# Date 2008-01-16 Time 00:33:31 PST -0800 (1200472411.53 s)
#phil __OFF__

Command line arguments: "../64.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 12796
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 64

-------------------------------------------------------------------------------
  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, 46.93, 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: 3.36, per 1000 atoms: 1.19


================================== 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, 46.93, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8637 1.95095
Completeness in resolution range: 0.921705
Completeness with d_max=infinity: 0.918938

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8637
                             d_min =   1.9509

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, 46.93, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8637 1.95095
Completeness in resolution range: 0.921705
Completeness with d_max=infinity: 0.918938

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8641 -  4.1751 [2231/2259]  2004   227  10.2%
  bin  2:  4.1751 -  3.3261 [2140/2163]  1926   214  10.0%
  bin  3:  3.3261 -  2.9092 [2122/2144]  1916   206   9.7%
  bin  4:  2.9092 -  2.6449 [2098/2117]  1881   217  10.3%
  bin  5:  2.6449 -  2.4562 [2070/2099]  1857   213  10.3%
  bin  6:  2.4562 -  2.3119 [2081/2123]  1882   199   9.6%
  bin  7:  2.3119 -  2.1965 [2055/2091]  1851   204   9.9%
  bin  8:  2.1965 -  2.1012 [2071/2112]  1864   207  10.0%
  bin  9:  2.1012 -  2.0205 [1975/2057]  1785   190   9.6%
  bin 10:  2.0205 -  1.9509 [ 746/2088]   664    82  11.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_64/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:
        1.03 -     1.80: 12
        1.80 -     2.58: 73
        2.58 -     3.35: 4058
        3.35 -     4.13: 9483
        4.13 -     4.90: 14907
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.031 3.040 -x+1,y+1/2,-z+1/2
  " NH1 ARG A  24 " - " O   GLY A  91 "  1.140 3.120 -x+1,y+1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 176 "  1.314 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.324 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  57 " - " O   HOH Z 104 "  1.444 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28528 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_64/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_64/model_refine_001.geo

CPU time processing inputs: 9.51


============================ 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 46.93 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 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4888   r_free= 0.4835   ksol= 0.00   Bsol= 0.00   scale= 0.789    |
|                                                                             |
| 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:   0.78 A                  |
| x-ray target function (ml) for work reflections: 6.289382                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8641 -  4.6569 0.99   1447  159 0.3937 0.3823      6.6035      6.6134|
|  2:  4.6569 -  3.7153 0.99   1403  156 0.3950 0.4475      6.7583      6.8697|
|  3:  3.7153 -  3.2513 0.99   1366  156 0.4654 0.4287      6.6878      6.6756|
|  4:  3.2513 -  2.9566 0.99   1358  144 0.4908 0.4879      6.5195      6.4998|
|  5:  2.9566 -  2.7461 0.98   1347  151 0.5082 0.5158      6.3572       6.419|
|  6:  2.7461 -  2.5850 0.98   1344  153 0.5243 0.5336      6.2931       6.201|
|  7:  2.5850 -  2.4562 0.99   1319  158 0.5218 0.5046       6.231      6.1667|
|  8:  2.4562 -  2.3497 0.99   1354  139 0.5315 0.5038      6.1707      6.1384|
|  9:  2.3497 -  2.2596 0.98   1336  141 0.5481 0.5036      6.1333      6.1877|
| 10:  2.2596 -  2.1818 0.98   1310  150 0.5410 0.5421      6.0981      6.1053|
| 11:  2.1818 -  2.1138 0.98   1316  155 0.5300 0.5015       6.004      6.0045|
| 12:  2.1138 -  2.0536 0.99   1333  142 0.5425 0.5309      5.9561      5.9386|
| 13:  2.0536 -  1.9996 0.82   1106  116 0.5475 0.5154      5.8932      5.8459|
| 14:  1.9996 -  1.9509 0.22    291   39 0.5313 0.5719      5.9087      5.7685|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8641 -  4.6569  1447   159  0.69  35.33   0.79     0.71      74875.04|
|  2:  4.6569 -  3.7153  1403   156  0.67  37.72   0.89     0.74     117175.43|
|  3:  3.7153 -  3.2513  1366   156  0.56  46.75   0.82     0.68     123978.37|
|  4:  3.2513 -  2.9566  1358   144  0.44  56.45   0.78     0.55     113340.38|
|  5:  2.9566 -  2.7461  1347   151  0.34  64.54   0.73     0.41      92206.11|
|  6:  2.7461 -  2.5850  1344   153  0.27  69.83   0.72     0.33      84080.86|
|  7:  2.5850 -  2.4562  1319   158  0.29  68.05   0.73     0.34      72085.57|
|  8:  2.4562 -  2.3497  1354   139  0.34  64.63   0.72     0.41      60474.62|
|  9:  2.3497 -  2.2596  1336   141  0.38  61.28   0.71     0.48      53132.54|
| 10:  2.2596 -  2.1818  1310   150  0.38  61.85   0.75     0.45      45932.02|
| 11:  2.1818 -  2.1138  1316   155  0.31  67.17   0.73     0.40      48992.25|
| 12:  2.1138 -  2.0536  1333   142  0.26  70.83   0.75     0.34      45899.95|
| 13:  2.0536 -  1.9996  1106   116  0.26  70.79   0.72     0.35      40916.83|
| 14:  1.9996 -  1.9509   291    39  0.36  62.66   0.77     0.39      29102.05|
|alpha:            min =        0.33 max =            0.74 mean =         0.48|
|beta:             min =    29102.05 max =       123978.37 mean =     74913.16|
|figures of merit: min =        0.00 max =            1.00 mean =         0.40|
|phase err.(work): min =        0.00 max =           90.00 mean =        59.26|
|phase err.(test): min =        0.00 max =           89.95 mean =        59.78|
|-----------------------------------------------------------------------------|

============================== 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 = 15.539013             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.401   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.368929              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.026   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.040 -  1.426:        8 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.426 -  1.812:       17 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.812 -  2.198:      115 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.198 -  2.584:      555 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.584 -  2.970:     1361 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.970 -  3.356:     2479 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.356 -  3.742:     3988 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.742 -  4.128:     5174 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.128 -  4.514:     6810 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.514 -  4.900:     8054 |
|-----------------------------------------------------------------------------|
|-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 |       53.456 |
| 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  1.040 |       3.096 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.673)------------------------------------------|
|    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 = 11.673)------------------------------------------|
|    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 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4948   r_free= 0.4869   ksol= 0.00   Bsol= 0.00   scale= 0.759    |
|                                                                             |
| 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:   0.79 A                  |
| x-ray target function (ml) for work reflections: 6.290335                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4800   r_free= 0.4774   ksol= 0.33   Bsol= 6.44   scale= 1.001    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.36,7.54,11.16,0.00,0.00,0.00); trace/3= 9.02                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.77 A                  |
| x-ray target function (ml) for work reflections: 6.281991                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.932111             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.871   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.425167              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.021   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4800      final r-factor (work) = 0.4044          |
| start r-factor (free) = 0.4774      final r-factor (free) = 0.4228          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 97.2525 = 13.93 * 0.50 * 6.2871 + 1.00 * 53.4564                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 43.4366 = 13.93 * 0.50 * 6.2144 + 1.00 * 0.1469                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4044      final r-factor (work) = 0.3596          |
| start r-factor (free) = 0.4228      final r-factor (free) = 0.4100          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.8709 = 1.43 * 1.00 * 6.2144 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.7531 = 1.43 * 1.00 * 6.1289 + 1.00 * 0.0185                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.673)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    72.02   14.12    None  None   None       |
|    all(noH): 2823   0      0.00    72.02   14.12    None  None   None       |
|    Sol.    : 438    0      0.00    72.02   26.20    None  None   None       |
|    Mac.    : 2385   0      0.00    65.26   11.90    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.203: 1007   |   5:    36.012 -  43.215:  101        |
|      1:     7.203 -  14.405:  700   |   6:    43.215 -  50.417:   53        |
|      2:    14.405 -  21.607:  478   |   7:    50.417 -  57.620:   22        |
|      3:    21.607 -  28.810:  286   |   8:    57.620 -  64.822:   10        |
|      4:    28.810 -  36.012:  162   |   9:    64.822 -  72.024:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3596 r_free = 0.4100             target_work(ml) = 6.109         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3596 r_free = 0.4103             target_work(ml) = 6.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3596   r_free= 0.4103   ksol= 0.33   Bsol= 6.44   scale= 1.122    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.36,7.54,11.16,0.00,0.00,0.00); trace/3= 9.02                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.108313                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3550   r_free= 0.4061   ksol= 0.32   Bsol= 36.38   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.12,3.47,6.90,0.00,0.00,0.00); trace/3= 4.83                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.109856                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.784866              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.979   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.532817              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 124.604  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3550      final r-factor (work) = 0.2786          |
| start r-factor (free) = 0.4061      final r-factor (free) = 0.3330          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.8632 = 5.78 * 0.50 * 6.1250 + 1.00 * 0.1469                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.4688 = 5.78 * 0.50 * 6.0112 + 1.00 * 0.0817                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2786      final r-factor (work) = 0.2567          |
| start r-factor (free) = 0.3330      final r-factor (free) = 0.3145          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2213 = 0.53 * 1.00 * 6.0112 + 1.00 * 0.0184                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1438 = 0.53 * 1.00 * 5.8775 + 1.00 * 0.0122                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.673)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    74.56   14.09    None  None   None       |
|    all(noH): 2823   0      0.00    74.56   14.09    None  None   None       |
|    Sol.    : 438    0      0.00    71.84   32.57    None  None   None       |
|    Mac.    : 2385   0      0.00    74.56   10.70    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.456: 1130   |   5:    37.281 -  44.737:   91        |
|      1:     7.456 -  14.912:  750   |   6:    44.737 -  52.193:   64        |
|      2:    14.912 -  22.369:  387   |   7:    52.193 -  59.650:   27        |
|      3:    22.369 -  29.825:  196   |   8:    59.650 -  67.106:   22        |
|      4:    29.825 -  37.281:  150   |   9:    67.106 -  74.562:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2567 r_free = 0.3145             target_work(ml) = 5.853         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2566 r_free = 0.3147             target_work(ml) = 5.852         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2566   r_free= 0.3147   ksol= 0.32   Bsol= 36.38   scale= 1.062   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.12,3.47,6.90,0.00,0.00,0.00); trace/3= 4.83                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.852302                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2544   r_free= 0.3127   ksol= 0.33   Bsol= 49.21   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.78,2.23,4.41,0.00,0.00,0.00); trace/3= 2.81                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.850998                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.639179              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.073   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.324687              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.900  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2544      final r-factor (work) = 0.1831          |
| start r-factor (free) = 0.3127      final r-factor (free) = 0.2355          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.6616 = 5.64 * 0.50 * 5.8802 + 1.00 * 0.0817                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.2060 = 5.64 * 0.50 * 5.7207 + 1.00 * 0.0759                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1831      final r-factor (work) = 0.1667          |
| start r-factor (free) = 0.2355      final r-factor (free) = 0.2193          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8697 = 0.32 * 1.00 * 5.7207 + 1.00 * 0.0123                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8054 = 0.32 * 1.00 * 5.5166 + 1.00 * 0.0142                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.673)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    73.08   14.02    None  None   None       |
|    all(noH): 2823   0      0.00    73.08   14.02    None  None   None       |
|    Sol.    : 438    0      1.22    73.08   36.29    None  None   None       |
|    Mac.    : 2385   0      0.00    72.21   9.93     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.308: 1133   |   5:    36.542 -  43.850:  111        |
|      1:     7.308 -  14.617:  885   |   6:    43.850 -  51.158:   91        |
|      2:    14.617 -  21.925:  287   |   7:    51.158 -  58.467:   46        |
|      3:    21.925 -  29.233:  126   |   8:    58.467 -  65.775:   17        |
|      4:    29.233 -  36.542:  113   |   9:    65.775 -  73.083:   14        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1667 r_free = 0.2193             target_work(ml) = 5.481         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1663 r_free = 0.2188             target_work(ml) = 5.480         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1663   r_free= 0.2188   ksol= 0.33   Bsol= 49.21   scale= 1.036   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.78,2.23,4.41,0.00,0.00,0.00); trace/3= 2.81                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.479768                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1653   r_free= 0.2184   ksol= 0.32   Bsol= 45.53   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.29,1.18,3.01,0.00,0.00,0.00); trace/3= 1.49                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.479484                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.243355              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.525  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.435990              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 96.576   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1653      final r-factor (work) = 0.1354          |
| start r-factor (free) = 0.2184      final r-factor (free) = 0.1813          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.0383 = 3.24 * 0.50 * 5.5266 + 1.00 * 0.0759                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.8268 = 3.24 * 0.50 * 5.4016 + 1.00 * 0.0671                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1354      final r-factor (work) = 0.1286          |
| start r-factor (free) = 0.1813      final r-factor (free) = 0.1750          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3808 = 0.44 * 1.00 * 5.4016 + 1.00 * 0.0258                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3444 = 0.44 * 1.00 * 5.2805 + 1.00 * 0.0421                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.673)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.46   14.13    None  None   None       |
|    all(noH): 2823   0      0.00    80.46   14.13    None  None   None       |
|    Sol.    : 438    0      2.94    76.21   38.03    None  None   None       |
|    Mac.    : 2385   0      0.00    80.46   9.74     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 -   8.046: 1310   |   5:    40.230 -  48.276:  105        |
|      1:     8.046 -  16.092:  838   |   6:    48.276 -  56.322:   81        |
|      2:    16.092 -  24.138:  203   |   7:    56.322 -  64.368:   37        |
|      3:    24.138 -  32.184:  114   |   8:    64.368 -  72.414:   23        |
|      4:    32.184 -  40.230:  105   |   9:    72.414 -  80.461:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1286 r_free = 0.1750             target_work(ml) = 5.264         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1282 r_free = 0.1752             target_work(ml) = 5.263         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1282   r_free= 0.1752   ksol= 0.32   Bsol= 45.53   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.29,1.18,3.01,0.00,0.00,0.00); trace/3= 1.49                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.263345                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1284   r_free= 0.1754   ksol= 0.32   Bsol= 49.42   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.09,1.08,2.76,0.00,0.00,0.00); trace/3= 1.31                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.264166                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.489770              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 125.628  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.633675              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.004   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1284      final r-factor (work) = 0.1199          |
| start r-factor (free) = 0.1754      final r-factor (free) = 0.1666          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6403 = 2.49 * 0.50 * 5.2801 + 1.00 * 0.0671                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5840 = 2.49 * 0.50 * 5.2367 + 1.00 * 0.0650                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1199      final r-factor (work) = 0.1181          |
| start r-factor (free) = 0.1666      final r-factor (free) = 0.1652          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3310 = 0.63 * 1.00 * 5.2367 + 1.00 * 0.0127                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3092 = 0.63 * 1.00 * 5.2040 + 1.00 * 0.0116                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.673)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.89   14.03    None  None   None       |
|    all(noH): 2823   0      0.00    82.89   14.03    None  None   None       |
|    Sol.    : 438    0      2.91    80.14   37.96    None  None   None       |
|    Mac.    : 2385   0      0.00    82.89   9.64     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 -   8.290: 1383   |   5:    41.447 -  49.737:  100        |
|      1:     8.290 -  16.579:  798   |   6:    49.737 -  58.026:   75        |
|      2:    16.579 -  24.868:  194   |   7:    58.026 -  66.316:   34        |
|      3:    24.868 -  33.158:  104   |   8:    66.316 -  74.605:   14        |
|      4:    33.158 -  41.447:  111   |   9:    74.605 -  82.894:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1181 r_free = 0.1652             target_work(ml) = 5.200         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1180 r_free = 0.1651             target_work(ml) = 5.199         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1180   r_free= 0.1651   ksol= 0.32   Bsol= 49.42   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.09,1.08,2.76,0.00,0.00,0.00); trace/3= 1.31                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.199365                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8641 -  4.6569 0.99   1447  159 0.1025 0.1372      5.4362      5.6173|
|  2:  4.6569 -  3.7153 0.99   1403  156 0.0873 0.1150      5.4669      5.6803|
|  3:  3.7153 -  3.2513 0.99   1366  156 0.1122 0.1535      5.5195      5.8216|
|  4:  3.2513 -  2.9566 0.99   1358  144 0.1299 0.1725      5.4778      5.6758|
|  5:  2.9566 -  2.7461 0.98   1347  151 0.1404 0.1584       5.381      5.5224|
|  6:  2.7461 -  2.5850 0.98   1344  153 0.1313 0.2234      5.2597      5.5759|
|  7:  2.5850 -  2.4562 0.99   1319  158 0.1324 0.1719      5.2115      5.3702|
|  8:  2.4562 -  2.3497 0.99   1354  139 0.1230 0.1823      5.1102      5.3349|
|  9:  2.3497 -  2.2596 0.98   1336  141 0.1235 0.1909      5.0605      5.3719|
| 10:  2.2596 -  2.1818 0.98   1310  150 0.1192 0.1721      4.9879      5.1899|
| 11:  2.1818 -  2.1138 0.98   1316  155 0.1234 0.1929      4.9575      5.3192|
| 12:  2.1138 -  2.0536 0.99   1333  142 0.1204 0.1702      4.9196      5.1622|
| 13:  2.0536 -  1.9996 0.82   1106  116 0.1134 0.1759      4.7908      4.9643|
| 14:  1.9996 -  1.9509 0.22    291   39 0.1013 0.1655      4.6866      4.9495|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8641 -  4.6569  1447   159  0.93  10.06   0.97     0.95       8471.99|
|  2:  4.6569 -  3.7153  1403   156  0.95   8.73   1.02     1.00       9948.80|
|  3:  3.7153 -  3.2513  1366   156  0.93  12.15   1.03     1.03      11371.74|
|  4:  3.2513 -  2.9566  1358   144  0.91  14.68   1.02     1.01      10887.60|
|  5:  2.9566 -  2.7461  1347   151  0.89  17.29   1.00     0.97       9699.13|
|  6:  2.7461 -  2.5850  1344   153  0.89  17.41   0.97     0.93       7627.33|
|  7:  2.5850 -  2.4562  1319   158  0.89  16.81   0.98     0.94       6875.28|
|  8:  2.4562 -  2.3497  1354   139  0.90  16.39   1.00     0.97       5908.12|
|  9:  2.3497 -  2.2596  1336   141  0.89  16.95   1.00     0.96       5425.81|
| 10:  2.2596 -  2.1818  1310   150  0.89  16.64   1.00     0.96       4764.04|
| 11:  2.1818 -  2.1138  1316   155  0.89  17.68   0.99     0.95       4695.54|
| 12:  2.1138 -  2.0536  1333   142  0.89  17.38   1.00     1.01       4399.33|
| 13:  2.0536 -  1.9996  1106   116  0.90  16.62   0.98     0.95       3421.59|
| 14:  1.9996 -  1.9509   291    39  0.92  13.10   0.98     0.95       2530.43|
|alpha:            min =        0.93 max =            1.03 mean =         0.97|
|beta:             min =     2530.43 max =        11371.74 mean =      7202.17|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.96 mean =        15.17|
|phase err.(test): min =        0.00 max =           89.96 mean =        14.70|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1180   r_free= 0.1651   ksol= 0.32   Bsol= 50.85   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.22,-0.22,1.45,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.199450                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1180   r_free= 0.1651   ksol= 0.32   Bsol= 50.85   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.22,-0.22,1.45,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.199450                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8641 -  4.6569 0.99   1447  159 0.1026 0.1373      5.4367      5.6182|
|  2:  4.6569 -  3.7153 0.99   1403  156 0.0873 0.1150      5.4672      5.6801|
|  3:  3.7153 -  3.2513 0.99   1366  156 0.1122 0.1535      5.5194      5.8216|
|  4:  3.2513 -  2.9566 0.99   1358  144 0.1299 0.1725      5.4778      5.6757|
|  5:  2.9566 -  2.7461 0.98   1347  151 0.1404 0.1584       5.381      5.5223|
|  6:  2.7461 -  2.5850 0.98   1344  153 0.1313 0.2234      5.2598       5.576|
|  7:  2.5850 -  2.4562 0.99   1319  158 0.1324 0.1719      5.2116      5.3703|
|  8:  2.4562 -  2.3497 0.99   1354  139 0.1230 0.1823      5.1103       5.335|
|  9:  2.3497 -  2.2596 0.98   1336  141 0.1235 0.1909      5.0607      5.3719|
| 10:  2.2596 -  2.1818 0.98   1310  150 0.1192 0.1721       4.988      5.1899|
| 11:  2.1818 -  2.1138 0.98   1316  155 0.1234 0.1929      4.9576      5.3193|
| 12:  2.1138 -  2.0536 0.99   1333  142 0.1204 0.1702      4.9195       5.162|
| 13:  2.0536 -  1.9996 0.82   1106  116 0.1134 0.1759      4.7908      4.9643|
| 14:  1.9996 -  1.9509 0.22    291   39 0.1013 0.1655      4.6867      4.9496|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8641 -  4.6569  1447   159  0.93  10.07   0.97     0.95       8482.03|
|  2:  4.6569 -  3.7153  1403   156  0.95   8.73   1.02     1.01       9954.36|
|  3:  3.7153 -  3.2513  1366   156  0.93  12.15   1.03     1.03      11372.64|
|  4:  3.2513 -  2.9566  1358   144  0.91  14.68   1.02     1.01      10888.52|
|  5:  2.9566 -  2.7461  1347   151  0.89  17.30   1.00     0.98       9699.86|
|  6:  2.7461 -  2.5850  1344   153  0.89  17.41   0.98     0.94       7626.74|
|  7:  2.5850 -  2.4562  1319   158  0.89  16.82   0.98     0.95       6875.03|
|  8:  2.4562 -  2.3497  1354   139  0.90  16.39   1.00     0.98       5908.68|
|  9:  2.3497 -  2.2596  1336   141  0.89  16.95   1.01     0.97       5426.24|
| 10:  2.2596 -  2.1818  1310   150  0.89  16.64   1.00     0.97       4764.01|
| 11:  2.1818 -  2.1138  1316   155  0.89  17.68   1.00     0.95       4694.75|
| 12:  2.1138 -  2.0536  1333   142  0.89  17.38   1.01     1.01       4399.07|
| 13:  2.0536 -  1.9996  1106   116  0.90  16.62   0.98     0.96       3421.43|
| 14:  1.9996 -  1.9509   291    39  0.92  13.10   0.99     0.95       2530.53|
|alpha:            min =        0.94 max =            1.03 mean =         0.98|
|beta:             min =     2530.53 max =        11372.64 mean =      7203.56|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.96 mean =        15.17|
|phase err.(test): min =        0.00 max =           89.96 mean =        14.71|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.673)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.42    84.32   15.45    None  None   None       |
|    all(noH): 2823   0      1.42    84.32   15.45    None  None   None       |
|    Sol.    : 438    0      4.33    81.56   39.39    None  None   None       |
|    Mac.    : 2385   0      1.42    84.32   11.06    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:     1.422 -   9.712: 1383   |   5:    42.870 -  51.159:  100        |
|      1:     9.712 -  18.001:  798   |   6:    51.159 -  59.448:   75        |
|      2:    18.001 -  26.291:  194   |   7:    59.448 -  67.738:   34        |
|      3:    26.291 -  34.580:  104   |   8:    67.738 -  76.027:   14        |
|      4:    34.580 -  42.870:  111   |   9:    76.027 -  84.317:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 315         
Filter by distance & map next to the model:
   mapped sites are within: 0.546 - 5.640
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 310 from: 315
   mapped sites are within: 0.710 - 5.640

peak=   11.137 closest distance to " CB  VAL A 230 " =    1.486
peak=    9.022 closest distance to " CG2 VAL A 296 " =    1.579
peak=    5.833 closest distance to " CG  LEU A   5 " =    1.208
peak=    5.825 closest distance to " O   HOH Z 188 " =    1.784
peak=    5.794 closest distance to " CD2 LEU A   5 " =    1.149
peak=    5.672 closest distance to " NE2 GLN A  11 " =    1.141
peak=    5.485 closest distance to " CG  PRO A  54 " =    1.382
peak=    5.367 closest distance to " CG  LEU A 228 " =    1.204
peak=    5.362 closest distance to " O   HOH Z 248 " =    1.357
peak=    5.325 closest distance to " O   HOH Z  43 " =    1.567
peak=    5.300 closest distance to " CB  GLN A 223 " =    1.495
peak=    5.198 closest distance to " CB  ARG A 275 " =    0.963
peak=    4.903 closest distance to " O   HOH Z 232 " =    2.363
peak=    4.902 closest distance to " O   HOH Z 193 " =    1.867
peak=    4.895 closest distance to " NH2 ARG A  56 " =    2.128
peak=    4.751 closest distance to " CZ  PHE A 218 " =    1.169
peak=    4.687 closest distance to " O   HOH Z 142 " =    1.621
peak=    4.685 closest distance to " O   HOH Z 238 " =    1.421
peak=    4.558 closest distance to " CB  PRO A  54 " =    1.004
peak=    4.478 closest distance to " O   HOH Z 346 " =    1.602
peak=    4.466 closest distance to " CB  VAL A 230 " =    1.196
peak=    4.463 closest distance to " O   SER A  87 " =    2.330
peak=    4.456 closest distance to " O   HOH Z  95 " =    1.312
peak=    4.452 closest distance to " CD2 TRP A 179 " =    1.415
peak=    4.448 closest distance to " NH2AARG A 145 " =    1.118
peak=    4.428 closest distance to " O   HOH Z  69 " =    2.298
peak=    4.411 closest distance to " O   HOH Z   3 " =    2.022
peak=    4.408 closest distance to " O   HOH Z 124 " =    1.300
peak=    4.401 closest distance to " O   HOH Z 203 " =    1.085
peak=    4.365 closest distance to " O   HOH Z 403 " =    1.641
peak=    4.357 closest distance to " CB  GLN A 183 " =    1.294
peak=    4.346 closest distance to " CG  PRO A 243 " =    1.161
peak=    4.338 closest distance to " CG  GLN A  58 " =    1.118
peak=    4.337 closest distance to " NH2AARG A 190 " =    2.005
peak=    4.301 closest distance to " CB  ASN A 148 " =    1.342
peak=    4.297 closest distance to " O   HOH Z  78 " =    1.695
peak=    4.294 closest distance to " O   HOH Z 251 " =    1.691
peak=    4.289 closest distance to " CB  ASN A 142 " =    1.174
peak=    4.262 closest distance to " O   HOH Z 126 " =    1.859
peak=    4.254 closest distance to " CB  ARG A  79 " =    1.498
peak=    4.246 closest distance to " O   HOH Z 287 " =    1.837
peak=    4.216 closest distance to " O   HOH Z 143 " =    1.497
peak=    4.201 closest distance to " O   HOH Z 265 " =    2.098
peak=    4.200 closest distance to " CG2 ILE A 234 " =    1.107
peak=    4.194 closest distance to " CA  ALA A  51 " =    1.008
peak=    4.186 closest distance to " CB  SER A  63 " =    1.204
peak=    4.181 closest distance to " O   HOH Z 406 " =    1.499
peak=    4.166 closest distance to " O   HOH Z  97 " =    1.389
peak=    4.157 closest distance to " CB  ALA A   9 " =    1.618
peak=    4.154 closest distance to " O   HOH Z  61 " =    1.816
peak=    4.154 closest distance to " O   HOH Z 255 " =    1.156
peak=    4.144 closest distance to " O   HOH Z 126 " =    1.583
peak=    4.128 closest distance to " O   HOH Z 375 " =    0.984
peak=    4.118 closest distance to " O   HOH Z 272 " =    1.853
peak=    4.093 closest distance to " O   HOH Z 359 " =    1.517
peak=    4.075 closest distance to " O   HOH Z 422 " =    2.534
peak=    4.060 closest distance to " O   HOH Z  85 " =    1.513
peak=    4.060 closest distance to " CB  ASN A 110 " =    1.097
peak=    4.053 closest distance to " O   HOH Z 369 " =    2.522
peak=    4.051 closest distance to " O   HOH Z 402 " =    1.353
peak=    4.050 closest distance to " CG  PRO A 280 " =    0.901
peak=    4.042 closest distance to " O   HOH Z  63 " =    1.974
peak=    4.037 closest distance to " CG  PRO A 213 " =    1.193
peak=    4.032 closest distance to " CB  SER A  26 " =    1.823
peak=    4.015 closest distance to " O   HOH Z 427 " =    2.872
peak=    4.004 closest distance to " O   HOH Z 188 " =    2.399
peak=    4.003 closest distance to " O   HOH Z  80 " =    1.772
peak=    4.001 closest distance to " O   HOH Z 261 " =    2.484
peak=    3.999 closest distance to " CD2 LEU A 228 " =    1.256
peak=    3.999 closest distance to " CD  LYS A  76 " =    1.747
peak=    3.994 closest distance to " CB  THR A  52 " =    0.869
peak=    3.993 closest distance to " O   HOH Z 368 " =    2.280
peak=    3.980 closest distance to " CG2 VAL A 257 " =    0.784
peak=    3.970 closest distance to " O   HOH Z  59 " =    1.975
peak=    3.969 closest distance to " CB  VAL A 265 " =    1.316
peak=    3.958 closest distance to " CD1AILE A 234 " =    0.823
peak=    3.952 closest distance to " CG  PRO A 198 " =    1.203
peak=    3.950 closest distance to " CB  GLU A 152 " =    1.172
peak=    3.939 closest distance to " CB  GLU A 277 " =    3.620
peak=    3.932 closest distance to " CA  TYR A  30 " =    0.947
peak=    3.927 closest distance to " ND2 ASN A 249 " =    0.904
peak=    3.914 closest distance to " CD  ARG A 269 " =    1.024
peak=    3.907 closest distance to " N   PHE A 130 " =    1.354
peak=    3.897 closest distance to " O   HOH Z 303 " =    2.154
peak=    3.896 closest distance to " O   HOH Z  76 " =    1.088
peak=    3.894 closest distance to " CA  ARG A  36 " =    0.990
peak=    3.884 closest distance to " CB  ARG A 190 " =    1.684
peak=    3.872 closest distance to " O   HOH Z 234 " =    3.518
peak=    3.868 closest distance to " O   HOH Z 246 " =    1.222
peak=    3.866 closest distance to " O   HOH Z 425 " =    1.362
peak=    3.866 closest distance to " CD  ARG A 159 " =    0.712
peak=    3.856 closest distance to " O   HOH Z 411 " =    4.055
peak=    3.848 closest distance to " O   HOH Z 112 " =    1.061
peak=    3.842 closest distance to " CB  THR A  31 " =    1.481
peak=    3.841 closest distance to " CG AARG A 275 " =    1.214
peak=    3.841 closest distance to " CB  ARG A  79 " =    1.015
peak=    3.822 closest distance to " CB  ARG A 156 " =    1.151
peak=    3.819 closest distance to " O   HOH Z 128 " =    2.348
peak=    3.797 closest distance to " O   PRO A 198 " =    1.586
peak=    3.797 closest distance to " CD  LYS A 166 " =    1.368
peak=    3.792 closest distance to " O   HOH Z  19 " =    2.055
peak=    3.788 closest distance to " OG ASER A 258 " =    2.968
peak=    3.782 closest distance to " O   HOH Z  44 " =    2.164
peak=    3.779 closest distance to " CG  LEU A 167 " =    1.259
peak=    3.775 closest distance to " O   HOH Z 365 " =    2.567
peak=    3.771 closest distance to " N   ASN A  39 " =    1.316
peak=    3.758 closest distance to " O   HOH Z 130 " =    2.524
peak=    3.730 closest distance to " CB  VAL A 202 " =    1.605
peak=    3.729 closest distance to " O   HOH Z 141 " =    1.698
peak=    3.717 closest distance to " NZ  LYS A 117 " =    2.753
peak=    3.713 closest distance to " ND2 ASN A 187 " =    1.665
peak=    3.705 closest distance to " O   HOH Z 298 " =    1.691
peak=    3.693 closest distance to " CE  LYS A  76 " =    0.894
peak=    3.688 closest distance to " O   HOH Z  40 " =    1.614
peak=    3.658 closest distance to " O   HOH Z  30 " =    1.378
peak=    3.656 closest distance to " CA  ASN A 215 " =    0.983
peak=    3.655 closest distance to " O   HOH Z 169 " =    0.981
peak=    3.654 closest distance to " O   HOH Z 258 " =    2.194
peak=    3.651 closest distance to " O   HOH Z 130 " =    2.184
peak=    3.643 closest distance to " O   HOH Z 350 " =    1.957
peak=    3.640 closest distance to " CB  ALA A 248 " =    1.349
peak=    3.632 closest distance to " O   HOH Z 236 " =    1.446
peak=    3.623 closest distance to " O   HOH Z  15 " =    2.154
peak=    3.615 closest distance to " CG2 ILE A 120 " =    1.491
peak=    3.594 closest distance to " CD1 LEU A  96 " =    0.710
peak=    3.584 closest distance to " CB  TRP A 266 " =    1.125
peak=    3.567 closest distance to " O   HOH Z 329 " =    4.063
peak=    3.564 closest distance to " CB  ARG A 138 " =    0.807
peak=    3.561 closest distance to " CZ  PHE A  38 " =    1.072
peak=    3.559 closest distance to " N   ARG A 156 " =    1.353
peak=    3.559 closest distance to " O   HOH Z 128 " =    1.477
peak=    3.556 closest distance to " O   HOH Z 371 " =    2.874
peak=    3.554 closest distance to " O  BHOH Z 338 " =    2.380
peak=    3.553 closest distance to " CB  ASN A  39 " =    0.885
peak=    3.553 closest distance to " CB  GLN A  88 " =    1.251
peak=    3.547 closest distance to " CA  ASN A 217 " =    1.211
peak=    3.547 closest distance to " O   HOH Z 423 " =    1.820
peak=    3.546 closest distance to " O   HOH Z 214 " =    2.788
peak=    3.546 closest distance to " O   HOH Z 337 " =    1.874
peak=    3.543 closest distance to " O   HOH Z 410 " =    3.059
peak=    3.541 closest distance to " CG  LYS A 289 " =    1.437
peak=    3.541 closest distance to " CB  VAL A 296 " =    0.961
peak=    3.539 closest distance to " O   HOH Z 263 " =    1.810
peak=    3.539 closest distance to " O   HOH Z 132 " =    2.666
peak=    3.537 closest distance to " O   HOH Z 213 " =    1.893
peak=    3.526 closest distance to " OE1 GLU A   2 " =    2.072
peak=    3.525 closest distance to " CA  ASP A 162 " =    1.021
peak=    3.525 closest distance to " CG  MET A 185 " =    1.283
peak=    3.521 closest distance to " CE1 TYR A 186 " =    1.232
peak=    3.520 closest distance to " O   HOH Z  10 " =    1.724
peak=    3.519 closest distance to " OG1 THR A 264 " =    0.744
peak=    3.514 closest distance to " CB  SER A   3 " =    1.237
peak=    3.513 closest distance to " O   HOH Z 132 " =    2.406
peak=    3.502 closest distance to " N   ASP A 162 " =    1.193
peak=    3.480 closest distance to " O   HOH Z  88 " =    3.505
peak=    3.477 closest distance to " CG2AVAL A 121 " =    2.362
peak=    3.477 closest distance to " NH1AARG A 145 " =    1.240
peak=    3.471 closest distance to " CB  TYR A 169 " =    0.856
peak=    3.469 closest distance to " O   HOH Z  88 " =    2.531
peak=    3.469 closest distance to " O   HOH Z 375 " =    1.549
peak=    3.467 closest distance to " O   GLY A  91 " =    1.498
peak=    3.466 closest distance to " O   HOH Z 417 " =    1.073
peak=    3.463 closest distance to " CG AARG A 102 " =    1.076
peak=    3.452 closest distance to " CB  THR A 235 " =    1.293
peak=    3.449 closest distance to " CB  LYS A 117 " =    1.221
peak=    3.449 closest distance to " CD  LYS A 119 " =    1.798
peak=    3.446 closest distance to " O   HOH Z 353 " =    2.666
peak=    3.443 closest distance to " O   HOH Z 421 " =    2.166
peak=    3.442 closest distance to " O   HOH Z 156 " =    3.337
peak=    3.442 closest distance to " CB  PHE A 204 " =    1.004
peak=    3.434 closest distance to " O   HOH Z 107 " =    0.848
peak=    3.433 closest distance to " O   HOH Z 280 " =    2.957
peak=    3.432 closest distance to " N   SER A 135 " =    1.364
peak=    3.430 closest distance to " O   GLY A  23 " =    2.413
peak=    3.423 closest distance to " O   HOH Z 419 " =    1.720
peak=    3.420 closest distance to " NH2BARG A 145 " =    2.226
peak=    3.416 closest distance to " O   HOH Z 272 " =    2.141
peak=    3.414 closest distance to " CD2 TYR A 186 " =    1.112
peak=    3.408 closest distance to " O   THR A 182 " =    1.455
peak=    3.400 closest distance to " CD2 LEU A 297 " =    0.955
peak=    3.391 closest distance to " CA  PHE A 283 " =    1.158
peak=    3.387 closest distance to " O   HOH Z 371 " =    1.331
peak=    3.387 closest distance to " O   HOH Z 273 " =    3.053
peak=    3.384 closest distance to " O   HOH Z 200 " =    2.160
peak=    3.379 closest distance to " O   HOH Z 389 " =    1.380
peak=    3.375 closest distance to " O   ASP A 124 " =    1.189
peak=    3.373 closest distance to " CB  ASP A 298 " =    1.150
peak=    3.370 closest distance to " CG1 ILE A  49 " =    1.611
peak=    3.367 closest distance to " O   HOH Z 415 " =    3.450
peak=    3.366 closest distance to " CA  ASP A 149 " =    1.160
peak=    3.361 closest distance to " O   HOH Z 293 " =    1.978
peak=    3.360 closest distance to " O   HOH Z  41 " =    2.014
peak=    3.359 closest distance to " CA  ILE A 234 " =    0.974
peak=    3.358 closest distance to " O   HOH Z 207 " =    1.161
peak=    3.352 closest distance to " OG BSER A 164 " =    2.174
peak=    3.351 closest distance to " O   HOH Z 388 " =    2.252
peak=    3.351 closest distance to " CB BVAL A  41 " =    1.280
peak=    3.345 closest distance to " O   HOH Z  28 " =    1.673
peak=    3.337 closest distance to " OG  SER A  62 " =    2.713
peak=    3.337 closest distance to " O   HOH Z  97 " =    1.878
peak=    3.334 closest distance to " NH2BARG A 190 " =    1.766
peak=    3.333 closest distance to " CA  LYS A 290 " =    1.226
peak=    3.331 closest distance to " O   HOH Z 193 " =    1.388
peak=    3.330 closest distance to " CZ3 TRP A 266 " =    1.078
peak=    3.330 closest distance to " CB  SER A 212 " =    1.394
peak=    3.327 closest distance to " O   HOH Z 193 " =    1.520
peak=    3.326 closest distance to " CB  GLU A  46 " =    0.984
peak=    3.325 closest distance to " CE  LYS A 119 " =    1.125
peak=    3.324 closest distance to " CA  ALA A 129 " =    1.519
peak=    3.318 closest distance to " CD1 ILE A 199 " =    1.200
peak=    3.313 closest distance to " CB  PRO A  90 " =    1.129
peak=    3.309 closest distance to " O   HOH Z  68 " =    2.165
peak=    3.305 closest distance to " CG  GLU A  37 " =    0.834
peak=    3.299 closest distance to " NZ  LYS A  48 " =    1.026
peak=    3.298 closest distance to " CA  ARG A 195 " =    1.189
peak=    3.295 closest distance to " CB  SER A 273 " =    0.897
peak=    3.294 closest distance to " CA  TYR A 116 " =    1.522
peak=    3.292 closest distance to " CB  ASP A 191 " =    1.234
peak=    3.291 closest distance to " O   HOH Z 325 " =    2.210
peak=    3.291 closest distance to " O   HOH Z 109 " =    1.531
peak=    3.291 closest distance to " CB  TRP A 179 " =    1.356
peak=    3.291 closest distance to " O   HOH Z 352 " =    1.314
peak=    3.286 closest distance to " CG  GLN A  88 " =    1.090
peak=    3.285 closest distance to " O   HOH Z 368 " =    4.737
peak=    3.285 closest distance to " CG2 VAL A 197 " =    1.071
peak=    3.285 closest distance to " O   HOH Z 380 " =    2.031
peak=    3.284 closest distance to " CB  SER A 141 " =    1.138
peak=    3.283 closest distance to " O   HOH Z  78 " =    2.424
peak=    3.279 closest distance to " CB  SER A  62 " =    1.129
peak=    3.278 closest distance to " O   HOH Z 345 " =    3.192
peak=    3.276 closest distance to " O   HOH Z  94 " =    2.153
peak=    3.268 closest distance to " O   HOH Z 162 " =    2.864
peak=    3.266 closest distance to " O   HOH Z 130 " =    1.106
peak=    3.261 closest distance to " CG BARG A 102 " =    1.798
peak=    3.257 closest distance to " OD1 ASN A  69 " =    2.444
peak=    3.256 closest distance to " CG  LYS A 119 " =    1.135
peak=    3.255 closest distance to " O   HOH Z 389 " =    1.614
peak=    3.255 closest distance to " O   ASP A 191 " =    1.713
peak=    3.252 closest distance to " O   HOH Z 361 " =    3.592
peak=    3.251 closest distance to " O   HOH Z 392 " =    2.761
peak=    3.249 closest distance to " CE3 TRP A 150 " =    1.077
peak=    3.247 closest distance to " CG1 VAL A 153 " =    0.865
peak=    3.246 closest distance to " O   HOH Z 357 " =    2.004
peak=    3.241 closest distance to " NH1AARG A 275 " =    0.941
peak=    3.241 closest distance to " CA  LYS A 117 " =    1.191
peak=    3.234 closest distance to " CB  GLN A  89 " =    1.228
peak=    3.233 closest distance to " CG2 ILE A  20 " =    1.528
peak=    3.232 closest distance to " O   HOH Z   1 " =    1.860
peak=    3.228 closest distance to " OG1 THR A 221 " =    1.385
peak=    3.226 closest distance to " CG1 VAL A 296 " =    1.258
peak=    3.225 closest distance to " CD  ARG A 195 " =    0.953
peak=    3.223 closest distance to " CB  ALA A 295 " =    1.298
peak=    3.216 closest distance to " O   HOH Z 327 " =    1.544
peak=    3.216 closest distance to " O   HOH Z 322 " =    1.930
peak=    3.213 closest distance to " CB  ALA A 114 " =    1.233
peak=    3.211 closest distance to " O   HOH Z  49 " =    0.984
peak=    3.208 closest distance to " CB  ASP A 140 " =    1.210
peak=    3.206 closest distance to " O   HOH Z 173 " =    2.068
peak=    3.205 closest distance to " O   HOH Z 209 " =    2.696
peak=    3.205 closest distance to " NE2 GLN A  77 " =    3.130
peak=    3.204 closest distance to " CA  THR A 221 " =    1.077
peak=    3.200 closest distance to " O   HOH Z 368 " =    3.439
peak=    3.198 closest distance to " CB  ASN A 215 " =    1.079
peak=    3.194 closest distance to " CG1 ILE A 120 " =    1.060
peak=    3.187 closest distance to " O   ALA A   1 " =    1.817
peak=    3.186 closest distance to " CB  ALA A 291 " =    1.039
peak=    3.176 closest distance to " O   HOH Z 162 " =    1.710
peak=    3.175 closest distance to " O   HOH Z 409 " =    1.247
peak=    3.174 closest distance to " CA  ASN A 127 " =    1.066
peak=    3.174 closest distance to " O   HOH Z  85 " =    1.788
peak=    3.170 closest distance to " O   HOH Z 250 " =    1.343
peak=    3.167 closest distance to " O   ASN A 284 " =    1.780
peak=    3.165 closest distance to " CG  GLN A  55 " =    2.394
peak=    3.159 closest distance to " O   HOH Z 337 " =    3.594
peak=    3.159 closest distance to " O   HOH Z 298 " =    4.178
peak=    3.159 closest distance to " CB  ASP A 124 " =    0.898
peak=    3.158 closest distance to " O   HOH Z 299 " =    4.064
peak=    3.152 closest distance to " CA  LEU A 282 " =    1.254
peak=    3.150 closest distance to " O   HOH Z  21 " =    1.920
peak=    3.149 closest distance to " CA  GLY A 267 " =    1.038
peak=    3.149 closest distance to " CB  HIS A 108 " =    0.871
peak=    3.144 closest distance to " O   HOH Z 407 " =    2.547
peak=    3.143 closest distance to " O   HOH Z 403 " =    1.516
peak=    3.140 closest distance to " O   THR A 220 " =    1.229
peak=    3.139 closest distance to " O   HOH Z 102 " =    1.261
peak=    3.139 closest distance to " O   HOH Z   4 " =    1.435
peak=    3.138 closest distance to " O   HOH Z  80 " =    2.050
peak=    3.138 closest distance to " C   SER A  32 " =    1.869
peak=    3.130 closest distance to " CG2 THR A 221 " =    1.234
peak=    3.126 closest distance to " CA  SER A  87 " =    0.960
peak=    3.122 closest distance to " CA  SER A 146 " =    1.970
peak=    3.119 closest distance to " CG  ARG A  66 " =    2.510
peak=    3.113 closest distance to " O   HOH Z 345 " =    1.550
peak=    3.108 closest distance to " CG2 THR A  18 " =    1.505
peak=    3.108 closest distance to " CB  ARG A 219 " =    1.105
peak=    3.104 closest distance to " OD1 ASN A 301 " =    1.583
peak=    3.096 closest distance to " O   HOH Z 301 " =    1.667
peak=    3.090 closest distance to " O   SER A 164 " =    1.230
peak=    3.086 closest distance to " O   HOH Z 172 " =    3.674
peak=    3.085 closest distance to " O   HOH Z 344 " =    2.765
peak=    3.079 closest distance to " CB  SER A  99 " =    1.345
peak=    3.077 closest distance to " OH  TYR A 116 " =    1.209
peak=    3.073 closest distance to " O   HOH Z 187 " =    2.198
peak=    3.068 closest distance to " CA  VAL A  41 " =    0.909
peak=    3.068 closest distance to " O   HOH Z 430 " =    5.640
peak=    3.053 closest distance to " CB  ASN A 173 " =    0.952
peak=    3.044 closest distance to " O   HOH Z 305 " =    3.387
peak=    3.043 closest distance to " CD  ARG A 138 " =    0.867
peak=    3.030 closest distance to " OG ASER A 212 " =    1.777
peak=    3.025 closest distance to " O   HOH Z 363 " =    3.056

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 207         
Filter by distance & map next to the model:
   mapped sites are within: 0.424 - 5.544
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 206 from: 207
   mapped sites are within: 0.721 - 5.544

peak=   -4.835 closest distance to " CG2 VAL A 230 " =    0.721
peak=   -4.760 closest distance to " CD  ARG A  14 " =    3.165
peak=   -4.676 closest distance to " CG  GLN A  58 " =    0.936
peak=   -4.636 closest distance to " O   HOH Z 193 " =    0.920
peak=   -4.616 closest distance to " OG BSER A 134 " =    1.386
peak=   -4.490 closest distance to " C   HIS A 108 " =    1.197
peak=   -4.447 closest distance to " O   HOH Z 169 " =    0.857
peak=   -4.421 closest distance to " O   HOH Z 203 " =    1.275
peak=   -4.259 closest distance to " OE1 GLN A 223 " =    2.292
peak=   -4.175 closest distance to " CD2 TYR A 293 " =    1.943
peak=   -4.166 closest distance to " O   VAL A  67 " =    2.550
peak=   -4.155 closest distance to " O   HOH Z 211 " =    1.206
peak=   -4.082 closest distance to " O   PRO A 163 " =    2.110
peak=   -4.081 closest distance to " CD  ARG A 156 " =    2.004
peak=   -4.009 closest distance to " CD1 LEU A 101 " =    2.349
peak=   -3.998 closest distance to " O   PRO A 198 " =    1.229
peak=   -3.985 closest distance to " O   HOH Z 394 " =    1.632
peak=   -3.975 closest distance to " CD1 ILE A 263 " =    2.708
peak=   -3.957 closest distance to " OXT GLY A 302 " =    2.851
peak=   -3.879 closest distance to " O   HOH Z 216 " =    1.113
peak=   -3.872 closest distance to " CB  ALA A  43 " =    2.458
peak=   -3.838 closest distance to " O   HOH Z 131 " =    4.169
peak=   -3.819 closest distance to " NE2 GLN A  88 " =    1.165
peak=   -3.817 closest distance to " OG  SER A  97 " =    2.267
peak=   -3.782 closest distance to " CE2 TYR A  30 " =    2.783
peak=   -3.781 closest distance to " O   HOH Z 267 " =    5.483
peak=   -3.777 closest distance to " O   HOH Z 351 " =    1.522
peak=   -3.775 closest distance to " O   HOH Z  69 " =    1.785
peak=   -3.754 closest distance to " OH  TYR A 172 " =    1.790
peak=   -3.749 closest distance to " CD2 PHE A  61 " =    2.225
peak=   -3.742 closest distance to " O   ALA A 227 " =    1.337
peak=   -3.732 closest distance to " O   HOH Z 166 " =    1.907
peak=   -3.721 closest distance to " O   HOH Z 290 " =    1.109
peak=   -3.708 closest distance to " CD1 ILE A 199 " =    2.291
peak=   -3.704 closest distance to " NE2 GLN A  11 " =    1.770
peak=   -3.701 closest distance to " CA  VAL A  67 " =    2.991
peak=   -3.685 closest distance to " O   HOH Z 387 " =    2.671
peak=   -3.678 closest distance to " CE  MET A 105 " =    2.412
peak=   -3.669 closest distance to " O   HOH Z 116 " =    1.455
peak=   -3.669 closest distance to " CG1 VAL A 112 " =    2.709
peak=   -3.669 closest distance to " N   ALA A 248 " =    1.580
peak=   -3.668 closest distance to " CB  ALA A  51 " =    1.900
peak=   -3.661 closest distance to " CB  PHE A 192 " =    2.060
peak=   -3.646 closest distance to " ND2 ASN A 249 " =    2.328
peak=   -3.642 closest distance to " CA  ASP A 298 " =    1.041
peak=   -3.641 closest distance to " O   VAL A 174 " =    2.233
peak=   -3.640 closest distance to " CG2 ILE A  49 " =    2.791
peak=   -3.631 closest distance to " OG  SER A  87 " =    1.490
peak=   -3.620 closest distance to " O   ASN A 187 " =    1.617
peak=   -3.618 closest distance to " O   HOH Z 100 " =    0.899
peak=   -3.612 closest distance to " CE BMET A  47 " =    1.264
peak=   -3.591 closest distance to " O   HOH Z 231 " =    2.299
peak=   -3.584 closest distance to " NH2 ARG A  66 " =    1.125
peak=   -3.575 closest distance to " N   THR A  52 " =    1.714
peak=   -3.564 closest distance to " O   HOH Z 128 " =    1.249
peak=   -3.542 closest distance to " CG2 VAL A 296 " =    1.958
peak=   -3.532 closest distance to " OD2 ASP A 191 " =    1.351
peak=   -3.529 closest distance to " O   HOH Z 265 " =    2.379
peak=   -3.520 closest distance to " NE2 GLN A  88 " =    1.951
peak=   -3.519 closest distance to " ND2 ASN A  45 " =    1.217
peak=   -3.510 closest distance to " CA  GLY A 241 " =    2.413
peak=   -3.508 closest distance to " ND2 ASN A 187 " =    1.685
peak=   -3.500 closest distance to " O   HOH Z 423 " =    2.310
peak=   -3.497 closest distance to " O   HOH Z 281 " =    2.991
peak=   -3.492 closest distance to " O   HOH Z 114 " =    3.240
peak=   -3.484 closest distance to " O   PHE A 218 " =    1.526
peak=   -3.479 closest distance to " CB  ALA A 248 " =    2.342
peak=   -3.477 closest distance to " CB  SER A 210 " =    1.137
peak=   -3.464 closest distance to " CB  ASP A 132 " =    2.341
peak=   -3.464 closest distance to " O   HOH Z 109 " =    0.834
peak=   -3.463 closest distance to " CB  GLN A  55 " =    1.242
peak=   -3.460 closest distance to " O   HOH Z 371 " =    2.371
peak=   -3.455 closest distance to " O   HOH Z 174 " =    3.848
peak=   -3.453 closest distance to " CZ3 TRP A 179 " =    1.332
peak=   -3.451 closest distance to " CG  TRP A 266 " =    1.954
peak=   -3.448 closest distance to " CD  PRO A 243 " =    1.968
peak=   -3.445 closest distance to " OE1 GLN A 183 " =    1.469
peak=   -3.441 closest distance to " O   HOH Z 191 " =    5.544
peak=   -3.439 closest distance to " O   HOH Z 165 " =    1.937
peak=   -3.437 closest distance to " OE2 GLU A 152 " =    1.413
peak=   -3.437 closest distance to " NE  ARG A  66 " =    4.279
peak=   -3.426 closest distance to " O   HOH Z 285 " =    2.015
peak=   -3.424 closest distance to " O   SER A 210 " =    1.757
peak=   -3.419 closest distance to " O   SER A 146 " =    1.297
peak=   -3.417 closest distance to " CB  ALA A 161 " =    2.404
peak=   -3.417 closest distance to " O   HOH Z 372 " =    2.251
peak=   -3.416 closest distance to " ND2 ASN A  39 " =    1.138
peak=   -3.403 closest distance to " CA  GLY A 133 " =    1.982
peak=   -3.397 closest distance to " OD1 ASN A 301 " =    1.949
peak=   -3.396 closest distance to " O   HOH Z 429 " =    1.552
peak=   -3.382 closest distance to " N   PHE A  59 " =    2.085
peak=   -3.380 closest distance to " CG2 THR A  18 " =    2.831
peak=   -3.374 closest distance to " O   HOH Z 252 " =    3.773
peak=   -3.374 closest distance to " CE3 TRP A 274 " =    2.141
peak=   -3.374 closest distance to " CG  GLN A 103 " =    2.420
peak=   -3.372 closest distance to " CE3 TRP A 150 " =    2.089
peak=   -3.361 closest distance to " O   HOH Z 102 " =    1.756
peak=   -3.360 closest distance to " O   VAL A 189 " =    2.632
peak=   -3.349 closest distance to " O   HOH Z 275 " =    1.767
peak=   -3.339 closest distance to " O   HOH Z 185 " =    2.292
peak=   -3.338 closest distance to " C   MET A 188 " =    1.438
peak=   -3.337 closest distance to " O   HOH Z 407 " =    2.652
peak=   -3.336 closest distance to " O   HOH Z 421 " =    3.167
peak=   -3.335 closest distance to " O   HOH Z 404 " =    1.466
peak=   -3.334 closest distance to " CG  ASP A 231 " =    0.787
peak=   -3.334 closest distance to " CB  ALA A 248 " =    2.103
peak=   -3.330 closest distance to " N   SER A 276 " =    1.412
peak=   -3.328 closest distance to " O   GLY A  80 " =    2.472
peak=   -3.326 closest distance to " CZ  ARG A 259 " =    0.990
peak=   -3.321 closest distance to " CB  PRO A 163 " =    2.439
peak=   -3.320 closest distance to " CB  ASN A  39 " =    2.306
peak=   -3.319 closest distance to " C   LEU A 143 " =    0.944
peak=   -3.316 closest distance to " CA  SER A 135 " =    1.217
peak=   -3.314 closest distance to " O   HOH Z 107 " =    1.083
peak=   -3.313 closest distance to " O   HOH Z 101 " =    1.584
peak=   -3.310 closest distance to " O   TRP A  70 " =    1.572
peak=   -3.307 closest distance to " O   ASN A 252 " =    1.323
peak=   -3.296 closest distance to " NH2AARG A 275 " =    4.754
peak=   -3.295 closest distance to " CE1 TYR A 247 " =    2.602
peak=   -3.294 closest distance to " O   HOH Z 137 " =    1.660
peak=   -3.287 closest distance to " CD1 LEU A 255 " =    2.688
peak=   -3.286 closest distance to " N   ALA A 226 " =    1.943
peak=   -3.286 closest distance to " CZ  PHE A  38 " =    2.276
peak=   -3.277 closest distance to " O   HOH Z 166 " =    2.239
peak=   -3.275 closest distance to " OD2 ASP A  50 " =    1.381
peak=   -3.273 closest distance to " N   GLY A 196 " =    1.767
peak=   -3.272 closest distance to " OXT GLY A 302 " =    3.624
peak=   -3.267 closest distance to " CD2 PHE A 225 " =    1.062
peak=   -3.265 closest distance to " O   HOH Z 179 " =    2.127
peak=   -3.265 closest distance to " CZ  PHE A  38 " =    2.175
peak=   -3.257 closest distance to " O   HOH Z 111 " =    4.446
peak=   -3.252 closest distance to " N   ASP A 286 " =    2.050
peak=   -3.252 closest distance to " O   HOH Z 250 " =    1.754
peak=   -3.246 closest distance to " O   HOH Z  60 " =    1.380
peak=   -3.246 closest distance to " N   HIS A 115 " =    2.239
peak=   -3.245 closest distance to " O   HOH Z 359 " =    2.894
peak=   -3.242 closest distance to " CA  GLY A  23 " =    1.787
peak=   -3.241 closest distance to " O   HOH Z  11 " =    2.099
peak=   -3.240 closest distance to " O   HOH Z 218 " =    3.982
peak=   -3.236 closest distance to " O   GLY A 196 " =    1.050
peak=   -3.233 closest distance to " O   HOH Z 286 " =    1.838
peak=   -3.232 closest distance to " O   HOH Z 390 " =    2.206
peak=   -3.232 closest distance to " O   HOH Z 236 " =    1.668
peak=   -3.228 closest distance to " O   HOH Z  64 " =    3.036
peak=   -3.228 closest distance to " ND2 ASN A  69 " =    1.916
peak=   -3.227 closest distance to " CG  ARG A  66 " =    2.324
peak=   -3.222 closest distance to " CB  HIS A  86 " =    1.137
peak=   -3.220 closest distance to " CG1BVAL A  72 " =    2.513
peak=   -3.219 closest distance to " OG ASER A 134 " =    1.546
peak=   -3.218 closest distance to " O   ILE A 106 " =    1.724
peak=   -3.215 closest distance to " O   HOH Z 148 " =    3.743
peak=   -3.215 closest distance to " O   HOH Z  11 " =    1.864
peak=   -3.215 closest distance to " O   HOH Z 374 " =    1.751
peak=   -3.209 closest distance to " OG1 THR A  52 " =    2.702
peak=   -3.208 closest distance to " O   SER A 276 " =    1.655
peak=   -3.207 closest distance to " CD  GLN A  88 " =    0.906
peak=   -3.205 closest distance to " O   HOH Z 392 " =    1.969
peak=   -3.204 closest distance to " CG  LEU A   5 " =    0.984
peak=   -3.203 closest distance to " O   HOH Z 431 " =    2.135
peak=   -3.200 closest distance to " CG2 THR A 178 " =    2.418
peak=   -3.198 closest distance to " NH2 ARG A  79 " =    1.597
peak=   -3.195 closest distance to " O   GLY A  80 " =    2.605
peak=   -3.195 closest distance to " O   TRP A  92 " =    2.020
peak=   -3.193 closest distance to " CG2 ILE A 263 " =    2.303
peak=   -3.193 closest distance to " CA  LYS A 166 " =    2.100
peak=   -3.191 closest distance to " CG1 VAL A 125 " =    1.881
peak=   -3.189 closest distance to " O   HOH Z 174 " =    2.404
peak=   -3.185 closest distance to " OD2 ASP A 140 " =    1.008
peak=   -3.182 closest distance to " N   ALA A 248 " =    2.477
peak=   -3.182 closest distance to " O   ILE A 120 " =    1.277
peak=   -3.182 closest distance to " O   HOH Z  40 " =    3.032
peak=   -3.181 closest distance to " ND2 ASN A 173 " =    1.356
peak=   -3.179 closest distance to " O   HOH Z 183 " =    1.626
peak=   -3.175 closest distance to " O   HOH Z 326 " =    4.978
peak=   -3.173 closest distance to " CG2 VAL A 189 " =    2.061
peak=   -3.168 closest distance to " N   THR A 157 " =    1.434
peak=   -3.165 closest distance to " CZ2 TRP A 274 " =    0.936
peak=   -3.164 closest distance to " O   HOH Z 154 " =    1.647
peak=   -3.162 closest distance to " CG2 VAL A 296 " =    1.865
peak=   -3.162 closest distance to " C   SER A 206 " =    1.441
peak=   -3.152 closest distance to " CZ  PHE A  59 " =    1.610
peak=   -3.149 closest distance to " NH2 ARG A 159 " =    2.365
peak=   -3.146 closest distance to " CG  LEU A  83 " =    2.137
peak=   -3.144 closest distance to " O   HOH Z 427 " =    1.551
peak=   -3.144 closest distance to " CB  PRO A 213 " =    2.291
peak=   -3.142 closest distance to " CG  PRO A 243 " =    1.670
peak=   -3.140 closest distance to " OG BSER A 210 " =    1.555
peak=   -3.139 closest distance to " O   HOH Z 283 " =    2.558
peak=   -3.136 closest distance to " O   HOH Z  64 " =    1.621
peak=   -3.134 closest distance to " O   HOH Z 134 " =    3.474
peak=   -3.130 closest distance to " O   HOH Z 198 " =    0.907
peak=   -3.129 closest distance to " CB  ASP A 132 " =    2.261
peak=   -3.126 closest distance to " CG  ARG A 269 " =    2.130
peak=   -3.123 closest distance to " OD1 ASP A 171 " =    1.491
peak=   -3.122 closest distance to " O   HOH Z 377 " =    2.041
peak=   -3.120 closest distance to " OG BSER A  99 " =    1.157
peak=   -3.106 closest distance to " CA  GLY A  57 " =    2.011
peak=   -3.102 closest distance to " O   HOH Z 313 " =    1.706
peak=   -3.098 closest distance to " OG1 THR A  82 " =    1.655
peak=   -3.091 closest distance to " O   HOH Z 201 " =    2.142
peak=   -3.084 closest distance to " OG  SER A   3 " =    1.617
peak=   -3.081 closest distance to " O   HOH Z  38 " =    1.923
peak=   -3.064 closest distance to " O   HOH Z 139 " =    3.236
peak=   -3.038 closest distance to " O   HOH Z 423 " =    2.550
peak=   -3.019 closest distance to " O   HOH Z 111 " =    1.692
peak=   -3.014 closest distance to " CZ  PHE A  38 " =    2.199

================= 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    :  0.4888 0.4835   6.289382e+00   6.284577e+00
   1_bss:  0.4800 0.4774   6.281991e+00   6.278753e+00
   1_xyz:  0.4044 0.4228   6.184399e+00   6.223967e+00
   1_adp:  0.3596 0.4100   6.109086e+00   6.197163e+00
   1_occ:  0.3596 0.4103   6.108313e+00   6.198398e+00
   2_bss:  0.3550 0.4061   6.109856e+00   6.199704e+00
   2_xyz:  0.2786 0.3330   5.913933e+00   6.061210e+00
   2_adp:  0.2567 0.3145   5.852544e+00   6.010709e+00
   2_occ:  0.2566 0.3147   5.852302e+00   6.010136e+00
   3_bss:  0.2544 0.3127   5.850998e+00   6.007873e+00
   3_xyz:  0.1831 0.2355   5.562831e+00   5.762593e+00
   3_adp:  0.1667 0.2193   5.480707e+00   5.689575e+00
   3_occ:  0.1663 0.2188   5.479768e+00   5.689133e+00
   4_bss:  0.1653 0.2184   5.479484e+00   5.688598e+00
   4_xyz:  0.1354 0.1813   5.304509e+00   5.520989e+00
   4_adp:  0.1286 0.1750   5.264246e+00   5.486991e+00
   4_occ:  0.1282 0.1752   5.263345e+00   5.487481e+00
   5_bss:  0.1284 0.1754   5.264166e+00   5.487756e+00
   5_xyz:  0.1199 0.1666   5.210780e+00   5.442724e+00
   5_adp:  0.1181 0.1652   5.199755e+00   5.433726e+00
   5_occ:  0.1180 0.1651   5.199365e+00   5.433438e+00
   5_bss:  0.1180 0.1651   5.199450e+00   5.433490e+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:  0.333   6.443   8.355   7.541  11.158   0.000   0.000   0.000
   1_xyz:  0.333   6.443   8.355   7.541  11.158   0.000   0.000   0.000
   1_adp:  0.333   6.443   8.355   7.541  11.158   0.000   0.000   0.000
   1_occ:  0.333   6.443   8.355   7.541  11.158   0.000   0.000   0.000
   2_bss:  0.323  36.378   4.124   3.473   6.904   0.000   0.000   0.000
   2_xyz:  0.323  36.378   4.124   3.473   6.904   0.000   0.000   0.000
   2_adp:  0.323  36.378   4.124   3.473   6.904   0.000   0.000   0.000
   2_occ:  0.323  36.378   4.124   3.473   6.904   0.000   0.000   0.000
   3_bss:  0.335  49.209   1.782   2.230   4.414   0.000   0.000   0.000
   3_xyz:  0.335  49.209   1.782   2.230   4.414   0.000   0.000   0.000
   3_adp:  0.335  49.209   1.782   2.230   4.414   0.000   0.000   0.000
   3_occ:  0.335  49.209   1.782   2.230   4.414   0.000   0.000   0.000
   4_bss:  0.323  45.526   0.289   1.176   3.012   0.000   0.000   0.000
   4_xyz:  0.323  45.526   0.289   1.176   3.012   0.000   0.000   0.000
   4_adp:  0.323  45.526   0.289   1.176   3.012   0.000   0.000   0.000
   4_occ:  0.323  45.526   0.289   1.176   3.012   0.000   0.000   0.000
   5_bss:  0.324  49.423   0.090   1.083   2.764   0.000   0.000   0.000
   5_xyz:  0.324  49.423   0.090   1.083   2.764   0.000   0.000   0.000
   5_adp:  0.324  49.423   0.090   1.083   2.764   0.000   0.000   0.000
   5_occ:  0.324  49.423   0.090   1.083   2.764   0.000   0.000   0.000
   5_bss:  0.324  50.846  -1.222  -0.224   1.445   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  59.316 0.4027  0.4790    74915.641
   1_bss:  59.642 0.3970  0.6171    73427.982
   1_xyz:  49.595 0.5245  0.7918    54602.784
   1_adp:  45.562 0.5752  0.9268    49167.807
   1_occ:  45.633 0.5743  0.9228    49275.877
   2_bss:  45.406 0.5773  0.8051    49421.244
   2_xyz:  35.351 0.6967  0.9425    30698.042
   2_adp:  32.464 0.7303  0.9844    26754.657
   2_occ:  32.460 0.7303  0.9846    26761.304
   3_bss:  32.263 0.7325  0.9175    26520.624
   3_xyz:  23.143 0.8304  0.9981    14291.171
   3_adp:  21.072 0.8516  1.0122    12415.021
   3_occ:  21.063 0.8517  1.0122    12386.793
   4_bss:  21.003 0.8522  0.9659    12338.682
   4_xyz:  17.085 0.8888  0.9801     8621.191
   4_adp:  16.354 0.8955  0.9754     8079.899
   4_occ:  16.366 0.8953  0.9751     8084.665
   5_bss:  16.366 0.8954  0.9691     8110.994
   5_xyz:  15.322 0.9042  0.9759     7327.218
   5_adp:  15.133 0.9059  0.9724     7211.004
   5_occ:  15.122 0.9060  0.9724     7202.102
   5_bss:  15.126 0.9060  0.9762     7203.486
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.088   5.3456e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.088   5.3456e+01
   1_xyz:   1.724  0.014  0.107 18.280  0.007  4.106   1.4691e-01
   1_adp:   1.724  0.014  0.107 18.280  0.007  4.106   1.4691e-01
   1_occ:   1.724  0.014  0.107 18.280  0.007  4.106   1.4691e-01
   2_bss:   1.724  0.014  0.107 18.280  0.007  4.106   1.4691e-01
   2_xyz:   1.214  0.008  0.081 16.141  0.005  4.107   8.1730e-02
   2_adp:   1.214  0.008  0.081 16.141  0.005  4.107   8.1730e-02
   2_occ:   1.214  0.008  0.081 16.141  0.005  4.107   8.1730e-02
   3_bss:   1.214  0.008  0.081 16.141  0.005  4.107   8.1730e-02
   3_xyz:   1.163  0.008  0.083 15.809  0.004  4.123   7.5879e-02
   3_adp:   1.163  0.008  0.083 15.809  0.004  4.123   7.5879e-02
   3_occ:   1.163  0.008  0.083 15.809  0.004  4.123   7.5879e-02
   4_bss:   1.163  0.008  0.083 15.809  0.004  4.123   7.5879e-02
   4_xyz:   1.069  0.008  0.078 15.587  0.004  4.111   6.7135e-02
   4_adp:   1.069  0.008  0.078 15.587  0.004  4.111   6.7135e-02
   4_occ:   1.069  0.008  0.078 15.587  0.004  4.111   6.7135e-02
   5_bss:   1.069  0.008  0.078 15.587  0.004  4.111   6.7135e-02
   5_xyz:   1.049  0.007  0.080 15.393  0.004  4.111   6.4974e-02
   5_adp:   1.049  0.007  0.080 15.393  0.004  4.111   6.4974e-02
   5_occ:   1.049  0.007  0.080 15.393  0.004  4.111   6.4974e-02
   5_bss:   1.049  0.007  0.080 15.393  0.004  4.111   6.4974e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.040   6.9198e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.040   6.9198e+00
   1_xyz:  14.882  0.164  0.457 86.855  0.052  2.053   1.0152e-01
   1_adp:  14.882  0.164  0.457 86.855  0.052  2.053   1.0152e-01
   1_occ:  14.882  0.164  0.457 86.855  0.052  2.053   1.0152e-01
   2_bss:  14.882  0.164  0.457 86.855  0.052  2.053   1.0152e-01
   2_xyz:   8.436  0.079  0.276 83.462  0.043  2.219   7.3497e-02
   2_adp:   8.436  0.079  0.276 83.462  0.043  2.219   7.3497e-02
   2_occ:   8.436  0.079  0.276 83.462  0.043  2.219   7.3497e-02
   3_bss:   8.436  0.079  0.276 83.462  0.043  2.219   7.3497e-02
   3_xyz:   7.421  0.066  0.416 89.212  0.031  2.213   6.5772e-02
   3_adp:   7.421  0.066  0.416 89.212  0.031  2.213   6.5772e-02
   3_occ:   7.421  0.066  0.416 89.212  0.031  2.213   6.5772e-02
   4_bss:   7.421  0.066  0.416 89.212  0.031  2.213   6.5772e-02
   4_xyz:   6.896  0.055  0.341 83.910  0.035  2.332   4.8902e-02
   4_adp:   6.896  0.055  0.341 83.910  0.035  2.332   4.8902e-02
   4_occ:   6.896  0.055  0.341 83.910  0.035  2.332   4.8902e-02
   5_bss:   6.896  0.055  0.341 83.910  0.035  2.332   4.8902e-02
   5_xyz:   6.853  0.042  0.358 82.960  0.026  2.280   4.6205e-02
   5_adp:   6.853  0.042  0.358 82.960  0.026  2.280   4.6205e-02
   5_occ:   6.853  0.042  0.358 82.960  0.026  2.280   4.6205e-02
   5_bss:   6.853  0.042  0.358 82.960  0.026  2.280   4.6205e-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:  72.02   0.00  14.12  65.26   0.00  11.90  72.02   0.00  26.20
   1_occ:  72.02   0.00  14.12  65.26   0.00  11.90  72.02   0.00  26.20
   2_bss:  72.02   0.00  14.12  65.26   0.00  11.90  72.02   0.00  26.20
   2_xyz:  72.02   0.00  14.12  65.26   0.00  11.90  72.02   0.00  26.20
   2_adp:  74.56   0.00  14.09  74.56   0.00  10.70  71.84   0.00  32.57
   2_occ:  74.56   0.00  14.09  74.56   0.00  10.70  71.84   0.00  32.57
   3_bss:  74.56   0.00  14.09  74.56   0.00  10.70  71.84   0.00  32.57
   3_xyz:  74.56   0.00  14.09  74.56   0.00  10.70  71.84   0.00  32.57
   3_adp:  73.08   0.00  14.02  72.21   0.00   9.93  73.08   1.22  36.29
   3_occ:  73.08   0.00  14.02  72.21   0.00   9.93  73.08   1.22  36.29
   4_bss:  73.08   0.00  14.02  72.21   0.00   9.93  73.08   1.22  36.29
   4_xyz:  73.08   0.00  14.02  72.21   0.00   9.93  73.08   1.22  36.29
   4_adp:  80.46   0.00  14.13  80.46   0.00   9.74  76.21   2.94  38.03
   4_occ:  80.46   0.00  14.13  80.46   0.00   9.74  76.21   2.94  38.03
   5_bss:  80.46   0.00  14.13  80.46   0.00   9.74  76.21   2.94  38.03
   5_xyz:  80.46   0.00  14.13  80.46   0.00   9.74  76.21   2.94  38.03
   5_adp:  82.89   0.00  14.03  82.89   0.00   9.64  80.14   2.91  37.96
   5_occ:  82.89   0.00  14.03  82.89   0.00   9.64  80.14   2.91  37.96
   5_bss:  84.32   1.42  15.45  84.32   1.42  11.06  81.56   4.33  39.39
------------------------------------------------------------------------
 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:    1.302    0.026    0.414
   1_adp:    1.302    0.026    0.414
   1_occ:    1.302    0.026    0.414
   2_bss:    1.302    0.026    0.414
   2_xyz:    1.901    0.044    0.570
   2_adp:    1.901    0.044    0.570
   2_occ:    1.901    0.044    0.570
   3_bss:    1.901    0.044    0.570
   3_xyz:    1.730    0.045    0.667
   3_adp:    1.730    0.045    0.667
   3_occ:    1.730    0.045    0.667
   4_bss:    1.730    0.045    0.667
   4_xyz:    1.842    0.050    0.728
   4_adp:    1.842    0.050    0.728
   4_occ:    1.842    0.050    0.728
   5_bss:    1.842    0.050    0.728
   5_xyz:    1.916    0.058    0.743
   5_adp:    1.916    0.058    0.743
   5_occ:    1.916    0.058    0.743
   5_bss:    1.916    0.058    0.743
------------------------------------------------------------------------

CPU time actual refinement: 356.18


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_64/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_64/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_64/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_64/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_64/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 356.02 
  Macro-tasks:
    bulk solvent and scale       = 40.54  
    individual site refinement   = 151.91 
    weights calculation          = 32.15  
    collect and process          = 6.60   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 231.33 
  Micro-tasks:
    mask                            = 2.46   
    f_calc                          = 112.63 
    alpha_beta                      = 8.33   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 123.78 
    fmodel                         = 7.58   
    r_factors                      = 0.32   
    phase_errors                   = 10.33  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 266.89 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.968 micro seconds
Total CPU time: 6.17 minutes
from_scatterers_fft:    666 calls, 112.17 s
gradients_fft:          612 calls, 109.91 s

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

# Date 2008-01-16 Time 00:39:41 PST -0800 (1200472781.13 s)
Start R-work = 0.4888, R-free = 0.4835 (no bulk solvent and anisotropic scale)
Final R-work = 0.1360, R-free = 0.1803 (no bulk solvent and anisotropic scale)

Start R-work = 0.4800, R-free = 0.4774
Final R-work = 0.1180, R-free = 0.1651