# Date 2008-01-16 Time 00:33:39 PST -0800 (1200472419.95 s)
#phil __OFF__

Command line arguments: "../75.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 29255
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 75

-------------------------------------------------------------------------------
  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: (68.4938, 47.1647, 88.1178, 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: 3.30, per 1000 atoms: 1.17


================================== 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: (68.4938, 47.1647, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8711 1.95096
Completeness in resolution range: 0.917002
Completeness with d_max=infinity: 0.914263

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8711
                             d_min =   1.9510

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: (68.4938, 47.1647, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8711 1.95096
Completeness in resolution range: 0.917002
Completeness with d_max=infinity: 0.914263

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8715 -  4.1751 [2239/2267]  2009   230  10.3%
  bin  2:  4.1751 -  3.3261 [2155/2178]  1941   214   9.9%
  bin  3:  3.3261 -  2.9093 [2127/2152]  1923   204   9.6%
  bin  4:  2.9093 -  2.6449 [2113/2129]  1893   220  10.4%
  bin  5:  2.6449 -  2.4562 [2075/2115]  1863   212  10.2%
  bin  6:  2.4562 -  2.3120 [2093/2124]  1890   203   9.7%
  bin  7:  2.3120 -  2.1966 [2062/2099]  1858   204   9.9%
  bin  8:  2.1966 -  2.1012 [2084/2126]  1880   204   9.8%
  bin  9:  2.1012 -  2.0205 [1979/2077]  1784   195   9.9%
  bin 10:  2.0205 -  1.9510 [ 662/2095]   589    73  11.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_75/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:
        1.04 -     1.82: 13
        1.82 -     2.59: 72
        2.59 -     3.36: 4104
        3.36 -     4.13: 9426
        4.13 -     4.90: 14830
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.045 3.040 -x+1,y+1/2,-z+1/2
  " NH1 ARG A  24 " - " O   GLY A  91 "  1.190 3.120 -x+1,y+1/2,-z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.227 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 176 "  1.326 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  57 " - " O   HOH Z 104 "  1.409 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28440 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_75/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_75/model_refine_001.geo

CPU time processing inputs: 9.45


============================ 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 = 68.49375 47.16465 88.1178 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: 1.95 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4932   r_free= 0.4858   ksol= 0.00   Bsol= 0.00   scale= 0.785    |
|                                                                             |
| 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:   0.81 A                  |
| x-ray target function (ml) for work reflections: 6.292646                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8715 -  4.6570 0.99   1453  161 0.3951 0.3933      6.6084      6.6289|
|  2:  4.6570 -  3.7154 0.99   1412  154 0.4003 0.4565      6.7741      6.8895|
|  3:  3.7154 -  3.2513 0.99   1370  156 0.4713 0.4360      6.6917      6.6837|
|  4:  3.2513 -  2.9566 0.99   1363  146 0.4946 0.4722      6.5182      6.4939|
|  5:  2.9566 -  2.7461 0.98   1357  152 0.5157 0.5104      6.3631      6.4186|
|  6:  2.7461 -  2.5851 0.99   1353  154 0.5253 0.5535      6.2911      6.2074|
|  7:  2.5851 -  2.4562 0.99   1321  157 0.5291 0.4732      6.2276      6.1603|
|  8:  2.4562 -  2.3497 0.99   1361  141 0.5385 0.5117      6.1811      6.1517|
|  9:  2.3497 -  2.2596 0.99   1339  145 0.5493 0.4876      6.1271      6.1638|
| 10:  2.2596 -  2.1819 0.98   1334  148 0.5428 0.5641       6.092      6.1083|
| 11:  2.1819 -  2.1138 0.98   1303  155 0.5374 0.5478      6.0118      6.0256|
| 12:  2.1138 -  2.0536 1.00   1339  144 0.5462 0.5213      5.9484      5.9247|
| 13:  2.0536 -  1.9996 0.78   1075  114 0.5455 0.5036       5.881      5.8367|
| 14:  1.9996 -  1.9510 0.19    250   32 0.5324 0.5676       5.933       5.733|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8715 -  4.6570  1453   161  0.68  35.95   0.79     0.69      76637.50|
|  2:  4.6570 -  3.7154  1412   154  0.66  38.32   0.89     0.73     120434.16|
|  3:  3.7154 -  3.2513  1370   156  0.55  47.62   0.81     0.67     127203.99|
|  4:  3.2513 -  2.9566  1363   146  0.43  57.08   0.77     0.54     114537.43|
|  5:  2.9566 -  2.7461  1357   152  0.33  65.23   0.72     0.40      92978.15|
|  6:  2.7461 -  2.5851  1353   154  0.26  70.16   0.72     0.32      84417.21|
|  7:  2.5851 -  2.4562  1321   157  0.29  68.34   0.73     0.34      71656.77|
|  8:  2.4562 -  2.3497  1361   141  0.34  64.24   0.72     0.41      59737.25|
|  9:  2.3497 -  2.2596  1339   145  0.38  61.28   0.70     0.48      52765.19|
| 10:  2.2596 -  2.1819  1334   148  0.36  63.02   0.74     0.44      46835.78|
| 11:  2.1819 -  2.1138  1303   155  0.27  69.79   0.73     0.35      50213.94|
| 12:  2.1138 -  2.0536  1339   144  0.21  74.05   0.74     0.29      47866.95|
| 13:  2.0536 -  1.9996  1075   114  0.22  73.88   0.72     0.30      42244.15|
| 14:  1.9996 -  1.9510   250    32  0.36  63.22   0.78     0.36      28735.23|
|alpha:            min =        0.29 max =            0.73 mean =         0.46|
|beta:             min =    28735.23 max =       127203.99 mean =     76199.12|
|figures of merit: min =        0.00 max =            1.00 mean =         0.39|
|phase err.(work): min =        0.00 max =           89.99 mean =        60.24|
|phase err.(test): min =        0.00 max =           89.98 mean =        60.68|
|-----------------------------------------------------------------------------|

============================== 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 = 16.798383             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.699   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.463414              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.976   (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 |  0.936 -  1.332:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.332 -  1.729:       17 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.729 -  2.125:       75 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.125 -  2.521:      458 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.521 -  2.918:     1246 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.918 -  3.314:     2383 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.314 -  3.711:     3918 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.711 -  4.107:     5245 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.107 -  4.504:     6914 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.504 -  4.900:     8237 |
|-----------------------------------------------------------------------------|
|-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 |       53.552 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.088    4.900  0.936 |       3.104 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.729)------------------------------------------|
|    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 = 11.729)------------------------------------------|
|    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: 1.95 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4989   r_free= 0.4865   ksol= 0.00   Bsol= 0.00   scale= 0.755    |
|                                                                             |
| 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:   0.81 A                  |
| x-ray target function (ml) for work reflections: 6.293464                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4844   r_free= 0.4790   ksol= 0.32   Bsol= 3.25   scale= 0.998    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.29,8.00,11.20,0.00,0.00,0.00); trace/3= 9.17                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.80 A                  |
| x-ray target function (ml) for work reflections: 6.285376                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 15.277323             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.054   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.525343              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.730   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4844      final r-factor (work) = 0.4087          |
| start r-factor (free) = 0.4790      final r-factor (free) = 0.4309          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 101.6062 = 15.28 * 0.50 * 6.2909 + 1.00 * 53.5522                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 47.6619 = 15.28 * 0.50 * 6.2196 + 1.00 * 0.1526                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4087      final r-factor (work) = 0.3653          |
| start r-factor (free) = 0.4309      final r-factor (free) = 0.4212          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.5015 = 1.53 * 1.00 * 6.2196 + 1.00 * 0.0145                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.3850 = 1.53 * 1.00 * 6.1392 + 1.00 * 0.0206                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.729)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.53   14.72    None  None   None       |
|    all(noH): 2823   0      0.00    92.53   14.72    None  None   None       |
|    Sol.    : 438    0      0.00    92.53   27.50    None  None   None       |
|    Mac.    : 2385   0      0.00    89.38   12.37    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 -   9.253: 1207   |   5:    46.263 -  55.516:   43        |
|      1:     9.253 -  18.505:  782   |   6:    55.516 -  64.769:   30        |
|      2:    18.505 -  27.758:  426   |   7:    64.769 -  74.022:   12        |
|      3:    27.758 -  37.011:  203   |   8:    74.022 -  83.274:    5        |
|      4:    37.011 -  46.263:  111   |   9:    83.274 -  92.527:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3653 r_free = 0.4212             target_work(ml) = 6.123         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3650 r_free = 0.4213             target_work(ml) = 6.123         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3650   r_free= 0.4213   ksol= 0.32   Bsol= 3.25   scale= 1.122    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.29,8.00,11.20,0.00,0.00,0.00); trace/3= 9.17                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.122703                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3609   r_free= 0.4181   ksol= 0.34   Bsol= 38.43   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.12,3.98,7.01,0.00,0.00,0.00); trace/3= 5.04                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.123257                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.230708             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.509   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.581599              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 117.472  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3609      final r-factor (work) = 0.2721          |
| start r-factor (free) = 0.4181      final r-factor (free) = 0.3267          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 31.5381 = 10.23 * 0.50 * 6.1355 + 1.00 * 0.1526                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.8854 = 10.23 * 0.50 * 6.0184 + 1.00 * 0.0992                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2721      final r-factor (work) = 0.2459          |
| start r-factor (free) = 0.3267      final r-factor (free) = 0.3023          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5258 = 0.58 * 1.00 * 6.0184 + 1.00 * 0.0255                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4476 = 0.58 * 1.00 * 5.8421 + 1.00 * 0.0498                               |
|-----------------------------------------------------------------------------|
| number of iterations = 14      |    number of function evaluations = 20     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.729)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    109.48  14.51    None  None   None       |
|    all(noH): 2823   0      0.00    109.48  14.51    None  None   None       |
|    Sol.    : 438    0      0.00    92.43   33.71    None  None   None       |
|    Mac.    : 2385   0      0.00    109.48  10.99    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 -  10.948: 1537   |   5:    54.738 -  65.686:   32        |
|      1:    10.948 -  21.895:  683   |   6:    65.686 -  76.634:   11        |
|      2:    21.895 -  32.843:  284   |   7:    76.634 -  87.582:    5        |
|      3:    32.843 -  43.791:  177   |   8:    87.582 -  98.529:    1        |
|      4:    43.791 -  54.738:   92   |   9:    98.529 - 109.477:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2459 r_free = 0.3023             target_work(ml) = 5.811         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2457 r_free = 0.3025             target_work(ml) = 5.811         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2457   r_free= 0.3025   ksol= 0.34   Bsol= 38.43   scale= 1.073   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.12,3.98,7.01,0.00,0.00,0.00); trace/3= 5.04                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.810518                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2428   r_free= 0.3005   ksol= 0.32   Bsol= 38.43   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.58,2.42,4.20,0.00,0.00,0.00); trace/3= 2.73                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.808951                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.440507              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.041  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.601866              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.971   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2428      final r-factor (work) = 0.1780          |
| start r-factor (free) = 0.3005      final r-factor (free) = 0.2277          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.0071 = 5.44 * 0.50 * 5.8480 + 1.00 * 0.0992                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.5538 = 5.44 * 0.50 * 5.6895 + 1.00 * 0.0769                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1780      final r-factor (work) = 0.1582          |
| start r-factor (free) = 0.2277      final r-factor (free) = 0.2112          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4684 = 0.60 * 1.00 * 5.6895 + 1.00 * 0.0441                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3168 = 0.60 * 1.00 * 5.4817 + 1.00 * 0.0176                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.729)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.33   14.77    None  None   None       |
|    all(noH): 2823   0      0.00    85.33   14.77    None  None   None       |
|    Sol.    : 438    0      2.13    85.33   39.45    None  None   None       |
|    Mac.    : 2385   0      0.00    84.16   10.24    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.533: 1352   |   5:    42.665 -  51.198:   92        |
|      1:     8.533 -  17.066:  783   |   6:    51.198 -  59.731:   81        |
|      2:    17.066 -  25.599:  215   |   7:    59.731 -  68.264:   39        |
|      3:    25.599 -  34.132:  125   |   8:    68.264 -  76.797:   13        |
|      4:    34.132 -  42.665:  112   |   9:    76.797 -  85.330:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1582 r_free = 0.2112             target_work(ml) = 5.441         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1580 r_free = 0.2113             target_work(ml) = 5.441         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1580   r_free= 0.2113   ksol= 0.32   Bsol= 38.43   scale= 1.037   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.58,2.42,4.20,0.00,0.00,0.00); trace/3= 2.73                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.440722                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1567   r_free= 0.2102   ksol= 0.32   Bsol= 49.62   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.19,1.30,2.86,0.00,0.00,0.00); trace/3= 1.45                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.437529                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.087089              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 110.875  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.353940              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 94.525   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1567      final r-factor (work) = 0.1324          |
| start r-factor (free) = 0.2102      final r-factor (free) = 0.1804          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.5539 = 3.09 * 0.50 * 5.4919 + 1.00 * 0.0769                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.3600 = 3.09 * 0.50 * 5.3721 + 1.00 * 0.0679                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1324      final r-factor (work) = 0.1279          |
| start r-factor (free) = 0.1804      final r-factor (free) = 0.1730          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9168 = 0.35 * 1.00 * 5.3721 + 1.00 * 0.0154                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8787 = 0.35 * 1.00 * 5.2767 + 1.00 * 0.0111                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.729)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.86   14.35    None  None   None       |
|    all(noH): 2823   0      0.00    86.86   14.35    None  None   None       |
|    Sol.    : 438    0      3.05    83.73   38.74    None  None   None       |
|    Mac.    : 2385   0      0.00    86.86   9.86     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 -   8.686: 1415   |   5:    43.432 -  52.118:  105        |
|      1:     8.686 -  17.373:  782   |   6:    52.118 -  60.804:   63        |
|      2:    17.373 -  26.059:  183   |   7:    60.804 -  69.491:   29        |
|      3:    26.059 -  34.745:  121   |   8:    69.491 -  78.177:   15        |
|      4:    34.745 -  43.432:  103   |   9:    78.177 -  86.863:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1279 r_free = 0.1730             target_work(ml) = 5.258         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1277 r_free = 0.1730             target_work(ml) = 5.257         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1277   r_free= 0.1730   ksol= 0.32   Bsol= 49.62   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.19,1.30,2.86,0.00,0.00,0.00); trace/3= 1.45                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.257401                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1279   r_free= 0.1736   ksol= 0.32   Bsol= 49.62   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.19,1.30,2.86,0.00,0.00,0.00); trace/3= 1.45                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.259159                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.688844              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 132.916  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.190602              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 151.572  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1279      final r-factor (work) = 0.1190          |
| start r-factor (free) = 0.1736      final r-factor (free) = 0.1661          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1624 = 2.69 * 0.50 * 5.2770 + 1.00 * 0.0679                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1021 = 2.69 * 0.50 * 5.2296 + 1.00 * 0.0713                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1190      final r-factor (work) = 0.1186          |
| start r-factor (free) = 0.1661      final r-factor (free) = 0.1642          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0078 = 0.19 * 1.00 * 5.2296 + 1.00 * 0.0110                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0017 = 0.19 * 1.00 * 5.2078 + 1.00 * 0.0091                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.729)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.65    85.16   13.78    None  None   None       |
|    all(noH): 2823   0      0.65    85.16   13.78    None  None   None       |
|    Sol.    : 438    0      3.25    80.23   36.12    None  None   None       |
|    Mac.    : 2385   0      0.65    85.16   9.67     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:     0.655 -   9.106: 1530   |   5:    42.910 -  51.361:   95        |
|      1:     9.106 -  17.557:  698   |   6:    51.361 -  59.812:   51        |
|      2:    17.557 -  26.008:  175   |   7:    59.812 -  68.263:   23        |
|      3:    26.008 -  34.459:  130   |   8:    68.263 -  76.714:    8        |
|      4:    34.459 -  42.910:  107   |   9:    76.714 -  85.165:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1186 r_free = 0.1642             target_work(ml) = 5.201         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1185 r_free = 0.1641             target_work(ml) = 5.200         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1185   r_free= 0.1641   ksol= 0.32   Bsol= 49.62   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.19,1.30,2.86,0.00,0.00,0.00); trace/3= 1.45                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.199902                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8715 -  4.6570 0.99   1453  161 0.1025 0.1375      5.4291      5.6049|
|  2:  4.6570 -  3.7154 0.99   1412  154 0.0872 0.1158      5.4657      5.6949|
|  3:  3.7154 -  3.2513 0.99   1370  156 0.1133 0.1553      5.5236      5.8251|
|  4:  3.2513 -  2.9566 0.99   1363  146 0.1310 0.1683      5.4739        5.65|
|  5:  2.9566 -  2.7461 0.98   1357  152 0.1419 0.1621      5.3841      5.5309|
|  6:  2.7461 -  2.5851 0.99   1353  154 0.1319 0.2178      5.2596      5.5468|
|  7:  2.5851 -  2.4562 0.99   1321  157 0.1350 0.1709      5.2178      5.3848|
|  8:  2.4562 -  2.3497 0.99   1361  141 0.1237 0.1806      5.1184      5.3256|
|  9:  2.3497 -  2.2596 0.99   1339  145 0.1259 0.1886      5.0606      5.3562|
| 10:  2.2596 -  2.1819 0.98   1334  148 0.1207 0.1807      4.9906      5.2124|
| 11:  2.1819 -  2.1138 0.98   1303  155 0.1224 0.1847      4.9518      5.2825|
| 12:  2.1138 -  2.0536 1.00   1339  144 0.1190 0.1622      4.8938      5.1115|
| 13:  2.0536 -  1.9996 0.78   1075  114 0.1155 0.1811      4.7782      4.9832|
| 14:  1.9996 -  1.9510 0.19    250   32 0.1067 0.1526      4.7331      4.8879|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8715 -  4.6570  1453   161  0.94   9.89   0.98     0.95       8275.58|
|  2:  4.6570 -  3.7154  1412   154  0.95   8.69   1.02     1.00       9924.84|
|  3:  3.7154 -  3.2513  1370   156  0.93  12.05   1.03     1.03      11341.56|
|  4:  3.2513 -  2.9566  1363   146  0.91  14.73   1.01     1.01      10788.21|
|  5:  2.9566 -  2.7461  1357   152  0.89  17.14   1.00     0.98       9487.33|
|  6:  2.7461 -  2.5851  1353   154  0.89  17.18   0.98     0.94       7524.57|
|  7:  2.5851 -  2.4562  1321   157  0.89  16.95   0.99     0.95       6883.39|
|  8:  2.4562 -  2.3497  1361   141  0.90  16.31   1.01     0.98       5935.09|
|  9:  2.3497 -  2.2596  1339   145  0.89  17.01   1.01     0.98       5402.97|
| 10:  2.2596 -  2.1819  1334   148  0.89  16.65   1.01     0.98       4731.76|
| 11:  2.1819 -  2.1138  1303   155  0.89  17.24   1.01     0.96       4558.74|
| 12:  2.1138 -  2.0536  1339   144  0.90  16.52   1.02     1.03       4061.29|
| 13:  2.0536 -  1.9996  1075   114  0.90  16.56   1.00     0.98       3280.26|
| 14:  1.9996 -  1.9510   250    32  0.93  13.02   1.00     0.96       2665.18|
|alpha:            min =        0.94 max =            1.03 mean =         0.98|
|beta:             min =     2665.18 max =        11341.56 mean =      7125.56|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.92 mean =        15.03|
|phase err.(test): min =        0.00 max =           89.77 mean =        14.60|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1185   r_free= 0.1641   ksol= 0.32   Bsol= 50.81   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.26,-0.14,1.40,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.199709                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1185   r_free= 0.1641   ksol= 0.32   Bsol= 50.81   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.26,-0.14,1.40,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.199709                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8715 -  4.6570 0.99   1453  161 0.1024 0.1373      5.4279      5.6028|
|  2:  4.6570 -  3.7154 0.99   1412  154 0.0871 0.1158      5.4651      5.6953|
|  3:  3.7154 -  3.2513 0.99   1370  156 0.1133 0.1553      5.5238       5.825|
|  4:  3.2513 -  2.9566 0.99   1363  146 0.1310 0.1684       5.474      5.6502|
|  5:  2.9566 -  2.7461 0.98   1357  152 0.1419 0.1621      5.3841      5.5314|
|  6:  2.7461 -  2.5851 0.99   1353  154 0.1319 0.2178      5.2594      5.5466|
|  7:  2.5851 -  2.4562 0.99   1321  157 0.1350 0.1709      5.2176      5.3844|
|  8:  2.4562 -  2.3497 0.99   1361  141 0.1237 0.1806      5.1183      5.3258|
|  9:  2.3497 -  2.2596 0.99   1339  145 0.1259 0.1887      5.0603      5.3561|
| 10:  2.2596 -  2.1819 0.98   1334  148 0.1207 0.1807      4.9905      5.2126|
| 11:  2.1819 -  2.1138 0.98   1303  155 0.1224 0.1846      4.9514      5.2818|
| 12:  2.1138 -  2.0536 1.00   1339  144 0.1190 0.1623      4.8943      5.1123|
| 13:  2.0536 -  1.9996 0.78   1075  114 0.1155 0.1811      4.7783      4.9838|
| 14:  1.9996 -  1.9510 0.19    250   32 0.1066 0.1526      4.7328      4.8875|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8715 -  4.6570  1453   161  0.94   9.87   0.97     0.95       8253.28|
|  2:  4.6570 -  3.7154  1412   154  0.95   8.69   1.01     1.00       9912.44|
|  3:  3.7154 -  3.2513  1370   156  0.93  12.05   1.02     1.02      11341.02|
|  4:  3.2513 -  2.9566  1363   146  0.91  14.73   1.01     1.00      10786.72|
|  5:  2.9566 -  2.7461  1357   152  0.89  17.14   1.00     0.97       9488.63|
|  6:  2.7461 -  2.5851  1353   154  0.89  17.18   0.97     0.93       7525.14|
|  7:  2.5851 -  2.4562  1321   157  0.89  16.94   0.98     0.94       6883.17|
|  8:  2.4562 -  2.3497  1361   141  0.90  16.30   1.00     0.97       5934.88|
|  9:  2.3497 -  2.2596  1339   145  0.89  17.00   1.00     0.97       5401.79|
| 10:  2.2596 -  2.1819  1334   148  0.89  16.65   1.00     0.97       4731.28|
| 11:  2.1819 -  2.1138  1303   155  0.89  17.23   1.00     0.95       4557.37|
| 12:  2.1138 -  2.0536  1339   144  0.90  16.51   1.01     1.02       4061.36|
| 13:  2.0536 -  1.9996  1075   114  0.90  16.55   0.98     0.96       3280.87|
| 14:  1.9996 -  1.9510   250    32  0.93  13.02   0.99     0.95       2665.76|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2665.76 max =        11341.02 mean =      7122.51|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.92 mean =        15.02|
|phase err.(test): min =        0.00 max =           89.77 mean =        14.59|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.729)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.84    86.35   14.97    None  None   None       |
|    all(noH): 2823   0      1.84    86.35   14.97    None  None   None       |
|    Sol.    : 438    0      4.44    81.42   37.31    None  None   None       |
|    Mac.    : 2385   0      1.84    86.35   10.86    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.844 -  10.295: 1530   |   5:    44.099 -  52.550:   95        |
|      1:    10.295 -  18.746:  698   |   6:    52.550 -  61.001:   51        |
|      2:    18.746 -  27.197:  175   |   7:    61.001 -  69.452:   23        |
|      3:    27.197 -  35.648:  130   |   8:    69.452 -  77.903:    8        |
|      4:    35.648 -  44.099:  107   |   9:    77.903 -  86.354:    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)= 323         
Filter by distance & map next to the model:
   mapped sites are within: 0.509 - 4.689
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 316 from: 323
   mapped sites are within: 0.726 - 4.689

peak=   11.204 closest distance to " CB  VAL A 230 " =    1.505
peak=    5.849 closest distance to " CG  LEU A   5 " =    1.334
peak=    5.761 closest distance to " O   HOH Z 188 " =    1.730
peak=    5.691 closest distance to " CB  VAL A 296 " =    1.125
peak=    5.484 closest distance to " O   HOH Z 255 " =    1.210
peak=    5.475 closest distance to " CD2 LEU A   5 " =    1.215
peak=    5.376 closest distance to " O   HOH Z 248 " =    1.448
peak=    5.324 closest distance to " NE2 GLN A  11 " =    1.175
peak=    5.307 closest distance to " CG  PRO A  54 " =    1.386
peak=    5.269 closest distance to " O   HOH Z  43 " =    1.677
peak=    5.209 closest distance to " CB  ARG A 275 " =    0.937
peak=    5.005 closest distance to " NH2 ARG A  56 " =    2.152
peak=    4.956 closest distance to " CZ  PHE A 218 " =    1.168
peak=    4.923 closest distance to " O   HOH Z 203 " =    0.973
peak=    4.904 closest distance to " CB  GLN A 223 " =    1.507
peak=    4.902 closest distance to " CG  LEU A 228 " =    1.247
peak=    4.889 closest distance to " CG2 VAL A 296 " =    1.043
peak=    4.887 closest distance to " O   HOH Z 251 " =    1.715
peak=    4.865 closest distance to " CG1 VAL A 296 " =    1.169
peak=    4.846 closest distance to " O   HOH Z 193 " =    1.804
peak=    4.708 closest distance to " O   HOH Z 126 " =    1.587
peak=    4.700 closest distance to " O   HOH Z 238 " =    1.520
peak=    4.618 closest distance to " O   HOH Z 169 " =    1.025
peak=    4.605 closest distance to " O   HOH Z 142 " =    1.674
peak=    4.591 closest distance to " O   HOH Z 232 " =    2.354
peak=    4.586 closest distance to " CB  ARG A  79 " =    1.510
peak=    4.564 closest distance to " O   HOH Z 209 " =    2.318
peak=    4.463 closest distance to " O   HOH Z 403 " =    1.629
peak=    4.459 closest distance to " CA  ALA A  51 " =    1.029
peak=    4.442 closest distance to " O   HOH Z 346 " =    1.524
peak=    4.430 closest distance to " CB  SER A  63 " =    1.155
peak=    4.429 closest distance to " O   HOH Z 272 " =    1.861
peak=    4.411 closest distance to " CB  GLU A 152 " =    1.188
peak=    4.344 closest distance to " CB  PRO A  54 " =    0.970
peak=    4.311 closest distance to " O   HOH Z  63 " =    1.978
peak=    4.296 closest distance to " O   HOH Z 313 " =    1.916
peak=    4.295 closest distance to " CG  PRO A 243 " =    1.167
peak=    4.293 closest distance to " O   HOH Z  85 " =    1.647
peak=    4.293 closest distance to " CB  SER A  26 " =    1.838
peak=    4.259 closest distance to " CD2 LEU A 228 " =    1.249
peak=    4.256 closest distance to " CB  GLN A 183 " =    1.284
peak=    4.238 closest distance to " CD2 TRP A 179 " =    1.382
peak=    4.233 closest distance to " CB  VAL A 230 " =    1.219
peak=    4.230 closest distance to " O   HOH Z  76 " =    1.190
peak=    4.225 closest distance to " CB  ASN A 148 " =    1.322
peak=    4.220 closest distance to " CB  ASN A 142 " =    1.160
peak=    4.207 closest distance to " O   HOH Z 359 " =    1.664
peak=    4.203 closest distance to " O   HOH Z 368 " =    2.248
peak=    4.201 closest distance to " O   HOH Z 406 " =    1.584
peak=    4.180 closest distance to " O   HOH Z  97 " =    1.550
peak=    4.166 closest distance to " O   SER A  87 " =    2.306
peak=    4.158 closest distance to " O   HOH Z 126 " =    1.783
peak=    4.147 closest distance to " ND2 ASN A 187 " =    1.671
peak=    4.135 closest distance to " CD  LYS A 166 " =    1.364
peak=    4.124 closest distance to " O   PRO A 198 " =    1.611
peak=    4.097 closest distance to " O   HOH Z 188 " =    2.457
peak=    4.095 closest distance to " O   HOH Z 124 " =    1.264
peak=    4.091 closest distance to " CB  VAL A 265 " =    1.332
peak=    4.072 closest distance to " CB  ALA A   9 " =    1.716
peak=    4.027 closest distance to " CB  ARG A  79 " =    1.033
peak=    4.008 closest distance to " O   HOH Z  95 " =    1.278
peak=    4.005 closest distance to " O   HOH Z 422 " =    2.575
peak=    3.999 closest distance to " O   HOH Z 234 " =    3.487
peak=    3.986 closest distance to " O   HOH Z  80 " =    1.844
peak=    3.971 closest distance to " O   HOH Z  61 " =    1.777
peak=    3.967 closest distance to " O   HOH Z 402 " =    1.363
peak=    3.952 closest distance to " O   HOH Z 265 " =    2.034
peak=    3.950 closest distance to " O   HOH Z 287 " =    1.927
peak=    3.936 closest distance to " CA  TYR A  30 " =    1.037
peak=    3.928 closest distance to " O   HOH Z  40 " =    1.676
peak=    3.922 closest distance to " CG  GLN A  58 " =    1.126
peak=    3.916 closest distance to " CD  LYS A  76 " =    1.804
peak=    3.904 closest distance to " O   HOH Z 425 " =    1.406
peak=    3.897 closest distance to " O   HOH Z 261 " =    2.468
peak=    3.893 closest distance to " O   HOH Z 369 " =    2.376
peak=    3.891 closest distance to " O   HOH Z 128 " =    1.561
peak=    3.887 closest distance to " CD  ARG A 159 " =    0.726
peak=    3.880 closest distance to " CD  ARG A 269 " =    1.016
peak=    3.879 closest distance to " O   HOH Z 394 " =    1.529
peak=    3.873 closest distance to " O   HOH Z 419 " =    1.835
peak=    3.857 closest distance to " CB  GLU A 277 " =    3.616
peak=    3.857 closest distance to " O   HOH Z 303 " =    2.182
peak=    3.851 closest distance to " O   HOH Z  78 " =    1.692
peak=    3.848 closest distance to " O   HOH Z 423 " =    1.853
peak=    3.835 closest distance to " CA  ARG A  36 " =    0.998
peak=    3.829 closest distance to " CB  ASN A 110 " =    1.077
peak=    3.825 closest distance to " ND2 ASN A 249 " =    0.918
peak=    3.819 closest distance to " CB  ASP A 298 " =    1.170
peak=    3.814 closest distance to " O   HOH Z 411 " =    3.914
peak=    3.813 closest distance to " O   HOH Z 365 " =    2.530
peak=    3.807 closest distance to " O   HOH Z 141 " =    1.640
peak=    3.800 closest distance to " CB  TRP A 266 " =    1.135
peak=    3.796 closest distance to " N   ASN A  39 " =    1.202
peak=    3.795 closest distance to " CA  ASP A 162 " =    0.962
peak=    3.792 closest distance to " O   HOH Z 120 " =    2.700
peak=    3.775 closest distance to " N   PHE A 130 " =    1.361
peak=    3.766 closest distance to " O   HOH Z 132 " =    2.521
peak=    3.760 closest distance to " O   HOH Z 375 " =    1.048
peak=    3.758 closest distance to " O   HOH Z  94 " =    2.253
peak=    3.747 closest distance to " CG  PRO A 213 " =    1.224
peak=    3.741 closest distance to " O   HOH Z  59 " =    2.028
peak=    3.739 closest distance to " OG ASER A 258 " =    3.020
peak=    3.733 closest distance to " CD1 LEU A  96 " =    0.792
peak=    3.723 closest distance to " O   ASN A  74 " =    1.516
peak=    3.710 closest distance to " CB  SER A   3 " =    1.239
peak=    3.704 closest distance to " CB  ARG A 190 " =    1.655
peak=    3.701 closest distance to " CB  THR A  31 " =    1.526
peak=    3.701 closest distance to " O   HOH Z 407 " =    2.630
peak=    3.701 closest distance to " O   HOH Z 427 " =    2.855
peak=    3.689 closest distance to " O   HOH Z 227 " =    1.618
peak=    3.688 closest distance to " CG2AVAL A 121 " =    2.325
peak=    3.671 closest distance to " CB  PHE A 204 " =    0.805
peak=    3.669 closest distance to " OG BSER A 212 " =    2.663
peak=    3.660 closest distance to " O   HOH Z 187 " =    2.246
peak=    3.658 closest distance to " O   HOH Z 246 " =    1.251
peak=    3.646 closest distance to " CG  ARG A  66 " =    2.617
peak=    3.643 closest distance to " O   HOH Z 154 " =    1.772
peak=    3.642 closest distance to " CD  LYS A 119 " =    1.856
peak=    3.625 closest distance to " CG  PRO A 198 " =    1.181
peak=    3.623 closest distance to " O   HOH Z 214 " =    2.818
peak=    3.622 closest distance to " O   HOH Z 126 " =    1.507
peak=    3.615 closest distance to " CA  TYR A 116 " =    1.592
peak=    3.606 closest distance to " O   HOH Z 350 " =    1.820
peak=    3.603 closest distance to " O   HOH Z 173 " =    2.131
peak=    3.584 closest distance to " O   HOH Z 112 " =    1.087
peak=    3.580 closest distance to " O   HOH Z  97 " =    1.889
peak=    3.574 closest distance to " O   HOH Z   3 " =    1.763
peak=    3.572 closest distance to " O   HOH Z 295 " =    1.305
peak=    3.571 closest distance to " CG2 VAL A 257 " =    0.783
peak=    3.571 closest distance to " CG AARG A 275 " =    1.239
peak=    3.568 closest distance to " CB  THR A  52 " =    0.953
peak=    3.567 closest distance to " CG  LEU A 167 " =    1.258
peak=    3.563 closest distance to " O   HOH Z   1 " =    1.971
peak=    3.562 closest distance to " O   HOH Z 148 " =    3.363
peak=    3.558 closest distance to " O   HOH Z 263 " =    1.801
peak=    3.558 closest distance to " CB  VAL A 202 " =    1.500
peak=    3.554 closest distance to " OG  SER A 276 " =    1.420
peak=    3.552 closest distance to " O   HOH Z 102 " =    1.300
peak=    3.550 closest distance to " CA  ASN A 217 " =    1.201
peak=    3.548 closest distance to " O   HOH Z  15 " =    2.052
peak=    3.548 closest distance to " CG  GLN A  88 " =    1.103
peak=    3.546 closest distance to " O   HOH Z 337 " =    1.885
peak=    3.535 closest distance to " CB  ARG A 156 " =    1.098
peak=    3.533 closest distance to " CG1 ILE A  49 " =    1.595
peak=    3.524 closest distance to " CG2 ILE A  20 " =    1.313
peak=    3.521 closest distance to " CB  ALA A 114 " =    0.921
peak=    3.517 closest distance to " CB  ALA A 248 " =    1.284
peak=    3.511 closest distance to " CZ  PHE A  38 " =    1.018
peak=    3.503 closest distance to " O   HOH Z  28 " =    1.633
peak=    3.500 closest distance to " O   HOH Z 371 " =    2.767
peak=    3.499 closest distance to " O   GLY A  23 " =    2.430
peak=    3.497 closest distance to " O   HOH Z  30 " =    1.360
peak=    3.493 closest distance to " O   HOH Z 213 " =    1.868
peak=    3.491 closest distance to " O   HOH Z 107 " =    0.917
peak=    3.487 closest distance to " O   HOH Z 421 " =    1.693
peak=    3.477 closest distance to " O   HOH Z  44 " =    2.133
peak=    3.473 closest distance to " CE  LYS A  76 " =    0.899
peak=    3.471 closest distance to " CG  PHE A 204 " =    0.966
peak=    3.460 closest distance to " O   ASP A 124 " =    1.372
peak=    3.457 closest distance to " CB  ASP A 124 " =    0.766
peak=    3.451 closest distance to " O   HOH Z 298 " =    1.699
peak=    3.450 closest distance to " CB  SER A  62 " =    1.112
peak=    3.446 closest distance to " O   HOH Z 388 " =    2.215
peak=    3.445 closest distance to " CA  SER A  87 " =    0.926
peak=    3.444 closest distance to " CG  MET A 185 " =    1.266
peak=    3.443 closest distance to " O   HOH Z 280 " =    2.973
peak=    3.441 closest distance to " CG AARG A 102 " =    1.040
peak=    3.432 closest distance to " O   HOH Z 236 " =    1.547
peak=    3.432 closest distance to " CB  GLN A  89 " =    1.264
peak=    3.431 closest distance to " O   HOH Z 327 " =    1.597
peak=    3.426 closest distance to " CB  ASN A  39 " =    0.814
peak=    3.424 closest distance to " CA  ASP A 149 " =    1.131
peak=    3.409 closest distance to " CB  GLU A  46 " =    0.970
peak=    3.408 closest distance to " CG2 ILE A 234 " =    1.201
peak=    3.404 closest distance to " CB  GLN A  88 " =    1.192
peak=    3.397 closest distance to " O   HOH Z 438 " =    3.013
peak=    3.393 closest distance to " CB  TRP A 179 " =    1.366
peak=    3.390 closest distance to " CA  ASN A 215 " =    0.977
peak=    3.389 closest distance to " O   HOH Z 132 " =    2.778
peak=    3.389 closest distance to " CB  ARG A 219 " =    1.162
peak=    3.386 closest distance to " NH2AARG A 145 " =    1.015
peak=    3.384 closest distance to " NH2BARG A 145 " =    2.204
peak=    3.383 closest distance to " OG BSER A 164 " =    2.289
peak=    3.383 closest distance to " CG2 ILE A 120 " =    1.485
peak=    3.378 closest distance to " CA  LEU A 282 " =    1.222
peak=    3.369 closest distance to " O   HOH Z 410 " =    3.132
peak=    3.367 closest distance to " O   HOH Z 329 " =    4.078
peak=    3.365 closest distance to " O   HOH Z 380 " =    1.966
peak=    3.361 closest distance to " O   HOH Z 298 " =    4.274
peak=    3.357 closest distance to " NE2 GLN A  77 " =    3.290
peak=    3.357 closest distance to " CB  THR A 235 " =    1.287
peak=    3.354 closest distance to " O   THR A 182 " =    1.431
peak=    3.354 closest distance to " CA  ARG A 195 " =    1.220
peak=    3.353 closest distance to " O   HOH Z 130 " =    2.280
peak=    3.349 closest distance to " O  BHOH Z 338 " =    2.277
peak=    3.348 closest distance to " O   HOH Z 156 " =    3.244
peak=    3.347 closest distance to " O   HOH Z  19 " =    1.637
peak=    3.347 closest distance to " CB  PRO A  90 " =    1.115
peak=    3.345 closest distance to " O   HOH Z 368 " =    4.689
peak=    3.344 closest distance to " CA  PHE A 283 " =    1.063
peak=    3.339 closest distance to " CE1 TYR A 186 " =    1.199
peak=    3.339 closest distance to " CA  ALA A 158 " =    1.442
peak=    3.335 closest distance to " O   HOH Z  68 " =    2.093
peak=    3.335 closest distance to " O   HOH Z 258 " =    1.880
peak=    3.333 closest distance to " O   HOH Z 143 " =    1.369
peak=    3.330 closest distance to " O   HOH Z 425 " =    1.897
peak=    3.329 closest distance to " CB  ALA A 295 " =    1.205
peak=    3.327 closest distance to " OD1 ASN A 301 " =    1.637
peak=    3.322 closest distance to " O   HOH Z  85 " =    1.803
peak=    3.322 closest distance to " O   HOH Z   1 " =    1.987
peak=    3.322 closest distance to " O   HOH Z 315 " =    1.904
peak=    3.313 closest distance to " CB  ARG A 139 " =    1.095
peak=    3.305 closest distance to " O   HOH Z 322 " =    1.966
peak=    3.305 closest distance to " O   HOH Z 337 " =    3.515
peak=    3.303 closest distance to " CA  SER A  32 " =    1.748
peak=    3.295 closest distance to " O   HOH Z 332 " =    1.416
peak=    3.293 closest distance to " CG2 VAL A 197 " =    1.015
peak=    3.293 closest distance to " CD2 LEU A 297 " =    0.932
peak=    3.289 closest distance to " O   HOH Z   9 " =    2.210
peak=    3.286 closest distance to " O   HOH Z  99 " =    1.819
peak=    3.285 closest distance to " CA  ILE A 234 " =    0.907
peak=    3.278 closest distance to " O   HOH Z 345 " =    1.632
peak=    3.272 closest distance to " O   HOH Z 385 " =    3.838
peak=    3.271 closest distance to " O   THR A  31 " =    1.895
peak=    3.268 closest distance to " N   ARG A 156 " =    1.339
peak=    3.265 closest distance to " O   HOH Z  10 " =    1.752
peak=    3.265 closest distance to " NZ  LYS A 117 " =    2.809
peak=    3.263 closest distance to " CB  PRO A 198 " =    1.028
peak=    3.260 closest distance to " O   HOH Z 371 " =    1.259
peak=    3.258 closest distance to " O   HOH Z 383 " =    1.635
peak=    3.255 closest distance to " O   HOH Z 109 " =    1.624
peak=    3.255 closest distance to " O   HOH Z  83 " =    1.545
peak=    3.252 closest distance to " O   HOH Z 345 " =    3.024
peak=    3.250 closest distance to " OE1 GLN A  73 " =    2.479
peak=    3.250 closest distance to " O   HOH Z 293 " =    1.918
peak=    3.249 closest distance to " CB  SER A  99 " =    1.431
peak=    3.246 closest distance to " O   ALA A 165 " =    1.426
peak=    3.246 closest distance to " N   ASP A 162 " =    1.204
peak=    3.244 closest distance to " CZ3 TRP A 266 " =    1.073
peak=    3.242 closest distance to " O   LEU A 228 " =    1.646
peak=    3.240 closest distance to " O   HOH Z 200 " =    2.231
peak=    3.239 closest distance to " CB  ALA A 104 " =    0.727
peak=    3.234 closest distance to " OE1 GLU A   2 " =    2.126
peak=    3.229 closest distance to " O   TRP A 274 " =    1.721
peak=    3.228 closest distance to " CB BVAL A  41 " =    1.222
peak=    3.227 closest distance to " CB  ASP A 191 " =    1.165
peak=    3.227 closest distance to " OG  SER A  62 " =    2.679
peak=    3.226 closest distance to " O   HOH Z 421 " =    3.039
peak=    3.224 closest distance to " O   HOH Z 272 " =    2.161
peak=    3.220 closest distance to " CA  LYS A 290 " =    1.205
peak=    3.215 closest distance to " CG  MET A 185 " =    0.943
peak=    3.211 closest distance to " CB  ALA A 291 " =    0.824
peak=    3.210 closest distance to " O   HOH Z 409 " =    1.408
peak=    3.210 closest distance to " N   CYS A 260 " =    0.767
peak=    3.210 closest distance to " O   HOH Z 130 " =    1.182
peak=    3.209 closest distance to " O   HOH Z 361 " =    2.663
peak=    3.208 closest distance to " CE1 HIS A 108 " =    1.204
peak=    3.206 closest distance to " O   SER A 164 " =    1.145
peak=    3.204 closest distance to " O   HOH Z 299 " =    4.125
peak=    3.203 closest distance to " CE3 TRP A 150 " =    1.073
peak=    3.200 closest distance to " O   HOH Z 357 " =    1.988
peak=    3.199 closest distance to " O   HOH Z 355 " =    1.905
peak=    3.195 closest distance to " O   HOH Z 162 " =    2.972
peak=    3.192 closest distance to " CG  LEU A 237 " =    1.392
peak=    3.191 closest distance to " O   HOH Z  80 " =    1.860
peak=    3.187 closest distance to " CG  GLN A  55 " =    2.343
peak=    3.187 closest distance to " CD1 ILE A 199 " =    1.108
peak=    3.186 closest distance to " O   HOH Z 254 " =    1.484
peak=    3.183 closest distance to " CE2 TYR A 169 " =    1.333
peak=    3.183 closest distance to " O   HOH Z 325 " =    2.207
peak=    3.180 closest distance to " CD1 LEU A 228 " =    1.924
peak=    3.178 closest distance to " CB  SER A 288 " =    1.523
peak=    3.176 closest distance to " CA  VAL A  41 " =    0.792
peak=    3.172 closest distance to " CD2 TYR A 186 " =    1.074
peak=    3.171 closest distance to " CA  ALA A 291 " =    0.828
peak=    3.167 closest distance to " O   HOH Z 209 " =    2.640
peak=    3.166 closest distance to " O   HOH Z 285 " =    2.235
peak=    3.166 closest distance to " CB  SER A 141 " =    1.130
peak=    3.165 closest distance to " CG2 THR A 221 " =    1.242
peak=    3.157 closest distance to " CZ3 TRP A  85 " =    0.918
peak=    3.156 closest distance to " CB  SER A 212 " =    1.457
peak=    3.152 closest distance to " CA  SER A 146 " =    2.020
peak=    3.150 closest distance to " O   HOH Z 392 " =    2.625
peak=    3.149 closest distance to " O   HOH Z 183 " =    1.815
peak=    3.148 closest distance to " CB  LYS A 117 " =    1.134
peak=    3.143 closest distance to " CB  ALA A  84 " =    0.734
peak=    3.143 closest distance to " O   HOH Z 147 " =    1.737
peak=    3.135 closest distance to " CB  ASP A 140 " =    1.129
peak=    3.134 closest distance to " O   HOH Z 344 " =    1.805
peak=    3.131 closest distance to " O   HOH Z  94 " =    1.935
peak=    3.125 closest distance to " OG1 THR A 221 " =    1.385
peak=    3.113 closest distance to " O   HOH Z 250 " =    1.337
peak=    3.112 closest distance to " O   HOH Z 163 " =    1.971
peak=    3.111 closest distance to " O   HOH Z 301 " =    1.708
peak=    3.111 closest distance to " CA  THR A 221 " =    1.034
peak=    3.107 closest distance to " O   HOH Z 344 " =    2.888
peak=    3.107 closest distance to " NH1AARG A 145 " =    1.372
peak=    3.102 closest distance to " O   HOH Z 162 " =    1.663
peak=    3.097 closest distance to " O   HOH Z 172 " =    3.825
peak=    3.094 closest distance to " O   HOH Z 233 " =    1.831
peak=    3.092 closest distance to " O   HOH Z 305 " =    3.466
peak=    3.091 closest distance to " CG2 THR A  18 " =    1.579
peak=    3.087 closest distance to " O   ALA A   1 " =    1.858
peak=    3.084 closest distance to " CB  ALA A  10 " =    0.752
peak=    3.084 closest distance to " O   HOH Z 421 " =    2.520
peak=    3.080 closest distance to " O   HOH Z 438 " =    2.141
peak=    3.077 closest distance to " O   HOH Z 193 " =    1.547
peak=    3.077 closest distance to " CG2 ILE A  20 " =    1.130
peak=    3.074 closest distance to " CG  MET A 185 " =    2.102
peak=    3.061 closest distance to " O   HOH Z 361 " =    3.634
peak=    3.056 closest distance to " CD  ARG A  66 " =    2.607
peak=    3.056 closest distance to " O   HOH Z 197 " =    2.014
peak=    3.053 closest distance to " O   HOH Z 361 " =    3.545
peak=    3.048 closest distance to " O   HOH Z  41 " =    2.006
peak=    3.016 closest distance to " O   GLY A 302 " =    1.895
peak=    3.013 closest distance to " CA  ALA A 129 " =    1.564

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 197         
Filter by distance & map next to the model:
   mapped sites are within: 0.425 - 5.858
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 191 from: 197
   mapped sites are within: 0.745 - 5.858

peak=   -5.156 closest distance to " O   HOH Z 169 " =    0.753
peak=   -4.860 closest distance to " O   HOH Z 203 " =    1.204
peak=   -4.836 closest distance to " CG  GLN A  58 " =    0.926
peak=   -4.766 closest distance to " O   HOH Z 193 " =    0.940
peak=   -4.675 closest distance to " CD  ARG A  14 " =    3.177
peak=   -4.578 closest distance to " O   HOH Z 100 " =    0.782
peak=   -4.390 closest distance to " C   HIS A 108 " =    1.180
peak=   -4.343 closest distance to " CD1 LEU A 101 " =    2.387
peak=   -4.342 closest distance to " CD2 TYR A 293 " =    1.907
peak=   -4.283 closest distance to " O   VAL A  67 " =    2.517
peak=   -4.225 closest distance to " NE2 GLN A  88 " =    1.065
peak=   -4.222 closest distance to " O   HOH Z 211 " =    1.229
peak=   -4.219 closest distance to " OG BSER A 134 " =    1.376
peak=   -4.136 closest distance to " CD  ARG A 156 " =    2.005
peak=   -4.107 closest distance to " OE1 GLN A 223 " =    2.211
peak=   -4.106 closest distance to " O   PRO A 163 " =    2.155
peak=   -4.066 closest distance to " O   HOH Z 216 " =    1.012
peak=   -4.058 closest distance to " O   HOH Z 109 " =    0.745
peak=   -4.048 closest distance to " O   HOH Z 290 " =    0.991
peak=   -4.024 closest distance to " O   PRO A 198 " =    1.211
peak=   -4.005 closest distance to " O   HOH Z 166 " =    1.831
peak=   -3.982 closest distance to " O   HOH Z 394 " =    1.765
peak=   -3.957 closest distance to " CD1 ILE A 263 " =    2.723
peak=   -3.935 closest distance to " O   HOH Z 267 " =    5.504
peak=   -3.935 closest distance to " O   HOH Z 131 " =    4.174
peak=   -3.892 closest distance to " CG1 VAL A 112 " =    2.561
peak=   -3.866 closest distance to " OXT GLY A 302 " =    2.944
peak=   -3.857 closest distance to " CB  PRO A 243 " =    2.815
peak=   -3.856 closest distance to " OG  SER A  97 " =    2.333
peak=   -3.841 closest distance to " O   HOH Z 128 " =    1.213
peak=   -3.816 closest distance to " O   HOH Z 351 " =    1.577
peak=   -3.782 closest distance to " CG2 ILE A  49 " =    2.803
peak=   -3.769 closest distance to " CB  PHE A 192 " =    2.082
peak=   -3.757 closest distance to " CE  MET A 105 " =    2.232
peak=   -3.755 closest distance to " O   GLY A 241 " =    2.432
peak=   -3.738 closest distance to " CB  ALA A  43 " =    2.428
peak=   -3.734 closest distance to " CA  VAL A  67 " =    2.956
peak=   -3.729 closest distance to " OH  TYR A 172 " =    1.797
peak=   -3.700 closest distance to " CB  ALA A 248 " =    2.379
peak=   -3.685 closest distance to " O   HOH Z 174 " =    3.861
peak=   -3.671 closest distance to " O   VAL A 174 " =    2.267
peak=   -3.666 closest distance to " N   PHE A  59 " =    2.115
peak=   -3.633 closest distance to " O   ASN A 187 " =    1.590
peak=   -3.628 closest distance to " CA  ASP A 298 " =    1.076
peak=   -3.622 closest distance to " O   HOH Z 196 " =    2.091
peak=   -3.613 closest distance to " CB  ALA A 248 " =    2.138
peak=   -3.610 closest distance to " O   ALA A 227 " =    1.301
peak=   -3.607 closest distance to " CB  ALA A  51 " =    1.943
peak=   -3.606 closest distance to " CB  VAL A 296 " =    0.971
peak=   -3.603 closest distance to " CE1 TYR A 247 " =    2.651
peak=   -3.589 closest distance to " O   ILE A  49 " =    1.732
peak=   -3.583 closest distance to " OXT GLY A 302 " =    3.621
peak=   -3.582 closest distance to " CG  LEU A   5 " =    0.901
peak=   -3.576 closest distance to " O   HOH Z 423 " =    2.375
peak=   -3.570 closest distance to " O   HOH Z 246 " =    0.839
peak=   -3.568 closest distance to " O   HOH Z 210 " =    0.849
peak=   -3.554 closest distance to " CG2 VAL A 296 " =    1.203
peak=   -3.537 closest distance to " N   GLY A 196 " =    1.715
peak=   -3.531 closest distance to " CB  SER A 210 " =    1.163
peak=   -3.514 closest distance to " CE2 TYR A  30 " =    2.761
peak=   -3.513 closest distance to " O   HOH Z 407 " =    2.659
peak=   -3.487 closest distance to " CE BMET A  47 " =    1.186
peak=   -3.471 closest distance to " NH2 ARG A  66 " =    1.106
peak=   -3.467 closest distance to " OG ASER A 134 " =    1.571
peak=   -3.464 closest distance to " O   HOH Z 165 " =    1.827
peak=   -3.462 closest distance to " NE2 GLN A  11 " =    1.763
peak=   -3.461 closest distance to " CB  PRO A 163 " =    2.503
peak=   -3.451 closest distance to " CB  TRP A  85 " =    2.779
peak=   -3.450 closest distance to " OG  SER A  87 " =    1.484
peak=   -3.446 closest distance to " O   HOH Z 116 " =    1.376
peak=   -3.445 closest distance to " CG  ARG A 269 " =    2.123
peak=   -3.439 closest distance to " NH2AARG A 275 " =    4.810
peak=   -3.435 closest distance to " N   SER A 276 " =    1.428
peak=   -3.435 closest distance to " CG  ASP A 231 " =    0.763
peak=   -3.430 closest distance to " O   HOH Z 119 " =    2.140
peak=   -3.426 closest distance to " O   HOH Z 429 " =    1.625
peak=   -3.420 closest distance to " CD2 PHE A 225 " =    1.082
peak=   -3.417 closest distance to " NE2 GLN A  88 " =    1.855
peak=   -3.413 closest distance to " CD1 ILE A 199 " =    2.382
peak=   -3.410 closest distance to " ND2 ASN A  69 " =    1.946
peak=   -3.410 closest distance to " ND2 ASN A 249 " =    2.318
peak=   -3.402 closest distance to " O   HOH Z 185 " =    2.517
peak=   -3.402 closest distance to " CH2 TRP A 179 " =    1.268
peak=   -3.400 closest distance to " CD1 PHE A 130 " =    2.304
peak=   -3.382 closest distance to " O   HOH Z 371 " =    2.405
peak=   -3.380 closest distance to " O   PHE A 218 " =    1.521
peak=   -3.380 closest distance to " O   HOH Z 191 " =    5.717
peak=   -3.377 closest distance to " ND2 ASN A  45 " =    1.234
peak=   -3.374 closest distance to " O   ILE A 106 " =    1.746
peak=   -3.369 closest distance to " CB  PHE A 208 " =    2.313
peak=   -3.354 closest distance to " O   HOH Z 114 " =    3.345
peak=   -3.351 closest distance to " OD1 ASN A 301 " =    1.867
peak=   -3.348 closest distance to " OG BSER A 210 " =    1.560
peak=   -3.348 closest distance to " O   GLY A 196 " =    1.101
peak=   -3.342 closest distance to " O   GLY A  80 " =    2.637
peak=   -3.342 closest distance to " O   LEU A 282 " =    2.212
peak=   -3.339 closest distance to " O   HOH Z 421 " =    3.394
peak=   -3.336 closest distance to " O   HOH Z 423 " =    2.523
peak=   -3.334 closest distance to " CG2 THR A  18 " =    2.863
peak=   -3.332 closest distance to " CD  PRO A 243 " =    1.912
peak=   -3.331 closest distance to " O   HOH Z 372 " =    0.949
peak=   -3.325 closest distance to " CG  MET A 105 " =    0.871
peak=   -3.323 closest distance to " N   THR A 157 " =    1.497
peak=   -3.322 closest distance to " O   HOH Z 154 " =    1.386
peak=   -3.320 closest distance to " CD1 PHE A  59 " =    2.020
peak=   -3.313 closest distance to " OG1 THR A  52 " =    2.730
peak=   -3.312 closest distance to " O   HOH Z 111 " =    1.641
peak=   -3.308 closest distance to " ND2 ASN A 187 " =    1.661
peak=   -3.304 closest distance to " CZ  PHE A  38 " =    2.164
peak=   -3.303 closest distance to " CE3 TRP A 150 " =    2.105
peak=   -3.298 closest distance to " CA  SER A 135 " =    1.279
peak=   -3.297 closest distance to " CB  ASN A  39 " =    2.329
peak=   -3.288 closest distance to " OD2 ASP A 191 " =    1.383
peak=   -3.282 closest distance to " CE3 TRP A 274 " =    2.266
peak=   -3.281 closest distance to " CD1 LEU A 255 " =    2.689
peak=   -3.279 closest distance to " O   SER A 146 " =    1.324
peak=   -3.276 closest distance to " CB  ASP A 132 " =    2.367
peak=   -3.273 closest distance to " O   HOH Z 431 " =    2.093
peak=   -3.271 closest distance to " C   LEU A 143 " =    0.995
peak=   -3.268 closest distance to " CA  GLY A 133 " =    1.913
peak=   -3.264 closest distance to " CA  ALA A 114 " =    0.992
peak=   -3.263 closest distance to " OG1 THR A 157 " =    1.593
peak=   -3.260 closest distance to " CB  GLN A  55 " =    1.312
peak=   -3.257 closest distance to " CZ  PHE A  38 " =    2.356
peak=   -3.251 closest distance to " O   HOH Z 102 " =    1.677
peak=   -3.247 closest distance to " O   ASP A  27 " =    2.100
peak=   -3.245 closest distance to " CD  GLN A 223 " =    0.777
peak=   -3.243 closest distance to " O   HOH Z 427 " =    1.427
peak=   -3.240 closest distance to " ND2 ASN A  60 " =    1.267
peak=   -3.238 closest distance to " CB  ALA A 291 " =    1.982
peak=   -3.237 closest distance to " CG  ASP A 132 " =    2.246
peak=   -3.231 closest distance to " CA  GLY A  23 " =    1.783
peak=   -3.228 closest distance to " O   HOH Z 183 " =    1.516
peak=   -3.227 closest distance to " CG  TRP A 266 " =    1.987
peak=   -3.227 closest distance to " CB  ALA A 161 " =    2.345
peak=   -3.227 closest distance to " O   HOH Z 140 " =    1.119
peak=   -3.225 closest distance to " O   SER A 276 " =    1.748
peak=   -3.225 closest distance to " CG2 ILE A 263 " =    2.267
peak=   -3.225 closest distance to " C   ASN A 285 " =    2.118
peak=   -3.222 closest distance to " O   HOH Z 265 " =    2.462
peak=   -3.222 closest distance to " NE  ARG A  66 " =    4.317
peak=   -3.220 closest distance to " CA  LYS A 166 " =    2.086
peak=   -3.220 closest distance to " OD2 ASP A 140 " =    0.948
peak=   -3.214 closest distance to " O   HOH Z 252 " =    3.641
peak=   -3.211 closest distance to " O   HOH Z 269 " =    1.102
peak=   -3.208 closest distance to " NH2 ARG A  66 " =    5.858
peak=   -3.207 closest distance to " O   HOH Z  59 " =    3.899
peak=   -3.207 closest distance to " N   ALA A 248 " =    1.567
peak=   -3.199 closest distance to " O   HOH Z 137 " =    1.644
peak=   -3.189 closest distance to " O   HOH Z 275 " =    1.838
peak=   -3.186 closest distance to " O   HOH Z 198 " =    0.800
peak=   -3.185 closest distance to " O   HOH Z 313 " =    1.896
peak=   -3.185 closest distance to " OE1 GLN A 183 " =    1.464
peak=   -3.182 closest distance to " CG1 VAL A 296 " =    1.091
peak=   -3.177 closest distance to " CG  GLN A 103 " =    2.532
peak=   -3.174 closest distance to " O   TRP A  70 " =    1.646
peak=   -3.174 closest distance to " O   GLY A  80 " =    2.595
peak=   -3.172 closest distance to " O   HOH Z 329 " =    1.040
peak=   -3.169 closest distance to " O   HOH Z 179 " =    2.162
peak=   -3.169 closest distance to " C   GLN A  58 " =    2.170
peak=   -3.157 closest distance to " N   ALA A 226 " =    1.931
peak=   -3.155 closest distance to " CA  VAL A 296 " =    0.998
peak=   -3.152 closest distance to " O   HOH Z 281 " =    2.893
peak=   -3.152 closest distance to " N   HIS A 115 " =    2.186
peak=   -3.149 closest distance to " O   SER A 210 " =    1.842
peak=   -3.149 closest distance to " CG2 VAL A 202 " =    2.695
peak=   -3.146 closest distance to " O   HOH Z 353 " =    1.222
peak=   -3.145 closest distance to " O   HOH Z 374 " =    1.781
peak=   -3.141 closest distance to " CG1 VAL A 125 " =    1.913
peak=   -3.136 closest distance to " O   HOH Z 232 " =    1.594
peak=   -3.126 closest distance to " OD2 ASP A  50 " =    1.397
peak=   -3.117 closest distance to " CE2 PHE A  61 " =    2.721
peak=   -3.116 closest distance to " O   HOH Z 392 " =    1.917
peak=   -3.109 closest distance to " O   ASN A 252 " =    1.347
peak=   -3.105 closest distance to " O   HOH Z 236 " =    1.658
peak=   -3.105 closest distance to " CG2 THR A 178 " =    2.426
peak=   -3.103 closest distance to " O   HOH Z 301 " =    2.536
peak=   -3.102 closest distance to " O   HOH Z 110 " =    1.550
peak=   -3.101 closest distance to " CD1 ILE A 239 " =    2.296
peak=   -3.093 closest distance to " CH2 TRP A 150 " =    1.127
peak=   -3.092 closest distance to " O   HOH Z 255 " =    0.931
peak=   -3.088 closest distance to " O   HOH Z  60 " =    1.412
peak=   -3.085 closest distance to " O   ALA A   1 " =    1.635
peak=   -3.082 closest distance to " OE2 GLU A 152 " =    1.492
peak=   -3.076 closest distance to " ND2 ASN A  39 " =    1.116
peak=   -3.073 closest distance to " CB  ALA A   9 " =    2.365
peak=   -3.059 closest distance to " CG1BVAL A  72 " =    2.596
peak=   -3.056 closest distance to " O   HOH Z  11 " =    1.879
peak=   -3.040 closest distance to " CB  HIS A  86 " =    1.196
peak=   -3.005 closest distance to " NH2 ARG A  79 " =    1.955
peak=   -3.001 closest distance to " CB  ASP A 132 " =    2.228

================= 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    :  0.4932 0.4858   6.292646e+00   6.288344e+00
   1_bss:  0.4844 0.4790   6.285376e+00   6.283497e+00
   1_xyz:  0.4087 0.4309   6.190853e+00   6.231570e+00
   1_adp:  0.3653 0.4212   6.123493e+00   6.209982e+00
   1_occ:  0.3650 0.4213   6.122703e+00   6.210715e+00
   2_bss:  0.3609 0.4181   6.123257e+00   6.210980e+00
   2_xyz:  0.2721 0.3267   5.887743e+00   6.038969e+00
   2_adp:  0.2459 0.3023   5.810859e+00   5.977095e+00
   2_occ:  0.2457 0.3025   5.810518e+00   5.976804e+00
   3_bss:  0.2428 0.3005   5.808951e+00   5.974875e+00
   3_xyz:  0.1780 0.2277   5.537643e+00   5.736345e+00
   3_adp:  0.1582 0.2112   5.440990e+00   5.662285e+00
   3_occ:  0.1580 0.2113   5.440722e+00   5.662638e+00
   4_bss:  0.1567 0.2102   5.437529e+00   5.658685e+00
   4_xyz:  0.1324 0.1804   5.290845e+00   5.517125e+00
   4_adp:  0.1279 0.1730   5.257678e+00   5.479626e+00
   4_occ:  0.1277 0.1730   5.257401e+00   5.479915e+00
   5_bss:  0.1279 0.1736   5.259159e+00   5.481293e+00
   5_xyz:  0.1190 0.1661   5.207047e+00   5.441673e+00
   5_adp:  0.1186 0.1642   5.200523e+00   5.427611e+00
   5_occ:  0.1185 0.1641   5.199902e+00   5.427090e+00
   5_bss:  0.1185 0.1641   5.199709e+00   5.427001e+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:  0.323   3.247   8.294   8.003  11.205   0.000   0.000   0.000
   1_xyz:  0.323   3.247   8.294   8.003  11.205   0.000   0.000   0.000
   1_adp:  0.323   3.247   8.294   8.003  11.205   0.000   0.000   0.000
   1_occ:  0.323   3.247   8.294   8.003  11.205   0.000   0.000   0.000
   2_bss:  0.336  38.429   4.118   3.984   7.013   0.000   0.000   0.000
   2_xyz:  0.336  38.429   4.118   3.984   7.013   0.000   0.000   0.000
   2_adp:  0.336  38.429   4.118   3.984   7.013   0.000   0.000   0.000
   2_occ:  0.336  38.429   4.118   3.984   7.013   0.000   0.000   0.000
   3_bss:  0.318  38.429   1.582   2.418   4.204   0.000   0.000   0.000
   3_xyz:  0.318  38.429   1.582   2.418   4.204   0.000   0.000   0.000
   3_adp:  0.318  38.429   1.582   2.418   4.204   0.000   0.000   0.000
   3_occ:  0.318  38.429   1.582   2.418   4.204   0.000   0.000   0.000
   4_bss:  0.322  49.625   0.193   1.296   2.856   0.000   0.000   0.000
   4_xyz:  0.322  49.625   0.193   1.296   2.856   0.000   0.000   0.000
   4_adp:  0.322  49.625   0.193   1.296   2.856   0.000   0.000   0.000
   4_occ:  0.322  49.625   0.193   1.296   2.856   0.000   0.000   0.000
   5_bss:  0.323  49.625   0.193   1.296   2.856   0.000   0.000   0.000
   5_xyz:  0.323  49.625   0.193   1.296   2.856   0.000   0.000   0.000
   5_adp:  0.323  49.625   0.193   1.296   2.856   0.000   0.000   0.000
   5_occ:  0.323  49.625   0.193   1.296   2.856   0.000   0.000   0.000
   5_bss:  0.323  50.814  -1.258  -0.141   1.398   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  60.281 0.3901  0.4633    76197.984
   1_bss:  60.734 0.3827  0.5961    75197.178
   1_xyz:  50.934 0.5075  0.7706    56830.846
   1_adp:  47.703 0.5484  0.8927    52684.844
   1_occ:  47.731 0.5480  0.8901    52727.579
   2_bss:  47.358 0.5528  0.7827    52504.468
   2_xyz:  34.505 0.7063  0.9645    29162.116
   2_adp:  31.262 0.7437  1.0101    24801.110
   2_occ:  31.242 0.7439  1.0106    24800.021
   3_bss:  31.001 0.7466  0.9320    24540.853
   3_xyz:  22.469 0.8371  1.0028    13472.511
   3_adp:  20.345 0.8586  1.0145    11630.117
   3_occ:  20.352 0.8585  1.0143    11639.632
   4_bss:  20.214 0.8597  0.9700    11506.006
   4_xyz:  17.000 0.8893  0.9803     8459.656
   4_adp:  16.163 0.8970  0.9775     7905.172
   4_occ:  16.167 0.8970  0.9773     7902.254
   5_bss:  16.196 0.8968  0.9773     7954.826
   5_xyz:  15.297 0.9044  0.9833     7278.317
   5_adp:  14.994 0.9071  0.9822     7136.040
   5_occ:  14.986 0.9072  0.9821     7125.510
   5_bss:  14.979 0.9073  0.9733     7122.458
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.088   5.3552e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.088   5.3552e+01
   1_xyz:   1.761  0.014  0.109 18.367  0.007  4.106   1.5258e-01
   1_adp:   1.761  0.014  0.109 18.367  0.007  4.106   1.5258e-01
   1_occ:   1.761  0.014  0.109 18.367  0.007  4.106   1.5258e-01
   2_bss:   1.761  0.014  0.109 18.367  0.007  4.106   1.5258e-01
   2_xyz:   1.300  0.010  0.085 16.661  0.006  4.107   9.9182e-02
   2_adp:   1.300  0.010  0.085 16.661  0.006  4.107   9.9182e-02
   2_occ:   1.300  0.010  0.085 16.661  0.006  4.107   9.9182e-02
   3_bss:   1.300  0.010  0.085 16.661  0.006  4.107   9.9182e-02
   3_xyz:   1.163  0.008  0.082 15.847  0.004  4.115   7.6867e-02
   3_adp:   1.163  0.008  0.082 15.847  0.004  4.115   7.6867e-02
   3_occ:   1.163  0.008  0.082 15.847  0.004  4.115   7.6867e-02
   4_bss:   1.163  0.008  0.082 15.847  0.004  4.115   7.6867e-02
   4_xyz:   1.075  0.008  0.079 15.616  0.004  4.110   6.7904e-02
   4_adp:   1.075  0.008  0.079 15.616  0.004  4.110   6.7904e-02
   4_occ:   1.075  0.008  0.079 15.616  0.004  4.110   6.7904e-02
   5_bss:   1.075  0.008  0.079 15.616  0.004  4.110   6.7904e-02
   5_xyz:   1.106  0.008  0.085 15.473  0.004  4.115   7.1305e-02
   5_adp:   1.106  0.008  0.085 15.473  0.004  4.115   7.1305e-02
   5_occ:   1.106  0.008  0.085 15.473  0.004  4.115   7.1305e-02
   5_bss:   1.106  0.008  0.085 15.473  0.004  4.115   7.1305e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  0.936   6.9321e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  0.936   6.9321e+00
   1_xyz:  15.544  0.168  0.490 85.985  0.045  2.049   1.0517e-01
   1_adp:  15.544  0.168  0.490 85.985  0.045  2.049   1.0517e-01
   1_occ:  15.544  0.168  0.490 85.985  0.045  2.049   1.0517e-01
   2_bss:  15.544  0.168  0.490 85.985  0.045  2.049   1.0517e-01
   2_xyz:   7.774  0.139  0.306 88.469  0.065  2.223   8.3066e-02
   2_adp:   7.774  0.139  0.306 88.469  0.065  2.223   8.3066e-02
   2_occ:   7.774  0.139  0.306 88.469  0.065  2.223   8.3066e-02
   3_bss:   7.774  0.139  0.306 88.469  0.065  2.223   8.3066e-02
   3_xyz:   7.812  0.051  0.306 88.183  0.034  2.219   5.7691e-02
   3_adp:   7.812  0.051  0.306 88.183  0.034  2.219   5.7691e-02
   3_occ:   7.812  0.051  0.306 88.183  0.034  2.219   5.7691e-02
   4_bss:   7.812  0.051  0.306 88.183  0.034  2.219   5.7691e-02
   4_xyz:   7.199  0.046  0.383 82.538  0.043  2.312   4.7798e-02
   4_adp:   7.199  0.046  0.383 82.538  0.043  2.312   4.7798e-02
   4_occ:   7.199  0.046  0.383 82.538  0.043  2.312   4.7798e-02
   5_bss:   7.199  0.046  0.383 82.538  0.043  2.312   4.7798e-02
   5_xyz:   7.290  0.052  0.461 83.055  0.036  2.200   4.7118e-02
   5_adp:   7.290  0.052  0.461 83.055  0.036  2.200   4.7118e-02
   5_occ:   7.290  0.052  0.461 83.055  0.036  2.200   4.7118e-02
   5_bss:   7.290  0.052  0.461 83.055  0.036  2.200   4.7118e-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:  92.53   0.00  14.72  89.38   0.00  12.37  92.53   0.00  27.50
   1_occ:  92.53   0.00  14.72  89.38   0.00  12.37  92.53   0.00  27.50
   2_bss:  92.53   0.00  14.72  89.38   0.00  12.37  92.53   0.00  27.50
   2_xyz:  92.53   0.00  14.72  89.38   0.00  12.37  92.53   0.00  27.50
   2_adp: 109.48   0.00  14.51 109.48   0.00  10.99  92.43   0.00  33.71
   2_occ: 109.48   0.00  14.51 109.48   0.00  10.99  92.43   0.00  33.71
   3_bss: 109.48   0.00  14.51 109.48   0.00  10.99  92.43   0.00  33.71
   3_xyz: 109.48   0.00  14.51 109.48   0.00  10.99  92.43   0.00  33.71
   3_adp:  85.33   0.00  14.77  84.16   0.00  10.24  85.33   2.13  39.45
   3_occ:  85.33   0.00  14.77  84.16   0.00  10.24  85.33   2.13  39.45
   4_bss:  85.33   0.00  14.77  84.16   0.00  10.24  85.33   2.13  39.45
   4_xyz:  85.33   0.00  14.77  84.16   0.00  10.24  85.33   2.13  39.45
   4_adp:  86.86   0.00  14.35  86.86   0.00   9.86  83.73   3.05  38.74
   4_occ:  86.86   0.00  14.35  86.86   0.00   9.86  83.73   3.05  38.74
   5_bss:  86.86   0.00  14.35  86.86   0.00   9.86  83.73   3.05  38.74
   5_xyz:  86.86   0.00  14.35  86.86   0.00   9.86  83.73   3.05  38.74
   5_adp:  85.16   0.65  13.78  85.16   0.65   9.67  80.23   3.25  36.12
   5_occ:  85.16   0.65  13.78  85.16   0.65   9.67  80.23   3.25  36.12
   5_bss:  86.35   1.84  14.97  86.35   1.84  10.86  81.42   4.44  37.31
------------------------------------------------------------------------
 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:    1.314    0.031    0.417
   1_adp:    1.314    0.031    0.417
   1_occ:    1.314    0.031    0.417
   2_bss:    1.314    0.031    0.417
   2_xyz:    1.900    0.029    0.604
   2_adp:    1.900    0.029    0.604
   2_occ:    1.900    0.029    0.604
   3_bss:    1.900    0.029    0.604
   3_xyz:    1.874    0.047    0.702
   3_adp:    1.874    0.047    0.702
   3_occ:    1.874    0.047    0.702
   4_bss:    1.874    0.047    0.702
   4_xyz:    1.922    0.055    0.744
   4_adp:    1.922    0.055    0.744
   4_occ:    1.922    0.055    0.744
   5_bss:    1.922    0.055    0.744
   5_xyz:    1.952    0.076    0.764
   5_adp:    1.952    0.076    0.764
   5_occ:    1.952    0.076    0.764
   5_bss:    1.952    0.076    0.764
------------------------------------------------------------------------

CPU time actual refinement: 354.89


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_75/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_75/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_75/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_75/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_75/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 354.73 
  Macro-tasks:
    bulk solvent and scale       = 40.08  
    individual site refinement   = 149.95 
    weights calculation          = 32.09  
    collect and process          = 6.40   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 228.63 
  Micro-tasks:
    mask                            = 2.74   
    f_calc                          = 113.93 
    alpha_beta                      = 8.36   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 123.06 
    fmodel                         = 6.92   
    r_factors                      = 0.29   
    phase_errors                   = 10.13  
    foms                           = 0.22   
    TOTAL for micro-tasks          = 266.84 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.927 micro seconds
Total CPU time: 6.14 minutes
from_scatterers_fft:    666 calls, 113.60 s
gradients_fft:          610 calls, 109.19 s

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

# Date 2008-01-16 Time 00:39:47 PST -0800 (1200472787.19 s)
Start R-work = 0.4932, R-free = 0.4858 (no bulk solvent and anisotropic scale)
Final R-work = 0.1370, R-free = 0.1795 (no bulk solvent and anisotropic scale)

Start R-work = 0.4844, R-free = 0.4790
Final R-work = 0.1185, R-free = 0.1641