# Date 2008-01-16 Time 02:02:01 PST -0800 (1200477721.72 s)
#phil __OFF__

Command line arguments: "../656.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 12655
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 656

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.25, 46.6953, 87.2539, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 46.6953, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0342 1.99202
Completeness in resolution range: 0.969273
Completeness with d_max=infinity: 0.966261

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0342
                             d_min =   1.9920

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 46.6953, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0342 1.99202
Completeness in resolution range: 0.969273
Completeness with d_max=infinity: 0.966261

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0346 -  4.2621 [2127/2151]  1913   214  10.1%
  bin  2:  4.2621 -  3.3958 [2032/2052]  1830   202   9.9%
  bin  3:  3.3958 -  2.9703 [2016/2035]  1813   203  10.1%
  bin  4:  2.9703 -  2.7005 [1981/2011]  1783   198  10.0%
  bin  5:  2.7005 -  2.5078 [1992/2011]  1790   202  10.1%
  bin  6:  2.5078 -  2.3606 [1974/1999]  1779   195   9.9%
  bin  7:  2.3606 -  2.2428 [1947/1975]  1752   195  10.0%
  bin  8:  2.2428 -  2.1454 [1971/2007]  1779   192   9.7%
  bin  9:  2.1454 -  2.0630 [1930/1972]  1732   198  10.3%
  bin 10:  2.0630 -  1.9920 [1619/1997]  1459   160   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_656/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: 0.15 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 12
        2.42 -     3.04: 2192
        3.04 -     3.66: 4656
        3.66 -     4.28: 9015
        4.28 -     4.90: 12343
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " OE1 GLN A  55 " - " O   HOH Z 403 "  2.053 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 183 "  2.072 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  2.214 3.040 -x+1,y+1/2,-z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  ... (remaining 28213 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_656/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_656/model_refine_001.geo

CPU time processing inputs: 9.16


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.25 46.69535 87.2539 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4264   r_free= 0.4089   ksol= 0.00   Bsol= 0.00   scale= 0.825    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.216046                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0346 -  4.7536 0.99   1382  152 0.3601 0.3327      6.5219      6.4292|
|  2:  4.7536 -  3.7930 0.99   1318  151 0.3124 0.3143      6.6057      6.6501|
|  3:  3.7930 -  3.3195 0.99   1300  142 0.3625 0.3299      6.5294       6.505|
|  4:  3.3195 -  3.0186 0.99   1300  142 0.4067 0.3699      6.4452      6.3566|
|  5:  3.0186 -  2.8038 0.99   1269  145 0.4379 0.4363      6.3019      6.3133|
|  6:  2.8038 -  2.6394 0.99   1295  140 0.4460 0.5148        6.22      6.1881|
|  7:  2.6394 -  2.5078 0.99   1265  147 0.4754 0.4755      6.2028      6.1699|
|  8:  2.5078 -  2.3991 0.98   1278  134 0.4795 0.4305      6.1402      6.1381|
|  9:  2.3991 -  2.3071 0.98   1256  142 0.4651 0.4603      6.0739      6.0899|
| 10:  2.3071 -  2.2278 1.00   1277  144 0.5018 0.4269      6.1137       6.009|
| 11:  2.2278 -  2.1583 0.97   1242  138 0.4933 0.4550      6.0206      5.9932|
| 12:  2.1583 -  2.0968 0.98   1254  134 0.5003 0.4665      5.9728      5.9768|
| 13:  2.0968 -  2.0417 0.99   1252  140 0.4872 0.4847      5.8694       5.844|
| 14:  2.0417 -  1.9920 0.74    942  108 0.5000 0.4633      5.8435      5.7265|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0346 -  4.7536  1382   152  0.75  29.78   0.81     0.78      54827.67|
|  2:  4.7536 -  3.7930  1318   151  0.79  26.99   0.91     0.84      67675.41|
|  3:  3.7930 -  3.3195  1300   142  0.73  32.83   0.89     0.81      70393.37|
|  4:  3.3195 -  3.0186  1300   142  0.67  38.39   0.83     0.72      64665.60|
|  5:  3.0186 -  2.8038  1269   145  0.58  45.74   0.79     0.65      58752.27|
|  6:  2.8038 -  2.6394  1295   140  0.54  48.88   0.76     0.60      54965.04|
|  7:  2.6394 -  2.5078  1265   147  0.50  51.78   0.76     0.58      52046.75|
|  8:  2.5078 -  2.3991  1278   134  0.50  52.09   0.75     0.57      46735.83|
|  9:  2.3991 -  2.3071  1256   142  0.54  49.19   0.76     0.60      40267.65|
| 10:  2.3071 -  2.2278  1277   144  0.54  49.00   0.77     0.62      34865.51|
| 11:  2.2278 -  2.1583  1242   138  0.54  49.38   0.77     0.62      32562.43|
| 12:  2.1583 -  2.0968  1254   134  0.50  52.43   0.79     0.59      32184.56|
| 13:  2.0968 -  2.0417  1252   140  0.48  54.04   0.75     0.56      28996.50|
| 14:  2.0417 -  1.9920   942   108  0.51  51.86   0.75     0.53      23390.47|
|alpha:            min =        0.53 max =            0.84 mean =         0.65|
|beta:             min =    23390.47 max =        70393.37 mean =     47991.34|
|figures of merit: min =        0.00 max =            1.00 mean =         0.59|
|phase err.(work): min =        0.00 max =           89.99 mean =        44.85|
|phase err.(test): min =        0.00 max =           89.75 mean =        44.99|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.571668              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 74.630   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.573257              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.105   (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:       22 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      170 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      682 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1479 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2626 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3915 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5075 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6530 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7726 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.861 |
| 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 |       1.681 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.951)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 11.951)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4360   r_free= 0.4145   ksol= 0.00   Bsol= 0.00   scale= 0.793    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.224012                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4186   r_free= 0.3969   ksol= 0.34   Bsol= 18.90   scale= 1.028   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.16,8.25,9.73,0.00,0.00,0.00); trace/3= 8.38                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.212202                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.085061              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 76.550   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.533636              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 75.096   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4186      final r-factor (work) = 0.3044          |
| start r-factor (free) = 0.3969      final r-factor (free) = 0.3212          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 72.8208 = 6.09 * 0.50 * 6.2317 + 1.00 * 53.8607                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.4895 = 6.09 * 0.50 * 6.0399 + 1.00 * 0.1131                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3044      final r-factor (work) = 0.2358          |
| start r-factor (free) = 0.3212      final r-factor (free) = 0.2689          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2378 = 0.53 * 1.00 * 6.0399 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1220 = 0.53 * 1.00 * 5.8296 + 1.00 * 0.0111                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.951)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    58.06   10.53    None  None   None       |
|    all(noH): 2823   0      0.00    58.06   10.53    None  None   None       |
|    Sol.    : 438    0      0.00    58.06   27.89    None  None   None       |
|    Mac.    : 2385   0      0.00    52.87   7.34     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   5.806: 1279   |   5:    29.032 -  34.838:   89        |
|      1:     5.806 -  11.613:  742   |   6:    34.838 -  40.645:   91        |
|      2:    11.613 -  17.419:  277   |   7:    40.645 -  46.451:   40        |
|      3:    17.419 -  23.226:  143   |   8:    46.451 -  52.257:   21        |
|      4:    23.226 -  29.032:  129   |   9:    52.257 -  58.064:   12        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2358 r_free = 0.2689             target_work(ml) = 5.751         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2350 r_free = 0.2691             target_work(ml) = 5.750         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2350   r_free= 0.2691   ksol= 0.34   Bsol= 18.90   scale= 1.095   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.16,8.25,9.73,0.00,0.00,0.00); trace/3= 8.38                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.750244                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2288   r_free= 0.2632   ksol= 0.34   Bsol= 45.20   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.83,4.33,6.20,0.00,0.00,0.00); trace/3= 4.79                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.747499                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.602011              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.264   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.291791              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 123.293  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2288      final r-factor (work) = 0.1563          |
| start r-factor (free) = 0.2632      final r-factor (free) = 0.1956          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7171 = 2.60 * 0.50 * 5.8450 + 1.00 * 0.1127                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3062 = 2.60 * 0.50 * 5.5685 + 1.00 * 0.0615                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1563      final r-factor (work) = 0.1436          |
| start r-factor (free) = 0.1956      final r-factor (free) = 0.1848          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6359 = 0.29 * 1.00 * 5.5685 + 1.00 * 0.0110                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5745 = 0.29 * 1.00 * 5.3613 + 1.00 * 0.0102                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.951)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    59.08   10.82    None  None   None       |
|    all(noH): 2823   0      0.00    59.08   10.82    None  None   None       |
|    Sol.    : 438    0      0.00    59.08   30.87    None  None   None       |
|    Mac.    : 2385   0      0.00    56.46   7.14     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   5.908: 1359   |   5:    29.539 -  35.447:  103        |
|      1:     5.908 -  11.816:  712   |   6:    35.447 -  41.354:  105        |
|      2:    11.816 -  17.723:  234   |   7:    41.354 -  47.262:   58        |
|      3:    17.723 -  23.631:  105   |   8:    47.262 -  53.170:   31        |
|      4:    23.631 -  29.539:  105   |   9:    53.170 -  59.078:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1436 r_free = 0.1848             target_work(ml) = 5.334         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1435 r_free = 0.1846             target_work(ml) = 5.333         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1435   r_free= 0.1846   ksol= 0.34   Bsol= 45.20   scale= 1.025   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.83,4.33,6.20,0.00,0.00,0.00); trace/3= 4.79                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.332940                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1432   r_free= 0.1841   ksol= 0.33   Bsol= 45.20   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.09,3.42,4.98,0.00,0.00,0.00); trace/3= 3.83                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.333799                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.794039              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.907  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.484049              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 137.057  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1432      final r-factor (work) = 0.1203          |
| start r-factor (free) = 0.1841      final r-factor (free) = 0.1637          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5604 = 2.79 * 0.50 * 5.3678 + 1.00 * 0.0615                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.4058 = 2.79 * 0.50 * 5.2535 + 1.00 * 0.0667                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1203      final r-factor (work) = 0.1153          |
| start r-factor (free) = 0.1637      final r-factor (free) = 0.1615          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.0599 = 2.48 * 1.00 * 5.2535 + 1.00 * 0.0101                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.8730 = 2.48 * 1.00 * 5.1766 + 1.00 * 0.0141                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.951)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.24   11.64    None  None   None       |
|    all(noH): 2823   0      0.00    76.24   11.64    None  None   None       |
|    Sol.    : 438    0      0.38    70.85   34.99    None  None   None       |
|    Mac.    : 2385   0      0.00    76.24   7.35     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.624: 1652   |   5:    38.119 -  45.743:   82        |
|      1:     7.624 -  15.248:  563   |   6:    45.743 -  53.367:   78        |
|      2:    15.248 -  22.872:  163   |   7:    53.367 -  60.991:   46        |
|      3:    22.872 -  30.496:  109   |   8:    60.991 -  68.615:   21        |
|      4:    30.496 -  38.119:  103   |   9:    68.615 -  76.239:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1153 r_free = 0.1615             target_work(ml) = 5.171         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1152 r_free = 0.1615             target_work(ml) = 5.171         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1152   r_free= 0.1615   ksol= 0.33   Bsol= 45.20   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.09,3.42,4.98,0.00,0.00,0.00); trace/3= 3.83                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.170953                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1152   r_free= 0.1615   ksol= 0.32   Bsol= 45.20   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.12,3.37,4.88,0.00,0.00,0.00); trace/3= 3.79                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.170635                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.103412              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 144.737  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.248842              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.260  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1152      final r-factor (work) = 0.1131          |
| start r-factor (free) = 0.1615      final r-factor (free) = 0.1595          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5104 = 2.10 * 0.50 * 5.1762 + 1.00 * 0.0667                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4916 = 2.10 * 0.50 * 5.1641 + 1.00 * 0.0605                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1131      final r-factor (work) = 0.1140          |
| start r-factor (free) = 0.1595      final r-factor (free) = 0.1578          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2991 = 0.25 * 1.00 * 5.1641 + 1.00 * 0.0140                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3058 = 0.25 * 1.00 * 5.1635 + 1.00 * 0.0209                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.951)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.03   11.11    None  None   None       |
|    all(noH): 2823   0      0.00    76.03   11.11    None  None   None       |
|    Sol.    : 438    0      0.92    68.22   32.85    None  None   None       |
|    Mac.    : 2385   0      0.00    76.03   7.12     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.603: 1700   |   5:    38.013 -  45.616:   82        |
|      1:     7.603 -  15.205:  549   |   6:    45.616 -  53.218:   71        |
|      2:    15.205 -  22.808:  148   |   7:    53.218 -  60.821:   32        |
|      3:    22.808 -  30.411:  113   |   8:    60.821 -  68.424:   17        |
|      4:    30.411 -  38.013:  109   |   9:    68.424 -  76.026:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1140 r_free = 0.1578             target_work(ml) = 5.156         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1139 r_free = 0.1577             target_work(ml) = 5.156         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1139   r_free= 0.1577   ksol= 0.32   Bsol= 45.20   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.12,3.37,4.88,0.00,0.00,0.00); trace/3= 3.79                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.155695                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1140   r_free= 0.1573   ksol= 0.32   Bsol= 45.20   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.12,3.37,4.88,0.00,0.00,0.00); trace/3= 3.79                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.155519                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.795188              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 156.727  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.581872              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.153   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1140      final r-factor (work) = 0.1127          |
| start r-factor (free) = 0.1573      final r-factor (free) = 0.1568          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.6952 = 1.80 * 0.50 * 5.1634 + 1.00 * 0.0605                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.6828 = 1.80 * 0.50 * 5.1502 + 1.00 * 0.0600                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1127      final r-factor (work) = 0.1121          |
| start r-factor (free) = 0.1568      final r-factor (free) = 0.1571          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0093 = 0.58 * 1.00 * 5.1502 + 1.00 * 0.0126                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0223 = 0.58 * 1.00 * 5.1458 + 1.00 * 0.0281                               |
|-----------------------------------------------------------------------------|
| number of iterations = 9       |    number of function evaluations = 10     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.951)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.46   11.11    None  None   None       |
|    all(noH): 2823   0      0.00    76.46   11.11    None  None   None       |
|    Sol.    : 438    0      0.75    68.17   32.98    None  None   None       |
|    Mac.    : 2385   0      0.00    76.46   7.10     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.646: 1700   |   5:    38.228 -  45.873:   81        |
|      1:     7.646 -  15.291:  541   |   6:    45.873 -  53.519:   69        |
|      2:    15.291 -  22.937:  154   |   7:    53.519 -  61.164:   30        |
|      3:    22.937 -  30.582:  111   |   8:    61.164 -  68.810:   17        |
|      4:    30.582 -  38.228:  117   |   9:    68.810 -  76.455:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1121 r_free = 0.1571             target_work(ml) = 5.149         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1121 r_free = 0.1571             target_work(ml) = 5.149         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1121   r_free= 0.1571   ksol= 0.32   Bsol= 45.20   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.12,3.37,4.88,0.00,0.00,0.00); trace/3= 3.79                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.148641                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0346 -  4.7536 0.99   1382  152 0.1009 0.1262      5.3855       5.499|
|  2:  4.7536 -  3.7930 0.99   1318  151 0.0864 0.1125      5.4432      5.6485|
|  3:  3.7930 -  3.3195 0.99   1300  142 0.1052 0.1484      5.4802      5.8351|
|  4:  3.3195 -  3.0186 0.99   1300  142 0.1195 0.1625      5.4511      5.5981|
|  5:  3.0186 -  2.8038 0.99   1269  145 0.1322 0.1681      5.3369      5.5489|
|  6:  2.8038 -  2.6394 0.99   1295  140 0.1188 0.2046      5.1995      5.5245|
|  7:  2.6394 -  2.5078 0.99   1265  147 0.1270 0.1575      5.1741      5.3337|
|  8:  2.5078 -  2.3991 0.98   1278  134 0.1187 0.1710      5.0842      5.3539|
|  9:  2.3991 -  2.3071 0.98   1256  142 0.1187 0.1820      5.0576      5.3017|
| 10:  2.3071 -  2.2278 1.00   1277  144 0.1152 0.1647       4.979      5.2232|
| 11:  2.2278 -  2.1583 0.97   1242  138 0.1141 0.1714      4.9548      5.2226|
| 12:  2.1583 -  2.0968 0.98   1254  134 0.1128 0.1744      4.8794      5.2702|
| 13:  2.0968 -  2.0417 0.99   1252  140 0.1125 0.1650       4.792      5.0149|
| 14:  2.0417 -  1.9920 0.74    942  108 0.1026 0.1744      4.6828      4.9544|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0346 -  4.7536  1382   152  0.94   8.96   0.97     0.95       6926.85|
|  2:  4.7536 -  3.7930  1318   151  0.95   7.87   1.01     1.00       8931.21|
|  3:  3.7930 -  3.3195  1300   142  0.93  11.14   1.02     1.01      10423.93|
|  4:  3.3195 -  3.0186  1300   142  0.92  13.36   1.00     0.98      10295.51|
|  5:  3.0186 -  2.8038  1269   145  0.90  15.63   0.99     0.97       8403.16|
|  6:  2.8038 -  2.6394  1295   140  0.90  15.96   0.98     0.95       6971.55|
|  7:  2.6394 -  2.5078  1265   147  0.90  15.65   0.98     0.95       6173.83|
|  8:  2.5078 -  2.3991  1278   134  0.91  15.01   0.99     0.97       5334.59|
|  9:  2.3991 -  2.3071  1256   142  0.91  15.67   1.01     0.97       5288.67|
| 10:  2.3071 -  2.2278  1277   144  0.90  15.91   1.00     0.96       4528.60|
| 11:  2.2278 -  2.1583  1242   138  0.90  16.44   1.00     0.96       4550.45|
| 12:  2.1583 -  2.0968  1254   134  0.91  15.38   1.01     1.00       3917.05|
| 13:  2.0968 -  2.0417  1252   140  0.90  15.88   0.99     0.97       3344.67|
| 14:  2.0417 -  1.9920   942   108  0.92  14.38   0.98     0.95       2679.71|
|alpha:            min =        0.95 max =            1.01 mean =         0.97|
|beta:             min =     2679.71 max =        10423.93 mean =      6369.81|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.89 mean =        14.02|
|phase err.(test): min =        0.00 max =           89.98 mean =        13.53|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1121   r_free= 0.1571   ksol= 0.32   Bsol= 49.54   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.66,-0.42,1.08,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.148572                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1121   r_free= 0.1571   ksol= 0.32   Bsol= 49.54   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.66,-0.42,1.08,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.148572                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0346 -  4.7536 0.99   1382  152 0.1009 0.1263      5.3855      5.4991|
|  2:  4.7536 -  3.7930 0.99   1318  151 0.0865 0.1126      5.4437      5.6492|
|  3:  3.7930 -  3.3195 0.99   1300  142 0.1052 0.1484      5.4806      5.8353|
|  4:  3.3195 -  3.0186 0.99   1300  142 0.1194 0.1625       5.451       5.598|
|  5:  3.0186 -  2.8038 0.99   1269  145 0.1321 0.1680      5.3366      5.5486|
|  6:  2.8038 -  2.6394 0.99   1295  140 0.1188 0.2045      5.1992      5.5241|
|  7:  2.6394 -  2.5078 0.99   1265  147 0.1270 0.1575      5.1739      5.3336|
|  8:  2.5078 -  2.3991 0.98   1278  134 0.1187 0.1710      5.0841      5.3538|
|  9:  2.3991 -  2.3071 0.98   1256  142 0.1186 0.1820      5.0575      5.3017|
| 10:  2.3071 -  2.2278 1.00   1277  144 0.1152 0.1647      4.9789      5.2232|
| 11:  2.2278 -  2.1583 0.97   1242  138 0.1141 0.1713      4.9547      5.2223|
| 12:  2.1583 -  2.0968 0.98   1254  134 0.1128 0.1743      4.8793      5.2699|
| 13:  2.0968 -  2.0417 0.99   1252  140 0.1125 0.1650      4.7919      5.0149|
| 14:  2.0417 -  1.9920 0.74    942  108 0.1026 0.1743      4.6827      4.9541|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0346 -  4.7536  1382   152  0.94   8.97   0.97     0.95       6928.06|
|  2:  4.7536 -  3.7930  1318   151  0.95   7.88   1.01     1.00       8938.20|
|  3:  3.7930 -  3.3195  1300   142  0.93  11.14   1.02     1.01      10432.44|
|  4:  3.3195 -  3.0186  1300   142  0.92  13.36   1.00     0.98      10293.20|
|  5:  3.0186 -  2.8038  1269   145  0.90  15.62   1.00     0.97       8397.62|
|  6:  2.8038 -  2.6394  1295   140  0.90  15.95   0.98     0.95       6966.78|
|  7:  2.6394 -  2.5078  1265   147  0.90  15.65   0.98     0.95       6170.87|
|  8:  2.5078 -  2.3991  1278   134  0.91  15.02   0.99     0.97       5333.82|
|  9:  2.3991 -  2.3071  1256   142  0.91  15.67   1.01     0.97       5288.89|
| 10:  2.3071 -  2.2278  1277   144  0.90  15.91   1.00     0.96       4527.02|
| 11:  2.2278 -  2.1583  1242   138  0.90  16.44   1.00     0.96       4548.26|
| 12:  2.1583 -  2.0968  1254   134  0.91  15.37   1.01     1.00       3915.34|
| 13:  2.0968 -  2.0417  1252   140  0.90  15.88   1.00     0.97       3343.28|
| 14:  2.0417 -  1.9920   942   108  0.92  14.37   0.98     0.95       2678.04|
|alpha:            min =        0.95 max =            1.01 mean =         0.97|
|beta:             min =     2678.04 max =        10432.44 mean =      6369.31|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.02|
|phase err.(test): min =        0.00 max =           90.00 mean =        13.53|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.951)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.80    80.25   14.91    None  None   None       |
|    all(noH): 2823   0      3.80    80.25   14.91    None  None   None       |
|    Sol.    : 438    0      4.55    71.97   36.78    None  None   None       |
|    Mac.    : 2385   0      3.80    80.25   10.90    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     3.797 -  11.443: 1700   |   5:    42.025 -  49.670:   81        |
|      1:    11.443 -  19.088:  541   |   6:    49.670 -  57.316:   69        |
|      2:    19.088 -  26.734:  154   |   7:    57.316 -  64.961:   30        |
|      3:    26.734 -  34.379:  111   |   8:    64.961 -  72.607:   17        |
|      4:    34.379 -  42.025:  117   |   9:    72.607 -  80.253:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 304         
Filter by distance & map next to the model:
   mapped sites are within: 0.293 - 4.111
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 295 from: 304
   mapped sites are within: 0.716 - 4.111

peak=   11.302 closest distance to " CB  VAL A 230 " =    1.488
peak=    7.960 closest distance to " CG2 VAL A 296 " =    1.196
peak=    6.302 closest distance to " CG  LEU A   5 " =    1.237
peak=    6.182 closest distance to " NH2 ARG A  56 " =    2.186
peak=    5.726 closest distance to " CD2 LEU A   5 " =    1.205
peak=    5.530 closest distance to " CG  LEU A 228 " =    1.171
peak=    5.489 closest distance to " NE2 GLN A  11 " =    1.191
peak=    5.387 closest distance to " O   HOH Z 142 " =    1.874
peak=    5.384 closest distance to " CB  GLN A 223 " =    1.458
peak=    5.255 closest distance to " O   HOH Z 232 " =    2.327
peak=    4.972 closest distance to " CB  GLN A 183 " =    1.243
peak=    4.835 closest distance to " CB  ARG A 275 " =    0.898
peak=    4.613 closest distance to " CG  PRO A 213 " =    1.249
peak=    4.586 closest distance to " CG  PRO A 243 " =    1.118
peak=    4.572 closest distance to " O   HOH Z 427 " =    3.040
peak=    4.561 closest distance to " O   HOH Z 126 " =    1.915
peak=    4.533 closest distance to " CB  VAL A 296 " =    1.058
peak=    4.488 closest distance to " CZ  PHE A 218 " =    1.122
peak=    4.466 closest distance to " O   HOH Z  61 " =    1.689
peak=    4.460 closest distance to " C   PRO A 198 " =    1.516
peak=    4.459 closest distance to " ND2 ASN A 187 " =    1.561
peak=    4.452 closest distance to " CB  SER A  63 " =    1.247
peak=    4.420 closest distance to " O   HOH Z 346 " =    1.610
peak=    4.413 closest distance to " O   HOH Z 209 " =    2.268
peak=    4.392 closest distance to " O   HOH Z   9 " =    1.362
peak=    4.391 closest distance to " CB  ARG A  79 " =    1.448
peak=    4.387 closest distance to " CB  VAL A 230 " =    1.148
peak=    4.316 closest distance to " CG  PRO A 198 " =    1.268
peak=    4.307 closest distance to " O   SER A  87 " =    2.296
peak=    4.306 closest distance to " CD2 LEU A 228 " =    1.190
peak=    4.298 closest distance to " O   HOH Z 369 " =    2.070
peak=    4.287 closest distance to " CB  TRP A 266 " =    1.028
peak=    4.282 closest distance to " O   HOH Z  43 " =    1.959
peak=    4.280 closest distance to " O   HOH Z 272 " =    1.854
peak=    4.236 closest distance to " CB  ASN A 148 " =    1.376
peak=    4.211 closest distance to " CB  VAL A 265 " =    1.322
peak=    4.159 closest distance to " O   HOH Z 265 " =    2.344
peak=    4.150 closest distance to " O   HOH Z 298 " =    1.778
peak=    4.148 closest distance to " O   HOH Z 158 " =    3.289
peak=    4.144 closest distance to " CB  GLU A 152 " =    1.215
peak=    4.119 closest distance to " O   HOH Z  78 " =    1.816
peak=    4.109 closest distance to " CB  ASN A 142 " =    1.089
peak=    4.098 closest distance to " OG  SER A  97 " =    2.910
peak=    4.097 closest distance to " O   HOH Z 303 " =    2.086
peak=    4.097 closest distance to " O   HOH Z 368 " =    2.105
peak=    4.052 closest distance to " OG ASER A 258 " =    3.085
peak=    4.027 closest distance to " CB  SER A   3 " =    1.260
peak=    4.026 closest distance to " O   HOH Z 126 " =    1.891
peak=    4.022 closest distance to " O   HOH Z 248 " =    1.595
peak=    4.015 closest distance to " O   HOH Z 261 " =    1.993
peak=    4.008 closest distance to " O   HOH Z 126 " =    1.646
peak=    4.000 closest distance to " O   HOH Z 234 " =    3.698
peak=    3.997 closest distance to " O   HOH Z 423 " =    1.796
peak=    3.965 closest distance to " O   HOH Z 287 " =    2.147
peak=    3.962 closest distance to " CB  ALA A   9 " =    1.585
peak=    3.954 closest distance to " CB  GLU A 128 " =    0.982
peak=    3.949 closest distance to " CA  TYR A  30 " =    0.982
peak=    3.914 closest distance to " CG2 VAL A 257 " =    0.869
peak=    3.897 closest distance to " O   HOH Z 425 " =    1.384
peak=    3.887 closest distance to " CB  VAL A 202 " =    1.608
peak=    3.882 closest distance to " CB  ASN A  39 " =    0.934
peak=    3.879 closest distance to " CB  PRO A  54 " =    0.842
peak=    3.878 closest distance to " N   PHE A 130 " =    1.240
peak=    3.876 closest distance to " N   ASN A  39 " =    1.166
peak=    3.870 closest distance to " O   HOH Z 214 " =    2.125
peak=    3.855 closest distance to " OD1 ASN A  69 " =    2.633
peak=    3.854 closest distance to " O   HOH Z 313 " =    1.882
peak=    3.842 closest distance to " CB  GLU A 277 " =    3.611
peak=    3.822 closest distance to " CG1BVAL A  72 " =    1.652
peak=    3.811 closest distance to " O   HOH Z 411 " =    3.849
peak=    3.804 closest distance to " CB BVAL A  41 " =    1.181
peak=    3.803 closest distance to " CE  LYS A  76 " =    0.859
peak=    3.793 closest distance to " O   HOH Z 193 " =    1.826
peak=    3.783 closest distance to " CG  LEU A 167 " =    1.210
peak=    3.781 closest distance to " CB  ARG A 190 " =    1.613
peak=    3.775 closest distance to " CB  ASN A 187 " =    1.203
peak=    3.772 closest distance to " CB  ASP A 140 " =    0.926
peak=    3.771 closest distance to " O   HOH Z  68 " =    2.279
peak=    3.764 closest distance to " O   HOH Z 203 " =    1.728
peak=    3.745 closest distance to " O   HOH Z  21 " =    1.784
peak=    3.744 closest distance to " CA  ALA A  51 " =    0.948
peak=    3.728 closest distance to " O   HOH Z 371 " =    2.936
peak=    3.727 closest distance to " NH1AARG A 145 " =    1.130
peak=    3.724 closest distance to " CB  ARG A  79 " =    0.904
peak=    3.724 closest distance to " CA  ASN A 215 " =    1.034
peak=    3.714 closest distance to " CD  LYS A 166 " =    1.276
peak=    3.706 closest distance to " CG1 ILE A  49 " =    1.463
peak=    3.691 closest distance to " CB  SER A 212 " =    1.245
peak=    3.690 closest distance to " O   HOH Z 353 " =    2.539
peak=    3.673 closest distance to " O   HOH Z 126 " =    1.557
peak=    3.672 closest distance to " CA  ARG A 195 " =    1.159
peak=    3.663 closest distance to " OG BSER A 164 " =    2.203
peak=    3.656 closest distance to " CG1 VAL A 153 " =    0.946
peak=    3.650 closest distance to " O   HOH Z  10 " =    1.767
peak=    3.644 closest distance to " CA  THR A 264 " =    0.787
peak=    3.636 closest distance to " CB  TRP A 179 " =    1.449
peak=    3.627 closest distance to " CA  SER A  87 " =    1.005
peak=    3.613 closest distance to " O   HOH Z 180 " =    2.130
peak=    3.611 closest distance to " O   HOH Z 128 " =    2.188
peak=    3.609 closest distance to " O   HOH Z  59 " =    1.898
peak=    3.608 closest distance to " O   HOH Z  92 " =    2.478
peak=    3.603 closest distance to " O   HOH Z 280 " =    3.020
peak=    3.600 closest distance to " O   HOH Z 273 " =    2.807
peak=    3.600 closest distance to " CB  LEU A 228 " =    1.247
peak=    3.584 closest distance to " CA  ALA A  21 " =    1.125
peak=    3.581 closest distance to " O   HOH Z 147 " =    1.764
peak=    3.571 closest distance to " CB  GLU A  46 " =    0.946
peak=    3.569 closest distance to " CA  ARG A  36 " =    1.055
peak=    3.561 closest distance to " CB  GLN A  88 " =    1.168
peak=    3.552 closest distance to " CG  ARG A  66 " =    2.663
peak=    3.551 closest distance to " CD1 ILE A  33 " =    1.748
peak=    3.549 closest distance to " O   HOH Z  97 " =    2.450
peak=    3.547 closest distance to " O   HOH Z 251 " =    1.533
peak=    3.541 closest distance to " CD1 LEU A  96 " =    0.734
peak=    3.537 closest distance to " O   HOH Z 419 " =    1.877
peak=    3.531 closest distance to " CG  GLN A  88 " =    1.078
peak=    3.529 closest distance to " CB  THR A  31 " =    1.538
peak=    3.528 closest distance to " CG  MET A 185 " =    1.205
peak=    3.519 closest distance to " CB  SER A 216 " =    0.838
peak=    3.510 closest distance to " O   HOH Z  40 " =    1.506
peak=    3.508 closest distance to " O   HOH Z 402 " =    1.404
peak=    3.507 closest distance to " CB  ASN A 110 " =    1.053
peak=    3.504 closest distance to " O   HOH Z 261 " =    1.550
peak=    3.502 closest distance to " CB  ALA A 291 " =    1.337
peak=    3.502 closest distance to " O   HOH Z   9 " =    1.976
peak=    3.501 closest distance to " CD BLYS A 290 " =    1.130
peak=    3.499 closest distance to " CB  LYS A 117 " =    1.250
peak=    3.497 closest distance to " O   HOH Z 250 " =    1.342
peak=    3.492 closest distance to " CB  LEU A 143 " =    1.190
peak=    3.481 closest distance to " O   HOH Z 132 " =    2.716
peak=    3.481 closest distance to " CG2 ILE A  20 " =    1.501
peak=    3.476 closest distance to " CA  VAL A  41 " =    0.780
peak=    3.475 closest distance to " O   HOH Z 366 " =    2.976
peak=    3.472 closest distance to " O   HOH Z 285 " =    2.613
peak=    3.468 closest distance to " NE2 GLN A  77 " =    3.225
peak=    3.465 closest distance to " CD2 TRP A 179 " =    1.330
peak=    3.464 closest distance to " O   HOH Z   3 " =    1.972
peak=    3.463 closest distance to " O   HOH Z 148 " =    3.411
peak=    3.461 closest distance to " CB  ALA A 248 " =    1.384
peak=    3.461 closest distance to " CA  ALA A 291 " =    0.867
peak=    3.455 closest distance to " CA  ASP A 162 " =    0.998
peak=    3.454 closest distance to " O   HOH Z 263 " =    1.696
peak=    3.452 closest distance to " O   HOH Z 299 " =    4.111
peak=    3.452 closest distance to " O   HOH Z 389 " =    1.812
peak=    3.451 closest distance to " O   HOH Z 305 " =    3.579
peak=    3.446 closest distance to " O  BHOH Z 338 " =    2.399
peak=    3.445 closest distance to " O   HOH Z 193 " =    1.968
peak=    3.444 closest distance to " O   GLN A 278 " =    1.380
peak=    3.443 closest distance to " CB  MET A  40 " =    0.812
peak=    3.437 closest distance to " CA  TYR A 116 " =    1.413
peak=    3.436 closest distance to " CB  HIS A 108 " =    0.801
peak=    3.435 closest distance to " CD  ARG A 269 " =    0.972
peak=    3.429 closest distance to " CA  LYS A 117 " =    1.183
peak=    3.427 closest distance to " CB  THR A 157 " =    1.134
peak=    3.426 closest distance to " O   HOH Z 133 " =    2.430
peak=    3.425 closest distance to " CE1 TYR A 186 " =    1.357
peak=    3.425 closest distance to " CB  SER A 273 " =    0.893
peak=    3.423 closest distance to " O   HOH Z 344 " =    3.005
peak=    3.419 closest distance to " O   HOH Z   1 " =    1.740
peak=    3.419 closest distance to " O   HOH Z 145 " =    2.077
peak=    3.413 closest distance to " N   SER A 135 " =    1.316
peak=    3.411 closest distance to " O   HOH Z 128 " =    2.098
peak=    3.410 closest distance to " NZ  LYS A 117 " =    3.286
peak=    3.408 closest distance to " O   HOH Z 403 " =    1.586
peak=    3.408 closest distance to " O   HOH Z 187 " =    2.299
peak=    3.408 closest distance to " O   HOH Z 291 " =    1.593
peak=    3.407 closest distance to " O   HOH Z 422 " =    2.645
peak=    3.406 closest distance to " CB  THR A  82 " =    1.401
peak=    3.397 closest distance to " O   ASN A  74 " =    1.503
peak=    3.388 closest distance to " O   HOH Z  97 " =    1.947
peak=    3.385 closest distance to " O   HOH Z 290 " =    1.140
peak=    3.383 closest distance to " N   ARG A 156 " =    1.339
peak=    3.381 closest distance to " CD1 LEU A 228 " =    2.042
peak=    3.381 closest distance to " O   TRP A 274 " =    1.846
peak=    3.370 closest distance to " O   HOH Z 213 " =    2.075
peak=    3.369 closest distance to " O   ASP A 124 " =    1.104
peak=    3.366 closest distance to " O   HOH Z  88 " =    3.008
peak=    3.365 closest distance to " NZ  LYS A  48 " =    1.226
peak=    3.361 closest distance to " CB  ALA A 242 " =    0.795
peak=    3.358 closest distance to " CB  ARG A 139 " =    0.914
peak=    3.356 closest distance to " O   HOH Z 435 " =    1.972
peak=    3.354 closest distance to " ND1 HIS A  86 " =    1.674
peak=    3.348 closest distance to " O   HOH Z 368 " =    3.547
peak=    3.348 closest distance to " CZ  PHE A  38 " =    1.156
peak=    3.342 closest distance to " O   HOH Z 193 " =    1.693
peak=    3.342 closest distance to " O   HOH Z 329 " =    3.986
peak=    3.340 closest distance to " O   HOH Z 392 " =    3.193
peak=    3.333 closest distance to " O   HOH Z  40 " =    2.235
peak=    3.331 closest distance to " CD1 ILE A 106 " =    1.003
peak=    3.326 closest distance to " CA  LEU A 282 " =    1.142
peak=    3.326 closest distance to " CB  PRO A  90 " =    1.144
peak=    3.323 closest distance to " CA  ALA A 233 " =    1.182
peak=    3.321 closest distance to " CD1 ILE A 263 " =    1.237
peak=    3.320 closest distance to " O   HOH Z 409 " =    3.128
peak=    3.319 closest distance to " O   HOH Z 337 " =    3.580
peak=    3.315 closest distance to " ND2 ASN A 249 " =    0.868
peak=    3.315 closest distance to " O   HOH Z 350 " =    1.608
peak=    3.311 closest distance to " CG1 VAL A 296 " =    1.247
peak=    3.309 closest distance to " CA  ALA A 158 " =    1.272
peak=    3.307 closest distance to " O   HOH Z 437 " =    1.769
peak=    3.303 closest distance to " CB  GLN A  89 " =    1.255
peak=    3.298 closest distance to " CZ3 TRP A 266 " =    1.132
peak=    3.297 closest distance to " CB  SER A  26 " =    1.699
peak=    3.296 closest distance to " CB  ALA A 114 " =    1.230
peak=    3.295 closest distance to " O   HOH Z 403 " =    1.470
peak=    3.294 closest distance to " O   HOH Z 172 " =    3.288
peak=    3.294 closest distance to " O   MET A 105 " =    1.833
peak=    3.291 closest distance to " O   HOH Z 406 " =    1.523
peak=    3.287 closest distance to " N   GLN A 278 " =    1.245
peak=    3.285 closest distance to " CB  TRP A 150 " =    1.396
peak=    3.283 closest distance to " OD2 ASP A 286 " =    2.781
peak=    3.280 closest distance to " O   HOH Z 359 " =    3.802
peak=    3.278 closest distance to " O   HOH Z 425 " =    2.052
peak=    3.273 closest distance to " CG2 ILE A 120 " =    1.088
peak=    3.271 closest distance to " CA  ALA A 154 " =    0.989
peak=    3.266 closest distance to " C   ALA A 299 " =    0.917
peak=    3.266 closest distance to " CG  MET A 185 " =    1.043
peak=    3.261 closest distance to " CA  GLY A 267 " =    0.716
peak=    3.260 closest distance to " CG1 ILE A 151 " =    1.047
peak=    3.256 closest distance to " CB  ASN A 224 " =    1.006
peak=    3.253 closest distance to " CG BARG A 102 " =    1.785
peak=    3.248 closest distance to " CD1 LEU A 261 " =    1.193
peak=    3.233 closest distance to " NH2 ARG A 156 " =    1.103
peak=    3.232 closest distance to " CA  ILE A 234 " =    0.931
peak=    3.231 closest distance to " O   HOH Z 421 " =    3.009
peak=    3.231 closest distance to " CD1 LEU A 300 " =    1.271
peak=    3.231 closest distance to " O   HOH Z 258 " =    2.315
peak=    3.229 closest distance to " CG2 THR A 221 " =    1.170
peak=    3.221 closest distance to " CA  ASN A 127 " =    1.057
peak=    3.219 closest distance to " O   HOH Z 380 " =    1.801
peak=    3.219 closest distance to " CG  LEU A 281 " =    1.066
peak=    3.219 closest distance to " CB  GLN A 278 " =    0.904
peak=    3.217 closest distance to " O   HOH Z  30 " =    1.387
peak=    3.217 closest distance to " O   HOH Z 294 " =    1.516
peak=    3.211 closest distance to " CZ  PHE A 192 " =    0.973
peak=    3.211 closest distance to " CB  ASN A 215 " =    1.153
peak=    3.209 closest distance to " CA  ASN A 217 " =    1.235
peak=    3.207 closest distance to " CA  SER A 146 " =    1.733
peak=    3.206 closest distance to " CB  PHE A 204 " =    0.874
peak=    3.206 closest distance to " CB  LYS A 290 " =    0.904
peak=    3.205 closest distance to " NE2 HIS A 207 " =    1.288
peak=    3.203 closest distance to " CE3 TRP A 150 " =    0.955
peak=    3.198 closest distance to " CG  MET A 113 " =    1.120
peak=    3.192 closest distance to " CB  GLN A 205 " =    1.082
peak=    3.191 closest distance to " CD  ARG A 195 " =    3.500
peak=    3.190 closest distance to " CG  GLN A 278 " =    1.278
peak=    3.189 closest distance to " CB  ILE A  20 " =    1.438
peak=    3.188 closest distance to " CB  GLN A 103 " =    0.994
peak=    3.185 closest distance to " CA  LYS A 290 " =    1.192
peak=    3.185 closest distance to " O   LYS A 290 " =    2.415
peak=    3.184 closest distance to " O   HOH Z  88 " =    2.704
peak=    3.178 closest distance to " O   HOH Z  48 " =    1.605
peak=    3.173 closest distance to " CA  TYR A  30 " =    1.074
peak=    3.172 closest distance to " O   HOH Z 417 " =    3.151
peak=    3.170 closest distance to " CD2 TYR A 186 " =    1.044
peak=    3.169 closest distance to " CA  MET A 105 " =    0.951
peak=    3.167 closest distance to " O   HOH Z 325 " =    2.222
peak=    3.164 closest distance to " OG BSER A 134 " =    3.043
peak=    3.163 closest distance to " O   HOH Z 417 " =    2.125
peak=    3.161 closest distance to " N   ASP A 162 " =    1.263
peak=    3.161 closest distance to " CB  ALA A 248 " =    1.018
peak=    3.160 closest distance to " CA  ILE A 106 " =    0.738
peak=    3.159 closest distance to " O   ARG A  56 " =    2.876
peak=    3.158 closest distance to " CB  LEU A 300 " =    0.842
peak=    3.156 closest distance to " O   HOH Z  88 " =    3.377
peak=    3.155 closest distance to " CG  GLN A  77 " =    2.311
peak=    3.153 closest distance to " CA  ASP A 191 " =    1.113
peak=    3.149 closest distance to " O   PHE A 192 " =    1.396
peak=    3.142 closest distance to " OG1 THR A 264 " =    0.773
peak=    3.138 closest distance to " N   ASN A 127 " =    1.220
peak=    3.137 closest distance to " CA  ARG A 159 " =    1.212
peak=    3.136 closest distance to " O   SER A 164 " =    1.266
peak=    3.124 closest distance to " OE2 GLU A  53 " =    1.981
peak=    3.122 closest distance to " OG  SER A  22 " =    2.774
peak=    3.122 closest distance to " O   HOH Z 141 " =    1.720
peak=    3.119 closest distance to " CB  VAL A 268 " =    0.846
peak=    3.118 closest distance to " CA  ALA A 248 " =    1.169
peak=    3.098 closest distance to " O   HOH Z  80 " =    1.550
peak=    3.095 closest distance to " CG1 ILE A  33 " =    1.284
peak=    3.094 closest distance to " CB  ASN A 173 " =    1.030
peak=    3.093 closest distance to " O   HOH Z 342 " =    1.254
peak=    3.093 closest distance to " CB  ALA A 180 " =    1.225
peak=    3.090 closest distance to " O   HOH Z 357 " =    1.974
peak=    3.086 closest distance to " O   HOH Z 245 " =    1.351
peak=    3.085 closest distance to " O   HOH Z 345 " =    3.374
peak=    3.085 closest distance to " O   HOH Z  85 " =    2.238
peak=    3.077 closest distance to " ND1 HIS A  81 " =    1.728
peak=    3.075 closest distance to " O   HOH Z 238 " =    3.709
peak=    3.072 closest distance to " CG  ARG A 159 " =    0.950
peak=    3.069 closest distance to " CA  ARG A 102 " =    1.162
peak=    3.059 closest distance to " OE2 GLU A   2 " =    1.790
peak=    3.059 closest distance to " O   HOH Z 384 " =    3.224
peak=    3.056 closest distance to " O   HOH Z 154 " =    2.038
peak=    3.044 closest distance to " O   HOH Z 116 " =    1.715
peak=    3.035 closest distance to " O   HOH Z  47 " =    1.775

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 197         
Filter by distance & map next to the model:
   mapped sites are within: 0.716 - 5.433
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 196 from: 197
   mapped sites are within: 0.716 - 5.433

peak=   -5.470 closest distance to " CG2 VAL A 230 " =    0.716
peak=   -4.619 closest distance to " CD  ARG A 156 " =    2.029
peak=   -4.495 closest distance to " CD  GLN A  58 " =    1.024
peak=   -4.417 closest distance to " SG  CYS A 254 " =    3.342
peak=   -4.319 closest distance to " CB  PRO A 243 " =    2.697
peak=   -4.271 closest distance to " CB  PHE A 192 " =    1.986
peak=   -4.210 closest distance to " OG BSER A 134 " =    1.222
peak=   -4.182 closest distance to " O   HOH Z 266 " =    5.296
peak=   -4.129 closest distance to " CG  GLN A 223 " =    2.036
peak=   -4.074 closest distance to " C   HIS A 108 " =    1.208
peak=   -4.067 closest distance to " CG2 VAL A 296 " =    1.328
peak=   -3.991 closest distance to " O   HOH Z 290 " =    1.192
peak=   -3.967 closest distance to " O   HOH Z 185 " =    2.350
peak=   -3.923 closest distance to " CD1 LEU A 255 " =    2.873
peak=   -3.888 closest distance to " O   HOH Z 114 " =    3.014
peak=   -3.881 closest distance to " O   VAL A  67 " =    2.614
peak=   -3.880 closest distance to " O   HOH Z 231 " =    2.051
peak=   -3.858 closest distance to " O   HOH Z 351 " =    1.505
peak=   -3.852 closest distance to " CA  ASN A 110 " =    2.581
peak=   -3.852 closest distance to " CE2 TYR A  30 " =    2.767
peak=   -3.850 closest distance to " CB  ALA A 248 " =    2.147
peak=   -3.847 closest distance to " O   VAL A  67 " =    2.882
peak=   -3.817 closest distance to " CG1 VAL A 112 " =    2.625
peak=   -3.795 closest distance to " O   HOH Z 196 " =    2.230
peak=   -3.789 closest distance to " N   THR A 157 " =    1.501
peak=   -3.779 closest distance to " CZ3 TRP A 179 " =    1.200
peak=   -3.776 closest distance to " CE  MET A 105 " =    2.250
peak=   -3.754 closest distance to " CB  ALA A 248 " =    2.393
peak=   -3.752 closest distance to " CB  ALA A  43 " =    2.496
peak=   -3.744 closest distance to " CA  GLY A 241 " =    2.301
peak=   -3.707 closest distance to " O   PRO A 198 " =    1.194
peak=   -3.698 closest distance to " C   MET A 188 " =    1.416
peak=   -3.694 closest distance to " CG  ASP A 231 " =    0.792
peak=   -3.676 closest distance to " CG1 VAL A 112 " =    2.834
peak=   -3.669 closest distance to " ND2 ASN A  45 " =    1.802
peak=   -3.666 closest distance to " O   HOH Z  44 " =    2.283
peak=   -3.655 closest distance to " O   HOH Z 394 " =    1.516
peak=   -3.654 closest distance to " O   HOH Z 389 " =    2.096
peak=   -3.641 closest distance to " O   HOH Z  11 " =    1.945
peak=   -3.625 closest distance to " O   PRO A 163 " =    2.083
peak=   -3.622 closest distance to " O   HOH Z 211 " =    1.576
peak=   -3.621 closest distance to " CB  PRO A 280 " =    2.153
peak=   -3.617 closest distance to " ND2 ASN A 249 " =    2.465
peak=   -3.616 closest distance to " OG  SER A  97 " =    2.306
peak=   -3.591 closest distance to " O   VAL A 189 " =    2.604
peak=   -3.588 closest distance to " CE3 TRP A 150 " =    2.083
peak=   -3.577 closest distance to " CA  GLY A 241 " =    3.108
peak=   -3.564 closest distance to " N   ALA A 248 " =    1.751
peak=   -3.563 closest distance to " ND2 ASN A  45 " =    1.192
peak=   -3.561 closest distance to " CG2 ILE A  49 " =    2.819
peak=   -3.557 closest distance to " C   LEU A 222 " =    0.807
peak=   -3.551 closest distance to " N   ALA A 226 " =    2.117
peak=   -3.548 closest distance to " OXT GLY A 302 " =    2.934
peak=   -3.544 closest distance to " CA  ASP A 298 " =    1.090
peak=   -3.540 closest distance to " CE BMET A  47 " =    1.477
peak=   -3.535 closest distance to " O   HOH Z  73 " =    2.269
peak=   -3.523 closest distance to " CG2 VAL A 202 " =    2.701
peak=   -3.514 closest distance to " O   HOH Z 166 " =    2.056
peak=   -3.503 closest distance to " CD2 LEU A 237 " =    2.870
peak=   -3.503 closest distance to " CG1 VAL A 250 " =    2.780
peak=   -3.500 closest distance to " CD1 LEU A 101 " =    2.364
peak=   -3.489 closest distance to " O   HOH Z  13 " =    1.697
peak=   -3.487 closest distance to " OD1 ASN A 148 " =    1.409
peak=   -3.484 closest distance to " N   ALA A  43 " =    2.500
peak=   -3.483 closest distance to " O   HOH Z 102 " =    1.633
peak=   -3.473 closest distance to " O   HOH Z 140 " =    1.626
peak=   -3.469 closest distance to " CB  ALA A 291 " =    2.247
peak=   -3.464 closest distance to " ND2 ASN A 187 " =    1.454
peak=   -3.463 closest distance to " NH2AARG A 275 " =    5.232
peak=   -3.462 closest distance to " CB  ALA A 291 " =    2.206
peak=   -3.452 closest distance to " CG  TRP A 266 " =    1.880
peak=   -3.450 closest distance to " O   MET A  40 " =    2.782
peak=   -3.444 closest distance to " O   GLY A  80 " =    2.503
peak=   -3.441 closest distance to " O   HOH Z 407 " =    3.037
peak=   -3.431 closest distance to " CG2 ILE A 263 " =    2.376
peak=   -3.427 closest distance to " O   HOH Z 191 " =    5.433
peak=   -3.417 closest distance to " O   SER A  22 " =    2.328
peak=   -3.409 closest distance to " O   ALA A 161 " =    1.715
peak=   -3.406 closest distance to " CB  PRO A 163 " =    2.533
peak=   -3.404 closest distance to " CB  ASN A  39 " =    2.162
peak=   -3.400 closest distance to " CG1 VAL A 296 " =    1.375
peak=   -3.393 closest distance to " CD  ARG A 139 " =    1.622
peak=   -3.389 closest distance to " OG  SER A  87 " =    1.448
peak=   -3.385 closest distance to " O   HOH Z 243 " =    1.899
peak=   -3.380 closest distance to " CZ  TYR A 169 " =    1.672
peak=   -3.378 closest distance to " C   GLY A  17 " =    1.275
peak=   -3.372 closest distance to " C   PHE A  59 " =    1.353
peak=   -3.367 closest distance to " C   ALA A 158 " =    1.373
peak=   -3.358 closest distance to " NE2 GLN A  88 " =    1.901
peak=   -3.356 closest distance to " CA  ASN A 127 " =    1.058
peak=   -3.354 closest distance to " OD2 ASP A 171 " =    2.271
peak=   -3.353 closest distance to " O   HOH Z 198 " =    2.051
peak=   -3.351 closest distance to " CG  PHE A 283 " =    2.654
peak=   -3.349 closest distance to " O   HOH Z 426 " =    1.687
peak=   -3.347 closest distance to " O   HOH Z  60 " =    1.922
peak=   -3.344 closest distance to " O   HOH Z 350 " =    2.000
peak=   -3.343 closest distance to " CG2 VAL A 296 " =    1.829
peak=   -3.343 closest distance to " CB  ASP A 132 " =    2.298
peak=   -3.343 closest distance to " O   HOH Z 313 " =    1.159
peak=   -3.335 closest distance to " O   ALA A  51 " =    1.371
peak=   -3.334 closest distance to " C   LEU A 143 " =    1.081
peak=   -3.326 closest distance to " N   THR A  52 " =    1.742
peak=   -3.325 closest distance to " N   ALA A 248 " =    2.275
peak=   -3.323 closest distance to " CA  GLY A  98 " =    1.842
peak=   -3.319 closest distance to " O   PRO A 198 " =    1.385
peak=   -3.319 closest distance to " NE2 GLN A 278 " =    1.904
peak=   -3.317 closest distance to " O   HOH Z 313 " =    1.655
peak=   -3.313 closest distance to " CB  ASP A 132 " =    2.377
peak=   -3.311 closest distance to " OD1 ASN A 187 " =    1.664
peak=   -3.307 closest distance to " O   HOH Z 134 " =    3.146
peak=   -3.307 closest distance to " N   GLN A  58 " =    1.880
peak=   -3.307 closest distance to " OH  TYR A 247 " =    2.077
peak=   -3.304 closest distance to " N   ASP A 171 " =    2.338
peak=   -3.301 closest distance to " O   HOH Z 103 " =    1.844
peak=   -3.299 closest distance to " O   HOH Z 353 " =    2.064
peak=   -3.296 closest distance to " O   HOH Z 359 " =    3.264
peak=   -3.292 closest distance to " CD  LYS A 289 " =    2.513
peak=   -3.292 closest distance to " C   ASP A 231 " =    2.484
peak=   -3.288 closest distance to " CB  ASN A  69 " =    1.209
peak=   -3.285 closest distance to " O   HOH Z  38 " =    1.702
peak=   -3.284 closest distance to " O   SER A 210 " =    1.952
peak=   -3.282 closest distance to " NH2 ARG A  79 " =    2.019
peak=   -3.272 closest distance to " CA  ASP A  27 " =    2.417
peak=   -3.265 closest distance to " CD2 TYR A 293 " =    2.057
peak=   -3.264 closest distance to " NH2 ARG A  79 " =    1.579
peak=   -3.263 closest distance to " CB  GLN A  11 " =    1.837
peak=   -3.260 closest distance to " OG  SER A 206 " =    1.717
peak=   -3.260 closest distance to " O   HOH Z 417 " =    2.963
peak=   -3.258 closest distance to " CD1 PHE A  59 " =    1.990
peak=   -3.253 closest distance to " NE2 GLN A 194 " =    1.781
peak=   -3.251 closest distance to " O   ALA A  10 " =    1.751
peak=   -3.246 closest distance to " O   HOH Z  52 " =    1.521
peak=   -3.239 closest distance to " CG1 VAL A 125 " =    1.886
peak=   -3.235 closest distance to " CE2 PHE A  61 " =    2.606
peak=   -3.231 closest distance to " CD2 LEU A 300 " =    2.838
peak=   -3.228 closest distance to " O   HOH Z 346 " =    1.786
peak=   -3.228 closest distance to " O   ARG A 145 " =    1.622
peak=   -3.227 closest distance to " OG BSER A 134 " =    1.792
peak=   -3.226 closest distance to " CG2 VAL A 189 " =    1.973
peak=   -3.223 closest distance to " CG  HIS A  86 " =    1.075
peak=   -3.223 closest distance to " CZ  PHE A 192 " =    2.833
peak=   -3.222 closest distance to " O   SER A 271 " =    2.229
peak=   -3.219 closest distance to " CD1 LEU A 228 " =    2.226
peak=   -3.218 closest distance to " CG  LEU A 228 " =    0.982
peak=   -3.214 closest distance to " CD1 ILE A 239 " =    2.268
peak=   -3.213 closest distance to " N   PHE A  59 " =    2.081
peak=   -3.210 closest distance to " CG2 THR A 178 " =    2.236
peak=   -3.209 closest distance to " O   HOH Z 187 " =    1.611
peak=   -3.201 closest distance to " CG  GLU A 277 " =    1.256
peak=   -3.197 closest distance to " O   HOH Z 139 " =    5.103
peak=   -3.192 closest distance to " N   HIS A 115 " =    2.159
peak=   -3.192 closest distance to " CD1 LEU A 101 " =    2.609
peak=   -3.188 closest distance to " O   HOH Z 281 " =    2.656
peak=   -3.185 closest distance to " O   GLY A 196 " =    1.219
peak=   -3.182 closest distance to " SG BCYS A 201 " =    2.043
peak=   -3.179 closest distance to " NE2 GLN A  88 " =    1.099
peak=   -3.179 closest distance to " CA  GLY A 203 " =    2.444
peak=   -3.175 closest distance to " NE2 GLN A 278 " =    1.830
peak=   -3.164 closest distance to " ND2 ASN A 252 " =    1.897
peak=   -3.163 closest distance to " O   SER A 135 " =    1.440
peak=   -3.159 closest distance to " CE2 PHE A 218 " =    2.531
peak=   -3.149 closest distance to " O   HOH Z 256 " =    1.320
peak=   -3.149 closest distance to " O   HOH Z 131 " =    4.103
peak=   -3.147 closest distance to " O   HOH Z 166 " =    1.547
peak=   -3.141 closest distance to " CD2 LEU A   5 " =    1.187
peak=   -3.140 closest distance to " OH  TYR A 214 " =    1.221
peak=   -3.140 closest distance to " O   HOH Z 193 " =    2.051
peak=   -3.135 closest distance to " CA  PRO A 243 " =    2.239
peak=   -3.133 closest distance to " CB  ASN A 252 " =    1.802
peak=   -3.131 closest distance to " O   HOH Z  10 " =    1.459
peak=   -3.131 closest distance to " ND2 ASN A  60 " =    1.376
peak=   -3.130 closest distance to " O   HOH Z  22 " =    2.414
peak=   -3.124 closest distance to " CG1 VAL A  67 " =    3.072
peak=   -3.124 closest distance to " N   SER A 276 " =    1.323
peak=   -3.121 closest distance to " O   HOH Z 175 " =    4.230
peak=   -3.119 closest distance to " OXT GLY A 302 " =    3.553
peak=   -3.117 closest distance to " OD2 ASP A  50 " =    2.229
peak=   -3.114 closest distance to " ND2BASN A 224 " =    1.697
peak=   -3.113 closest distance to " CE  LYS A  76 " =    2.658
peak=   -3.107 closest distance to " CD1 ILE A 199 " =    2.485
peak=   -3.107 closest distance to " CA  SER A 135 " =    1.389
peak=   -3.107 closest distance to " CD2 PHE A 225 " =    1.045
peak=   -3.105 closest distance to " O   HOH Z 210 " =    1.117
peak=   -3.104 closest distance to " C   ASP A 270 " =    1.312
peak=   -3.095 closest distance to " CB  TRP A  85 " =    2.560
peak=   -3.089 closest distance to " CD  PRO A 243 " =    2.129
peak=   -3.089 closest distance to " CB  ALA A 114 " =    2.513
peak=   -3.086 closest distance to " CD2 LEU A 300 " =    2.873
peak=   -3.082 closest distance to " OG  SER A  62 " =    1.642
peak=   -3.074 closest distance to " OD1 ASP A 171 " =    1.647
peak=   -3.059 closest distance to " CE1 TYR A 247 " =    2.734
peak=   -3.053 closest distance to " O   HOH Z 128 " =    2.578
peak=   -3.045 closest distance to " O   HOH Z 371 " =    1.703
peak=   -3.042 closest distance to " O   HOH Z 200 " =    4.343
peak=   -3.031 closest distance to " CG1 VAL A 197 " =    2.271
peak=   -3.015 closest distance to " OD1 ASN A 301 " =    1.962

================= 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    :  0.4264 0.4089   6.216046e+00   6.183579e+00
   1_bss:  0.4186 0.3969   6.212202e+00   6.167609e+00
   1_xyz:  0.3044 0.3212   5.978670e+00   6.010951e+00
   1_adp:  0.2358 0.2689   5.751361e+00   5.866099e+00
   1_occ:  0.2350 0.2691   5.750244e+00   5.867974e+00
   2_bss:  0.2288 0.2632   5.747499e+00   5.863124e+00
   2_xyz:  0.1563 0.1956   5.406809e+00   5.582281e+00
   2_adp:  0.1436 0.1848   5.333723e+00   5.524851e+00
   2_occ:  0.1435 0.1846   5.332940e+00   5.524150e+00
   3_bss:  0.1432 0.1841   5.333799e+00   5.524498e+00
   3_xyz:  0.1203 0.1637   5.197379e+00   5.424033e+00
   3_adp:  0.1153 0.1615   5.170860e+00   5.410692e+00
   3_occ:  0.1152 0.1615   5.170953e+00   5.410892e+00
   4_bss:  0.1152 0.1615   5.170635e+00   5.410760e+00
   4_xyz:  0.1131 0.1595   5.158849e+00   5.402689e+00
   4_adp:  0.1140 0.1578   5.156171e+00   5.391280e+00
   4_occ:  0.1139 0.1577   5.155695e+00   5.390944e+00
   5_bss:  0.1140 0.1573   5.155519e+00   5.389267e+00
   5_xyz:  0.1127 0.1568   5.148812e+00   5.387502e+00
   5_adp:  0.1121 0.1571   5.149020e+00   5.391194e+00
   5_occ:  0.1121 0.1571   5.148641e+00   5.390934e+00
   5_bss:  0.1121 0.1571   5.148572e+00   5.390885e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.341  18.899   7.160   8.251   9.728   0.000   0.000   0.000
   1_xyz:  0.341  18.899   7.160   8.251   9.728   0.000   0.000   0.000
   1_adp:  0.341  18.899   7.160   8.251   9.728   0.000   0.000   0.000
   1_occ:  0.341  18.899   7.160   8.251   9.728   0.000   0.000   0.000
   2_bss:  0.341  45.196   3.834   4.326   6.202   0.000   0.000   0.000
   2_xyz:  0.341  45.196   3.834   4.326   6.202   0.000   0.000   0.000
   2_adp:  0.341  45.196   3.834   4.326   6.202   0.000   0.000   0.000
   2_occ:  0.341  45.196   3.834   4.326   6.202   0.000   0.000   0.000
   3_bss:  0.326  45.197   3.095   3.425   4.980   0.000   0.000   0.000
   3_xyz:  0.326  45.197   3.095   3.425   4.980   0.000   0.000   0.000
   3_adp:  0.326  45.197   3.095   3.425   4.980   0.000   0.000   0.000
   3_occ:  0.326  45.197   3.095   3.425   4.980   0.000   0.000   0.000
   4_bss:  0.319  45.197   3.116   3.373   4.876   0.000   0.000   0.000
   4_xyz:  0.319  45.197   3.116   3.373   4.876   0.000   0.000   0.000
   4_adp:  0.319  45.197   3.116   3.373   4.876   0.000   0.000   0.000
   4_occ:  0.319  45.197   3.116   3.373   4.876   0.000   0.000   0.000
   5_bss:  0.322  45.197   3.116   3.373   4.876   0.000   0.000   0.000
   5_xyz:  0.322  45.197   3.116   3.373   4.876   0.000   0.000   0.000
   5_adp:  0.322  45.197   3.116   3.373   4.876   0.000   0.000   0.000
   5_occ:  0.322  45.197   3.116   3.373   4.876   0.000   0.000   0.000
   5_bss:  0.321  49.537  -0.657  -0.422   1.079  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  44.863 0.5858  0.6510    47990.040
   1_bss:  44.482 0.5885  0.8402    45186.682
   1_xyz:  33.802 0.7145  0.9818    27333.207
   1_adp:  26.272 0.7992  1.0626    18182.510
   1_occ:  26.354 0.7982  1.0605    18241.890
   2_bss:  26.073 0.8011  0.9343    17916.499
   2_xyz:  18.326 0.8773  0.9971     9392.955
   2_adp:  16.832 0.8914  1.0068     8406.105
   2_occ:  16.813 0.8915  1.0069     8387.110
   3_bss:  16.799 0.8917  0.9721     8408.911
   3_xyz:  14.755 0.9087  0.9798     6819.129
   3_adp:  14.483 0.9112  0.9776     6636.681
   3_occ:  14.487 0.9111  0.9775     6636.512
   4_bss:  14.482 0.9111  0.9759     6634.200
   4_xyz:  14.222 0.9136  0.9763     6541.099
   4_adp:  13.956 0.9158  0.9748     6415.996
   4_occ:  13.950 0.9158  0.9749     6410.303
   5_bss:  13.940 0.9158  0.9745     6380.764
   5_xyz:  13.895 0.9162  0.9749     6336.971
   5_adp:  13.978 0.9155  0.9715     6371.943
   5_occ:  13.974 0.9155  0.9714     6369.593
   5_bss:  13.973 0.9155  0.9717     6369.087
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.3861e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.3861e+01
   1_xyz:   1.482  0.011  0.100 18.014  0.005  4.122   1.1310e-01
   1_adp:   1.482  0.011  0.100 18.014  0.005  4.122   1.1310e-01
   1_occ:   1.482  0.011  0.100 18.014  0.005  4.122   1.1310e-01
   2_bss:   1.482  0.011  0.100 18.014  0.005  4.122   1.1310e-01
   2_xyz:   0.968  0.007  0.073 16.344  0.004  4.123   6.1460e-02
   2_adp:   0.968  0.007  0.073 16.344  0.004  4.123   6.1460e-02
   2_occ:   0.968  0.007  0.073 16.344  0.004  4.123   6.1460e-02
   3_bss:   0.968  0.007  0.073 16.344  0.004  4.123   6.1460e-02
   3_xyz:   1.042  0.008  0.084 16.013  0.004  4.132   6.6651e-02
   3_adp:   1.042  0.008  0.084 16.013  0.004  4.132   6.6651e-02
   3_occ:   1.042  0.008  0.084 16.013  0.004  4.132   6.6651e-02
   4_bss:   1.042  0.008  0.084 16.013  0.004  4.132   6.6651e-02
   4_xyz:   0.975  0.007  0.080 15.768  0.004  4.134   6.0509e-02
   4_adp:   0.975  0.007  0.080 15.768  0.004  4.134   6.0509e-02
   4_occ:   0.975  0.007  0.080 15.768  0.004  4.134   6.0509e-02
   5_bss:   0.975  0.007  0.080 15.768  0.004  4.134   6.0509e-02
   5_xyz:   0.978  0.007  0.080 15.636  0.004  4.137   6.0002e-02
   5_adp:   0.978  0.007  0.080 15.636  0.004  4.137   6.0002e-02
   5_occ:   0.978  0.007  0.080 15.636  0.004  4.137   6.0002e-02
   5_bss:   0.978  0.007  0.080 15.636  0.004  4.137   6.0002e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9835e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9835e+00
   1_xyz:  11.309  0.137  0.409 88.984  0.033  2.209   8.2916e-02
   1_adp:  11.309  0.137  0.409 88.984  0.033  2.209   8.2916e-02
   1_occ:  11.309  0.137  0.409 88.984  0.033  2.209   8.2916e-02
   2_bss:  11.309  0.137  0.409 88.984  0.033  2.209   8.2916e-02
   2_xyz:   6.757  0.053  0.328 88.122  0.037  2.315   7.3056e-02
   2_adp:   6.757  0.053  0.328 88.122  0.037  2.315   7.3056e-02
   2_occ:   6.757  0.053  0.328 88.122  0.037  2.315   7.3056e-02
   3_bss:   6.757  0.053  0.328 88.122  0.037  2.315   7.3056e-02
   3_xyz:   6.495  0.041  0.532 82.618  0.036  2.275   4.5072e-02
   3_adp:   6.495  0.041  0.532 82.618  0.036  2.275   4.5072e-02
   3_occ:   6.495  0.041  0.532 82.618  0.036  2.275   4.5072e-02
   4_bss:   6.495  0.041  0.532 82.618  0.036  2.275   4.5072e-02
   4_xyz:   6.871  0.043  0.500 83.601  0.037  2.374   3.9489e-02
   4_adp:   6.871  0.043  0.500 83.601  0.037  2.374   3.9489e-02
   4_occ:   6.871  0.043  0.500 83.601  0.037  2.374   3.9489e-02
   5_bss:   6.871  0.043  0.500 83.601  0.037  2.374   3.9489e-02
   5_xyz:   6.540  0.044  0.483 83.208  0.037  2.320   3.7295e-02
   5_adp:   6.540  0.044  0.483 83.208  0.037  2.320   3.7295e-02
   5_occ:   6.540  0.044  0.483 83.208  0.037  2.320   3.7295e-02
   5_bss:   6.540  0.044  0.483 83.208  0.037  2.320   3.7295e-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:  58.06   0.00  10.53  52.87   0.00   7.34  58.06   0.00  27.89
   1_occ:  58.06   0.00  10.53  52.87   0.00   7.34  58.06   0.00  27.89
   2_bss:  58.06   0.00  10.53  52.87   0.00   7.34  58.06   0.00  27.89
   2_xyz:  58.06   0.00  10.53  52.87   0.00   7.34  58.06   0.00  27.89
   2_adp:  59.08   0.00  10.82  56.46   0.00   7.14  59.08   0.00  30.87
   2_occ:  59.08   0.00  10.82  56.46   0.00   7.14  59.08   0.00  30.87
   3_bss:  59.08   0.00  10.82  56.46   0.00   7.14  59.08   0.00  30.87
   3_xyz:  59.08   0.00  10.82  56.46   0.00   7.14  59.08   0.00  30.87
   3_adp:  76.24   0.00  11.64  76.24   0.00   7.35  70.85   0.38  34.99
   3_occ:  76.24   0.00  11.64  76.24   0.00   7.35  70.85   0.38  34.99
   4_bss:  76.24   0.00  11.64  76.24   0.00   7.35  70.85   0.38  34.99
   4_xyz:  76.24   0.00  11.64  76.24   0.00   7.35  70.85   0.38  34.99
   4_adp:  76.03   0.00  11.11  76.03   0.00   7.12  68.22   0.92  32.85
   4_occ:  76.03   0.00  11.11  76.03   0.00   7.12  68.22   0.92  32.85
   5_bss:  76.03   0.00  11.11  76.03   0.00   7.12  68.22   0.92  32.85
   5_xyz:  76.03   0.00  11.11  76.03   0.00   7.12  68.22   0.92  32.85
   5_adp:  76.46   0.00  11.11  76.46   0.00   7.10  68.17   0.75  32.98
   5_occ:  76.46   0.00  11.11  76.46   0.00   7.10  68.17   0.75  32.98
   5_bss:  80.25   3.80  14.91  80.25   3.80  10.90  71.97   4.55  36.78
------------------------------------------------------------------------
 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:    1.198    0.021    0.398
   1_adp:    1.198    0.021    0.398
   1_occ:    1.198    0.021    0.398
   2_bss:    1.198    0.021    0.398
   2_xyz:    1.455    0.040    0.487
   2_adp:    1.455    0.040    0.487
   2_occ:    1.455    0.040    0.487
   3_bss:    1.455    0.040    0.487
   3_xyz:    1.450    0.031    0.516
   3_adp:    1.450    0.031    0.516
   3_occ:    1.450    0.031    0.516
   4_bss:    1.450    0.031    0.516
   4_xyz:    1.571    0.049    0.526
   4_adp:    1.571    0.049    0.526
   4_occ:    1.571    0.049    0.526
   5_bss:    1.571    0.049    0.526
   5_xyz:    1.641    0.059    0.534
   5_adp:    1.641    0.059    0.534
   5_occ:    1.641    0.059    0.534
   5_bss:    1.641    0.059    0.534
------------------------------------------------------------------------

CPU time actual refinement: 337.80


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_656/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_656/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_656/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_656/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_656/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 337.65 
  Macro-tasks:
    bulk solvent and scale       = 41.29  
    individual site refinement   = 142.62 
    weights calculation          = 32.43  
    collect and process          = 6.69   
    model show statistics        = 0.14   
    TOTAL for macro-tasks        = 223.17 
  Micro-tasks:
    mask                            = 1.77   
    f_calc                          = 103.84 
    alpha_beta                      = 8.40   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 114.99 
    fmodel                         = 7.53   
    r_factors                      = 0.32   
    phase_errors                   = 11.05  
    foms                           = 0.24   
    TOTAL for micro-tasks          = 249.30 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.692 micro seconds
Total CPU time: 5.85 minutes
from_scatterers_fft:    652 calls, 103.60 s
gradients_fft:          596 calls, 101.11 s

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

# Date 2008-01-16 Time 02:07:51 PST -0800 (1200478071.49 s)
Start R-work = 0.4264, R-free = 0.4089 (no bulk solvent and anisotropic scale)
Final R-work = 0.1298, R-free = 0.1744 (no bulk solvent and anisotropic scale)

Start R-work = 0.4186, R-free = 0.3969
Final R-work = 0.1121, R-free = 0.1571