# Date 2008-01-16 Time 01:03:41 PST -0800 (1200474221.55 s)
#phil __OFF__

Command line arguments: "../263.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 18692
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 263

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.1963, 45.9914, 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: 3.26, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 45.9914, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9247 1.96247
Completeness in resolution range: 0.942096
Completeness with d_max=infinity: 0.93925

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9247
                             d_min =   1.9625

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 45.9914, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9247 1.96247
Completeness in resolution range: 0.942096
Completeness with d_max=infinity: 0.93925

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9251 -  4.1996 [2187/2211]  1965   222  10.2%
  bin  2:  4.1996 -  3.3457 [2099/2119]  1891   208   9.9%
  bin  3:  3.3457 -  2.9264 [2080/2099]  1877   203   9.8%
  bin  4:  2.9264 -  2.6605 [2034/2064]  1820   214  10.5%
  bin  5:  2.6605 -  2.4707 [2045/2064]  1841   204  10.0%
  bin  6:  2.4707 -  2.3256 [2039/2064]  1837   202   9.9%
  bin  7:  2.3256 -  2.2095 [2018/2046]  1819   199   9.9%
  bin  8:  2.2095 -  2.1136 [2007/2043]  1808   199   9.9%
  bin  9:  2.1136 -  2.0324 [1979/2049]  1787   192   9.7%
  bin 10:  2.0324 -  1.9625 [1101/2034]   985   116  10.5%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_263/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:
        0.95 -     1.74: 7
        1.74 -     2.53: 71
        2.53 -     3.32: 3906
        3.32 -     4.11: 9483
        4.11 -     4.90: 15095
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OE1 GLN A  55 " - " O   HOH Z 403 "  0.949 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.485 3.040 -x+1,y+1/2,-z+1/2
  " NH1 ARG A  24 " - " O   GLY A  91 "  1.506 3.120 -x+1,y+1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.589 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  53 " - " O   HOH Z 102 "  1.616 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28557 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_263/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_263/model_refine_001.geo

CPU time processing inputs: 9.14


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.19625 45.9914 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: 1.96 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5195   r_free= 0.5114   ksol= 0.00   Bsol= 0.00   scale= 0.767    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.97 A                  |
| x-ray target function (ml) for work reflections: 6.311908                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9251 -  4.6841 0.99   1421  154 0.4351 0.4229      6.6618      6.6496|
|  2:  4.6841 -  3.7372 0.99   1367  155 0.4603 0.4710      6.8594      6.8916|
|  3:  3.7372 -  3.2704 0.99   1332  150 0.5014 0.4430      6.7413      6.7244|
|  4:  3.2704 -  2.9740 0.99   1329  148 0.5258 0.5122       6.572      6.5266|
|  5:  2.9740 -  2.7623 0.99   1327  144 0.5482 0.5025      6.3861      6.4434|
|  6:  2.7623 -  2.6003 0.99   1324  150 0.5506 0.5681      6.3086      6.2203|
|  7:  2.6003 -  2.4707 0.99   1294  150 0.5477 0.5196      6.2483      6.1589|
|  8:  2.4707 -  2.3636 0.98   1318  143 0.5673 0.5400      6.1958      6.2313|
|  9:  2.3636 -  2.2729 0.98   1293  138 0.5417 0.5735       6.124      6.2131|
| 10:  2.2729 -  2.1947 1.00   1309  145 0.5519 0.5906      6.1159      6.1105|
| 11:  2.1947 -  2.1263 0.98   1281  147 0.5449 0.5354      6.0258      6.0523|
| 12:  2.1263 -  2.0657 0.98   1297  140 0.5471 0.5357      5.9744      5.9747|
| 13:  2.0657 -  2.0114 0.90   1186  129 0.5479 0.5307      5.8995      5.8396|
| 14:  2.0114 -  1.9625 0.43    552   66 0.5478 0.5314      5.8969      5.7944|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9251 -  4.6841  1421   154  0.64  39.67   0.77     0.70      94105.14|
|  2:  4.6841 -  3.7372  1367   155  0.62  42.07   0.84     0.71     142377.85|
|  3:  3.7372 -  3.2704  1332   150  0.48  53.20   0.81     0.62     150586.71|
|  4:  3.2704 -  2.9740  1329   148  0.36  62.54   0.75     0.47     135201.86|
|  5:  2.9740 -  2.7623  1327   144  0.26  70.66   0.70     0.33     102953.46|
|  6:  2.7623 -  2.6003  1324   150  0.21  74.15   0.70     0.26      89380.02|
|  7:  2.6003 -  2.4707  1294   150  0.16  77.78   0.71     0.19      79091.30|
|  8:  2.4707 -  2.3636  1318   143  0.17  77.38   0.71     0.21      71597.18|
|  9:  2.3636 -  2.2729  1293   138  0.16  78.18   0.71     0.19      65598.90|
| 10:  2.2729 -  2.1947  1309   145  0.16  78.05   0.73     0.19      58347.63|
| 11:  2.1947 -  2.1263  1281   147  0.11  81.60   0.74     0.15      58017.60|
| 12:  2.1263 -  2.0657  1297   140  0.13  80.41   0.73     0.17      51375.43|
| 13:  2.0657 -  2.0114  1186   129  0.20  75.40   0.71     0.26      42733.28|
| 14:  2.0114 -  1.9625   552    66  0.37  62.46   0.73     0.41      29745.35|
|alpha:            min =        0.15 max =            0.71 mean =         0.35|
|beta:             min =    29745.35 max =       150586.71 mean =     86757.70|
|figures of merit: min =        0.00 max =            1.00 mean =         0.29|
|phase err.(work): min =        0.00 max =           90.00 mean =        67.97|
|phase err.(test): min =        0.00 max =           89.98 mean =        68.21|
|-----------------------------------------------------------------------------|

============================== 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 = 30.297025             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 85.819   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.843934              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.939   (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 |  0.994 -  1.384:        6 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.384 -  1.775:       14 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.775 -  2.166:       99 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.166 -  2.556:      512 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.556 -  2.947:     1326 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.947 -  3.337:     2442 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.337 -  3.728:     3990 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.728 -  4.119:     5243 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.119 -  4.509:     6789 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.509 -  4.900:     8179 |
|-----------------------------------------------------------------------------|
|-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 |       53.362 |
| 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  0.994 |       2.564 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.619)------------------------------------------|
|    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 = 11.619)------------------------------------------|
|    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: 1.96 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5239   r_free= 0.5143   ksol= 0.00   Bsol= 0.00   scale= 0.737    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.95 A                  |
| x-ray target function (ml) for work reflections: 6.311988                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5110   r_free= 0.5035   ksol= 0.34   Bsol= 0.00   scale= 0.940    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.49,7.59,9.97,0.00,0.00,0.00); trace/3= 7.68                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.96 A                  |
| x-ray target function (ml) for work reflections: 6.306984                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 21.889532             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 86.785   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.140856              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.671   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.5110      final r-factor (work) = 0.4568          |
| start r-factor (free) = 0.5035      final r-factor (free) = 0.4813          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 122.3767 = 21.89 * 0.50 * 6.3057 + 1.00 * 53.3623                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 68.7403 = 21.89 * 0.50 * 6.2658 + 1.00 * 0.1628                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4568      final r-factor (work) = 0.4200          |
| start r-factor (free) = 0.4813      final r-factor (free) = 0.4785          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.4286 = 2.14 * 1.00 * 6.2658 + 1.00 * 0.0144                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.3501 = 2.14 * 1.00 * 6.2254 + 1.00 * 0.0224                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.619)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.31   17.11    None  None   None       |
|    all(noH): 2823   0      0.00    89.31   17.11    None  None   None       |
|    Sol.    : 438    0      0.00    89.31   23.26    None  None   None       |
|    Mac.    : 2385   0      0.00    79.24   15.98    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.931:  879   |   5:    44.656 -  53.587:   64        |
|      1:     8.931 -  17.862:  833   |   6:    53.587 -  62.518:   33        |
|      2:    17.862 -  26.794:  544   |   7:    62.518 -  71.449:    7        |
|      3:    26.794 -  35.725:  292   |   8:    71.449 -  80.381:    5        |
|      4:    35.725 -  44.656:  162   |   9:    80.381 -  89.312:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.4200 r_free = 0.4785             target_work(ml) = 6.220         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.4194 r_free = 0.4793             target_work(ml) = 6.220         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4194   r_free= 0.4793   ksol= 0.34   Bsol= 0.00   scale= 1.099    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.49,7.59,9.97,0.00,0.00,0.00); trace/3= 7.68                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.79 A                  |
| x-ray target function (ml) for work reflections: 6.219717                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4187   r_free= 0.4795   ksol= 0.37   Bsol= 50.00   scale= 1.029   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.14,4.53,6.93,0.00,0.00,0.00); trace/3= 4.87                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.79 A                  |
| x-ray target function (ml) for work reflections: 6.222213                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 23.187636             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.130  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.973001              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 138.314  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4187      final r-factor (work) = 0.3508          |
| start r-factor (free) = 0.4795      final r-factor (free) = 0.4274          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 72.3223 = 23.19 * 0.50 * 6.2240 + 1.00 * 0.1628                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 71.6046 = 23.19 * 0.50 * 6.1635 + 1.00 * 0.1458                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3508      final r-factor (work) = 0.3250          |
| start r-factor (free) = 0.4274      final r-factor (free) = 0.4083          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.0195 = 0.97 * 1.00 * 6.1635 + 1.00 * 0.0224                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.9236 = 0.97 * 1.00 * 6.0710 + 1.00 * 0.0165                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.619)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.87   16.17    None  None   None       |
|    all(noH): 2823   0      0.00    76.87   16.17    None  None   None       |
|    Sol.    : 438    0      0.00    76.87   28.91    None  None   None       |
|    Mac.    : 2385   0      0.00    62.30   13.83    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.687:  771   |   5:    38.434 -  46.121:   82        |
|      1:     7.687 -  15.374:  818   |   6:    46.121 -  53.808:   48        |
|      2:    15.374 -  23.061:  584   |   7:    53.808 -  61.495:   14        |
|      3:    23.061 -  30.747:  317   |   8:    61.495 -  69.182:   12        |
|      4:    30.747 -  38.434:  169   |   9:    69.182 -  76.869:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3250 r_free = 0.4083             target_work(ml) = 6.051         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3247 r_free = 0.4079             target_work(ml) = 6.051         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3247   r_free= 0.4079   ksol= 0.37   Bsol= 50.00   scale= 1.080   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.14,4.53,6.93,0.00,0.00,0.00); trace/3= 4.87                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.050801                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3233   r_free= 0.4072   ksol= 0.34   Bsol= 50.00   scale= 1.026   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.44,2.38,4.36,0.00,0.00,0.00); trace/3= 2.73                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.050268                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.120962             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.115  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.447421              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 110.535  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3233      final r-factor (work) = 0.2561          |
| start r-factor (free) = 0.4072      final r-factor (free) = 0.3265          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 33.8973 = 11.12 * 0.50 * 6.0699 + 1.00 * 0.1458                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 33.3425 = 11.12 * 0.50 * 5.9769 + 1.00 * 0.1080                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2561      final r-factor (work) = 0.2291          |
| start r-factor (free) = 0.3265      final r-factor (free) = 0.3003          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6898 = 0.45 * 1.00 * 5.9769 + 1.00 * 0.0155                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6107 = 0.45 * 1.00 * 5.8115 + 1.00 * 0.0105                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.619)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.70   15.47    None  None   None       |
|    all(noH): 2823   0      0.00    79.70   15.47    None  None   None       |
|    Sol.    : 438    0      0.77    79.70   35.71    None  None   None       |
|    Mac.    : 2385   0      0.00    67.30   11.75    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.970:  982   |   5:    39.851 -  47.821:  113        |
|      1:     7.970 -  15.941:  934   |   6:    47.821 -  55.792:   58        |
|      2:    15.941 -  23.911:  348   |   7:    55.792 -  63.762:   24        |
|      3:    23.911 -  31.881:  198   |   8:    63.762 -  71.732:   10        |
|      4:    31.881 -  39.851:  150   |   9:    71.732 -  79.702:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2291 r_free = 0.3003             target_work(ml) = 5.764         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2286 r_free = 0.2997             target_work(ml) = 5.762         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2286   r_free= 0.2997   ksol= 0.34   Bsol= 50.00   scale= 1.056   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.44,2.38,4.36,0.00,0.00,0.00); trace/3= 2.73                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.762052                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2270   r_free= 0.2975   ksol= 0.33   Bsol= 50.00   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.09,0.59,2.72,0.00,0.00,0.00); trace/3= 1.07                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.759158                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.072256              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.628   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.366288              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 137.584  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2270      final r-factor (work) = 0.1720          |
| start r-factor (free) = 0.2975      final r-factor (free) = 0.2305          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.7620 = 6.07 * 0.50 * 5.8147 + 1.00 * 0.1078                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.2429 = 6.07 * 0.50 * 5.6515 + 1.00 * 0.0843                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1720      final r-factor (work) = 0.1606          |
| start r-factor (free) = 0.2305      final r-factor (free) = 0.2193          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0806 = 0.37 * 1.00 * 5.6515 + 1.00 * 0.0105                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3620 = 0.37 * 1.00 * 5.4821 + 1.00 * 0.3539                               |
|-----------------------------------------------------------------------------|
| number of iterations = 11      |    number of function evaluations = 15     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.619)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.58   15.14    None  None   None       |
|    all(noH): 2823   0      0.00    80.58   15.14    None  None   None       |
|    Sol.    : 438    0      2.61    80.58   37.17    None  None   None       |
|    Mac.    : 2385   0      0.00    68.17   11.10    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.058: 1061   |   5:    40.291 -  48.350:  120        |
|      1:     8.058 -  16.117:  943   |   6:    48.350 -  56.408:   65        |
|      2:    16.117 -  24.175:  292   |   7:    56.408 -  64.466:   22        |
|      3:    24.175 -  32.233:  157   |   8:    64.466 -  72.524:   10        |
|      4:    32.233 -  40.291:  147   |   9:    72.524 -  80.582:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1606 r_free = 0.2193             target_work(ml) = 5.459         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1603 r_free = 0.2186             target_work(ml) = 5.457         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1603   r_free= 0.2186   ksol= 0.33   Bsol= 50.00   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.09,0.59,2.72,0.00,0.00,0.00); trace/3= 1.07                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.457106                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1603   r_free= 0.2184   ksol= 0.31   Bsol= 47.27   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.63,-0.15,2.12,-0.00,0.00,0.00); trace/3= 0.45                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.456906                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.070212              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 116.335  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 6.501581              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.279   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1603      final r-factor (work) = 0.1474          |
| start r-factor (free) = 0.2184      final r-factor (free) = 0.1970          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7607 = 2.07 * 0.50 * 5.4838 + 1.00 * 0.0844                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6713 = 2.07 * 0.50 * 5.4260 + 1.00 * 0.0549                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1474      final r-factor (work) = 0.1395          |
| start r-factor (free) = 0.1970      final r-factor (free) = 0.1910          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 35.4958 = 6.50 * 1.00 * 5.4260 + 1.00 * 0.2184                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 34.7810 = 6.50 * 1.00 * 5.3473 + 1.00 * 0.0154                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.619)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.66   16.42    None  None   None       |
|    all(noH): 2823   0      0.00    98.66   16.42    None  None   None       |
|    Sol.    : 438    0      3.79    98.66   45.33    None  None   None       |
|    Mac.    : 2385   0      0.00    89.23   11.11    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.866: 1453   |   5:    49.329 -  59.194:   83        |
|      1:     9.866 -  19.732:  736   |   6:    59.194 -  69.060:   77        |
|      2:    19.732 -  29.597:  192   |   7:    69.060 -  78.926:   38        |
|      3:    29.597 -  39.463:  112   |   8:    78.926 -  88.792:   23        |
|      4:    39.463 -  49.329:  102   |   9:    88.792 -  98.657:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1395 r_free = 0.1910             target_work(ml) = 5.331         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1394 r_free = 0.1909             target_work(ml) = 5.331         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1394   r_free= 0.1909   ksol= 0.31   Bsol= 47.27   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.63,-0.15,2.12,-0.00,0.00,0.00); trace/3= 0.45                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.330817                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9251 -  4.6841 0.99   1421  154 0.1067 0.1365      5.4661      5.6242|
|  2:  4.6841 -  3.7372 0.99   1367  155 0.0991 0.1331      5.5788      5.8108|
|  3:  3.7372 -  3.2704 0.99   1332  150 0.1333 0.1823      5.6744      5.9895|
|  4:  3.2704 -  2.9740 0.99   1329  148 0.1598 0.2129      5.6695      5.8239|
|  5:  2.9740 -  2.7623 0.99   1327  144 0.1706 0.2008      5.5651      5.7337|
|  6:  2.7623 -  2.6003 0.99   1324  150 0.1597 0.2605      5.4145      5.7183|
|  7:  2.6003 -  2.4707 0.99   1294  150 0.1637 0.2002      5.3759      5.5019|
|  8:  2.4707 -  2.3636 0.98   1318  143 0.1560 0.1990      5.2868      5.5193|
|  9:  2.3636 -  2.2729 0.98   1293  138 0.1528 0.2160      5.2292      5.4976|
| 10:  2.2729 -  2.1947 1.00   1309  145 0.1419 0.1956      5.1388      5.3008|
| 11:  2.1947 -  2.1263 0.98   1281  147 0.1405 0.2276      5.1152      5.4554|
| 12:  2.1263 -  2.0657 0.98   1297  140 0.1436 0.2169      5.0562       5.431|
| 13:  2.0657 -  2.0114 0.90   1186  129 0.1238 0.1818      4.8917      5.0553|
| 14:  2.0114 -  1.9625 0.43    552   66 0.1083 0.1827      4.7421      5.0175|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9251 -  4.6841  1421   154  0.93  10.73   0.97     0.94       8976.71|
|  2:  4.6841 -  3.7372  1367   155  0.94  10.07   1.03     1.01      12153.52|
|  3:  3.7372 -  3.2704  1332   150  0.90  15.13   1.05     1.05      15620.74|
|  4:  3.2704 -  2.9740  1329   148  0.88  18.18   1.03     1.00      15739.31|
|  5:  2.9740 -  2.7623  1327   144  0.85  21.18   1.00     0.98      14309.90|
|  6:  2.7623 -  2.6003  1324   150  0.86  20.75   0.98     0.92      10378.36|
|  7:  2.6003 -  2.4707  1294   150  0.86  20.97   1.00     0.96       9720.39|
|  8:  2.4707 -  2.3636  1318   143  0.87  19.87   1.01     0.96       8075.84|
|  9:  2.3636 -  2.2729  1293   138  0.87  19.70   1.00     0.95       7297.83|
| 10:  2.2729 -  2.1947  1309   145  0.87  19.07   1.00     0.95       6178.81|
| 11:  2.1947 -  2.1263  1281   147  0.86  20.39   1.00     0.95       6504.00|
| 12:  2.1263 -  2.0657  1297   140  0.87  19.97   1.00     0.98       5698.37|
| 13:  2.0657 -  2.0114  1186   129  0.88  19.06   0.98     0.94       4250.25|
| 14:  2.0114 -  1.9625   552    66  0.92  14.24   0.99     0.96       2970.62|
|alpha:            min =        0.92 max =            1.05 mean =         0.97|
|beta:             min =     2970.62 max =        15739.31 mean =      9470.99|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.77 mean =        17.88|
|phase err.(test): min =        0.00 max =           89.67 mean =        17.14|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1394   r_free= 0.1909   ksol= 0.32   Bsol= 55.33   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.05,-0.66,1.71,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.330697                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1394   r_free= 0.1909   ksol= 0.32   Bsol= 55.33   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.05,-0.66,1.71,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.330697                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9251 -  4.6841 0.99   1421  154 0.1066 0.1365      5.4651       5.627|
|  2:  4.6841 -  3.7372 0.99   1367  155 0.0996 0.1342       5.582      5.8177|
|  3:  3.7372 -  3.2704 0.99   1332  150 0.1338 0.1827      5.6773      5.9919|
|  4:  3.2704 -  2.9740 0.99   1329  148 0.1596 0.2128      5.6692       5.823|
|  5:  2.9740 -  2.7623 0.99   1327  144 0.1705 0.2004      5.5641      5.7316|
|  6:  2.7623 -  2.6003 0.99   1324  150 0.1595 0.2599      5.4132      5.7166|
|  7:  2.6003 -  2.4707 0.99   1294  150 0.1636 0.2005       5.375      5.5026|
|  8:  2.4707 -  2.3636 0.98   1318  143 0.1559 0.1987      5.2861      5.5178|
|  9:  2.3636 -  2.2729 0.98   1293  138 0.1527 0.2156      5.2288      5.4972|
| 10:  2.2729 -  2.1947 1.00   1309  145 0.1417 0.1956      5.1379       5.301|
| 11:  2.1947 -  2.1263 0.98   1281  147 0.1404 0.2276      5.1149      5.4553|
| 12:  2.1263 -  2.0657 0.98   1297  140 0.1434 0.2169      5.0559      5.4318|
| 13:  2.0657 -  2.0114 0.90   1186  129 0.1237 0.1815      4.8912      5.0538|
| 14:  2.0114 -  1.9625 0.43    552   66 0.1084 0.1823      4.7411       5.017|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9251 -  4.6841  1421   154  0.93  10.74   0.97     0.94       8997.83|
|  2:  4.6841 -  3.7372  1367   155  0.94  10.12   1.03     1.01      12232.85|
|  3:  3.7372 -  3.2704  1332   150  0.90  15.22   1.05     1.05      15753.72|
|  4:  3.2704 -  2.9740  1329   148  0.88  18.20   1.03     1.00      15777.28|
|  5:  2.9740 -  2.7623  1327   144  0.85  21.16   1.01     0.98      14272.59|
|  6:  2.7623 -  2.6003  1324   150  0.86  20.71   0.98     0.92      10346.63|
|  7:  2.6003 -  2.4707  1294   150  0.86  20.95   1.00     0.97       9702.32|
|  8:  2.4707 -  2.3636  1318   143  0.87  19.86   1.01     0.96       8065.08|
|  9:  2.3636 -  2.2729  1293   138  0.87  19.70   1.00     0.95       7290.94|
| 10:  2.2729 -  2.1947  1309   145  0.87  19.05   1.00     0.96       6175.14|
| 11:  2.1947 -  2.1263  1281   147  0.86  20.39   1.01     0.95       6501.37|
| 12:  2.1263 -  2.0657  1297   140  0.87  19.97   1.00     0.99       5699.48|
| 13:  2.0657 -  2.0114  1186   129  0.88  19.05   0.99     0.94       4244.35|
| 14:  2.0114 -  1.9625   552    66  0.92  14.20   0.99     0.96       2960.54|
|alpha:            min =        0.92 max =            1.05 mean =         0.97|
|beta:             min =     2960.54 max =        15777.28 mean =      9482.83|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.82 mean =        17.88|
|phase err.(test): min =        0.00 max =           89.38 mean =        17.14|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.619)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.52    99.17   16.93    None  None   None       |
|    all(noH): 2823   0      0.52    99.17   16.93    None  None   None       |
|    Sol.    : 438    0      4.31    99.17   45.84    None  None   None       |
|    Mac.    : 2385   0      0.52    89.75   11.62    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:     0.516 -  10.382: 1453   |   5:    49.845 -  59.711:   83        |
|      1:    10.382 -  20.248:  736   |   6:    59.711 -  69.577:   77        |
|      2:    20.248 -  30.114:  192   |   7:    69.577 -  79.442:   38        |
|      3:    30.114 -  39.979:  112   |   8:    79.442 -  89.308:   23        |
|      4:    39.979 -  49.845:  102   |   9:    89.308 -  99.174:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 330         
Filter by distance & map next to the model:
   mapped sites are within: 0.224 - 5.260
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 323 from: 330
   mapped sites are within: 0.767 - 5.260

peak=    8.939 closest distance to " CB  VAL A 230 " =    1.444
peak=    7.950 closest distance to " CB  VAL A 296 " =    1.534
peak=    7.592 closest distance to " O   HOH Z 103 " =    1.252
peak=    7.345 closest distance to " O   HOH Z 130 " =    1.988
peak=    6.812 closest distance to " O   ALA A 114 " =    0.900
peak=    6.623 closest distance to " O  BHOH Z  74 " =    1.035
peak=    6.498 closest distance to " CD2 LEU A   5 " =    1.415
peak=    5.841 closest distance to " O   HOH Z 246 " =    1.767
peak=    5.779 closest distance to " O   HOH Z 385 " =    1.284
peak=    5.730 closest distance to " O   HOH Z 105 " =    1.405
peak=    5.623 closest distance to " O   HOH Z 375 " =    1.507
peak=    5.569 closest distance to " O   HOH Z 258 " =    1.299
peak=    5.315 closest distance to " O   HOH Z 425 " =    1.504
peak=    5.274 closest distance to " CB  VAL A 230 " =    1.208
peak=    5.205 closest distance to " O   HOH Z 222 " =    1.470
peak=    5.123 closest distance to " O   HOH Z   7 " =    2.108
peak=    5.074 closest distance to " O   HOH Z 427 " =    2.218
peak=    5.065 closest distance to " O   HOH Z 124 " =    1.639
peak=    5.027 closest distance to " OD1 ASN A  69 " =    1.083
peak=    4.945 closest distance to " CB  ALA A 114 " =    0.977
peak=    4.941 closest distance to " O   HOH Z  83 " =    1.290
peak=    4.932 closest distance to " CG  PRO A  54 " =    1.540
peak=    4.918 closest distance to " CD1AILE A 234 " =    0.930
peak=    4.910 closest distance to " O   HOH Z 236 " =    1.604
peak=    4.891 closest distance to " O   HOH Z  65 " =    1.970
peak=    4.883 closest distance to " C   GLN A  73 " =    1.070
peak=    4.837 closest distance to " NE2 GLN A  11 " =    1.171
peak=    4.835 closest distance to " O   HOH Z 350 " =    1.434
peak=    4.662 closest distance to " O   HOH Z 255 " =    0.882
peak=    4.655 closest distance to " O   HOH Z  69 " =    1.736
peak=    4.643 closest distance to " O   HOH Z  66 " =    1.067
peak=    4.640 closest distance to " O   PRO A 198 " =    1.471
peak=    4.631 closest distance to " CG  GLN A  58 " =    1.273
peak=    4.624 closest distance to " NH2AARG A 145 " =    1.225
peak=    4.592 closest distance to " O   HOH Z 406 " =    1.727
peak=    4.565 closest distance to " O   HOH Z 112 " =    1.335
peak=    4.552 closest distance to " O   HOH Z 369 " =    2.248
peak=    4.519 closest distance to " O   HOH Z  59 " =    1.942
peak=    4.503 closest distance to " O   HOH Z 417 " =    2.294
peak=    4.503 closest distance to " O   HOH Z 287 " =    1.876
peak=    4.497 closest distance to " O   HOH Z 422 " =    1.017
peak=    4.453 closest distance to " CG2 VAL A 257 " =    0.929
peak=    4.443 closest distance to " O   HOH Z  46 " =    1.161
peak=    4.417 closest distance to " O   HOH Z 263 " =    1.522
peak=    4.405 closest distance to " CB  GLN A 223 " =    1.563
peak=    4.402 closest distance to " O   HOH Z 330 " =    1.152
peak=    4.400 closest distance to " CG2 ILE A 234 " =    0.947
peak=    4.388 closest distance to " O   HOH Z 127 " =    1.101
peak=    4.380 closest distance to " O   HOH Z 414 " =    1.575
peak=    4.374 closest distance to " O   HOH Z 142 " =    1.718
peak=    4.354 closest distance to " O   HOH Z 368 " =    1.477
peak=    4.346 closest distance to " CB  ASN A 142 " =    0.996
peak=    4.340 closest distance to " O   HOH Z 123 " =    1.778
peak=    4.328 closest distance to " CG  PRO A 243 " =    1.097
peak=    4.328 closest distance to " O   HOH Z 423 " =    1.814
peak=    4.327 closest distance to " O   HOH Z  39 " =    1.716
peak=    4.304 closest distance to " O   HOH Z 331 " =    1.286
peak=    4.304 closest distance to " CB  SER A 216 " =    1.070
peak=    4.301 closest distance to " CG AARG A 275 " =    1.306
peak=    4.291 closest distance to " CB  ARG A 275 " =    1.178
peak=    4.278 closest distance to " O   HOH Z 177 " =    1.178
peak=    4.263 closest distance to " O   HOH Z 245 " =    1.047
peak=    4.259 closest distance to " C   VAL A  72 " =    0.896
peak=    4.252 closest distance to " O   HOH Z 249 " =    1.350
peak=    4.235 closest distance to " O   HOH Z   9 " =    2.576
peak=    4.209 closest distance to " O   HOH Z 365 " =    3.024
peak=    4.158 closest distance to " O   HOH Z 344 " =    1.349
peak=    4.133 closest distance to " CB  SER A 276 " =    1.145
peak=    4.104 closest distance to " CB  PRO A  54 " =    1.042
peak=    4.104 closest distance to " CA  ALA A 129 " =    1.226
peak=    4.103 closest distance to " CB  VAL A 265 " =    1.202
peak=    4.099 closest distance to " NZ  LYS A 117 " =    3.094
peak=    4.080 closest distance to " O   HOH Z 303 " =    2.029
peak=    4.078 closest distance to " CB  ARG A  79 " =    0.840
peak=    4.072 closest distance to " O   HOH Z 126 " =    1.748
peak=    4.064 closest distance to " CG  LYS A  76 " =    1.687
peak=    4.051 closest distance to " CB  ASN A 110 " =    1.146
peak=    4.038 closest distance to " O   HOH Z 211 " =    1.392
peak=    4.029 closest distance to " O   HOH Z 422 " =    2.305
peak=    4.024 closest distance to " O   HOH Z 392 " =    1.060
peak=    4.018 closest distance to " O   HOH Z 143 " =    1.673
peak=    4.015 closest distance to " O   HOH Z 147 " =    1.398
peak=    4.014 closest distance to " O   HOH Z 238 " =    1.440
peak=    4.007 closest distance to " CD2 TRP A 179 " =    1.391
peak=    4.006 closest distance to " O   HOH Z 298 " =    1.592
peak=    3.994 closest distance to " O   HOH Z 232 " =    2.186
peak=    3.981 closest distance to " CH2 TRP A 266 " =    1.161
peak=    3.957 closest distance to " O   HOH Z  24 " =    1.778
peak=    3.956 closest distance to " O   HOH Z 193 " =    2.047
peak=    3.952 closest distance to " O   HOH Z  66 " =    2.325
peak=    3.940 closest distance to " CG  PRO A 198 " =    1.319
peak=    3.933 closest distance to " O   HOH Z  80 " =    1.663
peak=    3.933 closest distance to " O   HOH Z   4 " =    2.207
peak=    3.933 closest distance to " O   HOH Z  63 " =    1.394
peak=    3.924 closest distance to " ND2BASN A 224 " =    0.909
peak=    3.921 closest distance to " O   HOH Z 425 " =    2.021
peak=    3.920 closest distance to " O   HOH Z  78 " =    1.804
peak=    3.919 closest distance to " O   HOH Z 427 " =    1.206
peak=    3.918 closest distance to " CA  PHE A 283 " =    1.228
peak=    3.917 closest distance to " CB  SER A  63 " =    1.334
peak=    3.895 closest distance to " O   HOH Z 199 " =    1.141
peak=    3.880 closest distance to " CA  ILE A 234 " =    1.076
peak=    3.880 closest distance to " O   HOH Z 272 " =    1.859
peak=    3.868 closest distance to " CB  ALA A  43 " =    1.015
peak=    3.858 closest distance to " CG  LEU A 228 " =    1.214
peak=    3.844 closest distance to " CA  ARG A 195 " =    1.357
peak=    3.839 closest distance to " O   HOH Z  49 " =    1.414
peak=    3.837 closest distance to " CZ  PHE A  38 " =    1.136
peak=    3.832 closest distance to " O   HOH Z 388 " =    1.138
peak=    3.831 closest distance to " O   HOH Z 389 " =    1.922
peak=    3.830 closest distance to " O   HOH Z 403 " =    1.926
peak=    3.827 closest distance to " O   HOH Z 342 " =    0.912
peak=    3.799 closest distance to " O   HOH Z 216 " =    3.842
peak=    3.796 closest distance to " O   HOH Z  11 " =    1.026
peak=    3.792 closest distance to " O   HOH Z 148 " =    1.632
peak=    3.786 closest distance to " CG  GLN A  11 " =    2.182
peak=    3.783 closest distance to " O   HOH Z 368 " =    2.540
peak=    3.774 closest distance to " O   HOH Z 316 " =    3.032
peak=    3.772 closest distance to " CD2 LEU A 228 " =    1.261
peak=    3.765 closest distance to " NE1 TRP A 274 " =    0.951
peak=    3.759 closest distance to " O   HOH Z 213 " =    1.841
peak=    3.755 closest distance to " O   HOH Z 434 " =    1.561
peak=    3.748 closest distance to " CB  ASN A 148 " =    1.306
peak=    3.747 closest distance to " O   HOH Z  26 " =    1.651
peak=    3.747 closest distance to " N   ARG A 156 " =    1.216
peak=    3.738 closest distance to " O   HOH Z   1 " =    1.777
peak=    3.736 closest distance to " O   HOH Z 359 " =    1.497
peak=    3.735 closest distance to " O   HOH Z 139 " =    1.160
peak=    3.725 closest distance to " O   HOH Z  76 " =    1.437
peak=    3.721 closest distance to " O   HOH Z 130 " =    2.231
peak=    3.717 closest distance to " CB  SER A  62 " =    1.083
peak=    3.717 closest distance to " NH2AARG A 190 " =    1.905
peak=    3.714 closest distance to " CE3 TRP A 150 " =    1.142
peak=    3.707 closest distance to " NH2 ARG A  56 " =    2.032
peak=    3.707 closest distance to " CD  ARG A 159 " =    0.769
peak=    3.705 closest distance to " O   ARG A 275 " =    1.109
peak=    3.705 closest distance to " CB  ASN A 215 " =    1.226
peak=    3.701 closest distance to " O   HOH Z 411 " =    3.235
peak=    3.699 closest distance to " CG2 ILE A 120 " =    0.853
peak=    3.686 closest distance to " O  BHOH Z 338 " =    2.348
peak=    3.683 closest distance to " CB  ASN A  39 " =    0.918
peak=    3.670 closest distance to " O   HOH Z 203 " =    1.789
peak=    3.670 closest distance to " O   HOH Z 437 " =    2.237
peak=    3.655 closest distance to " N   TYR A  15 " =    1.200
peak=    3.649 closest distance to " O   HOH Z 284 " =    1.452
peak=    3.646 closest distance to " O   HOH Z 251 " =    1.714
peak=    3.645 closest distance to " OG  SER A  62 " =    2.936
peak=    3.644 closest distance to " CB  ALA A 292 " =    0.961
peak=    3.636 closest distance to " O   HOH Z 207 " =    1.036
peak=    3.635 closest distance to " NE2 GLN A  73 " =    1.642
peak=    3.631 closest distance to " O   HOH Z 132 " =    2.669
peak=    3.629 closest distance to " O   HOH Z 104 " =    1.839
peak=    3.626 closest distance to " O   HOH Z 153 " =    3.599
peak=    3.616 closest distance to " CG  ARG A 138 " =    1.284
peak=    3.613 closest distance to " O   HOH Z 293 " =    1.490
peak=    3.606 closest distance to " NE BARG A 275 " =    1.369
peak=    3.605 closest distance to " O   HOH Z 407 " =    1.505
peak=    3.602 closest distance to " CB  SER A   3 " =    1.353
peak=    3.598 closest distance to " O   HOH Z 180 " =    2.215
peak=    3.596 closest distance to " CB  THR A  31 " =    1.459
peak=    3.591 closest distance to " C   ASN A 209 " =    1.672
peak=    3.589 closest distance to " CB BVAL A  41 " =    0.968
peak=    3.572 closest distance to " O   HOH Z  51 " =    2.267
peak=    3.571 closest distance to " CB  TRP A 179 " =    1.372
peak=    3.568 closest distance to " CB  HIS A 108 " =    0.860
peak=    3.564 closest distance to " O   HOH Z 329 " =    4.241
peak=    3.560 closest distance to " CE2 PHE A  16 " =    0.875
peak=    3.556 closest distance to " O   HOH Z 371 " =    2.791
peak=    3.554 closest distance to " CG  LEU A 281 " =    1.003
peak=    3.538 closest distance to " N   PHE A 208 " =    0.871
peak=    3.537 closest distance to " O   HOH Z 158 " =    2.782
peak=    3.532 closest distance to " CB  THR A  52 " =    0.879
peak=    3.527 closest distance to " O   HOH Z 346 " =    1.529
peak=    3.523 closest distance to " CA  TYR A  30 " =    1.015
peak=    3.523 closest distance to " CB  LYS A 117 " =    1.211
peak=    3.519 closest distance to " CG  LEU A   5 " =    1.139
peak=    3.518 closest distance to " O   HOH Z 181 " =    1.372
peak=    3.512 closest distance to " CE3 TRP A 274 " =    1.211
peak=    3.508 closest distance to " O   HOH Z 296 " =    1.070
peak=    3.503 closest distance to " O   HOH Z  61 " =    1.453
peak=    3.503 closest distance to " CZ  PHE A 218 " =    1.090
peak=    3.496 closest distance to " OG  SER A 276 " =    0.999
peak=    3.489 closest distance to " O   HOH Z 380 " =    2.055
peak=    3.487 closest distance to " O   HOH Z 389 " =    2.356
peak=    3.485 closest distance to " CA  ALA A  51 " =    0.965
peak=    3.477 closest distance to " CB  GLU A 128 " =    0.985
peak=    3.472 closest distance to " ND2 ASN A 249 " =    0.853
peak=    3.467 closest distance to " CB  LEU A 300 " =    0.966
peak=    3.465 closest distance to " O   HOH Z  40 " =    1.515
peak=    3.464 closest distance to " N   PHE A 130 " =    1.279
peak=    3.457 closest distance to " CB  PHE A 204 " =    0.793
peak=    3.455 closest distance to " O   HOH Z  70 " =    1.090
peak=    3.453 closest distance to " O   HOH Z 424 " =    0.926
peak=    3.452 closest distance to " CG BARG A 102 " =    2.112
peak=    3.446 closest distance to " CE  LYS A  48 " =    1.159
peak=    3.444 closest distance to " O   HOH Z 145 " =    2.930
peak=    3.440 closest distance to " CG  LEU A 167 " =    1.247
peak=    3.421 closest distance to " O   HOH Z 132 " =    2.426
peak=    3.413 closest distance to " CG  ARG A 269 " =    1.820
peak=    3.412 closest distance to " NH1AARG A 102 " =    0.895
peak=    3.411 closest distance to " O   HOH Z 404 " =    1.502
peak=    3.405 closest distance to " CA  GLN A  58 " =    0.981
peak=    3.405 closest distance to " O   HOH Z 181 " =    2.397
peak=    3.404 closest distance to " O   HOH Z   6 " =    1.510
peak=    3.400 closest distance to " O   HOH Z 110 " =    0.944
peak=    3.396 closest distance to " O   PHE A 192 " =    1.260
peak=    3.389 closest distance to " CA  GLY A  57 " =    1.046
peak=    3.388 closest distance to " CA  ASN A 127 " =    1.108
peak=    3.377 closest distance to " O   HOH Z 150 " =    1.394
peak=    3.374 closest distance to " CB  MET A  47 " =    1.232
peak=    3.373 closest distance to " O   HOH Z 158 " =    1.040
peak=    3.373 closest distance to " CD1 ILE A 199 " =    1.466
peak=    3.372 closest distance to " CA  CYS A 260 " =    1.308
peak=    3.364 closest distance to " O   HOH Z  67 " =    1.101
peak=    3.357 closest distance to " O   HOH Z 402 " =    1.447
peak=    3.355 closest distance to " O   GLN A  55 " =    0.785
peak=    3.349 closest distance to " CB  ARG A 138 " =    0.849
peak=    3.347 closest distance to " CB  SER A 210 " =    0.923
peak=    3.344 closest distance to " O   HOH Z  61 " =    1.863
peak=    3.341 closest distance to " O   HOH Z  10 " =    1.705
peak=    3.333 closest distance to " OE1 GLN A  55 " =    1.461
peak=    3.332 closest distance to " CB  GLU A 277 " =    3.448
peak=    3.329 closest distance to " N   ASN A  74 " =    1.058
peak=    3.325 closest distance to " NZ  LYS A 289 " =    1.230
peak=    3.325 closest distance to " O   HOH Z  41 " =    2.389
peak=    3.324 closest distance to " O   HOH Z 362 " =    2.164
peak=    3.324 closest distance to " O   TYR A 116 " =    1.100
peak=    3.323 closest distance to " O   HOH Z  71 " =    1.943
peak=    3.313 closest distance to " CB  ASP A 124 " =    0.947
peak=    3.310 closest distance to " O   HOH Z 392 " =    1.646
peak=    3.309 closest distance to " O   HOH Z  55 " =    1.889
peak=    3.304 closest distance to " NE2 GLN A 103 " =    0.991
peak=    3.304 closest distance to " CA  ALA A 154 " =    1.217
peak=    3.300 closest distance to " CB  SER A 273 " =    0.896
peak=    3.296 closest distance to " O   HOH Z 389 " =    1.590
peak=    3.291 closest distance to " CE  LYS A  76 " =    0.914
peak=    3.283 closest distance to " O   HOH Z 343 " =    2.709
peak=    3.282 closest distance to " O   HOH Z  53 " =    2.237
peak=    3.282 closest distance to " CG1 VAL A 153 " =    0.868
peak=    3.278 closest distance to " CB  ALA A  10 " =    0.860
peak=    3.278 closest distance to " O   HOH Z 253 " =    2.084
peak=    3.278 closest distance to " N   PHE A  16 " =    1.503
peak=    3.272 closest distance to " O   HOH Z 410 " =    3.132
peak=    3.271 closest distance to " N   ASP A 162 " =    1.141
peak=    3.266 closest distance to " O   HOH Z 184 " =    1.763
peak=    3.266 closest distance to " CA  ALA A 184 " =    1.364
peak=    3.259 closest distance to " CB  VAL A 202 " =    1.625
peak=    3.255 closest distance to " CB  ASP A 107 " =    1.089
peak=    3.251 closest distance to " CD  LYS A 119 " =    1.813
peak=    3.250 closest distance to " CA  LEU A 282 " =    1.218
peak=    3.237 closest distance to " CB  ASP A 140 " =    1.119
peak=    3.234 closest distance to " O   GLY A 211 " =    1.067
peak=    3.233 closest distance to " O   ARG A 275 " =    1.503
peak=    3.230 closest distance to " CA  VAL A 125 " =    1.030
peak=    3.230 closest distance to " O   HIS A 115 " =    1.016
peak=    3.229 closest distance to " OG BSER A 212 " =    2.678
peak=    3.227 closest distance to " NH1AARG A 275 " =    0.908
peak=    3.227 closest distance to " CB  PHE A 130 " =    0.947
peak=    3.224 closest distance to " O   HOH Z 409 " =    5.260
peak=    3.223 closest distance to " ND1 HIS A  81 " =    1.475
peak=    3.223 closest distance to " CD1 LEU A   5 " =    1.490
peak=    3.223 closest distance to " CG  GLN A  89 " =    1.428
peak=    3.216 closest distance to " O   HOH Z 155 " =    1.837
peak=    3.215 closest distance to " OG BSER A 164 " =    2.340
peak=    3.215 closest distance to " CB  ASP A 191 " =    1.368
peak=    3.214 closest distance to " O   THR A 157 " =    1.489
peak=    3.214 closest distance to " OD1 ASN A 301 " =    1.540
peak=    3.210 closest distance to " O   HOH Z 383 " =    2.659
peak=    3.209 closest distance to " CB  SER A 212 " =    1.531
peak=    3.207 closest distance to " NE AARG A 145 " =    0.931
peak=    3.206 closest distance to " OG  SER A 135 " =    1.171
peak=    3.205 closest distance to " O   HOH Z 418 " =    0.959
peak=    3.204 closest distance to " O   HOH Z 265 " =    1.480
peak=    3.204 closest distance to " CE  LYS A 119 " =    1.202
peak=    3.201 closest distance to " CG2 ILE A 106 " =    1.083
peak=    3.199 closest distance to " O   THR A 220 " =    1.294
peak=    3.196 closest distance to " O   HOH Z 423 " =    1.912
peak=    3.186 closest distance to " O   HOH Z 426 " =    1.021
peak=    3.184 closest distance to " O   HOH Z  47 " =    1.805
peak=    3.182 closest distance to " O   HOH Z 118 " =    2.862
peak=    3.181 closest distance to " O   HOH Z  32 " =    2.178
peak=    3.173 closest distance to " CA  TRP A 150 " =    0.951
peak=    3.170 closest distance to " ND2 ASN A 176 " =    0.889
peak=    3.169 closest distance to " CB  MET A  40 " =    0.889
peak=    3.169 closest distance to " O   HOH Z 182 " =    1.058
peak=    3.169 closest distance to " O   HOH Z 162 " =    1.370
peak=    3.165 closest distance to " CA  ALA A 291 " =    0.767
peak=    3.159 closest distance to " O   VAL A 153 " =    1.126
peak=    3.153 closest distance to " CA  ALA A 160 " =    0.913
peak=    3.149 closest distance to " O   HOH Z   7 " =    3.158
peak=    3.148 closest distance to " O   HOH Z 287 " =    2.460
peak=    3.147 closest distance to " NH1 ARG A  14 " =    1.157
peak=    3.142 closest distance to " O   HOH Z 357 " =    2.075
peak=    3.140 closest distance to " O   HOH Z 119 " =    4.539
peak=    3.138 closest distance to " O   HOH Z  94 " =    1.352
peak=    3.137 closest distance to " CB  ALA A 291 " =    0.797
peak=    3.133 closest distance to " CB  ASN A 217 " =    0.855
peak=    3.131 closest distance to " O   HOH Z 328 " =    1.724
peak=    3.129 closest distance to " O   ASP A 124 " =    1.017
peak=    3.128 closest distance to " O   HOH Z 117 " =    1.834
peak=    3.128 closest distance to " O   HOH Z 196 " =    2.997
peak=    3.121 closest distance to " CD1 ILE A 120 " =    0.897
peak=    3.118 closest distance to " OE1 GLN A  89 " =    1.671
peak=    3.117 closest distance to " O   HOH Z 126 " =    1.396
peak=    3.116 closest distance to " CD  ARG A  79 " =    1.006
peak=    3.115 closest distance to " CA  ASN A 215 " =    1.017
peak=    3.115 closest distance to " CB  GLU A 152 " =    1.147
peak=    3.112 closest distance to " O   HOH Z 371 " =    2.607
peak=    3.110 closest distance to " CG2 ILE A  20 " =    1.613
peak=    3.102 closest distance to " O   HOH Z 323 " =    1.510
peak=    3.101 closest distance to " O   HOH Z 270 " =    1.386
peak=    3.098 closest distance to " O   HOH Z 274 " =    2.512
peak=    3.098 closest distance to " O   HOH Z  20 " =    1.288
peak=    3.085 closest distance to " O   HOH Z 365 " =    2.517
peak=    3.083 closest distance to " O   HOH Z 356 " =    1.347
peak=    3.082 closest distance to " CD2 LEU A 143 " =    1.341
peak=    3.080 closest distance to " O   HOH Z 191 " =    3.265
peak=    3.074 closest distance to " CB  ILE A 234 " =    1.510
peak=    3.073 closest distance to " CB  LEU A 143 " =    1.106
peak=    3.046 closest distance to " N   GLN A 122 " =    0.840
peak=    3.034 closest distance to " N   GLY A 203 " =    2.055
peak=    3.030 closest distance to " NZ  LYS A 289 " =    1.369
peak=    3.016 closest distance to " O   HOH Z 213 " =    1.222

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 198         
Filter by distance & map next to the model:
   mapped sites are within: 0.663 - 5.732
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 197 from: 198
   mapped sites are within: 0.705 - 5.732

peak=   -5.367 closest distance to " CB  GLN A  55 " =    1.148
peak=   -5.026 closest distance to " O   PRO A 198 " =    1.099
peak=   -4.456 closest distance to " CB  VAL A 230 " =    1.024
peak=   -4.342 closest distance to " O   HOH Z 147 " =    1.979
peak=   -4.325 closest distance to " O   HOH Z 276 " =    1.224
peak=   -4.288 closest distance to " O   HOH Z  69 " =    1.572
peak=   -4.255 closest distance to " NE2 GLN A 223 " =    1.752
peak=   -4.231 closest distance to " O   HOH Z  22 " =    2.969
peak=   -4.212 closest distance to " O   HOH Z 131 " =    4.005
peak=   -4.185 closest distance to " O   ALA A 114 " =    0.842
peak=   -4.073 closest distance to " OG  SER A  87 " =    1.736
peak=   -3.981 closest distance to " CG  ARG A 219 " =    2.293
peak=   -3.979 closest distance to " O   HOH Z 385 " =    1.476
peak=   -3.967 closest distance to " CG2 ILE A  20 " =    2.508
peak=   -3.892 closest distance to " CB  ASP A 132 " =    2.573
peak=   -3.876 closest distance to " O   HOH Z 100 " =    0.777
peak=   -3.873 closest distance to " O   HOH Z  67 " =    1.439
peak=   -3.866 closest distance to " O   HOH Z 415 " =    1.109
peak=   -3.857 closest distance to " O   HOH Z 165 " =    2.315
peak=   -3.851 closest distance to " CA  GLY A  57 " =    2.252
peak=   -3.841 closest distance to " O  BHOH Z  74 " =    0.783
peak=   -3.827 closest distance to " CA  GLN A  58 " =    1.154
peak=   -3.812 closest distance to " CD2 TYR A 293 " =    1.918
peak=   -3.811 closest distance to " OE1 GLU A 277 " =    2.122
peak=   -3.774 closest distance to " N   THR A 157 " =    1.399
peak=   -3.761 closest distance to " O   HOH Z  24 " =    1.133
peak=   -3.759 closest distance to " O   HOH Z  39 " =    1.156
peak=   -3.750 closest distance to " O   HOH Z 177 " =    2.127
peak=   -3.737 closest distance to " SG BCYS A 201 " =    2.289
peak=   -3.724 closest distance to " CB  ALA A  43 " =    2.468
peak=   -3.708 closest distance to " O   HOH Z 278 " =    1.133
peak=   -3.703 closest distance to " O   HOH Z 412 " =    5.629
peak=   -3.699 closest distance to " CA  HIS A 207 " =    1.200
peak=   -3.697 closest distance to " O   HOH Z  53 " =    1.683
peak=   -3.696 closest distance to " CD2 HIS A 207 " =    1.697
peak=   -3.685 closest distance to " O   HOH Z 105 " =    2.029
peak=   -3.676 closest distance to " OG  SER A  97 " =    2.216
peak=   -3.671 closest distance to " O   HOH Z 245 " =    0.908
peak=   -3.660 closest distance to " CA  ASN A 127 " =    1.404
peak=   -3.632 closest distance to " C   SER A 276 " =    1.612
peak=   -3.631 closest distance to " O   HOH Z 359 " =    3.302
peak=   -3.627 closest distance to " CE  MET A 188 " =    2.333
peak=   -3.622 closest distance to " O   SER A  22 " =    2.372
peak=   -3.612 closest distance to " O   HOH Z 134 " =    4.103
peak=   -3.609 closest distance to " O   HOH Z 193 " =    0.735
peak=   -3.608 closest distance to " CG2 THR A 178 " =    2.204
peak=   -3.608 closest distance to " CZ2 TRP A 274 " =    0.938
peak=   -3.594 closest distance to " O   HOH Z 231 " =    0.705
peak=   -3.590 closest distance to " O   HOH Z  52 " =    1.571
peak=   -3.587 closest distance to " O   HOH Z 177 " =    1.002
peak=   -3.579 closest distance to " O   HOH Z 257 " =    1.165
peak=   -3.576 closest distance to " O   HOH Z 211 " =    1.289
peak=   -3.572 closest distance to " NZ  LYS A 289 " =    0.742
peak=   -3.568 closest distance to " SG  CYS A 254 " =    3.174
peak=   -3.568 closest distance to " NE2 GLN A  55 " =    0.986
peak=   -3.567 closest distance to " C   VAL A  72 " =    0.877
peak=   -3.556 closest distance to " ND2 ASN A 285 " =    2.071
peak=   -3.552 closest distance to " O   HOH Z 242 " =    1.590
peak=   -3.551 closest distance to " CD1 TYR A 247 " =    2.724
peak=   -3.549 closest distance to " OG BSER A 134 " =    1.566
peak=   -3.547 closest distance to " CG  GLU A 277 " =    1.123
peak=   -3.546 closest distance to " CG2 VAL A 189 " =    2.095
peak=   -3.545 closest distance to " ND2 ASN A 249 " =    2.522
peak=   -3.544 closest distance to " O   HOH Z 426 " =    1.566
peak=   -3.542 closest distance to " OD1 ASN A  69 " =    0.793
peak=   -3.528 closest distance to " O   HOH Z  64 " =    1.334
peak=   -3.526 closest distance to " O   VAL A  67 " =    2.573
peak=   -3.523 closest distance to " CG2 VAL A 202 " =    2.792
peak=   -3.523 closest distance to " CG  LEU A 281 " =    1.853
peak=   -3.512 closest distance to " O   HOH Z 368 " =    0.939
peak=   -3.508 closest distance to " N   GLN A  58 " =    1.291
peak=   -3.503 closest distance to " ND2 ASN A  39 " =    1.447
peak=   -3.499 closest distance to " CG  LEU A  83 " =    2.370
peak=   -3.498 closest distance to " OE2 GLU A 152 " =    1.313
peak=   -3.494 closest distance to " O   HOH Z 255 " =    0.885
peak=   -3.490 closest distance to " CB  TYR A  68 " =    1.033
peak=   -3.489 closest distance to " CG2 VAL A 296 " =    2.226
peak=   -3.488 closest distance to " OE1 GLU A  44 " =    1.230
peak=   -3.488 closest distance to " O   SER A 245 " =    1.418
peak=   -3.470 closest distance to " O   HOH Z 298 " =    2.836
peak=   -3.458 closest distance to " CZ  PHE A  38 " =    2.282
peak=   -3.456 closest distance to " CZ2 TRP A  92 " =    2.802
peak=   -3.452 closest distance to " CE2 TYR A  30 " =    2.730
peak=   -3.451 closest distance to " CG  GLN A  88 " =    0.767
peak=   -3.447 closest distance to " O   HOH Z 352 " =    1.524
peak=   -3.443 closest distance to " O   ALA A  51 " =    1.185
peak=   -3.438 closest distance to " CG  GLN A  58 " =    1.086
peak=   -3.429 closest distance to " O   GLN A 144 " =    1.297
peak=   -3.427 closest distance to " NE2 GLN A  11 " =    1.746
peak=   -3.426 closest distance to " O   HOH Z 185 " =    1.790
peak=   -3.423 closest distance to " C   HIS A 108 " =    1.195
peak=   -3.410 closest distance to " O   HOH Z 133 " =    1.297
peak=   -3.394 closest distance to " O   HOH Z 128 " =    2.576
peak=   -3.389 closest distance to " CG2 VAL A 230 " =    0.736
peak=   -3.386 closest distance to " NE2 GLN A 194 " =    1.997
peak=   -3.377 closest distance to " O   HOH Z 135 " =    2.282
peak=   -3.376 closest distance to " OG  SER A  28 " =    1.805
peak=   -3.371 closest distance to " CB  ASP A 200 " =    2.574
peak=   -3.371 closest distance to " CE1 TYR A 186 " =    2.193
peak=   -3.370 closest distance to " N   LYS A 290 " =    1.184
peak=   -3.369 closest distance to " O   ASN A 187 " =    1.354
peak=   -3.357 closest distance to " O   HOH Z 427 " =    1.985
peak=   -3.354 closest distance to " CD  PRO A 213 " =    2.214
peak=   -3.352 closest distance to " N   ASP A 270 " =    1.277
peak=   -3.349 closest distance to " O   GLU A 152 " =    1.426
peak=   -3.349 closest distance to " CG2 ILE A 120 " =    1.323
peak=   -3.349 closest distance to " N   ALA A  43 " =    2.389
peak=   -3.344 closest distance to " CB  ALA A  10 " =    2.256
peak=   -3.344 closest distance to " O   HOH Z  89 " =    2.835
peak=   -3.342 closest distance to " CG  ARG A 259 " =    2.257
peak=   -3.338 closest distance to " CB  ASN A  45 " =    2.091
peak=   -3.338 closest distance to " C   GLU A   2 " =    1.927
peak=   -3.338 closest distance to " O   HOH Z 350 " =    1.183
peak=   -3.338 closest distance to " O   HOH Z 368 " =    1.837
peak=   -3.333 closest distance to " O   HOH Z  44 " =    1.150
peak=   -3.333 closest distance to " O   HOH Z 163 " =    2.056
peak=   -3.324 closest distance to " OE1 GLN A 223 " =    2.058
peak=   -3.316 closest distance to " CG1 VAL A 125 " =    2.370
peak=   -3.309 closest distance to " CA  GLY A 133 " =    2.086
peak=   -3.304 closest distance to " O   HOH Z  70 " =    0.950
peak=   -3.303 closest distance to " O   HOH Z 275 " =    1.810
peak=   -3.297 closest distance to " O   ASN A 252 " =    1.356
peak=   -3.297 closest distance to " O   HOH Z 281 " =    2.507
peak=   -3.292 closest distance to " CG2 THR A  18 " =    2.847
peak=   -3.288 closest distance to " N   ALA A 244 " =    1.252
peak=   -3.284 closest distance to " CB  PHE A 155 " =    2.480
peak=   -3.283 closest distance to " CG  PHE A  59 " =    1.260
peak=   -3.280 closest distance to " CA  GLY A 241 " =    2.392
peak=   -3.280 closest distance to " OG BSER A  99 " =    1.137
peak=   -3.275 closest distance to " CZ  ARG A 259 " =    0.924
peak=   -3.275 closest distance to " CD2 TYR A 116 " =    2.268
peak=   -3.274 closest distance to " OG  SER A 245 " =    1.584
peak=   -3.274 closest distance to " OD1 ASP A 107 " =    0.956
peak=   -3.270 closest distance to " O   HOH Z 286 " =    1.662
peak=   -3.264 closest distance to " CG2 THR A 178 " =    2.315
peak=   -3.259 closest distance to " OD2 ASP A 171 " =    2.067
peak=   -3.256 closest distance to " O   HOH Z 425 " =    0.858
peak=   -3.244 closest distance to " CZ  TYR A 169 " =    2.033
peak=   -3.234 closest distance to " N   ARG A 275 " =    0.777
peak=   -3.230 closest distance to " O   HOH Z 411 " =    5.179
peak=   -3.229 closest distance to " O   HOH Z 193 " =    1.762
peak=   -3.216 closest distance to " CB  ALA A   1 " =    3.025
peak=   -3.216 closest distance to " CD1 TRP A 179 " =    1.161
peak=   -3.215 closest distance to " CA  GLY A 203 " =    2.574
peak=   -3.213 closest distance to " CG1 VAL A 265 " =    2.533
peak=   -3.210 closest distance to " O   HOH Z 423 " =    2.745
peak=   -3.210 closest distance to " NZ  LYS A 289 " =    1.622
peak=   -3.208 closest distance to " CB  ALA A 248 " =    2.057
peak=   -3.205 closest distance to " O   THR A  52 " =    1.104
peak=   -3.204 closest distance to " N   SER A 206 " =    2.034
peak=   -3.195 closest distance to " CG  PRO A 243 " =    1.640
peak=   -3.194 closest distance to " CD  ARG A 156 " =    1.914
peak=   -3.187 closest distance to " CD1 TYR A 214 " =    1.531
peak=   -3.187 closest distance to " OG  SER A  63 " =    1.177
peak=   -3.182 closest distance to " C   ILE A 239 " =    1.900
peak=   -3.173 closest distance to " O   HOH Z 362 " =    4.355
peak=   -3.173 closest distance to " O   SER A  28 " =    1.144
peak=   -3.172 closest distance to " O   HOH Z 199 " =    1.375
peak=   -3.168 closest distance to " O   HOH Z 292 " =    1.525
peak=   -3.168 closest distance to " O   HOH Z  99 " =    1.565
peak=   -3.166 closest distance to " CB  ALA A   9 " =    2.552
peak=   -3.164 closest distance to " N   TYR A 172 " =    1.631
peak=   -3.160 closest distance to " CE2 PHE A  61 " =    2.650
peak=   -3.158 closest distance to " CZ3 TRP A 274 " =    2.189
peak=   -3.156 closest distance to " O   HOH Z 389 " =    1.274
peak=   -3.154 closest distance to " O   ALA A   1 " =    1.743
peak=   -3.154 closest distance to " O   HOH Z 155 " =    1.168
peak=   -3.145 closest distance to " CD  LYS A 289 " =    2.272
peak=   -3.144 closest distance to " CG1 ILE A 263 " =    2.161
peak=   -3.143 closest distance to " CA  GLY A  57 " =    2.147
peak=   -3.135 closest distance to " CD2 LEU A 228 " =    1.319
peak=   -3.132 closest distance to " O   HOH Z 147 " =    1.208
peak=   -3.125 closest distance to " O   HOH Z 414 " =    2.331
peak=   -3.124 closest distance to " O   GLN A 205 " =    1.486
peak=   -3.122 closest distance to " O   TRP A  70 " =    1.333
peak=   -3.121 closest distance to " O   CYS A 260 " =    1.423
peak=   -3.117 closest distance to " CG2 THR A  52 " =    3.094
peak=   -3.116 closest distance to " O   ILE A 234 " =    1.390
peak=   -3.116 closest distance to " SG ACYS A 201 " =    1.308
peak=   -3.108 closest distance to " O   HOH Z  60 " =    1.870
peak=   -3.106 closest distance to " OE1 GLN A  88 " =    1.282
peak=   -3.105 closest distance to " CE2 PHE A 218 " =    2.601
peak=   -3.103 closest distance to " O   HOH Z 434 " =    4.443
peak=   -3.092 closest distance to " O   ILE A  49 " =    1.664
peak=   -3.082 closest distance to " CA  GLU A  44 " =    2.426
peak=   -3.080 closest distance to " N   ALA A   1 " =    1.644
peak=   -3.075 closest distance to " CB  ASN A  39 " =    2.151
peak=   -3.073 closest distance to " O   SER A 271 " =    1.609
peak=   -3.070 closest distance to " CG1 VAL A 125 " =    2.281
peak=   -3.060 closest distance to " OG ASER A  12 " =    1.648
peak=   -3.059 closest distance to " N   MET A 188 " =    2.075
peak=   -3.047 closest distance to " CG  GLN A  58 " =    5.136
peak=   -3.047 closest distance to " O   HOH Z 216 " =    1.454
peak=   -3.041 closest distance to " CB  ASP A 132 " =    2.458
peak=   -3.037 closest distance to " O   HOH Z 328 " =    1.063
peak=   -3.037 closest distance to " O   HOH Z 171 " =    2.557
peak=   -3.022 closest distance to " O   HOH Z 191 " =    5.732

================= 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    :  0.5195 0.5114   6.311908e+00   6.303197e+00
   1_bss:  0.5110 0.5035   6.306984e+00   6.296821e+00
   1_xyz:  0.4568 0.4813   6.253451e+00   6.275088e+00
   1_adp:  0.4200 0.4785   6.220072e+00   6.273720e+00
   1_occ:  0.4194 0.4793   6.219717e+00   6.274626e+00
   2_bss:  0.4187 0.4795   6.222213e+00   6.275967e+00
   2_xyz:  0.3508 0.4274   6.094871e+00   6.209497e+00
   2_adp:  0.3250 0.4083   6.050762e+00   6.179988e+00
   2_occ:  0.3247 0.4079   6.050801e+00   6.180009e+00
   3_bss:  0.3233 0.4072   6.050268e+00   6.178822e+00
   3_xyz:  0.2561 0.3265   5.857093e+00   6.026620e+00
   3_adp:  0.2291 0.3003   5.763705e+00   5.945998e+00
   3_occ:  0.2286 0.2997   5.762052e+00   5.944590e+00
   4_bss:  0.2270 0.2975   5.759158e+00   5.942937e+00
   4_xyz:  0.1720 0.2305   5.513902e+00   5.731139e+00
   4_adp:  0.1606 0.2193   5.458634e+00   5.686401e+00
   4_occ:  0.1603 0.2186   5.457106e+00   5.684743e+00
   5_bss:  0.1603 0.2184   5.456906e+00   5.684546e+00
   5_xyz:  0.1474 0.1970   5.375223e+00   5.596634e+00
   5_adp:  0.1395 0.1910   5.331186e+00   5.563455e+00
   5_occ:  0.1394 0.1909   5.330817e+00   5.563016e+00
   5_bss:  0.1394 0.1909   5.330697e+00   5.563482e+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:  0.342   0.000   5.489   7.586   9.966   0.000   0.000   0.000
   1_xyz:  0.342   0.000   5.489   7.586   9.966   0.000   0.000   0.000
   1_adp:  0.342   0.000   5.489   7.586   9.966   0.000   0.000   0.000
   1_occ:  0.342   0.000   5.489   7.586   9.966   0.000   0.000   0.000
   2_bss:  0.369  50.000   3.135   4.535   6.929   0.000   0.000   0.000
   2_xyz:  0.369  50.000   3.135   4.535   6.929   0.000   0.000   0.000
   2_adp:  0.369  50.000   3.135   4.535   6.929   0.000   0.000   0.000
   2_occ:  0.369  50.000   3.135   4.535   6.929   0.000   0.000   0.000
   3_bss:  0.344  50.000   1.442   2.378   4.365   0.000   0.000   0.000
   3_xyz:  0.344  50.000   1.442   2.378   4.365   0.000   0.000   0.000
   3_adp:  0.344  50.000   1.442   2.378   4.365   0.000   0.000   0.000
   3_occ:  0.344  50.000   1.442   2.378   4.365   0.000   0.000   0.000
   4_bss:  0.329  50.000  -0.088   0.592   2.716   0.000   0.000   0.000
   4_xyz:  0.329  50.000  -0.088   0.592   2.716   0.000   0.000   0.000
   4_adp:  0.329  50.000  -0.088   0.592   2.716   0.000   0.000   0.000
   4_occ:  0.329  50.000  -0.088   0.592   2.716   0.000   0.000   0.000
   5_bss:  0.313  47.272  -0.627  -0.146   2.123  -0.000   0.000   0.000
   5_xyz:  0.313  47.272  -0.627  -0.146   2.123  -0.000   0.000   0.000
   5_adp:  0.313  47.272  -0.627  -0.146   2.123  -0.000   0.000   0.000
   5_occ:  0.313  47.272  -0.627  -0.146   2.123  -0.000   0.000   0.000
   5_bss:  0.316  55.329  -1.052  -0.659   1.711  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  67.998 0.2890  0.3499    86770.195
   1_bss:  67.451 0.2954  0.4383    84982.852
   1_xyz:  60.973 0.3792  0.5558    74593.880
   1_adp:  60.440 0.3858  0.6291    74222.541
   1_occ:  60.572 0.3841  0.6253    74545.280
   2_bss:  60.217 0.3889  0.5835    74366.635
   2_xyz:  48.778 0.5344  0.8081    53453.495
   2_adp:  45.614 0.5739  0.8637    48054.214
   2_occ:  45.692 0.5729  0.8618    48075.577
   3_bss:  45.539 0.5746  0.8021    47749.521
   3_xyz:  34.340 0.7080  0.9568    28923.364
   3_adp:  29.904 0.7590  0.9919    23455.625
   3_occ:  29.849 0.7596  0.9920    23342.745
   4_bss:  29.712 0.7609  0.9352    23102.396
   4_xyz:  22.466 0.8372  0.9848    13740.884
   4_adp:  21.120 0.8509  0.9838    12508.815
   4_occ:  21.079 0.8512  0.9838    12450.783
   5_bss:  21.062 0.8513  0.9621    12445.098
   5_xyz:  18.623 0.8749  0.9743    10192.421
   5_adp:  17.813 0.8825  0.9685     9487.161
   5_occ:  17.803 0.8826  0.9686     9471.839
   5_bss:  17.804 0.8826  0.9710     9483.700
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.087   5.3362e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.087   5.3362e+01
   1_xyz:   1.828  0.014  0.109 18.484  0.007  4.103   1.6285e-01
   1_adp:   1.828  0.014  0.109 18.484  0.007  4.103   1.6285e-01
   1_occ:   1.828  0.014  0.109 18.484  0.007  4.103   1.6285e-01
   2_bss:   1.828  0.014  0.109 18.484  0.007  4.103   1.6285e-01
   2_xyz:   1.513  0.012  0.100 17.506  0.007  4.105   1.4576e-01
   2_adp:   1.513  0.012  0.100 17.506  0.007  4.105   1.4576e-01
   2_occ:   1.513  0.012  0.100 17.506  0.007  4.105   1.4576e-01
   3_bss:   1.513  0.012  0.100 17.506  0.007  4.105   1.4576e-01
   3_xyz:   1.346  0.010  0.094 16.985  0.005  4.110   1.0796e-01
   3_adp:   1.346  0.010  0.094 16.985  0.005  4.110   1.0796e-01
   3_occ:   1.346  0.010  0.094 16.985  0.005  4.110   1.0796e-01
   4_bss:   1.346  0.010  0.094 16.985  0.005  4.110   1.0796e-01
   4_xyz:   1.201  0.009  0.083 15.964  0.005  4.123   8.4339e-02
   4_adp:   1.201  0.009  0.083 15.964  0.005  4.123   8.4339e-02
   4_occ:   1.201  0.009  0.083 15.964  0.005  4.123   8.4339e-02
   5_bss:   1.201  0.009  0.083 15.964  0.005  4.123   8.4339e-02
   5_xyz:   0.900  0.006  0.065 15.433  0.003  4.115   5.4866e-02
   5_adp:   0.900  0.006  0.065 15.433  0.003  4.115   5.4866e-02
   5_occ:   0.900  0.006  0.065 15.433  0.003  4.115   5.4866e-02
   5_bss:   0.900  0.006  0.065 15.433  0.003  4.115   5.4866e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  0.994   6.9120e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  0.994   6.9120e+00
   1_xyz:  14.499  0.182  0.452 84.337  0.039  2.081   1.0670e-01
   1_adp:  14.499  0.182  0.452 84.337  0.039  2.081   1.0670e-01
   1_occ:  14.499  0.182  0.452 84.337  0.039  2.081   1.0670e-01
   2_bss:  14.499  0.182  0.452 84.337  0.039  2.081   1.0670e-01
   2_xyz:   9.100  0.178  0.339 85.242  0.059  1.960   1.1123e-01
   2_adp:   9.100  0.178  0.339 85.242  0.059  1.960   1.1123e-01
   2_occ:   9.100  0.178  0.339 85.242  0.059  1.960   1.1123e-01
   3_bss:   9.100  0.178  0.339 85.242  0.059  1.960   1.1123e-01
   3_xyz:   8.827  0.060  0.348 85.439  0.051  2.051   1.0550e-01
   3_adp:   8.827  0.060  0.348 85.439  0.051  2.051   1.0550e-01
   3_occ:   8.827  0.060  0.348 85.439  0.051  2.051   1.0550e-01
   4_bss:   8.827  0.060  0.348 85.439  0.051  2.051   1.0550e-01
   4_xyz:   8.157  0.068  0.285 86.798  0.048  2.110   6.3164e-02
   4_adp:   8.157  0.068  0.285 86.798  0.048  2.110   6.3164e-02
   4_occ:   8.157  0.068  0.285 86.798  0.048  2.110   6.3164e-02
   5_bss:   8.157  0.068  0.285 86.798  0.048  2.110   6.3164e-02
   5_xyz:   6.702  0.050  0.211 80.797  0.038  2.331   5.6996e-02
   5_adp:   6.702  0.050  0.211 80.797  0.038  2.331   5.6996e-02
   5_occ:   6.702  0.050  0.211 80.797  0.038  2.331   5.6996e-02
   5_bss:   6.702  0.050  0.211 80.797  0.038  2.331   5.6996e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00
   1_bss:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_xyz:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_adp:  89.31   0.00  17.11  79.24   0.00  15.98  89.31   0.00  23.26
   1_occ:  89.31   0.00  17.11  79.24   0.00  15.98  89.31   0.00  23.26
   2_bss:  89.31   0.00  17.11  79.24   0.00  15.98  89.31   0.00  23.26
   2_xyz:  89.31   0.00  17.11  79.24   0.00  15.98  89.31   0.00  23.26
   2_adp:  76.87   0.00  16.17  62.30   0.00  13.83  76.87   0.00  28.91
   2_occ:  76.87   0.00  16.17  62.30   0.00  13.83  76.87   0.00  28.91
   3_bss:  76.87   0.00  16.17  62.30   0.00  13.83  76.87   0.00  28.91
   3_xyz:  76.87   0.00  16.17  62.30   0.00  13.83  76.87   0.00  28.91
   3_adp:  79.70   0.00  15.47  67.30   0.00  11.75  79.70   0.77  35.71
   3_occ:  79.70   0.00  15.47  67.30   0.00  11.75  79.70   0.77  35.71
   4_bss:  79.70   0.00  15.47  67.30   0.00  11.75  79.70   0.77  35.71
   4_xyz:  79.70   0.00  15.47  67.30   0.00  11.75  79.70   0.77  35.71
   4_adp:  80.58   0.00  15.14  68.17   0.00  11.10  80.58   2.61  37.17
   4_occ:  80.58   0.00  15.14  68.17   0.00  11.10  80.58   2.61  37.17
   5_bss:  80.58   0.00  15.14  68.17   0.00  11.10  80.58   2.61  37.17
   5_xyz:  80.58   0.00  15.14  68.17   0.00  11.10  80.58   2.61  37.17
   5_adp:  98.66   0.00  16.42  89.23   0.00  11.11  98.66   3.79  45.33
   5_occ:  98.66   0.00  16.42  89.23   0.00  11.11  98.66   3.79  45.33
   5_bss:  99.17   0.52  16.93  89.75   0.52  11.62  99.17   4.31  45.84
------------------------------------------------------------------------
 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:    1.317    0.021    0.418
   1_adp:    1.317    0.021    0.418
   1_occ:    1.317    0.021    0.418
   2_bss:    1.317    0.021    0.418
   2_xyz:    1.780    0.037    0.646
   2_adp:    1.780    0.037    0.646
   2_occ:    1.780    0.037    0.646
   3_bss:    1.780    0.037    0.646
   3_xyz:    1.958    0.034    0.810
   3_adp:    1.958    0.034    0.810
   3_occ:    1.958    0.034    0.810
   4_bss:    1.958    0.034    0.810
   4_xyz:    1.874    0.033    0.896
   4_adp:    1.874    0.033    0.896
   4_occ:    1.874    0.033    0.896
   5_bss:    1.874    0.033    0.896
   5_xyz:    2.011    0.076    0.919
   5_adp:    2.011    0.076    0.919
   5_occ:    2.011    0.076    0.919
   5_bss:    2.011    0.076    0.919
------------------------------------------------------------------------

CPU time actual refinement: 336.03


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_263/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_263/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_263/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_263/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_263/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 335.87 
  Macro-tasks:
    bulk solvent and scale       = 39.13  
    individual site refinement   = 138.39 
    weights calculation          = 32.19  
    collect and process          = 6.29   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 216.13 
  Micro-tasks:
    mask                            = 2.39   
    f_calc                          = 105.60 
    alpha_beta                      = 8.16   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 115.31 
    fmodel                         = 6.74   
    r_factors                      = 0.23   
    phase_errors                   = 9.90   
    foms                           = 0.31   
    TOTAL for micro-tasks          = 249.78 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.766 micro seconds
Total CPU time: 5.82 minutes
from_scatterers_fft:    646 calls, 105.27 s
gradients_fft:          591 calls, 102.38 s

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

# Date 2008-01-16 Time 01:09:30 PST -0800 (1200474570.59 s)
Start R-work = 0.5195, R-free = 0.5114 (no bulk solvent and anisotropic scale)
Final R-work = 0.1556, R-free = 0.2060 (no bulk solvent and anisotropic scale)

Start R-work = 0.5110, R-free = 0.5035
Final R-work = 0.1394, R-free = 0.1909