# Date 2008-01-16 Time 02:37:33 PST -0800 (1200479853.43 s)
#phil __OFF__

Command line arguments: "../905.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 29215
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 905

-------------------------------------------------------------------------------
  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: (70.9525, 46.93, 85.5261, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 2.77, per 1000 atoms: 0.98


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 46.93, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0608 1.9811
Completeness in resolution range: 0.958976
Completeness with d_max=infinity: 0.956074

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0608
                             d_min =   1.9811

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: (70.9525, 46.93, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0608 1.9811
Completeness in resolution range: 0.958976
Completeness with d_max=infinity: 0.956074

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0612 -  4.2394 [2140/2169]  1929   211   9.9%
  bin  2:  4.2394 -  3.3774 [2053/2069]  1846   207  10.1%
  bin  3:  3.3774 -  2.9541 [2038/2057]  1832   206  10.1%
  bin  4:  2.9541 -  2.6857 [2028/2058]  1827   201   9.9%
  bin  5:  2.6857 -  2.4941 [1999/2018]  1803   196   9.8%
  bin  6:  2.4941 -  2.3477 [2001/2026]  1794   207  10.3%
  bin  7:  2.3477 -  2.2305 [1956/1989]  1762   194   9.9%
  bin  8:  2.2305 -  2.1337 [1991/2022]  1792   199  10.0%
  bin  9:  2.1337 -  2.0517 [1986/2028]  1787   199  10.0%
  bin 10:  2.0517 -  1.9811 [1397/1991]  1258   139   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_905/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: 0.12 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 11
        2.42 -     3.04: 2201
        3.04 -     3.66: 4673
        3.66 -     4.28: 9036
        4.28 -     4.90: 12357
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.131 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  2.172 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  2.176 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  ... (remaining 28273 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_905/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_905/model_refine_001.geo

CPU time processing inputs: 8.21


============================ 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 = 70.9525 46.93 85.5261 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4250   r_free= 0.4129   ksol= 0.00   Bsol= 0.00   scale= 0.827    |
|                                                                             |
| 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:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.215237                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0612 -  4.7285 0.99   1388  155 0.3638 0.3485      6.5175      6.4672|
|  2:  4.7285 -  3.7726 0.99   1347  146 0.3180 0.3238      6.6227      6.6341|
|  3:  3.7726 -  3.3015 0.99   1316  147 0.3700 0.3361      6.5353      6.5612|
|  4:  3.3015 -  3.0022 0.99   1313  153 0.3937 0.3711      6.4311      6.3515|
|  5:  3.0022 -  2.7885 0.99   1294  139 0.4398 0.4549      6.2993      6.3429|
|  6:  2.7885 -  2.6250 0.99   1287  146 0.4465 0.4535      6.2129      6.1923|
|  7:  2.6250 -  2.4941 0.99   1292  135 0.4788 0.4637      6.2229      6.1802|
|  8:  2.4941 -  2.3860 0.98   1268  150 0.4732 0.4503      6.1253      6.1112|
|  9:  2.3860 -  2.2945 0.98   1271  142 0.4712 0.4502      6.0859      6.0487|
| 10:  2.2945 -  2.2156 0.99   1282  137 0.4758 0.4848      6.0762      6.0712|
| 11:  2.2156 -  2.1465 0.99   1283  143 0.4849 0.4378      6.0163       5.996|
| 12:  2.1465 -  2.0853 0.97   1246  139 0.4747 0.4919      5.9489       5.998|
| 13:  2.0853 -  2.0305 0.99   1269  141 0.5064 0.5199      5.8719      5.8209|
| 14:  2.0305 -  1.9811 0.60    774   86 0.5014 0.4720       5.816      5.7344|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0612 -  4.7285  1388   155  0.74  30.85   0.82     0.76      57691.80|
|  2:  4.7285 -  3.7726  1347   146  0.78  27.71   0.91     0.83      70486.00|
|  3:  3.7726 -  3.3015  1316   147  0.71  34.53   0.88     0.81      73729.81|
|  4:  3.3015 -  3.0022  1313   153  0.65  39.32   0.85     0.74      68368.77|
|  5:  3.0022 -  2.7885  1294   139  0.56  47.50   0.77     0.64      61802.33|
|  6:  2.7885 -  2.6250  1287   146  0.53  49.76   0.77     0.60      55449.53|
|  7:  2.6250 -  2.4941  1292   135  0.53  49.92   0.76     0.59      50415.11|
|  8:  2.4941 -  2.3860  1268   150  0.52  50.83   0.75     0.60      45214.94|
|  9:  2.3860 -  2.2945  1271   142  0.53  49.88   0.76     0.60      39913.93|
| 10:  2.2945 -  2.2156  1282   137  0.52  50.76   0.79     0.59      36708.22|
| 11:  2.2156 -  2.1465  1283   143  0.49  52.73   0.78     0.56      34866.52|
| 12:  2.1465 -  2.0853  1246   139  0.46  55.55   0.79     0.54      35650.34|
| 13:  2.0853 -  2.0305  1269   141  0.42  58.81   0.75     0.50      31851.14|
| 14:  2.0305 -  1.9811   774    86  0.45  56.50   0.73     0.49      25692.09|
|alpha:            min =        0.49 max =            0.83 mean =         0.64|
|beta:             min =    25692.09 max =        73729.81 mean =     50077.79|
|figures of merit: min =        0.00 max =            1.00 mean =         0.57|
|phase err.(work): min =        0.00 max =           89.97 mean =        46.25|
|phase err.(test): min =        0.00 max =           89.91 mean =        46.29|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.813721              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 74.080   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.611167              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.034   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       21 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      165 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      685 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1515 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2622 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3917 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5076 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6562 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7729 |
|-----------------------------------------------------------------------------|
|-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 |       53.758 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.092    4.900  1.196 |       1.653 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.929)------------------------------------------|
|    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 = 11.929)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4339   r_free= 0.4214   ksol= 0.00   Bsol= 0.00   scale= 0.795    |
|                                                                             |
| 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:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.221209                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4172   r_free= 0.4025   ksol= 0.35   Bsol= 20.00   scale= 1.025   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.10,8.04,8.30,0.00,0.00,0.00); trace/3= 8.15                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.211834                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.162420              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 76.249   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.616402              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.149   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4172      final r-factor (work) = 0.3081          |
| start r-factor (free) = 0.4025      final r-factor (free) = 0.3384          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 76.0619 = 7.16 * 0.50 * 6.2282 + 1.00 * 53.7576                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.7970 = 7.16 * 0.50 * 6.0543 + 1.00 * 0.1154                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3081      final r-factor (work) = 0.2423          |
| start r-factor (free) = 0.3384      final r-factor (free) = 0.2845          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7466 = 0.62 * 1.00 * 6.0543 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6256 = 0.62 * 1.00 * 5.8637 + 1.00 * 0.0112                               |
|-----------------------------------------------------------------------------|
| number of iterations = 19      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.929)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    61.90   10.37    None  None   None       |
|    all(noH): 2823   0      0.00    61.90   10.37    None  None   None       |
|    Sol.    : 438    0      0.00    61.90   27.77    None  None   None       |
|    Mac.    : 2385   0      0.00    57.89   7.17     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.190: 1373   |   5:    30.950 -  37.139:   98        |
|      1:     6.190 -  12.380:  730   |   6:    37.139 -  43.329:   75        |
|      2:    12.380 -  18.570:  238   |   7:    43.329 -  49.519:   36        |
|      3:    18.570 -  24.760:  122   |   8:    49.519 -  55.709:    7        |
|      4:    24.760 -  30.950:  140   |   9:    55.709 -  61.899:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2423 r_free = 0.2845             target_work(ml) = 5.788         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2416 r_free = 0.2845             target_work(ml) = 5.787         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2416   r_free= 0.2845   ksol= 0.35   Bsol= 20.00   scale= 1.088   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.10,8.04,8.30,0.00,0.00,0.00); trace/3= 8.15                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.787099                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2366   r_free= 0.2779   ksol= 0.33   Bsol= 40.88   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.63,4.29,5.41,0.00,0.00,0.00); trace/3= 4.78                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.784007                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.447678              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.238   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.319118              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 116.471  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2366      final r-factor (work) = 0.1663          |
| start r-factor (free) = 0.2779      final r-factor (free) = 0.2087          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3024 = 2.45 * 0.50 * 5.8729 + 1.00 * 0.1149                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9405 = 2.45 * 0.50 * 5.6263 + 1.00 * 0.0549                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1663      final r-factor (work) = 0.1544          |
| start r-factor (free) = 0.2087      final r-factor (free) = 0.1969          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8065 = 0.32 * 1.00 * 5.6263 + 1.00 * 0.0111                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7599 = 0.32 * 1.00 * 5.4316 + 1.00 * 0.0266                               |
|-----------------------------------------------------------------------------|
| number of iterations = 12      |    number of function evaluations = 16     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.929)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    63.01   10.75    None  None   None       |
|    all(noH): 2823   0      0.00    63.01   10.75    None  None   None       |
|    Sol.    : 438    0      1.18    63.01   29.86    None  None   None       |
|    Mac.    : 2385   0      0.00    58.49   7.24     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.301: 1412   |   5:    31.505 -  37.805:  128        |
|      1:     6.301 -  12.602:  703   |   6:    37.805 -  44.106:   88        |
|      2:    12.602 -  18.903:  212   |   7:    44.106 -  50.407:   34        |
|      3:    18.903 -  25.204:  117   |   8:    50.407 -  56.708:    8        |
|      4:    25.204 -  31.505:  117   |   9:    56.708 -  63.009:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1544 r_free = 0.1969             target_work(ml) = 5.405         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1543 r_free = 0.1968             target_work(ml) = 5.405         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1543   r_free= 0.1968   ksol= 0.33   Bsol= 40.88   scale= 1.027   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.63,4.29,5.41,0.00,0.00,0.00); trace/3= 4.78                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.404853                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1535   r_free= 0.1952   ksol= 0.34   Bsol= 40.88   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.36,3.29,4.25,0.00,0.00,0.00); trace/3= 3.63                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.405164                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.689268              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 110.727  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.737453              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 95.039   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1535      final r-factor (work) = 0.1291          |
| start r-factor (free) = 0.1952      final r-factor (free) = 0.1709          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.6494 = 1.69 * 0.50 * 5.4397 + 1.00 * 0.0549                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.5548 = 1.69 * 0.50 * 5.3261 + 1.00 * 0.0562                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1291      final r-factor (work) = 0.1220          |
| start r-factor (free) = 0.1709      final r-factor (free) = 0.1648          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9402 = 0.74 * 1.00 * 5.3261 + 1.00 * 0.0125                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8765 = 0.74 * 1.00 * 5.2300 + 1.00 * 0.0196                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.929)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    70.90   11.60    None  None   None       |
|    all(noH): 2823   0      0.00    70.90   11.60    None  None   None       |
|    Sol.    : 438    0      0.99    68.58   34.16    None  None   None       |
|    Mac.    : 2385   0      0.00    70.90   7.45     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 -   7.090: 1555   |   5:    35.448 -  42.538:   87        |
|      1:     7.090 -  14.179:  617   |   6:    42.538 -  49.627:   85        |
|      2:    14.179 -  21.269:  187   |   7:    49.627 -  56.717:   58        |
|      3:    21.269 -  28.359:   97   |   8:    56.717 -  63.807:   21        |
|      4:    28.359 -  35.448:  106   |   9:    63.807 -  70.896:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1220 r_free = 0.1648             target_work(ml) = 5.211         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1219 r_free = 0.1648             target_work(ml) = 5.211         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1219   r_free= 0.1648   ksol= 0.34   Bsol= 40.88   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.36,3.29,4.25,0.00,0.00,0.00); trace/3= 3.63                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.211201                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1221   r_free= 0.1649   ksol= 0.33   Bsol= 45.53   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.18,3.18,3.96,0.00,0.00,0.00); trace/3= 3.44                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.211467                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.583586              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 117.569  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.491553              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 96.975   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1221      final r-factor (work) = 0.1125          |
| start r-factor (free) = 0.1649      final r-factor (free) = 0.1581          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8120 = 2.58 * 0.50 * 5.2298 + 1.00 * 0.0562                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7543 = 2.58 * 0.50 * 5.1763 + 1.00 * 0.0676                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1125      final r-factor (work) = 0.1117          |
| start r-factor (free) = 0.1581      final r-factor (free) = 0.1577          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5595 = 0.49 * 1.00 * 5.1763 + 1.00 * 0.0151                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5541 = 0.49 * 1.00 * 5.1528 + 1.00 * 0.0212                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.929)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.49   11.50    None  None   None       |
|    all(noH): 2823   0      0.00    77.49   11.50    None  None   None       |
|    Sol.    : 438    0      1.07    69.81   33.69    None  None   None       |
|    Mac.    : 2385   0      0.00    77.49   7.42     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 -   7.749: 1665   |   5:    38.745 -  46.494:   85        |
|      1:     7.749 -  15.498:  575   |   6:    46.494 -  54.243:   73        |
|      2:    15.498 -  23.247:  150   |   7:    54.243 -  61.992:   30        |
|      3:    23.247 -  30.996:  112   |   8:    61.992 -  69.741:   12        |
|      4:    30.996 -  38.745:  115   |   9:    69.741 -  77.490:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1117 r_free = 0.1577             target_work(ml) = 5.150         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1116 r_free = 0.1576             target_work(ml) = 5.149         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1116   r_free= 0.1576   ksol= 0.33   Bsol= 45.53   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.18,3.18,3.96,0.00,0.00,0.00); trace/3= 3.44                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.149486                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1116   r_free= 0.1576   ksol= 0.33   Bsol= 45.53   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.21,3.24,4.00,0.00,0.00,0.00); trace/3= 3.49                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.149515                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.125579              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 149.194  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.338902              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 99.173   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1116      final r-factor (work) = 0.1112          |
| start r-factor (free) = 0.1576      final r-factor (free) = 0.1573          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5438 = 2.13 * 0.50 * 5.1525 + 1.00 * 0.0678                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5325 = 2.13 * 0.50 * 5.1488 + 1.00 * 0.0604                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1112      final r-factor (work) = 0.1115          |
| start r-factor (free) = 0.1573      final r-factor (free) = 0.1571          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7595 = 0.34 * 1.00 * 5.1488 + 1.00 * 0.0145                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7833 = 0.34 * 1.00 * 5.1491 + 1.00 * 0.0383                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 34     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.929)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.13   11.29    None  None   None       |
|    all(noH): 2823   0      0.00    79.13   11.29    None  None   None       |
|    Sol.    : 438    0      0.99    67.23   32.80    None  None   None       |
|    Mac.    : 2385   0      0.00    79.13   7.34     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.913: 1705   |   5:    39.565 -  47.478:   91        |
|      1:     7.913 -  15.826:  552   |   6:    47.478 -  55.391:   57        |
|      2:    15.826 -  23.739:  147   |   7:    55.391 -  63.304:   21        |
|      3:    23.739 -  31.652:  126   |   8:    63.304 -  71.217:    7        |
|      4:    31.652 -  39.565:  112   |   9:    71.217 -  79.130:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1115 r_free = 0.1571             target_work(ml) = 5.148         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1114 r_free = 0.1570             target_work(ml) = 5.148         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1114   r_free= 0.1570   ksol= 0.33   Bsol= 45.53   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.21,3.24,4.00,0.00,0.00,0.00); trace/3= 3.49                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.147605                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0612 -  4.7285 0.99   1388  155 0.0990 0.1310      5.3862      5.5292|
|  2:  4.7285 -  3.7726 0.99   1347  146 0.0869 0.1108      5.4448       5.639|
|  3:  3.7726 -  3.3015 0.99   1316  147 0.1047 0.1524      5.4646      5.8631|
|  4:  3.3015 -  3.0022 0.99   1313  153 0.1186 0.1504       5.448      5.5622|
|  5:  3.0022 -  2.7885 0.99   1294  139 0.1311 0.1776      5.3251      5.5647|
|  6:  2.7885 -  2.6250 0.99   1287  146 0.1197 0.1785      5.2019      5.4636|
|  7:  2.6250 -  2.4941 0.99   1292  135 0.1255 0.1634      5.1743      5.3727|
|  8:  2.4941 -  2.3860 0.98   1268  150 0.1161 0.1726      5.0614      5.3329|
|  9:  2.3860 -  2.2945 0.98   1271  142 0.1191 0.1792      5.0515      5.3366|
| 10:  2.2945 -  2.2156 0.99   1282  137 0.1110 0.1688      4.9556      5.1957|
| 11:  2.2156 -  2.1465 0.99   1283  143 0.1152 0.1803      4.9473      5.3081|
| 12:  2.1465 -  2.0853 0.97   1246  139 0.1081 0.1573      4.8635      5.0886|
| 13:  2.0853 -  2.0305 0.99   1269  141 0.1182 0.1802      4.8044      5.0897|
| 14:  2.0305 -  1.9811 0.60    774   86 0.1097 0.1688      4.6912         4.9|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0612 -  4.7285  1388   155  0.94   9.05   0.98     0.95       7217.99|
|  2:  4.7285 -  3.7726  1347   146  0.95   7.95   1.01     1.00       9085.53|
|  3:  3.7726 -  3.3015  1316   147  0.93  11.30   1.02     1.01      10303.17|
|  4:  3.3015 -  3.0022  1313   153  0.92  13.57   1.01     0.99      10363.45|
|  5:  3.0022 -  2.7885  1294   139  0.90  16.14   0.99     0.96       8282.62|
|  6:  2.7885 -  2.6250  1287   146  0.90  15.85   0.98     0.96       7082.06|
|  7:  2.6250 -  2.4941  1292   135  0.91  15.35   0.99     0.96       6191.01|
|  8:  2.4941 -  2.3860  1268   150  0.91  15.26   0.99     0.97       5319.76|
|  9:  2.3860 -  2.2945  1271   142  0.91  15.39   1.01     0.99       5138.42|
| 10:  2.2945 -  2.2156  1282   137  0.90  15.44   1.00     0.96       4306.17|
| 11:  2.2156 -  2.1465  1283   143  0.90  16.50   1.00     0.97       4441.74|
| 12:  2.1465 -  2.0853  1246   139  0.92  14.53   1.01     0.99       3858.82|
| 13:  2.0853 -  2.0305  1269   141  0.89  16.77   1.00     0.99       3454.79|
| 14:  2.0305 -  1.9811   774    86  0.91  15.30   0.98     0.95       2694.86|
|alpha:            min =        0.95 max =            1.01 mean =         0.98|
|beta:             min =     2694.86 max =        10363.45 mean =      6411.10|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.08|
|phase err.(test): min =        0.00 max =           89.07 mean =        13.56|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1114   r_free= 0.1571   ksol= 0.33   Bsol= 49.03   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.28,-0.24,0.52,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.147622                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1114   r_free= 0.1571   ksol= 0.33   Bsol= 49.03   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.28,-0.24,0.52,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.147622                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0612 -  4.7285 0.99   1388  155 0.0990 0.1310      5.3863      5.5293|
|  2:  4.7285 -  3.7726 0.99   1347  146 0.0869 0.1108      5.4448      5.6389|
|  3:  3.7726 -  3.3015 0.99   1316  147 0.1047 0.1524      5.4646       5.863|
|  4:  3.3015 -  3.0022 0.99   1313  153 0.1186 0.1504       5.448      5.5622|
|  5:  3.0022 -  2.7885 0.99   1294  139 0.1312 0.1777      5.3251      5.5648|
|  6:  2.7885 -  2.6250 0.99   1287  146 0.1197 0.1784      5.2019      5.4635|
|  7:  2.6250 -  2.4941 0.99   1292  135 0.1255 0.1634      5.1742      5.3726|
|  8:  2.4941 -  2.3860 0.98   1268  150 0.1161 0.1726      5.0613      5.3329|
|  9:  2.3860 -  2.2945 0.98   1271  142 0.1191 0.1792      5.0515      5.3366|
| 10:  2.2945 -  2.2156 0.99   1282  137 0.1110 0.1688      4.9557      5.1958|
| 11:  2.2156 -  2.1465 0.99   1283  143 0.1152 0.1804      4.9474      5.3083|
| 12:  2.1465 -  2.0853 0.97   1246  139 0.1081 0.1573      4.8637      5.0887|
| 13:  2.0853 -  2.0305 0.99   1269  141 0.1182 0.1803      4.8045      5.0899|
| 14:  2.0305 -  1.9811 0.60    774   86 0.1097 0.1688      4.6913      4.8999|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0612 -  4.7285  1388   155  0.94   9.06   0.98     0.95       7218.78|
|  2:  4.7285 -  3.7726  1347   146  0.95   7.95   1.01     1.00       9085.02|
|  3:  3.7726 -  3.3015  1316   147  0.93  11.29   1.02     1.01      10300.99|
|  4:  3.3015 -  3.0022  1313   153  0.92  13.57   1.01     0.99      10363.72|
|  5:  3.0022 -  2.7885  1294   139  0.90  16.14   0.99     0.96       8282.20|
|  6:  2.7885 -  2.6250  1287   146  0.90  15.86   0.98     0.96       7082.23|
|  7:  2.6250 -  2.4941  1292   135  0.91  15.35   0.99     0.96       6189.97|
|  8:  2.4941 -  2.3860  1268   150  0.91  15.26   0.99     0.97       5319.37|
|  9:  2.3860 -  2.2945  1271   142  0.91  15.39   1.01     0.99       5137.81|
| 10:  2.2945 -  2.2156  1282   137  0.90  15.44   1.00     0.96       4306.69|
| 11:  2.2156 -  2.1465  1283   143  0.90  16.51   1.00     0.97       4442.33|
| 12:  2.1465 -  2.0853  1246   139  0.92  14.53   1.01     0.99       3860.29|
| 13:  2.0853 -  2.0305  1269   141  0.89  16.77   1.00     0.99       3455.33|
| 14:  2.0305 -  1.9811   774    86  0.91  15.31   0.99     0.95       2694.75|
|alpha:            min =        0.95 max =            1.01 mean =         0.98|
|beta:             min =     2694.75 max =        10363.72 mean =      6411.04|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.08|
|phase err.(test): min =        0.00 max =           89.07 mean =        13.56|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.929)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.50    82.63   14.79    None  None   None       |
|    all(noH): 2823   0      3.50    82.63   14.79    None  None   None       |
|    Sol.    : 438    0      4.49    70.73   36.30    None  None   None       |
|    Mac.    : 2385   0      3.50    82.63   10.84    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     3.499 -  11.412: 1705   |   5:    43.064 -  50.977:   91        |
|      1:    11.412 -  19.325:  552   |   6:    50.977 -  58.890:   57        |
|      2:    19.325 -  27.238:  147   |   7:    58.890 -  66.803:   21        |
|      3:    27.238 -  35.151:  126   |   8:    66.803 -  74.716:    7        |
|      4:    35.151 -  43.064:  112   |   9:    74.716 -  82.629:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 320         
Filter by distance & map next to the model:
   mapped sites are within: 0.368 - 5.814
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 316 from: 320
   mapped sites are within: 0.722 - 5.814

peak=   11.215 closest distance to " CB  VAL A 230 " =    1.468
peak=    7.690 closest distance to " CG2 VAL A 296 " =    1.159
peak=    6.301 closest distance to " CG  LEU A   5 " =    1.257
peak=    5.764 closest distance to " NH2 ARG A  56 " =    2.203
peak=    5.612 closest distance to " CD2 LEU A   5 " =    1.207
peak=    5.505 closest distance to " CG  PRO A  54 " =    1.287
peak=    5.445 closest distance to " CG  LEU A 228 " =    1.188
peak=    5.404 closest distance to " CB  GLN A 223 " =    1.430
peak=    5.089 closest distance to " CB  SER A  63 " =    1.295
peak=    5.021 closest distance to " CB  PRO A  54 " =    0.975
peak=    4.982 closest distance to " O   HOH Z 126 " =    1.904
peak=    4.896 closest distance to " CB  GLN A 183 " =    1.257
peak=    4.783 closest distance to " NE2 GLN A  11 " =    1.109
peak=    4.782 closest distance to " O   HOH Z 232 " =    2.307
peak=    4.770 closest distance to " CB  VAL A 296 " =    1.081
peak=    4.735 closest distance to " CG  PRO A 213 " =    1.203
peak=    4.675 closest distance to " CG  PRO A 243 " =    1.168
peak=    4.623 closest distance to " CB  ARG A 275 " =    0.868
peak=    4.616 closest distance to " OD1 ASN A  69 " =    2.632
peak=    4.592 closest distance to " C   PRO A 198 " =    1.514
peak=    4.581 closest distance to " CB  GLU A 152 " =    1.155
peak=    4.526 closest distance to " O   HOH Z 272 " =    1.869
peak=    4.496 closest distance to " O   HOH Z 298 " =    1.763
peak=    4.496 closest distance to " O   HOH Z 142 " =    1.663
peak=    4.494 closest distance to " CD2 LEU A 228 " =    1.168
peak=    4.453 closest distance to " CG  PRO A 198 " =    1.225
peak=    4.406 closest distance to " CB  ASN A 148 " =    1.300
peak=    4.395 closest distance to " O   HOH Z 316 " =    3.018
peak=    4.390 closest distance to " CB  SER A   3 " =    1.349
peak=    4.388 closest distance to " CB  VAL A 230 " =    1.179
peak=    4.363 closest distance to " O   HOH Z 369 " =    2.077
peak=    4.346 closest distance to " CB  GLU A 128 " =    1.059
peak=    4.337 closest distance to " CB  TYR A 169 " =    0.746
peak=    4.260 closest distance to " ND2 ASN A 187 " =    1.481
peak=    4.259 closest distance to " O   HOH Z 427 " =    3.031
peak=    4.254 closest distance to " O   HOH Z 368 " =    2.143
peak=    4.252 closest distance to " O   HOH Z 236 " =    1.880
peak=    4.193 closest distance to " O   HOH Z 265 " =    2.455
peak=    4.151 closest distance to " CB  VAL A 265 " =    1.295
peak=    4.111 closest distance to " O   HOH Z 193 " =    1.830
peak=    4.084 closest distance to " OD2 ASP A 286 " =    2.831
peak=    4.040 closest distance to " CB  TRP A 266 " =    0.932
peak=    4.038 closest distance to " O   SER A  87 " =    2.296
peak=    4.033 closest distance to " O   HOH Z 303 " =    2.086
peak=    4.029 closest distance to " O   HOH Z  78 " =    1.677
peak=    4.015 closest distance to " CB  ASN A 187 " =    1.293
peak=    4.012 closest distance to " O   HOH Z  61 " =    1.667
peak=    4.009 closest distance to " O   HOH Z 263 " =    1.630
peak=    4.008 closest distance to " O   HOH Z 203 " =    1.738
peak=    4.002 closest distance to " ND2 ASN A 249 " =    1.936
peak=    3.994 closest distance to " O   HOH Z 158 " =    3.087
peak=    3.993 closest distance to " CA  TYR A  30 " =    0.925
peak=    3.992 closest distance to " CB  ARG A  79 " =    1.410
peak=    3.943 closest distance to " CB  LEU A 143 " =    1.157
peak=    3.938 closest distance to " O   HOH Z 234 " =    3.667
peak=    3.936 closest distance to " O   HOH Z 346 " =    1.575
peak=    3.936 closest distance to " CG1BVAL A  72 " =    1.620
peak=    3.928 closest distance to " CA  THR A 264 " =    0.777
peak=    3.924 closest distance to " O   HOH Z 209 " =    2.349
peak=    3.909 closest distance to " CA  ALA A  51 " =    1.018
peak=    3.907 closest distance to " O   HOH Z  88 " =    3.204
peak=    3.892 closest distance to " O   HOH Z 403 " =    1.675
peak=    3.887 closest distance to " CG  ARG A  66 " =    2.713
peak=    3.887 closest distance to " CA  THR A 221 " =    0.939
peak=    3.877 closest distance to " CD1 LEU A 300 " =    1.189
peak=    3.871 closest distance to " CB  GLU A 277 " =    3.588
peak=    3.866 closest distance to " CB  TRP A 179 " =    1.376
peak=    3.861 closest distance to " CB  ASN A  39 " =    0.903
peak=    3.856 closest distance to " O   HOH Z 411 " =    3.781
peak=    3.840 closest distance to " O   HOH Z 423 " =    1.719
peak=    3.837 closest distance to " O   HOH Z 189 " =    2.702
peak=    3.837 closest distance to " CB  ASP A 140 " =    0.902
peak=    3.817 closest distance to " CA  ALA A  21 " =    1.171
peak=    3.816 closest distance to " O   HOH Z 128 " =    2.078
peak=    3.811 closest distance to " CB  ALA A   9 " =    1.597
peak=    3.808 closest distance to " CA  ASN A 215 " =    1.211
peak=    3.792 closest distance to " O   TRP A 274 " =    1.883
peak=    3.779 closest distance to " O   HOH Z 280 " =    2.960
peak=    3.774 closest distance to " O   HOH Z  68 " =    2.081
peak=    3.774 closest distance to " O   HOH Z  97 " =    1.997
peak=    3.767 closest distance to " O   HOH Z 273 " =    2.613
peak=    3.764 closest distance to " O   HOH Z  15 " =    2.174
peak=    3.754 closest distance to " O   HOH Z 193 " =    1.699
peak=    3.754 closest distance to " CZ  PHE A 218 " =    1.062
peak=    3.748 closest distance to " CD BLYS A 290 " =    1.099
peak=    3.746 closest distance to " O   HOH Z 261 " =    2.074
peak=    3.745 closest distance to " CD  ARG A 269 " =    0.980
peak=    3.744 closest distance to " O   HOH Z 344 " =    2.906
peak=    3.743 closest distance to " O   HOH Z 425 " =    1.359
peak=    3.737 closest distance to " CB  LEU A 228 " =    1.285
peak=    3.728 closest distance to " NH2 ARG A 156 " =    1.150
peak=    3.727 closest distance to " CB BVAL A  41 " =    1.065
peak=    3.726 closest distance to " O   HOH Z 197 " =    3.151
peak=    3.716 closest distance to " CB  SER A 216 " =    0.792
peak=    3.699 closest distance to " CB  ARG A 139 " =    0.923
peak=    3.696 closest distance to " O   HOH Z 145 " =    1.993
peak=    3.686 closest distance to " CB  SER A 212 " =    1.194
peak=    3.684 closest distance to " NH1AARG A 145 " =    1.096
peak=    3.668 closest distance to " CA  LYS A 117 " =    1.204
peak=    3.665 closest distance to " CG  LEU A 167 " =    1.192
peak=    3.664 closest distance to " CG2 THR A 221 " =    1.125
peak=    3.663 closest distance to " O   HOH Z 329 " =    3.802
peak=    3.660 closest distance to " ND2 ASN A 110 " =    1.763
peak=    3.655 closest distance to " CD  ARG A 159 " =    0.773
peak=    3.651 closest distance to " CG1 ILE A  33 " =    1.320
peak=    3.650 closest distance to " CB  ALA A 248 " =    1.440
peak=    3.644 closest distance to " O   HOH Z 133 " =    1.673
peak=    3.635 closest distance to " O   HOH Z 250 " =    1.368
peak=    3.632 closest distance to " O   HOH Z 193 " =    1.934
peak=    3.632 closest distance to " OG BSER A 164 " =    2.182
peak=    3.623 closest distance to " O   HOH Z 425 " =    2.033
peak=    3.623 closest distance to " NZ  LYS A 117 " =    3.244
peak=    3.622 closest distance to " O   HOH Z 371 " =    3.105
peak=    3.611 closest distance to " O   HOH Z  59 " =    2.097
peak=    3.593 closest distance to " O   HOH Z 402 " =    1.464
peak=    3.591 closest distance to " O   MET A 105 " =    1.793
peak=    3.590 closest distance to " CG1 VAL A 153 " =    0.886
peak=    3.579 closest distance to " CA  ALA A 158 " =    1.160
peak=    3.576 closest distance to " ND1 HIS A  81 " =    1.679
peak=    3.576 closest distance to " O   HOH Z 112 " =    1.631
peak=    3.555 closest distance to " O   HOH Z  43 " =    2.130
peak=    3.555 closest distance to " CA  MET A  40 " =    1.111
peak=    3.553 closest distance to " O   HOH Z 245 " =    1.401
peak=    3.551 closest distance to " CB  VAL A 202 " =    1.625
peak=    3.550 closest distance to " O   HOH Z  93 " =    2.705
peak=    3.545 closest distance to " CA  SER A  87 " =    0.945
peak=    3.544 closest distance to " O   HOH Z 214 " =    2.069
peak=    3.540 closest distance to " O   HOH Z 345 " =    3.479
peak=    3.538 closest distance to " O   HOH Z 132 " =    2.611
peak=    3.536 closest distance to " CB  ARG A 190 " =    1.662
peak=    3.532 closest distance to " O   HOH Z 135 " =    1.774
peak=    3.524 closest distance to " CA  LEU A 282 " =    1.075
peak=    3.515 closest distance to " O   HOH Z 426 " =    1.545
peak=    3.511 closest distance to " CZ  PHE A 192 " =    0.983
peak=    3.511 closest distance to " CA  ASP A 140 " =    1.248
peak=    3.510 closest distance to " CG BARG A 102 " =    1.826
peak=    3.500 closest distance to " CA  VAL A  41 " =    0.835
peak=    3.494 closest distance to " CB  GLN A  88 " =    1.224
peak=    3.492 closest distance to " CE1 TYR A 186 " =    1.321
peak=    3.488 closest distance to " O   HOH Z  40 " =    2.377
peak=    3.484 closest distance to " O   HOH Z 437 " =    1.985
peak=    3.483 closest distance to " CB  ASN A 142 " =    1.017
peak=    3.470 closest distance to " CB  GLN A 278 " =    0.888
peak=    3.469 closest distance to " CD1 ILE A 106 " =    1.050
peak=    3.464 closest distance to " CB  ALA A 291 " =    1.399
peak=    3.463 closest distance to " O   HOH Z 368 " =    3.626
peak=    3.460 closest distance to " O   HOH Z 407 " =    2.419
peak=    3.454 closest distance to " O   HOH Z 108 " =    2.506
peak=    3.454 closest distance to " O   HOH Z   9 " =    1.998
peak=    3.444 closest distance to " CA  GLY A 267 " =    0.816
peak=    3.434 closest distance to " O   HOH Z 248 " =    1.751
peak=    3.430 closest distance to " N   ASN A  39 " =    1.157
peak=    3.429 closest distance to " CG  MET A 185 " =    1.257
peak=    3.428 closest distance to " O   HOH Z  10 " =    1.849
peak=    3.428 closest distance to " O   HOH Z  61 " =    1.582
peak=    3.424 closest distance to " O   HOH Z 171 " =    2.384
peak=    3.422 closest distance to " CB  HIS A 108 " =    0.795
peak=    3.421 closest distance to " CB  MET A  40 " =    0.811
peak=    3.418 closest distance to " N   SER A 135 " =    1.364
peak=    3.413 closest distance to " CB  THR A 157 " =    1.134
peak=    3.408 closest distance to " CE  LYS A  76 " =    0.879
peak=    3.408 closest distance to " O   HOH Z  21 " =    1.694
peak=    3.406 closest distance to " O   HOH Z 147 " =    1.708
peak=    3.406 closest distance to " N   PHE A 130 " =    1.267
peak=    3.404 closest distance to " O   HOH Z 128 " =    2.158
peak=    3.399 closest distance to " O   HOH Z 134 " =    1.417
peak=    3.398 closest distance to " N   VAL A 126 " =    1.335
peak=    3.396 closest distance to " O   HOH Z 291 " =    1.541
peak=    3.394 closest distance to " CB  TRP A 150 " =    1.410
peak=    3.393 closest distance to " CG  MET A 185 " =    1.088
peak=    3.389 closest distance to " OG  SER A 206 " =    1.207
peak=    3.389 closest distance to " CD  LYS A 166 " =    1.295
peak=    3.383 closest distance to " C   ALA A 299 " =    0.951
peak=    3.382 closest distance to " O   HOH Z 359 " =    3.810
peak=    3.380 closest distance to " CG1 ILE A  49 " =    1.429
peak=    3.379 closest distance to " CG  GLN A  88 " =    1.033
peak=    3.377 closest distance to " CB  THR A  31 " =    1.685
peak=    3.370 closest distance to " O   HOH Z   1 " =    1.888
peak=    3.367 closest distance to " O   HOH Z 227 " =    2.081
peak=    3.365 closest distance to " CG2 ILE A 120 " =    1.271
peak=    3.364 closest distance to " CA  VAL A 126 " =    0.853
peak=    3.357 closest distance to " CG2 VAL A 257 " =    0.904
peak=    3.355 closest distance to " O   HOH Z 227 " =    1.663
peak=    3.354 closest distance to " CA  ALA A 295 " =    1.051
peak=    3.352 closest distance to " O   HOH Z 180 " =    2.091
peak=    3.351 closest distance to " O   HOH Z 247 " =    1.308
peak=    3.351 closest distance to " O   ALA A 158 " =    1.376
peak=    3.349 closest distance to " O   HOH Z 411 " =    1.833
peak=    3.349 closest distance to " NH1BARG A 190 " =    1.832
peak=    3.348 closest distance to " CA  ALA A 233 " =    1.359
peak=    3.347 closest distance to " ND1 HIS A  86 " =    1.613
peak=    3.346 closest distance to " CA  ARG A 195 " =    1.226
peak=    3.343 closest distance to " CA  ALA A 291 " =    0.978
peak=    3.338 closest distance to " OG  SER A  22 " =    2.835
peak=    3.336 closest distance to " CG1 VAL A 296 " =    1.219
peak=    3.330 closest distance to " OG1 THR A 294 " =    2.376
peak=    3.329 closest distance to " CA  ARG A  36 " =    1.102
peak=    3.328 closest distance to " CD1 LEU A  96 " =    0.722
peak=    3.327 closest distance to " CB  ARG A  79 " =    0.879
peak=    3.322 closest distance to " O   ALA A   1 " =    1.558
peak=    3.320 closest distance to " CD2 LEU A 255 " =    1.577
peak=    3.318 closest distance to " OG BSER A 134 " =    2.850
peak=    3.312 closest distance to " CD  LYS A 119 " =    1.522
peak=    3.311 closest distance to " O   HOH Z 435 " =    2.000
peak=    3.311 closest distance to " CD2 HIS A  81 " =    1.141
peak=    3.309 closest distance to " O   HOH Z 281 " =    4.669
peak=    3.306 closest distance to " O   HOH Z 423 " =    2.851
peak=    3.305 closest distance to " N   ARG A 156 " =    1.344
peak=    3.304 closest distance to " O   HOH Z 302 " =    1.924
peak=    3.304 closest distance to " NZ  LYS A  48 " =    1.438
peak=    3.301 closest distance to " O   HOH Z 128 " =    1.666
peak=    3.299 closest distance to " CD2 TRP A 179 " =    1.403
peak=    3.295 closest distance to " O   HOH Z 409 " =    3.279
peak=    3.289 closest distance to " CA  GLN A 194 " =    1.256
peak=    3.289 closest distance to " N   ARG A 190 " =    1.066
peak=    3.288 closest distance to " CB  ALA A 248 " =    0.997
peak=    3.287 closest distance to " OD1BASN A 224 " =    2.268
peak=    3.287 closest distance to " CG2 THR A 294 " =    1.702
peak=    3.285 closest distance to " O   HOH Z 128 " =    1.977
peak=    3.284 closest distance to " CA  GLY A 211 " =    1.270
peak=    3.282 closest distance to " CD1 ILE A  33 " =    1.584
peak=    3.282 closest distance to " O   HOH Z 286 " =    2.346
peak=    3.282 closest distance to " O   HOH Z 172 " =    3.734
peak=    3.280 closest distance to " O   HOH Z 313 " =    1.790
peak=    3.280 closest distance to " O   HOH Z 285 " =    3.097
peak=    3.275 closest distance to " CB  VAL A 268 " =    0.847
peak=    3.274 closest distance to " O   HOH Z  20 " =    1.618
peak=    3.271 closest distance to " O  BHOH Z 338 " =    2.422
peak=    3.271 closest distance to " CB  ASN A 224 " =    1.069
peak=    3.270 closest distance to " CG1 ILE A 151 " =    1.054
peak=    3.270 closest distance to " O   HOH Z 353 " =    2.696
peak=    3.268 closest distance to " CB  ASN A 110 " =    1.159
peak=    3.262 closest distance to " CA  ILE A 106 " =    0.781
peak=    3.261 closest distance to " CB  ILE A  20 " =    1.470
peak=    3.260 closest distance to " CG2 THR A 220 " =    0.926
peak=    3.260 closest distance to " O   HOH Z 216 " =    2.606
peak=    3.257 closest distance to " CD1 LEU A   5 " =    1.377
peak=    3.253 closest distance to " CA  ALA A 154 " =    0.978
peak=    3.249 closest distance to " O   HOH Z 145 " =    3.638
peak=    3.245 closest distance to " O   HOH Z 189 " =    2.958
peak=    3.241 closest distance to " O   HOH Z 175 " =    2.123
peak=    3.239 closest distance to " CB  LEU A 255 " =    0.799
peak=    3.239 closest distance to " O   HOH Z  54 " =    1.576
peak=    3.231 closest distance to " CB  MET A  47 " =    1.096
peak=    3.231 closest distance to " O   HOH Z 126 " =    1.610
peak=    3.230 closest distance to " CB  LYS A 117 " =    1.172
peak=    3.229 closest distance to " CB  ILE A 120 " =    1.342
peak=    3.227 closest distance to " NH2BARG A 145 " =    2.079
peak=    3.223 closest distance to " CB  ALA A 114 " =    1.276
peak=    3.223 closest distance to " O   HOH Z 213 " =    1.772
peak=    3.219 closest distance to " CA  LYS A 290 " =    1.277
peak=    3.215 closest distance to " O   HOH Z 130 " =    2.240
peak=    3.213 closest distance to " N   ASN A 127 " =    1.235
peak=    3.212 closest distance to " O   HOH Z 116 " =    1.763
peak=    3.211 closest distance to " CA  ASP A 191 " =    0.761
peak=    3.210 closest distance to " CB  PRO A 198 " =    1.011
peak=    3.209 closest distance to " O   HOH Z 290 " =    1.118
peak=    3.205 closest distance to " O   HOH Z 383 " =    2.136
peak=    3.202 closest distance to " CG1 VAL A 174 " =    1.076
peak=    3.202 closest distance to " OE1 GLU A   2 " =    2.120
peak=    3.201 closest distance to " CB  ALA A 161 " =    0.841
peak=    3.201 closest distance to " N   GLN A 278 " =    1.006
peak=    3.198 closest distance to " O   HOH Z 213 " =    1.818
peak=    3.194 closest distance to " CZ2 TRP A 274 " =    1.571
peak=    3.194 closest distance to " O   HOH Z 250 " =    1.346
peak=    3.193 closest distance to " O   HOH Z  48 " =    1.350
peak=    3.192 closest distance to " O   HOH Z  48 " =    1.736
peak=    3.187 closest distance to " O   HOH Z 185 " =    2.284
peak=    3.186 closest distance to " CD1 LEU A 228 " =    1.808
peak=    3.185 closest distance to " CB  SER A  26 " =    1.614
peak=    3.184 closest distance to " O   HOH Z 422 " =    2.693
peak=    3.182 closest distance to " O   HOH Z 374 " =    2.612
peak=    3.180 closest distance to " O   HOH Z 305 " =    3.566
peak=    3.179 closest distance to " CG BARG A 275 " =    1.442
peak=    3.178 closest distance to " OD1 ASN A 217 " =    1.664
peak=    3.176 closest distance to " O   HOH Z 271 " =    2.013
peak=    3.174 closest distance to " O   HOH Z 286 " =    2.507
peak=    3.174 closest distance to " O   ASN A 217 " =    1.245
peak=    3.174 closest distance to " O   HOH Z 303 " =    1.741
peak=    3.174 closest distance to " NH2AARG A 275 " =    3.658
peak=    3.174 closest distance to " CB  GLU A  46 " =    1.070
peak=    3.170 closest distance to " O   HOH Z 279 " =    2.188
peak=    3.169 closest distance to " CB  ALA A 137 " =    1.087
peak=    3.166 closest distance to " C   SER A  32 " =    1.019
peak=    3.164 closest distance to " CB  SER A  62 " =    1.267
peak=    3.163 closest distance to " O   HOH Z 148 " =    3.289
peak=    3.161 closest distance to " CG2 ILE A  20 " =    1.500
peak=    3.158 closest distance to " O   HOH Z  49 " =    2.547
peak=    3.153 closest distance to " O   HOH Z 417 " =    2.100
peak=    3.143 closest distance to " O   HOH Z  92 " =    2.494
peak=    3.140 closest distance to " O   HOH Z 367 " =    3.515
peak=    3.140 closest distance to " O   HOH Z 163 " =    1.821
peak=    3.136 closest distance to " NE2 GLN A  58 " =    5.814
peak=    3.133 closest distance to " NH2 ARG A  79 " =    1.414
peak=    3.126 closest distance to " O   HOH Z 313 " =    1.769
peak=    3.122 closest distance to " CB  PHE A 283 " =    0.762
peak=    3.121 closest distance to " O   HOH Z  80 " =    1.583
peak=    3.120 closest distance to " CG  GLN A  77 " =    2.195
peak=    3.116 closest distance to " OH  TYR A 214 " =    1.151
peak=    3.116 closest distance to " CB  ALA A 295 " =    1.264
peak=    3.113 closest distance to " O   HOH Z 350 " =    1.587
peak=    3.111 closest distance to " CA  ASN A 176 " =    1.101
peak=    3.110 closest distance to " CG  GLN A  89 " =    1.477
peak=    3.108 closest distance to " CA  SER A 146 " =    1.737
peak=    3.100 closest distance to " O   GLN A 278 " =    1.524
peak=    3.094 closest distance to " CG2 VAL A 202 " =    1.165
peak=    3.089 closest distance to " O   HOH Z 124 " =    1.347
peak=    3.085 closest distance to " O   HOH Z 366 " =    2.994
peak=    3.084 closest distance to " O   HOH Z 357 " =    1.873
peak=    3.082 closest distance to " OD2 ASP A 200 " =    1.374
peak=    3.080 closest distance to " CB  GLN A 205 " =    1.075
peak=    3.057 closest distance to " CB  ASN A 215 " =    1.104
peak=    3.056 closest distance to " O   HOH Z  68 " =    1.460
peak=    3.045 closest distance to " O   HOH Z 133 " =    2.441
peak=    3.038 closest distance to " O   HOH Z 294 " =    1.557
peak=    3.021 closest distance to " O   HOH Z 201 " =    3.207

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 191         
Filter by distance & map next to the model:
   mapped sites are within: 0.541 - 5.468
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 189 from: 191
   mapped sites are within: 0.763 - 5.468

peak=   -5.603 closest distance to " CG2 VAL A 230 " =    0.763
peak=   -4.509 closest distance to " CD  ARG A 156 " =    1.973
peak=   -4.327 closest distance to " O   HOH Z 290 " =    1.125
peak=   -4.293 closest distance to " SG  CYS A 254 " =    3.164
peak=   -4.195 closest distance to " O   HOH Z 266 " =    4.818
peak=   -4.160 closest distance to " CB  PRO A 243 " =    2.628
peak=   -4.102 closest distance to " O   ILE A 109 " =    2.606
peak=   -4.075 closest distance to " CG  GLN A 223 " =    2.046
peak=   -3.990 closest distance to " O   HOH Z 231 " =    1.766
peak=   -3.972 closest distance to " O   VAL A  67 " =    2.627
peak=   -3.962 closest distance to " C   HIS A 108 " =    1.212
peak=   -3.955 closest distance to " CD2 LEU A 300 " =    2.813
peak=   -3.953 closest distance to " CE2 TYR A  30 " =    2.835
peak=   -3.912 closest distance to " CG  ASP A 231 " =    0.783
peak=   -3.910 closest distance to " CG2 VAL A 296 " =    1.468
peak=   -3.893 closest distance to " O   HOH Z 351 " =    1.465
peak=   -3.884 closest distance to " OG BSER A 134 " =    1.164
peak=   -3.881 closest distance to " O   PRO A 163 " =    2.042
peak=   -3.877 closest distance to " O   HOH Z 389 " =    1.911
peak=   -3.849 closest distance to " CZ3 TRP A 179 " =    1.206
peak=   -3.838 closest distance to " CG  LEU A 101 " =    2.492
peak=   -3.814 closest distance to " O   HOH Z 118 " =    3.079
peak=   -3.805 closest distance to " CD1 LEU A 228 " =    2.310
peak=   -3.775 closest distance to " O   HOH Z  52 " =    1.582
peak=   -3.755 closest distance to " OXT GLY A 302 " =    2.918
peak=   -3.749 closest distance to " N   GLN A  58 " =    1.822
peak=   -3.748 closest distance to " ND2 ASN A  45 " =    1.033
peak=   -3.729 closest distance to " CD1 LEU A 101 " =    2.463
peak=   -3.713 closest distance to " CB  PRO A 163 " =    2.560
peak=   -3.692 closest distance to " N   ALA A 226 " =    2.130
peak=   -3.686 closest distance to " O   HOH Z 211 " =    1.610
peak=   -3.677 closest distance to " NE2 GLN A  88 " =    2.167
peak=   -3.670 closest distance to " NH2AARG A 275 " =    5.234
peak=   -3.670 closest distance to " C   ALA A 158 " =    1.305
peak=   -3.670 closest distance to " CB  ALA A  43 " =    2.486
peak=   -3.662 closest distance to " N   ALA A  43 " =    2.499
peak=   -3.658 closest distance to " CD  ARG A 139 " =    1.616
peak=   -3.658 closest distance to " OG  SER A  97 " =    2.252
peak=   -3.645 closest distance to " O   HOH Z 185 " =    2.332
peak=   -3.642 closest distance to " NH2 ARG A  79 " =    1.964
peak=   -3.641 closest distance to " CG  PHE A 283 " =    2.827
peak=   -3.624 closest distance to " O   HOH Z 103 " =    1.884
peak=   -3.622 closest distance to " O   HOH Z 196 " =    2.149
peak=   -3.619 closest distance to " CE  MET A 105 " =    2.095
peak=   -3.610 closest distance to " O   HOH Z 435 " =    2.775
peak=   -3.599 closest distance to " O   HOH Z  11 " =    1.943
peak=   -3.596 closest distance to " CG  TRP A 266 " =    1.830
peak=   -3.590 closest distance to " O   HOH Z  43 " =    1.725
peak=   -3.584 closest distance to " CG1 VAL A 112 " =    2.644
peak=   -3.584 closest distance to " O   HOH Z 394 " =    1.518
peak=   -3.583 closest distance to " CG  ARG A 269 " =    2.342
peak=   -3.583 closest distance to " CB  PRO A 280 " =    2.048
peak=   -3.573 closest distance to " CD  LYS A 289 " =    2.511
peak=   -3.569 closest distance to " CG1 VAL A 112 " =    2.924
peak=   -3.569 closest distance to " O   HOH Z 166 " =    1.928
peak=   -3.565 closest distance to " O   HOH Z 222 " =    1.405
peak=   -3.565 closest distance to " CB  PHE A 192 " =    1.845
peak=   -3.549 closest distance to " O   GLY A 196 " =    1.159
peak=   -3.546 closest distance to " OG  SER A  87 " =    1.459
peak=   -3.541 closest distance to " OD1 ASN A 148 " =    1.516
peak=   -3.540 closest distance to " CA  ASP A 298 " =    1.065
peak=   -3.511 closest distance to " CG2 ILE A 263 " =    2.367
peak=   -3.491 closest distance to " CB  TYR A  15 " =    2.216
peak=   -3.489 closest distance to " CG1 VAL A 296 " =    1.384
peak=   -3.487 closest distance to " CG1 VAL A 250 " =    2.734
peak=   -3.487 closest distance to " OG BSER A 134 " =    1.730
peak=   -3.481 closest distance to " O   VAL A  67 " =    2.711
peak=   -3.479 closest distance to " N   THR A 157 " =    1.472
peak=   -3.466 closest distance to " CB  ALA A 248 " =    2.065
peak=   -3.466 closest distance to " C   GLN A  58 " =    2.276
peak=   -3.464 closest distance to " O   HOH Z 241 " =    1.288
peak=   -3.464 closest distance to " CD  GLN A  58 " =    1.081
peak=   -3.456 closest distance to " CE2 PHE A 218 " =    2.615
peak=   -3.454 closest distance to " O   PRO A 198 " =    1.212
peak=   -3.442 closest distance to " O   VAL A 189 " =    2.589
peak=   -3.441 closest distance to " C   MET A 188 " =    1.437
peak=   -3.439 closest distance to " O   HOH Z 102 " =    1.700
peak=   -3.430 closest distance to " CE3 TRP A 150 " =    2.042
peak=   -3.430 closest distance to " C   ASN A 187 " =    1.872
peak=   -3.425 closest distance to " O   HOH Z  38 " =    1.615
peak=   -3.423 closest distance to " CB  ALA A 291 " =    2.153
peak=   -3.422 closest distance to " O   HOH Z 311 " =    3.703
peak=   -3.420 closest distance to " CB  ALA A 291 " =    2.284
peak=   -3.419 closest distance to " O   HOH Z  13 " =    1.364
peak=   -3.416 closest distance to " CB  ASP A 132 " =    2.324
peak=   -3.415 closest distance to " O   HOH Z 292 " =    4.515
peak=   -3.411 closest distance to " O   HOH Z  60 " =    2.163
peak=   -3.411 closest distance to " O   HOH Z 198 " =    1.428
peak=   -3.408 closest distance to " ND2 ASN A 187 " =    1.678
peak=   -3.400 closest distance to " O   HOH Z 407 " =    3.128
peak=   -3.399 closest distance to " NH2 ARG A  66 " =    1.967
peak=   -3.399 closest distance to " CA  GLY A 241 " =    3.070
peak=   -3.398 closest distance to " CZ  TYR A 169 " =    1.633
peak=   -3.377 closest distance to " O   HOH Z 372 " =    2.404
peak=   -3.370 closest distance to " CD1 PHE A  59 " =    1.931
peak=   -3.368 closest distance to " NZ  LYS A 119 " =    3.461
peak=   -3.366 closest distance to " O   HOH Z 417 " =    2.739
peak=   -3.364 closest distance to " CG  ASP A  50 " =    2.409
peak=   -3.360 closest distance to " CG  LEU A 228 " =    0.954
peak=   -3.357 closest distance to " O   HOH Z 426 " =    1.680
peak=   -3.357 closest distance to " OD1 ASN A 187 " =    1.595
peak=   -3.356 closest distance to " O   HOH Z  63 " =    1.122
peak=   -3.355 closest distance to " O   GLY A 211 " =    1.456
peak=   -3.353 closest distance to " CZ  PHE A  59 " =    1.575
peak=   -3.353 closest distance to " CG2 VAL A 112 " =    2.563
peak=   -3.348 closest distance to " CB  ASN A  69 " =    1.180
peak=   -3.344 closest distance to " O   HOH Z  19 " =    2.435
peak=   -3.343 closest distance to " O   GLY A 203 " =    2.388
peak=   -3.342 closest distance to " N   MET A 105 " =    2.658
peak=   -3.340 closest distance to " O   HOH Z 184 " =    1.734
peak=   -3.338 closest distance to " N   THR A 235 " =    1.319
peak=   -3.333 closest distance to " OG  SER A  62 " =    1.614
peak=   -3.333 closest distance to " O   HOH Z  10 " =    1.487
peak=   -3.332 closest distance to " O   HOH Z 275 " =    1.477
peak=   -3.329 closest distance to " O   SER A  22 " =    2.204
peak=   -3.328 closest distance to " C   LEU A 222 " =    0.787
peak=   -3.321 closest distance to " CG  GLU A 277 " =    1.116
peak=   -3.319 closest distance to " O   HOH Z 353 " =    2.086
peak=   -3.319 closest distance to " CG1 VAL A 197 " =    2.266
peak=   -3.312 closest distance to " CG  MET A 105 " =    0.960
peak=   -3.308 closest distance to " O   SER A 271 " =    2.189
peak=   -3.306 closest distance to " O   HOH Z 388 " =    2.108
peak=   -3.295 closest distance to " O   HOH Z 166 " =    1.518
peak=   -3.293 closest distance to " OG ASER A 134 " =    1.300
peak=   -3.293 closest distance to " CD2 LEU A 237 " =    2.757
peak=   -3.287 closest distance to " O   HOH Z 262 " =    2.784
peak=   -3.286 closest distance to " CA  GLY A  98 " =    1.959
peak=   -3.285 closest distance to " O   HOH Z  47 " =    1.545
peak=   -3.281 closest distance to " O   LYS A 117 " =    1.707
peak=   -3.281 closest distance to " C   ASN A 285 " =    2.488
peak=   -3.281 closest distance to " N   SER A 212 " =    2.011
peak=   -3.281 closest distance to " O   HOH Z  98 " =    2.149
peak=   -3.279 closest distance to " CB  ASP A 132 " =    2.285
peak=   -3.276 closest distance to " O   HOH Z  44 " =    2.149
peak=   -3.274 closest distance to " CB  ASN A  39 " =    2.180
peak=   -3.274 closest distance to " O   GLY A  80 " =    2.485
peak=   -3.271 closest distance to " OG  SER A 206 " =    1.708
peak=   -3.266 closest distance to " CE BMET A  47 " =    1.844
peak=   -3.265 closest distance to " O   HOH Z 436 " =    1.520
peak=   -3.265 closest distance to " O   HOH Z 283 " =    2.003
peak=   -3.264 closest distance to " O   HOH Z 191 " =    5.468
peak=   -3.264 closest distance to " CD1 ILE A 239 " =    2.096
peak=   -3.260 closest distance to " C   ASP A 231 " =    2.585
peak=   -3.256 closest distance to " CA  GLY A 203 " =    2.346
peak=   -3.254 closest distance to " CD2 TYR A 293 " =    2.117
peak=   -3.251 closest distance to " O   ALA A 161 " =    1.685
peak=   -3.246 closest distance to " O   PRO A 198 " =    1.327
peak=   -3.239 closest distance to " O   HOH Z 295 " =    1.469
peak=   -3.229 closest distance to " O   HOH Z 231 " =    1.322
peak=   -3.216 closest distance to " ND2 ASN A  60 " =    1.425
peak=   -3.215 closest distance to " CG  PRO A 163 " =    2.570
peak=   -3.214 closest distance to " O   HOH Z  90 " =    2.945
peak=   -3.206 closest distance to " O   HOH Z 359 " =    3.182
peak=   -3.199 closest distance to " O   HOH Z 174 " =    2.380
peak=   -3.198 closest distance to " NE2 GLN A  88 " =    0.938
peak=   -3.195 closest distance to " O   MET A  40 " =    2.653
peak=   -3.189 closest distance to " OG1 THR A 178 " =    1.253
peak=   -3.182 closest distance to " NH1 ARG A 195 " =    2.595
peak=   -3.181 closest distance to " O   HOH Z 210 " =    1.052
peak=   -3.164 closest distance to " O   HOH Z 148 " =    1.749
peak=   -3.159 closest distance to " O   HOH Z 350 " =    1.793
peak=   -3.156 closest distance to " OG  SER A  26 " =    1.285
peak=   -3.153 closest distance to " O   HOH Z 207 " =    2.141
peak=   -3.147 closest distance to " O   HOH Z 281 " =    2.639
peak=   -3.145 closest distance to " OG1 THR A 246 " =    1.446
peak=   -3.143 closest distance to " NE2 GLN A 103 " =    1.719
peak=   -3.142 closest distance to " CG1 VAL A 230 " =    1.889
peak=   -3.134 closest distance to " CD1 TYR A 247 " =    2.369
peak=   -3.134 closest distance to " O   HOH Z 423 " =    2.088
peak=   -3.131 closest distance to " N   ALA A 248 " =    1.617
peak=   -3.128 closest distance to " O   HOH Z 313 " =    1.777
peak=   -3.122 closest distance to " O   HOH Z  37 " =    2.152
peak=   -3.119 closest distance to " O   GLN A 240 " =    2.377
peak=   -3.107 closest distance to " CD1 ILE A 199 " =    2.525
peak=   -3.105 closest distance to " OXT GLY A 302 " =    3.455
peak=   -3.103 closest distance to " OE1 GLN A  88 " =    1.123
peak=   -3.098 closest distance to " O   HOH Z 139 " =    3.060
peak=   -3.092 closest distance to " CD  GLN A  88 " =    0.816
peak=   -3.089 closest distance to " O   VAL A 125 " =    2.292
peak=   -3.073 closest distance to " O   HOH Z 148 " =    3.231
peak=   -3.066 closest distance to " O   HOH Z 417 " =    2.656
peak=   -3.064 closest distance to " O   HOH Z 175 " =    4.307
peak=   -3.057 closest distance to " N   THR A  18 " =    1.352
peak=   -3.056 closest distance to " CG  ARG A 269 " =    2.043
peak=   -3.052 closest distance to " CE  MET A  93 " =    1.137
peak=   -3.048 closest distance to " O   HOH Z 128 " =    4.219
peak=   -3.048 closest distance to " O   HOH Z 244 " =    2.001
peak=   -3.035 closest distance to " O   HOH Z 396 " =    1.695
peak=   -3.025 closest distance to " O   TRP A  70 " =    1.489

================= 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    :  0.4250 0.4129   6.215237e+00   6.196916e+00
   1_bss:  0.4172 0.4025   6.211834e+00   6.187429e+00
   1_xyz:  0.3081 0.3384   5.992441e+00   6.053583e+00
   1_adp:  0.2423 0.2845   5.788328e+00   5.919940e+00
   1_occ:  0.2416 0.2845   5.787099e+00   5.920369e+00
   2_bss:  0.2366 0.2779   5.784007e+00   5.914262e+00
   2_xyz:  0.1663 0.2087   5.470741e+00   5.655278e+00
   2_adp:  0.1544 0.1969   5.405316e+00   5.604364e+00
   2_occ:  0.1543 0.1968   5.404853e+00   5.603926e+00
   3_bss:  0.1535 0.1952   5.405164e+00   5.602886e+00
   3_xyz:  0.1291 0.1709   5.254883e+00   5.473837e+00
   3_adp:  0.1220 0.1648   5.211333e+00   5.437157e+00
   3_occ:  0.1219 0.1648   5.211201e+00   5.437252e+00
   4_bss:  0.1221 0.1649   5.211467e+00   5.436712e+00
   4_xyz:  0.1125 0.1581   5.155540e+00   5.400800e+00
   4_adp:  0.1117 0.1577   5.149857e+00   5.395258e+00
   4_occ:  0.1116 0.1576   5.149486e+00   5.395130e+00
   5_bss:  0.1116 0.1576   5.149515e+00   5.395146e+00
   5_xyz:  0.1112 0.1573   5.147870e+00   5.394804e+00
   5_adp:  0.1115 0.1571   5.147934e+00   5.393120e+00
   5_occ:  0.1114 0.1570   5.147605e+00   5.392900e+00
   5_bss:  0.1114 0.1571   5.147622e+00   5.392909e+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:  0.350  20.000   8.097   8.041   8.305   0.000   0.000   0.000
   1_xyz:  0.350  20.000   8.097   8.041   8.305   0.000   0.000   0.000
   1_adp:  0.350  20.000   8.097   8.041   8.305   0.000   0.000   0.000
   1_occ:  0.350  20.000   8.097   8.041   8.305   0.000   0.000   0.000
   2_bss:  0.327  40.883   4.628   4.293   5.412   0.000   0.000   0.000
   2_xyz:  0.327  40.883   4.628   4.293   5.412   0.000   0.000   0.000
   2_adp:  0.327  40.883   4.628   4.293   5.412   0.000   0.000   0.000
   2_occ:  0.327  40.883   4.628   4.293   5.412   0.000   0.000   0.000
   3_bss:  0.335  40.883   3.360   3.289   4.252   0.000   0.000   0.000
   3_xyz:  0.335  40.883   3.360   3.289   4.252   0.000   0.000   0.000
   3_adp:  0.335  40.883   3.360   3.289   4.252   0.000   0.000   0.000
   3_occ:  0.335  40.883   3.360   3.289   4.252   0.000   0.000   0.000
   4_bss:  0.326  45.527   3.180   3.177   3.961   0.000   0.000   0.000
   4_xyz:  0.326  45.527   3.180   3.177   3.961   0.000   0.000   0.000
   4_adp:  0.326  45.527   3.180   3.177   3.961   0.000   0.000   0.000
   4_occ:  0.326  45.527   3.180   3.177   3.961   0.000   0.000   0.000
   5_bss:  0.326  45.527   3.215   3.244   3.997   0.000   0.000   0.000
   5_xyz:  0.326  45.527   3.215   3.244   3.997   0.000   0.000   0.000
   5_adp:  0.326  45.527   3.215   3.244   3.997   0.000   0.000   0.000
   5_occ:  0.326  45.527   3.215   3.244   3.997   0.000   0.000   0.000
   5_bss:  0.326  49.026  -0.282  -0.239   0.522   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  46.252 0.5685  0.6382    50079.968
   1_bss:  46.600 0.5617  0.8030    48005.744
   1_xyz:  36.098 0.6877  0.9580    30876.925
   1_adp:  28.466 0.7751  1.0512    20801.468
   1_occ:  28.459 0.7751  1.0506    20792.340
   2_bss:  28.148 0.7782  0.9337    20371.266
   2_xyz:  19.954 0.8621  0.9965    10961.443
   2_adp:  18.505 0.8764  1.0094     9864.826
   2_occ:  18.496 0.8765  1.0091     9847.719
   3_bss:  18.467 0.8767  0.9678     9815.560
   3_xyz:  15.698 0.9011  0.9802     7550.577
   3_adp:  14.951 0.9075  0.9823     7025.325
   3_occ:  14.945 0.9075  0.9822     7023.585
   4_bss:  14.937 0.9076  0.9749     7032.978
   4_xyz:  14.244 0.9132  0.9770     6511.958
   4_adp:  14.116 0.9143  0.9760     6446.424
   4_occ:  14.117 0.9143  0.9758     6445.712
   5_bss:  14.119 0.9143  0.9774     6446.116
   5_xyz:  14.083 0.9146  0.9767     6433.067
   5_adp:  14.032 0.9151  0.9754     6416.225
   5_occ:  14.026 0.9151  0.9753     6411.877
   5_bss:  14.027 0.9151  0.9758     6411.810
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.3758e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.3758e+01
   1_xyz:   1.500  0.011  0.100 17.790  0.006  4.122   1.1540e-01
   1_adp:   1.500  0.011  0.100 17.790  0.006  4.122   1.1540e-01
   1_occ:   1.500  0.011  0.100 17.790  0.006  4.122   1.1540e-01
   2_bss:   1.500  0.011  0.100 17.790  0.006  4.122   1.1540e-01
   2_xyz:   0.913  0.006  0.067 15.794  0.004  4.123   5.4874e-02
   2_adp:   0.913  0.006  0.067 15.794  0.004  4.123   5.4874e-02
   2_occ:   0.913  0.006  0.067 15.794  0.004  4.123   5.4874e-02
   3_bss:   0.913  0.006  0.067 15.794  0.004  4.123   5.4874e-02
   3_xyz:   0.956  0.006  0.075 15.569  0.003  4.129   5.6202e-02
   3_adp:   0.956  0.006  0.075 15.569  0.003  4.129   5.6202e-02
   3_occ:   0.956  0.006  0.075 15.569  0.003  4.129   5.6202e-02
   4_bss:   0.956  0.006  0.075 15.569  0.003  4.129   5.6202e-02
   4_xyz:   1.057  0.008  0.087 15.673  0.004  4.133   6.7602e-02
   4_adp:   1.057  0.008  0.087 15.673  0.004  4.133   6.7602e-02
   4_occ:   1.057  0.008  0.087 15.673  0.004  4.133   6.7602e-02
   5_bss:   1.057  0.008  0.087 15.673  0.004  4.133   6.7602e-02
   5_xyz:   0.988  0.007  0.081 15.363  0.004  4.117   6.0420e-02
   5_adp:   0.988  0.007  0.081 15.363  0.004  4.117   6.0420e-02
   5_occ:   0.988  0.007  0.081 15.363  0.004  4.117   6.0420e-02
   5_bss:   0.988  0.007  0.081 15.363  0.004  4.117   6.0420e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9704e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9704e+00
   1_xyz:  12.708  0.137  0.422 89.460  0.041  2.256   8.6644e-02
   1_adp:  12.708  0.137  0.422 89.460  0.041  2.256   8.6644e-02
   1_occ:  12.708  0.137  0.422 89.460  0.041  2.256   8.6644e-02
   2_bss:  12.708  0.137  0.422 89.460  0.041  2.256   8.6644e-02
   2_xyz:   6.137  0.049  0.239 80.028  0.037  2.375   3.7898e-02
   2_adp:   6.137  0.049  0.239 80.028  0.037  2.375   3.7898e-02
   2_occ:   6.137  0.049  0.239 80.028  0.037  2.375   3.7898e-02
   3_bss:   6.137  0.049  0.239 80.028  0.037  2.375   3.7898e-02
   3_xyz:   7.448  0.048  0.425 83.646  0.036  2.370   4.1221e-02
   3_adp:   7.448  0.048  0.425 83.646  0.036  2.370   4.1221e-02
   3_occ:   7.448  0.048  0.425 83.646  0.036  2.370   4.1221e-02
   4_bss:   7.448  0.048  0.425 83.646  0.036  2.370   4.1221e-02
   4_xyz:   7.309  0.055  0.584 83.981  0.039  2.326   5.1555e-02
   4_adp:   7.309  0.055  0.584 83.981  0.039  2.326   5.1555e-02
   4_occ:   7.309  0.055  0.584 83.981  0.039  2.326   5.1555e-02
   5_bss:   7.309  0.055  0.584 83.981  0.039  2.326   5.1555e-02
   5_xyz:   7.181  0.043  0.528 83.373  0.038  2.335   4.2697e-02
   5_adp:   7.181  0.043  0.528 83.373  0.038  2.335   4.2697e-02
   5_occ:   7.181  0.043  0.528 83.373  0.038  2.335   4.2697e-02
   5_bss:   7.181  0.043  0.528 83.373  0.038  2.335   4.2697e-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:  61.90   0.00  10.37  57.89   0.00   7.17  61.90   0.00  27.77
   1_occ:  61.90   0.00  10.37  57.89   0.00   7.17  61.90   0.00  27.77
   2_bss:  61.90   0.00  10.37  57.89   0.00   7.17  61.90   0.00  27.77
   2_xyz:  61.90   0.00  10.37  57.89   0.00   7.17  61.90   0.00  27.77
   2_adp:  63.01   0.00  10.75  58.49   0.00   7.24  63.01   1.18  29.86
   2_occ:  63.01   0.00  10.75  58.49   0.00   7.24  63.01   1.18  29.86
   3_bss:  63.01   0.00  10.75  58.49   0.00   7.24  63.01   1.18  29.86
   3_xyz:  63.01   0.00  10.75  58.49   0.00   7.24  63.01   1.18  29.86
   3_adp:  70.90   0.00  11.60  70.90   0.00   7.45  68.58   0.99  34.16
   3_occ:  70.90   0.00  11.60  70.90   0.00   7.45  68.58   0.99  34.16
   4_bss:  70.90   0.00  11.60  70.90   0.00   7.45  68.58   0.99  34.16
   4_xyz:  70.90   0.00  11.60  70.90   0.00   7.45  68.58   0.99  34.16
   4_adp:  77.49   0.00  11.50  77.49   0.00   7.42  69.81   1.07  33.69
   4_occ:  77.49   0.00  11.50  77.49   0.00   7.42  69.81   1.07  33.69
   5_bss:  77.49   0.00  11.50  77.49   0.00   7.42  69.81   1.07  33.69
   5_xyz:  77.49   0.00  11.50  77.49   0.00   7.42  69.81   1.07  33.69
   5_adp:  79.13   0.00  11.29  79.13   0.00   7.34  67.23   0.99  32.80
   5_occ:  79.13   0.00  11.29  79.13   0.00   7.34  67.23   0.99  32.80
   5_bss:  82.63   3.50  14.79  82.63   3.50  10.84  70.73   4.49  36.30
------------------------------------------------------------------------
 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:    1.164    0.015    0.402
   1_adp:    1.164    0.015    0.402
   1_occ:    1.164    0.015    0.402
   2_bss:    1.164    0.015    0.402
   2_xyz:    1.460    0.023    0.492
   2_adp:    1.460    0.023    0.492
   2_occ:    1.460    0.023    0.492
   3_bss:    1.460    0.023    0.492
   3_xyz:    1.472    0.021    0.521
   3_adp:    1.472    0.021    0.521
   3_occ:    1.472    0.021    0.521
   4_bss:    1.472    0.021    0.521
   4_xyz:    1.585    0.049    0.542
   4_adp:    1.585    0.049    0.542
   4_occ:    1.585    0.049    0.542
   5_bss:    1.585    0.049    0.542
   5_xyz:    1.637    0.042    0.548
   5_adp:    1.637    0.042    0.548
   5_occ:    1.637    0.042    0.548
   5_bss:    1.637    0.042    0.548
------------------------------------------------------------------------

CPU time actual refinement: 276.69


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_905/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_905/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_905/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_905/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_905/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 276.55 
  Macro-tasks:
    bulk solvent and scale       = 34.10  
    individual site refinement   = 120.30 
    weights calculation          = 26.76  
    collect and process          = 5.46   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 186.71 
  Micro-tasks:
    mask                            = 1.45   
    f_calc                          = 83.69  
    alpha_beta                      = 6.82   
    target                          = 1.02   
    gradients_wrt_atomic_parameters = 95.26  
    fmodel                         = 5.96   
    r_factors                      = 0.27   
    phase_errors                   = 8.97   
    foms                           = 0.24   
    TOTAL for micro-tasks          = 203.68 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 3.818 micro seconds
Total CPU time: 4.81 minutes
from_scatterers_fft:    654 calls, 83.29 s
gradients_fft:          599 calls, 82.78 s

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

# Date 2008-01-16 Time 02:42:21 PST -0800 (1200480141.85 s)
Start R-work = 0.4250, R-free = 0.4129 (no bulk solvent and anisotropic scale)
Final R-work = 0.1286, R-free = 0.1729 (no bulk solvent and anisotropic scale)

Start R-work = 0.4172, R-free = 0.4025
Final R-work = 0.1114, R-free = 0.1571