# Date 2008-01-16 Time 01:51:00 PST -0800 (1200477060.37 s)
#phil __OFF__

Command line arguments: "../586.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 8332
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 586

-------------------------------------------------------------------------------
  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: (69.8988, 47.8686, 85.5261, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.25, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 47.8686, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9494 1.98135
Completeness in resolution range: 0.954537
Completeness with d_max=infinity: 0.951569

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9494
                             d_min =   1.9814

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: (69.8988, 47.8686, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9494 1.98135
Completeness in resolution range: 0.954537
Completeness with d_max=infinity: 0.951569

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9498 -  4.2393 [2158/2186]  1942   216  10.0%
  bin  2:  4.2393 -  3.3776 [2059/2082]  1853   206  10.0%
  bin  3:  3.3776 -  2.9544 [2046/2071]  1840   206  10.1%
  bin  4:  2.9544 -  2.6860 [2031/2047]  1830   201   9.9%
  bin  5:  2.6860 -  2.4944 [1999/2036]  1796   203  10.2%
  bin  6:  2.4944 -  2.3479 [1995/2029]  1804   191   9.6%
  bin  7:  2.3479 -  2.2307 [1978/2015]  1777   201  10.2%
  bin  8:  2.2307 -  2.1339 [1988/2030]  1784   204  10.3%
  bin  9:  2.1339 -  2.0520 [1977/2012]  1785   192   9.7%
  bin 10:  2.0520 -  1.9813 [1358/2014]  1219   139  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_586/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: 27
        2.42 -     3.04: 2199
        3.04 -     3.66: 4678
        3.66 -     4.28: 8964
        4.28 -     4.90: 12408
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 206 " - " O   HOH Z 342 "  1.865 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A 246 " - " O   HOH Z 201 "  1.868 3.040 -x+1/2,-y+1,z-1/2
  " OD2 ASP A 107 " - " OG BSER A 216 "  1.881 3.040 -x+1/2,-y+1,z+1/2
  " O   TYR A 214 " - " O   HOH Z 204 "  1.982 3.040 -x+1/2,-y+1,z-1/2
  ... (remaining 28271 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_586/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_586/model_refine_001.geo

CPU time processing inputs: 9.18


============================ 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 = 69.89875 47.8686 85.5261 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4813   r_free= 0.4694   ksol= 0.00   Bsol= 0.00   scale= 0.791    |
|                                                                             |
| 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:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.283754                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9498 -  4.7281 0.99   1396  158 0.3951 0.3950      6.5906      6.6093|
|  2:  4.7281 -  3.7727 0.99   1353  145 0.4106 0.4188      6.8031      6.8279|
|  3:  3.7727 -  3.3017 0.99   1314  152 0.4396 0.4129      6.6841      6.6642|
|  4:  3.3017 -  3.0025 0.99   1323  141 0.4665 0.4194      6.5219      6.4697|
|  5:  3.0025 -  2.7887 0.98   1286  145 0.5151 0.5144      6.3908      6.3948|
|  6:  2.7887 -  2.6253 0.99   1296  144 0.5085 0.5249      6.2792      6.1912|
|  7:  2.6253 -  2.4944 0.99   1293  147 0.4984 0.4343       6.255      6.1594|
|  8:  2.4944 -  2.3863 0.99   1296  138 0.5249 0.4870      6.1767      6.1581|
|  9:  2.3863 -  2.2948 0.99   1281  142 0.5352 0.5413      6.1218       6.186|
| 10:  2.2948 -  2.2158 0.97   1261  142 0.5227 0.5394      6.1201      6.1097|
| 11:  2.2158 -  2.1467 0.98   1270  147 0.5294 0.5226      6.0391      6.0446|
| 12:  2.1467 -  2.0855 1.00   1270  136 0.5277 0.5063      5.9826      6.0072|
| 13:  2.0855 -  2.0308 0.96   1261  137 0.5236 0.5334      5.8755      5.8822|
| 14:  2.0308 -  1.9813 0.56    730   85 0.5607 0.5239      5.8646      5.7486|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9498 -  4.7281  1396   158  0.67  37.00   0.80     0.69      80496.53|
|  2:  4.7281 -  3.7727  1353   145  0.69  36.33   0.88     0.74     107558.56|
|  3:  3.7727 -  3.3017  1314   152  0.60  43.50   0.83     0.71     112053.95|
|  4:  3.3017 -  3.0025  1323   141  0.52  50.10   0.80     0.61      95552.27|
|  5:  3.0025 -  2.7887  1286   145  0.43  57.08   0.73     0.51      80656.25|
|  6:  2.7887 -  2.6253  1296   144  0.42  58.53   0.73     0.48      68215.91|
|  7:  2.6253 -  2.4944  1293   147  0.42  58.28   0.74     0.47      62136.28|
|  8:  2.4944 -  2.3863  1296   138  0.39  60.87   0.72     0.45      57291.09|
|  9:  2.3863 -  2.2948  1281   142  0.34  64.85   0.72     0.41      55036.88|
| 10:  2.2948 -  2.2158  1261   142  0.32  66.23   0.75     0.36      52137.30|
| 11:  2.2158 -  2.1467  1270   147  0.29  68.72   0.75     0.35      49241.48|
| 12:  2.1467 -  2.0855  1270   136  0.29  68.54   0.75     0.36      45952.78|
| 13:  2.0855 -  2.0308  1261   137  0.28  69.38   0.73     0.35      38818.88|
| 14:  2.0308 -  1.9813   730    85  0.30  67.86   0.72     0.33      30529.17|
|alpha:            min =        0.33 max =            0.74 mean =         0.50|
|beta:             min =    30529.17 max =       112053.95 mean =     68443.49|
|figures of merit: min =        0.00 max =            1.00 mean =         0.43|
|phase err.(work): min =        0.00 max =           89.99 mean =        57.04|
|phase err.(test): min =        0.00 max =           89.98 mean =        57.08|
|-----------------------------------------------------------------------------|

============================== 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 = 13.828213             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.115   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.293304              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.593   (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 |  1.069 -  1.452:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.452 -  1.835:        7 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.835 -  2.218:      114 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.218 -  2.601:      567 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.601 -  2.984:     1361 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.984 -  3.367:     2491 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.367 -  3.751:     3927 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.751 -  4.134:     5132 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.134 -  4.517:     6705 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.517 -  4.900:     7953 |
|-----------------------------------------------------------------------------|
|-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 |       53.826 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.091    4.900  1.069 |       1.922 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.920)------------------------------------------|
|    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 = 11.920)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4872   r_free= 0.4785   ksol= 0.00   Bsol= 0.00   scale= 0.761    |
|                                                                             |
| 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: 6.285230                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4741   r_free= 0.4648   ksol= 0.32   Bsol= 7.27   scale= 0.988    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.60,11.89,7.55,0.00,0.00,0.00); trace/3= 8.68                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.77 A                  |
| x-ray target function (ml) for work reflections: 6.277398                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.241251             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.801   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.226322              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.976   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4741      final r-factor (work) = 0.3971          |
| start r-factor (free) = 0.4648      final r-factor (free) = 0.4125          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 95.4340 = 13.24 * 0.50 * 6.2846 + 1.00 * 53.8258                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 41.1898 = 13.24 * 0.50 * 6.1997 + 1.00 * 0.1438                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3971      final r-factor (work) = 0.3507          |
| start r-factor (free) = 0.4125      final r-factor (free) = 0.3936          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.6176 = 1.23 * 1.00 * 6.1997 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.5234 = 1.23 * 1.00 * 6.1202 + 1.00 * 0.0180                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.920)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.97   13.70    None  None   None       |
|    all(noH): 2823   0      0.00    93.97   13.70    None  None   None       |
|    Sol.    : 438    0      0.00    93.97   26.32    None  None   None       |
|    Mac.    : 2385   0      0.00    74.17   11.38    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 -   9.397: 1319   |   5:    46.983 -  56.379:   38        |
|      1:     9.397 -  18.793:  771   |   6:    56.379 -  65.776:   13        |
|      2:    18.793 -  28.190:  382   |   7:    65.776 -  75.172:   13        |
|      3:    28.190 -  37.586:  194   |   8:    75.172 -  84.569:    1        |
|      4:    37.586 -  46.983:   90   |   9:    84.569 -  93.965:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3507 r_free = 0.3936             target_work(ml) = 6.100         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3503 r_free = 0.3928             target_work(ml) = 6.099         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3503   r_free= 0.3928   ksol= 0.32   Bsol= 7.27   scale= 1.100    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.60,11.89,7.55,0.00,0.00,0.00); trace/3= 8.68                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.099121                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3479   r_free= 0.3869   ksol= 0.31   Bsol= 30.14   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.95,7.43,4.36,0.00,0.00,0.00); trace/3= 4.91                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.099664                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.359823              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.408   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.503854              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 124.583  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3479      final r-factor (work) = 0.2660          |
| start r-factor (free) = 0.3869      final r-factor (free) = 0.3204          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.7629 = 9.36 * 0.50 * 6.1155 + 1.00 * 0.1431                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.0610 = 9.36 * 0.50 * 5.9738 + 1.00 * 0.1041                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2660      final r-factor (work) = 0.2434          |
| start r-factor (free) = 0.3204      final r-factor (free) = 0.3036          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0274 = 0.50 * 1.00 * 5.9738 + 1.00 * 0.0175                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9574 = 0.50 * 1.00 * 5.8471 + 1.00 * 0.0113                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.920)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.12   13.18    None  None   None       |
|    all(noH): 2823   0      0.00    88.12   13.18    None  None   None       |
|    Sol.    : 438    0      0.00    88.12   30.40    None  None   None       |
|    Mac.    : 2385   0      0.00    76.05   10.02    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 -   8.812: 1392   |   5:    44.060 -  52.871:   60        |
|      1:     8.812 -  17.624:  755   |   6:    52.871 -  61.683:   30        |
|      2:    17.624 -  26.436:  292   |   7:    61.683 -  70.495:   11        |
|      3:    26.436 -  35.248:  176   |   8:    70.495 -  79.307:    3        |
|      4:    35.248 -  44.060:  102   |   9:    79.307 -  88.119:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2434 r_free = 0.3036             target_work(ml) = 5.823         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2433 r_free = 0.3038             target_work(ml) = 5.823         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2433   r_free= 0.3038   ksol= 0.31   Bsol= 30.14   scale= 1.045   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.95,7.43,4.36,0.00,0.00,0.00); trace/3= 4.91                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.823116                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2415   r_free= 0.3029   ksol= 0.30   Bsol= 43.33   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.78,4.54,2.97,0.00,0.00,0.00); trace/3= 3.10                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.821824                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.300175              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.484  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.277520              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.144  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2415      final r-factor (work) = 0.1765          |
| start r-factor (free) = 0.3029      final r-factor (free) = 0.2209          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.6043 = 5.30 * 0.50 * 5.8489 + 1.00 * 0.1041                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.1882 = 5.30 * 0.50 * 5.7032 + 1.00 * 0.0743                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1765      final r-factor (work) = 0.1601          |
| start r-factor (free) = 0.2209      final r-factor (free) = 0.2013          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5941 = 0.28 * 1.00 * 5.7032 + 1.00 * 0.0114                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5288 = 0.28 * 1.00 * 5.4743 + 1.00 * 0.0096                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.920)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.65   13.22    None  None   None       |
|    all(noH): 2823   0      0.00    80.65   13.22    None  None   None       |
|    Sol.    : 438    0      2.04    80.65   34.53    None  None   None       |
|    Mac.    : 2385   0      0.00    76.77   9.30     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 -   8.065: 1382   |   5:    40.325 -  48.390:  107        |
|      1:     8.065 -  16.130:  783   |   6:    48.390 -  56.455:   60        |
|      2:    16.130 -  24.195:  221   |   7:    56.455 -  64.520:   22        |
|      3:    24.195 -  32.260:  117   |   8:    64.520 -  72.585:   11        |
|      4:    32.260 -  40.325:  116   |   9:    72.585 -  80.650:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1601 r_free = 0.2013             target_work(ml) = 5.433         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1597 r_free = 0.2015             target_work(ml) = 5.432         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1597   r_free= 0.2015   ksol= 0.30   Bsol= 43.33   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.78,4.54,2.97,0.00,0.00,0.00); trace/3= 3.10                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.431994                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1591   r_free= 0.2003   ksol= 0.31   Bsol= 43.33   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.08,2.91,2.33,0.00,0.00,0.00); trace/3= 2.11                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.431087                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.900872              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.791  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.537273              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 145.189  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1591      final r-factor (work) = 0.1374          |
| start r-factor (free) = 0.2003      final r-factor (free) = 0.1774          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2820 = 1.90 * 0.50 * 5.4789 + 1.00 * 0.0746                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1529 = 1.90 * 0.50 * 5.3621 + 1.00 * 0.0565                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1374      final r-factor (work) = 0.1320          |
| start r-factor (free) = 0.1774      final r-factor (free) = 0.1749          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8905 = 0.54 * 1.00 * 5.3621 + 1.00 * 0.0096                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8483 = 0.54 * 1.00 * 5.2800 + 1.00 * 0.0115                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.920)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.93   13.49    None  None   None       |
|    all(noH): 2823   0      0.00    79.93   13.49    None  None   None       |
|    Sol.    : 438    0      1.98    79.42   36.67    None  None   None       |
|    Mac.    : 2385   0      0.00    79.93   9.24     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 -   7.994: 1376   |   5:    39.967 -  47.961:  100        |
|      1:     7.994 -  15.987:  789   |   6:    47.961 -  55.954:   82        |
|      2:    15.987 -  23.980:  201   |   7:    55.954 -  63.947:   33        |
|      3:    23.980 -  31.974:  110   |   8:    63.947 -  71.941:   21        |
|      4:    31.974 -  39.967:  107   |   9:    71.941 -  79.934:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1320 r_free = 0.1749             target_work(ml) = 5.274         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1320 r_free = 0.1748             target_work(ml) = 5.274         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1320   r_free= 0.1748   ksol= 0.31   Bsol= 43.33   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.08,2.91,2.33,0.00,0.00,0.00); trace/3= 2.11                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.273894                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1318   r_free= 0.1748   ksol= 0.32   Bsol= 50.39   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.99,2.44,2.29,0.00,0.00,0.00); trace/3= 1.91                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.273662                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.591633              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 135.216  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.200160              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 142.309  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1318      final r-factor (work) = 0.1191          |
| start r-factor (free) = 0.1748      final r-factor (free) = 0.1643          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8982 = 2.59 * 0.50 * 5.2798 + 1.00 * 0.0565                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8457 = 2.59 * 0.50 * 5.2297 + 1.00 * 0.0690                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1191      final r-factor (work) = 0.1167          |
| start r-factor (free) = 0.1643      final r-factor (free) = 0.1640          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.2879 = 1.20 * 1.00 * 5.2297 + 1.00 * 0.0115                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.2384 = 1.20 * 1.00 * 5.1871 + 1.00 * 0.0130                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.920)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.51   13.63    None  None   None       |
|    all(noH): 2823   0      0.00    87.51   13.63    None  None   None       |
|    Sol.    : 438    0      1.45    79.00   38.06    None  None   None       |
|    Mac.    : 2385   0      0.00    87.51   9.14     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 -   8.751: 1563   |   5:    43.754 -  52.504:   98        |
|      1:     8.751 -  17.502:  666   |   6:    52.504 -  61.255:   68        |
|      2:    17.502 -  26.252:  173   |   7:    61.255 -  70.006:   33        |
|      3:    26.252 -  35.003:  108   |   8:    70.006 -  78.757:   11        |
|      4:    35.003 -  43.754:   97   |   9:    78.757 -  87.507:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1167 r_free = 0.1640             target_work(ml) = 5.185         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1167 r_free = 0.1640             target_work(ml) = 5.185         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1167   r_free= 0.1640   ksol= 0.32   Bsol= 50.39   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.99,2.44,2.29,0.00,0.00,0.00); trace/3= 1.91                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.184855                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9498 -  4.7281 0.99   1396  158 0.0998 0.1292       5.382      5.5335|
|  2:  4.7281 -  3.7727 0.99   1353  145 0.0864 0.1096      5.4472      5.6505|
|  3:  3.7727 -  3.3017 0.99   1314  152 0.1090 0.1595       5.507      5.8964|
|  4:  3.3017 -  3.0025 0.99   1323  141 0.1274 0.1633      5.4885      5.6839|
|  5:  3.0025 -  2.7887 0.98   1286  145 0.1388 0.1660      5.3727      5.4938|
|  6:  2.7887 -  2.6253 0.99   1296  144 0.1350 0.2137      5.2811      5.5366|
|  7:  2.6253 -  2.4944 0.99   1293  147 0.1285 0.1803       5.202       5.442|
|  8:  2.4944 -  2.3863 0.99   1296  138 0.1250 0.1799      5.1342      5.3726|
|  9:  2.3863 -  2.2948 0.99   1281  142 0.1239 0.1874      5.0729        5.38|
| 10:  2.2948 -  2.2158 0.97   1261  142 0.1200 0.1894      5.0306      5.2531|
| 11:  2.2158 -  2.1467 0.98   1270  147 0.1218 0.1836      4.9748      5.2782|
| 12:  2.1467 -  2.0855 1.00   1270  136 0.1129 0.1772      4.8916      5.1807|
| 13:  2.0855 -  2.0308 0.96   1261  137 0.1196 0.1716      4.8195      5.0727|
| 14:  2.0308 -  1.9813 0.56    730   85 0.1106 0.1757      4.7185      4.9353|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9498 -  4.7281  1396   158  0.94   9.09   0.97     0.96       7323.81|
|  2:  4.7281 -  3.7727  1353   145  0.95   8.39   1.01     1.00       9371.99|
|  3:  3.7727 -  3.3017  1314   152  0.93  11.71   1.02     1.02      11223.88|
|  4:  3.3017 -  3.0025  1323   141  0.91  14.43   1.01     0.98      10918.91|
|  5:  3.0025 -  2.7887  1286   145  0.89  16.63   0.99     0.97       9009.26|
|  6:  2.7887 -  2.6253  1296   144  0.89  17.31   0.98     0.95       7972.48|
|  7:  2.6253 -  2.4944  1293   147  0.90  16.07   0.98     0.96       6656.94|
|  8:  2.4944 -  2.3863  1296   138  0.90  16.47   1.00     0.96       6175.31|
|  9:  2.3863 -  2.2948  1281   142  0.89  16.95   0.99     0.96       5549.88|
| 10:  2.2948 -  2.2158  1261   142  0.89  16.87   0.99     0.96       5205.76|
| 11:  2.2158 -  2.1467  1270   147  0.89  16.91   0.99     0.95       4595.91|
| 12:  2.1467 -  2.0855  1270   136  0.91  15.48   1.00     0.97       4042.50|
| 13:  2.0855 -  2.0308  1261   137  0.89  17.02   0.99     0.98       3565.46|
| 14:  2.0308 -  1.9813   730    85  0.91  15.52   0.97     0.93       2828.40|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2828.40 max =        11223.88 mean =      6910.52|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.91 mean =        14.83|
|phase err.(test): min =        0.00 max =           88.80 mean =        14.27|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1169   r_free= 0.1637   ksol= 0.32   Bsol= 54.17   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.83,0.42,0.41,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.185961                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1169   r_free= 0.1637   ksol= 0.32   Bsol= 54.17   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.83,0.42,0.41,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.185961                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9498 -  4.7281 0.99   1396  158 0.0999 0.1276      5.3882      5.5398|
|  2:  4.7281 -  3.7727 0.99   1353  145 0.0880 0.1095      5.4565      5.6567|
|  3:  3.7727 -  3.3017 0.99   1314  152 0.1094 0.1607      5.5125      5.8964|
|  4:  3.3017 -  3.0025 0.99   1323  141 0.1278 0.1635        5.49      5.6849|
|  5:  3.0025 -  2.7887 0.98   1286  145 0.1387 0.1660      5.3729      5.4912|
|  6:  2.7887 -  2.6253 0.99   1296  144 0.1348 0.2136      5.2803      5.5365|
|  7:  2.6253 -  2.4944 0.99   1293  147 0.1283 0.1806      5.2005      5.4443|
|  8:  2.4944 -  2.3863 0.99   1296  138 0.1247 0.1789      5.1328      5.3704|
|  9:  2.3863 -  2.2948 0.99   1281  142 0.1236 0.1865      5.0711      5.3759|
| 10:  2.2948 -  2.2158 0.97   1261  142 0.1199 0.1899      5.0298      5.2549|
| 11:  2.2158 -  2.1467 0.98   1270  147 0.1217 0.1831       4.974      5.2767|
| 12:  2.1467 -  2.0855 1.00   1270  136 0.1128 0.1774      4.8909      5.1816|
| 13:  2.0855 -  2.0308 0.96   1261  137 0.1197 0.1712       4.819      5.0721|
| 14:  2.0308 -  1.9813 0.56    730   85 0.1105 0.1755      4.7179      4.9333|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9498 -  4.7281  1396   158  0.94   9.29   0.97     0.95       7384.62|
|  2:  4.7281 -  3.7727  1353   145  0.95   8.50   1.01     1.00       9442.52|
|  3:  3.7727 -  3.3017  1314   152  0.93  11.74   1.03     1.02      11358.17|
|  4:  3.3017 -  3.0025  1323   141  0.91  14.43   1.01     0.98      10901.98|
|  5:  3.0025 -  2.7887  1286   145  0.89  16.66   1.00     0.97       9015.93|
|  6:  2.7887 -  2.6253  1296   144  0.89  17.31   0.98     0.96       7976.95|
|  7:  2.6253 -  2.4944  1293   147  0.90  16.07   0.99     0.96       6651.41|
|  8:  2.4944 -  2.3863  1296   138  0.90  16.43   1.00     0.97       6152.98|
|  9:  2.3863 -  2.2948  1281   142  0.89  16.91   1.00     0.96       5528.31|
| 10:  2.2948 -  2.2158  1261   142  0.89  16.85   1.00     0.97       5193.17|
| 11:  2.2158 -  2.1467  1270   147  0.89  16.91   1.00     0.95       4593.98|
| 12:  2.1467 -  2.0855  1270   136  0.91  15.47   1.00     0.98       4040.60|
| 13:  2.0855 -  2.0308  1261   137  0.89  17.00   1.00     0.99       3558.83|
| 14:  2.0308 -  1.9813   730    85  0.91  15.49   0.98     0.94       2820.79|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2820.79 max =        11358.17 mean =      6924.73|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.96 mean =        14.84|
|phase err.(test): min =        0.00 max =           89.16 mean =        14.25|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.920)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.02    89.53   15.64    None  None   None       |
|    all(noH): 2823   0      2.02    89.53   15.64    None  None   None       |
|    Sol.    : 438    0      3.47    81.01   40.07    None  None   None       |
|    Mac.    : 2385   0      2.02    89.53   11.16    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.018 -  10.769: 1563   |   5:    45.771 -  54.522:   98        |
|      1:    10.769 -  19.519:  666   |   6:    54.522 -  63.273:   68        |
|      2:    19.519 -  28.270:  173   |   7:    63.273 -  72.024:   33        |
|      3:    28.270 -  37.021:  108   |   8:    72.024 -  80.774:   11        |
|      4:    37.021 -  45.771:   97   |   9:    80.774 -  89.525:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 327         
Filter by distance & map next to the model:
   mapped sites are within: 0.399 - 5.120
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 324 from: 327
   mapped sites are within: 0.734 - 5.120

peak=    9.409 closest distance to " CG2 VAL A 230 " =    1.393
peak=    7.005 closest distance to " CG2 VAL A 296 " =    1.133
peak=    6.369 closest distance to " CD1AILE A 234 " =    1.263
peak=    5.999 closest distance to " CG  LEU A   5 " =    1.203
peak=    5.850 closest distance to " O   HOH Z 210 " =    1.152
peak=    5.545 closest distance to " NH2 ARG A  56 " =    2.346
peak=    5.456 closest distance to " O   HOH Z 124 " =    1.637
peak=    5.421 closest distance to " O   HOH Z 402 " =    1.679
peak=    5.407 closest distance to " O   HOH Z 120 " =    1.133
peak=    5.293 closest distance to " CB  SER A  63 " =    1.202
peak=    5.275 closest distance to " O   HOH Z 403 " =    1.842
peak=    5.133 closest distance to " CG  LEU A 228 " =    1.187
peak=    5.111 closest distance to " CG  PRO A  54 " =    1.258
peak=    4.922 closest distance to " CB  VAL A 296 " =    1.037
peak=    4.877 closest distance to " O   HOH Z 247 " =    1.468
peak=    4.818 closest distance to " O   HOH Z 209 " =    2.379
peak=    4.781 closest distance to " CB  GLN A 223 " =    1.373
peak=    4.750 closest distance to " O   HOH Z 433 " =    1.640
peak=    4.679 closest distance to " CG  PRO A 213 " =    1.249
peak=    4.661 closest distance to " CB  VAL A 230 " =    1.174
peak=    4.636 closest distance to " CA  TYR A  30 " =    0.946
peak=    4.636 closest distance to " CB  GLN A 183 " =    1.345
peak=    4.593 closest distance to " CG1 ILE A  33 " =    1.264
peak=    4.580 closest distance to " O   HOH Z 126 " =    1.720
peak=    4.552 closest distance to " CB  ARG A 275 " =    0.891
peak=    4.548 closest distance to " C   PRO A 198 " =    1.511
peak=    4.519 closest distance to " CB  PRO A  54 " =    0.873
peak=    4.485 closest distance to " O   HOH Z 154 " =    2.496
peak=    4.483 closest distance to " CD2 LEU A 228 " =    1.192
peak=    4.477 closest distance to " O   SER A  87 " =    2.369
peak=    4.459 closest distance to " O   HOH Z  80 " =    1.983
peak=    4.411 closest distance to " O   HOH Z 193 " =    1.785
peak=    4.401 closest distance to " CG  ARG A  66 " =    2.800
peak=    4.399 closest distance to " O   HOH Z 431 " =    1.282
peak=    4.358 closest distance to " O   HOH Z 128 " =    1.534
peak=    4.342 closest distance to " CG  PRO A 198 " =    1.160
peak=    4.330 closest distance to " O   HOH Z 263 " =    1.512
peak=    4.329 closest distance to " NE2 GLN A  11 " =    1.059
peak=    4.277 closest distance to " O   HOH Z  67 " =    2.004
peak=    4.267 closest distance to " O   HOH Z  48 " =    1.894
peak=    4.263 closest distance to " O   HOH Z 234 " =    3.628
peak=    4.256 closest distance to " O   HOH Z  49 " =    1.144
peak=    4.254 closest distance to " O   HOH Z 245 " =    1.418
peak=    4.229 closest distance to " CB  TRP A 179 " =    1.211
peak=    4.211 closest distance to " O   HOH Z 232 " =    2.367
peak=    4.185 closest distance to " O   HOH Z 346 " =    1.551
peak=    4.161 closest distance to " O   HOH Z  48 " =    1.697
peak=    4.159 closest distance to " O   HOH Z 134 " =    2.056
peak=    4.151 closest distance to " O   HOH Z 414 " =    1.902
peak=    4.120 closest distance to " O   GLY A  23 " =    2.343
peak=    4.117 closest distance to " O   HOH Z 394 " =    1.655
peak=    4.116 closest distance to " O   HOH Z 102 " =    1.329
peak=    4.100 closest distance to " CG  PRO A 280 " =    0.734
peak=    4.088 closest distance to " CB  SER A   3 " =    1.275
peak=    4.073 closest distance to " O   HOH Z 412 " =    3.378
peak=    4.065 closest distance to " OE1 GLU A   2 " =    2.091
peak=    4.057 closest distance to " O   HOH Z 389 " =    2.001
peak=    4.046 closest distance to " CG  PRO A  90 " =    1.198
peak=    4.025 closest distance to " CD2 LEU A   5 " =    1.177
peak=    4.004 closest distance to " O   HOH Z 345 " =    2.815
peak=    3.997 closest distance to " O   HOH Z  40 " =    1.923
peak=    3.996 closest distance to " O   HOH Z  15 " =    2.242
peak=    3.995 closest distance to " O   HOH Z 142 " =    1.496
peak=    3.991 closest distance to " O   HOH Z  63 " =    2.311
peak=    3.983 closest distance to " O   HOH Z 154 " =    1.435
peak=    3.977 closest distance to " CG2 THR A 221 " =    1.203
peak=    3.972 closest distance to " CB  GLU A 277 " =    3.653
peak=    3.964 closest distance to " O   HOH Z 130 " =    1.175
peak=    3.958 closest distance to " CG2 VAL A 296 " =    1.706
peak=    3.956 closest distance to " O   ASP A 124 " =    1.561
peak=    3.946 closest distance to " O   HOH Z 272 " =    1.941
peak=    3.942 closest distance to " O   HOH Z  43 " =    1.503
peak=    3.933 closest distance to " O   HOH Z 203 " =    1.782
peak=    3.933 closest distance to " CG1BVAL A  72 " =    1.799
peak=    3.922 closest distance to " O   HOH Z 408 " =    1.655
peak=    3.906 closest distance to " CB  ASN A 148 " =    1.306
peak=    3.904 closest distance to " O   HOH Z  85 " =    1.316
peak=    3.891 closest distance to " CB  GLU A 128 " =    1.173
peak=    3.888 closest distance to " O   HOH Z 214 " =    2.479
peak=    3.878 closest distance to " O   HOH Z 189 " =    2.529
peak=    3.878 closest distance to " O   HOH Z 369 " =    2.286
peak=    3.878 closest distance to " O   HOH Z  54 " =    2.284
peak=    3.871 closest distance to " O   HOH Z 327 " =    1.745
peak=    3.852 closest distance to " OG1 THR A 294 " =    2.285
peak=    3.848 closest distance to " CB  GLU A 152 " =    1.071
peak=    3.834 closest distance to " CD2 TRP A 179 " =    1.407
peak=    3.828 closest distance to " O   HOH Z 406 " =    1.589
peak=    3.825 closest distance to " O   HOH Z 280 " =    3.046
peak=    3.792 closest distance to " O   HOH Z   4 " =    1.661
peak=    3.791 closest distance to " O   HOH Z 132 " =    2.600
peak=    3.782 closest distance to " CA  ALA A  51 " =    1.042
peak=    3.772 closest distance to " CA  ARG A 195 " =    1.177
peak=    3.770 closest distance to " O   HOH Z 156 " =    3.235
peak=    3.769 closest distance to " O   HOH Z 303 " =    2.236
peak=    3.768 closest distance to " CB AVAL A  41 " =    1.037
peak=    3.765 closest distance to " O   HOH Z 426 " =    1.543
peak=    3.764 closest distance to " CA  VAL A  41 " =    0.867
peak=    3.764 closest distance to " O   HOH Z 316 " =    2.689
peak=    3.759 closest distance to " O   HOH Z  54 " =    1.451
peak=    3.758 closest distance to " O   HOH Z  44 " =    1.928
peak=    3.752 closest distance to " O   HOH Z  97 " =    1.858
peak=    3.745 closest distance to " O   HOH Z 357 " =    2.045
peak=    3.742 closest distance to " O   HOH Z  20 " =    1.486
peak=    3.722 closest distance to " O   HOH Z 386 " =    2.118
peak=    3.722 closest distance to " O   HOH Z 128 " =    2.031
peak=    3.719 closest distance to " O   GLY A  91 " =    1.315
peak=    3.717 closest distance to " O   HOH Z 146 " =    1.445
peak=    3.716 closest distance to " O   HOH Z 261 " =    2.076
peak=    3.715 closest distance to " CD  ARG A 159 " =    0.817
peak=    3.711 closest distance to " CA  ALA A  21 " =    1.275
peak=    3.702 closest distance to " O   HOH Z 423 " =    1.798
peak=    3.698 closest distance to " CG  ARG A  66 " =    1.004
peak=    3.670 closest distance to " O   HOH Z 395 " =    1.431
peak=    3.669 closest distance to " O   HOH Z 298 " =    1.976
peak=    3.666 closest distance to " NH2 ARG A 156 " =    1.146
peak=    3.664 closest distance to " NZ  LYS A 117 " =    2.968
peak=    3.663 closest distance to " CB  TYR A 169 " =    0.868
peak=    3.661 closest distance to " O   HOH Z 425 " =    1.346
peak=    3.659 closest distance to " OG BSER A 164 " =    2.108
peak=    3.652 closest distance to " CB  ALA A   9 " =    1.627
peak=    3.648 closest distance to " CD  ARG A 269 " =    1.155
peak=    3.643 closest distance to " O   HOH Z 189 " =    2.801
peak=    3.640 closest distance to " CB  PRO A  54 " =    1.307
peak=    3.640 closest distance to " O   HOH Z 365 " =    2.950
peak=    3.638 closest distance to " O   HOH Z 163 " =    1.406
peak=    3.637 closest distance to " O   HOH Z  40 " =    2.096
peak=    3.628 closest distance to " CB  ARG A 190 " =    1.695
peak=    3.628 closest distance to " O   HOH Z 136 " =    1.308
peak=    3.621 closest distance to " CB  ALA A 100 " =    1.370
peak=    3.621 closest distance to " O   HOH Z 166 " =    1.603
peak=    3.618 closest distance to " O   HOH Z 298 " =    5.120
peak=    3.617 closest distance to " CE  LYS A 119 " =    1.141
peak=    3.603 closest distance to " O   HOH Z 257 " =    2.300
peak=    3.600 closest distance to " O   HOH Z 359 " =    1.955
peak=    3.594 closest distance to " OE1 GLN A  11 " =    1.892
peak=    3.592 closest distance to " O   HOH Z  78 " =    1.735
peak=    3.576 closest distance to " NZ  LYS A 117 " =    1.554
peak=    3.574 closest distance to " O   HOH Z 368 " =    2.156
peak=    3.567 closest distance to " O   HOH Z  61 " =    1.476
peak=    3.564 closest distance to " CB  ALA A  71 " =    1.293
peak=    3.555 closest distance to " O   HOH Z 155 " =    1.462
peak=    3.549 closest distance to " CG2 VAL A 197 " =    1.166
peak=    3.547 closest distance to " CD  LYS A 166 " =    1.426
peak=    3.547 closest distance to " OD1 ASN A  69 " =    2.473
peak=    3.546 closest distance to " O   HOH Z 409 " =    4.144
peak=    3.545 closest distance to " O   HOH Z 128 " =    1.885
peak=    3.544 closest distance to " CB  SER A 141 " =    1.075
peak=    3.543 closest distance to " N   ASN A  39 " =    1.296
peak=    3.542 closest distance to " CA  ALA A 295 " =    1.067
peak=    3.536 closest distance to " N   ILE A  33 " =    1.125
peak=    3.534 closest distance to " CD2 LEU A 297 " =    0.942
peak=    3.531 closest distance to " O   HOH Z 248 " =    1.718
peak=    3.530 closest distance to " CE1 TYR A 186 " =    1.249
peak=    3.529 closest distance to " O   HOH Z 185 " =    1.624
peak=    3.522 closest distance to " O   HOH Z  88 " =    3.390
peak=    3.519 closest distance to " O   HOH Z  11 " =    1.295
peak=    3.519 closest distance to " CA  ASP A 191 " =    0.977
peak=    3.518 closest distance to " O   HOH Z 374 " =    2.652
peak=    3.518 closest distance to " CA  ASN A 176 " =    1.087
peak=    3.512 closest distance to " O   HOH Z 123 " =    2.126
peak=    3.512 closest distance to " O   HOH Z 271 " =    1.240
peak=    3.505 closest distance to " CB  ARG A 139 " =    0.990
peak=    3.504 closest distance to " O   HOH Z 373 " =    1.598
peak=    3.504 closest distance to " CB  ASN A  39 " =    0.829
peak=    3.498 closest distance to " O   HOH Z 380 " =    1.798
peak=    3.494 closest distance to " CA  LYS A 117 " =    1.284
peak=    3.493 closest distance to " O   HOH Z 383 " =    1.977
peak=    3.490 closest distance to " O   HOH Z 422 " =    2.504
peak=    3.480 closest distance to " O   HOH Z 158 " =    2.881
peak=    3.479 closest distance to " O   HOH Z 271 " =    2.376
peak=    3.476 closest distance to " CB  TRP A 266 " =    1.075
peak=    3.474 closest distance to " O   HOH Z 417 " =    3.204
peak=    3.473 closest distance to " CA  THR A  82 " =    1.522
peak=    3.472 closest distance to " NH2BARG A 145 " =    2.146
peak=    3.470 closest distance to " O   HOH Z 162 " =    1.444
peak=    3.467 closest distance to " CG  PRO A 243 " =    1.178
peak=    3.466 closest distance to " O   HOH Z  48 " =    2.231
peak=    3.466 closest distance to " CD1 LEU A 300 " =    1.214
peak=    3.463 closest distance to " O  BHOH Z  74 " =    1.458
peak=    3.460 closest distance to " CG2 ILE A  20 " =    1.519
peak=    3.453 closest distance to " O   ALA A 165 " =    1.295
peak=    3.449 closest distance to " O   HOH Z 227 " =    1.565
peak=    3.440 closest distance to " O   HOH Z 387 " =    2.519
peak=    3.436 closest distance to " CB  ARG A  79 " =    1.346
peak=    3.434 closest distance to " CD1 ILE A 199 " =    0.975
peak=    3.434 closest distance to " O   HOH Z 361 " =    3.389
peak=    3.433 closest distance to " O   HOH Z  90 " =    3.451
peak=    3.421 closest distance to " NH1 ARG A  14 " =    1.280
peak=    3.418 closest distance to " O   HOH Z 173 " =    2.367
peak=    3.418 closest distance to " O   HOH Z 197 " =    2.031
peak=    3.417 closest distance to " O   HOH Z 146 " =    1.328
peak=    3.416 closest distance to " O   HOH Z 301 " =    1.900
peak=    3.416 closest distance to " O   HOH Z  66 " =    2.173
peak=    3.415 closest distance to " CD  LYS A 119 " =    1.818
peak=    3.414 closest distance to " CB  ASN A 187 " =    1.229
peak=    3.412 closest distance to " O   HOH Z 279 " =    1.339
peak=    3.411 closest distance to " O   HOH Z 112 " =    1.614
peak=    3.411 closest distance to " NH2 ARG A  79 " =    1.383
peak=    3.405 closest distance to " O   HOH Z 404 " =    1.478
peak=    3.400 closest distance to " CD1 LEU A 222 " =    0.757
peak=    3.397 closest distance to " O   HOH Z 155 " =    2.927
peak=    3.394 closest distance to " CE1 HIS A 108 " =    1.113
peak=    3.393 closest distance to " CB  LEU A 228 " =    1.415
peak=    3.393 closest distance to " O   HOH Z 344 " =    2.943
peak=    3.390 closest distance to " O   HOH Z 336 " =    1.783
peak=    3.390 closest distance to " O   HOH Z  28 " =    1.466
peak=    3.389 closest distance to " O   HOH Z  21 " =    1.797
peak=    3.386 closest distance to " OD1 ASN A 217 " =    1.791
peak=    3.386 closest distance to " O   HOH Z 345 " =    1.733
peak=    3.383 closest distance to " ND1 HIS A  81 " =    1.553
peak=    3.381 closest distance to " O   HOH Z 162 " =    1.773
peak=    3.381 closest distance to " O   HOH Z 423 " =    3.058
peak=    3.378 closest distance to " CB  VAL A 202 " =    1.457
peak=    3.370 closest distance to " CG2 ILE A 234 " =    0.962
peak=    3.367 closest distance to " CA  ILE A 263 " =    0.940
peak=    3.361 closest distance to " O   HOH Z 236 " =    1.626
peak=    3.360 closest distance to " NZ  LYS A  76 " =    1.806
peak=    3.356 closest distance to " O   HOH Z  97 " =    2.533
peak=    3.355 closest distance to " CB  LEU A   5 " =    1.240
peak=    3.355 closest distance to " O   HOH Z 126 " =    1.888
peak=    3.353 closest distance to " O   HOH Z 329 " =    3.761
peak=    3.351 closest distance to " O   HOH Z 196 " =    1.120
peak=    3.351 closest distance to " OD1 ASN A  60 " =    1.787
peak=    3.344 closest distance to " CD  PRO A  54 " =    1.084
peak=    3.341 closest distance to " O   HOH Z 403 " =    1.559
peak=    3.339 closest distance to " O   HOH Z 250 " =    1.681
peak=    3.335 closest distance to " CB  MET A  40 " =    0.772
peak=    3.335 closest distance to " O   HOH Z 438 " =    2.343
peak=    3.333 closest distance to " O   HOH Z 334 " =    1.426
peak=    3.330 closest distance to " NZ  LYS A 166 " =    2.947
peak=    3.328 closest distance to " O   ALA A 158 " =    1.288
peak=    3.328 closest distance to " CA  GLY A  80 " =    1.090
peak=    3.317 closest distance to " O   HOH Z 281 " =    4.334
peak=    3.310 closest distance to " CB  TYR A 247 " =    0.982
peak=    3.309 closest distance to " O   HOH Z 133 " =    1.407
peak=    3.309 closest distance to " O   HOH Z 273 " =    2.869
peak=    3.307 closest distance to " CD1 LEU A 101 " =    1.236
peak=    3.305 closest distance to " CA  ASP A 162 " =    1.168
peak=    3.305 closest distance to " CB  ARG A  79 " =    0.894
peak=    3.301 closest distance to " CA  ARG A  66 " =    0.937
peak=    3.296 closest distance to " O   HOH Z 427 " =    3.032
peak=    3.295 closest distance to " NH2AARG A 275 " =    3.767
peak=    3.295 closest distance to " CG  GLN A  58 " =    2.621
peak=    3.293 closest distance to " CA  LEU A  83 " =    1.414
peak=    3.290 closest distance to " O   HOH Z 151 " =    1.802
peak=    3.283 closest distance to " CD  ARG A 195 " =    0.928
peak=    3.282 closest distance to " CB  PRO A 198 " =    1.021
peak=    3.281 closest distance to " CG2 THR A 294 " =    1.531
peak=    3.278 closest distance to " O   HOH Z  35 " =    2.243
peak=    3.273 closest distance to " CG1 ILE A  49 " =    1.641
peak=    3.268 closest distance to " O   HOH Z 227 " =    1.743
peak=    3.267 closest distance to " CB  SER A  26 " =    1.656
peak=    3.266 closest distance to " O   HOH Z 419 " =    1.749
peak=    3.265 closest distance to " O   HOH Z 261 " =    2.197
peak=    3.264 closest distance to " CZ  PHE A  38 " =    1.237
peak=    3.262 closest distance to " O   HOH Z 279 " =    2.071
peak=    3.255 closest distance to " OD2 ASP A 286 " =    2.750
peak=    3.255 closest distance to " CA  ALA A 160 " =    0.814
peak=    3.252 closest distance to " CA  LYS A 290 " =    1.211
peak=    3.251 closest distance to " CA  CYS A 260 " =    1.651
peak=    3.250 closest distance to " O   HOH Z 291 " =    1.482
peak=    3.250 closest distance to " O   THR A  31 " =    1.616
peak=    3.248 closest distance to " OD1 ASP A 286 " =    1.852
peak=    3.244 closest distance to " O   HOH Z 402 " =    2.830
peak=    3.242 closest distance to " CG  MET A 185 " =    1.145
peak=    3.240 closest distance to " CD1 LEU A  96 " =    0.763
peak=    3.239 closest distance to " CG2 THR A  42 " =    0.814
peak=    3.238 closest distance to " O   HOH Z 435 " =    1.900
peak=    3.235 closest distance to " CD BLYS A 290 " =    0.939
peak=    3.223 closest distance to " C   ILE A 106 " =    1.839
peak=    3.221 closest distance to " CB  MET A  47 " =    1.166
peak=    3.217 closest distance to " CB  THR A  31 " =    1.595
peak=    3.217 closest distance to " CB  ALA A 248 " =    1.399
peak=    3.216 closest distance to " O   HOH Z 261 " =    2.174
peak=    3.213 closest distance to " CG BARG A 102 " =    1.833
peak=    3.210 closest distance to " CB  ALA A 295 " =    1.248
peak=    3.206 closest distance to " O   HOH Z 420 " =    1.849
peak=    3.206 closest distance to " CA  VAL A 126 " =    0.853
peak=    3.202 closest distance to " CG  MET A 188 " =    0.879
peak=    3.199 closest distance to " OG BSER A 134 " =    2.929
peak=    3.197 closest distance to " O   HOH Z 250 " =    1.355
peak=    3.194 closest distance to " O   HOH Z   1 " =    2.314
peak=    3.192 closest distance to " O   HOH Z 427 " =    2.669
peak=    3.192 closest distance to " O   HOH Z 133 " =    2.378
peak=    3.190 closest distance to " CG2 ILE A 120 " =    1.228
peak=    3.189 closest distance to " CG1 VAL A 153 " =    1.012
peak=    3.184 closest distance to " OG  SER A 245 " =    1.453
peak=    3.170 closest distance to " CG2 ILE A 234 " =    2.052
peak=    3.169 closest distance to " CG2AVAL A 121 " =    2.028
peak=    3.163 closest distance to " O   HOH Z   9 " =    2.432
peak=    3.162 closest distance to " CB  PHE A 283 " =    0.754
peak=    3.156 closest distance to " O   ALA A   1 " =    1.577
peak=    3.147 closest distance to " O   HOH Z 227 " =    2.167
peak=    3.146 closest distance to " O   HOH Z 419 " =    2.390
peak=    3.142 closest distance to " CB  ARG A 219 " =    1.611
peak=    3.141 closest distance to " O   HOH Z 368 " =    4.365
peak=    3.140 closest distance to " O   HOH Z 147 " =    1.797
peak=    3.139 closest distance to " O   HOH Z 236 " =    1.816
peak=    3.137 closest distance to " CB  ALA A 137 " =    1.344
peak=    3.136 closest distance to " CA  GLY A 196 " =    1.127
peak=    3.136 closest distance to " OD2 ASP A 298 " =    3.959
peak=    3.136 closest distance to " CB  ALA A 256 " =    0.899
peak=    3.136 closest distance to " ND2 ASN A 187 " =    1.536
peak=    3.135 closest distance to " CA  LEU A 282 " =    1.144
peak=    3.131 closest distance to " N   TYR A 247 " =    1.230
peak=    3.121 closest distance to " NE1 TRP A 274 " =    0.927
peak=    3.110 closest distance to " CB  SER A  62 " =    0.742
peak=    3.109 closest distance to " N   ASP A 162 " =    1.458
peak=    3.105 closest distance to " O   TRP A 274 " =    1.942
peak=    3.101 closest distance to " CZ3 TRP A  92 " =    1.068
peak=    3.092 closest distance to " CB  ASN A 215 " =    1.121
peak=    3.082 closest distance to " O   HOH Z 116 " =    1.740
peak=    3.079 closest distance to " O   HOH Z 280 " =    2.529
peak=    3.079 closest distance to " O   HOH Z 217 " =    2.009
peak=    3.077 closest distance to " O   HOH Z 145 " =    2.826
peak=    3.075 closest distance to " O   HOH Z 196 " =    1.209
peak=    3.074 closest distance to " CA  THR A 182 " =    1.355
peak=    3.065 closest distance to " N   ASP A 231 " =    1.537
peak=    3.054 closest distance to " O   HOH Z  83 " =    1.566
peak=    3.047 closest distance to " O   HOH Z 109 " =    2.125
peak=    3.047 closest distance to " CB  ALA A 242 " =    1.073
peak=    3.029 closest distance to " CD2 PHE A 218 " =    1.735
peak=    3.016 closest distance to " O   HOH Z  59 " =    1.985
peak=    3.009 closest distance to " CD  LYS A 119 " =    1.297

                           ----------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: 0.711 - 5.593
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 212 from: 213
   mapped sites are within: 0.711 - 5.593

peak=   -4.830 closest distance to " CG2 VAL A 230 " =    0.861
peak=   -4.548 closest distance to " CA  SER A 164 " =    2.105
peak=   -4.521 closest distance to " O   HOH Z 155 " =    1.691
peak=   -4.517 closest distance to " O   HOH Z 266 " =    4.674
peak=   -4.429 closest distance to " CD  ARG A 156 " =    2.030
peak=   -4.209 closest distance to " OXT GLY A 302 " =    2.854
peak=   -4.134 closest distance to " CE2 TYR A  30 " =    2.724
peak=   -4.108 closest distance to " O   HOH Z 166 " =    1.792
peak=   -4.081 closest distance to " CG2BVAL A  41 " =    2.769
peak=   -3.992 closest distance to " NH2 ARG A  66 " =    1.256
peak=   -3.967 closest distance to " SG  CYS A 254 " =    3.196
peak=   -3.956 closest distance to " CB  ALA A 161 " =    2.574
peak=   -3.944 closest distance to " CG1 VAL A 250 " =    2.729
peak=   -3.937 closest distance to " O   HOH Z 196 " =    2.469
peak=   -3.937 closest distance to " N   ALA A 226 " =    2.029
peak=   -3.912 closest distance to " O   HOH Z 351 " =    1.552
peak=   -3.911 closest distance to " O   HOH Z 426 " =    1.743
peak=   -3.910 closest distance to " O   VAL A  67 " =    2.721
peak=   -3.904 closest distance to " CD2 LEU A 300 " =    2.764
peak=   -3.901 closest distance to " C   THR A 279 " =    1.163
peak=   -3.897 closest distance to " O   HOH Z 103 " =    1.800
peak=   -3.879 closest distance to " O   HOH Z 165 " =    1.976
peak=   -3.875 closest distance to " CG  ASP A 231 " =    0.894
peak=   -3.875 closest distance to " CD1 LEU A 101 " =    2.527
peak=   -3.859 closest distance to " CD1 PHE A  59 " =    1.902
peak=   -3.855 closest distance to " O   HOH Z 151 " =    1.131
peak=   -3.853 closest distance to " CB  PHE A 208 " =    2.345
peak=   -3.848 closest distance to " O   HOH Z 120 " =    0.860
peak=   -3.839 closest distance to " CG  ARG A 269 " =    2.299
peak=   -3.830 closest distance to " CB  ALA A 248 " =    2.010
peak=   -3.815 closest distance to " O   HOH Z 210 " =    0.711
peak=   -3.808 closest distance to " OG BSER A 210 " =    1.239
peak=   -3.788 closest distance to " O   HOH Z 377 " =    1.157
peak=   -3.780 closest distance to " CG2 THR A 221 " =    2.349
peak=   -3.768 closest distance to " CD  GLN A  58 " =    1.189
peak=   -3.758 closest distance to " C   HIS A 108 " =    1.170
peak=   -3.755 closest distance to " OG  SER A  97 " =    2.253
peak=   -3.741 closest distance to " O   HOH Z  71 " =    1.517
peak=   -3.741 closest distance to " N   THR A 235 " =    1.316
peak=   -3.718 closest distance to " O   HOH Z 407 " =    3.159
peak=   -3.703 closest distance to " CD2 LEU A 167 " =    1.559
peak=   -3.700 closest distance to " OG BSER A 134 " =    1.312
peak=   -3.697 closest distance to " O   SER A 271 " =    1.852
peak=   -3.695 closest distance to " O   HOH Z 231 " =    2.150
peak=   -3.682 closest distance to " N   SER A 276 " =    1.472
peak=   -3.671 closest distance to " O   PRO A 198 " =    1.317
peak=   -3.669 closest distance to " CG  ASP A  50 " =    2.350
peak=   -3.665 closest distance to " CG1 VAL A 112 " =    2.468
peak=   -3.662 closest distance to " O   HOH Z 290 " =    0.956
peak=   -3.661 closest distance to " CZ  TYR A 169 " =    1.838
peak=   -3.659 closest distance to " O   TRP A  92 " =    1.966
peak=   -3.658 closest distance to " OG ASER A 134 " =    1.188
peak=   -3.639 closest distance to " OE1 GLN A 223 " =    2.505
peak=   -3.632 closest distance to " OG1 THR A   4 " =    1.880
peak=   -3.621 closest distance to " O   HOH Z 136 " =    2.337
peak=   -3.619 closest distance to " ND2 ASN A 187 " =    1.734
peak=   -3.615 closest distance to " CH2 TRP A 179 " =    1.229
peak=   -3.614 closest distance to " O   HOH Z 252 " =    3.809
peak=   -3.607 closest distance to " O   HOH Z 283 " =    1.946
peak=   -3.571 closest distance to " O   HOH Z 377 " =    2.112
peak=   -3.569 closest distance to " CG2 ILE A  49 " =    2.759
peak=   -3.566 closest distance to " O   HOH Z 234 " =    4.111
peak=   -3.555 closest distance to " OD1 ASN A  39 " =    2.176
peak=   -3.554 closest distance to " CA  GLY A 203 " =    2.171
peak=   -3.551 closest distance to " O   PHE A 218 " =    1.530
peak=   -3.538 closest distance to " OD1 ASN A 148 " =    1.535
peak=   -3.532 closest distance to " CA  ASP A 298 " =    1.012
peak=   -3.521 closest distance to " CG  MET A 105 " =    0.871
peak=   -3.514 closest distance to " O   ALA A   1 " =    1.935
peak=   -3.502 closest distance to " CG2 VAL A 189 " =    2.024
peak=   -3.501 closest distance to " C   ASN A 187 " =    1.979
peak=   -3.496 closest distance to " CD1 TYR A 247 " =    2.311
peak=   -3.488 closest distance to " CD1 LEU A 228 " =    2.279
peak=   -3.485 closest distance to " O   HOH Z  60 " =    2.244
peak=   -3.480 closest distance to " O   HOH Z 423 " =    2.303
peak=   -3.475 closest distance to " C   SER A 206 " =    1.539
peak=   -3.467 closest distance to " OG  SER A  26 " =    1.286
peak=   -3.462 closest distance to " CG  GLU A  53 " =    1.522
peak=   -3.460 closest distance to " ND2 ASN A  39 " =    1.230
peak=   -3.456 closest distance to " ND2 ASN A  45 " =    1.085
peak=   -3.456 closest distance to " O   HOH Z 174 " =    1.975
peak=   -3.450 closest distance to " C   ALA A 158 " =    1.228
peak=   -3.441 closest distance to " N   GLN A  58 " =    1.710
peak=   -3.441 closest distance to " CB  PRO A 243 " =    2.747
peak=   -3.439 closest distance to " ND2 ASN A  69 " =    1.641
peak=   -3.437 closest distance to " O   HOH Z   5 " =    1.592
peak=   -3.435 closest distance to " O   HOH Z 171 " =    2.377
peak=   -3.435 closest distance to " CE BMET A  47 " =    1.581
peak=   -3.435 closest distance to " CB  SER A 210 " =    1.294
peak=   -3.427 closest distance to " O   HOH Z  39 " =    1.818
peak=   -3.425 closest distance to " C   ASN A 285 " =    2.324
peak=   -3.424 closest distance to " O   HOH Z 292 " =    4.338
peak=   -3.417 closest distance to " CD  ARG A 195 " =    5.056
peak=   -3.414 closest distance to " O   HOH Z  19 " =    2.289
peak=   -3.411 closest distance to " OG1 THR A  82 " =    1.419
peak=   -3.406 closest distance to " O   HOH Z 150 " =    1.667
peak=   -3.397 closest distance to " O   ALA A  34 " =    2.177
peak=   -3.393 closest distance to " CD  ARG A  36 " =    1.823
peak=   -3.393 closest distance to " O   HOH Z  20 " =    1.206
peak=   -3.392 closest distance to " CG  PRO A 243 " =    1.654
peak=   -3.385 closest distance to " O   HOH Z 422 " =    1.611
peak=   -3.384 closest distance to " O   HOH Z 388 " =    1.945
peak=   -3.376 closest distance to " O   HOH Z  49 " =    0.969
peak=   -3.371 closest distance to " O   ALA A 256 " =    1.590
peak=   -3.370 closest distance to " CD1 TRP A 179 " =    1.147
peak=   -3.369 closest distance to " O   HOH Z 139 " =    3.269
peak=   -3.353 closest distance to " O   GLY A 196 " =    1.043
peak=   -3.347 closest distance to " NH2 ARG A  79 " =    1.947
peak=   -3.347 closest distance to " CG1 VAL A 296 " =    1.254
peak=   -3.346 closest distance to " O   HOH Z 385 " =    3.720
peak=   -3.344 closest distance to " NH2AARG A 275 " =    4.939
peak=   -3.341 closest distance to " CA  LYS A 166 " =    2.243
peak=   -3.339 closest distance to " CD1 LEU A  25 " =    2.493
peak=   -3.334 closest distance to " O  BHOH Z 338 " =    1.493
peak=   -3.331 closest distance to " O   SER A 146 " =    0.891
peak=   -3.328 closest distance to " CB  ASP A 162 " =    2.609
peak=   -3.323 closest distance to " CB  ALA A 291 " =    2.216
peak=   -3.316 closest distance to " O   HOH Z 166 " =    1.353
peak=   -3.315 closest distance to " O   HOH Z  15 " =    1.522
peak=   -3.314 closest distance to " O   HOH Z   6 " =    2.063
peak=   -3.314 closest distance to " NE2 GLN A  88 " =    1.108
peak=   -3.313 closest distance to " CG1 VAL A 112 " =    2.609
peak=   -3.308 closest distance to " CD  LYS A 289 " =    2.470
peak=   -3.305 closest distance to " CA  VAL A 197 " =    0.975
peak=   -3.303 closest distance to " O   HOH Z 350 " =    1.608
peak=   -3.299 closest distance to " OD1 ASN A 187 " =    1.776
peak=   -3.297 closest distance to " O   HOH Z 407 " =    1.444
peak=   -3.294 closest distance to " O   HOH Z 380 " =    4.622
peak=   -3.290 closest distance to " OG  SER A  62 " =    1.418
peak=   -3.285 closest distance to " N   LEU A 281 " =    1.837
peak=   -3.285 closest distance to " O   VAL A 125 " =    2.239
peak=   -3.280 closest distance to " CE3 TRP A 150 " =    2.271
peak=   -3.279 closest distance to " O   HOH Z 423 " =    1.091
peak=   -3.276 closest distance to " NH1 ARG A 195 " =    2.548
peak=   -3.262 closest distance to " CB  ALA A 248 " =    2.173
peak=   -3.258 closest distance to " CE  LYS A 166 " =    2.938
peak=   -3.258 closest distance to " OG BSER A 134 " =    1.717
peak=   -3.256 closest distance to " CB  ALA A  51 " =    1.888
peak=   -3.250 closest distance to " C   LEU A 143 " =    1.011
peak=   -3.249 closest distance to " O   LEU A 228 " =    2.495
peak=   -3.248 closest distance to " CG  GLN A  11 " =    1.951
peak=   -3.245 closest distance to " CG  ARG A 259 " =    2.476
peak=   -3.244 closest distance to " CA  PRO A 243 " =    2.764
peak=   -3.244 closest distance to " O   HOH Z  56 " =    2.297
peak=   -3.242 closest distance to " O   HOH Z 353 " =    2.276
peak=   -3.236 closest distance to " CA  GLY A 133 " =    2.303
peak=   -3.233 closest distance to " O   HOH Z 372 " =    2.591
peak=   -3.232 closest distance to " O   HOH Z 262 " =    2.396
peak=   -3.225 closest distance to " ND2 ASN A  45 " =    1.934
peak=   -3.223 closest distance to " O   PHE A  59 " =    2.333
peak=   -3.222 closest distance to " O   HOH Z 191 " =    5.593
peak=   -3.220 closest distance to " CD2 PHE A  61 " =    2.095
peak=   -3.219 closest distance to " CD2 TYR A 293 " =    1.964
peak=   -3.216 closest distance to " CG  LEU A  83 " =    2.012
peak=   -3.215 closest distance to " O   HOH Z 360 " =    2.456
peak=   -3.215 closest distance to " CG1 VAL A  78 " =    2.599
peak=   -3.215 closest distance to " ND2BASN A 224 " =    1.845
peak=   -3.215 closest distance to " O   HOH Z 198 " =    2.016
peak=   -3.214 closest distance to " O   ASN A 187 " =    1.604
peak=   -3.214 closest distance to " CG2 VAL A 296 " =    0.927
peak=   -3.211 closest distance to " O   HOH Z 412 " =    5.275
peak=   -3.210 closest distance to " CB  CYS A 254 " =    2.428
peak=   -3.203 closest distance to " O   HOH Z 200 " =    1.398
peak=   -3.198 closest distance to " NH1 ARG A 195 " =    2.299
peak=   -3.191 closest distance to " O   ALA A 161 " =    1.726
peak=   -3.191 closest distance to " ND2 ASN A 252 " =    1.689
peak=   -3.189 closest distance to " ND2 ASN A  60 " =    1.619
peak=   -3.188 closest distance to " O   SER A  26 " =    1.330
peak=   -3.188 closest distance to " ND2 ASN A  60 " =    1.473
peak=   -3.185 closest distance to " O   HOH Z 145 " =    1.954
peak=   -3.180 closest distance to " O   HOH Z  52 " =    2.005
peak=   -3.174 closest distance to " CE2 PHE A  38 " =    1.969
peak=   -3.173 closest distance to " O   HOH Z  22 " =    2.581
peak=   -3.170 closest distance to " O   HOH Z 132 " =    1.272
peak=   -3.168 closest distance to " OD1 ASP A 191 " =    1.960
peak=   -3.165 closest distance to " O   HOH Z 131 " =    4.063
peak=   -3.163 closest distance to " O   LYS A 117 " =    1.678
peak=   -3.162 closest distance to " O   HOH Z 157 " =    3.563
peak=   -3.160 closest distance to " O   HOH Z  39 " =    1.536
peak=   -3.159 closest distance to " O   ALA A 184 " =    1.820
peak=   -3.159 closest distance to " CA  ASN A 110 " =    1.067
peak=   -3.159 closest distance to " CD  ARG A 139 " =    1.664
peak=   -3.155 closest distance to " NE2 GLN A 223 " =    1.518
peak=   -3.151 closest distance to " CG2 THR A 251 " =    1.912
peak=   -3.149 closest distance to " O   HOH Z 311 " =    3.675
peak=   -3.148 closest distance to " CB  TRP A  85 " =    2.462
peak=   -3.148 closest distance to " O   HOH Z  43 " =    1.879
peak=   -3.146 closest distance to " O   HOH Z  11 " =    1.634
peak=   -3.145 closest distance to " O   HOH Z 193 " =    1.849
peak=   -3.140 closest distance to " CG2 VAL A 112 " =    2.556
peak=   -3.139 closest distance to " O   HOH Z 156 " =    1.387
peak=   -3.139 closest distance to " N   THR A  52 " =    1.603
peak=   -3.137 closest distance to " CE  MET A 105 " =    2.219
peak=   -3.135 closest distance to " O   ASP A  27 " =    2.131
peak=   -3.132 closest distance to " C   GLY A  91 " =    1.408
peak=   -3.126 closest distance to " O   VAL A 197 " =    1.351
peak=   -3.116 closest distance to " O   HOH Z 310 " =    3.500
peak=   -3.108 closest distance to " CE3 TRP A 179 " =    2.388
peak=   -3.105 closest distance to " OD1 ASN A 301 " =    1.943
peak=   -3.103 closest distance to " O   ALA A 160 " =    1.300
peak=   -3.102 closest distance to " O   HOH Z  51 " =    1.607
peak=   -3.102 closest distance to " O   HOH Z  78 " =    1.650
peak=   -3.101 closest distance to " O   HOH Z 418 " =    1.487
peak=   -3.100 closest distance to " N   ALA A 248 " =    1.701
peak=   -3.099 closest distance to " O   HOH Z 340 " =    1.117
peak=   -3.097 closest distance to " O   HOH Z 124 " =    1.584
peak=   -3.094 closest distance to " C   GLY A  80 " =    2.344
peak=   -3.076 closest distance to " CD  GLN A 223 " =    1.607
peak=   -3.068 closest distance to " CB  ASP A 132 " =    2.407
peak=   -3.067 closest distance to " O   HOH Z 285 " =    1.512
peak=   -3.067 closest distance to " O   HOH Z 184 " =    1.368
peak=   -3.019 closest distance to " OD1 ASN A 249 " =    2.212

================= 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    :  0.4813 0.4694   6.283754e+00   6.268279e+00
   1_bss:  0.4741 0.4648   6.277398e+00   6.260128e+00
   1_xyz:  0.3971 0.4125   6.178639e+00   6.199135e+00
   1_adp:  0.3507 0.3936   6.100089e+00   6.171133e+00
   1_occ:  0.3503 0.3928   6.099121e+00   6.171015e+00
   2_bss:  0.3479 0.3869   6.099664e+00   6.169226e+00
   2_xyz:  0.2660 0.3204   5.884185e+00   6.026955e+00
   2_adp:  0.2434 0.3036   5.823202e+00   5.980123e+00
   2_occ:  0.2433 0.3038   5.823116e+00   5.980283e+00
   3_bss:  0.2415 0.3029   5.821824e+00   5.978133e+00
   3_xyz:  0.1765 0.2209   5.523691e+00   5.705638e+00
   3_adp:  0.1601 0.2013   5.432669e+00   5.619600e+00
   3_occ:  0.1597 0.2015   5.431994e+00   5.619856e+00
   4_bss:  0.1591 0.2003   5.431087e+00   5.617620e+00
   4_xyz:  0.1374 0.1774   5.300157e+00   5.501373e+00
   4_adp:  0.1320 0.1749   5.274142e+00   5.487611e+00
   4_occ:  0.1320 0.1748   5.273894e+00   5.487683e+00
   5_bss:  0.1318 0.1748   5.273662e+00   5.488027e+00
   5_xyz:  0.1191 0.1643   5.197203e+00   5.431817e+00
   5_adp:  0.1167 0.1640   5.184753e+00   5.426535e+00
   5_occ:  0.1167 0.1640   5.184855e+00   5.426948e+00
   5_bss:  0.1169 0.1637   5.185961e+00   5.427462e+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:  0.320   7.269   6.601  11.887   7.552   0.000   0.000   0.000
   1_xyz:  0.320   7.269   6.601  11.887   7.552   0.000   0.000   0.000
   1_adp:  0.320   7.269   6.601  11.887   7.552   0.000   0.000   0.000
   1_occ:  0.320   7.269   6.601  11.887   7.552   0.000   0.000   0.000
   2_bss:  0.311  30.143   2.948   7.431   4.365   0.000   0.000   0.000
   2_xyz:  0.311  30.143   2.948   7.431   4.365   0.000   0.000   0.000
   2_adp:  0.311  30.143   2.948   7.431   4.365   0.000   0.000   0.000
   2_occ:  0.311  30.143   2.948   7.431   4.365   0.000   0.000   0.000
   3_bss:  0.303  43.333   1.784   4.537   2.966   0.000   0.000   0.000
   3_xyz:  0.303  43.333   1.784   4.537   2.966   0.000   0.000   0.000
   3_adp:  0.303  43.333   1.784   4.537   2.966   0.000   0.000   0.000
   3_occ:  0.303  43.333   1.784   4.537   2.966   0.000   0.000   0.000
   4_bss:  0.313  43.333   1.085   2.915   2.330   0.000   0.000   0.000
   4_xyz:  0.313  43.333   1.085   2.915   2.330   0.000   0.000   0.000
   4_adp:  0.313  43.333   1.085   2.915   2.330   0.000   0.000   0.000
   4_occ:  0.313  43.333   1.085   2.915   2.330   0.000   0.000   0.000
   5_bss:  0.324  50.391   0.994   2.444   2.294   0.000   0.000   0.000
   5_xyz:  0.324  50.391   0.994   2.444   2.294   0.000   0.000   0.000
   5_adp:  0.324  50.391   0.994   2.444   2.294   0.000   0.000   0.000
   5_occ:  0.324  50.391   0.994   2.444   2.294   0.000   0.000   0.000
   5_bss:  0.324  54.174  -0.830   0.416   0.414   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  57.048 0.4322  0.4962    68439.256
   1_bss:  57.467 0.4247  0.6223    66579.309
   1_xyz:  48.484 0.5377  0.7754    50395.791
   1_adp:  43.819 0.5964  0.9115    44220.185
   1_occ:  43.758 0.5971  0.9114    44071.506
   2_bss:  43.392 0.6016  0.8085    43600.254
   2_xyz:  34.726 0.7035  0.9325    28521.081
   2_adp:  32.107 0.7340  0.9531    25286.957
   2_occ:  32.136 0.7337  0.9526    25323.032
   3_bss:  31.955 0.7358  0.8965    25132.889
   3_xyz:  21.791 0.8438  0.9863    12609.487
   3_adp:  19.303 0.8685  1.0002    10467.890
   3_occ:  19.289 0.8687  1.0006    10471.282
   4_bss:  19.187 0.8696  0.9670    10379.625
   4_xyz:  16.432 0.8945  0.9785     7987.869
   4_adp:  16.070 0.8980  0.9763     7817.192
   4_occ:  16.065 0.8981  0.9761     7822.771
   5_bss:  16.063 0.8981  0.9699     7836.329
   5_xyz:  14.917 0.9077  0.9742     6995.085
   5_adp:  14.764 0.9090  0.9690     6903.358
   5_occ:  14.770 0.9090  0.9689     6910.049
   5_bss:  14.785 0.9089  0.9723     6924.291
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.3826e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.3826e+01
   1_xyz:   1.708  0.013  0.108 18.089  0.007  4.121   1.4378e-01
   1_adp:   1.708  0.013  0.108 18.089  0.007  4.121   1.4378e-01
   1_occ:   1.708  0.013  0.108 18.089  0.007  4.121   1.4378e-01
   2_bss:   1.708  0.013  0.108 18.089  0.007  4.121   1.4378e-01
   2_xyz:   1.348  0.011  0.088 16.436  0.006  4.110   1.0407e-01
   2_adp:   1.348  0.011  0.088 16.436  0.006  4.110   1.0407e-01
   2_occ:   1.348  0.011  0.088 16.436  0.006  4.110   1.0407e-01
   3_bss:   1.348  0.011  0.088 16.436  0.006  4.110   1.0407e-01
   3_xyz:   1.156  0.008  0.081 15.253  0.005  4.131   7.4274e-02
   3_adp:   1.156  0.008  0.081 15.253  0.005  4.131   7.4274e-02
   3_occ:   1.156  0.008  0.081 15.253  0.005  4.131   7.4274e-02
   4_bss:   1.156  0.008  0.081 15.253  0.005  4.131   7.4274e-02
   4_xyz:   0.963  0.006  0.074 14.948  0.003  4.117   5.6514e-02
   4_adp:   0.963  0.006  0.074 14.948  0.003  4.117   5.6514e-02
   4_occ:   0.963  0.006  0.074 14.948  0.003  4.117   5.6514e-02
   5_bss:   0.963  0.006  0.074 14.948  0.003  4.117   5.6514e-02
   5_xyz:   1.100  0.008  0.087 15.217  0.004  4.113   6.8955e-02
   5_adp:   1.100  0.008  0.087 15.217  0.004  4.113   6.8955e-02
   5_occ:   1.100  0.008  0.087 15.217  0.004  4.113   6.8955e-02
   5_bss:   1.100  0.008  0.087 15.217  0.004  4.113   6.8955e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.069   6.9772e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.069   6.9772e+00
   1_xyz:  15.322  0.161  0.521 88.087  0.050  2.269   1.0281e-01
   1_adp:  15.322  0.161  0.521 88.087  0.050  2.269   1.0281e-01
   1_occ:  15.322  0.161  0.521 88.087  0.050  2.269   1.0281e-01
   2_bss:  15.322  0.161  0.521 88.087  0.050  2.269   1.0281e-01
   2_xyz:  10.055  0.150  0.299 89.570  0.053  2.103   1.1329e-01
   2_adp:  10.055  0.150  0.299 89.570  0.053  2.103   1.1329e-01
   2_occ:  10.055  0.150  0.299 89.570  0.053  2.103   1.1329e-01
   3_bss:  10.055  0.150  0.299 89.570  0.053  2.103   1.1329e-01
   3_xyz:   6.449  0.049  0.331 88.644  0.040  2.247   6.4576e-02
   3_adp:   6.449  0.049  0.331 88.644  0.040  2.247   6.4576e-02
   3_occ:   6.449  0.049  0.331 88.644  0.040  2.247   6.4576e-02
   4_bss:   6.449  0.049  0.331 88.644  0.040  2.247   6.4576e-02
   4_xyz:   6.815  0.041  0.415 80.461  0.028  2.286   3.3305e-02
   4_adp:   6.815  0.041  0.415 80.461  0.028  2.286   3.3305e-02
   4_occ:   6.815  0.041  0.415 80.461  0.028  2.286   3.3305e-02
   5_bss:   6.815  0.041  0.415 80.461  0.028  2.286   3.3305e-02
   5_xyz:   7.726  0.052  0.623 83.233  0.036  2.282   4.8255e-02
   5_adp:   7.726  0.052  0.623 83.233  0.036  2.282   4.8255e-02
   5_occ:   7.726  0.052  0.623 83.233  0.036  2.282   4.8255e-02
   5_bss:   7.726  0.052  0.623 83.233  0.036  2.282   4.8255e-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:  93.97   0.00  13.70  74.17   0.00  11.38  93.97   0.00  26.32
   1_occ:  93.97   0.00  13.70  74.17   0.00  11.38  93.97   0.00  26.32
   2_bss:  93.97   0.00  13.70  74.17   0.00  11.38  93.97   0.00  26.32
   2_xyz:  93.97   0.00  13.70  74.17   0.00  11.38  93.97   0.00  26.32
   2_adp:  88.12   0.00  13.18  76.05   0.00  10.02  88.12   0.00  30.40
   2_occ:  88.12   0.00  13.18  76.05   0.00  10.02  88.12   0.00  30.40
   3_bss:  88.12   0.00  13.18  76.05   0.00  10.02  88.12   0.00  30.40
   3_xyz:  88.12   0.00  13.18  76.05   0.00  10.02  88.12   0.00  30.40
   3_adp:  80.65   0.00  13.22  76.77   0.00   9.30  80.65   2.04  34.53
   3_occ:  80.65   0.00  13.22  76.77   0.00   9.30  80.65   2.04  34.53
   4_bss:  80.65   0.00  13.22  76.77   0.00   9.30  80.65   2.04  34.53
   4_xyz:  80.65   0.00  13.22  76.77   0.00   9.30  80.65   2.04  34.53
   4_adp:  79.93   0.00  13.49  79.93   0.00   9.24  79.42   1.98  36.67
   4_occ:  79.93   0.00  13.49  79.93   0.00   9.24  79.42   1.98  36.67
   5_bss:  79.93   0.00  13.49  79.93   0.00   9.24  79.42   1.98  36.67
   5_xyz:  79.93   0.00  13.49  79.93   0.00   9.24  79.42   1.98  36.67
   5_adp:  87.51   0.00  13.63  87.51   0.00   9.14  79.00   1.45  38.06
   5_occ:  87.51   0.00  13.63  87.51   0.00   9.14  79.00   1.45  38.06
   5_bss:  89.53   2.02  15.64  89.53   2.02  11.16  81.01   3.47  40.07
------------------------------------------------------------------------
 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:    1.122    0.020    0.411
   1_adp:    1.122    0.020    0.411
   1_occ:    1.122    0.020    0.411
   2_bss:    1.122    0.020    0.411
   2_xyz:    1.692    0.020    0.615
   2_adp:    1.692    0.020    0.615
   2_occ:    1.692    0.020    0.615
   3_bss:    1.692    0.020    0.615
   3_xyz:    1.698    0.064    0.710
   3_adp:    1.698    0.064    0.710
   3_occ:    1.698    0.064    0.710
   4_bss:    1.698    0.064    0.710
   4_xyz:    1.839    0.054    0.755
   4_adp:    1.839    0.054    0.755
   4_occ:    1.839    0.054    0.755
   5_bss:    1.839    0.054    0.755
   5_xyz:    1.892    0.032    0.788
   5_adp:    1.892    0.032    0.788
   5_occ:    1.892    0.032    0.788
   5_bss:    1.892    0.032    0.788
------------------------------------------------------------------------

CPU time actual refinement: 333.60


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_586/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_586/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_586/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_586/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_586/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 333.44 
  Macro-tasks:
    bulk solvent and scale       = 40.88  
    individual site refinement   = 134.46 
    weights calculation          = 32.56  
    collect and process          = 6.41   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 214.42 
  Micro-tasks:
    mask                            = 2.44   
    f_calc                          = 103.45 
    alpha_beta                      = 8.16   
    target                          = 1.12   
    gradients_wrt_atomic_parameters = 112.99 
    fmodel                         = 7.03   
    r_factors                      = 0.24   
    phase_errors                   = 10.49  
    foms                           = 0.24   
    TOTAL for micro-tasks          = 246.16 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.731 micro seconds
Total CPU time: 5.79 minutes
from_scatterers_fft:    635 calls, 102.97 s
gradients_fft:          580 calls, 100.03 s

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

# Date 2008-01-16 Time 01:56:46 PST -0800 (1200477406.90 s)
Start R-work = 0.4813, R-free = 0.4694 (no bulk solvent and anisotropic scale)
Final R-work = 0.1333, R-free = 0.1789 (no bulk solvent and anisotropic scale)

Start R-work = 0.4741, R-free = 0.4648
Final R-work = 0.1169, R-free = 0.1637