# Date 2008-01-16 Time 00:39:42 PST -0800 (1200472782.66 s)
#phil __OFF__

Command line arguments: "../109.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 31864
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 109

-------------------------------------------------------------------------------
  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: (68.4938, 47.8686, 88.5498, 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: 3.31, per 1000 atoms: 1.17


================================== 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: (68.4938, 47.8686, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0111 1.95105
Completeness in resolution range: 0.898867
Completeness with d_max=infinity: 0.896235

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0111
                             d_min =   1.9511

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: (68.4938, 47.8686, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0111 1.95105
Completeness in resolution range: 0.898867
Completeness with d_max=infinity: 0.896235

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0116 -  4.1761 [2289/2317]  2057   232  10.1%
  bin  2:  4.1761 -  3.3265 [2200/2223]  1978   222  10.1%
  bin  3:  3.3265 -  2.9095 [2163/2188]  1955   208   9.6%
  bin  4:  2.9095 -  2.6451 [2135/2162]  1918   217  10.2%
  bin  5:  2.6451 -  2.4564 [2123/2156]  1902   221  10.4%
  bin  6:  2.4564 -  2.3121 [2139/2167]  1934   205   9.6%
  bin  7:  2.3121 -  2.1967 [2098/2134]  1891   207   9.9%
  bin  8:  2.1967 -  2.1013 [2104/2146]  1892   212  10.1%
  bin  9:  2.1013 -  2.0206 [1878/2158]  1695   183   9.7%
  bin 10:  2.0206 -  1.9511 [ 460/2142]   408    52  11.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_109/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:
        1.01 -     1.79: 15
        1.79 -     2.57: 68
        2.57 -     3.34: 3979
        3.34 -     4.12: 9353
        4.12 -     4.90: 14793
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.011 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.046 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  57 " - " O   HOH Z 104 "  1.209 3.040 -x+1,y+1/2,-z+1/2
  " NH1 ARG A  24 " - " O   GLY A  91 "  1.275 3.120 -x+1,y+1/2,-z+1/2
  " O   HOH Z  81 " - " O   HOH Z 186 "  1.296 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28203 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_109/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_109/model_refine_001.geo

CPU time processing inputs: 9.30


============================ 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 = 68.49375 47.8686 88.54975 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: 1.95 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5322   r_free= 0.5338   ksol= 0.00   Bsol= 0.00   scale= 0.748    |
|                                                                             |
| 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:   1.11 A                  |
| x-ray target function (ml) for work reflections: 6.320714                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0116 -  4.6584 0.99   1483  162 0.4415 0.4521       6.688      6.7257|
|  2:  4.6584 -  3.7160 0.99   1430  158 0.4871 0.5314       6.886      6.9518|
|  3:  3.7160 -  3.2517 0.99   1401  163 0.5218 0.5028      6.7316      6.7409|
|  4:  3.2517 -  2.9569 0.98   1387  145 0.5297 0.5131      6.5461      6.5305|
|  5:  2.9569 -  2.7463 0.99   1392  161 0.5693 0.5953      6.3842      6.4131|
|  6:  2.7463 -  2.5853 0.99   1378  154 0.5566 0.5518      6.2888       6.198|
|  7:  2.5853 -  2.4564 0.98   1339  157 0.5691 0.4708      6.2373      6.1704|
|  8:  2.4564 -  2.3499 0.98   1388  150 0.5496 0.5695      6.1717      6.2121|
|  9:  2.3499 -  2.2597 0.99   1348  136 0.5689 0.5725      6.1281      6.1712|
| 10:  2.2597 -  2.1820 0.99   1378  152 0.5570 0.6073      6.0807      6.0993|
| 11:  2.1820 -  2.1139 0.97   1344  154 0.5608 0.5509      6.0012      6.0231|
| 12:  2.1139 -  2.0537 0.98   1346  156 0.5700 0.5630      5.9485      5.9152|
| 13:  2.0537 -  1.9997 0.60    818   86 0.5541 0.5971      5.8744      5.8432|
| 14:  1.9997 -  1.9511 0.14    198   25 0.5917 0.4792      5.9098      5.7171|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0116 -  4.6584  1483   162  0.60  42.53   0.77     0.61     100676.80|
|  2:  4.6584 -  3.7160  1430   158  0.55  48.07   0.83     0.60     166958.28|
|  3:  3.7160 -  3.2517  1401   163  0.40  59.84   0.77     0.52     175553.21|
|  4:  3.2517 -  2.9569  1387   145  0.26  70.30   0.74     0.35     149049.24|
|  5:  2.9569 -  2.7463  1392   161  0.18  76.69   0.68     0.24     110618.29|
|  6:  2.7463 -  2.5853  1378   154  0.15  78.89   0.70     0.19      93018.36|
|  7:  2.5853 -  2.4564  1339   157  0.18  76.53   0.68     0.22      79119.65|
|  8:  2.4564 -  2.3499  1388   150  0.22  73.25   0.69     0.28      68309.27|
|  9:  2.3499 -  2.2597  1348   136  0.21  74.53   0.69     0.27      65536.10|
| 10:  2.2597 -  2.1820  1378   152  0.16  77.80   0.71     0.21      57626.80|
| 11:  2.1820 -  2.1139  1344   154  0.08  84.09   0.70     0.11      57336.98|
| 12:  2.1139 -  2.0537  1346   156  0.06  85.89   0.71     0.08      51599.58|
| 13:  2.0537 -  1.9997   818    86  0.07  84.48   0.73     0.11      46153.22|
| 14:  1.9997 -  1.9511   198    25  0.17  77.02   0.73     0.19      33685.24|
|alpha:            min =        0.08 max =            0.61 mean =         0.30|
|beta:             min =    33685.24 max =       175553.21 mean =     95424.80|
|figures of merit: min =        0.00 max =            1.00 mean =         0.25|
|phase err.(work): min =        0.00 max =           90.00 mean =        71.10|
|phase err.(test): min =        0.00 max =           90.00 mean =        71.54|
|-----------------------------------------------------------------------------|

============================== 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 = 37.198351             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 85.410   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.987453              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.761   (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 |  0.732 -  1.149:        1 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.149 -  1.566:       10 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.566 -  1.983:       49 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  1.983 -  2.399:      280 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.399 -  2.816:     1043 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.816 -  3.233:     2220 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.233 -  3.650:     3784 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.650 -  4.066:     5264 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.066 -  4.483:     7072 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.483 -  4.900:     8514 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.948 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.087    4.900  0.732 |       3.174 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.892)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 11.892)------------------------------------------|
|    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: 1.95 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5362   r_free= 0.5373   ksol= 0.00   Bsol= 0.00   scale= 0.721    |
|                                                                             |
| 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:   1.13 A                  |
| x-ray target function (ml) for work reflections: 6.320698                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5260   r_free= 0.5310   ksol= 0.34   Bsol= 20.00   scale= 0.937   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.22,9.58,9.96,0.00,0.00,0.00); trace/3= 8.58                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   1.24 A                  |
| x-ray target function (ml) for work reflections: 5.862305                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 30.728566             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 86.690   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.076679              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.883   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.5260      final r-factor (work) = 0.4798          |
| start r-factor (free) = 0.5310      final r-factor (free) = 0.5098          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 151.0343 = 30.73 * 0.50 * 6.3190 + 1.00 * 53.9478                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 89.7890 = 30.73 * 0.50 * 5.8326 + 1.00 * 0.1751                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4798      final r-factor (work) = 0.4415          |
| start r-factor (free) = 0.5098      final r-factor (free) = 0.5080          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 17.9595 = 3.08 * 1.00 * 5.8326 + 1.00 * 0.0145                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 19.0664 = 3.08 * 1.00 * 6.1880 + 1.00 * 0.0280                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.892)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    130.62  20.95    None  None   None       |
|    all(noH): 2823   0      0.00    130.62  20.95    None  None   None       |
|    Sol.    : 438    0      0.00    130.62  29.34    None  None   None       |
|    Mac.    : 2385   0      0.00    98.36   19.41    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 -  13.062: 1091   |   5:    65.311 -  78.373:   49        |
|      1:    13.062 -  26.124:  886   |   6:    78.373 -  91.435:    8        |
|      2:    26.124 -  39.186:  454   |   7:    91.435 - 104.497:    5        |
|      3:    39.186 -  52.248:  233   |   8:   104.497 - 117.559:    2        |
|      4:    52.248 -  65.311:   93   |   9:   117.559 - 130.621:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.4415 r_free = 0.5080             target_work(ml) = 6.247         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.4413 r_free = 0.5079             target_work(ml) = 6.247         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4413   r_free= 0.5079   ksol= 0.34   Bsol= 20.00   scale= 1.135   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.22,9.58,9.96,0.00,0.00,0.00); trace/3= 8.58                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.89 A                  |
| x-ray target function (ml) for work reflections: 6.246946                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4401   r_free= 0.5027   ksol= 0.34   Bsol= 50.00   scale= 1.034   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.57,5.19,5.89,0.00,0.00,0.00); trace/3= 4.55                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.89 A                  |
| x-ray target function (ml) for work reflections: 6.249096                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 25.854905             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.443  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.042847              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 123.453  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4401      final r-factor (work) = 0.3780          |
| start r-factor (free) = 0.5027      final r-factor (free) = 0.4436          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 80.1456 = 25.85 * 0.50 * 6.1861 + 1.00 * 0.1751                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 80.3107 = 25.85 * 0.50 * 6.2010 + 1.00 * 0.1479                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3780      final r-factor (work) = 0.3578          |
| start r-factor (free) = 0.4436      final r-factor (free) = 0.4301          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.4949 = 1.04 * 1.00 * 6.2010 + 1.00 * 0.0283                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.4052 = 1.04 * 1.00 * 6.1272 + 1.00 * 0.0154                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.892)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    133.33  19.31    None  None   None       |
|    all(noH): 2823   0      0.00    133.33  19.31    None  None   None       |
|    Sol.    : 438    0      0.00    133.33  31.96    None  None   None       |
|    Mac.    : 2385   0      0.00    86.98   16.99    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 -  13.333: 1177   |   5:    66.663 -  79.995:   15        |
|      1:    13.333 -  26.665:  951   |   6:    79.995 -  93.328:    7        |
|      2:    26.665 -  39.998:  451   |   7:    93.328 - 106.661:    0        |
|      3:    39.998 -  53.330:  165   |   8:   106.661 - 119.993:    1        |
|      4:    53.330 -  66.663:   55   |   9:   119.993 - 133.326:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3578 r_free = 0.4301             target_work(ml) = 6.114         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3574 r_free = 0.4297             target_work(ml) = 6.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3574   r_free= 0.4297   ksol= 0.34   Bsol= 50.00   scale= 1.092   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.57,5.19,5.89,0.00,0.00,0.00); trace/3= 4.55                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.112999                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3542   r_free= 0.4256   ksol= 0.32   Bsol= 47.53   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.20,2.00,2.66,0.00,0.00,0.00); trace/3= 1.49                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.112868                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.404837             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.894   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.363283              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 123.709  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3542      final r-factor (work) = 0.2914          |
| start r-factor (free) = 0.4256      final r-factor (free) = 0.3536          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 35.0892 = 11.40 * 0.50 * 6.1274 + 1.00 * 0.1479                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 34.6116 = 11.40 * 0.50 * 6.0516 + 1.00 * 0.1032                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2914      final r-factor (work) = 0.2761          |
| start r-factor (free) = 0.3536      final r-factor (free) = 0.3330          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2140 = 0.36 * 1.00 * 6.0516 + 1.00 * 0.0156                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1947 = 0.36 * 1.00 * 5.9373 + 1.00 * 0.0378                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.892)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    108.76  17.73    None  None   None       |
|    all(noH): 2823   0      0.00    108.76  17.73    None  None   None       |
|    Sol.    : 438    0      0.00    108.76  33.68    None  None   None       |
|    Mac.    : 2385   0      0.00    78.80   14.80    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.876: 1022   |   5:    54.382 -  65.259:   31        |
|      1:    10.876 -  21.753:  985   |   6:    65.259 -  76.135:    9        |
|      2:    21.753 -  32.629:  454   |   7:    76.135 -  87.011:    5        |
|      3:    32.629 -  43.506:  233   |   8:    87.011 -  97.888:    0        |
|      4:    43.506 -  54.382:   82   |   9:    97.888 - 108.764:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2761 r_free = 0.3330             target_work(ml) = 5.911         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2758 r_free = 0.3328             target_work(ml) = 5.910         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2758   r_free= 0.3328   ksol= 0.32   Bsol= 47.53   scale= 1.047   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.20,2.00,2.66,0.00,0.00,0.00); trace/3= 1.49                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.909583                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2743   r_free= 0.3322   ksol= 0.32   Bsol= 54.82   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.12,0.15,0.83,0.00,0.00,0.00); trace/3= -0.38                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.909149                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.682949              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.071  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.655242              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.152   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2743      final r-factor (work) = 0.2064          |
| start r-factor (free) = 0.3322      final r-factor (free) = 0.2595          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.9207 = 7.68 * 0.50 * 5.9398 + 1.00 * 0.1032                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.4016 = 7.68 * 0.50 * 5.8069 + 1.00 * 0.0945                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2064      final r-factor (work) = 0.1800          |
| start r-factor (free) = 0.2595      final r-factor (free) = 0.2441          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.6216 = 1.66 * 1.00 * 5.8069 + 1.00 * 0.0097                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.3002 = 1.66 * 1.00 * 5.6094 + 1.00 * 0.0152                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.892)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    105.49  18.88    None  None   None       |
|    all(noH): 2823   0      0.00    105.49  18.88    None  None   None       |
|    Sol.    : 438    0      3.77    105.49  46.30    None  None   None       |
|    Mac.    : 2385   0      0.00    102.13  13.85    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.549: 1137   |   5:    52.745 -  63.294:   89        |
|      1:    10.549 -  21.098:  953   |   6:    63.294 -  73.843:   68        |
|      2:    21.098 -  31.647:  253   |   7:    73.843 -  84.392:   38        |
|      3:    31.647 -  42.196:  155   |   8:    84.392 -  94.941:    9        |
|      4:    42.196 -  52.745:  118   |   9:    94.941 - 105.490:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1800 r_free = 0.2441             target_work(ml) = 5.574         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1799 r_free = 0.2440             target_work(ml) = 5.574         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1799   r_free= 0.2440   ksol= 0.32   Bsol= 54.82   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.12,0.15,0.83,0.00,0.00,0.00); trace/3= -0.38                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.573597                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1797   r_free= 0.2440   ksol= 0.34   Bsol= 67.75   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.70,-0.67,0.19,-0.00,0.00,0.00); trace/3= -1.06                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.573061                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.020469              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 111.805  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.712727              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 132.506  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1797      final r-factor (work) = 0.1500          |
| start r-factor (free) = 0.2440      final r-factor (free) = 0.2077          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.1801 = 5.02 * 0.50 * 5.6113 + 1.00 * 0.0945                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.9058 = 5.02 * 0.50 * 5.5069 + 1.00 * 0.0820                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1500      final r-factor (work) = 0.1431          |
| start r-factor (free) = 0.2077      final r-factor (free) = 0.1988          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9400 = 0.71 * 1.00 * 5.5069 + 1.00 * 0.0150                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8647 = 0.71 * 1.00 * 5.3978 + 1.00 * 0.0175                               |
|-----------------------------------------------------------------------------|
| number of iterations = 9       |    number of function evaluations = 12     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.892)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    106.88  18.55    None  None   None       |
|    all(noH): 2823   0      0.00    106.88  18.55    None  None   None       |
|    Sol.    : 438    0      5.37    106.88  46.32    None  None   None       |
|    Mac.    : 2385   0      0.00    102.81  13.45    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.688: 1224   |   5:    53.439 -  64.127:   92        |
|      1:    10.688 -  21.376:  944   |   6:    64.127 -  74.815:   64        |
|      2:    21.376 -  32.064:  201   |   7:    74.815 -  85.503:   35        |
|      3:    32.064 -  42.752:  134   |   8:    85.503 -  96.191:    8        |
|      4:    42.752 -  53.439:  118   |   9:    96.191 - 106.879:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1431 r_free = 0.1988             target_work(ml) = 5.374         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1428 r_free = 0.1990             target_work(ml) = 5.374         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1428   r_free= 0.1990   ksol= 0.34   Bsol= 67.75   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.70,-0.67,0.19,-0.00,0.00,0.00); trace/3= -1.06                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.373504                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0116 -  4.6584 0.99   1483  162 0.1038 0.1574      5.4912      5.7419|
|  2:  4.6584 -  3.7160 0.99   1430  158 0.0974 0.1236       5.581       5.795|
|  3:  3.7160 -  3.2517 0.99   1401  163 0.1352 0.1835      5.6899      5.9665|
|  4:  3.2517 -  2.9569 0.98   1387  145 0.1624 0.2266      5.6481      5.9048|
|  5:  2.9569 -  2.7463 0.99   1392  161 0.1780 0.2156      5.5969      5.7604|
|  6:  2.7463 -  2.5853 0.99   1378  154 0.1598 0.2490       5.433      5.6558|
|  7:  2.5853 -  2.4564 0.98   1339  157 0.1631 0.2027      5.3865      5.5119|
|  8:  2.4564 -  2.3499 0.98   1388  150 0.1641 0.2531       5.319      5.6201|
|  9:  2.3499 -  2.2597 0.99   1348  136 0.1513 0.2038      5.2307      5.4316|
| 10:  2.2597 -  2.1820 0.99   1378  152 0.1474 0.2231      5.1703      5.3981|
| 11:  2.1820 -  2.1139 0.97   1344  154 0.1489 0.2323       5.111       5.477|
| 12:  2.1139 -  2.0537 0.98   1346  156 0.1515 0.2022      5.0853      5.2974|
| 13:  2.0537 -  1.9997 0.60    818   86 0.1431 0.2208      4.9749      5.1643|
| 14:  1.9997 -  1.9511 0.14    198   25 0.1321 0.2171      4.9146      5.0999|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0116 -  4.6584  1483   162  0.92  11.84   0.96     0.94      10557.58|
|  2:  4.6584 -  3.7160  1430   158  0.93  10.76   1.03     1.01      13112.05|
|  3:  3.7160 -  3.2517  1401   163  0.90  15.49   1.04     1.03      16385.59|
|  4:  3.2517 -  2.9569  1387   145  0.87  19.47   1.03     1.00      15836.05|
|  5:  2.9569 -  2.7463  1392   161  0.84  22.72   1.02     1.00      15629.75|
|  6:  2.7463 -  2.5853  1378   154  0.85  21.79   0.99     0.94      11467.73|
|  7:  2.5853 -  2.4564  1339   157  0.85  21.61   1.00     0.96      10358.18|
|  8:  2.4564 -  2.3499  1388   150  0.84  22.20   1.02     0.97       9199.12|
|  9:  2.3499 -  2.2597  1348   136  0.85  21.35   1.00     0.94       7738.50|
| 10:  2.2597 -  2.1820  1378   152  0.86  20.87   1.01     0.99       7208.08|
| 11:  2.1820 -  2.1139  1344   154  0.85  21.75   1.00     0.95       6614.67|
| 12:  2.1139 -  2.0537  1346   156  0.84  22.31   1.00     0.99       6361.61|
| 13:  2.0537 -  1.9997   818    86  0.85  21.59   0.99     0.97       5139.98|
| 14:  1.9997 -  1.9511   198    25  0.89  17.17   0.96     0.91       3574.64|
|alpha:            min =        0.91 max =            1.03 mean =         0.97|
|beta:             min =     3574.64 max =        16385.59 mean =     10564.63|
|figures of merit: min =        0.00 max =            1.00 mean =         0.87|
|phase err.(work): min =        0.00 max =           89.87 mean =        19.34|
|phase err.(test): min =        0.00 max =           89.88 mean =        18.63|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1433   r_free= 0.1993   ksol= 0.33   Bsol= 63.91   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.84,-1.09,-0.06,-0.00,-0.00,-0.00); trace/3= -1.33                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.375589                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1433   r_free= 0.1993   ksol= 0.33   Bsol= 63.91   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.84,-1.09,-0.06,-0.00,-0.00,-0.00); trace/3= -1.33                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.375589                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0116 -  4.6584 0.99   1483  162 0.1054 0.1592      5.5025      5.7504|
|  2:  4.6584 -  3.7160 0.99   1430  158 0.0985 0.1237      5.5898      5.8025|
|  3:  3.7160 -  3.2517 0.99   1401  163 0.1355 0.1845      5.6938      5.9672|
|  4:  3.2517 -  2.9569 0.98   1387  145 0.1628 0.2264      5.6493      5.9061|
|  5:  2.9569 -  2.7463 0.99   1392  161 0.1780 0.2158      5.5972      5.7607|
|  6:  2.7463 -  2.5853 0.99   1378  154 0.1597 0.2493      5.4332      5.6555|
|  7:  2.5853 -  2.4564 0.98   1339  157 0.1631 0.2028      5.3867      5.5116|
|  8:  2.4564 -  2.3499 0.98   1388  150 0.1639 0.2530      5.3188      5.6209|
|  9:  2.3499 -  2.2597 0.99   1348  136 0.1511 0.2040      5.2299      5.4318|
| 10:  2.2597 -  2.1820 0.99   1378  152 0.1472 0.2231      5.1703      5.3988|
| 11:  2.1820 -  2.1139 0.97   1344  154 0.1489 0.2319      5.1109      5.4762|
| 12:  2.1139 -  2.0537 0.98   1346  156 0.1517 0.2022      5.0859      5.2983|
| 13:  2.0537 -  1.9997 0.60    818   86 0.1434 0.2203      4.9748      5.1608|
| 14:  1.9997 -  1.9511 0.14    198   25 0.1318 0.2170      4.9158      5.1038|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0116 -  4.6584  1483   162  0.92  11.93   0.96     0.93      10616.80|
|  2:  4.6584 -  3.7160  1430   158  0.93  10.89   1.02     1.00      13283.32|
|  3:  3.7160 -  3.2517  1401   163  0.90  15.60   1.04     1.03      16597.47|
|  4:  3.2517 -  2.9569  1387   145  0.87  19.46   1.02     0.99      15820.00|
|  5:  2.9569 -  2.7463  1392   161  0.84  22.72   1.01     0.99      15631.20|
|  6:  2.7463 -  2.5853  1378   154  0.85  21.78   0.98     0.93      11474.74|
|  7:  2.5853 -  2.4564  1339   157  0.85  21.63   0.99     0.95      10370.63|
|  8:  2.4564 -  2.3499  1388   150  0.84  22.19   1.01     0.96       9207.44|
|  9:  2.3499 -  2.2597  1348   136  0.85  21.33   0.98     0.93       7739.63|
| 10:  2.2597 -  2.1820  1378   152  0.86  20.86   1.00     0.98       7211.91|
| 11:  2.1820 -  2.1139  1344   154  0.85  21.74   0.99     0.94       6611.94|
| 12:  2.1139 -  2.0537  1346   156  0.84  22.29   0.98     0.97       6362.18|
| 13:  2.0537 -  1.9997   818    86  0.85  21.57   0.97     0.95       5127.68|
| 14:  1.9997 -  1.9511   198    25  0.89  17.14   0.95     0.89       3565.62|
|alpha:            min =        0.89 max =            1.03 mean =         0.96|
|beta:             min =     3565.62 max =        16597.47 mean =     10600.89|
|figures of merit: min =        0.00 max =            1.00 mean =         0.87|
|phase err.(work): min =        0.00 max =           89.98 mean =        19.36|
|phase err.(test): min =        0.00 max =           89.05 mean =        18.63|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.892)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    106.88  18.55    None  None   None       |
|    all(noH): 2823   0      0.00    106.88  18.55    None  None   None       |
|    Sol.    : 438    0      5.37    106.88  46.33    None  None   None       |
|    Mac.    : 2385   0      0.00    102.82  13.45    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:     0.003 -  10.691: 1224   |   5:    53.442 -  64.130:   92        |
|      1:    10.691 -  21.379:  944   |   6:    64.130 -  74.818:   64        |
|      2:    21.379 -  32.067:  201   |   7:    74.818 -  85.506:   35        |
|      3:    32.067 -  42.755:  134   |   8:    85.506 -  96.194:    8        |
|      4:    42.755 -  53.442:  118   |   9:    96.194 - 106.882:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 336         
Filter by distance & map next to the model:
   mapped sites are within: 0.654 - 4.549
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 329 from: 336
   mapped sites are within: 0.724 - 4.549

peak=    9.909 closest distance to " O   HOH Z 203 " =    1.386
peak=    9.176 closest distance to " O   HOH Z 190 " =    1.822
peak=    8.025 closest distance to " CB  VAL A 230 " =    1.303
peak=    7.697 closest distance to " O   HOH Z 109 " =    1.328
peak=    7.387 closest distance to " O   HOH Z 255 " =    1.693
peak=    6.408 closest distance to " O   GLN A  11 " =    0.960
peak=    6.071 closest distance to " O   HOH Z 404 " =    1.960
peak=    5.864 closest distance to " O   HOH Z 117 " =    1.623
peak=    5.863 closest distance to " CG1 VAL A 296 " =    1.263
peak=    5.801 closest distance to " O   HOH Z 248 " =    1.606
peak=    5.789 closest distance to " CD1AILE A 234 " =    1.404
peak=    5.491 closest distance to " O   HOH Z 239 " =    2.076
peak=    5.382 closest distance to " O   HOH Z 210 " =    1.588
peak=    5.382 closest distance to " O   HOH Z 169 " =    1.170
peak=    5.214 closest distance to " CD2 LEU A   5 " =    1.147
peak=    5.121 closest distance to " O   HOH Z 277 " =    1.906
peak=    5.002 closest distance to " O   HOH Z 403 " =    2.261
peak=    4.949 closest distance to " CD2 TRP A 179 " =    1.280
peak=    4.941 closest distance to " O   HOH Z 124 " =    1.622
peak=    4.939 closest distance to " O   HOH Z  54 " =    1.402
peak=    4.882 closest distance to " NH2AARG A 145 " =    1.068
peak=    4.859 closest distance to " O   HOH Z 128 " =    2.066
peak=    4.840 closest distance to " CB  VAL A 230 " =    1.463
peak=    4.813 closest distance to " CA  TYR A  30 " =    0.945
peak=    4.634 closest distance to " CZ3 TRP A 266 " =    1.088
peak=    4.564 closest distance to " O   HOH Z  69 " =    1.477
peak=    4.555 closest distance to " O   HOH Z 107 " =    1.038
peak=    4.547 closest distance to " O   HOH Z 431 " =    1.558
peak=    4.539 closest distance to " O   HOH Z 142 " =    2.340
peak=    4.511 closest distance to " CB  ARG A 275 " =    0.901
peak=    4.475 closest distance to " O   HOH Z 279 " =    0.976
peak=    4.456 closest distance to " O   HOH Z 158 " =    1.398
peak=    4.454 closest distance to " O   HOH Z 426 " =    1.253
peak=    4.428 closest distance to " N   ALA A   1 " =    2.091
peak=    4.424 closest distance to " O   HOH Z  97 " =    1.549
peak=    4.415 closest distance to " O   HOH Z 411 " =    3.715
peak=    4.411 closest distance to " O   HOH Z  67 " =    1.399
peak=    4.410 closest distance to " O   HOH Z 190 " =    1.424
peak=    4.386 closest distance to " O   HOH Z  76 " =    1.429
peak=    4.371 closest distance to " CD2 LEU A 228 " =    1.441
peak=    4.366 closest distance to " NH2 ARG A  56 " =    2.061
peak=    4.365 closest distance to " NH2 ARG A 156 " =    1.048
peak=    4.337 closest distance to " O   HOH Z  49 " =    1.725
peak=    4.302 closest distance to " O   HOH Z 169 " =    2.246
peak=    4.293 closest distance to " CZ  PHE A 218 " =    1.186
peak=    4.285 closest distance to " O   HOH Z 394 " =    1.896
peak=    4.273 closest distance to " O   HOH Z 406 " =    1.837
peak=    4.270 closest distance to " OD1 ASN A 301 " =    1.032
peak=    4.253 closest distance to " O   HOH Z 126 " =    1.619
peak=    4.252 closest distance to " O   HOH Z 331 " =    1.222
peak=    4.187 closest distance to " CA  ALA A 100 " =    1.079
peak=    4.178 closest distance to " CD  PRO A  54 " =    1.106
peak=    4.172 closest distance to " CG AARG A 102 " =    1.198
peak=    4.170 closest distance to " NE AARG A 145 " =    1.014
peak=    4.159 closest distance to " O   HOH Z 368 " =    3.106
peak=    4.159 closest distance to " CG  LEU A   5 " =    1.283
peak=    4.144 closest distance to " O   HOH Z 146 " =    1.334
peak=    4.138 closest distance to " O   HOH Z 402 " =    1.575
peak=    4.126 closest distance to " O   HOH Z 257 " =    1.374
peak=    4.125 closest distance to " CB  ASN A 285 " =    1.062
peak=    4.117 closest distance to " CB  GLN A  55 " =    0.899
peak=    4.114 closest distance to " CG  PRO A  54 " =    1.393
peak=    4.104 closest distance to " O   HOH Z   4 " =    1.848
peak=    4.103 closest distance to " O   HOH Z 193 " =    2.273
peak=    4.064 closest distance to " OE1 GLN A  55 " =    1.469
peak=    4.061 closest distance to " O   HOH Z 369 " =    1.220
peak=    4.046 closest distance to " O  BHOH Z 338 " =    1.434
peak=    4.038 closest distance to " CE2 PHE A  59 " =    0.932
peak=    4.024 closest distance to " O   HOH Z  45 " =    0.970
peak=    4.019 closest distance to " CB  TYR A  30 " =    1.111
peak=    4.019 closest distance to " O   HOH Z 132 " =    2.947
peak=    4.010 closest distance to " CG AARG A 275 " =    1.264
peak=    4.004 closest distance to " CB  SER A  99 " =    1.061
peak=    4.003 closest distance to " O   HOH Z  65 " =    0.901
peak=    4.002 closest distance to " CB  SER A  62 " =    1.197
peak=    3.999 closest distance to " O   HOH Z  88 " =    3.557
peak=    3.986 closest distance to " CD1 LEU A   5 " =    1.614
peak=    3.976 closest distance to " O   HOH Z 147 " =    1.304
peak=    3.971 closest distance to " CB  SER A  26 " =    1.721
peak=    3.970 closest distance to " CD  LYS A 166 " =    1.822
peak=    3.956 closest distance to " O   HOH Z  40 " =    2.221
peak=    3.944 closest distance to " O   HOH Z 368 " =    2.208
peak=    3.925 closest distance to " O   HOH Z 130 " =    2.370
peak=    3.923 closest distance to " O   HOH Z 246 " =    1.206
peak=    3.917 closest distance to " NH2 ARG A  56 " =    1.215
peak=    3.914 closest distance to " NH1AARG A 102 " =    0.992
peak=    3.913 closest distance to " O   HOH Z  63 " =    1.658
peak=    3.905 closest distance to " CB  GLU A 152 " =    1.153
peak=    3.900 closest distance to " CB  SER A 146 " =    1.122
peak=    3.883 closest distance to " O   HOH Z 214 " =    1.718
peak=    3.881 closest distance to " O   HOH Z 234 " =    1.951
peak=    3.866 closest distance to " NH1AARG A 275 " =    1.232
peak=    3.854 closest distance to " O   HOH Z 146 " =    1.547
peak=    3.854 closest distance to " O   HOH Z 222 " =    1.158
peak=    3.848 closest distance to " NE2 GLN A  11 " =    1.190
peak=    3.835 closest distance to " O   HOH Z 199 " =    1.411
peak=    3.815 closest distance to " CB  ASP A 191 " =    1.222
peak=    3.812 closest distance to " O   SER A  87 " =    2.332
peak=    3.800 closest distance to " O   HOH Z  30 " =    1.233
peak=    3.795 closest distance to " O   HOH Z 213 " =    1.806
peak=    3.788 closest distance to " O   HOH Z 144 " =    1.685
peak=    3.787 closest distance to " CG  PRO A 243 " =    1.068
peak=    3.786 closest distance to " O  BHOH Z  74 " =    1.239
peak=    3.784 closest distance to " O   HOH Z 120 " =    0.855
peak=    3.783 closest distance to " O   HOH Z 339 " =    1.680
peak=    3.772 closest distance to " CG1 ILE A  20 " =    1.446
peak=    3.771 closest distance to " O   HOH Z 422 " =    0.777
peak=    3.770 closest distance to " O   HOH Z  46 " =    1.413
peak=    3.766 closest distance to " O   HOH Z 357 " =    2.083
peak=    3.765 closest distance to " CG  ARG A  66 " =    1.047
peak=    3.762 closest distance to " CG1BVAL A  72 " =    1.668
peak=    3.762 closest distance to " O   HOH Z 392 " =    1.259
peak=    3.760 closest distance to " O   HOH Z 395 " =    1.660
peak=    3.754 closest distance to " CB  VAL A 296 " =    1.233
peak=    3.754 closest distance to " CB  SER A  63 " =    1.273
peak=    3.753 closest distance to " O   HOH Z 112 " =    1.220
peak=    3.743 closest distance to " O   HOH Z 154 " =    1.685
peak=    3.742 closest distance to " O   HOH Z 391 " =    3.108
peak=    3.741 closest distance to " O   HOH Z  35 " =    1.950
peak=    3.740 closest distance to " O   HOH Z 287 " =    1.571
peak=    3.738 closest distance to " O   HOH Z   9 " =    1.257
peak=    3.726 closest distance to " O   HOH Z 223 " =    1.137
peak=    3.716 closest distance to " O   HOH Z  44 " =    1.259
peak=    3.715 closest distance to " O   HOH Z 151 " =    1.653
peak=    3.702 closest distance to " ND2 ASN A 249 " =    2.019
peak=    3.700 closest distance to " CG  ARG A 138 " =    1.423
peak=    3.697 closest distance to " CE1 TYR A 186 " =    1.130
peak=    3.686 closest distance to " CG2 VAL A 197 " =    1.198
peak=    3.668 closest distance to " O   HOH Z 188 " =    1.220
peak=    3.661 closest distance to " O   HOH Z  85 " =    1.711
peak=    3.652 closest distance to " O   HOH Z 299 " =    4.549
peak=    3.652 closest distance to " O   GLU A   2 " =    1.900
peak=    3.649 closest distance to " CA  ARG A  36 " =    1.046
peak=    3.647 closest distance to " CB  GLN A 223 " =    1.476
peak=    3.633 closest distance to " O   HOH Z  80 " =    2.472
peak=    3.632 closest distance to " CE3 TRP A 274 " =    1.270
peak=    3.630 closest distance to " O   HOH Z 188 " =    2.848
peak=    3.624 closest distance to " NE2 GLN A  77 " =    3.070
peak=    3.608 closest distance to " CE1 TYR A  30 " =    1.184
peak=    3.605 closest distance to " O   HOH Z 191 " =    1.266
peak=    3.605 closest distance to " CB  GLN A  58 " =    1.025
peak=    3.598 closest distance to " O   HOH Z 301 " =    1.326
peak=    3.587 closest distance to " OE2 GLU A   2 " =    1.997
peak=    3.586 closest distance to " O   HOH Z 236 " =    1.758
peak=    3.585 closest distance to " CB  ASN A  45 " =    1.127
peak=    3.576 closest distance to " CD  ARG A 139 " =    1.101
peak=    3.570 closest distance to " CD  ARG A 159 " =    0.794
peak=    3.566 closest distance to " CZ  TYR A  68 " =    0.724
peak=    3.555 closest distance to " CD  LYS A  76 " =    1.781
peak=    3.552 closest distance to " O   HOH Z 359 " =    2.038
peak=    3.552 closest distance to " CD2 LEU A  83 " =    1.602
peak=    3.545 closest distance to " CG2 VAL A 268 " =    1.126
peak=    3.538 closest distance to " CB  TRP A 179 " =    1.292
peak=    3.537 closest distance to " NH1AARG A 145 " =    1.306
peak=    3.537 closest distance to " CB  ALA A 114 " =    0.914
peak=    3.523 closest distance to " CB  ASN A 148 " =    1.318
peak=    3.519 closest distance to " CA  ALA A  51 " =    1.129
peak=    3.510 closest distance to " O   HOH Z 234 " =    3.223
peak=    3.509 closest distance to " O   HOH Z 408 " =    3.491
peak=    3.506 closest distance to " O   HOH Z 272 " =    1.361
peak=    3.500 closest distance to " O   HOH Z 340 " =    1.460
peak=    3.488 closest distance to " CG  LEU A 237 " =    1.428
peak=    3.486 closest distance to " CB  PRO A 280 " =    1.183
peak=    3.482 closest distance to " O   HOH Z 286 " =    1.951
peak=    3.480 closest distance to " CB  GLU A 236 " =    1.131
peak=    3.478 closest distance to " O   HOH Z  70 " =    0.994
peak=    3.475 closest distance to " O   PRO A 198 " =    1.606
peak=    3.475 closest distance to " CA  GLU A 152 " =    0.868
peak=    3.472 closest distance to " O   HOH Z  85 " =    1.570
peak=    3.470 closest distance to " OG ASER A 258 " =    3.136
peak=    3.467 closest distance to " O   HOH Z 328 " =    1.505
peak=    3.459 closest distance to " O   HOH Z 433 " =    1.530
peak=    3.449 closest distance to " N   GLU A  44 " =    1.451
peak=    3.444 closest distance to " O   HOH Z 298 " =    4.364
peak=    3.441 closest distance to " O   HOH Z 142 " =    1.564
peak=    3.440 closest distance to " CG2 VAL A 296 " =    1.065
peak=    3.440 closest distance to " CE3 TRP A  85 " =    1.063
peak=    3.438 closest distance to " O   HOH Z 343 " =    2.735
peak=    3.434 closest distance to " CG  LEU A 228 " =    1.300
peak=    3.433 closest distance to " O   HOH Z 141 " =    1.643
peak=    3.417 closest distance to " O   HOH Z   4 " =    1.988
peak=    3.416 closest distance to " CB  ARG A 145 " =    0.865
peak=    3.414 closest distance to " CZ  PHE A  38 " =    1.072
peak=    3.413 closest distance to " CG  GLN A  58 " =    1.387
peak=    3.413 closest distance to " CB  THR A  31 " =    1.192
peak=    3.411 closest distance to " CB  THR A 235 " =    1.257
peak=    3.409 closest distance to " O   HOH Z 313 " =    1.854
peak=    3.407 closest distance to " CB  ASP A 124 " =    1.017
peak=    3.405 closest distance to " N   TYR A 247 " =    1.295
peak=    3.401 closest distance to " CA  CYS A 260 " =    1.346
peak=    3.399 closest distance to " O   HOH Z 417 " =    2.896
peak=    3.398 closest distance to " O   HOH Z 435 " =    3.050
peak=    3.397 closest distance to " O   HOH Z 211 " =    1.096
peak=    3.395 closest distance to " O   HOH Z 102 " =    1.542
peak=    3.395 closest distance to " CA  VAL A  41 " =    0.847
peak=    3.386 closest distance to " NE BARG A 190 " =    1.491
peak=    3.384 closest distance to " CB  MET A  40 " =    1.086
peak=    3.384 closest distance to " O   HOH Z 298 " =    2.236
peak=    3.382 closest distance to " CB  PHE A  16 " =    1.072
peak=    3.376 closest distance to " NE1 TRP A  92 " =    1.583
peak=    3.368 closest distance to " O   HOH Z  50 " =    1.505
peak=    3.365 closest distance to " CA  ARG A 156 " =    0.998
peak=    3.363 closest distance to " CB  TRP A 179 " =    1.707
peak=    3.359 closest distance to " O   HOH Z 232 " =    2.325
peak=    3.357 closest distance to " NE  ARG A  24 " =    1.088
peak=    3.355 closest distance to " CB  ARG A 156 " =    1.082
peak=    3.352 closest distance to " O   ALA A 292 " =    1.495
peak=    3.351 closest distance to " O   HOH Z 251 " =    1.757
peak=    3.344 closest distance to " CB  SER A  97 " =    1.072
peak=    3.343 closest distance to " CB  GLN A 183 " =    1.255
peak=    3.342 closest distance to " O   HOH Z 189 " =    2.562
peak=    3.342 closest distance to " CD  GLN A 194 " =    1.454
peak=    3.340 closest distance to " CB  ALA A  71 " =    1.480
peak=    3.338 closest distance to " NH2 ARG A 269 " =    1.260
peak=    3.338 closest distance to " O   HOH Z 414 " =    2.332
peak=    3.337 closest distance to " CB  SER A  62 " =    3.822
peak=    3.336 closest distance to " CA  ASP A 162 " =    1.001
peak=    3.334 closest distance to " O   HOH Z  68 " =    1.808
peak=    3.333 closest distance to " O   HOH Z 134 " =    1.832
peak=    3.332 closest distance to " CB  THR A  52 " =    0.869
peak=    3.324 closest distance to " O   HOH Z 158 " =    2.817
peak=    3.323 closest distance to " CZ3 TRP A  92 " =    1.282
peak=    3.322 closest distance to " ND2AASN A 224 " =    0.916
peak=    3.320 closest distance to " O   HOH Z 344 " =    1.624
peak=    3.318 closest distance to " CB  GLU A 175 " =    1.347
peak=    3.317 closest distance to " O   HOH Z 122 " =    1.988
peak=    3.316 closest distance to " O   HOH Z 241 " =    1.957
peak=    3.315 closest distance to " CB  ASN A 187 " =    1.560
peak=    3.310 closest distance to " O   HOH Z 337 " =    2.227
peak=    3.309 closest distance to " CB  ASP A 140 " =    1.064
peak=    3.308 closest distance to " CA  VAL A 112 " =    1.110
peak=    3.306 closest distance to " O   HOH Z 200 " =    3.416
peak=    3.303 closest distance to " OG  SER A  62 " =    2.680
peak=    3.300 closest distance to " O   HOH Z 350 " =    1.394
peak=    3.297 closest distance to " O   HOH Z 371 " =    1.536
peak=    3.295 closest distance to " O   HOH Z 423 " =    1.845
peak=    3.292 closest distance to " O   HOH Z 380 " =    2.984
peak=    3.290 closest distance to " CB  SER A 141 " =    1.203
peak=    3.289 closest distance to " NZ  LYS A 117 " =    2.735
peak=    3.288 closest distance to " CB  PHE A 204 " =    0.991
peak=    3.286 closest distance to " SG BCYS A 201 " =    1.317
peak=    3.278 closest distance to " CG2 THR A  29 " =    1.529
peak=    3.277 closest distance to " O   HOH Z 327 " =    1.740
peak=    3.274 closest distance to " N   THR A  52 " =    1.260
peak=    3.274 closest distance to " CA  ARG A 195 " =    1.149
peak=    3.270 closest distance to " CG2 ILE A 234 " =    1.187
peak=    3.269 closest distance to " CA  THR A 246 " =    1.012
peak=    3.269 closest distance to " CD1 ILE A 120 " =    0.875
peak=    3.267 closest distance to " O   HOH Z 419 " =    1.823
peak=    3.264 closest distance to " O   HOH Z 299 " =    3.717
peak=    3.263 closest distance to " CD1 LEU A  96 " =    0.876
peak=    3.258 closest distance to " O   HOH Z 371 " =    2.630
peak=    3.256 closest distance to " O   HOH Z 130 " =    1.110
peak=    3.253 closest distance to " CG1 ILE A 120 " =    0.962
peak=    3.253 closest distance to " CG1 ILE A  33 " =    1.267
peak=    3.250 closest distance to " O   HOH Z 209 " =    2.250
peak=    3.244 closest distance to " NE1 TRP A 266 " =    1.672
peak=    3.241 closest distance to " O   THR A 220 " =    1.165
peak=    3.238 closest distance to " OE1 GLU A   2 " =    1.275
peak=    3.231 closest distance to " O   HOH Z  59 " =    2.121
peak=    3.230 closest distance to " O   THR A 157 " =    1.305
peak=    3.226 closest distance to " N   GLY A 262 " =    1.200
peak=    3.226 closest distance to " NZ  LYS A 117 " =    0.876
peak=    3.225 closest distance to " CA  SER A  32 " =    1.809
peak=    3.224 closest distance to " CA  HIS A  86 " =    0.879
peak=    3.222 closest distance to " CZ2 TRP A 179 " =    3.310
peak=    3.222 closest distance to " O   HOH Z 299 " =    1.783
peak=    3.221 closest distance to " O   HOH Z  56 " =    1.840
peak=    3.221 closest distance to " O   HOH Z 306 " =    1.439
peak=    3.217 closest distance to " NH2AARG A 275 " =    2.489
peak=    3.215 closest distance to " OG BSER A 258 " =    2.409
peak=    3.213 closest distance to " CB  GLN A  88 " =    1.260
peak=    3.209 closest distance to " OD1 ASP A 231 " =    2.041
peak=    3.208 closest distance to " O   HOH Z  38 " =    1.487
peak=    3.207 closest distance to " CA  THR A  82 " =    1.589
peak=    3.203 closest distance to " CA  LEU A  83 " =    1.457
peak=    3.203 closest distance to " O   HOH Z 427 " =    3.009
peak=    3.202 closest distance to " CD  LYS A 119 " =    2.128
peak=    3.199 closest distance to " CE  MET A  93 " =    1.475
peak=    3.199 closest distance to " CB  PRO A  54 " =    0.896
peak=    3.197 closest distance to " CB  GLU A 277 " =    1.058
peak=    3.187 closest distance to " OG BSER A  99 " =    3.052
peak=    3.184 closest distance to " N   SER A 164 " =    0.898
peak=    3.183 closest distance to " CE  LYS A  76 " =    0.844
peak=    3.180 closest distance to " ND1 HIS A  81 " =    1.060
peak=    3.179 closest distance to " O   HOH Z  26 " =    1.325
peak=    3.175 closest distance to " O   THR A 251 " =    1.349
peak=    3.162 closest distance to " O   HOH Z 289 " =    1.639
peak=    3.162 closest distance to " CD2 LEU A 282 " =    1.968
peak=    3.162 closest distance to " OD1 ASN A 285 " =    1.579
peak=    3.161 closest distance to " O   HOH Z 154 " =    2.094
peak=    3.159 closest distance to " ND2 ASN A 110 " =    1.523
peak=    3.159 closest distance to " O   HOH Z 244 " =    1.623
peak=    3.156 closest distance to " O   HOH Z 221 " =    1.140
peak=    3.156 closest distance to " CG2 VAL A 126 " =    1.116
peak=    3.153 closest distance to " CG  GLN A  11 " =    1.491
peak=    3.144 closest distance to " CG2 THR A 294 " =    1.037
peak=    3.143 closest distance to " CB  ASN A 110 " =    1.083
peak=    3.141 closest distance to " CA  ASP A 140 " =    1.391
peak=    3.138 closest distance to " O   HOH Z 132 " =    2.451
peak=    3.138 closest distance to " O   HOH Z 111 " =    1.225
peak=    3.136 closest distance to " CG2 THR A  42 " =    0.837
peak=    3.132 closest distance to " CD  ARG A 195 " =    1.080
peak=    3.132 closest distance to " NH2BARG A 190 " =    2.064
peak=    3.132 closest distance to " OE1 GLN A 223 " =    2.135
peak=    3.130 closest distance to " CE1 PHE A  59 " =    1.241
peak=    3.129 closest distance to " NH2 ARG A  79 " =    1.318
peak=    3.129 closest distance to " O   HOH Z 422 " =    3.188
peak=    3.129 closest distance to " CD1 ILE A 199 " =    1.222
peak=    3.126 closest distance to " O   HOH Z 366 " =    2.646
peak=    3.119 closest distance to " O   HOH Z 166 " =    1.653
peak=    3.117 closest distance to " O   HOH Z 191 " =    1.298
peak=    3.114 closest distance to " CG  PRO A 198 " =    1.613
peak=    3.113 closest distance to " CA  SER A  12 " =    1.308
peak=    3.113 closest distance to " CB  ALA A 248 " =    1.580
peak=    3.113 closest distance to " O   HOH Z 379 " =    3.567
peak=    3.112 closest distance to " O   ALA A 165 " =    1.261
peak=    3.104 closest distance to " N   ILE A  33 " =    1.074
peak=    3.099 closest distance to " O   LYS A 289 " =    1.002
peak=    3.098 closest distance to " O   HOH Z 371 " =    2.548
peak=    3.088 closest distance to " O   HOH Z 327 " =    3.275
peak=    3.076 closest distance to " CG  ARG A 269 " =    1.443
peak=    3.075 closest distance to " O   HOH Z 113 " =    1.889
peak=    3.068 closest distance to " O   HOH Z 227 " =    1.584
peak=    3.066 closest distance to " O   HOH Z 247 " =    1.697
peak=    3.065 closest distance to " CB  PRO A 243 " =    1.067
peak=    3.059 closest distance to " O   THR A 182 " =    1.589
peak=    3.040 closest distance to " O   ILE A  49 " =    0.960
peak=    3.036 closest distance to " O   HOH Z 163 " =    2.021

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 194         
Filter by distance & map next to the model:
   mapped sites are within: 0.660 - 5.516
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 189 from: 194
   mapped sites are within: 0.768 - 5.516

peak=   -4.999 closest distance to " CG2 VAL A 230 " =    0.788
peak=   -4.850 closest distance to " O   HOH Z 203 " =    0.883
peak=   -4.514 closest distance to " O   PRO A 198 " =    1.291
peak=   -4.437 closest distance to " OG BSER A 134 " =    1.503
peak=   -4.330 closest distance to " CD1 PHE A  59 " =    2.058
peak=   -4.208 closest distance to " CG2 ILE A  20 " =    2.876
peak=   -4.207 closest distance to " CD2 TYR A  30 " =    2.509
peak=   -4.140 closest distance to " CG2 ILE A  49 " =    2.841
peak=   -4.136 closest distance to " O   GLY A 241 " =    2.398
peak=   -4.118 closest distance to " OD1 ASN A 301 " =    0.768
peak=   -4.107 closest distance to " CG1 VAL A 296 " =    1.034
peak=   -4.094 closest distance to " CG  PRO A 243 " =    1.697
peak=   -4.070 closest distance to " CD2 TYR A 293 " =    1.830
peak=   -3.933 closest distance to " CG2BVAL A  41 " =    2.478
peak=   -3.899 closest distance to " O   ASP A 107 " =    2.149
peak=   -3.880 closest distance to " O   HOH Z 190 " =    1.472
peak=   -3.873 closest distance to " CA  VAL A 121 " =    1.432
peak=   -3.854 closest distance to " O   HOH Z 345 " =    3.048
peak=   -3.848 closest distance to " CG2 VAL A 189 " =    2.027
peak=   -3.842 closest distance to " SD  MET A 105 " =    2.390
peak=   -3.827 closest distance to " O   HOH Z 216 " =    1.276
peak=   -3.826 closest distance to " O   HOH Z 422 " =    1.091
peak=   -3.823 closest distance to " O   HOH Z 166 " =    1.242
peak=   -3.816 closest distance to " CA  ASP A 298 " =    1.023
peak=   -3.802 closest distance to " CG  ARG A 269 " =    2.317
peak=   -3.789 closest distance to " CG1 VAL A 112 " =    2.506
peak=   -3.786 closest distance to " CD  ARG A  14 " =    3.096
peak=   -3.753 closest distance to " O   HOH Z 162 " =    5.435
peak=   -3.752 closest distance to " CG  GLN A  58 " =    0.875
peak=   -3.747 closest distance to " CA  ARG A 139 " =    2.198
peak=   -3.740 closest distance to " CG1 VAL A 250 " =    2.691
peak=   -3.730 closest distance to " O   HOH Z 155 " =    1.834
peak=   -3.724 closest distance to " O   HOH Z 109 " =    0.951
peak=   -3.706 closest distance to " O   HOH Z 433 " =    0.820
peak=   -3.696 closest distance to " O   HOH Z 269 " =    1.238
peak=   -3.688 closest distance to " O   HOH Z 405 " =    2.288
peak=   -3.685 closest distance to " O   HOH Z 116 " =    1.273
peak=   -3.680 closest distance to " NH2AARG A 145 " =    1.638
peak=   -3.673 closest distance to " CD  GLN A 223 " =    1.700
peak=   -3.668 closest distance to " CZ2 TRP A 274 " =    1.042
peak=   -3.667 closest distance to " N   ASN A 215 " =    1.815
peak=   -3.648 closest distance to " CB  ALA A 248 " =    2.250
peak=   -3.645 closest distance to " O   HOH Z 166 " =    1.429
peak=   -3.630 closest distance to " CB  ALA A   9 " =    2.348
peak=   -3.619 closest distance to " O   HOH Z 384 " =    1.695
peak=   -3.618 closest distance to " O   HOH Z 368 " =    1.988
peak=   -3.611 closest distance to " CG  ARG A 259 " =    2.422
peak=   -3.597 closest distance to " O   HOH Z 374 " =    2.020
peak=   -3.595 closest distance to " CG  PHE A  59 " =    1.562
peak=   -3.589 closest distance to " O   GLN A  11 " =    1.303
peak=   -3.587 closest distance to " O   HOH Z 408 " =    3.746
peak=   -3.581 closest distance to " O   HOH Z 119 " =    1.939
peak=   -3.558 closest distance to " O   GLU A   2 " =    2.430
peak=   -3.549 closest distance to " OD2 ASP A 298 " =    1.070
peak=   -3.541 closest distance to " O   HOH Z 103 " =    1.408
peak=   -3.536 closest distance to " CE3 TRP A 150 " =    2.360
peak=   -3.524 closest distance to " O   HOH Z 435 " =    1.577
peak=   -3.519 closest distance to " O   HOH Z 186 " =    2.173
peak=   -3.517 closest distance to " O   HOH Z  69 " =    1.318
peak=   -3.513 closest distance to " CA  GLN A  58 " =    1.162
peak=   -3.513 closest distance to " CB  ALA A 161 " =    2.471
peak=   -3.510 closest distance to " O   HOH Z 407 " =    2.657
peak=   -3.490 closest distance to " OG  SER A  97 " =    2.436
peak=   -3.482 closest distance to " O  BHOH Z 338 " =    1.184
peak=   -3.464 closest distance to " CD1 TRP A 179 " =    1.153
peak=   -3.460 closest distance to " O   SER A 273 " =    0.991
peak=   -3.458 closest distance to " O   HOH Z 150 " =    2.009
peak=   -3.455 closest distance to " CB  ASP A 286 " =    1.572
peak=   -3.450 closest distance to " OG  SER A  63 " =    1.280
peak=   -3.449 closest distance to " O   HOH Z  10 " =    1.476
peak=   -3.448 closest distance to " ND2 ASN A  39 " =    1.416
peak=   -3.446 closest distance to " CG  GLN A 103 " =    2.387
peak=   -3.444 closest distance to " O   HOH Z  56 " =    1.402
peak=   -3.444 closest distance to " O   HOH Z  90 " =    3.471
peak=   -3.422 closest distance to " O   HOH Z  54 " =    1.607
peak=   -3.420 closest distance to " CD  ARG A 156 " =    2.068
peak=   -3.410 closest distance to " CA  GLY A 203 " =    2.537
peak=   -3.405 closest distance to " CD2 LEU A 237 " =    2.228
peak=   -3.403 closest distance to " O   HOH Z 100 " =    0.842
peak=   -3.400 closest distance to " NE2 GLN A  11 " =    1.333
peak=   -3.399 closest distance to " C   VAL A 265 " =    1.037
peak=   -3.391 closest distance to " CG1 VAL A  78 " =    2.661
peak=   -3.390 closest distance to " CB  PHE A 208 " =    2.265
peak=   -3.387 closest distance to " OXT GLY A 302 " =    3.048
peak=   -3.382 closest distance to " O   HOH Z 198 " =    1.761
peak=   -3.380 closest distance to " CZ  TYR A 172 " =    1.805
peak=   -3.378 closest distance to " O   HOH Z 171 " =    2.453
peak=   -3.377 closest distance to " CD1 ILE A 109 " =    2.688
peak=   -3.374 closest distance to " O   GLN A  77 " =    1.781
peak=   -3.370 closest distance to " CG2 THR A  18 " =    2.892
peak=   -3.357 closest distance to " O   HOH Z 275 " =    1.868
peak=   -3.354 closest distance to " CA  ARG A  36 " =    1.364
peak=   -3.353 closest distance to " CB  VAL A  67 " =    2.872
peak=   -3.349 closest distance to " O   HOH Z 111 " =    1.241
peak=   -3.341 closest distance to " O   HOH Z 110 " =    1.323
peak=   -3.331 closest distance to " O   HOH Z 260 " =    1.633
peak=   -3.326 closest distance to " CG  ASP A 286 " =    1.312
peak=   -3.320 closest distance to " O   HOH Z 353 " =    1.278
peak=   -3.319 closest distance to " O   HOH Z 423 " =    3.076
peak=   -3.319 closest distance to " CA  PRO A 280 " =    0.926
peak=   -3.318 closest distance to " O   HOH Z 297 " =    2.671
peak=   -3.314 closest distance to " CE1 PHE A 218 " =    1.611
peak=   -3.311 closest distance to " CD  PRO A 243 " =    1.560
peak=   -3.311 closest distance to " CA  PRO A 243 " =    2.870
peak=   -3.309 closest distance to " O   HOH Z 107 " =    0.888
peak=   -3.307 closest distance to " CA  VAL A 230 " =    1.021
peak=   -3.301 closest distance to " O   HOH Z  52 " =    2.144
peak=   -3.301 closest distance to " O   HOH Z 151 " =    0.879
peak=   -3.297 closest distance to " O   HOH Z 214 " =    2.616
peak=   -3.296 closest distance to " O   HOH Z 116 " =    1.877
peak=   -3.282 closest distance to " SD  MET A  93 " =    1.884
peak=   -3.282 closest distance to " N   GLN A  55 " =    1.641
peak=   -3.278 closest distance to " O   HOH Z   6 " =    2.060
peak=   -3.275 closest distance to " O   HOH Z 278 " =    1.166
peak=   -3.272 closest distance to " CG1 VAL A 268 " =    2.339
peak=   -3.271 closest distance to " N   LEU A 282 " =    2.231
peak=   -3.271 closest distance to " CA  ALA A 114 " =    1.101
peak=   -3.270 closest distance to " CB  HIS A  86 " =    1.243
peak=   -3.263 closest distance to " ND2 ASN A 127 " =    1.974
peak=   -3.256 closest distance to " O   HOH Z 222 " =    1.219
peak=   -3.255 closest distance to " CA  GLY A  57 " =    2.132
peak=   -3.255 closest distance to " NE  ARG A 139 " =    1.098
peak=   -3.249 closest distance to " CD1 TYR A 247 " =    2.482
peak=   -3.246 closest distance to " O   HOH Z 137 " =    1.518
peak=   -3.246 closest distance to " O   HOH Z  71 " =    1.219
peak=   -3.246 closest distance to " O   HOH Z 135 " =    2.061
peak=   -3.242 closest distance to " O   HOH Z 136 " =    1.399
peak=   -3.241 closest distance to " OD2 ASP A 191 " =    2.329
peak=   -3.239 closest distance to " ND2 ASN A 209 " =    2.526
peak=   -3.239 closest distance to " CB  SER A  22 " =    1.934
peak=   -3.238 closest distance to " CE2 TRP A  70 " =    2.302
peak=   -3.238 closest distance to " O   HOH Z 388 " =    2.161
peak=   -3.229 closest distance to " CE  LYS A 289 " =    2.462
peak=   -3.228 closest distance to " CD1 ILE A 151 " =    2.642
peak=   -3.219 closest distance to " O   HOH Z  28 " =    2.041
peak=   -3.217 closest distance to " O   HOH Z 165 " =    1.694
peak=   -3.210 closest distance to " O   HOH Z 428 " =    1.610
peak=   -3.209 closest distance to " O   HOH Z  41 " =    1.965
peak=   -3.209 closest distance to " O   ASN A  45 " =    1.953
peak=   -3.209 closest distance to " O   HOH Z 131 " =    4.172
peak=   -3.209 closest distance to " O   HOH Z 377 " =    2.173
peak=   -3.204 closest distance to " O   HOH Z 196 " =    1.588
peak=   -3.198 closest distance to " CA  TRP A 150 " =    0.982
peak=   -3.198 closest distance to " CD1 TYR A 169 " =    2.028
peak=   -3.198 closest distance to " O   HOH Z 154 " =    1.414
peak=   -3.195 closest distance to " O   HOH Z 411 " =    1.491
peak=   -3.194 closest distance to " O   HOH Z 417 " =    1.581
peak=   -3.192 closest distance to " O   ILE A 234 " =    1.091
peak=   -3.192 closest distance to " CE1 HIS A  81 " =    1.441
peak=   -3.182 closest distance to " NH2 ARG A  66 " =    5.139
peak=   -3.179 closest distance to " CB  ASP A 132 " =    2.351
peak=   -3.175 closest distance to " O   HOH Z 223 " =    2.336
peak=   -3.174 closest distance to " OG1 THR A 294 " =    2.471
peak=   -3.169 closest distance to " O   GLN A 144 " =    1.262
peak=   -3.168 closest distance to " OG1 THR A 246 " =    1.822
peak=   -3.165 closest distance to " NE1 TRP A 266 " =    2.221
peak=   -3.157 closest distance to " O   HOH Z 113 " =    2.108
peak=   -3.153 closest distance to " CG  ASN A 110 " =    0.879
peak=   -3.150 closest distance to " O   HOH Z  55 " =    1.260
peak=   -3.149 closest distance to " O   HOH Z 134 " =    3.025
peak=   -3.146 closest distance to " O   GLY A  80 " =    2.712
peak=   -3.146 closest distance to " CB  PRO A 163 " =    2.559
peak=   -3.145 closest distance to " O   HOH Z 387 " =    2.921
peak=   -3.142 closest distance to " N   ASP A 191 " =    1.622
peak=   -3.142 closest distance to " CE BMET A  47 " =    1.380
peak=   -3.141 closest distance to " OD1 ASN A  39 " =    0.987
peak=   -3.139 closest distance to " O   HOH Z 108 " =    2.143
peak=   -3.136 closest distance to " N   ASP A 272 " =    0.989
peak=   -3.133 closest distance to " CB  SER A  62 " =    5.516
peak=   -3.126 closest distance to " CE1 TYR A 247 " =    2.708
peak=   -3.119 closest distance to " OD1 ASN A 301 " =    1.162
peak=   -3.109 closest distance to " CG1 VAL A  78 " =    2.503
peak=   -3.104 closest distance to " O   HOH Z 118 " =    4.956
peak=   -3.100 closest distance to " CA  GLY A 229 " =    2.213
peak=   -3.098 closest distance to " CB  ALA A 248 " =    2.161
peak=   -3.096 closest distance to " OH  TYR A 169 " =    0.801
peak=   -3.094 closest distance to " CZ2 TRP A 179 " =    2.419
peak=   -3.081 closest distance to " O   HOH Z 179 " =    2.032
peak=   -3.080 closest distance to " CA  ASP A  27 " =    2.478
peak=   -3.078 closest distance to " CE1 HIS A 207 " =    2.494
peak=   -3.072 closest distance to " C   HIS A 108 " =    1.212
peak=   -3.071 closest distance to " CD1 LEU A  25 " =    2.276
peak=   -3.061 closest distance to " C   LEU A 222 " =    0.900
peak=   -3.059 closest distance to " CZ  PHE A  38 " =    2.357
peak=   -3.057 closest distance to " CA  SER A 276 " =    1.501
peak=   -3.057 closest distance to " CG  GLN A  58 " =    1.555
peak=   -3.056 closest distance to " NE2 GLN A 183 " =    1.824
peak=   -3.050 closest distance to " O   HOH Z 150 " =    1.637
peak=   -3.009 closest distance to " OE1 GLN A 223 " =    2.161

================= 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    :  0.5322 0.5338   6.320714e+00   6.321264e+00
   1_bss:  0.5260 0.5310   5.862305e+00   5.851360e+00
   1_xyz:  0.4798 0.5098   6.212396e+00   6.233121e+00
   1_adp:  0.4415 0.5080   6.247306e+00   6.303671e+00
   1_occ:  0.4413 0.5079   6.246946e+00   6.304818e+00
   2_bss:  0.4401 0.5027   6.249096e+00   6.305534e+00
   2_xyz:  0.3780 0.4436   6.145965e+00   6.243758e+00
   2_adp:  0.3578 0.4301   6.113826e+00   6.225765e+00
   2_occ:  0.3574 0.4297   6.112999e+00   6.225648e+00
   3_bss:  0.3542 0.4256   6.112868e+00   6.225279e+00
   3_xyz:  0.2914 0.3536   5.954932e+00   6.105551e+00
   3_adp:  0.2761 0.3330   5.910744e+00   6.057793e+00
   3_occ:  0.2758 0.3328   5.909583e+00   6.057240e+00
   4_bss:  0.2743 0.3322   5.909149e+00   6.056446e+00
   4_xyz:  0.2064 0.2595   5.667476e+00   5.857681e+00
   4_adp:  0.1800 0.2441   5.574240e+00   5.796257e+00
   4_occ:  0.1799 0.2440   5.573597e+00   5.795541e+00
   5_bss:  0.1797 0.2440   5.573061e+00   5.794287e+00
   5_xyz:  0.1500 0.2077   5.415294e+00   5.649704e+00
   5_adp:  0.1431 0.1988   5.374342e+00   5.606513e+00
   5_occ:  0.1428 0.1990   5.373504e+00   5.605931e+00
   5_bss:  0.1433 0.1993   5.375589e+00   5.607406e+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:  0.335  20.000   6.217   9.578   9.959   0.000   0.000   0.000
   1_xyz:  0.335  20.000   6.217   9.578   9.959   0.000   0.000   0.000
   1_adp:  0.335  20.000   6.217   9.578   9.959   0.000   0.000   0.000
   1_occ:  0.335  20.000   6.217   9.578   9.959   0.000   0.000   0.000
   2_bss:  0.340  50.000   2.566   5.192   5.886   0.000   0.000   0.000
   2_xyz:  0.340  50.000   2.566   5.192   5.886   0.000   0.000   0.000
   2_adp:  0.340  50.000   2.566   5.192   5.886   0.000   0.000   0.000
   2_occ:  0.340  50.000   2.566   5.192   5.886   0.000   0.000   0.000
   3_bss:  0.321  47.529  -0.197   1.996   2.659   0.000   0.000   0.000
   3_xyz:  0.321  47.529  -0.197   1.996   2.659   0.000   0.000   0.000
   3_adp:  0.321  47.529  -0.197   1.996   2.659   0.000   0.000   0.000
   3_occ:  0.321  47.529  -0.197   1.996   2.659   0.000   0.000   0.000
   4_bss:  0.323  54.824  -2.118   0.152   0.832   0.000   0.000   0.000
   4_xyz:  0.323  54.824  -2.118   0.152   0.832   0.000   0.000   0.000
   4_adp:  0.323  54.824  -2.118   0.152   0.832   0.000   0.000   0.000
   4_occ:  0.323  54.824  -2.118   0.152   0.832   0.000   0.000   0.000
   5_bss:  0.336  67.751  -2.700  -0.670   0.195  -0.000   0.000   0.000
   5_xyz:  0.336  67.751  -2.700  -0.670   0.195  -0.000   0.000   0.000
   5_adp:  0.336  67.751  -2.700  -0.670   0.195  -0.000   0.000   0.000
   5_occ:  0.336  67.751  -2.700  -0.670   0.195  -0.000   0.000   0.000
   5_bss:  0.332  63.914  -2.836  -1.094  -0.063  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  71.140 0.2482  0.2993    95432.181
   1_bss:  72.498 0.2294  0.3469    96783.317
   1_xyz:  67.161 0.2981  0.4411    84003.819
   1_adp:  63.518 0.3465  0.6221    82032.163
   1_occ:  63.636 0.3449  0.6170    82232.319
   2_bss:  63.277 0.3498  0.5540    82174.280
   2_xyz:  52.466 0.4885  0.7743    61552.458
   2_adp:  49.704 0.5237  0.8377    57027.935
   2_occ:  49.652 0.5243  0.8386    56877.080
   3_bss:  49.432 0.5270  0.7584    56567.212
   3_xyz:  39.519 0.6473  0.9028    37088.224
   3_adp:  36.125 0.6882  0.9378    32122.429
   3_occ:  36.046 0.6891  0.9390    31987.315
   4_bss:  35.937 0.6904  0.8813    31902.553
   4_xyz:  26.899 0.7906  0.9656    18395.042
   4_adp:  24.562 0.8155  0.9728    15982.789
   4_occ:  24.541 0.8158  0.9731    15968.698
   5_bss:  24.468 0.8165  0.9508    15897.328
   5_xyz:  20.391 0.8574  0.9746    11417.916
   5_adp:  19.283 0.8685  0.9740    10578.290
   5_occ:  19.265 0.8686  0.9742    10566.266
   5_bss:  19.284 0.8685  0.9647    10602.602
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.087   5.3948e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.087   5.3948e+01
   1_xyz:   1.881  0.015  0.112 18.714  0.008  4.105   1.7514e-01
   1_adp:   1.881  0.015  0.112 18.714  0.008  4.105   1.7514e-01
   1_occ:   1.881  0.015  0.112 18.714  0.008  4.105   1.7514e-01
   2_bss:   1.881  0.015  0.112 18.714  0.008  4.105   1.7514e-01
   2_xyz:   1.572  0.012  0.090 17.719  0.006  4.105   1.4794e-01
   2_adp:   1.572  0.012  0.090 17.719  0.006  4.105   1.4794e-01
   2_occ:   1.572  0.012  0.090 17.719  0.006  4.105   1.4794e-01
   3_bss:   1.572  0.012  0.090 17.719  0.006  4.105   1.4794e-01
   3_xyz:   1.315  0.010  0.089 16.749  0.005  4.110   1.0316e-01
   3_adp:   1.315  0.010  0.089 16.749  0.005  4.110   1.0316e-01
   3_occ:   1.315  0.010  0.089 16.749  0.005  4.110   1.0316e-01
   4_bss:   1.315  0.010  0.089 16.749  0.005  4.110   1.0316e-01
   4_xyz:   1.262  0.010  0.087 16.185  0.004  4.112   9.4451e-02
   4_adp:   1.262  0.010  0.087 16.185  0.004  4.112   9.4451e-02
   4_occ:   1.262  0.010  0.087 16.185  0.004  4.112   9.4451e-02
   5_bss:   1.262  0.010  0.087 16.185  0.004  4.112   9.4451e-02
   5_xyz:   1.205  0.009  0.088 15.585  0.004  4.113   8.2038e-02
   5_adp:   1.205  0.009  0.088 15.585  0.004  4.113   8.2038e-02
   5_occ:   1.205  0.009  0.088 15.585  0.004  4.113   8.2038e-02
   5_bss:   1.205  0.009  0.088 15.585  0.004  4.113   8.2038e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  0.732   6.9823e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  0.732   6.9823e+00
   1_xyz:  16.325  0.178  0.512 86.606  0.053  2.007   1.1167e-01
   1_adp:  16.325  0.178  0.512 86.606  0.053  2.007   1.1167e-01
   1_occ:  16.325  0.178  0.512 86.606  0.053  2.007   1.1167e-01
   2_bss:  16.325  0.178  0.512 86.606  0.053  2.007   1.1167e-01
   2_xyz:  10.881  0.094  0.323 87.156  0.050  2.053   1.3053e-01
   2_adp:  10.881  0.094  0.323 87.156  0.050  2.053   1.3053e-01
   2_occ:  10.881  0.094  0.323 87.156  0.050  2.053   1.3053e-01
   3_bss:  10.881  0.094  0.323 87.156  0.050  2.053   1.3053e-01
   3_xyz:   8.266  0.068  0.298 86.152  0.042  2.127   6.5276e-02
   3_adp:   8.266  0.068  0.298 86.152  0.042  2.127   6.5276e-02
   3_occ:   8.266  0.068  0.298 86.152  0.042  2.127   6.5276e-02
   4_bss:   8.266  0.068  0.298 86.152  0.042  2.127   6.5276e-02
   4_xyz:   7.977  0.082  0.312 85.156  0.044  2.157   6.7398e-02
   4_adp:   7.977  0.082  0.312 85.156  0.044  2.157   6.7398e-02
   4_occ:   7.977  0.082  0.312 85.156  0.044  2.157   6.7398e-02
   5_bss:   7.977  0.082  0.312 85.156  0.044  2.157   6.7398e-02
   5_xyz:   8.208  0.053  0.387 83.731  0.052  2.149   5.6715e-02
   5_adp:   8.208  0.053  0.387 83.731  0.052  2.149   5.6715e-02
   5_occ:   8.208  0.053  0.387 83.731  0.052  2.149   5.6715e-02
   5_bss:   8.208  0.053  0.387 83.731  0.052  2.149   5.6715e-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: 130.62   0.00  20.95  98.36   0.00  19.41 130.62   0.00  29.34
   1_occ: 130.62   0.00  20.95  98.36   0.00  19.41 130.62   0.00  29.34
   2_bss: 130.62   0.00  20.95  98.36   0.00  19.41 130.62   0.00  29.34
   2_xyz: 130.62   0.00  20.95  98.36   0.00  19.41 130.62   0.00  29.34
   2_adp: 133.33   0.00  19.31  86.98   0.00  16.99 133.33   0.00  31.96
   2_occ: 133.33   0.00  19.31  86.98   0.00  16.99 133.33   0.00  31.96
   3_bss: 133.33   0.00  19.31  86.98   0.00  16.99 133.33   0.00  31.96
   3_xyz: 133.33   0.00  19.31  86.98   0.00  16.99 133.33   0.00  31.96
   3_adp: 108.76   0.00  17.73  78.80   0.00  14.80 108.76   0.00  33.68
   3_occ: 108.76   0.00  17.73  78.80   0.00  14.80 108.76   0.00  33.68
   4_bss: 108.76   0.00  17.73  78.80   0.00  14.80 108.76   0.00  33.68
   4_xyz: 108.76   0.00  17.73  78.80   0.00  14.80 108.76   0.00  33.68
   4_adp: 105.49   0.00  18.88 102.13   0.00  13.85 105.49   3.77  46.30
   4_occ: 105.49   0.00  18.88 102.13   0.00  13.85 105.49   3.77  46.30
   5_bss: 105.49   0.00  18.88 102.13   0.00  13.85 105.49   3.77  46.30
   5_xyz: 105.49   0.00  18.88 102.13   0.00  13.85 105.49   3.77  46.30
   5_adp: 106.88   0.00  18.55 102.81   0.00  13.45 106.88   5.37  46.32
   5_occ: 106.88   0.00  18.55 102.81   0.00  13.45 106.88   5.37  46.32
   5_bss: 106.88   0.00  18.55 102.82   0.00  13.45 106.88   5.37  46.33
------------------------------------------------------------------------
 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:    1.326    0.033    0.420
   1_adp:    1.326    0.033    0.420
   1_occ:    1.326    0.033    0.420
   2_bss:    1.326    0.033    0.420
   2_xyz:    1.973    0.040    0.649
   2_adp:    1.973    0.040    0.649
   2_occ:    1.973    0.040    0.649
   3_bss:    1.973    0.040    0.649
   3_xyz:    2.006    0.052    0.779
   3_adp:    2.006    0.052    0.779
   3_occ:    2.006    0.052    0.779
   4_bss:    2.006    0.052    0.779
   4_xyz:    2.231    0.055    0.939
   4_adp:    2.231    0.055    0.939
   4_occ:    2.231    0.055    0.939
   5_bss:    2.231    0.055    0.939
   5_xyz:    2.325    0.050    0.988
   5_adp:    2.325    0.050    0.988
   5_occ:    2.325    0.050    0.988
   5_bss:    2.325    0.050    0.988
------------------------------------------------------------------------

CPU time actual refinement: 377.61


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_109/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_109/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_109/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_109/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_109/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 377.45 
  Macro-tasks:
    bulk solvent and scale       = 42.49  
    individual site refinement   = 167.65 
    weights calculation          = 32.50  
    collect and process          = 6.16   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 248.91 
  Micro-tasks:
    mask                            = 3.20   
    f_calc                          = 122.81 
    alpha_beta                      = 8.28   
    target                          = 1.13   
    gradients_wrt_atomic_parameters = 135.03 
    fmodel                         = 7.28   
    r_factors                      = 0.22   
    phase_errors                   = 9.34   
    foms                           = 0.33   
    TOTAL for micro-tasks          = 287.62 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 5.281 micro seconds
Total CPU time: 6.52 minutes
from_scatterers_fft:    641 calls, 122.42 s
gradients_fft:          585 calls, 121.94 s

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

# Date 2008-01-16 Time 00:46:14 PST -0800 (1200473174.41 s)
Start R-work = 0.5322, R-free = 0.5338 (no bulk solvent and anisotropic scale)
Final R-work = 0.1646, R-free = 0.2161 (no bulk solvent and anisotropic scale)

Start R-work = 0.5260, R-free = 0.5310
Final R-work = 0.1433, R-free = 0.1993