# Date 2008-01-16 Time 02:14:04 PST -0800 (1200478444.32 s)
#phil __OFF__

Command line arguments: "../745.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 31590
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 745

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.6012, 45.9914, 87.6859, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.23, per 1000 atoms: 1.14


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 45.9914, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1092 1.96344
Completeness in resolution range: 0.933743
Completeness with d_max=infinity: 0.931036

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1092
                             d_min =   1.9634

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 45.9914, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1092 1.96344
Completeness in resolution range: 0.933743
Completeness with d_max=infinity: 0.931036

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1096 -  4.2026 [2203/2229]  1982   221  10.0%
  bin  2:  4.2026 -  3.3477 [2124/2144]  1912   212  10.0%
  bin  3:  3.3477 -  2.9280 [2084/2103]  1878   206   9.9%
  bin  4:  2.9280 -  2.6619 [2068/2098]  1854   214  10.3%
  bin  5:  2.6619 -  2.4720 [2063/2082]  1866   197   9.5%
  bin  6:  2.4720 -  2.3268 [2055/2080]  1844   211  10.3%
  bin  7:  2.3268 -  2.2106 [2009/2037]  1804   205  10.2%
  bin  8:  2.2106 -  2.1147 [2064/2100]  1856   208  10.1%
  bin  9:  2.1147 -  2.0335 [2021/2063]  1828   193   9.5%
  bin 10:  2.0335 -  1.9634 [ 898/2043]   806    92  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_745/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 39
        2.42 -     3.04: 2204
        3.04 -     3.66: 4702
        3.66 -     4.28: 9028
        4.28 -     4.90: 12331
  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
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.883 3.040 x,y+1,z
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.941 3.040 x,y+1,z
  " O   HOH Z  70 " - " O   HOH Z 302 "  1.966 3.040 -x+1/2,-y+1,z+1/2
  " N   ASN A 148 " - " O   HOH Z 138 "  2.019 3.120 x,y-1,z
  ... (remaining 28299 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_745/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_745/model_refine_001.geo

CPU time processing inputs: 9.01


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.60125 45.9914 87.68585 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4940   r_free= 0.4827   ksol= 0.00   Bsol= 0.00   scale= 0.782    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.77 A                  |
| x-ray target function (ml) for work reflections: 6.296573                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1096 -  4.6880 0.99   1426  157 0.4188 0.3981      6.6323      6.6256|
|  2:  4.6880 -  3.7396 0.99   1385  156 0.4207 0.3920      6.8361      6.7857|
|  3:  3.7396 -  3.2723 0.99   1352  147 0.4477 0.4018      6.6783      6.6309|
|  4:  3.2723 -  2.9756 0.99   1337  151 0.4874 0.4695      6.5522      6.5014|
|  5:  2.9756 -  2.7638 0.99   1335  151 0.5327 0.5226       6.377      6.3971|
|  6:  2.7638 -  2.6017 0.99   1325  145 0.5226 0.5379      6.2744      6.2136|
|  7:  2.6017 -  2.4720 0.99   1332  143 0.5318 0.5016      6.2488      6.2009|
|  8:  2.4720 -  2.3648 0.98   1296  151 0.5442 0.5071      6.1808      6.1783|
|  9:  2.3648 -  2.2741 0.98   1313  145 0.5331 0.5565      6.1259      6.2159|
| 10:  2.2741 -  2.1958 1.00   1324  150 0.5309 0.5328      6.0948      6.0737|
| 11:  2.1958 -  2.1274 0.98   1306  139 0.5095 0.5471      6.0374      6.0215|
| 12:  2.1274 -  2.0667 0.98   1298  143 0.5416 0.5603      5.9436      5.9788|
| 13:  2.0667 -  2.0124 0.95   1249  139 0.5510 0.5553      5.8872      5.8028|
| 14:  2.0124 -  1.9634 0.27    352   42 0.5497 0.4577      5.8728      5.8403|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1096 -  4.6880  1426   157  0.68  36.21   0.78     0.73      78966.11|
|  2:  4.6880 -  3.7396  1385   156  0.70  34.86   0.85     0.79     107877.06|
|  3:  3.7396 -  3.2723  1352   147  0.59  44.58   0.84     0.72     114396.05|
|  4:  3.2723 -  2.9756  1337   151  0.49  52.30   0.77     0.59     105230.55|
|  5:  2.9756 -  2.7638  1335   151  0.38  61.33   0.72     0.47      87799.81|
|  6:  2.7638 -  2.6017  1325   145  0.34  64.06   0.70     0.41      77336.88|
|  7:  2.6017 -  2.4720  1332   143  0.29  68.37   0.73     0.34      71829.30|
|  8:  2.4720 -  2.3648  1296   151  0.26  70.73   0.71     0.31      65762.41|
|  9:  2.3648 -  2.2741  1313   145  0.24  72.13   0.72     0.29      62489.65|
| 10:  2.2741 -  2.1958  1324   150  0.26  70.42   0.74     0.32      54215.82|
| 11:  2.1958 -  2.1274  1306   139  0.26  70.51   0.77     0.33      52433.75|
| 12:  2.1274 -  2.0667  1298   143  0.26  70.98   0.73     0.33      46147.49|
| 13:  2.0667 -  2.0124  1249   139  0.25  71.28   0.71     0.34      40569.76|
| 14:  2.0124 -  1.9634   352    42  0.32  66.36   0.71     0.36      31806.40|
|alpha:            min =        0.29 max =            0.79 mean =         0.46|
|beta:             min =    31806.40 max =       114396.05 mean =     73853.49|
|figures of merit: min =        0.00 max =            1.00 mean =         0.39|
|phase err.(work): min =        0.00 max =           90.00 mean =        60.36|
|phase err.(test): min =        0.00 max =           89.88 mean =        60.70|
|-----------------------------------------------------------------------------|

============================== 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 = 18.211598             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.346   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.585186              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.104   (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:       35 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      171 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      691 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1510 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2633 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3930 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5096 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6538 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7702 |
|-----------------------------------------------------------------------------|
|-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 |       53.761 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.089    4.900  1.196 |       2.017 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.844)------------------------------------------|
|    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 = 11.844)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4992   r_free= 0.4836   ksol= 0.00   Bsol= 0.00   scale= 0.753    |
|                                                                             |
| 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:   0.76 A                  |
| x-ray target function (ml) for work reflections: 6.297827                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4861   r_free= 0.4686   ksol= 0.37   Bsol= 20.00   scale= 0.980   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.53,9.19,9.59,0.00,0.00,0.00); trace/3= 8.44                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.77 A                  |
| x-ray target function (ml) for work reflections: 6.292096                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 14.481536             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.499   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.424400              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.405   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4861      final r-factor (work) = 0.4100          |
| start r-factor (free) = 0.4686      final r-factor (free) = 0.4326          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 99.3024 = 14.48 * 0.50 * 6.2895 + 1.00 * 53.7614                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 45.2008 = 14.48 * 0.50 * 6.2218 + 1.00 * 0.1501                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4100      final r-factor (work) = 0.3692          |
| start r-factor (free) = 0.4326      final r-factor (free) = 0.4349          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.8768 = 1.42 * 1.00 * 6.2218 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.7893 = 1.42 * 1.00 * 6.1572 + 1.00 * 0.0190                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.844)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.97   15.11    None  None   None       |
|    all(noH): 2823   0      0.00    81.97   15.11    None  None   None       |
|    Sol.    : 438    0      0.00    81.97   25.25    None  None   None       |
|    Mac.    : 2385   0      0.00    69.95   13.24    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 -   8.197:  966   |   5:    40.983 -  49.180:   74        |
|      1:     8.197 -  16.393:  824   |   6:    49.180 -  57.377:   32        |
|      2:    16.393 -  24.590:  512   |   7:    57.377 -  65.574:   16        |
|      3:    24.590 -  32.787:  260   |   8:    65.574 -  73.770:    9        |
|      4:    32.787 -  40.983:  128   |   9:    73.770 -  81.967:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3692 r_free = 0.4349             target_work(ml) = 6.149         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3690 r_free = 0.4349             target_work(ml) = 6.149         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3690   r_free= 0.4349   ksol= 0.37   Bsol= 20.00   scale= 1.122   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.53,9.19,9.59,0.00,0.00,0.00); trace/3= 8.44                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.148755                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3668   r_free= 0.4301   ksol= 0.36   Bsol= 50.00   scale= 1.030   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.53,5.35,5.89,0.00,0.00,0.00); trace/3= 4.92                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.150382                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.722490              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.842  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.634148              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.758  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3668      final r-factor (work) = 0.3002          |
| start r-factor (free) = 0.4301      final r-factor (free) = 0.3682          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.9871 = 8.72 * 0.50 * 6.1535 + 1.00 * 0.1501                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.5693 = 8.72 * 0.50 * 6.0713 + 1.00 * 0.0908                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3002      final r-factor (work) = 0.2783          |
| start r-factor (free) = 0.3682      final r-factor (free) = 0.3514          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8692 = 0.63 * 1.00 * 6.0713 + 1.00 * 0.0190                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7961 = 0.63 * 1.00 * 5.9639 + 1.00 * 0.0141                               |
|-----------------------------------------------------------------------------|
| number of iterations = 14      |    number of function evaluations = 20     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.844)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.51   14.69    None  None   None       |
|    all(noH): 2823   0      0.00    85.51   14.69    None  None   None       |
|    Sol.    : 438    0      0.00    85.51   30.69    None  None   None       |
|    Mac.    : 2385   0      0.00    62.04   11.75    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.551: 1101   |   5:    42.753 -  51.304:   56        |
|      1:     8.551 -  17.101:  819   |   6:    51.304 -  59.855:   23        |
|      2:    17.101 -  25.652:  438   |   7:    59.855 -  68.405:   13        |
|      3:    25.652 -  34.203:  233   |   8:    68.405 -  76.956:    4        |
|      4:    34.203 -  42.753:  135   |   9:    76.956 -  85.507:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2783 r_free = 0.3514             target_work(ml) = 5.945         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2781 r_free = 0.3512             target_work(ml) = 5.945         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2781   r_free= 0.3512   ksol= 0.36   Bsol= 50.00   scale= 1.073   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.53,5.35,5.89,0.00,0.00,0.00); trace/3= 4.92                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.44 A                  |
| x-ray target function (ml) for work reflections: 5.944821                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2767   r_free= 0.3495   ksol= 0.34   Bsol= 50.00   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.92,2.67,3.63,0.00,0.00,0.00); trace/3= 2.74                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.45 A                  |
| x-ray target function (ml) for work reflections: 5.945414                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.020046              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.105  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.663105              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 122.656  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2767      final r-factor (work) = 0.2155          |
| start r-factor (free) = 0.3495      final r-factor (free) = 0.2769          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.0627 = 5.02 * 0.50 * 5.9649 + 1.00 * 0.0908                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.7546 = 5.02 * 0.50 * 5.8476 + 1.00 * 0.0769                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2155      final r-factor (work) = 0.1974          |
| start r-factor (free) = 0.2769      final r-factor (free) = 0.2608          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8935 = 0.66 * 1.00 * 5.8476 + 1.00 * 0.0159                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7825 = 0.66 * 1.00 * 5.6727 + 1.00 * 0.0210                               |
|-----------------------------------------------------------------------------|
| number of iterations = 13      |    number of function evaluations = 20     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.844)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.71   14.65    None  None   None       |
|    all(noH): 2823   0      0.00    86.71   14.65    None  None   None       |
|    Sol.    : 438    0      1.92    86.71   34.07    None  None   None       |
|    Mac.    : 2385   0      0.00    65.69   11.09    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.671: 1186   |   5:    43.355 -  52.026:   74        |
|      1:     8.671 -  17.342:  806   |   6:    52.026 -  60.698:   26        |
|      2:    17.342 -  26.013:  356   |   7:    60.698 -  69.369:   12        |
|      3:    26.013 -  34.684:  200   |   8:    69.369 -  78.040:    4        |
|      4:    34.684 -  43.355:  158   |   9:    78.040 -  86.711:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1974 r_free = 0.2608             target_work(ml) = 5.645         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1972 r_free = 0.2606             target_work(ml) = 5.644         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1972   r_free= 0.2606   ksol= 0.34   Bsol= 50.00   scale= 1.040   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.92,2.67,3.63,0.00,0.00,0.00); trace/3= 2.74                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.643595                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1967   r_free= 0.2600   ksol= 0.33   Bsol= 50.00   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.97,1.30,2.77,0.00,0.00,0.00); trace/3= 1.68                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.642981                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.473850              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.524   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.938592              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 94.284   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1967      final r-factor (work) = 0.1600          |
| start r-factor (free) = 0.2600      final r-factor (free) = 0.2189          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.9340 = 3.47 * 0.50 * 5.6750 + 1.00 * 0.0769                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.7123 = 3.47 * 0.50 * 5.5557 + 1.00 * 0.0625                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1600      final r-factor (work) = 0.1446          |
| start r-factor (free) = 0.2189      final r-factor (free) = 0.2014          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 16.3400 = 2.94 * 1.00 * 5.5557 + 1.00 * 0.0141                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 15.9578 = 2.94 * 1.00 * 5.4251 + 1.00 * 0.0156                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.844)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.70   15.35    None  None   None       |
|    all(noH): 2823   0      0.00    93.70   15.35    None  None   None       |
|    Sol.    : 438    0      3.23    93.70   42.65    None  None   None       |
|    Mac.    : 2385   0      0.00    85.11   10.34    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 -   9.370: 1459   |   5:    46.848 -  56.218:   90        |
|      1:     9.370 -  18.739:  726   |   6:    56.218 -  65.588:   73        |
|      2:    18.739 -  28.109:  188   |   7:    65.588 -  74.957:   43        |
|      3:    28.109 -  37.479:  122   |   8:    74.957 -  84.327:   12        |
|      4:    37.479 -  46.848:  102   |   9:    84.327 -  93.697:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1446 r_free = 0.2014             target_work(ml) = 5.381         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1444 r_free = 0.2013             target_work(ml) = 5.380         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1444   r_free= 0.2013   ksol= 0.33   Bsol= 50.00   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.97,1.30,2.77,0.00,0.00,0.00); trace/3= 1.68                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.380355                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1449   r_free= 0.2007   ksol= 0.33   Bsol= 60.91   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.98,0.82,2.67,0.00,0.00,0.00); trace/3= 1.49                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.378781                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.977292              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 119.424  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.252032              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 128.019  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1449      final r-factor (work) = 0.1329          |
| start r-factor (free) = 0.2007      final r-factor (free) = 0.1879          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4263 = 1.98 * 0.50 * 5.4254 + 1.00 * 0.0625                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3407 = 1.98 * 0.50 * 5.3477 + 1.00 * 0.0537                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1329      final r-factor (work) = 0.1308          |
| start r-factor (free) = 0.1879      final r-factor (free) = 0.1799          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3634 = 0.25 * 1.00 * 5.3477 + 1.00 * 0.0156                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3485 = 0.25 * 1.00 * 5.3067 + 1.00 * 0.0110                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.844)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.84   14.46    None  None   None       |
|    all(noH): 2823   0      0.00    89.84   14.46    None  None   None       |
|    Sol.    : 438    0      3.00    89.84   39.84    None  None   None       |
|    Mac.    : 2385   0      0.00    85.37   9.80     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.984: 1478   |   5:    44.919 -  53.902:   87        |
|      1:     8.984 -  17.968:  734   |   6:    53.902 -  62.886:   65        |
|      2:    17.968 -  26.951:  194   |   7:    62.886 -  71.870:   38        |
|      3:    26.951 -  35.935:  112   |   8:    71.870 -  80.854:   10        |
|      4:    35.935 -  44.919:   96   |   9:    80.854 -  89.837:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1308 r_free = 0.1799             target_work(ml) = 5.285         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1307 r_free = 0.1798             target_work(ml) = 5.284         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1307   r_free= 0.1798   ksol= 0.33   Bsol= 60.91   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.98,0.82,2.67,0.00,0.00,0.00); trace/3= 1.49                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.283866                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1096 -  4.6880 0.99   1426  157 0.1011 0.1330      5.4026      5.5947|
|  2:  4.6880 -  3.7396 0.99   1385  156 0.0934 0.1268       5.515       5.755|
|  3:  3.7396 -  3.2723 0.99   1352  147 0.1207 0.1681      5.5833       5.887|
|  4:  3.2723 -  2.9756 0.99   1337  151 0.1431 0.1908      5.5779      5.7282|
|  5:  2.9756 -  2.7638 0.99   1335  151 0.1566 0.2002      5.4665      5.6785|
|  6:  2.7638 -  2.6017 0.99   1325  145 0.1453 0.2262      5.3382      5.6125|
|  7:  2.6017 -  2.4720 0.99   1332  143 0.1514 0.1829      5.3089      5.4364|
|  8:  2.4720 -  2.3648 0.98   1296  151 0.1492 0.1993      5.2444      5.4633|
|  9:  2.3648 -  2.2741 0.98   1313  145 0.1449 0.2084       5.192      5.4548|
| 10:  2.2741 -  2.1958 1.00   1324  150 0.1393 0.1977      5.1063      5.3177|
| 11:  2.1958 -  2.1274 0.98   1306  139 0.1351 0.2196      5.0887      5.4459|
| 12:  2.1274 -  2.0667 0.98   1298  143 0.1397 0.2040      5.0261      5.2835|
| 13:  2.0667 -  2.0124 0.95   1249  139 0.1326 0.1721      4.9111      5.0625|
| 14:  2.0124 -  1.9634 0.27    352   42 0.1227 0.1841      4.7881      5.0064|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1096 -  4.6880  1426   157  0.94   9.59   0.97     0.94       7547.76|
|  2:  4.6880 -  3.7396  1385   156  0.94   9.17   1.02     1.00      10530.66|
|  3:  3.7396 -  3.2723  1352   147  0.92  13.51   1.04     1.03      13213.67|
|  4:  3.2723 -  2.9756  1337   151  0.90  16.43   1.02     1.00      13361.71|
|  5:  2.9756 -  2.7638  1335   151  0.88  18.27   1.01     0.98      10744.54|
|  6:  2.7638 -  2.6017  1325   145  0.87  19.06   0.99     0.95       9093.88|
|  7:  2.6017 -  2.4720  1332   143  0.88  18.52   1.00     0.96       8141.89|
|  8:  2.4720 -  2.3648  1296   151  0.88  19.09   1.00     0.98       7467.57|
|  9:  2.3648 -  2.2741  1313   145  0.88  18.99   1.00     0.94       6798.38|
| 10:  2.2741 -  2.1958  1324   150  0.88  18.87   1.01     0.96       5891.29|
| 11:  2.1958 -  2.1274  1306   139  0.88  19.09   1.00     0.94       5812.69|
| 12:  2.1274 -  2.0667  1298   143  0.88  19.01   1.01     1.00       5346.05|
| 13:  2.0667 -  2.0124  1249   139  0.87  19.50   1.00     0.98       4337.08|
| 14:  2.0124 -  1.9634   352    42  0.91  15.21   0.99     0.97       3081.76|
|alpha:            min =        0.94 max =            1.03 mean =         0.97|
|beta:             min =     3081.76 max =        13361.71 mean =      8267.30|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.89 mean =        16.73|
|phase err.(test): min =        0.00 max =           89.33 mean =        16.10|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1307   r_free= 0.1798   ksol= 0.32   Bsol= 54.86   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.51,-0.71,1.22,0.00,0.00,0.00); trace/3= -0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.283736                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1307   r_free= 0.1798   ksol= 0.32   Bsol= 54.86   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.51,-0.71,1.22,0.00,0.00,0.00); trace/3= -0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.283736                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1096 -  4.6880 0.99   1426  157 0.1007 0.1328      5.4005      5.5917|
|  2:  4.6880 -  3.7396 0.99   1385  156 0.0930 0.1262      5.5115      5.7498|
|  3:  3.7396 -  3.2723 0.99   1352  147 0.1204 0.1676       5.581       5.884|
|  4:  3.2723 -  2.9756 0.99   1337  151 0.1432 0.1912      5.5781        5.73|
|  5:  2.9756 -  2.7638 0.99   1335  151 0.1568 0.2004      5.4673      5.6801|
|  6:  2.7638 -  2.6017 0.99   1325  145 0.1455 0.2261      5.3391      5.6128|
|  7:  2.6017 -  2.4720 0.99   1332  143 0.1515 0.1831      5.3099      5.4371|
|  8:  2.4720 -  2.3648 0.98   1296  151 0.1493 0.2000      5.2456      5.4654|
|  9:  2.3648 -  2.2741 0.98   1313  145 0.1450 0.2083      5.1929      5.4544|
| 10:  2.2741 -  2.1958 1.00   1324  150 0.1395 0.1979      5.1072      5.3196|
| 11:  2.1958 -  2.1274 0.98   1306  139 0.1350 0.2199       5.089      5.4466|
| 12:  2.1274 -  2.0667 0.98   1298  143 0.1397 0.2040      5.0265      5.2835|
| 13:  2.0667 -  2.0124 0.95   1249  139 0.1326 0.1721      4.9112      5.0623|
| 14:  2.0124 -  1.9634 0.27    352   42 0.1227 0.1842      4.7878      5.0064|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1096 -  4.6880  1426   157  0.94   9.56   0.97     0.94       7512.55|
|  2:  4.6880 -  3.7396  1385   156  0.94   9.11   1.02     1.00      10465.44|
|  3:  3.7396 -  3.2723  1352   147  0.92  13.45   1.03     1.03      13133.02|
|  4:  3.2723 -  2.9756  1337   151  0.90  16.42   1.02     0.99      13344.77|
|  5:  2.9756 -  2.7638  1335   151  0.88  18.27   1.00     0.98      10756.72|
|  6:  2.7638 -  2.6017  1325   145  0.87  19.08   0.98     0.94       9114.24|
|  7:  2.6017 -  2.4720  1332   143  0.88  18.54   0.99     0.95       8163.16|
|  8:  2.4720 -  2.3648  1296   151  0.87  19.12   1.00     0.97       7492.54|
|  9:  2.3648 -  2.2741  1313   145  0.88  19.01   1.00     0.94       6815.84|
| 10:  2.2741 -  2.1958  1324   150  0.88  18.89   1.00     0.96       5907.35|
| 11:  2.1958 -  2.1274  1306   139  0.87  19.11   0.99     0.94       5826.28|
| 12:  2.1274 -  2.0667  1298   143  0.88  19.02   1.00     1.00       5354.13|
| 13:  2.0667 -  2.0124  1249   139  0.87  19.50   1.00     0.98       4338.35|
| 14:  2.0124 -  1.9634   352    42  0.91  15.20   0.98     0.96       3079.60|
|alpha:            min =        0.94 max =            1.03 mean =         0.97|
|beta:             min =     3079.60 max =        13344.77 mean =      8261.91|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.90 mean =        16.73|
|phase err.(test): min =        0.00 max =           89.52 mean =        16.10|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.844)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.38    91.21   15.84    None  None   None       |
|    all(noH): 2823   0      1.38    91.21   15.84    None  None   None       |
|    Sol.    : 438    0      4.38    91.21   41.22    None  None   None       |
|    Mac.    : 2385   0      1.38    86.75   11.18    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:     1.377 -  10.361: 1478   |   5:    46.296 -  55.280:   87        |
|      1:    10.361 -  19.345:  734   |   6:    55.280 -  64.263:   65        |
|      2:    19.345 -  28.328:  194   |   7:    64.263 -  73.247:   38        |
|      3:    28.328 -  37.312:  112   |   8:    73.247 -  82.231:   10        |
|      4:    37.312 -  46.296:   96   |   9:    82.231 -  91.214:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 335         
Filter by distance & map next to the model:
   mapped sites are within: 0.310 - 4.725
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 330 from: 335
   mapped sites are within: 0.721 - 4.725

peak=    9.413 closest distance to " CB  VAL A 230 " =    1.440
peak=    8.279 closest distance to " CG2 VAL A 296 " =    1.507
peak=    7.819 closest distance to " O   HOH Z 130 " =    1.771
peak=    7.355 closest distance to " CD2 LEU A   5 " =    1.439
peak=    6.860 closest distance to " CG  ARG A 138 " =    1.222
peak=    6.618 closest distance to " CD1AILE A 234 " =    1.095
peak=    5.701 closest distance to " NH1 ARG A 138 " =    1.051
peak=    5.653 closest distance to " O   HOH Z 222 " =    1.521
peak=    5.566 closest distance to " O   HOH Z 268 " =    1.168
peak=    5.338 closest distance to " O   HOH Z  65 " =    1.547
peak=    5.247 closest distance to " NE2 GLN A  11 " =    1.145
peak=    5.201 closest distance to " CG  PRO A  54 " =    1.520
peak=    5.100 closest distance to " O   HOH Z 127 " =    1.214
peak=    5.060 closest distance to " O   HOH Z 232 " =    2.183
peak=    4.892 closest distance to " CG  LEU A 228 " =    1.208
peak=    4.889 closest distance to " O   HOH Z 375 " =    1.195
peak=    4.880 closest distance to " CB  VAL A 230 " =    1.300
peak=    4.837 closest distance to " O   HOH Z 425 " =    1.777
peak=    4.809 closest distance to " O   HOH Z   7 " =    1.727
peak=    4.804 closest distance to " O   PRO A 198 " =    1.413
peak=    4.772 closest distance to " O   HOH Z  63 " =    1.510
peak=    4.764 closest distance to " NH2 ARG A  56 " =    2.108
peak=    4.725 closest distance to " CB  PRO A  54 " =    1.177
peak=    4.671 closest distance to " CG  LEU A   5 " =    1.190
peak=    4.653 closest distance to " O   HOH Z 287 " =    1.939
peak=    4.643 closest distance to " O   HOH Z  69 " =    2.277
peak=    4.614 closest distance to " O   HOH Z 385 " =    1.046
peak=    4.612 closest distance to " O   HOH Z   9 " =    2.267
peak=    4.590 closest distance to " O   HOH Z 427 " =    1.231
peak=    4.573 closest distance to " O   HOH Z 142 " =    2.135
peak=    4.552 closest distance to " CG  PRO A 198 " =    1.362
peak=    4.549 closest distance to " O   HOH Z 369 " =    2.062
peak=    4.538 closest distance to " CG  PRO A 280 " =    1.012
peak=    4.536 closest distance to " O   HOH Z 417 " =    1.793
peak=    4.484 closest distance to " O   HOH Z 427 " =    2.198
peak=    4.484 closest distance to " O   HOH Z 424 " =    1.146
peak=    4.423 closest distance to " CB  SER A 216 " =    0.989
peak=    4.414 closest distance to " O   HOH Z 225 " =    1.746
peak=    4.372 closest distance to " CG  PRO A 243 " =    1.172
peak=    4.371 closest distance to " CG  LEU A 167 " =    1.260
peak=    4.363 closest distance to " CD  ARG A 138 " =    1.002
peak=    4.310 closest distance to " CB  SER A   3 " =    1.503
peak=    4.302 closest distance to " CB  ASN A 148 " =    1.424
peak=    4.294 closest distance to " O   HOH Z 389 " =    1.559
peak=    4.292 closest distance to " O   HOH Z  66 " =    1.186
peak=    4.266 closest distance to " O   HOH Z 316 " =    3.011
peak=    4.246 closest distance to " CB  GLN A 223 " =    1.531
peak=    4.223 closest distance to " O   HOH Z 139 " =    1.187
peak=    4.204 closest distance to " CB  ASN A  39 " =    0.945
peak=    4.176 closest distance to " CG2 ILE A 234 " =    1.144
peak=    4.160 closest distance to " O   HOH Z 126 " =    1.968
peak=    4.159 closest distance to " O   HOH Z  59 " =    1.686
peak=    4.145 closest distance to " O   HOH Z 419 " =    1.895
peak=    4.133 closest distance to " O   HOH Z  78 " =    1.749
peak=    4.132 closest distance to " O   HOH Z 298 " =    1.765
peak=    4.125 closest distance to " CB  ASP A 124 " =    0.871
peak=    4.119 closest distance to " O   HOH Z 361 " =    1.455
peak=    4.117 closest distance to " O   HOH Z 418 " =    1.090
peak=    4.099 closest distance to " CB  GLN A 183 " =    1.166
peak=    4.075 closest distance to " O   HOH Z 258 " =    2.263
peak=    4.075 closest distance to " CA  ALA A  51 " =    1.113
peak=    4.065 closest distance to " CG  LYS A  76 " =    1.760
peak=    4.063 closest distance to " CB  ARG A 275 " =    1.040
peak=    4.045 closest distance to " O   HOH Z 350 " =    1.557
peak=    4.036 closest distance to " O   HOH Z 392 " =    1.366
peak=    4.028 closest distance to " CZ3 TRP A 266 " =    1.191
peak=    4.017 closest distance to " CD  ARG A 269 " =    1.050
peak=    4.007 closest distance to " NH2AARG A 145 " =    1.113
peak=    3.997 closest distance to " CG2 THR A 221 " =    1.231
peak=    3.982 closest distance to " N   SER A 271 " =    1.035
peak=    3.981 closest distance to " O   HOH Z 146 " =    1.654
peak=    3.952 closest distance to " CA  ILE A 234 " =    1.017
peak=    3.946 closest distance to " CB  SER A  63 " =    1.274
peak=    3.945 closest distance to " CB  ASN A 142 " =    0.965
peak=    3.939 closest distance to " O   HOH Z 303 " =    2.209
peak=    3.937 closest distance to " CD2 LEU A 228 " =    1.265
peak=    3.914 closest distance to " O   HOH Z 272 " =    1.883
peak=    3.907 closest distance to " O   HOH Z  24 " =    2.039
peak=    3.883 closest distance to " CE3 TRP A 274 " =    1.328
peak=    3.869 closest distance to " O   HOH Z 214 " =    2.350
peak=    3.868 closest distance to " O   HOH Z 373 " =    1.596
peak=    3.867 closest distance to " O   HOH Z 195 " =    1.675
peak=    3.850 closest distance to " C   ASN A 209 " =    1.619
peak=    3.842 closest distance to " O   HOH Z 153 " =    3.653
peak=    3.836 closest distance to " O   HOH Z 124 " =    1.360
peak=    3.821 closest distance to " O   HOH Z  39 " =    1.375
peak=    3.819 closest distance to " O   HOH Z 362 " =    1.812
peak=    3.819 closest distance to " CD1 LEU A   5 " =    1.280
peak=    3.814 closest distance to " O   HOH Z   1 " =    1.863
peak=    3.811 closest distance to " CB  SER A 276 " =    1.147
peak=    3.805 closest distance to " CE3 TRP A 150 " =    1.130
peak=    3.794 closest distance to " CD  ARG A  66 " =    2.291
peak=    3.792 closest distance to " O   HOH Z   2 " =    1.944
peak=    3.792 closest distance to " O   HOH Z 414 " =    1.404
peak=    3.784 closest distance to " CG2 ILE A 120 " =    1.202
peak=    3.783 closest distance to " NZ BLYS A 290 " =    1.012
peak=    3.781 closest distance to " CB  TRP A 266 " =    0.974
peak=    3.781 closest distance to " CB  GLU A 277 " =    3.623
peak=    3.775 closest distance to " O   HOH Z  61 " =    1.742
peak=    3.768 closest distance to " OG BSER A 212 " =    2.768
peak=    3.764 closest distance to " N   GLN A 278 " =    1.141
peak=    3.759 closest distance to " CB  ALA A  43 " =    0.937
peak=    3.746 closest distance to " ND2BASN A 224 " =    0.902
peak=    3.741 closest distance to " O   HOH Z 423 " =    1.771
peak=    3.737 closest distance to " CD  GLN A  77 " =    1.250
peak=    3.733 closest distance to " O   HOH Z 380 " =    1.912
peak=    3.724 closest distance to " O   HOH Z 293 " =    1.613
peak=    3.722 closest distance to " O   HOH Z  91 " =    2.418
peak=    3.721 closest distance to " CA  LEU A 282 " =    1.202
peak=    3.697 closest distance to " O   HOH Z 143 " =    1.427
peak=    3.696 closest distance to " NH2AARG A 190 " =    1.667
peak=    3.696 closest distance to " CB  TRP A 179 " =    1.447
peak=    3.693 closest distance to " CG BARG A 102 " =    2.007
peak=    3.692 closest distance to " O   HOH Z  68 " =    2.093
peak=    3.688 closest distance to " CB  LYS A 290 " =    0.896
peak=    3.688 closest distance to " O   HOH Z 236 " =    1.659
peak=    3.682 closest distance to " CB  GLU A 128 " =    1.035
peak=    3.679 closest distance to " CA  ALA A 160 " =    1.201
peak=    3.677 closest distance to " O   HOH Z 133 " =    1.341
peak=    3.675 closest distance to " O   HOH Z 371 " =    2.821
peak=    3.674 closest distance to " O   HOH Z 438 " =    2.072
peak=    3.665 closest distance to " CG  PRO A 213 " =    1.307
peak=    3.664 closest distance to " O   HOH Z 365 " =    3.120
peak=    3.664 closest distance to " CD1 ILE A  33 " =    1.850
peak=    3.658 closest distance to " O   HOH Z 218 " =    1.961
peak=    3.657 closest distance to " OG  SER A 276 " =    0.971
peak=    3.654 closest distance to " O   HOH Z 422 " =    2.635
peak=    3.651 closest distance to " CB  SER A 210 " =    0.999
peak=    3.650 closest distance to " O   ILE A  20 " =    1.936
peak=    3.642 closest distance to " N   SER A  97 " =    0.859
peak=    3.639 closest distance to " N   GLY A 133 " =    3.876
peak=    3.634 closest distance to " C   GLN A  73 " =    1.100
peak=    3.631 closest distance to " O   HOH Z 126 " =    1.485
peak=    3.628 closest distance to " NH1AARG A 145 " =    1.221
peak=    3.628 closest distance to " O   HOH Z  11 " =    1.151
peak=    3.624 closest distance to " O   HOH Z 245 " =    1.315
peak=    3.616 closest distance to " O   HOH Z 410 " =    1.654
peak=    3.614 closest distance to " O  BHOH Z  74 " =    1.120
peak=    3.613 closest distance to " CB  MET A  40 " =    0.869
peak=    3.612 closest distance to " O   HOH Z  56 " =    1.974
peak=    3.607 closest distance to " CB  VAL A 202 " =    1.555
peak=    3.607 closest distance to " O   HOH Z  55 " =    1.780
peak=    3.604 closest distance to " CB  VAL A 265 " =    1.426
peak=    3.586 closest distance to " CD  GLN A 240 " =    1.655
peak=    3.586 closest distance to " ND2 ASN A 249 " =    0.884
peak=    3.585 closest distance to " NE2 HIS A 207 " =    1.054
peak=    3.581 closest distance to " CA  ASN A 127 " =    1.112
peak=    3.577 closest distance to " O   HOH Z  43 " =    1.236
peak=    3.574 closest distance to " CB  HIS A 108 " =    0.833
peak=    3.573 closest distance to " O   TYR A 116 " =    1.174
peak=    3.569 closest distance to " CB  MET A  47 " =    1.061
peak=    3.568 closest distance to " O   HOH Z 368 " =    3.451
peak=    3.566 closest distance to " O   HOH Z  26 " =    1.458
peak=    3.564 closest distance to " O   VAL A  72 " =    0.918
peak=    3.561 closest distance to " O   HOH Z 148 " =    2.331
peak=    3.557 closest distance to " O   HOH Z 181 " =    2.370
peak=    3.549 closest distance to " CB  LEU A 143 " =    1.120
peak=    3.541 closest distance to " OG ASER A 212 " =    1.518
peak=    3.538 closest distance to " NH2BARG A 190 " =    1.333
peak=    3.533 closest distance to " O   HOH Z 211 " =    1.171
peak=    3.530 closest distance to " ND1 HIS A  86 " =    1.843
peak=    3.526 closest distance to " O   HOH Z  88 " =    3.653
peak=    3.518 closest distance to " CD1 LEU A 300 " =    1.124
peak=    3.518 closest distance to " O   HOH Z  10 " =    1.816
peak=    3.513 closest distance to " CB  LEU A 228 " =    1.344
peak=    3.507 closest distance to " ND1 HIS A  81 " =    1.713
peak=    3.505 closest distance to " N   GLU A   2 " =    1.449
peak=    3.503 closest distance to " CA  GLY A 136 " =    1.064
peak=    3.499 closest distance to " CZ  PHE A 218 " =    1.131
peak=    3.496 closest distance to " CB  VAL A 250 " =    1.069
peak=    3.493 closest distance to " O   HOH Z 359 " =    1.391
peak=    3.491 closest distance to " NE AARG A 275 " =    1.491
peak=    3.488 closest distance to " NZ  LYS A 117 " =    3.204
peak=    3.488 closest distance to " OE2 GLU A   2 " =    2.119
peak=    3.487 closest distance to " CB  ALA A 114 " =    1.160
peak=    3.486 closest distance to " O   HOH Z 360 " =    1.193
peak=    3.484 closest distance to " O   HOH Z 258 " =    1.202
peak=    3.480 closest distance to " CB  ARG A 138 " =    1.095
peak=    3.473 closest distance to " CB  ALA A 104 " =    0.721
peak=    3.472 closest distance to " O   HOH Z 145 " =    2.505
peak=    3.472 closest distance to " CA  ALA A 295 " =    0.915
peak=    3.468 closest distance to " CA  SER A  87 " =    0.900
peak=    3.459 closest distance to " CG1 VAL A 296 " =    1.187
peak=    3.457 closest distance to " O   HOH Z 425 " =    2.117
peak=    3.454 closest distance to " O   HOH Z 425 " =    2.013
peak=    3.454 closest distance to " CD  ARG A 159 " =    0.730
peak=    3.452 closest distance to " CG1 ILE A 151 " =    1.186
peak=    3.452 closest distance to " O   HOH Z  51 " =    1.814
peak=    3.448 closest distance to " N   ARG A 156 " =    1.342
peak=    3.447 closest distance to " O   HOH Z   3 " =    2.236
peak=    3.446 closest distance to " O   HOH Z 310 " =    2.292
peak=    3.442 closest distance to " CG  GLN A  58 " =    1.105
peak=    3.439 closest distance to " NH1 ARG A  14 " =    1.039
peak=    3.434 closest distance to " O   HOH Z  98 " =    1.791
peak=    3.433 closest distance to " CA  ARG A 159 " =    1.281
peak=    3.432 closest distance to " CG2 ILE A  20 " =    1.667
peak=    3.431 closest distance to " O   HOH Z 193 " =    1.635
peak=    3.430 closest distance to " CG  ARG A 156 " =    1.245
peak=    3.426 closest distance to " N   TYR A  15 " =    0.986
peak=    3.424 closest distance to " CE  MET A  93 " =    1.477
peak=    3.423 closest distance to " O   HOH Z 172 " =    2.208
peak=    3.423 closest distance to " O   HOH Z 233 " =    1.575
peak=    3.422 closest distance to " O   HOH Z 158 " =    3.084
peak=    3.418 closest distance to " O   HOH Z 368 " =    4.324
peak=    3.416 closest distance to " N   PHE A 130 " =    1.244
peak=    3.416 closest distance to " CD1 LEU A 281 " =    1.006
peak=    3.414 closest distance to " O   HOH Z 411 " =    3.226
peak=    3.412 closest distance to " CD  LYS A 166 " =    1.356
peak=    3.410 closest distance to " CG BARG A 275 " =    1.295
peak=    3.402 closest distance to " OG  SER A  62 " =    2.637
peak=    3.393 closest distance to " CA  ILE A 106 " =    0.766
peak=    3.389 closest distance to " CB  SER A 273 " =    1.002
peak=    3.382 closest distance to " O   HOH Z 109 " =    2.380
peak=    3.382 closest distance to " O   HOH Z 353 " =    1.685
peak=    3.372 closest distance to " CB  GLN A  88 " =    1.378
peak=    3.365 closest distance to " O   HOH Z 238 " =    1.306
peak=    3.352 closest distance to " CA  ILE A 263 " =    1.074
peak=    3.351 closest distance to " CB  LYS A 117 " =    1.223
peak=    3.350 closest distance to " O   HOH Z 421 " =    2.085
peak=    3.348 closest distance to " O   HOH Z  49 " =    0.927
peak=    3.342 closest distance to " CB  LEU A 237 " =    0.942
peak=    3.339 closest distance to " CG  GLN A  89 " =    1.565
peak=    3.338 closest distance to " ND2 ASN A 187 " =    1.984
peak=    3.337 closest distance to " O   HOH Z  40 " =    2.029
peak=    3.335 closest distance to " CB  PRO A  90 " =    1.091
peak=    3.335 closest distance to " OD1 ASP A 200 " =    1.522
peak=    3.334 closest distance to " O   HOH Z 218 " =    1.397
peak=    3.332 closest distance to " O   HOH Z 196 " =    1.265
peak=    3.330 closest distance to " O   HOH Z 110 " =    1.688
peak=    3.328 closest distance to " CB  ALA A  10 " =    0.885
peak=    3.328 closest distance to " O   CYS A 168 " =    1.323
peak=    3.325 closest distance to " O   HOH Z 119 " =    1.572
peak=    3.323 closest distance to " O   HOH Z 403 " =    1.358
peak=    3.323 closest distance to " O   HOH Z 222 " =    1.902
peak=    3.322 closest distance to " CE  LYS A  76 " =    0.915
peak=    3.321 closest distance to " OE1 GLU A   2 " =    1.611
peak=    3.320 closest distance to " N   CYS A 260 " =    0.885
peak=    3.318 closest distance to " CB  ASN A 110 " =    1.002
peak=    3.312 closest distance to " O   HOH Z 112 " =    1.097
peak=    3.311 closest distance to " O   HOH Z  44 " =    1.920
peak=    3.310 closest distance to " CB  TRP A 150 " =    1.287
peak=    3.309 closest distance to " C   GLN A  11 " =    1.421
peak=    3.305 closest distance to " CZ3 TRP A  92 " =    1.224
peak=    3.304 closest distance to " OG BSER A 210 " =    1.206
peak=    3.303 closest distance to " OD2 ASP A 286 " =    2.522
peak=    3.300 closest distance to " O   HOH Z 424 " =    2.630
peak=    3.298 closest distance to " O   GLY A 302 " =    2.128
peak=    3.296 closest distance to " CB  LEU A 300 " =    0.952
peak=    3.295 closest distance to " CA  ASN A 284 " =    0.836
peak=    3.295 closest distance to " CA  THR A 264 " =    0.767
peak=    3.292 closest distance to " NH1BARG A 145 " =    1.357
peak=    3.290 closest distance to " O   HOH Z 184 " =    1.386
peak=    3.289 closest distance to " O   HOH Z  83 " =    1.236
peak=    3.289 closest distance to " CG  LYS A 119 " =    1.115
peak=    3.283 closest distance to " O   HOH Z 201 " =    1.691
peak=    3.283 closest distance to " NE2 GLN A  58 " =    4.200
peak=    3.282 closest distance to " O   HOH Z 180 " =    2.194
peak=    3.279 closest distance to " CB  ASN A 215 " =    1.267
peak=    3.275 closest distance to " ND2 ASN A 110 " =    1.748
peak=    3.274 closest distance to " CB  ARG A 156 " =    1.244
peak=    3.271 closest distance to " CA  LEU A 101 " =    1.337
peak=    3.270 closest distance to " CE3 TRP A 274 " =    2.367
peak=    3.268 closest distance to " CG  ARG A 159 " =    0.925
peak=    3.267 closest distance to " O   HOH Z 356 " =    1.424
peak=    3.267 closest distance to " CB  ARG A  79 " =    0.898
peak=    3.265 closest distance to " CA  VAL A 296 " =    1.053
peak=    3.264 closest distance to " O   HOH Z 329 " =    4.044
peak=    3.263 closest distance to " O   HOH Z 222 " =    1.704
peak=    3.262 closest distance to " O   HOH Z 368 " =    1.903
peak=    3.262 closest distance to " O   HOH Z  11 " =    1.656
peak=    3.258 closest distance to " O   HOH Z 290 " =    1.046
peak=    3.254 closest distance to " CD  ARG A  24 " =    1.109
peak=    3.251 closest distance to " CB  SER A  62 " =    1.066
peak=    3.249 closest distance to " O   HOH Z 392 " =    1.879
peak=    3.248 closest distance to " CA  ARG A  36 " =    0.988
peak=    3.247 closest distance to " CB  GLU A 277 " =    0.870
peak=    3.236 closest distance to " CA  GLY A 267 " =    1.151
peak=    3.230 closest distance to " CB  TRP A 150 " =    0.971
peak=    3.228 closest distance to " O   THR A 294 " =    1.084
peak=    3.226 closest distance to " N   ASN A 127 " =    1.316
peak=    3.225 closest distance to " O   HOH Z 379 " =    1.302
peak=    3.219 closest distance to " CB  PHE A  16 " =    1.079
peak=    3.210 closest distance to " CB  ARG A 190 " =    1.811
peak=    3.207 closest distance to " O   HOH Z 328 " =    1.619
peak=    3.207 closest distance to " O   HOH Z 423 " =    1.346
peak=    3.204 closest distance to " O   THR A 182 " =    1.606
peak=    3.204 closest distance to " O   HOH Z 145 " =    1.987
peak=    3.201 closest distance to " CA  MET A 105 " =    0.828
peak=    3.197 closest distance to " CA  GLU A 152 " =    0.973
peak=    3.194 closest distance to " O   HOH Z 390 " =    1.216
peak=    3.193 closest distance to " O   HOH Z  78 " =    2.010
peak=    3.192 closest distance to " CB  ARG A 139 " =    1.230
peak=    3.190 closest distance to " O   HOH Z 327 " =    1.634
peak=    3.187 closest distance to " O   HOH Z 261 " =    2.385
peak=    3.185 closest distance to " CB  ALA A   1 " =    4.725
peak=    3.179 closest distance to " CB  ASP A 107 " =    1.074
peak=    3.178 closest distance to " O   HOH Z 357 " =    2.108
peak=    3.177 closest distance to " CD1 LEU A 167 " =    1.213
peak=    3.174 closest distance to " CE2 PHE A  16 " =    0.932
peak=    3.170 closest distance to " O   ALA A 165 " =    1.318
peak=    3.169 closest distance to " OD1 ASN A 217 " =    1.629
peak=    3.169 closest distance to " CA  VAL A 125 " =    1.086
peak=    3.157 closest distance to " N   ALA A 256 " =    0.971
peak=    3.155 closest distance to " CB  ALA A 248 " =    1.313
peak=    3.152 closest distance to " CE3 TRP A 274 " =    1.637
peak=    3.149 closest distance to " O   HOH Z  88 " =    3.236
peak=    3.147 closest distance to " N   ASP A 162 " =    1.204
peak=    3.145 closest distance to " CA  VAL A 153 " =    1.057
peak=    3.145 closest distance to " O   HOH Z 352 " =    1.652
peak=    3.141 closest distance to " CZ  PHE A  38 " =    1.313
peak=    3.139 closest distance to " O   HOH Z 384 " =    1.459
peak=    3.139 closest distance to " O   HOH Z 264 " =    1.580
peak=    3.136 closest distance to " O   HOH Z  57 " =    1.118
peak=    3.134 closest distance to " CG2 VAL A 268 " =    0.909
peak=    3.127 closest distance to " CA  ARG A 195 " =    1.218
peak=    3.124 closest distance to " CG2 VAL A 257 " =    0.813
peak=    3.123 closest distance to " O   ASP A 200 " =    1.445
peak=    3.119 closest distance to " CB  SER A  22 " =    0.999
peak=    3.119 closest distance to " CB  TYR A  30 " =    1.307
peak=    3.118 closest distance to " OE2 GLU A  53 " =    0.920
peak=    3.117 closest distance to " O   HOH Z   3 " =    2.353
peak=    3.115 closest distance to " O   HOH Z 148 " =    1.580
peak=    3.102 closest distance to " O   HOH Z 207 " =    2.520
peak=    3.098 closest distance to " O   HOH Z 154 " =    1.844
peak=    3.087 closest distance to " O   HOH Z  48 " =    1.531
peak=    3.082 closest distance to " O   HOH Z 215 " =    1.371
peak=    3.081 closest distance to " N   GLN A 122 " =    0.761
peak=    3.065 closest distance to " CB  ASN A 187 " =    1.056
peak=    3.044 closest distance to " O   HOH Z 380 " =    1.501
peak=    3.023 closest distance to " O   HOH Z 251 " =    1.651

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 213         
Filter by distance & map next to the model:
   mapped sites are within: 0.397 - 5.982
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 207 from: 213
   mapped sites are within: 0.711 - 5.982

peak=   -5.411 closest distance to " CG2 VAL A 230 " =    0.757
peak=   -4.881 closest distance to " CD  ARG A 138 " =    1.234
peak=   -4.457 closest distance to " O   PRO A 198 " =    1.051
peak=   -4.421 closest distance to " O   HOH Z 131 " =    3.855
peak=   -4.349 closest distance to " CD  ARG A  14 " =    2.998
peak=   -4.279 closest distance to " OG BSER A 134 " =    1.561
peak=   -4.224 closest distance to " CB  VAL A 230 " =    0.949
peak=   -4.194 closest distance to " O   HOH Z  39 " =    0.881
peak=   -4.084 closest distance to " O   SER A 135 " =    1.440
peak=   -4.050 closest distance to " CG  ARG A 138 " =    0.922
peak=   -4.043 closest distance to " CB  GLN A  55 " =    1.209
peak=   -4.024 closest distance to " CA  ASP A  27 " =    2.432
peak=   -4.015 closest distance to " N   THR A 157 " =    1.557
peak=   -3.986 closest distance to " O   HOH Z 100 " =    0.951
peak=   -3.962 closest distance to " CB  PHE A 130 " =    1.249
peak=   -3.951 closest distance to " O   HOH Z 211 " =    1.017
peak=   -3.904 closest distance to " CE1 PHE A  59 " =    2.091
peak=   -3.904 closest distance to " CD2 LEU A   5 " =    0.825
peak=   -3.903 closest distance to " O   HOH Z 275 " =    1.706
peak=   -3.899 closest distance to " CB  ALA A   9 " =    2.428
peak=   -3.899 closest distance to " CB  PRO A 243 " =    2.656
peak=   -3.881 closest distance to " CB  ALA A  43 " =    2.439
peak=   -3.853 closest distance to " O   HOH Z 385 " =    0.951
peak=   -3.848 closest distance to " CG  MET A 105 " =    0.985
peak=   -3.842 closest distance to " CG  ARG A 219 " =    2.335
peak=   -3.839 closest distance to " O   HOH Z 359 " =    1.635
peak=   -3.829 closest distance to " O   HOH Z 266 " =    5.170
peak=   -3.811 closest distance to " CA  GLY A  98 " =    1.881
peak=   -3.792 closest distance to " O   HOH Z 286 " =    1.608
peak=   -3.779 closest distance to " O   HOH Z  60 " =    1.671
peak=   -3.770 closest distance to " O   HOH Z 389 " =    1.184
peak=   -3.757 closest distance to " CG2 VAL A 202 " =    2.725
peak=   -3.751 closest distance to " CE2 PHE A 218 " =    2.497
peak=   -3.724 closest distance to " CG  TRP A 266 " =    1.816
peak=   -3.718 closest distance to " CD2 TYR A 293 " =    1.850
peak=   -3.713 closest distance to " O   SER A  22 " =    2.670
peak=   -3.696 closest distance to " CD  LYS A 166 " =    2.516
peak=   -3.695 closest distance to " O   HOH Z  24 " =    1.002
peak=   -3.681 closest distance to " CD  ARG A 156 " =    1.962
peak=   -3.676 closest distance to " O   HOH Z 377 " =    0.859
peak=   -3.670 closest distance to " O   ILE A  49 " =    1.616
peak=   -3.670 closest distance to " CB  ALA A 248 " =    2.085
peak=   -3.664 closest distance to " OE1 GLU A 277 " =    2.328
peak=   -3.655 closest distance to " O   PRO A 163 " =    1.811
peak=   -3.648 closest distance to " OG  SER A  97 " =    2.150
peak=   -3.645 closest distance to " NH2AARG A 275 " =    5.317
peak=   -3.642 closest distance to " N   PRO A 163 " =    1.501
peak=   -3.631 closest distance to " CB  TYR A  68 " =    1.438
peak=   -3.609 closest distance to " C   GLU A   2 " =    1.977
peak=   -3.608 closest distance to " O   ALA A  10 " =    1.676
peak=   -3.606 closest distance to " O   HOH Z 415 " =    1.073
peak=   -3.598 closest distance to " O   ALA A  84 " =    1.748
peak=   -3.594 closest distance to " O   SER A 141 " =    1.759
peak=   -3.587 closest distance to " C   MET A 188 " =    1.604
peak=   -3.580 closest distance to " O   VAL A  67 " =    2.512
peak=   -3.580 closest distance to " CG  PRO A 163 " =    2.578
peak=   -3.576 closest distance to " CZ2 TRP A 274 " =    0.959
peak=   -3.561 closest distance to " NH2 ARG A  79 " =    2.183
peak=   -3.555 closest distance to " ND2 ASN A 285 " =    2.148
peak=   -3.553 closest distance to " NE2 GLN A  55 " =    1.110
peak=   -3.553 closest distance to " CD  LYS A 289 " =    2.304
peak=   -3.552 closest distance to " C   ARG A 269 " =    1.364
peak=   -3.549 closest distance to " O   HOH Z 385 " =    1.264
peak=   -3.549 closest distance to " O   GLY A 203 " =    2.515
peak=   -3.545 closest distance to " O   HOH Z 163 " =    1.938
peak=   -3.543 closest distance to " CD1 LEU A 255 " =    2.906
peak=   -3.541 closest distance to " OG  SER A  87 " =    1.382
peak=   -3.533 closest distance to " CE2 TYR A  30 " =    2.601
peak=   -3.531 closest distance to " O   HOH Z 185 " =    2.094
peak=   -3.527 closest distance to " O   HOH Z  53 " =    1.735
peak=   -3.523 closest distance to " O   HOH Z 238 " =    0.888
peak=   -3.522 closest distance to " N   VAL A  72 " =    2.163
peak=   -3.519 closest distance to " CA  GLY A 241 " =    2.261
peak=   -3.510 closest distance to " CB  ASP A 132 " =    2.409
peak=   -3.493 closest distance to " O   HOH Z 100 " =    1.154
peak=   -3.488 closest distance to " O   HOH Z 298 " =    2.858
peak=   -3.481 closest distance to " O   HOH Z 435 " =    2.205
peak=   -3.469 closest distance to " CG2 ILE A 151 " =    2.545
peak=   -3.455 closest distance to " O   ALA A  51 " =    1.285
peak=   -3.451 closest distance to " O   HOH Z 359 " =    3.322
peak=   -3.451 closest distance to " N   ALA A  43 " =    2.648
peak=   -3.440 closest distance to " CG2AVAL A  41 " =    2.790
peak=   -3.434 closest distance to " CA  ASN A 127 " =    1.197
peak=   -3.432 closest distance to " O   HOH Z 111 " =    1.604
peak=   -3.431 closest distance to " O   GLY A  80 " =    2.556
peak=   -3.430 closest distance to " O   HOH Z 105 " =    2.042
peak=   -3.430 closest distance to " CE BMET A  47 " =    1.016
peak=   -3.427 closest distance to " O   HOH Z 368 " =    2.485
peak=   -3.425 closest distance to " O   HOH Z 389 " =    2.332
peak=   -3.422 closest distance to " O   PRO A 243 " =    2.521
peak=   -3.420 closest distance to " OG  SER A 245 " =    1.426
peak=   -3.417 closest distance to " O   HOH Z  52 " =    0.916
peak=   -3.412 closest distance to " O   HOH Z 368 " =    1.488
peak=   -3.401 closest distance to " CE2 TRP A  70 " =    2.399
peak=   -3.391 closest distance to " O   HOH Z 216 " =    1.547
peak=   -3.390 closest distance to " CB  ALA A 114 " =    2.514
peak=   -3.389 closest distance to " CD2 TYR A 116 " =    2.186
peak=   -3.383 closest distance to " O   HOH Z 186 " =    1.521
peak=   -3.380 closest distance to " O   HOH Z  11 " =    1.872
peak=   -3.374 closest distance to " O   HOH Z 353 " =    1.269
peak=   -3.373 closest distance to " OG  SER A  62 " =    4.222
peak=   -3.368 closest distance to " O   HOH Z 409 " =    5.982
peak=   -3.367 closest distance to " O   HOH Z 427 " =    1.857
peak=   -3.359 closest distance to " O   HOH Z  43 " =    1.990
peak=   -3.359 closest distance to " O   HOH Z 134 " =    4.165
peak=   -3.350 closest distance to " O   HOH Z 290 " =    1.146
peak=   -3.347 closest distance to " O   HOH Z 166 " =    1.675
peak=   -3.332 closest distance to " O   HOH Z 421 " =    3.248
peak=   -3.332 closest distance to " O   HOH Z 133 " =    1.481
peak=   -3.331 closest distance to " O   GLY A  17 " =    1.252
peak=   -3.328 closest distance to " ND2 ASN A 187 " =    1.578
peak=   -3.326 closest distance to " O   HOH Z 147 " =    2.047
peak=   -3.326 closest distance to " CG  LEU A   5 " =    0.916
peak=   -3.325 closest distance to " CD  GLN A  77 " =    1.281
peak=   -3.324 closest distance to " CB  TRP A  85 " =    2.589
peak=   -3.318 closest distance to " O   HOH Z 351 " =    1.616
peak=   -3.313 closest distance to " CG2 ILE A 120 " =    1.261
peak=   -3.311 closest distance to " O   HOH Z 300 " =    1.250
peak=   -3.308 closest distance to " CG2 THR A  52 " =    2.878
peak=   -3.307 closest distance to " O   HOH Z 198 " =    2.091
peak=   -3.306 closest distance to " O   HOH Z 165 " =    2.161
peak=   -3.305 closest distance to " O   HOH Z 231 " =    1.965
peak=   -3.304 closest distance to " CD1 LEU A 297 " =    2.283
peak=   -3.303 closest distance to " O   HOH Z 292 " =    1.779
peak=   -3.301 closest distance to " O   HOH Z 374 " =    1.760
peak=   -3.297 closest distance to " ND2 ASN A 249 " =    2.394
peak=   -3.295 closest distance to " CD2 LEU A 237 " =    2.824
peak=   -3.294 closest distance to " O   HOH Z 300 " =    2.213
peak=   -3.294 closest distance to " CG  GLN A 240 " =    2.407
peak=   -3.288 closest distance to " CG1 VAL A 250 " =    2.708
peak=   -3.283 closest distance to " CD  PRO A 213 " =    2.058
peak=   -3.279 closest distance to " C   ARG A  79 " =    2.601
peak=   -3.279 closest distance to " CG  LEU A 281 " =    1.765
peak=   -3.279 closest distance to " O   HOH Z 350 " =    1.804
peak=   -3.276 closest distance to " OH  TYR A 169 " =    0.900
peak=   -3.273 closest distance to " O   HOH Z 276 " =    1.374
peak=   -3.272 closest distance to " CB  PRO A 163 " =    2.365
peak=   -3.270 closest distance to " CZ2 TRP A  92 " =    2.813
peak=   -3.269 closest distance to " CD  GLU A 277 " =    0.870
peak=   -3.263 closest distance to " O   HOH Z 200 " =    3.371
peak=   -3.257 closest distance to " O   GLY A 211 " =    1.135
peak=   -3.257 closest distance to " C   ASN A 285 " =    2.173
peak=   -3.253 closest distance to " OG  SER A 206 " =    1.735
peak=   -3.247 closest distance to " CG1 VAL A 125 " =    2.338
peak=   -3.244 closest distance to " O   HOH Z 144 " =    0.897
peak=   -3.236 closest distance to " CA  GLY A 203 " =    2.477
peak=   -3.233 closest distance to " OG  SER A  28 " =    2.000
peak=   -3.231 closest distance to " CG2 THR A 157 " =    2.227
peak=   -3.230 closest distance to " NE1 TRP A 177 " =    1.889
peak=   -3.229 closest distance to " N   ASP A 191 " =    1.142
peak=   -3.229 closest distance to " O   HOH Z  52 " =    2.100
peak=   -3.228 closest distance to " NH2 ARG A 219 " =    1.801
peak=   -3.227 closest distance to " O   HOH Z  64 " =    1.268
peak=   -3.227 closest distance to " C   HIS A 108 " =    1.209
peak=   -3.226 closest distance to " O   LYS A 289 " =    3.026
peak=   -3.224 closest distance to " C   GLN A 205 " =    2.073
peak=   -3.222 closest distance to " O   HOH Z 313 " =    1.303
peak=   -3.220 closest distance to " O   HOH Z 111 " =    1.215
peak=   -3.220 closest distance to " O   HOH Z 414 " =    2.065
peak=   -3.216 closest distance to " C   VAL A  72 " =    0.860
peak=   -3.215 closest distance to " O   HOH Z 174 " =    3.098
peak=   -3.211 closest distance to " O   HOH Z 139 " =    5.145
peak=   -3.211 closest distance to " CB  CYS A 254 " =    1.941
peak=   -3.211 closest distance to " O   ARG A 145 " =    1.368
peak=   -3.209 closest distance to " C   ALA A 158 " =    1.407
peak=   -3.204 closest distance to " O   HOH Z  83 " =    1.368
peak=   -3.204 closest distance to " O   HOH Z 318 " =    1.882
peak=   -3.203 closest distance to " C   PHE A 155 " =    0.711
peak=   -3.202 closest distance to " OD1 ASP A 238 " =    1.359
peak=   -3.188 closest distance to " CD1 LEU A   5 " =    2.533
peak=   -3.188 closest distance to " CB  ALA A 291 " =    2.066
peak=   -3.187 closest distance to " O   HOH Z 331 " =    1.164
peak=   -3.181 closest distance to " O   ALA A   1 " =    1.414
peak=   -3.180 closest distance to " OE1 GLN A 183 " =    1.677
peak=   -3.178 closest distance to " O   HOH Z 365 " =    1.486
peak=   -3.177 closest distance to " CG2 VAL A 296 " =    2.024
peak=   -3.177 closest distance to " O   HOH Z 377 " =    2.002
peak=   -3.176 closest distance to " OE1 GLN A  88 " =    1.115
peak=   -3.175 closest distance to " O   ALA A   1 " =    1.753
peak=   -3.173 closest distance to " CB  TYR A  15 " =    2.197
peak=   -3.163 closest distance to " O   HOH Z 111 " =    4.777
peak=   -3.159 closest distance to " OE1 GLU A  44 " =    1.011
peak=   -3.155 closest distance to " ND2 ASN A  45 " =    2.446
peak=   -3.154 closest distance to " CG  LEU A  83 " =    2.059
peak=   -3.154 closest distance to " O   HOH Z 121 " =    3.881
peak=   -3.149 closest distance to " CD2 PHE A 130 " =    2.923
peak=   -3.136 closest distance to " O   HOH Z 404 " =    1.445
peak=   -3.136 closest distance to " CD2 HIS A 207 " =    2.340
peak=   -3.131 closest distance to " O   HOH Z 407 " =    2.937
peak=   -3.128 closest distance to " O   HOH Z 336 " =    5.946
peak=   -3.127 closest distance to " CB  ALA A 291 " =    2.186
peak=   -3.125 closest distance to " CB  ALA A 227 " =    2.407
peak=   -3.123 closest distance to " O   HOH Z  52 " =    1.683
peak=   -3.100 closest distance to " O   HOH Z  52 " =    2.211
peak=   -3.094 closest distance to " OH  TYR A 247 " =    1.599
peak=   -3.091 closest distance to " O   HOH Z 429 " =    2.086
peak=   -3.091 closest distance to " CG  PHE A 283 " =    2.610
peak=   -3.076 closest distance to " CB  ALA A 161 " =    1.620
peak=   -3.075 closest distance to " O   THR A  52 " =    1.138
peak=   -3.072 closest distance to " O   HOH Z  68 " =    1.342
peak=   -3.072 closest distance to " ND2 ASN A 173 " =    1.707
peak=   -3.066 closest distance to " O   HOH Z 414 " =    1.628
peak=   -3.063 closest distance to " O   HOH Z  52 " =    0.746
peak=   -3.048 closest distance to " CG1 VAL A 296 " =    1.365
peak=   -3.042 closest distance to " N   HIS A 115 " =    2.228
peak=   -3.041 closest distance to " O   HOH Z 292 " =    2.493
peak=   -3.014 closest distance to " CB  SER A  62 " =    5.470

================= 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    :  0.4940 0.4827   6.296573e+00   6.277708e+00
   1_bss:  0.4861 0.4686   6.292096e+00   6.270858e+00
   1_xyz:  0.4100 0.4326   6.203156e+00   6.230508e+00
   1_adp:  0.3692 0.4349   6.149095e+00   6.228138e+00
   1_occ:  0.3690 0.4349   6.148755e+00   6.228258e+00
   2_bss:  0.3668 0.4301   6.150382e+00   6.228032e+00
   2_xyz:  0.3002 0.3682   5.990200e+00   6.119819e+00
   2_adp:  0.2783 0.3514   5.945297e+00   6.088867e+00
   2_occ:  0.2781 0.3512   5.944821e+00   6.088831e+00
   3_bss:  0.2767 0.3495   5.945414e+00   6.088588e+00
   3_xyz:  0.2155 0.2769   5.716428e+00   5.895861e+00
   3_adp:  0.1974 0.2608   5.644567e+00   5.849737e+00
   3_occ:  0.1972 0.2606   5.643595e+00   5.849586e+00
   4_bss:  0.1967 0.2600   5.642981e+00   5.848122e+00
   4_xyz:  0.1600 0.2189   5.469146e+00   5.697355e+00
   4_adp:  0.1446 0.2014   5.381111e+00   5.615585e+00
   4_occ:  0.1444 0.2013   5.380355e+00   5.614864e+00
   5_bss:  0.1449 0.2007   5.378781e+00   5.613047e+00
   5_xyz:  0.1329 0.1879   5.308052e+00   5.549940e+00
   5_adp:  0.1308 0.1799   5.284553e+00   5.511279e+00
   5_occ:  0.1307 0.1798   5.283866e+00   5.510575e+00
   5_bss:  0.1307 0.1798   5.283736e+00   5.510327e+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:  0.365  20.000   6.525   9.193   9.588   0.000   0.000   0.000
   1_xyz:  0.365  20.000   6.525   9.193   9.588   0.000   0.000   0.000
   1_adp:  0.365  20.000   6.525   9.193   9.588   0.000   0.000   0.000
   1_occ:  0.365  20.000   6.525   9.193   9.588   0.000   0.000   0.000
   2_bss:  0.359  50.000   3.535   5.348   5.887   0.000   0.000   0.000
   2_xyz:  0.359  50.000   3.535   5.348   5.887   0.000   0.000   0.000
   2_adp:  0.359  50.000   3.535   5.348   5.887   0.000   0.000   0.000
   2_occ:  0.359  50.000   3.535   5.348   5.887   0.000   0.000   0.000
   3_bss:  0.335  50.000   1.919   2.671   3.635   0.000   0.000   0.000
   3_xyz:  0.335  50.000   1.919   2.671   3.635   0.000   0.000   0.000
   3_adp:  0.335  50.000   1.919   2.671   3.635   0.000   0.000   0.000
   3_occ:  0.335  50.000   1.919   2.671   3.635   0.000   0.000   0.000
   4_bss:  0.329  50.000   0.966   1.297   2.766   0.000   0.000   0.000
   4_xyz:  0.329  50.000   0.966   1.297   2.766   0.000   0.000   0.000
   4_adp:  0.329  50.000   0.966   1.297   2.766   0.000   0.000   0.000
   4_occ:  0.329  50.000   0.966   1.297   2.766   0.000   0.000   0.000
   5_bss:  0.327  60.906   0.981   0.818   2.668   0.000   0.000   0.000
   5_xyz:  0.327  60.906   0.981   0.818   2.668   0.000   0.000   0.000
   5_adp:  0.327  60.906   0.981   0.818   2.668   0.000   0.000   0.000
   5_occ:  0.327  60.906   0.981   0.818   2.668   0.000   0.000   0.000
   5_bss:  0.319  54.856  -0.507  -0.711   1.218   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  60.396 0.3879  0.4628    73852.606
   1_bss:  59.505 0.3987  0.6069    71774.012
   1_xyz:  52.256 0.4903  0.7259    57852.432
   1_adp:  51.223 0.5031  0.8133    56967.007
   1_occ:  51.299 0.5021  0.8111    57093.676
   2_bss:  50.956 0.5064  0.7275    56557.671
   2_xyz:  40.650 0.6331  0.8952    38141.804
   2_adp:  37.952 0.6661  0.9312    34752.091
   2_occ:  37.948 0.6662  0.9306    34710.816
   3_bss:  37.798 0.6679  0.8638    34596.699
   3_xyz:  28.018 0.7782  0.9738    20073.387
   3_adp:  25.821 0.8022  0.9870    17617.549
   3_occ:  25.798 0.8024  0.9870    17577.741
   4_bss:  25.755 0.8028  0.9507    17525.571
   4_xyz:  21.507 0.8463  0.9760    12352.151
   4_adp:  19.464 0.8663  0.9726    10376.676
   4_occ:  19.436 0.8665  0.9725    10348.008
   5_bss:  19.375 0.8670  0.9662    10276.583
   5_xyz:  17.713 0.8827  0.9751     8885.050
   5_adp:  16.678 0.8926  0.9747     8295.870
   5_occ:  16.663 0.8927  0.9745     8267.267
   5_bss:  16.663 0.8927  0.9705     8261.883
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.089   5.3761e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.089   5.3761e+01
   1_xyz:   1.747  0.014  0.109 18.469  0.006  4.106   1.5007e-01
   1_adp:   1.747  0.014  0.109 18.469  0.006  4.106   1.5007e-01
   1_occ:   1.747  0.014  0.109 18.469  0.006  4.106   1.5007e-01
   2_bss:   1.747  0.014  0.109 18.469  0.006  4.106   1.5007e-01
   2_xyz:   1.207  0.009  0.084 16.513  0.005  4.107   9.0793e-02
   2_adp:   1.207  0.009  0.084 16.513  0.005  4.107   9.0793e-02
   2_occ:   1.207  0.009  0.084 16.513  0.005  4.107   9.0793e-02
   3_bss:   1.207  0.009  0.084 16.513  0.005  4.107   9.0793e-02
   3_xyz:   1.122  0.009  0.085 15.889  0.005  4.125   7.6910e-02
   3_adp:   1.122  0.009  0.085 15.889  0.005  4.125   7.6910e-02
   3_occ:   1.122  0.009  0.085 15.889  0.005  4.125   7.6910e-02
   4_bss:   1.122  0.009  0.085 15.889  0.005  4.125   7.6910e-02
   4_xyz:   0.998  0.007  0.075 15.577  0.003  4.109   6.2512e-02
   4_adp:   0.998  0.007  0.075 15.577  0.003  4.109   6.2512e-02
   4_occ:   0.998  0.007  0.075 15.577  0.003  4.109   6.2512e-02
   5_bss:   0.998  0.007  0.075 15.577  0.003  4.109   6.2512e-02
   5_xyz:   0.920  0.006  0.070 15.212  0.003  4.113   5.3708e-02
   5_adp:   0.920  0.006  0.070 15.212  0.003  4.113   5.3708e-02
   5_occ:   0.920  0.006  0.070 15.212  0.003  4.113   5.3708e-02
   5_bss:   0.920  0.006  0.070 15.212  0.003  4.113   5.3708e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9681e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9681e+00
   1_xyz:  13.700  0.192  0.424 85.071  0.033  2.119   1.0350e-01
   1_adp:  13.700  0.192  0.424 85.071  0.033  2.119   1.0350e-01
   1_occ:  13.700  0.192  0.424 85.071  0.033  2.119   1.0350e-01
   2_bss:  13.700  0.192  0.424 85.071  0.033  2.119   1.0350e-01
   2_xyz:   6.960  0.090  0.298 89.815  0.041  2.030   6.0116e-02
   2_adp:   6.960  0.090  0.298 89.815  0.041  2.030   6.0116e-02
   2_occ:   6.960  0.090  0.298 89.815  0.041  2.030   6.0116e-02
   3_bss:   6.960  0.090  0.298 89.815  0.041  2.030   6.0116e-02
   3_xyz:   7.904  0.095  0.365 84.909  0.028  2.324   9.0244e-02
   3_adp:   7.904  0.095  0.365 84.909  0.028  2.324   9.0244e-02
   3_occ:   7.904  0.095  0.365 84.909  0.028  2.324   9.0244e-02
   4_bss:   7.904  0.095  0.365 84.909  0.028  2.324   9.0244e-02
   4_xyz:   6.626  0.062  0.289 84.927  0.029  2.351   4.4819e-02
   4_adp:   6.626  0.062  0.289 84.927  0.029  2.351   4.4819e-02
   4_occ:   6.626  0.062  0.289 84.927  0.029  2.351   4.4819e-02
   5_bss:   6.626  0.062  0.289 84.927  0.029  2.351   4.4819e-02
   5_xyz:   7.160  0.040  0.266 80.338  0.026  2.337   3.0488e-02
   5_adp:   7.160  0.040  0.266 80.338  0.026  2.337   3.0488e-02
   5_occ:   7.160  0.040  0.266 80.338  0.026  2.337   3.0488e-02
   5_bss:   7.160  0.040  0.266 80.338  0.026  2.337   3.0488e-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:  81.97   0.00  15.11  69.95   0.00  13.24  81.97   0.00  25.25
   1_occ:  81.97   0.00  15.11  69.95   0.00  13.24  81.97   0.00  25.25
   2_bss:  81.97   0.00  15.11  69.95   0.00  13.24  81.97   0.00  25.25
   2_xyz:  81.97   0.00  15.11  69.95   0.00  13.24  81.97   0.00  25.25
   2_adp:  85.51   0.00  14.69  62.04   0.00  11.75  85.51   0.00  30.69
   2_occ:  85.51   0.00  14.69  62.04   0.00  11.75  85.51   0.00  30.69
   3_bss:  85.51   0.00  14.69  62.04   0.00  11.75  85.51   0.00  30.69
   3_xyz:  85.51   0.00  14.69  62.04   0.00  11.75  85.51   0.00  30.69
   3_adp:  86.71   0.00  14.65  65.69   0.00  11.09  86.71   1.92  34.07
   3_occ:  86.71   0.00  14.65  65.69   0.00  11.09  86.71   1.92  34.07
   4_bss:  86.71   0.00  14.65  65.69   0.00  11.09  86.71   1.92  34.07
   4_xyz:  86.71   0.00  14.65  65.69   0.00  11.09  86.71   1.92  34.07
   4_adp:  93.70   0.00  15.35  85.11   0.00  10.34  93.70   3.23  42.65
   4_occ:  93.70   0.00  15.35  85.11   0.00  10.34  93.70   3.23  42.65
   5_bss:  93.70   0.00  15.35  85.11   0.00  10.34  93.70   3.23  42.65
   5_xyz:  93.70   0.00  15.35  85.11   0.00  10.34  93.70   3.23  42.65
   5_adp:  89.84   0.00  14.46  85.37   0.00   9.80  89.84   3.00  39.84
   5_occ:  89.84   0.00  14.46  85.37   0.00   9.80  89.84   3.00  39.84
   5_bss:  91.21   1.38  15.84  86.75   1.38  11.18  91.21   4.38  41.22
------------------------------------------------------------------------
 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:    1.281    0.041    0.413
   1_adp:    1.281    0.041    0.413
   1_occ:    1.281    0.041    0.413
   2_bss:    1.281    0.041    0.413
   2_xyz:    1.675    0.048    0.581
   2_adp:    1.675    0.048    0.581
   2_occ:    1.675    0.048    0.581
   3_bss:    1.675    0.048    0.581
   3_xyz:    1.589    0.017    0.695
   3_adp:    1.589    0.017    0.695
   3_occ:    1.589    0.017    0.695
   4_bss:    1.589    0.017    0.695
   4_xyz:    1.791    0.025    0.770
   4_adp:    1.791    0.025    0.770
   4_occ:    1.791    0.025    0.770
   5_bss:    1.791    0.025    0.770
   5_xyz:    1.881    0.053    0.790
   5_adp:    1.881    0.053    0.790
   5_occ:    1.881    0.053    0.790
   5_bss:    1.881    0.053    0.790
------------------------------------------------------------------------

CPU time actual refinement: 335.02


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_745/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_745/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_745/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_745/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_745/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 334.87 
  Macro-tasks:
    bulk solvent and scale       = 40.86  
    individual site refinement   = 142.72 
    weights calculation          = 30.85  
    collect and process          = 6.31   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 220.84 
  Micro-tasks:
    mask                            = 2.37   
    f_calc                          = 103.94 
    alpha_beta                      = 7.98   
    target                          = 1.12   
    gradients_wrt_atomic_parameters = 115.38 
    fmodel                         = 6.83   
    r_factors                      = 0.16   
    phase_errors                   = 10.40  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 248.45 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.653 micro seconds
Total CPU time: 5.80 minutes
from_scatterers_fft:    657 calls, 103.49 s
gradients_fft:          601 calls, 101.55 s

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

# Date 2008-01-16 Time 02:19:51 PST -0800 (1200478791.17 s)
Start R-work = 0.4940, R-free = 0.4827 (no bulk solvent and anisotropic scale)
Final R-work = 0.1468, R-free = 0.1960 (no bulk solvent and anisotropic scale)

Start R-work = 0.4861, R-free = 0.4686
Final R-work = 0.1307, R-free = 0.1798