# Date 2008-01-16 Time 02:35:21 PST -0800 (1200479721.45 s)
#phil __OFF__

Command line arguments: "../894.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 9311
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 894

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.9525, 46.6953, 85.5261, 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: 3.40, per 1000 atoms: 1.20


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 46.6953, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0608 1.98103
Completeness in resolution range: 0.963409
Completeness with d_max=infinity: 0.960481

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0608
                             d_min =   1.9810

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 46.6953, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0608 1.98103
Completeness in resolution range: 0.963409
Completeness with d_max=infinity: 0.960481

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0612 -  4.2392 [2133/2159]  1922   211   9.9%
  bin  2:  4.2392 -  3.3773 [2046/2065]  1840   206  10.1%
  bin  3:  3.3773 -  2.9540 [2030/2049]  1825   205  10.1%
  bin  4:  2.9540 -  2.6856 [2010/2040]  1810   200  10.0%
  bin  5:  2.6856 -  2.4940 [1992/2011]  1798   194   9.7%
  bin  6:  2.4940 -  2.3476 [1980/2005]  1775   205  10.4%
  bin  7:  2.3476 -  2.2304 [1967/1995]  1770   197  10.0%
  bin  8:  2.2304 -  2.1336 [1975/2011]  1780   195   9.9%
  bin  9:  2.1336 -  2.0517 [1970/2012]  1771   199  10.1%
  bin 10:  2.0517 -  1.9810 [1486/1986]  1339   147   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_894/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 16
        2.42 -     3.04: 2199
        3.04 -     3.66: 4704
        3.66 -     4.28: 9065
        4.28 -     4.90: 12346
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 113 " - " O   HOH Z 350 "  2.210 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z 100 " - " O   HOH Z 352 "  2.248 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 107 " - " O   HOH Z 340 "  2.259 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28325 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_894/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_894/model_refine_001.geo

CPU time processing inputs: 9.09


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.9525 46.69535 85.5261 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: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4327   r_free= 0.4174   ksol= 0.00   Bsol= 0.00   scale= 0.824    |
|                                                                             |
| 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:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.225117                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0612 -  4.7284 0.99   1386  155 0.3697 0.3618      6.5255      6.4884|
|  2:  4.7284 -  3.7725 0.99   1340  146 0.3275 0.3353       6.648      6.6522|
|  3:  3.7725 -  3.3013 0.99   1306  144 0.3780 0.3414      6.5527      6.5846|
|  4:  3.3013 -  3.0021 0.99   1299  153 0.4051 0.3753      6.4505      6.3745|
|  5:  3.0021 -  2.7884 0.99   1298  139 0.4536 0.4467      6.3131      6.3188|
|  6:  2.7884 -  2.6249 0.99   1277  143 0.4490 0.4702      6.2245      6.2167|
|  7:  2.6249 -  2.4940 0.99   1289  136 0.4846 0.4591      6.2266      6.1921|
|  8:  2.4940 -  2.3859 0.98   1266  151 0.4833 0.4359      6.1393      6.1328|
|  9:  2.3859 -  2.2944 0.98   1263  142 0.4666 0.4385      6.0886      6.0383|
| 10:  2.2944 -  2.2155 0.99   1274  137 0.4860 0.4857      6.0889      6.0854|
| 11:  2.2155 -  2.1464 0.98   1277  140 0.4979 0.4488      6.0285      5.9969|
| 12:  2.1464 -  2.0852 0.97   1239  143 0.4697 0.5015      5.9494      5.9933|
| 13:  2.0852 -  2.0305 1.00   1279  135 0.5139 0.5038      5.8817      5.8285|
| 14:  2.0305 -  1.9810 0.65    837   95 0.5107 0.5115      5.8282      5.7573|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0612 -  4.7284  1386   155  0.72  32.07   0.81     0.76      61892.24|
|  2:  4.7284 -  3.7725  1340   146  0.78  28.55   0.91     0.83      75275.82|
|  3:  3.7725 -  3.3013  1306   144  0.70  35.24   0.88     0.81      77701.32|
|  4:  3.3013 -  3.0021  1299   153  0.64  40.10   0.84     0.73      70740.23|
|  5:  3.0021 -  2.7884  1298   139  0.55  48.32   0.77     0.63      63521.96|
|  6:  2.7884 -  2.6249  1277   143  0.52  50.45   0.77     0.59      57183.05|
|  7:  2.6249 -  2.4940  1289   136  0.51  51.15   0.75     0.57      52498.35|
|  8:  2.4940 -  2.3859  1266   151  0.51  51.72   0.75     0.59      46609.66|
|  9:  2.3859 -  2.2944  1263   142  0.52  50.38   0.76     0.59      41289.67|
| 10:  2.2944 -  2.2155  1274   137  0.51  51.57   0.79     0.58      37592.02|
| 11:  2.2155 -  2.1464  1277   140  0.48  53.52   0.78     0.56      35838.69|
| 12:  2.1464 -  2.0852  1239   143  0.46  55.77   0.79     0.53      35928.82|
| 13:  2.0852 -  2.0305  1279   135  0.40  59.79   0.75     0.49      32447.71|
| 14:  2.0305 -  1.9810   837    95  0.42  58.46   0.73     0.46      26834.43|
|alpha:            min =        0.46 max =            0.83 mean =         0.63|
|beta:             min =    26834.43 max =        77701.32 mean =     51982.88|
|figures of merit: min =        0.00 max =            1.00 mean =         0.56|
|phase err.(work): min =        0.00 max =           89.96 mean =        47.17|
|phase err.(test): min =        0.00 max =           89.97 mean =        47.25|
|-----------------------------------------------------------------------------|

============================== 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 = 8.006484              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 74.731   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.653527              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.404   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       21 |
| 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:      685 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1515 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2651 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3913 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5094 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6567 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7760 |
|-----------------------------------------------------------------------------|
|-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 |       53.637 |
| 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 |       1.669 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.870)------------------------------------------|
|    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 = 11.870)------------------------------------------|
|    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: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4407   r_free= 0.4259   ksol= 0.00   Bsol= 0.00   scale= 0.792    |
|                                                                             |
| 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:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.230502                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4238   r_free= 0.4077   ksol= 0.36   Bsol= 20.00   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.03,8.22,8.18,0.00,0.00,0.00); trace/3= 8.14                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.220533                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.357115              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 76.745   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.653826              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.640   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4238      final r-factor (work) = 0.3184          |
| start r-factor (free) = 0.4077      final r-factor (free) = 0.3446          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 76.5735 = 7.36 * 0.50 * 6.2352 + 1.00 * 53.6370                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.4585 = 7.36 * 0.50 * 6.0732 + 1.00 * 0.1180                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3184      final r-factor (work) = 0.2555          |
| start r-factor (free) = 0.3446      final r-factor (free) = 0.2993          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9855 = 0.65 * 1.00 * 6.0732 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8663 = 0.65 * 1.00 * 5.8954 + 1.00 * 0.0118                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.870)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    68.84   10.79    None  None   None       |
|    all(noH): 2823   0      0.00    68.84   10.79    None  None   None       |
|    Sol.    : 438    0      0.00    68.34   28.29    None  None   None       |
|    Mac.    : 2385   0      0.00    68.84   7.58     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 -   6.884: 1442   |   5:    34.420 -  41.304:  104        |
|      1:     6.884 -  13.768:  708   |   6:    41.304 -  48.189:   45        |
|      2:    13.768 -  20.652:  219   |   7:    48.189 -  55.073:   20        |
|      3:    20.652 -  27.536:  152   |   8:    55.073 -  61.957:    7        |
|      4:    27.536 -  34.420:  122   |   9:    61.957 -  68.841:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2555 r_free = 0.2993             target_work(ml) = 5.833         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2549 r_free = 0.2998             target_work(ml) = 5.832         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2549   r_free= 0.2998   ksol= 0.36   Bsol= 20.00   scale= 1.092   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.03,8.22,8.18,0.00,0.00,0.00); trace/3= 8.14                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.832197                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2499   r_free= 0.2935   ksol= 0.34   Bsol= 50.00   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.43,4.11,5.15,0.00,0.00,0.00); trace/3= 4.56                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.829614                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.615267              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 93.986   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.349104              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 124.196  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2499      final r-factor (work) = 0.1652          |
| start r-factor (free) = 0.2935      final r-factor (free) = 0.2105          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.7904 = 3.62 * 0.50 * 5.9043 + 1.00 * 0.1176                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.2852 = 3.62 * 0.50 * 5.6565 + 1.00 * 0.0603                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1652      final r-factor (work) = 0.1498          |
| start r-factor (free) = 0.2105      final r-factor (free) = 0.1943          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9863 = 0.35 * 1.00 * 5.6565 + 1.00 * 0.0116                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9567 = 0.35 * 1.00 * 5.4179 + 1.00 * 0.0653                               |
|-----------------------------------------------------------------------------|
| number of iterations = 14      |    number of function evaluations = 15     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.870)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    68.08   11.16    None  None   None       |
|    all(noH): 2823   0      0.00    68.08   11.16    None  None   None       |
|    Sol.    : 438    0      0.81    67.85   31.40    None  None   None       |
|    Mac.    : 2385   0      0.00    68.08   7.44     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 -   6.808: 1500   |   5:    34.038 -  40.846:  131        |
|      1:     6.808 -  13.615:  647   |   6:    40.846 -  47.654:   80        |
|      2:    13.615 -  20.423:  197   |   7:    47.654 -  54.461:   25        |
|      3:    20.423 -  27.231:  116   |   8:    54.461 -  61.269:   10        |
|      4:    27.231 -  34.038:  113   |   9:    61.269 -  68.077:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1498 r_free = 0.1943             target_work(ml) = 5.381         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1497 r_free = 0.1942             target_work(ml) = 5.381         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1497   r_free= 0.1942   ksol= 0.34   Bsol= 50.00   scale= 1.028   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.43,4.11,5.15,0.00,0.00,0.00); trace/3= 4.56                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.380842                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1493   r_free= 0.1932   ksol= 0.35   Bsol= 50.00   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.29,3.09,4.11,0.00,0.00,0.00); trace/3= 3.50                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.381718                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.570450              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.626  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.765117              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.100   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1493      final r-factor (work) = 0.1289          |
| start r-factor (free) = 0.1932      final r-factor (free) = 0.1697          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.3211 = 1.57 * 0.50 * 5.4262 + 1.00 * 0.0603                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.2269 = 1.57 * 0.50 * 5.3139 + 1.00 * 0.0543                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1289      final r-factor (work) = 0.1230          |
| start r-factor (free) = 0.1697      final r-factor (free) = 0.1661          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.3944 = 1.77 * 1.00 * 5.3139 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.2381 = 1.77 * 1.00 * 5.2259 + 1.00 * 0.0138                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.870)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.29   12.01    None  None   None       |
|    all(noH): 2823   0      0.00    77.29   12.01    None  None   None       |
|    Sol.    : 438    0      1.32    74.50   35.50    None  None   None       |
|    Mac.    : 2385   0      0.00    77.29   7.70     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.729: 1625   |   5:    38.646 -  46.375:   86        |
|      1:     7.729 -  15.458:  573   |   6:    46.375 -  54.104:   92        |
|      2:    15.458 -  23.188:  187   |   7:    54.104 -  61.834:   42        |
|      3:    23.188 -  30.917:   89   |   8:    61.834 -  69.563:   15        |
|      4:    30.917 -  38.646:  107   |   9:    69.563 -  77.292:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1230 r_free = 0.1661             target_work(ml) = 5.215         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1230 r_free = 0.1660             target_work(ml) = 5.214         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1230   r_free= 0.1660   ksol= 0.35   Bsol= 50.00   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.29,3.09,4.11,0.00,0.00,0.00); trace/3= 3.50                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.214323                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1230   r_free= 0.1659   ksol= 0.33   Bsol= 46.26   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.11,2.98,3.89,0.00,0.00,0.00); trace/3= 3.33                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.213471                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.745123              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 129.658  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.194059              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 128.640  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1230      final r-factor (work) = 0.1155          |
| start r-factor (free) = 0.1659      final r-factor (free) = 0.1611          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.6137 = 1.75 * 0.50 * 5.2253 + 1.00 * 0.0543                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.5848 = 1.75 * 0.50 * 5.1866 + 1.00 * 0.0592                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1155      final r-factor (work) = 0.1165          |
| start r-factor (free) = 0.1611      final r-factor (free) = 0.1592          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0203 = 0.19 * 1.00 * 5.1866 + 1.00 * 0.0138                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0150 = 0.19 * 1.00 * 5.1784 + 1.00 * 0.0101                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.870)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.56   11.50    None  None   None       |
|    all(noH): 2823   0      0.00    77.56   11.50    None  None   None       |
|    Sol.    : 438    0      1.39    73.90   33.18    None  None   None       |
|    Mac.    : 2385   0      0.00    77.56   7.52     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.757: 1670   |   5:    38.782 -  46.539:   89        |
|      1:     7.757 -  15.513:  582   |   6:    46.539 -  54.295:   68        |
|      2:    15.513 -  23.269:  151   |   7:    54.295 -  62.052:   26        |
|      3:    23.269 -  31.026:  115   |   8:    62.052 -  69.808:    8        |
|      4:    31.026 -  38.782:  109   |   9:    69.808 -  77.565:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1165 r_free = 0.1592             target_work(ml) = 5.169         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1164 r_free = 0.1590             target_work(ml) = 5.168         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1164   r_free= 0.1590   ksol= 0.33   Bsol= 46.26   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.11,2.98,3.89,0.00,0.00,0.00); trace/3= 3.33                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.168354                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1166   r_free= 0.1589   ksol= 0.33   Bsol= 46.26   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.97,2.88,3.77,0.00,0.00,0.00); trace/3= 3.20                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.169303                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.474085              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 142.995  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.398433              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 150.369  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1166      final r-factor (work) = 0.1154          |
| start r-factor (free) = 0.1589      final r-factor (free) = 0.1581          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8757 = 1.47 * 0.50 * 5.1781 + 1.00 * 0.0592                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8622 = 1.47 * 0.50 * 5.1647 + 1.00 * 0.0556                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1154      final r-factor (work) = 0.1145          |
| start r-factor (free) = 0.1581      final r-factor (free) = 0.1585          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0679 = 0.40 * 1.00 * 5.1647 + 1.00 * 0.0101                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0696 = 0.40 * 1.00 * 5.1583 + 1.00 * 0.0144                               |
|-----------------------------------------------------------------------------|
| number of iterations = 16      |    number of function evaluations = 18     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.870)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.89   11.52    None  None   None       |
|    all(noH): 2823   0      0.00    78.89   11.52    None  None   None       |
|    Sol.    : 438    0      1.61    72.95   33.23    None  None   None       |
|    Mac.    : 2385   0      0.00    78.89   7.53     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.889: 1676   |   5:    39.446 -  47.335:   87        |
|      1:     7.889 -  15.778:  568   |   6:    47.335 -  55.224:   62        |
|      2:    15.778 -  23.668:  160   |   7:    55.224 -  63.113:   24        |
|      3:    23.668 -  31.557:  116   |   8:    63.113 -  71.003:    6        |
|      4:    31.557 -  39.446:  118   |   9:    71.003 -  78.892:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1145 r_free = 0.1585             target_work(ml) = 5.161         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1145 r_free = 0.1584             target_work(ml) = 5.161         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1145   r_free= 0.1584   ksol= 0.33   Bsol= 46.26   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.97,2.88,3.77,0.00,0.00,0.00); trace/3= 3.20                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.160652                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0612 -  4.7284 0.99   1386  155 0.1021 0.1290      5.3989      5.5168|
|  2:  4.7284 -  3.7725 0.99   1340  146 0.0908 0.1141      5.4711       5.653|
|  3:  3.7725 -  3.3013 0.99   1306  144 0.1077 0.1550      5.4924      5.8723|
|  4:  3.3013 -  3.0021 0.99   1299  153 0.1225 0.1531       5.465      5.5718|
|  5:  3.0021 -  2.7884 0.99   1298  139 0.1356 0.1824      5.3415      5.5837|
|  6:  2.7884 -  2.6249 0.99   1277  143 0.1206 0.1834      5.2098      5.4735|
|  7:  2.6249 -  2.4940 0.99   1289  136 0.1283 0.1565      5.1886      5.3426|
|  8:  2.4940 -  2.3859 0.98   1266  151 0.1200 0.1777      5.0763      5.3645|
|  9:  2.3859 -  2.2944 0.98   1263  142 0.1215 0.1824      5.0606      5.3492|
| 10:  2.2944 -  2.2155 0.99   1274  137 0.1156 0.1662      4.9756      5.1716|
| 11:  2.2155 -  2.1464 0.98   1277  140 0.1177 0.1800      4.9661       5.314|
| 12:  2.1464 -  2.0852 0.97   1239  143 0.1135 0.1620      4.8978      5.1238|
| 13:  2.0852 -  2.0305 1.00   1279  135 0.1179 0.1806      4.8169      5.1429|
| 14:  2.0305 -  1.9810 0.65    837   95 0.1035 0.1687      4.6524      4.8864|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0612 -  4.7284  1386   155  0.94   8.84   0.98     0.96       7032.16|
|  2:  4.7284 -  3.7725  1340   146  0.95   7.97   1.01     1.00       9167.29|
|  3:  3.7725 -  3.3013  1306   144  0.93  11.47   1.02     1.02      10734.32|
|  4:  3.3013 -  3.0021  1299   153  0.92  13.71   1.00     0.99      10401.47|
|  5:  3.0021 -  2.7884  1298   139  0.90  15.97   0.99     0.96       8318.17|
|  6:  2.7884 -  2.6249  1277   143  0.90  15.80   0.98     0.96       7131.67|
|  7:  2.6249 -  2.4940  1289   136  0.91  15.61   0.99     0.96       6332.44|
|  8:  2.4940 -  2.3859  1266   151  0.91  15.34   0.99     0.96       5305.74|
|  9:  2.3859 -  2.2944  1263   142  0.91  15.52   1.01     0.98       5160.29|
| 10:  2.2944 -  2.2155  1274   137  0.91  15.34   1.00     0.96       4351.56|
| 11:  2.2155 -  2.1464  1277   140  0.90  16.60   1.00     0.96       4521.60|
| 12:  2.1464 -  2.0852  1239   143  0.92  14.97   1.01     0.99       4080.47|
| 13:  2.0852 -  2.0305  1279   135  0.90  16.73   1.01     1.00       3528.99|
| 14:  2.0305 -  1.9810   837    95  0.92  14.49   0.98     0.95       2486.92|
|alpha:            min =        0.95 max =            1.02 mean =         0.97|
|beta:             min =     2486.92 max =        10734.32 mean =      6456.68|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           90.00 mean =        14.10|
|phase err.(test): min =        0.00 max =           88.26 mean =        13.63|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1145   r_free= 0.1584   ksol= 0.33   Bsol= 49.48   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.23,-0.32,0.56,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.160661                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1145   r_free= 0.1584   ksol= 0.33   Bsol= 49.48   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.23,-0.32,0.56,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.160661                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0612 -  4.7284 0.99   1386  155 0.1021 0.1290       5.399      5.5169|
|  2:  4.7284 -  3.7725 0.99   1340  146 0.0908 0.1141      5.4711       5.653|
|  3:  3.7725 -  3.3013 0.99   1306  144 0.1077 0.1550      5.4923      5.8723|
|  4:  3.3013 -  3.0021 0.99   1299  153 0.1225 0.1531       5.465      5.5718|
|  5:  3.0021 -  2.7884 0.99   1298  139 0.1355 0.1824      5.3415      5.5837|
|  6:  2.7884 -  2.6249 0.99   1277  143 0.1206 0.1835      5.2098      5.4735|
|  7:  2.6249 -  2.4940 0.99   1289  136 0.1283 0.1565      5.1886      5.3426|
|  8:  2.4940 -  2.3859 0.98   1266  151 0.1200 0.1777      5.0763      5.3645|
|  9:  2.3859 -  2.2944 0.98   1263  142 0.1215 0.1824      5.0606      5.3493|
| 10:  2.2944 -  2.2155 0.99   1274  137 0.1156 0.1662      4.9756      5.1716|
| 11:  2.2155 -  2.1464 0.98   1277  140 0.1177 0.1800      4.9661       5.314|
| 12:  2.1464 -  2.0852 0.97   1239  143 0.1135 0.1620      4.8977      5.1238|
| 13:  2.0852 -  2.0305 1.00   1279  135 0.1179 0.1805      4.8169      5.1428|
| 14:  2.0305 -  1.9810 0.65    837   95 0.1035 0.1687      4.6524      4.8865|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0612 -  4.7284  1386   155  0.94   8.84   0.98     0.96       7033.97|
|  2:  4.7284 -  3.7725  1340   146  0.95   7.97   1.01     1.00       9168.60|
|  3:  3.7725 -  3.3013  1306   144  0.93  11.47   1.02     1.02      10734.34|
|  4:  3.3013 -  3.0021  1299   153  0.92  13.71   1.00     0.99      10401.25|
|  5:  3.0021 -  2.7884  1298   139  0.90  15.97   0.99     0.96       8318.34|
|  6:  2.7884 -  2.6249  1277   143  0.90  15.80   0.98     0.96       7131.67|
|  7:  2.6249 -  2.4940  1289   136  0.91  15.61   0.99     0.96       6332.82|
|  8:  2.4940 -  2.3859  1266   151  0.91  15.34   0.99     0.96       5305.85|
|  9:  2.3859 -  2.2944  1263   142  0.91  15.52   1.01     0.99       5160.41|
| 10:  2.2944 -  2.2155  1274   137  0.91  15.34   1.00     0.96       4351.48|
| 11:  2.2155 -  2.1464  1277   140  0.90  16.60   1.00     0.96       4521.28|
| 12:  2.1464 -  2.0852  1239   143  0.92  14.97   1.01     0.99       4079.98|
| 13:  2.0852 -  2.0305  1279   135  0.90  16.73   1.01     1.00       3528.83|
| 14:  2.0305 -  1.9810   837    95  0.92  14.49   0.99     0.95       2487.17|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2487.17 max =        10734.34 mean =      6456.90|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           90.00 mean =        14.10|
|phase err.(test): min =        0.00 max =           88.26 mean =        13.63|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.870)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.22    82.12   14.74    None  None   None       |
|    all(noH): 2823   0      3.22    82.12   14.74    None  None   None       |
|    Sol.    : 438    0      4.83    76.18   36.46    None  None   None       |
|    Mac.    : 2385   0      3.22    82.12   10.75    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:     3.224 -  11.114: 1676   |   5:    42.670 -  50.559:   87        |
|      1:    11.114 -  19.003:  568   |   6:    50.559 -  58.449:   62        |
|      2:    19.003 -  26.892:  160   |   7:    58.449 -  66.338:   24        |
|      3:    26.892 -  34.781:  116   |   8:    66.338 -  74.227:    6        |
|      4:    34.781 -  42.670:  118   |   9:    74.227 -  82.116:    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: 0.374 - 5.704
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 298 from: 304
   mapped sites are within: 0.735 - 5.704

peak=   11.353 closest distance to " CB  VAL A 230 " =    1.479
peak=    8.704 closest distance to " CG2 VAL A 296 " =    1.229
peak=    7.073 closest distance to " CG  ARG A 138 " =    1.092
peak=    6.029 closest distance to " CD2 LEU A   5 " =    1.220
peak=    6.022 closest distance to " CG  LEU A   5 " =    1.267
peak=    5.957 closest distance to " NH2 ARG A  56 " =    2.202
peak=    5.509 closest distance to " CB  GLN A 223 " =    1.412
peak=    5.467 closest distance to " NH1 ARG A 138 " =    0.975
peak=    5.170 closest distance to " CG  LEU A 228 " =    1.174
peak=    5.108 closest distance to " CB  GLN A 183 " =    1.217
peak=    5.081 closest distance to " NE2 GLN A  11 " =    1.129
peak=    5.046 closest distance to " O   HOH Z 126 " =    2.015
peak=    4.952 closest distance to " CD1AILE A 234 " =    1.032
peak=    4.880 closest distance to " CG  PRO A 213 " =    1.252
peak=    4.782 closest distance to " CG  PRO A 198 " =    1.238
peak=    4.781 closest distance to " O   HOH Z 232 " =    2.311
peak=    4.762 closest distance to " O   HOH Z 142 " =    1.777
peak=    4.687 closest distance to " O   HOH Z 298 " =    1.788
peak=    4.682 closest distance to " CD2 LEU A 228 " =    1.173
peak=    4.671 closest distance to " CB  ARG A 275 " =    0.853
peak=    4.608 closest distance to " CB  ASN A 148 " =    1.370
peak=    4.584 closest distance to " O   HOH Z 369 " =    2.027
peak=    4.566 closest distance to " CB  SER A  63 " =    1.310
peak=    4.525 closest distance to " O   HOH Z 272 " =    1.873
peak=    4.506 closest distance to " CB  VAL A 230 " =    1.159
peak=    4.456 closest distance to " CG  PRO A 243 " =    1.151
peak=    4.446 closest distance to " CB  GLU A 152 " =    1.218
peak=    4.422 closest distance to " C   PRO A 198 " =    1.537
peak=    4.391 closest distance to " O   HOH Z 209 " =    2.284
peak=    4.386 closest distance to " CB  VAL A 265 " =    1.250
peak=    4.357 closest distance to " O   HOH Z 427 " =    2.986
peak=    4.342 closest distance to " CD  ARG A 138 " =    1.100
peak=    4.333 closest distance to " O   HOH Z 316 " =    3.034
peak=    4.312 closest distance to " OD1 ASN A  69 " =    2.680
peak=    4.288 closest distance to " O   HOH Z 368 " =    2.084
peak=    4.278 closest distance to " CB  TRP A 266 " =    0.981
peak=    4.255 closest distance to " CB  VAL A 296 " =    1.073
peak=    4.214 closest distance to " CB  GLU A 128 " =    1.025
peak=    4.207 closest distance to " O   HOH Z 236 " =    1.996
peak=    4.195 closest distance to " CB  SER A   3 " =    1.375
peak=    4.168 closest distance to " O   HOH Z  78 " =    1.714
peak=    4.166 closest distance to " O   HOH Z 263 " =    1.610
peak=    4.163 closest distance to " O   HOH Z 303 " =    2.047
peak=    4.140 closest distance to " O   HOH Z   9 " =    2.193
peak=    4.127 closest distance to " O   HOH Z 425 " =    1.397
peak=    4.126 closest distance to " O   HOH Z 158 " =    3.060
peak=    4.116 closest distance to " CB  SER A 216 " =    0.803
peak=    4.083 closest distance to " ND2 ASN A 187 " =    1.502
peak=    4.080 closest distance to " O   HOH Z  55 " =    2.386
peak=    4.080 closest distance to " O   HOH Z  68 " =    2.144
peak=    4.072 closest distance to " OD2 ASP A 286 " =    2.834
peak=    4.040 closest distance to " O   HOH Z 193 " =    1.789
peak=    4.011 closest distance to " CD  ARG A 159 " =    0.751
peak=    4.004 closest distance to " O   HOH Z 346 " =    1.577
peak=    4.001 closest distance to " O   HOH Z  61 " =    1.634
peak=    3.998 closest distance to " O   HOH Z  88 " =    3.225
peak=    3.996 closest distance to " CB  ASN A  39 " =    0.920
peak=    3.985 closest distance to " CB  LEU A 143 " =    1.162
peak=    3.944 closest distance to " O   HOH Z 193 " =    1.746
peak=    3.944 closest distance to " O   HOH Z 344 " =    2.879
peak=    3.934 closest distance to " CG  LEU A 167 " =    1.149
peak=    3.900 closest distance to " O   SER A  87 " =    2.369
peak=    3.894 closest distance to " CB  ASN A 187 " =    1.376
peak=    3.893 closest distance to " O   HOH Z 403 " =    1.689
peak=    3.877 closest distance to " O   HOH Z 411 " =    3.777
peak=    3.876 closest distance to " CB  TRP A 179 " =    1.355
peak=    3.859 closest distance to " CG  ARG A  66 " =    2.630
peak=    3.856 closest distance to " CA  THR A 264 " =    0.794
peak=    3.851 closest distance to " O   HOH Z 203 " =    1.775
peak=    3.843 closest distance to " O   HOH Z 189 " =    2.727
peak=    3.837 closest distance to " CZ  PHE A 218 " =    1.068
peak=    3.834 closest distance to " CA  ALA A  21 " =    1.162
peak=    3.827 closest distance to " O   HOH Z 234 " =    3.629
peak=    3.800 closest distance to " ND2 ASN A 249 " =    1.928
peak=    3.800 closest distance to " CA  ASN A 215 " =    1.120
peak=    3.782 closest distance to " O   TRP A 274 " =    1.894
peak=    3.777 closest distance to " CB  GLU A 277 " =    3.573
peak=    3.776 closest distance to " CG2 VAL A 257 " =    0.934
peak=    3.773 closest distance to " CB  PRO A  54 " =    0.791
peak=    3.770 closest distance to " CA  ALA A  51 " =    1.051
peak=    3.769 closest distance to " O   HOH Z  43 " =    1.982
peak=    3.756 closest distance to " O   HOH Z 280 " =    2.961
peak=    3.751 closest distance to " O   HOH Z 261 " =    2.166
peak=    3.742 closest distance to " CA  SER A  87 " =    0.976
peak=    3.735 closest distance to " CB  ARG A 139 " =    0.927
peak=    3.728 closest distance to " CE  LYS A  76 " =    0.931
peak=    3.713 closest distance to " O   HOH Z  59 " =    1.964
peak=    3.712 closest distance to " CD  ARG A 269 " =    1.026
peak=    3.712 closest distance to " O   HOH Z  97 " =    2.043
peak=    3.701 closest distance to " NH1AARG A 145 " =    1.096
peak=    3.696 closest distance to " CB  LEU A 228 " =    1.289
peak=    3.693 closest distance to " O   HOH Z 128 " =    2.026
peak=    3.688 closest distance to " CA  TYR A  30 " =    0.938
peak=    3.685 closest distance to " CB  VAL A 202 " =    1.616
peak=    3.674 closest distance to " CZ  PHE A 192 " =    0.994
peak=    3.673 closest distance to " CG1BVAL A  72 " =    1.598
peak=    3.669 closest distance to " O   HOH Z 197 " =    3.274
peak=    3.665 closest distance to " NZ  LYS A 117 " =    3.279
peak=    3.661 closest distance to " N   PHE A 130 " =    1.264
peak=    3.654 closest distance to " CB  SER A 212 " =    1.195
peak=    3.654 closest distance to " O   HOH Z 132 " =    2.583
peak=    3.644 closest distance to " CG1 VAL A 153 " =    0.895
peak=    3.642 closest distance to " O   MET A 105 " =    1.794
peak=    3.642 closest distance to " CD BLYS A 290 " =    1.081
peak=    3.641 closest distance to " CG  GLN A  88 " =    1.096
peak=    3.637 closest distance to " CA  VAL A  41 " =    0.884
peak=    3.633 closest distance to " CA  LEU A 282 " =    1.018
peak=    3.626 closest distance to " CA  ILE A 234 " =    0.898
peak=    3.624 closest distance to " O   HOH Z 368 " =    3.581
peak=    3.619 closest distance to " O   HOH Z 273 " =    2.653
peak=    3.611 closest distance to " CA  ALA A 158 " =    1.152
peak=    3.601 closest distance to " O   HOH Z 437 " =    1.998
peak=    3.596 closest distance to " CD1 LEU A 300 " =    1.186
peak=    3.595 closest distance to " CB  MET A  40 " =    0.786
peak=    3.588 closest distance to " CB  ARG A  79 " =    1.445
peak=    3.567 closest distance to " O   HOH Z 147 " =    1.659
peak=    3.567 closest distance to " ND2 ASN A 110 " =    1.776
peak=    3.559 closest distance to " CA  THR A 221 " =    0.923
peak=    3.555 closest distance to " CA  LYS A 117 " =    1.180
peak=    3.550 closest distance to " O   HOH Z 124 " =    1.287
peak=    3.540 closest distance to " CB  ALA A 248 " =    1.381
peak=    3.537 closest distance to " CG2 THR A 220 " =    0.993
peak=    3.535 closest distance to " CB  HIS A 108 " =    0.858
peak=    3.533 closest distance to " N   ASN A  39 " =    1.094
peak=    3.525 closest distance to " CG2 THR A 221 " =    1.119
peak=    3.523 closest distance to " O   GLN A 278 " =    1.404
peak=    3.523 closest distance to " O   HOH Z 214 " =    2.017
peak=    3.523 closest distance to " O   HOH Z 133 " =    1.680
peak=    3.520 closest distance to " O   HOH Z 193 " =    1.930
peak=    3.513 closest distance to " CG BARG A 102 " =    1.826
peak=    3.511 closest distance to " O   HOH Z 248 " =    1.781
peak=    3.510 closest distance to " O   HOH Z 329 " =    3.805
peak=    3.507 closest distance to " O   HOH Z 175 " =    2.043
peak=    3.505 closest distance to " CB  ALA A 291 " =    1.384
peak=    3.505 closest distance to " O   HOH Z 371 " =    3.019
peak=    3.502 closest distance to " CB  PRO A 198 " =    1.008
peak=    3.497 closest distance to " O   HOH Z 135 " =    1.868
peak=    3.493 closest distance to " CD1 LEU A  96 " =    0.743
peak=    3.493 closest distance to " CD2 LEU A 255 " =    1.607
peak=    3.492 closest distance to " N   VAL A 126 " =    1.273
peak=    3.491 closest distance to " CB  ALA A   9 " =    1.575
peak=    3.490 closest distance to " CB  ASP A 140 " =    0.791
peak=    3.482 closest distance to " NH1 ARG A  14 " =    0.957
peak=    3.480 closest distance to " ND1 HIS A  81 " =    1.680
peak=    3.477 closest distance to " CA  ASP A 140 " =    1.262
peak=    3.477 closest distance to " O   HOH Z 402 " =    1.408
peak=    3.477 closest distance to " O   HOH Z   3 " =    1.840
peak=    3.473 closest distance to " CG  MET A 185 " =    1.031
peak=    3.470 closest distance to " CB  GLN A  88 " =    1.231
peak=    3.468 closest distance to " CA  VAL A 126 " =    0.942
peak=    3.454 closest distance to " CB  LEU A 237 " =    0.811
peak=    3.452 closest distance to " CA  PHE A 283 " =    1.132
peak=    3.451 closest distance to " CB BVAL A  41 " =    1.276
peak=    3.450 closest distance to " O   HOH Z 250 " =    1.323
peak=    3.450 closest distance to " O   HOH Z 305 " =    3.490
peak=    3.449 closest distance to " CE1 TYR A 186 " =    1.359
peak=    3.446 closest distance to " O   HOH Z 290 " =    1.136
peak=    3.444 closest distance to " CD1 ILE A 106 " =    0.960
peak=    3.443 closest distance to " O   HOH Z   1 " =    1.804
peak=    3.441 closest distance to " O   HOH Z  93 " =    2.600
peak=    3.440 closest distance to " CD  LYS A 166 " =    1.304
peak=    3.434 closest distance to " NH2 ARG A 156 " =    1.087
peak=    3.432 closest distance to " CG1 ILE A  33 " =    1.358
peak=    3.427 closest distance to " CB  ASN A 142 " =    1.013
peak=    3.424 closest distance to " O   HOH Z 128 " =    2.188
peak=    3.417 closest distance to " CB  ALA A 161 " =    0.866
peak=    3.414 closest distance to " O   HOH Z 345 " =    3.490
peak=    3.409 closest distance to " O   HOH Z 227 " =    2.063
peak=    3.407 closest distance to " OG BSER A 164 " =    2.205
peak=    3.405 closest distance to " O   HOH Z   2 " =    1.593
peak=    3.404 closest distance to " CD1 ILE A  33 " =    1.650
peak=    3.399 closest distance to " OG  SER A 206 " =    1.211
peak=    3.398 closest distance to " OG  SER A  97 " =    2.670
peak=    3.393 closest distance to " CB  LEU A 255 " =    0.791
peak=    3.390 closest distance to " O   HOH Z 145 " =    1.848
peak=    3.385 closest distance to " NH2BARG A 145 " =    1.995
peak=    3.381 closest distance to " O   HOH Z 350 " =    1.534
peak=    3.380 closest distance to " CB  LYS A 117 " =    1.183
peak=    3.380 closest distance to " O   HOH Z 247 " =    1.320
peak=    3.379 closest distance to " O   ALA A 158 " =    1.389
peak=    3.369 closest distance to " ND1 HIS A  86 " =    1.611
peak=    3.365 closest distance to " CB  ASN A 110 " =    1.162
peak=    3.365 closest distance to " O   HOH Z 108 " =    2.321
peak=    3.363 closest distance to " CG2 ILE A 106 " =    0.969
peak=    3.361 closest distance to " CA  GLY A 267 " =    0.928
peak=    3.360 closest distance to " CG1 ILE A 151 " =    1.041
peak=    3.359 closest distance to " O   HOH Z 295 " =    1.495
peak=    3.359 closest distance to " CB  THR A 157 " =    1.074
peak=    3.357 closest distance to " O   HOH Z   1 " =    1.902
peak=    3.355 closest distance to " N   ARG A 156 " =    1.346
peak=    3.354 closest distance to " O   HOH Z 180 " =    2.125
peak=    3.354 closest distance to " O   HOH Z 172 " =    3.591
peak=    3.352 closest distance to " O   HOH Z 407 " =    2.331
peak=    3.346 closest distance to " O   HOH Z 423 " =    1.670
peak=    3.346 closest distance to " O   HOH Z 271 " =    1.980
peak=    3.344 closest distance to " CA  ASP A 162 " =    1.073
peak=    3.341 closest distance to " O   HOH Z  58 " =    1.477
peak=    3.334 closest distance to " CA  LYS A 290 " =    1.289
peak=    3.330 closest distance to " O   HOH Z 425 " =    2.052
peak=    3.326 closest distance to " CA  ALA A 154 " =    1.064
peak=    3.325 closest distance to " O   HOH Z 286 " =    2.380
peak=    3.324 closest distance to " O   HOH Z 112 " =    1.581
peak=    3.321 closest distance to " O   HOH Z 313 " =    1.827
peak=    3.321 closest distance to " O   HOH Z  10 " =    1.804
peak=    3.321 closest distance to " O   HOH Z 148 " =    3.338
peak=    3.320 closest distance to " CB  SER A  62 " =    1.250
peak=    3.315 closest distance to " O   HOH Z   9 " =    1.954
peak=    3.312 closest distance to " CA  ASN A 127 " =    1.095
peak=    3.312 closest distance to " CG1 VAL A 296 " =    1.214
peak=    3.311 closest distance to " CD  LYS A 119 " =    1.397
peak=    3.309 closest distance to " CB  VAL A 268 " =    0.880
peak=    3.307 closest distance to " C   ALA A 299 " =    0.967
peak=    3.301 closest distance to " O   HOH Z 353 " =    2.694
peak=    3.301 closest distance to " O   HOH Z 116 " =    1.704
peak=    3.300 closest distance to " CG2 THR A 294 " =    1.728
peak=    3.299 closest distance to " CB  SER A 273 " =    0.909
peak=    3.299 closest distance to " O   HOH Z 227 " =    1.630
peak=    3.292 closest distance to " CA  GLN A 194 " =    1.270
peak=    3.288 closest distance to " O   HOH Z 367 " =    2.271
peak=    3.288 closest distance to " CG  PRO A 280 " =    0.815
peak=    3.286 closest distance to " O   HOH Z  48 " =    1.372
peak=    3.279 closest distance to " CA  ALA A 291 " =    0.934
peak=    3.277 closest distance to " O   HOH Z 419 " =    1.798
peak=    3.271 closest distance to " O   HOH Z  92 " =    2.560
peak=    3.271 closest distance to " NE2 GLN A  58 " =    5.704
peak=    3.271 closest distance to " O   HOH Z  30 " =    1.291
peak=    3.269 closest distance to " CG  MET A 185 " =    1.160
peak=    3.265 closest distance to " O   HOH Z 417 " =    2.065
peak=    3.264 closest distance to " CA  ARG A  36 " =    1.104
peak=    3.261 closest distance to " O   HOH Z 185 " =    2.180
peak=    3.259 closest distance to " CB  GLN A 278 " =    0.871
peak=    3.259 closest distance to " NH2AARG A 190 " =    1.803
peak=    3.259 closest distance to " O   HOH Z 359 " =    3.778
peak=    3.253 closest distance to " CB  TRP A 150 " =    1.495
peak=    3.252 closest distance to " CB  ARG A 190 " =    1.680
peak=    3.251 closest distance to " O   HOH Z 216 " =    2.622
peak=    3.251 closest distance to " O   HOH Z 189 " =    2.970
peak=    3.247 closest distance to " O   HOH Z  44 " =    1.684
peak=    3.247 closest distance to " O   HOH Z 435 " =    2.012
peak=    3.244 closest distance to " CA  ARG A 195 " =    1.175
peak=    3.243 closest distance to " O   HOH Z 163 " =    1.831
peak=    3.243 closest distance to " N   SER A 135 " =    1.299
peak=    3.242 closest distance to " O   HOH Z 128 " =    2.028
peak=    3.240 closest distance to " NH2BARG A 190 " =    1.667
peak=    3.240 closest distance to " N   GLN A 278 " =    0.996
peak=    3.236 closest distance to " O   HOH Z 409 " =    3.072
peak=    3.233 closest distance to " CB  ALA A 114 " =    1.279
peak=    3.229 closest distance to " NH2AARG A 275 " =    3.760
peak=    3.226 closest distance to " O   HOH Z 423 " =    2.834
peak=    3.220 closest distance to " O  BHOH Z 338 " =    2.464
peak=    3.219 closest distance to " CG  GLN A  77 " =    2.288
peak=    3.217 closest distance to " CB  MET A  47 " =    1.061
peak=    3.215 closest distance to " N   SER A  12 " =    1.605
peak=    3.215 closest distance to " CB  ALA A 104 " =    0.735
peak=    3.214 closest distance to " CG BARG A 275 " =    1.431
peak=    3.210 closest distance to " OG  SER A  22 " =    2.830
peak=    3.210 closest distance to " O   HOH Z 392 " =    1.343
peak=    3.208 closest distance to " CZ3 TRP A 123 " =    1.275
peak=    3.208 closest distance to " O   HOH Z 392 " =    1.960
peak=    3.207 closest distance to " O   HOH Z  21 " =    1.717
peak=    3.192 closest distance to " NZ ALYS A 290 " =    1.156
peak=    3.191 closest distance to " CG  LEU A 281 " =    1.089
peak=    3.186 closest distance to " O   HOH Z  54 " =    1.559
peak=    3.181 closest distance to " O   HOH Z 109 " =    2.637
peak=    3.178 closest distance to " CB  THR A  31 " =    1.693
peak=    3.176 closest distance to " O   HOH Z 303 " =    1.748
peak=    3.166 closest distance to " CG1 VAL A 174 " =    1.081
peak=    3.164 closest distance to " CB  GLU A  46 " =    1.068
peak=    3.156 closest distance to " O   HOH Z 302 " =    1.852
peak=    3.156 closest distance to " O   HOH Z 291 " =    1.642
peak=    3.154 closest distance to " CB  ILE A 120 " =    1.304
peak=    3.153 closest distance to " O   HOH Z 171 " =    2.450
peak=    3.150 closest distance to " O   HOH Z 406 " =    1.608
peak=    3.146 closest distance to " CB  SER A  26 " =    1.620
peak=    3.127 closest distance to " O   ALA A   1 " =    1.778
peak=    3.122 closest distance to " CG2 ILE A 120 " =    1.297
peak=    3.121 closest distance to " CB  ILE A  20 " =    1.431
peak=    3.119 closest distance to " CA  ASP A 191 " =    0.752
peak=    3.119 closest distance to " O   HOH Z 285 " =    1.914
peak=    3.116 closest distance to " N   TYR A  15 " =    0.779
peak=    3.110 closest distance to " CD2 TRP A 179 " =    1.389
peak=    3.104 closest distance to " O   HOH Z 245 " =    1.350
peak=    3.103 closest distance to " CG  GLN A 278 " =    1.286
peak=    3.103 closest distance to " CA  ARG A 102 " =    1.166
peak=    3.098 closest distance to " O   HOH Z 366 " =    2.862
peak=    3.098 closest distance to " O   HOH Z 148 " =    2.160
peak=    3.092 closest distance to " O   HOH Z 141 " =    1.602
peak=    3.091 closest distance to " OD1 ASN A  45 " =    1.491
peak=    3.090 closest distance to " O   ALA A   1 " =    1.557
peak=    3.088 closest distance to " CB  GLN A 205 " =    1.134
peak=    3.087 closest distance to " CA  ALA A 233 " =    1.616
peak=    3.085 closest distance to " NZ  LYS A  76 " =    1.329
peak=    3.084 closest distance to " CB  VAL A 250 " =    1.098
peak=    3.067 closest distance to " CB  GLN A 103 " =    1.015
peak=    3.062 closest distance to " OH  TYR A 214 " =    1.186
peak=    3.058 closest distance to " CA  GLY A  80 " =    0.982
peak=    3.045 closest distance to " O   HOH Z 222 " =    2.506
peak=    3.025 closest distance to " OE1 GLU A   2 " =    2.172

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 206         
Filter by distance & map next to the model:
   mapped sites are within: 0.554 - 5.366
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 203 from: 206
   mapped sites are within: 0.763 - 5.366

peak=   -5.407 closest distance to " CG2 VAL A 230 " =    0.785
peak=   -4.777 closest distance to " CG  ARG A 138 " =    0.926
peak=   -4.546 closest distance to " CD  ARG A 156 " =    2.037
peak=   -4.342 closest distance to " O   HOH Z 266 " =    4.850
peak=   -4.266 closest distance to " CD  ARG A 138 " =    1.166
peak=   -4.238 closest distance to " O   HOH Z 290 " =    1.114
peak=   -4.173 closest distance to " CD  ARG A  14 " =    3.332
peak=   -4.101 closest distance to " CE2 TYR A  30 " =    2.870
peak=   -4.064 closest distance to " CG  ASP A 231 " =    0.763
peak=   -4.031 closest distance to " CG  GLN A 223 " =    2.019
peak=   -3.998 closest distance to " O   HOH Z 231 " =    1.671
peak=   -3.976 closest distance to " CB  ALA A 161 " =    2.546
peak=   -3.970 closest distance to " OG BSER A 134 " =    1.139
peak=   -3.970 closest distance to " CB  PRO A 243 " =    2.632
peak=   -3.883 closest distance to " CG2 VAL A 296 " =    1.441
peak=   -3.880 closest distance to " CG1 VAL A 296 " =    1.323
peak=   -3.864 closest distance to " O   HOH Z 435 " =    2.818
peak=   -3.859 closest distance to " C   HIS A 108 " =    1.191
peak=   -3.807 closest distance to " CZ3 TRP A 179 " =    1.216
peak=   -3.800 closest distance to " O   HOH Z 351 " =    1.360
peak=   -3.783 closest distance to " C   ALA A 158 " =    1.298
peak=   -3.781 closest distance to " O   HOH Z 388 " =    2.140
peak=   -3.779 closest distance to " CB  PRO A 163 " =    2.577
peak=   -3.759 closest distance to " CD1 LEU A 101 " =    2.393
peak=   -3.744 closest distance to " O   VAL A  67 " =    2.651
peak=   -3.741 closest distance to " O   PRO A 163 " =    1.939
peak=   -3.727 closest distance to " CD1 LEU A 228 " =    2.299
peak=   -3.721 closest distance to " O   PRO A 198 " =    1.202
peak=   -3.705 closest distance to " CG2 THR A   4 " =    1.876
peak=   -3.695 closest distance to " N   ALA A 226 " =    2.107
peak=   -3.695 closest distance to " CG  PHE A 283 " =    2.718
peak=   -3.693 closest distance to " CB  PHE A 192 " =    1.878
peak=   -3.671 closest distance to " CB  PRO A 280 " =    2.027
peak=   -3.648 closest distance to " N   GLN A  58 " =    1.766
peak=   -3.630 closest distance to " C   ASP A 231 " =    2.598
peak=   -3.629 closest distance to " O   HOH Z 118 " =    2.945
peak=   -3.621 closest distance to " O   GLY A 203 " =    2.378
peak=   -3.617 closest distance to " O   HOH Z 185 " =    2.231
peak=   -3.617 closest distance to " O   HOH Z 389 " =    1.914
peak=   -3.601 closest distance to " O   ARG A 145 " =    1.616
peak=   -3.598 closest distance to " O   HOH Z 196 " =    2.208
peak=   -3.590 closest distance to " N   THR A 157 " =    1.426
peak=   -3.589 closest distance to " O   HOH Z 372 " =    2.366
peak=   -3.584 closest distance to " OXT GLY A 302 " =    2.942
peak=   -3.578 closest distance to " O   HOH Z 211 " =    1.545
peak=   -3.574 closest distance to " O   HOH Z 102 " =    1.687
peak=   -3.573 closest distance to " CG1 VAL A 112 " =    2.987
peak=   -3.570 closest distance to " OE1 GLN A  88 " =    1.074
peak=   -3.565 closest distance to " CA  ASP A  27 " =    2.389
peak=   -3.559 closest distance to " CE  MET A 105 " =    2.193
peak=   -3.558 closest distance to " CD  LYS A 289 " =    2.627
peak=   -3.548 closest distance to " CD  ARG A 139 " =    1.579
peak=   -3.547 closest distance to " CD2 LEU A 300 " =    2.859
peak=   -3.539 closest distance to " O   VAL A  67 " =    2.576
peak=   -3.534 closest distance to " NZ  LYS A 119 " =    3.418
peak=   -3.529 closest distance to " O   HOH Z  43 " =    1.760
peak=   -3.528 closest distance to " CB  ALA A 248 " =    2.009
peak=   -3.528 closest distance to " N   ALA A  43 " =    2.360
peak=   -3.525 closest distance to " C   ASN A 285 " =    2.474
peak=   -3.520 closest distance to " O   HOH Z  52 " =    1.529
peak=   -3.516 closest distance to " NH2AARG A 275 " =    5.232
peak=   -3.513 closest distance to " O   HOH Z  44 " =    2.174
peak=   -3.512 closest distance to " CD  GLN A  58 " =    0.996
peak=   -3.510 closest distance to " NH2 ARG A  79 " =    1.972
peak=   -3.509 closest distance to " ND2 ASN A  45 " =    1.237
peak=   -3.507 closest distance to " OG  SER A  87 " =    1.414
peak=   -3.487 closest distance to " OD1 ASN A 187 " =    1.623
peak=   -3.485 closest distance to " CG  TRP A 266 " =    1.847
peak=   -3.481 closest distance to " CG  LEU A 101 " =    2.517
peak=   -3.480 closest distance to " OG  SER A  97 " =    2.165
peak=   -3.473 closest distance to " O   HOH Z  13 " =    1.297
peak=   -3.471 closest distance to " O   HOH Z 166 " =    1.516
peak=   -3.467 closest distance to " CE2 PHE A 218 " =    2.633
peak=   -3.467 closest distance to " O   GLY A  80 " =    2.474
peak=   -3.460 closest distance to " O   TYR A  30 " =    2.893
peak=   -3.459 closest distance to " CD2 LEU A 237 " =    2.848
peak=   -3.452 closest distance to " CG1 VAL A 265 " =    2.410
peak=   -3.446 closest distance to " O   HOH Z  38 " =    1.823
peak=   -3.444 closest distance to " OG ASER A 134 " =    1.184
peak=   -3.444 closest distance to " O   HOH Z 241 " =    1.279
peak=   -3.443 closest distance to " CB  TYR A  15 " =    2.161
peak=   -3.442 closest distance to " CG1 VAL A 112 " =    2.686
peak=   -3.436 closest distance to " CG  MET A 105 " =    0.919
peak=   -3.431 closest distance to " CG  ASP A  50 " =    2.348
peak=   -3.429 closest distance to " O   HOH Z 222 " =    1.468
peak=   -3.425 closest distance to " O   HOH Z 166 " =    1.984
peak=   -3.425 closest distance to " O   HOH Z  60 " =    2.139
peak=   -3.423 closest distance to " O   HOH Z 350 " =    1.790
peak=   -3.413 closest distance to " O   HOH Z 394 " =    1.541
peak=   -3.405 closest distance to " N   THR A  18 " =    1.322
peak=   -3.401 closest distance to " CB  ASN A  39 " =    2.101
peak=   -3.397 closest distance to " O   HOH Z 417 " =    2.868
peak=   -3.396 closest distance to " O   HOH Z 256 " =    1.269
peak=   -3.392 closest distance to " O   HOH Z 134 " =    2.638
peak=   -3.391 closest distance to " C   LEU A 222 " =    0.859
peak=   -3.382 closest distance to " N   THR A 235 " =    1.250
peak=   -3.382 closest distance to " CG  ASP A 132 " =    2.250
peak=   -3.381 closest distance to " CE3 TRP A 150 " =    2.114
peak=   -3.381 closest distance to " CD1 ILE A 239 " =    2.074
peak=   -3.379 closest distance to " CG  LEU A 228 " =    0.961
peak=   -3.374 closest distance to " O   HOH Z 436 " =    1.465
peak=   -3.365 closest distance to " OG BSER A 134 " =    1.747
peak=   -3.362 closest distance to " CG  ARG A 269 " =    2.349
peak=   -3.360 closest distance to " O   HOH Z  22 " =    2.577
peak=   -3.353 closest distance to " O   HOH Z 165 " =    1.897
peak=   -3.352 closest distance to " CA  GLY A 241 " =    2.253
peak=   -3.351 closest distance to " O   HOH Z 309 " =    2.409
peak=   -3.351 closest distance to " NE2 GLN A  88 " =    1.002
peak=   -3.348 closest distance to " CG1 VAL A 250 " =    2.747
peak=   -3.346 closest distance to " CD2 TYR A 293 " =    2.130
peak=   -3.345 closest distance to " N   ALA A 248 " =    1.601
peak=   -3.343 closest distance to " CE1 TYR A 169 " =    2.410
peak=   -3.343 closest distance to " CB  ALA A  43 " =    2.392
peak=   -3.337 closest distance to " CB  ALA A 248 " =    2.443
peak=   -3.336 closest distance to " O   HOH Z 275 " =    1.500
peak=   -3.331 closest distance to " CA  ARG A 139 " =    1.032
peak=   -3.328 closest distance to " C   MET A 188 " =    1.506
peak=   -3.326 closest distance to " O   HOH Z 407 " =    3.088
peak=   -3.323 closest distance to " CG1 VAL A 296 " =    1.256
peak=   -3.317 closest distance to " O   HOH Z 103 " =    1.803
peak=   -3.315 closest distance to " O   MET A  40 " =    2.719
peak=   -3.310 closest distance to " O   GLY A 211 " =    1.273
peak=   -3.307 closest distance to " CG1 VAL A 197 " =    2.320
peak=   -3.303 closest distance to " CE BMET A  47 " =    1.713
peak=   -3.292 closest distance to " O   PRO A 198 " =    1.292
peak=   -3.289 closest distance to " O   HOH Z 423 " =    2.116
peak=   -3.289 closest distance to " NH2 ARG A  66 " =    2.043
peak=   -3.277 closest distance to " CB  ASP A 132 " =    2.299
peak=   -3.277 closest distance to " CA  ASP A 298 " =    1.080
peak=   -3.276 closest distance to " C   GLY A 229 " =    1.203
peak=   -3.276 closest distance to " CD  PRO A 243 " =    2.153
peak=   -3.271 closest distance to " OD1 ASN A 148 " =    1.464
peak=   -3.267 closest distance to " O   HOH Z 437 " =    1.735
peak=   -3.266 closest distance to " O   HOH Z 198 " =    1.450
peak=   -3.262 closest distance to " CZ  PHE A  59 " =    1.492
peak=   -3.261 closest distance to " O   VAL A 189 " =    2.591
peak=   -3.259 closest distance to " O   HOH Z 359 " =    3.260
peak=   -3.258 closest distance to " O   HOH Z 281 " =    2.716
peak=   -3.258 closest distance to " CB  ASN A  69 " =    1.142
peak=   -3.256 closest distance to " O   THR A  18 " =    1.625
peak=   -3.255 closest distance to " CZ  TYR A 169 " =    1.568
peak=   -3.255 closest distance to " O   HOH Z 295 " =    1.440
peak=   -3.249 closest distance to " OG  SER A 206 " =    1.667
peak=   -3.247 closest distance to " N   SER A 212 " =    1.713
peak=   -3.245 closest distance to " CD1 LEU A 297 " =    2.394
peak=   -3.244 closest distance to " O   HOH Z  98 " =    2.200
peak=   -3.241 closest distance to " C   GLN A 205 " =    2.018
peak=   -3.236 closest distance to " CA  GLY A 241 " =    2.993
peak=   -3.236 closest distance to " C   ALA A   8 " =    1.551
peak=   -3.233 closest distance to " O   HOH Z 191 " =    5.366
peak=   -3.233 closest distance to " CA  GLY A  98 " =    1.937
peak=   -3.233 closest distance to " O   HOH Z 111 " =    4.382
peak=   -3.233 closest distance to " O   HOH Z 231 " =    1.233
peak=   -3.230 closest distance to " O   HOH Z 429 " =    2.070
peak=   -3.230 closest distance to " CB  ALA A 291 " =    2.110
peak=   -3.229 closest distance to " CA  VAL A 296 " =    1.078
peak=   -3.225 closest distance to " CG1 VAL A 230 " =    1.886
peak=   -3.224 closest distance to " ND2BASN A 224 " =    1.671
peak=   -3.222 closest distance to " OG1 THR A 178 " =    1.258
peak=   -3.213 closest distance to " ND2 ASN A  60 " =    1.781
peak=   -3.210 closest distance to " CG  GLU A 277 " =    1.149
peak=   -3.209 closest distance to " CG  PRO A 163 " =    2.494
peak=   -3.207 closest distance to " OG1 THR A 246 " =    1.420
peak=   -3.206 closest distance to " CD1 PHE A  59 " =    1.874
peak=   -3.205 closest distance to " O   HOH Z 426 " =    2.297
peak=   -3.199 closest distance to " O   ALA A 161 " =    1.510
peak=   -3.198 closest distance to " NE2 GLN A  88 " =    2.135
peak=   -3.196 closest distance to " CG2 VAL A 112 " =    2.541
peak=   -3.196 closest distance to " O   SER A  22 " =    2.188
peak=   -3.193 closest distance to " O   HOH Z 222 " =    3.274
peak=   -3.193 closest distance to " N   PHE A  59 " =    2.269
peak=   -3.192 closest distance to " O   GLY A 196 " =    1.127
peak=   -3.192 closest distance to " NH2BARG A 275 " =    1.764
peak=   -3.187 closest distance to " O   VAL A 121 " =    1.359
peak=   -3.184 closest distance to " O   HOH Z 311 " =    3.729
peak=   -3.182 closest distance to " C   ASN A 187 " =    1.796
peak=   -3.179 closest distance to " O   HOH Z  63 " =    1.298
peak=   -3.169 closest distance to " O   HOH Z  90 " =    2.946
peak=   -3.169 closest distance to " NH1 ARG A  56 " =    2.524
peak=   -3.167 closest distance to " O   HOH Z 184 " =    1.744
peak=   -3.160 closest distance to " O   HOH Z 140 " =    1.585
peak=   -3.153 closest distance to " NH2 ARG A 159 " =    2.311
peak=   -3.150 closest distance to " CD1 ILE A 199 " =    2.585
peak=   -3.146 closest distance to " CA  GLY A 133 " =    2.181
peak=   -3.144 closest distance to " O   HOH Z 359 " =    1.563
peak=   -3.141 closest distance to " O   HOH Z  71 " =    1.144
peak=   -3.137 closest distance to " O   ALA A  51 " =    1.433
peak=   -3.125 closest distance to " NH1 ARG A  36 " =    2.066
peak=   -3.123 closest distance to " CG  ASN A  45 " =    1.745
peak=   -3.121 closest distance to " N   ALA A 248 " =    1.883
peak=   -3.115 closest distance to " ND2 ASN A  60 " =    1.480
peak=   -3.110 closest distance to " O   HOH Z 113 " =    2.397
peak=   -3.110 closest distance to " CG2AVAL A  72 " =    4.338
peak=   -3.103 closest distance to " O   HOH Z 250 " =    1.379
peak=   -3.101 closest distance to " O   HOH Z 292 " =    1.773
peak=   -3.095 closest distance to " O   HOH Z 177 " =    1.714
peak=   -3.092 closest distance to " OXT GLY A 302 " =    3.514
peak=   -3.089 closest distance to " O   HOH Z 134 " =    3.412
peak=   -3.085 closest distance to " O   TRP A  70 " =    1.456
peak=   -3.083 closest distance to " O   HOH Z 174 " =    2.492
peak=   -3.065 closest distance to " CD1 ILE A 239 " =    2.320
peak=   -3.065 closest distance to " O   HOH Z 371 " =    2.235
peak=   -3.050 closest distance to " CD1 TYR A 247 " =    2.536

================= 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    :  0.4327 0.4174   6.225117e+00   6.205927e+00
   1_bss:  0.4238 0.4077   6.220533e+00   6.195910e+00
   1_xyz:  0.3184 0.3446   6.016099e+00   6.067728e+00
   1_adp:  0.2555 0.2993   5.832704e+00   5.956288e+00
   1_occ:  0.2549 0.2998   5.832197e+00   5.958174e+00
   2_bss:  0.2499 0.2935   5.829614e+00   5.954731e+00
   2_xyz:  0.1652 0.2105   5.467293e+00   5.660677e+00
   2_adp:  0.1498 0.1943   5.381457e+00   5.588355e+00
   2_occ:  0.1497 0.1942   5.380842e+00   5.587802e+00
   3_bss:  0.1493 0.1932   5.381718e+00   5.587382e+00
   3_xyz:  0.1289 0.1697   5.247801e+00   5.464222e+00
   3_adp:  0.1230 0.1661   5.214811e+00   5.441526e+00
   3_occ:  0.1230 0.1660   5.214323e+00   5.440922e+00
   4_bss:  0.1230 0.1659   5.213471e+00   5.440231e+00
   4_xyz:  0.1155 0.1611   5.172579e+00   5.414428e+00
   4_adp:  0.1165 0.1592   5.168796e+00   5.400141e+00
   4_occ:  0.1164 0.1590   5.168354e+00   5.399613e+00
   5_bss:  0.1166 0.1589   5.169303e+00   5.399135e+00
   5_xyz:  0.1154 0.1581   5.162675e+00   5.396441e+00
   5_adp:  0.1145 0.1585   5.160767e+00   5.399458e+00
   5_occ:  0.1145 0.1584   5.160652e+00   5.399326e+00
   5_bss:  0.1145 0.1584   5.160661e+00   5.399330e+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:  0.358  20.001   8.025   8.221   8.182   0.000   0.000   0.000
   1_xyz:  0.358  20.001   8.025   8.221   8.182   0.000   0.000   0.000
   1_adp:  0.358  20.001   8.025   8.221   8.182   0.000   0.000   0.000
   1_occ:  0.358  20.001   8.025   8.221   8.182   0.000   0.000   0.000
   2_bss:  0.342  50.001   4.425   4.114   5.146   0.000   0.000   0.000
   2_xyz:  0.342  50.001   4.425   4.114   5.146   0.000   0.000   0.000
   2_adp:  0.342  50.001   4.425   4.114   5.146   0.000   0.000   0.000
   2_occ:  0.342  50.001   4.425   4.114   5.146   0.000   0.000   0.000
   3_bss:  0.345  50.000   3.290   3.090   4.110   0.000   0.000   0.000
   3_xyz:  0.345  50.000   3.290   3.090   4.110   0.000   0.000   0.000
   3_adp:  0.345  50.000   3.290   3.090   4.110   0.000   0.000   0.000
   3_occ:  0.345  50.000   3.290   3.090   4.110   0.000   0.000   0.000
   4_bss:  0.329  46.259   3.113   2.975   3.892   0.000   0.000   0.000
   4_xyz:  0.329  46.259   3.113   2.975   3.892   0.000   0.000   0.000
   4_adp:  0.329  46.259   3.113   2.975   3.892   0.000   0.000   0.000
   4_occ:  0.329  46.259   3.113   2.975   3.892   0.000   0.000   0.000
   5_bss:  0.330  46.259   2.969   2.876   3.765   0.000   0.000   0.000
   5_xyz:  0.330  46.259   2.969   2.876   3.765   0.000   0.000   0.000
   5_adp:  0.330  46.259   2.969   2.876   3.765   0.000   0.000   0.000
   5_occ:  0.330  46.259   2.969   2.876   3.765   0.000   0.000   0.000
   5_bss:  0.330  49.484  -0.232  -0.325   0.557   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  47.176 0.5571  0.6299    51985.130
   1_bss:  47.639 0.5489  0.7891    49786.294
   1_xyz:  36.960 0.6779  0.9500    32445.086
   1_adp:  29.954 0.7590  1.0469    23159.474
   1_occ:  30.059 0.7578  1.0446    23268.797
   2_bss:  29.792 0.7605  0.9209    22904.425
   2_xyz:  20.050 0.8611  0.9983    11046.937
   2_adp:  18.132 0.8797  1.0119     9587.029
   2_occ:  18.116 0.8799  1.0118     9569.100
   3_bss:  18.098 0.8800  0.9733     9552.980
   3_xyz:  15.435 0.9033  0.9848     7414.418
   3_adp:  14.943 0.9077  0.9854     7092.334
   3_occ:  14.927 0.9078  0.9855     7082.285
   4_bss:  14.912 0.9079  0.9792     7058.170
   4_xyz:  14.412 0.9119  0.9804     6667.559
   4_adp:  14.057 0.9150  0.9824     6498.825
   4_occ:  14.045 0.9151  0.9823     6487.037
   5_bss:  14.058 0.9150  0.9775     6501.190
   5_xyz:  13.984 0.9155  0.9770     6424.484
   5_adp:  14.056 0.9149  0.9751     6460.568
   5_occ:  14.053 0.9149  0.9749     6457.367
   5_bss:  14.053 0.9149  0.9757     6457.585
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.3637e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.3637e+01
   1_xyz:   1.514  0.011  0.100 17.989  0.006  4.121   1.1802e-01
   1_adp:   1.514  0.011  0.100 17.989  0.006  4.121   1.1802e-01
   1_occ:   1.514  0.011  0.100 17.989  0.006  4.121   1.1802e-01
   2_bss:   1.514  0.011  0.100 17.989  0.006  4.121   1.1802e-01
   2_xyz:   0.953  0.006  0.072 16.243  0.004  4.121   6.0313e-02
   2_adp:   0.953  0.006  0.072 16.243  0.004  4.121   6.0313e-02
   2_occ:   0.953  0.006  0.072 16.243  0.004  4.121   6.0313e-02
   3_bss:   0.953  0.006  0.072 16.243  0.004  4.121   6.0313e-02
   3_xyz:   0.912  0.005  0.071 15.894  0.003  4.125   5.4269e-02
   3_adp:   0.912  0.005  0.071 15.894  0.003  4.125   5.4269e-02
   3_occ:   0.912  0.005  0.071 15.894  0.003  4.125   5.4269e-02
   4_bss:   0.912  0.005  0.071 15.894  0.003  4.125   5.4269e-02
   4_xyz:   0.969  0.006  0.077 15.963  0.003  4.128   5.9232e-02
   4_adp:   0.969  0.006  0.077 15.963  0.003  4.128   5.9232e-02
   4_occ:   0.969  0.006  0.077 15.963  0.003  4.128   5.9232e-02
   5_bss:   0.969  0.006  0.077 15.963  0.003  4.128   5.9232e-02
   5_xyz:   0.927  0.006  0.074 15.828  0.003  4.130   5.5612e-02
   5_adp:   0.927  0.006  0.074 15.828  0.003  4.130   5.5612e-02
   5_occ:   0.927  0.006  0.074 15.828  0.003  4.130   5.5612e-02
   5_bss:   0.927  0.006  0.074 15.828  0.003  4.130   5.5612e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9546e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9546e+00
   1_xyz:  12.862  0.143  0.419 88.731  0.034  2.261   8.7599e-02
   1_adp:  12.862  0.143  0.419 88.731  0.034  2.261   8.7599e-02
   1_occ:  12.862  0.143  0.419 88.731  0.034  2.261   8.7599e-02
   2_bss:  12.862  0.143  0.419 88.731  0.034  2.261   8.7599e-02
   2_xyz:   6.791  0.049  0.306 86.759  0.041  2.320   5.1330e-02
   2_adp:   6.791  0.049  0.306 86.759  0.041  2.320   5.1330e-02
   2_occ:   6.791  0.049  0.306 86.759  0.041  2.320   5.1330e-02
   3_bss:   6.791  0.049  0.306 86.759  0.041  2.320   5.1330e-02
   3_xyz:   7.803  0.045  0.378 82.903  0.032  2.370   3.0469e-02
   3_adp:   7.803  0.045  0.378 82.903  0.032  2.370   3.0469e-02
   3_occ:   7.803  0.045  0.378 82.903  0.032  2.370   3.0469e-02
   4_bss:   7.803  0.045  0.378 82.903  0.032  2.370   3.0469e-02
   4_xyz:   7.630  0.052  0.475 84.392  0.035  2.361   3.5812e-02
   4_adp:   7.630  0.052  0.475 84.392  0.035  2.361   3.5812e-02
   4_occ:   7.630  0.052  0.475 84.392  0.035  2.361   3.5812e-02
   5_bss:   7.630  0.052  0.475 84.392  0.035  2.361   3.5812e-02
   5_xyz:   7.809  0.045  0.419 83.303  0.033  2.337   3.2024e-02
   5_adp:   7.809  0.045  0.419 83.303  0.033  2.337   3.2024e-02
   5_occ:   7.809  0.045  0.419 83.303  0.033  2.337   3.2024e-02
   5_bss:   7.809  0.045  0.419 83.303  0.033  2.337   3.2024e-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:  68.84   0.00  10.79  68.84   0.00   7.58  68.34   0.00  28.29
   1_occ:  68.84   0.00  10.79  68.84   0.00   7.58  68.34   0.00  28.29
   2_bss:  68.84   0.00  10.79  68.84   0.00   7.58  68.34   0.00  28.29
   2_xyz:  68.84   0.00  10.79  68.84   0.00   7.58  68.34   0.00  28.29
   2_adp:  68.08   0.00  11.16  68.08   0.00   7.44  67.85   0.81  31.40
   2_occ:  68.08   0.00  11.16  68.08   0.00   7.44  67.85   0.81  31.40
   3_bss:  68.08   0.00  11.16  68.08   0.00   7.44  67.85   0.81  31.40
   3_xyz:  68.08   0.00  11.16  68.08   0.00   7.44  67.85   0.81  31.40
   3_adp:  77.29   0.00  12.01  77.29   0.00   7.70  74.50   1.32  35.50
   3_occ:  77.29   0.00  12.01  77.29   0.00   7.70  74.50   1.32  35.50
   4_bss:  77.29   0.00  12.01  77.29   0.00   7.70  74.50   1.32  35.50
   4_xyz:  77.29   0.00  12.01  77.29   0.00   7.70  74.50   1.32  35.50
   4_adp:  77.56   0.00  11.50  77.56   0.00   7.52  73.90   1.39  33.18
   4_occ:  77.56   0.00  11.50  77.56   0.00   7.52  73.90   1.39  33.18
   5_bss:  77.56   0.00  11.50  77.56   0.00   7.52  73.90   1.39  33.18
   5_xyz:  77.56   0.00  11.50  77.56   0.00   7.52  73.90   1.39  33.18
   5_adp:  78.89   0.00  11.52  78.89   0.00   7.53  72.95   1.61  33.23
   5_occ:  78.89   0.00  11.52  78.89   0.00   7.53  72.95   1.61  33.23
   5_bss:  82.12   3.22  14.74  82.12   3.22  10.75  76.18   4.83  36.46
------------------------------------------------------------------------
 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:    1.163    0.021    0.402
   1_adp:    1.163    0.021    0.402
   1_occ:    1.163    0.021    0.402
   2_bss:    1.163    0.021    0.402
   2_xyz:    1.355    0.042    0.509
   2_adp:    1.355    0.042    0.509
   2_occ:    1.355    0.042    0.509
   3_bss:    1.355    0.042    0.509
   3_xyz:    1.459    0.021    0.533
   3_adp:    1.459    0.021    0.533
   3_occ:    1.459    0.021    0.533
   4_bss:    1.459    0.021    0.533
   4_xyz:    1.653    0.040    0.554
   4_adp:    1.653    0.040    0.554
   4_occ:    1.653    0.040    0.554
   5_bss:    1.653    0.040    0.554
   5_xyz:    1.746    0.043    0.562
   5_adp:    1.746    0.043    0.562
   5_occ:    1.746    0.043    0.562
   5_bss:    1.746    0.043    0.562
------------------------------------------------------------------------

CPU time actual refinement: 336.92


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_894/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_894/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_894/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_894/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_894/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 336.78 
  Macro-tasks:
    bulk solvent and scale       = 44.22  
    individual site refinement   = 141.56 
    weights calculation          = 32.08  
    collect and process          = 6.59   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 224.56 
  Micro-tasks:
    mask                            = 1.61   
    f_calc                          = 103.61 
    alpha_beta                      = 8.31   
    target                          = 1.21   
    gradients_wrt_atomic_parameters = 110.91 
    fmodel                         = 7.65   
    r_factors                      = 0.28   
    phase_errors                   = 11.73  
    foms                           = 0.24   
    TOTAL for micro-tasks          = 245.55 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.632 micro seconds
Total CPU time: 5.84 minutes
from_scatterers_fft:    667 calls, 103.12 s
gradients_fft:          612 calls,  98.45 s

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

# Date 2008-01-16 Time 02:41:11 PST -0800 (1200480071.80 s)
Start R-work = 0.4327, R-free = 0.4174 (no bulk solvent and anisotropic scale)
Final R-work = 0.1313, R-free = 0.1749 (no bulk solvent and anisotropic scale)

Start R-work = 0.4238, R-free = 0.4077
Final R-work = 0.1145, R-free = 0.1584