# Date 2008-01-16 Time 01:28:21 PST -0800 (1200475701.43 s)
#phil __OFF__

Command line arguments: "../439.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 23893
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 439

-------------------------------------------------------------------------------
  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: (69.5475, 47.1647, 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: 3.33, per 1000 atoms: 1.18


================================== 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: (69.5475, 47.1647, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.981 1.98083
Completeness in resolution range: 0.939881
Completeness with d_max=infinity: 0.937004

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9810
                             d_min =   1.9808

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: (69.5475, 47.1647, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.981 1.98083
Completeness in resolution range: 0.939881
Completeness with d_max=infinity: 0.937004

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9814 -  4.2384 [2195/2222]  1974   221  10.1%
  bin  2:  4.2384 -  3.3768 [2096/2112]  1882   214  10.2%
  bin  3:  3.3768 -  2.9537 [2077/2096]  1876   201   9.7%
  bin  4:  2.9537 -  2.6853 [2055/2085]  1848   207  10.1%
  bin  5:  2.6853 -  2.4938 [2028/2047]  1824   204  10.1%
  bin  6:  2.4938 -  2.3473 [2033/2069]  1827   206  10.1%
  bin  7:  2.3473 -  2.2302 [2024/2057]  1830   194   9.6%
  bin  8:  2.2302 -  2.1334 [2020/2055]  1807   213  10.5%
  bin  9:  2.1334 -  2.0515 [2014/2041]  1818   196   9.7%
  bin 10:  2.0515 -  1.9808 [1047/2058]   944   103   9.8%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_439/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.41 -     2.11: 13
        2.11 -     2.80: 751
        2.80 -     3.50: 4403
        3.50 -     4.20: 9257
        4.20 -     4.90: 13630
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.408 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.413 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.613 3.040 -x+1,y+1/2,-z+1/2
  " NH2 ARG A  24 " - " OG  SER A  95 "  1.740 3.120 -x+1,y+1/2,-z+1/2
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.760 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28049 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_439/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_439/model_refine_001.geo

CPU time processing inputs: 9.80


============================ 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 = 69.5475 47.16465 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: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4763   r_free= 0.4609   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:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.279339                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9814 -  4.7272 0.99   1421  158 0.3846 0.3673      6.5976      6.5476|
|  2:  4.7272 -  3.7718 0.99   1375  152 0.3864 0.4434      6.7552        6.92|
|  3:  3.7718 -  3.3009 0.99   1337  149 0.4463 0.3978      6.6758      6.6278|
|  4:  3.3009 -  3.0017 0.99   1332  143 0.4650 0.4464       6.509      6.4667|
|  5:  3.0017 -  2.7880 0.99   1310  154 0.5012 0.4781      6.3609      6.3855|
|  6:  2.7880 -  2.6246 0.99   1330  144 0.5012 0.5561      6.2728      6.2134|
|  7:  2.6246 -  2.4938 0.99   1299  147 0.5080 0.4678       6.223      6.1369|
|  8:  2.4938 -  2.3857 0.98   1312  142 0.5352 0.4260      6.1988      6.1406|
|  9:  2.3857 -  2.2942 0.98   1314  146 0.5236 0.5134      6.1227      6.1393|
| 10:  2.2942 -  2.2153 0.98   1291  138 0.5359 0.4881       6.104      6.0925|
| 11:  2.2153 -  2.1462 1.00   1307  158 0.5142 0.5385       6.018      6.0494|
| 12:  2.1462 -  2.0850 0.97   1286  133 0.5300 0.5017      5.9515      5.9707|
| 13:  2.0850 -  2.0303 0.94   1247  138 0.5284 0.5180      5.8929      5.8293|
| 14:  2.0303 -  1.9808 0.36    469   57 0.5003 0.3863      5.8855      5.6945|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9814 -  4.7272  1421   158  0.72  32.66   0.80     0.73      65048.52|
|  2:  4.7272 -  3.7718  1375   152  0.71  34.47   0.88     0.76     102519.14|
|  3:  3.7718 -  3.3009  1337   149  0.61  42.65   0.82     0.72     108372.84|
|  4:  3.3009 -  3.0017  1332   143  0.52  50.52   0.79     0.60      96950.09|
|  5:  3.0017 -  2.7880  1310   154  0.41  58.56   0.74     0.48      81330.36|
|  6:  2.7880 -  2.6246  1330   144  0.36  63.22   0.72     0.41      75448.02|
|  7:  2.6246 -  2.4938  1299   147  0.38  61.53   0.74     0.43      64579.19|
|  8:  2.4938 -  2.3857  1312   142  0.43  57.82   0.72     0.50      52993.04|
|  9:  2.3857 -  2.2942  1314   146  0.45  56.21   0.71     0.53      47409.53|
| 10:  2.2942 -  2.2153  1291   138  0.41  59.20   0.73     0.48      44373.63|
| 11:  2.2153 -  2.1462  1307   158  0.34  64.49   0.75     0.43      47314.06|
| 12:  2.1462 -  2.0850  1286   133  0.33  65.58   0.74     0.42      42858.51|
| 13:  2.0850 -  2.0303  1247   138  0.36  63.34   0.73     0.45      36218.35|
| 14:  2.0303 -  1.9808   469    57  0.48  53.69   0.77     0.49      24043.92|
|alpha:            min =        0.41 max =            0.76 mean =         0.54|
|beta:             min =    24043.92 max =       108372.84 mean =     65837.35|
|figures of merit: min =        0.00 max =            1.00 mean =         0.47|
|phase err.(work): min =        0.00 max =           89.98 mean =        54.33|
|phase err.(test): min =        0.00 max =           89.95 mean =        54.68|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.914409             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.995   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.069955              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.730   (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 |  1.135 -  1.512:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.512 -  1.888:       19 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.888 -  2.265:      140 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.265 -  2.641:      625 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.641 -  3.018:     1433 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.018 -  3.394:     2512 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.394 -  3.771:     3900 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.771 -  4.147:     5095 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.147 -  4.523:     6607 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.523 -  4.900:     7726 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       54.133 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.091    4.900  1.135 |       1.971 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.032)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 12.032)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4819   r_free= 0.4636   ksol= 0.00   Bsol= 0.00   scale= 0.760    |
|                                                                             |
| 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:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.282818                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4660   r_free= 0.4511   ksol= 0.34   Bsol= 20.00   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.64,7.60,12.22,0.00,0.00,0.00); trace/3= 8.82                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.272594                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.232954             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.934   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.978551              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 75.896   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4660      final r-factor (work) = 0.3796          |
| start r-factor (free) = 0.4511      final r-factor (free) = 0.4039          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 89.3955 = 11.23 * 0.50 * 6.2784 + 1.00 * 54.1328                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 34.8302 = 11.23 * 0.50 * 6.1764 + 1.00 * 0.1408                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3796      final r-factor (work) = 0.3348          |
| start r-factor (free) = 0.4039      final r-factor (free) = 0.3807          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.0583 = 0.98 * 1.00 * 6.1764 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.9666 = 0.98 * 1.00 * 6.0823 + 1.00 * 0.0148                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.032)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    71.15   13.04    None  None   None       |
|    all(noH): 2823   0      0.00    71.15   13.04    None  None   None       |
|    Sol.    : 438    0      0.00    71.15   26.38    None  None   None       |
|    Mac.    : 2385   0      0.00    60.95   10.59    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 -   7.115: 1038   |   5:    35.576 -  42.691:   75        |
|      1:     7.115 -  14.231:  823   |   6:    42.691 -  49.807:   52        |
|      2:    14.231 -  21.346:  424   |   7:    49.807 -  56.922:   23        |
|      3:    21.346 -  28.461:  231   |   8:    56.922 -  64.037:    8        |
|      4:    28.461 -  35.576:  145   |   9:    64.037 -  71.152:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3348 r_free = 0.3807             target_work(ml) = 6.058         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3344 r_free = 0.3818             target_work(ml) = 6.057         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3344   r_free= 0.3818   ksol= 0.34   Bsol= 20.00   scale= 1.101   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.64,7.60,12.22,0.00,0.00,0.00); trace/3= 8.82                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.057263                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3309   r_free= 0.3793   ksol= 0.33   Bsol= 49.78   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.68,3.66,8.03,0.00,0.00,0.00); trace/3= 4.79                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.50 A                  |
| x-ray target function (ml) for work reflections: 6.058672                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.694368              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.435   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.443865              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.610  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3309      final r-factor (work) = 0.2564          |
| start r-factor (free) = 0.3793      final r-factor (free) = 0.3084          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.4111 = 4.69 * 0.50 * 6.0797 + 1.00 * 0.1408                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.0315 = 4.69 * 0.50 * 5.9452 + 1.00 * 0.0770                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2564      final r-factor (work) = 0.2375          |
| start r-factor (free) = 0.3084      final r-factor (free) = 0.2914          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6536 = 0.44 * 1.00 * 5.9452 + 1.00 * 0.0148                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5906 = 0.44 * 1.00 * 5.8114 + 1.00 * 0.0111                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.032)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    67.78   13.10    None  None   None       |
|    all(noH): 2823   0      0.00    67.78   13.10    None  None   None       |
|    Sol.    : 438    0      0.00    67.78   31.69    None  None   None       |
|    Mac.    : 2385   0      0.00    65.84   9.68     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 -   6.778: 1076   |   5:    33.888 -  40.665:  117        |
|      1:     6.778 -  13.555:  815   |   6:    40.665 -  47.443:   78        |
|      2:    13.555 -  20.333:  376   |   7:    47.443 -  54.221:   36        |
|      3:    20.333 -  27.110:  184   |   8:    54.221 -  60.998:   16        |
|      4:    27.110 -  33.888:  116   |   9:    60.998 -  67.776:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2375 r_free = 0.2914             target_work(ml) = 5.791         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2373 r_free = 0.2911             target_work(ml) = 5.790         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2373   r_free= 0.2911   ksol= 0.33   Bsol= 49.78   scale= 1.040   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.68,3.66,8.03,0.00,0.00,0.00); trace/3= 4.79                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.790401                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2360   r_free= 0.2917   ksol= 0.32   Bsol= 49.78   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.47,2.59,5.43,0.00,0.00,0.00); trace/3= 3.16                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.791784                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.848853              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.368  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.241065              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 129.080  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2360      final r-factor (work) = 0.1744          |
| start r-factor (free) = 0.2917      final r-factor (free) = 0.2271          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.2650 = 3.85 * 0.50 * 5.8137 + 1.00 * 0.0770                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.9746 = 3.85 * 0.50 * 5.6637 + 1.00 * 0.0753                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1744      final r-factor (work) = 0.1613          |
| start r-factor (free) = 0.2271      final r-factor (free) = 0.2103          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3768 = 0.24 * 1.00 * 5.6637 + 1.00 * 0.0115                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3377 = 0.24 * 1.00 * 5.4855 + 1.00 * 0.0153                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.032)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.97   12.85    None  None   None       |
|    all(noH): 2823   0      0.00    79.97   12.85    None  None   None       |
|    Sol.    : 438    0      1.81    69.03   33.81    None  None   None       |
|    Mac.    : 2385   0      0.00    79.97   9.00     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.997: 1395   |   5:    39.985 -  47.982:  113        |
|      1:     7.997 -  15.994:  795   |   6:    47.982 -  55.979:   50        |
|      2:    15.994 -  23.991:  200   |   7:    55.979 -  63.976:   15        |
|      3:    23.991 -  31.988:  118   |   8:    63.976 -  71.973:    4        |
|      4:    31.988 -  39.985:  132   |   9:    71.973 -  79.970:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1613 r_free = 0.2103             target_work(ml) = 5.450         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1611 r_free = 0.2103             target_work(ml) = 5.450         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1611   r_free= 0.2103   ksol= 0.32   Bsol= 49.78   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.47,2.59,5.43,0.00,0.00,0.00); trace/3= 3.16                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.449612                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1607   r_free= 0.2096   ksol= 0.32   Bsol= 58.01   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.87,1.81,3.90,0.00,0.00,0.00); trace/3= 2.19                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.449174                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.321387              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.865  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.785292              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 102.222  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1607      final r-factor (work) = 0.1331          |
| start r-factor (free) = 0.2096      final r-factor (free) = 0.1772          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.1937 = 3.32 * 0.50 * 5.4907 + 1.00 * 0.0753                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.9919 = 3.32 * 0.50 * 5.3698 + 1.00 * 0.0742                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1331      final r-factor (work) = 0.1287          |
| start r-factor (free) = 0.1772      final r-factor (free) = 0.1747          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2332 = 0.79 * 1.00 * 5.3698 + 1.00 * 0.0163                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.2017 = 0.79 * 1.00 * 5.2700 + 1.00 * 1.0632                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 6      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.032)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.35   12.83    None  None   None       |
|    all(noH): 2823   0      0.00    83.35   12.83    None  None   None       |
|    Sol.    : 438    0      1.28    70.45   34.50    None  None   None       |
|    Mac.    : 2385   0      0.00    83.35   8.85     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.335: 1490   |   5:    41.675 -  50.010:  112        |
|      1:     8.335 -  16.670:  712   |   6:    50.010 -  58.345:   43        |
|      2:    16.670 -  25.005:  193   |   7:    58.345 -  66.680:   13        |
|      3:    25.005 -  33.340:  124   |   8:    66.680 -  75.015:    4        |
|      4:    33.340 -  41.675:  131   |   9:    75.015 -  83.350:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1287 r_free = 0.1747             target_work(ml) = 5.265         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1285 r_free = 0.1746             target_work(ml) = 5.265         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1285   r_free= 0.1746   ksol= 0.32   Bsol= 58.01   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.87,1.81,3.90,0.00,0.00,0.00); trace/3= 2.19                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.264512                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1283   r_free= 0.1743   ksol= 0.33   Bsol= 58.01   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.04,1.87,3.68,0.00,0.00,0.00); trace/3= 2.20                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.263086                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.604588              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 134.237  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 16.109946             wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.548   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1283      final r-factor (work) = 0.1220          |
| start r-factor (free) = 0.1743      final r-factor (free) = 0.1676          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9366 = 2.60 * 0.50 * 5.2694 + 1.00 * 0.0742                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8971 = 2.60 * 0.50 * 5.2428 + 1.00 * 0.0694                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1220      final r-factor (work) = 0.1184          |
| start r-factor (free) = 0.1676      final r-factor (free) = 0.1666          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 84.4876 = 16.11 * 1.00 * 5.2428 + 1.00 * 0.0263                             |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 84.0114 = 16.11 * 1.00 * 5.2140 + 1.00 * 0.0149                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.032)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    94.92   13.52    None  None   None       |
|    all(noH): 2823   0      0.00    94.92   13.52    None  None   None       |
|    Sol.    : 438    0      1.38    94.92   38.28    None  None   None       |
|    Mac.    : 2385   0      0.00    81.82   8.98     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 -   9.492: 1696   |   5:    47.459 -  56.951:   98        |
|      1:     9.492 -  18.984:  572   |   6:    56.951 -  66.443:   53        |
|      2:    18.984 -  28.476:  163   |   7:    66.443 -  75.935:   20        |
|      3:    28.476 -  37.967:  118   |   8:    75.935 -  85.427:   11        |
|      4:    37.967 -  47.459:   91   |   9:    85.427 -  94.918:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1184 r_free = 0.1666             target_work(ml) = 5.211         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1183 r_free = 0.1666             target_work(ml) = 5.211         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1183   r_free= 0.1666   ksol= 0.33   Bsol= 58.01   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.04,1.87,3.68,0.00,0.00,0.00); trace/3= 2.20                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.211042                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9814 -  4.7272 0.99   1421  158 0.0987 0.1334      5.4152      5.5823|
|  2:  4.7272 -  3.7718 0.99   1375  152 0.0872 0.1094      5.4614      5.6714|
|  3:  3.7718 -  3.3009 0.99   1337  149 0.1134 0.1538      5.5182       5.846|
|  4:  3.3009 -  3.0017 0.99   1332  143 0.1274 0.1690      5.4842      5.6611|
|  5:  3.0017 -  2.7880 0.99   1310  154 0.1408 0.1675      5.3835      5.5525|
|  6:  2.7880 -  2.6246 0.99   1330  144 0.1325 0.2242      5.2773      5.5913|
|  7:  2.6246 -  2.4938 0.99   1299  147 0.1368 0.1714      5.2415      5.3873|
|  8:  2.4938 -  2.3857 0.98   1312  142 0.1235 0.1806      5.1517      5.3932|
|  9:  2.3857 -  2.2942 0.98   1314  146 0.1280 0.2116      5.1033      5.4356|
| 10:  2.2942 -  2.2153 0.98   1291  138 0.1212 0.1661      5.0291      5.2174|
| 11:  2.2153 -  2.1462 1.00   1307  158 0.1240 0.2046      5.0041      5.3651|
| 12:  2.1462 -  2.0850 0.97   1286  133 0.1241 0.1601      4.9499      5.1721|
| 13:  2.0850 -  2.0303 0.94   1247  138 0.1138 0.1914      4.8384      5.0901|
| 14:  2.0303 -  1.9808 0.36    469   57 0.0971 0.1864      4.7053      5.0374|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9814 -  4.7272  1421   158  0.93   9.90   0.97     0.94       8213.35|
|  2:  4.7272 -  3.7718  1375   152  0.95   8.60   1.01     0.99       9741.90|
|  3:  3.7718 -  3.3009  1337   149  0.93  11.96   1.02     1.02      11102.95|
|  4:  3.3009 -  3.0017  1332   143  0.92  14.16   1.01     0.99      10900.56|
|  5:  3.0017 -  2.7880  1310   154  0.89  17.09   0.99     0.97       9457.00|
|  6:  2.7880 -  2.6246  1330   144  0.88  18.16   0.97     0.94       8315.81|
|  7:  2.6246 -  2.4938  1299   147  0.89  17.11   0.98     0.94       7252.23|
|  8:  2.4938 -  2.3857  1312   142  0.89  17.06   0.99     0.95       6501.34|
|  9:  2.3857 -  2.2942  1314   146  0.89  17.44   0.99     0.95       5870.94|
| 10:  2.2942 -  2.2153  1291   138  0.89  17.70   0.99     0.94       5286.66|
| 11:  2.2153 -  2.1462  1307   158  0.88  18.14   0.98     0.93       5124.07|
| 12:  2.1462 -  2.0850  1286   133  0.89  17.75   0.99     0.97       4696.77|
| 13:  2.0850 -  2.0303  1247   138  0.89  17.70   0.97     0.95       3907.80|
| 14:  2.0303 -  1.9808   469    57  0.91  15.18   0.95     0.91       2928.78|
|alpha:            min =        0.91 max =            1.02 mean =         0.96|
|beta:             min =     2928.78 max =        11102.95 mean =      7337.09|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.84 mean =        15.51|
|phase err.(test): min =        0.00 max =           89.05 mean =        14.95|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1182   r_free= 0.1664   ksol= 0.32   Bsol= 60.44   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.10,-0.31,1.41,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.211125                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1182   r_free= 0.1664   ksol= 0.32   Bsol= 60.44   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.10,-0.31,1.41,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.211125                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9814 -  4.7272 0.99   1421  158 0.0985 0.1333       5.414      5.5833|
|  2:  4.7272 -  3.7718 0.99   1375  152 0.0873 0.1096      5.4625      5.6722|
|  3:  3.7718 -  3.3009 0.99   1337  149 0.1135 0.1540      5.5187      5.8467|
|  4:  3.3009 -  3.0017 0.99   1332  143 0.1274 0.1690      5.4841      5.6615|
|  5:  3.0017 -  2.7880 0.99   1310  154 0.1407 0.1674      5.3833      5.5519|
|  6:  2.7880 -  2.6246 0.99   1330  144 0.1325 0.2243      5.2773      5.5916|
|  7:  2.6246 -  2.4938 0.99   1299  147 0.1367 0.1714      5.2417      5.3875|
|  8:  2.4938 -  2.3857 0.98   1312  142 0.1235 0.1807      5.1523      5.3939|
|  9:  2.3857 -  2.2942 0.98   1314  146 0.1280 0.2116      5.1036      5.4358|
| 10:  2.2942 -  2.2153 0.98   1291  138 0.1213 0.1660      5.0294      5.2171|
| 11:  2.2153 -  2.1462 1.00   1307  158 0.1240 0.2042      5.0038      5.3643|
| 12:  2.1462 -  2.0850 0.97   1286  133 0.1240 0.1601      4.9498       5.172|
| 13:  2.0850 -  2.0303 0.94   1247  138 0.1138 0.1915      4.8383      5.0903|
| 14:  2.0303 -  1.9808 0.36    469   57 0.0971 0.1861      4.7059      5.0371|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9814 -  4.7272  1421   158  0.93   9.90   0.97     0.94       8201.40|
|  2:  4.7272 -  3.7718  1375   152  0.95   8.61   1.01     0.99       9755.20|
|  3:  3.7718 -  3.3009  1337   149  0.93  11.98   1.03     1.02      11127.55|
|  4:  3.3009 -  3.0017  1332   143  0.92  14.17   1.01     1.00      10902.91|
|  5:  3.0017 -  2.7880  1310   154  0.89  17.09   1.00     0.98       9459.51|
|  6:  2.7880 -  2.6246  1330   144  0.88  18.17   0.98     0.94       8313.95|
|  7:  2.6246 -  2.4938  1299   147  0.89  17.12   0.99     0.95       7257.25|
|  8:  2.4938 -  2.3857  1312   142  0.89  17.08   1.00     0.95       6512.20|
|  9:  2.3857 -  2.2942  1314   146  0.89  17.46   1.00     0.96       5876.16|
| 10:  2.2942 -  2.2153  1291   138  0.89  17.70   1.00     0.95       5286.59|
| 11:  2.2153 -  2.1462  1307   158  0.88  18.13   0.99     0.95       5115.37|
| 12:  2.1462 -  2.0850  1286   133  0.89  17.74   1.00     0.98       4695.16|
| 13:  2.0850 -  2.0303  1247   138  0.89  17.69   0.99     0.96       3905.08|
| 14:  2.0303 -  1.9808   469    57  0.91  15.19   0.97     0.93       2927.09|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2927.09 max =        11127.55 mean =      7339.82|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.86 mean =        15.51|
|phase err.(test): min =        0.00 max =           89.00 mean =        14.95|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.032)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.43    97.35   15.95    None  None   None       |
|    all(noH): 2823   0      2.43    97.35   15.95    None  None   None       |
|    Sol.    : 438    0      3.80    97.35   40.71    None  None   None       |
|    Mac.    : 2385   0      2.43    84.25   11.40    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:     2.427 -  11.919: 1696   |   5:    49.886 -  59.378:   98        |
|      1:    11.919 -  21.411:  572   |   6:    59.378 -  68.870:   53        |
|      2:    21.411 -  30.902:  163   |   7:    68.870 -  78.362:   20        |
|      3:    30.902 -  40.394:  118   |   8:    78.362 -  87.853:   11        |
|      4:    40.394 -  49.886:   91   |   9:    87.853 -  97.345:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 304         
Filter by distance & map next to the model:
   mapped sites are within: 0.235 - 5.585
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 294 from: 304
   mapped sites are within: 0.710 - 5.585

peak=   10.469 closest distance to " CB  VAL A 230 " =    1.461
peak=    5.773 closest distance to " CG  LEU A   5 " =    1.175
peak=    5.515 closest distance to " NH2 ARG A  56 " =    2.087
peak=    5.396 closest distance to " CG  PRO A  54 " =    1.363
peak=    5.366 closest distance to " NE2 GLN A  11 " =    1.051
peak=    5.317 closest distance to " CG  LEU A 228 " =    1.222
peak=    5.308 closest distance to " CB  VAL A 296 " =    1.095
peak=    5.261 closest distance to " O   HOH Z 142 " =    1.814
peak=    5.250 closest distance to " CD2 LEU A   5 " =    1.170
peak=    5.244 closest distance to " CG1 VAL A 296 " =    1.194
peak=    5.229 closest distance to " CB  GLN A 223 " =    1.497
peak=    5.157 closest distance to " CG  PRO A 280 " =    0.958
peak=    4.956 closest distance to " O   HOH Z 248 " =    1.306
peak=    4.854 closest distance to " CG2 VAL A 296 " =    1.038
peak=    4.687 closest distance to " CB  ARG A 275 " =    0.933
peak=    4.630 closest distance to " CB  VAL A 230 " =    1.122
peak=    4.616 closest distance to " CZ  PHE A 218 " =    1.176
peak=    4.501 closest distance to " O   HOH Z 251 " =    1.722
peak=    4.453 closest distance to " CG  PRO A 243 " =    1.114
peak=    4.448 closest distance to " O   HOH Z 265 " =    2.110
peak=    4.439 closest distance to " CD1AILE A 234 " =    0.972
peak=    4.438 closest distance to " O   HOH Z 232 " =    2.338
peak=    4.388 closest distance to " CB  ARG A 190 " =    1.648
peak=    4.358 closest distance to " CB  ASN A 148 " =    1.491
peak=    4.358 closest distance to " CB  ARG A  79 " =    1.382
peak=    4.335 closest distance to " O   HOH Z 126 " =    1.597
peak=    4.329 closest distance to " O   HOH Z 369 " =    2.244
peak=    4.309 closest distance to " CB  GLN A 183 " =    1.295
peak=    4.290 closest distance to " CZ3 TRP A 266 " =    1.112
peak=    4.277 closest distance to " O   HOH Z 313 " =    1.984
peak=    4.270 closest distance to " CD2 TRP A 179 " =    1.289
peak=    4.245 closest distance to " O   HOH Z  91 " =    2.402
peak=    4.245 closest distance to " O   PRO A 198 " =    1.571
peak=    4.228 closest distance to " CB  GLU A 277 " =    3.722
peak=    4.209 closest distance to " O   HOH Z  76 " =    1.205
peak=    4.198 closest distance to " CG  ARG A 138 " =    1.357
peak=    4.196 closest distance to " CA  TYR A  30 " =    0.952
peak=    4.189 closest distance to " CE  LYS A  76 " =    0.910
peak=    4.180 closest distance to " CB  PRO A  54 " =    0.978
peak=    4.167 closest distance to " CB  ASN A 142 " =    1.228
peak=    4.165 closest distance to " O   HOH Z 427 " =    2.973
peak=    4.154 closest distance to " O   HOH Z 261 " =    2.462
peak=    4.089 closest distance to " O   HOH Z 188 " =    2.819
peak=    4.088 closest distance to " CD2 LEU A 228 " =    1.222
peak=    4.077 closest distance to " O   HOH Z 287 " =    1.891
peak=    4.074 closest distance to " O   HOH Z 303 " =    2.133
peak=    4.057 closest distance to " O   HOH Z 128 " =    1.343
peak=    4.036 closest distance to " O   HOH Z 359 " =    1.864
peak=    4.034 closest distance to " CB  SER A  63 " =    1.144
peak=    4.023 closest distance to " NH2AARG A 145 " =    1.188
peak=    4.022 closest distance to " O   HOH Z 368 " =    2.442
peak=    3.998 closest distance to " O   HOH Z 411 " =    3.911
peak=    3.974 closest distance to " CA  ARG A  36 " =    1.034
peak=    3.968 closest distance to " CB  VAL A 265 " =    1.243
peak=    3.952 closest distance to " O   HOH Z 280 " =    2.997
peak=    3.946 closest distance to " O   HOH Z  92 " =    2.084
peak=    3.928 closest distance to " O  BHOH Z 338 " =    2.227
peak=    3.921 closest distance to " O   HOH Z 214 " =    2.839
peak=    3.920 closest distance to " CB  GLU A 152 " =    1.121
peak=    3.916 closest distance to " O   HOH Z 403 " =    1.576
peak=    3.909 closest distance to " O   HOH Z  43 " =    2.033
peak=    3.907 closest distance to " O   HOH Z  78 " =    1.687
peak=    3.903 closest distance to " O   HOH Z 126 " =    1.932
peak=    3.891 closest distance to " CB  PRO A  90 " =    1.131
peak=    3.885 closest distance to " CB  ASP A 124 " =    0.852
peak=    3.885 closest distance to " CA  ALA A  51 " =    0.967
peak=    3.880 closest distance to " O   HOH Z 422 " =    2.615
peak=    3.873 closest distance to " O   HOH Z 425 " =    1.458
peak=    3.870 closest distance to " ND2 ASN A 249 " =    0.940
peak=    3.868 closest distance to " CB  TRP A 266 " =    1.093
peak=    3.865 closest distance to " CD  ARG A 159 " =    0.744
peak=    3.863 closest distance to " CA  ARG A 195 " =    1.217
peak=    3.860 closest distance to " CB  ASP A 298 " =    1.183
peak=    3.856 closest distance to " OG BSER A 164 " =    2.293
peak=    3.850 closest distance to " CZ  PHE A  38 " =    1.162
peak=    3.843 closest distance to " CG  ARG A  66 " =    2.522
peak=    3.833 closest distance to " CB  THR A  31 " =    1.480
peak=    3.827 closest distance to " O   HOH Z 353 " =    2.754
peak=    3.812 closest distance to " CD1 ILE A 199 " =    1.161
peak=    3.808 closest distance to " CB  ASN A 110 " =    1.179
peak=    3.799 closest distance to " O   HOH Z 298 " =    1.786
peak=    3.799 closest distance to " O   HOH Z 214 " =    1.339
peak=    3.796 closest distance to " O   HOH Z 346 " =    1.544
peak=    3.792 closest distance to " CG  PRO A 213 " =    1.130
peak=    3.790 closest distance to " CG2AVAL A 121 " =    2.307
peak=    3.780 closest distance to " CB  TRP A 179 " =    1.461
peak=    3.778 closest distance to " CB  LYS A 117 " =    1.190
peak=    3.772 closest distance to " O   HOH Z 402 " =    1.363
peak=    3.772 closest distance to " CA  VAL A 125 " =    1.104
peak=    3.770 closest distance to " CG  PRO A 198 " =    1.253
peak=    3.758 closest distance to " O   HOH Z 365 " =    2.679
peak=    3.755 closest distance to " CD1 LEU A  96 " =    0.760
peak=    3.751 closest distance to " NZ  LYS A 117 " =    3.044
peak=    3.740 closest distance to " N   ASP A 162 " =    1.236
peak=    3.739 closest distance to " O   ASP A 124 " =    1.142
peak=    3.717 closest distance to " CG  GLN A  58 " =    0.984
peak=    3.705 closest distance to " O   HOH Z 154 " =    1.522
peak=    3.702 closest distance to " O   HOH Z 406 " =    1.482
peak=    3.701 closest distance to " CA  TYR A 116 " =    1.459
peak=    3.696 closest distance to " N   ASN A  39 " =    1.259
peak=    3.695 closest distance to " CB  SER A  26 " =    1.847
peak=    3.692 closest distance to " CG2 ILE A 234 " =    1.073
peak=    3.690 closest distance to " CB  GLU A 128 " =    1.156
peak=    3.688 closest distance to " CB  ARG A 138 " =    0.812
peak=    3.683 closest distance to " O   HOH Z 209 " =    2.267
peak=    3.679 closest distance to " NZ  LYS A  48 " =    1.125
peak=    3.679 closest distance to " CD2 LEU A   5 " =    0.728
peak=    3.676 closest distance to " O  BHOH Z  74 " =    1.235
peak=    3.670 closest distance to " O   HOH Z 371 " =    2.865
peak=    3.670 closest distance to " CG AARG A 275 " =    1.196
peak=    3.660 closest distance to " O   HOH Z 299 " =    4.254
peak=    3.659 closest distance to " CG  MET A 185 " =    1.241
peak=    3.655 closest distance to " CG1 VAL A 153 " =    0.938
peak=    3.646 closest distance to " CB  THR A  52 " =    0.755
peak=    3.638 closest distance to " CB  VAL A 202 " =    1.488
peak=    3.632 closest distance to " O   HOH Z  61 " =    1.777
peak=    3.627 closest distance to " O   HOH Z 193 " =    1.540
peak=    3.622 closest distance to " CG  PHE A 204 " =    0.933
peak=    3.616 closest distance to " O   HOH Z  80 " =    1.885
peak=    3.614 closest distance to " CD  ARG A 269 " =    0.981
peak=    3.614 closest distance to " O   HOH Z 162 " =    1.420
peak=    3.613 closest distance to " NE2 HIS A 207 " =    1.134
peak=    3.604 closest distance to " OE1 GLN A  55 " =    1.446
peak=    3.602 closest distance to " CB  ASN A  39 " =    0.903
peak=    3.600 closest distance to " O   HOH Z 247 " =    1.331
peak=    3.593 closest distance to " CA  ALA A 160 " =    0.952
peak=    3.591 closest distance to " O   HOH Z 337 " =    1.987
peak=    3.587 closest distance to " CB  ASP A 140 " =    1.222
peak=    3.586 closest distance to " OG  SER A 276 " =    1.401
peak=    3.582 closest distance to " O   HOH Z 368 " =    3.438
peak=    3.573 closest distance to " CB AVAL A  41 " =    1.169
peak=    3.568 closest distance to " O   HOH Z  68 " =    2.163
peak=    3.566 closest distance to " O   HOH Z 207 " =    1.178
peak=    3.562 closest distance to " CG  LEU A 167 " =    1.232
peak=    3.561 closest distance to " O   HOH Z 238 " =    1.034
peak=    3.559 closest distance to " NH1AARG A 145 " =    1.277
peak=    3.549 closest distance to " O   HOH Z 203 " =    1.482
peak=    3.549 closest distance to " ND2 ASN A 187 " =    1.682
peak=    3.539 closest distance to " O   HOH Z 438 " =    2.807
peak=    3.537 closest distance to " CB  ARG A 145 " =    0.933
peak=    3.532 closest distance to " CB  ALA A 248 " =    1.417
peak=    3.531 closest distance to " CA  MET A 105 " =    1.053
peak=    3.531 closest distance to " O   HOH Z 193 " =    1.677
peak=    3.520 closest distance to " O   HOH Z 430 " =    5.585
peak=    3.519 closest distance to " O   HOH Z 316 " =    3.039
peak=    3.518 closest distance to " CB  SER A 273 " =    0.920
peak=    3.515 closest distance to " O   GLN A  88 " =    1.661
peak=    3.513 closest distance to " O   HOH Z   3 " =    1.855
peak=    3.505 closest distance to " CB  GLN A  89 " =    1.225
peak=    3.505 closest distance to " O   ASN A  74 " =    1.310
peak=    3.498 closest distance to " CB  PHE A 204 " =    0.968
peak=    3.491 closest distance to " O   HOH Z   4 " =    1.536
peak=    3.487 closest distance to " O   HOH Z 290 " =    1.014
peak=    3.485 closest distance to " CE1 TYR A 186 " =    1.296
peak=    3.483 closest distance to " CG  GLU A  37 " =    0.966
peak=    3.481 closest distance to " CA  ASP A 162 " =    1.025
peak=    3.481 closest distance to " OD1 ASN A  69 " =    2.484
peak=    3.479 closest distance to " O   HOH Z 234 " =    3.613
peak=    3.478 closest distance to " O   HOH Z  63 " =    1.734
peak=    3.464 closest distance to " O   HOH Z 258 " =    1.978
peak=    3.461 closest distance to " CD  LYS A 119 " =    1.851
peak=    3.447 closest distance to " CD  LYS A  76 " =    1.968
peak=    3.447 closest distance to " CD1 ILE A  33 " =    1.797
peak=    3.445 closest distance to " O   HOH Z   9 " =    1.235
peak=    3.444 closest distance to " CD  LYS A 166 " =    1.388
peak=    3.441 closest distance to " CG1 ILE A  49 " =    1.620
peak=    3.438 closest distance to " CB  SER A   3 " =    1.323
peak=    3.427 closest distance to " CA  SER A  87 " =    1.019
peak=    3.426 closest distance to " O   HOH Z 158 " =    3.105
peak=    3.425 closest distance to " O   HOH Z 154 " =    2.203
peak=    3.425 closest distance to " CA  ASN A 217 " =    1.134
peak=    3.419 closest distance to " O   HOH Z 213 " =    1.873
peak=    3.414 closest distance to " CA  ALA A 291 " =    0.864
peak=    3.414 closest distance to " N   PHE A 130 " =    1.297
peak=    3.409 closest distance to " CG2 VAL A 257 " =    0.729
peak=    3.408 closest distance to " O   HOH Z  97 " =    2.284
peak=    3.403 closest distance to " CD2 LEU A 297 " =    0.867
peak=    3.402 closest distance to " CA  ASP A 191 " =    1.309
peak=    3.399 closest distance to " CA  ALA A 158 " =    1.339
peak=    3.399 closest distance to " O   HOH Z 345 " =    3.428
peak=    3.395 closest distance to " CG AARG A 102 " =    1.209
peak=    3.392 closest distance to " O   HOH Z 417 " =    3.202
peak=    3.389 closest distance to " O   HOH Z  85 " =    1.190
peak=    3.382 closest distance to " CG2 ILE A  20 " =    1.487
peak=    3.375 closest distance to " OG BSER A 134 " =    2.977
peak=    3.371 closest distance to " CA  ALA A  21 " =    1.095
peak=    3.371 closest distance to " O   HOH Z  21 " =    1.746
peak=    3.369 closest distance to " CB  SER A  62 " =    0.928
peak=    3.362 closest distance to " CB  PRO A 198 " =    1.192
peak=    3.355 closest distance to " O   HOH Z 171 " =    3.977
peak=    3.355 closest distance to " O   HOH Z 421 " =    3.010
peak=    3.343 closest distance to " O   ALA A 165 " =    1.502
peak=    3.341 closest distance to " CD1 LEU A 101 " =    1.172
peak=    3.340 closest distance to " O   HOH Z 148 " =    3.450
peak=    3.340 closest distance to " CA  ASN A  74 " =    1.159
peak=    3.337 closest distance to " O   THR A 220 " =    1.305
peak=    3.332 closest distance to " CA  LEU A 282 " =    1.187
peak=    3.331 closest distance to " O   HOH Z 329 " =    4.225
peak=    3.330 closest distance to " O   THR A 182 " =    1.451
peak=    3.318 closest distance to " CD BLYS A 290 " =    1.033
peak=    3.316 closest distance to " CB  GLU A  46 " =    0.978
peak=    3.315 closest distance to " C   GLN A  73 " =    1.096
peak=    3.314 closest distance to " O   ASP A 200 " =    1.646
peak=    3.312 closest distance to " CB  ASN A 215 " =    1.181
peak=    3.311 closest distance to " CB  ARG A 156 " =    1.175
peak=    3.310 closest distance to " CE3 TRP A 150 " =    1.127
peak=    3.306 closest distance to " O   HOH Z  88 " =    3.598
peak=    3.304 closest distance to " O   ARG A  56 " =    3.100
peak=    3.302 closest distance to " O   HOH Z 327 " =    2.540
peak=    3.302 closest distance to " O   HOH Z 128 " =    1.118
peak=    3.298 closest distance to " O   HOH Z 383 " =    1.856
peak=    3.296 closest distance to " CB  ALA A   9 " =    1.656
peak=    3.294 closest distance to " CG  LEU A 281 " =    1.014
peak=    3.294 closest distance to " O   HOH Z 272 " =    1.823
peak=    3.291 closest distance to " CE  LYS A  48 " =    1.174
peak=    3.286 closest distance to " O   HOH Z 293 " =    1.954
peak=    3.285 closest distance to " O   HOH Z 187 " =    2.269
peak=    3.283 closest distance to " O   HOH Z 368 " =    4.227
peak=    3.281 closest distance to " O   ASN A 284 " =    1.822
peak=    3.280 closest distance to " CB  ALA A 114 " =    0.710
peak=    3.276 closest distance to " O   PHE A 192 " =    1.310
peak=    3.275 closest distance to " CA  ALA A 154 " =    1.074
peak=    3.274 closest distance to " CA  ASN A 215 " =    0.984
peak=    3.268 closest distance to " O   ASP A 191 " =    1.580
peak=    3.264 closest distance to " O   HOH Z 193 " =    1.562
peak=    3.263 closest distance to " O   HOH Z 281 " =    2.572
peak=    3.262 closest distance to " O   HOH Z 393 " =    3.130
peak=    3.260 closest distance to " O   HOH Z 371 " =    2.384
peak=    3.257 closest distance to " O   HOH Z 245 " =    1.284
peak=    3.251 closest distance to " O   HOH Z 172 " =    3.842
peak=    3.249 closest distance to " O   HOH Z 263 " =    1.670
peak=    3.247 closest distance to " CA  ALA A 100 " =    0.832
peak=    3.245 closest distance to " CA  LYS A 290 " =    1.193
peak=    3.243 closest distance to " O   HOH Z 357 " =    2.136
peak=    3.242 closest distance to " O   HOH Z 361 " =    3.707
peak=    3.239 closest distance to " OG BSER A 164 " =    2.516
peak=    3.224 closest distance to " O   ALA A   1 " =    1.794
peak=    3.222 closest distance to " O   HOH Z 180 " =    2.136
peak=    3.220 closest distance to " CG BARG A 102 " =    1.820
peak=    3.220 closest distance to " O   HOH Z  40 " =    1.886
peak=    3.220 closest distance to " OE2 GLU A  53 " =    1.935
peak=    3.217 closest distance to " O   LEU A 228 " =    1.782
peak=    3.216 closest distance to " CB  GLN A 205 " =    1.069
peak=    3.216 closest distance to " O   HOH Z 410 " =    3.105
peak=    3.213 closest distance to " CB  ASN A 285 " =    1.011
peak=    3.206 closest distance to " O   HOH Z  83 " =    1.484
peak=    3.202 closest distance to " OG1 THR A 264 " =    0.715
peak=    3.201 closest distance to " O   HOH Z 392 " =    2.892
peak=    3.194 closest distance to " CB  GLN A  88 " =    1.282
peak=    3.192 closest distance to " O   HOH Z 189 " =    2.937
peak=    3.188 closest distance to " O   HOH Z 106 " =    1.982
peak=    3.187 closest distance to " O   TRP A 274 " =    1.767
peak=    3.186 closest distance to " CA  GLN A  94 " =    0.788
peak=    3.183 closest distance to " CD  ARG A 138 " =    0.838
peak=    3.175 closest distance to " OG  SER A 245 " =    1.560
peak=    3.172 closest distance to " C   ILE A 106 " =    1.874
peak=    3.172 closest distance to " CB  SER A 288 " =    1.519
peak=    3.171 closest distance to " O   HOH Z 145 " =    2.504
peak=    3.171 closest distance to " ND2BASN A 224 " =    0.855
peak=    3.162 closest distance to " CB  ARG A 139 " =    0.896
peak=    3.162 closest distance to " O   HOH Z 133 " =    2.773
peak=    3.161 closest distance to " O   HOH Z 389 " =    1.827
peak=    3.157 closest distance to " CB  SER A  97 " =    0.767
peak=    3.156 closest distance to " CB  ASP A 107 " =    1.166
peak=    3.156 closest distance to " CB  PRO A 243 " =    1.116
peak=    3.153 closest distance to " CZ3 TRP A  85 " =    0.914
peak=    3.150 closest distance to " O   HOH Z  88 " =    2.599
peak=    3.140 closest distance to " CA  LYS A 117 " =    1.326
peak=    3.139 closest distance to " O   HOH Z  10 " =    1.771
peak=    3.138 closest distance to " O   HOH Z 117 " =    2.062
peak=    3.134 closest distance to " CG2 VAL A 197 " =    0.984
peak=    3.131 closest distance to " OG  SER A  62 " =    2.822
peak=    3.128 closest distance to " O   HOH Z 199 " =    1.567
peak=    3.126 closest distance to " O   HOH Z 188 " =    1.337
peak=    3.122 closest distance to " O   HOH Z 285 " =    2.140
peak=    3.113 closest distance to " O   HOH Z  35 " =    4.431
peak=    3.112 closest distance to " CG1 ILE A  20 " =    1.240
peak=    3.112 closest distance to " O   ILE A  49 " =    1.133
peak=    3.111 closest distance to " O   HOH Z  94 " =    2.469
peak=    3.103 closest distance to " O   SER A 164 " =    1.342
peak=    3.100 closest distance to " CA  ARG A 102 " =    1.161
peak=    3.100 closest distance to " O   HOH Z 305 " =    3.441
peak=    3.096 closest distance to " O   HOH Z 391 " =    2.990
peak=    3.089 closest distance to " CA  ILE A 106 " =    0.783
peak=    3.087 closest distance to " N   ALA A 256 " =    1.070
peak=    3.077 closest distance to " CB  ALA A  43 " =    0.741
peak=    3.076 closest distance to " CG2 VAL A 126 " =    0.857
peak=    3.074 closest distance to " CB  TYR A  30 " =    1.121
peak=    3.073 closest distance to " CA  ARG A 139 " =    1.109
peak=    3.068 closest distance to " O   HOH Z 272 " =    2.420
peak=    3.057 closest distance to " CD  ARG A 195 " =    1.043
peak=    3.050 closest distance to " N   GLY A 133 " =    3.798
peak=    3.041 closest distance to " CE2 PHE A  16 " =    0.870
peak=    3.033 closest distance to " CG  GLN A  11 " =    2.086

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 220         
Filter by distance & map next to the model:
   mapped sites are within: 0.791 - 5.649
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 219 from: 220
   mapped sites are within: 0.791 - 5.649

peak=   -5.171 closest distance to " SG  CYS A 254 " =    3.346
peak=   -4.585 closest distance to " C   HIS A 108 " =    1.193
peak=   -4.437 closest distance to " O   HOH Z 211 " =    1.162
peak=   -4.409 closest distance to " CG2 VAL A 230 " =    0.791
peak=   -4.309 closest distance to " O   VAL A  67 " =    2.665
peak=   -4.278 closest distance to " CG1 VAL A 112 " =    2.743
peak=   -4.259 closest distance to " O   HOH Z 193 " =    0.847
peak=   -4.244 closest distance to " CB  PRO A 243 " =    2.766
peak=   -4.202 closest distance to " CD  ARG A 156 " =    2.045
peak=   -4.192 closest distance to " OE1 GLN A 223 " =    2.397
peak=   -4.175 closest distance to " CG  GLN A  58 " =    1.048
peak=   -4.173 closest distance to " OG BSER A 134 " =    1.484
peak=   -4.149 closest distance to " CE3 TRP A 150 " =    2.316
peak=   -4.109 closest distance to " O   PRO A 198 " =    1.254
peak=   -4.064 closest distance to " CA  ASP A 298 " =    1.108
peak=   -4.044 closest distance to " CG1 VAL A 250 " =    2.725
peak=   -3.994 closest distance to " CG1 VAL A 296 " =    1.025
peak=   -3.983 closest distance to " CB  ALA A  43 " =    2.568
peak=   -3.970 closest distance to " O   HOH Z 267 " =    5.649
peak=   -3.949 closest distance to " CB  PHE A 192 " =    1.973
peak=   -3.923 closest distance to " O   HOH Z 196 " =    2.236
peak=   -3.914 closest distance to " OG  SER A  97 " =    2.394
peak=   -3.911 closest distance to " O   PRO A 163 " =    2.173
peak=   -3.899 closest distance to " O   HOH Z 166 " =    1.861
peak=   -3.888 closest distance to " O   HOH Z 359 " =    2.877
peak=   -3.885 closest distance to " OXT GLY A 302 " =    2.898
peak=   -3.860 closest distance to " O   HOH Z 198 " =    1.967
peak=   -3.858 closest distance to " O   SER A 271 " =    2.216
peak=   -3.854 closest distance to " CG2 VAL A 189 " =    2.058
peak=   -3.853 closest distance to " CD2 TYR A 293 " =    1.998
peak=   -3.842 closest distance to " O   HOH Z 133 " =    1.049
peak=   -3.838 closest distance to " O   HOH Z 231 " =    2.128
peak=   -3.838 closest distance to " CD1 LEU A 101 " =    2.373
peak=   -3.830 closest distance to " O   HOH Z 214 " =    2.602
peak=   -3.825 closest distance to " O   HOH Z 131 " =    4.125
peak=   -3.787 closest distance to " CG2 ILE A  20 " =    3.009
peak=   -3.773 closest distance to " CB  VAL A 230 " =    1.081
peak=   -3.770 closest distance to " CZ2 TRP A  92 " =    2.858
peak=   -3.760 closest distance to " CG  GLU A 277 " =    1.263
peak=   -3.733 closest distance to " O   HOH Z 216 " =    1.232
peak=   -3.729 closest distance to " O   HOH Z  73 " =    2.427
peak=   -3.719 closest distance to " N   THR A  52 " =    1.665
peak=   -3.707 closest distance to " CE2 TYR A  30 " =    2.696
peak=   -3.702 closest distance to " CG  ARG A 269 " =    2.220
peak=   -3.679 closest distance to " O   MET A  40 " =    2.897
peak=   -3.678 closest distance to " ND2 ASN A  45 " =    1.178
peak=   -3.669 closest distance to " O   HOH Z 252 " =    3.582
peak=   -3.663 closest distance to " O   HOH Z 128 " =    2.483
peak=   -3.658 closest distance to " CB  ALA A 161 " =    2.495
peak=   -3.657 closest distance to " CG  PRO A 243 " =    1.650
peak=   -3.644 closest distance to " O   HOH Z 154 " =    1.537
peak=   -3.640 closest distance to " O   HOH Z 394 " =    1.637
peak=   -3.615 closest distance to " O   HOH Z 128 " =    1.077
peak=   -3.610 closest distance to " CE BMET A  47 " =    1.298
peak=   -3.609 closest distance to " O   HOH Z 275 " =    1.813
peak=   -3.602 closest distance to " O   HOH Z  38 " =    1.748
peak=   -3.601 closest distance to " O   HOH Z  19 " =    2.335
peak=   -3.600 closest distance to " O   HOH Z 127 " =    1.092
peak=   -3.597 closest distance to " NE2 GLN A  11 " =    1.698
peak=   -3.585 closest distance to " CE2 TRP A  70 " =    2.092
peak=   -3.581 closest distance to " O   HOH Z 107 " =    0.962
peak=   -3.566 closest distance to " O   HOH Z 102 " =    1.516
peak=   -3.559 closest distance to " O   HOH Z 191 " =    5.623
peak=   -3.546 closest distance to " O   HOH Z 110 " =    1.409
peak=   -3.541 closest distance to " O   HOH Z 285 " =    1.973
peak=   -3.535 closest distance to " O   HOH Z 165 " =    1.977
peak=   -3.533 closest distance to " CG2 THR A 178 " =    2.492
peak=   -3.532 closest distance to " CB  HIS A  86 " =    1.164
peak=   -3.528 closest distance to " CG2 VAL A 296 " =    1.285
peak=   -3.524 closest distance to " O   HOH Z 174 " =    2.464
peak=   -3.519 closest distance to " CA  GLY A 241 " =    2.425
peak=   -3.500 closest distance to " NE  ARG A  66 " =    4.317
peak=   -3.493 closest distance to " O   ALA A 227 " =    1.333
peak=   -3.484 closest distance to " O   HOH Z  52 " =    1.717
peak=   -3.464 closest distance to " O   HOH Z  43 " =    1.668
peak=   -3.464 closest distance to " O   HOH Z 351 " =    1.703
peak=   -3.462 closest distance to " CA  GLY A 133 " =    2.357
peak=   -3.462 closest distance to " O   HOH Z 251 " =    5.045
peak=   -3.453 closest distance to " CD1 ILE A 199 " =    2.393
peak=   -3.446 closest distance to " CD2 HIS A 207 " =    2.213
peak=   -3.436 closest distance to " O   HOH Z 286 " =    1.859
peak=   -3.434 closest distance to " CB  ALA A 248 " =    2.284
peak=   -3.430 closest distance to " O   SER A 210 " =    1.733
peak=   -3.425 closest distance to " O   HOH Z 139 " =    5.136
peak=   -3.422 closest distance to " O   HOH Z 295 " =    1.662
peak=   -3.422 closest distance to " O   HOH Z  91 " =    1.333
peak=   -3.417 closest distance to " CD1 LEU A 255 " =    2.797
peak=   -3.416 closest distance to " CG1 VAL A 197 " =    2.214
peak=   -3.415 closest distance to " CA  GLY A 203 " =    2.420
peak=   -3.411 closest distance to " O   HOH Z 106 " =    1.802
peak=   -3.410 closest distance to " OD1 ASN A 148 " =    1.329
peak=   -3.407 closest distance to " N   ALA A 226 " =    2.034
peak=   -3.404 closest distance to " CG1 VAL A 112 " =    2.662
peak=   -3.400 closest distance to " CE  MET A 105 " =    2.413
peak=   -3.398 closest distance to " CG  GLN A 103 " =    2.511
peak=   -3.398 closest distance to " O   ASP A  27 " =    1.991
peak=   -3.397 closest distance to " O   HOH Z 103 " =    1.774
peak=   -3.395 closest distance to " O   ILE A 106 " =    1.816
peak=   -3.390 closest distance to " CZ3 TRP A 179 " =    1.303
peak=   -3.379 closest distance to " O   HOH Z  64 " =    1.584
peak=   -3.379 closest distance to " O   HOH Z 149 " =    1.989
peak=   -3.377 closest distance to " N   SER A 276 " =    1.381
peak=   -3.377 closest distance to " CB  PRO A 163 " =    2.511
peak=   -3.369 closest distance to " O   HOH Z   6 " =    2.234
peak=   -3.368 closest distance to " ND2 ASN A 249 " =    2.332
peak=   -3.367 closest distance to " ND2 ASN A 187 " =    1.543
peak=   -3.367 closest distance to " NE2 GLN A  88 " =    1.135
peak=   -3.366 closest distance to " CG2 ILE A 263 " =    2.369
peak=   -3.361 closest distance to " CD  LYS A 289 " =    2.456
peak=   -3.358 closest distance to " O   HOH Z 348 " =    2.240
peak=   -3.358 closest distance to " O   HOH Z 357 " =    2.181
peak=   -3.357 closest distance to " CG  LEU A   5 " =    1.034
peak=   -3.351 closest distance to " O   HOH Z 119 " =    2.173
peak=   -3.339 closest distance to " ND2 ASN A  45 " =    1.216
peak=   -3.337 closest distance to " CD1 PHE A  59 " =    2.112
peak=   -3.334 closest distance to " O   SER A 276 " =    1.671
peak=   -3.332 closest distance to " O   GLY A  17 " =    1.127
peak=   -3.329 closest distance to " O   HOH Z 431 " =    1.994
peak=   -3.328 closest distance to " O   LEU A 300 " =    2.339
peak=   -3.321 closest distance to " ND2 ASN A  45 " =    1.921
peak=   -3.316 closest distance to " O   HOH Z   6 " =    1.546
peak=   -3.316 closest distance to " O   TRP A  70 " =    1.654
peak=   -3.312 closest distance to " CE3 TRP A 274 " =    2.368
peak=   -3.312 closest distance to " OD2 ASP A  50 " =    2.150
peak=   -3.310 closest distance to " O   HOH Z  68 " =    1.198
peak=   -3.308 closest distance to " O   HOH Z 236 " =    1.466
peak=   -3.308 closest distance to " O   HOH Z 265 " =    1.961
peak=   -3.308 closest distance to " O   GLN A  77 " =    1.703
peak=   -3.305 closest distance to " C   ALA A 158 " =    1.152
peak=   -3.302 closest distance to " O   HOH Z 340 " =    1.821
peak=   -3.300 closest distance to " C   ILE A 239 " =    2.124
peak=   -3.299 closest distance to " O   HOH Z 210 " =    1.099
peak=   -3.297 closest distance to " N   ALA A 248 " =    2.381
peak=   -3.297 closest distance to " O   HOH Z 275 " =    1.565
peak=   -3.290 closest distance to " CD2 PHE A 225 " =    1.055
peak=   -3.286 closest distance to " CA  GLY A 241 " =    3.210
peak=   -3.280 closest distance to " ND2 ASN A  69 " =    2.004
peak=   -3.279 closest distance to " N   ASP A 286 " =    2.257
peak=   -3.278 closest distance to " CZ2 TRP A 274 " =    1.051
peak=   -3.278 closest distance to " C   MET A 188 " =    1.400
peak=   -3.276 closest distance to " O   HOH Z 423 " =    2.301
peak=   -3.271 closest distance to " CB  ASN A  39 " =    2.400
peak=   -3.268 closest distance to " CB  ASP A 171 " =    2.276
peak=   -3.268 closest distance to " CB  ALA A  10 " =    2.253
peak=   -3.268 closest distance to " NH2AARG A 275 " =    5.040
peak=   -3.265 closest distance to " CB  ASN A 148 " =    1.832
peak=   -3.261 closest distance to " O   TYR A 186 " =    1.775
peak=   -3.257 closest distance to " CD  PRO A 243 " =    1.908
peak=   -3.241 closest distance to " O   GLN A  94 " =    2.396
peak=   -3.240 closest distance to " N   ALA A 248 " =    1.868
peak=   -3.239 closest distance to " OE1 GLN A  88 " =    1.052
peak=   -3.237 closest distance to " NH2 ARG A  66 " =    1.295
peak=   -3.237 closest distance to " CG1 VAL A  67 " =    2.886
peak=   -3.230 closest distance to " CB  ALA A 114 " =    2.622
peak=   -3.223 closest distance to " C   LEU A 143 " =    1.005
peak=   -3.223 closest distance to " CG2AVAL A  72 " =    2.626
peak=   -3.222 closest distance to " CG  GLU A  53 " =    1.650
peak=   -3.221 closest distance to " CG  TRP A 266 " =    1.783
peak=   -3.218 closest distance to " OE1 GLN A 223 " =    2.272
peak=   -3.218 closest distance to " O   HOH Z 371 " =    2.328
peak=   -3.218 closest distance to " O   HOH Z 407 " =    2.866
peak=   -3.217 closest distance to " CB  ALA A  51 " =    1.949
peak=   -3.216 closest distance to " O   HOH Z 292 " =    1.745
peak=   -3.214 closest distance to " O   HOH Z  10 " =    1.460
peak=   -3.213 closest distance to " CA  HIS A  86 " =    2.302
peak=   -3.213 closest distance to " O   ALA A  34 " =    2.599
peak=   -3.212 closest distance to " O   HOH Z 426 " =    1.703
peak=   -3.210 closest distance to " O   HOH Z   9 " =    1.567
peak=   -3.207 closest distance to " O   HOH Z 177 " =    1.810
peak=   -3.204 closest distance to " O   HOH Z 137 " =    1.788
peak=   -3.201 closest distance to " NE2 GLN A 278 " =    1.894
peak=   -3.201 closest distance to " NE2 GLN A 194 " =    1.937
peak=   -3.200 closest distance to " O   HOH Z  11 " =    1.869
peak=   -3.197 closest distance to " CB  PHE A  16 " =    2.424
peak=   -3.195 closest distance to " CE1 TYR A 247 " =    2.657
peak=   -3.193 closest distance to " O   HOH Z 429 " =    1.746
peak=   -3.190 closest distance to " CB  SER A 210 " =    1.036
peak=   -3.187 closest distance to " CG  LYS A 193 " =    2.709
peak=   -3.187 closest distance to " CB  TRP A  85 " =    2.619
peak=   -3.178 closest distance to " N   ALA A  43 " =    2.705
peak=   -3.176 closest distance to " CG  LEU A  83 " =    2.098
peak=   -3.176 closest distance to " O   HOH Z 365 " =    1.269
peak=   -3.172 closest distance to " NH2 ARG A  56 " =    2.022
peak=   -3.169 closest distance to " CB  ALA A 248 " =    2.200
peak=   -3.166 closest distance to " NE2 GLN A 103 " =    1.629
peak=   -3.163 closest distance to " CD1 ILE A 239 " =    2.209
peak=   -3.158 closest distance to " O   ASN A 252 " =    1.461
peak=   -3.157 closest distance to " OG1 THR A  82 " =    1.446
peak=   -3.152 closest distance to " O   HOH Z  91 " =    1.319
peak=   -3.152 closest distance to " CZ  TYR A 169 " =    1.865
peak=   -3.149 closest distance to " O   HOH Z  71 " =    2.587
peak=   -3.147 closest distance to " CB  GLN A  55 " =    1.195
peak=   -3.145 closest distance to " CD2 LEU A 237 " =    2.812
peak=   -3.144 closest distance to " OD1 ASP A 171 " =    1.567
peak=   -3.143 closest distance to " O   GLY A 196 " =    1.185
peak=   -3.140 closest distance to " O   HOH Z 265 " =    2.445
peak=   -3.137 closest distance to " O   HOH Z 116 " =    1.612
peak=   -3.137 closest distance to " O   HOH Z 411 " =    1.492
peak=   -3.136 closest distance to " O   HOH Z 278 " =    1.247
peak=   -3.136 closest distance to " O   PHE A 218 " =    1.431
peak=   -3.134 closest distance to " CG  ASP A 231 " =    0.922
peak=   -3.132 closest distance to " O   SER A 146 " =    1.358
peak=   -3.131 closest distance to " O   HOH Z 185 " =    2.410
peak=   -3.130 closest distance to " NH2 ARG A  79 " =    1.555
peak=   -3.117 closest distance to " OD1 ASP A 200 " =    1.604
peak=   -3.116 closest distance to " CB  ALA A 291 " =    2.200
peak=   -3.114 closest distance to " O   HOH Z  44 " =    0.877
peak=   -3.107 closest distance to " O   ALA A 161 " =    1.774
peak=   -3.102 closest distance to " OD1 ASN A 173 " =    1.396
peak=   -3.100 closest distance to " O   HOH Z 238 " =    0.807
peak=   -3.098 closest distance to " NE2 GLN A 194 " =    2.018
peak=   -3.095 closest distance to " O   HOH Z 244 " =    1.371
peak=   -3.090 closest distance to " CG1 VAL A 125 " =    1.861
peak=   -3.079 closest distance to " CA  SER A  62 " =    2.524
peak=   -3.077 closest distance to " CG  MET A 105 " =    0.940
peak=   -3.052 closest distance to " ND2 ASN A  39 " =    1.227
peak=   -3.031 closest distance to " O   HOH Z 162 " =    2.945
peak=   -3.025 closest distance to " CD1 ILE A 109 " =    2.893
peak=   -3.016 closest distance to " CG1 VAL A 197 " =    2.362

================= 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    :  0.4763 0.4609   6.279339e+00   6.261813e+00
   1_bss:  0.4660 0.4511   6.272594e+00   6.250742e+00
   1_xyz:  0.3796 0.4039   6.148928e+00   6.183571e+00
   1_adp:  0.3348 0.3807   6.057875e+00   6.140266e+00
   1_occ:  0.3344 0.3818   6.057263e+00   6.142095e+00
   2_bss:  0.3309 0.3793   6.058672e+00   6.143151e+00
   2_xyz:  0.2564 0.3084   5.846758e+00   5.987971e+00
   2_adp:  0.2375 0.2914   5.790638e+00   5.949307e+00
   2_occ:  0.2373 0.2911   5.790401e+00   5.949519e+00
   3_bss:  0.2360 0.2917   5.791784e+00   5.951618e+00
   3_xyz:  0.1744 0.2271   5.521633e+00   5.718997e+00
   3_adp:  0.1613 0.2103   5.449912e+00   5.648033e+00
   3_occ:  0.1611 0.2103   5.449612e+00   5.648330e+00
   4_bss:  0.1607 0.2096   5.449174e+00   5.646589e+00
   4_xyz:  0.1331 0.1772   5.286638e+00   5.502354e+00
   4_adp:  0.1287 0.1747   5.265171e+00   5.490935e+00
   4_occ:  0.1285 0.1746   5.264512e+00   5.490531e+00
   5_bss:  0.1283 0.1743   5.263086e+00   5.488523e+00
   5_xyz:  0.1220 0.1676   5.228143e+00   5.461256e+00
   5_adp:  0.1184 0.1666   5.211263e+00   5.452582e+00
   5_occ:  0.1183 0.1666   5.211042e+00   5.452478e+00
   5_bss:  0.1182 0.1664   5.211125e+00   5.452666e+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:  0.335  20.000   6.639   7.597  12.221   0.000   0.000   0.000
   1_xyz:  0.335  20.000   6.639   7.597  12.221   0.000   0.000   0.000
   1_adp:  0.335  20.000   6.639   7.597  12.221   0.000   0.000   0.000
   1_occ:  0.335  20.000   6.639   7.597  12.221   0.000   0.000   0.000
   2_bss:  0.334  49.777   2.680   3.656   8.032   0.000   0.000   0.000
   2_xyz:  0.334  49.777   2.680   3.656   8.032   0.000   0.000   0.000
   2_adp:  0.334  49.777   2.680   3.656   8.032   0.000   0.000   0.000
   2_occ:  0.334  49.777   2.680   3.656   8.032   0.000   0.000   0.000
   3_bss:  0.321  49.778   1.469   2.593   5.433   0.000   0.000   0.000
   3_xyz:  0.321  49.778   1.469   2.593   5.433   0.000   0.000   0.000
   3_adp:  0.321  49.778   1.469   2.593   5.433   0.000   0.000   0.000
   3_occ:  0.321  49.778   1.469   2.593   5.433   0.000   0.000   0.000
   4_bss:  0.317  58.014   0.869   1.806   3.897   0.000   0.000   0.000
   4_xyz:  0.317  58.014   0.869   1.806   3.897   0.000   0.000   0.000
   4_adp:  0.317  58.014   0.869   1.806   3.897   0.000   0.000   0.000
   4_occ:  0.317  58.014   0.869   1.806   3.897   0.000   0.000   0.000
   5_bss:  0.329  58.014   1.041   1.866   3.682   0.000   0.000   0.000
   5_xyz:  0.329  58.014   1.041   1.866   3.682   0.000   0.000   0.000
   5_adp:  0.329  58.014   1.041   1.866   3.682   0.000   0.000   0.000
   5_occ:  0.329  58.014   1.041   1.866   3.682   0.000   0.000   0.000
   5_bss:  0.323  60.440  -1.099  -0.311   1.410  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  54.362 0.4665  0.5359    65831.939
   1_bss:  53.259 0.4796  0.7182    63424.575
   1_xyz:  45.528 0.5751  0.8364    47198.263
   1_adp:  41.395 0.6261  0.9473    41084.512
   1_occ:  41.477 0.6251  0.9445    41247.262
   2_bss:  41.258 0.6279  0.8255    41238.605
   2_xyz:  31.956 0.7359  0.9453    25583.182
   2_adp:  29.673 0.7618  0.9719    23041.887
   2_occ:  29.690 0.7616  0.9716    23052.681
   3_bss:  29.647 0.7622  0.9175    23131.135
   3_xyz:  22.126 0.8408  0.9779    13194.234
   3_adp:  20.070 0.8616  0.9865    11428.676
   3_occ:  20.092 0.8613  0.9863    11430.428
   4_bss:  19.993 0.8623  0.9539    11365.304
   4_xyz:  16.589 0.8932  0.9688     8247.434
   4_adp:  16.318 0.8957  0.9614     8097.328
   4_occ:  16.303 0.8958  0.9615     8088.514
   5_bss:  16.263 0.8962  0.9620     8041.187
   5_xyz:  15.620 0.9019  0.9662     7538.656
   5_adp:  15.459 0.9032  0.9595     7339.892
   5_occ:  15.452 0.9033  0.9595     7336.506
   5_bss:  15.456 0.9032  0.9672     7339.226
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.4133e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.4133e+01
   1_xyz:   1.691  0.013  0.106 18.158  0.007  4.111   1.4083e-01
   1_adp:   1.691  0.013  0.106 18.158  0.007  4.111   1.4083e-01
   1_occ:   1.691  0.013  0.106 18.158  0.007  4.111   1.4083e-01
   2_bss:   1.691  0.013  0.106 18.158  0.007  4.111   1.4083e-01
   2_xyz:   1.178  0.008  0.077 15.957  0.004  4.111   7.6967e-02
   2_adp:   1.178  0.008  0.077 15.957  0.004  4.111   7.6967e-02
   2_occ:   1.178  0.008  0.077 15.957  0.004  4.111   7.6967e-02
   3_bss:   1.178  0.008  0.077 15.957  0.004  4.111   7.6967e-02
   3_xyz:   1.128  0.009  0.082 15.763  0.004  4.129   7.5266e-02
   3_adp:   1.128  0.009  0.082 15.763  0.004  4.129   7.5266e-02
   3_occ:   1.128  0.009  0.082 15.763  0.004  4.129   7.5266e-02
   4_bss:   1.128  0.009  0.082 15.763  0.004  4.129   7.5266e-02
   4_xyz:   1.121  0.009  0.084 15.780  0.004  4.116   7.4234e-02
   4_adp:   1.121  0.009  0.084 15.780  0.004  4.116   7.4234e-02
   4_occ:   1.121  0.009  0.084 15.780  0.004  4.116   7.4234e-02
   5_bss:   1.121  0.009  0.084 15.780  0.004  4.116   7.4234e-02
   5_xyz:   1.075  0.009  0.085 15.414  0.004  4.122   6.9386e-02
   5_adp:   1.075  0.009  0.085 15.414  0.004  4.122   6.9386e-02
   5_occ:   1.075  0.009  0.085 15.414  0.004  4.122   6.9386e-02
   5_bss:   1.075  0.009  0.085 15.414  0.004  4.122   6.9386e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.135   7.0163e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.135   7.0163e+00
   1_xyz:  14.191  0.164  0.446 86.535  0.051  2.160   1.0461e-01
   1_adp:  14.191  0.164  0.446 86.535  0.051  2.160   1.0461e-01
   1_occ:  14.191  0.164  0.446 86.535  0.051  2.160   1.0461e-01
   2_bss:  14.191  0.164  0.446 86.535  0.051  2.160   1.0461e-01
   2_xyz:   7.753  0.087  0.245 83.906  0.023  2.235   6.5735e-02
   2_adp:   7.753  0.087  0.245 83.906  0.023  2.235   6.5735e-02
   2_occ:   7.753  0.087  0.245 83.906  0.023  2.235   6.5735e-02
   3_bss:   7.753  0.087  0.245 83.906  0.023  2.235   6.5735e-02
   3_xyz:   6.677  0.059  0.278 86.080  0.041  2.241   1.0784e-01
   3_adp:   6.677  0.059  0.278 86.080  0.041  2.241   1.0784e-01
   3_occ:   6.677  0.059  0.278 86.080  0.041  2.241   1.0784e-01
   4_bss:   6.677  0.059  0.278 86.080  0.041  2.241   1.0784e-01
   4_xyz:   8.645  0.052  0.403 83.987  0.033  2.256   4.8233e-02
   4_adp:   8.645  0.052  0.403 83.987  0.033  2.256   4.8233e-02
   4_occ:   8.645  0.052  0.403 83.987  0.033  2.256   4.8233e-02
   5_bss:   8.645  0.052  0.403 83.987  0.033  2.256   4.8233e-02
   5_xyz:   7.106  0.049  0.436 82.263  0.029  2.339   4.6847e-02
   5_adp:   7.106  0.049  0.436 82.263  0.029  2.339   4.6847e-02
   5_occ:   7.106  0.049  0.436 82.263  0.029  2.339   4.6847e-02
   5_bss:   7.106  0.049  0.436 82.263  0.029  2.339   4.6847e-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:  71.15   0.00  13.04  60.95   0.00  10.59  71.15   0.00  26.38
   1_occ:  71.15   0.00  13.04  60.95   0.00  10.59  71.15   0.00  26.38
   2_bss:  71.15   0.00  13.04  60.95   0.00  10.59  71.15   0.00  26.38
   2_xyz:  71.15   0.00  13.04  60.95   0.00  10.59  71.15   0.00  26.38
   2_adp:  67.78   0.00  13.10  65.84   0.00   9.68  67.78   0.00  31.69
   2_occ:  67.78   0.00  13.10  65.84   0.00   9.68  67.78   0.00  31.69
   3_bss:  67.78   0.00  13.10  65.84   0.00   9.68  67.78   0.00  31.69
   3_xyz:  67.78   0.00  13.10  65.84   0.00   9.68  67.78   0.00  31.69
   3_adp:  79.97   0.00  12.85  79.97   0.00   9.00  69.03   1.81  33.81
   3_occ:  79.97   0.00  12.85  79.97   0.00   9.00  69.03   1.81  33.81
   4_bss:  79.97   0.00  12.85  79.97   0.00   9.00  69.03   1.81  33.81
   4_xyz:  79.97   0.00  12.85  79.97   0.00   9.00  69.03   1.81  33.81
   4_adp:  83.35   0.00  12.83  83.35   0.00   8.85  70.45   1.28  34.50
   4_occ:  83.35   0.00  12.83  83.35   0.00   8.85  70.45   1.28  34.50
   5_bss:  83.35   0.00  12.83  83.35   0.00   8.85  70.45   1.28  34.50
   5_xyz:  83.35   0.00  12.83  83.35   0.00   8.85  70.45   1.28  34.50
   5_adp:  94.92   0.00  13.52  81.82   0.00   8.98  94.92   1.38  38.28
   5_occ:  94.92   0.00  13.52  81.82   0.00   8.98  94.92   1.38  38.28
   5_bss:  97.35   2.43  15.95  84.25   2.43  11.40  97.35   3.80  40.71
------------------------------------------------------------------------
 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:    1.275    0.016    0.412
   1_adp:    1.275    0.016    0.412
   1_occ:    1.275    0.016    0.412
   2_bss:    1.275    0.016    0.412
   2_xyz:    1.951    0.022    0.557
   2_adp:    1.951    0.022    0.557
   2_occ:    1.951    0.022    0.557
   3_bss:    1.951    0.022    0.557
   3_xyz:    1.784    0.032    0.643
   3_adp:    1.784    0.032    0.643
   3_occ:    1.784    0.032    0.643
   4_bss:    1.784    0.032    0.643
   4_xyz:    1.893    0.053    0.696
   4_adp:    1.893    0.053    0.696
   4_occ:    1.893    0.053    0.696
   5_bss:    1.893    0.053    0.696
   5_xyz:    1.900    0.038    0.709
   5_adp:    1.900    0.038    0.709
   5_occ:    1.900    0.038    0.709
   5_bss:    1.900    0.038    0.709
------------------------------------------------------------------------

CPU time actual refinement: 329.92


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_439/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_439/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_439/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_439/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_439/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 329.77 
  Macro-tasks:
    bulk solvent and scale       = 42.31  
    individual site refinement   = 132.65 
    weights calculation          = 31.92  
    collect and process          = 6.50   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 213.50 
  Micro-tasks:
    mask                            = 2.39   
    f_calc                          = 99.96  
    alpha_beta                      = 8.00   
    target                          = 1.13   
    gradients_wrt_atomic_parameters = 110.09 
    fmodel                         = 7.34   
    r_factors                      = 0.23   
    phase_errors                   = 10.45  
    foms                           = 0.26   
    TOTAL for micro-tasks          = 239.85 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.677 micro seconds
Total CPU time: 5.73 minutes
from_scatterers_fft:    644 calls, 99.69 s
gradients_fft:          589 calls, 97.07 s

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

# Date 2008-01-16 Time 01:34:04 PST -0800 (1200476044.03 s)
Start R-work = 0.4763, R-free = 0.4609 (no bulk solvent and anisotropic scale)
Final R-work = 0.1359, R-free = 0.1820 (no bulk solvent and anisotropic scale)

Start R-work = 0.4660, R-free = 0.4511
Final R-work = 0.1182, R-free = 0.1664