# Date 2008-01-16 Time 02:07:38 PST -0800 (1200478058.77 s)
#phil __OFF__

Command line arguments: "../698.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 15302
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 698

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.25, 47.6339, 86.39, 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: 3.26, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 47.6339, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.994 2.00047
Completeness in resolution range: 0.971773
Completeness with d_max=infinity: 0.968697

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9940
                             d_min =   2.0005

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 47.6339, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.994 2.00047
Completeness in resolution range: 0.971773
Completeness with d_max=infinity: 0.968697

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9944 -  4.2796 [2114/2141]  1903   211  10.0%
  bin  2:  4.2796 -  3.4100 [2030/2046]  1826   204  10.0%
  bin  3:  3.4100 -  2.9828 [2012/2031]  1809   203  10.1%
  bin  4:  2.9828 -  2.7118 [1985/2015]  1793   192   9.7%
  bin  5:  2.7118 -  2.5184 [1967/1986]  1766   201  10.2%
  bin  6:  2.5184 -  2.3706 [1964/2000]  1769   195   9.9%
  bin  7:  2.3706 -  2.2523 [1959/1992]  1765   194   9.9%
  bin  8:  2.2523 -  2.1545 [1940/1974]  1742   198  10.2%
  bin  9:  2.1545 -  2.0718 [1941/1969]  1747   194  10.0%
  bin 10:  2.0718 -  2.0005 [1677/2004]  1510   167  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_698/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 13
        2.42 -     3.04: 2168
        3.04 -     3.66: 4660
        3.66 -     4.28: 8922
        4.28 -     4.90: 12348
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.000 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 206 " - " O   HOH Z 342 "  2.143 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " OG1 THR A 246 " - " O   HOH Z 201 "  2.219 3.040 -x+1/2,-y+1,z-1/2
  ... (remaining 28106 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_698/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_698/model_refine_001.geo

CPU time processing inputs: 9.16


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.25 47.63395 86.39 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: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4531   r_free= 0.4379   ksol= 0.00   Bsol= 0.00   scale= 0.806    |
|                                                                             |
| 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:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.252073                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9944 -  4.7728 0.99   1374  153 0.3704 0.3586      6.5384      6.5052|
|  2:  4.7728 -  3.8088 0.99   1321  146 0.3600 0.3858      6.7082      6.7763|
|  3:  3.8088 -  3.3333 0.99   1299  146 0.4014 0.3645      6.6333       6.595|
|  4:  3.3333 -  3.0313 0.99   1285  138 0.4342 0.3712       6.494      6.3671|
|  5:  3.0313 -  2.8156 0.99   1275  143 0.4810 0.4731      6.3549      6.3673|
|  6:  2.8156 -  2.6505 0.99   1278  146 0.4808 0.4977      6.2689      6.2325|
|  7:  2.6505 -  2.5184 0.99   1265  139 0.4750 0.4626      6.2202      6.1216|
|  8:  2.5184 -  2.4093 0.98   1270  142 0.4979 0.4354      6.1809      6.1451|
|  9:  2.4093 -  2.3169 0.98   1260  139 0.5081 0.5134      6.1051      6.1259|
| 10:  2.3169 -  2.2372 0.98   1247  136 0.5185 0.4974      6.1247      6.0982|
| 11:  2.2372 -  2.1675 1.00   1263  147 0.5076 0.4443      6.0266      6.0583|
| 12:  2.1675 -  2.1057 0.97   1256  128 0.5147 0.4898      5.9758      6.0037|
| 13:  2.1057 -  2.0504 0.98   1241  138 0.5092 0.5489      5.8937      5.8865|
| 14:  2.0504 -  2.0005 0.79    996  118 0.5222 0.4981      5.8471       5.748|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9944 -  4.7728  1374   153  0.71  33.18   0.81     0.73      65477.52|
|  2:  4.7728 -  3.8088  1321   146  0.75  30.92   0.90     0.79      84485.70|
|  3:  3.8088 -  3.3333  1299   146  0.68  37.00   0.85     0.76      87188.83|
|  4:  3.3333 -  3.0313  1285   138  0.62  42.03   0.82     0.68      73946.23|
|  5:  3.0313 -  2.8156  1275   143  0.53  49.95   0.76     0.59      65360.07|
|  6:  2.8156 -  2.6505  1278   146  0.51  51.23   0.74     0.56      57588.47|
|  7:  2.6505 -  2.5184  1265   139  0.49  52.54   0.75     0.55      53807.24|
|  8:  2.5184 -  2.4093  1270   142  0.49  53.19   0.76     0.55      48852.64|
|  9:  2.4093 -  2.3169  1260   139  0.45  55.82   0.72     0.53      46038.12|
| 10:  2.3169 -  2.2372  1247   136  0.45  56.18   0.73     0.51      43592.45|
| 11:  2.2372 -  2.1675  1263   147  0.41  58.90   0.77     0.49      41344.94|
| 12:  2.1675 -  2.1057  1256   128  0.39  61.00   0.76     0.47      39762.90|
| 13:  2.1057 -  2.0504  1241   138  0.34  64.63   0.74     0.40      36096.08|
| 14:  2.0504 -  2.0005   996   118  0.28  69.29   0.73     0.31      31881.86|
|alpha:            min =        0.31 max =            0.79 mean =         0.57|
|beta:             min =    31881.86 max =        87188.83 mean =     56039.16|
|figures of merit: min =        0.00 max =            1.00 mean =         0.51|
|phase err.(work): min =        0.00 max =           89.96 mean =        50.61|
|phase err.(test): min =        0.00 max =           89.86 mean =        50.76|
|-----------------------------------------------------------------------------|

============================== 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 = 9.580862              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 77.194   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.841439              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.460   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       23 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      159 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      683 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1490 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2610 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3876 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5035 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6548 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7683 |
|-----------------------------------------------------------------------------|
|-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 |       54.038 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.093    4.900  1.196 |       1.702 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.072)------------------------------------------|
|    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 = 12.072)------------------------------------------|
|    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: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4602   r_free= 0.4444   ksol= 0.00   Bsol= 0.00   scale= 0.776    |
|                                                                             |
| 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:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.255525                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4452   r_free= 0.4272   ksol= 0.33   Bsol= 20.00   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.74,11.17,7.74,0.00,0.00,0.00); trace/3= 8.55                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.64 A                  |
| x-ray target function (ml) for work reflections: 6.243980                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.154479              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.612   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.822479              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.093   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4452      final r-factor (work) = 0.3448          |
| start r-factor (free) = 0.4272      final r-factor (free) = 0.3635          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 82.6971 = 9.15 * 0.50 * 6.2612 + 1.00 * 54.0381                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.1374 = 9.15 * 0.50 * 6.1192 + 1.00 * 0.1286                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3448      final r-factor (work) = 0.2873          |
| start r-factor (free) = 0.3635      final r-factor (free) = 0.3226          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.0476 = 0.82 * 1.00 * 6.1192 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9374 = 0.82 * 1.00 * 5.9856 + 1.00 * 0.0144                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.072)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.24   11.62    None  None   None       |
|    all(noH): 2823   0      0.00    81.24   11.62    None  None   None       |
|    Sol.    : 438    0      0.00    81.24   26.99    None  None   None       |
|    Mac.    : 2385   0      0.00    66.25   8.80     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.124: 1460   |   5:    40.622 -  48.746:   74        |
|      1:     8.124 -  16.249:  693   |   6:    48.746 -  56.870:   28        |
|      2:    16.249 -  24.373:  292   |   7:    56.870 -  64.995:    3        |
|      3:    24.373 -  32.497:  163   |   8:    64.995 -  73.119:    4        |
|      4:    32.497 -  40.622:  103   |   9:    73.119 -  81.243:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2873 r_free = 0.3226             target_work(ml) = 5.946         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2868 r_free = 0.3220             target_work(ml) = 5.945         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2868   r_free= 0.3220   ksol= 0.33   Bsol= 20.00   scale= 1.086   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.74,11.17,7.74,0.00,0.00,0.00); trace/3= 8.55                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.944823                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2834   r_free= 0.3178   ksol= 0.33   Bsol= 45.69   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.63,7.30,4.95,0.00,0.00,0.00); trace/3= 5.29                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.944980                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.242001              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.739   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.391314              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 126.116  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2834      final r-factor (work) = 0.1902          |
| start r-factor (free) = 0.3178      final r-factor (free) = 0.2332          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.7990 = 7.24 * 0.50 * 5.9847 + 1.00 * 0.1282                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.9434 = 7.24 * 0.50 * 5.7600 + 1.00 * 0.0866                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1902      final r-factor (work) = 0.1685          |
| start r-factor (free) = 0.2332      final r-factor (free) = 0.2104          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2709 = 0.39 * 1.00 * 5.7600 + 1.00 * 0.0169                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1878 = 0.39 * 1.00 * 5.5211 + 1.00 * 0.0273                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.072)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.18   11.76    None  None   None       |
|    all(noH): 2823   0      0.00    76.18   11.76    None  None   None       |
|    Sol.    : 438    0      0.00    73.93   32.19    None  None   None       |
|    Mac.    : 2385   0      0.00    76.18   8.00     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:     0.000 -   7.618: 1535   |   5:    38.091 -  45.709:  101        |
|      1:     7.618 -  15.237:  649   |   6:    45.709 -  53.328:   64        |
|      2:    15.237 -  22.855:  199   |   7:    53.328 -  60.946:   25        |
|      3:    22.855 -  30.473:  132   |   8:    60.946 -  68.564:    8        |
|      4:    30.473 -  38.091:  106   |   9:    68.564 -  76.182:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1685 r_free = 0.2104             target_work(ml) = 5.479         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1681 r_free = 0.2104             target_work(ml) = 5.478         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1681   r_free= 0.2104   ksol= 0.33   Bsol= 45.69   scale= 1.039   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.63,7.30,4.95,0.00,0.00,0.00); trace/3= 5.29                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.478412                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1662   r_free= 0.2101   ksol= 0.32   Bsol= 58.01   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.51,4.27,3.95,0.00,0.00,0.00); trace/3= 3.58                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.475160                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.435026              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.087  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.409128              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 93.888   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1662      final r-factor (work) = 0.1320          |
| start r-factor (free) = 0.2101      final r-factor (free) = 0.1712          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.5878 = 3.44 * 0.50 * 5.5318 + 1.00 * 0.0869                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.3024 = 3.44 * 0.50 * 5.3758 + 1.00 * 0.0694                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1320      final r-factor (work) = 0.1247          |
| start r-factor (free) = 0.1712      final r-factor (free) = 0.1646          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2127 = 0.41 * 1.00 * 5.3758 + 1.00 * 0.0133                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1545 = 0.41 * 1.00 * 5.2374 + 1.00 * 0.0118                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.072)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.89   12.05    None  None   None       |
|    all(noH): 2823   0      0.00    77.89   12.05    None  None   None       |
|    Sol.    : 438    0      1.13    73.27   35.00    None  None   None       |
|    Mac.    : 2385   0      0.00    77.89   7.83     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 -   7.789: 1614   |   5:    38.944 -  46.733:   85        |
|      1:     7.789 -  15.578:  608   |   6:    46.733 -  54.522:   69        |
|      2:    15.578 -  23.367:  164   |   7:    54.522 -  62.311:   45        |
|      3:    23.367 -  31.156:  107   |   8:    62.311 -  70.100:   16        |
|      4:    31.156 -  38.944:  109   |   9:    70.100 -  77.889:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1247 r_free = 0.1646             target_work(ml) = 5.221         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1247 r_free = 0.1646             target_work(ml) = 5.220         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1247   r_free= 0.1646   ksol= 0.32   Bsol= 58.01   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.51,4.27,3.95,0.00,0.00,0.00); trace/3= 3.58                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.220442                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1248   r_free= 0.1650   ksol= 0.33   Bsol= 58.01   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.34,3.54,3.80,0.00,0.00,0.00); trace/3= 3.23                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.221245                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.007383              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 131.189  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.145748              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.289  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1248      final r-factor (work) = 0.1146          |
| start r-factor (free) = 0.1650      final r-factor (free) = 0.1593          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9459 = 3.01 * 0.50 * 5.2381 + 1.00 * 0.0694                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.8732 = 3.01 * 0.50 * 5.1851 + 1.00 * 0.0765                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1146      final r-factor (work) = 0.1159          |
| start r-factor (free) = 0.1593      final r-factor (free) = 0.1582          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7674 = 0.15 * 1.00 * 5.1851 + 1.00 * 0.0117                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7631 = 0.15 * 1.00 * 5.1706 + 1.00 * 0.0095                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.072)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    73.16   11.36    None  None   None       |
|    all(noH): 2823   0      0.00    73.16   11.36    None  None   None       |
|    Sol.    : 438    0      1.23    71.58   32.00    None  None   None       |
|    Mac.    : 2385   0      0.00    73.16   7.57     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 -   7.316: 1578   |   5:    36.581 -  43.898:   87        |
|      1:     7.316 -  14.633:  641   |   6:    43.898 -  51.214:   67        |
|      2:    14.633 -  21.949:  168   |   7:    51.214 -  58.530:   30        |
|      3:    21.949 -  29.265:  123   |   8:    58.530 -  65.846:   10        |
|      4:    29.265 -  36.581:  112   |   9:    65.846 -  73.163:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1159 r_free = 0.1582             target_work(ml) = 5.166         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1159 r_free = 0.1583             target_work(ml) = 5.166         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1159   r_free= 0.1583   ksol= 0.33   Bsol= 58.01   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.34,3.54,3.80,0.00,0.00,0.00); trace/3= 3.23                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.165672                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1158   r_free= 0.1582   ksol= 0.34   Bsol= 58.01   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.31,3.27,3.77,0.00,0.00,0.00); trace/3= 3.12                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.165449                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.470592              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 138.109  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.276343              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 96.314   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1158      final r-factor (work) = 0.1121          |
| start r-factor (free) = 0.1582      final r-factor (free) = 0.1566          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.0479 = 3.47 * 0.50 * 5.1700 + 1.00 * 0.0765                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.0228 = 3.47 * 0.50 * 5.1501 + 1.00 * 0.0858                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1121      final r-factor (work) = 0.1107          |
| start r-factor (free) = 0.1566      final r-factor (free) = 0.1564          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4325 = 0.28 * 1.00 * 5.1501 + 1.00 * 0.0093                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4362 = 0.28 * 1.00 * 5.1387 + 1.00 * 0.0161                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.072)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    75.55   11.44    None  None   None       |
|    all(noH): 2823   0      0.00    75.55   11.44    None  None   None       |
|    Sol.    : 438    0      1.02    67.86   32.66    None  None   None       |
|    Mac.    : 2385   0      0.00    75.55   7.55     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 -   7.555: 1634   |   5:    37.775 -  45.330:   88        |
|      1:     7.555 -  15.110:  593   |   6:    45.330 -  52.885:   77        |
|      2:    15.110 -  22.665:  168   |   7:    52.885 -  60.439:   21        |
|      3:    22.665 -  30.220:  110   |   8:    60.439 -  67.994:   12        |
|      4:    30.220 -  37.775:  115   |   9:    67.994 -  75.549:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1107 r_free = 0.1564             target_work(ml) = 5.139         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1106 r_free = 0.1564             target_work(ml) = 5.139         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1106   r_free= 0.1564   ksol= 0.34   Bsol= 58.01   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.31,3.27,3.77,0.00,0.00,0.00); trace/3= 3.12                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.139223                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9944 -  4.7728 0.99   1374  153 0.1022 0.1281      5.3933      5.5075|
|  2:  4.7728 -  3.8088 0.99   1321  146 0.0870 0.1142      5.4485      5.6629|
|  3:  3.8088 -  3.3333 0.99   1299  146 0.1046 0.1484      5.4754      5.8638|
|  4:  3.3333 -  3.0313 0.99   1285  138 0.1192 0.1480      5.4359      5.5706|
|  5:  3.0313 -  2.8156 0.99   1275  143 0.1313 0.1664      5.3268      5.5066|
|  6:  2.8156 -  2.6505 0.99   1278  146 0.1218 0.1881      5.2212      5.4846|
|  7:  2.6505 -  2.5184 0.99   1265  139 0.1223 0.1670       5.164      5.3677|
|  8:  2.5184 -  2.4093 0.98   1270  142 0.1157 0.1748      5.0784      5.3752|
|  9:  2.4093 -  2.3169 0.98   1260  139 0.1147 0.1749      5.0167      5.2585|
| 10:  2.3169 -  2.2372 0.98   1247  136 0.1112 0.1724      4.9811      5.2397|
| 11:  2.2372 -  2.1675 1.00   1263  147 0.1123 0.1750      4.9351      5.2742|
| 12:  2.1675 -  2.1057 0.97   1256  128 0.1087 0.1706      4.8693      5.1751|
| 13:  2.1057 -  2.0504 0.98   1241  138 0.1096 0.1690      4.7784      5.0516|
| 14:  2.0504 -  2.0005 0.79    996  118 0.1009 0.1753      4.6598      4.9508|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9944 -  4.7728  1374   153  0.94   8.87   0.98     0.95       7132.21|
|  2:  4.7728 -  3.8088  1321   146  0.95   8.01   1.00     0.99       9135.20|
|  3:  3.8088 -  3.3333  1299   146  0.93  11.27   1.01     1.00      10517.74|
|  4:  3.3333 -  3.0313  1285   138  0.93  12.94   0.99     0.97       9740.86|
|  5:  3.0313 -  2.8156  1275   143  0.90  15.70   0.98     0.95       8221.67|
|  6:  2.8156 -  2.6505  1278   146  0.90  15.87   0.97     0.94       7067.52|
|  7:  2.6505 -  2.5184  1265   139  0.91  15.58   0.98     0.95       6273.14|
|  8:  2.5184 -  2.4093  1270   142  0.91  15.06   0.98     0.96       5407.91|
|  9:  2.4093 -  2.3169  1260   139  0.91  15.65   0.99     0.96       4928.64|
| 10:  2.3169 -  2.2372  1247   136  0.90  15.76   0.99     0.96       4637.49|
| 11:  2.2372 -  2.1675  1263   147  0.90  15.93   0.99     0.95       4327.96|
| 12:  2.1675 -  2.1057  1256   128  0.91  14.97   0.99     0.97       3905.19|
| 13:  2.1057 -  2.0504  1241   138  0.91  15.45   0.99     0.97       3293.63|
| 14:  2.0504 -  2.0005   996   118  0.91  14.94   0.97     0.93       2597.77|
|alpha:            min =        0.93 max =            1.00 mean =         0.96|
|beta:             min =     2597.77 max =        10517.74 mean =      6319.01|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.86 mean =        13.93|
|phase err.(test): min =        0.00 max =           89.42 mean =        13.42|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1106   r_free= 0.1564   ksol= 0.33   Bsol= 55.21   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.77,0.10,0.67,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.139129                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1106   r_free= 0.1564   ksol= 0.33   Bsol= 55.21   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.77,0.10,0.67,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.139129                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9944 -  4.7728 0.99   1374  153 0.1018 0.1282      5.3896      5.5043|
|  2:  4.7728 -  3.8088 0.99   1321  146 0.0866 0.1135      5.4449      5.6575|
|  3:  3.8088 -  3.3333 0.99   1299  146 0.1044 0.1483      5.4736      5.8645|
|  4:  3.3333 -  3.0313 0.99   1285  138 0.1192 0.1481      5.4366      5.5709|
|  5:  3.0313 -  2.8156 0.99   1275  143 0.1316 0.1665      5.3288      5.5081|
|  6:  2.8156 -  2.6505 0.99   1278  146 0.1221 0.1884      5.2228      5.4856|
|  7:  2.6505 -  2.5184 0.99   1265  139 0.1224 0.1671      5.1653      5.3689|
|  8:  2.5184 -  2.4093 0.98   1270  142 0.1158 0.1749      5.0793      5.3758|
|  9:  2.4093 -  2.3169 0.98   1260  139 0.1147 0.1749      5.0172       5.259|
| 10:  2.3169 -  2.2372 0.98   1247  136 0.1112 0.1726      4.9817      5.2414|
| 11:  2.2372 -  2.1675 1.00   1263  147 0.1124 0.1749      4.9355       5.274|
| 12:  2.1675 -  2.1057 0.97   1256  128 0.1087 0.1706      4.8696      5.1754|
| 13:  2.1057 -  2.0504 0.98   1241  138 0.1096 0.1690      4.7783      5.0519|
| 14:  2.0504 -  2.0005 0.79    996  118 0.1010 0.1753      4.6601      4.9509|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9944 -  4.7728  1374   153  0.94   8.83   0.98     0.95       7083.03|
|  2:  4.7728 -  3.8088  1321   146  0.95   7.96   1.01     0.99       9074.78|
|  3:  3.8088 -  3.3333  1299   146  0.93  11.23   1.01     1.01      10471.56|
|  4:  3.3333 -  3.0313  1285   138  0.93  12.95   0.99     0.98       9758.67|
|  5:  3.0313 -  2.8156  1275   143  0.90  15.72   0.99     0.96       8247.92|
|  6:  2.8156 -  2.6505  1278   146  0.90  15.89   0.98     0.94       7088.64|
|  7:  2.6505 -  2.5184  1265   139  0.91  15.60   0.98     0.96       6287.56|
|  8:  2.5184 -  2.4093  1270   142  0.91  15.07   0.99     0.96       5416.10|
|  9:  2.4093 -  2.3169  1260   139  0.91  15.66   1.00     0.97       4937.51|
| 10:  2.3169 -  2.2372  1247   136  0.90  15.77   1.00     0.97       4644.00|
| 11:  2.2372 -  2.1675  1263   147  0.90  15.94   0.99     0.96       4331.98|
| 12:  2.1675 -  2.1057  1256   128  0.91  14.99   1.00     0.98       3907.69|
| 13:  2.1057 -  2.0504  1241   138  0.91  15.46   1.00     0.98       3293.98|
| 14:  2.0504 -  2.0005   996   118  0.91  14.94   0.98     0.94       2597.86|
|alpha:            min =        0.94 max =            1.01 mean =         0.97|
|beta:             min =     2597.86 max =        10471.56 mean =      6315.19|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.98 mean =        13.93|
|phase err.(test): min =        0.00 max =           89.85 mean =        13.43|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.072)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.28    78.83   14.72    None  None   None       |
|    all(noH): 2823   0      3.28    78.83   14.72    None  None   None       |
|    Sol.    : 438    0      4.30    71.14   35.94    None  None   None       |
|    Mac.    : 2385   0      3.28    78.83   10.82    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:     3.278 -  10.833: 1634   |   5:    41.053 -  48.608:   88        |
|      1:    10.833 -  18.388:  593   |   6:    48.608 -  56.163:   77        |
|      2:    18.388 -  25.943:  168   |   7:    56.163 -  63.718:   21        |
|      3:    25.943 -  33.498:  110   |   8:    63.718 -  71.273:   12        |
|      4:    33.498 -  41.053:  115   |   9:    71.273 -  78.828:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 338         
Filter by distance & map next to the model:
   mapped sites are within: 0.322 - 5.585
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 330 from: 338
   mapped sites are within: 0.701 - 5.585

peak=    6.233 closest distance to " CG2 VAL A 230 " =    1.158
peak=    6.169 closest distance to " CG  LEU A   5 " =    1.213
peak=    6.155 closest distance to " CB  VAL A 230 " =    1.252
peak=    6.117 closest distance to " NH2 ARG A  56 " =    2.329
peak=    5.936 closest distance to " CG  LEU A 228 " =    1.214
peak=    5.721 closest distance to " CB  VAL A 296 " =    1.214
peak=    5.395 closest distance to " CG2 VAL A 296 " =    1.017
peak=    5.190 closest distance to " CB  GLN A 223 " =    1.392
peak=    4.993 closest distance to " CG  PRO A  54 " =    1.224
peak=    4.950 closest distance to " CB  ARG A 275 " =    0.885
peak=    4.858 closest distance to " CB  SER A  63 " =    1.213
peak=    4.769 closest distance to " CB  GLN A 183 " =    1.262
peak=    4.691 closest distance to " CB  GLU A 152 " =    1.171
peak=    4.654 closest distance to " O   HOH Z 232 " =    2.393
peak=    4.560 closest distance to " NE2 GLN A  11 " =    1.069
peak=    4.518 closest distance to " O   HOH Z 272 " =    1.916
peak=    4.459 closest distance to " O   SER A  87 " =    2.251
peak=    4.449 closest distance to " C   PRO A 198 " =    1.494
peak=    4.429 closest distance to " O   HOH Z 402 " =    1.548
peak=    4.419 closest distance to " CD2 LEU A   5 " =    1.179
peak=    4.408 closest distance to " CB  ASN A 148 " =    1.453
peak=    4.388 closest distance to " O   HOH Z 236 " =    1.841
peak=    4.380 closest distance to " CA  TYR A  30 " =    0.923
peak=    4.347 closest distance to " O   HOH Z 126 " =    1.845
peak=    4.292 closest distance to " O   HOH Z  43 " =    2.127
peak=    4.289 closest distance to " OD1 ASN A  69 " =    2.626
peak=    4.282 closest distance to " O   HOH Z 234 " =    3.644
peak=    4.275 closest distance to " CZ  PHE A 218 " =    1.175
peak=    4.261 closest distance to " O   HOH Z 423 " =    1.880
peak=    4.254 closest distance to " O   HOH Z 193 " =    1.854
peak=    4.236 closest distance to " O   HOH Z 403 " =    1.652
peak=    4.228 closest distance to " CB  ARG A 190 " =    1.634
peak=    4.203 closest distance to " CG  PRO A 213 " =    1.212
peak=    4.187 closest distance to " CB  SER A   3 " =    1.239
peak=    4.178 closest distance to " O   HOH Z 303 " =    2.089
peak=    4.161 closest distance to " O   HOH Z  44 " =    2.285
peak=    4.133 closest distance to " O   HOH Z 298 " =    1.838
peak=    4.129 closest distance to " O   HOH Z  63 " =    2.011
peak=    4.103 closest distance to " CB  ARG A  79 " =    1.439
peak=    4.096 closest distance to " CB  ASN A  39 " =    0.822
peak=    4.095 closest distance to " O   HOH Z 368 " =    2.301
peak=    4.058 closest distance to " CB  PRO A  54 " =    0.841
peak=    4.050 closest distance to " CG  PRO A 280 " =    0.798
peak=    4.046 closest distance to " CG1 VAL A 230 " =    1.144
peak=    4.033 closest distance to " O   HOH Z  97 " =    1.931
peak=    4.013 closest distance to " O   HOH Z  61 " =    1.533
peak=    4.007 closest distance to " O   HOH Z 197 " =    2.616
peak=    4.007 closest distance to " O   HOH Z 280 " =    2.915
peak=    4.000 closest distance to " CG  PRO A 243 " =    1.116
peak=    3.999 closest distance to " O   HOH Z 158 " =    3.207
peak=    3.998 closest distance to " O   HOH Z  48 " =    1.712
peak=    3.974 closest distance to " O   HOH Z 147 " =    1.821
peak=    3.946 closest distance to " O   HOH Z 346 " =    1.653
peak=    3.928 closest distance to " O   HOH Z 369 " =    2.165
peak=    3.898 closest distance to " O   HOH Z  97 " =    2.497
peak=    3.895 closest distance to " O   HOH Z 189 " =    2.694
peak=    3.894 closest distance to " CB  GLU A 277 " =    3.619
peak=    3.893 closest distance to " O   HOH Z 316 " =    3.084
peak=    3.888 closest distance to " O   HOH Z 126 " =    1.643
peak=    3.885 closest distance to " CB  TRP A 266 " =    0.923
peak=    3.882 closest distance to " O   HOH Z 427 " =    2.986
peak=    3.878 closest distance to " O   HOH Z 142 " =    1.503
peak=    3.865 closest distance to " CB BVAL A  41 " =    0.877
peak=    3.861 closest distance to " CD  LYS A 166 " =    1.303
peak=    3.860 closest distance to " O   HOH Z  54 " =    1.655
peak=    3.857 closest distance to " O   HOH Z 420 " =    2.047
peak=    3.856 closest distance to " O   HOH Z  80 " =    1.814
peak=    3.855 closest distance to " O   HOH Z  59 " =    2.336
peak=    3.853 closest distance to " O   HOH Z 383 " =    2.031
peak=    3.833 closest distance to " O   HOH Z  40 " =    1.816
peak=    3.830 closest distance to " CG1BVAL A  72 " =    1.743
peak=    3.810 closest distance to " CG1 VAL A 296 " =    1.156
peak=    3.810 closest distance to " CB  ARG A 139 " =    0.958
peak=    3.799 closest distance to " O   HOH Z 193 " =    2.134
peak=    3.787 closest distance to " O   HOH Z 344 " =    3.023
peak=    3.782 closest distance to " CB  THR A  31 " =    1.641
peak=    3.782 closest distance to " O   HOH Z 248 " =    1.628
peak=    3.777 closest distance to " CA  ALA A  51 " =    0.944
peak=    3.775 closest distance to " O   HOH Z 214 " =    2.333
peak=    3.751 closest distance to " CB  TRP A 179 " =    1.459
peak=    3.749 closest distance to " CB  VAL A 265 " =    1.304
peak=    3.744 closest distance to " CD2 LEU A 228 " =    1.100
peak=    3.743 closest distance to " O   HOH Z  21 " =    1.766
peak=    3.739 closest distance to " O   HOH Z 128 " =    2.018
peak=    3.739 closest distance to " CB  VAL A 202 " =    1.406
peak=    3.736 closest distance to " CA  ARG A 195 " =    1.222
peak=    3.724 closest distance to " CB  GLU A 128 " =    1.061
peak=    3.724 closest distance to " O   HOH Z 134 " =    1.501
peak=    3.721 closest distance to " CB  GLU A  46 " =    0.978
peak=    3.716 closest distance to " O   HOH Z 426 " =    1.571
peak=    3.715 closest distance to " CG1 ILE A  49 " =    1.572
peak=    3.713 closest distance to " CB  ASP A 140 " =    0.933
peak=    3.708 closest distance to " O   HOH Z  15 " =    2.067
peak=    3.708 closest distance to " O   HOH Z 412 " =    3.733
peak=    3.706 closest distance to " O   HOH Z 265 " =    2.173
peak=    3.706 closest distance to " CA  THR A 264 " =    0.809
peak=    3.704 closest distance to " O   HOH Z 389 " =    1.952
peak=    3.695 closest distance to " CG1 ILE A  33 " =    1.251
peak=    3.689 closest distance to " CE1 HIS A 108 " =    1.159
peak=    3.688 closest distance to " NH2 ARG A 156 " =    1.130
peak=    3.681 closest distance to " CA  ALA A  21 " =    1.129
peak=    3.677 closest distance to " O   HOH Z 130 " =    2.308
peak=    3.676 closest distance to " O   HOH Z 250 " =    1.383
peak=    3.662 closest distance to " CB  ILE A 120 " =    1.328
peak=    3.659 closest distance to " OG BSER A 164 " =    2.193
peak=    3.649 closest distance to " O   HOH Z 203 " =    1.778
peak=    3.642 closest distance to " CG  GLN A  58 " =    2.824
peak=    3.638 closest distance to " ND2 ASN A 187 " =    1.521
peak=    3.633 closest distance to " O   MET A 105 " =    1.861
peak=    3.633 closest distance to " CG2 THR A 221 " =    1.073
peak=    3.628 closest distance to " O   HOH Z 371 " =    3.243
peak=    3.620 closest distance to " O   HOH Z  78 " =    1.688
peak=    3.619 closest distance to " CA  LYS A 117 " =    1.291
peak=    3.618 closest distance to " O   TRP A 274 " =    1.908
peak=    3.617 closest distance to " O   ASP A 124 " =    1.227
peak=    3.605 closest distance to " O   HOH Z 422 " =    2.702
peak=    3.603 closest distance to " O   ALA A 165 " =    1.453
peak=    3.600 closest distance to " O   HOH Z 180 " =    2.114
peak=    3.597 closest distance to " O   HOH Z 417 " =    3.195
peak=    3.596 closest distance to " CB  ALA A 291 " =    1.327
peak=    3.592 closest distance to " CG  ARG A  66 " =    2.710
peak=    3.587 closest distance to " O   HOH Z 245 " =    1.388
peak=    3.577 closest distance to " OD2 ASP A 286 " =    2.945
peak=    3.576 closest distance to " O   HOH Z 345 " =    3.063
peak=    3.566 closest distance to " O   HOH Z  48 " =    1.569
peak=    3.562 closest distance to " O   HOH Z  88 " =    2.540
peak=    3.562 closest distance to " CB  ASN A 187 " =    1.234
peak=    3.550 closest distance to " N   ASN A  39 " =    1.232
peak=    3.547 closest distance to " O   HOH Z 133 " =    2.438
peak=    3.542 closest distance to " O   HOH Z 271 " =    2.624
peak=    3.534 closest distance to " CE1 TYR A 186 " =    1.308
peak=    3.529 closest distance to " CA  THR A  52 " =    1.028
peak=    3.528 closest distance to " CG2 ILE A  20 " =    1.425
peak=    3.527 closest distance to " CG  MET A 185 " =    1.086
peak=    3.527 closest distance to " O   HOH Z 261 " =    2.270
peak=    3.523 closest distance to " O   HOH Z 285 " =    3.107
peak=    3.520 closest distance to " CB  ALA A   9 " =    1.605
peak=    3.520 closest distance to " OD2 ASP A 298 " =    3.807
peak=    3.519 closest distance to " CD1 LEU A 300 " =    1.137
peak=    3.519 closest distance to " O   HOH Z 365 " =    2.997
peak=    3.515 closest distance to " O   HOH Z 171 " =    2.651
peak=    3.510 closest distance to " CD2 TRP A 179 " =    1.325
peak=    3.504 closest distance to " CB  GLN A 278 " =    0.809
peak=    3.502 closest distance to " CB  TRP A 150 " =    1.445
peak=    3.498 closest distance to " O   HOH Z 411 " =    1.799
peak=    3.497 closest distance to " O   HOH Z 199 " =    1.572
peak=    3.497 closest distance to " CG  GLN A  77 " =    1.901
peak=    3.495 closest distance to " CA  TYR A 116 " =    1.435
peak=    3.492 closest distance to " O   HOH Z 407 " =    2.602
peak=    3.485 closest distance to " CA  ALA A 248 " =    1.265
peak=    3.480 closest distance to " N   SER A 135 " =    1.468
peak=    3.469 closest distance to " CG1 VAL A 153 " =    0.958
peak=    3.468 closest distance to " O   HOH Z  68 " =    1.738
peak=    3.465 closest distance to " O   HOH Z 128 " =    2.252
peak=    3.463 closest distance to " O   HOH Z  35 " =    2.424
peak=    3.459 closest distance to " CB  LEU A 143 " =    1.133
peak=    3.457 closest distance to " ND1 HIS A  81 " =    1.698
peak=    3.448 closest distance to " CB  GLN A  88 " =    1.145
peak=    3.447 closest distance to " O   HOH Z 291 " =    1.583
peak=    3.447 closest distance to " O   HOH Z 437 " =    1.978
peak=    3.447 closest distance to " CB  ARG A  79 " =    0.910
peak=    3.443 closest distance to " CG BARG A 275 " =    1.338
peak=    3.440 closest distance to " CB  ALA A 248 " =    0.976
peak=    3.438 closest distance to " OG  SER A  22 " =    2.702
peak=    3.436 closest distance to " CB  HIS A 108 " =    0.804
peak=    3.426 closest distance to " NZ  LYS A  48 " =    1.281
peak=    3.424 closest distance to " O   HOH Z 263 " =    1.745
peak=    3.423 closest distance to " O   HOH Z 419 " =    1.734
peak=    3.420 closest distance to " CD  ARG A 159 " =    0.749
peak=    3.419 closest distance to " O   HOH Z 421 " =    1.550
peak=    3.413 closest distance to " OG1 THR A 294 " =    2.439
peak=    3.406 closest distance to " O   HOH Z 435 " =    1.943
peak=    3.405 closest distance to " O   HOH Z 155 " =    3.316
peak=    3.399 closest distance to " CB  GLN A 103 " =    0.936
peak=    3.396 closest distance to " CA  ALA A  84 " =    1.278
peak=    3.396 closest distance to " O   HOH Z 258 " =    1.719
peak=    3.395 closest distance to " O   HOH Z 126 " =    1.883
peak=    3.393 closest distance to " CA  ASP A 162 " =    1.092
peak=    3.392 closest distance to " CA  ASP A 140 " =    1.209
peak=    3.390 closest distance to " CB  ALA A 100 " =    1.224
peak=    3.379 closest distance to " CA  ASN A 215 " =    1.129
peak=    3.378 closest distance to " CA  THR A 221 " =    0.863
peak=    3.374 closest distance to " O   HOH Z  48 " =    1.371
peak=    3.373 closest distance to " CB  LEU A 228 " =    1.278
peak=    3.373 closest distance to " CD1 LEU A   5 " =    1.357
peak=    3.372 closest distance to " O   HOH Z  66 " =    2.343
peak=    3.365 closest distance to " O   HOH Z 403 " =    1.386
peak=    3.364 closest distance to " CB  SER A  26 " =    1.710
peak=    3.362 closest distance to " CA  ARG A  36 " =    1.063
peak=    3.362 closest distance to " O   HOH Z 299 " =    4.290
peak=    3.359 closest distance to " O   HOH Z 187 " =    2.351
peak=    3.353 closest distance to " O   HOH Z 332 " =    1.441
peak=    3.352 closest distance to " N   ASP A 162 " =    1.323
peak=    3.350 closest distance to " O   HOH Z 380 " =    1.912
peak=    3.349 closest distance to " O   HOH Z  83 " =    1.617
peak=    3.347 closest distance to " CA  ASP A 191 " =    0.853
peak=    3.344 closest distance to " CD ALYS A 290 " =    1.066
peak=    3.340 closest distance to " O   HOH Z 247 " =    1.369
peak=    3.337 closest distance to " OH  TYR A 116 " =    1.185
peak=    3.336 closest distance to " O   HOH Z 132 " =    2.832
peak=    3.331 closest distance to " CA  ALA A 295 " =    0.998
peak=    3.331 closest distance to " O   HOH Z 193 " =    1.592
peak=    3.329 closest distance to " CG  PRO A 198 " =    1.287
peak=    3.328 closest distance to " O   HOH Z 261 " =    1.969
peak=    3.327 closest distance to " CD  ARG A 269 " =    0.921
peak=    3.325 closest distance to " CG  GLN A  88 " =    1.037
peak=    3.323 closest distance to " CE  LYS A  76 " =    0.829
peak=    3.323 closest distance to " O   HOH Z  20 " =    1.489
peak=    3.322 closest distance to " CB  ALA A 256 " =    1.254
peak=    3.321 closest distance to " N   VAL A 126 " =    1.488
peak=    3.319 closest distance to " O   HOH Z  90 " =    3.448
peak=    3.318 closest distance to " O   HOH Z 227 " =    1.576
peak=    3.313 closest distance to " CB  PRO A 198 " =    1.132
peak=    3.309 closest distance to " CA  ALA A 158 " =    1.249
peak=    3.307 closest distance to " OG BSER A 134 " =    2.924
peak=    3.302 closest distance to " OE1 GLN A  11 " =    1.904
peak=    3.302 closest distance to " CB  ALA A 242 " =    0.889
peak=    3.301 closest distance to " O   HOH Z 273 " =    2.940
peak=    3.300 closest distance to " O   HOH Z 171 " =    3.879
peak=    3.295 closest distance to " O   HOH Z 305 " =    3.695
peak=    3.294 closest distance to " O   HOH Z 425 " =    1.962
peak=    3.292 closest distance to " O   HOH Z 227 " =    1.679
peak=    3.290 closest distance to " CD1 LEU A  96 " =    0.701
peak=    3.288 closest distance to " CB  PHE A 204 " =    0.877
peak=    3.277 closest distance to " CB  MET A  40 " =    0.827
peak=    3.276 closest distance to " CD1 ILE A 106 " =    1.032
peak=    3.276 closest distance to " CB  THR A 157 " =    1.195
peak=    3.271 closest distance to " O   HOH Z 189 " =    2.709
peak=    3.270 closest distance to " CG  MET A 185 " =    1.100
peak=    3.266 closest distance to " OD1 ASN A 217 " =    1.685
peak=    3.266 closest distance to " NH2 ARG A  79 " =    1.279
peak=    3.265 closest distance to " CZ2 TRP A 179 " =    1.796
peak=    3.263 closest distance to " CA  GLY A 211 " =    1.308
peak=    3.262 closest distance to " O   GLN A 278 " =    1.503
peak=    3.258 closest distance to " O   HOH Z 329 " =    4.033
peak=    3.251 closest distance to " O   HOH Z  47 " =    1.749
peak=    3.249 closest distance to " CB  ALA A 295 " =    1.268
peak=    3.249 closest distance to " O   HOH Z 256 " =    2.364
peak=    3.249 closest distance to " O   HOH Z 261 " =    1.790
peak=    3.249 closest distance to " CZ  PHE A 192 " =    0.999
peak=    3.248 closest distance to " O   GLU A   2 " =    1.764
peak=    3.248 closest distance to " CD  PRO A  54 " =    0.992
peak=    3.247 closest distance to " CB  GLN A 205 " =    1.168
peak=    3.247 closest distance to " CG2 ILE A 234 " =    2.087
peak=    3.245 closest distance to " O   HOH Z 409 " =    3.482
peak=    3.245 closest distance to " O   HOH Z 258 " =    2.093
peak=    3.244 closest distance to " CA  ILE A 106 " =    0.749
peak=    3.243 closest distance to " O   HOH Z 240 " =    2.275
peak=    3.239 closest distance to " CG2 ILE A 120 " =    1.190
peak=    3.237 closest distance to " O   HOH Z 145 " =    2.723
peak=    3.237 closest distance to " O   HOH Z 109 " =    2.675
peak=    3.237 closest distance to " CG AARG A 275 " =    1.253
peak=    3.233 closest distance to " O   HOH Z 336 " =    1.765
peak=    3.226 closest distance to " CB  ARG A 259 " =    1.917
peak=    3.226 closest distance to " CB  ASN A 142 " =    1.169
peak=    3.225 closest distance to " O   HOH Z 258 " =    2.199
peak=    3.225 closest distance to " C   TYR A 214 " =    1.438
peak=    3.222 closest distance to " O   HOH Z 417 " =    2.543
peak=    3.222 closest distance to " O   HOH Z 282 " =    2.011
peak=    3.220 closest distance to " O   HOH Z 367 " =    2.164
peak=    3.217 closest distance to " O   HOH Z 406 " =    1.579
peak=    3.215 closest distance to " O   HOH Z 281 " =    4.877
peak=    3.210 closest distance to " O   ALA A 158 " =    1.265
peak=    3.209 closest distance to " O   HOH Z 214 " =    2.490
peak=    3.208 closest distance to " O   HOH Z  10 " =    1.743
peak=    3.206 closest distance to " O   HOH Z 251 " =    1.437
peak=    3.205 closest distance to " CG2 VAL A 197 " =    1.074
peak=    3.202 closest distance to " OE1 GLU A   2 " =    1.965
peak=    3.201 closest distance to " CG  GLU A 277 " =    2.217
peak=    3.201 closest distance to " O   HOH Z 163 " =    1.566
peak=    3.200 closest distance to " O   HOH Z 123 " =    2.286
peak=    3.198 closest distance to " OG1 THR A 294 " =    1.661
peak=    3.191 closest distance to " N   GLY A  98 " =    1.123
peak=    3.190 closest distance to " O   HOH Z 294 " =    1.551
peak=    3.188 closest distance to " O   HOH Z 353 " =    2.777
peak=    3.188 closest distance to " O   HOH Z  85 " =    2.122
peak=    3.187 closest distance to " CA  ASN A 176 " =    1.132
peak=    3.181 closest distance to " CZ3 TRP A  85 " =    0.931
peak=    3.177 closest distance to " O   HOH Z 188 " =    1.994
peak=    3.172 closest distance to " O   VAL A  72 " =    3.180
peak=    3.170 closest distance to " O   HOH Z 292 " =    1.641
peak=    3.170 closest distance to " O   HOH Z  50 " =    2.026
peak=    3.165 closest distance to " ND2 ASN A 110 " =    1.563
peak=    3.164 closest distance to " NH1AARG A 145 " =    1.198
peak=    3.164 closest distance to " OG BSER A 212 " =    2.404
peak=    3.158 closest distance to " CB  SER A 212 " =    1.220
peak=    3.157 closest distance to " NZ  LYS A 117 " =    3.299
peak=    3.154 closest distance to " OE2 GLU A   2 " =    1.923
peak=    3.153 closest distance to " O   HOH Z 387 " =    2.545
peak=    3.151 closest distance to " NH2BARG A 145 " =    2.029
peak=    3.151 closest distance to " O   HOH Z 148 " =    3.255
peak=    3.151 closest distance to " O   HOH Z 216 " =    2.747
peak=    3.146 closest distance to " CB  SER A 273 " =    0.797
peak=    3.142 closest distance to " N   GLU A  44 " =    2.182
peak=    3.142 closest distance to " O   HOH Z 420 " =    5.585
peak=    3.137 closest distance to " CD  LYS A  76 " =    1.916
peak=    3.134 closest distance to " CB  ALA A 114 " =    1.296
peak=    3.133 closest distance to " CD  LYS A 119 " =    2.118
peak=    3.132 closest distance to " CA  VAL A  41 " =    0.832
peak=    3.132 closest distance to " CA  GLY A 267 " =    0.853
peak=    3.128 closest distance to " N   PHE A 130 " =    1.274
peak=    3.128 closest distance to " O   GLU A   2 " =    1.572
peak=    3.125 closest distance to " CA  SER A  87 " =    1.008
peak=    3.124 closest distance to " CD  ARG A  66 " =    2.751
peak=    3.124 closest distance to " CG  GLN A 205 " =    1.031
peak=    3.123 closest distance to " O   HOH Z  78 " =    2.139
peak=    3.123 closest distance to " O   HOH Z 163 " =    1.921
peak=    3.122 closest distance to " O   HOH Z 368 " =    3.553
peak=    3.122 closest distance to " O   HOH Z  88 " =    3.106
peak=    3.121 closest distance to " O   HOH Z 359 " =    1.494
peak=    3.119 closest distance to " O   HOH Z  85 " =    1.314
peak=    3.117 closest distance to " CG2AVAL A 121 " =    2.153
peak=    3.115 closest distance to " CD2 TYR A  30 " =    0.868
peak=    3.111 closest distance to " OG  SER A 245 " =    1.568
peak=    3.110 closest distance to " O   HOH Z 357 " =    1.957
peak=    3.104 closest distance to " NZ  LYS A  76 " =    1.503
peak=    3.101 closest distance to " CA  ALA A 233 " =    1.507
peak=    3.100 closest distance to " CG2 VAL A 257 " =    0.841
peak=    3.099 closest distance to " CB  SER A 216 " =    0.787
peak=    3.094 closest distance to " O   HOH Z 139 " =    4.669
peak=    3.080 closest distance to " O   HOH Z 302 " =    2.053
peak=    3.074 closest distance to " O   HOH Z  89 " =    1.634
peak=    3.074 closest distance to " CA  ALA A 299 " =    0.954
peak=    3.072 closest distance to " CG  LEU A 281 " =    1.078
peak=    3.070 closest distance to " CB  ASN A 285 " =    0.896
peak=    3.070 closest distance to " O   HOH Z 298 " =    4.902
peak=    3.069 closest distance to " N   ASN A 127 " =    1.278
peak=    3.067 closest distance to " O   HOH Z 128 " =    1.900
peak=    3.057 closest distance to " O   THR A  31 " =    1.541
peak=    3.009 closest distance to " O   ASP A 124 " =    1.764

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 222         
Filter by distance & map next to the model:
   mapped sites are within: 0.665 - 5.606
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 219 from: 222
   mapped sites are within: 0.746 - 5.606

peak=   -4.535 closest distance to " CD  ARG A 156 " =    1.982
peak=   -4.450 closest distance to " O   HOH Z 196 " =    2.159
peak=   -4.428 closest distance to " CB  PRO A 243 " =    2.650
peak=   -4.415 closest distance to " SG  CYS A 254 " =    3.255
peak=   -4.327 closest distance to " O   HOH Z 266 " =    4.940
peak=   -4.281 closest distance to " CD  GLN A  58 " =    1.059
peak=   -4.198 closest distance to " C   HIS A 108 " =    1.208
peak=   -4.117 closest distance to " CG2BVAL A  41 " =    2.683
peak=   -4.102 closest distance to " O   VAL A  67 " =    2.769
peak=   -4.079 closest distance to " OG  SER A  97 " =    2.344
peak=   -4.064 closest distance to " O   HOH Z 166 " =    1.665
peak=   -4.031 closest distance to " CZ3 TRP A 179 " =    1.218
peak=   -4.030 closest distance to " O   HOH Z 290 " =    1.335
peak=   -3.962 closest distance to " CG  ASP A 231 " =    0.827
peak=   -3.961 closest distance to " CB  ALA A 161 " =    2.496
peak=   -3.919 closest distance to " O   PRO A 163 " =    2.131
peak=   -3.909 closest distance to " O   HOH Z 351 " =    1.630
peak=   -3.899 closest distance to " CD1 LEU A 101 " =    2.468
peak=   -3.896 closest distance to " O   HOH Z  13 " =    1.581
peak=   -3.893 closest distance to " OE1 GLN A 223 " =    2.158
peak=   -3.891 closest distance to " CG2 VAL A 230 " =    1.092
peak=   -3.865 closest distance to " CB  PHE A 192 " =    1.835
peak=   -3.853 closest distance to " O   HOH Z 394 " =    1.552
peak=   -3.820 closest distance to " CB  ALA A 291 " =    2.258
peak=   -3.787 closest distance to " OXT GLY A 302 " =    2.734
peak=   -3.781 closest distance to " O   HOH Z 114 " =    3.258
peak=   -3.752 closest distance to " O   HOH Z 231 " =    2.066
peak=   -3.742 closest distance to " O   HOH Z  11 " =    1.876
peak=   -3.720 closest distance to " O   HOH Z 283 " =    2.045
peak=   -3.720 closest distance to " O   HOH Z  52 " =    1.482
peak=   -3.702 closest distance to " CD1 PHE A  59 " =    1.946
peak=   -3.701 closest distance to " O   PRO A 198 " =    1.281
peak=   -3.669 closest distance to " CB  PRO A 163 " =    2.560
peak=   -3.666 closest distance to " OG BSER A 134 " =    1.257
peak=   -3.666 closest distance to " CD2 LEU A 300 " =    2.661
peak=   -3.656 closest distance to " CB  ALA A 248 " =    2.296
peak=   -3.651 closest distance to " NE2 GLN A 103 " =    1.763
peak=   -3.646 closest distance to " O   HOH Z 165 " =    1.894
peak=   -3.644 closest distance to " O   HOH Z 311 " =    3.676
peak=   -3.627 closest distance to " CB  ALA A 248 " =    2.053
peak=   -3.625 closest distance to " CA  ASP A 298 " =    1.080
peak=   -3.616 closest distance to " CZ  TYR A 169 " =    1.765
peak=   -3.614 closest distance to " NE2 GLN A  88 " =    1.823
peak=   -3.604 closest distance to " CG1 VAL A 112 " =    2.637
peak=   -3.599 closest distance to " CD  LYS A 289 " =    2.452
peak=   -3.571 closest distance to " CE3 TRP A 150 " =    2.131
peak=   -3.570 closest distance to " OG ASER A 134 " =    1.303
peak=   -3.563 closest distance to " CE2 TYR A  30 " =    2.704
peak=   -3.563 closest distance to " O   HOH Z 234 " =    4.174
peak=   -3.558 closest distance to " CE2 PHE A 218 " =    2.571
peak=   -3.551 closest distance to " O   HOH Z  37 " =    1.939
peak=   -3.551 closest distance to " O   HOH Z 185 " =    2.480
peak=   -3.551 closest distance to " C   ALA A 158 " =    1.304
peak=   -3.549 closest distance to " CG2 ILE A 263 " =    2.370
peak=   -3.546 closest distance to " OD2 ASP A  50 " =    2.306
peak=   -3.542 closest distance to " C   LEU A 143 " =    0.979
peak=   -3.537 closest distance to " O   HOH Z  15 " =    1.461
peak=   -3.535 closest distance to " O   VAL A 189 " =    2.626
peak=   -3.533 closest distance to " O   HOH Z  44 " =    2.203
peak=   -3.529 closest distance to " NH2AARG A 275 " =    5.067
peak=   -3.528 closest distance to " CD1 ILE A 263 " =    2.807
peak=   -3.527 closest distance to " O   VAL A  67 " =    2.214
peak=   -3.514 closest distance to " CG  ARG A 269 " =    2.333
peak=   -3.513 closest distance to " O   HOH Z 407 " =    3.094
peak=   -3.512 closest distance to " C   SER A 206 " =    1.493
peak=   -3.507 closest distance to " CB  ASP A 171 " =    2.411
peak=   -3.507 closest distance to " CD  ARG A 139 " =    1.583
peak=   -3.499 closest distance to " NE2 GLN A  88 " =    1.002
peak=   -3.496 closest distance to " OD1 ASN A 148 " =    1.473
peak=   -3.495 closest distance to " O   HOH Z 264 " =    1.734
peak=   -3.494 closest distance to " OG  SER A  26 " =    1.186
peak=   -3.491 closest distance to " CB  ASP A 132 " =    2.280
peak=   -3.488 closest distance to " N   ALA A  43 " =    2.565
peak=   -3.485 closest distance to " CB  LEU A  83 " =    2.343
peak=   -3.484 closest distance to " O   HOH Z 285 " =    1.481
peak=   -3.483 closest distance to " NH2 ARG A  79 " =    2.022
peak=   -3.481 closest distance to " O   HOH Z 389 " =    1.764
peak=   -3.480 closest distance to " CE BMET A  47 " =    2.033
peak=   -3.476 closest distance to " N   ALA A 226 " =    2.091
peak=   -3.475 closest distance to " ND2 ASN A 187 " =    1.691
peak=   -3.470 closest distance to " C   MET A 188 " =    1.501
peak=   -3.459 closest distance to " ND2 ASN A  45 " =    1.645
peak=   -3.457 closest distance to " O   GLY A 196 " =    1.182
peak=   -3.457 closest distance to " NH2 ARG A 159 " =    2.313
peak=   -3.457 closest distance to " OG BSER A 134 " =    1.850
peak=   -3.455 closest distance to " CB  ALA A 291 " =    2.246
peak=   -3.452 closest distance to " NE2 GLN A 194 " =    1.864
peak=   -3.452 closest distance to " CG2 VAL A 296 " =    1.199
peak=   -3.450 closest distance to " CG  GLU A 277 " =    1.107
peak=   -3.449 closest distance to " C   ILE A 239 " =    2.125
peak=   -3.448 closest distance to " O   HOH Z  63 " =    1.097
peak=   -3.439 closest distance to " CG  LEU A 101 " =    2.450
peak=   -3.430 closest distance to " O   HOH Z  60 " =    2.256
peak=   -3.428 closest distance to " O   HOH Z 177 " =    1.730
peak=   -3.427 closest distance to " O   HOH Z 211 " =    1.625
peak=   -3.422 closest distance to " O   HOH Z 252 " =    3.873
peak=   -3.416 closest distance to " ND2 ASN A  69 " =    1.815
peak=   -3.409 closest distance to " O   HOH Z 313 " =    1.117
peak=   -3.409 closest distance to " ND2 ASN A  45 " =    1.087
peak=   -3.405 closest distance to " CD1 LEU A  25 " =    2.483
peak=   -3.400 closest distance to " N   THR A 235 " =    1.309
peak=   -3.399 closest distance to " CD  ARG A 195 " =    5.200
peak=   -3.398 closest distance to " CB  ALA A 114 " =    2.529
peak=   -3.389 closest distance to " O   HOH Z 241 " =    1.371
peak=   -3.386 closest distance to " O   HOH Z 193 " =    2.093
peak=   -3.384 closest distance to " CG1 VAL A 296 " =    1.199
peak=   -3.381 closest distance to " O   HOH Z 292 " =    4.505
peak=   -3.378 closest distance to " N   SER A   3 " =    2.019
peak=   -3.370 closest distance to " CG2 VAL A 189 " =    2.028
peak=   -3.364 closest distance to " O   HOH Z  10 " =    1.608
peak=   -3.362 closest distance to " N   GLN A  58 " =    1.588
peak=   -3.358 closest distance to " CG1 VAL A 197 " =    2.164
peak=   -3.352 closest distance to " O   HOH Z 136 " =    2.304
peak=   -3.348 closest distance to " O   HOH Z 222 " =    1.532
peak=   -3.347 closest distance to " CA  GLY A 241 " =    3.015
peak=   -3.346 closest distance to " O   HOH Z   6 " =    1.780
peak=   -3.344 closest distance to " O   HOH Z  90 " =    1.708
peak=   -3.343 closest distance to " CG1 VAL A 112 " =    2.650
peak=   -3.343 closest distance to " O   HOH Z 166 " =    1.609
peak=   -3.341 closest distance to " CD  GLN A 223 " =    0.746
peak=   -3.339 closest distance to " CE  MET A 105 " =    2.060
peak=   -3.338 closest distance to " CD  PRO A 213 " =    2.237
peak=   -3.332 closest distance to " N   GLY A  23 " =    2.155
peak=   -3.314 closest distance to " O   HOH Z  17 " =    1.423
peak=   -3.312 closest distance to " O   ALA A 161 " =    1.698
peak=   -3.310 closest distance to " CB  ASN A  39 " =    2.247
peak=   -3.309 closest distance to " O   HOH Z 414 " =    1.405
peak=   -3.299 closest distance to " CD2 TYR A 293 " =    2.123
peak=   -3.296 closest distance to " CG  GLU A  53 " =    1.621
peak=   -3.294 closest distance to " CG  PHE A 283 " =    2.732
peak=   -3.290 closest distance to " CD2 LEU A 167 " =    1.767
peak=   -3.289 closest distance to " O   SER A 271 " =    2.084
peak=   -3.288 closest distance to " O   LEU A 167 " =    1.477
peak=   -3.287 closest distance to " CB  VAL A 230 " =    1.012
peak=   -3.286 closest distance to " O   SER A 210 " =    1.868
peak=   -3.285 closest distance to " CG1 VAL A 230 " =    2.024
peak=   -3.280 closest distance to " CG1 VAL A 112 " =    2.923
peak=   -3.279 closest distance to " O   HOH Z  38 " =    1.644
peak=   -3.279 closest distance to " CD1 ILE A 151 " =    2.381
peak=   -3.279 closest distance to " NZ  LYS A 119 " =    3.699
peak=   -3.277 closest distance to " O   HOH Z 426 " =    1.739
peak=   -3.276 closest distance to " O   GLY A  75 " =    1.857
peak=   -3.274 closest distance to " CG  TRP A 266 " =    1.995
peak=   -3.273 closest distance to " O   GLN A 240 " =    2.093
peak=   -3.266 closest distance to " N   MET A 188 " =    1.903
peak=   -3.265 closest distance to " CD1 LEU A 101 " =    2.654
peak=   -3.261 closest distance to " O   HOH Z 288 " =    1.546
peak=   -3.259 closest distance to " CG  LEU A  83 " =    1.883
peak=   -3.251 closest distance to " OG  SER A   3 " =    1.741
peak=   -3.251 closest distance to " CG  ARG A 219 " =    2.627
peak=   -3.250 closest distance to " OG  SER A  62 " =    1.563
peak=   -3.246 closest distance to " ND2 ASN A  60 " =    1.703
peak=   -3.242 closest distance to " O   HOH Z 131 " =    4.074
peak=   -3.241 closest distance to " O   HOH Z  47 " =    1.689
peak=   -3.234 closest distance to " CD2 PHE A  61 " =    2.456
peak=   -3.228 closest distance to " NH1 ARG A 195 " =    2.559
peak=   -3.223 closest distance to " CB  ASP A 132 " =    2.392
peak=   -3.218 closest distance to " CB  ALA A  64 " =    2.648
peak=   -3.212 closest distance to " NH2 ARG A  66 " =    1.640
peak=   -3.210 closest distance to " O   ARG A  24 " =    2.060
peak=   -3.210 closest distance to " O   HOH Z 353 " =    2.153
peak=   -3.204 closest distance to " O   HOH Z  71 " =    1.425
peak=   -3.201 closest distance to " O   ASN A 187 " =    1.594
peak=   -3.199 closest distance to " N   SER A 276 " =    1.410
peak=   -3.192 closest distance to " O   HOH Z 292 " =    1.868
peak=   -3.192 closest distance to " O   HOH Z  19 " =    2.255
peak=   -3.192 closest distance to " N   THR A  52 " =    1.711
peak=   -3.185 closest distance to " O   HOH Z 339 " =    1.758
peak=   -3.185 closest distance to " O   HOH Z 102 " =    1.578
peak=   -3.184 closest distance to " O   HOH Z 174 " =    4.302
peak=   -3.180 closest distance to " NH2 ARG A  79 " =    1.651
peak=   -3.180 closest distance to " C   ASP A 270 " =    1.236
peak=   -3.176 closest distance to " O   HOH Z  43 " =    1.749
peak=   -3.176 closest distance to " O   ILE A 234 " =    1.293
peak=   -3.174 closest distance to " N   PHE A  59 " =    2.164
peak=   -3.163 closest distance to " O   HOH Z 435 " =    2.664
peak=   -3.162 closest distance to " O   LYS A 117 " =    1.682
peak=   -3.160 closest distance to " O   HOH Z 191 " =    5.606
peak=   -3.157 closest distance to " NE1 TRP A 266 " =    2.398
peak=   -3.151 closest distance to " CD1 LEU A 228 " =    2.251
peak=   -3.148 closest distance to " O   HOH Z 171 " =    2.022
peak=   -3.147 closest distance to " CZ2 TRP A 274 " =    1.144
peak=   -3.143 closest distance to " CG  PRO A 163 " =    2.689
peak=   -3.143 closest distance to " CG  LYS A 119 " =    2.863
peak=   -3.142 closest distance to " CG  ASP A 286 " =    1.446
peak=   -3.142 closest distance to " O   HOH Z 232 " =    1.729
peak=   -3.138 closest distance to " CG1 VAL A  78 " =    2.574
peak=   -3.132 closest distance to " CG2 THR A 221 " =    2.252
peak=   -3.132 closest distance to " O   HOH Z 262 " =    2.770
peak=   -3.132 closest distance to " O   SER A  95 " =    1.699
peak=   -3.127 closest distance to " O   HOH Z 377 " =    1.881
peak=   -3.126 closest distance to " CD2 LEU A 237 " =    2.728
peak=   -3.123 closest distance to " ND2 ASN A 252 " =    1.807
peak=   -3.119 closest distance to " CE1 HIS A  81 " =    1.387
peak=   -3.119 closest distance to " CD1 ILE A 199 " =    2.515
peak=   -3.104 closest distance to " N   VAL A 230 " =    1.114
peak=   -3.103 closest distance to " OE2 GLU A   2 " =    1.788
peak=   -3.100 closest distance to " CB  VAL A 296 " =    1.000
peak=   -3.093 closest distance to " CB  ASP A 286 " =    2.210
peak=   -3.091 closest distance to " OG1 THR A  82 " =    1.446
peak=   -3.087 closest distance to " CG1 VAL A  67 " =    3.100
peak=   -3.082 closest distance to " O   HOH Z 139 " =    3.143
peak=   -3.082 closest distance to " OD1 ASN A 301 " =    1.950
peak=   -3.078 closest distance to " O   HOH Z 244 " =    1.442
peak=   -3.075 closest distance to " O   HOH Z 111 " =    1.340
peak=   -3.070 closest distance to " CA  SER A  62 " =    2.643
peak=   -3.064 closest distance to " O   HOH Z 421 " =    3.349
peak=   -3.061 closest distance to " O   HOH Z 350 " =    1.991
peak=   -3.057 closest distance to " OD1 ASN A 249 " =    1.969
peak=   -3.054 closest distance to " O   ASP A 171 " =    2.008
peak=   -3.054 closest distance to " O   PRO A 198 " =    1.264
peak=   -3.049 closest distance to " CB  ALA A  10 " =    2.258
peak=   -3.049 closest distance to " N   ASP A 171 " =    2.295
peak=   -3.039 closest distance to " CD2 TYR A 247 " =    2.263
peak=   -3.036 closest distance to " O   HOH Z 298 " =    2.643
peak=   -3.034 closest distance to " O   SER A 276 " =    1.755
peak=   -3.017 closest distance to " O   HOH Z 236 " =    1.495
peak=   -3.006 closest distance to " O   HOH Z 111 " =    2.372
peak=   -3.003 closest distance to " O   HOH Z 377 " =    1.705

================= 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    :  0.4531 0.4379   6.252073e+00   6.228002e+00
   1_bss:  0.4452 0.4272   6.243980e+00   6.216251e+00
   1_xyz:  0.3448 0.3635   6.080553e+00   6.110216e+00
   1_adp:  0.2873 0.3226   5.946013e+00   6.033119e+00
   1_occ:  0.2868 0.3220   5.944823e+00   6.033128e+00
   2_bss:  0.2834 0.3178   5.944980e+00   6.029435e+00
   2_xyz:  0.1902 0.2332   5.585765e+00   5.754627e+00
   2_adp:  0.1685 0.2104   5.478808e+00   5.666785e+00
   2_occ:  0.1681 0.2104   5.478412e+00   5.667609e+00
   3_bss:  0.1662 0.2101   5.475160e+00   5.663086e+00
   3_xyz:  0.1320 0.1712   5.263442e+00   5.474809e+00
   3_adp:  0.1247 0.1646   5.220526e+00   5.440735e+00
   3_occ:  0.1247 0.1646   5.220442e+00   5.440965e+00
   4_bss:  0.1248 0.1650   5.221245e+00   5.441204e+00
   4_xyz:  0.1146 0.1593   5.164350e+00   5.403560e+00
   4_adp:  0.1159 0.1582   5.165936e+00   5.397200e+00
   4_occ:  0.1159 0.1583   5.165672e+00   5.397346e+00
   5_bss:  0.1158 0.1582   5.165449e+00   5.397159e+00
   5_xyz:  0.1121 0.1566   5.145549e+00   5.388329e+00
   5_adp:  0.1107 0.1564   5.139391e+00   5.387476e+00
   5_occ:  0.1106 0.1564   5.139223e+00   5.387670e+00
   5_bss:  0.1106 0.1564   5.139129e+00   5.387604e+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:  0.327  20.001   6.742  11.173   7.742   0.000   0.000   0.000
   1_xyz:  0.327  20.001   6.742  11.173   7.742   0.000   0.000   0.000
   1_adp:  0.327  20.001   6.742  11.173   7.742   0.000   0.000   0.000
   1_occ:  0.327  20.001   6.742  11.173   7.742   0.000   0.000   0.000
   2_bss:  0.327  45.688   3.634   7.298   4.952   0.000   0.000   0.000
   2_xyz:  0.327  45.688   3.634   7.298   4.952   0.000   0.000   0.000
   2_adp:  0.327  45.688   3.634   7.298   4.952   0.000   0.000   0.000
   2_occ:  0.327  45.688   3.634   7.298   4.952   0.000   0.000   0.000
   3_bss:  0.323  58.011   2.508   4.270   3.952   0.000   0.000   0.000
   3_xyz:  0.323  58.011   2.508   4.270   3.952   0.000   0.000   0.000
   3_adp:  0.323  58.011   2.508   4.270   3.952   0.000   0.000   0.000
   3_occ:  0.323  58.011   2.508   4.270   3.952   0.000   0.000   0.000
   4_bss:  0.332  58.011   2.341   3.543   3.795   0.000   0.000   0.000
   4_xyz:  0.332  58.011   2.341   3.543   3.795   0.000   0.000   0.000
   4_adp:  0.332  58.011   2.341   3.543   3.795   0.000   0.000   0.000
   4_occ:  0.332  58.011   2.341   3.543   3.795   0.000   0.000   0.000
   5_bss:  0.335  58.011   2.312   3.267   3.772   0.000   0.000   0.000
   5_xyz:  0.335  58.011   2.312   3.267   3.772   0.000   0.000   0.000
   5_adp:  0.335  58.011   2.312   3.267   3.772   0.000   0.000   0.000
   5_occ:  0.335  58.011   2.312   3.267   3.772   0.000   0.000   0.000
   5_bss:  0.326  55.210  -0.772   0.102   0.670   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  50.627 0.5136  0.5709    56034.850
   1_bss:  50.027 0.5197  0.7445    53786.730
   1_xyz:  40.368 0.6372  0.8912    36940.581
   1_adp:  34.337 0.7093  0.9916    28940.578
   1_occ:  34.321 0.7095  0.9908    28892.620
   2_bss:  33.994 0.7132  0.8874    28438.499
   2_xyz:  23.292 0.8285  0.9981    14003.219
   2_adp:  20.640 0.8554  1.0153    11562.622
   2_occ:  20.665 0.8551  1.0147    11576.723
   3_bss:  20.502 0.8568  0.9561    11465.010
   3_xyz:  15.879 0.8990  0.9799     7480.189
   3_adp:  15.082 0.9061  0.9809     7021.263
   3_occ:  15.085 0.9061  0.9809     7026.088
   4_bss:  15.081 0.9062  0.9687     7042.940
   4_xyz:  14.262 0.9131  0.9711     6558.428
   4_adp:  14.060 0.9149  0.9697     6513.756
   4_occ:  14.060 0.9149  0.9697     6517.143
   5_bss:  14.052 0.9150  0.9662     6515.765
   5_xyz:  13.894 0.9162  0.9668     6349.619
   5_adp:  13.874 0.9164  0.9624     6315.175
   5_occ:  13.875 0.9164  0.9624     6318.310
   5_bss:  13.877 0.9164  0.9680     6314.488
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.093   5.4038e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.093   5.4038e+01
   1_xyz:   1.606  0.012  0.106 17.837  0.006  4.125   1.2855e-01
   1_adp:   1.606  0.012  0.106 17.837  0.006  4.125   1.2855e-01
   1_occ:   1.606  0.012  0.106 17.837  0.006  4.125   1.2855e-01
   2_bss:   1.606  0.012  0.106 17.837  0.006  4.125   1.2855e-01
   2_xyz:   1.218  0.010  0.080 16.106  0.005  4.131   8.6572e-02
   2_adp:   1.218  0.010  0.080 16.106  0.005  4.131   8.6572e-02
   2_occ:   1.218  0.010  0.080 16.106  0.005  4.131   8.6572e-02
   3_bss:   1.218  0.010  0.080 16.106  0.005  4.131   8.6572e-02
   3_xyz:   1.084  0.008  0.084 15.453  0.004  4.128   6.9376e-02
   3_adp:   1.084  0.008  0.084 15.453  0.004  4.128   6.9376e-02
   3_occ:   1.084  0.008  0.084 15.453  0.004  4.128   6.9376e-02
   4_bss:   1.084  0.008  0.084 15.453  0.004  4.128   6.9376e-02
   4_xyz:   1.125  0.010  0.093 15.458  0.004  4.116   7.6468e-02
   4_adp:   1.125  0.010  0.093 15.458  0.004  4.116   7.6468e-02
   4_occ:   1.125  0.010  0.093 15.458  0.004  4.116   7.6468e-02
   5_bss:   1.125  0.010  0.093 15.458  0.004  4.116   7.6468e-02
   5_xyz:   1.196  0.011  0.101 15.441  0.005  4.117   8.5794e-02
   5_adp:   1.196  0.011  0.101 15.441  0.005  4.117   8.5794e-02
   5_occ:   1.196  0.011  0.101 15.441  0.005  4.117   8.5794e-02
   5_bss:   1.196  0.011  0.101 15.441  0.005  4.117   8.5794e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0064e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0064e+00
   1_xyz:  14.356  0.151  0.490 86.845  0.040  2.308   9.7163e-02
   1_adp:  14.356  0.151  0.490 86.845  0.040  2.308   9.7163e-02
   1_occ:  14.356  0.151  0.490 86.845  0.040  2.308   9.7163e-02
   2_bss:  14.356  0.151  0.490 86.845  0.040  2.308   9.7163e-02
   2_xyz:   7.713  0.137  0.271 82.130  0.042  2.111   7.9775e-02
   2_adp:   7.713  0.137  0.271 82.130  0.042  2.111   7.9775e-02
   2_occ:   7.713  0.137  0.271 82.130  0.042  2.111   7.9775e-02
   3_bss:   7.713  0.137  0.271 82.130  0.042  2.111   7.9775e-02
   3_xyz:   7.129  0.056  0.563 82.016  0.040  2.262   4.7755e-02
   3_adp:   7.129  0.056  0.563 82.016  0.040  2.262   4.7755e-02
   3_occ:   7.129  0.056  0.563 82.016  0.040  2.262   4.7755e-02
   4_bss:   7.129  0.056  0.563 82.016  0.040  2.262   4.7755e-02
   4_xyz:   7.830  0.047  0.684 82.662  0.037  2.301   6.8436e-02
   4_adp:   7.830  0.047  0.684 82.662  0.037  2.301   6.8436e-02
   4_occ:   7.830  0.047  0.684 82.662  0.037  2.301   6.8436e-02
   5_bss:   7.830  0.047  0.684 82.662  0.037  2.301   6.8436e-02
   5_xyz:   8.469  0.050  0.764 81.741  0.038  2.255   6.5360e-02
   5_adp:   8.469  0.050  0.764 81.741  0.038  2.255   6.5360e-02
   5_occ:   8.469  0.050  0.764 81.741  0.038  2.255   6.5360e-02
   5_bss:   8.469  0.050  0.764 81.741  0.038  2.255   6.5360e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00
   1_bss:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_xyz:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_adp:  81.24   0.00  11.62  66.25   0.00   8.80  81.24   0.00  26.99
   1_occ:  81.24   0.00  11.62  66.25   0.00   8.80  81.24   0.00  26.99
   2_bss:  81.24   0.00  11.62  66.25   0.00   8.80  81.24   0.00  26.99
   2_xyz:  81.24   0.00  11.62  66.25   0.00   8.80  81.24   0.00  26.99
   2_adp:  76.18   0.00  11.76  76.18   0.00   8.00  73.93   0.00  32.19
   2_occ:  76.18   0.00  11.76  76.18   0.00   8.00  73.93   0.00  32.19
   3_bss:  76.18   0.00  11.76  76.18   0.00   8.00  73.93   0.00  32.19
   3_xyz:  76.18   0.00  11.76  76.18   0.00   8.00  73.93   0.00  32.19
   3_adp:  77.89   0.00  12.05  77.89   0.00   7.83  73.27   1.13  35.00
   3_occ:  77.89   0.00  12.05  77.89   0.00   7.83  73.27   1.13  35.00
   4_bss:  77.89   0.00  12.05  77.89   0.00   7.83  73.27   1.13  35.00
   4_xyz:  77.89   0.00  12.05  77.89   0.00   7.83  73.27   1.13  35.00
   4_adp:  73.16   0.00  11.36  73.16   0.00   7.57  71.58   1.23  32.00
   4_occ:  73.16   0.00  11.36  73.16   0.00   7.57  71.58   1.23  32.00
   5_bss:  73.16   0.00  11.36  73.16   0.00   7.57  71.58   1.23  32.00
   5_xyz:  73.16   0.00  11.36  73.16   0.00   7.57  71.58   1.23  32.00
   5_adp:  75.55   0.00  11.44  75.55   0.00   7.55  67.86   1.02  32.66
   5_occ:  75.55   0.00  11.44  75.55   0.00   7.55  67.86   1.02  32.66
   5_bss:  78.83   3.28  14.72  78.83   3.28  10.82  71.14   4.30  35.94
------------------------------------------------------------------------
 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:    1.175    0.013    0.408
   1_adp:    1.175    0.013    0.408
   1_occ:    1.175    0.013    0.408
   2_bss:    1.175    0.013    0.408
   2_xyz:    1.539    0.027    0.577
   2_adp:    1.539    0.027    0.577
   2_occ:    1.539    0.027    0.577
   3_bss:    1.539    0.027    0.577
   3_xyz:    1.477    0.049    0.618
   3_adp:    1.477    0.049    0.618
   3_occ:    1.477    0.049    0.618
   4_bss:    1.477    0.049    0.618
   4_xyz:    1.519    0.060    0.648
   4_adp:    1.519    0.060    0.648
   4_occ:    1.519    0.060    0.648
   5_bss:    1.519    0.060    0.648
   5_xyz:    1.531    0.055    0.655
   5_adp:    1.531    0.055    0.655
   5_occ:    1.531    0.055    0.655
   5_bss:    1.531    0.055    0.655
------------------------------------------------------------------------

CPU time actual refinement: 327.70


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_698/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_698/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_698/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_698/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_698/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 327.53 
  Macro-tasks:
    bulk solvent and scale       = 42.06  
    individual site refinement   = 136.79 
    weights calculation          = 31.83  
    collect and process          = 6.43   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 217.22 
  Micro-tasks:
    mask                            = 1.78   
    f_calc                          = 99.08  
    alpha_beta                      = 8.05   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 110.88 
    fmodel                         = 7.22   
    r_factors                      = 0.22   
    phase_errors                   = 10.77  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 239.39 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.566 micro seconds
Total CPU time: 5.68 minutes
from_scatterers_fft:    653 calls, 98.79 s
gradients_fft:          598 calls, 97.19 s

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

# Date 2008-01-16 Time 02:13:18 PST -0800 (1200478398.62 s)
Start R-work = 0.4531, R-free = 0.4379 (no bulk solvent and anisotropic scale)
Final R-work = 0.1275, R-free = 0.1721 (no bulk solvent and anisotropic scale)

Start R-work = 0.4452, R-free = 0.4272
Final R-work = 0.1106, R-free = 0.1564