# Date 2008-01-16 Time 01:09:21 PST -0800 (1200474561.25 s)
#phil __OFF__

Command line arguments: "../296.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 20905
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 296

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.1963, 46.6953, 88.5498, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 46.6953, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9364 1.97086
Completeness in resolution range: 0.93952
Completeness with d_max=infinity: 0.936645

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9364
                             d_min =   1.9709

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 46.6953, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9364 1.97086
Completeness in resolution range: 0.93952
Completeness with d_max=infinity: 0.936645

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9368 -  4.2172 [2191/2218]  1969   222  10.1%
  bin  2:  4.2172 -  3.3599 [2104/2120]  1892   212  10.1%
  bin  3:  3.3599 -  2.9388 [2084/2103]  1882   202   9.7%
  bin  4:  2.9388 -  2.6718 [2056/2086]  1843   213  10.4%
  bin  5:  2.6718 -  2.4812 [2025/2044]  1826   199   9.8%
  bin  6:  2.4812 -  2.3355 [2037/2062]  1830   207  10.2%
  bin  7:  2.3355 -  2.2189 [2017/2051]  1826   191   9.5%
  bin  8:  2.2189 -  2.1226 [2042/2072]  1830   212  10.4%
  bin  9:  2.1226 -  2.0411 [1979/2030]  1785   194   9.8%
  bin 10:  2.0411 -  1.9709 [1054/2064]   947   107  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_296/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.16 -     1.91: 11
        1.91 -     2.65: 86
        2.65 -     3.40: 4352
        3.40 -     4.15: 9372
        4.15 -     4.90: 14483
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.157 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.430 3.040 -x+1,y+1/2,-z+1/2
  " NH1 ARG A  24 " - " O   GLY A  91 "  1.538 3.120 -x+1,y+1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.572 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.630 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28299 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_296/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_296/model_refine_001.geo

CPU time processing inputs: 9.06


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.19625 46.69535 88.54975 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: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4844   r_free= 0.4697   ksol= 0.00   Bsol= 0.00   scale= 0.789    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.285899                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9368 -  4.7037 0.99   1422  157 0.3942 0.3701      6.6052      6.5559|
|  2:  4.7037 -  3.7530 0.99   1367  153 0.3928 0.4417      6.7585      6.8815|
|  3:  3.7530 -  3.2843 0.99   1340  149 0.4550 0.4045      6.6829      6.6515|
|  4:  3.2843 -  2.9866 0.99   1339  144 0.4836 0.4770      6.5326      6.4931|
|  5:  2.9866 -  2.7740 0.99   1315  150 0.5094 0.4819      6.3602      6.3935|
|  6:  2.7740 -  2.6114 0.99   1327  147 0.5118 0.5562      6.2847      6.2361|
|  7:  2.6114 -  2.4812 0.99   1302  148 0.5111 0.4735      6.2397      6.1348|
|  8:  2.4812 -  2.3737 0.98   1314  145 0.5353 0.5118      6.1861       6.175|
|  9:  2.3737 -  2.2826 0.98   1299  144 0.5331 0.5091      6.1189      6.1785|
| 10:  2.2826 -  2.2041 0.99   1316  138 0.5399 0.4929      6.1083      6.0758|
| 11:  2.2041 -  2.1354 0.99   1282  154 0.5271 0.5076      6.0256      6.0455|
| 12:  2.1354 -  2.0745 0.97   1304  134 0.5271 0.4887      5.9642      5.9923|
| 13:  2.0745 -  2.0200 0.92   1199  135 0.5474 0.4892      5.8981      5.8334|
| 14:  2.0200 -  1.9709 0.39    504   61 0.5051 0.4755      5.8923      5.7337|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9368 -  4.7037  1422   157  0.70  33.99   0.79     0.73      70402.77|
|  2:  4.7037 -  3.7530  1367   153  0.70  35.59   0.88     0.76     108274.74|
|  3:  3.7530 -  3.2843  1340   149  0.59  44.27   0.83     0.72     115304.75|
|  4:  3.2843 -  2.9866  1339   144  0.48  53.09   0.78     0.58     106273.35|
|  5:  2.9866 -  2.7740  1315   150  0.37  62.17   0.73     0.44      88251.66|
|  6:  2.7740 -  2.6114  1327   147  0.30  67.83   0.71     0.35      81772.38|
|  7:  2.6114 -  2.4812  1302   148  0.31  66.50   0.74     0.36      70497.95|
|  8:  2.4812 -  2.3737  1314   145  0.35  63.88   0.72     0.41      59919.75|
|  9:  2.3737 -  2.2826  1299   144  0.39  60.99   0.71     0.47      52848.62|
| 10:  2.2826 -  2.2041  1316   138  0.38  61.20   0.73     0.45      46201.65|
| 11:  2.2041 -  2.1354  1282   154  0.33  65.19   0.75     0.43      48192.39|
| 12:  2.1354 -  2.0745  1304   134  0.33  65.33   0.75     0.42      42676.58|
| 13:  2.0745 -  2.0200  1199   135  0.34  65.04   0.72     0.44      37179.11|
| 14:  2.0200 -  1.9709   504    61  0.44  56.98   0.76     0.46      26129.45|
|alpha:            min =        0.35 max =            0.76 mean =         0.51|
|beta:             min =    26129.45 max =       115304.75 mean =     70598.42|
|figures of merit: min =        0.00 max =            1.00 mean =         0.43|
|phase err.(work): min =        0.00 max =           89.98 mean =        57.00|
|phase err.(test): min =        0.00 max =           89.93 mean =        57.33|
|-----------------------------------------------------------------------------|

============================== 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 = 13.718958             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.449   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.187810              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.399   (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 |  1.195 -  1.565:        6 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.565 -  1.936:       30 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.936 -  2.306:      176 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.306 -  2.677:      693 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.047:     1530 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.047 -  3.418:     2600 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.788:     3924 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.788 -  4.159:     5115 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.529:     6519 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.529 -  4.900:     7752 |
|-----------------------------------------------------------------------------|
|-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 |       53.717 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.090    4.900  1.195 |       2.180 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.828)------------------------------------------|
|    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 = 11.828)------------------------------------------|
|    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: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4906   r_free= 0.4776   ksol= 0.00   Bsol= 0.00   scale= 0.759    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.287634                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4751   r_free= 0.4621   ksol= 0.35   Bsol= 20.00   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.15,7.46,12.04,0.00,0.00,0.00); trace/3= 8.88                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.277964                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.937333             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.480   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.147656              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.679   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4751      final r-factor (work) = 0.3990          |
| start r-factor (free) = 0.4621      final r-factor (free) = 0.4151          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 91.2161 = 11.94 * 0.50 * 6.2827 + 1.00 * 53.7169                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 37.1656 = 11.94 * 0.50 * 6.2037 + 1.00 * 0.1375                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3990      final r-factor (work) = 0.3542          |
| start r-factor (free) = 0.4151      final r-factor (free) = 0.4020          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.1342 = 1.15 * 1.00 * 6.2037 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.0348 = 1.15 * 1.00 * 6.1153 + 1.00 * 0.0166                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.828)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    68.29   13.89    None  None   None       |
|    all(noH): 2823   0      0.00    68.29   13.89    None  None   None       |
|    Sol.    : 438    0      0.00    68.29   26.64    None  None   None       |
|    Mac.    : 2385   0      0.00    64.87   11.55    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.829:  972   |   5:    34.147 -  40.976:   78        |
|      1:     6.829 -  13.659:  700   |   6:    40.976 -  47.806:   59        |
|      2:    13.659 -  20.488:  485   |   7:    47.806 -  54.635:   38        |
|      3:    20.488 -  27.318:  294   |   8:    54.635 -  61.465:   18        |
|      4:    27.318 -  34.147:  173   |   9:    61.465 -  68.294:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3542 r_free = 0.4020             target_work(ml) = 6.097         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3537 r_free = 0.4029             target_work(ml) = 6.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3537   r_free= 0.4029   ksol= 0.35   Bsol= 20.00   scale= 1.116   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.15,7.46,12.04,0.00,0.00,0.00); trace/3= 8.88                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.095681                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3506   r_free= 0.3979   ksol= 0.34   Bsol= 41.41   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.43,3.72,8.25,0.00,0.00,0.00); trace/3= 5.14                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.096687                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.077101              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.231   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.514870              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.238  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3506      final r-factor (work) = 0.2631          |
| start r-factor (free) = 0.3979      final r-factor (free) = 0.3147          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.7624 = 7.08 * 0.50 * 6.1112 + 1.00 * 0.1375                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.2345 = 7.08 * 0.50 * 5.9740 + 1.00 * 0.0953                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2631      final r-factor (work) = 0.2379          |
| start r-factor (free) = 0.3147      final r-factor (free) = 0.2940          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0924 = 0.51 * 1.00 * 5.9740 + 1.00 * 0.0166                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0040 = 0.51 * 1.00 * 5.8108 + 1.00 * 0.0122                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.828)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.32   13.84    None  None   None       |
|    all(noH): 2823   0      0.00    76.32   13.84    None  None   None       |
|    Sol.    : 438    0      0.00    76.32   33.08    None  None   None       |
|    Mac.    : 2385   0      0.00    65.71   10.31    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 -   7.632: 1149   |   5:    38.162 -  45.794:   95        |
|      1:     7.632 -  15.265:  807   |   6:    45.794 -  53.427:   55        |
|      2:    15.265 -  22.897:  354   |   7:    53.427 -  61.059:   26        |
|      3:    22.897 -  30.530:  178   |   8:    61.059 -  68.692:   14        |
|      4:    30.530 -  38.162:  141   |   9:    68.692 -  76.324:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2379 r_free = 0.2940             target_work(ml) = 5.781         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2376 r_free = 0.2938             target_work(ml) = 5.781         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2376   r_free= 0.2938   ksol= 0.34   Bsol= 41.41   scale= 1.069   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.43,3.72,8.25,0.00,0.00,0.00); trace/3= 5.14                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.781247                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2353   r_free= 0.2936   ksol= 0.32   Bsol= 47.91   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.44,2.04,4.99,0.00,0.00,0.00); trace/3= 2.82                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.781227                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.267675              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.666   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.281007              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 121.811  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2353      final r-factor (work) = 0.1761          |
| start r-factor (free) = 0.2936      final r-factor (free) = 0.2332          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.5132 = 4.27 * 0.50 * 5.8195 + 1.00 * 0.0953                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.1581 = 4.27 * 0.50 * 5.6648 + 1.00 * 0.0704                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1761      final r-factor (work) = 0.1635          |
| start r-factor (free) = 0.2332      final r-factor (free) = 0.2182          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6042 = 0.28 * 1.00 * 5.6648 + 1.00 * 0.0124                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5631 = 0.28 * 1.00 * 5.5017 + 1.00 * 0.0171                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 36     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.828)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    117.14  13.52    None  None   None       |
|    all(noH): 2823   0      0.00    117.14  13.52    None  None   None       |
|    Sol.    : 438    0      1.86    74.90   35.20    None  None   None       |
|    Mac.    : 2385   0      0.00    117.14  9.54     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.714: 1812   |   5:    58.570 -  70.284:   22        |
|      1:    11.714 -  23.428:  542   |   6:    70.284 -  81.998:    3        |
|      2:    23.428 -  35.142:  187   |   7:    81.998 -  93.711:    0        |
|      3:    35.142 -  46.856:  184   |   8:    93.711 - 105.425:    0        |
|      4:    46.856 -  58.570:   72   |   9:   105.425 - 117.139:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1635 r_free = 0.2182             target_work(ml) = 5.467         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1631 r_free = 0.2179             target_work(ml) = 5.466         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1631   r_free= 0.2179   ksol= 0.32   Bsol= 47.91   scale= 1.025   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.44,2.04,4.99,0.00,0.00,0.00); trace/3= 2.82                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.466284                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1628   r_free= 0.2172   ksol= 0.33   Bsol= 54.78   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.64,1.33,3.73,0.00,0.00,0.00); trace/3= 1.90                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.467282                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.089844              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.947  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.798132              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 106.052  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1628      final r-factor (work) = 0.1399          |
| start r-factor (free) = 0.2172      final r-factor (free) = 0.1863          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8244 = 2.09 * 0.50 * 5.5065 + 1.00 * 0.0705                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7065 = 2.09 * 0.50 * 5.4048 + 1.00 * 0.0589                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1399      final r-factor (work) = 0.1325          |
| start r-factor (free) = 0.1863      final r-factor (free) = 0.1822          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3335 = 0.80 * 1.00 * 5.4048 + 1.00 * 0.0197                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2464 = 0.80 * 1.00 * 5.3035 + 1.00 * 0.0135                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.828)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.13   14.32    None  None   None       |
|    all(noH): 2823   0      0.00    98.13   14.32    None  None   None       |
|    Sol.    : 438    0      1.97    98.13   40.24    None  None   None       |
|    Mac.    : 2385   0      0.00    88.68   9.56     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.813: 1637   |   5:    49.064 -  58.877:   97        |
|      1:     9.813 -  19.626:  628   |   6:    58.877 -  68.690:   58        |
|      2:    19.626 -  29.439:  163   |   7:    68.690 -  78.503:   21        |
|      3:    29.439 -  39.251:  119   |   8:    78.503 -  88.315:    5        |
|      4:    39.251 -  49.064:   92   |   9:    88.315 -  98.128:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1325 r_free = 0.1822             target_work(ml) = 5.294         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1324 r_free = 0.1821             target_work(ml) = 5.294         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1324   r_free= 0.1821   ksol= 0.33   Bsol= 54.78   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.64,1.33,3.73,0.00,0.00,0.00); trace/3= 1.90                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.294243                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1325   r_free= 0.1826   ksol= 0.33   Bsol= 60.93   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.62,1.32,3.40,0.00,0.00,0.00); trace/3= 1.78                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.294067                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.117674              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 114.989  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.429534              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.291  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1325      final r-factor (work) = 0.1225          |
| start r-factor (free) = 0.1826      final r-factor (free) = 0.1698          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6740 = 2.12 * 0.50 * 5.3031 + 1.00 * 0.0589                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6336 = 2.12 * 0.50 * 5.2608 + 1.00 * 0.0633                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1225      final r-factor (work) = 0.1209          |
| start r-factor (free) = 0.1698      final r-factor (free) = 0.1677          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2731 = 0.43 * 1.00 * 5.2608 + 1.00 * 0.0134                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2560 = 0.43 * 1.00 * 5.2237 + 1.00 * 0.0122                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.828)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.47   13.93    None  None   None       |
|    all(noH): 2823   0      0.00    96.47   13.93    None  None   None       |
|    Sol.    : 438    0      2.03    96.47   38.85    None  None   None       |
|    Mac.    : 2385   0      0.00    90.95   9.36     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.647: 1650   |   5:    48.234 -  57.881:   90        |
|      1:     9.647 -  19.294:  623   |   6:    57.881 -  67.528:   54        |
|      2:    19.294 -  28.941:  161   |   7:    67.528 -  77.175:   21        |
|      3:    28.941 -  38.587:  120   |   8:    77.175 -  86.821:    6        |
|      4:    38.587 -  48.234:   94   |   9:    86.821 -  96.468:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1209 r_free = 0.1677             target_work(ml) = 5.217         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1208 r_free = 0.1676             target_work(ml) = 5.217         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1208   r_free= 0.1676   ksol= 0.33   Bsol= 60.93   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.62,1.32,3.40,0.00,0.00,0.00); trace/3= 1.78                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.216898                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9368 -  4.7037 0.99   1422  157 0.1018 0.1364      5.4319      5.5965|
|  2:  4.7037 -  3.7530 0.99   1367  153 0.0898 0.1193      5.4937      5.7056|
|  3:  3.7530 -  3.2843 0.99   1340  149 0.1159 0.1621      5.5555      5.8893|
|  4:  3.2843 -  2.9866 0.99   1339  144 0.1330 0.1773       5.511      5.6873|
|  5:  2.9866 -  2.7740 0.99   1315  150 0.1444 0.1608      5.4133      5.5514|
|  6:  2.7740 -  2.6114 0.99   1327  147 0.1335 0.2258      5.2704      5.5976|
|  7:  2.6114 -  2.4812 0.99   1302  148 0.1382 0.1754      5.2493      5.3808|
|  8:  2.4812 -  2.3737 0.98   1314  145 0.1253 0.1770      5.1403      5.3652|
|  9:  2.3737 -  2.2826 0.98   1299  144 0.1304 0.1893      5.0931      5.4004|
| 10:  2.2826 -  2.2041 0.99   1316  138 0.1232 0.1666      5.0186      5.2016|
| 11:  2.2041 -  2.1354 0.99   1282  154 0.1248 0.2104      4.9978      5.4033|
| 12:  2.1354 -  2.0745 0.97   1304  134 0.1278 0.1642      4.9727      5.1845|
| 13:  2.0745 -  2.0200 0.92   1199  135 0.1131 0.1808       4.806      5.0374|
| 14:  2.0200 -  1.9709 0.39    504   61 0.0995 0.1642      4.6444      4.8917|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9368 -  4.7037  1422   157  0.93  10.12   0.97     0.95       8410.30|
|  2:  4.7037 -  3.7530  1367   153  0.95   8.93   1.01     1.00      10345.37|
|  3:  3.7530 -  3.2843  1340   149  0.92  12.80   1.03     1.02      12101.88|
|  4:  3.2843 -  2.9866  1339   144  0.91  14.53   1.01     1.01      11358.36|
|  5:  2.9866 -  2.7740  1315   150  0.89  17.63   1.00     0.97      10087.49|
|  6:  2.7740 -  2.6114  1327   147  0.89  17.74   0.97     0.93       7932.66|
|  7:  2.6114 -  2.4812  1302   148  0.89  17.18   0.99     0.95       7248.57|
|  8:  2.4812 -  2.3737  1314   145  0.90  16.56   1.00     0.97       6162.81|
|  9:  2.3737 -  2.2826  1299   144  0.90  16.84   1.00     0.96       5548.54|
| 10:  2.2826 -  2.2041  1316   138  0.89  17.15   1.00     0.96       4982.44|
| 11:  2.2041 -  2.1354  1282   154  0.88  18.03   0.99     0.95       5119.57|
| 12:  2.1354 -  2.0745  1304   134  0.89  17.62   1.00     0.99       4778.28|
| 13:  2.0745 -  2.0200  1199   135  0.90  16.84   0.99     0.96       3555.76|
| 14:  2.0200 -  1.9709   504    61  0.93  13.02   0.98     0.95       2356.47|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2356.47 max =        12101.88 mean =      7422.79|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.92 mean =        15.39|
|phase err.(test): min =        0.00 max =           89.06 mean =        14.88|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1208   r_free= 0.1676   ksol= 0.33   Bsol= 62.78   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.10,-0.46,1.55,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.216985                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1208   r_free= 0.1676   ksol= 0.33   Bsol= 62.78   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.10,-0.46,1.55,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.216985                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9368 -  4.7037 0.99   1422  157 0.1018 0.1365      5.4322      5.5971|
|  2:  4.7037 -  3.7530 0.99   1367  153 0.0898 0.1193      5.4941      5.7058|
|  3:  3.7530 -  3.2843 0.99   1340  149 0.1159 0.1622      5.5558        5.89|
|  4:  3.2843 -  2.9866 0.99   1339  144 0.1330 0.1773       5.511      5.6876|
|  5:  2.9866 -  2.7740 0.99   1315  150 0.1443 0.1607      5.4134      5.5513|
|  6:  2.7740 -  2.6114 0.99   1327  147 0.1335 0.2258      5.2704      5.5979|
|  7:  2.6114 -  2.4812 0.99   1302  148 0.1382 0.1755      5.2494      5.3809|
|  8:  2.4812 -  2.3737 0.98   1314  145 0.1253 0.1771      5.1405      5.3658|
|  9:  2.3737 -  2.2826 0.98   1299  144 0.1304 0.1894      5.0933      5.4007|
| 10:  2.2826 -  2.2041 0.99   1316  138 0.1232 0.1666      5.0187      5.2014|
| 11:  2.2041 -  2.1354 0.99   1282  154 0.1248 0.2102      4.9974      5.4026|
| 12:  2.1354 -  2.0745 0.97   1304  134 0.1278 0.1642      4.9727      5.1845|
| 13:  2.0745 -  2.0200 0.92   1199  135 0.1131 0.1810      4.8057      5.0378|
| 14:  2.0200 -  1.9709 0.39    504   61 0.0996 0.1639      4.6444      4.8906|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9368 -  4.7037  1422   157  0.93  10.13   0.97     0.95       8417.24|
|  2:  4.7037 -  3.7530  1367   153  0.95   8.93   1.01     1.00      10354.23|
|  3:  3.7530 -  3.2843  1340   149  0.92  12.81   1.03     1.03      12116.95|
|  4:  3.2843 -  2.9866  1339   144  0.91  14.54   1.02     1.01      11364.07|
|  5:  2.9866 -  2.7740  1315   150  0.89  17.64   1.00     0.98      10094.01|
|  6:  2.7740 -  2.6114  1327   147  0.89  17.74   0.97     0.94       7932.10|
|  7:  2.6114 -  2.4812  1302   148  0.89  17.18   0.99     0.95       7250.97|
|  8:  2.4812 -  2.3737  1314   145  0.90  16.58   1.00     0.98       6169.26|
|  9:  2.3737 -  2.2826  1299   144  0.90  16.85   1.00     0.96       5552.80|
| 10:  2.2826 -  2.2041  1316   138  0.89  17.15   1.01     0.97       4982.46|
| 11:  2.2041 -  2.1354  1282   154  0.88  18.02   0.99     0.96       5113.06|
| 12:  2.1354 -  2.0745  1304   134  0.89  17.61   1.00     0.99       4777.84|
| 13:  2.0745 -  2.0200  1199   135  0.90  16.83   0.99     0.97       3552.08|
| 14:  2.0200 -  1.9709   504    61  0.93  13.01   0.98     0.95       2351.87|
|alpha:            min =        0.94 max =            1.03 mean =         0.97|
|beta:             min =     2351.87 max =        12116.95 mean =      7426.15|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.91 mean =        15.39|
|phase err.(test): min =        0.00 max =           89.06 mean =        14.88|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.828)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.85    98.32   15.79    None  None   None       |
|    all(noH): 2823   0      1.85    98.32   15.79    None  None   None       |
|    Sol.    : 438    0      3.88    98.32   40.70    None  None   None       |
|    Mac.    : 2385   0      1.85    92.80   11.21    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.855 -  11.501: 1650   |   5:    50.089 -  59.735:   90        |
|      1:    11.501 -  21.148:  623   |   6:    59.735 -  69.382:   54        |
|      2:    21.148 -  30.795:  161   |   7:    69.382 -  79.029:   21        |
|      3:    30.795 -  40.442:  120   |   8:    79.029 -  88.676:    6        |
|      4:    40.442 -  50.089:   94   |   9:    88.676 -  98.323:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 306         
Filter by distance & map next to the model:
   mapped sites are within: 0.582 - 4.371
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 300 from: 306
   mapped sites are within: 0.709 - 4.371

peak=   10.552 closest distance to " CB  VAL A 230 " =    1.462
peak=    8.664 closest distance to " CB  VAL A 296 " =    1.576
peak=    6.564 closest distance to " CD2 LEU A   5 " =    1.261
peak=    5.669 closest distance to " CG  PRO A  54 " =    1.392
peak=    5.572 closest distance to " NE2 GLN A  11 " =    1.146
peak=    5.530 closest distance to " NH1 ARG A 138 " =    0.992
peak=    5.310 closest distance to " CG  LEU A   5 " =    1.300
peak=    5.273 closest distance to " CB  GLN A 223 " =    1.503
peak=    5.220 closest distance to " NH2 ARG A  56 " =    2.014
peak=    5.181 closest distance to " CG  ARG A 138 " =    1.003
peak=    5.072 closest distance to " O   HOH Z 232 " =    2.377
peak=    4.918 closest distance to " O   HOH Z 142 " =    1.845
peak=    4.911 closest distance to " CG  LEU A 228 " =    1.224
peak=    4.803 closest distance to " CB  ASN A 148 " =    1.423
peak=    4.757 closest distance to " O   HOH Z 248 " =    1.345
peak=    4.743 closest distance to " CB  ARG A 275 " =    0.958
peak=    4.708 closest distance to " CG  PRO A 280 " =    0.957
peak=    4.665 closest distance to " O   HOH Z   9 " =    1.661
peak=    4.569 closest distance to " O   HOH Z 369 " =    2.223
peak=    4.516 closest distance to " O   HOH Z 425 " =    1.518
peak=    4.513 closest distance to " CG  PRO A 243 " =    1.188
peak=    4.456 closest distance to " NH2AARG A 190 " =    2.078
peak=    4.446 closest distance to " CB  ASN A 142 " =    1.085
peak=    4.438 closest distance to " O   HOH Z  78 " =    1.610
peak=    4.423 closest distance to " O   HOH Z 246 " =    1.100
peak=    4.415 closest distance to " CZ  PHE A 218 " =    1.132
peak=    4.396 closest distance to " O   HOH Z 251 " =    1.751
peak=    4.311 closest distance to " O   HOH Z  91 " =    2.401
peak=    4.311 closest distance to " O   HOH Z   3 " =    2.162
peak=    4.242 closest distance to " O   HOH Z 261 " =    2.188
peak=    4.220 closest distance to " CD2 TRP A 179 " =    1.347
peak=    4.218 closest distance to " O   HOH Z  69 " =    0.859
peak=    4.206 closest distance to " O   HOH Z  76 " =    1.257
peak=    4.193 closest distance to " NH2AARG A 145 " =    1.072
peak=    4.172 closest distance to " CB  GLN A 183 " =    1.200
peak=    4.169 closest distance to " O   PRO A 198 " =    1.582
peak=    4.153 closest distance to " O   HOH Z 265 " =    2.066
peak=    4.145 closest distance to " O   HOH Z 188 " =    1.411
peak=    4.122 closest distance to " O   HOH Z 427 " =    2.932
peak=    4.112 closest distance to " CG AARG A 275 " =    1.284
peak=    4.109 closest distance to " O   HOH Z 406 " =    1.564
peak=    4.100 closest distance to " CG  PRO A 198 " =    1.277
peak=    4.099 closest distance to " CB  ASN A  39 " =    0.909
peak=    4.096 closest distance to " CE  LYS A  76 " =    0.935
peak=    4.089 closest distance to " CZ3 TRP A 266 " =    1.074
peak=    4.089 closest distance to " CG2 ILE A 234 " =    1.129
peak=    4.085 closest distance to " CB  TYR A 169 " =    0.905
peak=    4.084 closest distance to " O   HOH Z 188 " =    2.563
peak=    4.065 closest distance to " CG  GLN A  58 " =    1.142
peak=    4.061 closest distance to " O  BHOH Z 338 " =    2.362
peak=    4.059 closest distance to " O   HOH Z 112 " =    1.019
peak=    4.052 closest distance to " O   HOH Z 303 " =    2.159
peak=    4.033 closest distance to " O   HOH Z 193 " =    1.560
peak=    4.033 closest distance to " O   HOH Z 143 " =    1.402
peak=    4.025 closest distance to " O   HOH Z 126 " =    1.597
peak=    4.015 closest distance to " CB  PRO A  54 " =    0.951
peak=    4.007 closest distance to " O   HOH Z 402 " =    1.372
peak=    4.004 closest distance to " O   HOH Z 238 " =    1.282
peak=    3.982 closest distance to " O   HOH Z 346 " =    1.514
peak=    3.976 closest distance to " N   ASN A  39 " =    1.305
peak=    3.968 closest distance to " CB  VAL A 265 " =    1.338
peak=    3.950 closest distance to " O   HOH Z 403 " =    1.542
peak=    3.947 closest distance to " ND2 ASN A 249 " =    0.922
peak=    3.942 closest distance to " O   HOH Z 272 " =    1.820
peak=    3.936 closest distance to " CD1AILE A 234 " =    0.887
peak=    3.933 closest distance to " O   HOH Z 207 " =    1.258
peak=    3.922 closest distance to " O   HOH Z 287 " =    2.062
peak=    3.918 closest distance to " O   HOH Z 203 " =    1.241
peak=    3.914 closest distance to " CG  PRO A 213 " =    1.237
peak=    3.886 closest distance to " CG  LEU A 167 " =    1.232
peak=    3.885 closest distance to " CB  ARG A  79 " =    1.493
peak=    3.883 closest distance to " CB  GLU A 152 " =    1.155
peak=    3.878 closest distance to " CD  ARG A 269 " =    1.026
peak=    3.877 closest distance to " O   HOH Z 353 " =    2.608
peak=    3.872 closest distance to " CD2 LEU A 228 " =    1.274
peak=    3.869 closest distance to " CB  TRP A 266 " =    1.072
peak=    3.865 closest distance to " O   HOH Z 359 " =    1.802
peak=    3.862 closest distance to " O   HOH Z 126 " =    1.957
peak=    3.859 closest distance to " CB  VAL A 230 " =    1.214
peak=    3.852 closest distance to " O   HOH Z 214 " =    3.172
peak=    3.846 closest distance to " O   HOH Z 365 " =    2.718
peak=    3.843 closest distance to " CD  LYS A  76 " =    1.740
peak=    3.841 closest distance to " CB  ASP A 124 " =    0.864
peak=    3.839 closest distance to " CG2 VAL A 257 " =    0.756
peak=    3.831 closest distance to " CB  GLU A 277 " =    3.660
peak=    3.830 closest distance to " ND2 ASN A 187 " =    1.624
peak=    3.825 closest distance to " O   HOH Z  43 " =    2.040
peak=    3.824 closest distance to " O   HOH Z 411 " =    4.019
peak=    3.817 closest distance to " O   HOH Z 222 " =    2.375
peak=    3.803 closest distance to " O   HOH Z 130 " =    2.557
peak=    3.797 closest distance to " OG ASER A 258 " =    3.027
peak=    3.788 closest distance to " O   HOH Z  59 " =    1.950
peak=    3.774 closest distance to " O   HOH Z 298 " =    1.740
peak=    3.755 closest distance to " CB  THR A  31 " =    1.508
peak=    3.755 closest distance to " CD  ARG A 159 " =    0.709
peak=    3.749 closest distance to " CB  PRO A  90 " =    1.082
peak=    3.747 closest distance to " CB  ARG A 190 " =    1.686
peak=    3.743 closest distance to " CB  VAL A 202 " =    1.546
peak=    3.740 closest distance to " CB  SER A  26 " =    1.836
peak=    3.740 closest distance to " CB  SER A  63 " =    1.157
peak=    3.739 closest distance to " O   HOH Z 124 " =    1.270
peak=    3.727 closest distance to " NH1AARG A 145 " =    1.203
peak=    3.718 closest distance to " CB  THR A  52 " =    0.906
peak=    3.714 closest distance to " CB  ARG A 156 " =    1.201
peak=    3.711 closest distance to " CA  TYR A  30 " =    1.036
peak=    3.699 closest distance to " N   PHE A 130 " =    1.280
peak=    3.688 closest distance to " CZ  PHE A  38 " =    1.127
peak=    3.682 closest distance to " O   HOH Z  85 " =    1.287
peak=    3.676 closest distance to " O   HOH Z  92 " =    2.068
peak=    3.675 closest distance to " O   THR A 182 " =    1.432
peak=    3.672 closest distance to " O   HOH Z 422 " =    2.610
peak=    3.669 closest distance to " O   HOH Z 193 " =    1.655
peak=    3.668 closest distance to " CA  ARG A 195 " =    1.173
peak=    3.667 closest distance to " CB  PRO A 198 " =    1.137
peak=    3.667 closest distance to " CB  ASN A 215 " =    1.163
peak=    3.666 closest distance to " CA  ASP A 162 " =    0.952
peak=    3.663 closest distance to " CD  LYS A 166 " =    1.302
peak=    3.659 closest distance to " CB  ASN A 110 " =    1.155
peak=    3.654 closest distance to " O   HOH Z 258 " =    1.990
peak=    3.653 closest distance to " O   HOH Z 290 " =    1.097
peak=    3.640 closest distance to " CB  SER A 273 " =    0.978
peak=    3.637 closest distance to " CA  ALA A  51 " =    0.972
peak=    3.634 closest distance to " CB  ARG A  79 " =    0.948
peak=    3.634 closest distance to " O   HOH Z  88 " =    3.562
peak=    3.629 closest distance to " CA  LEU A 282 " =    1.203
peak=    3.611 closest distance to " CA  ILE A 234 " =    1.074
peak=    3.604 closest distance to " O   HOH Z  40 " =    1.711
peak=    3.602 closest distance to " CB AVAL A  41 " =    1.298
peak=    3.593 closest distance to " CG  MET A 185 " =    1.196
peak=    3.591 closest distance to " CG2 ILE A  20 " =    1.546
peak=    3.590 closest distance to " O   HOH Z 258 " =    1.294
peak=    3.589 closest distance to " CA  PHE A 283 " =    1.143
peak=    3.583 closest distance to " O   HOH Z 368 " =    3.328
peak=    3.579 closest distance to " N   ASP A 162 " =    1.253
peak=    3.576 closest distance to " O   HOH Z 193 " =    1.432
peak=    3.574 closest distance to " O   HOH Z 329 " =    4.170
peak=    3.571 closest distance to " CE3 TRP A 150 " =    1.131
peak=    3.567 closest distance to " N   ALA A 256 " =    0.942
peak=    3.566 closest distance to " O   HOH Z 299 " =    4.371
peak=    3.559 closest distance to " NH2AARG A 275 " =    3.422
peak=    3.542 closest distance to " CD1 ILE A 199 " =    1.202
peak=    3.535 closest distance to " CD1 ILE A  33 " =    1.769
peak=    3.525 closest distance to " O   HOH Z 263 " =    1.731
peak=    3.522 closest distance to " CB  PHE A 204 " =    0.847
peak=    3.515 closest distance to " O   HOH Z 368 " =    2.339
peak=    3.513 closest distance to " O   HOH Z  61 " =    1.791
peak=    3.510 closest distance to " CA  ALA A 158 " =    1.387
peak=    3.509 closest distance to " O   HOH Z 419 " =    2.010
peak=    3.505 closest distance to " CB  SER A   3 " =    1.300
peak=    3.505 closest distance to " O   ASN A  74 " =    1.339
peak=    3.504 closest distance to " CB  GLN A  89 " =    1.261
peak=    3.503 closest distance to " O   HOH Z  88 " =    2.582
peak=    3.503 closest distance to " O   HOH Z 423 " =    1.798
peak=    3.502 closest distance to " O   HOH Z 417 " =    1.108
peak=    3.502 closest distance to " O   HOH Z 234 " =    3.572
peak=    3.502 closest distance to " OD1 ASN A  69 " =    2.505
peak=    3.496 closest distance to " CG2 ILE A 120 " =    1.379
peak=    3.493 closest distance to " O   HOH Z  63 " =    1.775
peak=    3.486 closest distance to " O   HOH Z   4 " =    1.433
peak=    3.484 closest distance to " CG  GLU A  37 " =    0.881
peak=    3.483 closest distance to " CA  ARG A  36 " =    1.002
peak=    3.483 closest distance to " O   HOH Z 371 " =    2.578
peak=    3.482 closest distance to " O   ASP A 124 " =    1.156
peak=    3.482 closest distance to " O   HOH Z 405 " =    1.373
peak=    3.480 closest distance to " CB  GLU A  46 " =    0.972
peak=    3.479 closest distance to " CB  ARG A 102 " =    0.905
peak=    3.454 closest distance to " O   HOH Z  55 " =    2.429
peak=    3.451 closest distance to " CA  VAL A 125 " =    1.178
peak=    3.450 closest distance to " CA  ASN A 217 " =    1.163
peak=    3.450 closest distance to " CB  SER A 216 " =    0.894
peak=    3.442 closest distance to " CB  TRP A 179 " =    1.423
peak=    3.441 closest distance to " O   HOH Z 130 " =    2.162
peak=    3.438 closest distance to " NZ  LYS A  48 " =    1.120
peak=    3.432 closest distance to " CB  ASP A 191 " =    1.192
peak=    3.431 closest distance to " O   LEU A 228 " =    1.817
peak=    3.427 closest distance to " O   HOH Z 331 " =    0.953
peak=    3.425 closest distance to " O   HOH Z 162 " =    1.587
peak=    3.423 closest distance to " O   HOH Z 130 " =    0.974
peak=    3.417 closest distance to " NZ  LYS A 117 " =    2.792
peak=    3.415 closest distance to " CA  ALA A 160 " =    0.981
peak=    3.413 closest distance to " CB  GLN A  88 " =    1.254
peak=    3.406 closest distance to " O   HOH Z 410 " =    2.968
peak=    3.401 closest distance to " O   HOH Z  44 " =    1.706
peak=    3.395 closest distance to " CB  ASP A 298 " =    1.111
peak=    3.395 closest distance to " O   HOH Z  80 " =    1.686
peak=    3.389 closest distance to " O   HOH Z 280 " =    3.002
peak=    3.388 closest distance to " O   HOH Z 148 " =    3.556
peak=    3.385 closest distance to " O   HOH Z 421 " =    2.308
peak=    3.382 closest distance to " O   HOH Z  68 " =    2.209
peak=    3.380 closest distance to " OG BSER A 164 " =    2.194
peak=    3.379 closest distance to " O   HOH Z 361 " =    3.664
peak=    3.379 closest distance to " O   HOH Z 415 " =    3.368
peak=    3.377 closest distance to " CB  ARG A 138 " =    1.236
peak=    3.376 closest distance to " OG BSER A 164 " =    2.259
peak=    3.375 closest distance to " O   HOH Z 303 " =    2.880
peak=    3.375 closest distance to " N   ARG A 156 " =    1.389
peak=    3.373 closest distance to " O   HOH Z 236 " =    1.496
peak=    3.368 closest distance to " O   HOH Z 438 " =    2.924
peak=    3.364 closest distance to " O   HOH Z 200 " =    1.873
peak=    3.358 closest distance to " O   HOH Z 180 " =    2.186
peak=    3.354 closest distance to " O   HOH Z 172 " =    3.555
peak=    3.353 closest distance to " CE  LYS A 119 " =    1.140
peak=    3.350 closest distance to " CB  THR A 235 " =    1.396
peak=    3.349 closest distance to " CA  ARG A 139 " =    1.057
peak=    3.349 closest distance to " O   HOH Z  85 " =    1.716
peak=    3.342 closest distance to " CA  LYS A 117 " =    1.219
peak=    3.341 closest distance to " O   HOH Z 403 " =    1.947
peak=    3.333 closest distance to " CB  LEU A 300 " =    0.958
peak=    3.327 closest distance to " OG  SER A  62 " =    2.832
peak=    3.326 closest distance to " O   HOH Z 128 " =    2.176
peak=    3.326 closest distance to " NH1 ARG A  66 " =    1.422
peak=    3.320 closest distance to " CA  LYS A 290 " =    1.202
peak=    3.320 closest distance to " O   HOH Z 148 " =    2.203
peak=    3.310 closest distance to " CG  PHE A 204 " =    1.044
peak=    3.309 closest distance to " O   HOH Z 398 " =    1.269
peak=    3.307 closest distance to " O   ASP A 191 " =    1.654
peak=    3.304 closest distance to " O   HOH Z 123 " =    1.001
peak=    3.304 closest distance to " O   HOH Z  49 " =    1.077
peak=    3.299 closest distance to " CB  ALA A 248 " =    1.358
peak=    3.297 closest distance to " O   HOH Z 389 " =    1.386
peak=    3.292 closest distance to " O   ASN A 284 " =    1.759
peak=    3.283 closest distance to " CB  SER A  62 " =    0.899
peak=    3.281 closest distance to " CB  ALA A   9 " =    1.673
peak=    3.272 closest distance to " O   HOH Z  10 " =    1.665
peak=    3.271 closest distance to " O   HOH Z 244 " =    1.726
peak=    3.270 closest distance to " N   TYR A  15 " =    1.078
peak=    3.269 closest distance to " O   HOH Z 380 " =    1.805
peak=    3.266 closest distance to " CB  LYS A 117 " =    1.228
peak=    3.259 closest distance to " O   HOH Z 403 " =    1.527
peak=    3.256 closest distance to " CA  GLY A 267 " =    1.010
peak=    3.253 closest distance to " OG1 THR A 279 " =    1.383
peak=    3.246 closest distance to " CG  LYS A 119 " =    1.043
peak=    3.245 closest distance to " O   HOH Z 171 " =    3.774
peak=    3.243 closest distance to " N   SER A 135 " =    1.402
peak=    3.243 closest distance to " O   HOH Z 272 " =    2.317
peak=    3.243 closest distance to " CA  ASN A 215 " =    0.966
peak=    3.238 closest distance to " CD  LYS A 119 " =    2.003
peak=    3.236 closest distance to " O   HOH Z 385 " =    3.919
peak=    3.232 closest distance to " O   HOH Z 254 " =    1.341
peak=    3.229 closest distance to " OG1 THR A 221 " =    1.196
peak=    3.227 closest distance to " O   HOH Z 325 " =    2.054
peak=    3.225 closest distance to " OE2 GLU A  53 " =    1.956
peak=    3.224 closest distance to " CD ALYS A 290 " =    1.179
peak=    3.223 closest distance to " O   HOH Z   7 " =    1.548
peak=    3.223 closest distance to " CB  LEU A 143 " =    1.182
peak=    3.222 closest distance to " O   HOH Z 227 " =    1.345
peak=    3.219 closest distance to " N   TYR A 247 " =    1.283
peak=    3.217 closest distance to " CE1 TYR A 186 " =    1.320
peak=    3.215 closest distance to " CA  ALA A 160 " =    1.377
peak=    3.214 closest distance to " CD1 LEU A 261 " =    1.137
peak=    3.210 closest distance to " CG1 VAL A 153 " =    0.832
peak=    3.209 closest distance to " O   HOH Z 133 " =    2.836
peak=    3.209 closest distance to " N   GLN A 278 " =    1.485
peak=    3.205 closest distance to " O   HOH Z  30 " =    1.560
peak=    3.205 closest distance to " O   HOH Z 302 " =    1.837
peak=    3.202 closest distance to " O   GLN A  88 " =    1.596
peak=    3.202 closest distance to " CA  GLY A 133 " =    3.768
peak=    3.201 closest distance to " CB  SER A 212 " =    1.453
peak=    3.199 closest distance to " O   HOH Z 350 " =    1.604
peak=    3.199 closest distance to " CA  ALA A 154 " =    1.099
peak=    3.193 closest distance to " CA  SER A  87 " =    0.971
peak=    3.193 closest distance to " O   HOH Z 293 " =    1.883
peak=    3.192 closest distance to " CG2AVAL A  72 " =    1.699
peak=    3.192 closest distance to " NH2 ARG A  56 " =    1.087
peak=    3.189 closest distance to " CD2 TYR A 186 " =    1.101
peak=    3.188 closest distance to " O   GLY A  91 " =    1.419
peak=    3.185 closest distance to " CA  TYR A 116 " =    1.427
peak=    3.185 closest distance to " O   SER A 164 " =    1.259
peak=    3.181 closest distance to " O   HOH Z 141 " =    1.653
peak=    3.180 closest distance to " NH2BARG A 190 " =    1.753
peak=    3.179 closest distance to " O   HOH Z   1 " =    1.830
peak=    3.173 closest distance to " CA  TRP A 150 " =    0.989
peak=    3.168 closest distance to " CA  ARG A 102 " =    1.139
peak=    3.168 closest distance to " CB  PRO A 243 " =    1.305
peak=    3.164 closest distance to " CB  ALA A 104 " =    0.728
peak=    3.159 closest distance to " CG1 ILE A  49 " =    1.601
peak=    3.150 closest distance to " O   HOH Z  47 " =    2.007
peak=    3.147 closest distance to " CB  SER A 271 " =    1.312
peak=    3.146 closest distance to " CG  LEU A 281 " =    0.979
peak=    3.144 closest distance to " O   HOH Z 394 " =    3.546
peak=    3.143 closest distance to " CZ3 TRP A  92 " =    1.437
peak=    3.143 closest distance to " O   HOH Z 213 " =    2.633
peak=    3.140 closest distance to " O   HOH Z 392 " =    2.908
peak=    3.135 closest distance to " O   HOH Z 305 " =    3.361
peak=    3.133 closest distance to " CG1 VAL A 126 " =    1.479
peak=    3.129 closest distance to " O   ILE A  49 " =    1.089
peak=    3.126 closest distance to " O   HOH Z 344 " =    2.833
peak=    3.123 closest distance to " O   PHE A 192 " =    1.338
peak=    3.122 closest distance to " CA  ASP A 149 " =    1.173
peak=    3.119 closest distance to " CG1 VAL A 257 " =    1.391
peak=    3.112 closest distance to " CB  ASN A 173 " =    1.001
peak=    3.107 closest distance to " O   HOH Z 156 " =    3.064
peak=    3.107 closest distance to " O   HOH Z 421 " =    2.906
peak=    3.096 closest distance to " CB  GLN A 240 " =    1.224
peak=    3.074 closest distance to " CB  ASN A  74 " =    1.465
peak=    3.067 closest distance to " NE2 GLN A  73 " =    1.435
peak=    3.059 closest distance to " CA  ILE A 106 " =    0.775
peak=    3.046 closest distance to " O   HOH Z  63 " =    1.766
peak=    3.035 closest distance to " O   HOH Z 235 " =    1.601
peak=    3.000 closest distance to " O   HOH Z 213 " =    2.248

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 200         
Filter by distance & map next to the model:
   mapped sites are within: 0.688 - 5.671
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 198 from: 200
   mapped sites are within: 0.721 - 5.671

peak=   -4.565 closest distance to " CD  ARG A  14 " =    3.265
peak=   -4.544 closest distance to " O   HOH Z 211 " =    1.021
peak=   -4.534 closest distance to " O   HOH Z  69 " =    1.444
peak=   -4.508 closest distance to " C   HIS A 108 " =    1.220
peak=   -4.472 closest distance to " O   HOH Z 203 " =    1.185
peak=   -4.452 closest distance to " O   PRO A 198 " =    1.233
peak=   -4.329 closest distance to " CD1 LEU A 101 " =    2.357
peak=   -4.156 closest distance to " OG BSER A 134 " =    1.314
peak=   -4.154 closest distance to " O   VAL A  67 " =    2.656
peak=   -4.119 closest distance to " O   PRO A 163 " =    2.028
peak=   -4.103 closest distance to " CG  GLN A  58 " =    0.952
peak=   -4.070 closest distance to " O   HOH Z 100 " =    0.920
peak=   -4.039 closest distance to " O   HOH Z 131 " =    4.069
peak=   -4.013 closest distance to " CZ2 TRP A  92 " =    2.773
peak=   -3.983 closest distance to " O   HOH Z 394 " =    1.590
peak=   -3.962 closest distance to " CG  GLN A 223 " =    2.190
peak=   -3.913 closest distance to " CG  TRP A 266 " =    1.871
peak=   -3.908 closest distance to " O   HOH Z 267 " =    5.565
peak=   -3.895 closest distance to " O   HOH Z 387 " =    2.615
peak=   -3.887 closest distance to " CG2 VAL A 202 " =    2.688
peak=   -3.859 closest distance to " CG1 VAL A 112 " =    2.822
peak=   -3.851 closest distance to " CG1 VAL A 250 " =    2.664
peak=   -3.807 closest distance to " O   HOH Z 295 " =    1.585
peak=   -3.794 closest distance to " CD2 TYR A 293 " =    2.035
peak=   -3.787 closest distance to " CB  PHE A 192 " =    1.987
peak=   -3.785 closest distance to " O   ALA A 227 " =    1.295
peak=   -3.780 closest distance to " OG  SER A  97 " =    2.304
peak=   -3.779 closest distance to " O   HOH Z 359 " =    2.942
peak=   -3.776 closest distance to " CD  ARG A 156 " =    2.070
peak=   -3.763 closest distance to " O   HOH Z 231 " =    2.177
peak=   -3.752 closest distance to " O   HOH Z 166 " =    1.966
peak=   -3.742 closest distance to " NE2 GLN A  11 " =    1.788
peak=   -3.714 closest distance to " CG2 ILE A  20 " =    2.849
peak=   -3.705 closest distance to " O   HOH Z 216 " =    1.363
peak=   -3.688 closest distance to " N   THR A  52 " =    1.669
peak=   -3.675 closest distance to " CE BMET A  47 " =    1.376
peak=   -3.673 closest distance to " O   HOH Z 201 " =    2.217
peak=   -3.664 closest distance to " O   HOH Z 128 " =    1.107
peak=   -3.659 closest distance to " CB  ALA A  43 " =    2.510
peak=   -3.644 closest distance to " C   ASN A 285 " =    2.206
peak=   -3.627 closest distance to " NE2 GLN A  88 " =    1.081
peak=   -3.622 closest distance to " CE1 PHE A 192 " =    1.914
peak=   -3.616 closest distance to " CG2 THR A 178 " =    2.468
peak=   -3.612 closest distance to " O   HOH Z  73 " =    2.549
peak=   -3.604 closest distance to " CA  ASP A  27 " =    2.416
peak=   -3.594 closest distance to " O   HOH Z 377 " =    2.123
peak=   -3.592 closest distance to " ND2 ASN A  45 " =    1.284
peak=   -3.591 closest distance to " O   HOH Z 107 " =    1.000
peak=   -3.588 closest distance to " O   HOH Z 149 " =    1.735
peak=   -3.564 closest distance to " CD1 ILE A 199 " =    2.383
peak=   -3.554 closest distance to " CE  MET A 105 " =    2.364
peak=   -3.547 closest distance to " OD2 ASP A 191 " =    1.299
peak=   -3.543 closest distance to " O   SER A 271 " =    2.090
peak=   -3.536 closest distance to " CB  HIS A  86 " =    1.110
peak=   -3.525 closest distance to " CG  LEU A   5 " =    0.917
peak=   -3.518 closest distance to " O   HOH Z 371 " =    2.484
peak=   -3.506 closest distance to " O   HOH Z 106 " =    1.721
peak=   -3.504 closest distance to " CD  PRO A 243 " =    1.911
peak=   -3.496 closest distance to " O   HOH Z 285 " =    2.031
peak=   -3.495 closest distance to " O   HOH Z  64 " =    1.500
peak=   -3.494 closest distance to " OH  TYR A 172 " =    1.813
peak=   -3.494 closest distance to " CB  ALA A 161 " =    2.363
peak=   -3.493 closest distance to " CD1 LEU A 255 " =    2.816
peak=   -3.474 closest distance to " CB  ALA A   7 " =    2.192
peak=   -3.471 closest distance to " O   HOH Z 429 " =    1.557
peak=   -3.470 closest distance to " CG  PHE A 283 " =    2.623
peak=   -3.467 closest distance to " O   HOH Z 236 " =    1.370
peak=   -3.465 closest distance to " O   HOH Z 290 " =    1.148
peak=   -3.462 closest distance to " CE3 TRP A 150 " =    2.301
peak=   -3.439 closest distance to " O   HOH Z 256 " =    1.449
peak=   -3.436 closest distance to " C   MET A 188 " =    1.408
peak=   -3.431 closest distance to " CB  PRO A 163 " =    2.443
peak=   -3.431 closest distance to " O   ASN A 187 " =    1.611
peak=   -3.426 closest distance to " CA  ASP A 298 " =    1.088
peak=   -3.422 closest distance to " O   HOH Z 191 " =    5.671
peak=   -3.422 closest distance to " CG  GLN A 103 " =    2.418
peak=   -3.406 closest distance to " O   HOH Z 166 " =    2.228
peak=   -3.406 closest distance to " CD  PRO A 213 " =    2.026
peak=   -3.406 closest distance to " OG  SER A  63 " =    1.082
peak=   -3.406 closest distance to " O   HOH Z  37 " =    1.792
peak=   -3.401 closest distance to " NH2 ARG A  79 " =    2.167
peak=   -3.399 closest distance to " CE2 TRP A  70 " =    2.202
peak=   -3.399 closest distance to " O   HOH Z 115 " =    1.901
peak=   -3.389 closest distance to " CD2 HIS A 207 " =    2.153
peak=   -3.385 closest distance to " O   HOH Z 352 " =    1.395
peak=   -3.380 closest distance to " CB  ALA A 114 " =    2.563
peak=   -3.379 closest distance to " CD2 PHE A 225 " =    1.069
peak=   -3.374 closest distance to " OH  TYR A 169 " =    0.879
peak=   -3.370 closest distance to " CB  SER A 210 " =    1.141
peak=   -3.369 closest distance to " O   HOH Z  44 " =    0.859
peak=   -3.364 closest distance to " SG BCYS A 201 " =    2.261
peak=   -3.363 closest distance to " CG2 THR A  18 " =    2.881
peak=   -3.359 closest distance to " O   HOH Z 345 " =    2.121
peak=   -3.358 closest distance to " CG  GLU A 277 " =    1.294
peak=   -3.358 closest distance to " N   PHE A  59 " =    2.067
peak=   -3.356 closest distance to " O   HOH Z  65 " =    1.024
peak=   -3.353 closest distance to " CG2 VAL A 189 " =    1.996
peak=   -3.351 closest distance to " O   HOH Z  68 " =    1.301
peak=   -3.346 closest distance to " O   HOH Z 369 " =    2.188
peak=   -3.344 closest distance to " CB  VAL A 230 " =    1.077
peak=   -3.342 closest distance to " O   SER A 276 " =    1.647
peak=   -3.340 closest distance to " CE3 TRP A 274 " =    2.226
peak=   -3.334 closest distance to " O   HOH Z 252 " =    3.719
peak=   -3.333 closest distance to " OXT GLY A 302 " =    3.000
peak=   -3.332 closest distance to " O   HOH Z 238 " =    0.721
peak=   -3.331 closest distance to " O   HOH Z 380 " =    1.039
peak=   -3.331 closest distance to " NE2 GLN A 278 " =    1.750
peak=   -3.330 closest distance to " CE2 TYR A  30 " =    2.732
peak=   -3.326 closest distance to " OD1 ASP A 171 " =    1.511
peak=   -3.321 closest distance to " CG  ASP A 231 " =    0.805
peak=   -3.315 closest distance to " C   ALA A 158 " =    1.184
peak=   -3.302 closest distance to " O   VAL A 174 " =    2.151
peak=   -3.300 closest distance to " O   HOH Z  20 " =    1.329
peak=   -3.291 closest distance to " O   HOH Z   9 " =    1.496
peak=   -3.291 closest distance to " CA  GLY A 241 " =    2.365
peak=   -3.283 closest distance to " O   HOH Z 165 " =    1.899
peak=   -3.283 closest distance to " CG2BVAL A  41 " =    1.817
peak=   -3.265 closest distance to " O   TRP A  70 " =    1.591
peak=   -3.265 closest distance to " O   PHE A 218 " =    1.490
peak=   -3.265 closest distance to " O   SER A 210 " =    1.856
peak=   -3.264 closest distance to " O   HOH Z 281 " =    3.036
peak=   -3.262 closest distance to " C   GLY A  17 " =    1.135
peak=   -3.260 closest distance to " NH2AARG A 275 " =    4.834
peak=   -3.260 closest distance to " O   HOH Z 198 " =    1.316
peak=   -3.259 closest distance to " CZ2 TRP A 274 " =    1.054
peak=   -3.257 closest distance to " O   VAL A 189 " =    2.693
peak=   -3.250 closest distance to " CG  ARG A 138 " =    0.926
peak=   -3.246 closest distance to " CG2 VAL A 296 " =    1.736
peak=   -3.245 closest distance to " N   SER A 276 " =    1.358
peak=   -3.244 closest distance to " CG1 VAL A 125 " =    1.905
peak=   -3.244 closest distance to " CG  MET A 105 " =    0.974
peak=   -3.243 closest distance to " O   HOH Z 351 " =    1.583
peak=   -3.241 closest distance to " CG  LEU A 228 " =    0.986
peak=   -3.233 closest distance to " OE1 GLN A 183 " =    1.619
peak=   -3.232 closest distance to " N   TRP A 274 " =    1.136
peak=   -3.229 closest distance to " O   HOH Z 185 " =    2.209
peak=   -3.221 closest distance to " O   HOH Z 102 " =    1.654
peak=   -3.220 closest distance to " CD2 PHE A  61 " =    2.244
peak=   -3.216 closest distance to " CB  GLN A  55 " =    1.393
peak=   -3.216 closest distance to " O   HOH Z 144 " =    1.172
peak=   -3.216 closest distance to " N   ALA A 226 " =    1.922
peak=   -3.215 closest distance to " CG  ARG A 269 " =    2.244
peak=   -3.214 closest distance to " O   HOH Z  11 " =    1.821
peak=   -3.212 closest distance to " CB  ASN A  39 " =    2.248
peak=   -3.208 closest distance to " O   GLY A 241 " =    1.461
peak=   -3.206 closest distance to " O   HOH Z 404 " =    1.438
peak=   -3.200 closest distance to " OE1 GLN A 223 " =    2.926
peak=   -3.199 closest distance to " O   HOH Z 140 " =    1.643
peak=   -3.196 closest distance to " CA  HIS A 207 " =    1.231
peak=   -3.196 closest distance to " ND2 ASN A 173 " =    1.566
peak=   -3.191 closest distance to " OE1 GLN A  88 " =    1.037
peak=   -3.186 closest distance to " O   HOH Z 281 " =    2.565
peak=   -3.184 closest distance to " CG  PRO A 243 " =    1.632
peak=   -3.181 closest distance to " CB  TYR A  15 " =    2.178
peak=   -3.179 closest distance to " O   HOH Z 127 " =    1.242
peak=   -3.179 closest distance to " ND2 ASN A 187 " =    1.523
peak=   -3.177 closest distance to " CE1 TYR A 247 " =    2.558
peak=   -3.176 closest distance to " O   HOH Z 174 " =    3.815
peak=   -3.175 closest distance to " CG2 VAL A 296 " =    0.788
peak=   -3.173 closest distance to " O   HOH Z 108 " =    1.302
peak=   -3.172 closest distance to " O   HOH Z 307 " =    2.016
peak=   -3.171 closest distance to " ND2 ASN A 249 " =    2.163
peak=   -3.171 closest distance to " NH2 ARG A 219 " =    1.588
peak=   -3.170 closest distance to " ND2 ASN A 252 " =    1.972
peak=   -3.168 closest distance to " O   HOH Z 374 " =    1.838
peak=   -3.166 closest distance to " O   HOH Z 421 " =    3.096
peak=   -3.164 closest distance to " O   HOH Z 116 " =    1.634
peak=   -3.159 closest distance to " OD1 ASP A 200 " =    1.698
peak=   -3.154 closest distance to " CA  GLY A 302 " =    2.905
peak=   -3.153 closest distance to " CG2 ILE A 151 " =    2.555
peak=   -3.153 closest distance to " OE1 GLN A 183 " =    1.799
peak=   -3.152 closest distance to " O   HOH Z 407 " =    2.712
peak=   -3.151 closest distance to " NH2 ARG A  79 " =    1.522
peak=   -3.150 closest distance to " O   HOH Z  60 " =    1.612
peak=   -3.143 closest distance to " CA  GLY A 133 " =    2.250
peak=   -3.142 closest distance to " OG ASER A 134 " =    1.328
peak=   -3.140 closest distance to " O   HOH Z 128 " =    2.016
peak=   -3.140 closest distance to " O   HOH Z 113 " =    1.589
peak=   -3.139 closest distance to " CZ3 TRP A 179 " =    1.336
peak=   -3.134 closest distance to " O   ALA A  51 " =    1.174
peak=   -3.131 closest distance to " O   HOH Z 110 " =    1.417
peak=   -3.117 closest distance to " O   HOH Z 108 " =    1.687
peak=   -3.116 closest distance to " O   HOH Z 174 " =    2.487
peak=   -3.114 closest distance to " O   HOH Z 166 " =    1.571
peak=   -3.114 closest distance to " O   HOH Z 134 " =    4.132
peak=   -3.111 closest distance to " O   HOH Z  52 " =    1.566
peak=   -3.108 closest distance to " CD  LYS A 289 " =    2.334
peak=   -3.107 closest distance to " O   GLY A  80 " =    2.589
peak=   -3.107 closest distance to " OE1 GLN A 223 " =    2.009
peak=   -3.105 closest distance to " O   SER A 135 " =    1.616
peak=   -3.104 closest distance to " O   ALA A 180 " =    1.406
peak=   -3.092 closest distance to " NE  ARG A  79 " =    1.071
peak=   -3.070 closest distance to " CD2 LEU A 237 " =    2.886
peak=   -3.066 closest distance to " OD1 ASN A 301 " =    1.966
peak=   -3.060 closest distance to " O   HOH Z 111 " =    4.432
peak=   -3.060 closest distance to " OG  SER A 271 " =    1.167
peak=   -3.045 closest distance to " O   HOH Z 351 " =    1.705
peak=   -3.028 closest distance to " NE2 GLN A  55 " =    1.183

================= 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    :  0.4844 0.4697   6.285899e+00   6.271937e+00
   1_bss:  0.4751 0.4621   6.277964e+00   6.262877e+00
   1_xyz:  0.3990 0.4151   6.176884e+00   6.203136e+00
   1_adp:  0.3542 0.4020   6.096622e+00   6.171711e+00
   1_occ:  0.3537 0.4029   6.095681e+00   6.173538e+00
   2_bss:  0.3506 0.3979   6.096687e+00   6.173680e+00
   2_xyz:  0.2631 0.3147   5.859376e+00   6.001256e+00
   2_adp:  0.2379 0.2940   5.781497e+00   5.949681e+00
   2_occ:  0.2376 0.2938   5.781247e+00   5.949691e+00
   3_bss:  0.2353 0.2936   5.781227e+00   5.950646e+00
   3_xyz:  0.1761 0.2332   5.535768e+00   5.744452e+00
   3_adp:  0.1635 0.2182   5.467193e+00   5.677041e+00
   3_occ:  0.1631 0.2179   5.466284e+00   5.676596e+00
   4_bss:  0.1628 0.2172   5.467282e+00   5.676753e+00
   4_xyz:  0.1399 0.1863   5.329449e+00   5.540078e+00
   4_adp:  0.1325 0.1822   5.294313e+00   5.517582e+00
   4_occ:  0.1324 0.1821   5.294243e+00   5.517901e+00
   5_bss:  0.1325 0.1826   5.294067e+00   5.518235e+00
   5_xyz:  0.1225 0.1698   5.228906e+00   5.463621e+00
   5_adp:  0.1209 0.1677   5.217300e+00   5.451192e+00
   5_occ:  0.1208 0.1676   5.216898e+00   5.451097e+00
   5_bss:  0.1208 0.1676   5.216985e+00   5.451248e+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:  0.354  20.000   7.153   7.456  12.040   0.000   0.000   0.000
   1_xyz:  0.354  20.000   7.153   7.456  12.040   0.000   0.000   0.000
   1_adp:  0.354  20.000   7.153   7.456  12.040   0.000   0.000   0.000
   1_occ:  0.354  20.000   7.153   7.456  12.040   0.000   0.000   0.000
   2_bss:  0.344  41.408   3.430   3.725   8.250   0.000   0.000   0.000
   2_xyz:  0.344  41.408   3.430   3.725   8.250   0.000   0.000   0.000
   2_adp:  0.344  41.408   3.430   3.725   8.250   0.000   0.000   0.000
   2_occ:  0.344  41.408   3.430   3.725   8.250   0.000   0.000   0.000
   3_bss:  0.318  47.914   1.442   2.040   4.987   0.000   0.000   0.000
   3_xyz:  0.318  47.914   1.442   2.040   4.987   0.000   0.000   0.000
   3_adp:  0.318  47.914   1.442   2.040   4.987   0.000   0.000   0.000
   3_occ:  0.318  47.914   1.442   2.040   4.987   0.000   0.000   0.000
   4_bss:  0.333  54.776   0.642   1.329   3.730   0.000   0.000   0.000
   4_xyz:  0.333  54.776   0.642   1.329   3.730   0.000   0.000   0.000
   4_adp:  0.333  54.776   0.642   1.329   3.730   0.000   0.000   0.000
   4_occ:  0.333  54.776   0.642   1.329   3.730   0.000   0.000   0.000
   5_bss:  0.330  60.927   0.624   1.315   3.395   0.000   0.000   0.000
   5_xyz:  0.330  60.927   0.624   1.315   3.395   0.000   0.000   0.000
   5_adp:  0.330  60.927   0.624   1.315   3.395   0.000   0.000   0.000
   5_occ:  0.330  60.927   0.624   1.315   3.395   0.000   0.000   0.000
   5_bss:  0.330  62.782  -1.096  -0.457   1.553  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  57.033 0.4322  0.5061    70594.358
   1_bss:  56.886 0.4329  0.6618    68924.497
   1_xyz:  47.395 0.5525  0.8198    51008.137
   1_adp:  43.993 0.5947  0.9370    46009.678
   1_occ:  44.113 0.5931  0.9328    46158.637
   2_bss:  43.890 0.5957  0.8211    45803.003
   2_xyz:  32.800 0.7257  0.9737    26485.249
   2_adp:  29.823 0.7597  1.0052    22894.425
   2_occ:  29.838 0.7596  1.0048    22909.366
   3_bss:  29.732 0.7607  0.9264    22877.039
   3_xyz:  22.610 0.8360  0.9849    13780.986
   3_adp:  20.638 0.8561  0.9936    12080.728
   3_occ:  20.631 0.8562  0.9936    12057.046
   4_bss:  20.603 0.8565  0.9620    12063.629
   4_xyz:  17.360 0.8866  0.9753     9003.654
   4_adp:  16.862 0.8912  0.9696     8611.307
   4_occ:  16.867 0.8912  0.9696     8612.143
   5_bss:  16.860 0.8913  0.9656     8621.749
   5_xyz:  15.639 0.9017  0.9740     7600.845
   5_adp:  15.343 0.9043  0.9713     7426.789
   5_occ:  15.340 0.9043  0.9714     7422.048
   5_bss:  15.343 0.9043  0.9741     7425.400
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.090   5.3717e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.090   5.3717e+01
   1_xyz:   1.674  0.013  0.104 18.183  0.006  4.108   1.3746e-01
   1_adp:   1.674  0.013  0.104 18.183  0.006  4.108   1.3746e-01
   1_occ:   1.674  0.013  0.104 18.183  0.006  4.108   1.3746e-01
   2_bss:   1.674  0.013  0.104 18.183  0.006  4.108   1.3746e-01
   2_xyz:   1.278  0.010  0.084 16.170  0.005  4.110   9.5271e-02
   2_adp:   1.278  0.010  0.084 16.170  0.005  4.110   9.5271e-02
   2_occ:   1.278  0.010  0.084 16.170  0.005  4.110   9.5271e-02
   3_bss:   1.278  0.010  0.084 16.170  0.005  4.110   9.5271e-02
   3_xyz:   1.090  0.008  0.079 15.864  0.004  4.128   7.0374e-02
   3_adp:   1.090  0.008  0.079 15.864  0.004  4.128   7.0374e-02
   3_occ:   1.090  0.008  0.079 15.864  0.004  4.128   7.0374e-02
   4_bss:   1.090  0.008  0.079 15.864  0.004  4.128   7.0374e-02
   4_xyz:   0.961  0.006  0.072 15.610  0.004  4.124   5.8894e-02
   4_adp:   0.961  0.006  0.072 15.610  0.004  4.124   5.8894e-02
   4_occ:   0.961  0.006  0.072 15.610  0.004  4.124   5.8894e-02
   5_bss:   0.961  0.006  0.072 15.610  0.004  4.124   5.8894e-02
   5_xyz:   1.028  0.007  0.078 15.422  0.003  4.112   6.3347e-02
   5_adp:   1.028  0.007  0.078 15.422  0.003  4.112   6.3347e-02
   5_occ:   1.028  0.007  0.078 15.422  0.003  4.112   6.3347e-02
   5_bss:   1.028  0.007  0.078 15.422  0.003  4.112   6.3347e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.195   6.9607e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.195   6.9607e+00
   1_xyz:  13.539  0.169  0.398 87.722  0.052  2.124   9.7972e-02
   1_adp:  13.539  0.169  0.398 87.722  0.052  2.124   9.7972e-02
   1_occ:  13.539  0.169  0.398 87.722  0.052  2.124   9.7972e-02
   2_bss:  13.539  0.169  0.398 87.722  0.052  2.124   9.7972e-02
   2_xyz:   7.779  0.113  0.299 88.722  0.037  2.115   1.4514e-01
   2_adp:   7.779  0.113  0.299 88.722  0.037  2.115   1.4514e-01
   2_occ:   7.779  0.113  0.299 88.722  0.037  2.115   1.4514e-01
   3_bss:   7.779  0.113  0.299 88.722  0.037  2.115   1.4514e-01
   3_xyz:   6.823  0.045  0.345 88.442  0.033  2.223   6.3165e-02
   3_adp:   6.823  0.045  0.345 88.442  0.033  2.223   6.3165e-02
   3_occ:   6.823  0.045  0.345 88.442  0.033  2.223   6.3165e-02
   4_bss:   6.823  0.045  0.345 88.442  0.033  2.223   6.3165e-02
   4_xyz:   7.605  0.050  0.291 85.580  0.035  2.304   5.3891e-02
   4_adp:   7.605  0.050  0.291 85.580  0.035  2.304   5.3891e-02
   4_occ:   7.605  0.050  0.291 85.580  0.035  2.304   5.3891e-02
   5_bss:   7.605  0.050  0.291 85.580  0.035  2.304   5.3891e-02
   5_xyz:   8.107  0.054  0.326 81.977  0.027  2.293   5.1929e-02
   5_adp:   8.107  0.054  0.326 81.977  0.027  2.293   5.1929e-02
   5_occ:   8.107  0.054  0.326 81.977  0.027  2.293   5.1929e-02
   5_bss:   8.107  0.054  0.326 81.977  0.027  2.293   5.1929e-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:  68.29   0.00  13.89  64.87   0.00  11.55  68.29   0.00  26.64
   1_occ:  68.29   0.00  13.89  64.87   0.00  11.55  68.29   0.00  26.64
   2_bss:  68.29   0.00  13.89  64.87   0.00  11.55  68.29   0.00  26.64
   2_xyz:  68.29   0.00  13.89  64.87   0.00  11.55  68.29   0.00  26.64
   2_adp:  76.32   0.00  13.84  65.71   0.00  10.31  76.32   0.00  33.08
   2_occ:  76.32   0.00  13.84  65.71   0.00  10.31  76.32   0.00  33.08
   3_bss:  76.32   0.00  13.84  65.71   0.00  10.31  76.32   0.00  33.08
   3_xyz:  76.32   0.00  13.84  65.71   0.00  10.31  76.32   0.00  33.08
   3_adp: 117.14   0.00  13.52 117.14   0.00   9.54  74.90   1.86  35.20
   3_occ: 117.14   0.00  13.52 117.14   0.00   9.54  74.90   1.86  35.20
   4_bss: 117.14   0.00  13.52 117.14   0.00   9.54  74.90   1.86  35.20
   4_xyz: 117.14   0.00  13.52 117.14   0.00   9.54  74.90   1.86  35.20
   4_adp:  98.13   0.00  14.32  88.68   0.00   9.56  98.13   1.97  40.24
   4_occ:  98.13   0.00  14.32  88.68   0.00   9.56  98.13   1.97  40.24
   5_bss:  98.13   0.00  14.32  88.68   0.00   9.56  98.13   1.97  40.24
   5_xyz:  98.13   0.00  14.32  88.68   0.00   9.56  98.13   1.97  40.24
   5_adp:  96.47   0.00  13.93  90.95   0.00   9.36  96.47   2.03  38.85
   5_occ:  96.47   0.00  13.93  90.95   0.00   9.36  96.47   2.03  38.85
   5_bss:  98.32   1.85  15.79  92.80   1.85  11.21  98.32   3.88  40.70
------------------------------------------------------------------------
 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:    1.278    0.012    0.407
   1_adp:    1.278    0.012    0.407
   1_occ:    1.278    0.012    0.407
   2_bss:    1.278    0.012    0.407
   2_xyz:    1.865    0.048    0.588
   2_adp:    1.865    0.048    0.588
   2_occ:    1.865    0.048    0.588
   3_bss:    1.865    0.048    0.588
   3_xyz:    1.718    0.036    0.662
   3_adp:    1.718    0.036    0.662
   3_occ:    1.718    0.036    0.662
   4_bss:    1.718    0.036    0.662
   4_xyz:    1.851    0.041    0.707
   4_adp:    1.851    0.041    0.707
   4_occ:    1.851    0.041    0.707
   5_bss:    1.851    0.041    0.707
   5_xyz:    2.030    0.027    0.729
   5_adp:    2.030    0.027    0.729
   5_occ:    2.030    0.027    0.729
   5_bss:    2.030    0.027    0.729
------------------------------------------------------------------------

CPU time actual refinement: 331.60


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_296/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_296/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_296/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_296/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_296/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 331.45 
  Macro-tasks:
    bulk solvent and scale       = 42.59  
    individual site refinement   = 134.44 
    weights calculation          = 32.03  
    collect and process          = 6.55   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 215.71 
  Micro-tasks:
    mask                            = 2.37   
    f_calc                          = 100.66 
    alpha_beta                      = 8.37   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 110.66 
    fmodel                         = 7.14   
    r_factors                      = 0.34   
    phase_errors                   = 10.60  
    foms                           = 0.23   
    TOTAL for micro-tasks          = 241.54 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.688 micro seconds
Total CPU time: 5.75 minutes
from_scatterers_fft:    642 calls, 100.28 s
gradients_fft:          587 calls,  97.64 s

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

# Date 2008-01-16 Time 01:15:04 PST -0800 (1200474904.80 s)
Start R-work = 0.4844, R-free = 0.4697 (no bulk solvent and anisotropic scale)
Final R-work = 0.1384, R-free = 0.1837 (no bulk solvent and anisotropic scale)

Start R-work = 0.4751, R-free = 0.4621
Final R-work = 0.1208, R-free = 0.1676