# Date 2008-01-16 Time 02:25:44 PST -0800 (1200479144.46 s)
#phil __OFF__

Command line arguments: "../822.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 5360
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 822

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.6012, 47.6339, 87.6859, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 47.6339, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1092 2.0106
Completeness in resolution range: 0.968267
Completeness with d_max=infinity: 0.965213

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1092
                             d_min =   2.0106

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 47.6339, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1092 2.0106
Completeness in resolution range: 0.968267
Completeness with d_max=infinity: 0.965213

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1096 -  4.3015 [2129/2156]  1915   214  10.1%
  bin  2:  4.3015 -  3.4273 [2037/2053]  1834   203  10.0%
  bin  3:  3.4273 -  2.9979 [2027/2046]  1825   202  10.0%
  bin  4:  2.9979 -  2.7256 [1987/2017]  1785   202  10.2%
  bin  5:  2.7256 -  2.5312 [1988/2007]  1791   197   9.9%
  bin  6:  2.5312 -  2.3826 [1976/2001]  1781   195   9.9%
  bin  7:  2.3826 -  2.2637 [1966/1999]  1772   194   9.9%
  bin  8:  2.2637 -  2.1654 [1940/1971]  1742   198  10.2%
  bin  9:  2.1654 -  2.0823 [1946/1988]  1751   195  10.0%
  bin 10:  2.0823 -  2.0106 [1593/1993]  1434   159  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_822/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: 0.13 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: 15
        2.42 -     3.04: 2148
        3.04 -     3.66: 4588
        3.66 -     4.28: 8839
        4.28 -     4.90: 12230
  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 "  1.926 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.933 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  50 " - " O   HOH Z  95 "  2.142 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  95 " - " O   HOH Z  50 "  2.142 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 27815 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_822/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_822/model_refine_001.geo

CPU time processing inputs: 9.10


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.60125 47.63395 87.68585 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.01 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4785   r_free= 0.4655   ksol= 0.00   Bsol= 0.00   scale= 0.783    |
|                                                                             |
| 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:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.276573                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1096 -  4.7973 0.99   1383  153 0.3845 0.3646      6.5754      6.5109|
|  2:  4.7973 -  3.8282 0.99   1318  150 0.3923 0.4322      6.7705      6.9044|
|  3:  3.8282 -  3.3503 0.99   1314  144 0.4411 0.4079      6.6874      6.6291|
|  4:  3.3503 -  3.0467 0.99   1293  139 0.4645 0.4090      6.5332      6.4311|
|  5:  3.0467 -  2.8299 0.99   1282  143 0.5084 0.4816       6.379      6.3914|
|  6:  2.8299 -  2.6640 0.99   1278  145 0.5070 0.5335      6.2889      6.2072|
|  7:  2.6640 -  2.5312 0.99   1282  144 0.5045 0.4526      6.2389        6.16|
|  8:  2.5312 -  2.4215 0.98   1278  139 0.5156 0.4418      6.1886      6.1386|
|  9:  2.4215 -  2.3286 0.98   1248  140 0.5194 0.6062      6.1091      6.1807|
| 10:  2.3286 -  2.2485 0.99   1267  139 0.5432 0.4857       6.135      6.0887|
| 11:  2.2485 -  2.1784 0.99   1264  143 0.5221 0.5021      6.0297      6.0968|
| 12:  2.1784 -  2.1163 0.97   1245  134 0.5365 0.5297      5.9825       6.024|
| 13:  2.1163 -  2.0608 0.99   1280  143 0.5365 0.5193      5.8989       5.845|
| 14:  2.0608 -  2.0106 0.72    898  103 0.5447 0.5402      5.8621      5.7743|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1096 -  4.7973  1383   153  0.71  33.35   0.80     0.73      66659.01|
|  2:  4.7973 -  3.8282  1318   150  0.72  33.80   0.87     0.76      99262.86|
|  3:  3.8282 -  3.3503  1314   144  0.62  41.77   0.82     0.71     104843.14|
|  4:  3.3503 -  3.0467  1293   139  0.55  48.04   0.79     0.62      91264.40|
|  5:  3.0467 -  2.8299  1282   143  0.47  54.50   0.73     0.54      74037.72|
|  6:  2.8299 -  2.6640  1278   145  0.45  55.89   0.71     0.50      65481.60|
|  7:  2.6640 -  2.5312  1282   144  0.43  57.34   0.74     0.48      59721.61|
|  8:  2.5312 -  2.4215  1278   139  0.42  58.74   0.74     0.48      55152.46|
|  9:  2.4215 -  2.3286  1248   140  0.38  61.44   0.69     0.44      53132.15|
| 10:  2.3286 -  2.2485  1267   139  0.36  62.73   0.72     0.42      49866.47|
| 11:  2.2485 -  2.1784  1264   143  0.34  64.62   0.74     0.41      46602.30|
| 12:  2.1784 -  2.1163  1245   134  0.33  65.03   0.74     0.41      42345.82|
| 13:  2.1163 -  2.0608  1280   143  0.31  67.01   0.71     0.36      37340.76|
| 14:  2.0608 -  2.0106   898   103  0.27  70.12   0.70     0.29      32026.64|
|alpha:            min =        0.29 max =            0.76 mean =         0.52|
|beta:             min =    32026.64 max =       104843.14 mean =     63647.65|
|figures of merit: min =        0.00 max =            1.00 mean =         0.46|
|phase err.(work): min =        0.00 max =           89.99 mean =        54.74|
|phase err.(test): min =        0.00 max =           89.88 mean =        54.85|
|-----------------------------------------------------------------------------|

============================== 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 = 12.416901             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.078   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.201335              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.278   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       27 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      156 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      676 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1477 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2569 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3839 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     4978 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6487 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7645 |
|-----------------------------------------------------------------------------|
|-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 |       54.428 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.094    4.900  1.196 |       1.684 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.292)------------------------------------------|
|    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 = 12.292)------------------------------------------|
|    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: 2.01 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4842   r_free= 0.4664   ksol= 0.00   Bsol= 0.00   scale= 0.755    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.279003                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4706   r_free= 0.4542   ksol= 0.30   Bsol= 20.00   scale= 0.984   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.42,10.07,9.86,0.00,0.00,0.00); trace/3= 8.78                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.270152                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.303794             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.174   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.077131              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.036   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4706      final r-factor (work) = 0.3798          |
| start r-factor (free) = 0.4542      final r-factor (free) = 0.3972          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 89.9165 = 11.30 * 0.50 * 6.2791 + 1.00 * 54.4278                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 35.0236 = 11.30 * 0.50 * 6.1717 + 1.00 * 0.1420                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3798      final r-factor (work) = 0.3325          |
| start r-factor (free) = 0.3972      final r-factor (free) = 0.3795          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.6621 = 1.08 * 1.00 * 6.1717 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.5580 = 1.08 * 1.00 * 6.0717 + 1.00 * 0.0180                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.292)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    111.29  13.05    None  None   None       |
|    all(noH): 2823   0      0.00    111.29  13.05    None  None   None       |
|    Sol.    : 438    0      0.00    111.29  27.90    None  None   None       |
|    Mac.    : 2385   0      0.00    75.47   10.33    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 -  11.129: 1610   |   5:    55.644 -  66.772:   19        |
|      1:    11.129 -  22.258:  714   |   6:    66.772 -  77.901:   10        |
|      2:    22.258 -  33.386:  273   |   7:    77.901 -  89.030:    3        |
|      3:    33.386 -  44.515:  142   |   8:    89.030 - 100.159:    1        |
|      4:    44.515 -  55.644:   50   |   9:   100.159 - 111.287:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3325 r_free = 0.3795             target_work(ml) = 6.050         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3318 r_free = 0.3799             target_work(ml) = 6.049         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3318   r_free= 0.3799   ksol= 0.30   Bsol= 20.00   scale= 1.084   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.42,10.07,9.86,0.00,0.00,0.00); trace/3= 8.78                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.49 A                  |
| x-ray target function (ml) for work reflections: 6.048991                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3289   r_free= 0.3753   ksol= 0.32   Bsol= 52.20   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.26,6.39,6.11,0.00,0.00,0.00); trace/3= 5.25                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.50 A                  |
| x-ray target function (ml) for work reflections: 6.050458                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.725266              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.875   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.422520              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 123.432  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3289      final r-factor (work) = 0.2487          |
| start r-factor (free) = 0.3753      final r-factor (free) = 0.2986          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.4769 = 4.73 * 0.50 * 6.0674 + 1.00 * 0.1420                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.0630 = 4.73 * 0.50 * 5.9205 + 1.00 * 0.0751                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2487      final r-factor (work) = 0.2297          |
| start r-factor (free) = 0.2986      final r-factor (free) = 0.2760          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5199 = 0.42 * 1.00 * 5.9205 + 1.00 * 0.0184                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4712 = 0.42 * 1.00 * 5.7815 + 1.00 * 0.0284                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.292)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    110.67  12.43    None  None   None       |
|    all(noH): 2823   0      0.00    110.67  12.43    None  None   None       |
|    Sol.    : 438    0      0.00    110.67  31.88    None  None   None       |
|    Mac.    : 2385   0      0.00    67.46   8.86     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.067: 1820   |   5:    55.334 -  66.401:   31        |
|      1:    11.067 -  22.134:  535   |   6:    66.401 -  77.467:    9        |
|      2:    22.134 -  33.200:  215   |   7:    77.467 -  88.534:    2        |
|      3:    33.200 -  44.267:  136   |   8:    88.534 -  99.601:    0        |
|      4:    44.267 -  55.334:   74   |   9:    99.601 - 110.668:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2297 r_free = 0.2760             target_work(ml) = 5.755         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2293 r_free = 0.2765             target_work(ml) = 5.755         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2293   r_free= 0.2765   ksol= 0.32   Bsol= 52.20   scale= 1.029   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.26,6.39,6.11,0.00,0.00,0.00); trace/3= 5.25                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.754826                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2287   r_free= 0.2761   ksol= 0.31   Bsol= 52.20   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.45,4.32,4.38,0.00,0.00,0.00); trace/3= 3.72                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.755817                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.130001              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.195  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.511254              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 93.097   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2287      final r-factor (work) = 0.1630          |
| start r-factor (free) = 0.2761      final r-factor (free) = 0.2013          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.0182 = 4.13 * 0.50 * 5.7835 + 1.00 * 0.0753                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.6817 = 4.13 * 0.50 * 5.6201 + 1.00 * 0.0763                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1630      final r-factor (work) = 0.1470          |
| start r-factor (free) = 0.2013      final r-factor (free) = 0.1911          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.5343 = 1.51 * 1.00 * 5.6201 + 1.00 * 0.0410                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.1653 = 1.51 * 1.00 * 5.3923 + 1.00 * 0.0161                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.292)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    105.28  13.34    None  None   None       |
|    all(noH): 2823   0      0.00    105.28  13.34    None  None   None       |
|    Sol.    : 438    0      0.19    105.28  38.60    None  None   None       |
|    Mac.    : 2385   0      0.00    80.43   8.70     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.528: 1808   |   5:    52.640 -  63.167:   80        |
|      1:    10.528 -  21.056:  503   |   6:    63.167 -  73.695:   38        |
|      2:    21.056 -  31.584:  152   |   7:    73.695 -  84.223:   10        |
|      3:    31.584 -  42.112:  113   |   8:    84.223 -  94.751:    1        |
|      4:    42.112 -  52.640:  117   |   9:    94.751 - 105.279:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1470 r_free = 0.1911             target_work(ml) = 5.367         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1469 r_free = 0.1913             target_work(ml) = 5.367         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1469   r_free= 0.1913   ksol= 0.31   Bsol= 52.20   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.45,4.32,4.38,0.00,0.00,0.00); trace/3= 3.72                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.366936                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1469   r_free= 0.1914   ksol= 0.33   Bsol= 67.35   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.18,3.27,4.02,0.00,0.00,0.00); trace/3= 3.16                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.366344                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.063680              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 114.031  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.662443              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 124.280  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1469      final r-factor (work) = 0.1269          |
| start r-factor (free) = 0.1914      final r-factor (free) = 0.1754          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.3390 = 3.06 * 0.50 * 5.3940 + 1.00 * 0.0763                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.1992 = 3.06 * 0.50 * 5.3045 + 1.00 * 0.0736                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1269      final r-factor (work) = 0.1237          |
| start r-factor (free) = 0.1754      final r-factor (free) = 0.1715          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5300 = 0.66 * 1.00 * 5.3045 + 1.00 * 0.0161                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5116 = 0.66 * 1.00 * 5.2452 + 1.00 * 0.0369                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.292)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.12   12.94    None  None   None       |
|    all(noH): 2823   0      0.00    95.12   12.94    None  None   None       |
|    Sol.    : 438    0      0.08    95.12   38.29    None  None   None       |
|    Mac.    : 2385   0      0.00    87.05   8.28     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.512: 1764   |   5:    47.561 -  57.073:   76        |
|      1:     9.512 -  19.024:  522   |   6:    57.073 -  66.585:   64        |
|      2:    19.024 -  28.536:  155   |   7:    66.585 -  76.097:   22        |
|      3:    28.536 -  38.048:  107   |   8:    76.097 -  85.609:    8        |
|      4:    38.048 -  47.561:  101   |   9:    85.609 -  95.121:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1237 r_free = 0.1715             target_work(ml) = 5.233         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1236 r_free = 0.1714             target_work(ml) = 5.233         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1236   r_free= 0.1714   ksol= 0.33   Bsol= 67.35   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.18,3.27,4.02,0.00,0.00,0.00); trace/3= 3.16                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.232531                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1236   r_free= 0.1713   ksol= 0.33   Bsol= 67.35   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.35,3.12,4.09,0.00,0.00,0.00); trace/3= 3.19                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.232344                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.827572              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 132.368  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.242763              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 95.365   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1236      final r-factor (work) = 0.1230          |
| start r-factor (free) = 0.1713      final r-factor (free) = 0.1683          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8672 = 1.83 * 0.50 * 5.2451 + 1.00 * 0.0743                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8403 = 1.83 * 0.50 * 5.2312 + 1.00 * 0.0601                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1230      final r-factor (work) = 0.1223          |
| start r-factor (free) = 0.1683      final r-factor (free) = 0.1686          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.5244 = 1.24 * 1.00 * 5.2312 + 1.00 * 0.0232                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.5013 = 1.24 * 1.00 * 5.2189 + 1.00 * 0.0154                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.292)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.16   12.80    None  None   None       |
|    all(noH): 2823   0      0.00    93.16   12.80    None  None   None       |
|    Sol.    : 438    0      0.39    93.16   38.19    None  None   None       |
|    Mac.    : 2385   0      0.00    88.78   8.14     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.316: 1769   |   5:    46.582 -  55.898:   81        |
|      1:     9.316 -  18.633:  506   |   6:    55.898 -  65.215:   58        |
|      2:    18.633 -  27.949:  160   |   7:    65.215 -  74.531:   30        |
|      3:    27.949 -  37.265:  107   |   8:    74.531 -  83.847:   11        |
|      4:    37.265 -  46.582:   95   |   9:    83.847 -  93.164:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1223 r_free = 0.1686             target_work(ml) = 5.221         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1222 r_free = 0.1686             target_work(ml) = 5.221         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1222   r_free= 0.1686   ksol= 0.33   Bsol= 67.35   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.35,3.12,4.09,0.00,0.00,0.00); trace/3= 3.19                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.221047                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1096 -  4.7973 0.99   1383  153 0.1050 0.1346      5.4341      5.5509|
|  2:  4.7973 -  3.8282 0.99   1318  150 0.0869 0.1098      5.4544      5.6543|
|  3:  3.8282 -  3.3503 0.99   1314  144 0.1106 0.1537      5.5133      5.8793|
|  4:  3.3503 -  3.0467 0.99   1293  139 0.1278 0.1628      5.5028      5.6511|
|  5:  3.0467 -  2.8299 0.99   1282  143 0.1496 0.1849      5.4332      5.5893|
|  6:  2.8299 -  2.6640 0.99   1278  145 0.1362 0.2238      5.3142      5.6096|
|  7:  2.6640 -  2.5312 0.99   1282  144 0.1411 0.1768      5.2627      5.4278|
|  8:  2.5312 -  2.4215 0.98   1278  139 0.1338 0.1820      5.1892      5.4099|
|  9:  2.4215 -  2.3286 0.98   1248  140 0.1313 0.2094      5.1188      5.4013|
| 10:  2.3286 -  2.2485 0.99   1267  139 0.1290 0.1758      5.0813      5.2683|
| 11:  2.2485 -  2.1784 0.99   1264  143 0.1295 0.1891      5.0244      5.3059|
| 12:  2.1784 -  2.1163 0.97   1245  134 0.1264 0.1825      4.9625      5.2896|
| 13:  2.1163 -  2.0608 0.99   1280  143 0.1232 0.1749      4.8654       5.078|
| 14:  2.0608 -  2.0106 0.72    898  103 0.1126 0.1954      4.7489      5.0586|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1096 -  4.7973  1383   153  0.94   9.63   0.96     0.94       7985.33|
|  2:  4.7973 -  3.8282  1318   150  0.95   8.27   1.00     0.98       9336.25|
|  3:  3.8282 -  3.3503  1314   144  0.93  11.32   1.02     1.01      10839.66|
|  4:  3.3503 -  3.0467  1293   139  0.92  14.11   1.00     0.98      11032.54|
|  5:  3.0467 -  2.8299  1282   143  0.89  17.59   1.00     0.97       9995.22|
|  6:  2.8299 -  2.6640  1278   145  0.89  17.85   0.97     0.94       8702.47|
|  7:  2.6640 -  2.5312  1282   144  0.89  17.18   0.98     0.95       7449.80|
|  8:  2.5312 -  2.4215  1278   139  0.89  16.86   0.98     0.95       6476.84|
|  9:  2.4215 -  2.3286  1248   140  0.89  17.28   0.99     0.95       5968.58|
| 10:  2.3286 -  2.2485  1267   139  0.88  17.64   0.98     0.93       5417.43|
| 11:  2.2485 -  2.1784  1264   143  0.89  17.61   0.98     0.93       5020.87|
| 12:  2.1784 -  2.1163  1245   134  0.90  16.82   0.99     0.98       4576.24|
| 13:  2.1163 -  2.0608  1280   143  0.90  16.92   0.97     0.95       3832.00|
| 14:  2.0608 -  2.0106   898   103  0.90  16.14   0.95     0.90       2989.08|
|alpha:            min =        0.90 max =            1.01 mean =         0.96|
|beta:             min =     2989.08 max =        11032.54 mean =      7235.77|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.94 mean =        15.29|
|phase err.(test): min =        0.00 max =           87.80 mean =        14.67|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1223   r_free= 0.1686   ksol= 0.33   Bsol= 69.21   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.78,-0.14,0.93,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.220971                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1223   r_free= 0.1686   ksol= 0.33   Bsol= 69.21   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.78,-0.14,0.93,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.220971                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1096 -  4.7973 0.99   1383  153 0.1047 0.1318      5.4273      5.5368|
|  2:  4.7973 -  3.8282 0.99   1318  150 0.0875 0.1099      5.4586      5.6557|
|  3:  3.8282 -  3.3503 0.99   1314  144 0.1106 0.1537      5.5144      5.8799|
|  4:  3.3503 -  3.0467 0.99   1293  139 0.1284 0.1639      5.5049      5.6562|
|  5:  3.0467 -  2.8299 0.99   1282  143 0.1495 0.1848      5.4332      5.5883|
|  6:  2.8299 -  2.6640 0.99   1278  145 0.1362 0.2230      5.3137      5.6071|
|  7:  2.6640 -  2.5312 0.99   1282  144 0.1409 0.1772      5.2625      5.4286|
|  8:  2.5312 -  2.4215 0.98   1278  139 0.1338 0.1820      5.1893      5.4101|
|  9:  2.4215 -  2.3286 0.98   1248  140 0.1312 0.2092      5.1184      5.4009|
| 10:  2.3286 -  2.2485 0.99   1267  139 0.1289 0.1758      5.0811      5.2686|
| 11:  2.2485 -  2.1784 0.99   1264  143 0.1294 0.1892      5.0244      5.3063|
| 12:  2.1784 -  2.1163 0.97   1245  134 0.1265 0.1825      4.9629      5.2897|
| 13:  2.1163 -  2.0608 0.99   1280  143 0.1231 0.1747      4.8652      5.0781|
| 14:  2.0608 -  2.0106 0.72    898  103 0.1126 0.1952      4.7486      5.0581|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1096 -  4.7973  1383   153  0.94   9.67   0.96     0.94       7839.02|
|  2:  4.7973 -  3.8282  1318   150  0.95   8.26   1.00     0.98       9276.09|
|  3:  3.8282 -  3.3503  1314   144  0.93  11.35   1.02     1.01      10893.26|
|  4:  3.3503 -  3.0467  1293   139  0.92  14.15   1.00     0.98      11071.66|
|  5:  3.0467 -  2.8299  1282   143  0.89  17.57   1.00     0.97       9990.92|
|  6:  2.8299 -  2.6640  1278   145  0.89  17.84   0.98     0.94       8685.64|
|  7:  2.6640 -  2.5312  1282   144  0.89  17.17   0.98     0.96       7447.71|
|  8:  2.5312 -  2.4215  1278   139  0.89  16.86   0.98     0.95       6477.53|
|  9:  2.4215 -  2.3286  1248   140  0.89  17.28   1.00     0.95       5968.89|
| 10:  2.3286 -  2.2485  1267   139  0.88  17.64   0.99     0.94       5417.52|
| 11:  2.2485 -  2.1784  1264   143  0.89  17.62   0.98     0.93       5024.88|
| 12:  2.1784 -  2.1163  1245   134  0.90  16.83   1.00     0.98       4580.98|
| 13:  2.1163 -  2.0608  1280   143  0.90  16.91   0.98     0.95       3830.78|
| 14:  2.0608 -  2.0106   898   103  0.90  16.13   0.95     0.90       2985.81|
|alpha:            min =        0.90 max =            1.01 mean =         0.96|
|beta:             min =     2985.81 max =        11071.66 mean =      7225.42|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.95 mean =        15.29|
|phase err.(test): min =        0.00 max =           87.78 mean =        14.68|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.292)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.24    96.40   16.04    None  None   None       |
|    all(noH): 2823   0      3.24    96.40   16.04    None  None   None       |
|    Sol.    : 438    0      3.63    96.40   41.42    None  None   None       |
|    Mac.    : 2385   0      3.24    92.02   11.37    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     3.238 -  12.554: 1769   |   5:    49.819 -  59.136:   81        |
|      1:    12.554 -  21.870:  506   |   6:    59.136 -  68.452:   58        |
|      2:    21.870 -  31.187:  160   |   7:    68.452 -  77.768:   30        |
|      3:    31.187 -  40.503:  107   |   8:    77.768 -  87.085:   11        |
|      4:    40.503 -  49.819:   95   |   9:    87.085 -  96.401:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 346         
Filter by distance & map next to the model:
   mapped sites are within: 0.282 - 5.729
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 338 from: 346
   mapped sites are within: 0.706 - 5.729

peak=   10.114 closest distance to " CB  VAL A 230 " =    1.438
peak=    5.899 closest distance to " NH2 ARG A  56 " =    2.253
peak=    5.793 closest distance to " CG  LEU A   5 " =    1.181
peak=    5.663 closest distance to " O   HOH Z 210 " =    1.183
peak=    5.582 closest distance to " CB  GLN A 223 " =    1.441
peak=    5.537 closest distance to " CG  PRO A 280 " =    0.928
peak=    5.339 closest distance to " CG  LEU A 228 " =    1.223
peak=    5.311 closest distance to " CB  VAL A 296 " =    1.091
peak=    5.224 closest distance to " CD1AILE A 234 " =    1.081
peak=    5.197 closest distance to " CG2 VAL A 296 " =    1.018
peak=    5.112 closest distance to " CG  PRO A 198 " =    1.289
peak=    5.098 closest distance to " CG  PRO A  54 " =    1.399
peak=    4.996 closest distance to " CD2 LEU A   5 " =    1.114
peak=    4.829 closest distance to " CG1 VAL A 296 " =    1.168
peak=    4.821 closest distance to " CB  PRO A  54 " =    0.974
peak=    4.816 closest distance to " CB  SER A  63 " =    1.238
peak=    4.592 closest distance to " O   HOH Z 232 " =    2.221
peak=    4.567 closest distance to " CZ  PHE A 218 " =    1.126
peak=    4.554 closest distance to " CB  GLN A 183 " =    1.269
peak=    4.507 closest distance to " CB  ARG A 275 " =    0.913
peak=    4.504 closest distance to " O   HOH Z 128 " =    1.480
peak=    4.502 closest distance to " CA  VAL A 230 " =    1.170
peak=    4.445 closest distance to " O   HOH Z 403 " =    1.684
peak=    4.372 closest distance to " O   HOH Z 248 " =    1.500
peak=    4.362 closest distance to " CA  TYR A  30 " =    0.986
peak=    4.354 closest distance to " O   HOH Z  49 " =    1.298
peak=    4.353 closest distance to " CB  ARG A 190 " =    1.668
peak=    4.351 closest distance to " CG  PRO A 213 " =    1.251
peak=    4.334 closest distance to " CB  GLU A 128 " =    1.112
peak=    4.291 closest distance to " CA  ALA A  51 " =    1.005
peak=    4.258 closest distance to " CD2 LEU A 228 " =    1.396
peak=    4.235 closest distance to " O   PRO A 198 " =    1.547
peak=    4.198 closest distance to " O   HOH Z 365 " =    2.473
peak=    4.176 closest distance to " O   HOH Z 425 " =    1.525
peak=    4.167 closest distance to " CG  PRO A 243 " =    1.181
peak=    4.148 closest distance to " CD  LYS A 166 " =    1.377
peak=    4.145 closest distance to " O   HOH Z 411 " =    3.844
peak=    4.131 closest distance to " CZ3 TRP A 266 " =    1.143
peak=    4.110 closest distance to " O   SER A  87 " =    2.363
peak=    4.108 closest distance to " CB  GLU A 277 " =    3.768
peak=    4.107 closest distance to " O   HOH Z 234 " =    3.721
peak=    4.097 closest distance to " CA  ALA A 295 " =    1.069
peak=    4.096 closest distance to " NE2 GLN A  11 " =    1.025
peak=    4.094 closest distance to " O   HOH Z 126 " =    1.627
peak=    4.079 closest distance to " O   HOH Z 189 " =    3.041
peak=    4.070 closest distance to " CB  TRP A 266 " =    1.052
peak=    4.066 closest distance to " O   HOH Z 423 " =    1.783
peak=    4.059 closest distance to " O   HOH Z 265 " =    2.079
peak=    4.039 closest distance to " CB  ASP A 124 " =    0.777
peak=    4.039 closest distance to " O   HOH Z 402 " =    1.491
peak=    4.033 closest distance to " CB  ARG A  79 " =    1.401
peak=    4.030 closest distance to " CB  ASN A 148 " =    1.378
peak=    4.015 closest distance to " O   HOH Z 144 " =    1.904
peak=    4.014 closest distance to " O   HOH Z 251 " =    1.526
peak=    4.009 closest distance to " CA  ARG A 195 " =    1.161
peak=    4.007 closest distance to " O   HOH Z 130 " =    2.574
peak=    3.999 closest distance to " O   HOH Z  63 " =    1.937
peak=    3.995 closest distance to " O   HOH Z 131 " =    2.476
peak=    3.986 closest distance to " O   HOH Z  43 " =    2.011
peak=    3.980 closest distance to " CB  TYR A 169 " =    0.768
peak=    3.966 closest distance to " O   HOH Z 369 " =    2.138
peak=    3.952 closest distance to " O   HOH Z  40 " =    1.856
peak=    3.942 closest distance to " O   HOH Z 298 " =    1.862
peak=    3.935 closest distance to " O   HOH Z 394 " =    1.464
peak=    3.931 closest distance to " O   HOH Z   4 " =    1.710
peak=    3.927 closest distance to " O   HOH Z 214 " =    1.259
peak=    3.912 closest distance to " O   HOH Z 316 " =    3.145
peak=    3.905 closest distance to " CD2 TRP A 179 " =    1.322
peak=    3.896 closest distance to " OG BSER A 164 " =    2.189
peak=    3.870 closest distance to " O   HOH Z 142 " =    1.600
peak=    3.861 closest distance to " O   HOH Z  78 " =    1.672
peak=    3.859 closest distance to " CB  VAL A 202 " =    1.508
peak=    3.841 closest distance to " CB AVAL A  41 " =    1.159
peak=    3.841 closest distance to " O   HOH Z 433 " =    1.550
peak=    3.834 closest distance to " CB  TRP A 179 " =    1.334
peak=    3.827 closest distance to " CA  VAL A  41 " =    0.749
peak=    3.825 closest distance to " O   HOH Z  44 " =    2.018
peak=    3.823 closest distance to " CB  SER A 273 " =    0.951
peak=    3.816 closest distance to " O   HOH Z 285 " =    2.430
peak=    3.812 closest distance to " CG1 VAL A 153 " =    1.022
peak=    3.809 closest distance to " CD1 LEU A  96 " =    0.772
peak=    3.807 closest distance to " O   HOH Z 422 " =    2.690
peak=    3.803 closest distance to " NE2 GLN A  77 " =    3.360
peak=    3.802 closest distance to " CZ  PHE A 192 " =    1.045
peak=    3.789 closest distance to " CB  ASP A 140 " =    1.052
peak=    3.785 closest distance to " CB  GLU A  46 " =    0.980
peak=    3.782 closest distance to " O   ASP A 124 " =    1.202
peak=    3.782 closest distance to " O   HOH Z 287 " =    1.942
peak=    3.780 closest distance to " O   HOH Z 126 " =    1.941
peak=    3.777 closest distance to " O   HOH Z 272 " =    1.972
peak=    3.772 closest distance to " CZ  PHE A  38 " =    1.210
peak=    3.765 closest distance to " CD  ARG A 269 " =    0.997
peak=    3.763 closest distance to " O   HOH Z  80 " =    1.956
peak=    3.759 closest distance to " N   ASN A  39 " =    1.208
peak=    3.757 closest distance to " CA  TYR A  30 " =    1.064
peak=    3.748 closest distance to " O   HOH Z 102 " =    1.343
peak=    3.747 closest distance to " CD2 LEU A 297 " =    0.894
peak=    3.747 closest distance to " CA  ARG A  36 " =    1.089
peak=    3.745 closest distance to " CB  ASN A 142 " =    1.107
peak=    3.740 closest distance to " O   HOH Z 134 " =    1.514
peak=    3.740 closest distance to " O   HOH Z   9 " =    2.185
peak=    3.732 closest distance to " O   HOH Z 261 " =    2.016
peak=    3.732 closest distance to " O   HOH Z 280 " =    2.914
peak=    3.730 closest distance to " O   HOH Z 130 " =    1.122
peak=    3.730 closest distance to " O   HOH Z 427 " =    3.068
peak=    3.725 closest distance to " ND2 ASN A 187 " =    1.496
peak=    3.716 closest distance to " CA  MET A 105 " =    1.010
peak=    3.714 closest distance to " CA  ILE A 106 " =    0.752
peak=    3.702 closest distance to " CE1 TYR A 186 " =    1.319
peak=    3.699 closest distance to " O   HOH Z 359 " =    1.589
peak=    3.691 closest distance to " NH1AARG A 145 " =    1.304
peak=    3.685 closest distance to " O   HOH Z  63 " =    1.299
peak=    3.679 closest distance to " CE  LYS A  76 " =    0.823
peak=    3.677 closest distance to " CB  SER A   3 " =    1.353
peak=    3.672 closest distance to " O   HOH Z 247 " =    1.501
peak=    3.671 closest distance to " O   ALA A 165 " =    1.442
peak=    3.666 closest distance to " O   HOH Z  61 " =    1.561
peak=    3.665 closest distance to " O   HOH Z 214 " =    2.398
peak=    3.661 closest distance to " CB  GLU A 152 " =    1.154
peak=    3.661 closest distance to " CZ3 TRP A  85 " =    0.925
peak=    3.660 closest distance to " O   HOH Z 303 " =    2.230
peak=    3.660 closest distance to " CG1 ILE A  33 " =    1.265
peak=    3.659 closest distance to " CG2 THR A 221 " =    1.199
peak=    3.655 closest distance to " CG AARG A 275 " =    1.261
peak=    3.647 closest distance to " CG  LEU A 167 " =    1.068
peak=    3.645 closest distance to " CA  SER A  87 " =    1.034
peak=    3.642 closest distance to " CB  ALA A   9 " =    1.644
peak=    3.638 closest distance to " O   HOH Z 393 " =    3.781
peak=    3.637 closest distance to " ND2 ASN A 249 " =    1.900
peak=    3.634 closest distance to " O   HOH Z 383 " =    2.107
peak=    3.634 closest distance to " O  BHOH Z  74 " =    1.232
peak=    3.629 closest distance to " O   HOH Z  21 " =    1.769
peak=    3.629 closest distance to " OD1 ASN A  69 " =    2.544
peak=    3.618 closest distance to " O   HOH Z 313 " =    1.709
peak=    3.617 closest distance to " O   HOH Z 258 " =    2.069
peak=    3.615 closest distance to " O   HOH Z 199 " =    1.614
peak=    3.613 closest distance to " CB  ASN A  39 " =    0.855
peak=    3.612 closest distance to " CB  VAL A 265 " =    1.250
peak=    3.607 closest distance to " CG  MET A 185 " =    1.255
peak=    3.598 closest distance to " CB  MET A  40 " =    0.832
peak=    3.597 closest distance to " NH2 ARG A 156 " =    1.116
peak=    3.583 closest distance to " OE1 GLU A   2 " =    1.834
peak=    3.575 closest distance to " CA  ALA A 160 " =    0.912
peak=    3.572 closest distance to " CB  GLN A  89 " =    1.140
peak=    3.559 closest distance to " O   PRO A 213 " =    1.491
peak=    3.557 closest distance to " O   ASP A 200 " =    1.714
peak=    3.557 closest distance to " O   ASN A  74 " =    1.584
peak=    3.554 closest distance to " CG  GLU A  37 " =    0.854
peak=    3.552 closest distance to " O   HOH Z 368 " =    3.463
peak=    3.547 closest distance to " O   HOH Z 353 " =    2.592
peak=    3.547 closest distance to " CA  GLY A 267 " =    0.789
peak=    3.546 closest distance to " CD  ARG A 159 " =    0.774
peak=    3.546 closest distance to " CG2 VAL A 257 " =    0.865
peak=    3.543 closest distance to " O   HOH Z 346 " =    1.589
peak=    3.534 closest distance to " NZ  LYS A  48 " =    1.316
peak=    3.533 closest distance to " O   HOH Z 261 " =    1.536
peak=    3.531 closest distance to " CD1 ILE A 199 " =    1.027
peak=    3.531 closest distance to " O   HOH Z 273 " =    2.959
peak=    3.527 closest distance to " O   HOH Z  48 " =    1.516
peak=    3.513 closest distance to " CB  ASN A 285 " =    0.950
peak=    3.512 closest distance to " CB  LEU A  83 " =    0.788
peak=    3.510 closest distance to " CA  TYR A 116 " =    1.348
peak=    3.508 closest distance to " NZ  LYS A 117 " =    3.128
peak=    3.507 closest distance to " O   HOH Z 113 " =    1.772
peak=    3.502 closest distance to " O   HOH Z 203 " =    1.845
peak=    3.500 closest distance to " CD1 LEU A 300 " =    1.048
peak=    3.497 closest distance to " CB  MET A  47 " =    0.992
peak=    3.496 closest distance to " O   HOH Z 327 " =    2.241
peak=    3.495 closest distance to " ND2 ASN A 249 " =    0.927
peak=    3.495 closest distance to " CA  ALA A  21 " =    1.233
peak=    3.494 closest distance to " CD1 LEU A   5 " =    1.373
peak=    3.487 closest distance to " O   HOH Z 368 " =    1.843
peak=    3.485 closest distance to " CG2 ILE A 234 " =    0.896
peak=    3.485 closest distance to " O   HOH Z 227 " =    1.621
peak=    3.483 closest distance to " C   ALA A 299 " =    0.895
peak=    3.479 closest distance to " N   CYS A 260 " =    0.762
peak=    3.476 closest distance to " OG  SER A 276 " =    1.415
peak=    3.471 closest distance to " CB  TRP A 150 " =    1.392
peak=    3.469 closest distance to " CA  VAL A 125 " =    1.402
peak=    3.463 closest distance to " O   HOH Z 437 " =    1.817
peak=    3.451 closest distance to " CD1 LEU A 222 " =    0.706
peak=    3.451 closest distance to " CB  GLN A  88 " =    1.232
peak=    3.451 closest distance to " O   THR A 220 " =    1.223
peak=    3.450 closest distance to " N   SER A 164 " =    1.023
peak=    3.449 closest distance to " CD  ARG A  66 " =    2.089
peak=    3.447 closest distance to " O   HOH Z 158 " =    3.069
peak=    3.447 closest distance to " CB  SER A  62 " =    0.872
peak=    3.439 closest distance to " O  BHOH Z 338 " =    2.306
peak=    3.438 closest distance to " CD ALYS A 290 " =    1.027
peak=    3.435 closest distance to " CB  ALA A 248 " =    1.392
peak=    3.433 closest distance to " CA  ASP A 191 " =    0.972
peak=    3.432 closest distance to " O   HOH Z 420 " =    5.729
peak=    3.432 closest distance to " O   HOH Z 391 " =    2.960
peak=    3.426 closest distance to " O   HOH Z 417 " =    2.931
peak=    3.425 closest distance to " O   HOH Z  19 " =    1.724
peak=    3.424 closest distance to " CG  MET A 188 " =    0.844
peak=    3.423 closest distance to " O   HOH Z 146 " =    1.589
peak=    3.421 closest distance to " O   HOH Z  56 " =    1.652
peak=    3.418 closest distance to " O   HOH Z 141 " =    1.650
peak=    3.413 closest distance to " CA  ASN A 127 " =    1.155
peak=    3.407 closest distance to " O   HOH Z 371 " =    2.835
peak=    3.407 closest distance to " CB  THR A  52 " =    0.847
peak=    3.406 closest distance to " OG  SER A 245 " =    1.588
peak=    3.394 closest distance to " CB  ALA A 242 " =    0.858
peak=    3.394 closest distance to " OE1 GLN A  11 " =    1.899
peak=    3.393 closest distance to " CB  PRO A 243 " =    1.378
peak=    3.389 closest distance to " O   HOH Z 357 " =    2.650
peak=    3.386 closest distance to " CB  TYR A 247 " =    1.015
peak=    3.384 closest distance to " CG1 ILE A  49 " =    1.632
peak=    3.379 closest distance to " O   HOH Z 154 " =    1.323
peak=    3.373 closest distance to " O   HOH Z 406 " =    1.508
peak=    3.373 closest distance to " CG1BVAL A  72 " =    1.919
peak=    3.371 closest distance to " CB  ASN A 187 " =    1.219
peak=    3.367 closest distance to " O   HOH Z 294 " =    1.559
peak=    3.365 closest distance to " CA  ALA A 100 " =    0.930
peak=    3.362 closest distance to " CB  GLN A 103 " =    0.940
peak=    3.360 closest distance to " CA  THR A 264 " =    0.740
peak=    3.359 closest distance to " O   HOH Z   3 " =    1.847
peak=    3.356 closest distance to " CZ3 TRP A 274 " =    4.455
peak=    3.355 closest distance to " CB  ALA A 291 " =    1.244
peak=    3.355 closest distance to " CA  ASP A 162 " =    1.032
peak=    3.351 closest distance to " NE2 HIS A 115 " =    1.043
peak=    3.349 closest distance to " O   PHE A  61 " =    1.334
peak=    3.348 closest distance to " O   MET A 105 " =    1.887
peak=    3.346 closest distance to " O   HOH Z 407 " =    2.563
peak=    3.342 closest distance to " CA  ASN A 217 " =    1.238
peak=    3.340 closest distance to " CG1 ILE A  20 " =    1.224
peak=    3.340 closest distance to " CG  PHE A 204 " =    0.880
peak=    3.337 closest distance to " CB  SER A 210 " =    0.933
peak=    3.334 closest distance to " CB  LYS A 117 " =    1.197
peak=    3.334 closest distance to " O   HOH Z 431 " =    1.045
peak=    3.333 closest distance to " CG  GLN A  11 " =    1.307
peak=    3.332 closest distance to " O   TRP A 274 " =    1.866
peak=    3.332 closest distance to " CG  MET A 185 " =    0.966
peak=    3.330 closest distance to " O   HOH Z 139 " =    4.869
peak=    3.325 closest distance to " CE1 HIS A 108 " =    1.180
peak=    3.322 closest distance to " O   HOH Z 435 " =    2.013
peak=    3.317 closest distance to " CA  GLN A  88 " =    1.319
peak=    3.314 closest distance to " OD2 ASP A 298 " =    3.813
peak=    3.310 closest distance to " CB  LEU A 143 " =    1.232
peak=    3.306 closest distance to " N   TYR A 247 " =    1.228
peak=    3.298 closest distance to " O   HOH Z 344 " =    3.042
peak=    3.296 closest distance to " CE3 TRP A  85 " =    1.133
peak=    3.294 closest distance to " O   HOH Z 357 " =    2.153
peak=    3.294 closest distance to " CB  PRO A 198 " =    1.037
peak=    3.292 closest distance to " CB  SER A 288 " =    1.425
peak=    3.291 closest distance to " O   HOH Z 291 " =    1.543
peak=    3.289 closest distance to " CG  ARG A 138 " =    1.258
peak=    3.285 closest distance to " CB  SER A  26 " =    1.756
peak=    3.283 closest distance to " CE3 TRP A 150 " =    1.067
peak=    3.283 closest distance to " OD1 ASN A 217 " =    1.664
peak=    3.283 closest distance to " O   HOH Z 193 " =    2.048
peak=    3.277 closest distance to " O   HOH Z 365 " =    2.862
peak=    3.267 closest distance to " O   HOH Z 426 " =    1.419
peak=    3.264 closest distance to " N   PHE A 130 " =    1.274
peak=    3.261 closest distance to " CB  ASP A 107 " =    1.223
peak=    3.256 closest distance to " CA  ALA A 291 " =    0.872
peak=    3.255 closest distance to " O   ALA A 158 " =    1.274
peak=    3.254 closest distance to " CG2 THR A 220 " =    0.833
peak=    3.252 closest distance to " NH1 ARG A  14 " =    1.093
peak=    3.251 closest distance to " O   HOH Z 185 " =    1.705
peak=    3.249 closest distance to " O   HOH Z 271 " =    2.416
peak=    3.249 closest distance to " O   HOH Z 184 " =    1.473
peak=    3.248 closest distance to " CB  ASN A 110 " =    1.200
peak=    3.244 closest distance to " CB  ALA A 248 " =    1.130
peak=    3.243 closest distance to " CA  ASP A 140 " =    1.284
peak=    3.240 closest distance to " CB  PRO A  90 " =    1.194
peak=    3.240 closest distance to " CB  ALA A  43 " =    0.893
peak=    3.239 closest distance to " O   HOH Z 145 " =    2.145
peak=    3.238 closest distance to " N   ILE A  33 " =    1.022
peak=    3.237 closest distance to " CA  ALA A 154 " =    1.054
peak=    3.236 closest distance to " CG2 ILE A 106 " =    0.885
peak=    3.234 closest distance to " CA  LEU A 282 " =    1.132
peak=    3.231 closest distance to " N   ALA A 256 " =    1.094
peak=    3.228 closest distance to " O   HOH Z 213 " =    1.869
peak=    3.225 closest distance to " NH1 ARG A 269 " =    0.771
peak=    3.225 closest distance to " O   HOH Z  68 " =    1.769
peak=    3.221 closest distance to " N   ALA A 292 " =    1.042
peak=    3.221 closest distance to " O   HOH Z 163 " =    1.560
peak=    3.217 closest distance to " CB  LEU A 228 " =    1.202
peak=    3.213 closest distance to " O   HOH Z 124 " =    1.763
peak=    3.211 closest distance to " O   ASP A 124 " =    1.788
peak=    3.210 closest distance to " CB  ALA A  34 " =    0.769
peak=    3.209 closest distance to " O   HOH Z 133 " =    2.451
peak=    3.208 closest distance to " O   HOH Z 261 " =    1.130
peak=    3.207 closest distance to " O   HOH Z 166 " =    1.571
peak=    3.206 closest distance to " CE  LYS A 119 " =    0.996
peak=    3.201 closest distance to " O   HOH Z 301 " =    1.851
peak=    3.201 closest distance to " CB  SER A  62 " =    1.096
peak=    3.190 closest distance to " O   THR A 182 " =    1.425
peak=    3.189 closest distance to " O   HOH Z 329 " =    4.128
peak=    3.188 closest distance to " O   HOH Z 245 " =    1.345
peak=    3.187 closest distance to " CZ3 TRP A  92 " =    1.377
peak=    3.185 closest distance to " O   HOH Z 180 " =    2.152
peak=    3.185 closest distance to " O   HOH Z 227 " =    1.937
peak=    3.184 closest distance to " O   HOH Z 117 " =    1.983
peak=    3.177 closest distance to " OG BSER A 134 " =    2.746
peak=    3.172 closest distance to " NE2 HIS A 207 " =    1.091
peak=    3.171 closest distance to " O   HOH Z 132 " =    2.739
peak=    3.170 closest distance to " O   HOH Z  47 " =    2.744
peak=    3.169 closest distance to " OE1 GLN A  55 " =    1.368
peak=    3.169 closest distance to " CG2 ILE A 120 " =    1.056
peak=    3.166 closest distance to " CA  ARG A 156 " =    1.175
peak=    3.164 closest distance to " O   HOH Z 361 " =    3.653
peak=    3.163 closest distance to " O   HOH Z  68 " =    1.916
peak=    3.162 closest distance to " O   HOH Z 293 " =    1.983
peak=    3.160 closest distance to " OG1 THR A 294 " =    2.405
peak=    3.160 closest distance to " O   ALA A 292 " =    1.163
peak=    3.157 closest distance to " CG2 ILE A  20 " =    1.272
peak=    3.157 closest distance to " O   HOH Z 147 " =    1.758
peak=    3.155 closest distance to " CA  LYS A 117 " =    1.249
peak=    3.153 closest distance to " CD  PRO A  54 " =    1.044
peak=    3.153 closest distance to " O   HOH Z  88 " =    3.218
peak=    3.152 closest distance to " O   HOH Z 124 " =    1.121
peak=    3.150 closest distance to " O   HOH Z 433 " =    4.242
peak=    3.149 closest distance to " O   HOH Z 393 " =    3.295
peak=    3.143 closest distance to " CB  ASN A 215 " =    1.178
peak=    3.139 closest distance to " O   TYR A 116 " =    1.317
peak=    3.133 closest distance to " CG2 VAL A 197 " =    1.138
peak=    3.130 closest distance to " C   GLY A  80 " =    1.065
peak=    3.130 closest distance to " CA  THR A 221 " =    0.884
peak=    3.130 closest distance to " CD1 LEU A 101 " =    1.114
peak=    3.126 closest distance to " CB  THR A  31 " =    1.501
peak=    3.114 closest distance to " O   HOH Z 201 " =    2.937
peak=    3.110 closest distance to " O   HOH Z 213 " =    2.546
peak=    3.110 closest distance to " CE1 PHE A 218 " =    1.259
peak=    3.109 closest distance to " CB  ALA A 104 " =    0.766
peak=    3.109 closest distance to " CA  ASN A 176 " =    1.192
peak=    3.091 closest distance to " O   HOH Z  83 " =    1.463
peak=    3.080 closest distance to " CG2 VAL A 126 " =    0.889
peak=    3.079 closest distance to " O   HOH Z 148 " =    2.062
peak=    3.076 closest distance to " O   HOH Z 196 " =    1.001
peak=    3.070 closest distance to " O   HOH Z  90 " =    3.355
peak=    3.067 closest distance to " O   HOH Z 109 " =    2.559
peak=    3.064 closest distance to " CB  ARG A 219 " =    1.486
peak=    3.054 closest distance to " O   HOH Z 156 " =    2.562
peak=    3.048 closest distance to " CB  PHE A 204 " =    0.976
peak=    3.027 closest distance to " O   HOH Z 417 " =    2.193

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 215         
Filter by distance & map next to the model:
   mapped sites are within: 0.817 - 5.634
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 214 from: 215
   mapped sites are within: 0.817 - 5.634

peak=   -5.282 closest distance to " CG2 VAL A 230 " =    0.817
peak=   -4.515 closest distance to " CG1 VAL A 296 " =    1.098
peak=   -4.450 closest distance to " O   HOH Z 166 " =    1.569
peak=   -4.354 closest distance to " CD  GLN A  58 " =    0.996
peak=   -4.240 closest distance to " O   HOH Z 266 " =    5.507
peak=   -4.239 closest distance to " CG1 VAL A 250 " =    2.723
peak=   -4.215 closest distance to " O   VAL A  67 " =    2.826
peak=   -4.122 closest distance to " CD  ARG A 156 " =    2.100
peak=   -4.114 closest distance to " CA  ASP A 298 " =    1.064
peak=   -4.068 closest distance to " O   HOH Z 351 " =    1.496
peak=   -4.065 closest distance to " SG  CYS A 254 " =    3.380
peak=   -4.056 closest distance to " O   HOH Z 196 " =    2.549
peak=   -4.051 closest distance to " O   HOH Z  10 " =    1.585
peak=   -4.038 closest distance to " CE3 TRP A 150 " =    2.283
peak=   -4.030 closest distance to " CB  PRO A 243 " =    2.715
peak=   -4.008 closest distance to " CG1 VAL A 112 " =    2.776
peak=   -3.944 closest distance to " CZ2 TRP A  92 " =    2.790
peak=   -3.943 closest distance to " CG  ARG A 269 " =    2.352
peak=   -3.878 closest distance to " OXT GLY A 302 " =    2.985
peak=   -3.864 closest distance to " O   PRO A 163 " =    2.238
peak=   -3.841 closest distance to " CE2 TYR A  30 " =    2.751
peak=   -3.813 closest distance to " O   ILE A 109 " =    2.651
peak=   -3.811 closest distance to " O   SER A 271 " =    2.097
peak=   -3.789 closest distance to " OD1 ASN A 148 " =    1.368
peak=   -3.771 closest distance to " C   HIS A 108 " =    1.114
peak=   -3.770 closest distance to " O   HOH Z  37 " =    1.958
peak=   -3.751 closest distance to " O   HOH Z  73 " =    2.372
peak=   -3.738 closest distance to " O   PRO A 198 " =    1.248
peak=   -3.735 closest distance to " CA  VAL A  67 " =    2.894
peak=   -3.730 closest distance to " OD1 ASN A 249 " =    2.530
peak=   -3.716 closest distance to " CD2 TYR A 293 " =    1.880
peak=   -3.674 closest distance to " CD1 LEU A 101 " =    2.422
peak=   -3.672 closest distance to " O   HOH Z 394 " =    1.677
peak=   -3.671 closest distance to " OE1 GLN A 223 " =    2.090
peak=   -3.669 closest distance to " O   HOH Z 185 " =    2.439
peak=   -3.664 closest distance to " CG  ASP A 231 " =    0.840
peak=   -3.664 closest distance to " N   ALA A 226 " =    2.118
peak=   -3.659 closest distance to " CB  ALA A  10 " =    2.189
peak=   -3.650 closest distance to " O   HOH Z 231 " =    2.277
peak=   -3.636 closest distance to " CE3 TRP A  70 " =    1.810
peak=   -3.621 closest distance to " CB  ALA A 248 " =    2.274
peak=   -3.616 closest distance to " O   HOH Z 210 " =    0.946
peak=   -3.610 closest distance to " CG  GLU A  53 " =    1.560
peak=   -3.610 closest distance to " CZ  TYR A 169 " =    1.749
peak=   -3.607 closest distance to " O   HOH Z 211 " =    1.363
peak=   -3.603 closest distance to " O   HOH Z  13 " =    1.672
peak=   -3.597 closest distance to " CD1 PHE A  59 " =    2.025
peak=   -3.594 closest distance to " C   LEU A 143 " =    1.102
peak=   -3.587 closest distance to " OG BSER A 134 " =    1.364
peak=   -3.577 closest distance to " N   ALA A  43 " =    2.626
peak=   -3.575 closest distance to " O   GLY A  17 " =    1.294
peak=   -3.573 closest distance to " O   HOH Z  11 " =    1.911
peak=   -3.566 closest distance to " CG1 VAL A 112 " =    2.667
peak=   -3.563 closest distance to " NE2 GLN A 194 " =    1.898
peak=   -3.549 closest distance to " CG  GLU A 277 " =    1.172
peak=   -3.549 closest distance to " CA  GLY A 241 " =    2.329
peak=   -3.547 closest distance to " CG  PRO A 243 " =    1.683
peak=   -3.546 closest distance to " ND2 ASN A  45 " =    1.113
peak=   -3.542 closest distance to " CA  SER A  62 " =    2.638
peak=   -3.540 closest distance to " CD  GLN A 223 " =    1.319
peak=   -3.536 closest distance to " CZ3 TRP A 179 " =    1.240
peak=   -3.516 closest distance to " ND2BASN A 224 " =    1.861
peak=   -3.510 closest distance to " CB  PHE A 192 " =    1.994
peak=   -3.504 closest distance to " O   HOH Z 193 " =    1.491
peak=   -3.493 closest distance to " C   ASN A 285 " =    2.399
peak=   -3.477 closest distance to " O   HOH Z 222 " =    1.623
peak=   -3.475 closest distance to " O   ARG A  24 " =    2.131
peak=   -3.472 closest distance to " CD  LYS A 289 " =    2.401
peak=   -3.470 closest distance to " O   HOH Z  52 " =    1.691
peak=   -3.469 closest distance to " OG  SER A  97 " =    2.312
peak=   -3.460 closest distance to " O   HOH Z 113 " =    2.260
peak=   -3.458 closest distance to " O   HOH Z 348 " =    2.342
peak=   -3.457 closest distance to " CD2 PHE A  61 " =    2.061
peak=   -3.457 closest distance to " O   HOH Z 177 " =    1.937
peak=   -3.446 closest distance to " CG2 VAL A 189 " =    2.175
peak=   -3.440 closest distance to " CB  ALA A 248 " =    2.123
peak=   -3.438 closest distance to " O   HOH Z 133 " =    1.151
peak=   -3.437 closest distance to " O   SER A 210 " =    1.758
peak=   -3.434 closest distance to " O   HOH Z 251 " =    4.857
peak=   -3.433 closest distance to " O   HOH Z 165 " =    1.905
peak=   -3.428 closest distance to " O   HOH Z  92 " =    1.716
peak=   -3.427 closest distance to " ND2 ASN A 187 " =    1.680
peak=   -3.426 closest distance to " O   HOH Z 171 " =    2.230
peak=   -3.425 closest distance to " CD2 LEU A 167 " =    1.853
peak=   -3.420 closest distance to " C   ALA A 158 " =    1.353
peak=   -3.416 closest distance to " CA  VAL A 296 " =    1.019
peak=   -3.415 closest distance to " CA  GLY A 241 " =    3.176
peak=   -3.410 closest distance to " O   HOH Z 198 " =    1.984
peak=   -3.408 closest distance to " CD  PRO A 243 " =    1.969
peak=   -3.407 closest distance to " CD1 LEU A   5 " =    2.455
peak=   -3.405 closest distance to " O   HOH Z 290 " =    1.131
peak=   -3.404 closest distance to " O   HOH Z  19 " =    2.332
peak=   -3.403 closest distance to " CE2 TRP A  70 " =    2.136
peak=   -3.397 closest distance to " NE  ARG A  66 " =    4.168
peak=   -3.387 closest distance to " CG2 VAL A 230 " =    2.723
peak=   -3.384 closest distance to " ND2 ASN A  45 " =    1.993
peak=   -3.383 closest distance to " CE2 PHE A  61 " =    2.603
peak=   -3.383 closest distance to " NH2 ARG A 159 " =    2.311
peak=   -3.381 closest distance to " NH2 ARG A  79 " =    1.578
peak=   -3.380 closest distance to " O   HOH Z  44 " =    2.296
peak=   -3.376 closest distance to " O   HOH Z 200 " =    1.622
peak=   -3.376 closest distance to " O   HOH Z 350 " =    2.001
peak=   -3.374 closest distance to " O   ALA A  34 " =    2.582
peak=   -3.371 closest distance to " O   ALA A 227 " =    1.559
peak=   -3.370 closest distance to " O   HOH Z 234 " =    4.454
peak=   -3.368 closest distance to " C   SER A 206 " =    1.453
peak=   -3.365 closest distance to " CG2 ILE A 263 " =    2.337
peak=   -3.365 closest distance to " O   HOH Z 407 " =    3.158
peak=   -3.364 closest distance to " O   SER A  95 " =    1.940
peak=   -3.359 closest distance to " O   HOH Z 149 " =    2.070
peak=   -3.359 closest distance to " NH2 ARG A  66 " =    1.771
peak=   -3.357 closest distance to " O   HOH Z 231 " =    1.888
peak=   -3.356 closest distance to " OG1 THR A  82 " =    1.447
peak=   -3.347 closest distance to " O   HOH Z 435 " =    2.549
peak=   -3.346 closest distance to " CB  VAL A 230 " =    1.118
peak=   -3.342 closest distance to " CA  ALA A   8 " =    1.448
peak=   -3.341 closest distance to " CA  GLY A 133 " =    2.360
peak=   -3.341 closest distance to " CE BMET A  47 " =    1.888
peak=   -3.339 closest distance to " O   HOH Z 285 " =    1.807
peak=   -3.333 closest distance to " O   HOH Z  60 " =    1.828
peak=   -3.326 closest distance to " O   HOH Z 252 " =    3.824
peak=   -3.326 closest distance to " CA  VAL A 197 " =    1.032
peak=   -3.315 closest distance to " O   HOH Z 191 " =    5.634
peak=   -3.314 closest distance to " O   HOH Z 431 " =    2.272
peak=   -3.313 closest distance to " O   HOH Z 426 " =    1.759
peak=   -3.307 closest distance to " CA  ASN A 127 " =    1.053
peak=   -3.306 closest distance to " CG1 VAL A 112 " =    2.823
peak=   -3.303 closest distance to " O   GLY A  80 " =    2.625
peak=   -3.296 closest distance to " CG  LYS A 166 " =    2.135
peak=   -3.296 closest distance to " O   HOH Z 396 " =    2.064
peak=   -3.294 closest distance to " O   HOH Z 236 " =    1.525
peak=   -3.289 closest distance to " O   HOH Z 201 " =    2.102
peak=   -3.288 closest distance to " CG  GLN A  11 " =    1.581
peak=   -3.287 closest distance to " O   HOH Z 106 " =    1.936
peak=   -3.283 closest distance to " C   MET A 188 " =    1.357
peak=   -3.283 closest distance to " CD1 LEU A   5 " =    1.730
peak=   -3.283 closest distance to " O   GLU A  44 " =    1.667
peak=   -3.278 closest distance to " O   SER A   3 " =    1.127
peak=   -3.273 closest distance to " O   HOH Z 264 " =    1.707
peak=   -3.273 closest distance to " CB  ALA A 291 " =    2.374
peak=   -3.269 closest distance to " O   HOH Z 275 " =    1.586
peak=   -3.267 closest distance to " CD2 LEU A 300 " =    2.547
peak=   -3.263 closest distance to " CG  ASP A  50 " =    2.419
peak=   -3.257 closest distance to " NE  ARG A  79 " =    1.185
peak=   -3.254 closest distance to " CD1 ILE A 151 " =    2.452
peak=   -3.252 closest distance to " ND2 ASN A  45 " =    1.144
peak=   -3.252 closest distance to " O   TYR A 186 " =    1.794
peak=   -3.250 closest distance to " O   HOH Z 114 " =    3.152
peak=   -3.247 closest distance to " O   SER A 276 " =    1.785
peak=   -3.246 closest distance to " O   HOH Z 105 " =    2.134
peak=   -3.239 closest distance to " O   HOH Z 166 " =    1.656
peak=   -3.237 closest distance to " NE2 GLN A 103 " =    1.878
peak=   -3.234 closest distance to " OE2 GLU A 277 " =    2.948
peak=   -3.231 closest distance to " NH2 ARG A  36 " =    2.395
peak=   -3.229 closest distance to " O   HOH Z 377 " =    1.890
peak=   -3.226 closest distance to " NH2AARG A 275 " =    5.149
peak=   -3.216 closest distance to " O   HOH Z 411 " =    1.738
peak=   -3.215 closest distance to " O   HOH Z 259 " =    1.921
peak=   -3.215 closest distance to " OG1 THR A  82 " =    1.452
peak=   -3.214 closest distance to " O   HOH Z 238 " =    1.082
peak=   -3.212 closest distance to " O   HOH Z 216 " =    1.297
peak=   -3.209 closest distance to " N   GLN A  77 " =    1.540
peak=   -3.207 closest distance to " OXT GLY A 302 " =    3.382
peak=   -3.206 closest distance to " O   GLY A  75 " =    2.101
peak=   -3.201 closest distance to " O   HOH Z 340 " =    1.582
peak=   -3.201 closest distance to " CD  GLN A  88 " =    0.896
peak=   -3.200 closest distance to " O   HOH Z  94 " =    2.092
peak=   -3.190 closest distance to " O   HOH Z 423 " =    2.299
peak=   -3.189 closest distance to " NE2 GLN A  88 " =    1.049
peak=   -3.186 closest distance to " OE1 GLN A  88 " =    0.927
peak=   -3.184 closest distance to " O   HOH Z 241 " =    1.383
peak=   -3.183 closest distance to " CA  ARG A  36 " =    1.153
peak=   -3.181 closest distance to " O   HOH Z 139 " =    5.480
peak=   -3.181 closest distance to " O   ASP A 107 " =    1.636
peak=   -3.180 closest distance to " CD  GLU A 236 " =    1.121
peak=   -3.180 closest distance to " CZ  PHE A  38 " =    2.518
peak=   -3.175 closest distance to " CB  TRP A  85 " =    2.469
peak=   -3.173 closest distance to " O   GLY A 203 " =    2.346
peak=   -3.172 closest distance to " CG  TRP A 266 " =    1.815
peak=   -3.167 closest distance to " CB  ALA A 114 " =    2.550
peak=   -3.165 closest distance to " OG  SER A  63 " =    1.155
peak=   -3.160 closest distance to " O   HOH Z 292 " =    4.587
peak=   -3.159 closest distance to " O   HOH Z 136 " =    2.458
peak=   -3.159 closest distance to " O   HOH Z  38 " =    1.623
peak=   -3.158 closest distance to " CG  MET A 105 " =    0.919
peak=   -3.157 closest distance to " SD  MET A  40 " =    2.002
peak=   -3.148 closest distance to " SG  CYS A 260 " =    2.506
peak=   -3.137 closest distance to " N   SER A 276 " =    1.447
peak=   -3.137 closest distance to " CB  ALA A  51 " =    1.905
peak=   -3.136 closest distance to " CE  MET A 105 " =    2.232
peak=   -3.134 closest distance to " O   VAL A 189 " =    2.536
peak=   -3.133 closest distance to " O   HOH Z 150 " =    2.087
peak=   -3.130 closest distance to " O   HOH Z 110 " =    1.506
peak=   -3.130 closest distance to " CG2 VAL A 112 " =    2.560
peak=   -3.128 closest distance to " OD1 ASN A 173 " =    1.388
peak=   -3.121 closest distance to " CB  ASP A 171 " =    2.293
peak=   -3.119 closest distance to " O   HOH Z   6 " =    1.702
peak=   -3.117 closest distance to " CD2 PHE A 225 " =    1.297
peak=   -3.115 closest distance to " CA  GLY A 203 " =    2.473
peak=   -3.112 closest distance to " OD2 ASP A 171 " =    1.878
peak=   -3.110 closest distance to " ND2 ASN A  39 " =    1.318
peak=   -3.106 closest distance to " NE1 TRP A 266 " =    2.405
peak=   -3.099 closest distance to " N   ASN A  60 " =    1.240
peak=   -3.097 closest distance to " CD1 TYR A 247 " =    2.386
peak=   -3.094 closest distance to " C   THR A 279 " =    1.227
peak=   -3.089 closest distance to " CD2 HIS A 207 " =    2.425
peak=   -3.081 closest distance to " CG2 VAL A 296 " =    1.076
peak=   -3.080 closest distance to " CB  ASP A 132 " =    2.358
peak=   -3.077 closest distance to " CG  ARG A 219 " =    2.863
peak=   -3.075 closest distance to " C   THR A 264 " =    1.436
peak=   -3.066 closest distance to " O   HOH Z 227 " =    1.345
peak=   -3.048 closest distance to " OD2 ASP A 298 " =    0.988
peak=   -3.018 closest distance to " CB  PHE A  16 " =    2.453
peak=   -3.001 closest distance to " OG1 THR A 157 " =    2.934

================= 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    :  0.4785 0.4655   6.276573e+00   6.256228e+00
   1_bss:  0.4706 0.4542   6.270152e+00   6.248487e+00
   1_xyz:  0.3798 0.3972   6.143790e+00   6.165263e+00
   1_adp:  0.3325 0.3795   6.049760e+00   6.126580e+00
   1_occ:  0.3318 0.3799   6.048991e+00   6.127380e+00
   2_bss:  0.3289 0.3753   6.050458e+00   6.126062e+00
   2_xyz:  0.2487 0.2986   5.816610e+00   5.955767e+00
   2_adp:  0.2297 0.2760   5.754993e+00   5.900628e+00
   2_occ:  0.2293 0.2765   5.754826e+00   5.901812e+00
   3_bss:  0.2287 0.2761   5.755817e+00   5.901603e+00
   3_xyz:  0.1630 0.2013   5.443832e+00   5.627869e+00
   3_adp:  0.1470 0.1911   5.367244e+00   5.575991e+00
   3_occ:  0.1469 0.1913   5.366936e+00   5.575896e+00
   4_bss:  0.1469 0.1914   5.366344e+00   5.574703e+00
   4_xyz:  0.1269 0.1754   5.256333e+00   5.487829e+00
   4_adp:  0.1237 0.1715   5.233040e+00   5.464598e+00
   4_occ:  0.1236 0.1714   5.232531e+00   5.464169e+00
   5_bss:  0.1236 0.1713   5.232344e+00   5.464041e+00
   5_xyz:  0.1230 0.1683   5.223115e+00   5.449340e+00
   5_adp:  0.1223 0.1686   5.221278e+00   5.451409e+00
   5_occ:  0.1222 0.1686   5.221047e+00   5.451244e+00
   5_bss:  0.1223 0.1686   5.220971e+00   5.450495e+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:  0.300  20.000   6.416  10.073   9.858   0.000   0.000   0.000
   1_xyz:  0.300  20.000   6.416  10.073   9.858   0.000   0.000   0.000
   1_adp:  0.300  20.000   6.416  10.073   9.858   0.000   0.000   0.000
   1_occ:  0.300  20.000   6.416  10.073   9.858   0.000   0.000   0.000
   2_bss:  0.318  52.195   3.264   6.388   6.110   0.000   0.000   0.000
   2_xyz:  0.318  52.195   3.264   6.388   6.110   0.000   0.000   0.000
   2_adp:  0.318  52.195   3.264   6.388   6.110   0.000   0.000   0.000
   2_occ:  0.318  52.195   3.264   6.388   6.110   0.000   0.000   0.000
   3_bss:  0.307  52.195   2.452   4.322   4.384   0.000   0.000   0.000
   3_xyz:  0.307  52.195   2.452   4.322   4.384   0.000   0.000   0.000
   3_adp:  0.307  52.195   2.452   4.322   4.384   0.000   0.000   0.000
   3_occ:  0.307  52.195   2.452   4.322   4.384   0.000   0.000   0.000
   4_bss:  0.328  67.346   2.179   3.269   4.024   0.000   0.000   0.000
   4_xyz:  0.328  67.346   2.179   3.269   4.024   0.000   0.000   0.000
   4_adp:  0.328  67.346   2.179   3.269   4.024   0.000   0.000   0.000
   4_occ:  0.328  67.346   2.179   3.269   4.024   0.000   0.000   0.000
   5_bss:  0.330  67.346   2.347   3.124   4.089   0.000   0.000   0.000
   5_xyz:  0.330  67.346   2.347   3.124   4.089   0.000   0.000   0.000
   5_adp:  0.330  67.346   2.347   3.124   4.089   0.000   0.000   0.000
   5_occ:  0.330  67.346   2.347   3.124   4.089   0.000   0.000   0.000
   5_bss:  0.325  69.210  -0.784  -0.145   0.929   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  54.753 0.4612  0.5180    63641.571
   1_bss:  53.957 0.4705  0.6857    62222.958
   1_xyz:  44.762 0.5840  0.8252    44286.257
   1_adp:  40.842 0.6323  0.9231    39045.975
   1_occ:  40.880 0.6318  0.9220    39094.695
   2_bss:  40.695 0.6341  0.8195    38871.935
   2_xyz:  31.477 0.7408  0.9389    23941.973
   2_adp:  28.540 0.7741  0.9592    20669.363
   2_occ:  28.587 0.7736  0.9583    20711.720
   3_bss:  28.510 0.7745  0.9089    20686.321
   3_xyz:  19.625 0.8650  0.9759    10513.914
   3_adp:  18.156 0.8792  0.9753     9404.970
   3_occ:  18.152 0.8792  0.9753     9406.418
   4_bss:  18.102 0.8797  0.9566     9381.790
   4_xyz:  16.213 0.8963  0.9648     7806.768
   4_adp:  15.641 0.9015  0.9598     7500.358
   4_occ:  15.630 0.9016  0.9598     7495.477
   5_bss:  15.624 0.9017  0.9611     7495.114
   5_xyz:  15.216 0.9054  0.9628     7205.371
   5_adp:  15.232 0.9054  0.9560     7235.901
   5_occ:  15.226 0.9055  0.9560     7234.830
   5_bss:  15.231 0.9054  0.9575     7224.456
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.094   5.4428e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.094   5.4428e+01
   1_xyz:   1.700  0.014  0.108 17.997  0.007  4.112   1.4198e-01
   1_adp:   1.700  0.014  0.108 17.997  0.007  4.112   1.4198e-01
   1_occ:   1.700  0.014  0.108 17.997  0.007  4.112   1.4198e-01
   2_bss:   1.700  0.014  0.108 17.997  0.007  4.112   1.4198e-01
   2_xyz:   1.162  0.008  0.076 16.037  0.004  4.130   7.5120e-02
   2_adp:   1.162  0.008  0.076 16.037  0.004  4.130   7.5120e-02
   2_occ:   1.162  0.008  0.076 16.037  0.004  4.130   7.5120e-02
   3_bss:   1.162  0.008  0.076 16.037  0.004  4.130   7.5120e-02
   3_xyz:   1.153  0.009  0.086 15.924  0.004  4.136   7.6259e-02
   3_adp:   1.153  0.009  0.086 15.924  0.004  4.136   7.6259e-02
   3_occ:   1.153  0.009  0.086 15.924  0.004  4.136   7.6259e-02
   4_bss:   1.153  0.009  0.086 15.924  0.004  4.136   7.6259e-02
   4_xyz:   1.108  0.010  0.087 15.557  0.004  4.147   7.3569e-02
   4_adp:   1.108  0.010  0.087 15.557  0.004  4.147   7.3569e-02
   4_occ:   1.108  0.010  0.087 15.557  0.004  4.147   7.3569e-02
   5_bss:   1.108  0.010  0.087 15.557  0.004  4.147   7.3569e-02
   5_xyz:   0.985  0.008  0.078 15.125  0.003  4.127   6.0070e-02
   5_adp:   0.985  0.008  0.078 15.125  0.003  4.127   6.0070e-02
   5_occ:   0.985  0.008  0.078 15.125  0.003  4.127   6.0070e-02
   5_bss:   0.985  0.008  0.078 15.125  0.003  4.127   6.0070e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0570e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0570e+00
   1_xyz:  15.368  0.168  0.476 89.607  0.040  2.270   1.0659e-01
   1_adp:  15.368  0.168  0.476 89.607  0.040  2.270   1.0659e-01
   1_occ:  15.368  0.168  0.476 89.607  0.040  2.270   1.0659e-01
   2_bss:  15.368  0.168  0.476 89.607  0.040  2.270   1.0659e-01
   2_xyz:   8.743  0.080  0.285 83.587  0.025  2.102   6.1259e-02
   2_adp:   8.743  0.080  0.285 83.587  0.025  2.102   6.1259e-02
   2_occ:   8.743  0.080  0.285 83.587  0.025  2.102   6.1259e-02
   3_bss:   8.743  0.080  0.285 83.587  0.025  2.102   6.1259e-02
   3_xyz:   9.316  0.073  0.320 85.460  0.047  2.288   5.2994e-02
   3_adp:   9.316  0.073  0.320 85.460  0.047  2.288   5.2994e-02
   3_occ:   9.316  0.073  0.320 85.460  0.047  2.288   5.2994e-02
   4_bss:   9.316  0.073  0.320 85.460  0.047  2.288   5.2994e-02
   4_xyz:   7.593  0.050  0.486 82.433  0.033  2.283   5.6107e-02
   4_adp:   7.593  0.050  0.486 82.433  0.033  2.283   5.6107e-02
   4_occ:   7.593  0.050  0.486 82.433  0.033  2.283   5.6107e-02
   5_bss:   7.593  0.050  0.486 82.433  0.033  2.283   5.6107e-02
   5_xyz:   7.240  0.041  0.364 80.170  0.036  2.374   3.5775e-02
   5_adp:   7.240  0.041  0.364 80.170  0.036  2.374   3.5775e-02
   5_occ:   7.240  0.041  0.364 80.170  0.036  2.374   3.5775e-02
   5_bss:   7.240  0.041  0.364 80.170  0.036  2.374   3.5775e-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: 111.29   0.00  13.05  75.47   0.00  10.33 111.29   0.00  27.90
   1_occ: 111.29   0.00  13.05  75.47   0.00  10.33 111.29   0.00  27.90
   2_bss: 111.29   0.00  13.05  75.47   0.00  10.33 111.29   0.00  27.90
   2_xyz: 111.29   0.00  13.05  75.47   0.00  10.33 111.29   0.00  27.90
   2_adp: 110.67   0.00  12.43  67.46   0.00   8.86 110.67   0.00  31.88
   2_occ: 110.67   0.00  12.43  67.46   0.00   8.86 110.67   0.00  31.88
   3_bss: 110.67   0.00  12.43  67.46   0.00   8.86 110.67   0.00  31.88
   3_xyz: 110.67   0.00  12.43  67.46   0.00   8.86 110.67   0.00  31.88
   3_adp: 105.28   0.00  13.34  80.43   0.00   8.70 105.28   0.19  38.60
   3_occ: 105.28   0.00  13.34  80.43   0.00   8.70 105.28   0.19  38.60
   4_bss: 105.28   0.00  13.34  80.43   0.00   8.70 105.28   0.19  38.60
   4_xyz: 105.28   0.00  13.34  80.43   0.00   8.70 105.28   0.19  38.60
   4_adp:  95.12   0.00  12.94  87.05   0.00   8.28  95.12   0.08  38.29
   4_occ:  95.12   0.00  12.94  87.05   0.00   8.28  95.12   0.08  38.29
   5_bss:  95.12   0.00  12.94  87.05   0.00   8.28  95.12   0.08  38.29
   5_xyz:  95.12   0.00  12.94  87.05   0.00   8.28  95.12   0.08  38.29
   5_adp:  93.16   0.00  12.80  88.78   0.00   8.14  93.16   0.39  38.19
   5_occ:  93.16   0.00  12.80  88.78   0.00   8.14  93.16   0.39  38.19
   5_bss:  96.40   3.24  16.04  92.02   3.24  11.37  96.40   3.63  41.42
------------------------------------------------------------------------
 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:    1.248    0.017    0.412
   1_adp:    1.248    0.017    0.412
   1_occ:    1.248    0.017    0.412
   2_bss:    1.248    0.017    0.412
   2_xyz:    1.791    0.032    0.566
   2_adp:    1.791    0.032    0.566
   2_occ:    1.791    0.032    0.566
   3_bss:    1.791    0.032    0.566
   3_xyz:    1.736    0.061    0.656
   3_adp:    1.736    0.061    0.656
   3_occ:    1.736    0.061    0.656
   4_bss:    1.736    0.061    0.656
   4_xyz:    1.877    0.028    0.698
   4_adp:    1.877    0.028    0.698
   4_occ:    1.877    0.028    0.698
   5_bss:    1.877    0.028    0.698
   5_xyz:    2.024    0.024    0.713
   5_adp:    2.024    0.024    0.713
   5_occ:    2.024    0.024    0.713
   5_bss:    2.024    0.024    0.713
------------------------------------------------------------------------

CPU time actual refinement: 314.36


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_822/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_822/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_822/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_822/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_822/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 314.21 
  Macro-tasks:
    bulk solvent and scale       = 41.72  
    individual site refinement   = 124.89 
    weights calculation          = 31.63  
    collect and process          = 6.46   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 204.81 
  Micro-tasks:
    mask                            = 2.33   
    f_calc                          = 93.92  
    alpha_beta                      = 8.40   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 103.81 
    fmodel                         = 6.95   
    r_factors                      = 0.30   
    phase_errors                   = 10.72  
    foms                           = 0.22   
    TOTAL for micro-tasks          = 227.80 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.495 micro seconds
Total CPU time: 5.46 minutes
from_scatterers_fft:    621 calls, 93.59 s
gradients_fft:          566 calls, 91.23 s

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

# Date 2008-01-16 Time 02:31:10 PST -0800 (1200479470.95 s)
Start R-work = 0.4785, R-free = 0.4655 (no bulk solvent and anisotropic scale)
Final R-work = 0.1381, R-free = 0.1832 (no bulk solvent and anisotropic scale)

Start R-work = 0.4706, R-free = 0.4542
Final R-work = 0.1223, R-free = 0.1686