# Date 2008-01-16 Time 01:44:55 PST -0800 (1200476695.24 s)
#phil __OFF__

Command line arguments: "../542.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 7277
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 542

-------------------------------------------------------------------------------
  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, 85.5261, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 46.93, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8986 1.98108
Completeness in resolution range: 0.972738
Completeness with d_max=infinity: 0.969656

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8986
                             d_min =   1.9811

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, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8986 1.98108
Completeness in resolution range: 0.972738
Completeness with d_max=infinity: 0.969656

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8990 -  4.2384 [2113/2140]  1902   211  10.0%
  bin  2:  4.2384 -  3.3770 [2029/2045]  1826   203  10.0%
  bin  3:  3.3770 -  2.9539 [2005/2024]  1802   203  10.1%
  bin  4:  2.9539 -  2.6856 [1991/2021]  1796   195   9.8%
  bin  5:  2.6856 -  2.4940 [1962/1981]  1763   199  10.1%
  bin  6:  2.4940 -  2.3476 [1961/1986]  1767   194   9.9%
  bin  7:  2.3476 -  2.2304 [1965/1998]  1769   196  10.0%
  bin  8:  2.2304 -  2.1336 [1936/1967]  1741   195  10.1%
  bin  9:  2.1336 -  2.0517 [1944/1986]  1749   195  10.0%
  bin 10:  2.0517 -  1.9811 [1683/1990]  1515   168  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_542/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 18
        2.42 -     3.04: 2214
        3.04 -     3.66: 4718
        3.66 -     4.28: 9105
        4.28 -     4.90: 12426
  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 "  2.059 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  2.147 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  2.199 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  ... (remaining 28476 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_542/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_542/model_refine_001.geo

CPU time processing inputs: 9.01


============================ 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 85.5261 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4189   r_free= 0.4112   ksol= 0.00   Bsol= 0.00   scale= 0.835    |
|                                                                             |
| 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:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.207525                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8990 -  4.7270 0.99   1375  153 0.3552 0.3385      6.4973      6.4679|
|  2:  4.7270 -  3.7720 0.99   1319  145 0.3190 0.3166      6.6079       6.609|
|  3:  3.7720 -  3.3011 0.99   1302  145 0.3520 0.3493       6.519      6.5655|
|  4:  3.3011 -  3.0020 0.99   1284  145 0.3906 0.3813      6.4213      6.3461|
|  5:  3.0020 -  2.7883 0.99   1272  139 0.4236 0.4530      6.2922      6.3162|
|  6:  2.7883 -  2.6249 0.99   1278  143 0.4400 0.5032      6.2183      6.2391|
|  7:  2.6249 -  2.4940 0.99   1259  141 0.4640 0.4304      6.2003      6.1005|
|  8:  2.4940 -  2.3859 0.98   1266  140 0.4646 0.4492      6.1409       6.139|
|  9:  2.3859 -  2.2944 0.98   1270  138 0.4760 0.4577      6.0791      6.0685|
| 10:  2.2944 -  2.2155 0.98   1233  137 0.4735 0.4660      6.1008       6.034|
| 11:  2.2155 -  2.1464 0.99   1269  147 0.4792 0.4186      6.0241      5.9827|
| 12:  2.1464 -  2.0853 0.97   1250  130 0.4844 0.4557      5.9624      5.9818|
| 13:  2.0853 -  2.0305 0.99   1234  141 0.4864 0.5225      5.8729      5.8801|
| 14:  2.0305 -  1.9811 0.79   1019  115 0.4978 0.4693      5.8271      5.7376|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8990 -  4.7270  1375   153  0.73  31.52   0.82     0.75      59730.56|
|  2:  4.7270 -  3.7720  1319   145  0.78  27.94   0.92     0.83      70616.96|
|  3:  3.7720 -  3.3011  1302   145  0.72  33.51   0.89     0.81      72183.04|
|  4:  3.3011 -  3.0020  1284   145  0.66  38.78   0.85     0.73      65276.64|
|  5:  3.0020 -  2.7883  1272   139  0.57  46.36   0.79     0.64      59877.30|
|  6:  2.7883 -  2.6249  1278   143  0.54  48.90   0.78     0.61      54528.97|
|  7:  2.6249 -  2.4940  1259   141  0.53  49.77   0.76     0.60      50249.81|
|  8:  2.4940 -  2.3859  1266   140  0.54  49.37   0.78     0.61      44433.85|
|  9:  2.3859 -  2.2944  1270   138  0.55  48.34   0.76     0.62      38055.90|
| 10:  2.2944 -  2.2155  1233   137  0.57  46.33   0.79     0.64      32983.08|
| 11:  2.2155 -  2.1464  1269   147  0.55  47.95   0.79     0.64      31229.08|
| 12:  2.1464 -  2.0853  1250   130  0.50  52.18   0.78     0.59      32513.20|
| 13:  2.0853 -  2.0305  1234   141  0.45  56.18   0.79     0.53      30603.58|
| 14:  2.0305 -  1.9811  1019   115  0.45  56.45   0.75     0.49      25535.19|
|alpha:            min =        0.49 max =            0.83 mean =         0.65|
|beta:             min =    25535.19 max =        72183.04 mean =     48298.13|
|figures of merit: min =        0.00 max =            1.00 mean =         0.59|
|phase err.(work): min =        0.00 max =           89.96 mean =        44.91|
|phase err.(test): min =        0.00 max =           89.91 mean =        45.00|
|-----------------------------------------------------------------------------|

============================== 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 = 6.948995              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 73.788   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.551759              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.426   (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:        3 |
| 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:      164 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      692 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1530 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2651 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3948 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5108 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6607 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7771 |
|-----------------------------------------------------------------------------|
|-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 |       53.459 |
| 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 |       1.749 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.736)------------------------------------------|
|    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 = 11.736)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4286   r_free= 0.4199   ksol= 0.00   Bsol= 0.00   scale= 0.802    |
|                                                                             |
| 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:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.215057                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4108   r_free= 0.4027   ksol= 0.36   Bsol= 20.00   scale= 1.030   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.25,8.15,8.47,0.00,0.00,0.00); trace/3= 7.96                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.202308                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.380006              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 75.653   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.564022              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.094   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4108      final r-factor (work) = 0.3000          |
| start r-factor (free) = 0.4027      final r-factor (free) = 0.3234          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 73.3173 = 6.38 * 0.50 * 6.2253 + 1.00 * 53.4586                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.3646 = 6.38 * 0.50 * 6.0354 + 1.00 * 0.1116                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3000      final r-factor (work) = 0.2287          |
| start r-factor (free) = 0.3234      final r-factor (free) = 0.2631          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4188 = 0.56 * 1.00 * 6.0354 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2941 = 0.56 * 1.00 * 5.8212 + 1.00 * 0.0108                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.736)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    61.58   10.37    None  None   None       |
|    all(noH): 2823   0      0.00    61.58   10.37    None  None   None       |
|    Sol.    : 438    0      0.00    57.69   27.97    None  None   None       |
|    Mac.    : 2385   0      0.00    61.58   7.14     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 -   6.158: 1392   |   5:    30.788 -  36.946:  106        |
|      1:     6.158 -  12.315:  709   |   6:    36.946 -  43.103:   77        |
|      2:    12.315 -  18.473:  228   |   7:    43.103 -  49.261:   41        |
|      3:    18.473 -  24.630:  124   |   8:    49.261 -  55.418:   10        |
|      4:    24.630 -  30.788:  129   |   9:    55.418 -  61.576:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2287 r_free = 0.2631             target_work(ml) = 5.725         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2282 r_free = 0.2629             target_work(ml) = 5.724         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2282   r_free= 0.2629   ksol= 0.36   Bsol= 20.00   scale= 1.091   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.25,8.15,8.47,0.00,0.00,0.00); trace/3= 7.96                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.723834                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2228   r_free= 0.2559   ksol= 0.34   Bsol= 32.12   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.01,4.47,5.63,0.00,0.00,0.00); trace/3= 4.70                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.722445                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.571723              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 93.443   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.271914              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 117.764  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2228      final r-factor (work) = 0.1527          |
| start r-factor (free) = 0.2559      final r-factor (free) = 0.1894          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6125 = 2.57 * 0.50 * 5.8339 + 1.00 * 0.1109                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1885 = 2.57 * 0.50 * 5.5461 + 1.00 * 0.0569                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1527      final r-factor (work) = 0.1403          |
| start r-factor (free) = 0.1894      final r-factor (free) = 0.1775          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5187 = 0.27 * 1.00 * 5.5461 + 1.00 * 0.0107                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4618 = 0.27 * 1.00 * 5.3395 + 1.00 * 0.0099                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.736)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    65.82   10.91    None  None   None       |
|    all(noH): 2823   0      0.00    65.82   10.91    None  None   None       |
|    Sol.    : 438    0      1.36    58.62   31.34    None  None   None       |
|    Mac.    : 2385   0      0.00    65.82   7.15     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 -   6.582: 1519   |   5:    32.911 -  39.493:  120        |
|      1:     6.582 -  13.164:  633   |   6:    39.493 -  46.075:   91        |
|      2:    13.164 -  19.746:  194   |   7:    46.075 -  52.657:   45        |
|      3:    19.746 -  26.328:  100   |   8:    52.657 -  59.239:   11        |
|      4:    26.328 -  32.911:  106   |   9:    59.239 -  65.821:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1403 r_free = 0.1775             target_work(ml) = 5.310         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1402 r_free = 0.1772             target_work(ml) = 5.309         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1402   r_free= 0.1772   ksol= 0.34   Bsol= 32.12   scale= 1.031   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.01,4.47,5.63,0.00,0.00,0.00); trace/3= 4.70                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.309261                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1398   r_free= 0.1772   ksol= 0.33   Bsol= 37.10   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.01,3.55,4.40,0.00,0.00,0.00); trace/3= 3.66                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.309790                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.655751              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 112.224  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.585853              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.793  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1398      final r-factor (work) = 0.1177          |
| start r-factor (free) = 0.1772      final r-factor (free) = 0.1565          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1596 = 2.66 * 0.50 * 5.3489 + 1.00 * 0.0569                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0079 = 2.66 * 0.50 * 5.2296 + 1.00 * 0.0636                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1177      final r-factor (work) = 0.1134          |
| start r-factor (free) = 0.1565      final r-factor (free) = 0.1548          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0736 = 0.59 * 1.00 * 5.2296 + 1.00 * 0.0098                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0264 = 0.59 * 1.00 * 5.1459 + 1.00 * 0.0117                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.736)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    74.75   11.30    None  None   None       |
|    all(noH): 2823   0      0.00    74.75   11.30    None  None   None       |
|    Sol.    : 438    0      0.86    66.79   33.42    None  None   None       |
|    Mac.    : 2385   0      0.00    74.75   7.23     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 -   7.475: 1664   |   5:    37.377 -  44.852:  103        |
|      1:     7.475 -  14.951:  564   |   6:    44.852 -  52.328:   75        |
|      2:    14.951 -  22.426:  150   |   7:    52.328 -  59.803:   40        |
|      3:    22.426 -  29.902:  109   |   8:    59.803 -  67.279:   10        |
|      4:    29.902 -  37.377:  104   |   9:    67.279 -  74.754:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1134 r_free = 0.1548             target_work(ml) = 5.142         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1133 r_free = 0.1547             target_work(ml) = 5.141         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1133   r_free= 0.1547   ksol= 0.33   Bsol= 37.10   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.01,3.55,4.40,0.00,0.00,0.00); trace/3= 3.66                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.141450                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1133   r_free= 0.1547   ksol= 0.33   Bsol= 37.10   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.01,3.55,4.40,0.00,0.00,0.00); trace/3= 3.66                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.141450                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.508984              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 125.476  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.214850              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.923  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1133      final r-factor (work) = 0.1126          |
| start r-factor (free) = 0.1547      final r-factor (free) = 0.1552          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.9461 = 1.51 * 0.50 * 5.1458 + 1.00 * 0.0636                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.9318 = 1.51 * 0.50 * 5.1412 + 1.00 * 0.0528                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1126      final r-factor (work) = 0.1131          |
| start r-factor (free) = 0.1552      final r-factor (free) = 0.1547          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1162 = 0.21 * 1.00 * 5.1412 + 1.00 * 0.0116                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1176 = 0.21 * 1.00 * 5.1454 + 1.00 * 0.0121                               |
|-----------------------------------------------------------------------------|
| number of iterations = 9       |    number of function evaluations = 11     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.736)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    74.87   11.20    None  None   None       |
|    all(noH): 2823   0      0.00    74.87   11.20    None  None   None       |
|    Sol.    : 438    0      1.06    65.83   32.94    None  None   None       |
|    Mac.    : 2385   0      0.00    74.87   7.21     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.487: 1674   |   5:    37.433 -  44.920:   96        |
|      1:     7.487 -  14.973:  567   |   6:    44.920 -  52.406:   73        |
|      2:    14.973 -  22.460:  147   |   7:    52.406 -  59.893:   35        |
|      3:    22.460 -  29.946:  109   |   8:    59.893 -  67.379:   10        |
|      4:    29.946 -  37.433:  108   |   9:    67.379 -  74.866:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1131 r_free = 0.1547             target_work(ml) = 5.142         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1131 r_free = 0.1548             target_work(ml) = 5.142         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1131   r_free= 0.1548   ksol= 0.33   Bsol= 37.10   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.01,3.55,4.40,0.00,0.00,0.00); trace/3= 3.66                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.141874                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1134   r_free= 0.1549   ksol= 0.32   Bsol= 39.31   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.90,3.41,4.18,0.00,0.00,0.00); trace/3= 3.49                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.143290                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.724030              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 157.345  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.971199              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 95.827   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1134      final r-factor (work) = 0.1079          |
| start r-factor (free) = 0.1549      final r-factor (free) = 0.1528          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0608 = 2.72 * 0.50 * 5.1453 + 1.00 * 0.0528                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0439 = 2.72 * 0.50 * 5.1210 + 1.00 * 0.0690                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1079      final r-factor (work) = 0.1072          |
| start r-factor (free) = 0.1528      final r-factor (free) = 0.1547          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.1071 = 1.97 * 1.00 * 5.1210 + 1.00 * 0.0125                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.0934 = 1.97 * 1.00 * 5.1081 + 1.00 * 0.0244                              |
|-----------------------------------------------------------------------------|
| number of iterations = 9       |    number of function evaluations = 11     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.736)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    75.87   11.21    None  None   None       |
|    all(noH): 2823   0      0.00    75.87   11.21    None  None   None       |
|    Sol.    : 438    0      0.74    66.89   33.21    None  None   None       |
|    Mac.    : 2385   0      0.00    75.87   7.17     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 -   7.587: 1672   |   5:    37.933 -  45.520:   99        |
|      1:     7.587 -  15.173:  558   |   6:    45.520 -  53.106:   68        |
|      2:    15.173 -  22.760:  153   |   7:    53.106 -  60.693:   33        |
|      3:    22.760 -  30.346:  114   |   8:    60.693 -  68.279:   10        |
|      4:    30.346 -  37.933:  112   |   9:    68.279 -  75.866:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1072 r_free = 0.1547             target_work(ml) = 5.118         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1070 r_free = 0.1548             target_work(ml) = 5.117         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1070   r_free= 0.1548   ksol= 0.32   Bsol= 39.31   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.90,3.41,4.18,0.00,0.00,0.00); trace/3= 3.49                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.117044                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8990 -  4.7270 0.99   1375  153 0.0981 0.1280      5.3776      5.5198|
|  2:  4.7270 -  3.7720 0.99   1319  145 0.0850 0.1111      5.4281      5.6221|
|  3:  3.7720 -  3.3011 0.99   1302  145 0.1010 0.1495      5.4462      5.8408|
|  4:  3.3011 -  3.0020 0.99   1284  145 0.1160 0.1492      5.4256      5.5725|
|  5:  3.0020 -  2.7883 0.99   1272  139 0.1220 0.1696      5.2835       5.518|
|  6:  2.7883 -  2.6249 0.99   1278  143 0.1133 0.1715      5.1756      5.4019|
|  7:  2.6249 -  2.4940 0.99   1259  141 0.1191 0.1677       5.135      5.3965|
|  8:  2.4940 -  2.3859 0.98   1266  140 0.1117 0.1761      5.0555       5.365|
|  9:  2.3859 -  2.2944 0.98   1270  138 0.1143 0.1718      5.0205      5.2638|
| 10:  2.2944 -  2.2155 0.98   1233  137 0.1027 0.1726      4.9419      5.2164|
| 11:  2.2155 -  2.1464 0.99   1269  147 0.1088 0.1655      4.9154      5.2502|
| 12:  2.1464 -  2.0853 0.97   1250  130 0.1063 0.1658      4.8538      5.1866|
| 13:  2.0853 -  2.0305 0.99   1234  141 0.1084 0.1625       4.774      5.0278|
| 14:  2.0305 -  1.9811 0.79   1019  115 0.1012 0.1806      4.6481      4.9426|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8990 -  4.7270  1375   153  0.94   9.05   0.98     0.96       7180.89|
|  2:  4.7270 -  3.7720  1319   145  0.95   7.85   1.02     1.01       8944.87|
|  3:  3.7720 -  3.3011  1302   145  0.94  10.83   1.03     1.02       9951.49|
|  4:  3.3011 -  3.0020  1284   145  0.92  13.04   1.01     1.00       9895.31|
|  5:  3.0020 -  2.7883  1272   139  0.91  15.10   0.99     0.96       7742.47|
|  6:  2.7883 -  2.6249  1278   143  0.91  15.26   0.98     0.95       6698.65|
|  7:  2.6249 -  2.4940  1259   141  0.91  15.24   0.99     0.96       5973.12|
|  8:  2.4940 -  2.3859  1266   140  0.91  14.67   0.99     0.97       5245.96|
|  9:  2.3859 -  2.2944  1270   138  0.91  15.47   1.00     0.98       4989.00|
| 10:  2.2944 -  2.2155  1233   137  0.91  15.07   1.00     0.96       4360.85|
| 11:  2.2155 -  2.1464  1269   147  0.90  16.03   1.00     0.96       4266.85|
| 12:  2.1464 -  2.0853  1250   130  0.92  14.81   1.01     0.99       3807.60|
| 13:  2.0853 -  2.0305  1234   141  0.91  15.40   1.01     1.00       3276.18|
| 14:  2.0305 -  1.9811  1019   115  0.92  14.35   0.99     0.95       2480.43|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2480.43 max =         9951.49 mean =      6146.50|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.71 mean =        13.66|
|phase err.(test): min =        0.00 max =           89.62 mean =        13.25|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1069   r_free= 0.1548   ksol= 0.32   Bsol= 42.95   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.57,-0.09,0.67,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.117084                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1069   r_free= 0.1548   ksol= 0.32   Bsol= 42.95   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.57,-0.09,0.67,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.117084                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8990 -  4.7270 0.99   1375  153 0.0982 0.1281      5.3783      5.5207|
|  2:  4.7270 -  3.7720 0.99   1319  145 0.0850 0.1111      5.4284      5.6219|
|  3:  3.7720 -  3.3011 0.99   1302  145 0.1010 0.1495      5.4463      5.8412|
|  4:  3.3011 -  3.0020 0.99   1284  145 0.1160 0.1492      5.4255      5.5725|
|  5:  3.0020 -  2.7883 0.99   1272  139 0.1220 0.1695      5.2834      5.5177|
|  6:  2.7883 -  2.6249 0.99   1278  143 0.1133 0.1716      5.1755      5.4019|
|  7:  2.6249 -  2.4940 0.99   1259  141 0.1191 0.1678      5.1351      5.3968|
|  8:  2.4940 -  2.3859 0.98   1266  140 0.1118 0.1761      5.0556       5.365|
|  9:  2.3859 -  2.2944 0.98   1270  138 0.1143 0.1718      5.0206      5.2638|
| 10:  2.2944 -  2.2155 0.98   1233  137 0.1027 0.1726      4.9419      5.2164|
| 11:  2.2155 -  2.1464 0.99   1269  147 0.1088 0.1654      4.9153        5.25|
| 12:  2.1464 -  2.0853 0.97   1250  130 0.1063 0.1658      4.8535      5.1863|
| 13:  2.0853 -  2.0305 0.99   1234  141 0.1084 0.1624      4.7738      5.0275|
| 14:  2.0305 -  1.9811 0.79   1019  115 0.1012 0.1806      4.6481      4.9426|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8990 -  4.7270  1375   153  0.94   9.06   0.98     0.96       7194.60|
|  2:  4.7270 -  3.7720  1319   145  0.95   7.86   1.02     1.01       8953.88|
|  3:  3.7720 -  3.3011  1302   145  0.94  10.83   1.03     1.02       9953.78|
|  4:  3.3011 -  3.0020  1284   145  0.92  13.04   1.01     1.00       9893.88|
|  5:  3.0020 -  2.7883  1272   139  0.91  15.10   1.00     0.96       7740.80|
|  6:  2.7883 -  2.6249  1278   143  0.91  15.26   0.99     0.96       6696.75|
|  7:  2.6249 -  2.4940  1259   141  0.91  15.24   0.99     0.96       5974.00|
|  8:  2.4940 -  2.3859  1266   140  0.91  14.67   1.00     0.97       5246.15|
|  9:  2.3859 -  2.2944  1270   138  0.91  15.47   1.01     0.98       4990.45|
| 10:  2.2944 -  2.2155  1233   137  0.91  15.07   1.01     0.97       4359.69|
| 11:  2.2155 -  2.1464  1269   147  0.90  16.03   1.00     0.97       4265.16|
| 12:  2.1464 -  2.0853  1250   130  0.92  14.81   1.01     1.00       3805.16|
| 13:  2.0853 -  2.0305  1234   141  0.91  15.39   1.02     1.01       3274.55|
| 14:  2.0305 -  1.9811  1019   115  0.92  14.35   1.00     0.96       2480.03|
|alpha:            min =        0.96 max =            1.02 mean =         0.98|
|beta:             min =     2480.03 max =         9953.78 mean =      6147.71|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.71 mean =        13.66|
|phase err.(test): min =        0.00 max =           89.62 mean =        13.25|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.736)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.64    79.50   14.85    None  None   None       |
|    all(noH): 2823   0      3.64    79.50   14.85    None  None   None       |
|    Sol.    : 438    0      4.38    70.53   36.85    None  None   None       |
|    Mac.    : 2385   0      3.64    79.50   10.81    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:     3.639 -  11.225: 1672   |   5:    41.572 -  49.158:   99        |
|      1:    11.225 -  18.812:  558   |   6:    49.158 -  56.745:   68        |
|      2:    18.812 -  26.398:  153   |   7:    56.745 -  64.331:   33        |
|      3:    26.398 -  33.985:  114   |   8:    64.331 -  71.918:   10        |
|      4:    33.985 -  41.572:  112   |   9:    71.918 -  79.505:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 297         
Filter by distance & map next to the model:
   mapped sites are within: 0.327 - 5.897
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 292 from: 297
   mapped sites are within: 0.745 - 5.897

peak=   11.160 closest distance to " CB  VAL A 230 " =    1.473
peak=    6.670 closest distance to " CG2 VAL A 296 " =    1.095
peak=    6.325 closest distance to " CG  LEU A   5 " =    1.174
peak=    6.006 closest distance to " NH2 ARG A  56 " =    2.211
peak=    5.791 closest distance to " CG  LEU A 228 " =    1.168
peak=    5.715 closest distance to " CB  VAL A 296 " =    1.095
peak=    5.529 closest distance to " NE2 GLN A  11 " =    1.120
peak=    5.404 closest distance to " CD2 LEU A   5 " =    1.184
peak=    5.216 closest distance to " O   HOH Z 142 " =    1.727
peak=    5.213 closest distance to " CG  PRO A  54 " =    1.204
peak=    5.187 closest distance to " CB  GLN A 223 " =    1.474
peak=    5.185 closest distance to " CB  GLN A 183 " =    1.284
peak=    5.159 closest distance to " O   HOH Z 126 " =    1.967
peak=    4.889 closest distance to " CB  ARG A 275 " =    0.901
peak=    4.850 closest distance to " CB  SER A  63 " =    1.249
peak=    4.821 closest distance to " O   HOH Z 193 " =    1.710
peak=    4.818 closest distance to " O   HOH Z 209 " =    2.321
peak=    4.758 closest distance to " O   HOH Z 272 " =    1.910
peak=    4.726 closest distance to " CB  VAL A 230 " =    1.153
peak=    4.584 closest distance to " CB  GLU A 152 " =    1.197
peak=    4.506 closest distance to " O   HOH Z 232 " =    2.356
peak=    4.490 closest distance to " C   PRO A 198 " =    1.463
peak=    4.465 closest distance to " O   HOH Z 369 " =    2.162
peak=    4.455 closest distance to " O   HOH Z 298 " =    1.793
peak=    4.416 closest distance to " O   HOH Z 316 " =    3.011
peak=    4.408 closest distance to " O   HOH Z 303 " =    2.042
peak=    4.408 closest distance to " CB  PRO A  54 " =    0.895
peak=    4.402 closest distance to " O   HOH Z 427 " =    2.938
peak=    4.367 closest distance to " O   SER A  87 " =    2.296
peak=    4.348 closest distance to " CG  PRO A 213 " =    1.202
peak=    4.337 closest distance to " OD1 ASN A  69 " =    2.608
peak=    4.336 closest distance to " O   HOH Z 236 " =    1.973
peak=    4.303 closest distance to " CB  SER A   3 " =    1.274
peak=    4.291 closest distance to " O   HOH Z 124 " =    1.364
peak=    4.267 closest distance to " CB  TYR A 169 " =    0.748
peak=    4.260 closest distance to " O   HOH Z 368 " =    2.129
peak=    4.251 closest distance to " O   HOH Z  59 " =    2.053
peak=    4.210 closest distance to " CB  ARG A  79 " =    1.457
peak=    4.204 closest distance to " O   HOH Z  43 " =    2.040
peak=    4.201 closest distance to " CB  ASN A 148 " =    1.366
peak=    4.194 closest distance to " O   HOH Z 346 " =    1.572
peak=    4.191 closest distance to " O   HOH Z 158 " =    3.114
peak=    4.179 closest distance to " O   HOH Z  78 " =    1.706
peak=    4.178 closest distance to " O   HOH Z 203 " =    1.692
peak=    4.178 closest distance to " O   HOH Z 423 " =    1.799
peak=    4.176 closest distance to " O   HOH Z 197 " =    3.094
peak=    4.169 closest distance to " O   HOH Z  61 " =    1.644
peak=    4.150 closest distance to " O   HOH Z 234 " =    3.556
peak=    4.139 closest distance to " CB  TRP A 179 " =    1.338
peak=    4.104 closest distance to " CA  TYR A  30 " =    0.962
peak=    4.099 closest distance to " O   HOH Z  15 " =    2.220
peak=    4.065 closest distance to " O   HOH Z 402 " =    1.443
peak=    4.054 closest distance to " CB  VAL A 265 " =    1.318
peak=    4.015 closest distance to " O   HOH Z 403 " =    1.717
peak=    4.011 closest distance to " ND2 ASN A 187 " =    1.492
peak=    4.000 closest distance to " CB  ARG A 139 " =    0.957
peak=    3.993 closest distance to " CD2 LEU A 228 " =    1.129
peak=    3.972 closest distance to " O   HOH Z  66 " =    2.181
peak=    3.960 closest distance to " CB  GLU A 277 " =    3.527
peak=    3.952 closest distance to " O   HOH Z 261 " =    2.227
peak=    3.938 closest distance to " O   HOH Z 371 " =    3.126
peak=    3.920 closest distance to " O   HOH Z 280 " =    2.907
peak=    3.916 closest distance to " O   HOH Z 248 " =    1.675
peak=    3.909 closest distance to " OG BSER A 164 " =    2.143
peak=    3.909 closest distance to " CG1BVAL A  72 " =    1.568
peak=    3.892 closest distance to " O   HOH Z 250 " =    1.360
peak=    3.883 closest distance to " O   HOH Z  97 " =    1.932
peak=    3.865 closest distance to " O   HOH Z  97 " =    2.566
peak=    3.848 closest distance to " O   HOH Z 411 " =    3.802
peak=    3.826 closest distance to " CG  ARG A  66 " =    2.716
peak=    3.822 closest distance to " O   HOH Z 189 " =    2.549
peak=    3.800 closest distance to " CA  ASN A 215 " =    1.186
peak=    3.793 closest distance to " CB  GLU A 128 " =    1.019
peak=    3.783 closest distance to " O   HOH Z 345 " =    3.153
peak=    3.780 closest distance to " O   HOH Z 263 " =    1.578
peak=    3.779 closest distance to " CD2 TRP A 179 " =    1.403
peak=    3.768 closest distance to " OD2 ASP A 286 " =    2.755
peak=    3.749 closest distance to " O   HOH Z  54 " =    1.573
peak=    3.742 closest distance to " CB  ASP A 140 " =    1.008
peak=    3.735 closest distance to " O   HOH Z 389 " =    1.831
peak=    3.731 closest distance to " CB  VAL A 202 " =    1.611
peak=    3.705 closest distance to " CB  TRP A 266 " =    0.992
peak=    3.697 closest distance to " O   HOH Z 417 " =    3.159
peak=    3.696 closest distance to " CD BLYS A 290 " =    1.197
peak=    3.681 closest distance to " O   HOH Z 344 " =    2.980
peak=    3.681 closest distance to " CG  GLN A  77 " =    2.287
peak=    3.675 closest distance to " O   HOH Z 366 " =    2.921
peak=    3.672 closest distance to " CB  ARG A 190 " =    1.653
peak=    3.667 closest distance to " CA  VAL A  41 " =    0.818
peak=    3.666 closest distance to " O   HOH Z 128 " =    2.079
peak=    3.665 closest distance to " O   TRP A 274 " =    1.893
peak=    3.663 closest distance to " O   HOH Z 147 " =    1.706
peak=    3.660 closest distance to " CB  ALA A   9 " =    1.582
peak=    3.655 closest distance to " O   HOH Z  44 " =    1.731
peak=    3.650 closest distance to " O   HOH Z 245 " =    1.368
peak=    3.646 closest distance to " O   HOH Z 299 " =    4.272
peak=    3.644 closest distance to " O   HOH Z  40 " =    1.430
peak=    3.630 closest distance to " O   HOH Z 112 " =    1.634
peak=    3.629 closest distance to " CB  ASN A 148 " =    1.901
peak=    3.624 closest distance to " O   HOH Z 128 " =    2.030
peak=    3.622 closest distance to " CA  ALA A  21 " =    1.169
peak=    3.617 closest distance to " O   HOH Z 145 " =    2.126
peak=    3.616 closest distance to " OE1 GLU A   2 " =    2.125
peak=    3.606 closest distance to " CG2 ILE A  20 " =    1.453
peak=    3.604 closest distance to " O   HOH Z 407 " =    2.480
peak=    3.596 closest distance to " O   HOH Z  88 " =    2.932
peak=    3.594 closest distance to " CA  ALA A 158 " =    1.286
peak=    3.589 closest distance to " CB  ASN A  39 " =    0.904
peak=    3.587 closest distance to " O   HOH Z 193 " =    1.939
peak=    3.573 closest distance to " CZ  PHE A 218 " =    1.117
peak=    3.561 closest distance to " O   HOH Z  80 " =    1.603
peak=    3.559 closest distance to " O   HOH Z 286 " =    2.327
peak=    3.553 closest distance to " CB  THR A 157 " =    1.154
peak=    3.549 closest distance to " O   HOH Z 214 " =    2.152
peak=    3.544 closest distance to " NH2 ARG A 156 " =    1.073
peak=    3.542 closest distance to " O   HOH Z  85 " =    1.334
peak=    3.540 closest distance to " CA  LYS A 117 " =    1.257
peak=    3.535 closest distance to " CB  ALA A 248 " =    1.385
peak=    3.534 closest distance to " CB  THR A  31 " =    1.681
peak=    3.533 closest distance to " CG  PRO A 243 " =    1.169
peak=    3.533 closest distance to " O   HOH Z 425 " =    2.097
peak=    3.522 closest distance to " CA  ALA A  51 " =    0.941
peak=    3.521 closest distance to " CA  PHE A 283 " =    1.195
peak=    3.518 closest distance to " O   MET A 105 " =    1.863
peak=    3.514 closest distance to " O   HOH Z 322 " =    2.020
peak=    3.503 closest distance to " O   HOH Z 227 " =    2.087
peak=    3.500 closest distance to " CD1 ILE A 106 " =    1.068
peak=    3.498 closest distance to " CB  ASN A 142 " =    1.150
peak=    3.495 closest distance to " O   HOH Z 154 " =    2.007
peak=    3.491 closest distance to " CG1 ILE A  49 " =    1.371
peak=    3.491 closest distance to " CA  ARG A  36 " =    0.976
peak=    3.482 closest distance to " CB  SER A  26 " =    1.598
peak=    3.481 closest distance to " O   HOH Z 273 " =    2.639
peak=    3.481 closest distance to " N   ASN A  39 " =    1.249
peak=    3.480 closest distance to " O   HOH Z 329 " =    3.852
peak=    3.476 closest distance to " CG1 ILE A  33 " =    1.284
peak=    3.469 closest distance to " O   HOH Z 189 " =    2.677
peak=    3.467 closest distance to " OG1 THR A 294 " =    2.377
peak=    3.460 closest distance to " CA  VAL A 126 " =    0.881
peak=    3.459 closest distance to " CE1 TYR A 186 " =    1.304
peak=    3.454 closest distance to " O   HOH Z 291 " =    1.550
peak=    3.454 closest distance to " O   HOH Z 132 " =    2.675
peak=    3.453 closest distance to " CG  MET A 185 " =    1.119
peak=    3.448 closest distance to " O   HOH Z 337 " =    3.563
peak=    3.445 closest distance to " NZ  LYS A 117 " =    3.190
peak=    3.443 closest distance to " O   HOH Z   9 " =    2.075
peak=    3.442 closest distance to " O   HOH Z 423 " =    3.011
peak=    3.441 closest distance to " CG2 ILE A 120 " =    1.250
peak=    3.439 closest distance to " O   ASP A 124 " =    1.153
peak=    3.434 closest distance to " CB  VAL A 268 " =    0.847
peak=    3.433 closest distance to " O   HOH Z  10 " =    1.805
peak=    3.429 closest distance to " CG  PRO A 198 " =    1.141
peak=    3.427 closest distance to " O   HOH Z   1 " =    1.904
peak=    3.426 closest distance to " CA  ASP A 140 " =    1.175
peak=    3.423 closest distance to " O   HOH Z  48 " =    1.427
peak=    3.423 closest distance to " CB  TRP A 150 " =    1.412
peak=    3.422 closest distance to " O   HOH Z  61 " =    1.576
peak=    3.420 closest distance to " CG BARG A 102 " =    1.796
peak=    3.419 closest distance to " ND2 ASN A 110 " =    1.721
peak=    3.419 closest distance to " CG2 THR A 221 " =    1.247
peak=    3.418 closest distance to " CB  ALA A 291 " =    1.452
peak=    3.418 closest distance to " CB  LEU A 228 " =    1.327
peak=    3.415 closest distance to " O   HOH Z 148 " =    3.268
peak=    3.413 closest distance to " O   HOH Z 422 " =    2.672
peak=    3.411 closest distance to " CB  ASN A 110 " =    1.147
peak=    3.408 closest distance to " O   HOH Z 426 " =    1.515
peak=    3.404 closest distance to " CG2 VAL A 257 " =    0.807
peak=    3.402 closest distance to " CB  HIS A 108 " =    0.803
peak=    3.401 closest distance to " CD  LYS A 119 " =    1.468
peak=    3.392 closest distance to " CA  ALA A 291 " =    0.922
peak=    3.390 closest distance to " O   HOH Z 222 " =    2.485
peak=    3.377 closest distance to " O   HOH Z 368 " =    3.613
peak=    3.377 closest distance to " O   HOH Z 172 " =    3.746
peak=    3.373 closest distance to " CD1 ILE A  33 " =    1.596
peak=    3.364 closest distance to " CA  ASP A 162 " =    1.095
peak=    3.362 closest distance to " CB  GLN A 205 " =    1.186
peak=    3.360 closest distance to " O   HOH Z 425 " =    1.281
peak=    3.358 closest distance to " CA  ALA A 233 " =    1.354
peak=    3.357 closest distance to " CA  THR A 264 " =    0.787
peak=    3.352 closest distance to " O   HOH Z 180 " =    2.100
peak=    3.352 closest distance to " O   HOH Z 144 " =    1.674
peak=    3.351 closest distance to " O   HOH Z 437 " =    1.878
peak=    3.350 closest distance to " CB  ILE A  20 " =    1.479
peak=    3.349 closest distance to " CG  MET A 185 " =    1.192
peak=    3.347 closest distance to " O   HOH Z 227 " =    1.637
peak=    3.346 closest distance to " OE2 GLU A  53 " =    1.979
peak=    3.346 closest distance to " CB  GLN A  89 " =    1.202
peak=    3.343 closest distance to " O   HOH Z 313 " =    1.795
peak=    3.332 closest distance to " NH2 ARG A  79 " =    1.354
peak=    3.330 closest distance to " CA  ASN A 176 " =    1.066
peak=    3.327 closest distance to " CE  LYS A  76 " =    0.895
peak=    3.326 closest distance to " CB  GLN A  88 " =    1.200
peak=    3.322 closest distance to " O   HOH Z 145 " =    3.719
peak=    3.319 closest distance to " O   HOH Z 305 " =    3.547
peak=    3.315 closest distance to " CG  LEU A 167 " =    1.177
peak=    3.315 closest distance to " O   HOH Z 250 " =    1.366
peak=    3.312 closest distance to " O   HOH Z 261 " =    1.573
peak=    3.311 closest distance to " O   HOH Z 265 " =    2.431
peak=    3.309 closest distance to " O   HOH Z 193 " =    1.583
peak=    3.307 closest distance to " O   HOH Z 368 " =    2.632
peak=    3.306 closest distance to " O   HOH Z  19 " =    2.210
peak=    3.301 closest distance to " O   ARG A  56 " =    2.794
peak=    3.298 closest distance to " O   HOH Z 135 " =    1.831
peak=    3.296 closest distance to " CA  SER A 146 " =    1.743
peak=    3.294 closest distance to " CB  LEU A 143 " =    1.158
peak=    3.288 closest distance to " O   HOH Z 151 " =    1.767
peak=    3.288 closest distance to " N   VAL A 126 " =    1.334
peak=    3.287 closest distance to " CB  ALA A 248 " =    1.005
peak=    3.283 closest distance to " N   PHE A 130 " =    1.342
peak=    3.281 closest distance to " CD  LYS A 166 " =    1.361
peak=    3.279 closest distance to " CD  ARG A 269 " =    0.987
peak=    3.277 closest distance to " O  BHOH Z 338 " =    2.391
peak=    3.274 closest distance to " O   HOH Z 251 " =    1.592
peak=    3.270 closest distance to " O   HOH Z 367 " =    3.384
peak=    3.268 closest distance to " O   HOH Z 134 " =    1.346
peak=    3.265 closest distance to " O   HOH Z 417 " =    2.118
peak=    3.264 closest distance to " CB  SER A 212 " =    1.125
peak=    3.262 closest distance to " CB  LYS A 290 " =    1.075
peak=    3.259 closest distance to " O   HOH Z  49 " =    2.333
peak=    3.258 closest distance to " O   HOH Z 435 " =    1.893
peak=    3.257 closest distance to " O   SER A 164 " =    1.112
peak=    3.256 closest distance to " CB BVAL A  41 " =    1.260
peak=    3.255 closest distance to " O   HOH Z 130 " =    2.324
peak=    3.251 closest distance to " CB  LEU A 255 " =    0.745
peak=    3.251 closest distance to " N   ASP A 162 " =    1.298
peak=    3.249 closest distance to " CB  ASN A 215 " =    1.163
peak=    3.246 closest distance to " CD1 LEU A 228 " =    1.886
peak=    3.246 closest distance to " N   SER A 135 " =    1.438
peak=    3.244 closest distance to " O   HOH Z 123 " =    2.180
peak=    3.244 closest distance to " CD1 LEU A 300 " =    1.304
peak=    3.238 closest distance to " CB  SER A 216 " =    0.754
peak=    3.238 closest distance to " O   HOH Z 234 " =    1.820
peak=    3.237 closest distance to " CB  ASN A 224 " =    1.039
peak=    3.233 closest distance to " O   HOH Z 173 " =    2.224
peak=    3.232 closest distance to " CG1 VAL A 296 " =    1.223
peak=    3.228 closest distance to " OD1BASN A 224 " =    2.220
peak=    3.220 closest distance to " O   HOH Z 227 " =    1.527
peak=    3.220 closest distance to " CB  GLN A 278 " =    0.882
peak=    3.218 closest distance to " O   GLN A 278 " =    1.339
peak=    3.218 closest distance to " O   HOH Z 419 " =    1.576
peak=    3.216 closest distance to " CD2 TYR A  30 " =    0.962
peak=    3.214 closest distance to " CA  THR A 221 " =    0.937
peak=    3.213 closest distance to " O   HOH Z 285 " =    3.035
peak=    3.212 closest distance to " CA  ARG A 195 " =    1.166
peak=    3.212 closest distance to " ND1 HIS A  81 " =    1.623
peak=    3.206 closest distance to " O   HOH Z 357 " =    1.788
peak=    3.205 closest distance to " O   HOH Z 409 " =    3.376
peak=    3.198 closest distance to " O   HOH Z 374 " =    2.550
peak=    3.190 closest distance to " O   HOH Z 298 " =    4.709
peak=    3.186 closest distance to " O   HOH Z 365 " =    3.414
peak=    3.183 closest distance to " O   HOH Z 128 " =    1.979
peak=    3.183 closest distance to " CG AARG A 275 " =    1.086
peak=    3.178 closest distance to " OG  SER A  22 " =    2.739
peak=    3.177 closest distance to " CG  GLN A  88 " =    1.021
peak=    3.175 closest distance to " O   HOH Z 341 " =    2.111
peak=    3.175 closest distance to " CB  ALA A 100 " =    1.151
peak=    3.175 closest distance to " O   HOH Z 279 " =    2.171
peak=    3.174 closest distance to " NH2BARG A 145 " =    1.928
peak=    3.173 closest distance to " CG  LYS A  76 " =    1.005
peak=    3.172 closest distance to " N   ARG A 156 " =    1.363
peak=    3.170 closest distance to " O   HOH Z 199 " =    1.589
peak=    3.168 closest distance to " CB  MET A  47 " =    1.221
peak=    3.167 closest distance to " O   HOH Z 359 " =    1.814
peak=    3.165 closest distance to " CB  ALA A   1 " =    1.169
peak=    3.164 closest distance to " O   ALA A   1 " =    1.763
peak=    3.163 closest distance to " CE  LYS A  48 " =    1.149
peak=    3.160 closest distance to " CD2 LEU A 255 " =    1.463
peak=    3.156 closest distance to " CD2 HIS A  81 " =    1.101
peak=    3.154 closest distance to " O   HOH Z 175 " =    2.107
peak=    3.151 closest distance to " NE2 GLN A  58 " =    5.897
peak=    3.148 closest distance to " O   ALA A 158 " =    1.417
peak=    3.146 closest distance to " O   HOH Z 392 " =    1.519
peak=    3.142 closest distance to " O   HOH Z  21 " =    1.700
peak=    3.140 closest distance to " CG2 ILE A 234 " =    2.046
peak=    3.134 closest distance to " CZ2 TRP A 179 " =    1.691
peak=    3.120 closest distance to " O   HOH Z 336 " =    1.769
peak=    3.115 closest distance to " C   ALA A 299 " =    0.917
peak=    3.111 closest distance to " CB  ALA A 295 " =    1.317
peak=    3.107 closest distance to " O   HOH Z 163 " =    1.801
peak=    3.106 closest distance to " O   HOH Z 353 " =    2.657
peak=    3.103 closest distance to " CB  LYS A 117 " =    1.136
peak=    3.096 closest distance to " OE1 GLU A 236 " =    1.700
peak=    3.083 closest distance to " O   THR A  31 " =    1.529
peak=    3.082 closest distance to " O   HOH Z  40 " =    2.143
peak=    3.078 closest distance to " NH1BARG A 190 " =    2.119
peak=    3.078 closest distance to " O   HOH Z 303 " =    1.651
peak=    3.072 closest distance to " CB  ILE A 120 " =    1.362
peak=    3.060 closest distance to " O   HOH Z 281 " =    4.721
peak=    3.056 closest distance to " O   HOH Z 251 " =    1.424
peak=    3.054 closest distance to " O   HOH Z 371 " =    3.313
peak=    3.050 closest distance to " CA  MET A 105 " =    0.987
peak=    3.038 closest distance to " CZ3 TRP A  85 " =    0.912

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 211         
Filter by distance & map next to the model:
   mapped sites are within: 0.639 - 5.443
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 209 from: 211
   mapped sites are within: 0.753 - 5.443

peak=   -5.472 closest distance to " CG2 VAL A 230 " =    0.753
peak=   -4.780 closest distance to " SG  CYS A 254 " =    3.221
peak=   -4.662 closest distance to " CD  ARG A 156 " =    2.025
peak=   -4.622 closest distance to " O   HOH Z 266 " =    4.807
peak=   -4.299 closest distance to " OG BSER A 134 " =    1.207
peak=   -4.254 closest distance to " CG  GLN A 223 " =    2.062
peak=   -4.200 closest distance to " CB  PRO A 243 " =    2.619
peak=   -4.174 closest distance to " C   HIS A 108 " =    1.207
peak=   -4.170 closest distance to " CB  ALA A 161 " =    2.599
peak=   -4.139 closest distance to " O   HOH Z 290 " =    1.130
peak=   -4.130 closest distance to " CG2 VAL A 296 " =    1.220
peak=   -4.084 closest distance to " OXT GLY A 302 " =    2.793
peak=   -4.080 closest distance to " CG2BVAL A  41 " =    2.616
peak=   -4.068 closest distance to " O   VAL A  67 " =    2.761
peak=   -4.064 closest distance to " O   PRO A 163 " =    2.130
peak=   -4.038 closest distance to " N   GLN A  58 " =    1.676
peak=   -3.941 closest distance to " CD2 LEU A 300 " =    2.822
peak=   -3.930 closest distance to " O   HOH Z 231 " =    2.054
peak=   -3.906 closest distance to " O   HOH Z  11 " =    1.859
peak=   -3.882 closest distance to " CB  ALA A 248 " =    2.052
peak=   -3.836 closest distance to " O   HOH Z 389 " =    1.851
peak=   -3.825 closest distance to " CD  GLN A  58 " =    1.146
peak=   -3.804 closest distance to " N   ALA A 226 " =    1.981
peak=   -3.793 closest distance to " CG  ASP A 231 " =    0.805
peak=   -3.784 closest distance to " CE2 TYR A  30 " =    2.766
peak=   -3.773 closest distance to " CZ  TYR A 169 " =    1.655
peak=   -3.771 closest distance to " O   HOH Z 351 " =    1.530
peak=   -3.759 closest distance to " OG  SER A   3 " =    1.717
peak=   -3.751 closest distance to " ND2 ASN A 187 " =    1.537
peak=   -3.721 closest distance to " CB  PHE A 192 " =    1.885
peak=   -3.712 closest distance to " CD  ARG A 139 " =    1.626
peak=   -3.701 closest distance to " CG1 VAL A 112 " =    2.737
peak=   -3.698 closest distance to " CB  PRO A 280 " =    2.086
peak=   -3.693 closest distance to " OG  SER A  97 " =    2.204
peak=   -3.688 closest distance to " O   HOH Z 114 " =    3.050
peak=   -3.688 closest distance to " O   HOH Z 435 " =    2.768
peak=   -3.678 closest distance to " CD1 PHE A  59 " =    1.943
peak=   -3.675 closest distance to " O   HOH Z 196 " =    2.103
peak=   -3.668 closest distance to " NH2AARG A 275 " =    5.083
peak=   -3.655 closest distance to " O   HOH Z 166 " =    1.963
peak=   -3.640 closest distance to " CZ3 TRP A 179 " =    1.268
peak=   -3.640 closest distance to " O   HOH Z 198 " =    2.267
peak=   -3.635 closest distance to " CD  LYS A 289 " =    2.512
peak=   -3.626 closest distance to " CD1 LEU A 101 " =    2.391
peak=   -3.621 closest distance to " CE  MET A 105 " =    2.105
peak=   -3.619 closest distance to " NH2 ARG A  79 " =    1.944
peak=   -3.613 closest distance to " N   THR A 157 " =    1.486
peak=   -3.601 closest distance to " N   MET A 188 " =    1.896
peak=   -3.601 closest distance to " NE2 GLN A  88 " =    1.952
peak=   -3.600 closest distance to " CB  PRO A 163 " =    2.545
peak=   -3.598 closest distance to " CG1 VAL A 250 " =    2.722
peak=   -3.596 closest distance to " O   HOH Z 211 " =    1.621
peak=   -3.590 closest distance to " N   ALA A 248 " =    1.612
peak=   -3.588 closest distance to " ND2 ASN A  45 " =    1.432
peak=   -3.587 closest distance to " ND2 ASN A  45 " =    1.055
peak=   -3.581 closest distance to " CB  TYR A  15 " =    2.180
peak=   -3.575 closest distance to " CG  PHE A 283 " =    2.765
peak=   -3.569 closest distance to " CE2 PHE A 218 " =    2.589
peak=   -3.569 closest distance to " O   HOH Z 407 " =    2.974
peak=   -3.558 closest distance to " O   HOH Z 103 " =    1.833
peak=   -3.553 closest distance to " CA  ASP A 298 " =    1.034
peak=   -3.545 closest distance to " CB  ALA A 248 " =    2.330
peak=   -3.543 closest distance to " CG  LEU A 228 " =    1.014
peak=   -3.541 closest distance to " CB  ASP A 132 " =    2.330
peak=   -3.540 closest distance to " CB  ALA A 291 " =    2.310
peak=   -3.532 closest distance to " CG1 VAL A 230 " =    1.794
peak=   -3.530 closest distance to " O   HOH Z 165 " =    1.980
peak=   -3.523 closest distance to " CZ  PHE A  59 " =    1.520
peak=   -3.508 closest distance to " O   HOH Z 102 " =    1.612
peak=   -3.499 closest distance to " O   VAL A 189 " =    2.609
peak=   -3.498 closest distance to " CB  ASP A 132 " =    2.288
peak=   -3.498 closest distance to " OD2 ASP A 171 " =    2.336
peak=   -3.498 closest distance to " O   HOH Z  43 " =    1.828
peak=   -3.493 closest distance to " O   MET A  40 " =    2.657
peak=   -3.493 closest distance to " CG2 THR A 178 " =    2.204
peak=   -3.485 closest distance to " O   PRO A 198 " =    1.244
peak=   -3.478 closest distance to " O   ALA A  51 " =    1.321
peak=   -3.475 closest distance to " CD1 ILE A 199 " =    2.407
peak=   -3.466 closest distance to " O   HOH Z 166 " =    1.404
peak=   -3.463 closest distance to " O   HOH Z 394 " =    1.551
peak=   -3.454 closest distance to " O   HOH Z 234 " =    3.999
peak=   -3.453 closest distance to " CD1 LEU A 228 " =    2.120
peak=   -3.445 closest distance to " CG  ASP A  50 " =    2.343
peak=   -3.438 closest distance to " CB  ASN A  69 " =    1.104
peak=   -3.437 closest distance to " O   HOH Z  13 " =    1.479
peak=   -3.436 closest distance to " N   SER A 276 " =    1.307
peak=   -3.432 closest distance to " N   ALA A  43 " =    2.565
peak=   -3.429 closest distance to " N   THR A 235 " =    1.297
peak=   -3.422 closest distance to " NZ  LYS A 119 " =    3.430
peak=   -3.415 closest distance to " OG  SER A  62 " =    1.587
peak=   -3.408 closest distance to " OXT GLY A 302 " =    3.448
peak=   -3.407 closest distance to " C   ALA A 158 " =    1.248
peak=   -3.406 closest distance to " O   HOH Z 185 " =    2.324
peak=   -3.405 closest distance to " O   HOH Z  60 " =    1.968
peak=   -3.404 closest distance to " O   HOH Z 389 " =    4.700
peak=   -3.403 closest distance to " O   HOH Z 339 " =    1.838
peak=   -3.402 closest distance to " C   MET A 188 " =    1.437
peak=   -3.389 closest distance to " N   PHE A  59 " =    2.166
peak=   -3.389 closest distance to " C   LEU A 143 " =    0.994
peak=   -3.388 closest distance to " OG  SER A  26 " =    1.139
peak=   -3.388 closest distance to " CG  LYS A 193 " =    2.226
peak=   -3.387 closest distance to " O   HOH Z  47 " =    1.581
peak=   -3.387 closest distance to " O   GLY A  80 " =    2.403
peak=   -3.387 closest distance to " CE3 TRP A 150 " =    2.025
peak=   -3.385 closest distance to " O   HOH Z 313 " =    1.751
peak=   -3.383 closest distance to " CG1 VAL A 112 " =    2.578
peak=   -3.381 closest distance to " O   PHE A 218 " =    1.681
peak=   -3.381 closest distance to " CA  GLY A  98 " =    1.898
peak=   -3.376 closest distance to " O   ALA A 161 " =    1.625
peak=   -3.374 closest distance to " C   GLN A 205 " =    1.941
peak=   -3.374 closest distance to " O   HOH Z 198 " =    1.400
peak=   -3.370 closest distance to " CD1 LEU A 101 " =    2.751
peak=   -3.369 closest distance to " O   HOH Z 411 " =    3.856
peak=   -3.357 closest distance to " O   SER A 210 " =    1.980
peak=   -3.355 closest distance to " OG BSER A 134 " =    1.656
peak=   -3.352 closest distance to " OG ASER A 134 " =    1.177
peak=   -3.352 closest distance to " O   HOH Z 311 " =    3.647
peak=   -3.341 closest distance to " CG2 ILE A 263 " =    2.282
peak=   -3.340 closest distance to " O   PRO A 198 " =    1.309
peak=   -3.338 closest distance to " CG1 VAL A 112 " =    2.907
peak=   -3.332 closest distance to " OG  SER A  87 " =    1.351
peak=   -3.327 closest distance to " O   HOH Z 191 " =    5.443
peak=   -3.316 closest distance to " O   SER A  22 " =    2.226
peak=   -3.309 closest distance to " O   HOH Z  19 " =    2.335
peak=   -3.303 closest distance to " N   LYS A 289 " =    1.541
peak=   -3.300 closest distance to " O   SER A  95 " =    1.581
peak=   -3.298 closest distance to " OG1 THR A 178 " =    1.273
peak=   -3.296 closest distance to " O   GLY A 196 " =    1.033
peak=   -3.293 closest distance to " O   HOH Z 193 " =    1.696
peak=   -3.291 closest distance to " CG  ARG A 269 " =    2.287
peak=   -3.289 closest distance to " CB  ALA A 291 " =    2.111
peak=   -3.283 closest distance to " O   ALA A   8 " =    1.964
peak=   -3.283 closest distance to " O   GLY A  80 " =    2.545
peak=   -3.282 closest distance to " O   HOH Z 388 " =    2.083
peak=   -3.276 closest distance to " O   ALA A  10 " =    1.792
peak=   -3.275 closest distance to " O   HOH Z 134 " =    2.752
peak=   -3.271 closest distance to " OH  TYR A 214 " =    1.269
peak=   -3.268 closest distance to " O   HOH Z  52 " =    1.464
peak=   -3.265 closest distance to " O   HOH Z 281 " =    2.757
peak=   -3.261 closest distance to " O   HOH Z 426 " =    1.650
peak=   -3.259 closest distance to " CG  TRP A 266 " =    1.915
peak=   -3.247 closest distance to " O   HOH Z 359 " =    3.167
peak=   -3.244 closest distance to " O   HOH Z 436 " =    1.588
peak=   -3.243 closest distance to " OG  SER A 206 " =    1.651
peak=   -3.242 closest distance to " O   HOH Z 350 " =    1.782
peak=   -3.237 closest distance to " CD1 TYR A 247 " =    2.424
peak=   -3.237 closest distance to " C   ASP A 231 " =    2.557
peak=   -3.235 closest distance to " CD2 LEU A 237 " =    2.624
peak=   -3.234 closest distance to " O   HOH Z 139 " =    5.135
peak=   -3.230 closest distance to " OD1 ASN A 148 " =    1.502
peak=   -3.229 closest distance to " O   HOH Z 139 " =    3.058
peak=   -3.228 closest distance to " CG  GLU A 277 " =    1.156
peak=   -3.218 closest distance to " CG  GLU A   2 " =    1.936
peak=   -3.218 closest distance to " C   LEU A 222 " =    0.849
peak=   -3.216 closest distance to " CA  GLY A 133 " =    1.960
peak=   -3.212 closest distance to " O   HOH Z 385 " =    1.927
peak=   -3.211 closest distance to " CG1 VAL A 296 " =    1.268
peak=   -3.210 closest distance to " O   LYS A 117 " =    1.652
peak=   -3.208 closest distance to " CB  ASN A  39 " =    2.194
peak=   -3.207 closest distance to " O   HOH Z  97 " =    1.542
peak=   -3.193 closest distance to " O   HOH Z 262 " =    2.746
peak=   -3.190 closest distance to " O   HOH Z 174 " =    2.410
peak=   -3.189 closest distance to " CD2 TYR A 247 " =    2.402
peak=   -3.187 closest distance to " O   HOH Z  22 " =    2.519
peak=   -3.186 closest distance to " O   GLY A  75 " =    1.882
peak=   -3.186 closest distance to " O   HOH Z  11 " =    2.109
peak=   -3.186 closest distance to " O   LEU A 167 " =    1.526
peak=   -3.185 closest distance to " CA  GLY A 133 " =    2.220
peak=   -3.175 closest distance to " O   HOH Z 385 " =    2.076
peak=   -3.173 closest distance to " CG  PRO A 163 " =    2.644
peak=   -3.171 closest distance to " O   HOH Z 111 " =    2.538
peak=   -3.171 closest distance to " OE1 GLN A  77 " =    1.705
peak=   -3.171 closest distance to " O   HOH Z 148 " =    1.839
peak=   -3.163 closest distance to " N   HIS A 115 " =    2.002
peak=   -3.163 closest distance to " NH1 ARG A 195 " =    2.576
peak=   -3.162 closest distance to " CG  GLN A 278 " =    2.096
peak=   -3.161 closest distance to " CE BMET A  47 " =    1.530
peak=   -3.159 closest distance to " O   HOH Z 310 " =    1.786
peak=   -3.158 closest distance to " OG1 THR A  82 " =    1.460
peak=   -3.156 closest distance to " O   HOH Z 210 " =    1.206
peak=   -3.154 closest distance to " O   HOH Z 131 " =    4.042
peak=   -3.152 closest distance to " O   HOH Z  10 " =    1.428
peak=   -3.150 closest distance to " CA  GLY A 241 " =    3.017
peak=   -3.150 closest distance to " N   ASP A 171 " =    2.331
peak=   -3.147 closest distance to " O   HOH Z 423 " =    2.084
peak=   -3.143 closest distance to " CG  GLU A 152 " =    1.377
peak=   -3.135 closest distance to " SG ACYS A 201 " =    2.050
peak=   -3.133 closest distance to " O   VAL A 197 " =    1.327
peak=   -3.130 closest distance to " O   HOH Z 123 " =    2.361
peak=   -3.122 closest distance to " O   HOH Z 222 " =    1.539
peak=   -3.120 closest distance to " O   HOH Z 243 " =    1.995
peak=   -3.119 closest distance to " O   HOH Z 175 " =    4.331
peak=   -3.116 closest distance to " NH1 ARG A  36 " =    2.060
peak=   -3.114 closest distance to " NH2 ARG A  66 " =    1.832
peak=   -3.114 closest distance to " CB  ALA A  51 " =    1.879
peak=   -3.111 closest distance to " O   HOH Z 353 " =    2.037
peak=   -3.110 closest distance to " O   TRP A  70 " =    1.501
peak=   -3.098 closest distance to " N   ALA A 248 " =    2.362
peak=   -3.097 closest distance to " O   HOH Z   6 " =    1.686
peak=   -3.091 closest distance to " O   VAL A 125 " =    2.315
peak=   -3.088 closest distance to " O   VAL A 174 " =    2.001
peak=   -3.083 closest distance to " ND2 ASN A  60 " =    1.467
peak=   -3.079 closest distance to " CG  PHE A 283 " =    2.646
peak=   -3.079 closest distance to " CG  GLU A 152 " =    2.075
peak=   -3.077 closest distance to " ND2 ASN A 249 " =    2.433
peak=   -3.064 closest distance to " O   HOH Z 407 " =    3.138
peak=   -3.058 closest distance to " CG1 VAL A 197 " =    2.195
peak=   -3.057 closest distance to " OD1 ASP A 200 " =    1.330
peak=   -3.033 closest distance to " OD1 ASN A 301 " =    2.032

================= 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    :  0.4189 0.4112   6.207525e+00   6.186808e+00
   1_bss:  0.4108 0.4027   6.202308e+00   6.170142e+00
   1_xyz:  0.3000 0.3234   5.968088e+00   6.016988e+00
   1_adp:  0.2287 0.2631   5.725331e+00   5.846756e+00
   1_occ:  0.2282 0.2629   5.723834e+00   5.846676e+00
   2_bss:  0.2228 0.2559   5.722445e+00   5.839118e+00
   2_xyz:  0.1527 0.1894   5.384962e+00   5.564190e+00
   2_adp:  0.1403 0.1775   5.310033e+00   5.501919e+00
   2_occ:  0.1402 0.1772   5.309261e+00   5.501027e+00
   3_bss:  0.1398 0.1772   5.309790e+00   5.501124e+00
   3_xyz:  0.1177 0.1565   5.163476e+00   5.383765e+00
   3_adp:  0.1134 0.1548   5.141555e+00   5.373799e+00
   3_occ:  0.1133 0.1547   5.141450e+00   5.373763e+00
   4_bss:  0.1133 0.1547   5.141450e+00   5.373763e+00
   4_xyz:  0.1126 0.1552   5.143190e+00   5.379369e+00
   4_adp:  0.1131 0.1547   5.141544e+00   5.373716e+00
   4_occ:  0.1131 0.1548   5.141874e+00   5.374370e+00
   5_bss:  0.1134 0.1549   5.143290e+00   5.375368e+00
   5_xyz:  0.1079 0.1528   5.112665e+00   5.362622e+00
   5_adp:  0.1072 0.1547   5.117728e+00   5.375624e+00
   5_occ:  0.1070 0.1548   5.117044e+00   5.375467e+00
   5_bss:  0.1069 0.1548   5.117084e+00   5.375492e+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:  0.361  20.001   7.247   8.152   8.468   0.000   0.000   0.000
   1_xyz:  0.361  20.001   7.247   8.152   8.468   0.000   0.000   0.000
   1_adp:  0.361  20.001   7.247   8.152   8.468   0.000   0.000   0.000
   1_occ:  0.361  20.001   7.247   8.152   8.468   0.000   0.000   0.000
   2_bss:  0.335  32.125   4.009   4.465   5.625   0.000   0.000   0.000
   2_xyz:  0.335  32.125   4.009   4.465   5.625   0.000   0.000   0.000
   2_adp:  0.335  32.125   4.009   4.465   5.625   0.000   0.000   0.000
   2_occ:  0.335  32.125   4.009   4.465   5.625   0.000   0.000   0.000
   3_bss:  0.329  37.098   3.015   3.548   4.404   0.000   0.000   0.000
   3_xyz:  0.329  37.098   3.015   3.548   4.404   0.000   0.000   0.000
   3_adp:  0.329  37.098   3.015   3.548   4.404   0.000   0.000   0.000
   3_occ:  0.329  37.098   3.015   3.548   4.404   0.000   0.000   0.000
   4_bss:  0.329  37.098   3.015   3.548   4.404   0.000   0.000   0.000
   4_xyz:  0.329  37.098   3.015   3.548   4.404   0.000   0.000   0.000
   4_adp:  0.329  37.098   3.015   3.548   4.404   0.000   0.000   0.000
   4_occ:  0.329  37.098   3.015   3.548   4.404   0.000   0.000   0.000
   5_bss:  0.323  39.309   2.898   3.407   4.180   0.000   0.000   0.000
   5_xyz:  0.323  39.309   2.898   3.407   4.180   0.000   0.000   0.000
   5_adp:  0.323  39.309   2.898   3.407   4.180   0.000   0.000   0.000
   5_occ:  0.323  39.309   2.898   3.407   4.180   0.000   0.000   0.000
   5_bss:  0.323  42.947  -0.574  -0.094   0.669  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  44.915 0.5855  0.6544    48296.080
   1_bss:  45.142 0.5800  0.8225    45771.601
   1_xyz:  34.381 0.7074  0.9769    28072.070
   1_adp:  25.816 0.8036  1.0690    17389.103
   1_occ:  25.785 0.8039  1.0689    17327.920
   2_bss:  25.574 0.8059  0.9511    17017.596
   2_xyz:  17.829 0.8818  1.0069     9018.610
   2_adp:  16.299 0.8960  1.0180     8013.356
   2_occ:  16.282 0.8962  1.0179     7994.393
   3_bss:  16.290 0.8961  0.9790     8022.948
   3_xyz:  13.896 0.9157  0.9869     6247.451
   3_adp:  13.684 0.9176  0.9871     6137.569
   3_occ:  13.683 0.9176  0.9870     6135.786
   4_bss:  13.683 0.9176  0.9870     6135.786
   4_xyz:  13.675 0.9180  0.9861     6176.944
   4_adp:  13.524 0.9193  0.9869     6110.120
   4_occ:  13.534 0.9192  0.9867     6117.595
   5_bss:  13.569 0.9189  0.9804     6148.620
   5_xyz:  13.346 0.9204  0.9815     5999.789
   5_adp:  13.628 0.9183  0.9761     6147.020
   5_occ:  13.618 0.9184  0.9759     6146.423
   5_bss:  13.619 0.9184  0.9811     6147.640
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.3459e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.3459e+01
   1_xyz:   1.472  0.011  0.099 17.732  0.006  4.119   1.1156e-01
   1_adp:   1.472  0.011  0.099 17.732  0.006  4.119   1.1156e-01
   1_occ:   1.472  0.011  0.099 17.732  0.006  4.119   1.1156e-01
   2_bss:   1.472  0.011  0.099 17.732  0.006  4.119   1.1156e-01
   2_xyz:   0.946  0.006  0.071 15.860  0.003  4.118   5.6943e-02
   2_adp:   0.946  0.006  0.071 15.860  0.003  4.118   5.6943e-02
   2_occ:   0.946  0.006  0.071 15.860  0.003  4.118   5.6943e-02
   3_bss:   0.946  0.006  0.071 15.860  0.003  4.118   5.6943e-02
   3_xyz:   1.030  0.007  0.084 15.726  0.004  4.110   6.3634e-02
   3_adp:   1.030  0.007  0.084 15.726  0.004  4.110   6.3634e-02
   3_occ:   1.030  0.007  0.084 15.726  0.004  4.110   6.3634e-02
   4_bss:   1.030  0.007  0.084 15.726  0.004  4.110   6.3634e-02
   4_xyz:   0.901  0.005  0.074 15.351  0.003  4.110   5.2830e-02
   4_adp:   0.901  0.005  0.074 15.351  0.003  4.110   5.2830e-02
   4_occ:   0.901  0.005  0.074 15.351  0.003  4.110   5.2830e-02
   5_bss:   0.901  0.005  0.074 15.351  0.003  4.110   5.2830e-02
   5_xyz:   1.080  0.008  0.089 15.674  0.004  4.111   6.9000e-02
   5_adp:   1.080  0.008  0.089 15.674  0.004  4.111   6.9000e-02
   5_occ:   1.080  0.008  0.089 15.674  0.004  4.111   6.9000e-02
   5_bss:   1.080  0.008  0.089 15.674  0.004  4.111   6.9000e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9309e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9309e+00
   1_xyz:  12.266  0.132  0.416 87.880  0.042  2.242   8.2763e-02
   1_adp:  12.266  0.132  0.416 87.880  0.042  2.242   8.2763e-02
   1_occ:  12.266  0.132  0.416 87.880  0.042  2.242   8.2763e-02
   2_bss:  12.266  0.132  0.416 87.880  0.042  2.242   8.2763e-02
   2_xyz:   6.747  0.058  0.363 82.249  0.030  2.352   4.2489e-02
   2_adp:   6.747  0.058  0.363 82.249  0.030  2.352   4.2489e-02
   2_occ:   6.747  0.058  0.363 82.249  0.030  2.352   4.2489e-02
   3_bss:   6.747  0.058  0.363 82.249  0.030  2.352   4.2489e-02
   3_xyz:   6.688  0.047  0.602 83.793  0.038  2.327   5.6098e-02
   3_adp:   6.688  0.047  0.602 83.793  0.038  2.327   5.6098e-02
   3_occ:   6.688  0.047  0.602 83.793  0.038  2.327   5.6098e-02
   4_bss:   6.688  0.047  0.602 83.793  0.038  2.327   5.6098e-02
   4_xyz:   6.237  0.038  0.458 82.604  0.036  2.394   3.2200e-02
   4_adp:   6.237  0.038  0.458 82.604  0.036  2.394   3.2200e-02
   4_occ:   6.237  0.038  0.458 82.604  0.036  2.394   3.2200e-02
   5_bss:   6.237  0.038  0.458 82.604  0.036  2.394   3.2200e-02
   5_xyz:   6.936  0.047  0.678 83.269  0.038  2.246   5.1246e-02
   5_adp:   6.936  0.047  0.678 83.269  0.038  2.246   5.1246e-02
   5_occ:   6.936  0.047  0.678 83.269  0.038  2.246   5.1246e-02
   5_bss:   6.936  0.047  0.678 83.269  0.038  2.246   5.1246e-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:  61.58   0.00  10.37  61.58   0.00   7.14  57.69   0.00  27.97
   1_occ:  61.58   0.00  10.37  61.58   0.00   7.14  57.69   0.00  27.97
   2_bss:  61.58   0.00  10.37  61.58   0.00   7.14  57.69   0.00  27.97
   2_xyz:  61.58   0.00  10.37  61.58   0.00   7.14  57.69   0.00  27.97
   2_adp:  65.82   0.00  10.91  65.82   0.00   7.15  58.62   1.36  31.34
   2_occ:  65.82   0.00  10.91  65.82   0.00   7.15  58.62   1.36  31.34
   3_bss:  65.82   0.00  10.91  65.82   0.00   7.15  58.62   1.36  31.34
   3_xyz:  65.82   0.00  10.91  65.82   0.00   7.15  58.62   1.36  31.34
   3_adp:  74.75   0.00  11.30  74.75   0.00   7.23  66.79   0.86  33.42
   3_occ:  74.75   0.00  11.30  74.75   0.00   7.23  66.79   0.86  33.42
   4_bss:  74.75   0.00  11.30  74.75   0.00   7.23  66.79   0.86  33.42
   4_xyz:  74.75   0.00  11.30  74.75   0.00   7.23  66.79   0.86  33.42
   4_adp:  74.87   0.00  11.20  74.87   0.00   7.21  65.83   1.06  32.94
   4_occ:  74.87   0.00  11.20  74.87   0.00   7.21  65.83   1.06  32.94
   5_bss:  74.87   0.00  11.20  74.87   0.00   7.21  65.83   1.06  32.94
   5_xyz:  74.87   0.00  11.20  74.87   0.00   7.21  65.83   1.06  32.94
   5_adp:  75.87   0.00  11.21  75.87   0.00   7.17  66.89   0.74  33.21
   5_occ:  75.87   0.00  11.21  75.87   0.00   7.17  66.89   0.74  33.21
   5_bss:  79.50   3.64  14.85  79.50   3.64  10.81  70.53   4.38  36.85
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.164    0.025    0.400
   1_adp:    1.164    0.025    0.400
   1_occ:    1.164    0.025    0.400
   2_bss:    1.164    0.025    0.400
   2_xyz:    1.405    0.029    0.479
   2_adp:    1.405    0.029    0.479
   2_occ:    1.405    0.029    0.479
   3_bss:    1.405    0.029    0.479
   3_xyz:    1.415    0.029    0.510
   3_adp:    1.415    0.029    0.510
   3_occ:    1.415    0.029    0.510
   4_bss:    1.415    0.029    0.510
   4_xyz:    1.520    0.050    0.519
   4_adp:    1.520    0.050    0.519
   4_occ:    1.520    0.050    0.519
   5_bss:    1.520    0.050    0.519
   5_xyz:    1.491    0.027    0.529
   5_adp:    1.491    0.027    0.529
   5_occ:    1.491    0.027    0.529
   5_bss:    1.491    0.027    0.529
------------------------------------------------------------------------

CPU time actual refinement: 347.09


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_542/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_542/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_542/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_542/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_542/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 346.93 
  Macro-tasks:
    bulk solvent and scale       = 42.80  
    individual site refinement   = 145.71 
    weights calculation          = 32.45  
    collect and process          = 6.59   
    model show statistics        = 0.14   
    TOTAL for macro-tasks        = 227.69 
  Micro-tasks:
    mask                            = 1.77   
    f_calc                          = 106.78 
    alpha_beta                      = 8.23   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 118.81 
    fmodel                         = 7.80   
    r_factors                      = 0.27   
    phase_errors                   = 10.97  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 256.05 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.778 micro seconds
Total CPU time: 6.01 minutes
from_scatterers_fft:    674 calls, 106.36 s
gradients_fft:          619 calls, 104.60 s

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

# Date 2008-01-16 Time 01:50:55 PST -0800 (1200477055.53 s)
Start R-work = 0.4189, R-free = 0.4112 (no bulk solvent and anisotropic scale)
Final R-work = 0.1249, R-free = 0.1705 (no bulk solvent and anisotropic scale)

Start R-work = 0.4108, R-free = 0.4027
Final R-work = 0.1069, R-free = 0.1548