# Date 2008-01-16 Time 02:20:56 PST -0800 (1200478856.32 s)
#phil __OFF__

Command line arguments: "../793.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 28854
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 793

-------------------------------------------------------------------------------
  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, 47.1647, 84.6622, 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: 3.25, 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, 47.1647, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9645 1.9613
Completeness in resolution range: 0.940558
Completeness with d_max=infinity: 0.937721

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9645
                             d_min =   1.9613

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, 47.1647, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9645 1.9613
Completeness in resolution range: 0.940558
Completeness with d_max=infinity: 0.937721

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9649 -  4.1973 [2195/2224]  1977   218   9.9%
  bin  2:  4.1973 -  3.3438 [2089/2112]  1881   208  10.0%
  bin  3:  3.3438 -  2.9247 [2067/2089]  1856   211  10.2%
  bin  4:  2.9247 -  2.6589 [2061/2080]  1862   199   9.7%
  bin  5:  2.6589 -  2.4692 [2052/2081]  1841   211  10.3%
  bin  6:  2.4692 -  2.3242 [2030/2072]  1829   201   9.9%
  bin  7:  2.3242 -  2.2082 [2011/2047]  1810   201  10.0%
  bin  8:  2.2082 -  2.1124 [2004/2041]  1804   200  10.0%
  bin  9:  2.1124 -  2.0312 [2009/2041]  1804   205  10.2%
  bin 10:  2.0312 -  1.9613 [1071/2040]   966   105   9.8%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_793/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.70 -     2.34: 24
        2.34 -     2.98: 1795
        2.98 -     3.62: 4602
        3.62 -     4.26: 9191
        4.26 -     4.90: 12832
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.696 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.740 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " NH2 ARG A 259 " - " O   HOH Z   3 "  1.992 3.120 -x,y-1/2,-z+1/2
  " O   HOH Z  70 " - " O   HOH Z 294 "  2.003 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28439 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_793/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_793/model_refine_001.geo

CPU time processing inputs: 9.12


============================ 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 47.16465 84.6622 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4531   r_free= 0.4531   ksol= 0.00   Bsol= 0.00   scale= 0.813    |
|                                                                             |
| 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:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.253335                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9649 -  4.6818 0.99   1418  158 0.3748 0.3684      6.5517      6.5491|
|  2:  4.6818 -  3.7351 0.99   1367  147 0.3623 0.3604      6.7133      6.7087|
|  3:  3.7351 -  3.2686 0.99   1338  157 0.4072 0.3870      6.6119      6.6596|
|  4:  3.2686 -  2.9723 0.99   1336  145 0.4235 0.4358      6.4726      6.4696|
|  5:  2.9723 -  2.7607 0.99   1316  145 0.4718 0.4984      6.3416      6.3578|
|  6:  2.7607 -  2.5988 0.98   1319  146 0.4713 0.5132      6.2393      6.1851|
|  7:  2.5988 -  2.4692 0.99   1323  149 0.4949 0.4265      6.2451      6.1453|
|  8:  2.4692 -  2.3622 0.99   1291  145 0.5092 0.5264      6.1382      6.1751|
|  9:  2.3622 -  2.2716 0.98   1320  148 0.5063 0.4958      6.1156      6.1161|
| 10:  2.2716 -  2.1934 0.98   1283  143 0.5128 0.5090      6.0855      6.0948|
| 11:  2.1934 -  2.1250 0.98   1286  139 0.5048 0.5099      6.0221      6.0266|
| 12:  2.1250 -  2.0645 0.99   1290  143 0.5104 0.5575      5.9523      5.9962|
| 13:  2.0645 -  2.0102 0.97   1290  145 0.5302 0.4986      5.8674      5.8255|
| 14:  2.0102 -  1.9613 0.35    453   49 0.5378 0.5810      5.8516      5.7637|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9649 -  4.6818  1418   158  0.72  32.16   0.81     0.74      62685.04|
|  2:  4.6818 -  3.7351  1367   147  0.73  32.44   0.90     0.80      88997.57|
|  3:  3.7351 -  3.2686  1338   157  0.64  40.64   0.85     0.76      98225.03|
|  4:  3.2686 -  2.9723  1336   145  0.56  47.19   0.83     0.66      89686.20|
|  5:  2.9723 -  2.7607  1316   145  0.46  54.91   0.76     0.56      77121.58|
|  6:  2.7607 -  2.5988  1319   146  0.45  55.78   0.76     0.53      64246.15|
|  7:  2.5988 -  2.4692  1323   149  0.47  54.74   0.75     0.52      56031.13|
|  8:  2.4692 -  2.3622  1291   145  0.45  56.23   0.72     0.52      50950.22|
|  9:  2.3622 -  2.2716  1320   148  0.43  57.87   0.75     0.50      47770.72|
| 10:  2.2716 -  2.1934  1283   143  0.39  61.04   0.77     0.46      47434.64|
| 11:  2.1934 -  2.1250  1286   139  0.33  64.97   0.78     0.41      46056.75|
| 12:  2.1250 -  2.0645  1290   143  0.28  69.36   0.76     0.35      45947.59|
| 13:  2.0645 -  2.0102  1290   145  0.26  70.43   0.74     0.34      39112.73|
| 14:  2.0102 -  1.9613   453    49  0.32  65.83   0.71     0.37      30020.42|
|alpha:            min =        0.34 max =            0.80 mean =         0.55|
|beta:             min =    30020.42 max =        98225.03 mean =     62076.21|
|figures of merit: min =        0.00 max =            1.00 mean =         0.47|
|phase err.(work): min =        0.00 max =           89.99 mean =        53.69|
|phase err.(test): min =        0.00 max =           89.70 mean =        53.92|
|-----------------------------------------------------------------------------|

============================== 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 = 11.151205             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 77.640   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.961605              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.254   (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:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       24 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      167 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      706 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1510 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2656 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3946 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5073 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6624 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7731 |
|-----------------------------------------------------------------------------|
|-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 |       53.549 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.090    4.900  1.196 |       1.830 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.801)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 11.801)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4603   r_free= 0.4594   ksol= 0.00   Bsol= 0.00   scale= 0.782    |
|                                                                             |
| 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:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.256815                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4449   r_free= 0.4411   ksol= 0.36   Bsol= 20.00   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.04,8.13,9.38,0.00,0.00,0.00); trace/3= 8.18                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.252921                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.334962              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.044   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.888619              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.231   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4449      final r-factor (work) = 0.3539          |
| start r-factor (free) = 0.4411      final r-factor (free) = 0.3855          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 82.7489 = 9.33 * 0.50 * 6.2560 + 1.00 * 53.5492                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.7827 = 9.33 * 0.50 * 6.1386 + 1.00 * 0.1311                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3539      final r-factor (work) = 0.3024          |
| start r-factor (free) = 0.3855      final r-factor (free) = 0.3553          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.4692 = 0.89 * 1.00 * 6.1386 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.3631 = 0.89 * 1.00 * 6.0204 + 1.00 * 0.0133                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.801)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    73.19   11.78    None  None   None       |
|    all(noH): 2823   0      0.00    73.19   11.78    None  None   None       |
|    Sol.    : 438    0      0.00    73.19   27.27    None  None   None       |
|    Mac.    : 2385   0      0.00    61.14   8.93     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 -   7.319: 1296   |   5:    36.597 -  43.917:   90        |
|      1:     7.319 -  14.639:  743   |   6:    43.917 -  51.236:   43        |
|      2:    14.639 -  21.958:  352   |   7:    51.236 -  58.555:   16        |
|      3:    21.958 -  29.278:  171   |   8:    58.555 -  65.875:    5        |
|      4:    29.278 -  36.597:  106   |   9:    65.875 -  73.194:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3024 r_free = 0.3553             target_work(ml) = 5.990         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3021 r_free = 0.3553             target_work(ml) = 5.989         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3021   r_free= 0.3553   ksol= 0.36   Bsol= 20.00   scale= 1.096   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.04,8.13,9.38,0.00,0.00,0.00); trace/3= 8.18                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 5.989062                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2980   r_free= 0.3503   ksol= 0.34   Bsol= 37.30   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.62,4.40,6.21,0.00,0.00,0.00); trace/3= 4.74                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.44 A                  |
| x-ray target function (ml) for work reflections: 5.988106                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.463159              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.200   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.445461              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 127.951  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2980      final r-factor (work) = 0.2149          |
| start r-factor (free) = 0.3503      final r-factor (free) = 0.2721          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.5641 = 4.46 * 0.50 * 6.0195 + 1.00 * 0.1311                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.1265 = 4.46 * 0.50 * 5.8520 + 1.00 * 0.0673                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2149      final r-factor (work) = 0.1962          |
| start r-factor (free) = 0.2721      final r-factor (free) = 0.2510          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6202 = 0.45 * 1.00 * 5.8520 + 1.00 * 0.0133                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5475 = 0.45 * 1.00 * 5.6731 + 1.00 * 0.0203                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.801)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    74.04   12.16    None  None   None       |
|    all(noH): 2823   0      0.00    74.04   12.16    None  None   None       |
|    Sol.    : 438    0      1.21    74.04   32.04    None  None   None       |
|    Mac.    : 2385   0      0.00    65.06   8.51     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.404: 1401   |   5:    37.019 -  44.422:  110        |
|      1:     7.404 -  14.808:  732   |   6:    44.422 -  51.826:   69        |
|      2:    14.808 -  22.211:  221   |   7:    51.826 -  59.230:   20        |
|      3:    22.211 -  29.615:  130   |   8:    59.230 -  66.634:    7        |
|      4:    29.615 -  37.019:  132   |   9:    66.634 -  74.037:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1962 r_free = 0.2510             target_work(ml) = 5.634         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1961 r_free = 0.2513             target_work(ml) = 5.633         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1961   r_free= 0.2513   ksol= 0.34   Bsol= 37.30   scale= 1.045   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.62,4.40,6.21,0.00,0.00,0.00); trace/3= 4.74                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.632995                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1947   r_free= 0.2487   ksol= 0.32   Bsol= 37.30   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.41,2.92,3.86,0.00,0.00,0.00); trace/3= 3.06                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.630909                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.458198              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.046  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.862496              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 93.757   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1947      final r-factor (work) = 0.1447          |
| start r-factor (free) = 0.2487      final r-factor (free) = 0.1917          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.8896 = 3.46 * 0.50 * 5.6806 + 1.00 * 0.0673                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.5911 = 3.46 * 0.50 * 5.5113 + 1.00 * 0.0615                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1447      final r-factor (work) = 0.1337          |
| start r-factor (free) = 0.1917      final r-factor (free) = 0.1811          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7651 = 0.86 * 1.00 * 5.5113 + 1.00 * 0.0116                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6060 = 0.86 * 1.00 * 5.3260 + 1.00 * 0.0124                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.801)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.38   12.81    None  None   None       |
|    all(noH): 2823   0      0.00    79.38   12.81    None  None   None       |
|    Sol.    : 438    0      2.09    73.78   36.37    None  None   None       |
|    Mac.    : 2385   0      0.00    79.38   8.48     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 -   7.938: 1525   |   5:    39.688 -  47.625:  113        |
|      1:     7.938 -  15.875:  670   |   6:    47.625 -  55.563:   76        |
|      2:    15.875 -  23.813:  177   |   7:    55.563 -  63.501:   37        |
|      3:    23.813 -  31.750:   95   |   8:    63.501 -  71.438:   12        |
|      4:    31.750 -  39.688:  111   |   9:    71.438 -  79.376:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1337 r_free = 0.1811             target_work(ml) = 5.297         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1336 r_free = 0.1810             target_work(ml) = 5.296         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1336   r_free= 0.1810   ksol= 0.32   Bsol= 37.30   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.41,2.92,3.86,0.00,0.00,0.00); trace/3= 3.06                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.296158                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1335   r_free= 0.1807   ksol= 0.32   Bsol= 37.30   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.18,2.55,3.02,0.00,0.00,0.00); trace/3= 2.58                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.296762                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.456371              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 115.468  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.797804              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 138.177  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1335      final r-factor (work) = 0.1194          |
| start r-factor (free) = 0.1807      final r-factor (free) = 0.1646          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6053 = 2.46 * 0.50 * 5.3280 + 1.00 * 0.0615                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5152 = 2.46 * 0.50 * 5.2538 + 1.00 * 0.0625                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1194      final r-factor (work) = 0.1165          |
| start r-factor (free) = 0.1646      final r-factor (free) = 0.1621          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2038 = 0.80 * 1.00 * 5.2538 + 1.00 * 0.0123                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1556 = 0.80 * 1.00 * 5.1931 + 1.00 * 0.0125                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.801)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.04   12.80    None  None   None       |
|    all(noH): 2823   0      0.00    91.04   12.80    None  None   None       |
|    Sol.    : 438    0      1.38    76.71   36.53    None  None   None       |
|    Mac.    : 2385   0      0.00    91.04   8.44     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 -   9.104: 1706   |   5:    45.519 -  54.622:   76        |
|      1:     9.104 -  18.208:  570   |   6:    54.622 -  63.726:   52        |
|      2:    18.208 -  27.311:  152   |   7:    63.726 -  72.830:   20        |
|      3:    27.311 -  36.415:  115   |   8:    72.830 -  81.934:    8        |
|      4:    36.415 -  45.519:  121   |   9:    81.934 -  91.037:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1165 r_free = 0.1621             target_work(ml) = 5.186         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1163 r_free = 0.1622             target_work(ml) = 5.186         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1163   r_free= 0.1622   ksol= 0.32   Bsol= 37.30   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.18,2.55,3.02,0.00,0.00,0.00); trace/3= 2.58                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.186005                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1163   r_free= 0.1622   ksol= 0.32   Bsol= 37.30   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.18,2.55,3.02,0.00,0.00,0.00); trace/3= 2.58                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.186005                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.442657              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 139.232  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.484750              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.508  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1163      final r-factor (work) = 0.1160          |
| start r-factor (free) = 0.1622      final r-factor (free) = 0.1611          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8083 = 1.44 * 0.50 * 5.1928 + 1.00 * 0.0625                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.7927 = 1.44 * 0.50 * 5.1858 + 1.00 * 0.0521                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1160      final r-factor (work) = 0.1158          |
| start r-factor (free) = 0.1611      final r-factor (free) = 0.1599          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5263 = 0.48 * 1.00 * 5.1858 + 1.00 * 0.0125                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5240 = 0.48 * 1.00 * 5.1826 + 1.00 * 0.0118                               |
|-----------------------------------------------------------------------------|
| number of iterations = 19      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.801)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.21   12.63    None  None   None       |
|    all(noH): 2823   0      0.00    92.21   12.63    None  None   None       |
|    Sol.    : 438    0      1.31    76.07   35.93    None  None   None       |
|    Mac.    : 2385   0      0.00    92.21   8.35     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 -   9.221: 1736   |   5:    46.105 -  55.326:   74        |
|      1:     9.221 -  18.442:  555   |   6:    55.326 -  64.547:   41        |
|      2:    18.442 -  27.663:  147   |   7:    64.547 -  73.768:   17        |
|      3:    27.663 -  36.884:  120   |   8:    73.768 -  82.989:    7        |
|      4:    36.884 -  46.105:  123   |   9:    82.989 -  92.210:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1158 r_free = 0.1599             target_work(ml) = 5.179         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1158 r_free = 0.1599             target_work(ml) = 5.179         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1158   r_free= 0.1599   ksol= 0.32   Bsol= 37.30   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.18,2.55,3.02,0.00,0.00,0.00); trace/3= 2.58                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.178820                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9649 -  4.6818 0.99   1418  158 0.0981 0.1242      5.3766       5.516|
|  2:  4.6818 -  3.7351 0.99   1367  147 0.0879 0.1138      5.4392      5.6564|
|  3:  3.7351 -  3.2686 0.99   1338  157 0.1077 0.1585      5.4838      5.8648|
|  4:  3.2686 -  2.9723 0.99   1336  145 0.1257 0.1477      5.4752      5.5969|
|  5:  2.9723 -  2.7607 0.99   1316  145 0.1354 0.1719      5.3441      5.5052|
|  6:  2.7607 -  2.5988 0.98   1319  146 0.1299 0.1976      5.2517      5.5182|
|  7:  2.5988 -  2.4692 0.99   1323  149 0.1292 0.1745      5.2028      5.4327|
|  8:  2.4692 -  2.3622 0.99   1291  145 0.1225 0.1701      5.0971      5.3015|
|  9:  2.3622 -  2.2716 0.98   1320  148 0.1220 0.1819      5.0637      5.3214|
| 10:  2.2716 -  2.1934 0.98   1283  143 0.1201 0.1799      5.0094      5.2715|
| 11:  2.1934 -  2.1250 0.98   1286  139 0.1189 0.1782      4.9643      5.2902|
| 12:  2.1250 -  2.0645 0.99   1290  143 0.1159 0.1758      4.8921      5.1221|
| 13:  2.0645 -  2.0102 0.97   1290  145 0.1239 0.1836      4.8263      5.0694|
| 14:  2.0102 -  1.9613 0.35    453   49 0.1118 0.1867      4.7142      4.9541|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9649 -  4.6818  1418   158  0.94   8.76   0.98     0.96       6994.18|
|  2:  4.6818 -  3.7351  1367   147  0.95   8.01   1.02     1.00       8769.22|
|  3:  3.7351 -  3.2686  1338   157  0.93  11.47   1.03     1.03      10597.10|
|  4:  3.2686 -  2.9723  1336   145  0.92  14.00   1.01     0.99      10611.67|
|  5:  2.9723 -  2.7607  1316   145  0.89  16.59   0.99     0.96       8581.84|
|  6:  2.7607 -  2.5988  1319   146  0.89  16.70   0.99     0.97       7618.55|
|  7:  2.5988 -  2.4692  1323   149  0.90  15.97   0.99     0.96       6630.51|
|  8:  2.4692 -  2.3622  1291   145  0.90  16.38   0.99     0.96       5756.53|
|  9:  2.3622 -  2.2716  1320   148  0.90  16.43   1.01     0.98       5373.97|
| 10:  2.2716 -  2.1934  1283   143  0.90  16.24   1.00     0.97       4839.06|
| 11:  2.1934 -  2.1250  1286   139  0.90  16.68   1.00     0.96       4548.26|
| 12:  2.1250 -  2.0645  1290   143  0.91  15.69   1.00     0.99       4067.76|
| 13:  2.0645 -  2.0102  1290   145  0.89  17.10   1.01     1.00       3583.98|
| 14:  2.0102 -  1.9613   453    49  0.89  16.73   1.00     0.96       2927.92|
|alpha:            min =        0.96 max =            1.03 mean =         0.98|
|beta:             min =     2927.92 max =        10611.67 mean =      6701.99|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.96 mean =        14.60|
|phase err.(test): min =        0.00 max =           89.77 mean =        14.13|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1158   r_free= 0.1599   ksol= 0.32   Bsol= 39.89   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.41,-0.03,0.43,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.178820                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1158   r_free= 0.1599   ksol= 0.32   Bsol= 39.89   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.41,-0.03,0.43,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.178820                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9649 -  4.6818 0.99   1418  158 0.0981 0.1242      5.3766       5.516|
|  2:  4.6818 -  3.7351 0.99   1367  147 0.0879 0.1138      5.4392      5.6564|
|  3:  3.7351 -  3.2686 0.99   1338  157 0.1077 0.1585      5.4838      5.8648|
|  4:  3.2686 -  2.9723 0.99   1336  145 0.1257 0.1477      5.4752      5.5969|
|  5:  2.9723 -  2.7607 0.99   1316  145 0.1354 0.1719      5.3441      5.5052|
|  6:  2.7607 -  2.5988 0.98   1319  146 0.1299 0.1976      5.2517      5.5182|
|  7:  2.5988 -  2.4692 0.99   1323  149 0.1292 0.1745      5.2028      5.4327|
|  8:  2.4692 -  2.3622 0.99   1291  145 0.1225 0.1701      5.0971      5.3015|
|  9:  2.3622 -  2.2716 0.98   1320  148 0.1220 0.1819      5.0637      5.3214|
| 10:  2.2716 -  2.1934 0.98   1283  143 0.1201 0.1799      5.0094      5.2715|
| 11:  2.1934 -  2.1250 0.98   1286  139 0.1189 0.1782      4.9643      5.2902|
| 12:  2.1250 -  2.0645 0.99   1290  143 0.1159 0.1758      4.8921      5.1221|
| 13:  2.0645 -  2.0102 0.97   1290  145 0.1239 0.1836      4.8263      5.0694|
| 14:  2.0102 -  1.9613 0.35    453   49 0.1118 0.1867      4.7142      4.9541|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9649 -  4.6818  1418   158  0.94   8.76   0.98     0.96       6994.18|
|  2:  4.6818 -  3.7351  1367   147  0.95   8.01   1.02     1.00       8769.22|
|  3:  3.7351 -  3.2686  1338   157  0.93  11.47   1.03     1.03      10597.10|
|  4:  3.2686 -  2.9723  1336   145  0.92  14.00   1.01     0.99      10611.67|
|  5:  2.9723 -  2.7607  1316   145  0.89  16.59   0.99     0.96       8581.84|
|  6:  2.7607 -  2.5988  1319   146  0.89  16.70   0.99     0.97       7618.55|
|  7:  2.5988 -  2.4692  1323   149  0.90  15.97   0.99     0.96       6630.51|
|  8:  2.4692 -  2.3622  1291   145  0.90  16.38   0.99     0.96       5756.53|
|  9:  2.3622 -  2.2716  1320   148  0.90  16.43   1.01     0.98       5373.97|
| 10:  2.2716 -  2.1934  1283   143  0.90  16.24   1.00     0.97       4839.06|
| 11:  2.1934 -  2.1250  1286   139  0.90  16.68   1.00     0.96       4548.26|
| 12:  2.1250 -  2.0645  1290   143  0.91  15.69   1.00     0.99       4067.76|
| 13:  2.0645 -  2.0102  1290   145  0.89  17.10   1.01     1.00       3583.98|
| 14:  2.0102 -  1.9613   453    49  0.89  16.73   1.00     0.96       2927.92|
|alpha:            min =        0.96 max =            1.03 mean =         0.98|
|beta:             min =     2927.92 max =        10611.67 mean =      6701.99|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.96 mean =        14.60|
|phase err.(test): min =        0.00 max =           89.77 mean =        14.13|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.801)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.58    94.79   15.22    None  None   None       |
|    all(noH): 2823   0      2.58    94.79   15.22    None  None   None       |
|    Sol.    : 438    0      3.89    78.65   38.51    None  None   None       |
|    Mac.    : 2385   0      2.58    94.79   10.94    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.584 -  11.805: 1736   |   5:    48.689 -  57.910:   74        |
|      1:    11.805 -  21.026:  555   |   6:    57.910 -  67.130:   41        |
|      2:    21.026 -  30.247:  147   |   7:    67.130 -  76.351:   17        |
|      3:    30.247 -  39.468:  120   |   8:    76.351 -  85.572:    7        |
|      4:    39.468 -  48.689:  123   |   9:    85.572 -  94.793:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 339         
Filter by distance & map next to the model:
   mapped sites are within: 0.386 - 5.820
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 336 from: 339
   mapped sites are within: 0.764 - 5.820

peak=   10.624 closest distance to " CB  VAL A 230 " =    1.442
peak=    8.751 closest distance to " CG2 VAL A 296 " =    1.251
peak=    6.053 closest distance to " CG  LEU A   5 " =    1.290
peak=    5.927 closest distance to " NH2 ARG A  56 " =    2.191
peak=    5.866 closest distance to " CD2 LEU A   5 " =    1.214
peak=    5.435 closest distance to " O   HOH Z 278 " =    1.054
peak=    5.382 closest distance to " CB  GLN A 223 " =    1.402
peak=    5.271 closest distance to " CG  PRO A  54 " =    1.264
peak=    5.151 closest distance to " CB  PRO A  54 " =    0.915
peak=    5.089 closest distance to " CD1AILE A 234 " =    1.054
peak=    5.005 closest distance to " CG  PRO A 198 " =    1.270
peak=    4.981 closest distance to " O   HOH Z 124 " =    1.436
peak=    4.968 closest distance to " CG  LEU A 228 " =    1.258
peak=    4.953 closest distance to " CG  PRO A 213 " =    1.261
peak=    4.899 closest distance to " CB  SER A  63 " =    1.327
peak=    4.883 closest distance to " NE2 GLN A  11 " =    1.115
peak=    4.870 closest distance to " CB  GLN A 183 " =    1.318
peak=    4.781 closest distance to " CB  ARG A 275 " =    0.880
peak=    4.776 closest distance to " O   HOH Z 247 " =    1.339
peak=    4.691 closest distance to " O   HOH Z  48 " =    1.661
peak=    4.688 closest distance to " O   HOH Z 126 " =    1.945
peak=    4.640 closest distance to " O   HOH Z 193 " =    1.793
peak=    4.615 closest distance to " CB  SER A   3 " =    1.363
peak=    4.569 closest distance to " CB  GLU A 128 " =    1.112
peak=    4.566 closest distance to " CB  VAL A 230 " =    1.187
peak=    4.521 closest distance to " O   HOH Z 316 " =    2.750
peak=    4.511 closest distance to " CA  ALA A  21 " =    1.180
peak=    4.510 closest distance to " CD2 LEU A 228 " =    1.244
peak=    4.500 closest distance to " O   HOH Z 132 " =    1.067
peak=    4.489 closest distance to " C   PRO A 198 " =    1.535
peak=    4.421 closest distance to " O   HOH Z 128 " =    2.052
peak=    4.409 closest distance to " CB  VAL A 296 " =    1.045
peak=    4.386 closest distance to " O   HOH Z 142 " =    1.687
peak=    4.376 closest distance to " O   HOH Z 411 " =    3.658
peak=    4.373 closest distance to " CB  ASN A 148 " =    1.393
peak=    4.371 closest distance to " O   HOH Z  97 " =    1.941
peak=    4.358 closest distance to " O   HOH Z 427 " =    2.908
peak=    4.342 closest distance to " O   HOH Z 298 " =    1.870
peak=    4.321 closest distance to " OD1 ASN A  69 " =    2.606
peak=    4.307 closest distance to " CG  PRO A 280 " =    0.817
peak=    4.304 closest distance to " CG1BVAL A  72 " =    1.606
peak=    4.287 closest distance to " CB  GLU A 152 " =    1.115
peak=    4.282 closest distance to " O   HOH Z 279 " =    1.115
peak=    4.262 closest distance to " O   HOH Z 232 " =    2.189
peak=    4.256 closest distance to " CB  TYR A 169 " =    0.903
peak=    4.256 closest distance to " O   HOH Z  78 " =    1.831
peak=    4.230 closest distance to " CB  TRP A 179 " =    1.306
peak=    4.229 closest distance to " O   HOH Z 368 " =    2.114
peak=    4.226 closest distance to " O   HOH Z 263 " =    1.474
peak=    4.224 closest distance to " O   SER A  87 " =    2.277
peak=    4.127 closest distance to " O   HOH Z 344 " =    2.772
peak=    4.113 closest distance to " O   TRP A 274 " =    1.876
peak=    4.106 closest distance to " O   HOH Z 371 " =    3.247
peak=    4.098 closest distance to " O   HOH Z 389 " =    1.886
peak=    4.094 closest distance to " CA  VAL A  41 " =    0.844
peak=    4.087 closest distance to " CG  PRO A 243 " =    1.164
peak=    4.077 closest distance to " O   HOH Z 295 " =    1.566
peak=    4.070 closest distance to " O   HOH Z 234 " =    3.804
peak=    4.070 closest distance to " O   HOH Z 280 " =    2.967
peak=    4.064 closest distance to " O   HOH Z 426 " =    1.476
peak=    4.063 closest distance to " CA  TYR A  30 " =    0.985
peak=    4.039 closest distance to " O   HOH Z  20 " =    1.614
peak=    4.023 closest distance to " O   HOH Z 134 " =    1.479
peak=    4.018 closest distance to " O   HOH Z 272 " =    1.853
peak=    3.965 closest distance to " O   HOH Z 236 " =    1.850
peak=    3.958 closest distance to " CB  VAL A 265 " =    1.198
peak=    3.949 closest distance to " O   HOH Z  93 " =    2.592
peak=    3.939 closest distance to " CA  THR A 221 " =    0.909
peak=    3.936 closest distance to " O   HOH Z 112 " =    1.547
peak=    3.934 closest distance to " O   HOH Z 403 " =    1.704
peak=    3.929 closest distance to " O   HOH Z  80 " =    1.662
peak=    3.903 closest distance to " O   HOH Z 423 " =    1.801
peak=    3.899 closest distance to " O   HOH Z 108 " =    1.223
peak=    3.885 closest distance to " O   HOH Z 346 " =    1.486
peak=    3.882 closest distance to " O   HOH Z   9 " =    2.224
peak=    3.877 closest distance to " OD2 ASP A 286 " =    2.806
peak=    3.876 closest distance to " CD  ARG A 269 " =    0.956
peak=    3.858 closest distance to " O   HOH Z 303 " =    2.070
peak=    3.855 closest distance to " CA  ALA A  51 " =    1.005
peak=    3.826 closest distance to " CG  ARG A  66 " =    2.736
peak=    3.818 closest distance to " CB  VAL A 202 " =    1.605
peak=    3.815 closest distance to " O   HOH Z 260 " =    1.190
peak=    3.806 closest distance to " CB  PRO A 198 " =    0.996
peak=    3.805 closest distance to " CG1 ILE A  33 " =    1.369
peak=    3.798 closest distance to " O   HOH Z  61 " =    1.591
peak=    3.785 closest distance to " O   HOH Z 345 " =    3.292
peak=    3.781 closest distance to " O   HOH Z 202 " =    1.030
peak=    3.774 closest distance to " CB  ALA A 291 " =    1.346
peak=    3.774 closest distance to " CG2 THR A 221 " =    1.051
peak=    3.758 closest distance to " O   HOH Z  37 " =    1.173
peak=    3.754 closest distance to " O   HOH Z 189 " =    2.476
peak=    3.743 closest distance to " NH2 ARG A 156 " =    1.149
peak=    3.739 closest distance to " NH2BARG A 102 " =    0.926
peak=    3.734 closest distance to " O   HOH Z 133 " =    1.649
peak=    3.734 closest distance to " O   HOH Z  21 " =    1.741
peak=    3.731 closest distance to " CA  LEU A 282 " =    1.102
peak=    3.725 closest distance to " OG BSER A 164 " =    2.202
peak=    3.724 closest distance to " CB  LEU A 228 " =    1.413
peak=    3.721 closest distance to " CD1 LEU A 300 " =    1.150
peak=    3.720 closest distance to " N   ASN A  39 " =    1.204
peak=    3.719 closest distance to " CA  ALA A 295 " =    1.088
peak=    3.717 closest distance to " CA  ASP A 140 " =    1.203
peak=    3.716 closest distance to " NZ  LYS A 117 " =    3.231
peak=    3.713 closest distance to " O   HOH Z 203 " =    1.669
peak=    3.711 closest distance to " O   HOH Z  88 " =    3.156
peak=    3.704 closest distance to " CA  GLN A 194 " =    1.143
peak=    3.703 closest distance to " O   HOH Z  54 " =    1.567
peak=    3.702 closest distance to " CB  GLU A 277 " =    3.599
peak=    3.702 closest distance to " CG2 VAL A 257 " =    0.861
peak=    3.699 closest distance to " CD BLYS A 290 " =    1.063
peak=    3.697 closest distance to " O   THR A  31 " =    1.500
peak=    3.691 closest distance to " ND2 ASN A 187 " =    1.635
peak=    3.690 closest distance to " O   HOH Z 273 " =    2.728
peak=    3.685 closest distance to " CA  ASP A 191 " =    0.827
peak=    3.683 closest distance to " CB  TRP A 266 " =    0.968
peak=    3.677 closest distance to " CB  ALA A 248 " =    1.404
peak=    3.677 closest distance to " O   HOH Z 369 " =    1.992
peak=    3.676 closest distance to " O   HOH Z 214 " =    2.152
peak=    3.667 closest distance to " O   HOH Z 276 " =    1.275
peak=    3.657 closest distance to " CG1 VAL A 153 " =    0.973
peak=    3.655 closest distance to " O   HOH Z  11 " =    1.240
peak=    3.654 closest distance to " O   HOH Z  59 " =    2.291
peak=    3.642 closest distance to " CD2 LEU A 255 " =    1.217
peak=    3.632 closest distance to " O   HOH Z 193 " =    2.002
peak=    3.632 closest distance to " O   HOH Z  85 " =    1.219
peak=    3.632 closest distance to " O   HOH Z  54 " =    2.425
peak=    3.630 closest distance to " CE1 TYR A 186 " =    1.282
peak=    3.620 closest distance to " NE2 GLN A  58 " =    5.820
peak=    3.601 closest distance to " OE1 GLU A   2 " =    2.141
peak=    3.598 closest distance to " CG2 ILE A 120 " =    1.286
peak=    3.596 closest distance to " O   HOH Z 108 " =    2.192
peak=    3.595 closest distance to " O   HOH Z  48 " =    1.621
peak=    3.594 closest distance to " O   MET A 105 " =    1.848
peak=    3.589 closest distance to " O   HOH Z 236 " =    1.629
peak=    3.585 closest distance to " O   HOH Z 102 " =    1.256
peak=    3.583 closest distance to " CB  SER A 216 " =    0.794
peak=    3.572 closest distance to " O   HOH Z  68 " =    1.564
peak=    3.565 closest distance to " O   HOH Z 261 " =    2.047
peak=    3.553 closest distance to " O   HOH Z 425 " =    1.362
peak=    3.547 closest distance to " CB  ARG A 139 " =    0.853
peak=    3.539 closest distance to " O   HOH Z 126 " =    2.304
peak=    3.537 closest distance to " O   HOH Z 126 " =    1.519
peak=    3.535 closest distance to " O   HOH Z 172 " =    3.958
peak=    3.527 closest distance to " O   HOH Z 329 " =    3.695
peak=    3.526 closest distance to " CD  LYS A 119 " =    1.198
peak=    3.524 closest distance to " CA  VAL A 126 " =    0.998
peak=    3.519 closest distance to " O   HOH Z 227 " =    1.623
peak=    3.515 closest distance to " O   HOH Z  43 " =    2.254
peak=    3.511 closest distance to " C   ALA A 299 " =    0.973
peak=    3.507 closest distance to " CA  ALA A 158 " =    1.118
peak=    3.505 closest distance to " O   HOH Z 261 " =    1.907
peak=    3.495 closest distance to " OG  SER A  22 " =    2.826
peak=    3.492 closest distance to " NH1 ARG A  14 " =    1.025
peak=    3.490 closest distance to " CA  GLY A 211 " =    1.259
peak=    3.489 closest distance to " CA  LYS A 117 " =    1.256
peak=    3.486 closest distance to " O   HOH Z 215 " =    1.565
peak=    3.485 closest distance to " CA  ARG A  36 " =    1.077
peak=    3.483 closest distance to " O   HOH Z 357 " =    2.005
peak=    3.482 closest distance to " O   HOH Z 374 " =    2.456
peak=    3.477 closest distance to " CB  LEU A 255 " =    0.838
peak=    3.476 closest distance to " CA  THR A 264 " =    0.776
peak=    3.474 closest distance to " O   HOH Z 327 " =    2.458
peak=    3.473 closest distance to " O   HOH Z  44 " =    2.338
peak=    3.469 closest distance to " CB  TYR A 169 " =    0.919
peak=    3.466 closest distance to " O   HOH Z 116 " =    1.745
peak=    3.463 closest distance to " CD2 HIS A  81 " =    1.173
peak=    3.456 closest distance to " O   HOH Z  63 " =    1.136
peak=    3.456 closest distance to " CA  THR A 246 " =    1.228
peak=    3.447 closest distance to " CB  SER A  62 " =    1.252
peak=    3.447 closest distance to " CB  LEU A 143 " =    1.177
peak=    3.444 closest distance to " O   HOH Z 332 " =    1.556
peak=    3.441 closest distance to " O   HOH Z   9 " =    2.117
peak=    3.438 closest distance to " CB  ARG A  79 " =    1.387
peak=    3.437 closest distance to " O   HOH Z 422 " =    2.628
peak=    3.436 closest distance to " OE1 GLN A  11 " =    1.701
peak=    3.435 closest distance to " O   ALA A   1 " =    1.398
peak=    3.434 closest distance to " CG  GLN A  88 " =    1.033
peak=    3.434 closest distance to " O   HOH Z 371 " =    3.507
peak=    3.432 closest distance to " CD  ARG A 159 " =    0.776
peak=    3.431 closest distance to " CA  ASN A 215 " =    1.163
peak=    3.429 closest distance to " CA  ASN A 176 " =    1.081
peak=    3.429 closest distance to " O   HOH Z 197 " =    2.829
peak=    3.429 closest distance to " O   ALA A 158 " =    1.324
peak=    3.428 closest distance to " CB  GLN A  88 " =    1.236
peak=    3.425 closest distance to " O   HOH Z  49 " =    2.440
peak=    3.425 closest distance to " O   HOH Z 245 " =    1.348
peak=    3.423 closest distance to " CB  ARG A 190 " =    1.786
peak=    3.422 closest distance to " OD1 ASP A 231 " =    1.867
peak=    3.420 closest distance to " O   HOH Z  40 " =    1.446
peak=    3.419 closest distance to " CB  SER A 141 " =    1.090
peak=    3.418 closest distance to " O   HOH Z 130 " =    2.294
peak=    3.417 closest distance to " O   HOH Z  63 " =    1.671
peak=    3.416 closest distance to " CG  LEU A 167 " =    1.104
peak=    3.416 closest distance to " CB  ALA A 295 " =    1.289
peak=    3.406 closest distance to " O   SER A  26 " =    1.593
peak=    3.406 closest distance to " CD1 LEU A  96 " =    0.767
peak=    3.404 closest distance to " O   HOH Z 279 " =    2.171
peak=    3.401 closest distance to " CG  MET A 188 " =    1.314
peak=    3.400 closest distance to " CZ  PHE A 192 " =    1.052
peak=    3.399 closest distance to " CD  LYS A 166 " =    1.386
peak=    3.398 closest distance to " CG BARG A 102 " =    1.854
peak=    3.397 closest distance to " O   HOH Z 280 " =    1.569
peak=    3.394 closest distance to " CB BVAL A  41 " =    1.182
peak=    3.391 closest distance to " CB  ALA A   9 " =    1.577
peak=    3.390 closest distance to " O   HOH Z 132 " =    2.854
peak=    3.389 closest distance to " O   GLN A 278 " =    1.386
peak=    3.386 closest distance to " O   HOH Z 406 " =    1.623
peak=    3.386 closest distance to " O   HOH Z 374 " =    3.041
peak=    3.384 closest distance to " O   HOH Z 367 " =    3.409
peak=    3.384 closest distance to " C   LYS A 290 " =    1.274
peak=    3.380 closest distance to " CG2 THR A 220 " =    1.014
peak=    3.379 closest distance to " O   HOH Z 313 " =    1.824
peak=    3.378 closest distance to " CG AARG A 275 " =    1.105
peak=    3.376 closest distance to " O   HOH Z 271 " =    1.831
peak=    3.375 closest distance to " O   HOH Z 352 " =    1.328
peak=    3.374 closest distance to " CG1 VAL A 296 " =    1.170
peak=    3.371 closest distance to " O   HOH Z  44 " =    1.804
peak=    3.367 closest distance to " CG  ARG A 138 " =    1.076
peak=    3.360 closest distance to " NE2 GLN A  58 " =    4.149
peak=    3.360 closest distance to " O   HOH Z 128 " =    1.912
peak=    3.352 closest distance to " O   HOH Z 383 " =    2.051
peak=    3.351 closest distance to " O   HOH Z   4 " =    1.632
peak=    3.348 closest distance to " O   HOH Z 355 " =    1.786
peak=    3.348 closest distance to " O   HOH Z 135 " =    1.926
peak=    3.348 closest distance to " CB  ASN A  39 " =    0.867
peak=    3.344 closest distance to " O   HOH Z 180 " =    2.113
peak=    3.343 closest distance to " O   HOH Z 334 " =    1.358
peak=    3.343 closest distance to " NZ  LYS A  76 " =    1.257
peak=    3.339 closest distance to " CZ  PHE A 218 " =    1.102
peak=    3.335 closest distance to " O   HOH Z 411 " =    1.874
peak=    3.335 closest distance to " CG  MET A 185 " =    1.255
peak=    3.334 closest distance to " CA  ASN A  74 " =    1.192
peak=    3.332 closest distance to " CG2 VAL A 174 " =    1.338
peak=    3.312 closest distance to " CB  ILE A 234 " =    0.909
peak=    3.312 closest distance to " CD1 ILE A  33 " =    1.624
peak=    3.311 closest distance to " O   HOH Z  10 " =    1.807
peak=    3.311 closest distance to " OD1 ASN A 217 " =    1.765
peak=    3.311 closest distance to " O   HOH Z 284 " =    1.360
peak=    3.309 closest distance to " O   HOH Z 281 " =    4.404
peak=    3.308 closest distance to " O   HOH Z 394 " =    1.645
peak=    3.303 closest distance to " CB  LYS A 117 " =    1.146
peak=    3.299 closest distance to " O   HOH Z 419 " =    1.684
peak=    3.296 closest distance to " OD1 ASN A  45 " =    1.407
peak=    3.295 closest distance to " O   HOH Z 216 " =    2.438
peak=    3.289 closest distance to " O   HOH Z 209 " =    2.305
peak=    3.283 closest distance to " O   HOH Z 420 " =    1.965
peak=    3.280 closest distance to " O   HOH Z 158 " =    2.966
peak=    3.280 closest distance to " O   HOH Z 250 " =    1.350
peak=    3.275 closest distance to " O   HOH Z 133 " =    2.301
peak=    3.275 closest distance to " O   HOH Z 303 " =    1.677
peak=    3.275 closest distance to " CB  ALA A 248 " =    0.993
peak=    3.274 closest distance to " O   ALA A   1 " =    1.736
peak=    3.271 closest distance to " CB  SER A 273 " =    0.849
peak=    3.269 closest distance to " CA  MET A  40 " =    1.071
peak=    3.268 closest distance to " O   HOH Z 395 " =    1.327
peak=    3.268 closest distance to " O   HOH Z 175 " =    2.148
peak=    3.265 closest distance to " O   HOH Z 423 " =    3.153
peak=    3.265 closest distance to " N   ARG A 156 " =    1.329
peak=    3.262 closest distance to " CA  ALA A 160 " =    0.824
peak=    3.255 closest distance to " NH2 ARG A 219 " =    1.775
peak=    3.253 closest distance to " ND1 HIS A  81 " =    1.515
peak=    3.252 closest distance to " CA  ILE A 106 " =    0.828
peak=    3.247 closest distance to " CD1 TRP A 266 " =    1.196
peak=    3.247 closest distance to " C   GLY A  80 " =    1.106
peak=    3.247 closest distance to " CE1 HIS A 108 " =    1.167
peak=    3.245 closest distance to " O   HOH Z 280 " =    2.336
peak=    3.245 closest distance to " CG  MET A 185 " =    1.062
peak=    3.245 closest distance to " CB  SER A  26 " =    1.628
peak=    3.244 closest distance to " O   HOH Z  30 " =    1.173
peak=    3.233 closest distance to " OG  SER A 206 " =    1.317
peak=    3.232 closest distance to " O   HOH Z 163 " =    1.415
peak=    3.232 closest distance to " NH1AARG A 145 " =    0.955
peak=    3.232 closest distance to " O   HOH Z 366 " =    3.012
peak=    3.230 closest distance to " O   ASP A 124 " =    1.125
peak=    3.223 closest distance to " CB  ALA A   1 " =    1.289
peak=    3.221 closest distance to " O   HOH Z 163 " =    1.821
peak=    3.219 closest distance to " O   HOH Z 128 " =    2.058
peak=    3.218 closest distance to " ND1 HIS A  86 " =    1.685
peak=    3.217 closest distance to " CB  TYR A  30 " =    1.505
peak=    3.213 closest distance to " O   HOH Z 409 " =    3.730
peak=    3.213 closest distance to " C   SER A  32 " =    1.077
peak=    3.213 closest distance to " CZ2 TRP A 274 " =    1.810
peak=    3.212 closest distance to " O   HOH Z 344 " =    1.464
peak=    3.208 closest distance to " O   ALA A 165 " =    1.322
peak=    3.206 closest distance to " CB  SER A  28 " =    0.997
peak=    3.201 closest distance to " CA  SER A  87 " =    0.936
peak=    3.195 closest distance to " O   HOH Z 192 " =    1.461
peak=    3.194 closest distance to " CA  ALA A 154 " =    1.239
peak=    3.192 closest distance to " NH1 ARG A  56 " =    1.034
peak=    3.184 closest distance to " O   HOH Z 402 " =    1.440
peak=    3.181 closest distance to " CB  LYS A 193 " =    1.171
peak=    3.175 closest distance to " CB  ASN A 142 " =    1.032
peak=    3.175 closest distance to " O   HOH Z 211 " =    2.455
peak=    3.170 closest distance to " O   HOH Z 337 " =    3.720
peak=    3.169 closest distance to " O   HOH Z 353 " =    2.830
peak=    3.169 closest distance to " CD2 TYR A 186 " =    1.031
peak=    3.167 closest distance to " O   HOH Z 155 " =    2.864
peak=    3.165 closest distance to " N   GLN A 278 " =    1.064
peak=    3.165 closest distance to " NH2 ARG A  79 " =    1.384
peak=    3.163 closest distance to " O   HOH Z 291 " =    1.508
peak=    3.162 closest distance to " O   HOH Z   3 " =    1.484
peak=    3.160 closest distance to " O   SER A 164 " =    1.411
peak=    3.157 closest distance to " O   HOH Z 151 " =    1.668
peak=    3.154 closest distance to " CB  ALA A 137 " =    1.122
peak=    3.144 closest distance to " O   HOH Z 435 " =    2.048
peak=    3.138 closest distance to " OG  SER A  97 " =    2.550
peak=    3.135 closest distance to " CD1 ILE A 106 " =    1.020
peak=    3.132 closest distance to " NH2BARG A 145 " =    2.163
peak=    3.130 closest distance to " OD2 ASP A 200 " =    1.358
peak=    3.130 closest distance to " CB  ASP A 140 " =    0.764
peak=    3.128 closest distance to " O   HOH Z 120 " =    1.023
peak=    3.126 closest distance to " O   HOH Z 271 " =    2.039
peak=    3.124 closest distance to " CD2 TRP A 179 " =    1.379
peak=    3.124 closest distance to " CH2 TRP A 274 " =    2.274
peak=    3.121 closest distance to " O   HOH Z 175 " =    3.497
peak=    3.120 closest distance to " CA  GLY A 267 " =    0.959
peak=    3.119 closest distance to " CA  LEU A 101 " =    1.587
peak=    3.119 closest distance to " O   HOH Z 404 " =    2.283
peak=    3.118 closest distance to " NH2BARG A 190 " =    1.801
peak=    3.112 closest distance to " O   HOH Z 277 " =    2.585
peak=    3.110 closest distance to " O   HOH Z 197 " =    1.913
peak=    3.109 closest distance to " O   HOH Z 417 " =    2.008
peak=    3.103 closest distance to " O   HOH Z 227 " =    1.529
peak=    3.100 closest distance to " CB  MET A  47 " =    1.334
peak=    3.094 closest distance to " NH1 ARG A 269 " =    0.810
peak=    3.094 closest distance to " CG2 VAL A 202 " =    1.190
peak=    3.090 closest distance to " O   HOH Z 391 " =    3.025
peak=    3.090 closest distance to " O   HOH Z 193 " =    1.492
peak=    3.090 closest distance to " CB  THR A  31 " =    1.622
peak=    3.089 closest distance to " CB  GLU A 152 " =    1.392
peak=    3.084 closest distance to " O   HOH Z 128 " =    1.851
peak=    3.067 closest distance to " O   HOH Z 109 " =    2.733
peak=    3.051 closest distance to " CD  ARG A 219 " =    0.986
peak=    3.050 closest distance to " CE  MET A  93 " =    1.409
peak=    3.034 closest distance to " O   GLY A  91 " =    1.797
peak=    3.018 closest distance to " CA  TYR A 186 " =    1.356

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 212         
Filter by distance & map next to the model:
   mapped sites are within: 0.618 - 5.331
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 210 from: 212
   mapped sites are within: 0.808 - 5.331

peak=   -5.342 closest distance to " CG2 VAL A 230 " =    0.823
peak=   -4.442 closest distance to " O   ILE A 109 " =    2.611
peak=   -4.324 closest distance to " O   HOH Z 266 " =    4.466
peak=   -4.307 closest distance to " CD  ARG A 156 " =    2.004
peak=   -4.194 closest distance to " OXT GLY A 302 " =    2.879
peak=   -4.142 closest distance to " CE2 TYR A  30 " =    2.821
peak=   -4.131 closest distance to " CG2BVAL A  41 " =    2.742
peak=   -4.128 closest distance to " O   HOH Z 290 " =    1.028
peak=   -4.113 closest distance to " OG ASER A 134 " =    1.310
peak=   -4.111 closest distance to " O   HOH Z  92 " =    1.411
peak=   -4.048 closest distance to " O   HOH Z  13 " =    1.338
peak=   -4.039 closest distance to " SG  CYS A 254 " =    3.172
peak=   -3.996 closest distance to " O   HOH Z 103 " =    1.858
peak=   -3.992 closest distance to " O   HOH Z 231 " =    1.746
peak=   -3.929 closest distance to " CD1 LEU A 101 " =    2.677
peak=   -3.901 closest distance to " NH2 ARG A  66 " =    1.657
peak=   -3.875 closest distance to " O   HOH Z  43 " =    1.639
peak=   -3.873 closest distance to " O   HOH Z 166 " =    1.856
peak=   -3.867 closest distance to " O   HOH Z 198 " =    2.355
peak=   -3.858 closest distance to " CG  ASP A 231 " =    0.808
peak=   -3.848 closest distance to " CD  GLN A  88 " =    2.223
peak=   -3.824 closest distance to " CG2 THR A   4 " =    1.941
peak=   -3.811 closest distance to " C   ALA A 158 " =    1.247
peak=   -3.810 closest distance to " C   HIS A 108 " =    1.196
peak=   -3.791 closest distance to " O   HOH Z 388 " =    1.936
peak=   -3.754 closest distance to " N   GLN A  58 " =    1.818
peak=   -3.743 closest distance to " O   PRO A 163 " =    2.049
peak=   -3.736 closest distance to " CB  TYR A  15 " =    2.227
peak=   -3.732 closest distance to " CD2 LEU A 300 " =    2.903
peak=   -3.732 closest distance to " CG  LYS A 193 " =    2.262
peak=   -3.723 closest distance to " CG  ASP A  50 " =    2.501
peak=   -3.719 closest distance to " N   ALA A 226 " =    2.090
peak=   -3.703 closest distance to " OE1 GLN A 223 " =    2.268
peak=   -3.701 closest distance to " ND2 ASN A  45 " =    0.959
peak=   -3.690 closest distance to " CG1 VAL A 296 " =    1.239
peak=   -3.687 closest distance to " O   HOH Z  52 " =    1.680
peak=   -3.687 closest distance to " CD2 LEU A 237 " =    2.656
peak=   -3.667 closest distance to " CB  ALA A 248 " =    1.972
peak=   -3.665 closest distance to " O   HOH Z  11 " =    1.670
peak=   -3.660 closest distance to " N   THR A 157 " =    1.574
peak=   -3.654 closest distance to " CB  PRO A 243 " =    2.605
peak=   -3.651 closest distance to " O   HOH Z 423 " =    2.227
peak=   -3.643 closest distance to " O   HOH Z 222 " =    1.367
peak=   -3.642 closest distance to " C   ASN A 187 " =    1.869
peak=   -3.632 closest distance to " CD  ARG A 139 " =    1.647
peak=   -3.631 closest distance to " N   ALA A  43 " =    2.461
peak=   -3.616 closest distance to " CG  PHE A 283 " =    2.792
peak=   -3.603 closest distance to " O   HOH Z 185 " =    2.420
peak=   -3.600 closest distance to " O   HOH Z 407 " =    3.136
peak=   -3.593 closest distance to " CD  LYS A 289 " =    2.554
peak=   -3.591 closest distance to " O   HOH Z 292 " =    4.396
peak=   -3.584 closest distance to " O   HOH Z 351 " =    1.428
peak=   -3.569 closest distance to " O   SER A 271 " =    2.177
peak=   -3.567 closest distance to " CB  SER A 134 " =    1.804
peak=   -3.564 closest distance to " O   MET A  40 " =    2.650
peak=   -3.548 closest distance to " O   ALA A 161 " =    1.521
peak=   -3.547 closest distance to " O   HOH Z  19 " =    2.109
peak=   -3.546 closest distance to " O   HOH Z 151 " =    1.376
peak=   -3.546 closest distance to " O   HOH Z 166 " =    1.485
peak=   -3.540 closest distance to " NH2AARG A 275 " =    5.174
peak=   -3.539 closest distance to " O   HOH Z 165 " =    2.073
peak=   -3.537 closest distance to " CZ  TYR A 169 " =    1.813
peak=   -3.533 closest distance to " CG  MET A 105 " =    0.894
peak=   -3.532 closest distance to " CA  ASN A 127 " =    1.011
peak=   -3.531 closest distance to " O   HOH Z  71 " =    0.967
peak=   -3.529 closest distance to " O   HOH Z 266 " =    4.518
peak=   -3.526 closest distance to " CE  MET A 105 " =    2.152
peak=   -3.525 closest distance to " N   SER A 276 " =    1.279
peak=   -3.525 closest distance to " OE2 GLU A   2 " =    1.826
peak=   -3.511 closest distance to " CG  GLU A  53 " =    1.446
peak=   -3.509 closest distance to " NH2 ARG A  79 " =    1.903
peak=   -3.503 closest distance to " O   HOH Z  17 " =    1.418
peak=   -3.502 closest distance to " N   ALA A 248 " =    1.697
peak=   -3.495 closest distance to " NH2 ARG A 159 " =    2.308
peak=   -3.491 closest distance to " O   HOH Z 377 " =    1.889
peak=   -3.485 closest distance to " O   HOH Z 308 " =    1.726
peak=   -3.478 closest distance to " OG  SER A  62 " =    1.586
peak=   -3.476 closest distance to " O   PRO A 198 " =    1.232
peak=   -3.470 closest distance to " O   HOH Z  63 " =    0.827
peak=   -3.464 closest distance to " CZ3 TRP A 179 " =    1.326
peak=   -3.463 closest distance to " CD1 LEU A 228 " =    2.362
peak=   -3.461 closest distance to " CG2 VAL A 112 " =    2.611
peak=   -3.459 closest distance to " O   HOH Z  98 " =    1.931
peak=   -3.451 closest distance to " CB  CYS A 254 " =    2.336
peak=   -3.450 closest distance to " CB  ASN A  39 " =    2.035
peak=   -3.447 closest distance to " CA  ASP A 298 " =    1.028
peak=   -3.425 closest distance to " O   HOH Z  97 " =    1.704
peak=   -3.425 closest distance to " NE2 GLN A  88 " =    1.074
peak=   -3.424 closest distance to " O   GLY A 196 " =    1.046
peak=   -3.413 closest distance to " CD1 PHE A  59 " =    1.886
peak=   -3.410 closest distance to " OG BSER A 134 " =    1.210
peak=   -3.403 closest distance to " N   THR A 235 " =    1.162
peak=   -3.400 closest distance to " C   ASN A 285 " =    2.462
peak=   -3.392 closest distance to " O   HOH Z 252 " =    4.179
peak=   -3.391 closest distance to " O   HOH Z 353 " =    2.229
peak=   -3.388 closest distance to " CG  GLU A 277 " =    1.102
peak=   -3.381 closest distance to " CG  TRP A 266 " =    1.705
peak=   -3.380 closest distance to " CG1 VAL A 112 " =    2.859
peak=   -3.379 closest distance to " O   HOH Z 191 " =    5.331
peak=   -3.378 closest distance to " OG  SER A  32 " =    1.110
peak=   -3.370 closest distance to " O   HOH Z 389 " =    1.737
peak=   -3.370 closest distance to " OG  SER A  97 " =    2.240
peak=   -3.370 closest distance to " O   HOH Z 311 " =    3.540
peak=   -3.368 closest distance to " CB  SER A 245 " =    2.343
peak=   -3.364 closest distance to " CE3 TRP A 150 " =    2.030
peak=   -3.361 closest distance to " O   HOH Z 189 " =    2.124
peak=   -3.358 closest distance to " CG  LEU A 228 " =    1.019
peak=   -3.356 closest distance to " O   HOH Z 377 " =    1.493
peak=   -3.353 closest distance to " O   HOH Z 431 " =    1.727
peak=   -3.350 closest distance to " CD2 TYR A 293 " =    2.155
peak=   -3.349 closest distance to " O   HOH Z 211 " =    1.591
peak=   -3.346 closest distance to " O   ALA A 256 " =    1.511
peak=   -3.346 closest distance to " CD  GLN A  88 " =    0.852
peak=   -3.343 closest distance to " CD2 LEU A 167 " =    1.722
peak=   -3.329 closest distance to " OXT GLY A 302 " =    3.369
peak=   -3.326 closest distance to " CG2 VAL A 296 " =    1.606
peak=   -3.319 closest distance to " OD1 ASN A 249 " =    1.203
peak=   -3.314 closest distance to " O   HOH Z 196 " =    2.320
peak=   -3.311 closest distance to " ND2 ASN A  60 " =    1.475
peak=   -3.310 closest distance to " O   ALA A   7 " =    1.597
peak=   -3.310 closest distance to " O   ASN A 187 " =    1.476
peak=   -3.305 closest distance to " O   HOH Z  10 " =    1.551
peak=   -3.295 closest distance to " CB  ALA A  51 " =    1.824
peak=   -3.292 closest distance to " O   HOH Z 184 " =    1.450
peak=   -3.288 closest distance to " OD1 ASN A 148 " =    1.577
peak=   -3.282 closest distance to " CE2 PHE A 218 " =    2.684
peak=   -3.282 closest distance to " O   HOH Z 275 " =    1.479
peak=   -3.280 closest distance to " O   HOH Z 241 " =    1.311
peak=   -3.274 closest distance to " ND2 ASN A  39 " =    1.478
peak=   -3.274 closest distance to " O   HOH Z 341 " =    1.174
peak=   -3.273 closest distance to " O   VAL A  67 " =    2.527
peak=   -3.271 closest distance to " CB  GLN A  11 " =    1.869
peak=   -3.266 closest distance to " O   HOH Z 234 " =    4.295
peak=   -3.264 closest distance to " OG  SER A 206 " =    1.604
peak=   -3.264 closest distance to " CG2 ILE A 263 " =    2.349
peak=   -3.257 closest distance to " OD1 ASP A 191 " =    1.550
peak=   -3.253 closest distance to " O   HOH Z 295 " =    1.391
peak=   -3.253 closest distance to " O   HOH Z 118 " =    2.804
peak=   -3.250 closest distance to " O   HOH Z 350 " =    1.973
peak=   -3.249 closest distance to " O   HOH Z 339 " =    1.816
peak=   -3.242 closest distance to " N   SER A 212 " =    1.950
peak=   -3.231 closest distance to " O   HOH Z 292 " =    2.895
peak=   -3.227 closest distance to " O   HOH Z 426 " =    2.388
peak=   -3.227 closest distance to " O   GLY A 211 " =    1.493
peak=   -3.223 closest distance to " CB  GLN A  55 " =    1.479
peak=   -3.220 closest distance to " O   HOH Z  38 " =    1.674
peak=   -3.214 closest distance to " C   MET A 188 " =    1.582
peak=   -3.211 closest distance to " CB  PRO A 163 " =    2.719
peak=   -3.210 closest distance to " O   HOH Z 297 " =    2.770
peak=   -3.209 closest distance to " N   SER A 206 " =    2.014
peak=   -3.202 closest distance to " O   HOH Z  60 " =    2.297
peak=   -3.201 closest distance to " CB  ALA A 291 " =    2.175
peak=   -3.200 closest distance to " O   HOH Z 202 " =    2.364
peak=   -3.195 closest distance to " O   HOH Z 435 " =    2.739
peak=   -3.192 closest distance to " C   LEU A 143 " =    1.152
peak=   -3.191 closest distance to " CD2 LEU A   5 " =    1.087
peak=   -3.190 closest distance to " O   HOH Z  93 " =    1.430
peak=   -3.190 closest distance to " O   ALA A 100 " =    2.466
peak=   -3.189 closest distance to " OD1 ASP A 191 " =    1.552
peak=   -3.189 closest distance to " C   GLN A 240 " =    2.186
peak=   -3.187 closest distance to " OE1 GLN A  88 " =    1.015
peak=   -3.185 closest distance to " OE1 GLN A  73 " =    2.469
peak=   -3.183 closest distance to " CA  SER A 146 " =    2.336
peak=   -3.183 closest distance to " O   HOH Z 411 " =    3.573
peak=   -3.181 closest distance to " N   VAL A 230 " =    1.152
peak=   -3.181 closest distance to " CD1 ILE A 263 " =    2.401
peak=   -3.175 closest distance to " N   ALA A 248 " =    2.162
peak=   -3.175 closest distance to " O   HOH Z 123 " =    2.371
peak=   -3.173 closest distance to " OD1 ASN A 187 " =    1.633
peak=   -3.170 closest distance to " C   ASP A 231 " =    2.547
peak=   -3.169 closest distance to " CD  GLU A 236 " =    1.043
peak=   -3.167 closest distance to " C   LEU A 222 " =    0.870
peak=   -3.165 closest distance to " O   HOH Z 250 " =    1.439
peak=   -3.161 closest distance to " O   HOH Z 133 " =    3.338
peak=   -3.157 closest distance to " CE  LYS A  76 " =    2.915
peak=   -3.140 closest distance to " O   HOH Z 396 " =    1.584
peak=   -3.139 closest distance to " O   HOH Z 128 " =    2.473
peak=   -3.139 closest distance to " CA  GLY A 133 " =    2.262
peak=   -3.130 closest distance to " OD1 ASP A 200 " =    1.348
peak=   -3.127 closest distance to " OH  TYR A 169 " =    0.970
peak=   -3.127 closest distance to " OG  SER A  87 " =    1.438
peak=   -3.126 closest distance to " CG  GLU A 152 " =    2.407
peak=   -3.126 closest distance to " O   GLU A  44 " =    1.593
peak=   -3.121 closest distance to " O   HOH Z 352 " =    0.953
peak=   -3.121 closest distance to " CE2 PHE A 283 " =    2.560
peak=   -3.119 closest distance to " O   HOH Z 360 " =    2.551
peak=   -3.114 closest distance to " CD1 ILE A 199 " =    2.521
peak=   -3.113 closest distance to " CD  ARG A 259 " =    2.535
peak=   -3.110 closest distance to " N   GLY A  23 " =    2.046
peak=   -3.109 closest distance to " SG ACYS A 201 " =    2.403
peak=   -3.106 closest distance to " O   HOH Z 310 " =    1.643
peak=   -3.105 closest distance to " CB  ALA A  43 " =    2.414
peak=   -3.104 closest distance to " O   HOH Z 429 " =    2.170
peak=   -3.103 closest distance to " CG1 VAL A 197 " =    2.295
peak=   -3.102 closest distance to " O   VAL A 197 " =    1.187
peak=   -3.102 closest distance to " CG  PHE A  59 " =    2.255
peak=   -3.095 closest distance to " O   ALA A  51 " =    1.515
peak=   -3.093 closest distance to " OG1 THR A  82 " =    1.372
peak=   -3.085 closest distance to " CD  ARG A 195 " =    5.007
peak=   -3.079 closest distance to " NZ BLYS A 290 " =    1.265
peak=   -3.073 closest distance to " N   GLY A  17 " =    1.629
peak=   -3.069 closest distance to " O   LEU A 167 " =    1.527
peak=   -3.068 closest distance to " CA  VAL A 296 " =    0.928
peak=   -3.060 closest distance to " CA  TYR A  30 " =    1.016
peak=   -3.060 closest distance to " O   HOH Z 417 " =    2.710
peak=   -3.053 closest distance to " CE3 TRP A 274 " =    2.456
peak=   -3.049 closest distance to " O   HOH Z 313 " =    1.877
peak=   -3.049 closest distance to " O   ASN A 301 " =    1.827
peak=   -3.033 closest distance to " O   PRO A 198 " =    1.279
peak=   -3.014 closest distance to " NH2 ARG A  66 " =    1.537

================= 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    :  0.4531 0.4531   6.253335e+00   6.247854e+00
   1_bss:  0.4449 0.4411   6.252921e+00   6.238072e+00
   1_xyz:  0.3539 0.3855   6.100510e+00   6.149993e+00
   1_adp:  0.3024 0.3553   5.989625e+00   6.096159e+00
   1_occ:  0.3021 0.3553   5.989062e+00   6.096306e+00
   2_bss:  0.2980 0.3503   5.988106e+00   6.092887e+00
   2_xyz:  0.2149 0.2721   5.713262e+00   5.886015e+00
   2_adp:  0.1962 0.2510   5.633505e+00   5.818958e+00
   2_occ:  0.1961 0.2513   5.632995e+00   5.819113e+00
   3_bss:  0.1947 0.2487   5.630909e+00   5.814946e+00
   3_xyz:  0.1447 0.1917   5.360532e+00   5.581037e+00
   3_adp:  0.1337 0.1811   5.296531e+00   5.523873e+00
   3_occ:  0.1336 0.1810   5.296158e+00   5.523739e+00
   4_bss:  0.1335 0.1807   5.296762e+00   5.524365e+00
   4_xyz:  0.1194 0.1646   5.203322e+00   5.436593e+00
   4_adp:  0.1165 0.1621   5.186173e+00   5.423809e+00
   4_occ:  0.1163 0.1622   5.186005e+00   5.424020e+00
   5_bss:  0.1163 0.1622   5.186005e+00   5.424020e+00
   5_xyz:  0.1160 0.1611   5.183116e+00   5.419395e+00
   5_adp:  0.1158 0.1599   5.179057e+00   5.413352e+00
   5_occ:  0.1158 0.1599   5.178820e+00   5.413203e+00
   5_bss:  0.1158 0.1599   5.178820e+00   5.413203e+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:  0.360  20.001   7.042   8.132   9.377   0.000   0.000   0.000
   1_xyz:  0.360  20.001   7.042   8.132   9.377   0.000   0.000   0.000
   1_adp:  0.360  20.001   7.042   8.132   9.377   0.000   0.000   0.000
   1_occ:  0.360  20.001   7.042   8.132   9.377   0.000   0.000   0.000
   2_bss:  0.336  37.300   3.617   4.402   6.208   0.000   0.000   0.000
   2_xyz:  0.336  37.300   3.617   4.402   6.208   0.000   0.000   0.000
   2_adp:  0.336  37.300   3.617   4.402   6.208   0.000   0.000   0.000
   2_occ:  0.336  37.300   3.617   4.402   6.208   0.000   0.000   0.000
   3_bss:  0.322  37.302   2.412   2.925   3.856   0.000   0.000   0.000
   3_xyz:  0.322  37.302   2.412   2.925   3.856   0.000   0.000   0.000
   3_adp:  0.322  37.302   2.412   2.925   3.856   0.000   0.000   0.000
   3_occ:  0.322  37.302   2.412   2.925   3.856   0.000   0.000   0.000
   4_bss:  0.322  37.302   2.178   2.555   3.019   0.000   0.000   0.000
   4_xyz:  0.322  37.302   2.178   2.555   3.019   0.000   0.000   0.000
   4_adp:  0.322  37.302   2.178   2.555   3.019   0.000   0.000   0.000
   4_occ:  0.322  37.302   2.178   2.555   3.019   0.000   0.000   0.000
   5_bss:  0.322  37.302   2.178   2.555   3.019   0.000   0.000   0.000
   5_xyz:  0.322  37.302   2.178   2.555   3.019   0.000   0.000   0.000
   5_adp:  0.322  37.302   2.178   2.555   3.019   0.000   0.000   0.000
   5_occ:  0.322  37.302   2.178   2.555   3.019   0.000   0.000   0.000
   5_bss:  0.322  39.886  -0.406  -0.029   0.435   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  53.717 0.4739  0.5492    62079.902
   1_bss:  53.702 0.4711  0.6872    59013.062
   1_xyz:  43.397 0.5996  0.8655    41984.115
   1_adp:  38.582 0.6584  0.9677    35090.445
   1_occ:  38.618 0.6580  0.9671    35158.579
   2_bss:  38.311 0.6615  0.8605    34705.479
   2_xyz:  27.956 0.7791  0.9811    19627.524
   2_adp:  24.989 0.8116  1.0084    16483.679
   2_occ:  25.000 0.8115  1.0079    16480.752
   3_bss:  24.812 0.8133  0.9500    16265.551
   3_xyz:  18.373 0.8766  0.9892     9444.454
   3_adp:  17.021 0.8893  0.9934     8473.797
   3_occ:  17.011 0.8894  0.9933     8469.720
   4_bss:  17.015 0.8894  0.9760     8497.007
   4_xyz:  15.146 0.9055  0.9832     7074.865
   4_adp:  14.819 0.9084  0.9825     6903.008
   4_occ:  14.818 0.9085  0.9823     6908.198
   5_bss:  14.818 0.9085  0.9823     6908.198
   5_xyz:  14.699 0.9095  0.9816     6786.538
   5_adp:  14.562 0.9107  0.9802     6702.729
   5_occ:  14.554 0.9108  0.9801     6702.556
   5_bss:  14.554 0.9108  0.9801     6702.556
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.090   5.3549e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.090   5.3549e+01
   1_xyz:   1.628  0.012  0.105 18.011  0.007  4.111   1.3107e-01
   1_adp:   1.628  0.012  0.105 18.011  0.007  4.111   1.3107e-01
   1_occ:   1.628  0.012  0.105 18.011  0.007  4.111   1.3107e-01
   2_bss:   1.628  0.012  0.105 18.011  0.007  4.111   1.3107e-01
   2_xyz:   1.021  0.007  0.072 15.810  0.005  4.113   6.7251e-02
   2_adp:   1.021  0.007  0.072 15.810  0.005  4.113   6.7251e-02
   2_occ:   1.021  0.007  0.072 15.810  0.005  4.113   6.7251e-02
   3_bss:   1.021  0.007  0.072 15.810  0.005  4.113   6.7251e-02
   3_xyz:   1.022  0.006  0.076 15.426  0.004  4.122   6.1509e-02
   3_adp:   1.022  0.006  0.076 15.426  0.004  4.122   6.1509e-02
   3_occ:   1.022  0.006  0.076 15.426  0.004  4.122   6.1509e-02
   4_bss:   1.022  0.006  0.076 15.426  0.004  4.122   6.1509e-02
   4_xyz:   1.028  0.007  0.080 15.592  0.003  4.126   6.2540e-02
   4_adp:   1.028  0.007  0.080 15.592  0.003  4.126   6.2540e-02
   4_occ:   1.028  0.007  0.080 15.592  0.003  4.126   6.2540e-02
   5_bss:   1.028  0.007  0.080 15.592  0.003  4.126   6.2540e-02
   5_xyz:   0.916  0.005  0.071 15.103  0.003  4.114   5.2066e-02
   5_adp:   0.916  0.005  0.071 15.103  0.003  4.114   5.2066e-02
   5_occ:   0.916  0.005  0.071 15.103  0.003  4.114   5.2066e-02
   5_bss:   0.916  0.005  0.071 15.103  0.003  4.114   5.2066e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9420e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9420e+00
   1_xyz:  14.098  0.155  0.467 86.200  0.055  2.181   9.4433e-02
   1_adp:  14.098  0.155  0.467 86.200  0.055  2.181   9.4433e-02
   1_occ:  14.098  0.155  0.467 86.200  0.055  2.181   9.4433e-02
   2_bss:  14.098  0.155  0.467 86.200  0.055  2.181   9.4433e-02
   2_xyz:   6.234  0.062  0.242 84.040  0.035  2.290   6.5617e-02
   2_adp:   6.234  0.062  0.242 84.040  0.035  2.290   6.5617e-02
   2_occ:   6.234  0.062  0.242 84.040  0.035  2.290   6.5617e-02
   3_bss:   6.234  0.062  0.242 84.040  0.035  2.290   6.5617e-02
   3_xyz:   7.029  0.047  0.425 84.547  0.032  2.366   5.5407e-02
   3_adp:   7.029  0.047  0.425 84.547  0.032  2.366   5.5407e-02
   3_occ:   7.029  0.047  0.425 84.547  0.032  2.366   5.5407e-02
   4_bss:   7.029  0.047  0.425 84.547  0.032  2.366   5.5407e-02
   4_xyz:   7.513  0.042  0.523 82.088  0.029  2.326   4.3848e-02
   4_adp:   7.513  0.042  0.523 82.088  0.029  2.326   4.3848e-02
   4_occ:   7.513  0.042  0.523 82.088  0.029  2.326   4.3848e-02
   5_bss:   7.513  0.042  0.523 82.088  0.029  2.326   4.3848e-02
   5_xyz:   6.817  0.039  0.423 82.691  0.030  2.397   3.1527e-02
   5_adp:   6.817  0.039  0.423 82.691  0.030  2.397   3.1527e-02
   5_occ:   6.817  0.039  0.423 82.691  0.030  2.397   3.1527e-02
   5_bss:   6.817  0.039  0.423 82.691  0.030  2.397   3.1527e-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:  73.19   0.00  11.78  61.14   0.00   8.93  73.19   0.00  27.27
   1_occ:  73.19   0.00  11.78  61.14   0.00   8.93  73.19   0.00  27.27
   2_bss:  73.19   0.00  11.78  61.14   0.00   8.93  73.19   0.00  27.27
   2_xyz:  73.19   0.00  11.78  61.14   0.00   8.93  73.19   0.00  27.27
   2_adp:  74.04   0.00  12.16  65.06   0.00   8.51  74.04   1.21  32.04
   2_occ:  74.04   0.00  12.16  65.06   0.00   8.51  74.04   1.21  32.04
   3_bss:  74.04   0.00  12.16  65.06   0.00   8.51  74.04   1.21  32.04
   3_xyz:  74.04   0.00  12.16  65.06   0.00   8.51  74.04   1.21  32.04
   3_adp:  79.38   0.00  12.81  79.38   0.00   8.48  73.78   2.09  36.37
   3_occ:  79.38   0.00  12.81  79.38   0.00   8.48  73.78   2.09  36.37
   4_bss:  79.38   0.00  12.81  79.38   0.00   8.48  73.78   2.09  36.37
   4_xyz:  79.38   0.00  12.81  79.38   0.00   8.48  73.78   2.09  36.37
   4_adp:  91.04   0.00  12.80  91.04   0.00   8.44  76.71   1.38  36.53
   4_occ:  91.04   0.00  12.80  91.04   0.00   8.44  76.71   1.38  36.53
   5_bss:  91.04   0.00  12.80  91.04   0.00   8.44  76.71   1.38  36.53
   5_xyz:  91.04   0.00  12.80  91.04   0.00   8.44  76.71   1.38  36.53
   5_adp:  92.21   0.00  12.63  92.21   0.00   8.35  76.07   1.31  35.93
   5_occ:  92.21   0.00  12.63  92.21   0.00   8.35  76.07   1.31  35.93
   5_bss:  94.79   2.58  15.22  94.79   2.58  10.94  78.65   3.89  38.51
------------------------------------------------------------------------
 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:    1.213    0.021    0.409
   1_adp:    1.213    0.021    0.409
   1_occ:    1.213    0.021    0.409
   2_bss:    1.213    0.021    0.409
   2_xyz:    1.543    0.024    0.537
   2_adp:    1.543    0.024    0.537
   2_occ:    1.543    0.024    0.537
   3_bss:    1.543    0.024    0.537
   3_xyz:    1.512    0.020    0.599
   3_adp:    1.512    0.020    0.599
   3_occ:    1.512    0.020    0.599
   4_bss:    1.512    0.020    0.599
   4_xyz:    1.626    0.037    0.632
   4_adp:    1.626    0.037    0.632
   4_occ:    1.626    0.037    0.632
   5_bss:    1.626    0.037    0.632
   5_xyz:    1.656    0.041    0.637
   5_adp:    1.656    0.041    0.637
   5_occ:    1.656    0.041    0.637
   5_bss:    1.656    0.041    0.637
------------------------------------------------------------------------

CPU time actual refinement: 342.56


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_793/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_793/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_793/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_793/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_793/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 342.40 
  Macro-tasks:
    bulk solvent and scale       = 39.90  
    individual site refinement   = 148.18 
    weights calculation          = 32.21  
    collect and process          = 6.53   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 226.94 
  Micro-tasks:
    mask                            = 1.80   
    f_calc                          = 107.14 
    alpha_beta                      = 8.34   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 118.61 
    fmodel                         = 7.52   
    r_factors                      = 0.30   
    phase_errors                   = 10.76  
    foms                           = 0.23   
    TOTAL for micro-tasks          = 255.88 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.735 micro seconds
Total CPU time: 5.93 minutes
from_scatterers_fft:    659 calls, 106.77 s
gradients_fft:          603 calls, 104.38 s

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

# Date 2008-01-16 Time 02:26:52 PST -0800 (1200479212.50 s)
Start R-work = 0.4531, R-free = 0.4531 (no bulk solvent and anisotropic scale)
Final R-work = 0.1329, R-free = 0.1774 (no bulk solvent and anisotropic scale)

Start R-work = 0.4449, R-free = 0.4411
Final R-work = 0.1158, R-free = 0.1599