# Date 2008-01-16 Time 03:34:20 PST -0800 (1200483260.40 s)
#phil __OFF__

Command line arguments: "../1296.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 24759
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1296

-------------------------------------------------------------------------------
  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: (72.0062, 47.3993, 88.1178, 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: 3.34, per 1000 atoms: 1.18


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (72.0062, 47.3993, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.3484 2.02253
Completeness in resolution range: 0.966022
Completeness with d_max=infinity: 0.96303

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.3484
                             d_min =   2.0225

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: (72.0062, 47.3993, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.3484 2.02253
Completeness in resolution range: 0.966022
Completeness with d_max=infinity: 0.96303

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.3488 -  4.3279 [2125/2149]  1912   213  10.0%
  bin  2:  4.3279 -  3.4480 [2041/2061]  1837   204  10.0%
  bin  3:  3.4480 -  3.0159 [2028/2047]  1825   203  10.0%
  bin  4:  3.0159 -  2.7419 [2004/2034]  1807   197   9.8%
  bin  5:  2.7419 -  2.5463 [2003/2022]  1804   199   9.9%
  bin  6:  2.5463 -  2.3968 [1959/1984]  1758   201  10.3%
  bin  7:  2.3968 -  2.2771 [1966/1994]  1766   200  10.2%
  bin  8:  2.2771 -  2.1783 [1974/2010]  1782   192   9.7%
  bin  9:  2.1783 -  2.0946 [1958/2000]  1761   197  10.1%
  bin 10:  2.0946 -  2.0225 [1531/1977]  1378   153  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1296/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: 0.12 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:
        1.58 -     2.25: 3
        2.25 -     2.91: 1387
        2.91 -     3.57: 4347
        3.57 -     4.24: 8966
        4.24 -     4.90: 12892
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.583 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  " NH2BARG A 275 " - " O   HOH Z 335 "  2.406 3.120
  ... (remaining 27590 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_1296/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1296/model_refine_001.geo

CPU time processing inputs: 8.94


============================ 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 = 72.00625 47.3993 88.1178 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.02 - 15.35 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5002   r_free= 0.4908   ksol= 0.00   Bsol= 0.00   scale= 0.761    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.88 A                  |
| x-ray target function (ml) for work reflections: 6.296955                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3488 -  4.8272 0.99   1385  154 0.4072 0.3783      6.6197      6.5404|
|  2:  4.8272 -  3.8514 0.99   1333  148 0.4313 0.4643      6.8427      6.9294|
|  3:  3.8514 -  3.3704 0.99   1305  143 0.4684 0.4348      6.7155      6.7204|
|  4:  3.3704 -  3.0650 0.99   1295  146 0.4976 0.4265       6.567      6.4654|
|  5:  3.0650 -  2.8468 0.99   1283  144 0.5215 0.5154        6.39      6.4365|
|  6:  2.8468 -  2.6799 0.99   1299  139 0.5259 0.5577      6.3034      6.2098|
|  7:  2.6799 -  2.5463 0.99   1285  142 0.5452 0.5125      6.2536      6.2492|
|  8:  2.5463 -  2.4359 0.98   1257  145 0.5446 0.5015      6.1993       6.157|
|  9:  2.4359 -  2.3425 0.98   1272  139 0.5338 0.6016      6.1291      6.1678|
| 10:  2.3425 -  2.2619 1.00   1258  142 0.5490 0.5332      6.1282      6.1628|
| 11:  2.2619 -  2.1914 0.98   1268  139 0.5260 0.5419      6.0445      6.0808|
| 12:  2.1914 -  2.1289 0.98   1246  141 0.5351 0.5392      5.9937      6.0213|
| 13:  2.1289 -  2.0730 0.99   1285  139 0.5426 0.4897       5.896      5.8297|
| 14:  2.0730 -  2.0225 0.68    859   98 0.5483 0.5086      5.8539      5.7804|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.3488 -  4.8272  1385   154  0.69  34.91   0.78     0.72      74292.37|
|  2:  4.8272 -  3.8514  1333   148  0.68  36.91   0.85     0.73     114795.58|
|  3:  3.8514 -  3.3704  1305   143  0.58  45.78   0.79     0.66     122954.32|
|  4:  3.3704 -  3.0650  1295   146  0.47  54.09   0.77     0.56     109906.34|
|  5:  3.0650 -  2.8468  1283   144  0.38  61.66   0.71     0.44      88738.72|
|  6:  2.8468 -  2.6799  1299   139  0.33  65.29   0.70     0.37      78795.42|
|  7:  2.6799 -  2.5463  1285   142  0.26  70.16   0.69     0.30      73026.17|
|  8:  2.5463 -  2.4359  1257   145  0.21  74.33   0.70     0.24      69114.91|
|  9:  2.4359 -  2.3425  1272   139  0.18  76.88   0.69     0.20      64797.45|
| 10:  2.3425 -  2.2619  1258   142  0.18  76.94   0.71     0.20      58915.13|
| 11:  2.2619 -  2.1914  1268   139  0.23  72.74   0.73     0.28      52982.99|
| 12:  2.1914 -  2.1289  1246   141  0.27  70.11   0.71     0.32      47401.61|
| 13:  2.1289 -  2.0730  1285   139  0.27  70.07   0.69     0.33      39500.95|
| 14:  2.0730 -  2.0225   859    98  0.25  71.49   0.68     0.26      31589.74|
|alpha:            min =        0.20 max =            0.73 mean =         0.41|
|beta:             min =    31589.74 max =       122954.32 mean =     74662.58|
|figures of merit: min =        0.00 max =            1.00 mean =         0.36|
|phase err.(work): min =        0.00 max =           90.00 mean =        62.42|
|phase err.(test): min =        0.00 max =           89.92 mean =        62.23|
|-----------------------------------------------------------------------------|

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

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 1
total                    = 1

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 19.659161             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.965   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.078140              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 83.973   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       23 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      159 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      674 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1468 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2549 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3829 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     4936 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6424 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7531 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       54.829 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.092    4.900  1.196 |       1.613 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.539)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 12.539)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.35 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5041   r_free= 0.4948   ksol= 0.00   Bsol= 0.00   scale= 0.735    |
|                                                                             |
| 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:   0.84 A                  |
| x-ray target function (ml) for work reflections: 6.297083                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.35 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4933   r_free= 0.4829   ksol= 0.27   Bsol= 20.00   scale= 0.946   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.37,7.04,9.67,0.00,0.00,0.00); trace/3= 8.36                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.85 A                  |
| x-ray target function (ml) for work reflections: 6.292910                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 17.379512             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.529   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.629170              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 82.508   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4933      final r-factor (work) = 0.4163          |
| start r-factor (free) = 0.4829      final r-factor (free) = 0.4400          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 109.5326 = 17.38 * 0.50 * 6.2952 + 1.00 * 54.8289                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 54.2397 = 17.38 * 0.50 * 6.2228 + 1.00 * 0.1654                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4163      final r-factor (work) = 0.3764          |
| start r-factor (free) = 0.4400      final r-factor (free) = 0.4271          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.1524 = 1.63 * 1.00 * 6.2228 + 1.00 * 0.0145                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.0572 = 1.63 * 1.00 * 6.1593 + 1.00 * 0.0227                              |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.539)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    111.54  15.04    None  None   None       |
|    all(noH): 2823   0      0.00    111.54  15.04    None  None   None       |
|    Sol.    : 438    0      0.00    111.54  27.70    None  None   None       |
|    Mac.    : 2385   0      0.00    82.87   12.72    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.154: 1386   |   5:    55.770 -  66.924:   28        |
|      1:    11.154 -  22.308:  805   |   6:    66.924 -  78.078:   17        |
|      2:    22.308 -  33.462:  329   |   7:    78.078 -  89.232:    6        |
|      3:    33.462 -  44.616:  166   |   8:    89.232 - 100.386:    0        |
|      4:    44.616 -  55.770:   84   |   9:   100.386 - 111.540:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3764 r_free = 0.4271             target_work(ml) = 6.143         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3758 r_free = 0.4274             target_work(ml) = 6.142         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.35 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3758   r_free= 0.4274   ksol= 0.27   Bsol= 20.00   scale= 1.067   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.37,7.04,9.67,0.00,0.00,0.00); trace/3= 8.36                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.64 A                  |
| x-ray target function (ml) for work reflections: 6.141830                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.35 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3749   r_free= 0.4262   ksol= 0.30   Bsol= 50.00   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.70,4.69,6.82,0.00,0.00,0.00); trace/3= 5.74                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.143188                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.408174             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.833   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.680109              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 120.440  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3749      final r-factor (work) = 0.2902          |
| start r-factor (free) = 0.4262      final r-factor (free) = 0.3535          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 35.2661 = 11.41 * 0.50 * 6.1536 + 1.00 * 0.1654                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 34.5950 = 11.41 * 0.50 * 6.0465 + 1.00 * 0.1051                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2902      final r-factor (work) = 0.2632          |
| start r-factor (free) = 0.3535      final r-factor (free) = 0.3239          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1373 = 0.68 * 1.00 * 6.0465 + 1.00 * 0.0249                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0512 = 0.68 * 1.00 * 5.9060 + 1.00 * 0.0344                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.539)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    122.08  13.99    None  None   None       |
|    all(noH): 2823   0      0.00    122.08  13.99    None  None   None       |
|    Sol.    : 438    0      0.00    122.08  33.71    None  None   None       |
|    Mac.    : 2385   0      0.00    83.75   10.36    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 -  12.208: 1721   |   5:    61.038 -  73.246:   23        |
|      1:    12.208 -  24.415:  631   |   6:    73.246 -  85.453:   12        |
|      2:    24.415 -  36.623:  250   |   7:    85.453 -  97.661:    0        |
|      3:    36.623 -  48.830:  121   |   8:    97.661 - 109.868:    1        |
|      4:    48.830 -  61.038:   63   |   9:   109.868 - 122.076:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2632 r_free = 0.3239             target_work(ml) = 5.873         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2630 r_free = 0.3243             target_work(ml) = 5.873         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.35 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2630   r_free= 0.3243   ksol= 0.30   Bsol= 50.00   scale= 1.046   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.70,4.69,6.82,0.00,0.00,0.00); trace/3= 5.74                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.872580                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.35 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2615   r_free= 0.3225   ksol= 0.31   Bsol= 50.00   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.47,3.13,4.60,0.00,0.00,0.00); trace/3= 3.73                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.873652                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.021055              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.272  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.699186              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.655   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2615      final r-factor (work) = 0.2045          |
| start r-factor (free) = 0.3225      final r-factor (free) = 0.2586          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.9802 = 4.02 * 0.50 * 5.9065 + 1.00 * 0.1051                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.6962 = 4.02 * 0.50 * 5.7815 + 1.00 * 0.0724                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2045      final r-factor (work) = 0.1935          |
| start r-factor (free) = 0.2586      final r-factor (free) = 0.2493          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0599 = 0.70 * 1.00 * 5.7815 + 1.00 * 0.0176                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9642 = 0.70 * 1.00 * 5.6310 + 1.00 * 0.0270                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 13     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.539)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    121.95  13.95    None  None   None       |
|    all(noH): 2823   0      0.00    121.95  13.95    None  None   None       |
|    Sol.    : 438    0      0.33    121.95  34.83    None  None   None       |
|    Mac.    : 2385   0      0.00    86.12   10.11    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 -  12.195: 1753   |   5:    60.974 -  73.169:   25        |
|      1:    12.195 -  24.390:  591   |   6:    73.169 -  85.363:   11        |
|      2:    24.390 -  36.584:  243   |   7:    85.363 -  97.558:    2        |
|      3:    36.584 -  48.779:  129   |   8:    97.558 - 109.753:    0        |
|      4:    48.779 -  60.974:   68   |   9:   109.753 - 121.948:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1935 r_free = 0.2493             target_work(ml) = 5.618         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1933 r_free = 0.2494             target_work(ml) = 5.617         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.35 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1933   r_free= 0.2494   ksol= 0.31   Bsol= 50.00   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.47,3.13,4.60,0.00,0.00,0.00); trace/3= 3.73                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.617009                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.35 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1930   r_free= 0.2481   ksol= 0.33   Bsol= 68.16   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.24,2.16,3.45,0.00,0.00,0.00); trace/3= 2.62                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.615727                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.448483              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.142  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.364199              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 99.491   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1930      final r-factor (work) = 0.1677          |
| start r-factor (free) = 0.2481      final r-factor (free) = 0.2213          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9703 = 2.45 * 0.50 * 5.6344 + 1.00 * 0.0724                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8650 = 2.45 * 0.50 * 5.5547 + 1.00 * 0.0647                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1677      final r-factor (work) = 0.1561          |
| start r-factor (free) = 0.2213      final r-factor (free) = 0.2070          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0560 = 0.36 * 1.00 * 5.5547 + 1.00 * 0.0329                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0016 = 0.36 * 1.00 * 5.4624 + 1.00 * 0.0122                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.539)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    112.78  13.85    None  None   None       |
|    all(noH): 2823   0      0.00    112.78  13.85    None  None   None       |
|    Sol.    : 438    0      1.41    112.78  38.16    None  None   None       |
|    Mac.    : 2385   0      0.00    79.86   9.38     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 -  11.278: 1781   |   5:    56.391 -  67.670:   57        |
|      1:    11.278 -  22.557:  553   |   6:    67.670 -  78.948:   16        |
|      2:    22.557 -  33.835:  160   |   7:    78.948 -  90.226:    5        |
|      3:    33.835 -  45.113:  144   |   8:    90.226 - 101.504:    0        |
|      4:    45.113 -  56.391:  106   |   9:   101.504 - 112.782:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1561 r_free = 0.2070             target_work(ml) = 5.432         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1560 r_free = 0.2069             target_work(ml) = 5.432         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.35 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1560   r_free= 0.2069   ksol= 0.33   Bsol= 68.16   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.24,2.16,3.45,0.00,0.00,0.00); trace/3= 2.62                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.431833                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.35 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1562   r_free= 0.2071   ksol= 0.33   Bsol= 77.73   scale= 0.982   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.77,1.74,3.11,0.00,0.00,0.00); trace/3= 2.21                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.433196                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.092101              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 118.649  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.468368              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 158.019  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1562      final r-factor (work) = 0.1408          |
| start r-factor (free) = 0.2071      final r-factor (free) = 0.1897          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7796 = 2.09 * 0.50 * 5.4627 + 1.00 * 0.0654                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7048 = 2.09 * 0.50 * 5.3887 + 1.00 * 0.0680                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1408      final r-factor (work) = 0.1370          |
| start r-factor (free) = 0.1897      final r-factor (free) = 0.1875          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5360 = 0.47 * 1.00 * 5.3887 + 1.00 * 0.0121                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5097 = 0.47 * 1.00 * 5.3302 + 1.00 * 0.0132                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.539)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    103.02  13.90    None  None   None       |
|    all(noH): 2823   0      0.00    103.02  13.90    None  None   None       |
|    Sol.    : 438    0      1.96    103.02  39.31    None  None   None       |
|    Mac.    : 2385   0      0.00    79.51   9.23     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 -  10.302: 1714   |   5:    51.510 -  61.813:   81        |
|      1:    10.302 -  20.604:  586   |   6:    61.813 -  72.115:   36        |
|      2:    20.604 -  30.906:  151   |   7:    72.115 -  82.417:   19        |
|      3:    30.906 -  41.208:  128   |   8:    82.417 -  92.719:    3        |
|      4:    41.208 -  51.510:  103   |   9:    92.719 - 103.021:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1370 r_free = 0.1875             target_work(ml) = 5.324         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1369 r_free = 0.1873             target_work(ml) = 5.324         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.35 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1369   r_free= 0.1873   ksol= 0.33   Bsol= 77.73   scale= 0.982   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.77,1.74,3.11,0.00,0.00,0.00); trace/3= 2.21                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.323547                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3488 -  4.8272 0.99   1385  154 0.1099 0.1455      5.4746      5.6269|
|  2:  4.8272 -  3.8514 0.99   1333  148 0.0946 0.1239       5.535      5.7436|
|  3:  3.8514 -  3.3704 0.99   1305  143 0.1254 0.1615      5.6177      5.9104|
|  4:  3.3704 -  3.0650 0.99   1295  146 0.1468 0.1935      5.6138      5.7988|
|  5:  3.0650 -  2.8468 0.99   1283  144 0.1719 0.2166      5.5487      5.7462|
|  6:  2.8468 -  2.6799 0.99   1299  139 0.1521 0.2426      5.4163      5.6595|
|  7:  2.6799 -  2.5463 0.99   1285  142 0.1582 0.1867      5.3573      5.5014|
|  8:  2.5463 -  2.4359 0.98   1257  145 0.1544 0.2061      5.2978      5.5216|
|  9:  2.4359 -  2.3425 0.98   1272  139 0.1499 0.2273      5.2418      5.4757|
| 10:  2.3425 -  2.2619 1.00   1258  142 0.1467 0.2022      5.1778      5.3914|
| 11:  2.2619 -  2.1914 0.98   1268  139 0.1439 0.2180      5.1364       5.427|
| 12:  2.1914 -  2.1289 0.98   1246  141 0.1394 0.1967      5.0511      5.3447|
| 13:  2.1289 -  2.0730 0.99   1285  139 0.1437 0.2097      4.9843      5.1968|
| 14:  2.0730 -  2.0225 0.68    859   98 0.1366 0.2009      4.8915      5.1239|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.3488 -  4.8272  1385   154  0.93  10.56   0.96     0.93       8960.65|
|  2:  4.8272 -  3.8514  1333   148  0.94   9.33   0.99     0.97      11077.11|
|  3:  3.8514 -  3.3704  1305   143  0.92  13.39   1.01     1.00      13615.13|
|  4:  3.3704 -  3.0650  1295   146  0.90  16.51   0.99     0.97      13959.29|
|  5:  3.0650 -  2.8468  1283   144  0.86  20.21   0.99     0.97      12729.38|
|  6:  2.8468 -  2.6799  1299   139  0.87  19.66   0.97     0.94      10543.16|
|  7:  2.6799 -  2.5463  1285   142  0.87  19.66   0.99     0.94       9173.26|
|  8:  2.5463 -  2.4359  1257   145  0.87  19.98   0.97     0.93       8210.92|
|  9:  2.4359 -  2.3425  1272   139  0.87  19.48   0.98     0.92       7522.75|
| 10:  2.3425 -  2.2619  1258   142  0.87  19.55   0.99     0.93       6476.37|
| 11:  2.2619 -  2.1914  1268   139  0.87  19.55   0.98     0.91       6123.32|
| 12:  2.1914 -  2.1289  1246   141  0.88  18.44   0.99     0.97       5548.61|
| 13:  2.1289 -  2.0730  1285   139  0.86  20.53   0.97     0.94       5023.50|
| 14:  2.0730 -  2.0225   859    98  0.88  18.89   0.94     0.89       3949.10|
|alpha:            min =        0.89 max =            1.00 mean =         0.95|
|beta:             min =     3949.10 max =        13959.29 mean =      8927.91|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.96 mean =        17.44|
|phase err.(test): min =        0.00 max =           89.13 mean =        16.64|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.35 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1369   r_free= 0.1873   ksol= 0.33   Bsol= 75.51   scale= 0.984   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.44,-0.48,0.93,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.323526                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.35 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1369   r_free= 0.1873   ksol= 0.33   Bsol= 75.51   scale= 0.984   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.44,-0.48,0.93,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.323526                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3488 -  4.8272 0.99   1385  154 0.1097 0.1453      5.4729      5.6264|
|  2:  4.8272 -  3.8514 0.99   1333  148 0.0945 0.1236      5.5339      5.7412|
|  3:  3.8514 -  3.3704 0.99   1305  143 0.1253 0.1614      5.6169      5.9096|
|  4:  3.3704 -  3.0650 0.99   1295  146 0.1469 0.1935      5.6144      5.7988|
|  5:  3.0650 -  2.8468 0.99   1283  144 0.1721 0.2168      5.5495      5.7472|
|  6:  2.8468 -  2.6799 0.99   1299  139 0.1522 0.2425      5.4169      5.6596|
|  7:  2.6799 -  2.5463 0.99   1285  142 0.1583 0.1868      5.3577      5.5018|
|  8:  2.5463 -  2.4359 0.98   1257  145 0.1544 0.2062       5.298      5.5218|
|  9:  2.4359 -  2.3425 0.98   1272  139 0.1499 0.2271       5.242      5.4754|
| 10:  2.3425 -  2.2619 1.00   1258  142 0.1467 0.2024       5.178      5.3919|
| 11:  2.2619 -  2.1914 0.98   1268  139 0.1439 0.2182      5.1367      5.4274|
| 12:  2.1914 -  2.1289 0.98   1246  141 0.1394 0.1968      5.0513       5.345|
| 13:  2.1289 -  2.0730 0.99   1285  139 0.1437 0.2096      4.9844      5.1966|
| 14:  2.0730 -  2.0225 0.68    859   98 0.1366 0.2008      4.8915      5.1237|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.3488 -  4.8272  1385   154  0.93  10.55   0.96     0.93       8956.46|
|  2:  4.8272 -  3.8514  1333   148  0.94   9.32   0.99     0.97      11055.71|
|  3:  3.8514 -  3.3704  1305   143  0.92  13.36   1.01     1.00      13577.64|
|  4:  3.3704 -  3.0650  1295   146  0.90  16.51   1.00     0.97      13962.56|
|  5:  3.0650 -  2.8468  1283   144  0.86  20.22   0.99     0.97      12741.64|
|  6:  2.8468 -  2.6799  1299   139  0.87  19.67   0.97     0.94      10556.69|
|  7:  2.6799 -  2.5463  1285   142  0.87  19.67   0.99     0.95       9179.43|
|  8:  2.5463 -  2.4359  1257   145  0.87  19.98   0.98     0.93       8212.71|
|  9:  2.4359 -  2.3425  1272   139  0.87  19.49   0.99     0.93       7523.86|
| 10:  2.3425 -  2.2619  1258   142  0.87  19.56   0.99     0.93       6479.40|
| 11:  2.2619 -  2.1914  1268   139  0.87  19.56   0.98     0.91       6128.40|
| 12:  2.1914 -  2.1289  1246   141  0.88  18.45   0.99     0.97       5551.02|
| 13:  2.1289 -  2.0730  1285   139  0.86  20.53   0.98     0.95       5024.45|
| 14:  2.0730 -  2.0225   859    98  0.88  18.89   0.95     0.89       3948.69|
|alpha:            min =        0.89 max =            1.00 mean =         0.95|
|beta:             min =     3948.69 max =        13962.56 mean =      8926.78|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.88 mean =        17.44|
|phase err.(test): min =        0.00 max =           89.09 mean =        16.65|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.539)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.29    105.31  16.19    None  None   None       |
|    all(noH): 2823   0      2.29    105.31  16.19    None  None   None       |
|    Sol.    : 438    0      4.25    105.31  41.60    None  None   None       |
|    Mac.    : 2385   0      2.29    81.79   11.52    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.286 -  12.588: 1714   |   5:    53.796 -  64.098:   81        |
|      1:    12.588 -  22.890:  586   |   6:    64.098 -  74.400:   36        |
|      2:    22.890 -  33.192:  151   |   7:    74.400 -  84.702:   19        |
|      3:    33.192 -  43.494:  128   |   8:    84.702 -  95.005:    3        |
|      4:    43.494 -  53.796:  103   |   9:    95.005 - 105.307:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 342         
Filter by distance & map next to the model:
   mapped sites are within: 0.362 - 5.525
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 336 from: 342
   mapped sites are within: 0.707 - 5.525

peak=    9.466 closest distance to " CB  VAL A 230 " =    1.471
peak=    6.804 closest distance to " O   HOH Z  82 " =    1.086
peak=    6.478 closest distance to " CG  ARG A 138 " =    1.346
peak=    6.038 closest distance to " NH1 ARG A 138 " =    1.057
peak=    5.724 closest distance to " CG1 VAL A 296 " =    1.307
peak=    5.516 closest distance to " CD1AILE A 234 " =    1.158
peak=    5.277 closest distance to " CG2 VAL A 296 " =    1.037
peak=    5.176 closest distance to " CZ  PHE A 218 " =    1.166
peak=    5.130 closest distance to " CG  LEU A   5 " =    1.256
peak=    4.947 closest distance to " O   HOH Z 102 " =    1.508
peak=    4.946 closest distance to " O   HOH Z 425 " =    1.898
peak=    4.899 closest distance to " CB  GLN A 223 " =    1.479
peak=    4.822 closest distance to " CG  PRO A 280 " =    0.998
peak=    4.797 closest distance to " NH1 ARG A  56 " =    1.265
peak=    4.750 closest distance to " CG  PRO A 198 " =    1.321
peak=    4.745 closest distance to " O   HOH Z 411 " =    3.164
peak=    4.713 closest distance to " O   PRO A 198 " =    1.543
peak=    4.689 closest distance to " CD2 LEU A   5 " =    1.111
peak=    4.647 closest distance to " CG  LEU A 228 " =    1.335
peak=    4.646 closest distance to " CB  SER A  63 " =    1.440
peak=    4.629 closest distance to " CA  VAL A 230 " =    1.168
peak=    4.603 closest distance to " O   HOH Z 103 " =    0.949
peak=    4.583 closest distance to " O   HOH Z 369 " =    1.959
peak=    4.558 closest distance to " CB  ASP A 124 " =    0.819
peak=    4.546 closest distance to " CD2 LEU A 228 " =    1.200
peak=    4.512 closest distance to " CD  ARG A 138 " =    1.243
peak=    4.511 closest distance to " O   HOH Z 210 " =    1.240
peak=    4.359 closest distance to " O   HOH Z 182 " =    1.376
peak=    4.338 closest distance to " NH1AARG A 145 " =    1.262
peak=    4.275 closest distance to " O   HOH Z   4 " =    1.810
peak=    4.263 closest distance to " O   HOH Z 261 " =    1.808
peak=    4.252 closest distance to " N   SER A 164 " =    1.000
peak=    4.212 closest distance to " O   HOH Z 184 " =    1.958
peak=    4.207 closest distance to " CA  TYR A  30 " =    1.000
peak=    4.196 closest distance to " OD1 ASN A 217 " =    1.480
peak=    4.189 closest distance to " O   HOH Z 112 " =    1.543
peak=    4.187 closest distance to " O   HOH Z 111 " =    1.897
peak=    4.177 closest distance to " O   ASP A 124 " =    1.088
peak=    4.169 closest distance to " O   HOH Z 130 " =    1.070
peak=    4.134 closest distance to " CB  ASN A 148 " =    1.360
peak=    4.126 closest distance to " O   HOH Z 232 " =    2.052
peak=    4.104 closest distance to " CB  TYR A 169 " =    0.729
peak=    4.091 closest distance to " CE3 TRP A  85 " =    1.133
peak=    4.082 closest distance to " CG1 ILE A 120 " =    1.111
peak=    4.072 closest distance to " NE2 GLN A  11 " =    1.083
peak=    4.063 closest distance to " CB  TRP A 266 " =    0.953
peak=    4.052 closest distance to " O   HOH Z  41 " =    0.949
peak=    4.050 closest distance to " CD ALYS A 290 " =    1.114
peak=    4.038 closest distance to " CZ  PHE A 192 " =    1.019
peak=    4.034 closest distance to " CG2 THR A 221 " =    1.065
peak=    4.025 closest distance to " CB  VAL A 296 " =    1.172
peak=    4.011 closest distance to " O   ASN A 209 " =    1.440
peak=    3.996 closest distance to " CG BARG A 275 " =    1.291
peak=    3.990 closest distance to " CB  ALA A  10 " =    1.288
peak=    3.988 closest distance to " O   HOH Z 179 " =    0.868
peak=    3.977 closest distance to " CB  SER A   3 " =    1.817
peak=    3.974 closest distance to " CA  ALA A 295 " =    1.132
peak=    3.970 closest distance to " O   HOH Z 250 " =    1.321
peak=    3.969 closest distance to " CG2 ILE A 234 " =    1.008
peak=    3.968 closest distance to " CA  ALA A  51 " =    0.959
peak=    3.968 closest distance to " O   HOH Z  80 " =    2.252
peak=    3.967 closest distance to " NH2AARG A 145 " =    1.037
peak=    3.943 closest distance to " CA  ARG A 195 " =    1.354
peak=    3.935 closest distance to " CG  PRO A 243 " =    1.158
peak=    3.928 closest distance to " O   HOH Z  35 " =    4.885
peak=    3.925 closest distance to " CB  GLN A 183 " =    1.218
peak=    3.918 closest distance to " O   HOH Z 303 " =    2.512
peak=    3.916 closest distance to " CB  ASN A  39 " =    0.859
peak=    3.900 closest distance to " O   HOH Z 234 " =    3.969
peak=    3.896 closest distance to " CD  ARG A 159 " =    0.755
peak=    3.894 closest distance to " OE1 GLN A  55 " =    1.354
peak=    3.894 closest distance to " O   HOH Z  56 " =    1.856
peak=    3.880 closest distance to " CA  ASP A 124 " =    0.837
peak=    3.858 closest distance to " O   HOH Z 411 " =    1.564
peak=    3.857 closest distance to " O   HOH Z  49 " =    1.513
peak=    3.855 closest distance to " O   HOH Z  76 " =    1.450
peak=    3.839 closest distance to " CB  ASN A 142 " =    0.984
peak=    3.833 closest distance to " OG1 THR A 264 " =    0.867
peak=    3.829 closest distance to " N   GLN A  55 " =    0.910
peak=    3.817 closest distance to " O   HOH Z 265 " =    2.025
peak=    3.809 closest distance to " CB  GLU A 128 " =    1.108
peak=    3.803 closest distance to " CA  ALA A  21 " =    1.379
peak=    3.791 closest distance to " ND2 ASN A 249 " =    2.062
peak=    3.785 closest distance to " O   SER A  87 " =    2.398
peak=    3.774 closest distance to " OG  SER A 276 " =    1.609
peak=    3.771 closest distance to " O   HOH Z  70 " =    0.957
peak=    3.760 closest distance to " O   ASP A 200 " =    1.664
peak=    3.758 closest distance to " O   HOH Z 393 " =    3.848
peak=    3.754 closest distance to " O   HOH Z 290 " =    1.645
peak=    3.750 closest distance to " O   HOH Z 287 " =    2.098
peak=    3.746 closest distance to " CD1 LEU A 300 " =    1.115
peak=    3.745 closest distance to " O   THR A 251 " =    1.192
peak=    3.735 closest distance to " O   HOH Z 410 " =    1.199
peak=    3.722 closest distance to " O   HOH Z   9 " =    1.399
peak=    3.718 closest distance to " O   HOH Z  32 " =    2.162
peak=    3.709 closest distance to " CZ3 TRP A 266 " =    1.179
peak=    3.705 closest distance to " O   HOH Z 207 " =    1.379
peak=    3.702 closest distance to " CG2 ILE A 120 " =    1.034
peak=    3.689 closest distance to " CG1 ILE A  49 " =    1.855
peak=    3.686 closest distance to " O   HOH Z 214 " =    1.535
peak=    3.683 closest distance to " CB  ALA A 100 " =    1.475
peak=    3.682 closest distance to " O   HOH Z 183 " =    1.588
peak=    3.678 closest distance to " O   HOH Z 298 " =    2.307
peak=    3.677 closest distance to " CG  GLU A  37 " =    1.010
peak=    3.658 closest distance to " CB  SER A 216 " =    0.927
peak=    3.648 closest distance to " CG2BVAL A  41 " =    1.246
peak=    3.646 closest distance to " CD1 LEU A  96 " =    0.780
peak=    3.641 closest distance to " CG1 VAL A 153 " =    1.115
peak=    3.637 closest distance to " O   HOH Z 188 " =    3.080
peak=    3.636 closest distance to " O   HOH Z 368 " =    2.284
peak=    3.630 closest distance to " CA  MET A 105 " =    0.923
peak=    3.629 closest distance to " N   PHE A 130 " =    1.267
peak=    3.628 closest distance to " O   HOH Z 437 " =    1.589
peak=    3.627 closest distance to " CB  GLN A  89 " =    1.135
peak=    3.625 closest distance to " CG1 ILE A  33 " =    1.281
peak=    3.621 closest distance to " CG2 THR A  82 " =    0.707
peak=    3.619 closest distance to " CA  TYR A  30 " =    1.107
peak=    3.611 closest distance to " CB  ARG A 275 " =    0.944
peak=    3.611 closest distance to " CA  ILE A  33 " =    1.829
peak=    3.610 closest distance to " O   HOH Z 298 " =    2.239
peak=    3.608 closest distance to " CE  LYS A  76 " =    0.964
peak=    3.607 closest distance to " O   HOH Z 197 " =    2.011
peak=    3.607 closest distance to " CZ3 TRP A  85 " =    0.943
peak=    3.596 closest distance to " CA  LEU A 101 " =    1.261
peak=    3.592 closest distance to " CA  ALA A 160 " =    1.141
peak=    3.587 closest distance to " CG  PRO A 213 " =    1.288
peak=    3.587 closest distance to " CB  ARG A 259 " =    1.931
peak=    3.587 closest distance to " OG  SER A 245 " =    1.677
peak=    3.574 closest distance to " CE1 TYR A 186 " =    1.208
peak=    3.566 closest distance to " O   HOH Z  38 " =    2.438
peak=    3.564 closest distance to " O   HOH Z 427 " =    3.219
peak=    3.562 closest distance to " CA  ASP A 162 " =    0.964
peak=    3.558 closest distance to " CD1 LEU A   5 " =    1.362
peak=    3.556 closest distance to " N   ASN A  39 " =    1.206
peak=    3.552 closest distance to " CG  MET A 185 " =    1.428
peak=    3.544 closest distance to " CB  LEU A  83 " =    0.712
peak=    3.541 closest distance to " CG  GLN A  55 " =    0.789
peak=    3.541 closest distance to " CA  TYR A 116 " =    1.470
peak=    3.539 closest distance to " CB  ASN A 187 " =    1.117
peak=    3.535 closest distance to " CA  GLU A 152 " =    0.883
peak=    3.533 closest distance to " CA  MET A  40 " =    1.236
peak=    3.533 closest distance to " CB  ARG A  79 " =    1.528
peak=    3.532 closest distance to " NE2 HIS A 115 " =    1.156
peak=    3.531 closest distance to " CB  VAL A 265 " =    1.241
peak=    3.527 closest distance to " CA  ILE A 106 " =    0.864
peak=    3.524 closest distance to " CD2 LEU A 297 " =    0.878
peak=    3.522 closest distance to " CA  SER A  87 " =    0.833
peak=    3.519 closest distance to " O   HOH Z 148 " =    2.117
peak=    3.518 closest distance to " O   HOH Z 126 " =    1.764
peak=    3.517 closest distance to " CB  MET A  40 " =    0.739
peak=    3.515 closest distance to " CA  PRO A  54 " =    1.014
peak=    3.514 closest distance to " CA  ARG A 102 " =    1.196
peak=    3.514 closest distance to " O   HOH Z  19 " =    2.609
peak=    3.509 closest distance to " O   HOH Z  63 " =    2.002
peak=    3.501 closest distance to " N   SER A 271 " =    0.997
peak=    3.499 closest distance to " CA  ARG A 139 " =    1.264
peak=    3.495 closest distance to " CG  LYS A  76 " =    1.144
peak=    3.492 closest distance to " CD  LYS A 166 " =    1.414
peak=    3.487 closest distance to " N   ALA A 256 " =    1.116
peak=    3.486 closest distance to " N   TYR A  15 " =    0.837
peak=    3.486 closest distance to " O   HOH Z 359 " =    1.603
peak=    3.483 closest distance to " CD1 LEU A 101 " =    1.069
peak=    3.477 closest distance to " CB  TYR A  30 " =    1.037
peak=    3.471 closest distance to " CG  ARG A 269 " =    1.730
peak=    3.465 closest distance to " CB  ALA A 137 " =    1.074
peak=    3.462 closest distance to " O   HOH Z  48 " =    1.759
peak=    3.461 closest distance to " CB  GLU A  46 " =    0.951
peak=    3.460 closest distance to " O   THR A 294 " =    1.426
peak=    3.459 closest distance to " CA  HIS A  86 " =    0.768
peak=    3.456 closest distance to " CB  ASN A 173 " =    1.005
peak=    3.453 closest distance to " O   HOH Z 256 " =    2.071
peak=    3.453 closest distance to " CB  TRP A 150 " =    1.581
peak=    3.451 closest distance to " O   HOH Z 201 " =    2.764
peak=    3.450 closest distance to " CD  ARG A 269 " =    0.906
peak=    3.449 closest distance to " OG  SER A  28 " =    1.459
peak=    3.448 closest distance to " O   HOH Z 406 " =    1.491
peak=    3.447 closest distance to " O   HOH Z 193 " =    2.194
peak=    3.443 closest distance to " O   MET A 105 " =    1.556
peak=    3.442 closest distance to " CB  PRO A  54 " =    0.777
peak=    3.441 closest distance to " O   HOH Z 120 " =    1.110
peak=    3.441 closest distance to " CH2 TRP A  70 " =    1.096
peak=    3.434 closest distance to " O   HOH Z 332 " =    1.566
peak=    3.433 closest distance to " O   HOH Z 132 " =    2.695
peak=    3.428 closest distance to " CZ  PHE A  38 " =    1.273
peak=    3.425 closest distance to " CA  ARG A 156 " =    1.146
peak=    3.423 closest distance to " CB  PRO A 243 " =    1.178
peak=    3.420 closest distance to " CB  PRO A 198 " =    0.975
peak=    3.413 closest distance to " O   HOH Z 258 " =    2.236
peak=    3.411 closest distance to " O   HOH Z 117 " =    1.218
peak=    3.409 closest distance to " CB  VAL A 202 " =    1.515
peak=    3.401 closest distance to " C   ALA A 299 " =    0.939
peak=    3.397 closest distance to " O   THR A 182 " =    1.447
peak=    3.389 closest distance to " CB  GLU A 152 " =    1.295
peak=    3.387 closest distance to " CD  ARG A  66 " =    2.375
peak=    3.386 closest distance to " O   HOH Z 272 " =    1.935
peak=    3.385 closest distance to " O   HOH Z  68 " =    1.696
peak=    3.375 closest distance to " O   HOH Z 423 " =    1.671
peak=    3.373 closest distance to " NH1 ARG A 269 " =    0.760
peak=    3.373 closest distance to " NH1 ARG A  14 " =    1.067
peak=    3.372 closest distance to " CB  ALA A 242 " =    0.838
peak=    3.370 closest distance to " CB  ARG A 190 " =    1.650
peak=    3.366 closest distance to " O   HOH Z 142 " =    1.661
peak=    3.365 closest distance to " O   HOH Z 313 " =    1.824
peak=    3.365 closest distance to " CD2 TRP A 179 " =    1.324
peak=    3.360 closest distance to " CD  LYS A 289 " =    1.265
peak=    3.360 closest distance to " O   HOH Z 215 " =    1.560
peak=    3.358 closest distance to " CB  GLU A 277 " =    3.838
peak=    3.357 closest distance to " O   GLU A  53 " =    0.884
peak=    3.353 closest distance to " CB  SER A 273 " =    0.994
peak=    3.351 closest distance to " CB  ALA A 104 " =    0.875
peak=    3.346 closest distance to " OH  TYR A 186 " =    1.029
peak=    3.346 closest distance to " O   HOH Z 125 " =    3.789
peak=    3.344 closest distance to " CD  ARG A 219 " =    1.160
peak=    3.342 closest distance to " O   THR A 220 " =    1.265
peak=    3.342 closest distance to " O   PRO A  90 " =    1.459
peak=    3.341 closest distance to " CA  ALA A 100 " =    1.058
peak=    3.341 closest distance to " CA  VAL A 153 " =    0.947
peak=    3.337 closest distance to " CB  ILE A 199 " =    0.880
peak=    3.337 closest distance to " O   HOH Z 316 " =    3.138
peak=    3.329 closest distance to " CB  GLU A 175 " =    0.838
peak=    3.327 closest distance to " O  BHOH Z  74 " =    1.292
peak=    3.325 closest distance to " CD2 LEU A 255 " =    1.717
peak=    3.321 closest distance to " CB  THR A  82 " =    1.350
peak=    3.320 closest distance to " CA  ARG A  36 " =    1.028
peak=    3.312 closest distance to " O   HOH Z  57 " =    1.725
peak=    3.311 closest distance to " CD  LYS A 119 " =    1.482
peak=    3.310 closest distance to " CG1 ILE A 151 " =    1.257
peak=    3.307 closest distance to " O   HOH Z  99 " =    2.480
peak=    3.307 closest distance to " CA  ALA A 184 " =    1.106
peak=    3.298 closest distance to " O   HOH Z 247 " =    1.574
peak=    3.298 closest distance to " CE2 PHE A 204 " =    0.981
peak=    3.296 closest distance to " CG BARG A 275 " =    1.494
peak=    3.293 closest distance to " CA  ALA A 154 " =    1.004
peak=    3.291 closest distance to " OG1 THR A 279 " =    1.464
peak=    3.290 closest distance to " O   HOH Z 193 " =    1.782
peak=    3.290 closest distance to " NE2 GLN A 278 " =    2.307
peak=    3.289 closest distance to " CB  ALA A  43 " =    1.100
peak=    3.288 closest distance to " CG2AVAL A 121 " =    2.052
peak=    3.288 closest distance to " CB  ARG A 138 " =    1.727
peak=    3.285 closest distance to " CB  SER A 210 " =    0.947
peak=    3.285 closest distance to " CE2 TYR A 186 " =    0.938
peak=    3.285 closest distance to " O   HOH Z 344 " =    2.885
peak=    3.284 closest distance to " O   HOH Z 185 " =    2.057
peak=    3.280 closest distance to " N   ASN A 127 " =    1.171
peak=    3.276 closest distance to " N   GLU A  44 " =    0.976
peak=    3.276 closest distance to " CB  GLN A  88 " =    1.334
peak=    3.271 closest distance to " CB  ALA A   9 " =    1.677
peak=    3.270 closest distance to " O   ALA A 165 " =    1.376
peak=    3.265 closest distance to " ND2 ASN A 249 " =    0.826
peak=    3.263 closest distance to " O   HOH Z 346 " =    1.665
peak=    3.263 closest distance to " NE2 GLN A  58 " =    4.505
peak=    3.263 closest distance to " CA  GLY A 267 " =    0.958
peak=    3.262 closest distance to " O   HOH Z 158 " =    3.160
peak=    3.262 closest distance to " CA  ASN A 284 " =    0.846
peak=    3.259 closest distance to " O   HOH Z 186 " =    1.844
peak=    3.258 closest distance to " CA  ASN A 127 " =    1.161
peak=    3.257 closest distance to " O   HOH Z  78 " =    2.199
peak=    3.257 closest distance to " O   PHE A 192 " =    1.581
peak=    3.254 closest distance to " CA  GLN A 223 " =    0.888
peak=    3.250 closest distance to " CG  LEU A 167 " =    1.177
peak=    3.244 closest distance to " CB  ALA A 291 " =    1.181
peak=    3.243 closest distance to " CA  GLU A  46 " =    0.820
peak=    3.242 closest distance to " O   HOH Z 329 " =    4.071
peak=    3.241 closest distance to " O   HOH Z 194 " =    2.427
peak=    3.238 closest distance to " ND2 ASN A 187 " =    1.474
peak=    3.238 closest distance to " O   GLU A 152 " =    1.484
peak=    3.236 closest distance to " O   HOH Z 438 " =    2.704
peak=    3.235 closest distance to " CB  ALA A 248 " =    1.140
peak=    3.227 closest distance to " O   HOH Z 394 " =    1.796
peak=    3.227 closest distance to " O   HOH Z  59 " =    2.213
peak=    3.226 closest distance to " NE2 GLN A 103 " =    1.199
peak=    3.225 closest distance to " CB  ILE A 120 " =    1.412
peak=    3.221 closest distance to " CA  GLY A 196 " =    0.712
peak=    3.217 closest distance to " N   VAL A 126 " =    1.413
peak=    3.212 closest distance to " CE3 TRP A 150 " =    1.109
peak=    3.212 closest distance to " O   HOH Z 124 " =    1.958
peak=    3.211 closest distance to " ND1 HIS A  81 " =    1.788
peak=    3.210 closest distance to " O   HOH Z 285 " =    2.655
peak=    3.209 closest distance to " O   HOH Z 109 " =    2.789
peak=    3.208 closest distance to " CA  ILE A 234 " =    0.942
peak=    3.206 closest distance to " O   HOH Z   1 " =    1.992
peak=    3.202 closest distance to " CD1 ILE A 199 " =    0.936
peak=    3.201 closest distance to " NE AARG A 275 " =    1.629
peak=    3.199 closest distance to " CB  GLU A  37 " =    0.955
peak=    3.197 closest distance to " O   HOH Z 214 " =    2.363
peak=    3.195 closest distance to " N   GLU A 152 " =    1.521
peak=    3.194 closest distance to " CA  ASP A 191 " =    0.938
peak=    3.192 closest distance to " CB  LEU A 255 " =    2.031
peak=    3.189 closest distance to " CB  VAL A 296 " =    1.362
peak=    3.188 closest distance to " CA  ALA A 291 " =    0.986
peak=    3.185 closest distance to " CA  GLN A  94 " =    0.880
peak=    3.180 closest distance to " N   TYR A 247 " =    1.181
peak=    3.178 closest distance to " CA  GLN A  88 " =    0.981
peak=    3.177 closest distance to " O   HOH Z 213 " =    1.971
peak=    3.174 closest distance to " O   HOH Z 313 " =    1.610
peak=    3.173 closest distance to " O   HOH Z  59 " =    2.123
peak=    3.168 closest distance to " O   HOH Z 134 " =    2.680
peak=    3.163 closest distance to " CB  LEU A 281 " =    0.824
peak=    3.162 closest distance to " CB  TRP A 179 " =    1.372
peak=    3.161 closest distance to " CE1 PHE A 208 " =    1.045
peak=    3.158 closest distance to " OG BSER A 164 " =    2.033
peak=    3.154 closest distance to " CD  ARG A  14 " =    1.456
peak=    3.150 closest distance to " CD1 TRP A 266 " =    1.186
peak=    3.144 closest distance to " CG2 VAL A 126 " =    1.202
peak=    3.143 closest distance to " O   HOH Z 215 " =    3.005
peak=    3.139 closest distance to " CB  LYS A 193 " =    1.082
peak=    3.137 closest distance to " CB  ASN A 285 " =    0.863
peak=    3.136 closest distance to " CA  LYS A 290 " =    1.144
peak=    3.131 closest distance to " CA  LEU A 282 " =    1.045
peak=    3.131 closest distance to " CB  PHE A  61 " =    1.025
peak=    3.131 closest distance to " O   HOH Z 172 " =    5.525
peak=    3.130 closest distance to " O   HOH Z 250 " =    0.861
peak=    3.126 closest distance to " NH1BARG A 102 " =    1.128
peak=    3.121 closest distance to " CB  SER A 288 " =    1.503
peak=    3.120 closest distance to " NH2 ARG A  56 " =    1.144
peak=    3.119 closest distance to " O   HOH Z 433 " =    1.675
peak=    3.115 closest distance to " O   HOH Z 419 " =    3.051
peak=    3.109 closest distance to " O   HOH Z 188 " =    2.109
peak=    3.108 closest distance to " O   HOH Z 395 " =    1.356
peak=    3.108 closest distance to " O   HOH Z 391 " =    3.110
peak=    3.106 closest distance to " CB  ALA A  34 " =    0.938
peak=    3.103 closest distance to " CA  VAL A 112 " =    1.089
peak=    3.102 closest distance to " O   HOH Z 327 " =    1.973
peak=    3.100 closest distance to " O   HOH Z 424 " =    2.811
peak=    3.097 closest distance to " CB  THR A 235 " =    1.030
peak=    3.089 closest distance to " CB  PHE A 283 " =    0.958
peak=    3.088 closest distance to " CG2 ILE A 106 " =    0.932
peak=    3.088 closest distance to " NZ  LYS A  48 " =    1.422
peak=    3.077 closest distance to " O   HOH Z 272 " =    2.714
peak=    3.065 closest distance to " O   ALA A 292 " =    1.779
peak=    3.055 closest distance to " CA  THR A 264 " =    0.816
peak=    3.054 closest distance to " CG  ARG A 159 " =    1.036
peak=    3.050 closest distance to " OE1 GLU A  46 " =    1.345
peak=    3.048 closest distance to " CB  ASN A 215 " =    1.244
peak=    3.037 closest distance to " CZ3 TRP A  85 " =    1.149
peak=    3.030 closest distance to " CD  LYS A  76 " =    1.368

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 223         
Filter by distance & map next to the model:
   mapped sites are within: 0.497 - 5.448
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 219 from: 223
   mapped sites are within: 0.708 - 5.448

peak=   -5.484 closest distance to " CG1 VAL A 296 " =    1.049
peak=   -5.327 closest distance to " CD  ARG A 138 " =    1.205
peak=   -4.585 closest distance to " CG1 VAL A 250 " =    2.694
peak=   -4.584 closest distance to " O   HOH Z 166 " =    1.371
peak=   -4.476 closest distance to " O   HOH Z 103 " =    0.934
peak=   -4.412 closest distance to " O   HOH Z 102 " =    1.054
peak=   -4.402 closest distance to " O   HOH Z 231 " =    1.950
peak=   -4.373 closest distance to " CG2 VAL A 230 " =    0.799
peak=   -4.333 closest distance to " O   SER A 271 " =    2.242
peak=   -4.274 closest distance to " O   PRO A 198 " =    1.333
peak=   -4.263 closest distance to " CD  GLN A  55 " =    0.928
peak=   -4.160 closest distance to " CD  GLN A  58 " =    0.890
peak=   -4.158 closest distance to " O   HOH Z 216 " =    1.069
peak=   -4.155 closest distance to " CA  GLU A 277 " =    1.322
peak=   -4.044 closest distance to " CD1 PHE A  59 " =    2.065
peak=   -4.023 closest distance to " CD2 TYR A 293 " =    1.914
peak=   -4.017 closest distance to " O   HOH Z 394 " =    1.522
peak=   -4.014 closest distance to " O   HOH Z 103 " =    2.335
peak=   -3.944 closest distance to " CE3 TRP A  70 " =    1.884
peak=   -3.936 closest distance to " CD  GLN A  88 " =    1.072
peak=   -3.921 closest distance to " OE1 GLN A 223 " =    2.302
peak=   -3.920 closest distance to " O   HOH Z 255 " =    0.892
peak=   -3.917 closest distance to " O   HOH Z   5 " =    1.623
peak=   -3.857 closest distance to " CG  MET A 105 " =    1.012
peak=   -3.854 closest distance to " O   HOH Z 231 " =    1.019
peak=   -3.811 closest distance to " CA  ASP A 298 " =    1.052
peak=   -3.800 closest distance to " CB  PRO A 243 " =    2.809
peak=   -3.798 closest distance to " CG  ARG A 269 " =    2.316
peak=   -3.792 closest distance to " CA  ALA A 158 " =    1.346
peak=   -3.740 closest distance to " O   HOH Z  52 " =    2.270
peak=   -3.732 closest distance to " O   HOH Z  19 " =    2.042
peak=   -3.726 closest distance to " NE2 GLN A  55 " =    2.452
peak=   -3.723 closest distance to " CG2BVAL A  41 " =    2.403
peak=   -3.708 closest distance to " O   HOH Z 183 " =    1.232
peak=   -3.707 closest distance to " O   ILE A 109 " =    2.701
peak=   -3.696 closest distance to " OG1 THR A  82 " =    1.443
peak=   -3.693 closest distance to " O   HOH Z 118 " =    1.065
peak=   -3.692 closest distance to " CZ2 TRP A  92 " =    2.923
peak=   -3.691 closest distance to " CG1 VAL A 112 " =    2.805
peak=   -3.683 closest distance to " SG  CYS A 260 " =    2.466
peak=   -3.676 closest distance to " O   HOH Z 177 " =    1.410
peak=   -3.645 closest distance to " CD2 LEU A 167 " =    1.806
peak=   -3.642 closest distance to " NH2 ARG A  66 " =    2.029
peak=   -3.637 closest distance to " CD1 LEU A   5 " =    2.549
peak=   -3.631 closest distance to " O   HOH Z 251 " =    4.970
peak=   -3.629 closest distance to " CG1 VAL A 232 " =    2.252
peak=   -3.626 closest distance to " OE1 GLN A  88 " =    1.071
peak=   -3.625 closest distance to " N   ILE A 120 " =    1.060
peak=   -3.625 closest distance to " O   HOH Z  82 " =    1.335
peak=   -3.621 closest distance to " O   HOH Z 340 " =    1.335
peak=   -3.617 closest distance to " O   HOH Z  82 " =    0.708
peak=   -3.613 closest distance to " CA  ARG A  36 " =    1.299
peak=   -3.599 closest distance to " NE2 HIS A  86 " =    0.936
peak=   -3.595 closest distance to " O   HOH Z 166 " =    2.532
peak=   -3.591 closest distance to " O   HOH Z 407 " =    3.401
peak=   -3.589 closest distance to " CG1 VAL A 112 " =    2.722
peak=   -3.581 closest distance to " CD  ARG A  14 " =    3.251
peak=   -3.581 closest distance to " CG  PRO A 163 " =    2.194
peak=   -3.578 closest distance to " CD2 PHE A  61 " =    2.173
peak=   -3.566 closest distance to " O   HOH Z 368 " =    1.808
peak=   -3.562 closest distance to " O   GLY A 203 " =    2.432
peak=   -3.554 closest distance to " O   HOH Z 111 " =    2.142
peak=   -3.554 closest distance to " O   HOH Z 411 " =    1.717
peak=   -3.550 closest distance to " O   HOH Z  13 " =    1.712
peak=   -3.536 closest distance to " O   HOH Z 411 " =    5.026
peak=   -3.534 closest distance to " O   HOH Z 229 " =    2.064
peak=   -3.531 closest distance to " O   HOH Z  37 " =    1.504
peak=   -3.531 closest distance to " O   HOH Z  32 " =    2.135
peak=   -3.513 closest distance to " CD  ARG A 156 " =    2.087
peak=   -3.505 closest distance to " O   HOH Z   9 " =    1.376
peak=   -3.505 closest distance to " O   HOH Z 410 " =    1.404
peak=   -3.499 closest distance to " O   HOH Z 166 " =    1.856
peak=   -3.499 closest distance to " C   GLY A  17 " =    1.374
peak=   -3.492 closest distance to " SG ACYS A 201 " =    1.004
peak=   -3.490 closest distance to " OD1 ASN A 148 " =    1.355
peak=   -3.476 closest distance to " CG  ARG A 138 " =    0.852
peak=   -3.473 closest distance to " O   HOH Z 256 " =    1.274
peak=   -3.471 closest distance to " CD1 LEU A 101 " =    2.851
peak=   -3.469 closest distance to " CA  GLY A 241 " =    3.080
peak=   -3.467 closest distance to " O   HOH Z 232 " =    1.813
peak=   -3.467 closest distance to " OG  SER A  97 " =    2.178
peak=   -3.450 closest distance to " O   HOH Z 210 " =    0.966
peak=   -3.448 closest distance to " CB  HIS A  86 " =    1.187
peak=   -3.436 closest distance to " CE2 TYR A  30 " =    2.700
peak=   -3.435 closest distance to " O   HOH Z 198 " =    1.565
peak=   -3.431 closest distance to " O   HOH Z  73 " =    2.340
peak=   -3.431 closest distance to " O   HOH Z 377 " =    1.618
peak=   -3.428 closest distance to " CA  GLY A  98 " =    2.315
peak=   -3.423 closest distance to " O   HOH Z 317 " =    2.083
peak=   -3.415 closest distance to " O   ASN A  74 " =    1.844
peak=   -3.414 closest distance to " CG  LEU A   5 " =    0.935
peak=   -3.405 closest distance to " N   ALA A  43 " =    2.608
peak=   -3.399 closest distance to " CG2 VAL A 189 " =    2.168
peak=   -3.398 closest distance to " NH1 ARG A 138 " =    0.939
peak=   -3.396 closest distance to " O   HOH Z 275 " =    1.628
peak=   -3.395 closest distance to " CG1 VAL A 125 " =    1.871
peak=   -3.394 closest distance to " CG  GLU A  53 " =    1.389
peak=   -3.388 closest distance to " O   HOH Z  70 " =    1.814
peak=   -3.384 closest distance to " N   SER A   3 " =    2.354
peak=   -3.381 closest distance to " O   HOH Z 388 " =    2.038
peak=   -3.381 closest distance to " CD2 TYR A 169 " =    2.191
peak=   -3.378 closest distance to " O   HOH Z  92 " =    1.054
peak=   -3.378 closest distance to " CG  GLN A  55 " =    1.370
peak=   -3.376 closest distance to " ND2 ASN A  69 " =    1.786
peak=   -3.371 closest distance to " O   SER A 164 " =    1.942
peak=   -3.368 closest distance to " O   HOH Z  17 " =    1.278
peak=   -3.368 closest distance to " CA  GLY A 203 " =    2.438
peak=   -3.366 closest distance to " O   HOH Z 118 " =    4.955
peak=   -3.364 closest distance to " O   HOH Z 341 " =    1.083
peak=   -3.359 closest distance to " O   GLY A 211 " =    1.419
peak=   -3.355 closest distance to " O   VAL A 189 " =    2.473
peak=   -3.355 closest distance to " CB  PHE A 130 " =    1.315
peak=   -3.354 closest distance to " CG  ASP A 231 " =    0.775
peak=   -3.353 closest distance to " CD  GLN A 223 " =    1.095
peak=   -3.353 closest distance to " CB  PRO A 163 " =    2.509
peak=   -3.350 closest distance to " O   HOH Z 133 " =    0.995
peak=   -3.349 closest distance to " O   HOH Z 438 " =    2.915
peak=   -3.343 closest distance to " O   HOH Z 325 " =    1.545
peak=   -3.342 closest distance to " O   ASP A 253 " =    1.774
peak=   -3.337 closest distance to " OD1 ASN A 173 " =    1.314
peak=   -3.336 closest distance to " N   ASP A 191 " =    1.269
peak=   -3.334 closest distance to " CG1 VAL A  78 " =    2.443
peak=   -3.332 closest distance to " OG  SER A  87 " =    1.682
peak=   -3.330 closest distance to " NH2 ARG A  66 " =    1.614
peak=   -3.328 closest distance to " O   HOH Z  43 " =    1.619
peak=   -3.325 closest distance to " C   GLY A  13 " =    0.929
peak=   -3.323 closest distance to " C   MET A 188 " =    1.412
peak=   -3.322 closest distance to " O   HOH Z  60 " =    2.215
peak=   -3.320 closest distance to " CG  ARG A 259 " =    1.416
peak=   -3.317 closest distance to " CA  ALA A   8 " =    1.420
peak=   -3.317 closest distance to " O   PRO A 163 " =    2.138
peak=   -3.312 closest distance to " O   HOH Z 252 " =    3.603
peak=   -3.307 closest distance to " ND2 ASN A  45 " =    2.557
peak=   -3.306 closest distance to " O   HOH Z 114 " =    1.636
peak=   -3.304 closest distance to " CB  ARG A  79 " =    2.555
peak=   -3.303 closest distance to " C   GLY A 133 " =    1.164
peak=   -3.301 closest distance to " O   HOH Z 350 " =    1.744
peak=   -3.301 closest distance to " CB  SER A  63 " =    3.454
peak=   -3.301 closest distance to " OG  SER A  62 " =    4.433
peak=   -3.300 closest distance to " CE2 TRP A  70 " =    2.458
peak=   -3.297 closest distance to " CZ  ARG A  56 " =    0.954
peak=   -3.295 closest distance to " O   HOH Z  83 " =    1.423
peak=   -3.292 closest distance to " CB  SER A 146 " =    2.275
peak=   -3.291 closest distance to " OG1 THR A  82 " =    1.933
peak=   -3.291 closest distance to " CE  MET A  93 " =    1.881
peak=   -3.290 closest distance to " O   HOH Z 285 " =    1.828
peak=   -3.287 closest distance to " O   HOH Z 359 " =    3.042
peak=   -3.286 closest distance to " CB  ALA A   9 " =    2.571
peak=   -3.284 closest distance to " O   HOH Z 250 " =    1.065
peak=   -3.283 closest distance to " CZ  ARG A  66 " =    1.032
peak=   -3.281 closest distance to " O   HOH Z   6 " =    1.596
peak=   -3.279 closest distance to " O   HOH Z 168 " =    1.175
peak=   -3.276 closest distance to " CH2 TRP A 179 " =    1.109
peak=   -3.269 closest distance to " O   HOH Z 379 " =    0.957
peak=   -3.263 closest distance to " O   HOH Z 236 " =    1.470
peak=   -3.263 closest distance to " NE2 GLN A 103 " =    1.958
peak=   -3.259 closest distance to " CD  LYS A 289 " =    2.357
peak=   -3.258 closest distance to " O   HOH Z  44 " =    0.941
peak=   -3.258 closest distance to " O   HOH Z 142 " =    1.451
peak=   -3.256 closest distance to " N   ARG A 275 " =    1.318
peak=   -3.254 closest distance to " OD1 ASP A 171 " =    1.617
peak=   -3.253 closest distance to " N   VAL A  67 " =    1.169
peak=   -3.249 closest distance to " O   TRP A  70 " =    1.637
peak=   -3.246 closest distance to " CA  PRO A 198 " =    1.051
peak=   -3.240 closest distance to " O   HOH Z 351 " =    1.660
peak=   -3.240 closest distance to " CA  GLY A 241 " =    2.872
peak=   -3.238 closest distance to " O   HOH Z  93 " =    2.254
peak=   -3.237 closest distance to " O   HOH Z 113 " =    2.285
peak=   -3.236 closest distance to " C   GLY A 133 " =    2.411
peak=   -3.228 closest distance to " O   HOH Z 219 " =    4.774
peak=   -3.228 closest distance to " CD1 ILE A 151 " =    2.551
peak=   -3.212 closest distance to " O   HOH Z 112 " =    3.830
peak=   -3.212 closest distance to " OG  SER A  87 " =    1.221
peak=   -3.208 closest distance to " C   ASP A 270 " =    1.266
peak=   -3.202 closest distance to " O   GLY A  80 " =    2.669
peak=   -3.200 closest distance to " CD2 PHE A 225 " =    2.818
peak=   -3.198 closest distance to " CA  VAL A 296 " =    1.077
peak=   -3.196 closest distance to " O   HOH Z 431 " =    1.945
peak=   -3.188 closest distance to " C   LEU A 143 " =    1.141
peak=   -3.187 closest distance to " O   HOH Z 368 " =    1.260
peak=   -3.186 closest distance to " CA  TYR A  68 " =    2.816
peak=   -3.185 closest distance to " O   HOH Z 184 " =    1.739
peak=   -3.184 closest distance to " OD1 ASN A  60 " =    0.881
peak=   -3.182 closest distance to " O   HOH Z 357 " =    2.097
peak=   -3.181 closest distance to " OG  SER A  28 " =    2.067
peak=   -3.180 closest distance to " O   HOH Z 390 " =    1.887
peak=   -3.178 closest distance to " O   HOH Z  38 " =    1.147
peak=   -3.177 closest distance to " CG  ARG A 259 " =    2.511
peak=   -3.174 closest distance to " OE2 GLU A 277 " =    2.823
peak=   -3.173 closest distance to " CB  VAL A 189 " =    2.467
peak=   -3.170 closest distance to " NH2AARG A 275 " =    5.448
peak=   -3.168 closest distance to " O   HOH Z 265 " =    1.775
peak=   -3.167 closest distance to " CE  LYS A  76 " =    2.578
peak=   -3.166 closest distance to " N   THR A  52 " =    1.698
peak=   -3.166 closest distance to " CD1 LEU A   5 " =    1.672
peak=   -3.165 closest distance to " CG  TRP A 266 " =    1.797
peak=   -3.161 closest distance to " CE3 TRP A 274 " =    2.360
peak=   -3.157 closest distance to " C   VAL A 265 " =    0.883
peak=   -3.153 closest distance to " OE1 GLN A 240 " =    1.010
peak=   -3.151 closest distance to " N   TRP A 274 " =    1.213
peak=   -3.148 closest distance to " CZ  PHE A 130 " =    1.297
peak=   -3.146 closest distance to " O   HOH Z  64 " =    1.342
peak=   -3.145 closest distance to " OG  SER A  63 " =    0.987
peak=   -3.145 closest distance to " O   ILE A 106 " =    2.057
peak=   -3.140 closest distance to " O   HOH Z  60 " =    1.339
peak=   -3.139 closest distance to " CG2 THR A 178 " =    2.340
peak=   -3.131 closest distance to " SD  MET A 113 " =    3.026
peak=   -3.130 closest distance to " O   HOH Z 290 " =    1.546
peak=   -3.127 closest distance to " O   TYR A  30 " =    2.434
peak=   -3.122 closest distance to " OH  TYR A 247 " =    1.691
peak=   -3.106 closest distance to " OG BSER A 164 " =    1.218
peak=   -3.104 closest distance to " O   HOH Z 137 " =    1.884
peak=   -3.096 closest distance to " C   GLU A  46 " =    1.239
peak=   -3.090 closest distance to " O   HOH Z 426 " =    1.933
peak=   -3.082 closest distance to " CZ  PHE A 218 " =    1.126
peak=   -3.080 closest distance to " CG  ARG A 219 " =    2.756
peak=   -3.079 closest distance to " CA  GLY A 287 " =    1.797
peak=   -3.073 closest distance to " CD2 PHE A  61 " =    2.553
peak=   -3.039 closest distance to " O   HOH Z 174 " =    2.817

================= 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    :  0.5002 0.4908   6.296955e+00   6.284529e+00
   1_bss:  0.4933 0.4829   6.292910e+00   6.278638e+00
   1_xyz:  0.4163 0.4400   6.203074e+00   6.228706e+00
   1_adp:  0.3764 0.4271   6.142663e+00   6.206464e+00
   1_occ:  0.3758 0.4274   6.141830e+00   6.207269e+00
   2_bss:  0.3749 0.4262   6.143188e+00   6.206828e+00
   2_xyz:  0.2902 0.3535   5.946822e+00   6.077778e+00
   2_adp:  0.2632 0.3239   5.872694e+00   6.022766e+00
   2_occ:  0.2630 0.3243   5.872580e+00   6.023333e+00
   3_bss:  0.2615 0.3225   5.873652e+00   6.022465e+00
   3_xyz:  0.2045 0.2586   5.656887e+00   5.834459e+00
   3_adp:  0.1935 0.2493   5.617532e+00   5.809951e+00
   3_occ:  0.1933 0.2494   5.617009e+00   5.810040e+00
   4_bss:  0.1930 0.2481   5.615727e+00   5.808370e+00
   4_xyz:  0.1677 0.2213   5.493691e+00   5.701354e+00
   4_adp:  0.1561 0.2070   5.432231e+00   5.642088e+00
   4_occ:  0.1560 0.2069   5.431833e+00   5.641522e+00
   5_bss:  0.1562 0.2071   5.433196e+00   5.642534e+00
   5_xyz:  0.1408 0.1897   5.341908e+00   5.560689e+00
   5_adp:  0.1370 0.1875   5.324150e+00   5.546210e+00
   5_occ:  0.1369 0.1873   5.323547e+00   5.545422e+00
   5_bss:  0.1369 0.1873   5.323526e+00   5.545313e+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:  0.273  20.000   8.372   7.035   9.670   0.000   0.000   0.000
   1_xyz:  0.273  20.000   8.372   7.035   9.670   0.000   0.000   0.000
   1_adp:  0.273  20.000   8.372   7.035   9.670   0.000   0.000   0.000
   1_occ:  0.273  20.000   8.372   7.035   9.670   0.000   0.000   0.000
   2_bss:  0.300  50.000   5.698   4.692   6.818   0.000   0.000   0.000
   2_xyz:  0.300  50.000   5.698   4.692   6.818   0.000   0.000   0.000
   2_adp:  0.300  50.000   5.698   4.692   6.818   0.000   0.000   0.000
   2_occ:  0.300  50.000   5.698   4.692   6.818   0.000   0.000   0.000
   3_bss:  0.307  50.000   3.470   3.132   4.597   0.000   0.000   0.000
   3_xyz:  0.307  50.000   3.470   3.132   4.597   0.000   0.000   0.000
   3_adp:  0.307  50.000   3.470   3.132   4.597   0.000   0.000   0.000
   3_occ:  0.307  50.000   3.470   3.132   4.597   0.000   0.000   0.000
   4_bss:  0.329  68.164   2.238   2.164   3.445   0.000   0.000   0.000
   4_xyz:  0.329  68.164   2.238   2.164   3.445   0.000   0.000   0.000
   4_adp:  0.329  68.164   2.238   2.164   3.445   0.000   0.000   0.000
   4_occ:  0.329  68.164   2.238   2.164   3.445   0.000   0.000   0.000
   5_bss:  0.333  77.732   1.767   1.742   3.107   0.000   0.000   0.000
   5_xyz:  0.333  77.732   1.767   1.742   3.107   0.000   0.000   0.000
   5_adp:  0.333  77.732   1.767   1.742   3.107   0.000   0.000   0.000
   5_occ:  0.333  77.732   1.767   1.742   3.107   0.000   0.000   0.000
   5_bss:  0.327  75.515  -0.444  -0.484   0.928   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  62.401 0.3617  0.4086    74658.775
   1_bss:  60.863 0.3814  0.5484    73143.556
   1_xyz:  53.299 0.4770  0.6685    57800.969
   1_adp:  49.876 0.5209  0.7779    53107.705
   1_occ:  49.907 0.5204  0.7756    53195.305
   2_bss:  49.850 0.5211  0.7135    53197.836
   2_xyz:  38.401 0.6606  0.9018    34518.825
   2_adp:  34.571 0.7058  0.9414    28938.528
   2_occ:  34.633 0.7051  0.9399    28976.498
   3_bss:  34.596 0.7055  0.8766    28944.616
   3_xyz:  25.969 0.8011  0.9606    17461.745
   3_adp:  24.787 0.8139  0.9685    16350.752
   3_occ:  24.793 0.8139  0.9681    16349.685
   4_bss:  24.692 0.8148  0.9314    16209.732
   4_xyz:  21.372 0.8483  0.9536    12580.114
   4_adp:  19.760 0.8642  0.9544    10988.209
   4_occ:  19.750 0.8643  0.9543    10976.276
   5_bss:  19.777 0.8641  0.9405    11031.307
   5_xyz:  17.741 0.8832  0.9517     9201.101
   5_adp:  17.378 0.8867  0.9455     8943.885
   5_occ:  17.363 0.8868  0.9455     8927.419
   5_bss:  17.364 0.8868  0.9481     8926.286
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.4829e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.4829e+01
   1_xyz:   1.840  0.015  0.116 18.461  0.007  4.112   1.6536e-01
   1_adp:   1.840  0.015  0.116 18.461  0.007  4.112   1.6536e-01
   1_occ:   1.840  0.015  0.116 18.461  0.007  4.112   1.6536e-01
   2_bss:   1.840  0.015  0.116 18.461  0.007  4.112   1.6536e-01
   2_xyz:   1.333  0.010  0.089 17.270  0.005  4.113   1.0509e-01
   2_adp:   1.333  0.010  0.089 17.270  0.005  4.113   1.0509e-01
   2_occ:   1.333  0.010  0.089 17.270  0.005  4.113   1.0509e-01
   3_bss:   1.333  0.010  0.089 17.270  0.005  4.113   1.0509e-01
   3_xyz:   1.095  0.008  0.081 16.148  0.004  4.137   7.2375e-02
   3_adp:   1.095  0.008  0.081 16.148  0.004  4.137   7.2375e-02
   3_occ:   1.095  0.008  0.081 16.148  0.004  4.137   7.2375e-02
   4_bss:   1.095  0.008  0.081 16.148  0.004  4.137   7.2375e-02
   4_xyz:   1.012  0.008  0.075 15.731  0.003  4.149   6.4671e-02
   4_adp:   1.012  0.008  0.075 15.731  0.003  4.149   6.4671e-02
   4_occ:   1.012  0.008  0.075 15.731  0.003  4.149   6.4671e-02
   5_bss:   1.012  0.008  0.075 15.731  0.003  4.149   6.4671e-02
   5_xyz:   1.069  0.009  0.082 15.557  0.003  4.136   6.7964e-02
   5_adp:   1.069  0.009  0.082 15.557  0.003  4.136   6.7964e-02
   5_occ:   1.069  0.009  0.082 15.557  0.003  4.136   6.7964e-02
   5_bss:   1.069  0.009  0.082 15.557  0.003  4.136   6.7964e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.1096e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.1096e+00
   1_xyz:  15.351  0.183  0.496 86.549  0.047  2.125   1.1871e-01
   1_adp:  15.351  0.183  0.496 86.549  0.047  2.125   1.1871e-01
   1_occ:  15.351  0.183  0.496 86.549  0.047  2.125   1.1871e-01
   2_bss:  15.351  0.183  0.496 86.549  0.047  2.125   1.1871e-01
   2_xyz:   7.730  0.090  0.318 80.950  0.029  2.022   6.6173e-02
   2_adp:   7.730  0.090  0.318 80.950  0.029  2.022   6.6173e-02
   2_occ:   7.730  0.090  0.318 80.950  0.029  2.022   6.6173e-02
   3_bss:   7.730  0.090  0.318 80.950  0.029  2.022   6.6173e-02
   3_xyz:   7.838  0.068  0.260 81.020  0.040  2.245   5.9684e-02
   3_adp:   7.838  0.068  0.260 81.020  0.040  2.245   5.9684e-02
   3_occ:   7.838  0.068  0.260 81.020  0.040  2.245   5.9684e-02
   4_bss:   7.838  0.068  0.260 81.020  0.040  2.245   5.9684e-02
   4_xyz:   8.301  0.054  0.232 88.297  0.033  2.353   4.2749e-02
   4_adp:   8.301  0.054  0.232 88.297  0.033  2.353   4.2749e-02
   4_occ:   8.301  0.054  0.232 88.297  0.033  2.353   4.2749e-02
   5_bss:   8.301  0.054  0.232 88.297  0.033  2.353   4.2749e-02
   5_xyz:   8.268  0.063  0.328 81.352  0.038  2.355   3.8351e-02
   5_adp:   8.268  0.063  0.328 81.352  0.038  2.355   3.8351e-02
   5_occ:   8.268  0.063  0.328 81.352  0.038  2.355   3.8351e-02
   5_bss:   8.268  0.063  0.328 81.352  0.038  2.355   3.8351e-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: 111.54   0.00  15.04  82.87   0.00  12.72 111.54   0.00  27.70
   1_occ: 111.54   0.00  15.04  82.87   0.00  12.72 111.54   0.00  27.70
   2_bss: 111.54   0.00  15.04  82.87   0.00  12.72 111.54   0.00  27.70
   2_xyz: 111.54   0.00  15.04  82.87   0.00  12.72 111.54   0.00  27.70
   2_adp: 122.08   0.00  13.99  83.75   0.00  10.36 122.08   0.00  33.71
   2_occ: 122.08   0.00  13.99  83.75   0.00  10.36 122.08   0.00  33.71
   3_bss: 122.08   0.00  13.99  83.75   0.00  10.36 122.08   0.00  33.71
   3_xyz: 122.08   0.00  13.99  83.75   0.00  10.36 122.08   0.00  33.71
   3_adp: 121.95   0.00  13.95  86.12   0.00  10.11 121.95   0.33  34.83
   3_occ: 121.95   0.00  13.95  86.12   0.00  10.11 121.95   0.33  34.83
   4_bss: 121.95   0.00  13.95  86.12   0.00  10.11 121.95   0.33  34.83
   4_xyz: 121.95   0.00  13.95  86.12   0.00  10.11 121.95   0.33  34.83
   4_adp: 112.78   0.00  13.85  79.86   0.00   9.38 112.78   1.41  38.16
   4_occ: 112.78   0.00  13.85  79.86   0.00   9.38 112.78   1.41  38.16
   5_bss: 112.78   0.00  13.85  79.86   0.00   9.38 112.78   1.41  38.16
   5_xyz: 112.78   0.00  13.85  79.86   0.00   9.38 112.78   1.41  38.16
   5_adp: 103.02   0.00  13.90  79.51   0.00   9.23 103.02   1.96  39.31
   5_occ: 103.02   0.00  13.90  79.51   0.00   9.23 103.02   1.96  39.31
   5_bss: 105.31   2.29  16.19  81.79   2.29  11.52 105.31   4.25  41.60
------------------------------------------------------------------------
 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:    1.286    0.020    0.421
   1_adp:    1.286    0.020    0.421
   1_occ:    1.286    0.020    0.421
   2_bss:    1.286    0.020    0.421
   2_xyz:    1.767    0.025    0.624
   2_adp:    1.767    0.025    0.624
   2_occ:    1.767    0.025    0.624
   3_bss:    1.767    0.025    0.624
   3_xyz:    1.659    0.069    0.702
   3_adp:    1.659    0.069    0.702
   3_occ:    1.659    0.069    0.702
   4_bss:    1.659    0.069    0.702
   4_xyz:    1.835    0.056    0.760
   4_adp:    1.835    0.056    0.760
   4_occ:    1.835    0.056    0.760
   5_bss:    1.835    0.056    0.760
   5_xyz:    1.887    0.031    0.790
   5_adp:    1.887    0.031    0.790
   5_occ:    1.887    0.031    0.790
   5_bss:    1.887    0.031    0.790
------------------------------------------------------------------------

CPU time actual refinement: 348.13


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1296/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_1296/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1296/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1296/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1296/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 347.99 
  Macro-tasks:
    bulk solvent and scale       = 49.52  
    individual site refinement   = 141.54 
    weights calculation          = 31.89  
    collect and process          = 6.48   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 229.52 
  Micro-tasks:
    mask                            = 2.16   
    f_calc                          = 107.24 
    alpha_beta                      = 8.33   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 113.22 
    fmodel                         = 8.82   
    r_factors                      = 0.19   
    phase_errors                   = 10.98  
    foms                           = 0.21   
    TOTAL for micro-tasks          = 252.34 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.849 micro seconds
Total CPU time: 6.02 minutes
from_scatterers_fft:    661 calls, 106.83 s
gradients_fft:          606 calls, 101.50 s

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

# Date 2008-01-16 Time 03:40:21 PST -0800 (1200483621.65 s)
Start R-work = 0.5002, R-free = 0.4908 (no bulk solvent and anisotropic scale)
Final R-work = 0.1522, R-free = 0.2023 (no bulk solvent and anisotropic scale)

Start R-work = 0.4933, R-free = 0.4829
Final R-work = 0.1369, R-free = 0.1873