# Date 2008-01-16 Time 02:07:53 PST -0800 (1200478073.23 s)
#phil __OFF__

Command line arguments: "../700.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 27840
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 700

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.25, 47.6339, 87.2539, 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: 3.35, per 1000 atoms: 1.19


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 47.6339, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0342 2.00061
Completeness in resolution range: 0.963314
Completeness with d_max=infinity: 0.960292

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0342
                             d_min =   2.0006

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 47.6339, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0342 2.00061
Completeness in resolution range: 0.963314
Completeness with d_max=infinity: 0.960292

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0346 -  4.2801 [2143/2170]  1928   215  10.0%
  bin  2:  4.2801 -  3.4103 [2040/2056]  1837   203  10.0%
  bin  3:  3.4103 -  2.9831 [2041/2060]  1838   203   9.9%
  bin  4:  2.9831 -  2.7121 [1994/2024]  1792   202  10.1%
  bin  5:  2.7121 -  2.5186 [1993/2012]  1792   201  10.1%
  bin  6:  2.5186 -  2.3707 [1977/2013]  1785   192   9.7%
  bin  7:  2.3707 -  2.2524 [1984/2017]  1783   201  10.1%
  bin  8:  2.2524 -  2.1547 [1955/1989]  1757   198  10.1%
  bin  9:  2.1547 -  2.0719 [1949/1977]  1756   193   9.9%
  bin 10:  2.0719 -  2.0006 [1513/2017]  1362   151  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_700/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 16
        2.42 -     3.04: 2155
        3.04 -     3.66: 4625
        3.66 -     4.28: 8873
        4.28 -     4.90: 12299
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.032 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  42 " - " O   HOH Z 183 "  2.047 3.040 -x+1,y+1/2,-z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " OE1 GLN A  55 " - " O   HOH Z 403 "  2.277 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 27963 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_700/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_700/model_refine_001.geo

CPU time processing inputs: 9.18


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.25 47.63395 87.2539 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4660   r_free= 0.4517   ksol= 0.00   Bsol= 0.00   scale= 0.795    |
|                                                                             |
| 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:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.265496                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0346 -  4.7735 0.99   1387  153 0.3745 0.3594      6.5526      6.5078|
|  2:  4.7735 -  3.8092 0.99   1328  150 0.3756 0.4110      6.7386      6.8455|
|  3:  3.8092 -  3.3336 0.99   1318  149 0.4254 0.3898      6.6595      6.6014|
|  4:  3.3336 -  3.0316 0.99   1297  135 0.4479 0.4065      6.5068      6.4152|
|  5:  3.0316 -  2.8158 0.99   1287  146 0.4977 0.4849      6.3665      6.3838|
|  6:  2.8158 -  2.6507 0.99   1291  145 0.4992 0.5171      6.2812      6.1922|
|  7:  2.6507 -  2.5186 0.99   1279  146 0.4832 0.4622      6.2259      6.1364|
|  8:  2.5186 -  2.4095 0.98   1290  136 0.5129 0.4246      6.1794      6.1445|
|  9:  2.4095 -  2.3171 0.98   1261  144 0.5146 0.5551      6.1063      6.1449|
| 10:  2.3171 -  2.2374 0.98   1255  135 0.5375 0.4734      6.1301      6.0734|
| 11:  2.2374 -  2.1676 1.00   1281  150 0.5159 0.4774      6.0264      6.0862|
| 12:  2.1676 -  2.1058 0.97   1267  133 0.5212 0.5194      5.9729      6.0073|
| 13:  2.1058 -  2.0505 0.98   1255  139 0.5239 0.5234      5.8929      5.8397|
| 14:  2.0505 -  2.0006 0.66    834   98 0.5373 0.5173      5.8674      5.7633|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0346 -  4.7735  1387   153  0.71  33.14   0.80     0.73      65651.46|
|  2:  4.7735 -  3.8092  1328   150  0.73  32.41   0.89     0.77      92259.83|
|  3:  3.8092 -  3.3336  1318   149  0.65  39.74   0.83     0.73      96392.29|
|  4:  3.3336 -  3.0316  1297   135  0.58  45.25   0.80     0.64      82553.52|
|  5:  3.0316 -  2.8158  1287   146  0.50  52.34   0.74     0.56      69352.70|
|  6:  2.8158 -  2.6507  1291   145  0.48  53.65   0.73     0.54      61625.51|
|  7:  2.6507 -  2.5186  1279   146  0.47  54.73   0.75     0.52      56015.91|
|  8:  2.5186 -  2.4095  1290   136  0.46  55.40   0.74     0.53      51205.53|
|  9:  2.4095 -  2.3171  1261   144  0.44  57.18   0.71     0.51      48056.57|
| 10:  2.3171 -  2.2374  1255   135  0.42  58.15   0.73     0.50      45494.78|
| 11:  2.2374 -  2.1676  1281   150  0.39  60.66   0.75     0.47      43057.32|
| 12:  2.1676 -  2.1058  1267   133  0.37  62.51   0.75     0.45      40933.03|
| 13:  2.1058 -  2.0505  1255   139  0.34  64.32   0.72     0.41      35841.16|
| 14:  2.0505 -  2.0006   834    98  0.33  65.21   0.71     0.35      28463.78|
|alpha:            min =        0.35 max =            0.77 mean =         0.56|
|beta:             min =    28463.78 max =        96392.29 mean =     59423.98|
|figures of merit: min =        0.00 max =            1.00 mean =         0.50|
|phase err.(work): min =        0.00 max =           90.00 mean =        51.91|
|phase err.(test): min =        0.00 max =           89.95 mean =        52.14|
|-----------------------------------------------------------------------------|

============================== 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 = 10.567971             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.463   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.968080              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.798   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       26 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      160 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      677 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1484 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2586 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3861 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     4998 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6519 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7667 |
|-----------------------------------------------------------------------------|
|-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 |       54.237 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.093    4.900  1.196 |       1.686 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.171)------------------------------------------|
|    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 = 12.171)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4728   r_free= 0.4537   ksol= 0.00   Bsol= 0.00   scale= 0.766    |
|                                                                             |
| 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:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.268824                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4588   r_free= 0.4411   ksol= 0.32   Bsol= 18.52   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.58,10.76,9.15,0.00,0.00,0.00); trace/3= 8.83                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.258258                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.833141              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.777   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.893022              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.377   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4588      final r-factor (work) = 0.3602          |
| start r-factor (free) = 0.4411      final r-factor (free) = 0.3769          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 85.0713 = 9.83 * 0.50 * 6.2715 + 1.00 * 54.2371                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.3402 = 9.83 * 0.50 * 6.1437 + 1.00 * 0.1341                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3602      final r-factor (work) = 0.3083          |
| start r-factor (free) = 0.3769      final r-factor (free) = 0.3521          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.5009 = 0.89 * 1.00 * 6.1437 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.3957 = 0.89 * 1.00 * 6.0249 + 1.00 * 0.0153                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.171)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.47   12.28    None  None   None       |
|    all(noH): 2823   0      0.00    95.47   12.28    None  None   None       |
|    Sol.    : 438    0      0.00    95.47   27.43    None  None   None       |
|    Mac.    : 2385   0      0.00    70.31   9.50     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 -   9.547: 1544   |   5:    47.733 -  57.280:   36        |
|      1:     9.547 -  19.093:  708   |   6:    57.280 -  66.826:   16        |
|      2:    19.093 -  28.640:  277   |   7:    66.826 -  76.373:    4        |
|      3:    28.640 -  38.187:  153   |   8:    76.373 -  85.920:    0        |
|      4:    38.187 -  47.733:   82   |   9:    85.920 -  95.466:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3083 r_free = 0.3521             target_work(ml) = 5.997         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3076 r_free = 0.3523             target_work(ml) = 5.996         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3076   r_free= 0.3523   ksol= 0.32   Bsol= 18.52   scale= 1.091   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.58,10.76,9.15,0.00,0.00,0.00); trace/3= 8.83                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 5.995747                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3033   r_free= 0.3470   ksol= 0.33   Bsol= 50.00   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.14,6.72,5.38,0.00,0.00,0.00); trace/3= 5.08                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.45 A                  |
| x-ray target function (ml) for work reflections: 5.996119                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.600224              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.371   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.374666              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 126.029  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3033      final r-factor (work) = 0.2190          |
| start r-factor (free) = 0.3470      final r-factor (free) = 0.2622          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.0020 = 5.60 * 0.50 * 6.0240 + 1.00 * 0.1341                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.4380 = 5.60 * 0.50 * 5.8415 + 1.00 * 0.0812                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2190      final r-factor (work) = 0.1981          |
| start r-factor (free) = 0.2622      final r-factor (free) = 0.2400          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2191 = 0.37 * 1.00 * 5.8415 + 1.00 * 0.0305                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1557 = 0.37 * 1.00 * 5.6572 + 1.00 * 0.0362                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.171)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.21   12.14    None  None   None       |
|    all(noH): 2823   0      0.00    88.21   12.14    None  None   None       |
|    Sol.    : 438    0      1.26    88.21   32.04    None  None   None       |
|    Mac.    : 2385   0      0.00    66.32   8.48     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 -   8.821: 1621   |   5:    44.106 -  52.927:   85        |
|      1:     8.821 -  17.642:  618   |   6:    52.927 -  61.748:   26        |
|      2:    17.642 -  26.463:  221   |   7:    61.748 -  70.569:   16        |
|      3:    26.463 -  35.284:  140   |   8:    70.569 -  79.390:    0        |
|      4:    35.284 -  44.106:   94   |   9:    79.390 -  88.211:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1981 r_free = 0.2400             target_work(ml) = 5.624         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1978 r_free = 0.2407             target_work(ml) = 5.624         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1978   r_free= 0.2407   ksol= 0.33   Bsol= 50.00   scale= 1.033   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.14,6.72,5.38,0.00,0.00,0.00); trace/3= 5.08                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.624418                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1965   r_free= 0.2396   ksol= 0.33   Bsol= 67.26   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.25,4.07,4.02,0.00,0.00,0.00); trace/3= 3.45                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.623536                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.191729              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.733  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.891935              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.321   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1965      final r-factor (work) = 0.1543          |
| start r-factor (free) = 0.2396      final r-factor (free) = 0.1890          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2856 = 2.19 * 0.50 * 5.6614 + 1.00 * 0.0814                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1046 = 2.19 * 0.50 * 5.5164 + 1.00 * 0.0594                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1543      final r-factor (work) = 0.1431          |
| start r-factor (free) = 0.1890      final r-factor (free) = 0.1847          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.4509 = 1.89 * 1.00 * 5.5164 + 1.00 * 0.0143                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.2491 = 1.89 * 1.00 * 5.3567 + 1.00 * 0.1147                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.171)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.92   13.30    None  None   None       |
|    all(noH): 2823   0      0.00    86.92   13.30    None  None   None       |
|    Sol.    : 438    0      0.74    84.97   38.96    None  None   None       |
|    Mac.    : 2385   0      0.00    86.92   8.59     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 -   8.692: 1625   |   5:    43.459 -  52.151:   95        |
|      1:     8.692 -  17.384:  601   |   6:    52.151 -  60.842:   59        |
|      2:    17.384 -  26.075:  168   |   7:    60.842 -  69.534:   51        |
|      3:    26.075 -  34.767:  109   |   8:    69.534 -  78.226:   21        |
|      4:    34.767 -  43.459:   83   |   9:    78.226 -  86.917:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1431 r_free = 0.1847             target_work(ml) = 5.346         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1431 r_free = 0.1847             target_work(ml) = 5.346         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1431   r_free= 0.1847   ksol= 0.33   Bsol= 67.26   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.25,4.07,4.02,0.00,0.00,0.00); trace/3= 3.45                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.345713                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1432   r_free= 0.1855   ksol= 0.33   Bsol= 67.26   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.10,3.35,3.89,0.00,0.00,0.00); trace/3= 3.11                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.346901                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.859750              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 110.395  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.570918              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.530   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1432      final r-factor (work) = 0.1233          |
| start r-factor (free) = 0.1855      final r-factor (free) = 0.1710          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7199 = 2.86 * 0.50 * 5.3574 + 1.00 * 0.0594                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6222 = 2.86 * 0.50 * 5.2802 + 1.00 * 0.0721                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1233      final r-factor (work) = 0.1206          |
| start r-factor (free) = 0.1710      final r-factor (free) = 0.1676          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.3119 = 1.57 * 1.00 * 5.2802 + 1.00 * 0.0171                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.2239 = 1.57 * 1.00 * 5.2213 + 1.00 * 0.0216                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.171)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.00   13.08    None  None   None       |
|    all(noH): 2823   0      0.00    88.00   13.08    None  None   None       |
|    Sol.    : 438    0      0.32    85.58   38.96    None  None   None       |
|    Mac.    : 2385   0      0.00    88.00   8.33     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.800: 1686   |   5:    44.001 -  52.801:   90        |
|      1:     8.800 -  17.600:  567   |   6:    52.801 -  61.601:   56        |
|      2:    17.600 -  26.401:  151   |   7:    61.601 -  70.402:   51        |
|      3:    26.401 -  35.201:  107   |   8:    70.402 -  79.202:   18        |
|      4:    35.201 -  44.001:   86   |   9:    79.202 -  88.002:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1206 r_free = 0.1676             target_work(ml) = 5.210         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1205 r_free = 0.1675             target_work(ml) = 5.210         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1205   r_free= 0.1675   ksol= 0.33   Bsol= 67.26   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.10,3.35,3.89,0.00,0.00,0.00); trace/3= 3.11                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.209627                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1205   r_free= 0.1674   ksol= 0.33   Bsol= 65.56   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.34,3.28,4.05,0.00,0.00,0.00); trace/3= 3.22                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.209423                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.994869              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 149.947  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.792815              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 99.187   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1205      final r-factor (work) = 0.1195          |
| start r-factor (free) = 0.1674      final r-factor (free) = 0.1649          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2803 = 1.99 * 0.50 * 5.2216 + 1.00 * 0.0721                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2546 = 1.99 * 0.50 * 5.2070 + 1.00 * 0.0609                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1195      final r-factor (work) = 0.1194          |
| start r-factor (free) = 0.1649      final r-factor (free) = 0.1642          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1525 = 0.79 * 1.00 * 5.2070 + 1.00 * 0.0243                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3006 = 0.79 * 1.00 * 5.2016 + 1.00 * 0.1767                               |
|-----------------------------------------------------------------------------|
| number of iterations = 7       |    number of function evaluations = 10     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.171)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.50   12.94    None  None   None       |
|    all(noH): 2823   0      0.00    88.50   12.94    None  None   None       |
|    Sol.    : 438    0      0.73    85.98   38.64    None  None   None       |
|    Mac.    : 2385   0      0.00    88.50   8.22     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 -   8.850: 1727   |   5:    44.249 -  53.099:   85        |
|      1:     8.850 -  17.700:  527   |   6:    53.099 -  61.949:   54        |
|      2:    17.700 -  26.549:  159   |   7:    61.949 -  70.798:   47        |
|      3:    26.549 -  35.399:   97   |   8:    70.798 -  79.648:   17        |
|      4:    35.399 -  44.249:   97   |   9:    79.648 -  88.498:   13        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1194 r_free = 0.1642             target_work(ml) = 5.199         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1190 r_free = 0.1640             target_work(ml) = 5.198         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1190   r_free= 0.1640   ksol= 0.33   Bsol= 65.56   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.34,3.28,4.05,0.00,0.00,0.00); trace/3= 3.22                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.198222                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0346 -  4.7735 0.99   1387  153 0.1016 0.1307      5.4135      5.5339|
|  2:  4.7735 -  3.8092 0.99   1328  150 0.0854 0.1068      5.4402      5.6373|
|  3:  3.8092 -  3.3336 0.99   1318  149 0.1090 0.1520      5.4965      5.8787|
|  4:  3.3336 -  3.0316 0.99   1297  135 0.1262 0.1599      5.4819      5.6399|
|  5:  3.0316 -  2.8158 0.99   1287  146 0.1432 0.1714      5.4026        5.52|
|  6:  2.8158 -  2.6507 0.99   1291  145 0.1326 0.2185      5.2777      5.5796|
|  7:  2.6507 -  2.5186 0.99   1279  146 0.1352 0.1745      5.2281      5.4019|
|  8:  2.5186 -  2.4095 0.98   1290  136 0.1278 0.1726       5.151      5.3832|
|  9:  2.4095 -  2.3171 0.98   1261  144 0.1270 0.2027      5.0906       5.362|
| 10:  2.3171 -  2.2374 0.98   1255  135 0.1269 0.1745      5.0567      5.2536|
| 11:  2.2374 -  2.1676 1.00   1281  150 0.1265 0.1867      5.0047      5.3121|
| 12:  2.1676 -  2.1058 0.97   1267  133 0.1205 0.1789      4.9263       5.239|
| 13:  2.1058 -  2.0505 0.98   1255  139 0.1205 0.1759      4.8453      5.0611|
| 14:  2.0505 -  2.0006 0.66    834   98 0.1148 0.1908      4.7482      5.0485|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0346 -  4.7735  1387   153  0.94   9.48   0.97     0.94       7735.24|
|  2:  4.7735 -  3.8092  1328   150  0.95   8.05   1.01     0.99       9055.46|
|  3:  3.8092 -  3.3336  1318   149  0.94  11.15   1.02     1.02      10537.80|
|  4:  3.3336 -  3.0316  1297   135  0.92  13.71   1.00     0.98      10478.68|
|  5:  3.0316 -  2.8158  1287   146  0.89  16.89   1.00     0.98       9386.31|
|  6:  2.8158 -  2.6507  1291   145  0.89  17.35   0.98     0.95       7994.80|
|  7:  2.6507 -  2.5186  1279   146  0.90  16.25   0.99     0.96       6854.88|
|  8:  2.5186 -  2.4095  1290   136  0.90  16.29   0.99     0.95       6076.63|
|  9:  2.4095 -  2.3171  1261   144  0.90  16.86   1.00     0.96       5657.24|
| 10:  2.3171 -  2.2374  1255   135  0.89  17.30   0.99     0.95       5236.07|
| 11:  2.2374 -  2.1676  1281   150  0.89  17.18   0.99     0.94       4817.78|
| 12:  2.1676 -  2.1058  1267   133  0.90  16.10   1.00     0.98       4274.47|
| 13:  2.1058 -  2.0505  1255   139  0.90  16.71   0.98     0.97       3693.46|
| 14:  2.0505 -  2.0006   834    98  0.90  16.12   0.96     0.91       2927.94|
|alpha:            min =        0.91 max =            1.02 mean =         0.96|
|beta:             min =     2927.94 max =        10537.80 mean =      6897.98|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.86|
|phase err.(test): min =        0.00 max =           88.07 mean =        14.27|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1193   r_free= 0.1643   ksol= 0.33   Bsol= 66.57   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.83,-0.02,0.85,-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: 5.199453                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1193   r_free= 0.1643   ksol= 0.33   Bsol= 66.57   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.83,-0.02,0.85,-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: 5.199453                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0346 -  4.7735 0.99   1387  153 0.1026 0.1305      5.4194      5.5347|
|  2:  4.7735 -  3.8092 0.99   1328  150 0.0858 0.1063       5.447      5.6431|
|  3:  3.8092 -  3.3336 0.99   1318  149 0.1095 0.1525      5.4991      5.8797|
|  4:  3.3336 -  3.0316 0.99   1297  135 0.1264 0.1603       5.483      5.6448|
|  5:  3.0316 -  2.8158 0.99   1287  146 0.1432 0.1712      5.4031      5.5183|
|  6:  2.8158 -  2.6507 0.99   1291  145 0.1325 0.2183      5.2774      5.5793|
|  7:  2.6507 -  2.5186 0.99   1279  146 0.1351 0.1750       5.228      5.4035|
|  8:  2.5186 -  2.4095 0.98   1290  136 0.1277 0.1727      5.1513      5.3836|
|  9:  2.4095 -  2.3171 0.98   1261  144 0.1269 0.2028      5.0905      5.3622|
| 10:  2.3171 -  2.2374 0.98   1255  135 0.1268 0.1743      5.0564      5.2535|
| 11:  2.2374 -  2.1676 1.00   1281  150 0.1265 0.1868      5.0046      5.3122|
| 12:  2.1676 -  2.1058 0.97   1267  133 0.1205 0.1792      4.9265        5.24|
| 13:  2.1058 -  2.0505 0.98   1255  139 0.1205 0.1759       4.845      5.0611|
| 14:  2.0505 -  2.0006 0.66    834   98 0.1148 0.1906       4.748      5.0475|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0346 -  4.7735  1387   153  0.94   9.72   0.96     0.94       7843.65|
|  2:  4.7735 -  3.8092  1328   150  0.95   8.12   1.01     0.99       9142.49|
|  3:  3.8092 -  3.3336  1318   149  0.93  11.22   1.02     1.02      10631.78|
|  4:  3.3336 -  3.0316  1297   135  0.92  13.75   1.00     0.98      10521.40|
|  5:  3.0316 -  2.8158  1287   146  0.89  16.90   1.00     0.98       9410.82|
|  6:  2.8158 -  2.6507  1291   145  0.89  17.36   0.98     0.95       7998.58|
|  7:  2.6507 -  2.5186  1279   146  0.90  16.26   0.99     0.96       6863.92|
|  8:  2.5186 -  2.4095  1290   136  0.90  16.31   0.99     0.95       6086.58|
|  9:  2.4095 -  2.3171  1261   144  0.90  16.86   1.00     0.96       5660.66|
| 10:  2.3171 -  2.2374  1255   135  0.89  17.31   0.99     0.95       5234.45|
| 11:  2.2374 -  2.1676  1281   150  0.89  17.18   0.99     0.94       4821.10|
| 12:  2.1676 -  2.1058  1267   133  0.90  16.11   1.00     0.98       4278.53|
| 13:  2.1058 -  2.0505  1255   139  0.90  16.70   0.98     0.97       3692.87|
| 14:  2.0505 -  2.0006   834    98  0.90  16.11   0.96     0.91       2924.49|
|alpha:            min =        0.91 max =            1.02 mean =         0.96|
|beta:             min =     2924.49 max =        10631.78 mean =      6927.14|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.90|
|phase err.(test): min =        0.00 max =           88.22 mean =        14.29|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.171)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.22    91.72   16.16    None  None   None       |
|    all(noH): 2823   0      3.22    91.72   16.16    None  None   None       |
|    Sol.    : 438    0      3.95    89.20   41.85    None  None   None       |
|    Mac.    : 2385   0      3.22    91.72   11.44    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     3.219 -  12.069: 1727   |   5:    47.468 -  56.318:   85        |
|      1:    12.069 -  20.919:  527   |   6:    56.318 -  65.168:   54        |
|      2:    20.919 -  29.768:  159   |   7:    65.168 -  74.017:   47        |
|      3:    29.768 -  38.618:   97   |   8:    74.017 -  82.867:   17        |
|      4:    38.618 -  47.468:   97   |   9:    82.867 -  91.717:   13        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 326         
Filter by distance & map next to the model:
   mapped sites are within: 0.324 - 5.696
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 321 from: 326
   mapped sites are within: 0.739 - 5.696

peak=   10.118 closest distance to " CB  VAL A 230 " =    1.435
peak=    6.364 closest distance to " CG  LEU A   5 " =    1.128
peak=    5.856 closest distance to " NH2 ARG A  56 " =    2.299
peak=    5.683 closest distance to " CB  VAL A 296 " =    1.082
peak=    5.665 closest distance to " O   HOH Z 210 " =    1.111
peak=    5.495 closest distance to " CB  GLN A 223 " =    1.429
peak=    5.333 closest distance to " CG  LEU A 228 " =    1.218
peak=    5.128 closest distance to " CG  PRO A  54 " =    1.352
peak=    5.097 closest distance to " CG  PRO A 280 " =    0.878
peak=    5.083 closest distance to " CG2 VAL A 296 " =    1.007
peak=    5.074 closest distance to " CD1AILE A 234 " =    1.022
peak=    4.949 closest distance to " CG  PRO A 198 " =    1.278
peak=    4.943 closest distance to " CB  SER A  63 " =    1.239
peak=    4.784 closest distance to " CB  ARG A 275 " =    0.948
peak=    4.761 closest distance to " CG1 VAL A 296 " =    1.181
peak=    4.750 closest distance to " O   HOH Z 403 " =    1.819
peak=    4.716 closest distance to " O   HOH Z 128 " =    1.428
peak=    4.649 closest distance to " CD2 LEU A   5 " =    1.134
peak=    4.645 closest distance to " CB  PRO A  54 " =    0.996
peak=    4.624 closest distance to " CB  VAL A 230 " =    1.259
peak=    4.557 closest distance to " O   HOH Z 232 " =    2.255
peak=    4.527 closest distance to " C   PRO A 198 " =    1.542
peak=    4.462 closest distance to " O   HOH Z  49 " =    1.239
peak=    4.448 closest distance to " CA  TYR A  30 " =    1.015
peak=    4.438 closest distance to " O   HOH Z  63 " =    1.765
peak=    4.406 closest distance to " O   HOH Z 433 " =    1.502
peak=    4.396 closest distance to " CB  GLN A 183 " =    1.262
peak=    4.352 closest distance to " CB  GLU A 128 " =    1.109
peak=    4.337 closest distance to " CB  ARG A 190 " =    1.739
peak=    4.334 closest distance to " CG  PRO A 213 " =    1.275
peak=    4.331 closest distance to " NE2 GLN A  11 " =    0.985
peak=    4.327 closest distance to " O   HOH Z 402 " =    1.521
peak=    4.301 closest distance to " O   HOH Z 248 " =    1.448
peak=    4.242 closest distance to " CB  ARG A  79 " =    1.347
peak=    4.242 closest distance to " CA  VAL A  41 " =    0.782
peak=    4.204 closest distance to " O   HOH Z 368 " =    2.452
peak=    4.188 closest distance to " CZ  PHE A 218 " =    1.129
peak=    4.187 closest distance to " O   HOH Z 189 " =    2.834
peak=    4.182 closest distance to " CD2 LEU A 228 " =    1.259
peak=    4.179 closest distance to " CB  GLU A 277 " =    3.703
peak=    4.177 closest distance to " O   SER A  87 " =    2.303
peak=    4.135 closest distance to " O   HOH Z  44 " =    2.112
peak=    4.129 closest distance to " CA  ALA A  51 " =    1.024
peak=    4.128 closest distance to " O   HOH Z 126 " =    1.600
peak=    4.115 closest distance to " OG BSER A 164 " =    2.167
peak=    4.093 closest distance to " O   HOH Z 234 " =    3.642
peak=    4.086 closest distance to " O   HOH Z  59 " =    2.431
peak=    4.083 closest distance to " O   HOH Z 265 " =    2.118
peak=    4.077 closest distance to " O   HOH Z  43 " =    2.002
peak=    4.074 closest distance to " CA  ARG A 195 " =    1.143
peak=    4.047 closest distance to " O   HOH Z  40 " =    1.916
peak=    4.025 closest distance to " CB  ASN A 148 " =    1.363
peak=    4.022 closest distance to " O   HOH Z 316 " =    3.027
peak=    4.004 closest distance to " O   HOH Z 412 " =    3.804
peak=    3.979 closest distance to " O   HOH Z 369 " =    2.105
peak=    3.979 closest distance to " CA  ALA A 295 " =    1.015
peak=    3.977 closest distance to " NZ  LYS A 117 " =    3.098
peak=    3.972 closest distance to " CB  TYR A 169 " =    0.836
peak=    3.961 closest distance to " O   HOH Z 298 " =    1.857
peak=    3.959 closest distance to " CD2 TRP A 179 " =    1.300
peak=    3.950 closest distance to " CD  LYS A 166 " =    1.376
peak=    3.950 closest distance to " CG  PRO A 243 " =    1.195
peak=    3.949 closest distance to " CB  TRP A 179 " =    1.396
peak=    3.934 closest distance to " O   HOH Z 130 " =    2.555
peak=    3.912 closest distance to " CB  VAL A 202 " =    1.526
peak=    3.893 closest distance to " O   HOH Z 214 " =    2.784
peak=    3.889 closest distance to " O   HOH Z 134 " =    1.501
peak=    3.887 closest distance to " O   HOH Z 346 " =    1.556
peak=    3.874 closest distance to " O   HOH Z 425 " =    1.409
peak=    3.853 closest distance to " O   HOH Z 423 " =    1.750
peak=    3.841 closest distance to " O   HOH Z 431 " =    0.970
peak=    3.836 closest distance to " O   HOH Z 280 " =    2.934
peak=    3.835 closest distance to " CE1 TYR A 186 " =    1.285
peak=    3.832 closest distance to " O   HOH Z 272 " =    1.931
peak=    3.825 closest distance to " O   HOH Z  48 " =    1.772
peak=    3.806 closest distance to " O   HOH Z 427 " =    3.073
peak=    3.806 closest distance to " O   HOH Z 142 " =    1.559
peak=    3.805 closest distance to " O   ASN A  74 " =    1.585
peak=    3.794 closest distance to " O   HOH Z 251 " =    1.458
peak=    3.786 closest distance to " CZ  PHE A  38 " =    1.205
peak=    3.777 closest distance to " O   HOH Z  80 " =    1.918
peak=    3.777 closest distance to " O   HOH Z 102 " =    1.300
peak=    3.764 closest distance to " CG1 ILE A  33 " =    1.267
peak=    3.761 closest distance to " O   HOH Z 422 " =    2.677
peak=    3.754 closest distance to " CB  TRP A 266 " =    1.035
peak=    3.754 closest distance to " O   HOH Z 359 " =    1.502
peak=    3.749 closest distance to " OD1 ASN A  69 " =    2.553
peak=    3.747 closest distance to " CD  ARG A 269 " =    1.035
peak=    3.745 closest distance to " ND2 ASN A 249 " =    1.968
peak=    3.745 closest distance to " O   HOH Z 287 " =    1.778
peak=    3.739 closest distance to " O   ASP A 124 " =    1.182
peak=    3.739 closest distance to " O   HOH Z 261 " =    2.024
peak=    3.726 closest distance to " CB  ASP A 140 " =    0.979
peak=    3.722 closest distance to " O   HOH Z 126 " =    1.982
peak=    3.718 closest distance to " O   HOH Z 155 " =    3.310
peak=    3.716 closest distance to " O   HOH Z 371 " =    2.994
peak=    3.709 closest distance to " O   HOH Z  78 " =    1.668
peak=    3.706 closest distance to " O   HOH Z 247 " =    1.357
peak=    3.703 closest distance to " CA  ALA A  21 " =    1.242
peak=    3.701 closest distance to " CD2 LEU A 297 " =    0.956
peak=    3.698 closest distance to " CA  ALA A 160 " =    0.905
peak=    3.695 closest distance to " CZ3 TRP A 266 " =    1.093
peak=    3.690 closest distance to " ND2 ASN A 187 " =    1.530
peak=    3.684 closest distance to " CB  GLU A  46 " =    0.991
peak=    3.681 closest distance to " O   HOH Z 357 " =    2.056
peak=    3.673 closest distance to " CA  ILE A 106 " =    0.739
peak=    3.671 closest distance to " CB  GLN A  89 " =    1.194
peak=    3.671 closest distance to " CB  ASN A  39 " =    0.848
peak=    3.670 closest distance to " O   HOH Z   9 " =    2.313
peak=    3.667 closest distance to " O   HOH Z   4 " =    1.672
peak=    3.666 closest distance to " CA  ARG A  36 " =    1.069
peak=    3.665 closest distance to " NH2 ARG A 156 " =    1.107
peak=    3.665 closest distance to " O   HOH Z 303 " =    2.288
peak=    3.665 closest distance to " CB  ASP A 124 " =    0.750
peak=    3.661 closest distance to " CG  LEU A 167 " =    1.101
peak=    3.657 closest distance to " O   HOH Z 394 " =    1.495
peak=    3.656 closest distance to " CB AVAL A  41 " =    1.287
peak=    3.653 closest distance to " O   HOH Z 285 " =    2.722
peak=    3.644 closest distance to " CD  ARG A 159 " =    0.777
peak=    3.632 closest distance to " CG  MET A 185 " =    1.196
peak=    3.629 closest distance to " CG2 THR A 221 " =    1.133
peak=    3.626 closest distance to " N   ASN A  39 " =    1.204
peak=    3.604 closest distance to " O   HOH Z 417 " =    3.036
peak=    3.598 closest distance to " O   HOH Z 203 " =    1.860
peak=    3.595 closest distance to " O   HOH Z 227 " =    1.600
peak=    3.594 closest distance to " O  BHOH Z  74 " =    1.279
peak=    3.586 closest distance to " O   HOH Z  48 " =    1.502
peak=    3.583 closest distance to " CB  ALA A   9 " =    1.655
peak=    3.582 closest distance to " O   HOH Z 193 " =    1.684
peak=    3.577 closest distance to " O   HOH Z 368 " =    3.489
peak=    3.571 closest distance to " CZ3 TRP A  85 " =    0.982
peak=    3.569 closest distance to " CA  VAL A 125 " =    1.411
peak=    3.569 closest distance to " CG1 VAL A 153 " =    1.052
peak=    3.560 closest distance to " OG1 THR A 294 " =    2.322
peak=    3.557 closest distance to " CG AARG A 275 " =    1.253
peak=    3.557 closest distance to " CD1 LEU A  96 " =    0.798
peak=    3.556 closest distance to " O   HOH Z 437 " =    1.983
peak=    3.556 closest distance to " CB  THR A  52 " =    0.947
peak=    3.555 closest distance to " NH1AARG A 145 " =    1.234
peak=    3.555 closest distance to " CZ  PHE A 192 " =    1.072
peak=    3.550 closest distance to " O   HOH Z 193 " =    1.686
peak=    3.543 closest distance to " CA  ARG A 275 " =    1.854
peak=    3.542 closest distance to " CB  GLU A 152 " =    1.124
peak=    3.538 closest distance to " O   HOH Z 258 " =    2.195
peak=    3.522 closest distance to " CA  TYR A 116 " =    1.305
peak=    3.519 closest distance to " O   HOH Z 214 " =    1.150
peak=    3.510 closest distance to " O   HOH Z  61 " =    1.579
peak=    3.508 closest distance to " O   ALA A 165 " =    1.406
peak=    3.506 closest distance to " CG2 ILE A 106 " =    0.875
peak=    3.504 closest distance to " CA  ASN A 176 " =    1.113
peak=    3.499 closest distance to " O   HOH Z 383 " =    2.117
peak=    3.496 closest distance to " O   HOH Z 393 " =    3.752
peak=    3.490 closest distance to " OE1 GLU A   2 " =    1.851
peak=    3.490 closest distance to " CB  ALA A 242 " =    0.911
peak=    3.486 closest distance to " CB  ALA A 248 " =    1.339
peak=    3.485 closest distance to " CB  SER A   3 " =    1.262
peak=    3.479 closest distance to " O   PRO A 213 " =    1.489
peak=    3.471 closest distance to " O   HOH Z 313 " =    1.649
peak=    3.464 closest distance to " O   HOH Z  21 " =    1.794
peak=    3.464 closest distance to " CB  VAL A 265 " =    1.285
peak=    3.459 closest distance to " O   HOH Z 130 " =    1.078
peak=    3.459 closest distance to " NZ  LYS A  48 " =    1.214
peak=    3.455 closest distance to " CB  ASN A 142 " =    1.124
peak=    3.452 closest distance to " OE1 GLN A  11 " =    1.848
peak=    3.452 closest distance to " CA  ASP A 191 " =    0.940
peak=    3.451 closest distance to " O   HOH Z 344 " =    2.982
peak=    3.450 closest distance to " O   HOH Z 141 " =    1.632
peak=    3.449 closest distance to " O   HOH Z 291 " =    1.475
peak=    3.448 closest distance to " CB  SER A  62 " =    0.877
peak=    3.442 closest distance to " CE  LYS A 119 " =    0.959
peak=    3.439 closest distance to " CA  SER A  87 " =    0.978
peak=    3.434 closest distance to " CG1BVAL A  72 " =    1.780
peak=    3.433 closest distance to " CB  SER A 273 " =    0.925
peak=    3.433 closest distance to " N   CYS A 260 " =    0.751
peak=    3.432 closest distance to " CD  PRO A  54 " =    1.059
peak=    3.431 closest distance to " CD  ARG A  66 " =    2.283
peak=    3.429 closest distance to " CD1 LEU A   5 " =    1.391
peak=    3.429 closest distance to " CA  ASN A 217 " =    1.195
peak=    3.429 closest distance to " CB  PRO A 198 " =    1.058
peak=    3.424 closest distance to " CE1 HIS A 108 " =    1.165
peak=    3.422 closest distance to " ND2 ASN A 249 " =    0.904
peak=    3.420 closest distance to " N   ASP A 231 " =    1.656
peak=    3.420 closest distance to " CB  MET A  40 " =    0.852
peak=    3.416 closest distance to " CG2 ILE A 234 " =    0.985
peak=    3.412 closest distance to " CG  GLN A  11 " =    1.299
peak=    3.411 closest distance to " O   HOH Z 158 " =    3.060
peak=    3.408 closest distance to " CD1 LEU A 300 " =    1.092
peak=    3.407 closest distance to " CA  MET A 105 " =    1.044
peak=    3.399 closest distance to " O   HOH Z 199 " =    1.613
peak=    3.397 closest distance to " CB  TYR A 247 " =    1.003
peak=    3.394 closest distance to " O   HOH Z 124 " =    1.129
peak=    3.393 closest distance to " C   ALA A 299 " =    0.924
peak=    3.392 closest distance to " OG  SER A 276 " =    1.439
peak=    3.390 closest distance to " CG2 ILE A  20 " =    1.290
peak=    3.388 closest distance to " O   HOH Z 435 " =    2.015
peak=    3.382 closest distance to " O   HOH Z 353 " =    2.645
peak=    3.380 closest distance to " O   HOH Z  97 " =    2.027
peak=    3.372 closest distance to " O   HOH Z 166 " =    1.441
peak=    3.370 closest distance to " CB  LEU A  83 " =    0.758
peak=    3.369 closest distance to " CA  ASP A 162 " =    1.064
peak=    3.366 closest distance to " O   HOH Z 133 " =    2.462
peak=    3.365 closest distance to " CB  SER A  26 " =    1.735
peak=    3.365 closest distance to " O   HOH Z 357 " =    2.366
peak=    3.363 closest distance to " O   HOH Z 391 " =    2.965
peak=    3.360 closest distance to " CG  MET A 188 " =    0.845
peak=    3.353 closest distance to " O   HOH Z 327 " =    2.447
peak=    3.351 closest distance to " CA  ASP A 140 " =    1.246
peak=    3.349 closest distance to " CG1 ILE A  49 " =    1.633
peak=    3.343 closest distance to " CA  GLN A  88 " =    1.269
peak=    3.342 closest distance to " CA  LYS A 117 " =    1.215
peak=    3.341 closest distance to " O   HOH Z 271 " =    2.324
peak=    3.339 closest distance to " O   HOH Z  88 " =    3.270
peak=    3.338 closest distance to " CA  ALA A 100 " =    0.908
peak=    3.337 closest distance to " CB  PRO A 243 " =    1.200
peak=    3.336 closest distance to " O   HOH Z 185 " =    1.685
peak=    3.333 closest distance to " O   HOH Z 193 " =    2.112
peak=    3.331 closest distance to " O   HOH Z 426 " =    1.439
peak=    3.330 closest distance to " O   HOH Z 189 " =    2.898
peak=    3.328 closest distance to " N   TYR A 247 " =    1.173
peak=    3.326 closest distance to " CB  ASN A 187 " =    1.186
peak=    3.326 closest distance to " O   ALA A 158 " =    1.279
peak=    3.323 closest distance to " O   HOH Z 163 " =    1.482
peak=    3.320 closest distance to " CB  GLN A  88 " =    1.202
peak=    3.319 closest distance to " O   HOH Z 345 " =    3.122
peak=    3.318 closest distance to " CG2 VAL A 257 " =    0.872
peak=    3.314 closest distance to " OD1 ASN A 217 " =    1.722
peak=    3.314 closest distance to " CB  ALA A 291 " =    1.300
peak=    3.313 closest distance to " O   HOH Z 273 " =    2.976
peak=    3.313 closest distance to " O   HOH Z 245 " =    1.367
peak=    3.312 closest distance to " O   HOH Z  68 " =    1.760
peak=    3.308 closest distance to " CB  ALA A 248 " =    1.096
peak=    3.305 closest distance to " CB  THR A 235 " =    1.171
peak=    3.305 closest distance to " N   SER A 164 " =    0.974
peak=    3.297 closest distance to " CE  LYS A  76 " =    0.835
peak=    3.292 closest distance to " O   HOH Z 366 " =    2.825
peak=    3.292 closest distance to " CD1 ILE A 199 " =    1.084
peak=    3.290 closest distance to " N   ILE A  33 " =    1.041
peak=    3.288 closest distance to " O   HOH Z 294 " =    1.582
peak=    3.284 closest distance to " CB  ARG A 219 " =    1.393
peak=    3.283 closest distance to " O   HOH Z 238 " =    0.772
peak=    3.283 closest distance to " CB  ASN A 285 " =    0.932
peak=    3.279 closest distance to " O   HOH Z 132 " =    2.741
peak=    3.277 closest distance to " CB  TRP A 150 " =    1.442
peak=    3.268 closest distance to " CD1 LEU A 222 " =    0.758
peak=    3.268 closest distance to " CB  MET A  47 " =    1.045
peak=    3.264 closest distance to " CG2 THR A  29 " =    1.385
peak=    3.263 closest distance to " O   HOH Z 250 " =    1.390
peak=    3.260 closest distance to " CZ3 TRP A 274 " =    4.498
peak=    3.258 closest distance to " OD2 ASP A 298 " =    3.780
peak=    3.258 closest distance to " O   HOH Z 201 " =    2.949
peak=    3.256 closest distance to " CA  GLY A 267 " =    0.760
peak=    3.256 closest distance to " O   HOH Z 403 " =    1.339
peak=    3.255 closest distance to " CA  ASN A 127 " =    1.159
peak=    3.254 closest distance to " CD BLYS A 290 " =    0.974
peak=    3.254 closest distance to " N   ALA A 256 " =    1.064
peak=    3.251 closest distance to " C   ILE A 106 " =    1.884
peak=    3.250 closest distance to " NH1 ARG A  14 " =    1.117
peak=    3.249 closest distance to " O   HOH Z 154 " =    1.294
peak=    3.247 closest distance to " O   THR A 220 " =    1.249
peak=    3.243 closest distance to " O   HOH Z 145 " =    2.167
peak=    3.243 closest distance to " O   HOH Z 301 " =    1.921
peak=    3.242 closest distance to " O   ASP A 124 " =    1.776
peak=    3.241 closest distance to " CA  LYS A 290 " =    1.138
peak=    3.234 closest distance to " O   HOH Z 180 " =    2.183
peak=    3.230 closest distance to " CG  PHE A 204 " =    0.917
peak=    3.229 closest distance to " CA  TYR A 214 " =    1.396
peak=    3.220 closest distance to " O   ALA A 292 " =    1.179
peak=    3.220 closest distance to " O   HOH Z 139 " =    4.884
peak=    3.218 closest distance to " O  BHOH Z 338 " =    2.389
peak=    3.217 closest distance to " CG  MET A 185 " =    1.008
peak=    3.214 closest distance to " NE2 HIS A 115 " =    1.013
peak=    3.212 closest distance to " O   HOH Z 151 " =    1.660
peak=    3.211 closest distance to " O   HOH Z 406 " =    1.394
peak=    3.208 closest distance to " O   HOH Z 421 " =    1.663
peak=    3.208 closest distance to " O   HOH Z 197 " =    1.802
peak=    3.205 closest distance to " CB  PRO A  90 " =    1.149
peak=    3.204 closest distance to " O   HOH Z  68 " =    1.966
peak=    3.200 closest distance to " O   HOH Z 146 " =    1.402
peak=    3.200 closest distance to " NZ  LYS A 117 " =    1.269
peak=    3.197 closest distance to " CG2 VAL A 197 " =    1.129
peak=    3.190 closest distance to " CB  GLN A 103 " =    0.955
peak=    3.189 closest distance to " CG1 ILE A  20 " =    1.232
peak=    3.188 closest distance to " CA  CYS A 260 " =    1.592
peak=    3.186 closest distance to " N   ARG A 190 " =    1.035
peak=    3.185 closest distance to " O   HOH Z  90 " =    3.383
peak=    3.177 closest distance to " CB  SER A  62 " =    1.079
peak=    3.172 closest distance to " CG  ARG A 138 " =    1.315
peak=    3.171 closest distance to " OG  SER A 245 " =    1.568
peak=    3.171 closest distance to " CG  GLU A  37 " =    0.854
peak=    3.171 closest distance to " O   HOH Z 227 " =    2.030
peak=    3.169 closest distance to " O   HOH Z 261 " =    1.551
peak=    3.160 closest distance to " CB  ALA A 100 " =    1.288
peak=    3.159 closest distance to " O   HOH Z 420 " =    5.696
peak=    3.153 closest distance to " OG BSER A 134 " =    2.751
peak=    3.153 closest distance to " O   HOH Z 336 " =    1.544
peak=    3.150 closest distance to " CB  ASN A 215 " =    1.191
peak=    3.145 closest distance to " O   HOH Z  44 " =    1.756
peak=    3.145 closest distance to " CA  THR A 264 " =    0.768
peak=    3.143 closest distance to " CA  GLY A 211 " =    1.329
peak=    3.142 closest distance to " O   HOH Z 329 " =    4.089
peak=    3.139 closest distance to " CG2 ILE A 120 " =    1.189
peak=    3.139 closest distance to " CG BARG A 102 " =    1.852
peak=    3.138 closest distance to " CE3 TRP A 150 " =    1.050
peak=    3.137 closest distance to " O   GLY A  91 " =    1.235
peak=    3.135 closest distance to " CA  LEU A 282 " =    1.140
peak=    3.134 closest distance to " O   HOH Z 285 " =    1.741
peak=    3.126 closest distance to " OG  SER A  62 " =    2.920
peak=    3.125 closest distance to " CB  LYS A 117 " =    1.203
peak=    3.124 closest distance to " CG2 VAL A 202 " =    1.105
peak=    3.122 closest distance to " CB  ALA A 295 " =    1.359
peak=    3.117 closest distance to " CZ3 TRP A  92 " =    1.322
peak=    3.115 closest distance to " CD  LYS A 119 " =    1.960
peak=    3.112 closest distance to " CA  GLY A  80 " =    0.817
peak=    3.103 closest distance to " ND1 HIS A  81 " =    1.648
peak=    3.098 closest distance to " O   HOH Z 126 " =    1.728
peak=    3.094 closest distance to " O   HOH Z 109 " =    2.514
peak=    3.084 closest distance to " O   HOH Z  85 " =    1.480
peak=    3.079 closest distance to " O   HOH Z 256 " =    2.274
peak=    3.074 closest distance to " CD2 TYR A 186 " =    1.029
peak=    3.055 closest distance to " O   HOH Z 162 " =    1.848
peak=    3.018 closest distance to " CB  ALA A  43 " =    0.894

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 202         
Filter by distance & map next to the model:
   mapped sites are within: 0.785 - 5.619
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 201 from: 202
   mapped sites are within: 0.785 - 5.619

peak=   -5.707 closest distance to " CG2 VAL A 230 " =    0.785
peak=   -4.501 closest distance to " O   HOH Z 266 " =    5.354
peak=   -4.375 closest distance to " O   HOH Z 166 " =    1.609
peak=   -4.363 closest distance to " CG1 VAL A 296 " =    1.112
peak=   -4.306 closest distance to " CD  GLN A  58 " =    1.084
peak=   -4.305 closest distance to " CA  SER A 164 " =    2.237
peak=   -4.288 closest distance to " O   HOH Z 196 " =    2.503
peak=   -4.246 closest distance to " SG  CYS A 254 " =    3.355
peak=   -4.233 closest distance to " O   HOH Z 351 " =    1.546
peak=   -4.228 closest distance to " CA  ASP A 298 " =    1.059
peak=   -4.219 closest distance to " CG1 VAL A 250 " =    2.728
peak=   -4.193 closest distance to " O   VAL A  67 " =    2.798
peak=   -4.091 closest distance to " CD  ARG A 156 " =    2.067
peak=   -4.033 closest distance to " CE3 TRP A 150 " =    2.125
peak=   -4.018 closest distance to " OXT GLY A 302 " =    2.958
peak=   -3.923 closest distance to " CG  ARG A 269 " =    2.331
peak=   -3.921 closest distance to " CZ2 TRP A  92 " =    2.805
peak=   -3.895 closest distance to " CB  PRO A 243 " =    2.731
peak=   -3.866 closest distance to " O   ILE A 109 " =    2.647
peak=   -3.862 closest distance to " CE2 TYR A  30 " =    2.778
peak=   -3.861 closest distance to " O   HOH Z 231 " =    2.194
peak=   -3.853 closest distance to " O   HOH Z  10 " =    1.557
peak=   -3.848 closest distance to " C   HIS A 108 " =    1.136
peak=   -3.847 closest distance to " O   PRO A 198 " =    1.261
peak=   -3.836 closest distance to " CG1 VAL A 112 " =    2.691
peak=   -3.817 closest distance to " CB  ALA A  10 " =    2.209
peak=   -3.803 closest distance to " OG BSER A 134 " =    1.358
peak=   -3.794 closest distance to " CG  ASP A 231 " =    0.861
peak=   -3.793 closest distance to " ND2 ASN A  45 " =    1.110
peak=   -3.778 closest distance to " O   HOH Z  13 " =    1.755
peak=   -3.740 closest distance to " CD1 PHE A  59 " =    2.006
peak=   -3.737 closest distance to " O   SER A 271 " =    2.100
peak=   -3.725 closest distance to " CB  ALA A 248 " =    2.251
peak=   -3.718 closest distance to " CB  ALA A 248 " =    2.096
peak=   -3.714 closest distance to " CG  GLU A  53 " =    1.579
peak=   -3.707 closest distance to " CB  PHE A 208 " =    2.354
peak=   -3.694 closest distance to " O   HOH Z 283 " =    2.231
peak=   -3.679 closest distance to " OG1 THR A  82 " =    1.222
peak=   -3.675 closest distance to " CH2 TRP A 179 " =    1.209
peak=   -3.674 closest distance to " CD1 LEU A 101 " =    2.421
peak=   -3.662 closest distance to " OD1 ASN A 148 " =    1.429
peak=   -3.653 closest distance to " OE1 GLN A 223 " =    2.212
peak=   -3.641 closest distance to " C   LEU A 143 " =    1.127
peak=   -3.629 closest distance to " O   HOH Z 165 " =    1.970
peak=   -3.620 closest distance to " N   ALA A 226 " =    2.045
peak=   -3.606 closest distance to " N   ALA A  43 " =    2.629
peak=   -3.606 closest distance to " CD  LYS A 289 " =    2.445
peak=   -3.598 closest distance to " O   HOH Z  52 " =    1.694
peak=   -3.595 closest distance to " O   HOH Z 394 " =    1.689
peak=   -3.589 closest distance to " O   HOH Z  37 " =    1.957
peak=   -3.584 closest distance to " CD2 TYR A 293 " =    1.846
peak=   -3.581 closest distance to " O   HOH Z 285 " =    1.673
peak=   -3.570 closest distance to " O   HOH Z 210 " =    0.948
peak=   -3.564 closest distance to " OG  SER A  97 " =    2.311
peak=   -3.554 closest distance to " CG2 THR A   4 " =    1.952
peak=   -3.551 closest distance to " O   HOH Z  44 " =    2.258
peak=   -3.541 closest distance to " CD  GLN A 223 " =    1.512
peak=   -3.534 closest distance to " O   HOH Z 252 " =    3.813
peak=   -3.524 closest distance to " O   HOH Z 426 " =    1.848
peak=   -3.524 closest distance to " O   VAL A  67 " =    2.847
peak=   -3.522 closest distance to " CG2 ILE A 263 " =    2.321
peak=   -3.520 closest distance to " NH2 ARG A  66 " =    1.629
peak=   -3.518 closest distance to " O   HOH Z 113 " =    2.416
peak=   -3.517 closest distance to " CB  PHE A 192 " =    1.951
peak=   -3.517 closest distance to " CG  GLN A 103 " =    2.527
peak=   -3.516 closest distance to " O   HOH Z 185 " =    2.460
peak=   -3.508 closest distance to " O   SER A 210 " =    1.748
peak=   -3.504 closest distance to " NE2 GLN A 194 " =    1.903
peak=   -3.496 closest distance to " C   ASN A 285 " =    2.366
peak=   -3.496 closest distance to " O   HOH Z 200 " =    1.573
peak=   -3.491 closest distance to " O   HOH Z 407 " =    3.128
peak=   -3.488 closest distance to " O   HOH Z 275 " =    1.543
peak=   -3.484 closest distance to " ND2BASN A 224 " =    1.852
peak=   -3.475 closest distance to " O   HOH Z 308 " =    1.668
peak=   -3.472 closest distance to " O   HOH Z 171 " =    2.279
peak=   -3.471 closest distance to " ND2 ASN A  45 " =    1.130
peak=   -3.470 closest distance to " CA  VAL A 197 " =    1.031
peak=   -3.468 closest distance to " CD2 LEU A 167 " =    1.822
peak=   -3.461 closest distance to " O   GLY A  75 " =    2.064
peak=   -3.458 closest distance to " O   HOH Z  60 " =    2.076
peak=   -3.444 closest distance to " N   SER A 276 " =    1.496
peak=   -3.442 closest distance to " CZ  TYR A 169 " =    1.763
peak=   -3.431 closest distance to " O   HOH Z 301 " =    2.456
peak=   -3.419 closest distance to " O   HOH Z 251 " =    4.933
peak=   -3.419 closest distance to " C   SER A 206 " =    1.405
peak=   -3.416 closest distance to " O   GLY A  80 " =    2.539
peak=   -3.412 closest distance to " O   HOH Z 193 " =    1.525
peak=   -3.405 closest distance to " O   HOH Z 264 " =    1.760
peak=   -3.404 closest distance to " C   GLY A  17 " =    1.285
peak=   -3.404 closest distance to " ND2 ASN A  45 " =    1.845
peak=   -3.403 closest distance to " O   HOH Z 114 " =    3.235
peak=   -3.401 closest distance to " CG  PRO A 243 " =    1.633
peak=   -3.395 closest distance to " O   HOH Z 423 " =    2.297
peak=   -3.393 closest distance to " O   HOH Z 431 " =    2.282
peak=   -3.392 closest distance to " O   HOH Z  92 " =    1.687
peak=   -3.388 closest distance to " NE2 GLN A  88 " =    1.017
peak=   -3.385 closest distance to " O   HOH Z 136 " =    2.536
peak=   -3.375 closest distance to " O   HOH Z 290 " =    1.131
peak=   -3.374 closest distance to " O   HOH Z  19 " =    2.247
peak=   -3.373 closest distance to " CA  GLY A 203 " =    2.443
peak=   -3.372 closest distance to " O   HOH Z 222 " =    1.575
peak=   -3.370 closest distance to " ND2 ASN A  69 " =    1.818
peak=   -3.369 closest distance to " C   ALA A 158 " =    1.297
peak=   -3.354 closest distance to " O   HOH Z 198 " =    1.991
peak=   -3.352 closest distance to " O   HOH Z 128 " =    2.606
peak=   -3.351 closest distance to " O   HOH Z 174 " =    2.113
peak=   -3.351 closest distance to " O   ALA A  34 " =    2.592
peak=   -3.348 closest distance to " CA  ASN A 127 " =    1.039
peak=   -3.344 closest distance to " CA  GLY A 133 " =    2.362
peak=   -3.343 closest distance to " CD2 PHE A  61 " =    2.042
peak=   -3.337 closest distance to " NE  ARG A  66 " =    4.312
peak=   -3.335 closest distance to " O   HOH Z 411 " =    1.721
peak=   -3.333 closest distance to " CG  ASP A  50 " =    2.310
peak=   -3.331 closest distance to " N   THR A 235 " =    1.247
peak=   -3.328 closest distance to " CD1 LEU A  25 " =    2.468
peak=   -3.328 closest distance to " O   HOH Z 133 " =    1.452
peak=   -3.326 closest distance to " CB  ALA A  51 " =    1.893
peak=   -3.323 closest distance to " CG  TRP A 266 " =    1.827
peak=   -3.322 closest distance to " CA  GLY A 241 " =    2.331
peak=   -3.318 closest distance to " O   HOH Z 191 " =    5.619
peak=   -3.318 closest distance to " O   HOH Z 177 " =    1.871
peak=   -3.317 closest distance to " NH2 ARG A  79 " =    1.621
peak=   -3.306 closest distance to " O   HOH Z 150 " =    1.886
peak=   -3.304 closest distance to " O   ASP A  27 " =    2.104
peak=   -3.304 closest distance to " ND2 ASN A  39 " =    1.291
peak=   -3.292 closest distance to " O   SER A  95 " =    1.834
peak=   -3.291 closest distance to " C   LYS A  76 " =    1.514
peak=   -3.290 closest distance to " O   HOH Z 106 " =    1.939
peak=   -3.287 closest distance to " O   HOH Z  88 " =    4.493
peak=   -3.286 closest distance to " CB  ASP A 171 " =    2.284
peak=   -3.285 closest distance to " O   ALA A 227 " =    1.520
peak=   -3.283 closest distance to " CB  LEU A   5 " =    1.812
peak=   -3.283 closest distance to " CG  GLN A  11 " =    1.731
peak=   -3.275 closest distance to " CG2 VAL A 189 " =    2.143
peak=   -3.272 closest distance to " O   SER A 276 " =    1.743
peak=   -3.272 closest distance to " N   ASP A 171 " =    2.374
peak=   -3.271 closest distance to " O   HOH Z   6 " =    1.831
peak=   -3.270 closest distance to " C   THR A 279 " =    1.141
peak=   -3.270 closest distance to " O   HOH Z 113 " =    1.988
peak=   -3.267 closest distance to " OXT GLY A 302 " =    3.352
peak=   -3.263 closest distance to " CA  VAL A 296 " =    1.017
peak=   -3.257 closest distance to " O   HOH Z 435 " =    2.546
peak=   -3.256 closest distance to " O   TYR A 186 " =    1.777
peak=   -3.255 closest distance to " O   ALA A 161 " =    1.847
peak=   -3.255 closest distance to " CA  LYS A 166 " =    2.250
peak=   -3.254 closest distance to " CD1 TYR A 247 " =    2.364
peak=   -3.254 closest distance to " CB  TYR A  15 " =    2.204
peak=   -3.254 closest distance to " O   HOH Z 236 " =    1.519
peak=   -3.253 closest distance to " CD2 LEU A 300 " =    2.599
peak=   -3.252 closest distance to " O   HOH Z 353 " =    2.121
peak=   -3.248 closest distance to " CE BMET A  47 " =    1.836
peak=   -3.243 closest distance to " O   PHE A 218 " =    1.566
peak=   -3.234 closest distance to " O   HOH Z 111 " =    1.515
peak=   -3.229 closest distance to " CG2 THR A 182 " =    2.421
peak=   -3.228 closest distance to " N   ALA A 242 " =    1.956
peak=   -3.226 closest distance to " C   VAL A 265 " =    0.866
peak=   -3.221 closest distance to " O   HOH Z 139 " =    3.207
peak=   -3.217 closest distance to " OD1 ASN A 187 " =    1.623
peak=   -3.217 closest distance to " O   VAL A 189 " =    2.555
peak=   -3.214 closest distance to " CB  SER A 210 " =    1.110
peak=   -3.213 closest distance to " O   HOH Z 105 " =    2.123
peak=   -3.213 closest distance to " CB  ALA A 256 " =    2.826
peak=   -3.211 closest distance to " O   HOH Z 234 " =    4.318
peak=   -3.209 closest distance to " CE3 TRP A  70 " =    1.649
peak=   -3.208 closest distance to " CB  TRP A  85 " =    2.447
peak=   -3.201 closest distance to " CG1 VAL A 112 " =    2.666
peak=   -3.196 closest distance to " O   HOH Z 385 " =    3.737
peak=   -3.195 closest distance to " CG1 VAL A 112 " =    2.838
peak=   -3.195 closest distance to " O   HOH Z 265 " =    2.337
peak=   -3.194 closest distance to " SG  CYS A 260 " =    2.326
peak=   -3.190 closest distance to " CE  MET A 105 " =    2.566
peak=   -3.189 closest distance to " O   HOH Z 311 " =    3.812
peak=   -3.184 closest distance to " O   VAL A 125 " =    2.223
peak=   -3.184 closest distance to " NE2 GLN A 103 " =    1.844
peak=   -3.173 closest distance to " CE  MET A  93 " =    1.430
peak=   -3.169 closest distance to " CH2 TRP A 150 " =    1.038
peak=   -3.162 closest distance to " O   HOH Z  38 " =    1.670
peak=   -3.162 closest distance to " CG2 VAL A 112 " =    2.593
peak=   -3.161 closest distance to " CD  ARG A 139 " =    1.655
peak=   -3.159 closest distance to " NE2 GLN A  58 " =    2.491
peak=   -3.158 closest distance to " O   HOH Z 259 " =    1.884
peak=   -3.155 closest distance to " CG  GLU A 277 " =    1.169
peak=   -3.153 closest distance to " CB  ALA A 291 " =    2.381
peak=   -3.147 closest distance to " CG  MET A 105 " =    0.926
peak=   -3.140 closest distance to " CE2 PHE A  61 " =    2.576
peak=   -3.140 closest distance to " CB  ASP A 132 " =    2.364
peak=   -3.139 closest distance to " O   HOH Z 196 " =    2.144
peak=   -3.133 closest distance to " CB  PHE A  16 " =    2.429
peak=   -3.126 closest distance to " O   HOH Z 231 " =    1.931
peak=   -3.125 closest distance to " O   HOH Z 166 " =    1.729
peak=   -3.104 closest distance to " CG  ASP A 286 " =    1.520
peak=   -3.101 closest distance to " CB  PRO A  54 " =    2.563
peak=   -3.097 closest distance to " O   HOH Z 136 " =    1.381
peak=   -3.092 closest distance to " O   HOH Z 110 " =    1.497
peak=   -3.082 closest distance to " O   HOH Z  40 " =    2.444
peak=   -3.076 closest distance to " NH2AARG A 275 " =    5.056
peak=   -3.076 closest distance to " N   ASN A  60 " =    1.260
peak=   -3.075 closest distance to " CG2 VAL A 296 " =    1.338
peak=   -3.059 closest distance to " CD  GLN A  88 " =    0.872
peak=   -3.043 closest distance to " CD1 LEU A 101 " =    2.841
peak=   -3.033 closest distance to " CA  SER A  62 " =    2.518

================= 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    :  0.4660 0.4517   6.265496e+00   6.241385e+00
   1_bss:  0.4588 0.4411   6.258258e+00   6.232229e+00
   1_xyz:  0.3602 0.3769   6.110708e+00   6.130838e+00
   1_adp:  0.3083 0.3521   5.996962e+00   6.077696e+00
   1_occ:  0.3076 0.3523   5.995747e+00   6.078193e+00
   2_bss:  0.3033 0.3470   5.996119e+00   6.075911e+00
   2_xyz:  0.2190 0.2622   5.705931e+00   5.857713e+00
   2_adp:  0.1981 0.2400   5.624133e+00   5.785826e+00
   2_occ:  0.1978 0.2407   5.624418e+00   5.787988e+00
   3_bss:  0.1965 0.2396   5.623536e+00   5.785264e+00
   3_xyz:  0.1543 0.1890   5.395071e+00   5.575088e+00
   3_adp:  0.1431 0.1847   5.345995e+00   5.548133e+00
   3_occ:  0.1431 0.1847   5.345713e+00   5.547954e+00
   4_bss:  0.1432 0.1855   5.346901e+00   5.549048e+00
   4_xyz:  0.1233 0.1710   5.232299e+00   5.465113e+00
   4_adp:  0.1206 0.1676   5.209793e+00   5.444330e+00
   4_occ:  0.1205 0.1675   5.209627e+00   5.444272e+00
   5_bss:  0.1205 0.1674   5.209423e+00   5.444103e+00
   5_xyz:  0.1195 0.1649   5.201907e+00   5.435463e+00
   5_adp:  0.1194 0.1642   5.199464e+00   5.431338e+00
   5_occ:  0.1190 0.1640   5.198222e+00   5.430612e+00
   5_bss:  0.1193 0.1643   5.199453e+00   5.431554e+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:  0.322  18.525   6.582  10.758   9.149   0.000   0.000   0.000
   1_xyz:  0.322  18.525   6.582  10.758   9.149   0.000   0.000   0.000
   1_adp:  0.322  18.525   6.582  10.758   9.149   0.000   0.000   0.000
   1_occ:  0.322  18.525   6.582  10.758   9.149   0.000   0.000   0.000
   2_bss:  0.328  50.000   3.141   6.718   5.381   0.000   0.000   0.000
   2_xyz:  0.328  50.000   3.141   6.718   5.381   0.000   0.000   0.000
   2_adp:  0.328  50.000   3.141   6.718   5.381   0.000   0.000   0.000
   2_occ:  0.328  50.000   3.141   6.718   5.381   0.000   0.000   0.000
   3_bss:  0.335  67.260   2.248   4.071   4.022   0.000   0.000   0.000
   3_xyz:  0.335  67.260   2.248   4.071   4.022   0.000   0.000   0.000
   3_adp:  0.335  67.260   2.248   4.071   4.022   0.000   0.000   0.000
   3_occ:  0.335  67.260   2.248   4.071   4.022   0.000   0.000   0.000
   4_bss:  0.335  67.260   2.097   3.353   3.885   0.000   0.000   0.000
   4_xyz:  0.335  67.260   2.097   3.353   3.885   0.000   0.000   0.000
   4_adp:  0.335  67.260   2.097   3.353   3.885   0.000   0.000   0.000
   4_occ:  0.335  67.260   2.097   3.353   3.885   0.000   0.000   0.000
   5_bss:  0.332  65.556   2.344   3.277   4.045   0.000   0.000   0.000
   5_xyz:  0.332  65.556   2.344   3.277   4.045   0.000   0.000   0.000
   5_adp:  0.332  65.556   2.344   3.277   4.045   0.000   0.000   0.000
   5_occ:  0.332  65.556   2.344   3.277   4.045   0.000   0.000   0.000
   5_bss:  0.325  66.566  -0.834  -0.017   0.851  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  51.937 0.4974  0.5574    59419.835
   1_bss:  51.303 0.5043  0.7374    57705.080
   1_xyz:  41.868 0.6193  0.8771    39672.986
   1_adp:  37.271 0.6750  0.9712    33575.348
   1_occ:  37.264 0.6751  0.9710    33575.764
   2_bss:  37.024 0.6779  0.8551    33254.074
   2_xyz:  27.063 0.7892  0.9691    18323.176
   2_adp:  24.279 0.8192  0.9916    15405.437
   2_occ:  24.344 0.8185  0.9906    15476.446
   3_bss:  24.194 0.8201  0.9370    15382.107
   3_xyz:  18.196 0.8786  0.9734     9306.254
   3_adp:  17.444 0.8858  0.9719     8758.857
   3_occ:  17.437 0.8858  0.9719     8755.269
   4_bss:  17.449 0.8858  0.9606     8789.027
   4_xyz:  15.721 0.9006  0.9682     7406.709
   4_adp:  15.218 0.9051  0.9637     7144.197
   4_occ:  15.217 0.9051  0.9636     7142.986
   5_bss:  15.210 0.9052  0.9677     7141.777
   5_xyz:  14.947 0.9076  0.9689     6960.990
   5_adp:  14.813 0.9088  0.9647     6906.287
   5_occ:  14.804 0.9089  0.9645     6897.127
   5_bss:  14.838 0.9086  0.9639     6926.287
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.093   5.4237e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.093   5.4237e+01
   1_xyz:   1.646  0.013  0.107 17.870  0.006  4.113   1.3413e-01
   1_adp:   1.646  0.013  0.107 17.870  0.006  4.113   1.3413e-01
   1_occ:   1.646  0.013  0.107 17.870  0.006  4.113   1.3413e-01
   2_bss:   1.646  0.013  0.107 17.870  0.006  4.113   1.3413e-01
   2_xyz:   1.183  0.009  0.076 16.122  0.004  4.132   8.1231e-02
   2_adp:   1.183  0.009  0.076 16.122  0.004  4.132   8.1231e-02
   2_occ:   1.183  0.009  0.076 16.122  0.004  4.132   8.1231e-02
   3_bss:   1.183  0.009  0.076 16.122  0.004  4.132   8.1231e-02
   3_xyz:   0.991  0.007  0.074 15.349  0.003  4.128   5.9397e-02
   3_adp:   0.991  0.007  0.074 15.349  0.003  4.128   5.9397e-02
   3_occ:   0.991  0.007  0.074 15.349  0.003  4.128   5.9397e-02
   4_bss:   0.991  0.007  0.074 15.349  0.003  4.128   5.9397e-02
   4_xyz:   1.104  0.009  0.086 15.549  0.004  4.139   7.2129e-02
   4_adp:   1.104  0.009  0.086 15.549  0.004  4.139   7.2129e-02
   4_occ:   1.104  0.009  0.086 15.549  0.004  4.139   7.2129e-02
   5_bss:   1.104  0.009  0.086 15.549  0.004  4.139   7.2129e-02
   5_xyz:   0.999  0.008  0.079 15.241  0.003  4.141   6.0948e-02
   5_adp:   0.999  0.008  0.079 15.241  0.003  4.141   6.0948e-02
   5_occ:   0.999  0.008  0.079 15.241  0.003  4.141   6.0948e-02
   5_bss:   0.999  0.008  0.079 15.241  0.003  4.141   6.0948e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0322e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0322e+00
   1_xyz:  14.985  0.159  0.481 86.605  0.038  2.300   1.0131e-01
   1_adp:  14.985  0.159  0.481 86.605  0.038  2.300   1.0131e-01
   1_occ:  14.985  0.159  0.481 86.605  0.038  2.300   1.0131e-01
   2_bss:  14.985  0.159  0.481 86.605  0.038  2.300   1.0131e-01
   2_xyz:   8.175  0.117  0.264 84.465  0.044  2.057   8.3662e-02
   2_adp:   8.175  0.117  0.264 84.465  0.044  2.057   8.3662e-02
   2_occ:   8.175  0.117  0.264 84.465  0.044  2.057   8.3662e-02
   3_bss:   8.175  0.117  0.264 84.465  0.044  2.057   8.3662e-02
   3_xyz:   6.718  0.076  0.240 80.981  0.032  2.313   4.6891e-02
   3_adp:   6.718  0.076  0.240 80.981  0.032  2.313   4.6891e-02
   3_occ:   6.718  0.076  0.240 80.981  0.032  2.313   4.6891e-02
   4_bss:   6.718  0.076  0.240 80.981  0.032  2.313   4.6891e-02
   4_xyz:   7.626  0.050  0.499 83.198  0.034  2.230   4.6734e-02
   4_adp:   7.626  0.050  0.499 83.198  0.034  2.230   4.6734e-02
   4_occ:   7.626  0.050  0.499 83.198  0.034  2.230   4.6734e-02
   5_bss:   7.626  0.050  0.499 83.198  0.034  2.230   4.6734e-02
   5_xyz:   7.211  0.043  0.407 81.202  0.035  2.343   3.7280e-02
   5_adp:   7.211  0.043  0.407 81.202  0.035  2.343   3.7280e-02
   5_occ:   7.211  0.043  0.407 81.202  0.035  2.343   3.7280e-02
   5_bss:   7.211  0.043  0.407 81.202  0.035  2.343   3.7280e-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:  95.47   0.00  12.28  70.31   0.00   9.50  95.47   0.00  27.43
   1_occ:  95.47   0.00  12.28  70.31   0.00   9.50  95.47   0.00  27.43
   2_bss:  95.47   0.00  12.28  70.31   0.00   9.50  95.47   0.00  27.43
   2_xyz:  95.47   0.00  12.28  70.31   0.00   9.50  95.47   0.00  27.43
   2_adp:  88.21   0.00  12.14  66.32   0.00   8.48  88.21   1.26  32.04
   2_occ:  88.21   0.00  12.14  66.32   0.00   8.48  88.21   1.26  32.04
   3_bss:  88.21   0.00  12.14  66.32   0.00   8.48  88.21   1.26  32.04
   3_xyz:  88.21   0.00  12.14  66.32   0.00   8.48  88.21   1.26  32.04
   3_adp:  86.92   0.00  13.30  86.92   0.00   8.59  84.97   0.74  38.96
   3_occ:  86.92   0.00  13.30  86.92   0.00   8.59  84.97   0.74  38.96
   4_bss:  86.92   0.00  13.30  86.92   0.00   8.59  84.97   0.74  38.96
   4_xyz:  86.92   0.00  13.30  86.92   0.00   8.59  84.97   0.74  38.96
   4_adp:  88.00   0.00  13.08  88.00   0.00   8.33  85.58   0.32  38.96
   4_occ:  88.00   0.00  13.08  88.00   0.00   8.33  85.58   0.32  38.96
   5_bss:  88.00   0.00  13.08  88.00   0.00   8.33  85.58   0.32  38.96
   5_xyz:  88.00   0.00  13.08  88.00   0.00   8.33  85.58   0.32  38.96
   5_adp:  88.50   0.00  12.94  88.50   0.00   8.22  85.98   0.73  38.64
   5_occ:  88.50   0.00  12.94  88.50   0.00   8.22  85.98   0.73  38.64
   5_bss:  91.72   3.22  16.16  91.72   3.22  11.44  89.20   3.95  41.85
------------------------------------------------------------------------
 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:    1.230    0.018    0.410
   1_adp:    1.230    0.018    0.410
   1_occ:    1.230    0.018    0.410
   2_bss:    1.230    0.018    0.410
   2_xyz:    1.674    0.008    0.571
   2_adp:    1.674    0.008    0.571
   2_occ:    1.674    0.008    0.571
   3_bss:    1.674    0.008    0.571
   3_xyz:    1.693    0.040    0.612
   3_adp:    1.693    0.040    0.612
   3_occ:    1.693    0.040    0.612
   4_bss:    1.693    0.040    0.612
   4_xyz:    1.804    0.055    0.660
   4_adp:    1.804    0.055    0.660
   4_occ:    1.804    0.055    0.660
   5_bss:    1.804    0.055    0.660
   5_xyz:    1.944    0.048    0.669
   5_adp:    1.944    0.048    0.669
   5_occ:    1.944    0.048    0.669
   5_bss:    1.944    0.048    0.669
------------------------------------------------------------------------

CPU time actual refinement: 349.03


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_700/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_700/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_700/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_700/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_700/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 348.87 
  Macro-tasks:
    bulk solvent and scale       = 40.78  
    individual site refinement   = 149.95 
    weights calculation          = 31.53  
    collect and process          = 6.52   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 228.90 
  Micro-tasks:
    mask                            = 2.30   
    f_calc                          = 108.99 
    alpha_beta                      = 8.07   
    target                          = 1.12   
    gradients_wrt_atomic_parameters = 122.25 
    fmodel                         = 7.31   
    r_factors                      = 0.19   
    phase_errors                   = 10.85  
    foms                           = 0.30   
    TOTAL for micro-tasks          = 261.38 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.832 micro seconds
Total CPU time: 6.04 minutes
from_scatterers_fft:    679 calls, 108.59 s
gradients_fft:          624 calls, 108.49 s

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

# Date 2008-01-16 Time 02:13:55 PST -0800 (1200478435.02 s)
Start R-work = 0.4660, R-free = 0.4517 (no bulk solvent and anisotropic scale)
Final R-work = 0.1352, R-free = 0.1793 (no bulk solvent and anisotropic scale)

Start R-work = 0.4588, R-free = 0.4411
Final R-work = 0.1193, R-free = 0.1643