    1.298
peak=    3.243 closest distance to " O   HOH Z 380 " =    1.788
peak=    3.239 closest distance to " O   HOH Z 171 " =    2.339
peak=    3.239 closest distance to " CB  PRO A 198 " =    1.011
peak=    3.236 closest distance to " O   HOH Z 148 " =    3.342
peak=    3.232 closest distance to " CA  ASP A 140 " =    1.251
peak=    3.231 closest distance to " O   HOH Z 141 " =    1.607
peak=    3.228 closest distance to " O   HOH Z 359 " =    3.739
peak=    3.226 closest distance to " O   HOH Z 294 " =    1.594
peak=    3.223 closest distance to " CA  ASN A 127 " =    1.044
peak=    3.223 closest distance to " CG  LEU A 281 " =    1.077
peak=    3.221 closest distance to " CG1 ILE A 151 " =    0.997
peak=    3.220 closest distance to " CA  ALA A 233 " =    1.345
peak=    3.219 closest distance to " CB  VAL A 268 " =    0.839
peak=    3.218 closest distance to " O   HOH Z 286 " =    2.440
peak=    3.215 closest distance to " NE2 HIS A 207 " =    1.303
peak=    3.211 closest distance to " O   HOH Z 329 " =    3.935
peak=    3.209 closest distance to " ND1 HIS A  86 " =    1.720
peak=    3.205 closest distance to " N   ASP A 162 " =    1.230
peak=    3.200 closest distance to " O   HOH Z 250 " =    1.304
peak=    3.196 closest distance to " O   HOH Z 409 " =    3.207
peak=    3.192 closest distance to " CA  ILE A 106 " =    0.750
peak=    3.192 closest distance to " CB  ILE A 120 " =    1.281
peak=    3.191 closest distance to " CG2 THR A 294 " =    1.730
peak=    3.191 closest distance to " CD  LYS A 119 " =    1.595
peak=    3.190 closest distance to " CB  TYR A 247 " =    0.965
peak=    3.190 closest distance to " CZ3 TRP A 266 " =    1.121
peak=    3.189 closest distance to " O   HOH Z 295 " =    1.497
peak=    3.188 closest distance to " CA  SER A 146 " =    1.775
peak=    3.188 closest distance to " O   HOH Z 148 " =    2.077
peak=    3.188 closest distance to " NH1 ARG A 138 " =    1.075
peak=    3.187 closest distance to " O   HOH Z 392 " =    1.982
peak=    3.186 closest distance to " O   HOH Z 419 " =    1.820
peak=    3.184 closest distance to " O   HOH Z 417 " =    3.083
peak=    3.182 closest distance to " O   HOH Z 327 " =    1.875
peak=    3.175 closest distance to " CB  SER A 210 " =    0.848
peak=    3.174 closest distance to " NZ  LYS A  48 " =    1.356
peak=    3.173 closest distance to " CB  PRO A 243 " =    1.492
peak=    3.166 closest distance to " CA  ASP A 191 " =    0.887
peak=    3.166 closest distance to " O   HOH Z 313 " =    1.673
peak=    3.164 closest distance to " N   ASN A 127 " =    1.221
peak=    3.161 closest distance to " O   HOH Z 128 " =    1.856
peak=    3.157 closest distance to " CG  GLN A  88 " =    1.061
peak=    3.157 closest distance to " OE2 GLU A  53 " =    2.010
peak=    3.155 closest distance to " CB  ILE A  20 " =    1.396
peak=    3.148 closest distance to " O   HOH Z 245 " =    1.359
peak=    3.147 closest distance to " CB  LYS A 290 " =    0.928
peak=    3.146 closest distance to " O   HOH Z 325 " =    2.156
peak=    3.137 closest distance to " CE3 TRP A 150 " =    0.989
peak=    3.136 closest distance to " O   HOH Z 156 " =    3.404
peak=    3.132 closest distance to " O   HOH Z 173 " =    2.196
peak=    3.131 closest distance to " O   HOH Z 133 " =    1.589
peak=    3.111 closest distance to " O   HOH Z 426 " =    1.826
peak=    3.110 closest distance to " CB  ALA A 114 " =    1.216
peak=    3.100 closest distance to " CG  ARG A 159 " =    0.994
peak=    3.091 closest distance to " O   HOH Z 345 " =    3.405
peak=    3.084 closest distance to " C   ALA A 299 " =    0.937
peak=    3.073 closest distance to " OH  TYR A 214 " =    1.271
peak=    3.070 closest distance to " CD1 ILE A 199 " =    0.806
peak=    3.067 closest distance to " CB  ASN A 215 " =    1.163
peak=    3.067 closest distance to " O   HOH Z  88 " =    3.387
peak=    3.063 closest distance to " O   ALA A 292 " =    1.528
peak=    3.051 closest distance to " O   HOH Z  49 " =    2.504
peak=    3.047 closest distance to " C   ASN A  39 " =    1.002
peak=    3.041 closest distance to " N   ALA A   7 " =    1.270
peak=    3.024 closest distance to " CA  ALA A 248 " =    1.202
peak=    3.021 closest distance to " CE  MET A  40 " =    1.106

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 203         
Filter by distance & map next to the model:
   mapped sites are within: 0.750 - 5.444
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 201 from: 203
   mapped sites are within: 0.750 - 5.444

peak=   -5.355 closest distance to " CG2 VAL A 230 " =    0.750
peak=   -4.658 closest distance to " CD  ARG A 156 " =    2.050
peak=   -4.344 closest distance to " CB  PRO A 243 " =    2.676
peak=   -4.344 closest distance to " CD  GLN A  58 " =    1.020
peak=   -4.227 closest distance to " SG  CYS A 254 " =    3.387
peak=   -4.226 closest distance to " O   HOH Z 266 " =    5.288
peak=   -4.182 closest distance to " O   ILE A 109 " =    2.570
peak=   -4.156 closest distance to " C   HIS A 108 " =    1.166
peak=   -4.085 closest distance to " O   HOH Z 351 " =    1.494
peak=   -4.055 closest distance to " O   HOH Z 166 " =    1.971
peak=   -4.006 closest distance to " OG BSER A 134 " =    1.181
peak=   -3.995 closest distance to " CG  GLN A 223 " =    2.054
peak=   -3.960 closest distance to " CE2 TYR A  30 " =    2.775
peak=   -3.941 closest distance to " O   VAL A  67 " =    2.656
peak=   -3.916 closest distance to " O   HOH Z 231 " =    1.999
peak=   -3.892 closest distance to " CG2 VAL A 296 " =    1.385
peak=   -3.887 closest distance to " O   HOH Z 196 " =    2.218
peak=   -3.872 closest distance to " CB  PHE A 192 " =    1.980
peak=   -3.861 closest distance to " CG  ASP A 231 " =    0.787
peak=   -3.850 closest distance to " O   PRO A 163 " =    2.135
peak=   -3.824 closest distance to " O   HOH Z 114 " =    3.080
peak=   -3.821 closest distance to " CG2 THR A   4 " =    1.931
peak=   -3.813 closest distance to " O   HOH Z 290 " =    1.239
peak=   -3.800 closest distance to " O   VAL A  67 " =    2.770
peak=   -3.794 closest distance to " N   ALA A 226 " =    2.076
peak=   -3.776 closest distance to " NH2AARG A 275 " =    5.238
peak=   -3.767 closest distance to " O   HOH Z 185 " =    2.321
peak=   -3.763 closest distance to " OG  SER A  97 " =    2.236
peak=   -3.754 closest distance to " CG1 VAL A 112 " =    2.631
peak=   -3.753 closest distance to " ND2 ASN A  45 " =    1.078
peak=   -3.748 closest distance to " O   HOH Z 435 " =    2.806
peak=   -3.731 closest distance to " CB  ALA A 248 " =    2.135
peak=   -3.724 closest distance to " CG1 VAL A 112 " =    2.885
peak=   -3.708 closest distance to " O   HOH Z 377 " =    2.111
peak=   -3.687 closest distance to " O   HOH Z 102 " =    1.661
peak=   -3.685 closest distance to " CB  ALA A 248 " =    2.369
peak=   -3.668 closest distance to " O   HOH Z 211 " =    1.550
peak=   -3.662 closest distance to " CE3 TRP A 150 " =    2.168
peak=   -3.650 closest distance to " O   PRO A 198 " =    1.224
peak=   -3.649 closest distance to " CZ3 TRP A 179 " =    1.176
peak=   -3.646 closest distance to " CG2 ILE A 263 " =    2.418
peak=   -3.645 closest distance to " CE  MET A 105 " =    2.325
peak=   -3.644 closest distance to " O   HOH Z 394 " =    1.539
peak=   -3.636 closest distance to " O   HOH Z  44 " =    2.267
peak=   -3.636 closest distance to " CG1 VAL A 296 " =    1.396
peak=   -3.635 closest distance to " CB  ALA A  43 " =    2.588
peak=   -3.626 closest distance to " O   HOH Z 389 " =    2.023
peak=   -3.623 closest distance to " CA  GLY A 241 " =    3.101
peak=   -3.602 closest distance to " CD1 LEU A 101 " =    2.341
peak=   -3.584 closest distance to " O   HOH Z 113 " =    2.435
peak=   -3.569 closest distance to " C   ALA A 158 " =    1.315
peak=   -3.566 closest distance to " CA  GLY A 241 " =    2.311
peak=   -3.560 closest distance to " CG1 VAL A 250 " =    2.755
peak=   -3.556 closest distance to " CD2 LEU A 300 " =    2.776
peak=   -3.556 closest distance to " CA  ASP A 298 " =    1.056
peak=   -3.529 closest distance to " N   THR A 157 " =    1.470
peak=   -3.525 closest distance to " O   VAL A 189 " =    2.620
peak=   -3.518 closest distance to " OD1 ASN A 148 " =    1.406
peak=   -3.511 closest distance to " O   HOH Z 350 " =    1.912
peak=   -3.510 closest distance to " ND2 ASN A  45 " =    1.770
peak=   -3.507 closest distance to " O   GLY A 203 " =    2.330
peak=   -3.506 closest distance to " CA  ASP A  27 " =    2.464
peak=   -3.502 closest distance to " OXT GLY A 302 " =    2.925
peak=   -3.494 closest distance to " N   ALA A  43 " =    2.546
peak=   -3.483 closest distance to " CD1 LEU A 228 " =    2.271
peak=   -3.482 closest distance to " ND2 ASN A 187 " =    1.545
peak=   -3.476 closest distance to " NH2 ARG A  79 " =    2.027
peak=   -3.474 closest distance to " C   LEU A 143 " =    1.081
peak=   -3.472 closest distance to " CD  LYS A 289 " =    2.522
peak=   -3.461 closest distance to " CB  ASP A 132 " =    2.311
peak=   -3.453 closest distance to " SD BMET A  47 " =    0.974
peak=   -3.453 closest distance to " C   GLY A  17 " =    1.330
peak=   -3.452 closest distance to " O   HOH Z  13 " =    1.438
peak=   -3.451 closest distance to " CE BMET A  47 " =    1.664
peak=   -3.449 closest distance to " CG  TRP A 266 " =    1.841
peak=   -3.446 closest distance to " O   HOH Z  73 " =    2.183
peak=   -3.443 closest distance to " O   GLY A  80 " =    2.508
peak=   -3.442 closest distance to " CB  ALA A 291 " =    2.200
peak=   -3.440 closest distance to " CG  ASP A  50 " =    2.381
peak=   -3.427 closest distance to " O   HOH Z  52 " =    1.642
peak=   -3.422 closest distance to " CE2 PHE A 218 " =    2.554
peak=   -3.419 closest distance to " C   MET A 188 " =    1.415
peak=   -3.414 closest distance to " CG  ARG A 269 " =    2.397
peak=   -3.411 closest distance to " O   SER A 271 " =    2.238
peak=   -3.393 closest distance to " O   HOH Z 198 " =    2.171
peak=   -3.385 closest distance to " O   HOH Z  60 " =    2.011
peak=   -3.383 closest distance to " O   HOH Z 426 " =    1.630
peak=   -3.380 closest distance to " CG  GLU A 277 " =    1.167
peak=   -3.378 closest distance to " CZ  TYR A 169 " =    1.690
peak=   -3.375 closest distance to " O   HOH Z 241 " =    1.341
peak=   -3.374 closest distance to " O   HOH Z 165 " =    1.848
peak=   -3.373 closest distance to " CD  ARG A 139 " =    1.629
peak=   -3.369 closest distance to " CD1 LEU A 101 " =    2.670
peak=   -3.369 closest distance to " O   TYR A 247 " =    2.856
peak=   -3.367 closest distance to " O   HOH Z 407 " =    3.089
peak=   -3.367 closest distance to " OD1 ASN A 187 " =    1.675
peak=   -3.367 closest distance to " O   HOH Z 103 " =    1.876
peak=   -3.366 closest distance to " NE2 GLN A  88 " =    2.010
peak=   -3.365 closest distance to " CD1 ILE A 239 " =    2.134
peak=   -3.359 closest distance to " CB  ASN A  39 " =    2.251
peak=   -3.358 closest distance to " O   HOH Z 292 " =    4.633
peak=   -3.352 closest distance to " NE2 GLN A  88 " =    1.030
peak=   -3.352 closest distance to " N   ASN A  60 " =    1.294
peak=   -3.348 closest distance to " O   GLY A 196 " =    1.167
peak=   -3.342 closest distance to " CG  HIS A  86 " =    1.025
peak=   -3.342 closest distance to " C   LEU A 222 " =    0.840
peak=   -3.339 closest distance to " N   GLN A  58 " =    1.809
peak=   -3.334 closest distance to " CB  ALA A 291 " =    2.247
peak=   -3.332 closest distance to " CZ2 TRP A  92 " =    2.776
peak=   -3.332 closest distance to " O   HOH Z 201 " =    2.135
peak=   -3.331 closest distance to " CB  PRO A 163 " =    2.537
peak=   -3.327 closest distance to " O   HOH Z 252 " =    4.078
peak=   -3.323 closest distance to " CG  MET A 105 " =    0.945
peak=   -3.323 closest distance to " CA  GLY A 203 " =    2.475
peak=   -3.316 closest distance to " NE2 GLN A 194 " =    1.807
peak=   -3.308 closest distance to " NH2 ARG A  79 " =    1.545
peak=   -3.301 closest distance to " CG1 VAL A 197 " =    2.276
peak=   -3.293 closest distance to " O   SER A  22 " =    2.284
peak=   -3.291 closest distance to " NE2 GLN A 103 " =    1.730
peak=   -3.288 closest distance to " CD1 TYR A 247 " =    2.423
peak=   -3.285 closest distance to " CB  TYR A  15 " =    2.172
peak=   -3.276 closest distance to " O   HOH Z 326 " =    5.156
peak=   -3.275 closest distance to " CD2 TYR A 293 " =    2.002
peak=   -3.274 closest distance to " N   ALA A 248 " =    1.677
peak=   -3.273 closest distance to " OG  SER A  87 " =    1.459
peak=   -3.272 closest distance to " CD1 TRP A 274 " =    0.977
peak=   -3.262 closest distance to " O   HOH Z 134 " =    2.927
peak=   -3.260 closest distance to " CG  PHE A 283 " =    2.667
peak=   -3.256 closest distance to " O   HOH Z 222 " =    1.504
peak=   -3.256 closest distance to " O   LEU A 167 " =    1.496
peak=   -3.250 closest distance to " N   SER A 276 " =    1.361
peak=   -3.249 closest distance to " CD2 LEU A 167 " =    1.843
peak=   -3.248 closest distance to " CD1 PHE A  59 " =    1.990
peak=   -3.248 closest distance to " ND2 ASN A  60 " =    1.867
peak=   -3.246 closest distance to " O   HOH Z  63 " =    1.344
peak=   -3.244 closest distance to " O   HOH Z 149 " =    2.215
peak=   -3.243 closest distance to " NZ  LYS A 119 " =    3.523
peak=   -3.240 closest distance to " OE1 GLN A  88 " =    0.946
peak=   -3.239 closest distance to " O   HOH Z  10 " =    1.468
peak=   -3.238 closest distance to " CB  ASN A  69 " =    1.171
peak=   -3.237 closest distance to " CA  GLY A 133 " =    2.270
peak=   -3.236 closest distance to " O   HOH Z 191 " =    5.444
peak=   -3.235 closest distance to " O   MET A  40 " =    2.788
peak=   -3.229 closest distance to " CD2 LEU A   5 " =    1.258
peak=   -3.229 closest distance to " O   HOH Z 262 " =    2.849
peak=   -3.224 closest distance to " O   HOH Z 431 " =    1.733
peak=   -3.224 closest distance to " N   THR A  52 " =    1.693
peak=   -3.223 closest distance to " CD2 PHE A  61 " =    2.561
peak=   -3.221 closest distance to " O   HOH Z  38 " =    1.608
peak=   -3.217 closest distance to " CD1 PHE A 208 " =    2.455
peak=   -3.212 closest distance to " O   HOH Z 313 " =    1.658
peak=   -3.211 closest distance to " O   HOH Z 123 " =    2.541
peak=   -3.210 closest distance to " C   ASN A 187 " =    1.835
peak=   -3.209 closest distance to " O   HOH Z 275 " =    1.499
peak=   -3.206 closest distance to " CG2 VAL A 296 " =    1.839
peak=   -3.201 closest distance to " O   LYS A 117 " =    1.718
peak=   -3.201 closest distance to " OXT GLY A 302 " =    3.442
peak=   -3.199 closest distance to " O   HOH Z 295 " =    1.561
peak=   -3.197 closest distance to " O   HOH Z 256 " =    1.344
peak=   -3.193 closest distance to " O   HOH Z 357 " =    1.925
peak=   -3.190 closest distance to " C   ASP A 231 " =    2.538
peak=   -3.189 closest distance to " OG BSER A 134 " =    1.807
peak=   -3.184 closest distance to " CZ  PHE A  59 " =    1.553
peak=   -3.182 closest distance to " O   HOH Z  43 " =    1.779
peak=   -3.180 closest distance to " O   ILE A 106 " =    1.986
peak=   -3.178 closest distance to " CA  GLY A  98 " =    1.917
peak=   -3.177 closest distance to " CB  GLN A  11 " =    1.767
peak=   -3.172 closest distance to " CD2 TYR A 247 " =    2.346
peak=   -3.172 closest distance to " O   ALA A  51 " =    1.362
peak=   -3.172 closest distance to " NE2 GLN A 278 " =    1.946
peak=   -3.172 closest distance to " O   HOH Z 128 " =    2.584
peak=   -3.169 closest distance to " O   HOH Z 265 " =    1.921
peak=   -3.166 closest distance to " O   ARG A 145 " =    1.674
peak=   -3.165 closest distance to " N   ALA A 248 " =    2.572
peak=   -3.164 closest distance to " O   HOH Z 133 " =    1.419
peak=   -3.161 closest distance to " CG2 VAL A 189 " =    1.989
peak=   -3.160 closest distance to " CG1 VAL A 230 " =    1.953
peak=   -3.149 closest distance to " N   SER A 212 " =    1.927
peak=   -3.139 closest distance to " OG ASER A 134 " =    1.323
peak=   -3.138 closest distance to " CD  PRO A 213 " =    2.099
peak=   -3.133 closest distance to " CG  LEU A 228 " =    0.990
peak=   -3.128 closest distance to " O   HOH Z 353 " =    2.080
peak=   -3.119 closest distance to " OH  TYR A 214 " =    1.218
peak=   -3.116 closest distance to " CB  ASP A 171 " =    2.271
peak=   -3.115 closest distance to " O   HOH Z  90 " =    1.617
peak=   -3.115 closest distance to " OG  SER A 206 " =    1.727
peak=   -3.114 closest distance to " O   HOH Z 281 " =    2.654
peak=   -3.110 closest distance to " O   HOH Z 106 " =    1.895
peak=   -3.107 closest distance to " CG1 VAL A 296 " =    1.318
peak=   -3.103 closest distance to " O   PRO A 198 " =    1.343
peak=   -3.100 closest distance to " CD  PRO A 243 " =    2.109
peak=   -3.092 closest distance to " CD1 ILE A 151 " =    2.392
peak=   -3.081 closest distance to " CB  ASP A 132 " =    2.349
peak=   -3.079 closest distance to " CB  TYR A 172 " =    2.472
peak=   -3.061 closest distance to " CB  TRP A  85 " =    2.516
peak=   -3.056 closest distance to " O   HOH Z 139 " =    3.071
peak=   -3.053 closest distance to " OG  SER A  62 " =    1.798
peak=   -3.043 closest distance to " CG2BVAL A  41 " =    1.726
peak=   -3.037 closest distance to " O   HOH Z 313 " =    1.152
peak=   -3.036 closest distance to " O   HOH Z 234 " =    4.215
peak=   -3.029 closest distance to " O   HOH Z 193 " =    2.029

================= 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    :  0.4094 0.3944   6.191290e+00   6.158535e+00
   1_bss:  0.4016 0.3791   6.188430e+00   6.140305e+00
   1_xyz:  0.2831 0.3013   5.919577e+00   5.965370e+00
   1_adp:  0.2048 0.2325   5.619492e+00   5.743345e+00
   1_occ:  0.2039 0.2325   5.617631e+00   5.744729e+00
   2_bss:  0.1973 0.2254   5.612769e+00   5.736873e+00
   2_xyz:  0.1463 0.1803   5.343557e+00   5.517236e+00
   2_adp:  0.1373 0.1728   5.291855e+00   5.476030e+00
   2_occ:  0.1373 0.1729   5.291873e+00   5.476463e+00
   3_bss:  0.1372 0.1730   5.293050e+00   5.477757e+00
   3_xyz:  0.1219 0.1616   5.200001e+00   5.415690e+00
   3_adp:  0.1175 0.1608   5.180298e+00   5.411402e+00
   3_occ:  0.1174 0.1609   5.180313e+00   5.411544e+00
   4_bss:  0.1174 0.1609   5.179402e+00   5.410846e+00
   4_xyz:  0.1140 0.1596   5.163301e+00   5.405663e+00
   4_adp:  0.1147 0.1574   5.158290e+00   5.391192e+00
   4_occ:  0.1146 0.1572   5.157838e+00   5.391263e+00
   5_bss:  0.1146 0.1572   5.157838e+00   5.391263e+00
   5_xyz:  0.1138 0.1572   5.154340e+00   5.390990e+00
   5_adp:  0.1133 0.1576   5.154254e+00   5.394201e+00
   5_occ:  0.1133 0.1576   5.154173e+00   5.394230e+00
   5_bss:  0.1135 0.1574   5.155300e+00   5.393558e+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:  0.343  18.521   7.603   8.116   8.879   0.000   0.000   0.000
   1_xyz:  0.343  18.521   7.603   8.116   8.879   0.000   0.000   0.000
   1_adp:  0.343  18.521   7.603   8.116   8.879   0.000   0.000   0.000
   1_occ:  0.343  18.521   7.603   8.116   8.879   0.000   0.000   0.000
   2_bss:  0.343  50.001   4.079   4.341   5.462   0.000   0.000   0.000
   2_xyz:  0.343  50.001   4.079   4.341   5.462   0.000   0.000   0.000
   2_adp:  0.343  50.001   4.079   4.341   5.462   0.000   0.000   0.000
   2_occ:  0.343  50.001   4.079   4.341   5.462   0.000   0.000   0.000
   3_bss:  0.343  50.001   3.497   3.762   4.923   0.000   0.000   0.000
   3_xyz:  0.343  50.001   3.497   3.762   4.923   0.000   0.000   0.000
   3_adp:  0.343  50.001   3.497   3.762   4.923   0.000   0.000   0.000
   3_occ:  0.343  50.001   3.497   3.762   4.923   0.000   0.000   0.000
   4_bss:  0.327  50.001   3.497   3.762   4.923   0.000   0.000   0.000
   4_xyz:  0.327  50.001   3.497   3.762   4.923   0.000   0.000   0.000
   4_adp:  0.327  50.001   3.497   3.762   4.923   0.000   0.000   0.000
   4_occ:  0.327  50.001   3.497   3.762   4.923   0.000   0.000   0.000
   5_bss:  0.327  50.001   3.497   3.762   4.923   0.000   0.000   0.000
   5_xyz:  0.327  50.001   3.497   3.762   4.923   0.000   0.000   0.000
   5_adp:  0.327  50.001   3.497   3.762   4.923   0.000   0.000   0.000
   5_occ:  0.327  50.001   3.497   3.762   4.923   0.000   0.000   0.000
   5_bss:  0.323  52.412  -0.564  -0.298   0.863   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  42.444 0.6155  0.6720    43526.101
   1_bss:  41.699 0.6228  0.8697    40750.439
   1_xyz:  31.779 0.7373  0.9959    24342.659
   1_adp:  22.185 0.8415  1.0779    13476.126
   1_occ:  22.211 0.8412  1.0772    13491.977
   2_bss:  21.910 0.8441  0.9488    13159.564
   2_xyz:  16.713 0.8923  0.9838     8204.240
   2_adp:  15.675 0.9017  0.9925     7609.207
   2_occ:  15.688 0.9015  0.9924     7612.085
   3_bss:  15.723 0.9013  0.9713     7662.593
   3_xyz:  14.439 0.9117  0.9755     6719.231
   3_adp:  14.356 0.9125  0.9739     6632.472
   3_occ:  14.357 0.9125  0.9738     6632.916
   4_bss:  14.344 0.9126  0.9737     6614.593
   4_xyz:  14.205 0.9138  0.9741     6550.139
   4_adp:  13.873 0.9165  0.9766     6361.263
   4_occ:  13.880 0.9164  0.9765     6361.950
   5_bss:  13.880 0.9164  0.9765     6361.950
   5_xyz:  13.867 0.9166  0.9759     6361.782
   5_adp:  13.944 0.9160  0.9743     6402.158
   5_occ:  13.944 0.9160  0.9743     6401.990
   5_bss:  13.964 0.9158  0.9732     6392.704
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.093   5.3993e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.093   5.3993e+01
   1_xyz:   1.415  0.010  0.097 17.897  0.005  4.124   1.0601e-01
   1_adp:   1.415  0.010  0.097 17.897  0.005  4.124   1.0601e-01
   1_occ:   1.415  0.010  0.097 17.897  0.005  4.124   1.0601e-01
   2_bss:   1.415  0.010  0.097 17.897  0.005  4.124   1.0601e-01
   2_xyz:   0.939  0.006  0.072 16.333  0.003  4.124   5.7374e-02
   2_adp:   0.939  0.006  0.072 16.333  0.003  4.124   5.7374e-02
   2_occ:   0.939  0.006  0.072 16.333  0.003  4.124   5.7374e-02
   3_bss:   0.939  0.006  0.072 16.333  0.003  4.124   5.7374e-02
   3_xyz:   0.986  0.007  0.080 16.121  0.003  4.132   6.1204e-02
   3_adp:   0.986  0.007  0.080 16.121  0.003  4.132   6.1204e-02
   3_occ:   0.986  0.007  0.080 16.121  0.003  4.132   6.1204e-02
   4_bss:   0.986  0.007  0.080 16.121  0.003  4.132   6.1204e-02
   4_xyz:   0.968  0.007  0.079 15.740  0.003  4.135   5.8969e-02
   4_adp:   0.968  0.007  0.079 15.740  0.003  4.135   5.8969e-02
   4_occ:   0.968  0.007  0.079 15.740  0.003  4.135   5.8969e-02
   5_bss:   0.968  0.007  0.079 15.740  0.003  4.135   5.8969e-02
   5_xyz:   0.954  0.007  0.078 15.551  0.003  4.137   5.7689e-02
   5_adp:   0.954  0.007  0.078 15.551  0.003  4.137   5.7689e-02
   5_occ:   0.954  0.007  0.078 15.551  0.003  4.137   5.7689e-02
   5_bss:   0.954  0.007  0.078 15.551  0.003  4.137   5.7689e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0011e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0011e+00
   1_xyz:  10.968  0.121  0.409 89.596  0.035  2.273   7.7467e-02
   1_adp:  10.968  0.121  0.409 89.596  0.035  2.273   7.7467e-02
   1_occ:  10.968  0.121  0.409 89.596  0.035  2.273   7.7467e-02
   2_bss:  10.968  0.121  0.409 89.596  0.035  2.273   7.7467e-02
   2_xyz:   6.734  0.052  0.353 83.410  0.036  2.341   3.2440e-02
   2_adp:   6.734  0.052  0.353 83.410  0.036  2.341   3.2440e-02
   2_occ:   6.734  0.052  0.353 83.410  0.036  2.341   3.2440e-02
   3_bss:   6.734  0.052  0.353 83.410  0.036  2.341   3.2440e-02
   3_xyz:   8.642  0.056  0.494 83.228  0.036  2.359   3.8914e-02
   3_adp:   8.642  0.056  0.494 83.228  0.036  2.359   3.8914e-02
   3_occ:   8.642  0.056  0.494 83.228  0.036  2.359   3.8914e-02
   4_bss:   8.642  0.056  0.494 83.228  0.036  2.359   3.8914e-02
   4_xyz:   7.225  0.040  0.504 82.907  0.036  2.371   3.5988e-02
   4_adp:   7.225  0.040  0.504 82.907  0.036  2.371   3.5988e-02
   4_occ:   7.225  0.040  0.504 82.907  0.036  2.371   3.5988e-02
   5_bss:   7.225  0.040  0.504 82.907  0.036  2.371   3.5988e-02
   5_xyz:   7.113  0.043  0.477 82.971  0.037  2.383   3.3703e-02
   5_adp:   7.113  0.043  0.477 82.971  0.037  2.383   3.3703e-02
   5_occ:   7.113  0.043  0.477 82.971  0.037  2.383   3.3703e-02
   5_bss:   7.113  0.043  0.477 82.971  0.037  2.383   3.3703e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00
   1_bss:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_xyz:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_adp:  55.46   0.00  10.04  55.46   0.00   6.77  55.23   0.00  27.89
   1_occ:  55.46   0.00  10.04  55.46   0.00   6.77  55.23   0.00  27.89
   2_bss:  55.46   0.00  10.04  55.46   0.00   6.77  55.23   0.00  27.89
   2_xyz:  55.46   0.00  10.04  55.46   0.00   6.77  55.23   0.00  27.89
   2_adp:  57.00   0.00  10.38  57.00   0.00   6.79  56.34   0.00  29.95
   2_occ:  57.00   0.00  10.38  57.00   0.00   6.79  56.34   0.00  29.95
   3_bss:  57.00   0.00  10.38  57.00   0.00   6.79  56.34   0.00  29.95
   3_xyz:  57.00   0.00  10.38  57.00   0.00   6.79  56.34   0.00  29.95
   3_adp:  77.04   0.00  11.44  77.04   0.00   7.11  76.40   0.00  35.01
   3_occ:  77.04   0.00  11.44  77.04   0.00   7.11  76.40   0.00  35.01
   4_bss:  77.04   0.00  11.44  77.04   0.00   7.11  76.40   0.00  35.01
   4_xyz:  77.04   0.00  11.44  77.04   0.00   7.11  76.40   0.00  35.01
   4_adp:  77.06   0.00  11.28  77.06   0.00   7.07  74.42   0.58  34.20
   4_occ:  77.06   0.00  11.28  77.06   0.00   7.07  74.42   0.58  34.20
   5_bss:  77.06   0.00  11.28  77.06   0.00   7.07  74.42   0.58  34.20
   5_xyz:  77.06   0.00  11.28  77.06   0.00   7.07  74.42   0.58  34.20
   5_adp:  77.91   0.00  11.23  77.91   0.00   7.06  73.90   0.52  33.96
   5_occ:  77.91   0.00  11.23  77.91   0.00   7.06  73.90   0.52  33.96
   5_bss:  81.97   4.06  15.30  81.97   4.06  11.12  77.96   4.58  38.02
------------------------------------------------------------------------
 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:    1.166    0.025    0.395
   1_adp:    1.166    0.025    0.395
   1_occ:    1.166    0.025    0.395
   2_bss:    1.166    0.025    0.395
   2_xyz:    1.453    0.032    0.454
   2_adp:    1.453    0.032    0.454
   2_occ:    1.453    0.032    0.454
   3_bss:    1.453    0.032    0.454
   3_xyz:    1.438    0.049    0.479
   3_adp:    1.438    0.049    0.479
   3_occ:    1.438    0.049    0.479
   4_bss:    1.438    0.049    0.479
   4_xyz:    1.541    0.036    0.488
   4_adp:    1.541    0.036    0.488
   4_occ:    1.541    0.036    0.488
   5_bss:    1.541    0.036    0.488
   5_xyz:    1.578    0.026    0.495
   5_adp:    1.578    0.026    0.495
   5_occ:    1.578    0.026    0.495
   5_bss:    1.578    0.026    0.495
------------------------------------------------------------------------

CPU time actual refinement: 313.11


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_787/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_787/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_787/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_787/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_787/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 312.96 
  Macro-tasks:
    bulk solvent and scale       = 40.61  
    individual site refinement   = 123.14 
    weights calculation          = 30.93  
    collect and process          = 6.51   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 201.29 
  Micro-tasks:
    mask                            = 1.72   
    f_calc                          = 94.44  
    alpha_beta                      = 8.15   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 104.58 
    fmodel                         = 7.02   
    r_factors                      = 0.19   
    phase_errors                   = 11.10  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 228.64 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.438 micro seconds
Total CPU time: 5.44 minutes
from_scatterers_fft:    647 calls, 94.08 s
gradients_fft:          591 calls, 91.51 s

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

# Date 2008-01-16 Time 02:25:47 PST -0800 (1200479147.08 s)
Start R-work = 0.4094, R-free = 0.3944 (no bulk solvent and anisotropic scale)
Final R-work = 0.1307, R-free = 0.1735 (no bulk solvent and anisotropic scale)

Start R-work = 0.4016, R-free = 0.3791
Final R-work = 0.1135, R-free = 0.1574