# Date 2008-01-16 Time 02:42:25 PST -0800 (1200480145.25 s)
#phil __OFF__

Command line arguments: "../939.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 = 880
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 939

-------------------------------------------------------------------------------
  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: (70.9525, 47.6339, 85.9581, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 47.6339, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0819 1.99124
Completeness in resolution range: 0.955281
Completeness with d_max=infinity: 0.952309

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0819
                             d_min =   1.9912

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: (70.9525, 47.6339, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0819 1.99124
Completeness in resolution range: 0.955281
Completeness with d_max=infinity: 0.952309

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0824 -  4.2608 [2151/2179]  1939   212   9.9%
  bin  2:  4.2608 -  3.3946 [2063/2082]  1854   209  10.1%
  bin  3:  3.3946 -  2.9692 [2046/2066]  1842   204  10.0%
  bin  4:  2.9692 -  2.6994 [2032/2057]  1834   198   9.7%
  bin  5:  2.6994 -  2.5069 [2014/2033]  1809   205  10.2%
  bin  6:  2.5069 -  2.3597 [1998/2043]  1797   201  10.1%
  bin  7:  2.3597 -  2.2419 [1973/2007]  1774   199  10.1%
  bin  8:  2.2419 -  2.1446 [1992/2027]  1792   200  10.0%
  bin  9:  2.1446 -  2.0622 [1993/2022]  1799   194   9.7%
  bin 10:  2.0622 -  1.9912 [1327/1990]  1190   137  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_939/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.70 -     2.34: 10
        2.34 -     2.98: 1768
        2.98 -     3.62: 4540
        3.62 -     4.26: 9032
        4.26 -     4.90: 12672
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.698 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 206 " - " O   HOH Z 342 "  1.953 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A 246 " - " O   HOH Z 201 "  2.038 3.040 -x+1/2,-y+1,z-1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  ... (remaining 28017 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_939/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_939/model_refine_001.geo

CPU time processing inputs: 9.10


============================ 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 = 70.9525 47.63395 85.95805 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4609   r_free= 0.4425   ksol= 0.00   Bsol= 0.00   scale= 0.800    |
|                                                                             |
| 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:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.261375                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0824 -  4.7522 0.99   1393  154 0.3793 0.3594      6.5602      6.4849|
|  2:  4.7522 -  3.7917 0.99   1360  148 0.3676 0.3994      6.7387      6.8058|
|  3:  3.7917 -  3.3182 0.99   1306  153 0.4160 0.3613       6.635      6.5867|
|  4:  3.3182 -  3.0175 0.99   1327  143 0.4428 0.3944      6.4968      6.3902|
|  5:  3.0175 -  2.8027 0.99   1303  145 0.4905 0.4907      6.3626      6.4143|
|  6:  2.8027 -  2.6384 0.98   1285  143 0.4893 0.4892      6.2556       6.192|
|  7:  2.6384 -  2.5069 0.99   1304  142 0.4894 0.4602      6.2354      6.1648|
|  8:  2.5069 -  2.3982 0.98   1270  147 0.5005 0.4727      6.1666      6.1416|
|  9:  2.3982 -  2.3062 0.98   1298  141 0.5224 0.5207      6.1193      6.1594|
| 10:  2.3062 -  2.2269 0.98   1276  138 0.5044 0.5018      6.0972      6.1005|
| 11:  2.2269 -  2.1575 0.99   1267  146 0.5076 0.4569      6.0298      6.0382|
| 12:  2.1575 -  2.0960 0.98   1272  138 0.5246 0.5237      5.9777      6.0041|
| 13:  2.0960 -  2.0409 0.97   1263  141 0.5282 0.5014      5.8788      5.8347|
| 14:  2.0409 -  1.9912 0.55    706   80 0.5301 0.4895      5.8299      5.7577|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0824 -  4.7522  1393   154  0.72  32.65   0.81     0.74      64456.38|
|  2:  4.7522 -  3.7917  1360   148  0.74  31.55   0.89     0.78      87170.20|
|  3:  3.7917 -  3.3182  1306   153  0.66  39.01   0.83     0.75      92176.49|
|  4:  3.3182 -  3.0175  1327   143  0.59  45.00   0.81     0.66      81964.78|
|  5:  3.0175 -  2.8027  1303   145  0.49  52.36   0.75     0.57      70653.90|
|  6:  2.8027 -  2.6384  1285   143  0.48  53.92   0.74     0.54      61565.23|
|  7:  2.6384 -  2.5069  1304   142  0.48  53.58   0.75     0.53      55415.43|
|  8:  2.5069 -  2.3982  1270   147  0.45  55.97   0.73     0.52      51697.49|
|  9:  2.3982 -  2.3062  1298   141  0.42  58.77   0.71     0.48      48841.14|
| 10:  2.3062 -  2.2269  1276   138  0.40  60.06   0.76     0.46      46870.52|
| 11:  2.2269 -  2.1575  1267   146  0.38  61.33   0.76     0.45      42963.64|
| 12:  2.1575 -  2.0960  1272   138  0.36  62.98   0.75     0.44      41254.35|
| 13:  2.0960 -  2.0409  1263   141  0.33  65.25   0.72     0.40      35784.06|
| 14:  2.0409 -  1.9912   706    80  0.34  64.71   0.71     0.38      29826.08|
|alpha:            min =        0.38 max =            0.78 mean =         0.56|
|beta:             min =    29826.08 max =        92176.49 mean =     59157.42|
|figures of merit: min =        0.00 max =            1.00 mean =         0.50|
|phase err.(work): min =        0.00 max =           89.98 mean =        51.98|
|phase err.(test): min =        0.00 max =           89.76 mean =        51.79|
|-----------------------------------------------------------------------------|

============================== 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 = 10.979934             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.052   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.907040              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.752   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        3 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       26 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      160 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      681 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1481 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2608 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3846 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5055 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6511 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7663 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       54.156 |
| 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 |       1.713 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.147)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 12.147)------------------------------------------|
|    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 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4671   r_free= 0.4514   ksol= 0.00   Bsol= 0.00   scale= 0.771    |
|                                                                             |
| 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:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.263399                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4527   r_free= 0.4327   ksol= 0.32   Bsol= 20.53   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.30,10.81,7.37,0.00,0.00,0.00); trace/3= 8.49                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.256436                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.069546             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.882   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.860839              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.495   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4527      final r-factor (work) = 0.3587          |
| start r-factor (free) = 0.4327      final r-factor (free) = 0.3825          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 85.6995 = 10.07 * 0.50 * 6.2651 + 1.00 * 54.1564                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 31.0496 = 10.07 * 0.50 * 6.1401 + 1.00 * 0.1358                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3587      final r-factor (work) = 0.3076          |
| start r-factor (free) = 0.3825      final r-factor (free) = 0.3465          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.3000 = 0.86 * 1.00 * 6.1401 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.2030 = 0.86 * 1.00 * 6.0277 + 1.00 * 0.0141                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.147)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.84   11.71    None  None   None       |
|    all(noH): 2823   0      0.00    89.84   11.71    None  None   None       |
|    Sol.    : 438    0      0.00    89.84   26.72    None  None   None       |
|    Mac.    : 2385   0      0.00    75.57   8.95     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.984: 1563   |   5:    44.918 -  53.902:   46        |
|      1:     8.984 -  17.967:  674   |   6:    53.902 -  62.885:   18        |
|      2:    17.967 -  26.951:  291   |   7:    62.885 -  71.869:    6        |
|      3:    26.951 -  35.934:  139   |   8:    71.869 -  80.852:    1        |
|      4:    35.934 -  44.918:   82   |   9:    80.852 -  89.836:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3076 r_free = 0.3465             target_work(ml) = 5.995         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3074 r_free = 0.3463             target_work(ml) = 5.994         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3074   r_free= 0.3463   ksol= 0.32   Bsol= 20.53   scale= 1.078   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.30,10.81,7.37,0.00,0.00,0.00); trace/3= 8.49                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 5.993779                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3045   r_free= 0.3408   ksol= 0.32   Bsol= 48.32   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.15,6.97,4.66,0.00,0.00,0.00); trace/3= 5.26                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.45 A                  |
| x-ray target function (ml) for work reflections: 5.994411                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.757325              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.154   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.449409              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 124.833  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3045      final r-factor (work) = 0.2057          |
| start r-factor (free) = 0.3408      final r-factor (free) = 0.2562          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.5080 = 7.76 * 0.50 * 6.0258 + 1.00 * 0.1358                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.6757 = 7.76 * 0.50 * 5.8229 + 1.00 * 0.0905                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2057      final r-factor (work) = 0.1830          |
| start r-factor (free) = 0.2562      final r-factor (free) = 0.2299          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6347 = 0.45 * 1.00 * 5.8229 + 1.00 * 0.0178                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5519 = 0.45 * 1.00 * 5.6039 + 1.00 * 0.0334                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.147)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.30   12.16    None  None   None       |
|    all(noH): 2823   0      0.00    86.30   12.16    None  None   None       |
|    Sol.    : 438    0      0.00    86.30   32.99    None  None   None       |
|    Mac.    : 2385   0      0.00    80.28   8.34     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 -   8.630: 1615   |   5:    43.150 -  51.780:   95        |
|      1:     8.630 -  17.260:  630   |   6:    51.780 -  60.410:   41        |
|      2:    17.260 -  25.890:  184   |   7:    60.410 -  69.040:   12        |
|      3:    25.890 -  34.520:  136   |   8:    69.040 -  77.670:    3        |
|      4:    34.520 -  43.150:  103   |   9:    77.670 -  86.300:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1830 r_free = 0.2299             target_work(ml) = 5.558         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1827 r_free = 0.2299             target_work(ml) = 5.557         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1827   r_free= 0.2299   ksol= 0.32   Bsol= 48.32   scale= 1.040   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.15,6.97,4.66,0.00,0.00,0.00); trace/3= 5.26                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.556788                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1807   r_free= 0.2291   ksol= 0.32   Bsol= 61.96   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.65,4.04,3.53,0.00,0.00,0.00); trace/3= 3.41                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.556801                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.545513              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.370  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.553571              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 94.969   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1807      final r-factor (work) = 0.1402          |
| start r-factor (free) = 0.2291      final r-factor (free) = 0.1809          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.0449 = 3.55 * 0.50 * 5.6149 + 1.00 * 0.0910                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.7319 = 3.55 * 0.50 * 5.4508 + 1.00 * 0.0690                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1402      final r-factor (work) = 0.1312          |
| start r-factor (free) = 0.1809      final r-factor (free) = 0.1744          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0430 = 0.55 * 1.00 * 5.4508 + 1.00 * 0.0256                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9480 = 0.55 * 1.00 * 5.2851 + 1.00 * 0.0223                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.147)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.30   12.72    None  None   None       |
|    all(noH): 2823   0      0.00    87.30   12.72    None  None   None       |
|    Sol.    : 438    0      0.47    80.80   36.90    None  None   None       |
|    Mac.    : 2385   0      0.00    87.30   8.28     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.730: 1688   |   5:    43.648 -  52.378:   83        |
|      1:     8.730 -  17.459:  562   |   6:    52.378 -  61.108:   75        |
|      2:    17.459 -  26.189:  164   |   7:    61.108 -  69.837:   27        |
|      3:    26.189 -  34.919:  110   |   8:    69.837 -  78.567:    6        |
|      4:    34.919 -  43.648:  101   |   9:    78.567 -  87.296:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1312 r_free = 0.1744             target_work(ml) = 5.270         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1311 r_free = 0.1743             target_work(ml) = 5.270         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1311   r_free= 0.1743   ksol= 0.32   Bsol= 61.96   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.65,4.04,3.53,0.00,0.00,0.00); trace/3= 3.41                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.269744                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1311   r_free= 0.1748   ksol= 0.33   Bsol= 61.96   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.37,3.28,3.34,0.00,0.00,0.00); trace/3= 3.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.271113                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.549017              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 126.111  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.311681              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 97.142   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1311      final r-factor (work) = 0.1171          |
| start r-factor (free) = 0.1748      final r-factor (free) = 0.1638          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.4498 = 3.55 * 0.50 * 5.2864 + 1.00 * 0.0690                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.3512 = 3.55 * 0.50 * 5.2242 + 1.00 * 0.0808                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1171      final r-factor (work) = 0.1159          |
| start r-factor (free) = 0.1638      final r-factor (free) = 0.1621          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6457 = 0.31 * 1.00 * 5.2242 + 1.00 * 0.0174                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6278 = 0.31 * 1.00 * 5.1858 + 1.00 * 0.0115                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.147)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.32   12.33    None  None   None       |
|    all(noH): 2823   0      0.00    86.32   12.33    None  None   None       |
|    Sol.    : 438    0      0.80    81.94   35.68    None  None   None       |
|    Mac.    : 2385   0      0.00    86.32   8.04     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.632: 1703   |   5:    43.159 -  51.791:   79        |
|      1:     8.632 -  17.264:  569   |   6:    51.791 -  60.423:   66        |
|      2:    17.264 -  25.895:  152   |   7:    60.423 -  69.054:   21        |
|      3:    25.895 -  34.527:  118   |   8:    69.054 -  77.686:    7        |
|      4:    34.527 -  43.159:  100   |   9:    77.686 -  86.318:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1159 r_free = 0.1621             target_work(ml) = 5.179         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1159 r_free = 0.1620             target_work(ml) = 5.179         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1159   r_free= 0.1620   ksol= 0.33   Bsol= 61.96   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.37,3.28,3.34,0.00,0.00,0.00); trace/3= 3.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.179007                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1159   r_free= 0.1619   ksol= 0.33   Bsol= 61.96   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.43,3.08,3.41,0.00,0.00,0.00); trace/3= 2.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.178824                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.471569              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 150.965  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.924421              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.593  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1159      final r-factor (work) = 0.1153          |
| start r-factor (free) = 0.1619      final r-factor (free) = 0.1606          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4890 = 2.47 * 0.50 * 5.1855 + 1.00 * 0.0808                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4672 = 2.47 * 0.50 * 5.1783 + 1.00 * 0.0679                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1153      final r-factor (work) = 0.1142          |
| start r-factor (free) = 0.1606      final r-factor (free) = 0.1622          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.9767 = 1.92 * 1.00 * 5.1783 + 1.00 * 0.0114                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.9629 = 1.92 * 1.00 * 5.1699 + 1.00 * 0.0139                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 35     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.147)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.94   12.46    None  None   None       |
|    all(noH): 2823   0      0.00    92.94   12.46    None  None   None       |
|    Sol.    : 438    0      0.75    82.92   36.50    None  None   None       |
|    Mac.    : 2385   0      0.00    92.94   8.05     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.294: 1779   |   5:    46.470 -  55.764:   78        |
|      1:     9.294 -  18.588:  504   |   6:    55.764 -  65.058:   53        |
|      2:    18.588 -  27.882:  162   |   7:    65.058 -  74.352:   20        |
|      3:    27.882 -  37.176:  110   |   8:    74.352 -  83.645:    5        |
|      4:    37.176 -  46.470:  108   |   9:    83.645 -  92.939:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1142 r_free = 0.1622             target_work(ml) = 5.178         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1142 r_free = 0.1623             target_work(ml) = 5.178         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1142   r_free= 0.1623   ksol= 0.33   Bsol= 61.96   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.43,3.08,3.41,0.00,0.00,0.00); trace/3= 2.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.177653                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0824 -  4.7522 0.99   1393  154 0.1018 0.1324      5.4015      5.5392|
|  2:  4.7522 -  3.7917 0.99   1360  148 0.0864 0.1092      5.4395      5.6314|
|  3:  3.7917 -  3.3182 0.99   1306  153 0.1070 0.1526       5.485      5.8756|
|  4:  3.3182 -  3.0175 0.99   1327  143 0.1245 0.1600      5.4761      5.6228|
|  5:  3.0175 -  2.8027 0.99   1303  145 0.1349 0.1779      5.3639       5.539|
|  6:  2.8027 -  2.6384 0.98   1285  143 0.1275 0.2027      5.2557      5.5326|
|  7:  2.6384 -  2.5069 0.99   1304  142 0.1257 0.1720      5.1922      5.3992|
|  8:  2.5069 -  2.3982 0.98   1270  147 0.1200 0.1726      5.1069      5.3497|
|  9:  2.3982 -  2.3062 0.98   1298  141 0.1206 0.1899      5.0695      5.3709|
| 10:  2.3062 -  2.2269 0.98   1276  138 0.1178 0.1827      5.0103      5.2736|
| 11:  2.2269 -  2.1575 0.99   1267  146 0.1172 0.1785      4.9701      5.3027|
| 12:  2.1575 -  2.0960 0.98   1272  138 0.1115 0.1718      4.8996      5.1562|
| 13:  2.0960 -  2.0409 0.97   1263  141 0.1177 0.1809      4.8276      5.1082|
| 14:  2.0409 -  1.9912 0.55    706   80 0.1076 0.1843      4.7177      4.9946|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0824 -  4.7522  1393   154  0.94   9.05   0.97     0.95       7278.37|
|  2:  4.7522 -  3.7917  1360   148  0.95   7.97   1.00     0.99       8925.56|
|  3:  3.7917 -  3.3182  1306   153  0.93  11.49   1.02     1.02      10717.04|
|  4:  3.3182 -  3.0175  1327   143  0.91  14.38   1.00     0.97      10854.29|
|  5:  3.0175 -  2.8027  1303   145  0.89  17.03   0.99     0.96       9186.36|
|  6:  2.8027 -  2.6384  1285   143  0.89  16.93   0.98     0.95       7917.52|
|  7:  2.6384 -  2.5069  1304   142  0.90  15.87   0.98     0.95       6629.23|
|  8:  2.5069 -  2.3982  1270   147  0.90  16.37   0.98     0.95       5942.25|
|  9:  2.3982 -  2.3062  1298   141  0.90  16.30   0.99     0.95       5472.97|
| 10:  2.3062 -  2.2269  1276   138  0.89  16.87   0.98     0.94       4955.29|
| 11:  2.2269 -  2.1575  1267   146  0.89  16.96   0.98     0.94       4629.67|
| 12:  2.1575 -  2.0960  1272   138  0.91  15.43   0.99     0.96       4176.40|
| 13:  2.0960 -  2.0409  1263   141  0.89  17.49   0.99     0.98       3760.51|
| 14:  2.0409 -  1.9912   706    80  0.90  16.26   0.97     0.92       2927.77|
|alpha:            min =        0.92 max =            1.02 mean =         0.96|
|beta:             min =     2927.77 max =        10854.29 mean =      6831.21|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.77|
|phase err.(test): min =        0.00 max =           89.08 mean =        14.19|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1141   r_free= 0.1622   ksol= 0.32   Bsol= 59.63   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.51,0.06,0.45,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.177630                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1141   r_free= 0.1622   ksol= 0.32   Bsol= 59.63   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.51,0.06,0.45,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.177630                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0824 -  4.7522 0.99   1393  154 0.1013 0.1323       5.399      5.5381|
|  2:  4.7522 -  3.7917 0.99   1360  148 0.0862 0.1087      5.4378      5.6276|
|  3:  3.7917 -  3.3182 0.99   1306  153 0.1069 0.1525      5.4838      5.8761|
|  4:  3.3182 -  3.0175 0.99   1327  143 0.1246 0.1598      5.4767      5.6229|
|  5:  3.0175 -  2.8027 0.99   1303  145 0.1351 0.1781      5.3652      5.5402|
|  6:  2.8027 -  2.6384 0.98   1285  143 0.1277 0.2029      5.2566      5.5331|
|  7:  2.6384 -  2.5069 0.99   1304  142 0.1258 0.1721      5.1929         5.4|
|  8:  2.5069 -  2.3982 0.98   1270  147 0.1201 0.1727      5.1075      5.3501|
|  9:  2.3982 -  2.3062 0.98   1298  141 0.1205 0.1898      5.0699       5.371|
| 10:  2.3062 -  2.2269 0.98   1276  138 0.1178 0.1828      5.0108      5.2743|
| 11:  2.2269 -  2.1575 0.99   1267  146 0.1172 0.1784      4.9703      5.3025|
| 12:  2.1575 -  2.0960 0.98   1272  138 0.1114 0.1720      4.8997      5.1575|
| 13:  2.0960 -  2.0409 0.97   1263  141 0.1177 0.1809      4.8277      5.1076|
| 14:  2.0409 -  1.9912 0.55    706   80 0.1077 0.1841      4.7178      4.9943|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0824 -  4.7522  1393   154  0.94   9.03   0.97     0.95       7271.45|
|  2:  4.7522 -  3.7917  1360   148  0.95   7.94   1.01     0.99       8893.48|
|  3:  3.7917 -  3.3182  1306   153  0.93  11.46   1.02     1.02      10677.56|
|  4:  3.3182 -  3.0175  1327   143  0.91  14.39   1.00     0.98      10862.00|
|  5:  3.0175 -  2.8027  1303   145  0.89  17.05   0.99     0.96       9203.10|
|  6:  2.8027 -  2.6384  1285   143  0.89  16.95   0.98     0.96       7930.56|
|  7:  2.6384 -  2.5069  1304   142  0.90  15.88   0.99     0.96       6636.58|
|  8:  2.5069 -  2.3982  1270   147  0.90  16.38   0.99     0.96       5949.15|
|  9:  2.3982 -  2.3062  1298   141  0.90  16.31   1.00     0.96       5479.81|
| 10:  2.3062 -  2.2269  1276   138  0.89  16.88   0.99     0.95       4959.60|
| 11:  2.2269 -  2.1575  1267   146  0.89  16.96   0.99     0.95       4632.51|
| 12:  2.1575 -  2.0960  1272   138  0.91  15.44   0.99     0.97       4178.96|
| 13:  2.0960 -  2.0409  1263   141  0.89  17.49   0.99     0.98       3761.47|
| 14:  2.0409 -  1.9912   706    80  0.90  16.26   0.98     0.93       2926.91|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2926.91 max =        10862.00 mean =      6830.31|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.91 mean =        14.77|
|phase err.(test): min =        0.00 max =           89.04 mean =        14.20|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.147)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.12    96.06   15.58    None  None   None       |
|    all(noH): 2823   0      3.12    96.06   15.58    None  None   None       |
|    Sol.    : 438    0      3.87    86.04   39.62    None  None   None       |
|    Mac.    : 2385   0      3.12    96.06   11.17    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     3.120 -  12.413: 1779   |   5:    49.589 -  58.883:   78        |
|      1:    12.413 -  21.707:  504   |   6:    58.883 -  68.177:   53        |
|      2:    21.707 -  31.001:  162   |   7:    68.177 -  77.471:   20        |
|      3:    31.001 -  40.295:  110   |   8:    77.471 -  86.765:    5        |
|      4:    40.295 -  49.589:  108   |   9:    86.765 -  96.059:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 313         
Filter by distance & map next to the model:
   mapped sites are within: 0.347 - 5.738
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 308 from: 313
   mapped sites are within: 0.703 - 5.738

peak=    9.381 closest distance to " CG2 VAL A 230 " =    1.253
peak=    6.564 closest distance to " CG2 VAL A 296 " =    1.085
peak=    6.328 closest distance to " NH2 ARG A  56 " =    2.289
peak=    6.219 closest distance to " CG  LEU A   5 " =    1.177
peak=    5.721 closest distance to " CG  LEU A 228 " =    1.140
peak=    5.644 closest distance to " CB  GLN A 223 " =    1.377
peak=    5.393 closest distance to " CG  PRO A  54 " =    1.239
peak=    5.376 closest distance to " CB  VAL A 230 " =    1.231
peak=    5.310 closest distance to " CB  VAL A 296 " =    1.105
peak=    5.043 closest distance to " CB  SER A  63 " =    1.302
peak=    4.881 closest distance to " CB  PRO A  54 " =    0.905
peak=    4.821 closest distance to " CG  PRO A 213 " =    1.226
peak=    4.649 closest distance to " O   HOH Z 232 " =    2.310
peak=    4.636 closest distance to " CD2 LEU A   5 " =    1.164
peak=    4.624 closest distance to " CB  GLN A 183 " =    1.308
peak=    4.589 closest distance to " CB  ARG A 275 " =    0.872
peak=    4.573 closest distance to " CG  PRO A 280 " =    0.839
peak=    4.503 closest distance to " O   SER A  87 " =    2.340
peak=    4.480 closest distance to " O   HOH Z 423 " =    1.834
peak=    4.452 closest distance to " CA  TYR A  30 " =    0.923
peak=    4.407 closest distance to " CG  PRO A 198 " =    1.235
peak=    4.344 closest distance to " NE2 GLN A  11 " =    1.055
peak=    4.341 closest distance to " O   HOH Z  48 " =    1.721
peak=    4.328 closest distance to " CB  ASN A 148 " =    1.353
peak=    4.324 closest distance to " O   HOH Z 272 " =    1.945
peak=    4.312 closest distance to " CB  GLU A 128 " =    1.141
peak=    4.289 closest distance to " O   HOH Z 316 " =    3.090
peak=    4.250 closest distance to " CG  PRO A 243 " =    1.179
peak=    4.236 closest distance to " OD1 ASN A  69 " =    2.678
peak=    4.226 closest distance to " CB  ARG A 190 " =    1.674
peak=    4.218 closest distance to " O   PRO A 198 " =    1.569
peak=    4.182 closest distance to " O   HOH Z 134 " =    1.660
peak=    4.181 closest distance to " CB  GLU A 152 " =    1.114
peak=    4.179 closest distance to " O   HOH Z 426 " =    1.505
peak=    4.177 closest distance to " O   HOH Z 403 " =    1.725
peak=    4.149 closest distance to " O   HOH Z  63 " =    1.645
peak=    4.149 closest distance to " O   HOH Z 236 " =    1.862
peak=    4.143 closest distance to " CB  TYR A 169 " =    0.735
peak=    4.122 closest distance to " O   HOH Z 369 " =    2.310
peak=    4.108 closest distance to " CB  TRP A 179 " =    1.410
peak=    4.093 closest distance to " O   HOH Z 126 " =    1.620
peak=    4.075 closest distance to " O   HOH Z  78 " =    1.703
peak=    4.072 closest distance to " O   HOH Z 433 " =    1.498
peak=    4.060 closest distance to " O   HOH Z 247 " =    1.404
peak=    4.057 closest distance to " O   HOH Z 298 " =    1.869
peak=    4.045 closest distance to " CB  GLU A 277 " =    3.695
peak=    4.025 closest distance to " CG2 THR A 221 " =    1.063
peak=    4.022 closest distance to " NH2 ARG A 156 " =    1.150
peak=    4.021 closest distance to " CZ  PHE A 218 " =    1.110
peak=    4.011 closest distance to " O   HOH Z 427 " =    3.083
peak=    3.998 closest distance to " O   HOH Z  44 " =    2.259
peak=    3.995 closest distance to " CG  PRO A  90 " =    1.025
peak=    3.985 closest distance to " O   HOH Z 126 " =    2.014
peak=    3.976 closest distance to " CB  SER A   3 " =    1.286
peak=    3.965 closest distance to " O   HOH Z  43 " =    2.087
peak=    3.941 closest distance to " O   HOH Z  80 " =    1.805
peak=    3.930 closest distance to " O   HOH Z  20 " =    1.680
peak=    3.929 closest distance to " CB  TRP A 266 " =    1.002
peak=    3.929 closest distance to " O   HOH Z  68 " =    1.823
peak=    3.929 closest distance to " CZ  PHE A 192 " =    1.018
peak=    3.920 closest distance to " O   HOH Z 280 " =    2.902
peak=    3.902 closest distance to " CG1 ILE A  33 " =    1.273
peak=    3.899 closest distance to " CB  ARG A  79 " =    1.439
peak=    3.897 closest distance to " CA  ALA A  51 " =    1.003
peak=    3.894 closest distance to " O   HOH Z  15 " =    2.234
peak=    3.859 closest distance to " O   HOH Z 234 " =    3.618
peak=    3.855 closest distance to " O   HOH Z 189 " =    2.709
peak=    3.842 closest distance to " O   HOH Z 412 " =    3.727
peak=    3.841 closest distance to " O   HOH Z  61 " =    1.543
peak=    3.840 closest distance to " O   HOH Z 214 " =    2.348
peak=    3.835 closest distance to " O   HOH Z 265 " =    2.317
peak=    3.829 closest distance to " O   HOH Z 420 " =    2.081
peak=    3.825 closest distance to " O   HOH Z  97 " =    2.080
peak=    3.811 closest distance to " CG  ARG A  66 " =    2.812
peak=    3.809 closest distance to " CD2 LEU A 228 " =    1.136
peak=    3.805 closest distance to " CD1 LEU A 300 " =    1.117
peak=    3.802 closest distance to " ND2 ASN A 249 " =    1.931
peak=    3.802 closest distance to " O   HOH Z  21 " =    1.739
peak=    3.800 closest distance to " O   TRP A 274 " =    1.898
peak=    3.800 closest distance to " O   HOH Z 374 " =    3.100
peak=    3.796 closest distance to " CB  LEU A 228 " =    1.300
peak=    3.795 closest distance to " O   HOH Z 402 " =    1.525
peak=    3.790 closest distance to " CA  ALA A  21 " =    1.299
peak=    3.782 closest distance to " O   HOH Z 158 " =    3.111
peak=    3.777 closest distance to " OG BSER A 164 " =    2.187
peak=    3.768 closest distance to " O   HOH Z 193 " =    1.835
peak=    3.759 closest distance to " O   HOH Z 437 " =    2.144
peak=    3.756 closest distance to " CA  THR A 264 " =    0.783
peak=    3.748 closest distance to " O   HOH Z 303 " =    2.117
peak=    3.742 closest distance to " CB  VAL A 265 " =    1.287
peak=    3.739 closest distance to " CA  ARG A  36 " =    1.150
peak=    3.733 closest distance to " CB AVAL A  41 " =    1.104
peak=    3.717 closest distance to " O   HOH Z 193 " =    2.251
peak=    3.717 closest distance to " CA  ARG A 195 " =    1.185
peak=    3.708 closest distance to " O   HOH Z 329 " =    3.852
peak=    3.700 closest distance to " CD  LYS A 166 " =    1.357
peak=    3.686 closest distance to " CD  ARG A 269 " =    0.960
peak=    3.676 closest distance to " CG1BVAL A  72 " =    1.705
peak=    3.675 closest distance to " CD ALYS A 290 " =    1.010
peak=    3.664 closest distance to " NH1AARG A 145 " =    1.108
peak=    3.659 closest distance to " CA  ALA A 295 " =    1.089
peak=    3.656 closest distance to " O   HOH Z 133 " =    2.314
peak=    3.654 closest distance to " O   MET A 105 " =    1.886
peak=    3.653 closest distance to " CE1 TYR A 186 " =    1.316
peak=    3.647 closest distance to " O   HOH Z 197 " =    2.509
peak=    3.646 closest distance to " O   HOH Z 383 " =    2.108
peak=    3.643 closest distance to " O   HOH Z 346 " =    1.625
peak=    3.638 closest distance to " CB  ALA A   9 " =    1.622
peak=    3.637 closest distance to " CB  ASN A  39 " =    0.846
peak=    3.630 closest distance to " CA  LYS A 117 " =    1.276
peak=    3.629 closest distance to " NZ  LYS A 117 " =    3.277
peak=    3.621 closest distance to " CB  VAL A 202 " =    1.560
peak=    3.619 closest distance to " O   HOH Z 245 " =    1.355
peak=    3.617 closest distance to " O   ALA A 165 " =    1.402
peak=    3.607 closest distance to " O   HOH Z 344 " =    3.001
peak=    3.606 closest distance to " O   HOH Z 227 " =    1.667
peak=    3.603 closest distance to " CG1 VAL A 296 " =    1.197
peak=    3.602 closest distance to " O   HOH Z 368 " =    2.331
peak=    3.601 closest distance to " O   HOH Z 357 " =    2.092
peak=    3.595 closest distance to " O   HOH Z 295 " =    1.540
peak=    3.593 closest distance to " O   HOH Z 261 " =    1.913
peak=    3.589 closest distance to " CB  THR A  31 " =    1.736
peak=    3.586 closest distance to " O   HOH Z 271 " =    2.610
peak=    3.577 closest distance to " CB  SER A 216 " =    0.870
peak=    3.575 closest distance to " O   HOH Z 352 " =    1.821
peak=    3.573 closest distance to " O   HOH Z  59 " =    2.461
peak=    3.568 closest distance to " CA  ASP A 191 " =    0.892
peak=    3.564 closest distance to " CD  ARG A 159 " =    0.785
peak=    3.562 closest distance to " O   HOH Z 102 " =    1.334
peak=    3.545 closest distance to " CB  ARG A 139 " =    0.834
peak=    3.541 closest distance to " CD1 LEU A   5 " =    1.377
peak=    3.539 closest distance to " ND1 HIS A  81 " =    1.704
peak=    3.537 closest distance to " O   HOH Z 248 " =    1.814
peak=    3.535 closest distance to " O   HOH Z 133 " =    1.659
peak=    3.534 closest distance to " OD2 ASP A 286 " =    2.925
peak=    3.532 closest distance to " O   HOH Z 345 " =    3.278
peak=    3.531 closest distance to " O   HOH Z 371 " =    3.258
peak=    3.527 closest distance to " CE1 HIS A 108 " =    1.157
peak=    3.526 closest distance to " O   HOH Z 132 " =    2.820
peak=    3.522 closest distance to " O   HOH Z  54 " =    1.662
peak=    3.521 closest distance to " N   VAL A 126 " =    1.451
peak=    3.519 closest distance to " CB  TRP A 150 " =    1.425
peak=    3.516 closest distance to " CA  THR A 221 " =    0.932
peak=    3.513 closest distance to " CB  SER A 212 " =    1.070
peak=    3.511 closest distance to " CA  MET A  40 " =    1.171
peak=    3.505 closest distance to " CB  HIS A 108 " =    0.848
peak=    3.505 closest distance to " CB  ASP A 140 " =    0.866
peak=    3.501 closest distance to " O   HOH Z 171 " =    3.902
peak=    3.500 closest distance to " NZ  LYS A  76 " =    1.597
peak=    3.487 closest distance to " CB  ALA A 291 " =    1.340
peak=    3.483 closest distance to " CD1 LEU A  96 " =    0.707
peak=    3.480 closest distance to " O   HOH Z 327 " =    2.420
peak=    3.474 closest distance to " O   ASP A 124 " =    1.131
peak=    3.472 closest distance to " O   HOH Z  40 " =    1.768
peak=    3.467 closest distance to " CB  MET A  40 " =    0.836
peak=    3.467 closest distance to " C   SER A  32 " =    1.059
peak=    3.467 closest distance to " CB  SER A  28 " =    1.314
peak=    3.465 closest distance to " O   HOH Z 128 " =    2.143
peak=    3.463 closest distance to " CG  MET A 185 " =    1.221
peak=    3.453 closest distance to " O   HOH Z 109 " =    2.519
peak=    3.452 closest distance to " O   THR A  31 " =    1.572
peak=    3.445 closest distance to " O   HOH Z 112 " =    1.604
peak=    3.444 closest distance to " CG  MET A 188 " =    0.854
peak=    3.443 closest distance to " CB  GLU A  46 " =    0.986
peak=    3.442 closest distance to " ND2 ASN A 187 " =    1.481
peak=    3.442 closest distance to " OD1 ASN A 217 " =    1.642
peak=    3.440 closest distance to " CB  LEU A 143 " =    1.205
peak=    3.440 closest distance to " O   HOH Z 193 " =    1.640
peak=    3.439 closest distance to " O   HOH Z 142 " =    1.409
peak=    3.437 closest distance to " O   HOH Z 180 " =    2.191
peak=    3.436 closest distance to " N   ASN A  39 " =    1.238
peak=    3.429 closest distance to " CA  GLY A 267 " =    0.706
peak=    3.429 closest distance to " O   HOH Z 365 " =    3.058
peak=    3.427 closest distance to " CA  ALA A 248 " =    1.311
peak=    3.426 closest distance to " O   HOH Z  88 " =    3.202
peak=    3.425 closest distance to " O   HOH Z 155 " =    3.115
peak=    3.424 closest distance to " O   HOH Z 422 " =    2.751
peak=    3.420 closest distance to " CG1 VAL A 153 " =    1.027
peak=    3.415 closest distance to " O   HOH Z 130 " =    2.212
peak=    3.407 closest distance to " CB  ALA A 242 " =    0.936
peak=    3.401 closest distance to " CB  SER A 273 " =    0.827
peak=    3.401 closest distance to " O   HOH Z 425 " =    1.298
peak=    3.398 closest distance to " CB  GLN A  89 " =    1.173
peak=    3.396 closest distance to " O   ALA A 158 " =    1.298
peak=    3.396 closest distance to " O   HOH Z 147 " =    1.792
peak=    3.395 closest distance to " O   HOH Z 163 " =    1.549
peak=    3.388 closest distance to " OG  SER A  22 " =    2.886
peak=    3.386 closest distance to " O   HOH Z 391 " =    3.041
peak=    3.385 closest distance to " CA  SER A  87 " =    1.025
peak=    3.382 closest distance to " CG  GLN A  58 " =    2.793
peak=    3.376 closest distance to " N   SER A 135 " =    1.431
peak=    3.371 closest distance to " CA  VAL A  41 " =    0.833
peak=    3.366 closest distance to " O   HOH Z 281 " =    4.649
peak=    3.363 closest distance to " CG BARG A 275 " =    1.325
peak=    3.359 closest distance to " CG  LEU A 167 " =    1.115
peak=    3.358 closest distance to " O   HOH Z   1 " =    2.855
peak=    3.358 closest distance to " CG1 ILE A 151 " =    1.048
peak=    3.352 closest distance to " CB  ALA A 100 " =    1.329
peak=    3.342 closest distance to " OG1 THR A 294 " =    2.398
peak=    3.341 closest distance to " CD2 HIS A  81 " =    1.038
peak=    3.337 closest distance to " CB  TYR A 247 " =    0.978
peak=    3.336 closest distance to " NH2BARG A 145 " =    2.153
peak=    3.330 closest distance to " CG2 VAL A 202 " =    1.131
peak=    3.329 closest distance to " CD2 LEU A 297 " =    0.849
peak=    3.317 closest distance to " CB  ARG A  79 " =    0.904
peak=    3.315 closest distance to " O   HOH Z 420 " =    5.738
peak=    3.312 closest distance to " OG1 THR A 157 " =    1.205
peak=    3.312 closest distance to " O   HOH Z 273 " =    2.927
peak=    3.310 closest distance to " O   HOH Z 387 " =    2.740
peak=    3.310 closest distance to " CB  ASN A 187 " =    1.104
peak=    3.309 closest distance to " CB  PRO A 198 " =    1.133
peak=    3.307 closest distance to " N   ARG A 190 " =    1.113
peak=    3.301 closest distance to " CG  GLN A  88 " =    1.080
peak=    3.301 closest distance to " CA  ASP A 140 " =    1.226
peak=    3.300 closest distance to " CB  GLN A  88 " =    1.281
peak=    3.297 closest distance to " O   HOH Z 291 " =    1.503
peak=    3.297 closest distance to " CB  ALA A 256 " =    1.221
peak=    3.293 closest distance to " CA  ASN A 176 " =    1.212
peak=    3.292 closest distance to " O   HOH Z 128 " =    2.066
peak=    3.290 closest distance to " O   HOH Z 368 " =    3.611
peak=    3.290 closest distance to " C   GLY A  80 " =    1.071
peak=    3.286 closest distance to " CA  ALA A 160 " =    0.809
peak=    3.285 closest distance to " O  BHOH Z 338 " =    2.419
peak=    3.284 closest distance to " CE  LYS A  76 " =    0.832
peak=    3.282 closest distance to " CA  LEU A 282 " =    1.147
peak=    3.281 closest distance to " CA  ASP A 162 " =    1.229
peak=    3.280 closest distance to " CG2 VAL A 257 " =    0.892
peak=    3.275 closest distance to " OE1 GLU A   2 " =    1.842
peak=    3.271 closest distance to " O   HOH Z 166 " =    1.514
peak=    3.268 closest distance to " CA  VAL A 125 " =    1.426
peak=    3.267 closest distance to " O   HOH Z 394 " =    1.419
peak=    3.265 closest distance to " O   HOH Z 419 " =    1.681
peak=    3.263 closest distance to " O   HOH Z  49 " =    1.875
peak=    3.254 closest distance to " ND2 ASN A 110 " =    1.592
peak=    3.252 closest distance to " CG2 THR A 220 " =    0.898
peak=    3.246 closest distance to " O   HOH Z 197 " =    1.917
peak=    3.242 closest distance to " O   HOH Z 407 " =    2.762
peak=    3.240 closest distance to " CB  ALA A 248 " =    1.057
peak=    3.239 closest distance to " O   HOH Z 187 " =    2.373
peak=    3.238 closest distance to " O   HOH Z 313 " =    1.752
peak=    3.237 closest distance to " CG  MET A 185 " =    1.094
peak=    3.236 closest distance to " O   HOH Z 299 " =    4.369
peak=    3.235 closest distance to " O   HOH Z 417 " =    3.157
peak=    3.235 closest distance to " CA  ASN A 215 " =    1.196
peak=    3.234 closest distance to " CG1 ILE A  49 " =    1.584
peak=    3.232 closest distance to " OG  SER A 245 " =    1.607
peak=    3.232 closest distance to " CG2 VAL A  78 " =    1.006
peak=    3.231 closest distance to " C   ALA A 299 " =    0.945
peak=    3.228 closest distance to " O   HOH Z 423 " =    3.224
peak=    3.227 closest distance to " O   HOH Z 279 " =    2.231
peak=    3.226 closest distance to " OE1 GLN A  11 " =    1.824
peak=    3.226 closest distance to " CG BARG A 102 " =    1.890
peak=    3.226 closest distance to " CD1 LEU A 222 " =    0.703
peak=    3.224 closest distance to " CD2 TRP A 179 " =    1.385
peak=    3.223 closest distance to " CD  PRO A  54 " =    1.072
peak=    3.223 closest distance to " O   HOH Z 425 " =    2.014
peak=    3.221 closest distance to " CG2 ILE A  20 " =    1.417
peak=    3.220 closest distance to " CA  ILE A 106 " =    0.783
peak=    3.217 closest distance to " O   GLN A 278 " =    1.527
peak=    3.217 closest distance to " O   HOH Z 227 " =    2.166
peak=    3.209 closest distance to " CD  ARG A  66 " =    2.527
peak=    3.208 closest distance to " O   HOH Z 116 " =    1.850
peak=    3.206 closest distance to " OD1 ASP A 231 " =    1.883
peak=    3.205 closest distance to " CZ3 TRP A  85 " =    0.926
peak=    3.201 closest distance to " O   HOH Z 263 " =    1.733
peak=    3.199 closest distance to " O   HOH Z 145 " =    2.552
peak=    3.197 closest distance to " CA  ALA A  84 " =    1.470
peak=    3.193 closest distance to " O   HOH Z 374 " =    2.842
peak=    3.190 closest distance to " CB  ASN A 285 " =    0.860
peak=    3.188 closest distance to " O   HOH Z 282 " =    2.069
peak=    3.188 closest distance to " O   HOH Z 104 " =    2.839
peak=    3.185 closest distance to " CA  THR A 246 " =    1.057
peak=    3.182 closest distance to " CG2 VAL A 197 " =    1.070
peak=    3.180 closest distance to " CD1 ILE A 106 " =    0.984
peak=    3.174 closest distance to " O   HOH Z 261 " =    2.152
peak=    3.171 closest distance to " OG  SER A  62 " =    2.973
peak=    3.170 closest distance to " O   HOH Z 298 " =    4.949
peak=    3.168 closest distance to " CA  ALA A 158 " =    1.225
peak=    3.166 closest distance to " CB  LYS A 117 " =    1.153
peak=    3.165 closest distance to " OD2 ASP A 298 " =    3.858
peak=    3.164 closest distance to " CB  ILE A 120 " =    1.355
peak=    3.163 closest distance to " CB  ASN A 142 " =    1.135
peak=    3.161 closest distance to " O   THR A 220 " =    1.186
peak=    3.157 closest distance to " CA  GLN A 194 " =    1.194
peak=    3.152 closest distance to " CG  LEU A 281 " =    1.140
peak=    3.141 closest distance to " NH1 ARG A  14 " =    1.096
peak=    3.135 closest distance to " OH  TYR A 214 " =    1.175
peak=    3.133 closest distance to " CB  ASN A 215 " =    1.179
peak=    3.128 closest distance to " CA  ALA A 154 " =    1.087
peak=    3.122 closest distance to " CB  ALA A 137 " =    1.195
peak=    3.120 closest distance to " O   HOH Z 213 " =    2.491
peak=    3.115 closest distance to " CG  GLU A  37 " =    0.806
peak=    3.114 closest distance to " CD1 ILE A  33 " =    1.575
peak=    3.111 closest distance to " ND1 HIS A  86 " =    1.556
peak=    3.110 closest distance to " CB  THR A  52 " =    1.007
peak=    3.103 closest distance to " N   ASN A 127 " =    1.261
peak=    3.095 closest distance to " CB  TYR A  30 " =    1.112
peak=    3.089 closest distance to " O   HOH Z 124 " =    1.242
peak=    3.084 closest distance to " O   HOH Z 128 " =    1.987
peak=    3.083 closest distance to " CA  GLN A  88 " =    1.272
peak=    3.082 closest distance to " O   HOH Z 409 " =    3.336
peak=    3.080 closest distance to " O   HOH Z 327 " =    1.685
peak=    3.079 closest distance to " O   HOH Z 406 " =    1.462
peak=    3.073 closest distance to " O   HOH Z 406 " =    1.516
peak=    3.073 closest distance to " CA  ALA A 233 " =    1.699
peak=    3.068 closest distance to " O   HOH Z 302 " =    1.949
peak=    3.047 closest distance to " O   HOH Z  90 " =    3.406
peak=    3.035 closest distance to " O   HOH Z 353 " =    2.848

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 213         
Filter by distance & map next to the model:
   mapped sites are within: 0.822 - 5.605
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 211 from: 213
   mapped sites are within: 0.822 - 5.605

peak=   -4.935 closest distance to " CG2 VAL A 230 " =    0.928
peak=   -4.663 closest distance to " O   HOH Z 266 " =    4.863
peak=   -4.429 closest distance to " CG2BVAL A  41 " =    2.711
peak=   -4.356 closest distance to " CD  ARG A 156 " =    2.016
peak=   -4.196 closest distance to " O   HOH Z  37 " =    1.869
peak=   -4.182 closest distance to " O   HOH Z  52 " =    1.643
peak=   -4.117 closest distance to " CG1 VAL A 112 " =    2.591
peak=   -4.084 closest distance to " O   HOH Z 196 " =    2.488
peak=   -4.047 closest distance to " O   HOH Z 166 " =    1.734
peak=   -4.045 closest distance to " CG  ASP A 231 " =    0.868
peak=   -3.965 closest distance to " O   HOH Z  13 " =    1.584
peak=   -3.963 closest distance to " C   HIS A 108 " =    1.122
peak=   -3.960 closest distance to " CD1 LEU A 101 " =    2.569
peak=   -3.956 closest distance to " CB  PRO A 243 " =    2.677
peak=   -3.953 closest distance to " SG  CYS A 254 " =    3.266
peak=   -3.933 closest distance to " O   HOH Z 426 " =    1.838
peak=   -3.926 closest distance to " OE1 GLN A 223 " =    2.149
peak=   -3.914 closest distance to " NH2 ARG A  66 " =    1.570
peak=   -3.908 closest distance to " OG  SER A  97 " =    2.283
peak=   -3.903 closest distance to " O   PRO A 163 " =    2.170
peak=   -3.882 closest distance to " CE2 TYR A  30 " =    2.729
peak=   -3.871 closest distance to " CB  ALA A 161 " =    2.605
peak=   -3.856 closest distance to " CD2 LEU A 300 " =    2.796
peak=   -3.842 closest distance to " NH2AARG A 275 " =    5.148
peak=   -3.817 closest distance to " N   ALA A  43 " =    2.537
peak=   -3.808 closest distance to " O   HOH Z 351 " =    1.569
peak=   -3.799 closest distance to " OG ASER A 134 " =    1.244
peak=   -3.786 closest distance to " CG1 VAL A 296 " =    1.276
peak=   -3.782 closest distance to " CZ3 TRP A 179 " =    1.209
peak=   -3.763 closest distance to " O   HOH Z 292 " =    4.499
peak=   -3.761 closest distance to " O   HOH Z 283 " =    2.137
peak=   -3.751 closest distance to " NE2 GLN A  88 " =    1.986
peak=   -3.733 closest distance to " CG1 VAL A 250 " =    2.759
peak=   -3.726 closest distance to " CD1 PHE A  59 " =    1.863
peak=   -3.718 closest distance to " O   HOH Z 290 " =    1.171
peak=   -3.716 closest distance to " CD2 LEU A 167 " =    1.749
peak=   -3.714 closest distance to " O   HOH Z 165 " =    1.904
peak=   -3.702 closest distance to " CG  GLU A  53 " =    1.625
peak=   -3.688 closest distance to " O   HOH Z 252 " =    3.863
peak=   -3.677 closest distance to " CB  ALA A 248 " =    2.028
peak=   -3.671 closest distance to " O   HOH Z  11 " =    1.920
peak=   -3.663 closest distance to " O   HOH Z  17 " =    1.460
peak=   -3.662 closest distance to " C   ALA A 158 " =    1.258
peak=   -3.654 closest distance to " O   HOH Z 350 " =    1.908
peak=   -3.653 closest distance to " CD  GLN A  58 " =    1.104
peak=   -3.648 closest distance to " O   HOH Z 241 " =    1.252
peak=   -3.641 closest distance to " OG BSER A 134 " =    1.323
peak=   -3.635 closest distance to " CA  ASP A 298 " =    1.038
peak=   -3.632 closest distance to " OXT GLY A 302 " =    2.869
peak=   -3.628 closest distance to " O   HOH Z  19 " =    2.210
peak=   -3.623 closest distance to " O   HOH Z 185 " =    2.387
peak=   -3.601 closest distance to " N   ALA A 226 " =    2.206
peak=   -3.598 closest distance to " O   HOH Z 231 " =    2.064
peak=   -3.586 closest distance to " O   HOH Z  43 " =    1.610
peak=   -3.583 closest distance to " O   ALA A 256 " =    1.647
peak=   -3.579 closest distance to " CD1 LEU A  25 " =    2.440
peak=   -3.578 closest distance to " CG2BVAL A  41 " =    1.715
peak=   -3.573 closest distance to " O   HOH Z 234 " =    4.232
peak=   -3.563 closest distance to " CB  LEU A  83 " =    2.318
peak=   -3.558 closest distance to " CE BMET A  47 " =    2.066
peak=   -3.555 closest distance to " O   HOH Z   5 " =    1.622
peak=   -3.554 closest distance to " CG2 VAL A 112 " =    2.594
peak=   -3.554 closest distance to " CE3 TRP A 150 " =    2.160
peak=   -3.554 closest distance to " N   THR A 235 " =    1.254
peak=   -3.554 closest distance to " O   VAL A  67 " =    2.705
peak=   -3.534 closest distance to " CD  ARG A 139 " =    1.576
peak=   -3.529 closest distance to " ND2 ASN A  45 " =    1.019
peak=   -3.527 closest distance to " O   HOH Z 407 " =    3.196
peak=   -3.505 closest distance to " CG2 ILE A 263 " =    2.414
peak=   -3.503 closest distance to " OG  SER A  26 " =    1.336
peak=   -3.497 closest distance to " OD1 ASN A 148 " =    1.482
peak=   -3.490 closest distance to " CD2 TYR A 293 " =    2.023
peak=   -3.483 closest distance to " N   SER A   3 " =    2.189
peak=   -3.477 closest distance to " CG  ARG A 269 " =    2.320
peak=   -3.477 closest distance to " O   HOH Z 353 " =    2.235
peak=   -3.477 closest distance to " CD  LYS A 289 " =    2.492
peak=   -3.471 closest distance to " NE2 GLN A 103 " =    1.815
peak=   -3.469 closest distance to " C   SER A 206 " =    1.487
peak=   -3.468 closest distance to " CD  PRO A 213 " =    2.199
peak=   -3.467 closest distance to " O   PRO A 198 " =    1.282
peak=   -3.461 closest distance to " O   VAL A 189 " =    2.588
peak=   -3.459 closest distance to " O   HOH Z 285 " =    1.473
peak=   -3.458 closest distance to " CG  TRP A 266 " =    1.915
peak=   -3.446 closest distance to " O   HOH Z 118 " =    3.345
peak=   -3.442 closest distance to " C   LEU A 143 " =    1.106
peak=   -3.441 closest distance to " CE  MET A 105 " =    2.101
peak=   -3.439 closest distance to " CB  PHE A 192 " =    1.837
peak=   -3.436 closest distance to " CB  ALA A 291 " =    2.241
peak=   -3.434 closest distance to " O   HOH Z 311 " =    3.764
peak=   -3.421 closest distance to " CA  GLY A 241 " =    3.054
peak=   -3.421 closest distance to " O   HOH Z 222 " =    1.530
peak=   -3.412 closest distance to " CD1 LEU A 228 " =    2.358
peak=   -3.407 closest distance to " O   HOH Z 348 " =    2.291
peak=   -3.407 closest distance to " CE2 PHE A 218 " =    2.611
peak=   -3.401 closest distance to " O   HOH Z 308 " =    1.729
peak=   -3.401 closest distance to " CB  ALA A  10 " =    2.191
peak=   -3.386 closest distance to " CA  GLY A 203 " =    2.352
peak=   -3.384 closest distance to " OG  SER A  62 " =    1.592
peak=   -3.383 closest distance to " O   HOH Z 177 " =    1.709
peak=   -3.383 closest distance to " ND2 ASN A  45 " =    1.789
peak=   -3.383 closest distance to " CG  GLU A 277 " =    1.060
peak=   -3.381 closest distance to " CB  ASP A 132 " =    2.327
peak=   -3.381 closest distance to " OD1 ASP A 191 " =    1.576
peak=   -3.373 closest distance to " CG2 VAL A 296 " =    1.380
peak=   -3.370 closest distance to " O   SER A 271 " =    2.117
peak=   -3.367 closest distance to " OG  SER A  87 " =    1.564
peak=   -3.364 closest distance to " CG  ASP A  50 " =    2.374
peak=   -3.357 closest distance to " N   GLN A  58 " =    1.586
peak=   -3.349 closest distance to " OD1 ASN A 187 " =    1.575
peak=   -3.348 closest distance to " NE2 GLN A 194 " =    1.839
peak=   -3.346 closest distance to " ND2 ASN A  60 " =    1.451
peak=   -3.344 closest distance to " O   ALA A 161 " =    1.671
peak=   -3.335 closest distance to " CG1 VAL A 112 " =    2.841
peak=   -3.334 closest distance to " O   HOH Z 253 " =    4.089
peak=   -3.333 closest distance to " N   SER A 276 " =    1.405
peak=   -3.333 closest distance to " OG BSER A 134 " =    1.881
peak=   -3.326 closest distance to " NH1 ARG A 195 " =    2.251
peak=   -3.325 closest distance to " CG  GLU A   2 " =    1.835
peak=   -3.322 closest distance to " O   HOH Z  15 " =    1.554
peak=   -3.321 closest distance to " CB  TRP A  85 " =    2.460
peak=   -3.315 closest distance to " CD1 LEU A 101 " =    2.663
peak=   -3.312 closest distance to " O   HOH Z 198 " =    2.488
peak=   -3.309 closest distance to " C   THR A 279 " =    1.176
peak=   -3.307 closest distance to " CB  ALA A 291 " =    2.333
peak=   -3.303 closest distance to " O   HOH Z 184 " =    1.428
peak=   -3.303 closest distance to " C   ALA A   8 " =    1.583
peak=   -3.301 closest distance to " O   HOH Z 389 " =    1.780
peak=   -3.297 closest distance to " O   HOH Z  90 " =    3.256
peak=   -3.296 closest distance to " CA  ASN A 127 " =    1.019
peak=   -3.295 closest distance to " CZ  TYR A 169 " =    1.759
peak=   -3.294 closest distance to " CB  PRO A 163 " =    2.626
peak=   -3.292 closest distance to " O   HOH Z 275 " =    1.513
peak=   -3.284 closest distance to " NH2 ARG A  79 " =    2.028
peak=   -3.279 closest distance to " CG  LEU A 228 " =    1.067
peak=   -3.276 closest distance to " CA  GLY A 133 " =    2.336
peak=   -3.276 closest distance to " O   HOH Z  38 " =    1.587
peak=   -3.274 closest distance to " O   SER A 258 " =    1.998
peak=   -3.272 closest distance to " O   HOH Z  90 " =    1.613
peak=   -3.272 closest distance to " O   HOH Z 264 " =    1.767
peak=   -3.266 closest distance to " O   HOH Z 150 " =    1.770
peak=   -3.263 closest distance to " N   THR A 157 " =    1.538
peak=   -3.260 closest distance to " O   ILE A 234 " =    1.274
peak=   -3.259 closest distance to " O   HOH Z 136 " =    2.202
peak=   -3.258 closest distance to " O   HOH Z 123 " =    2.390
peak=   -3.258 closest distance to " CB  ALA A  43 " =    2.526
peak=   -3.255 closest distance to " O   HOH Z 166 " =    1.841
peak=   -3.249 closest distance to " NE1 TRP A 266 " =    2.317
peak=   -3.248 closest distance to " CG  PRO A 243 " =    1.667
peak=   -3.246 closest distance to " O   GLY A 203 " =    2.349
peak=   -3.243 closest distance to " CG1 VAL A  78 " =    2.582
peak=   -3.243 closest distance to " O   HOH Z  71 " =    1.431
peak=   -3.242 closest distance to " CG  ARG A 259 " =    2.436
peak=   -3.241 closest distance to " CG2 VAL A 189 " =    2.132
peak=   -3.239 closest distance to " C   ASN A 285 " =    2.448
peak=   -3.237 closest distance to " CB  ASN A  39 " =    2.248
peak=   -3.235 closest distance to " O   HOH Z 262 " =    2.414
peak=   -3.233 closest distance to " ND2 ASN A  69 " =    1.710
peak=   -3.231 closest distance to " O   HOH Z 128 " =    2.551
peak=   -3.230 closest distance to " O   HOH Z 111 " =    2.383
peak=   -3.228 closest distance to " CA  TYR A  68 " =    2.842
peak=   -3.227 closest distance to " ND2 ASN A  60 " =    1.748
peak=   -3.226 closest distance to " C   ASN A 187 " =    1.841
peak=   -3.221 closest distance to " O   SER A 210 " =    1.858
peak=   -3.220 closest distance to " O   HOH Z 393 " =    1.720
peak=   -3.214 closest distance to " CD  GLN A 223 " =    1.361
peak=   -3.210 closest distance to " O   HOH Z 102 " =    1.478
peak=   -3.206 closest distance to " O   GLY A  17 " =    1.305
peak=   -3.203 closest distance to " O   HOH Z 191 " =    5.605
peak=   -3.200 closest distance to " O   HOH Z 431 " =    1.978
peak=   -3.195 closest distance to " NH1 ARG A 195 " =    2.665
peak=   -3.188 closest distance to " C   MET A 188 " =    1.606
peak=   -3.187 closest distance to " O   ALA A   1 " =    1.923
peak=   -3.187 closest distance to " O   ASP A  27 " =    2.172
peak=   -3.186 closest distance to " O   HOH Z 231 " =    1.891
peak=   -3.186 closest distance to " O   HOH Z 310 " =    1.825
peak=   -3.185 closest distance to " O   HOH Z 313 " =    1.230
peak=   -3.182 closest distance to " O   HOH Z 111 " =    1.338
peak=   -3.177 closest distance to " CB  VAL A 230 " =    1.097
peak=   -3.175 closest distance to " N   MET A 105 " =    2.678
peak=   -3.175 closest distance to " CG  GLN A  11 " =    1.675
peak=   -3.167 closest distance to " CG  MET A 105 " =    0.885
peak=   -3.166 closest distance to " O   HOH Z 211 " =    1.665
peak=   -3.164 closest distance to " O   HOH Z 189 " =    1.795
peak=   -3.164 closest distance to " O   HOH Z 423 " =    2.282
peak=   -3.152 closest distance to " O   HOH Z 174 " =    2.172
peak=   -3.151 closest distance to " O   LYS A 117 " =    1.692
peak=   -3.150 closest distance to " O   HOH Z 377 " =    2.037
peak=   -3.144 closest distance to " O   HOH Z 414 " =    1.727
peak=   -3.143 closest distance to " O   HOH Z 414 " =    1.502
peak=   -3.137 closest distance to " CA  VAL A 197 " =    1.074
peak=   -3.136 closest distance to " N   ASN A  60 " =    1.281
peak=   -3.129 closest distance to " O   HOH Z  60 " =    2.130
peak=   -3.127 closest distance to " NE2 GLN A  88 " =    1.052
peak=   -3.126 closest distance to " OD2 ASP A 171 " =    2.179
peak=   -3.110 closest distance to " CE  MET A  93 " =    1.231
peak=   -3.109 closest distance to " O   HOH Z  44 " =    2.123
peak=   -3.109 closest distance to " CD  GLN A 223 " =    0.822
peak=   -3.108 closest distance to " O   HOH Z 193 " =    1.814
peak=   -3.103 closest distance to " ND2BASN A 224 " =    1.726
peak=   -3.096 closest distance to " CD  ARG A 195 " =    5.100
peak=   -3.086 closest distance to " CD1 ILE A 151 " =    2.357
peak=   -3.083 closest distance to " O   HOH Z 380 " =    4.909
peak=   -3.079 closest distance to " CG1 VAL A 197 " =    2.302
peak=   -3.072 closest distance to " CE3 TRP A 274 " =    2.498
peak=   -3.060 closest distance to " CB  TYR A  15 " =    2.266
peak=   -3.058 closest distance to " CG1 VAL A 296 " =    1.300
peak=   -3.054 closest distance to " O   HOH Z   6 " =    1.780
peak=   -3.049 closest distance to " O   GLY A  80 " =    2.654
peak=   -3.044 closest distance to " CG2AVAL A  72 " =    4.528
peak=   -3.043 closest distance to " O   HOH Z 298 " =    2.814
peak=   -3.022 closest distance to " O   HOH Z 353 " =    2.187

================= 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    :  0.4609 0.4425   6.261375e+00   6.240447e+00
   1_bss:  0.4527 0.4327   6.256436e+00   6.230681e+00
   1_xyz:  0.3587 0.3825   6.106006e+00   6.147693e+00
   1_adp:  0.3076 0.3465   5.994654e+00   6.086479e+00
   1_occ:  0.3074 0.3463   5.993779e+00   6.086328e+00
   2_bss:  0.3045 0.3408   5.994411e+00   6.083768e+00
   2_xyz:  0.2057 0.2562   5.661242e+00   5.833801e+00
   2_adp:  0.1830 0.2299   5.557557e+00   5.745471e+00
   2_occ:  0.1827 0.2299   5.556788e+00   5.745345e+00
   3_bss:  0.1807 0.2291   5.556801e+00   5.744064e+00
   3_xyz:  0.1402 0.1809   5.316346e+00   5.527789e+00
   3_adp:  0.1312 0.1744   5.270195e+00   5.494791e+00
   3_occ:  0.1311 0.1743   5.269744e+00   5.494412e+00
   4_bss:  0.1311 0.1748   5.271113e+00   5.495020e+00
   4_xyz:  0.1171 0.1638   5.189939e+00   5.432950e+00
   4_adp:  0.1159 0.1621   5.179256e+00   5.420702e+00
   4_occ:  0.1159 0.1620   5.179007e+00   5.420624e+00
   5_bss:  0.1159 0.1619   5.178824e+00   5.420451e+00
   5_xyz:  0.1153 0.1606   5.175752e+00   5.414490e+00
   5_adp:  0.1142 0.1622   5.177720e+00   5.424946e+00
   5_occ:  0.1142 0.1623   5.177653e+00   5.424991e+00
   5_bss:  0.1141 0.1622   5.177630e+00   5.424954e+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:  0.319  20.530   7.303  10.807   7.374   0.000   0.000   0.000
   1_xyz:  0.319  20.530   7.303  10.807   7.374   0.000   0.000   0.000
   1_adp:  0.319  20.530   7.303  10.807   7.374   0.000   0.000   0.000
   1_occ:  0.319  20.530   7.303  10.807   7.374   0.000   0.000   0.000
   2_bss:  0.324  48.324   4.146   6.971   4.662   0.000   0.000   0.000
   2_xyz:  0.324  48.324   4.146   6.971   4.662   0.000   0.000   0.000
   2_adp:  0.324  48.324   4.146   6.971   4.662   0.000   0.000   0.000
   2_occ:  0.324  48.324   4.146   6.971   4.662   0.000   0.000   0.000
   3_bss:  0.319  61.961   2.650   4.044   3.530   0.000   0.000   0.000
   3_xyz:  0.319  61.961   2.650   4.044   3.530   0.000   0.000   0.000
   3_adp:  0.319  61.961   2.650   4.044   3.530   0.000   0.000   0.000
   3_occ:  0.319  61.961   2.650   4.044   3.530   0.000   0.000   0.000
   4_bss:  0.330  61.961   2.371   3.277   3.342   0.000   0.000   0.000
   4_xyz:  0.330  61.961   2.371   3.277   3.342   0.000   0.000   0.000
   4_adp:  0.330  61.961   2.371   3.277   3.342   0.000   0.000   0.000
   4_occ:  0.330  61.961   2.371   3.277   3.342   0.000   0.000   0.000
   5_bss:  0.332  61.961   2.425   3.077   3.406   0.000   0.000   0.000
   5_xyz:  0.332  61.961   2.425   3.077   3.406   0.000   0.000   0.000
   5_adp:  0.332  61.961   2.425   3.077   3.406   0.000   0.000   0.000
   5_occ:  0.332  61.961   2.425   3.077   3.406   0.000   0.000   0.000
   5_bss:  0.322  59.632  -0.511   0.062   0.450   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  51.959 0.4968  0.5595    59159.026
   1_bss:  52.135 0.4926  0.7109    57424.380
   1_xyz:  43.032 0.6047  0.8529    41376.611
   1_adp:  37.233 0.6753  0.9608    33307.202
   1_occ:  37.224 0.6754  0.9607    33295.177
   2_bss:  36.961 0.6785  0.8624    33024.774
   2_xyz:  26.007 0.8000  0.9876    17009.027
   2_adp:  22.789 0.8341  1.0105    13798.960
   2_occ:  22.779 0.8342  1.0102    13791.184
   3_bss:  22.690 0.8353  0.9473    13765.883
   3_xyz:  16.890 0.8904  0.9792     8339.673
   3_adp:  16.131 0.8973  0.9810     7823.307
   3_occ:  16.121 0.8974  0.9809     7817.345
   4_bss:  16.133 0.8974  0.9667     7849.845
   4_xyz:  14.902 0.9077  0.9710     6971.777
   4_adp:  14.626 0.9102  0.9685     6859.570
   4_occ:  14.623 0.9103  0.9685     6859.952
   5_bss:  14.618 0.9103  0.9678     6858.239
   5_xyz:  14.473 0.9115  0.9678     6713.999
   5_adp:  14.708 0.9096  0.9614     6829.548
   5_occ:  14.709 0.9096  0.9613     6831.346
   5_bss:  14.711 0.9096  0.9664     6830.436
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.4156e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.4156e+01
   1_xyz:   1.661  0.013  0.107 17.900  0.007  4.112   1.3577e-01
   1_adp:   1.661  0.013  0.107 17.900  0.007  4.112   1.3577e-01
   1_occ:   1.661  0.013  0.107 17.900  0.007  4.112   1.3577e-01
   2_bss:   1.661  0.013  0.107 17.900  0.007  4.112   1.3577e-01
   2_xyz:   1.249  0.010  0.082 16.330  0.005  4.134   9.0540e-02
   2_adp:   1.249  0.010  0.082 16.330  0.005  4.134   9.0540e-02
   2_occ:   1.249  0.010  0.082 16.330  0.005  4.134   9.0540e-02
   3_bss:   1.249  0.010  0.082 16.330  0.005  4.134   9.0540e-02
   3_xyz:   1.073  0.008  0.081 15.360  0.004  4.115   6.8986e-02
   3_adp:   1.073  0.008  0.081 15.360  0.004  4.115   6.8986e-02
   3_occ:   1.073  0.008  0.081 15.360  0.004  4.115   6.8986e-02
   4_bss:   1.073  0.008  0.081 15.360  0.004  4.115   6.8986e-02
   4_xyz:   1.169  0.010  0.093 15.585  0.004  4.121   8.0799e-02
   4_adp:   1.169  0.010  0.093 15.585  0.004  4.121   8.0799e-02
   4_occ:   1.169  0.010  0.093 15.585  0.004  4.121   8.0799e-02
   5_bss:   1.169  0.010  0.093 15.585  0.004  4.121   8.0799e-02
   5_xyz:   1.062  0.009  0.085 15.077  0.004  4.122   6.7878e-02
   5_adp:   1.062  0.009  0.085 15.077  0.004  4.122   6.7878e-02
   5_occ:   1.062  0.009  0.085 15.077  0.004  4.122   6.7878e-02
   5_bss:   1.062  0.009  0.085 15.077  0.004  4.122   6.7878e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0216e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0216e+00
   1_xyz:  14.894  0.163  0.499 87.737  0.044  2.312   1.0118e-01
   1_adp:  14.894  0.163  0.499 87.737  0.044  2.312   1.0118e-01
   1_occ:  14.894  0.163  0.499 87.737  0.044  2.312   1.0118e-01
   2_bss:  14.894  0.163  0.499 87.737  0.044  2.312   1.0118e-01
   2_xyz:   7.495  0.141  0.253 85.220  0.043  2.195   8.9325e-02
   2_adp:   7.495  0.141  0.253 85.220  0.043  2.195   8.9325e-02
   2_occ:   7.495  0.141  0.253 85.220  0.043  2.195   8.9325e-02
   3_bss:   7.495  0.141  0.253 85.220  0.043  2.195   8.9325e-02
   3_xyz:   6.869  0.056  0.477 82.869  0.035  2.321   4.8662e-02
   3_adp:   6.869  0.056  0.477 82.869  0.035  2.321   4.8662e-02
   3_occ:   6.869  0.056  0.477 82.869  0.035  2.321   4.8662e-02
   4_bss:   6.869  0.056  0.477 82.869  0.035  2.321   4.8662e-02
   4_xyz:   8.034  0.056  0.697 83.795  0.035  2.325   5.9100e-02
   4_adp:   8.034  0.056  0.697 83.795  0.035  2.325   5.9100e-02
   4_occ:   8.034  0.056  0.697 83.795  0.035  2.325   5.9100e-02
   5_bss:   8.034  0.056  0.697 83.795  0.035  2.325   5.9100e-02
   5_xyz:   7.634  0.044  0.582 81.565  0.034  2.368   4.6156e-02
   5_adp:   7.634  0.044  0.582 81.565  0.034  2.368   4.6156e-02
   5_occ:   7.634  0.044  0.582 81.565  0.034  2.368   4.6156e-02
   5_bss:   7.634  0.044  0.582 81.565  0.034  2.368   4.6156e-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:  89.84   0.00  11.71  75.57   0.00   8.95  89.84   0.00  26.72
   1_occ:  89.84   0.00  11.71  75.57   0.00   8.95  89.84   0.00  26.72
   2_bss:  89.84   0.00  11.71  75.57   0.00   8.95  89.84   0.00  26.72
   2_xyz:  89.84   0.00  11.71  75.57   0.00   8.95  89.84   0.00  26.72
   2_adp:  86.30   0.00  12.16  80.28   0.00   8.34  86.30   0.00  32.99
   2_occ:  86.30   0.00  12.16  80.28   0.00   8.34  86.30   0.00  32.99
   3_bss:  86.30   0.00  12.16  80.28   0.00   8.34  86.30   0.00  32.99
   3_xyz:  86.30   0.00  12.16  80.28   0.00   8.34  86.30   0.00  32.99
   3_adp:  87.30   0.00  12.72  87.30   0.00   8.28  80.80   0.47  36.90
   3_occ:  87.30   0.00  12.72  87.30   0.00   8.28  80.80   0.47  36.90
   4_bss:  87.30   0.00  12.72  87.30   0.00   8.28  80.80   0.47  36.90
   4_xyz:  87.30   0.00  12.72  87.30   0.00   8.28  80.80   0.47  36.90
   4_adp:  86.32   0.00  12.33  86.32   0.00   8.04  81.94   0.80  35.68
   4_occ:  86.32   0.00  12.33  86.32   0.00   8.04  81.94   0.80  35.68
   5_bss:  86.32   0.00  12.33  86.32   0.00   8.04  81.94   0.80  35.68
   5_xyz:  86.32   0.00  12.33  86.32   0.00   8.04  81.94   0.80  35.68
   5_adp:  92.94   0.00  12.46  92.94   0.00   8.05  82.92   0.75  36.50
   5_occ:  92.94   0.00  12.46  92.94   0.00   8.05  82.92   0.75  36.50
   5_bss:  96.06   3.12  15.58  96.06   3.12  11.17  86.04   3.87  39.62
------------------------------------------------------------------------
 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:    1.184    0.013    0.412
   1_adp:    1.184    0.013    0.412
   1_occ:    1.184    0.013    0.412
   2_bss:    1.184    0.013    0.412
   2_xyz:    1.506    0.029    0.584
   2_adp:    1.506    0.029    0.584
   2_occ:    1.506    0.029    0.584
   3_bss:    1.506    0.029    0.584
   3_xyz:    1.493    0.010    0.639
   3_adp:    1.493    0.010    0.639
   3_occ:    1.493    0.010    0.639
   4_bss:    1.493    0.010    0.639
   4_xyz:    1.531    0.008    0.674
   4_adp:    1.531    0.008    0.674
   4_occ:    1.531    0.008    0.674
   5_bss:    1.531    0.008    0.674
   5_xyz:    1.590    0.012    0.684
   5_adp:    1.590    0.012    0.684
   5_occ:    1.590    0.012    0.684
   5_bss:    1.590    0.012    0.684
------------------------------------------------------------------------

CPU time actual refinement: 322.42


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_939/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_939/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_939/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_939/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_939/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 322.27 
  Macro-tasks:
    bulk solvent and scale       = 43.17  
    individual site refinement   = 128.79 
    weights calculation          = 31.89  
    collect and process          = 6.49   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 210.45 
  Micro-tasks:
    mask                            = 1.80   
    f_calc                          = 97.11  
    alpha_beta                      = 8.20   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 106.73 
    fmodel                         = 7.00   
    r_factors                      = 0.30   
    phase_errors                   = 10.70  
    foms                           = 0.29   
    TOTAL for micro-tasks          = 233.27 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.602 micro seconds
Total CPU time: 5.60 minutes
from_scatterers_fft:    623 calls, 96.73 s
gradients_fft:          567 calls, 94.02 s

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

# Date 2008-01-16 Time 02:48:00 PST -0800 (1200480480.89 s)
Start R-work = 0.4609, R-free = 0.4425 (no bulk solvent and anisotropic scale)
Final R-work = 0.1300, R-free = 0.1775 (no bulk solvent and anisotropic scale)

Start R-work = 0.4527, R-free = 0.4327
Final R-work = 0.1141, R-free = 0.1622