# Date 2008-01-16 Time 01:45:01 PST -0800 (1200476701.30 s)
#phil __OFF__

Command line arguments: "../543.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 16492
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 543

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.8988, 46.93, 85.9581, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.26, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 46.93, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.919 1.99044
Completeness in resolution range: 0.981659
Completeness with d_max=infinity: 0.97852

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9190
                             d_min =   1.9904

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 46.93, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.919 1.99044
Completeness in resolution range: 0.981659
Completeness with d_max=infinity: 0.97852

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9194 -  4.2581 [2093/2118]  1884   209  10.0%
  bin  2:  4.2581 -  3.3929 [2024/2042]  1822   202  10.0%
  bin  3:  3.3929 -  2.9678 [1983/2002]  1784   199  10.0%
  bin  4:  2.9678 -  2.6982 [1956/1986]  1761   195  10.0%
  bin  5:  2.6982 -  2.5058 [1960/1979]  1764   196  10.0%
  bin  6:  2.5058 -  2.3587 [1949/1974]  1751   198  10.2%
  bin  7:  2.3587 -  2.2410 [1944/1972]  1755   189   9.7%
  bin  8:  2.2410 -  2.1437 [1941/1977]  1744   197  10.1%
  bin  9:  2.1437 -  2.0614 [1902/1944]  1711   191  10.0%
  bin 10:  2.0614 -  1.9904 [1837/1961]  1654   183  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_543/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 10
        2.42 -     3.04: 2220
        3.04 -     3.66: 4689
        3.66 -     4.28: 9087
        4.28 -     4.90: 12414
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  52 " - " O   HOH Z 183 "  2.171 3.040 -x+1,y+1/2,-z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z  18 " - " O   HOH Z 102 "  2.337 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  2.341 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28415 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_543/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_543/model_refine_001.geo

CPU time processing inputs: 9.09


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.89875 46.93 85.95805 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: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4082   r_free= 0.3984   ksol= 0.00   Bsol= 0.00   scale= 0.839    |
|                                                                             |
| 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:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.192092                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9194 -  4.7489 0.99   1370  153 0.3494 0.3315      6.4852      6.4461|
|  2:  4.7489 -  3.7897 0.99   1303  145 0.3030 0.3071      6.5658      6.5758|
|  3:  3.7897 -  3.3166 0.99   1280  142 0.3391 0.3290      6.4951      6.5051|
|  4:  3.3166 -  3.0161 0.99   1281  140 0.3805 0.3576       6.403      6.3143|
|  5:  3.0161 -  2.8015 0.99   1257  142 0.4092 0.4445      6.2694      6.3095|
|  6:  2.8015 -  2.6372 0.99   1274  140 0.4295 0.4845      6.2064      6.2379|
|  7:  2.6372 -  2.5058 0.99   1250  139 0.4527 0.4376       6.188      6.0905|
|  8:  2.5058 -  2.3972 0.98   1254  140 0.4502 0.4443      6.1294      6.1397|
|  9:  2.3972 -  2.3053 0.98   1241  140 0.4649 0.4592      6.0757      6.0456|
| 10:  2.3053 -  2.2260 0.99   1236  137 0.4699 0.4442      6.0946      6.0211|
| 11:  2.2260 -  2.1566 0.98   1253  137 0.4648 0.3819      6.0236      5.9195|
| 12:  2.1566 -  2.0951 0.97   1236  138 0.4734 0.4404      5.9665      5.9748|
| 13:  2.0951 -  2.0401 1.00   1229  134 0.4764 0.5207      5.8754      5.9164|
| 14:  2.0401 -  1.9904 0.91   1166  132 0.4826 0.4379      5.8197      5.7201|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9194 -  4.7489  1370   153  0.74  30.75   0.82     0.76      57222.34|
|  2:  4.7489 -  3.7897  1303   145  0.79  26.75   0.93     0.84      64997.01|
|  3:  3.7897 -  3.3166  1280   142  0.75  31.29   0.90     0.82      65145.62|
|  4:  3.3166 -  3.0161  1281   140  0.69  36.26   0.85     0.75      58823.64|
|  5:  3.0161 -  2.8015  1257   142  0.60  44.23   0.80     0.66      55325.00|
|  6:  2.8015 -  2.6372  1274   140  0.56  46.94   0.78     0.63      51581.57|
|  7:  2.6372 -  2.5058  1250   139  0.55  48.10   0.77     0.61      48099.80|
|  8:  2.5058 -  2.3972  1254   140  0.56  47.63   0.79     0.63      42252.95|
|  9:  2.3972 -  2.3053  1241   140  0.58  45.67   0.76     0.65      35308.28|
| 10:  2.3053 -  2.2260  1236   137  0.61  43.57   0.79     0.67      30151.59|
| 11:  2.2260 -  2.1566  1253   137  0.60  43.91   0.79     0.68      27942.94|
| 12:  2.1566 -  2.0951  1236   138  0.55  48.28   0.80     0.64      29573.96|
| 13:  2.0951 -  2.0401  1229   134  0.50  52.08   0.79     0.58      27711.39|
| 14:  2.0401 -  1.9904  1166   132  0.51  51.83   0.76     0.54      22608.05|
|alpha:            min =        0.54 max =            0.84 mean =         0.68|
|beta:             min =    22608.05 max =        65145.62 mean =     44427.84|
|figures of merit: min =        0.00 max =            1.00 mean =         0.62|
|phase err.(work): min =        0.00 max =           89.93 mean =        42.45|
|phase err.(test): min =        0.00 max =           89.99 mean =        42.62|
|-----------------------------------------------------------------------------|

============================== 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 = 6.188193              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 72.322   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.476457              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.747   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       24 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      165 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      679 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1527 |
| 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:     3932 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5095 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6592 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7758 |
|-----------------------------------------------------------------------------|
|-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 |       53.571 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.091    4.900  1.196 |       1.711 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.794)------------------------------------------|
|    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 = 11.794)------------------------------------------|
|    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: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4183   r_free= 0.4075   ksol= 0.00   Bsol= 0.00   scale= 0.806    |
|                                                                             |
| 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:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.200423                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4003   r_free= 0.3904   ksol= 0.35   Bsol= 20.00   scale= 1.033   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.34,8.25,8.16,0.00,0.00,0.00); trace/3= 7.92                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.186645                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.779181              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 74.223   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.490290              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 75.402   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4003      final r-factor (work) = 0.2854          |
| start r-factor (free) = 0.3904      final r-factor (free) = 0.3062          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 71.5352 = 5.78 * 0.50 * 6.2169 + 1.00 * 53.5710                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.4472 = 5.78 * 0.50 * 6.0016 + 1.00 * 0.1051                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2854      final r-factor (work) = 0.2074          |
| start r-factor (free) = 0.3062      final r-factor (free) = 0.2340          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9572 = 0.49 * 1.00 * 6.0016 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8330 = 0.49 * 1.00 * 5.7560 + 1.00 * 0.0109                               |
|-----------------------------------------------------------------------------|
| number of iterations = 16      |    number of function evaluations = 19     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.794)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    50.58   9.83     None  None   None       |
|    all(noH): 2823   0      0.00    50.58   9.83     None  None   None       |
|    Sol.    : 438    0      0.00    50.58   27.03    None  None   None       |
|    Mac.    : 2385   0      0.00    48.33   6.67     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 -   5.058: 1236   |   5:    25.291 -  30.349:  104        |
|      1:     5.058 -  10.116:  753   |   6:    30.349 -  35.407:  104        |
|      2:    10.116 -  15.174:  271   |   7:    35.407 -  40.465:   80        |
|      3:    15.174 -  20.232:  131   |   8:    40.465 -  45.523:   36        |
|      4:    20.232 -  25.291:   96   |   9:    45.523 -  50.581:   12        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2074 r_free = 0.2340             target_work(ml) = 5.628         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2069 r_free = 0.2336             target_work(ml) = 5.626         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2069   r_free= 0.2336   ksol= 0.35   Bsol= 20.00   scale= 1.087   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.34,8.25,8.16,0.00,0.00,0.00); trace/3= 7.92                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.626374                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2011   r_free= 0.2280   ksol= 0.34   Bsol= 35.75   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.14,4.59,5.45,0.00,0.00,0.00); trace/3= 4.72                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.624146                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.075488              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 92.473   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.228359              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 104.541  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2011      final r-factor (work) = 0.1380          |
| start r-factor (free) = 0.2280      final r-factor (free) = 0.1720          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.9849 = 3.08 * 0.50 * 5.7749 + 1.00 * 0.1045                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4307 = 3.08 * 0.50 * 5.4427 + 1.00 * 0.0611                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1380      final r-factor (work) = 0.1273          |
| start r-factor (free) = 0.1720      final r-factor (free) = 0.1633          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2551 = 0.23 * 1.00 * 5.4427 + 1.00 * 0.0122                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2173 = 0.23 * 1.00 * 5.2439 + 1.00 * 0.0198                               |
|-----------------------------------------------------------------------------|
| number of iterations = 14      |    number of function evaluations = 14     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.794)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    74.97   10.28    None  None   None       |
|    all(noH): 2823   0      0.00    74.97   10.28    None  None   None       |
|    Sol.    : 438    0      1.01    51.48   29.69    None  None   None       |
|    Mac.    : 2385   0      0.00    74.97   6.72     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 -   7.497: 1728   |   5:    37.487 -  44.984:  115        |
|      1:     7.497 -  14.995:  533   |   6:    44.984 -  52.482:   35        |
|      2:    14.995 -  22.492:  145   |   7:    52.482 -  59.979:    1        |
|      3:    22.492 -  29.990:  124   |   8:    59.979 -  67.477:    0        |
|      4:    29.990 -  37.487:  141   |   9:    67.477 -  74.974:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1273 r_free = 0.1633             target_work(ml) = 5.219         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1272 r_free = 0.1631             target_work(ml) = 5.219         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1272   r_free= 0.1631   ksol= 0.34   Bsol= 35.75   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.14,4.59,5.45,0.00,0.00,0.00); trace/3= 4.72                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.218933                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1270   r_free= 0.1630   ksol= 0.32   Bsol= 35.75   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.30,3.82,4.67,0.00,0.00,0.00); trace/3= 3.93                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.219558                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.402413              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 119.880  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.247286              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 99.269   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1270      final r-factor (work) = 0.1191          |
| start r-factor (free) = 0.1630      final r-factor (free) = 0.1557          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.7423 = 1.40 * 0.50 * 5.2499 + 1.00 * 0.0611                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.6907 = 1.40 * 0.50 * 5.1875 + 1.00 * 0.0531                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1191      final r-factor (work) = 0.1167          |
| start r-factor (free) = 0.1557      final r-factor (free) = 0.1540          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3114 = 0.25 * 1.00 * 5.1875 + 1.00 * 0.0286                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2862 = 0.25 * 1.00 * 5.1593 + 1.00 * 0.0103                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.794)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    63.33   10.62    None  None   None       |
|    all(noH): 2823   0      0.00    63.33   10.62    None  None   None       |
|    Sol.    : 438    0      0.72    58.44   31.32    None  None   None       |
|    Mac.    : 2385   0      0.00    63.33   6.82     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:     0.000 -   6.333: 1554   |   5:    31.663 -  37.995:  101        |
|      1:     6.333 -  12.665:  597   |   6:    37.995 -  44.328:   81        |
|      2:    12.665 -  18.998:  195   |   7:    44.328 -  50.660:   71        |
|      3:    18.998 -  25.330:  100   |   8:    50.660 -  56.993:   22        |
|      4:    25.330 -  31.663:   94   |   9:    56.993 -  63.325:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1167 r_free = 0.1540             target_work(ml) = 5.154         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1167 r_free = 0.1540             target_work(ml) = 5.154         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1167   r_free= 0.1540   ksol= 0.32   Bsol= 35.75   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.30,3.82,4.67,0.00,0.00,0.00); trace/3= 3.93                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.154053                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1167   r_free= 0.1540   ksol= 0.32   Bsol= 35.75   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.30,3.82,4.67,0.00,0.00,0.00); trace/3= 3.93                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.154053                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.513718              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 136.190  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.270835              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 104.083  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1167      final r-factor (work) = 0.1102          |
| start r-factor (free) = 0.1540      final r-factor (free) = 0.1525          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5374 = 2.51 * 0.50 * 5.1591 + 1.00 * 0.0531                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5111 = 2.51 * 0.50 * 5.1277 + 1.00 * 0.0663                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1102      final r-factor (work) = 0.1100          |
| start r-factor (free) = 0.1525      final r-factor (free) = 0.1532          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3993 = 0.27 * 1.00 * 5.1277 + 1.00 * 0.0106                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4035 = 0.27 * 1.00 * 5.1181 + 1.00 * 0.0173                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.794)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    69.47   10.59    None  None   None       |
|    all(noH): 2823   0      0.00    69.47   10.59    None  None   None       |
|    Sol.    : 438    0      0.75    60.82   31.15    None  None   None       |
|    Mac.    : 2385   0      0.00    69.47   6.82     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:     0.000 -   6.947: 1657   |   5:    34.735 -  41.682:   89        |
|      1:     6.947 -  13.894:  551   |   6:    41.682 -  48.630:   77        |
|      2:    13.894 -  20.841:  164   |   7:    48.630 -  55.577:   41        |
|      3:    20.841 -  27.788:  106   |   8:    55.577 -  62.524:   10        |
|      4:    27.788 -  34.735:  123   |   9:    62.524 -  69.471:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1100 r_free = 0.1532             target_work(ml) = 5.121         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1098 r_free = 0.1532             target_work(ml) = 5.120         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1098   r_free= 0.1532   ksol= 0.32   Bsol= 35.75   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.30,3.82,4.67,0.00,0.00,0.00); trace/3= 3.93                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.120310                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1098   r_free= 0.1531   ksol= 0.32   Bsol= 35.75   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.24,3.72,4.62,0.00,0.00,0.00); trace/3= 3.86                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.120071                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.772815              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 161.909  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.709039              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 97.302   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1098      final r-factor (work) = 0.1111          |
| start r-factor (free) = 0.1531      final r-factor (free) = 0.1542          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.6021 = 1.77 * 0.50 * 5.1171 + 1.00 * 0.0663                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.6010 = 1.77 * 0.50 * 5.1259 + 1.00 * 0.0573                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1111      final r-factor (work) = 0.1102          |
| start r-factor (free) = 0.1542      final r-factor (free) = 0.1546          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6483 = 0.71 * 1.00 * 5.1259 + 1.00 * 0.0138                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6467 = 0.71 * 1.00 * 5.1263 + 1.00 * 0.0120                               |
|-----------------------------------------------------------------------------|
| number of iterations = 18      |    number of function evaluations = 19     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.794)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    72.96   10.76    None  None   None       |
|    all(noH): 2823   0      0.00    72.96   10.76    None  None   None       |
|    Sol.    : 438    0      0.55    62.63   32.00    None  None   None       |
|    Mac.    : 2385   0      0.00    72.96   6.86     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 -   7.296: 1691   |   5:    36.478 -  43.774:   99        |
|      1:     7.296 -  14.591:  533   |   6:    43.774 -  51.069:   69        |
|      2:    14.591 -  21.887:  156   |   7:    51.069 -  58.365:   33        |
|      3:    21.887 -  29.182:  113   |   8:    58.365 -  65.660:    9        |
|      4:    29.182 -  36.478:  115   |   9:    65.660 -  72.956:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1102 r_free = 0.1546             target_work(ml) = 5.130         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1102 r_free = 0.1546             target_work(ml) = 5.130         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1102   r_free= 0.1546   ksol= 0.32   Bsol= 35.75   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.24,3.72,4.62,0.00,0.00,0.00); trace/3= 3.86                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.130038                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9194 -  4.7489 0.99   1370  153 0.1013 0.1256      5.3902      5.5076|
|  2:  4.7489 -  3.7897 0.99   1303  145 0.0864 0.1127      5.4409      5.6365|
|  3:  3.7897 -  3.3166 0.99   1280  142 0.1048 0.1494      5.4709      5.8498|
|  4:  3.3166 -  3.0161 0.99   1281  140 0.1194 0.1462      5.4443      5.5751|
|  5:  3.0161 -  2.8015 0.99   1257  142 0.1266 0.1717      5.3117      5.5282|
|  6:  2.8015 -  2.6372 0.99   1274  140 0.1180 0.1735      5.1954      5.4385|
|  7:  2.6372 -  2.5058 0.99   1250  139 0.1227 0.1629      5.1525      5.3704|
|  8:  2.5058 -  2.3972 0.98   1254  140 0.1137 0.1756      5.0677      5.3829|
|  9:  2.3972 -  2.3053 0.98   1241  140 0.1157 0.1705      5.0302      5.2483|
| 10:  2.3053 -  2.2260 0.99   1236  137 0.1086 0.1766      4.9569      5.2436|
| 11:  2.2260 -  2.1566 0.98   1253  137 0.1105 0.1614      4.9155      5.2081|
| 12:  2.1566 -  2.0951 0.97   1236  138 0.1097 0.1683        4.87      5.2106|
| 13:  2.0951 -  2.0401 1.00   1229  134 0.1106 0.1629      4.7959       5.047|
| 14:  2.0401 -  1.9904 0.91   1166  132 0.1055 0.1811      4.6814      4.9709|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9194 -  4.7489  1370   153  0.94   8.86   0.98     0.96       7025.36|
|  2:  4.7489 -  3.7897  1303   145  0.95   7.82   1.02     1.01       8909.86|
|  3:  3.7897 -  3.3166  1280   142  0.94  10.78   1.03     1.02      10136.14|
|  4:  3.3166 -  3.0161  1281   140  0.93  12.98   1.00     0.99       9979.58|
|  5:  3.0161 -  2.8015  1257   142  0.91  15.23   0.99     0.96       8022.95|
|  6:  2.8015 -  2.6372  1274   140  0.91  15.40   0.98     0.96       6848.85|
|  7:  2.6372 -  2.5058  1250   139  0.91  15.34   0.98     0.95       6019.12|
|  8:  2.5058 -  2.3972  1254   140  0.91  14.44   0.99     0.97       5212.85|
|  9:  2.3972 -  2.3053  1241   140  0.91  15.29   1.01     0.98       5008.21|
| 10:  2.3053 -  2.2260  1236   137  0.91  15.14   1.00     0.96       4302.16|
| 11:  2.2260 -  2.1566  1253   137  0.90  15.66   1.00     0.97       4195.40|
| 12:  2.1566 -  2.0951  1236   138  0.91  14.70   1.01     1.00       3806.00|
| 13:  2.0951 -  2.0401  1229   134  0.91  15.33   1.01     1.00       3370.92|
| 14:  2.0401 -  1.9904  1166   132  0.91  14.91   0.98     0.95       2645.72|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2645.72 max =        10136.14 mean =      6159.10|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.99 mean =        13.64|
|phase err.(test): min =        0.00 max =           89.73 mean =        13.26|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1101   r_free= 0.1546   ksol= 0.32   Bsol= 44.08   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.62,-0.14,0.76,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.129595                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1101   r_free= 0.1546   ksol= 0.32   Bsol= 44.08   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.62,-0.14,0.76,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.129595                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9194 -  4.7489 0.99   1370  153 0.1015 0.1260      5.3921        5.51|
|  2:  4.7489 -  3.7897 0.99   1303  145 0.0870 0.1132      5.4448      5.6403|
|  3:  3.7897 -  3.3166 0.99   1280  142 0.1050 0.1495      5.4725      5.8502|
|  4:  3.3166 -  3.0161 0.99   1281  140 0.1193 0.1459      5.4431      5.5736|
|  5:  3.0161 -  2.8015 0.99   1257  142 0.1264 0.1713      5.3094      5.5256|
|  6:  2.8015 -  2.6372 0.99   1274  140 0.1177 0.1731       5.193      5.4365|
|  7:  2.6372 -  2.5058 0.99   1250  139 0.1225 0.1626      5.1503      5.3686|
|  8:  2.5058 -  2.3972 0.98   1254  140 0.1136 0.1753      5.0663      5.3811|
|  9:  2.3972 -  2.3053 0.98   1241  140 0.1155 0.1705      5.0293      5.2483|
| 10:  2.3053 -  2.2260 0.99   1236  137 0.1086 0.1766      4.9565      5.2427|
| 11:  2.2260 -  2.1566 0.98   1253  137 0.1103 0.1612      4.9148      5.2077|
| 12:  2.1566 -  2.0951 0.97   1236  138 0.1097 0.1681      4.8696      5.2102|
| 13:  2.0951 -  2.0401 1.00   1229  134 0.1106 0.1629       4.795      5.0466|
| 14:  2.0401 -  1.9904 0.91   1166  132 0.1055 0.1806      4.6801      4.9689|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9194 -  4.7489  1370   153  0.94   8.90   0.98     0.96       7069.03|
|  2:  4.7489 -  3.7897  1303   145  0.95   7.87   1.02     1.01       8962.82|
|  3:  3.7897 -  3.3166  1280   142  0.94  10.81   1.03     1.02      10172.11|
|  4:  3.3166 -  3.0161  1281   140  0.93  12.95   1.01     0.99       9948.69|
|  5:  3.0161 -  2.8015  1257   142  0.91  15.19   0.99     0.96       7985.14|
|  6:  2.8015 -  2.6372  1274   140  0.91  15.35   0.99     0.96       6813.63|
|  7:  2.6372 -  2.5058  1250   139  0.91  15.30   0.99     0.96       5991.75|
|  8:  2.5058 -  2.3972  1254   140  0.91  14.42   0.99     0.97       5196.60|
|  9:  2.3972 -  2.3053  1241   140  0.91  15.27   1.01     0.99       4999.66|
| 10:  2.3053 -  2.2260  1236   137  0.91  15.13   1.01     0.96       4299.22|
| 11:  2.2260 -  2.1566  1253   137  0.90  15.65   1.00     0.97       4190.39|
| 12:  2.1566 -  2.0951  1236   138  0.91  14.68   1.01     1.00       3800.59|
| 13:  2.0951 -  2.0401  1229   134  0.91  15.30   1.01     1.00       3360.89|
| 14:  2.0401 -  1.9904  1166   132  0.91  14.88   0.99     0.95       2634.80|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2634.80 max =        10172.11 mean =      6155.48|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.82 mean =        13.63|
|phase err.(test): min =        0.00 max =           89.50 mean =        13.25|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.794)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.91    76.86   14.67    None  None   None       |
|    all(noH): 2823   0      3.91    76.86   14.67    None  None   None       |
|    Sol.    : 438    0      4.46    66.54   35.91    None  None   None       |
|    Mac.    : 2385   0      3.91    76.86   10.76    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     3.907 -  11.202: 1691   |   5:    40.385 -  47.680:   99        |
|      1:    11.202 -  18.498:  533   |   6:    47.680 -  54.976:   69        |
|      2:    18.498 -  25.794:  156   |   7:    54.976 -  62.271:   33        |
|      3:    25.794 -  33.089:  113   |   8:    62.271 -  69.567:    9        |
|      4:    33.089 -  40.385:  115   |   9:    69.567 -  76.863:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 298         
Filter by distance & map next to the model:
   mapped sites are within: 0.321 - 4.782
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 290 from: 298
   mapped sites are within: 0.729 - 4.782

peak=   10.891 closest distance to " CG2 VAL A 230 " =    1.407
peak=    7.136 closest distance to " CG2 VAL A 296 " =    1.124
peak=    6.437 closest distance to " CG  LEU A   5 " =    1.224
peak=    5.718 closest distance to " CG  LEU A 228 " =    1.164
peak=    5.628 closest distance to " CD2 LEU A   5 " =    1.203
peak=    5.624 closest distance to " CG  PRO A  54 " =    1.300
peak=    5.369 closest distance to " CB  ARG A 275 " =    0.935
peak=    5.343 closest distance to " CB  VAL A 296 " =    1.083
peak=    5.331 closest distance to " NH2 ARG A  56 " =    2.211
peak=    5.304 closest distance to " CB  GLN A 223 " =    1.437
peak=    5.046 closest distance to " O   HOH Z 142 " =    1.742
peak=    5.006 closest distance to " O   HOH Z 126 " =    1.906
peak=    4.992 closest distance to " CB  PRO A  54 " =    0.991
peak=    4.967 closest distance to " CB  VAL A 230 " =    1.160
peak=    4.895 closest distance to " NE2 GLN A  11 " =    1.111
peak=    4.854 closest distance to " O   HOH Z 209 " =    2.244
peak=    4.852 closest distance to " CB  GLN A 183 " =    1.296
peak=    4.821 closest distance to " CB  SER A  63 " =    1.257
peak=    4.727 closest distance to " CG  PRO A 213 " =    1.253
peak=    4.629 closest distance to " CB  GLU A 152 " =    1.187
peak=    4.573 closest distance to " O   HOH Z 232 " =    2.367
peak=    4.500 closest distance to " O   HOH Z 427 " =    2.962
peak=    4.490 closest distance to " CG  PRO A 243 " =    1.091
peak=    4.430 closest distance to " CG  PRO A 198 " =    1.171
peak=    4.425 closest distance to " O   HOH Z 193 " =    1.722
peak=    4.423 closest distance to " O   HOH Z 402 " =    1.466
peak=    4.402 closest distance to " O   HOH Z 316 " =    3.008
peak=    4.365 closest distance to " O   HOH Z 236 " =    1.894
peak=    4.281 closest distance to " O   SER A  87 " =    2.293
peak=    4.269 closest distance to " O   HOH Z 272 " =    1.879
peak=    4.254 closest distance to " CB  SER A   3 " =    1.264
peak=    4.247 closest distance to " CB  ASN A 148 " =    1.387
peak=    4.230 closest distance to " O   HOH Z  43 " =    2.082
peak=    4.222 closest distance to " C   PRO A 198 " =    1.490
peak=    4.219 closest distance to " O   HOH Z  61 " =    1.676
peak=    4.203 closest distance to " O   HOH Z 423 " =    1.789
peak=    4.159 closest distance to " O   HOH Z 369 " =    2.262
peak=    4.157 closest distance to " O   HOH Z 298 " =    1.778
peak=    4.148 closest distance to " ND2 ASN A 187 " =    1.516
peak=    4.127 closest distance to " O   HOH Z  78 " =    1.719
peak=    4.116 closest distance to " O   HOH Z 346 " =    1.603
peak=    4.107 closest distance to " O   HOH Z  59 " =    2.036
peak=    4.100 closest distance to " OD1 ASN A  69 " =    2.605
peak=    4.099 closest distance to " O   HOH Z 234 " =    3.544
peak=    4.084 closest distance to " O   HOH Z 203 " =    1.668
peak=    4.079 closest distance to " O   HOH Z 303 " =    2.039
peak=    4.062 closest distance to " CB  GLU A 128 " =    1.025
peak=    4.043 closest distance to " O   HOH Z 265 " =    2.463
peak=    4.027 closest distance to " CB  VAL A 265 " =    1.278
peak=    4.013 closest distance to " O   HOH Z 158 " =    3.119
peak=    4.001 closest distance to " CZ  PHE A 218 " =    1.095
peak=    3.997 closest distance to " CB  ARG A  79 " =    1.366
peak=    3.990 closest distance to " CD2 LEU A 228 " =    1.099
peak=    3.948 closest distance to " CB  TRP A 179 " =    1.314
peak=    3.932 closest distance to " O   HOH Z 392 " =    3.156
peak=    3.928 closest distance to " O   HOH Z 368 " =    2.139
peak=    3.920 closest distance to " O   HOH Z 248 " =    1.632
peak=    3.915 closest distance to " CG1BVAL A  72 " =    1.604
peak=    3.910 closest distance to " O   HOH Z 280 " =    2.919
peak=    3.910 closest distance to " CB  ARG A 139 " =    0.898
peak=    3.905 closest distance to " O   HOH Z  97 " =    1.968
peak=    3.895 closest distance to " O   HOH Z  66 " =    2.194
peak=    3.892 closest distance to " O   HOH Z 403 " =    1.675
peak=    3.875 closest distance to " O   HOH Z 389 " =    1.850
peak=    3.873 closest distance to " CB  ASN A  39 " =    0.932
peak=    3.863 closest distance to " CB  GLU A 277 " =    3.563
peak=    3.857 closest distance to " CG2 VAL A 257 " =    0.860
peak=    3.854 closest distance to " CB  TRP A 266 " =    0.979
peak=    3.847 closest distance to " O   HOH Z 371 " =    3.136
peak=    3.844 closest distance to " CA  ASN A 215 " =    1.171
peak=    3.839 closest distance to " CA  TYR A  30 " =    0.952
peak=    3.839 closest distance to " O   HOH Z 189 " =    2.642
peak=    3.833 closest distance to " O   HOH Z 263 " =    1.625
peak=    3.825 closest distance to " O   HOH Z 130 " =    2.268
peak=    3.816 closest distance to " CB  ALA A   9 " =    1.608
peak=    3.812 closest distance to " CB  ARG A 190 " =    1.665
peak=    3.807 closest distance to " O   HOH Z 245 " =    1.367
peak=    3.792 closest distance to " O   HOH Z 124 " =    1.324
peak=    3.771 closest distance to " N   ASN A  39 " =    1.148
peak=    3.765 closest distance to " O   HOH Z 250 " =    1.360
peak=    3.764 closest distance to " O   HOH Z 126 " =    2.067
peak=    3.736 closest distance to " O   HOH Z  97 " =    2.523
peak=    3.730 closest distance to " O   HOH Z  15 " =    2.158
peak=    3.729 closest distance to " O   HOH Z 261 " =    2.054
peak=    3.725 closest distance to " O   HOH Z 322 " =    2.054
peak=    3.723 closest distance to " O   HOH Z 425 " =    2.132
peak=    3.710 closest distance to " CB  ALA A 248 " =    1.509
peak=    3.700 closest distance to " O   TRP A 274 " =    1.855
peak=    3.697 closest distance to " O   HOH Z 407 " =    2.503
peak=    3.692 closest distance to " CB  ASP A 140 " =    0.970
peak=    3.681 closest distance to " O   HOH Z 193 " =    1.883
peak=    3.680 closest distance to " O   HOH Z 128 " =    2.076
peak=    3.679 closest distance to " CA  ALA A  21 " =    1.135
peak=    3.679 closest distance to " CB  VAL A 202 " =    1.567
peak=    3.677 closest distance to " OD2 ASP A 286 " =    2.718
peak=    3.664 closest distance to " O   HOH Z 344 " =    2.991
peak=    3.661 closest distance to " O   HOH Z 417 " =    3.203
peak=    3.659 closest distance to " CB  ALA A 291 " =    1.387
peak=    3.654 closest distance to " CB  ASN A 148 " =    1.912
peak=    3.651 closest distance to " CD BLYS A 290 " =    1.104
peak=    3.644 closest distance to " O   HOH Z 411 " =    3.751
peak=    3.640 closest distance to " O   HOH Z 273 " =    2.690
peak=    3.634 closest distance to " CB  SER A  26 " =    1.661
peak=    3.633 closest distance to " CA  VAL A  41 " =    0.798
peak=    3.618 closest distance to " CB  HIS A 108 " =    0.825
peak=    3.612 closest distance to " NZ  LYS A 117 " =    3.222
peak=    3.611 closest distance to " CA  PHE A 283 " =    1.125
peak=    3.610 closest distance to " O   HOH Z 145 " =    2.146
peak=    3.608 closest distance to " CG  ARG A  66 " =    2.725
peak=    3.605 closest distance to " OG BSER A 164 " =    2.179
peak=    3.602 closest distance to " O   HOH Z  88 " =    2.899
peak=    3.595 closest distance to " O   HOH Z 147 " =    1.744
peak=    3.593 closest distance to " O   HOH Z  54 " =    1.580
peak=    3.588 closest distance to " O   ASP A 124 " =    1.116
peak=    3.581 closest distance to " CE1 TYR A 186 " =    1.318
peak=    3.579 closest distance to " CB  LEU A 143 " =    1.144
peak=    3.578 closest distance to " CD2 TRP A 179 " =    1.404
peak=    3.575 closest distance to " CA  ARG A  36 " =    0.996
peak=    3.572 closest distance to " CA  ALA A  51 " =    0.950
peak=    3.565 closest distance to " CD1 ILE A 106 " =    1.035
peak=    3.556 closest distance to " CB  THR A  31 " =    1.625
peak=    3.544 closest distance to " O   HOH Z 187 " =    2.280
peak=    3.538 closest distance to " CG1 VAL A 296 " =    1.219
peak=    3.538 closest distance to " CG  MET A 185 " =    1.223
peak=    3.534 closest distance to " O   HOH Z 128 " =    2.091
peak=    3.527 closest distance to " CA  ALA A 158 " =    1.277
peak=    3.521 closest distance to " O   HOH Z 313 " =    1.808
peak=    3.517 closest distance to " O   HOH Z   9 " =    2.019
peak=    3.513 closest distance to " CG  GLN A  77 " =    2.127
peak=    3.512 closest distance to " O   MET A 105 " =    1.827
peak=    3.508 closest distance to " CB  ASN A 142 " =    1.126
peak=    3.502 closest distance to " O   HOH Z 214 " =    2.181
peak=    3.494 closest distance to " O   HOH Z 172 " =    3.577
peak=    3.491 closest distance to " O   HOH Z  40 " =    1.509
peak=    3.489 closest distance to " O   HOH Z 112 " =    1.641
peak=    3.487 closest distance to " CG2 ILE A 120 " =    1.135
peak=    3.486 closest distance to " CD  LYS A 119 " =    1.461
peak=    3.484 closest distance to " CD  ARG A 269 " =    0.970
peak=    3.473 closest distance to " O   HOH Z 435 " =    1.979
peak=    3.468 closest distance to " CG1 ILE A  49 " =    1.445
peak=    3.462 closest distance to " CB  ALA A 295 " =    1.146
peak=    3.462 closest distance to " CG1 ILE A  33 " =    1.335
peak=    3.461 closest distance to " CB  GLN A 278 " =    0.885
peak=    3.461 closest distance to " N   ARG A 156 " =    1.363
peak=    3.461 closest distance to " O   HOH Z 261 " =    1.610
peak=    3.460 closest distance to " CG1 VAL A 153 " =    0.961
peak=    3.459 closest distance to " CA  ASP A 140 " =    1.222
peak=    3.458 closest distance to " O   GLN A 278 " =    1.283
peak=    3.456 closest distance to " O   HOH Z 421 " =    1.730
peak=    3.455 closest distance to " NH2 ARG A 156 " =    1.108
peak=    3.454 closest distance to " O   HOH Z 329 " =    3.879
peak=    3.452 closest distance to " NH1AARG A 145 " =    1.089
peak=    3.451 closest distance to " CB  ASN A 110 " =    1.114
peak=    3.448 closest distance to " CA  LYS A 117 " =    1.254
peak=    3.447 closest distance to " CA  THR A 221 " =    0.931
peak=    3.432 closest distance to " O   HOH Z  49 " =    2.398
peak=    3.430 closest distance to " O   HOH Z 426 " =    1.580
peak=    3.425 closest distance to " CB BVAL A  41 " =    1.085
peak=    3.412 closest distance to " CB  GLU A  46 " =    1.073
peak=    3.409 closest distance to " CB  SER A 216 " =    0.776
peak=    3.407 closest distance to " ND2 ASN A 110 " =    1.679
peak=    3.400 closest distance to " O   HOH Z 422 " =    2.637
peak=    3.398 closest distance to " CB  GLN A  89 " =    1.192
peak=    3.398 closest distance to " N   PHE A 130 " =    1.266
peak=    3.396 closest distance to " OE1 GLU A   2 " =    2.122
peak=    3.395 closest distance to " CD  LYS A 166 " =    1.309
peak=    3.393 closest distance to " N   SER A 135 " =    1.323
peak=    3.390 closest distance to " CD1 LEU A 300 " =    1.277
peak=    3.389 closest distance to " O   HOH Z 345 " =    3.156
peak=    3.387 closest distance to " O   HOH Z 250 " =    1.389
peak=    3.381 closest distance to " CE  LYS A  76 " =    0.896
peak=    3.380 closest distance to " O   HOH Z 148 " =    3.319
peak=    3.380 closest distance to " CG2 ILE A  20 " =    1.468
peak=    3.377 closest distance to " CA  THR A 264 " =    0.777
peak=    3.365 closest distance to " O   HOH Z 286 " =    2.372
peak=    3.364 closest distance to " CG  MET A 185 " =    1.074
peak=    3.358 closest distance to " CD2 HIS A  81 " =    1.016
peak=    3.357 closest distance to " CA  ASP A 162 " =    1.058
peak=    3.356 closest distance to " O   HOH Z  21 " =    1.711
peak=    3.354 closest distance to " O   HOH Z 305 " =    3.604
peak=    3.353 closest distance to " CB  THR A 157 " =    1.163
peak=    3.349 closest distance to " O   HOH Z  10 " =    1.771
peak=    3.347 closest distance to " CB  ILE A  20 " =    1.381
peak=    3.345 closest distance to " O   HOH Z 291 " =    1.509
peak=    3.340 closest distance to " NE2 GLN A  77 " =    3.170
peak=    3.337 closest distance to " CB  LEU A 228 " =    1.289
peak=    3.336 closest distance to " O   HOH Z  80 " =    1.608
peak=    3.334 closest distance to " O   HOH Z 193 " =    1.589
peak=    3.329 closest distance to " CD2 LEU A 297 " =    0.924
peak=    3.325 closest distance to " O   HOH Z 366 " =    2.966
peak=    3.323 closest distance to " CA  VAL A 126 " =    0.855
peak=    3.315 closest distance to " O   HOH Z  48 " =    1.581
peak=    3.314 closest distance to " N   VAL A 126 " =    1.326
peak=    3.309 closest distance to " O   HOH Z  44 " =    1.715
peak=    3.308 closest distance to " CG AARG A 275 " =    1.212
peak=    3.306 closest distance to " O   HOH Z 368 " =    3.549
peak=    3.305 closest distance to " O   HOH Z 132 " =    2.623
peak=    3.299 closest distance to " CA  TYR A  30 " =    1.058
peak=    3.295 closest distance to " NZ  LYS A  48 " =    1.290
peak=    3.290 closest distance to " CA  ALA A 291 " =    0.922
peak=    3.289 closest distance to " CG  LEU A 167 " =    1.170
peak=    3.288 closest distance to " CB  PRO A 198 " =    1.094
peak=    3.287 closest distance to " CG2 THR A 221 " =    1.239
peak=    3.286 closest distance to " CB  ALA A 242 " =    0.841
peak=    3.283 closest distance to " CA  LYS A 290 " =    1.248
peak=    3.282 closest distance to " CB  LEU A 255 " =    0.764
peak=    3.282 closest distance to " OG  SER A  22 " =    2.702
peak=    3.277 closest distance to " O   HOH Z 299 " =    4.259
peak=    3.276 closest distance to " CB  SER A 212 " =    1.187
peak=    3.273 closest distance to " O   HOH Z 423 " =    2.998
peak=    3.270 closest distance to " O   HOH Z 222 " =    2.507
peak=    3.269 closest distance to " O   HOH Z 383 " =    1.859
peak=    3.268 closest distance to " O   HOH Z 227 " =    1.642
peak=    3.268 closest distance to " CB  ASN A 224 " =    1.046
peak=    3.260 closest distance to " OG1 THR A 294 " =    2.342
peak=    3.259 closest distance to " O   HOH Z 175 " =    2.102
peak=    3.258 closest distance to " CG2 VAL A 202 " =    1.105
peak=    3.256 closest distance to " CA  SER A  87 " =    1.021
peak=    3.255 closest distance to " O   HOH Z  19 " =    2.281
peak=    3.255 closest distance to " O   HOH Z 403 " =    1.356
peak=    3.253 closest distance to " CB  SER A 273 " =    0.833
peak=    3.249 closest distance to " CE  LYS A  48 " =    1.163
peak=    3.249 closest distance to " CB  LYS A 290 " =    1.032
peak=    3.249 closest distance to " CB  VAL A 268 " =    0.819
peak=    3.248 closest distance to " OG1 THR A 294 " =    1.713
peak=    3.248 closest distance to " CE1 HIS A 108 " =    1.124
peak=    3.247 closest distance to " CG2 ILE A 106 " =    0.781
peak=    3.244 closest distance to " O   HOH Z 234 " =    1.855
peak=    3.244 closest distance to " O   HOH Z 189 " =    2.681
peak=    3.242 closest distance to " CB  MET A  40 " =    0.799
peak=    3.239 closest distance to " CB  LYS A 117 " =    1.194
peak=    3.239 closest distance to " CA  ARG A 195 " =    1.167
peak=    3.238 closest distance to " O   HOH Z 298 " =    4.782
peak=    3.237 closest distance to " O   HOH Z 227 " =    2.112
peak=    3.232 closest distance to " O   HOH Z  90 " =    2.276
peak=    3.228 closest distance to " CA  SER A 146 " =    1.734
peak=    3.227 closest distance to " O   HOH Z 336 " =    1.788
peak=    3.225 closest distance to " CB  ASN A 215 " =    1.175
peak=    3.223 closest distance to " CB  ILE A 120 " =    1.268
peak=    3.222 closest distance to " O   HOH Z 180 " =    2.137
peak=    3.220 closest distance to " CB  GLN A 205 " =    1.138
peak=    3.219 closest distance to " CA  GLN A 194 " =    1.240
peak=    3.219 closest distance to " CD1 LEU A 228 " =    2.000
peak=    3.213 closest distance to " CA  ALA A 233 " =    1.307
peak=    3.211 closest distance to " O   HOH Z   1 " =    1.951
peak=    3.210 closest distance to " O   HOH Z 185 " =    1.752
peak=    3.208 closest distance to " O   HOH Z  85 " =    1.323
peak=    3.207 closest distance to " O   HOH Z 251 " =    1.636
peak=    3.201 closest distance to " CD1 ILE A  33 " =    1.636
peak=    3.201 closest distance to " O   HOH Z 302 " =    1.947
peak=    3.196 closest distance to " CD1 LEU A 261 " =    1.163
peak=    3.194 closest distance to " O   HOH Z 425 " =    1.332
peak=    3.191 closest distance to " O   HOH Z 337 " =    3.527
peak=    3.189 closest distance to " CD2 LEU A   5 " =    0.729
peak=    3.188 closest distance to " CB  TRP A 150 " =    1.422
peak=    3.185 closest distance to " O   HOH Z 123 " =    2.188
peak=    3.182 closest distance to " CA  ASN A 176 " =    1.092
peak=    3.182 closest distance to " ND1 HIS A  81 " =    1.652
peak=    3.177 closest distance to " N   SER A  12 " =    1.548
peak=    3.167 closest distance to " O   HOH Z   3 " =    1.749
peak=    3.165 closest distance to " O   HOH Z 173 " =    2.268
peak=    3.163 closest distance to " CD2 TYR A  30 " =    0.935
peak=    3.161 closest distance to " OE2 GLU A  53 " =    1.975
peak=    3.154 closest distance to " CA  MET A 105 " =    0.976
peak=    3.150 closest distance to " CG BARG A 102 " =    1.770
peak=    3.149 closest distance to " O   HOH Z 417 " =    2.479
peak=    3.143 closest distance to " N   ASP A 162 " =    1.296
peak=    3.142 closest distance to " CG  MET A 113 " =    1.082
peak=    3.139 closest distance to " O   HOH Z 359 " =    3.657
peak=    3.135 closest distance to " NZ  LYS A  76 " =    1.396
peak=    3.127 closest distance to " O   SER A 164 " =    1.153
peak=    3.126 closest distance to " O   HOH Z 282 " =    2.028
peak=    3.124 closest distance to " CB  MET A  47 " =    1.064
peak=    3.123 closest distance to " O   HOH Z 285 " =    3.035
peak=    3.122 closest distance to " O   ALA A   1 " =    1.751
peak=    3.116 closest distance to " O   HOH Z  48 " =    1.391
peak=    3.111 closest distance to " O   HOH Z 325 " =    2.200
peak=    3.110 closest distance to " O   HOH Z 367 " =    3.581
peak=    3.107 closest distance to " CA  ILE A 234 " =    0.793
peak=    3.093 closest distance to " O   HOH Z 357 " =    1.860
peak=    3.091 closest distance to " CB  ALA A 114 " =    1.247
peak=    3.088 closest distance to " CZ2 TRP A 274 " =    1.557
peak=    3.088 closest distance to " CA  ASP A 191 " =    0.965
peak=    3.087 closest distance to " CD2 LEU A 255 " =    1.559
peak=    3.081 closest distance to " O   HOH Z  43 " =    2.862
peak=    3.052 closest distance to " CZ3 TRP A  85 " =    0.891
peak=    3.041 closest distance to " ND2 ASN A 249 " =    0.870
peak=    3.041 closest distance to " O   HOH Z 353 " =    2.706
peak=    3.037 closest distance to " CB  PRO A 243 " =    1.527
peak=    3.018 closest distance to " O   HOH Z  47 " =    1.679

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 187         
Filter by distance & map next to the model:
   mapped sites are within: 0.540 - 5.431
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 184 from: 187
   mapped sites are within: 0.768 - 5.431

peak=   -5.411 closest distance to " CG2 VAL A 230 " =    0.768
peak=   -4.529 closest distance to " CD  ARG A 156 " =    2.028
peak=   -4.447 closest distance to " SG  CYS A 254 " =    3.260
peak=   -4.368 closest distance to " OG BSER A 134 " =    1.172
peak=   -4.318 closest distance to " O   HOH Z 266 " =    5.001
peak=   -4.250 closest distance to " O   HOH Z 290 " =    1.106
peak=   -4.246 closest distance to " C   HIS A 108 " =    1.191
peak=   -4.156 closest distance to " CG  GLN A 223 " =    2.036
peak=   -4.129 closest distance to " O   HOH Z 351 " =    1.478
peak=   -4.096 closest distance to " CD  GLN A  58 " =    1.099
peak=   -4.096 closest distance to " CB  PRO A 243 " =    2.634
peak=   -4.067 closest distance to " CG2 VAL A 296 " =    1.343
peak=   -4.026 closest distance to " CG  ASP A 231 " =    0.796
peak=   -3.969 closest distance to " O   HOH Z 114 " =    3.073
peak=   -3.963 closest distance to " CB  ALA A 161 " =    2.593
peak=   -3.958 closest distance to " CE2 TYR A  30 " =    2.756
peak=   -3.949 closest distance to " CB  PHE A 192 " =    1.935
peak=   -3.936 closest distance to " CG2BVAL A  41 " =    2.641
peak=   -3.928 closest distance to " O   PRO A 163 " =    2.130
peak=   -3.921 closest distance to " OG  SER A   3 " =    1.708
peak=   -3.898 closest distance to " O   HOH Z 389 " =    1.863
peak=   -3.890 closest distance to " OXT GLY A 302 " =    2.768
peak=   -3.874 closest distance to " N   GLN A  58 " =    1.711
peak=   -3.826 closest distance to " O   HOH Z 429 " =    2.021
peak=   -3.826 closest distance to " CE2 PHE A 218 " =    2.607
peak=   -3.825 closest distance to " O   HOH Z 231 " =    1.974
peak=   -3.819 closest distance to " N   ALA A 226 " =    2.042
peak=   -3.813 closest distance to " ND2 ASN A  45 " =    1.144
peak=   -3.807 closest distance to " CA  VAL A  67 " =    2.719
peak=   -3.780 closest distance to " CZ3 TRP A 179 " =    1.243
peak=   -3.779 closest distance to " N   THR A 157 " =    1.456
peak=   -3.770 closest distance to " O   HOH Z 166 " =    1.965
peak=   -3.764 closest distance to " OG  SER A  97 " =    2.246
peak=   -3.711 closest distance to " O   HOH Z 185 " =    2.344
peak=   -3.711 closest distance to " CG1 VAL A 112 " =    2.784
peak=   -3.706 closest distance to " ND2 ASN A 187 " =    1.516
peak=   -3.698 closest distance to " NE2 GLN A  88 " =    1.965
peak=   -3.693 closest distance to " O   HOH Z 435 " =    2.831
peak=   -3.684 closest distance to " CD  ARG A 139 " =    1.601
peak=   -3.683 closest distance to " CB  ALA A  43 " =    2.395
peak=   -3.681 closest distance to " NH2AARG A 275 " =    5.088
peak=   -3.681 closest distance to " O   HOH Z 196 " =    2.152
peak=   -3.666 closest distance to " CB  ALA A 291 " =    2.301
peak=   -3.636 closest distance to " CB  PRO A 163 " =    2.553
peak=   -3.634 closest distance to " O   HOH Z 103 " =    1.839
peak=   -3.618 closest distance to " CD1 LEU A 101 " =    2.406
peak=   -3.601 closest distance to " O   HOH Z  11 " =    1.852
peak=   -3.596 closest distance to " CG1 VAL A 230 " =    1.832
peak=   -3.588 closest distance to " C   MET A 188 " =    1.423
peak=   -3.588 closest distance to " CZ  PHE A  59 " =    1.490
peak=   -3.585 closest distance to " O   HOH Z 166 " =    1.538
peak=   -3.584 closest distance to " O   HOH Z 211 " =    1.674
peak=   -3.569 closest distance to " O   HOH Z 407 " =    2.993
peak=   -3.564 closest distance to " OD2 ASP A 171 " =    2.267
peak=   -3.555 closest distance to " CZ  TYR A 169 " =    1.701
peak=   -3.552 closest distance to " CG1 VAL A 296 " =    1.213
peak=   -3.552 closest distance to " CB  ASP A 132 " =    2.371
peak=   -3.539 closest distance to " CG  ARG A 269 " =    2.299
peak=   -3.538 closest distance to " O   HOH Z 102 " =    1.590
peak=   -3.533 closest distance to " CG  GLU A 277 " =    1.123
peak=   -3.528 closest distance to " CB  ASP A 132 " =    2.302
peak=   -3.524 closest distance to " NH2 ARG A  79 " =    1.930
peak=   -3.514 closest distance to " CG  PHE A 283 " =    2.813
peak=   -3.514 closest distance to " O   HOH Z  52 " =    1.504
peak=   -3.509 closest distance to " O   PRO A 198 " =    1.216
peak=   -3.504 closest distance to " CE  MET A 105 " =    2.080
peak=   -3.498 closest distance to " CA  ASP A 298 " =    1.047
peak=   -3.495 closest distance to " O   GLY A 196 " =    1.094
peak=   -3.488 closest distance to " OD1 ASN A 148 " =    1.463
peak=   -3.483 closest distance to " CD2 LEU A 300 " =    2.718
peak=   -3.482 closest distance to " O   VAL A 189 " =    2.591
peak=   -3.482 closest distance to " CG2 ILE A 263 " =    2.301
peak=   -3.477 closest distance to " N   THR A 235 " =    1.318
peak=   -3.476 closest distance to " O   HOH Z  44 " =    2.208
peak=   -3.470 closest distance to " C   ALA A 158 " =    1.275
peak=   -3.469 closest distance to " CB  PRO A 280 " =    2.067
peak=   -3.468 closest distance to " N   VAL A 230 " =    1.126
peak=   -3.467 closest distance to " O   SER A  95 " =    1.626
peak=   -3.459 closest distance to " O   MET A  40 " =    2.675
peak=   -3.458 closest distance to " CG1 VAL A 112 " =    2.652
peak=   -3.457 closest distance to " CB  ALA A 291 " =    2.143
peak=   -3.456 closest distance to " C   ASP A 231 " =    2.518
peak=   -3.444 closest distance to " O   HOH Z 394 " =    1.567
peak=   -3.439 closest distance to " CG  TRP A 266 " =    1.927
peak=   -3.435 closest distance to " O   HOH Z 262 " =    2.766
peak=   -3.435 closest distance to " NZ  LYS A 119 " =    3.480
peak=   -3.432 closest distance to " N   ALA A  43 " =    2.492
peak=   -3.431 closest distance to " O   HOH Z 369 " =    2.263
peak=   -3.431 closest distance to " CA  GLY A 241 " =    3.027
peak=   -3.427 closest distance to " O   SER A  22 " =    2.202
peak=   -3.413 closest distance to " CB  VAL A 296 " =    1.193
peak=   -3.409 closest distance to " CB  ALA A 248 " =    2.310
peak=   -3.407 closest distance to " O   HOH Z  43 " =    1.748
peak=   -3.402 closest distance to " CB  ASN A  69 " =    1.136
peak=   -3.388 closest distance to " N   HIS A 115 " =    2.053
peak=   -3.386 closest distance to " N   MET A 188 " =    1.922
peak=   -3.384 closest distance to " O   HOH Z  13 " =    1.557
peak=   -3.384 closest distance to " CG  LEU A 228 " =    1.024
peak=   -3.382 closest distance to " O   HOH Z 175 " =    4.343
peak=   -3.376 closest distance to " N   SER A 212 " =    1.994
peak=   -3.374 closest distance to " O   HOH Z 198 " =    2.164
peak=   -3.372 closest distance to " N   ALA A 248 " =    1.703
peak=   -3.360 closest distance to " CD  LYS A 289 " =    2.488
peak=   -3.357 closest distance to " CB  ASN A  39 " =    2.236
peak=   -3.355 closest distance to " O   HOH Z  60 " =    1.909
peak=   -3.353 closest distance to " O   HOH Z 423 " =    2.111
peak=   -3.353 closest distance to " C   LEU A 143 " =    1.026
peak=   -3.345 closest distance to " CB  GLN A  11 " =    1.806
peak=   -3.344 closest distance to " O   HOH Z 417 " =    2.758
peak=   -3.331 closest distance to " O   HOH Z 372 " =    2.277
peak=   -3.327 closest distance to " O   ALA A 161 " =    1.655
peak=   -3.326 closest distance to " O   HOH Z  47 " =    1.595
peak=   -3.321 closest distance to " CA  GLY A 133 " =    1.989
peak=   -3.319 closest distance to " O   HOH Z 339 " =    1.795
peak=   -3.318 closest distance to " CD1 ILE A 199 " =    2.487
peak=   -3.307 closest distance to " OG ASER A 134 " =    1.185
peak=   -3.304 closest distance to " CG1 VAL A 250 " =    2.713
peak=   -3.302 closest distance to " CG1 VAL A 197 " =    2.232
peak=   -3.296 closest distance to " O   HOH Z 165 " =    1.897
peak=   -3.290 closest distance to " NE2 GLN A 278 " =    1.955
peak=   -3.284 closest distance to " CD1 PHE A  59 " =    1.912
peak=   -3.283 closest distance to " O   HOH Z 295 " =    1.594
peak=   -3.280 closest distance to " CD1 LEU A 228 " =    2.127
peak=   -3.273 closest distance to " OG  SER A 206 " =    1.648
peak=   -3.271 closest distance to " CE BMET A  47 " =    1.675
peak=   -3.265 closest distance to " N   SER A 276 " =    1.294
peak=   -3.265 closest distance to " O   HOH Z 313 " =    1.615
peak=   -3.259 closest distance to " O   HOH Z 123 " =    2.385
peak=   -3.258 closest distance to " OG BSER A 134 " =    1.701
peak=   -3.258 closest distance to " CG  ASP A  50 " =    2.415
peak=   -3.257 closest distance to " CA  GLY A 203 " =    2.359
peak=   -3.255 closest distance to " OXT GLY A 302 " =    3.521
peak=   -3.252 closest distance to " CD1 LEU A 101 " =    2.814
peak=   -3.248 closest distance to " OG  SER A  62 " =    1.597
peak=   -3.246 closest distance to " CE3 TRP A 150 " =    2.022
peak=   -3.239 closest distance to " O   PRO A 198 " =    1.284
peak=   -3.238 closest distance to " CG  ARG A  66 " =    2.461
peak=   -3.234 closest distance to " O   HOH Z 139 " =    3.173
peak=   -3.224 closest distance to " O   HOH Z 385 " =    2.155
peak=   -3.224 closest distance to " CG2 THR A 221 " =    2.057
peak=   -3.221 closest distance to " O   LYS A 117 " =    1.633
peak=   -3.216 closest distance to " CA  GLY A  98 " =    1.892
peak=   -3.214 closest distance to " CD2 TYR A 293 " =    2.098
peak=   -3.211 closest distance to " O   HOH Z 309 " =    2.497
peak=   -3.204 closest distance to " O   GLY A  75 " =    1.931
peak=   -3.199 closest distance to " N   GLN A  77 " =    1.501
peak=   -3.198 closest distance to " O   HOH Z 191 " =    5.431
peak=   -3.194 closest distance to " N   ASP A 171 " =    2.289
peak=   -3.192 closest distance to " O   HOH Z 222 " =    1.497
peak=   -3.191 closest distance to " CD  PRO A 243 " =    2.125
peak=   -3.189 closest distance to " O   HOH Z 417 " =    2.689
peak=   -3.188 closest distance to " O   HOH Z 426 " =    1.665
peak=   -3.187 closest distance to " C   SER A 206 " =    1.592
peak=   -3.183 closest distance to " ND2 ASN A 252 " =    1.820
peak=   -3.181 closest distance to " O   HOH Z 384 " =    3.291
peak=   -3.176 closest distance to " NE2 GLN A  88 " =    1.031
peak=   -3.176 closest distance to " O   HOH Z 210 " =    1.119
peak=   -3.164 closest distance to " O   ALA A  10 " =    1.762
peak=   -3.161 closest distance to " OG1 THR A 246 " =    1.431
peak=   -3.158 closest distance to " O   ALA A  51 " =    1.356
peak=   -3.153 closest distance to " O   GLY A  80 " =    2.494
peak=   -3.151 closest distance to " O   ILE A 106 " =    1.952
peak=   -3.142 closest distance to " O   HOH Z 389 " =    4.788
peak=   -3.142 closest distance to " NH2 ARG A  79 " =    1.541
peak=   -3.142 closest distance to " CD1 ILE A 239 " =    2.263
peak=   -3.141 closest distance to " CG1 VAL A 296 " =    1.294
peak=   -3.138 closest distance to " O   HOH Z  10 " =    1.437
peak=   -3.133 closest distance to " O   HOH Z 244 " =    2.067
peak=   -3.125 closest distance to " O   HOH Z 281 " =    2.784
peak=   -3.122 closest distance to " CB  TYR A  15 " =    2.201
peak=   -3.116 closest distance to " O   HOH Z 234 " =    4.000
peak=   -3.115 closest distance to " O   HOH Z 313 " =    1.081
peak=   -3.107 closest distance to " O   HOH Z 311 " =    3.700
peak=   -3.105 closest distance to " O   LEU A 167 " =    1.477
peak=   -3.094 closest distance to " O   HOH Z   6 " =    1.666
peak=   -3.088 closest distance to " C   LEU A 222 " =    0.817
peak=   -3.077 closest distance to " NH2 ARG A  66 " =    1.889
peak=   -3.072 closest distance to " O   VAL A 125 " =    2.321
peak=   -3.066 closest distance to " O   HOH Z 371 " =    1.946
peak=   -3.065 closest distance to " CB  ASP A 132 " =    2.240
peak=   -3.063 closest distance to " CG  PRO A 163 " =    2.626
peak=   -3.061 closest distance to " N   LYS A 289 " =    1.551
peak=   -3.059 closest distance to " O   HOH Z 298 " =    2.529
peak=   -3.018 closest distance to " O   TRP A  70 " =    1.459

================= 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    :  0.4082 0.3984   6.192092e+00   6.165127e+00
   1_bss:  0.4003 0.3904   6.186645e+00   6.148409e+00
   1_xyz:  0.2854 0.3062   5.925848e+00   5.977274e+00
   1_adp:  0.2074 0.2340   5.628178e+00   5.751061e+00
   1_occ:  0.2069 0.2336   5.626374e+00   5.750667e+00
   2_bss:  0.2011 0.2280   5.624146e+00   5.743858e+00
   2_xyz:  0.1380 0.1720   5.288195e+00   5.471125e+00
   2_adp:  0.1273 0.1633   5.219455e+00   5.418308e+00
   2_occ:  0.1272 0.1631   5.218933e+00   5.417615e+00
   3_bss:  0.1270 0.1630   5.219558e+00   5.417655e+00
   3_xyz:  0.1191 0.1557   5.168856e+00   5.382920e+00
   3_adp:  0.1167 0.1540   5.154095e+00   5.372768e+00
   3_occ:  0.1167 0.1540   5.154053e+00   5.372867e+00
   4_bss:  0.1167 0.1540   5.154053e+00   5.372867e+00
   4_xyz:  0.1102 0.1525   5.119636e+00   5.361200e+00
   4_adp:  0.1100 0.1532   5.121023e+00   5.364920e+00
   4_occ:  0.1098 0.1532   5.120310e+00   5.364639e+00
   5_bss:  0.1098 0.1531   5.120071e+00   5.364411e+00
   5_xyz:  0.1111 0.1542   5.130899e+00   5.373298e+00
   5_adp:  0.1102 0.1546   5.129921e+00   5.377932e+00
   5_occ:  0.1102 0.1546   5.130038e+00   5.378154e+00
   5_bss:  0.1101 0.1546   5.129595e+00   5.377665e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.354  20.000   7.343   8.245   8.158   0.000   0.000   0.000
   1_xyz:  0.354  20.000   7.343   8.245   8.158   0.000   0.000   0.000
   1_adp:  0.354  20.000   7.343   8.245   8.158   0.000   0.000   0.000
   1_occ:  0.354  20.000   7.343   8.245   8.158   0.000   0.000   0.000
   2_bss:  0.337  35.752   4.136   4.588   5.446   0.000   0.000   0.000
   2_xyz:  0.337  35.752   4.136   4.588   5.446   0.000   0.000   0.000
   2_adp:  0.337  35.752   4.136   4.588   5.446   0.000   0.000   0.000
   2_occ:  0.337  35.752   4.136   4.588   5.446   0.000   0.000   0.000
   3_bss:  0.324  35.752   3.301   3.817   4.673   0.000   0.000   0.000
   3_xyz:  0.324  35.752   3.301   3.817   4.673   0.000   0.000   0.000
   3_adp:  0.324  35.752   3.301   3.817   4.673   0.000   0.000   0.000
   3_occ:  0.324  35.752   3.301   3.817   4.673   0.000   0.000   0.000
   4_bss:  0.324  35.752   3.301   3.817   4.673   0.000   0.000   0.000
   4_xyz:  0.324  35.752   3.301   3.817   4.673   0.000   0.000   0.000
   4_adp:  0.324  35.752   3.301   3.817   4.673   0.000   0.000   0.000
   4_occ:  0.324  35.752   3.301   3.817   4.673   0.000   0.000   0.000
   5_bss:  0.320  35.752   3.239   3.723   4.617   0.000   0.000   0.000
   5_xyz:  0.320  35.752   3.239   3.723   4.617   0.000   0.000   0.000
   5_adp:  0.320  35.752   3.239   3.723   4.617   0.000   0.000   0.000
   5_occ:  0.320  35.752   3.239   3.723   4.617   0.000   0.000   0.000
   5_bss:  0.324  44.078  -0.619  -0.141   0.760  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  42.468 0.6158  0.6780    44427.387
   1_bss:  42.787 0.6093  0.8530    42207.797
   1_xyz:  32.169 0.7328  0.9958    24974.820
   1_adp:  22.502 0.8381  1.0806    13708.975
   1_occ:  22.465 0.8384  1.0805    13658.460
   2_bss:  22.251 0.8404  0.9626    13398.125
   2_xyz:  15.667 0.9010  1.0025     7412.548
   2_adp:  14.525 0.9108  1.0101     6746.049
   2_occ:  14.515 0.9109  1.0099     6732.282
   3_bss:  14.543 0.9107  0.9799     6758.101
   3_xyz:  13.735 0.9174  0.9821     6243.633
   3_adp:  13.519 0.9192  0.9838     6118.930
   3_occ:  13.521 0.9192  0.9837     6119.870
   4_bss:  13.521 0.9192  0.9837     6119.870
   4_xyz:  13.271 0.9210  0.9839     5970.623
   4_adp:  13.350 0.9205  0.9821     6007.625
   4_occ:  13.344 0.9206  0.9819     6006.392
   5_bss:  13.339 0.9206  0.9794     6001.037
   5_xyz:  13.487 0.9195  0.9786     6114.436
   5_adp:  13.599 0.9186  0.9762     6155.777
   5_occ:  13.603 0.9186  0.9761     6158.777
   5_bss:  13.592 0.9187  0.9781     6155.153
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.3571e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.3571e+01
   1_xyz:   1.416  0.010  0.098 17.697  0.006  4.120   1.0513e-01
   1_adp:   1.416  0.010  0.098 17.697  0.006  4.120   1.0513e-01
   1_occ:   1.416  0.010  0.098 17.697  0.006  4.120   1.0513e-01
   2_bss:   1.416  0.010  0.098 17.697  0.006  4.120   1.0513e-01
   2_xyz:   0.994  0.007  0.078 15.848  0.003  4.122   6.1144e-02
   2_adp:   0.994  0.007  0.078 15.848  0.003  4.122   6.1144e-02
   2_occ:   0.994  0.007  0.078 15.848  0.003  4.122   6.1144e-02
   3_bss:   0.994  0.007  0.078 15.848  0.003  4.122   6.1144e-02
   3_xyz:   0.913  0.005  0.074 15.471  0.003  4.116   5.3126e-02
   3_adp:   0.913  0.005  0.074 15.471  0.003  4.116   5.3126e-02
   3_occ:   0.913  0.005  0.074 15.471  0.003  4.116   5.3126e-02
   4_bss:   0.913  0.005  0.074 15.471  0.003  4.116   5.3126e-02
   4_xyz:   1.048  0.008  0.087 15.649  0.004  4.121   6.6257e-02
   4_adp:   1.048  0.008  0.087 15.649  0.004  4.121   6.6257e-02
   4_occ:   1.048  0.008  0.087 15.649  0.004  4.121   6.6257e-02
   5_bss:   1.048  0.008  0.087 15.649  0.004  4.121   6.6257e-02
   5_xyz:   0.957  0.006  0.079 15.366  0.004  4.120   5.7294e-02
   5_adp:   0.957  0.006  0.079 15.366  0.004  4.120   5.7294e-02
   5_occ:   0.957  0.006  0.079 15.366  0.004  4.120   5.7294e-02
   5_bss:   0.957  0.006  0.079 15.366  0.004  4.120   5.7294e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9457e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9457e+00
   1_xyz:  11.346  0.121  0.424 87.726  0.039  2.274   7.6729e-02
   1_adp:  11.346  0.121  0.424 87.726  0.039  2.274   7.6729e-02
   1_occ:  11.346  0.121  0.424 87.726  0.039  2.274   7.6729e-02
   2_bss:  11.346  0.121  0.424 87.726  0.039  2.274   7.6729e-02
   2_xyz:   6.588  0.043  0.502 83.639  0.032  2.277   4.6220e-02
   2_adp:   6.588  0.043  0.502 83.639  0.032  2.277   4.6220e-02
   2_occ:   6.588  0.043  0.502 83.639  0.032  2.277   4.6220e-02
   3_bss:   6.588  0.043  0.502 83.639  0.032  2.277   4.6220e-02
   3_xyz:   6.215  0.040  0.489 83.028  0.034  2.390   3.5464e-02
   3_adp:   6.215  0.040  0.489 83.028  0.034  2.390   3.5464e-02
   3_occ:   6.215  0.040  0.489 83.028  0.034  2.390   3.5464e-02
   4_bss:   6.215  0.040  0.489 83.028  0.034  2.390   3.5464e-02
   4_xyz:   6.853  0.045  0.653 83.206  0.038  2.292   4.9268e-02
   4_adp:   6.853  0.045  0.653 83.206  0.038  2.292   4.9268e-02
   4_occ:   6.853  0.045  0.653 83.206  0.038  2.292   4.9268e-02
   5_bss:   6.853  0.045  0.653 83.206  0.038  2.292   4.9268e-02
   5_xyz:   6.399  0.044  0.534 83.091  0.035  2.360   3.7453e-02
   5_adp:   6.399  0.044  0.534 83.091  0.035  2.360   3.7453e-02
   5_occ:   6.399  0.044  0.534 83.091  0.035  2.360   3.7453e-02
   5_bss:   6.399  0.044  0.534 83.091  0.035  2.360   3.7453e-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:  50.58   0.00   9.83  48.33   0.00   6.67  50.58   0.00  27.03
   1_occ:  50.58   0.00   9.83  48.33   0.00   6.67  50.58   0.00  27.03
   2_bss:  50.58   0.00   9.83  48.33   0.00   6.67  50.58   0.00  27.03
   2_xyz:  50.58   0.00   9.83  48.33   0.00   6.67  50.58   0.00  27.03
   2_adp:  74.97   0.00  10.28  74.97   0.00   6.72  51.48   1.01  29.69
   2_occ:  74.97   0.00  10.28  74.97   0.00   6.72  51.48   1.01  29.69
   3_bss:  74.97   0.00  10.28  74.97   0.00   6.72  51.48   1.01  29.69
   3_xyz:  74.97   0.00  10.28  74.97   0.00   6.72  51.48   1.01  29.69
   3_adp:  63.33   0.00  10.62  63.33   0.00   6.82  58.44   0.72  31.32
   3_occ:  63.33   0.00  10.62  63.33   0.00   6.82  58.44   0.72  31.32
   4_bss:  63.33   0.00  10.62  63.33   0.00   6.82  58.44   0.72  31.32
   4_xyz:  63.33   0.00  10.62  63.33   0.00   6.82  58.44   0.72  31.32
   4_adp:  69.47   0.00  10.59  69.47   0.00   6.82  60.82   0.75  31.15
   4_occ:  69.47   0.00  10.59  69.47   0.00   6.82  60.82   0.75  31.15
   5_bss:  69.47   0.00  10.59  69.47   0.00   6.82  60.82   0.75  31.15
   5_xyz:  69.47   0.00  10.59  69.47   0.00   6.82  60.82   0.75  31.15
   5_adp:  72.96   0.00  10.76  72.96   0.00   6.86  62.63   0.55  32.00
   5_occ:  72.96   0.00  10.76  72.96   0.00   6.86  62.63   0.55  32.00
   5_bss:  76.86   3.91  14.67  76.86   3.91  10.76  66.54   4.46  35.91
------------------------------------------------------------------------
 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:    1.147    0.014    0.395
   1_adp:    1.147    0.014    0.395
   1_occ:    1.147    0.014    0.395
   2_bss:    1.147    0.014    0.395
   2_xyz:    1.328    0.051    0.473
   2_adp:    1.328    0.051    0.473
   2_occ:    1.328    0.051    0.473
   3_bss:    1.328    0.051    0.473
   3_xyz:    1.384    0.056    0.482
   3_adp:    1.384    0.056    0.482
   3_occ:    1.384    0.056    0.482
   4_bss:    1.384    0.056    0.482
   4_xyz:    1.376    0.050    0.495
   4_adp:    1.376    0.050    0.495
   4_occ:    1.376    0.050    0.495
   5_bss:    1.376    0.050    0.495
   5_xyz:    1.431    0.047    0.499
   5_adp:    1.431    0.047    0.499
   5_occ:    1.431    0.047    0.499
   5_bss:    1.431    0.047    0.499
------------------------------------------------------------------------

CPU time actual refinement: 325.83


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_543/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_543/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_543/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_543/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_543/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 325.68 
  Macro-tasks:
    bulk solvent and scale       = 39.90  
    individual site refinement   = 139.43 
    weights calculation          = 32.52  
    collect and process          = 6.58   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 218.54 
  Micro-tasks:
    mask                            = 1.14   
    f_calc                          = 98.24  
    alpha_beta                      = 8.35   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 111.01 
    fmodel                         = 7.02   
    r_factors                      = 0.23   
    phase_errors                   = 11.10  
    foms                           = 0.21   
    TOTAL for micro-tasks          = 238.47 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.496 micro seconds
Total CPU time: 5.65 minutes
from_scatterers_fft:    659 calls, 97.86 s
gradients_fft:          603 calls, 96.80 s

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

# Date 2008-01-16 Time 01:50:40 PST -0800 (1200477040.48 s)
Start R-work = 0.4082, R-free = 0.3984 (no bulk solvent and anisotropic scale)
Final R-work = 0.1280, R-free = 0.1708 (no bulk solvent and anisotropic scale)

Start R-work = 0.4003, R-free = 0.3904
Final R-work = 0.1101, R-free = 0.1546