# Date 2008-01-16 Time 01:44:32 PST -0800 (1200476672.66 s)
#phil __OFF__

Command line arguments: "../537.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 3948
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 537

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.8988, 46.6953, 88.1178, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 46.6953, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0179 1.99041
Completeness in resolution range: 0.961612
Completeness with d_max=infinity: 0.958647

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0179
                             d_min =   1.9904

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 46.6953, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0179 1.99041
Completeness in resolution range: 0.961612
Completeness with d_max=infinity: 0.958647

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0183 -  4.2587 [2143/2167]  1924   219  10.2%
  bin  2:  4.2587 -  3.3931 [2050/2070]  1848   202   9.9%
  bin  3:  3.3931 -  2.9679 [2032/2051]  1834   198   9.7%
  bin  4:  2.9679 -  2.6983 [1994/2024]  1789   205  10.3%
  bin  5:  2.6983 -  2.5058 [2003/2022]  1802   201  10.0%
  bin  6:  2.5058 -  2.3587 [1995/2020]  1794   201  10.1%
  bin  7:  2.3587 -  2.2410 [1983/2011]  1786   197   9.9%
  bin  8:  2.2410 -  2.1437 [1955/1991]  1760   195  10.0%
  bin  9:  2.1437 -  2.0614 [1958/2000]  1765   193   9.9%
  bin 10:  2.0614 -  1.9904 [1476/2015]  1328   148  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_537/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.56 -     2.22: 12
        2.22 -     2.89: 1336
        2.89 -     3.56: 4427
        3.56 -     4.23: 9143
        4.23 -     4.90: 13242
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.555 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.618 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.742 3.040 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  95 " - " O   HOH Z  50 "  1.926 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28155 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_537/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_537/model_refine_001.geo

CPU time processing inputs: 9.24


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.89875 46.69535 88.1178 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4564   r_free= 0.4382   ksol= 0.00   Bsol= 0.00   scale= 0.805    |
|                                                                             |
| 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:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.257527                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0183 -  4.7497 0.99   1394  152 0.3790 0.3479      6.5693      6.4725|
|  2:  4.7497 -  3.7900 0.99   1329  154 0.3523 0.3797      6.6932      6.7915|
|  3:  3.7900 -  3.3168 0.99   1307  143 0.4046 0.3670       6.626      6.5853|
|  4:  3.3168 -  3.0162 0.99   1304  140 0.4512 0.4222      6.5089      6.4433|
|  5:  3.0162 -  2.8015 0.99   1290  147 0.4818 0.4445      6.3478      6.3349|
|  6:  2.8015 -  2.6373 0.99   1301  145 0.4731 0.5412      6.2563      6.2212|
|  7:  2.6373 -  2.5058 0.99   1272  144 0.4951 0.4734      6.2231      6.1663|
|  8:  2.5058 -  2.3972 0.98   1270  136 0.5102 0.4684      6.1811      6.1669|
|  9:  2.3972 -  2.3052 0.98   1281  148 0.4977 0.5202      6.1024      6.1537|
| 10:  2.3052 -  2.2260 1.00   1275  139 0.5318 0.4094      6.1262       6.021|
| 11:  2.2260 -  2.1566 0.97   1266  134 0.5005 0.5089      6.0331      6.0538|
| 12:  2.1566 -  2.0951 0.98   1247  145 0.5154 0.4654      5.9623      5.9945|
| 13:  2.0951 -  2.0401 1.00   1273  137 0.5034 0.4939      5.8888      5.8352|
| 14:  2.0401 -  1.9904 0.63    821   95 0.5191 0.4705      5.8807      5.7328|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0183 -  4.7497  1394   152  0.73  31.70   0.80     0.76      61973.95|
|  2:  4.7497 -  3.7900  1329   154  0.75  30.68   0.89     0.81      85423.57|
|  3:  3.7900 -  3.3168  1307   143  0.68  37.34   0.85     0.77      89832.42|
|  4:  3.3168 -  3.0162  1304   140  0.59  44.34   0.80     0.66      80685.13|
|  5:  3.0162 -  2.8015  1290   147  0.49  52.49   0.77     0.56      70808.56|
|  6:  2.8015 -  2.6373  1301   145  0.45  56.13   0.73     0.50      66067.61|
|  7:  2.6373 -  2.5058  1272   144  0.42  58.09   0.75     0.49      61123.87|
|  8:  2.5058 -  2.3972  1270   136  0.44  56.88   0.72     0.50      52993.22|
|  9:  2.3972 -  2.3052  1281   148  0.46  55.19   0.74     0.53      46862.65|
| 10:  2.3052 -  2.2260  1275   139  0.46  55.75   0.74     0.53      41701.62|
| 11:  2.2260 -  2.1566  1266   134  0.44  56.64   0.76     0.54      40805.27|
| 12:  2.1566 -  2.0951  1247   145  0.43  57.98   0.76     0.52      37020.26|
| 13:  2.0951 -  2.0401  1273   137  0.43  57.84   0.74     0.51      32199.05|
| 14:  2.0401 -  1.9904   821    95  0.47  55.09   0.74     0.50      25317.11|
|alpha:            min =        0.49 max =            0.81 mean =         0.59|
|beta:             min =    25317.11 max =        89832.42 mean =     57724.96|
|figures of merit: min =        0.00 max =            1.00 mean =         0.52|
|phase err.(work): min =        0.00 max =           89.99 mean =        50.09|
|phase err.(test): min =        0.00 max =           89.71 mean =        50.34|
|-----------------------------------------------------------------------------|

============================== Outliers rejection =============================

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 0
total                    = 0

====================== Target weights (before refinement) =====================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.698140              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.434   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.793572              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.828   (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:        3 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       28 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      167 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      684 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1497 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2604 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3896 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5076 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6548 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7674 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.946 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.091    4.900  1.196 |       1.815 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.957)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

|-Occupancies statistics------------------------------------------------------|
| occupancies: max = 1.00   min = 0.30   number of occupancies < 0.1 = 0      |
|-----------------------------------------------------------------------------|

                ----------Modify initial isotropic ADP----------               

Randomizing
|-ADP statistics (Wilson B = 11.957)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4656   r_free= 0.4464   ksol= 0.00   Bsol= 0.00   scale= 0.774    |
|                                                                             |
| 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:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.261778                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4482   r_free= 0.4299   ksol= 0.35   Bsol= 20.00   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.85,7.79,11.67,0.00,0.00,0.00); trace/3= 8.77                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.249514                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.512805              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.729   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.743303              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 75.916   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4482      final r-factor (work) = 0.3514          |
| start r-factor (free) = 0.4299      final r-factor (free) = 0.3707          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 80.5926 = 8.51 * 0.50 * 6.2605 + 1.00 * 53.9456                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.2192 = 8.51 * 0.50 * 6.1298 + 1.00 * 0.1285                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3514      final r-factor (work) = 0.2977          |
| start r-factor (free) = 0.3707      final r-factor (free) = 0.3411          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5707 = 0.74 * 1.00 * 6.1298 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.4705 = 0.74 * 1.00 * 5.9965 + 1.00 * 0.0133                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.957)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    62.77   11.78    None  None   None       |
|    all(noH): 2823   0      0.00    62.77   11.78    None  None   None       |
|    Sol.    : 438    0      0.00    62.77   26.86    None  None   None       |
|    Mac.    : 2385   0      0.00    52.41   9.00     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.277: 1093   |   5:    31.386 -  37.664:  102        |
|      1:     6.277 -  12.555:  769   |   6:    37.664 -  43.941:   50        |
|      2:    12.555 -  18.832:  404   |   7:    43.941 -  50.218:   40        |
|      3:    18.832 -  25.109:  224   |   8:    50.218 -  56.496:   15        |
|      4:    25.109 -  31.386:  119   |   9:    56.496 -  62.773:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2977 r_free = 0.3411             target_work(ml) = 5.966         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2972 r_free = 0.3418             target_work(ml) = 5.965         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2972   r_free= 0.3418   ksol= 0.35   Bsol= 20.00   scale= 1.102   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.85,7.79,11.67,0.00,0.00,0.00); trace/3= 8.77                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.965485                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2929   r_free= 0.3370   ksol= 0.34   Bsol= 43.59   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.43,3.89,7.90,0.00,0.00,0.00); trace/3= 5.07                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.965278                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.673385              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.244   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.399599              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.654  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2929      final r-factor (work) = 0.2053          |
| start r-factor (free) = 0.3370      final r-factor (free) = 0.2526          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.1445 = 4.67 * 0.50 * 5.9982 + 1.00 * 0.1285                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.6350 = 4.67 * 0.50 * 5.8050 + 1.00 * 0.0706                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2053      final r-factor (work) = 0.1859          |
| start r-factor (free) = 0.2526      final r-factor (free) = 0.2355          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3330 = 0.40 * 1.00 * 5.8050 + 1.00 * 0.0134                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2510 = 0.40 * 1.00 * 5.5999 + 1.00 * 0.0133                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.957)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    61.51   11.77    None  None   None       |
|    all(noH): 2823   0      0.00    61.51   11.77    None  None   None       |
|    Sol.    : 438    0      0.00    61.51   30.71    None  None   None       |
|    Mac.    : 2385   0      0.00    53.20   8.29     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 -   6.151: 1188   |   5:    30.753 -  36.903:  127        |
|      1:     6.151 -  12.301:  764   |   6:    36.903 -  43.054:   76        |
|      2:    12.301 -  18.452:  330   |   7:    43.054 -  49.204:   51        |
|      3:    18.452 -  24.602:  130   |   8:    49.204 -  55.355:   22        |
|      4:    24.602 -  30.753:  124   |   9:    55.355 -  61.505:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1859 r_free = 0.2355             target_work(ml) = 5.565         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1858 r_free = 0.2353             target_work(ml) = 5.565         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1858   r_free= 0.2353   ksol= 0.34   Bsol= 43.59   scale= 1.044   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.43,3.89,7.90,0.00,0.00,0.00); trace/3= 5.07                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.565214                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1842   r_free= 0.2354   ksol= 0.32   Bsol= 43.59   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.39,2.93,5.31,0.00,0.00,0.00); trace/3= 3.54                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.565615                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.430883              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.591  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 5.541570              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 110.587  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1842      final r-factor (work) = 0.1378          |
| start r-factor (free) = 0.2354      final r-factor (free) = 0.1869          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.4912 = 4.43 * 0.50 * 5.6064 + 1.00 * 0.0705                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.1400 = 4.43 * 0.50 * 5.4455 + 1.00 * 0.0758                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1378      final r-factor (work) = 0.1251          |
| start r-factor (free) = 0.1869      final r-factor (free) = 0.1773          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 30.1881 = 5.54 * 1.00 * 5.4455 + 1.00 * 0.0116                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 29.2593 = 5.54 * 1.00 * 5.2771 + 1.00 * 0.0160                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.957)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.34   12.71    None  None   None       |
|    all(noH): 2823   0      0.00    82.34   12.71    None  None   None       |
|    Sol.    : 438    0      0.86    82.34   37.27    None  None   None       |
|    Mac.    : 2385   0      0.00    74.55   8.20     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.234: 1603   |   5:    41.170 -  49.404:   95        |
|      1:     8.234 -  16.468:  603   |   6:    49.404 -  57.638:   76        |
|      2:    16.468 -  24.702:  181   |   7:    57.638 -  65.872:   49        |
|      3:    24.702 -  32.936:  107   |   8:    65.872 -  74.106:   14        |
|      4:    32.936 -  41.170:   90   |   9:    74.106 -  82.340:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1251 r_free = 0.1773             target_work(ml) = 5.249         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1250 r_free = 0.1774             target_work(ml) = 5.250         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1250   r_free= 0.1774   ksol= 0.32   Bsol= 43.59   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.39,2.93,5.31,0.00,0.00,0.00); trace/3= 3.54                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.249676                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1250   r_free= 0.1773   ksol= 0.31   Bsol= 43.59   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.27,2.72,4.71,0.00,0.00,0.00); trace/3= 3.23                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.249306                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.323337              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 130.614  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.653248              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 120.418  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1250      final r-factor (work) = 0.1189          |
| start r-factor (free) = 0.1773      final r-factor (free) = 0.1686          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2068 = 2.32 * 0.50 * 5.2777 + 1.00 * 0.0758                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1396 = 2.32 * 0.50 * 5.2320 + 1.00 * 0.0618                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1189      final r-factor (work) = 0.1177          |
| start r-factor (free) = 0.1686      final r-factor (free) = 0.1654          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4377 = 0.65 * 1.00 * 5.2320 + 1.00 * 0.0200                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4124 = 0.65 * 1.00 * 5.2032 + 1.00 * 0.0134                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.957)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.39   12.35    None  None   None       |
|    all(noH): 2823   0      0.00    82.39   12.35    None  None   None       |
|    Sol.    : 438    0      0.92    82.39   36.05    None  None   None       |
|    Mac.    : 2385   0      0.00    78.96   7.99     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.239: 1649   |   5:    41.197 -  49.437:   83        |
|      1:     8.239 -  16.479:  583   |   6:    49.437 -  57.676:   70        |
|      2:    16.479 -  24.718:  168   |   7:    57.676 -  65.915:   43        |
|      3:    24.718 -  32.958:  108   |   8:    65.915 -  74.155:   12        |
|      4:    32.958 -  41.197:  101   |   9:    74.155 -  82.394:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1177 r_free = 0.1654             target_work(ml) = 5.193         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1176 r_free = 0.1653             target_work(ml) = 5.193         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1176   r_free= 0.1653   ksol= 0.31   Bsol= 43.59   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.27,2.72,4.71,0.00,0.00,0.00); trace/3= 3.23                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.193048                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1176   r_free= 0.1654   ksol= 0.31   Bsol= 43.59   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.40,2.76,4.64,0.00,0.00,0.00); trace/3= 3.26                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.193050                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.556051              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 150.821  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.374503              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 145.270  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1176      final r-factor (work) = 0.1174          |
| start r-factor (free) = 0.1654      final r-factor (free) = 0.1635          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.1099 = 1.56 * 0.50 * 5.2030 + 1.00 * 0.0618                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.0948 = 1.56 * 0.50 * 5.1926 + 1.00 * 0.0548                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1174      final r-factor (work) = 0.1175          |
| start r-factor (free) = 0.1635      final r-factor (free) = 0.1621          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9580 = 0.37 * 1.00 * 5.1926 + 1.00 * 0.0134                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9563 = 0.37 * 1.00 * 5.1907 + 1.00 * 0.0123                               |
|-----------------------------------------------------------------------------|
| number of iterations = 16      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.957)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.43   12.07    None  None   None       |
|    all(noH): 2823   0      0.00    81.43   12.07    None  None   None       |
|    Sol.    : 438    0      1.03    81.43   35.22    None  None   None       |
|    Mac.    : 2385   0      0.00    79.51   7.81     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.143: 1675   |   5:    40.715 -  48.858:   80        |
|      1:     8.143 -  16.286:  572   |   6:    48.858 -  57.001:   67        |
|      2:    16.286 -  24.429:  165   |   7:    57.001 -  65.144:   41        |
|      3:    24.429 -  32.572:   98   |   8:    65.144 -  73.287:   12        |
|      4:    32.572 -  40.715:  107   |   9:    73.287 -  81.430:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1175 r_free = 0.1621             target_work(ml) = 5.187         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1174 r_free = 0.1621             target_work(ml) = 5.186         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1174   r_free= 0.1621   ksol= 0.31   Bsol= 43.59   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.40,2.76,4.64,0.00,0.00,0.00); trace/3= 3.26                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.186468                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0183 -  4.7497 0.99   1394  152 0.1042 0.1317      5.4364      5.5495|
|  2:  4.7497 -  3.7900 0.99   1329  154 0.0879 0.1127      5.4629      5.6481|
|  3:  3.7900 -  3.3168 0.99   1307  143 0.1081 0.1500      5.4955      5.8451|
|  4:  3.3168 -  3.0162 0.99   1304  140 0.1256 0.1744      5.4837       5.668|
|  5:  3.0162 -  2.8015 0.99   1290  147 0.1375 0.1720      5.3701      5.5697|
|  6:  2.8015 -  2.6373 0.99   1301  145 0.1279 0.2115      5.2541      5.5537|
|  7:  2.6373 -  2.5058 0.99   1272  144 0.1363 0.1681      5.2351      5.3688|
|  8:  2.5058 -  2.3972 0.98   1270  136 0.1247 0.1688      5.1333      5.3761|
|  9:  2.3972 -  2.3052 0.98   1281  148 0.1232 0.1981      5.0815      5.3749|
| 10:  2.3052 -  2.2260 1.00   1275  139 0.1216 0.1582      5.0042      5.1781|
| 11:  2.2260 -  2.1566 0.97   1266  134 0.1229 0.1828      4.9932      5.2727|
| 12:  2.1566 -  2.0951 0.98   1247  145 0.1229 0.1786      4.9292      5.2846|
| 13:  2.0951 -  2.0401 1.00   1273  137 0.1177 0.1717      4.8205      5.0394|
| 14:  2.0401 -  1.9904 0.63    821   95 0.1003 0.1688      4.6646      4.9278|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0183 -  4.7497  1394   152  0.93   9.94   0.97     0.95       8167.68|
|  2:  4.7497 -  3.7900  1329   154  0.95   8.22   1.01     0.99       9402.58|
|  3:  3.7900 -  3.3168  1307   143  0.93  11.26   1.03     1.02      10551.03|
|  4:  3.3168 -  3.0162  1304   140  0.92  13.83   1.01     0.99      10893.50|
|  5:  3.0162 -  2.8015  1290   147  0.90  16.21   1.00     0.97       8891.44|
|  6:  2.8015 -  2.6373  1301   145  0.89  17.02   0.98     0.96       7784.64|
|  7:  2.6373 -  2.5058  1272   144  0.90  16.56   0.98     0.95       6840.39|
|  8:  2.5058 -  2.3972  1270   136  0.90  16.02   0.99     0.97       5972.02|
|  9:  2.3972 -  2.3052  1281   148  0.91  15.84   1.00     0.96       5475.84|
| 10:  2.3052 -  2.2260  1275   139  0.89  17.01   1.00     0.96       4777.56|
| 11:  2.2260 -  2.1566  1266   134  0.90  16.83   0.99     0.95       4774.25|
| 12:  2.1566 -  2.0951  1247   145  0.90  16.69   1.01     1.00       4299.29|
| 13:  2.0951 -  2.0401  1273   137  0.91  15.90   0.99     0.97       3464.88|
| 14:  2.0401 -  1.9904   821    95  0.92  14.06   0.98     0.95       2537.64|
|alpha:            min =        0.95 max =            1.02 mean =         0.97|
|beta:             min =     2537.64 max =        10893.50 mean =      6850.02|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.95 mean =        14.63|
|phase err.(test): min =        0.00 max =           88.63 mean =        14.16|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1174   r_free= 0.1621   ksol= 0.32   Bsol= 52.72   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.85,-0.51,1.35,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.186056                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1174   r_free= 0.1621   ksol= 0.32   Bsol= 52.72   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.85,-0.51,1.35,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.186056                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0183 -  4.7497 0.99   1394  152 0.1045 0.1320      5.4381      5.5514|
|  2:  4.7497 -  3.7900 0.99   1329  154 0.0883 0.1133       5.466      5.6526|
|  3:  3.7900 -  3.3168 0.99   1307  143 0.1083 0.1503      5.4972       5.846|
|  4:  3.3168 -  3.0162 0.99   1304  140 0.1255 0.1743      5.4826      5.6666|
|  5:  3.0162 -  2.8015 0.99   1290  147 0.1373 0.1713      5.3677      5.5666|
|  6:  2.8015 -  2.6373 0.99   1301  145 0.1276 0.2109      5.2516      5.5513|
|  7:  2.6373 -  2.5058 0.99   1272  144 0.1361 0.1678       5.233      5.3666|
|  8:  2.5058 -  2.3972 0.98   1270  136 0.1246 0.1688      5.1324       5.376|
|  9:  2.3972 -  2.3052 0.98   1281  148 0.1231 0.1980      5.0809      5.3748|
| 10:  2.3052 -  2.2260 1.00   1275  139 0.1215 0.1580      5.0036      5.1772|
| 11:  2.2260 -  2.1566 0.97   1266  134 0.1228 0.1828      4.9923      5.2716|
| 12:  2.1566 -  2.0951 0.98   1247  145 0.1230 0.1784      4.9289      5.2839|
| 13:  2.0951 -  2.0401 1.00   1273  137 0.1177 0.1717      4.8201      5.0394|
| 14:  2.0401 -  1.9904 0.63    821   95 0.1003 0.1685      4.6639      4.9266|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0183 -  4.7497  1394   152  0.93   9.96   0.97     0.95       8198.82|
|  2:  4.7497 -  3.7900  1329   154  0.95   8.26   1.01     0.99       9459.59|
|  3:  3.7900 -  3.3168  1307   143  0.93  11.30   1.02     1.02      10606.79|
|  4:  3.3168 -  3.0162  1304   140  0.92  13.82   1.01     0.99      10873.05|
|  5:  3.0162 -  2.8015  1290   147  0.90  16.17   1.00     0.97       8850.54|
|  6:  2.8015 -  2.6373  1301   145  0.89  16.97   0.98     0.96       7740.74|
|  7:  2.6373 -  2.5058  1272   144  0.90  16.52   0.99     0.95       6807.28|
|  8:  2.5058 -  2.3972  1270   136  0.90  16.01   0.99     0.97       5963.20|
|  9:  2.3972 -  2.3052  1281   148  0.91  15.83   1.00     0.96       5468.37|
| 10:  2.3052 -  2.2260  1275   139  0.89  17.00   1.00     0.97       4771.58|
| 11:  2.2260 -  2.1566  1266   134  0.90  16.81   1.00     0.95       4763.06|
| 12:  2.1566 -  2.0951  1247   145  0.90  16.67   1.01     1.00       4292.70|
| 13:  2.0951 -  2.0401  1273   137  0.91  15.89   0.99     0.97       3459.64|
| 14:  2.0401 -  1.9904   821    95  0.92  14.04   0.98     0.95       2531.97|
|alpha:            min =        0.95 max =            1.02 mean =         0.97|
|beta:             min =     2531.97 max =        10873.05 mean =      6847.26|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.62|
|phase err.(test): min =        0.00 max =           88.53 mean =        14.15|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.957)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.27    84.70   15.33    None  None   None       |
|    all(noH): 2823   0      3.27    84.70   15.33    None  None   None       |
|    Sol.    : 438    0      4.29    84.70   38.49    None  None   None       |
|    Mac.    : 2385   0      3.27    82.78   11.08    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:     3.266 -  11.409: 1675   |   5:    43.981 -  52.124:   80        |
|      1:    11.409 -  19.552:  572   |   6:    52.124 -  60.267:   67        |
|      2:    19.552 -  27.695:  165   |   7:    60.267 -  68.410:   41        |
|      3:    27.695 -  35.838:   98   |   8:    68.410 -  76.553:   12        |
|      4:    35.838 -  43.981:  107   |   9:    76.553 -  84.696:    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)= 304         
Filter by distance & map next to the model:
   mapped sites are within: 0.230 - 4.176
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 295 from: 304
   mapped sites are within: 0.705 - 4.176

peak=   11.069 closest distance to " CB  VAL A 230 " =    1.464
peak=    8.535 closest distance to " CG2 VAL A 296 " =    1.329
peak=    6.114 closest distance to " CG  LEU A   5 " =    1.269
peak=    6.042 closest distance to " CD2 LEU A   5 " =    1.213
peak=    5.857 closest distance to " NH2 ARG A  56 " =    2.123
peak=    5.764 closest distance to " CG  PRO A  54 " =    1.424
peak=    5.634 closest distance to " NE2 GLN A  11 " =    1.152
peak=    5.389 closest distance to " O   HOH Z 142 " =    1.982
peak=    5.337 closest distance to " CB  GLN A 223 " =    1.465
peak=    5.176 closest distance to " CB  PRO A  54 " =    1.048
peak=    5.167 closest distance to " CG  LEU A 228 " =    1.206
peak=    4.984 closest distance to " CG  PRO A 198 " =    1.290
peak=    4.881 closest distance to " O   HOH Z   9 " =    1.749
peak=    4.731 closest distance to " CB  ASN A 142 " =    1.102
peak=    4.673 closest distance to " ND2 ASN A 187 " =    1.653
peak=    4.667 closest distance to " O   HOH Z 265 " =    2.085
peak=    4.665 closest distance to " O   HOH Z 232 " =    2.283
peak=    4.613 closest distance to " CB  ARG A 275 " =    0.930
peak=    4.558 closest distance to " CZ  PHE A 218 " =    1.163
peak=    4.550 closest distance to " O   HOH Z 313 " =    2.008
peak=    4.547 closest distance to " CG  PRO A 213 " =    1.249
peak=    4.542 closest distance to " CG  PRO A 243 " =    1.147
peak=    4.520 closest distance to " CB  GLN A 183 " =    1.210
peak=    4.467 closest distance to " CB  VAL A 265 " =    1.367
peak=    4.433 closest distance to " O   HOH Z 248 " =    1.334
peak=    4.409 closest distance to " CB  ASN A 148 " =    1.406
peak=    4.399 closest distance to " O   HOH Z 427 " =    3.025
peak=    4.386 closest distance to " O   SER A  87 " =    2.369
peak=    4.342 closest distance to " O   HOH Z 346 " =    1.568
peak=    4.243 closest distance to " ND2 ASN A 249 " =    0.897
peak=    4.237 closest distance to " O   PRO A 198 " =    1.571
peak=    4.223 closest distance to " O   HOH Z  43 " =    2.009
peak=    4.218 closest distance to " O   HOH Z 126 " =    1.950
peak=    4.203 closest distance to " O   HOH Z  61 " =    1.786
peak=    4.199 closest distance to " O   HOH Z 369 " =    2.211
peak=    4.185 closest distance to " CG2 VAL A 257 " =    0.907
peak=    4.182 closest distance to " CB  ARG A 190 " =    1.460
peak=    4.164 closest distance to " O   HOH Z 303 " =    2.063
peak=    4.128 closest distance to " CB  ASP A 124 " =    0.754
peak=    4.124 closest distance to " N   ASN A  39 " =    1.174
peak=    4.111 closest distance to " CB  SER A  63 " =    1.231
peak=    4.106 closest distance to " CD2 LEU A 228 " =    1.174
peak=    4.091 closest distance to " OG  SER A  97 " =    2.992
peak=    4.086 closest distance to " CB  ARG A  79 " =    1.402
peak=    4.065 closest distance to " O   HOH Z  78 " =    1.591
peak=    4.017 closest distance to " CB  TRP A 266 " =    1.063
peak=    4.004 closest distance to " O   HOH Z 353 " =    2.542
peak=    3.997 closest distance to " CA  TYR A  30 " =    0.979
peak=    3.984 closest distance to " O   HOH Z 287 " =    2.110
peak=    3.971 closest distance to " O   HOH Z 425 " =    1.382
peak=    3.964 closest distance to " O   HOH Z 359 " =    1.537
peak=    3.958 closest distance to " CZ3 TRP A 266 " =    1.155
peak=    3.950 closest distance to " CB  ASN A  39 " =    0.912
peak=    3.940 closest distance to " CB  VAL A 202 " =    1.583
peak=    3.938 closest distance to " CG  LEU A 167 " =    1.226
peak=    3.937 closest distance to " CA  VAL A 296 " =    1.013
peak=    3.934 closest distance to " CA  ALA A  51 " =    0.953
peak=    3.924 closest distance to " CB  VAL A 230 " =    1.185
peak=    3.913 closest distance to " N   PHE A 130 " =    1.250
peak=    3.906 closest distance to " O   HOH Z 214 " =    2.293
peak=    3.889 closest distance to " CG  MET A 185 " =    1.166
peak=    3.876 closest distance to " O   HOH Z 411 " =    3.885
peak=    3.854 closest distance to " CA  SER A  87 " =    1.032
peak=    3.854 closest distance to " O   HOH Z 272 " =    1.785
peak=    3.848 closest distance to " CB  GLU A 277 " =    3.650
peak=    3.835 closest distance to " O  BHOH Z 338 " =    2.360
peak=    3.834 closest distance to " O   HOH Z   3 " =    2.044
peak=    3.833 closest distance to " CD  LYS A 166 " =    1.299
peak=    3.829 closest distance to " O   HOH Z 209 " =    2.286
peak=    3.821 closest distance to " O   HOH Z 251 " =    1.591
peak=    3.807 closest distance to " O   HOH Z 290 " =    1.108
peak=    3.802 closest distance to " CZ  PHE A  38 " =    1.118
peak=    3.800 closest distance to " CB  SER A   3 " =    1.306
peak=    3.792 closest distance to " CB  GLU A 152 " =    1.178
peak=    3.791 closest distance to " O   HOH Z 234 " =    3.706
peak=    3.784 closest distance to " O   HOH Z 261 " =    1.903
peak=    3.780 closest distance to " O   HOH Z 126 " =    1.539
peak=    3.755 closest distance to " O   HOH Z 402 " =    1.381
peak=    3.749 closest distance to " O   HOH Z  92 " =    2.292
peak=    3.746 closest distance to " CD  ARG A 269 " =    1.010
peak=    3.743 closest distance to " O   HOH Z  40 " =    1.635
peak=    3.739 closest distance to " CE  LYS A  76 " =    0.889
peak=    3.739 closest distance to " CB  ASN A 110 " =    1.113
peak=    3.737 closest distance to " CB  ALA A   9 " =    1.550
peak=    3.727 closest distance to " CA  ARG A 195 " =    1.148
peak=    3.714 closest distance to " CB  PRO A  90 " =    1.112
peak=    3.708 closest distance to " CA  ARG A  36 " =    1.098
peak=    3.707 closest distance to " CB  SER A 212 " =    1.366
peak=    3.706 closest distance to " CB  SER A 210 " =    0.767
peak=    3.696 closest distance to " CB  GLU A 128 " =    0.920
peak=    3.682 closest distance to " CD2 TRP A 179 " =    1.303
peak=    3.680 closest distance to " O   HOH Z 422 " =    2.608
peak=    3.678 closest distance to " NH1AARG A 145 " =    1.183
peak=    3.674 closest distance to " O   HOH Z 406 " =    1.628
peak=    3.673 closest distance to " OG ASER A 258 " =    3.087
peak=    3.658 closest distance to " O   HOH Z 368 " =    2.112
peak=    3.653 closest distance to " CG1 ILE A  49 " =    1.594
peak=    3.646 closest distance to " NH2AARG A 145 " =    1.100
peak=    3.642 closest distance to " CA  THR A 264 " =    0.850
peak=    3.636 closest distance to " CB  ASN A 173 " =    1.015
peak=    3.633 closest distance to " CA  PHE A 283 " =    1.102
peak=    3.632 closest distance to " CB  LYS A 117 " =    1.222
peak=    3.630 closest distance to " O   HOH Z  21 " =    1.791
peak=    3.629 closest distance to " O   HOH Z 371 " =    2.790
peak=    3.628 closest distance to " O   HOH Z 158 " =    3.247
peak=    3.613 closest distance to " O   HOH Z 298 " =    1.704
peak=    3.607 closest distance to " CG AARG A 275 " =    1.238
peak=    3.607 closest distance to " CA  ILE A 234 " =    0.931
peak=    3.601 closest distance to " O   HOH Z 423 " =    1.806
peak=    3.596 closest distance to " CB  GLN A  89 " =    1.254
peak=    3.595 closest distance to " OG BSER A 164 " =    2.223
peak=    3.589 closest distance to " O   HOH Z 258 " =    2.205
peak=    3.585 closest distance to " CB AVAL A  41 " =    1.288
peak=    3.581 closest distance to " CG  MET A 185 " =    0.949
peak=    3.576 closest distance to " CB  GLU A  46 " =    0.932
peak=    3.573 closest distance to " CG  GLN A  58 " =    0.953
peak=    3.568 closest distance to " O   HOH Z  88 " =    3.628
peak=    3.566 closest distance to " CA  ASN A 215 " =    1.028
peak=    3.565 closest distance to " O   HOH Z  10 " =    1.735
peak=    3.563 closest distance to " CD1 ILE A 199 " =    1.042
peak=    3.557 closest distance to " CG2AVAL A 121 " =    2.538
peak=    3.556 closest distance to " O   HOH Z 273 " =    2.947
peak=    3.553 closest distance to " CB  THR A  31 " =    1.561
peak=    3.553 closest distance to " CA  VAL A  41 " =    0.713
peak=    3.539 closest distance to " CB  ASN A 187 " =    1.145
peak=    3.538 closest distance to " CB  GLN A  88 " =    1.186
peak=    3.536 closest distance to " CG  ARG A  66 " =    2.716
peak=    3.528 closest distance to " O   HOH Z 180 " =    2.129
peak=    3.521 closest distance to " OD1 ASN A  69 " =    2.522
peak=    3.519 closest distance to " CD1 LEU A  96 " =    0.762
peak=    3.518 closest distance to " CG1 ILE A 120 " =    1.065
peak=    3.507 closest distance to " CB  ALA A 104 " =    0.705
peak=    3.505 closest distance to " CB  SER A 216 " =    0.825
peak=    3.502 closest distance to " CG1 VAL A 153 " =    0.978
peak=    3.501 closest distance to " CB  SER A  26 " =    1.799
peak=    3.494 closest distance to " O   HOH Z 365 " =    2.917
peak=    3.493 closest distance to " CA  TYR A 116 " =    1.410
peak=    3.491 closest distance to " O   HOH Z 299 " =    4.146
peak=    3.485 closest distance to " CA  LEU A 282 " =    1.170
peak=    3.484 closest distance to " CD1 ILE A  33 " =    1.786
peak=    3.483 closest distance to " N   SER A 135 " =    1.384
peak=    3.482 closest distance to " O   ASN A  74 " =    1.471
peak=    3.470 closest distance to " CB  ASN A 215 " =    1.153
peak=    3.464 closest distance to " O   HOH Z  97 " =    2.071
peak=    3.462 closest distance to " CG  GLN A  88 " =    1.061
peak=    3.458 closest distance to " O   HOH Z 172 " =    3.495
peak=    3.452 closest distance to " CG2 ILE A 120 " =    1.185
peak=    3.452 closest distance to " CA  TYR A  30 " =    1.093
peak=    3.437 closest distance to " O   HOH Z  90 " =    2.325
peak=    3.437 closest distance to " O   HOH Z 128 " =    2.116
peak=    3.436 closest distance to " C   ALA A 299 " =    0.863
peak=    3.433 closest distance to " NH1 ARG A 138 " =    1.149
peak=    3.432 closest distance to " CD  LYS A  76 " =    2.013
peak=    3.421 closest distance to " O   HOH Z  68 " =    2.220
peak=    3.419 closest distance to " O   HOH Z 368 " =    3.461
peak=    3.416 closest distance to " O   HOH Z  30 " =    1.340
peak=    3.413 closest distance to " CB  SER A 273 " =    0.922
peak=    3.412 closest distance to " CB  ASP A 140 " =    0.950
peak=    3.407 closest distance to " O   HOH Z 280 " =    3.057
peak=    3.407 closest distance to " O   HOH Z 171 " =    4.005
peak=    3.406 closest distance to " O   THR A 182 " =    1.377
peak=    3.404 closest distance to " CD2 LEU A 297 " =    0.949
peak=    3.402 closest distance to " CG2AVAL A  72 " =    1.687
peak=    3.402 closest distance to " O   HOH Z 187 " =    2.306
peak=    3.400 closest distance to " CA  VAL A 125 " =    1.206
peak=    3.396 closest distance to " CA  ASP A 162 " =    0.932
peak=    3.394 closest distance to " CG  GLU A  37 " =    0.907
peak=    3.393 closest distance to " CB  THR A  52 " =    0.871
peak=    3.389 closest distance to " CA  ASN A 127 " =    1.033
peak=    3.386 closest distance to " O   HOH Z 261 " =    1.625
peak=    3.384 closest distance to " CG1 VAL A 296 " =    1.242
peak=    3.384 closest distance to " CB  SER A  62 " =    1.103
peak=    3.382 closest distance to " O   HOH Z 329 " =    4.176
peak=    3.382 closest distance to " O   HOH Z  97 " =    2.389
peak=    3.381 closest distance to " CA  LYS A 290 " =    1.159
peak=    3.379 closest distance to " O   HOH Z 389 " =    1.719
peak=    3.378 closest distance to " O   HOH Z 128 " =    2.172
peak=    3.373 closest distance to " CA  ASN A 217 " =    1.251
peak=    3.373 closest distance to " CG2 ILE A  20 " =    1.546
peak=    3.372 closest distance to " O   HOH Z 419 " =    1.939
peak=    3.372 closest distance to " O   HOH Z 337 " =    3.521
peak=    3.369 closest distance to " O   HOH Z 285 " =    2.265
peak=    3.369 closest distance to " CG2 ILE A 239 " =    0.746
peak=    3.367 closest distance to " O   HOH Z 126 " =    1.880
peak=    3.366 closest distance to " OE2 GLU A   2 " =    1.896
peak=    3.364 closest distance to " NZ  LYS A  48 " =    1.174
peak=    3.362 closest distance to " CA  ALA A 233 " =    1.300
peak=    3.362 closest distance to " O   HOH Z 250 " =    1.357
peak=    3.356 closest distance to " CG BARG A 102 " =    1.839
peak=    3.355 closest distance to " CA  ALA A 154 " =    1.020
peak=    3.355 closest distance to " OE2 GLU A  53 " =    1.909
peak=    3.354 closest distance to " O   HOH Z  48 " =    1.616
peak=    3.354 closest distance to " CA  ILE A 263 " =    0.996
peak=    3.354 closest distance to " CB  ALA A 248 " =    1.405
peak=    3.352 closest distance to " NE2 HIS A 207 " =    1.112
peak=    3.345 closest distance to " O   ASP A 124 " =    1.089
peak=    3.335 closest distance to " CB  ALA A 291 " =    1.206
peak=    3.328 closest distance to " CA  LYS A 117 " =    1.219
peak=    3.328 closest distance to " CA  ASP A 191 " =    1.156
peak=    3.325 closest distance to " O   HOH Z 403 " =    1.495
peak=    3.325 closest distance to " CB  TRP A 179 " =    1.398
peak=    3.323 closest distance to " CD  ARG A  66 " =    2.570
peak=    3.322 closest distance to " CB  LEU A 143 " =    1.225
peak=    3.320 closest distance to " CB  ALA A 114 " =    0.824
peak=    3.320 closest distance to " NZ  LYS A 117 " =    3.268
peak=    3.320 closest distance to " O   HOH Z 263 " =    1.676
peak=    3.317 closest distance to " CE1 TYR A 186 " =    1.301
peak=    3.314 closest distance to " O   HOH Z 294 " =    1.557
peak=    3.308 closest distance to " O   PHE A 192 " =    1.375
peak=    3.308 closest distance to " CB  PHE A 204 " =    0.871
peak=    3.308 closest distance to " CB  PRO A 243 " =    1.387
peak=    3.307 closest distance to " N   ALA A 256 " =    1.109
peak=    3.306 closest distance to " ND2BASN A 224 " =    0.741
peak=    3.305 closest distance to " CA  MET A 105 " =    0.960
peak=    3.305 closest distance to " O   HOH Z 421 " =    2.102
peak=    3.295 closest distance to " O   HOH Z  59 " =    1.778
peak=    3.292 closest distance to " O   HOH Z   4 " =    1.601
peak=    3.289 closest distance to " CB  PRO A 198 " =    1.031
peak=    3.288 closest distance to " O   HOH Z 145 " =    2.186
peak=    3.286 closest distance to " CD  ARG A 195 " =    3.503
peak=    3.279 closest distance to " N   GLN A 278 " =    1.423
peak=    3.276 closest distance to " O   HOH Z 153 " =    3.768
peak=    3.273 closest distance to " CA  ARG A 139 " =    1.013
peak=    3.271 closest distance to " CD1 LEU A 261 " =    1.181
peak=    3.270 closest distance to " CB  GLN A 278 " =    0.885
peak=    3.268 closest distance to " OG1 THR A 279 " =    1.370
peak=    3.268 closest distance to " O   HOH Z 148 " =    3.497
peak=    3.263 closest distance to " CB  THR A 157 " =    1.191
peak=    3.261 closest distance to " CE3 TRP A 150 " =    1.070
peak=    3.260 closest distance to " O   GLN A  88 " =    1.675
peak=    3.257 closest distance to " CG1 ILE A 151 " =    1.102
peak=    3.254 closest distance to " CB  ALA A 227 " =    1.027
peak=    3.253 closest distance to " CB  ALA A  43 " =    0.847
peak=    3.247 closest distance to " CA  ALA A 295 " =    1.084
peak=    3.240 closest distance to " O   HOH Z 250 " =    1.350
peak=    3.239 closest distance to " CA  ALA A 160 " =    1.094
peak=    3.239 closest distance to " CA  ARG A 102 " =    1.165
peak=    3.239 closest distance to " O   HOH Z 162 " =    3.591
peak=    3.236 closest distance to " CA  ILE A 106 " =    0.723
peak=    3.229 closest distance to " CB  LEU A 228 " =    1.257
peak=    3.227 closest distance to " O   HOH Z  88 " =    2.745
peak=    3.227 closest distance to " N   ASP A 162 " =    1.193
peak=    3.227 closest distance to " O   HOH Z 403 " =    1.572
peak=    3.227 closest distance to " O   HOH Z  80 " =    1.656
peak=    3.227 closest distance to " CA  ALA A 129 " =    1.520
peak=    3.225 closest distance to " CG  MET A 113 " =    1.089
peak=    3.224 closest distance to " O   HOH Z 421 " =    2.987
peak=    3.215 closest distance to " CB  MET A  40 " =    0.773
peak=    3.214 closest distance to " CB  LEU A 300 " =    0.909
peak=    3.214 closest distance to " O   HOH Z  88 " =    2.865
peak=    3.206 closest distance to " CB  HIS A 108 " =    0.816
peak=    3.205 closest distance to " CB  ARG A 102 " =    0.756
peak=    3.204 closest distance to " N   ARG A 156 " =    1.370
peak=    3.202 closest distance to " O   HOH Z 437 " =    1.475
peak=    3.196 closest distance to " O   HOH Z 392 " =    3.107
peak=    3.195 closest distance to " CD BLYS A 290 " =    1.084
peak=    3.195 closest distance to " O   SER A 164 " =    1.354
peak=    3.193 closest distance to " CG2BVAL A 121 " =    0.716
peak=    3.192 closest distance to " CB  TYR A 172 " =    0.727
peak=    3.190 closest distance to " CG  PHE A 204 " =    1.003
peak=    3.188 closest distance to " CA  ASP A 149 " =    1.139
peak=    3.187 closest distance to " CB  GLN A 205 " =    1.113
peak=    3.184 closest distance to " O   HOH Z 130 " =    2.134
peak=    3.181 closest distance to " O   HOH Z 350 " =    1.641
peak=    3.179 closest distance to " O   HOH Z   1 " =    1.679
peak=    3.177 closest distance to " CB  VAL A 257 " =    0.808
peak=    3.176 closest distance to " O   HOH Z 389 " =    1.302
peak=    3.168 closest distance to " O   HOH Z 409 " =    3.231
peak=    3.166 closest distance to " O   HOH Z 303 " =    2.669
peak=    3.159 closest distance to " CB  ALA A 242 " =    0.742
peak=    3.159 closest distance to " O   HOH Z 337 " =    1.696
peak=    3.152 closest distance to " O   HOH Z 305 " =    3.537
peak=    3.150 closest distance to " O  BHOH Z  74 " =    1.275
peak=    3.147 closest distance to " CG  LEU A 281 " =    1.028
peak=    3.146 closest distance to " O   TYR A 116 " =    1.309
peak=    3.144 closest distance to " O   PRO A 213 " =    1.395
peak=    3.142 closest distance to " O   LEU A 228 " =    1.896
peak=    3.138 closest distance to " CD1 LEU A 300 " =    1.074
peak=    3.137 closest distance to " N   ASN A 127 " =    1.245
peak=    3.134 closest distance to " CB  TYR A 247 " =    0.977
peak=    3.124 closest distance to " O   THR A 220 " =    1.288
peak=    3.122 closest distance to " O   HOH Z 193 " =    1.345
peak=    3.112 closest distance to " O   PHE A  61 " =    1.386
peak=    3.111 closest distance to " OG  SER A  62 " =    2.862
peak=    3.108 closest distance to " CB  VAL A 268 " =    0.839
peak=    3.106 closest distance to " O   HOH Z 203 " =    1.610
peak=    3.099 closest distance to " O   HOH Z 371 " =    3.384
peak=    3.071 closest distance to " CG  ARG A 138 " =    1.319
peak=    3.055 closest distance to " CD1 ILE A 106 " =    0.955
peak=    3.040 closest distance to " CA  VAL A 153 " =    1.036
peak=    3.037 closest distance to " OE1 GLU A  37 " =    1.221
peak=    3.033 closest distance to " O   HOH Z 148 " =    2.182
peak=    3.024 closest distance to " O   HOH Z 345 " =    3.394
peak=    3.003 closest distance to " O   HOH Z 235 " =    1.440
peak=    3.002 closest distance to " CB  ASN A 173 " =    1.221

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 207         
Filter by distance & map next to the model:
   mapped sites are within: 0.743 - 5.636
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 207 from: 207
   mapped sites are within: 0.743 - 5.636

peak=   -5.042 closest distance to " CG2 VAL A 230 " =    0.743
peak=   -4.619 closest distance to " CD  ARG A  14 " =    3.245
peak=   -4.424 closest distance to " CB  PHE A 192 " =    1.915
peak=   -4.364 closest distance to " OG BSER A 134 " =    1.291
peak=   -4.302 closest distance to " CD  GLN A  58 " =    0.990
peak=   -4.254 closest distance to " CB  PRO A 243 " =    2.739
peak=   -4.253 closest distance to " CD  ARG A 156 " =    2.042
peak=   -4.210 closest distance to " O   VAL A  67 " =    2.532
peak=   -4.204 closest distance to " O   HOH Z 211 " =    1.170
peak=   -4.128 closest distance to " CG1 VAL A 112 " =    2.685
peak=   -4.111 closest distance to " CG2 VAL A 202 " =    2.737
peak=   -4.095 closest distance to " O   PRO A 198 " =    1.201
peak=   -4.009 closest distance to " NE  ARG A 156 " =    5.636
peak=   -4.001 closest distance to " O   HOH Z 231 " =    2.118
peak=   -3.990 closest distance to " C   HIS A 108 " =    1.171
peak=   -3.959 closest distance to " CE2 TYR A  30 " =    2.659
peak=   -3.937 closest distance to " O   HOH Z 394 " =    1.557
peak=   -3.891 closest distance to " CZ2 TRP A  92 " =    2.851
peak=   -3.890 closest distance to " O   HOH Z 166 " =    2.059
peak=   -3.887 closest distance to " OE1 GLN A 223 " =    2.187
peak=   -3.883 closest distance to " CG2 VAL A 296 " =    1.638
peak=   -3.847 closest distance to " O   HOH Z 351 " =    1.466
peak=   -3.812 closest distance to " CB  ALA A 248 " =    2.374
peak=   -3.805 closest distance to " CB  ALA A 161 " =    2.494
peak=   -3.783 closest distance to " CA  VAL A  67 " =    2.878
peak=   -3.744 closest distance to " O   HOH Z 429 " =    2.028
peak=   -3.742 closest distance to " CB  ALA A  43 " =    2.529
peak=   -3.738 closest distance to " O   HOH Z 290 " =    1.227
peak=   -3.712 closest distance to " CE BMET A  47 " =    1.331
peak=   -3.678 closest distance to " CG1 VAL A 125 " =    1.923
peak=   -3.673 closest distance to " CG1 VAL A 112 " =    2.846
peak=   -3.655 closest distance to " O   HOH Z 166 " =    2.235
peak=   -3.642 closest distance to " N   THR A  52 " =    1.673
peak=   -3.641 closest distance to " O   MET A  40 " =    2.887
peak=   -3.635 closest distance to " CB  VAL A 230 " =    1.171
peak=   -3.628 closest distance to " O   HOH Z 193 " =    1.206
peak=   -3.627 closest distance to " OG  SER A  97 " =    2.347
peak=   -3.609 closest distance to " O   PRO A 163 " =    2.044
peak=   -3.601 closest distance to " CG2 VAL A 296 " =    0.829
peak=   -3.595 closest distance to " ND2 ASN A  45 " =    1.692
peak=   -3.588 closest distance to " O   SER A 271 " =    2.175
peak=   -3.587 closest distance to " CA  ASP A 298 " =    1.097
peak=   -3.586 closest distance to " CA  GLY A 241 " =    2.385
peak=   -3.582 closest distance to " O   HOH Z 103 " =    1.804
peak=   -3.568 closest distance to " CD2 TYR A 293 " =    2.030
peak=   -3.567 closest distance to " CG  ASP A 231 " =    0.796
peak=   -3.555 closest distance to " CZ3 TRP A 179 " =    1.237
peak=   -3.554 closest distance to " O   HOH Z  73 " =    2.338
peak=   -3.547 closest distance to " O   HOH Z 243 " =    1.885
peak=   -3.544 closest distance to " N   THR A 157 " =    1.468
peak=   -3.534 closest distance to " ND2 ASN A  45 " =    1.252
peak=   -3.533 closest distance to " CD1 LEU A 101 " =    2.330
peak=   -3.532 closest distance to " CE3 TRP A 150 " =    2.247
peak=   -3.531 closest distance to " OE1 GLN A  88 " =    0.970
peak=   -3.530 closest distance to " OH  TYR A 172 " =    1.841
peak=   -3.528 closest distance to " O   HOH Z  44 " =    2.426
peak=   -3.527 closest distance to " O   HOH Z  11 " =    1.845
peak=   -3.524 closest distance to " CE  MET A 105 " =    2.394
peak=   -3.523 closest distance to " O   HOH Z 285 " =    2.112
peak=   -3.521 closest distance to " O   HOH Z 185 " =    2.404
peak=   -3.518 closest distance to " O   HOH Z 357 " =    2.051
peak=   -3.518 closest distance to " N   ALA A  43 " =    2.577
peak=   -3.516 closest distance to " O   HOH Z 286 " =    1.860
peak=   -3.512 closest distance to " CA  GLY A 241 " =    3.152
peak=   -3.496 closest distance to " CG  LEU A   5 " =    0.887
peak=   -3.494 closest distance to " CG1 VAL A 250 " =    2.778
peak=   -3.490 closest distance to " NH2AARG A 275 " =    5.147
peak=   -3.483 closest distance to " O   HOH Z 100 " =    1.042
peak=   -3.473 closest distance to " O   HOH Z 216 " =    1.257
peak=   -3.470 closest distance to " O   HOH Z 198 " =    1.876
peak=   -3.467 closest distance to " CD1 LEU A 255 " =    2.863
peak=   -3.463 closest distance to " O   HOH Z 256 " =    1.419
peak=   -3.459 closest distance to " OG  SER A  63 " =    1.129
peak=   -3.456 closest distance to " O   HOH Z 114 " =    3.016
peak=   -3.453 closest distance to " N   ALA A 226 " =    2.052
peak=   -3.451 closest distance to " O   HOH Z 377 " =    2.100
peak=   -3.441 closest distance to " ND2 ASN A 249 " =    2.433
peak=   -3.430 closest distance to " ND2 ASN A 187 " =    1.465
peak=   -3.427 closest distance to " O   VAL A 189 " =    2.639
peak=   -3.414 closest distance to " CD  PRO A 213 " =    2.053
peak=   -3.410 closest distance to " CG  TRP A 266 " =    1.909
peak=   -3.408 closest distance to " CB  GLN A  11 " =    1.840
peak=   -3.408 closest distance to " N   HIS A 115 " =    2.199
peak=   -3.406 closest distance to " C   MET A 188 " =    1.432
peak=   -3.404 closest distance to " O   HOH Z 191 " =    5.517
peak=   -3.382 closest distance to " O   SER A  22 " =    2.297
peak=   -3.380 closest distance to " O   HOH Z 106 " =    1.857
peak=   -3.380 closest distance to " O   HOH Z 359 " =    2.993
peak=   -3.379 closest distance to " CZ  PHE A 192 " =    2.767
peak=   -3.378 closest distance to " CB  HIS A  86 " =    1.096
peak=   -3.375 closest distance to " O   HOH Z 371 " =    2.186
peak=   -3.374 closest distance to " O   HOH Z 295 " =    1.528
peak=   -3.367 closest distance to " O   TYR A 247 " =    2.877
peak=   -3.367 closest distance to " O   HOH Z 102 " =    1.729
peak=   -3.361 closest distance to " O   GLY A  17 " =    1.231
peak=   -3.360 closest distance to " O   HOH Z 140 " =    1.601
peak=   -3.357 closest distance to " CD2 LEU A   5 " =    1.207
peak=   -3.355 closest distance to " N   ALA A 248 " =    1.702
peak=   -3.352 closest distance to " NE2 GLN A  88 " =    1.116
peak=   -3.352 closest distance to " O   HOH Z 149 " =    2.204
peak=   -3.348 closest distance to " CD  PRO A 243 " =    2.013
peak=   -3.343 closest distance to " O   HOH Z   9 " =    1.648
peak=   -3.342 closest distance to " O   HOH Z 345 " =    2.053
peak=   -3.338 closest distance to " O   SER A 210 " =    1.974
peak=   -3.331 closest distance to " OXT GLY A 302 " =    2.953
peak=   -3.328 closest distance to " OG  SER A  87 " =    1.493
peak=   -3.317 closest distance to " OD1 ASN A 148 " =    1.358
peak=   -3.315 closest distance to " CA  GLY A  98 " =    1.853
peak=   -3.312 closest distance to " CE2 TRP A  70 " =    2.110
peak=   -3.303 closest distance to " O   HOH Z 407 " =    2.962
peak=   -3.302 closest distance to " NH2 ARG A  79 " =    1.475
peak=   -3.301 closest distance to " CG2 ILE A 263 " =    2.397
peak=   -3.292 closest distance to " O   ASN A 252 " =    1.333
peak=   -3.285 closest distance to " CZ2 TRP A 274 " =    1.029
peak=   -3.282 closest distance to " CG  GLU A 277 " =    1.320
peak=   -3.280 closest distance to " O   HOH Z 131 " =    4.111
peak=   -3.275 closest distance to " O   HOH Z 275 " =    1.437
peak=   -3.275 closest distance to " O   HOH Z  38 " =    1.842
peak=   -3.263 closest distance to " O   HOH Z 123 " =    2.494
peak=   -3.262 closest distance to " CB  ALA A  10 " =    2.311
peak=   -3.261 closest distance to " CG  MET A 105 " =    0.962
peak=   -3.260 closest distance to " CB  ASP A 171 " =    2.349
peak=   -3.259 closest distance to " O   GLY A 196 " =    1.246
peak=   -3.255 closest distance to " CD1 PHE A  59 " =    2.036
peak=   -3.253 closest distance to " O   HOH Z  11 " =    2.223
peak=   -3.251 closest distance to " O   ILE A 106 " =    1.969
peak=   -3.250 closest distance to " NE2 GLN A 194 " =    1.876
peak=   -3.250 closest distance to " O   HOH Z 389 " =    1.448
peak=   -3.250 closest distance to " OD2 ASP A 191 " =    1.360
peak=   -3.245 closest distance to " O   HOH Z 236 " =    1.443
peak=   -3.241 closest distance to " O   GLY A  80 " =    2.551
peak=   -3.241 closest distance to " O   HOH Z 165 " =    1.954
peak=   -3.235 closest distance to " O   ARG A 145 " =    1.590
peak=   -3.234 closest distance to " CA  ASP A  27 " =    2.426
peak=   -3.233 closest distance to " O   HOH Z 437 " =    1.527
peak=   -3.224 closest distance to " O   HOH Z  52 " =    1.547
peak=   -3.214 closest distance to " CB  ALA A 291 " =    2.264
peak=   -3.212 closest distance to " NE2 GLN A 278 " =    1.744
peak=   -3.209 closest distance to " CG1 VAL A  67 " =    2.906
peak=   -3.205 closest distance to " CA  SER A 135 " =    1.315
peak=   -3.203 closest distance to " CB  TRP A  85 " =    2.570
peak=   -3.200 closest distance to " OG  SER A  62 " =    4.325
peak=   -3.197 closest distance to " ND2 ASN A 252 " =    1.940
peak=   -3.197 closest distance to " C   GLN A  58 " =    2.152
peak=   -3.196 closest distance to " O   HOH Z 421 " =    3.068
peak=   -3.195 closest distance to " O   HOH Z 136 " =    2.507
peak=   -3.195 closest distance to " CB  ASN A  39 " =    2.256
peak=   -3.192 closest distance to " N   TRP A 274 " =    0.994
peak=   -3.189 closest distance to " O   HOH Z 411 " =    1.412
peak=   -3.189 closest distance to " O   HOH Z  51 " =    1.099
peak=   -3.186 closest distance to " O   HOH Z 232 " =    1.779
peak=   -3.183 closest distance to " O   TRP A  70 " =    1.446
peak=   -3.183 closest distance to " CA  GLY A 133 " =    1.933
peak=   -3.175 closest distance to " C   LEU A 222 " =    0.882
peak=   -3.174 closest distance to " CZ  PHE A 155 " =    1.063
peak=   -3.173 closest distance to " O   ALA A 227 " =    1.412
peak=   -3.169 closest distance to " CB  ILE A 263 " =    1.243
peak=   -3.168 closest distance to " CB  ALA A 129 " =    2.484
peak=   -3.168 closest distance to " O   SER A 276 " =    1.647
peak=   -3.160 closest distance to " CD1 LEU A   5 " =    2.465
peak=   -3.159 closest distance to " NH2 ARG A  79 " =    2.110
peak=   -3.158 closest distance to " CD  GLU A 236 " =    1.071
peak=   -3.158 closest distance to " CE2 PHE A  61 " =    2.680
peak=   -3.155 closest distance to " CD  LYS A 289 " =    2.469
peak=   -3.155 closest distance to " O   HOH Z 350 " =    1.955
peak=   -3.155 closest distance to " O   ALA A 180 " =    1.356
peak=   -3.151 closest distance to " O   HOH Z 231 " =    1.800
peak=   -3.150 closest distance to " CA  GLY A 203 " =    2.516
peak=   -3.149 closest distance to " O   HOH Z 252 " =    3.894
peak=   -3.147 closest distance to " O   HOH Z 238 " =    1.050
peak=   -3.144 closest distance to " OE1 GLN A  77 " =    1.953
peak=   -3.144 closest distance to " O   HOH Z 313 " =    1.634
peak=   -3.142 closest distance to " CG  GLN A 103 " =    2.461
peak=   -3.136 closest distance to " O   HOH Z 380 " =    1.197
peak=   -3.130 closest distance to " CG  PHE A 283 " =    2.679
peak=   -3.128 closest distance to " CD1 ILE A 239 " =    2.296
peak=   -3.122 closest distance to " O   HOH Z  10 " =    1.454
peak=   -3.121 closest distance to " OD1 ASN A 187 " =    1.745
peak=   -3.110 closest distance to " CD1 LEU A 228 " =    2.277
peak=   -3.108 closest distance to " O   HOH Z 189 " =    2.198
peak=   -3.107 closest distance to " O   HOH Z 174 " =    2.441
peak=   -3.106 closest distance to " OG  SER A 206 " =    1.657
peak=   -3.105 closest distance to " CG2 VAL A 189 " =    1.886
peak=   -3.104 closest distance to " CE1 TYR A 247 " =    2.622
peak=   -3.101 closest distance to " O   PHE A 218 " =    1.508
peak=   -3.101 closest distance to " OE1 GLN A 183 " =    1.524
peak=   -3.100 closest distance to " O   PRO A 198 " =    1.378
peak=   -3.098 closest distance to " O   TYR A 186 " =    1.649
peak=   -3.097 closest distance to " CD2 HIS A 207 " =    2.268
peak=   -3.092 closest distance to " N   ALA A 248 " =    2.391
peak=   -3.091 closest distance to " CG1 VAL A 197 " =    2.308
peak=   -3.091 closest distance to " O   ASP A  27 " =    1.914
peak=   -3.090 closest distance to " O   HOH Z 390 " =    2.331
peak=   -3.090 closest distance to " CG1 VAL A  78 " =    2.887
peak=   -3.089 closest distance to " O   ALA A  51 " =    1.327
peak=   -3.079 closest distance to " CB  GLN A  55 " =    1.309
peak=   -3.078 closest distance to " CD2 PHE A  61 " =    2.043
peak=   -3.073 closest distance to " CG  ARG A 269 " =    2.352
peak=   -3.067 closest distance to " OXT GLY A 302 " =    3.541
peak=   -3.063 closest distance to " CD2 PHE A 225 " =    1.106
peak=   -3.060 closest distance to " O   HOH Z 251 " =    5.059
peak=   -3.058 closest distance to " N   ASP A 191 " =    1.086
peak=   -3.042 closest distance to " O   ASN A 127 " =    1.475
peak=   -3.039 closest distance to " CG  LEU A   5 " =    1.452
peak=   -3.035 closest distance to " ND2 ASN A 249 " =    2.227
peak=   -3.029 closest distance to " CZ  TYR A 169 " =    1.804
peak=   -3.008 closest distance to " NE2 GLN A 240 " =    1.662

================= 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    :  0.4564 0.4382   6.257527e+00   6.230489e+00
   1_bss:  0.4482 0.4299   6.249514e+00   6.217388e+00
   1_xyz:  0.3514 0.3707   6.091916e+00   6.117421e+00
   1_adp:  0.2977 0.3411   5.966453e+00   6.059231e+00
   1_occ:  0.2972 0.3418   5.965485e+00   6.060998e+00
   2_bss:  0.2929 0.3370   5.965278e+00   6.059178e+00
   2_xyz:  0.2053 0.2526   5.650143e+00   5.817161e+00
   2_adp:  0.1859 0.2355   5.565466e+00   5.748867e+00
   2_occ:  0.1858 0.2353   5.565214e+00   5.749243e+00
   3_bss:  0.1842 0.2354   5.565615e+00   5.750215e+00
   3_xyz:  0.1378 0.1869   5.319627e+00   5.543342e+00
   3_adp:  0.1251 0.1773   5.249488e+00   5.491196e+00
   3_occ:  0.1250 0.1774   5.249676e+00   5.491779e+00
   4_bss:  0.1250 0.1773   5.249306e+00   5.490938e+00
   4_xyz:  0.1189 0.1686   5.207068e+00   5.449649e+00
   4_adp:  0.1177 0.1654   5.193460e+00   5.432623e+00
   4_occ:  0.1176 0.1653   5.193048e+00   5.432513e+00
   5_bss:  0.1176 0.1654   5.193050e+00   5.432655e+00
   5_xyz:  0.1174 0.1635   5.190230e+00   5.427836e+00
   5_adp:  0.1175 0.1621   5.186515e+00   5.419596e+00
   5_occ:  0.1174 0.1621   5.186468e+00   5.419896e+00
   5_bss:  0.1174 0.1621   5.186056e+00   5.419527e+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:  0.349  20.000   6.851   7.788  11.671   0.000   0.000   0.000
   1_xyz:  0.349  20.000   6.851   7.788  11.671   0.000   0.000   0.000
   1_adp:  0.349  20.000   6.851   7.788  11.671   0.000   0.000   0.000
   1_occ:  0.349  20.000   6.851   7.788  11.671   0.000   0.000   0.000
   2_bss:  0.338  43.592   3.432   3.890   7.902   0.000   0.000   0.000
   2_xyz:  0.338  43.592   3.432   3.890   7.902   0.000   0.000   0.000
   2_adp:  0.338  43.592   3.432   3.890   7.902   0.000   0.000   0.000
   2_occ:  0.338  43.592   3.432   3.890   7.902   0.000   0.000   0.000
   3_bss:  0.323  43.592   2.388   2.934   5.308   0.000   0.000   0.000
   3_xyz:  0.323  43.592   2.388   2.934   5.308   0.000   0.000   0.000
   3_adp:  0.323  43.592   2.388   2.934   5.308   0.000   0.000   0.000
   3_occ:  0.323  43.592   2.388   2.934   5.308   0.000   0.000   0.000
   4_bss:  0.314  43.592   2.265   2.717   4.707   0.000   0.000   0.000
   4_xyz:  0.314  43.592   2.265   2.717   4.707   0.000   0.000   0.000
   4_adp:  0.314  43.592   2.265   2.717   4.707   0.000   0.000   0.000
   4_occ:  0.314  43.592   2.265   2.717   4.707   0.000   0.000   0.000
   5_bss:  0.314  43.592   2.397   2.756   4.640   0.000   0.000   0.000
   5_xyz:  0.314  43.592   2.397   2.756   4.640   0.000   0.000   0.000
   5_adp:  0.314  43.592   2.397   2.756   4.640   0.000   0.000   0.000
   5_occ:  0.314  43.592   2.397   2.756   4.640   0.000   0.000   0.000
   5_bss:  0.319  52.724  -0.849  -0.505   1.354   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  50.117 0.5204  0.5900    57725.779
   1_bss:  49.919 0.5215  0.7689    55499.888
   1_xyz:  40.069 0.6417  0.9132    37386.211
   1_adp:  35.733 0.6932  0.9961    31340.723
   1_occ:  35.814 0.6922  0.9935    31447.265
   2_bss:  35.562 0.6950  0.8750    31099.215
   2_xyz:  25.101 0.8103  0.9904    16236.575
   2_adp:  22.643 0.8361  1.0110    13910.023
   2_occ:  22.663 0.8359  1.0106    13912.865
   3_bss:  22.622 0.8364  0.9569    13959.465
   3_xyz:  17.549 0.8843  0.9857     8851.320
   3_adp:  16.392 0.8946  0.9813     7972.893
   3_occ:  16.405 0.8945  0.9812     7978.852
   4_bss:  16.373 0.8948  0.9704     7965.555
   4_xyz:  15.321 0.9043  0.9751     7280.095
   4_adp:  14.902 0.9080  0.9722     7048.598
   4_occ:  14.897 0.9080  0.9722     7044.202
   5_bss:  14.897 0.9081  0.9736     7047.149
   5_xyz:  14.764 0.9092  0.9734     6943.740
   5_adp:  14.576 0.9109  0.9703     6850.207
   5_occ:  14.580 0.9108  0.9702     6849.541
   5_bss:  14.570 0.9109  0.9705     6846.782
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.3946e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.3946e+01
   1_xyz:   1.614  0.012  0.104 17.992  0.006  4.110   1.2851e-01
   1_adp:   1.614  0.012  0.104 17.992  0.006  4.110   1.2851e-01
   1_occ:   1.614  0.012  0.104 17.992  0.006  4.110   1.2851e-01
   2_bss:   1.614  0.012  0.104 17.992  0.006  4.110   1.2851e-01
   2_xyz:   1.076  0.008  0.078 16.177  0.004  4.125   7.0579e-02
   2_adp:   1.076  0.008  0.078 16.177  0.004  4.125   7.0579e-02
   2_occ:   1.076  0.008  0.078 16.177  0.004  4.125   7.0579e-02
   3_bss:   1.076  0.008  0.078 16.177  0.004  4.125   7.0579e-02
   3_xyz:   1.111  0.010  0.086 15.953  0.004  4.113   7.5838e-02
   3_adp:   1.111  0.010  0.086 15.953  0.004  4.113   7.5838e-02
   3_occ:   1.111  0.010  0.086 15.953  0.004  4.113   7.5838e-02
   4_bss:   1.111  0.010  0.086 15.953  0.004  4.113   7.5838e-02
   4_xyz:   0.993  0.007  0.079 15.543  0.004  4.117   6.1805e-02
   4_adp:   0.993  0.007  0.079 15.543  0.004  4.117   6.1805e-02
   4_occ:   0.993  0.007  0.079 15.543  0.004  4.117   6.1805e-02
   5_bss:   0.993  0.007  0.079 15.543  0.004  4.117   6.1805e-02
   5_xyz:   0.929  0.006  0.074 15.232  0.003  4.118   5.4786e-02
   5_adp:   0.929  0.006  0.074 15.232  0.003  4.118   5.4786e-02
   5_occ:   0.929  0.006  0.074 15.232  0.003  4.118   5.4786e-02
   5_bss:   0.929  0.006  0.074 15.232  0.003  4.118   5.4786e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9934e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9934e+00
   1_xyz:  13.132  0.160  0.398 86.711  0.035  2.159   9.5189e-02
   1_adp:  13.132  0.160  0.398 86.711  0.035  2.159   9.5189e-02
   1_occ:  13.132  0.160  0.398 86.711  0.035  2.159   9.5189e-02
   2_bss:  13.132  0.160  0.398 86.711  0.035  2.159   9.5189e-02
   2_xyz:   6.307  0.074  0.276 87.420  0.033  2.310   5.9315e-02
   2_adp:   6.307  0.074  0.276 87.420  0.033  2.310   5.9315e-02
   2_occ:   6.307  0.074  0.276 87.420  0.033  2.310   5.9315e-02
   3_bss:   6.307  0.074  0.276 87.420  0.033  2.310   5.9315e-02
   3_xyz:   6.444  0.060  0.505 84.850  0.039  2.259   5.7055e-02
   3_adp:   6.444  0.060  0.505 84.850  0.039  2.259   5.7055e-02
   3_occ:   6.444  0.060  0.505 84.850  0.039  2.259   5.7055e-02
   4_bss:   6.444  0.060  0.505 84.850  0.039  2.259   5.7055e-02
   4_xyz:   6.494  0.044  0.437 82.237  0.041  2.363   3.9835e-02
   4_adp:   6.494  0.044  0.437 82.237  0.041  2.363   3.9835e-02
   4_occ:   6.494  0.044  0.437 82.237  0.041  2.363   3.9835e-02
   5_bss:   6.494  0.044  0.437 82.237  0.041  2.363   3.9835e-02
   5_xyz:   6.313  0.046  0.384 82.887  0.037  2.369   3.1339e-02
   5_adp:   6.313  0.046  0.384 82.887  0.037  2.369   3.1339e-02
   5_occ:   6.313  0.046  0.384 82.887  0.037  2.369   3.1339e-02
   5_bss:   6.313  0.046  0.384 82.887  0.037  2.369   3.1339e-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:  62.77   0.00  11.78  52.41   0.00   9.00  62.77   0.00  26.86
   1_occ:  62.77   0.00  11.78  52.41   0.00   9.00  62.77   0.00  26.86
   2_bss:  62.77   0.00  11.78  52.41   0.00   9.00  62.77   0.00  26.86
   2_xyz:  62.77   0.00  11.78  52.41   0.00   9.00  62.77   0.00  26.86
   2_adp:  61.51   0.00  11.77  53.20   0.00   8.29  61.51   0.00  30.71
   2_occ:  61.51   0.00  11.77  53.20   0.00   8.29  61.51   0.00  30.71
   3_bss:  61.51   0.00  11.77  53.20   0.00   8.29  61.51   0.00  30.71
   3_xyz:  61.51   0.00  11.77  53.20   0.00   8.29  61.51   0.00  30.71
   3_adp:  82.34   0.00  12.71  74.55   0.00   8.20  82.34   0.86  37.27
   3_occ:  82.34   0.00  12.71  74.55   0.00   8.20  82.34   0.86  37.27
   4_bss:  82.34   0.00  12.71  74.55   0.00   8.20  82.34   0.86  37.27
   4_xyz:  82.34   0.00  12.71  74.55   0.00   8.20  82.34   0.86  37.27
   4_adp:  82.39   0.00  12.35  78.96   0.00   7.99  82.39   0.92  36.05
   4_occ:  82.39   0.00  12.35  78.96   0.00   7.99  82.39   0.92  36.05
   5_bss:  82.39   0.00  12.35  78.96   0.00   7.99  82.39   0.92  36.05
   5_xyz:  82.39   0.00  12.35  78.96   0.00   7.99  82.39   0.92  36.05
   5_adp:  81.43   0.00  12.07  79.51   0.00   7.81  81.43   1.03  35.22
   5_occ:  81.43   0.00  12.07  79.51   0.00   7.81  81.43   1.03  35.22
   5_bss:  84.70   3.27  15.33  82.78   3.27  11.08  84.70   4.29  38.49
------------------------------------------------------------------------
 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:    1.259    0.016    0.406
   1_adp:    1.259    0.016    0.406
   1_occ:    1.259    0.016    0.406
   2_bss:    1.259    0.016    0.406
   2_xyz:    1.659    0.033    0.540
   2_adp:    1.659    0.033    0.540
   2_occ:    1.659    0.033    0.540
   3_bss:    1.659    0.033    0.540
   3_xyz:    1.659    0.046    0.608
   3_adp:    1.659    0.046    0.608
   3_occ:    1.659    0.046    0.608
   4_bss:    1.659    0.046    0.608
   4_xyz:    1.777    0.044    0.619
   4_adp:    1.777    0.044    0.619
   4_occ:    1.777    0.044    0.619
   5_bss:    1.777    0.044    0.619
   5_xyz:    1.814    0.054    0.630
   5_adp:    1.814    0.054    0.630
   5_occ:    1.814    0.054    0.630
   5_bss:    1.814    0.054    0.630
------------------------------------------------------------------------

CPU time actual refinement: 312.58


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_537/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_537/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_537/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_537/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_537/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 312.43 
  Macro-tasks:
    bulk solvent and scale       = 38.86  
    individual site refinement   = 127.80 
    weights calculation          = 31.11  
    collect and process          = 6.43   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 204.32 
  Micro-tasks:
    mask                            = 1.74   
    f_calc                          = 94.42  
    alpha_beta                      = 8.06   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 104.85 
    fmodel                         = 6.93   
    r_factors                      = 0.13   
    phase_errors                   = 10.88  
    foms                           = 0.23   
    TOTAL for micro-tasks          = 228.38 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.425 micro seconds
Total CPU time: 5.43 minutes
from_scatterers_fft:    634 calls, 94.04 s
gradients_fft:          579 calls, 91.47 s

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

# Date 2008-01-16 Time 01:49:57 PST -0800 (1200476997.21 s)
Start R-work = 0.4564, R-free = 0.4382 (no bulk solvent and anisotropic scale)
Final R-work = 0.1351, R-free = 0.1792 (no bulk solvent and anisotropic scale)

Start R-work = 0.4482, R-free = 0.4299
Final R-work = 0.1174, R-free = 0.1621