# Date 2008-01-16 Time 02:57:25 PST -0800 (1200481045.30 s)
#phil __OFF__

Command line arguments: "../1045.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 2614
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1045

-------------------------------------------------------------------------------
  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: (71.3037, 47.3993, 84.2302, 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: 2.77, per 1000 atoms: 0.98


================================== 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: (71.3037, 47.3993, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.049 1.95145
Completeness in resolution range: 0.91726
Completeness with d_max=infinity: 0.914562

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0490
                             d_min =   1.9515

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: (71.3037, 47.3993, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.049 1.95145
Completeness in resolution range: 0.91726
Completeness with d_max=infinity: 0.914562

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0495 -  4.1771 [2246/2275]  2023   223   9.9%
  bin  2:  4.1771 -  3.3273 [2145/2168]  1930   215  10.0%
  bin  3:  3.3273 -  2.9102 [2119/2144]  1902   217  10.2%
  bin  4:  2.9102 -  2.6456 [2107/2123]  1902   205   9.7%
  bin  5:  2.6456 -  2.4569 [2082/2126]  1877   205   9.8%
  bin  6:  2.4569 -  2.3126 [2082/2110]  1871   211  10.1%
  bin  7:  2.3126 -  2.1971 [2074/2110]  1863   211  10.2%
  bin  8:  2.1971 -  2.1018 [2055/2097]  1852   203   9.9%
  bin  9:  2.1018 -  2.0210 [2031/2105]  1826   205  10.1%
  bin 10:  2.0210 -  1.9515 [ 648/2098]   584    64   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1045/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: 0.11 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:
        1.49 -     2.17: 22
        2.17 -     2.85: 1143
        2.85 -     3.54: 4422
        3.54 -     4.22: 9276
        4.22 -     4.90: 13519
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.492 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.533 3.040 -x+1/2,-y+1,z+1/2
  " ND2 ASN A 215 " - " O   HOH Z 203 "  1.793 3.120 -x+1/2,-y+1,z-1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 324 " - " O   HOH Z 396 "  1.829 3.040 -x,y-1/2,-z+1/2
  ... (remaining 28377 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_1045/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1045/model_refine_001.geo

CPU time processing inputs: 8.30


============================ 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 = 71.30375 47.3993 84.23025 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4882   r_free= 0.4876   ksol= 0.00   Bsol= 0.00   scale= 0.787    |
|                                                                             |
| 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:   0.83 A                  |
| x-ray target function (ml) for work reflections: 6.291335                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0495 -  4.6597 0.99   1458  165 0.4009 0.3905      6.6163      6.5945|
|  2:  4.6597 -  3.7169 0.99   1393  151 0.4053 0.4272      6.8063      6.8679|
|  3:  3.7169 -  3.2524 0.99   1372  152 0.4533 0.4147      6.6748      6.6835|
|  4:  3.2524 -  2.9575 0.99   1364  150 0.4782 0.4912      6.5176      6.5188|
|  5:  2.9575 -  2.7469 0.98   1357  150 0.5141 0.5394      6.3687      6.3656|
|  6:  2.7469 -  2.5858 0.99   1351  156 0.5177 0.5318      6.2788      6.2189|
|  7:  2.5858 -  2.4569 0.98   1339  141 0.5232 0.4296      6.2468      6.1745|
|  8:  2.4569 -  2.3504 0.99   1338  153 0.5401 0.5506      6.1576      6.1967|
|  9:  2.3504 -  2.2602 0.99   1339  152 0.5435 0.5253      6.1509        6.11|
| 10:  2.2602 -  2.1824 0.98   1323  149 0.5297 0.5386       6.067      6.1347|
| 11:  2.1824 -  2.1144 0.97   1331  136 0.5249 0.5591      6.0389      5.9937|
| 12:  2.1144 -  2.0541 0.99   1317  157 0.5600 0.5560      5.9325      5.9655|
| 13:  2.0541 -  2.0001 0.79   1068  122 0.5363 0.5412      5.8736      5.8403|
| 14:  2.0001 -  1.9515 0.20    280   25 0.5592 0.5652      5.8064      5.8252|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0495 -  4.6597  1458   165  0.70  34.53   0.80     0.72      71985.28|
|  2:  4.6597 -  3.7169  1393   151  0.68  37.07   0.87     0.75     114096.33|
|  3:  3.7169 -  3.2524  1372   152  0.54  48.32   0.81     0.67     129056.72|
|  4:  3.2524 -  2.9575  1364   150  0.42  58.11   0.79     0.54     119755.33|
|  5:  2.9575 -  2.7469  1357   150  0.34  64.48   0.72     0.43      95735.83|
|  6:  2.7469 -  2.5858  1351   156  0.36  63.24   0.73     0.43      76581.54|
|  7:  2.5858 -  2.4569  1339   141  0.38  61.81   0.74     0.42      62491.47|
|  8:  2.4569 -  2.3504  1338   153  0.35  63.38   0.71     0.43      58315.18|
|  9:  2.3504 -  2.2602  1339   152  0.29  68.01   0.73     0.35      56634.72|
| 10:  2.2602 -  2.1824  1323   149  0.24  71.73   0.74     0.30      56626.99|
| 11:  2.1824 -  2.1144  1331   136  0.20  75.27   0.78     0.25      52816.54|
| 12:  2.1144 -  2.0541  1317   157  0.16  78.52   0.72     0.22      49805.11|
| 13:  2.0541 -  2.0001  1068   122  0.14  79.79   0.71     0.18      43423.29|
| 14:  2.0001 -  1.9515   280    25  0.11  81.68   0.69     0.14      36727.68|
|alpha:            min =        0.14 max =            0.75 mean =         0.44|
|beta:             min =    36727.68 max =       129056.72 mean =     76159.00|
|figures of merit: min =        0.00 max =            1.00 mean =         0.37|
|phase err.(work): min =        0.00 max =           89.98 mean =        61.58|
|phase err.(test): min =        0.00 max =           89.99 mean =        61.68|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 17.261775             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.241   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.604495              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.881   (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:        6 |
| 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:      173 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      709 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1496 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2647 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3942 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5036 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6589 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7791 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.604 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.091    4.900  1.196 |       2.064 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.884)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 11.884)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4924   r_free= 0.4946   ksol= 0.00   Bsol= 0.00   scale= 0.758    |
|                                                                             |
| 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:   0.88 A                  |
| x-ray target function (ml) for work reflections: 6.292447                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4797   r_free= 0.4771   ksol= 0.34   Bsol= 20.00   scale= 0.977   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.59,8.34,8.69,0.00,0.00,0.00); trace/3= 8.21                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   1.01 A                  |
| x-ray target function (ml) for work reflections: 5.842566                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.450936             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.405   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.322454              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.172   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4797      final r-factor (work) = 0.4140          |
| start r-factor (free) = 0.4771      final r-factor (free) = 0.4465          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 95.8959 = 13.45 * 0.50 * 6.2883 + 1.00 * 53.6040                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 38.9435 = 13.45 * 0.50 * 5.7683 + 1.00 * 0.1489                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4140      final r-factor (work) = 0.3779          |
| start r-factor (free) = 0.4465      final r-factor (free) = 0.4340          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.6427 = 1.32 * 1.00 * 5.7683 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.1672 = 1.32 * 1.00 * 6.1620 + 1.00 * 0.0182                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.884)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.21   14.40    None  None   None       |
|    all(noH): 2823   0      0.00    87.21   14.40    None  None   None       |
|    Sol.    : 438    0      0.00    83.29   26.28    None  None   None       |
|    Mac.    : 2385   0      0.00    87.21   12.21    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.721: 1079   |   5:    43.606 -  52.328:   51        |
|      1:     8.721 -  17.443:  900   |   6:    52.328 -  61.049:   27        |
|      2:    17.443 -  26.164:  409   |   7:    61.049 -  69.770:   11        |
|      3:    26.164 -  34.885:  241   |   8:    69.770 -  78.492:    5        |
|      4:    34.885 -  43.606:   95   |   9:    78.492 -  87.213:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3779 r_free = 0.4340             target_work(ml) = 6.147         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3774 r_free = 0.4345             target_work(ml) = 6.146         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3774   r_free= 0.4345   ksol= 0.34   Bsol= 20.00   scale= 1.101   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.59,8.34,8.69,0.00,0.00,0.00); trace/3= 8.21                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.145977                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3756   r_free= 0.4302   ksol= 0.34   Bsol= 40.56   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.01,4.97,5.81,0.00,0.00,0.00); trace/3= 4.93                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.146915                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.608204              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.595  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.691695              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 126.203  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3756      final r-factor (work) = 0.3023          |
| start r-factor (free) = 0.4302      final r-factor (free) = 0.3710          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.5743 = 7.61 * 0.50 * 6.1579 + 1.00 * 0.1489                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.1656 = 7.61 * 0.50 * 6.0673 + 1.00 * 0.0849                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3023      final r-factor (work) = 0.2846          |
| start r-factor (free) = 0.3710      final r-factor (free) = 0.3523          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2147 = 0.69 * 1.00 * 6.0673 + 1.00 * 0.0179                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1429 = 0.69 * 1.00 * 5.9725 + 1.00 * 0.0118                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.884)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.97   14.61    None  None   None       |
|    all(noH): 2823   0      0.00    79.97   14.61    None  None   None       |
|    Sol.    : 438    0      0.00    76.94   31.36    None  None   None       |
|    Mac.    : 2385   0      0.00    79.97   11.54    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.997: 1080   |   5:    39.983 -  47.979:   80        |
|      1:     7.997 -  15.993:  823   |   6:    47.979 -  55.976:   46        |
|      2:    15.993 -  23.990:  387   |   7:    55.976 -  63.972:   17        |
|      3:    23.990 -  31.986:  238   |   8:    63.972 -  71.969:   11        |
|      4:    31.986 -  39.983:  135   |   9:    71.969 -  79.966:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2846 r_free = 0.3523             target_work(ml) = 5.950         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2844 r_free = 0.3522             target_work(ml) = 5.950         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2844   r_free= 0.3522   ksol= 0.34   Bsol= 40.56   scale= 1.068   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.01,4.97,5.81,0.00,0.00,0.00); trace/3= 4.93                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.949704                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2825   r_free= 0.3486   ksol= 0.32   Bsol= 40.56   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.02,2.63,3.23,0.00,0.00,0.00); trace/3= 2.63                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.948426                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.326743              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.373  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.380885              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 145.793  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2825      final r-factor (work) = 0.2190          |
| start r-factor (free) = 0.3486      final r-factor (free) = 0.2821          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.0093 = 4.33 * 0.50 * 5.9742 + 1.00 * 0.0849                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.7386 = 4.33 * 0.50 * 5.8557 + 1.00 * 0.0706                              |
|-----------------------------------------------------------------------------|
| 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) = 0.1993          |
| start r-factor (free) = 0.2821      final r-factor (free) = 0.2661          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.0978 = 1.38 * 1.00 * 5.8557 + 1.00 * 0.0118                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.8849 = 1.38 * 1.00 * 5.6986 + 1.00 * 0.0158                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.884)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.29   15.54    None  None   None       |
|    all(noH): 2823   0      0.00    92.29   15.54    None  None   None       |
|    Sol.    : 438    0      1.12    92.29   40.14    None  None   None       |
|    Mac.    : 2385   0      0.00    92.24   11.02    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 -   9.229: 1343   |   5:    46.145 -  55.374:   86        |
|      1:     9.229 -  18.458:  757   |   6:    55.374 -  64.603:   65        |
|      2:    18.458 -  27.687:  257   |   7:    64.603 -  73.832:   34        |
|      3:    27.687 -  36.916:  130   |   8:    73.832 -  83.061:   11        |
|      4:    36.916 -  46.145:  131   |   9:    83.061 -  92.290:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1993 r_free = 0.2661             target_work(ml) = 5.668         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1991 r_free = 0.2663             target_work(ml) = 5.668         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1991   r_free= 0.2663   ksol= 0.32   Bsol= 40.56   scale= 1.034   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.02,2.63,3.23,0.00,0.00,0.00); trace/3= 2.63                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.667568                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1989   r_free= 0.2667   ksol= 0.32   Bsol= 50.44   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.17,1.64,1.75,0.00,0.00,0.00); trace/3= 1.52                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.667923                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.829253              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.945  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.836606              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.046  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1989      final r-factor (work) = 0.1586          |
| start r-factor (free) = 0.2667      final r-factor (free) = 0.2163          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.9875 = 3.83 * 0.50 * 5.7018 + 1.00 * 0.0706                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.7526 = 3.83 * 0.50 * 5.5833 + 1.00 * 0.0626                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1586      final r-factor (work) = 0.1475          |
| start r-factor (free) = 0.2163      final r-factor (free) = 0.2035          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6869 = 0.84 * 1.00 * 5.5833 + 1.00 * 0.0158                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5594 = 0.84 * 1.00 * 5.4334 + 1.00 * 0.0137                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.884)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.23  15.29    None  None   None       |
|    all(noH): 2823   0      0.00    101.23  15.29    None  None   None       |
|    Sol.    : 438    0      3.73    95.94   41.70    None  None   None       |
|    Mac.    : 2385   0      0.00    101.23  10.44    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.123: 1569   |   5:    50.613 -  60.735:   84        |
|      1:    10.123 -  20.245:  675   |   6:    60.735 -  70.858:   52        |
|      2:    20.245 -  30.368:  166   |   7:    70.858 -  80.980:   21        |
|      3:    30.368 -  40.490:  108   |   8:    80.980 -  91.103:    8        |
|      4:    40.490 -  50.613:  134   |   9:    91.103 - 101.226:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1475 r_free = 0.2035             target_work(ml) = 5.400         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1474 r_free = 0.2033             target_work(ml) = 5.399         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1474   r_free= 0.2033   ksol= 0.32   Bsol= 50.44   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.17,1.64,1.75,0.00,0.00,0.00); trace/3= 1.52                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.398902                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1476   r_free= 0.2034   ksol= 0.32   Bsol= 50.44   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.90,1.26,1.26,0.00,0.00,0.00); trace/3= 1.14                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.400670                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.715243              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 119.210  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.506227              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 142.377  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1476      final r-factor (work) = 0.1307          |
| start r-factor (free) = 0.2034      final r-factor (free) = 0.1804          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.4414 = 2.72 * 0.50 * 5.4349 + 1.00 * 0.0629                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3338 = 2.72 * 0.50 * 5.3554 + 1.00 * 0.0632                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1307      final r-factor (work) = 0.1273          |
| start r-factor (free) = 0.1804      final r-factor (free) = 0.1756          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7246 = 0.51 * 1.00 * 5.3554 + 1.00 * 0.0135                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6856 = 0.51 * 1.00 * 5.2813 + 1.00 * 0.0121                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.884)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.21  14.86    None  None   None       |
|    all(noH): 2823   0      0.00    104.21  14.86    None  None   None       |
|    Sol.    : 438    0      3.26    95.44   40.70    None  None   None       |
|    Mac.    : 2385   0      0.00    104.21  10.12    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 -  10.421: 1650   |   5:    52.106 -  62.527:   76        |
|      1:    10.421 -  20.842:  641   |   6:    62.527 -  72.948:   45        |
|      2:    20.842 -  31.264:  151   |   7:    72.948 -  83.369:   13        |
|      3:    31.264 -  41.685:  118   |   8:    83.369 -  93.790:    8        |
|      4:    41.685 -  52.106:  117   |   9:    93.790 - 104.212:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1273 r_free = 0.1756             target_work(ml) = 5.265         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1271 r_free = 0.1755             target_work(ml) = 5.264         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1271   r_free= 0.1755   ksol= 0.32   Bsol= 50.44   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.90,1.26,1.26,0.00,0.00,0.00); trace/3= 1.14                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.264339                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0495 -  4.6597 0.99   1458  165 0.1003 0.1310      5.3998      5.5945|
|  2:  4.6597 -  3.7169 0.99   1393  151 0.0936 0.1259       5.502      5.7548|
|  3:  3.7169 -  3.2524 0.99   1372  152 0.1205 0.1819      5.5823      5.9455|
|  4:  3.2524 -  2.9575 0.99   1364  150 0.1453 0.1654       5.564      5.6933|
|  5:  2.9575 -  2.7469 0.98   1357  150 0.1524 0.1868       5.444      5.5964|
|  6:  2.7469 -  2.5858 0.99   1351  156 0.1447 0.2293      5.3438      5.6237|
|  7:  2.5858 -  2.4569 0.98   1339  141 0.1446 0.1852      5.3003      5.4847|
|  8:  2.4569 -  2.3504 0.99   1338  153 0.1337 0.1778      5.1686      5.3495|
|  9:  2.3504 -  2.2602 0.99   1339  152 0.1294 0.2122      5.1066      5.3858|
| 10:  2.2602 -  2.1824 0.98   1323  149 0.1288 0.1922      5.0782      5.3951|
| 11:  2.1824 -  2.1144 0.97   1331  136 0.1328 0.1974      5.0417      5.2997|
| 12:  2.1144 -  2.0541 0.99   1317  157 0.1352 0.2037      4.9983      5.2251|
| 13:  2.0541 -  2.0001 0.79   1068  122 0.1353 0.1902      4.8876      5.0845|
| 14:  2.0001 -  1.9515 0.20    280   25 0.1285 0.1891      4.7707      5.1065|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0495 -  4.6597  1458   165  0.94   9.51   0.97     0.96       7765.50|
|  2:  4.6597 -  3.7169  1393   151  0.95   8.90   1.01     0.99      10259.67|
|  3:  3.7169 -  3.2524  1372   152  0.92  13.67   1.04     1.04      13201.18|
|  4:  3.2524 -  2.9575  1364   150  0.89  16.65   1.01     0.98      12702.46|
|  5:  2.9575 -  2.7469  1357   150  0.88  18.78   1.00     0.97      10850.20|
|  6:  2.7469 -  2.5858  1351   156  0.88  18.82   0.99     0.96       9415.02|
|  7:  2.5858 -  2.4569  1339   141  0.88  18.71   1.00     0.97       8438.44|
|  8:  2.4569 -  2.3504  1338   153  0.88  18.06   0.99     0.95       6598.78|
|  9:  2.3504 -  2.2602  1339   152  0.88  18.19   1.01     0.98       5999.81|
| 10:  2.2602 -  2.1824  1323   149  0.89  17.43   1.00     0.97       5645.83|
| 11:  2.1824 -  2.1144  1331   136  0.88  18.81   0.99     0.95       5419.22|
| 12:  2.1144 -  2.0541  1317   157  0.88  19.07   1.00     0.99       5200.82|
| 13:  2.0541 -  2.0001  1068   122  0.87  19.65   1.00     0.98       4175.03|
| 14:  2.0001 -  1.9515   280    25  0.88  18.65   0.99     0.97       3327.64|
|alpha:            min =        0.95 max =            1.04 mean =         0.98|
|beta:             min =     3327.64 max =        13201.18 mean =      8144.07|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.95 mean =        16.54|
|phase err.(test): min =        0.00 max =           89.29 mean =        15.83|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1271   r_free= 0.1754   ksol= 0.32   Bsol= 47.50   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.24,0.12,0.12,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.264236                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1271   r_free= 0.1754   ksol= 0.32   Bsol= 47.50   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.24,0.12,0.12,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.264236                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0495 -  4.6597 0.99   1458  165 0.1002 0.1302      5.3984      5.5913|
|  2:  4.6597 -  3.7169 0.99   1393  151 0.0933 0.1253      5.4992      5.7499|
|  3:  3.7169 -  3.2524 0.99   1372  152 0.1203 0.1816      5.5804      5.9448|
|  4:  3.2524 -  2.9575 0.99   1364  150 0.1453 0.1655      5.5638      5.6932|
|  5:  2.9575 -  2.7469 0.98   1357  150 0.1526 0.1867      5.4446       5.597|
|  6:  2.7469 -  2.5858 0.99   1351  156 0.1448 0.2293      5.3443       5.624|
|  7:  2.5858 -  2.4569 0.98   1339  141 0.1447 0.1850      5.3011      5.4851|
|  8:  2.4569 -  2.3504 0.99   1338  153 0.1337 0.1780      5.1693      5.3507|
|  9:  2.3504 -  2.2602 0.99   1339  152 0.1295 0.2123      5.1073      5.3864|
| 10:  2.2602 -  2.1824 0.98   1323  149 0.1289 0.1923      5.0788      5.3954|
| 11:  2.1824 -  2.1144 0.97   1331  136 0.1329 0.1975      5.0422      5.3001|
| 12:  2.1144 -  2.0541 0.99   1317  157 0.1353 0.2037      4.9988      5.2253|
| 13:  2.0541 -  2.0001 0.79   1068  122 0.1353 0.1903       4.888       5.085|
| 14:  2.0001 -  1.9515 0.20    280   25 0.1285 0.1891      4.7711      5.1068|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0495 -  4.6597  1458   165  0.94   9.49   0.97     0.96       7732.43|
|  2:  4.6597 -  3.7169  1393   151  0.95   8.87   1.01     0.99      10197.46|
|  3:  3.7169 -  3.2524  1372   152  0.92  13.61   1.04     1.04      13119.76|
|  4:  3.2524 -  2.9575  1364   150  0.89  16.64   1.01     0.98      12687.00|
|  5:  2.9575 -  2.7469  1357   150  0.88  18.78   1.00     0.97      10854.22|
|  6:  2.7469 -  2.5858  1351   156  0.88  18.84   0.99     0.96       9425.03|
|  7:  2.5858 -  2.4569  1339   141  0.88  18.72   1.00     0.97       8449.44|
|  8:  2.4569 -  2.3504  1338   153  0.88  18.07   0.99     0.95       6607.26|
|  9:  2.3504 -  2.2602  1339   152  0.88  18.20   1.01     0.98       6008.60|
| 10:  2.2602 -  2.1824  1323   149  0.89  17.45   1.00     0.97       5653.49|
| 11:  2.1824 -  2.1144  1331   136  0.88  18.83   0.99     0.95       5426.49|
| 12:  2.1144 -  2.0541  1317   157  0.88  19.08   1.00     0.99       5205.67|
| 13:  2.0541 -  2.0001  1068   122  0.87  19.66   1.00     0.97       4179.39|
| 14:  2.0001 -  1.9515   280    25  0.88  18.66   0.99     0.97       3331.14|
|alpha:            min =        0.95 max =            1.04 mean =         0.98|
|beta:             min =     3331.14 max =        13119.76 mean =      8133.92|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.96 mean =        16.54|
|phase err.(test): min =        0.00 max =           89.32 mean =        15.83|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.884)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.14    105.35  16.00    None  None   None       |
|    all(noH): 2823   0      1.14    105.35  16.00    None  None   None       |
|    Sol.    : 438    0      4.39    96.58   41.84    None  None   None       |
|    Mac.    : 2385   0      1.14    105.35  11.26    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.139 -  11.561: 1650   |   5:    53.245 -  63.666:   76        |
|      1:    11.561 -  21.982:  641   |   6:    63.666 -  74.088:   45        |
|      2:    21.982 -  32.403:  151   |   7:    74.088 -  84.509:   13        |
|      3:    32.403 -  42.824:  118   |   8:    84.509 -  94.930:    8        |
|      4:    42.824 -  53.245:  117   |   9:    94.930 - 105.351:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 355         
Filter by distance & map next to the model:
   mapped sites are within: 0.660 - 5.867
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 350 from: 355
   mapped sites are within: 0.725 - 5.867

peak=    9.005 closest distance to " CG2 VAL A 296 " =    1.415
peak=    8.989 closest distance to " CB  VAL A 230 " =    1.430
peak=    7.752 closest distance to " O   HOH Z 120 " =    1.382
peak=    7.201 closest distance to " O   HOH Z  37 " =    1.670
peak=    7.181 closest distance to " CG  ARG A 138 " =    1.235
peak=    6.993 closest distance to " O   HOH Z 279 " =    1.375
peak=    6.406 closest distance to " O   HOH Z 277 " =    1.560
peak=    6.372 closest distance to " NH2BARG A 102 " =    1.044
peak=    6.157 closest distance to " O   HOH Z 278 " =    1.491
peak=    5.671 closest distance to " CG  LEU A   5 " =    1.372
peak=    5.593 closest distance to " CD2 LEU A   5 " =    1.195
peak=    5.586 closest distance to " NH2 ARG A  56 " =    2.256
peak=    5.515 closest distance to " O   HOH Z 246 " =    1.559
peak=    5.465 closest distance to " O   HOH Z 199 " =    1.106
peak=    5.447 closest distance to " O   HOH Z 138 " =    1.084
peak=    5.161 closest distance to " O   HOH Z 124 " =    1.498
peak=    5.071 closest distance to " O   HOH Z  11 " =    1.308
peak=    5.041 closest distance to " CB  GLN A 223 " =    1.526
peak=    5.020 closest distance to " O   HOH Z  48 " =    2.098
peak=    5.001 closest distance to " CD1AILE A 234 " =    1.067
peak=    4.912 closest distance to " CG  PRO A 198 " =    1.418
peak=    4.897 closest distance to " O   HOH Z 291 " =    1.321
peak=    4.877 closest distance to " O   HOH Z 411 " =    3.329
peak=    4.872 closest distance to " O   HOH Z 132 " =    1.596
peak=    4.864 closest distance to " O   HOH Z 186 " =    1.278
peak=    4.810 closest distance to " CB  PRO A  54 " =    0.834
peak=    4.792 closest distance to " O   HOH Z 221 " =    1.352
peak=    4.757 closest distance to " O   HOH Z 202 " =    1.491
peak=    4.727 closest distance to " NH1 ARG A 138 " =    1.046
peak=    4.703 closest distance to " CG  PRO A  54 " =    1.245
peak=    4.701 closest distance to " O   HOH Z 272 " =    2.001
peak=    4.655 closest distance to " O   HOH Z 117 " =    1.063
peak=    4.623 closest distance to " O   HOH Z 112 " =    1.473
peak=    4.617 closest distance to " O   HOH Z 192 " =    1.333
peak=    4.534 closest distance to " O   HOH Z  97 " =    1.904
peak=    4.512 closest distance to " CB  SER A  63 " =    1.381
peak=    4.512 closest distance to " O   HOH Z  92 " =    1.262
peak=    4.472 closest distance to " O   HOH Z 142 " =    1.656
peak=    4.469 closest distance to " O   HOH Z  61 " =    1.405
peak=    4.460 closest distance to " O   HOH Z 126 " =    1.668
peak=    4.457 closest distance to " CA  ALA A  21 " =    1.298
peak=    4.455 closest distance to " O   HOH Z 389 " =    1.911
peak=    4.362 closest distance to " O   HOH Z 134 " =    1.608
peak=    4.358 closest distance to " O   HOH Z 394 " =    1.580
peak=    4.358 closest distance to " CB  TYR A 169 " =    0.938
peak=    4.321 closest distance to " CB  GLN A 183 " =    1.233
peak=    4.297 closest distance to " O   HOH Z 243 " =    1.186
peak=    4.290 closest distance to " C   PRO A 198 " =    1.433
peak=    4.282 closest distance to " O   HOH Z 263 " =    1.456
peak=    4.278 closest distance to " CB  ARG A 275 " =    0.923
peak=    4.267 closest distance to " O   HOH Z 193 " =    1.822
peak=    4.262 closest distance to " O   HOH Z 163 " =    1.645
peak=    4.260 closest distance to " O   HOH Z 371 " =    3.344
peak=    4.247 closest distance to " CG2 THR A 221 " =    0.986
peak=    4.213 closest distance to " CB  VAL A 230 " =    1.264
peak=    4.199 closest distance to " CD2 LEU A 228 " =    1.211
peak=    4.181 closest distance to " O   HOH Z  80 " =    1.894
peak=    4.178 closest distance to " CB  GLU A 152 " =    1.128
peak=    4.137 closest distance to " CD  LYS A 119 " =    1.135
peak=    4.132 closest distance to " O   ASP A 132 " =    3.769
peak=    4.131 closest distance to " O   HOH Z  78 " =    2.232
peak=    4.115 closest distance to " CG  PRO A 243 " =    1.273
peak=    4.109 closest distance to " O   HOH Z 284 " =    2.967
peak=    4.107 closest distance to " CG  LEU A 228 " =    1.279
peak=    4.106 closest distance to " CB  ASN A 148 " =    1.159
peak=    4.102 closest distance to " OD2 ASP A 286 " =    2.931
peak=    4.086 closest distance to " NE2 HIS A 115 " =    0.953
peak=    4.084 closest distance to " O   HOH Z 131 " =    2.396
peak=    4.078 closest distance to " O   HOH Z 236 " =    1.779
peak=    4.058 closest distance to " CG  PRO A 280 " =    0.819
peak=    4.019 closest distance to " OE1 GLN A  58 " =    5.692
peak=    4.016 closest distance to " NH1 ARG A  56 " =    1.066
peak=    4.002 closest distance to " O   HOH Z 260 " =    1.271
peak=    4.000 closest distance to " CB  LEU A 228 " =    1.339
peak=    3.999 closest distance to " CG1 VAL A 153 " =    1.024
peak=    3.989 closest distance to " CD2 LEU A 255 " =    1.387
peak=    3.985 closest distance to " O   HOH Z   4 " =    1.668
peak=    3.978 closest distance to " OE1 GLN A  11 " =    1.827
peak=    3.974 closest distance to " CG  PRO A 213 " =    1.259
peak=    3.971 closest distance to " O   HOH Z 316 " =    0.932
peak=    3.969 closest distance to " O   HOH Z 374 " =    1.102
peak=    3.967 closest distance to " CB  SER A   3 " =    1.472
peak=    3.942 closest distance to " O   HOH Z 183 " =    1.368
peak=    3.932 closest distance to " OG ASER A 164 " =    0.725
peak=    3.921 closest distance to " OD1 ASN A 217 " =    1.647
peak=    3.921 closest distance to " O   HOH Z 232 " =    2.098
peak=    3.905 closest distance to " CB  VAL A 265 " =    1.246
peak=    3.904 closest distance to " O   HOH Z 386 " =    2.127
peak=    3.903 closest distance to " O   HOH Z 331 " =    1.320
peak=    3.898 closest distance to " O   HOH Z 136 " =    1.462
peak=    3.890 closest distance to " O   HOH Z 128 " =    1.861
peak=    3.884 closest distance to " O   HOH Z 427 " =    3.205
peak=    3.871 closest distance to " O   HOH Z 276 " =    1.471
peak=    3.865 closest distance to " CD1 LEU A 300 " =    1.198
peak=    3.863 closest distance to " C   SER A  32 " =    1.124
peak=    3.863 closest distance to " NE2 GLN A  11 " =    1.121
peak=    3.858 closest distance to " CB  VAL A 202 " =    1.567
peak=    3.848 closest distance to " CA  ALA A 160 " =    0.879
peak=    3.837 closest distance to " O   MET A 105 " =    1.861
peak=    3.837 closest distance to " O   HOH Z  63 " =    1.492
peak=    3.835 closest distance to " CG1BVAL A 121 " =    1.259
peak=    3.834 closest distance to " CA  TYR A  30 " =    0.990
peak=    3.832 closest distance to " O   HOH Z 316 " =    2.276
peak=    3.830 closest distance to " O   HOH Z 215 " =    1.456
peak=    3.827 closest distance to " O   HOH Z 117 " =    1.944
peak=    3.818 closest distance to " O   HOH Z  13 " =    1.630
peak=    3.813 closest distance to " O   HOH Z 326 " =    1.391
peak=    3.812 closest distance to " O   HOH Z 369 " =    2.109
peak=    3.810 closest distance to " O   HOH Z 189 " =    2.468
peak=    3.809 closest distance to " CA  THR A 221 " =    0.903
peak=    3.806 closest distance to " O   HOH Z 118 " =    1.799
peak=    3.802 closest distance to " CA  LEU A 282 " =    1.138
peak=    3.802 closest distance to " O   HOH Z  19 " =    2.377
peak=    3.791 closest distance to " O   HOH Z 217 " =    1.779
peak=    3.788 closest distance to " O   HOH Z 133 " =    2.067
peak=    3.781 closest distance to " O   SER A  87 " =    2.392
peak=    3.780 closest distance to " O   HOH Z 180 " =    2.091
peak=    3.778 closest distance to " O   HOH Z  88 " =    3.211
peak=    3.773 closest distance to " O   HOH Z 184 " =    1.385
peak=    3.761 closest distance to " CB  TRP A 179 " =    1.332
peak=    3.755 closest distance to " NH1 ARG A  14 " =    1.099
peak=    3.753 closest distance to " O   HOH Z  54 " =    1.513
peak=    3.749 closest distance to " O   HOH Z 227 " =    1.990
peak=    3.745 closest distance to " O   HOH Z 102 " =    1.422
peak=    3.733 closest distance to " O   HOH Z 205 " =    1.116
peak=    3.727 closest distance to " O   HOH Z 215 " =    1.494
peak=    3.727 closest distance to " CD  ARG A 138 " =    1.114
peak=    3.718 closest distance to " CB  MET A  40 " =    0.758
peak=    3.708 closest distance to " O   HOH Z 155 " =    1.764
peak=    3.708 closest distance to " O   HOH Z 127 " =    1.238
peak=    3.704 closest distance to " O   HOH Z  43 " =    1.344
peak=    3.701 closest distance to " O   HOH Z  58 " =    1.556
peak=    3.689 closest distance to " CD  ARG A 269 " =    0.850
peak=    3.686 closest distance to " O   HOH Z  30 " =    1.701
peak=    3.679 closest distance to " O   HOH Z 303 " =    2.225
peak=    3.675 closest distance to " CA  ASP A 191 " =    0.886
peak=    3.661 closest distance to " O   HOH Z 128 " =    2.151
peak=    3.660 closest distance to " O   HOH Z  68 " =    1.848
peak=    3.656 closest distance to " O   HOH Z 126 " =    1.656
peak=    3.653 closest distance to " O   HOH Z 395 " =    1.450
peak=    3.644 closest distance to " CB  ILE A 199 " =    1.097
peak=    3.643 closest distance to " O   HOH Z  48 " =    1.992
peak=    3.640 closest distance to " O   HOH Z 108 " =    1.642
peak=    3.639 closest distance to " O   SER A 164 " =    0.988
peak=    3.635 closest distance to " O   HOH Z 352 " =    1.262
peak=    3.628 closest distance to " OD1 ASN A  69 " =    2.537
peak=    3.626 closest distance to " CG  ARG A  66 " =    2.830
peak=    3.619 closest distance to " O   HOH Z 203 " =    1.605
peak=    3.619 closest distance to " CB  PRO A 198 " =    0.990
peak=    3.616 closest distance to " OG  SER A  22 " =    2.972
peak=    3.615 closest distance to " O   HOH Z 346 " =    1.499
peak=    3.615 closest distance to " CB  ASP A 124 " =    0.825
peak=    3.614 closest distance to " O   GLY A  57 " =    2.342
peak=    3.613 closest distance to " CB  ARG A  56 " =    1.133
peak=    3.611 closest distance to " O   HOH Z 214 " =    2.045
peak=    3.608 closest distance to " CA  VAL A  41 " =    0.881
peak=    3.607 closest distance to " O   HOH Z 295 " =    1.598
peak=    3.605 closest distance to " CB  ALA A 100 " =    1.415
peak=    3.605 closest distance to " NZ  LYS A 117 " =    3.246
peak=    3.600 closest distance to " O   HOH Z 423 " =    1.927
peak=    3.589 closest distance to " O   HOH Z 214 " =    0.901
peak=    3.586 closest distance to " O   HOH Z 345 " =    3.383
peak=    3.580 closest distance to " O   HOH Z 207 " =    2.347
peak=    3.578 closest distance to " O   HOH Z 426 " =    1.466
peak=    3.573 closest distance to " CA  ASN A  74 " =    1.344
peak=    3.572 closest distance to " O   HOH Z   9 " =    2.173
peak=    3.568 closest distance to " CD1 TRP A 266 " =    1.159
peak=    3.566 closest distance to " O   HOH Z  40 " =    1.645
peak=    3.562 closest distance to " CB  GLU A 277 " =    3.639
peak=    3.560 closest distance to " O   HOH Z 298 " =    1.886
peak=    3.559 closest distance to " O   HOH Z 426 " =    3.022
peak=    3.559 closest distance to " O   HOH Z 236 " =    1.616
peak=    3.555 closest distance to " CB  GLU A 128 " =    1.184
peak=    3.554 closest distance to " O   HOH Z 327 " =    2.510
peak=    3.554 closest distance to " NZ  LYS A 117 " =    0.883
peak=    3.550 closest distance to " CD ALYS A 290 " =    1.011
peak=    3.546 closest distance to " O   HOH Z 261 " =    1.683
peak=    3.545 closest distance to " CG1BVAL A  72 " =    1.732
peak=    3.538 closest distance to " CA  LEU A 101 " =    1.640
peak=    3.535 closest distance to " O   GLN A 278 " =    1.231
peak=    3.534 closest distance to " CA  ALA A 295 " =    1.087
peak=    3.529 closest distance to " O   HOH Z 425 " =    1.423
peak=    3.528 closest distance to " CG  GLN A  77 " =    0.836
peak=    3.521 closest distance to " O   HOH Z 377 " =    1.323
peak=    3.511 closest distance to " O   HOH Z 422 " =    2.670
peak=    3.509 closest distance to " O   GLY A 211 " =    1.237
peak=    3.502 closest distance to " O   HOH Z 374 " =    2.980
peak=    3.502 closest distance to " O   HOH Z 280 " =    1.615
peak=    3.499 closest distance to " O   GLY A  91 " =    1.179
peak=    3.496 closest distance to " O   HOH Z 344 " =    2.798
peak=    3.492 closest distance to " CG1 ILE A  49 " =    1.736
peak=    3.489 closest distance to " CE  LYS A 119 " =    1.226
peak=    3.488 closest distance to " CD2 HIS A 115 " =    0.815
peak=    3.487 closest distance to " O   HOH Z 281 " =    3.995
peak=    3.486 closest distance to " O   HOH Z  37 " =    2.503
peak=    3.471 closest distance to " O   HOH Z 132 " =    3.308
peak=    3.470 closest distance to " CB  TRP A 266 " =    0.998
peak=    3.467 closest distance to " CG  GLN A  88 " =    1.027
peak=    3.466 closest distance to " CG1 ILE A  33 " =    1.292
peak=    3.465 closest distance to " CZ  PHE A 192 " =    1.124
peak=    3.464 closest distance to " O   HOH Z 149 " =    1.388
peak=    3.463 closest distance to " O   HOH Z 150 " =    1.820
peak=    3.462 closest distance to " O   HOH Z 429 " =    2.304
peak=    3.461 closest distance to " O   HOH Z 133 " =    1.603
peak=    3.456 closest distance to " CB  ALA A 256 " =    1.067
peak=    3.452 closest distance to " CB  MET A  47 " =    1.060
peak=    3.448 closest distance to " NH1 ARG A 269 " =    0.886
peak=    3.431 closest distance to " O   HOH Z 185 " =    1.736
peak=    3.427 closest distance to " O   HOH Z 172 " =    2.394
peak=    3.422 closest distance to " CA  ALA A 158 " =    1.086
peak=    3.420 closest distance to " CA  LYS A 117 " =    1.270
peak=    3.419 closest distance to " O   HOH Z 393 " =    3.643
peak=    3.418 closest distance to " CD  LYS A 166 " =    1.527
peak=    3.413 closest distance to " CB  GLN A  58 " =    0.890
peak=    3.413 closest distance to " CG2 THR A 220 " =    0.994
peak=    3.412 closest distance to " N   ASN A  39 " =    1.330
peak=    3.410 closest distance to " CG AARG A 275 " =    0.997
peak=    3.407 closest distance to " O   HOH Z 104 " =    3.406
peak=    3.407 closest distance to " CG2 VAL A 174 " =    1.307
peak=    3.404 closest distance to " O   HOH Z  93 " =    2.694
peak=    3.401 closest distance to " O   HOH Z  63 " =    1.855
peak=    3.397 closest distance to " O   HOH Z 174 " =    2.220
peak=    3.396 closest distance to " O   HOH Z 156 " =    2.455
peak=    3.395 closest distance to " O   THR A  31 " =    1.527
peak=    3.388 closest distance to " O   HOH Z 270 " =    1.804
peak=    3.386 closest distance to " O   HOH Z 329 " =    3.495
peak=    3.381 closest distance to " NE BARG A 102 " =    1.277
peak=    3.377 closest distance to " CG2 THR A  82 " =    1.028
peak=    3.375 closest distance to " CD1 ILE A 199 " =    1.051
peak=    3.375 closest distance to " O   HOH Z 143 " =    1.348
peak=    3.374 closest distance to " CA  GLY A 211 " =    1.151
peak=    3.373 closest distance to " O   HOH Z  21 " =    1.955
peak=    3.370 closest distance to " CD  ARG A  14 " =    1.259
peak=    3.367 closest distance to " CZ3 TRP A  92 " =    1.094
peak=    3.364 closest distance to " NZ  LYS A  76 " =    1.198
peak=    3.360 closest distance to " CD2 HIS A 115 " =    1.143
peak=    3.360 closest distance to " O   HOH Z 374 " =    2.477
peak=    3.359 closest distance to " O   HOH Z 114 " =    1.562
peak=    3.357 closest distance to " O   HOH Z 366 " =    2.995
peak=    3.355 closest distance to " O   HOH Z 355 " =    1.933
peak=    3.352 closest distance to " NH2BARG A 145 " =    2.197
peak=    3.350 closest distance to " O   HOH Z 403 " =    1.743
peak=    3.348 closest distance to " O   HOH Z 154 " =    1.335
peak=    3.346 closest distance to " O   HOH Z 271 " =    2.000
peak=    3.342 closest distance to " OG ASER A 134 " =    1.422
peak=    3.328 closest distance to " O   HOH Z 287 " =    1.860
peak=    3.328 closest distance to " O   HOH Z 150 " =    3.224
peak=    3.326 closest distance to " O   HOH Z 407 " =    2.714
peak=    3.324 closest distance to " O   HOH Z  87 " =    1.085
peak=    3.320 closest distance to " CG  ARG A 269 " =    0.939
peak=    3.319 closest distance to " CB  ARG A 139 " =    0.869
peak=    3.318 closest distance to " CA  TYR A 116 " =    1.591
peak=    3.317 closest distance to " CA  ASN A 217 " =    1.411
peak=    3.316 closest distance to " N   LYS A 166 " =    0.930
peak=    3.313 closest distance to " O   HOH Z  89 " =    3.620
peak=    3.310 closest distance to " O   HOH Z 194 " =    2.169
peak=    3.307 closest distance to " O   HOH Z  50 " =    1.863
peak=    3.305 closest distance to " O   ASN A 217 " =    1.483
peak=    3.304 closest distance to " NH1AARG A 145 " =    0.965
peak=    3.302 closest distance to " O   HOH Z 116 " =    1.695
peak=    3.296 closest distance to " O   HOH Z  87 " =    1.869
peak=    3.296 closest distance to " O   HOH Z  99 " =    1.969
peak=    3.294 closest distance to " CB  LEU A 255 " =    0.944
peak=    3.290 closest distance to " CD1 LEU A   5 " =    1.554
peak=    3.288 closest distance to " O   HOH Z 149 " =    1.970
peak=    3.287 closest distance to " CB  LEU A 143 " =    1.131
peak=    3.279 closest distance to " OE1 GLU A   2 " =    2.095
peak=    3.277 closest distance to " O   HOH Z 437 " =    2.536
peak=    3.275 closest distance to " CG  GLN A  58 " =    2.519
peak=    3.275 closest distance to " O   HOH Z 410 " =    1.365
peak=    3.274 closest distance to " CB  ASN A 170 " =    1.380
peak=    3.271 closest distance to " CG2 THR A  42 " =    0.965
peak=    3.270 closest distance to " CB  ALA A  34 " =    0.902
peak=    3.267 closest distance to " O   HOH Z  15 " =    1.674
peak=    3.267 closest distance to " CA  VAL A 126 " =    1.118
peak=    3.265 closest distance to " CA  ASP A 140 " =    1.284
peak=    3.260 closest distance to " CB  ALA A 291 " =    1.352
peak=    3.259 closest distance to " CA  SER A  32 " =    1.519
peak=    3.258 closest distance to " OD1 ASP A 238 " =    0.847
peak=    3.254 closest distance to " CA  ALA A   9 " =    1.160
peak=    3.254 closest distance to " O   HOH Z  99 " =    2.762
peak=    3.254 closest distance to " CB  GLN A 278 " =    1.152
peak=    3.252 closest distance to " O   HOH Z 344 " =    1.332
peak=    3.252 closest distance to " OD1 ASP A 231 " =    1.890
peak=    3.245 closest distance to " O   HOH Z 406 " =    1.720
peak=    3.242 closest distance to " CB  SER A 141 " =    1.001
peak=    3.237 closest distance to " O   HOH Z  44 " =    2.471
peak=    3.235 closest distance to " O   HOH Z 290 " =    1.231
peak=    3.234 closest distance to " CB  GLN A 194 " =    0.942
peak=    3.233 closest distance to " CG  LEU A 167 " =    1.097
peak=    3.231 closest distance to " CA  ARG A  36 " =    1.112
peak=    3.231 closest distance to " CA  ILE A  33 " =    1.417
peak=    3.230 closest distance to " O   HOH Z 279 " =    2.398
peak=    3.230 closest distance to " O   HOH Z 106 " =    2.409
peak=    3.230 closest distance to " O   HOH Z  49 " =    1.915
peak=    3.226 closest distance to " CA  MET A  40 " =    1.021
peak=    3.226 closest distance to " CE1 PHE A 208 " =    1.066
peak=    3.222 closest distance to " CA  ALA A 100 " =    1.149
peak=    3.221 closest distance to " OG BSER A 134 " =    3.505
peak=    3.216 closest distance to " CD  ARG A 159 " =    0.815
peak=    3.210 closest distance to " OD2 ASP A 200 " =    1.428
peak=    3.207 closest distance to " O   HOH Z 284 " =    1.267
peak=    3.196 closest distance to " CB  ARG A  79 " =    1.671
peak=    3.193 closest distance to " O   HOH Z 166 " =    1.536
peak=    3.192 closest distance to " O   HOH Z 126 " =    2.151
peak=    3.191 closest distance to " O   HOH Z  71 " =    1.260
peak=    3.187 closest distance to " O   HOH Z 373 " =    1.608
peak=    3.185 closest distance to " CD  ARG A 195 " =    3.420
peak=    3.183 closest distance to " O   HOH Z 253 " =    1.899
peak=    3.179 closest distance to " O   HOH Z 365 " =    5.867
peak=    3.177 closest distance to " O   HOH Z 313 " =    1.993
peak=    3.172 closest distance to " O   HOH Z 383 " =    2.064
peak=    3.163 closest distance to " CA  ALA A  51 " =    0.897
peak=    3.162 closest distance to " CB  SER A 216 " =    0.772
peak=    3.161 closest distance to " CB  ASN A 215 " =    1.130
peak=    3.158 closest distance to " O   HOH Z 259 " =    1.475
peak=    3.158 closest distance to " OE1 GLN A  58 " =    1.293
peak=    3.154 closest distance to " CA  GLY A 147 " =    0.827
peak=    3.153 closest distance to " O   HOH Z 368 " =    2.816
peak=    3.147 closest distance to " CG2 VAL A 112 " =    1.458
peak=    3.144 closest distance to " O   HOH Z 139 " =    5.364
peak=    3.143 closest distance to " CA  ARG A 156 " =    0.934
peak=    3.143 closest distance to " CG2 VAL A  67 " =    0.967
peak=    3.139 closest distance to " NE  ARG A 156 " =    1.066
peak=    3.138 closest distance to " O   HOH Z 218 " =    4.456
peak=    3.136 closest distance to " NH2 ARG A 156 " =    1.042
peak=    3.135 closest distance to " CB  PHE A  16 " =    1.257
peak=    3.130 closest distance to " OD2 ASP A 286 " =    2.305
peak=    3.129 closest distance to " NH1BARG A 145 " =    1.207
peak=    3.126 closest distance to " CA  ARG A 195 " =    1.253
peak=    3.123 closest distance to " CG  GLN A  77 " =    2.101
peak=    3.119 closest distance to " CG  MET A 188 " =    1.301
peak=    3.112 closest distance to " O   HOH Z 209 " =    2.332
peak=    3.108 closest distance to " CB  GLN A  89 " =    1.032
peak=    3.106 closest distance to " O   HOH Z 175 " =    2.191
peak=    3.105 closest distance to " CD  ARG A  56 " =    1.199
peak=    3.101 closest distance to " O   TRP A 274 " =    1.736
peak=    3.100 closest distance to " O   HOH Z 189 " =    3.431
peak=    3.099 closest distance to " N   ASN A 110 " =    1.212
peak=    3.097 closest distance to " CB  LYS A 117 " =    1.119
peak=    3.095 closest distance to " OG BSER A 164 " =    2.066
peak=    3.093 closest distance to " NH2BARG A 190 " =    1.744
peak=    3.090 closest distance to " CB  SER A 273 " =    0.842
peak=    3.087 closest distance to " CG1 VAL A 174 " =    1.204
peak=    3.081 closest distance to " O   HOH Z 345 " =    1.720
peak=    3.079 closest distance to " ND1 HIS A  81 " =    1.592
peak=    3.065 closest distance to " OH  TYR A 186 " =    1.048
peak=    3.051 closest distance to " CB  TYR A  30 " =    1.531
peak=    3.046 closest distance to " O   HOH Z 145 " =    2.287
peak=    3.036 closest distance to " O   HOH Z  85 " =    2.058

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 197         
Filter by distance & map next to the model:
   mapped sites are within: 0.677 - 5.593
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 195 from: 197
   mapped sites are within: 0.749 - 5.593

peak=   -5.139 closest distance to " CG2 VAL A 230 " =    0.930
peak=   -4.885 closest distance to " CD  ARG A 138 " =    1.304
peak=   -4.676 closest distance to " OG ASER A 134 " =    1.167
peak=   -4.502 closest distance to " O   HOH Z  13 " =    1.020
peak=   -4.459 closest distance to " O   HOH Z 166 " =    1.709
peak=   -4.438 closest distance to " CG  ARG A 138 " =    0.872
peak=   -4.390 closest distance to " O   HOH Z 221 " =    1.109
peak=   -4.174 closest distance to " O   HOH Z 231 " =    1.259
peak=   -4.171 closest distance to " O   HOH Z  52 " =    1.950
peak=   -4.128 closest distance to " C   ASN A 187 " =    1.853
peak=   -4.108 closest distance to " O   HOH Z 380 " =    4.816
peak=   -4.096 closest distance to " NH2 ARG A  66 " =    1.501
peak=   -4.058 closest distance to " O   HOH Z  11 " =    1.569
peak=   -4.004 closest distance to " O   HOH Z  19 " =    1.858
peak=   -4.000 closest distance to " N   ALA A 226 " =    2.033
peak=   -3.991 closest distance to " O   HOH Z 151 " =    1.280
peak=   -3.977 closest distance to " O   HOH Z 407 " =    3.331
peak=   -3.971 closest distance to " N   GLN A  58 " =    1.690
peak=   -3.950 closest distance to " O   HOH Z 290 " =    0.983
peak=   -3.925 closest distance to " O   HOH Z 266 " =    4.275
peak=   -3.915 closest distance to " NE2 GLN A  55 " =    2.451
peak=   -3.880 closest distance to " O   HOH Z  71 " =    0.749
peak=   -3.867 closest distance to " C   ALA A 158 " =    1.261
peak=   -3.851 closest distance to " CG2 VAL A 112 " =    2.586
peak=   -3.841 closest distance to " OD1 ASN A  39 " =    2.244
peak=   -3.790 closest distance to " O   HOH Z  93 " =    1.666
peak=   -3.786 closest distance to " CE2 TYR A  30 " =    2.804
peak=   -3.779 closest distance to " O   HOH Z 184 " =    1.076
peak=   -3.773 closest distance to " O   HOH Z 243 " =    1.520
peak=   -3.755 closest distance to " O   HOH Z 241 " =    1.106
peak=   -3.753 closest distance to " CG  ASP A 231 " =    0.864
peak=   -3.751 closest distance to " CB  ALA A 161 " =    2.711
peak=   -3.742 closest distance to " CE3 TRP A 150 " =    1.999
peak=   -3.735 closest distance to " CG  MET A 105 " =    0.880
peak=   -3.730 closest distance to " O   HOH Z 423 " =    2.176
peak=   -3.725 closest distance to " O   VAL A  67 " =    2.786
peak=   -3.723 closest distance to " O   HOH Z  92 " =    1.202
peak=   -3.723 closest distance to " CD1 PHE A  59 " =    1.756
peak=   -3.678 closest distance to " CD2 LEU A 143 " =    2.606
peak=   -3.660 closest distance to " CD  GLN A  88 " =    0.853
peak=   -3.656 closest distance to " O   HOH Z  88 " =    4.493
peak=   -3.650 closest distance to " O   HOH Z  17 " =    1.243
peak=   -3.648 closest distance to " O   HOH Z 274 " =    2.498
peak=   -3.618 closest distance to " CG2 THR A   4 " =    1.871
peak=   -3.617 closest distance to " O   HOH Z 177 " =    1.011
peak=   -3.609 closest distance to " O   GLY A 211 " =    1.426
peak=   -3.606 closest distance to " O   HOH Z 138 " =    0.895
peak=   -3.602 closest distance to " CB  CYS A 254 " =    2.437
peak=   -3.599 closest distance to " CB  ALA A 227 " =    2.355
peak=   -3.598 closest distance to " CD2 LEU A 300 " =    2.787
peak=   -3.584 closest distance to " CD1 LEU A 228 " =    2.492
peak=   -3.578 closest distance to " OE1 GLN A 223 " =    2.513
peak=   -3.568 closest distance to " CD  ARG A 156 " =    2.081
peak=   -3.566 closest distance to " O   HOH Z 366 " =    1.597
peak=   -3.566 closest distance to " CA  ASP A 298 " =    1.099
peak=   -3.563 closest distance to " OE2 GLU A   2 " =    1.461
peak=   -3.561 closest distance to " O   ASN A 301 " =    1.573
peak=   -3.553 closest distance to " O   HOH Z 275 " =    1.807
peak=   -3.542 closest distance to " N   ALA A  43 " =    2.418
peak=   -3.541 closest distance to " CB  ASP A 124 " =    2.205
peak=   -3.540 closest distance to " O   HOH Z 189 " =    2.208
peak=   -3.532 closest distance to " CA  GLY A  23 " =    2.213
peak=   -3.528 closest distance to " CG  ASN A  45 " =    1.770
peak=   -3.522 closest distance to " CA  SER A 164 " =    1.858
peak=   -3.510 closest distance to " CD1 LEU A 101 " =    2.750
peak=   -3.509 closest distance to " O   HOH Z  43 " =    1.587
peak=   -3.502 closest distance to " O   HOH Z 103 " =    1.869
peak=   -3.501 closest distance to " NH2AARG A 275 " =    5.302
peak=   -3.498 closest distance to " CG  PHE A  59 " =    2.564
peak=   -3.494 closest distance to " O   HOH Z 377 " =    1.996
peak=   -3.490 closest distance to " ND2 ASN A  45 " =    1.118
peak=   -3.486 closest distance to " C   LEU A 101 " =    0.850
peak=   -3.477 closest distance to " ND1 HIS A 115 " =    0.951
peak=   -3.475 closest distance to " CG  GLU A  53 " =    1.525
peak=   -3.474 closest distance to " N   GLN A 122 " =    1.688
peak=   -3.471 closest distance to " CB  GLN A  55 " =    1.398
peak=   -3.468 closest distance to " O   HOH Z  98 " =    1.614
peak=   -3.449 closest distance to " N   ARG A  56 " =    1.204
peak=   -3.447 closest distance to " O   HOH Z 138 " =    0.861
peak=   -3.443 closest distance to " O   HOH Z 420 " =    5.593
peak=   -3.439 closest distance to " O   LEU A 255 " =    1.731
peak=   -3.439 closest distance to " CE  MET A  93 " =    1.347
peak=   -3.437 closest distance to " O   HOH Z 265 " =    1.477
peak=   -3.425 closest distance to " N   THR A 235 " =    1.173
peak=   -3.423 closest distance to " CA  GLY A  98 " =    2.189
peak=   -3.418 closest distance to " O   HOH Z  60 " =    2.283
peak=   -3.416 closest distance to " OG  SER A  97 " =    2.298
peak=   -3.416 closest distance to " OG  SER A  26 " =    1.321
peak=   -3.414 closest distance to " O   HOH Z 345 " =    2.361
peak=   -3.413 closest distance to " O   HOH Z 275 " =    1.475
peak=   -3.410 closest distance to " CA  GLY A 133 " =    1.883
peak=   -3.405 closest distance to " CG  GLU A 152 " =    2.247
peak=   -3.403 closest distance to " O   HOH Z 221 " =    1.702
peak=   -3.398 closest distance to " OD1 ASN A 148 " =    1.543
peak=   -3.396 closest distance to " O   HOH Z 353 " =    2.230
peak=   -3.396 closest distance to " O   HOH Z 124 " =    1.433
peak=   -3.395 closest distance to " O   ALA A   7 " =    1.701
peak=   -3.393 closest distance to " OG  SER A  87 " =    1.329
peak=   -3.391 closest distance to " O   HOH Z 185 " =    2.069
peak=   -3.377 closest distance to " CD2 PHE A  61 " =    1.859
peak=   -3.376 closest distance to " O   LEU A 300 " =    2.563
peak=   -3.375 closest distance to " C   GLY A  91 " =    1.549
peak=   -3.370 closest distance to " CD2 LEU A 237 " =    2.508
peak=   -3.369 closest distance to " CD  LYS A 289 " =    2.419
peak=   -3.366 closest distance to " O   HOH Z 166 " =    1.770
peak=   -3.365 closest distance to " CB  ALA A 100 " =    2.034
peak=   -3.354 closest distance to " CA  SER A 276 " =    1.430
peak=   -3.352 closest distance to " O   GLY A 118 " =    2.106
peak=   -3.348 closest distance to " O   HOH Z 208 " =    1.260
peak=   -3.344 closest distance to " O   HOH Z 396 " =    1.477
peak=   -3.343 closest distance to " NH1BARG A 190 " =    2.189
peak=   -3.343 closest distance to " NE2 GLN A  73 " =    1.575
peak=   -3.342 closest distance to " OG ASER A 258 " =    2.819
peak=   -3.334 closest distance to " CD1 TRP A 179 " =    1.147
peak=   -3.326 closest distance to " O   HOH Z 118 " =    4.554
peak=   -3.325 closest distance to " CG  TYR A 169 " =    1.912
peak=   -3.321 closest distance to " CD  GLN A  88 " =    2.401
peak=   -3.319 closest distance to " C   VAL A 265 " =    0.901
peak=   -3.318 closest distance to " CZ3 TRP A  92 " =    1.194
peak=   -3.316 closest distance to " CG  ASP A  50 " =    2.090
peak=   -3.316 closest distance to " CZ  TYR A 172 " =    1.674
peak=   -3.304 closest distance to " O   HOH Z 125 " =    2.896
peak=   -3.301 closest distance to " O   HOH Z 385 " =    3.949
peak=   -3.301 closest distance to " CB  PRO A 163 " =    2.786
peak=   -3.300 closest distance to " CE2 TRP A  85 " =    1.109
peak=   -3.299 closest distance to " O   HOH Z 186 " =    1.458
peak=   -3.296 closest distance to " O   HOH Z  37 " =    1.583
peak=   -3.296 closest distance to " OG BSER A 212 " =    2.185
peak=   -3.289 closest distance to " CG1 VAL A 296 " =    1.541
peak=   -3.282 closest distance to " CZ  TYR A 169 " =    1.862
peak=   -3.271 closest distance to " O   HOH Z 410 " =    2.202
peak=   -3.270 closest distance to " CD  ARG A 139 " =    1.577
peak=   -3.269 closest distance to " CA  VAL A 232 " =    2.275
peak=   -3.268 closest distance to " O   HOH Z 227 " =    1.044
peak=   -3.267 closest distance to " O   HOH Z 252 " =    1.049
peak=   -3.264 closest distance to " CD  LYS A 119 " =    0.989
peak=   -3.259 closest distance to " O   HOH Z 120 " =    1.547
peak=   -3.256 closest distance to " CB  TRP A  85 " =    2.311
peak=   -3.255 closest distance to " CB  ALA A 248 " =    1.914
peak=   -3.252 closest distance to " O   HOH Z 108 " =    2.360
peak=   -3.247 closest distance to " O   HOH Z 377 " =    1.006
peak=   -3.247 closest distance to " O   HOH Z  10 " =    1.552
peak=   -3.242 closest distance to " NH1 ARG A  56 " =    2.375
peak=   -3.242 closest distance to " O   HOH Z 165 " =    2.105
peak=   -3.240 closest distance to " OD2 ASP A 171 " =    1.832
peak=   -3.240 closest distance to " O   HOH Z 427 " =    1.530
peak=   -3.237 closest distance to " O   HOH Z 388 " =    1.743
peak=   -3.233 closest distance to " O   ALA A 161 " =    1.349
peak=   -3.232 closest distance to " CD2 TYR A 293 " =    2.211
peak=   -3.227 closest distance to " O   HOH Z 430 " =    1.514
peak=   -3.227 closest distance to " CE  MET A 105 " =    2.228
peak=   -3.221 closest distance to " O   LEU A 143 " =    1.428
peak=   -3.221 closest distance to " O   ASP A 270 " =    1.871
peak=   -3.213 closest distance to " CG  LYS A 193 " =    2.448
peak=   -3.213 closest distance to " O   HOH Z 100 " =    0.998
peak=   -3.211 closest distance to " CE2 PHE A  38 " =    2.126
peak=   -3.209 closest distance to " CD  ARG A  14 " =    3.170
peak=   -3.209 closest distance to " N   ILE A 120 " =    1.197
peak=   -3.208 closest distance to " N   GLY A  17 " =    1.484
peak=   -3.208 closest distance to " O   GLY A 196 " =    1.255
peak=   -3.207 closest distance to " O   HOH Z 345 " =    4.754
peak=   -3.207 closest distance to " C   PRO A 213 " =    1.616
peak=   -3.204 closest distance to " CD1 LEU A   5 " =    2.440
peak=   -3.204 closest distance to " O   HOH Z 192 " =    1.705
peak=   -3.203 closest distance to " CB  SER A  63 " =    3.242
peak=   -3.202 closest distance to " OG BSER A 134 " =    1.826
peak=   -3.196 closest distance to " O   HOH Z   9 " =    2.097
peak=   -3.193 closest distance to " O   HOH Z  97 " =    1.555
peak=   -3.190 closest distance to " ND2 ASN A  60 " =    1.471
peak=   -3.189 closest distance to " O   HOH Z 283 " =    2.044
peak=   -3.189 closest distance to " O   HOH Z  92 " =    2.512
peak=   -3.187 closest distance to " O   HOH Z 113 " =    1.603
peak=   -3.186 closest distance to " CD2 LEU A   5 " =    1.013
peak=   -3.185 closest distance to " OG  SER A  62 " =    4.544
peak=   -3.181 closest distance to " O   ALA A 158 " =    1.078
peak=   -3.175 closest distance to " OH  TYR A 169 " =    1.004
peak=   -3.171 closest distance to " O   HOH Z 378 " =    1.268
peak=   -3.166 closest distance to " O   HOH Z 105 " =    1.976
peak=   -3.165 closest distance to " C   HIS A 108 " =    1.105
peak=   -3.159 closest distance to " O   HOH Z 147 " =    2.146
peak=   -3.143 closest distance to " NH2 ARG A  66 " =    4.848
peak=   -3.141 closest distance to " ND2BASN A 224 " =    1.824
peak=   -3.131 closest distance to " O   ALA A 100 " =    2.486
peak=   -3.130 closest distance to " OD2 ASP A 286 " =    2.547
peak=   -3.128 closest distance to " CG1 ILE A 234 " =    1.638
peak=   -3.119 closest distance to " OD2 ASP A 270 " =    1.416
peak=   -3.103 closest distance to " CE  MET A 105 " =    2.109
peak=   -3.102 closest distance to " O   HOH Z  97 " =    1.972
peak=   -3.098 closest distance to " O   HOH Z 325 " =    1.525
peak=   -3.097 closest distance to " C   LEU A 143 " =    1.343
peak=   -3.097 closest distance to " O   HOH Z 179 " =    2.219
peak=   -3.093 closest distance to " O   HOH Z 199 " =    1.302
peak=   -3.070 closest distance to " NE2 HIS A  86 " =    1.074
peak=   -3.055 closest distance to " O   HOH Z 426 " =    2.209
peak=   -3.033 closest distance to " O   PRO A 198 " =    1.288

================= 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    :  0.4882 0.4876   6.291335e+00   6.286468e+00
   1_bss:  0.4797 0.4771   5.842566e+00   5.842745e+00
   1_xyz:  0.4140 0.4465   6.202456e+00   6.242820e+00
   1_adp:  0.3779 0.4340   6.146537e+00   6.228123e+00
   1_occ:  0.3774 0.4345   6.145977e+00   6.227597e+00
   2_bss:  0.3756 0.4302   6.146915e+00   6.225777e+00
   2_xyz:  0.3023 0.3710   5.996773e+00   6.135722e+00
   2_adp:  0.2846 0.3523   5.950269e+00   6.101548e+00
   2_occ:  0.2844 0.3522   5.949704e+00   6.101230e+00
   3_bss:  0.2825 0.3486   5.948426e+00   6.098765e+00
   3_xyz:  0.2190 0.2821   5.736909e+00   5.933766e+00
   3_adp:  0.1993 0.2661   5.667782e+00   5.882622e+00
   3_occ:  0.1991 0.2663   5.667568e+00   5.882791e+00
   4_bss:  0.1989 0.2667   5.667923e+00   5.882460e+00
   4_xyz:  0.1586 0.2163   5.461296e+00   5.695349e+00
   4_adp:  0.1475 0.2035   5.399550e+00   5.633800e+00
   4_occ:  0.1474 0.2033   5.398902e+00   5.633189e+00
   5_bss:  0.1476 0.2034   5.400670e+00   5.634425e+00
   5_xyz:  0.1307 0.1804   5.290492e+00   5.525066e+00
   5_adp:  0.1273 0.1756   5.265102e+00   5.498258e+00
   5_occ:  0.1271 0.1755   5.264339e+00   5.497665e+00
   5_bss:  0.1271 0.1754   5.264236e+00   5.497316e+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:  0.341  20.001   7.586   8.344   8.687   0.000   0.000   0.000
   1_xyz:  0.341  20.001   7.586   8.344   8.687   0.000   0.000   0.000
   1_adp:  0.341  20.001   7.586   8.344   8.687   0.000   0.000   0.000
   1_occ:  0.341  20.001   7.586   8.344   8.687   0.000   0.000   0.000
   2_bss:  0.336  40.558   4.008   4.971   5.812   0.000   0.000   0.000
   2_xyz:  0.336  40.558   4.008   4.971   5.812   0.000   0.000   0.000
   2_adp:  0.336  40.558   4.008   4.971   5.812   0.000   0.000   0.000
   2_occ:  0.336  40.558   4.008   4.971   5.812   0.000   0.000   0.000
   3_bss:  0.319  40.558   2.021   2.629   3.231   0.000   0.000   0.000
   3_xyz:  0.319  40.558   2.021   2.629   3.231   0.000   0.000   0.000
   3_adp:  0.319  40.558   2.021   2.629   3.231   0.000   0.000   0.000
   3_occ:  0.319  40.558   2.021   2.629   3.231   0.000   0.000   0.000
   4_bss:  0.324  50.444   1.170   1.645   1.745   0.000   0.000   0.000
   4_xyz:  0.324  50.444   1.170   1.645   1.745   0.000   0.000   0.000
   4_adp:  0.324  50.444   1.170   1.645   1.745   0.000   0.000   0.000
   4_occ:  0.324  50.444   1.170   1.645   1.745   0.000   0.000   0.000
   5_bss:  0.324  50.444   0.897   1.260   1.261   0.000   0.000   0.000
   5_xyz:  0.324  50.444   0.897   1.260   1.261   0.000   0.000   0.000
   5_adp:  0.324  50.444   0.897   1.260   1.261   0.000   0.000   0.000
   5_occ:  0.324  50.444   0.897   1.260   1.261   0.000   0.000   0.000
   5_bss:  0.319  47.500  -0.242   0.121   0.121   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  61.591 0.3723  0.4421    76148.551
   1_bss:  62.226 0.3614  0.5313    73461.351
   1_xyz:  56.162 0.4383  0.6350    61107.299
   1_adp:  52.322 0.4882  0.7735    56480.905
   1_occ:  52.293 0.4886  0.7741    56571.593
   2_bss:  52.000 0.4922  0.7015    56199.981
   2_xyz:  41.330 0.6255  0.8908    40185.929
   2_adp:  38.608 0.6581  0.9403    35730.288
   2_occ:  38.567 0.6586  0.9408    35664.925
   3_bss:  38.323 0.6613  0.8702    35298.519
   3_xyz:  29.643 0.7601  0.9609    21829.725
   3_adp:  27.299 0.7861  0.9700    19081.576
   3_occ:  27.308 0.7860  0.9696    19090.046
   4_bss:  27.250 0.7868  0.9331    19112.698
   4_xyz:  21.504 0.8460  0.9747    12350.367
   4_adp:  19.718 0.8642  0.9780    10896.475
   4_occ:  19.700 0.8644  0.9778    10879.040
   5_bss:  19.723 0.8642  0.9649    10923.598
   5_xyz:  17.234 0.8871  0.9762     8618.488
   5_adp:  16.491 0.8941  0.9755     8151.270
   5_occ:  16.472 0.8943  0.9754     8143.215
   5_bss:  16.470 0.8943  0.9753     8133.071
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.3604e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.3604e+01
   1_xyz:   1.743  0.013  0.109 18.237  0.007  4.109   1.4893e-01
   1_adp:   1.743  0.013  0.109 18.237  0.007  4.109   1.4893e-01
   1_occ:   1.743  0.013  0.109 18.237  0.007  4.109   1.4893e-01
   2_bss:   1.743  0.013  0.109 18.237  0.007  4.109   1.4893e-01
   2_xyz:   1.167  0.008  0.077 16.232  0.005  4.109   8.4867e-02
   2_adp:   1.167  0.008  0.077 16.232  0.005  4.109   8.4867e-02
   2_occ:   1.167  0.008  0.077 16.232  0.005  4.109   8.4867e-02
   3_bss:   1.167  0.008  0.077 16.232  0.005  4.109   8.4867e-02
   3_xyz:   1.111  0.008  0.079 15.398  0.005  4.128   7.0640e-02
   3_adp:   1.111  0.008  0.079 15.398  0.005  4.128   7.0640e-02
   3_occ:   1.111  0.008  0.079 15.398  0.005  4.128   7.0640e-02
   4_bss:   1.111  0.008  0.079 15.398  0.005  4.128   7.0640e-02
   4_xyz:   1.018  0.007  0.074 15.306  0.004  4.135   6.2623e-02
   4_adp:   1.018  0.007  0.074 15.306  0.004  4.135   6.2623e-02
   4_occ:   1.018  0.007  0.074 15.306  0.004  4.135   6.2623e-02
   5_bss:   1.018  0.007  0.074 15.306  0.004  4.135   6.2623e-02
   5_xyz:   1.036  0.007  0.077 15.333  0.003  4.118   6.3225e-02
   5_adp:   1.036  0.007  0.077 15.333  0.003  4.118   6.3225e-02
   5_occ:   1.036  0.007  0.077 15.333  0.003  4.118   6.3225e-02
   5_bss:   1.036  0.007  0.077 15.333  0.003  4.118   6.3225e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9472e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9472e+00
   1_xyz:  15.167  0.176  0.476 85.567  0.053  2.204   1.0198e-01
   1_adp:  15.167  0.176  0.476 85.567  0.053  2.204   1.0198e-01
   1_occ:  15.167  0.176  0.476 85.567  0.053  2.204   1.0198e-01
   2_bss:  15.167  0.176  0.476 85.567  0.053  2.204   1.0198e-01
   2_xyz:   8.973  0.088  0.267 81.717  0.033  2.093   5.9898e-02
   2_adp:   8.973  0.088  0.267 81.717  0.033  2.093   5.9898e-02
   2_occ:   8.973  0.088  0.267 81.717  0.033  2.093   5.9898e-02
   3_bss:   8.973  0.088  0.267 81.717  0.033  2.093   5.9898e-02
   3_xyz:   7.712  0.074  0.285 76.550  0.058  2.316   6.2099e-02
   3_adp:   7.712  0.074  0.285 76.550  0.058  2.316   6.2099e-02
   3_occ:   7.712  0.074  0.285 76.550  0.058  2.316   6.2099e-02
   4_bss:   7.712  0.074  0.285 76.550  0.058  2.316   6.2099e-02
   4_xyz:   8.243  0.047  0.329 87.075  0.039  2.388   4.5056e-02
   4_adp:   8.243  0.047  0.329 87.075  0.039  2.388   4.5056e-02
   4_occ:   8.243  0.047  0.329 87.075  0.039  2.388   4.5056e-02
   5_bss:   8.243  0.047  0.329 87.075  0.039  2.388   4.5056e-02
   5_xyz:   7.697  0.050  0.403 81.096  0.030  2.357   4.0276e-02
   5_adp:   7.697  0.050  0.403 81.096  0.030  2.357   4.0276e-02
   5_occ:   7.697  0.050  0.403 81.096  0.030  2.357   4.0276e-02
   5_bss:   7.697  0.050  0.403 81.096  0.030  2.357   4.0276e-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:  87.21   0.00  14.40  87.21   0.00  12.21  83.29   0.00  26.28
   1_occ:  87.21   0.00  14.40  87.21   0.00  12.21  83.29   0.00  26.28
   2_bss:  87.21   0.00  14.40  87.21   0.00  12.21  83.29   0.00  26.28
   2_xyz:  87.21   0.00  14.40  87.21   0.00  12.21  83.29   0.00  26.28
   2_adp:  79.97   0.00  14.61  79.97   0.00  11.54  76.94   0.00  31.36
   2_occ:  79.97   0.00  14.61  79.97   0.00  11.54  76.94   0.00  31.36
   3_bss:  79.97   0.00  14.61  79.97   0.00  11.54  76.94   0.00  31.36
   3_xyz:  79.97   0.00  14.61  79.97   0.00  11.54  76.94   0.00  31.36
   3_adp:  92.29   0.00  15.54  92.24   0.00  11.02  92.29   1.12  40.14
   3_occ:  92.29   0.00  15.54  92.24   0.00  11.02  92.29   1.12  40.14
   4_bss:  92.29   0.00  15.54  92.24   0.00  11.02  92.29   1.12  40.14
   4_xyz:  92.29   0.00  15.54  92.24   0.00  11.02  92.29   1.12  40.14
   4_adp: 101.23   0.00  15.29 101.23   0.00  10.44  95.94   3.73  41.70
   4_occ: 101.23   0.00  15.29 101.23   0.00  10.44  95.94   3.73  41.70
   5_bss: 101.23   0.00  15.29 101.23   0.00  10.44  95.94   3.73  41.70
   5_xyz: 101.23   0.00  15.29 101.23   0.00  10.44  95.94   3.73  41.70
   5_adp: 104.21   0.00  14.86 104.21   0.00  10.12  95.44   3.26  40.70
   5_occ: 104.21   0.00  14.86 104.21   0.00  10.12  95.44   3.26  40.70
   5_bss: 105.35   1.14  16.00 105.35   1.14  11.26  96.58   4.39  41.84
------------------------------------------------------------------------
 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:    1.213    0.035    0.413
   1_adp:    1.213    0.035    0.413
   1_occ:    1.213    0.035    0.413
   2_bss:    1.213    0.035    0.413
   2_xyz:    1.763    0.031    0.567
   2_adp:    1.763    0.031    0.567
   2_occ:    1.763    0.031    0.567
   3_bss:    1.763    0.031    0.567
   3_xyz:    1.670    0.048    0.660
   3_adp:    1.670    0.048    0.660
   3_occ:    1.670    0.048    0.660
   4_bss:    1.670    0.048    0.660
   4_xyz:    1.814    0.016    0.743
   4_adp:    1.814    0.016    0.743
   4_occ:    1.814    0.016    0.743
   5_bss:    1.814    0.016    0.743
   5_xyz:    1.831    0.055    0.777
   5_adp:    1.831    0.055    0.777
   5_occ:    1.831    0.055    0.777
   5_bss:    1.831    0.055    0.777
------------------------------------------------------------------------

CPU time actual refinement: 298.37


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1045/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_1045/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1045/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1045/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1045/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 298.22 
  Macro-tasks:
    bulk solvent and scale       = 35.79  
    individual site refinement   = 122.34 
    weights calculation          = 28.38  
    collect and process          = 5.36   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 191.96 
  Micro-tasks:
    mask                            = 2.12   
    f_calc                          = 95.67  
    alpha_beta                      = 7.04   
    target                          = 0.99   
    gradients_wrt_atomic_parameters = 102.33 
    fmodel                         = 6.18   
    r_factors                      = 0.18   
    phase_errors                   = 8.30   
    foms                           = 0.25   
    TOTAL for micro-tasks          = 223.06 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.278 micro seconds
Total CPU time: 5.17 minutes
from_scatterers_fft:    621 calls, 95.33 s
gradients_fft:          566 calls, 91.66 s

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

# Date 2008-01-16 Time 03:02:34 PST -0800 (1200481354.52 s)
Start R-work = 0.4882, R-free = 0.4876 (no bulk solvent and anisotropic scale)
Final R-work = 0.1432, R-free = 0.1936 (no bulk solvent and anisotropic scale)

Start R-work = 0.4797, R-free = 0.4771
Final R-work = 0.1271, R-free = 0.1754