Starting phenix.real_space_refine
on Sat Aug 23 06:13:17 2025 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/8buz_16252/08_2025/8buz_16252_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8buz_16252/08_2025/8buz_16252.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8buz_16252/08_2025/8buz_16252.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8buz_16252/08_2025/8buz_16252.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8buz_16252/08_2025/8buz_16252_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8buz_16252/08_2025/8buz_16252_neut.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     Mg      1      5.21       5
     S      61      5.16       5
     C    6344      2.51       5
     N    1702      2.21       5
     O    1810      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9921
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 7120
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 890, 7120
          Classifications: {'peptide': 890}
          Link IDs: {'PTRANS': 19, 'TRANS': 870}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 2739
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 333, 2739
          Classifications: {'peptide': 333}
          Link IDs: {'PTRANS': 13, 'TRANS': 319}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 29
          Unusual residues: {'FOK': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Unusual residues: {' MG': 1, 'GSP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.36, per 1000 atoms: 0.24
  Number of scatterers: 9921
  At special positions: 0
  Unit cell: (151.8, 115.5, 129.36, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      61     16.00
     P       3     15.00
     Mg      1     11.99
     O    1810      8.00
     N    1702      7.00
     C    6344      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 457 " - pdb=" SG  CYS A 469 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 809 " - pdb=" SG  CYS A 832 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.70
  Conformation dependent library (CDL) restraints added in 370.8 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2422 Ramachandran restraints generated.
    1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2318

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 6 sheets defined
      63.3% alpha, 7.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.46
  Creating SS restraints...
    Processing helix  chain 'A' and resid 165 through 206
      removed outlier: 3.659A  pdb=" N   GLY A 178 " --> pdb=" O   ARG A 174 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   GLN A 179 " --> pdb=" O   TYR A 175 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   SER A 183 " --> pdb=" O   GLN A 179 " (cutoff:3.500A)
      removed outlier: 4.144A  pdb=" N   VAL A 186 " --> pdb=" O   LYS A 182 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   LEU A 193 " --> pdb=" O   VAL A 189 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   ALA A 206 " --> pdb=" O   HIS A 202 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 238
      removed outlier: 3.656A  pdb=" N   ILE A 216 " --> pdb=" O   PRO A 212 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   LEU A 217 " --> pdb=" O   LEU A 213 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   LEU A 218 " --> pdb=" O   LYS A 214 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   GLU A 225 " --> pdb=" O   PHE A 221 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   VAL A 226 " --> pdb=" O   THR A 222 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   VAL A 233 " --> pdb=" O   CYS A 229 " (cutoff:3.500A)
      removed outlier: 4.335A  pdb=" N   VAL A 234 " --> pdb=" O   ALA A 230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 264
      removed outlier: 3.532A  pdb=" N   VAL A 249 " --> pdb=" O   GLN A 245 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   ILE A 259 " --> pdb=" O   MET A 255 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   LEU A 260 " --> pdb=" O   THR A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 286
      removed outlier: 4.041A  pdb=" N   TYR A 284 " --> pdb=" O   LEU A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 290 through 312
      removed outlier: 3.631A  pdb=" N   LEU A 296 " --> pdb=" O   THR A 292 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   THR A 301 " --> pdb=" O   ALA A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 319
      removed outlier: 4.013A  pdb=" N   ALA A 316 " --> pdb=" O   ILE A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 322 through 377
      removed outlier: 4.142A  pdb=" N   MET A 333 " --> pdb=" O   LEU A 329 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ASN A 334 " --> pdb=" O   PHE A 330 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   PHE A 339 " --> pdb=" O   THR A 335 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   VAL A 359 " --> pdb=" O   THR A 355 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   LEU A 375 " --> pdb=" O   ARG A 371 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 381 through 393
      removed outlier: 4.808A  pdb=" N   GLU A 387 " --> pdb=" O   PHE A 383 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 424 through 430
      removed outlier: 3.628A  pdb=" N   THR A 430 " --> pdb=" O   THR A 426 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 433 through 455
    Processing helix  chain 'A' and resid 479 through 499
      removed outlier: 4.105A  pdb=" N   CYS A 483 " --> pdb=" O   ASP A 479 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   CYS A 484 " --> pdb=" O   HIS A 480 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 500 through 503
      removed outlier: 3.867A  pdb=" N   LYS A 503 " --> pdb=" O   SER A 500 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 500 through 503'
    Processing helix  chain 'A' and resid 533 through 546
      removed outlier: 3.850A  pdb=" N   ASP A 537 " --> pdb=" O   SER A 533 " (cutoff:3.500A)
      removed outlier: 4.429A  pdb=" N   GLY A 546 " --> pdb=" O   LEU A 542 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 554 through 562
      removed outlier: 4.419A  pdb=" N   CYS A 560 " --> pdb=" O   ALA A 556 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   ASN A 562 " --> pdb=" O   LEU A 558 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 672 through 685
      removed outlier: 3.549A  pdb=" N   SER A 681 " --> pdb=" O   ILE A 677 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 686 through 688
      No H-bonds generated for 'chain 'A' and resid 686 through 688'
    Processing helix  chain 'A' and resid 699 through 708
    Processing helix  chain 'A' and resid 713 through 734
      removed outlier: 3.902A  pdb=" N   LEU A 734 " --> pdb=" O   ALA A 730 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 739 through 762
    Processing helix  chain 'A' and resid 770 through 783
      removed outlier: 3.623A  pdb=" N   THR A 783 " --> pdb=" O   TRP A 779 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 783 through 809
      removed outlier: 3.619A  pdb=" N   ILE A 790 " --> pdb=" O   ALA A 786 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   ASN A 798 " --> pdb=" O   SER A 794 " (cutoff:3.500A)
      removed outlier: 4.456A  pdb=" N   ASN A 805 " --> pdb=" O   GLY A 801 " (cutoff:3.500A)
      removed outlier: 5.099A  pdb=" N   ILE A 806 " --> pdb=" O   ALA A 802 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 834 through 852
      removed outlier: 3.767A  pdb=" N   PHE A 838 " --> pdb=" O   TYR A 834 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   VAL A 839 " --> pdb=" O   PRO A 835 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   THR A 841 " --> pdb=" O   TYR A 837 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   GLY A 842 " --> pdb=" O   PHE A 838 " (cutoff:3.500A)
      removed outlier: 4.517A  pdb=" N   THR A 848 " --> pdb=" O   LEU A 844 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   CYS A 849 " --> pdb=" O   ALA A 845 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 856 through 876
      removed outlier: 3.519A  pdb=" N   MET A 867 " --> pdb=" O   VAL A 863 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 879 through 891
      removed outlier: 3.737A  pdb=" N   TYR A 886 " --> pdb=" O   LEU A 882 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 894 through 898
    Processing helix  chain 'A' and resid 899 through 957
      removed outlier: 3.584A  pdb=" N   LEU A 904 " --> pdb=" O   LYS A 900 " (cutoff:3.500A)
      removed outlier: 4.513A  pdb=" N   LEU A 905 " --> pdb=" O   GLU A 901 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 958 through 967
      removed outlier: 3.822A  pdb=" N   GLU A 967 " --> pdb=" O   ARG A 963 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 991 through 997
      removed outlier: 4.494A  pdb=" N   ASP A 995 " --> pdb=" O   PRO A 991 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1006 through 1025
    Processing helix  chain 'A' and resid 1059 through 1083
      removed outlier: 3.806A  pdb=" N   CYS A1063 " --> pdb=" O   TRP A1059 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1114 through 1126
      removed outlier: 4.053A  pdb=" N   ASN A1118 " --> pdb=" O   GLY A1114 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 52 through 64
    Processing helix  chain 'B' and resid 89 through 113
      removed outlier: 4.171A  pdb=" N   SER B 111 " --> pdb=" O   VAL B 107 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   LEU B 113 " --> pdb=" O   ALA B 109 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 125 through 137
      removed outlier: 3.705A  pdb=" N   ASN B 136 " --> pdb=" O   LEU B 132 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   VAL B 137 " --> pdb=" O   SER B 133 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 143 through 156
    Processing helix  chain 'B' and resid 156 through 165
    Processing helix  chain 'B' and resid 174 through 180
      removed outlier: 3.571A  pdb=" N   PHE B 178 " --> pdb=" O   CYS B 174 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 181 through 187
      removed outlier: 4.315A  pdb=" N   GLN B 187 " --> pdb=" O   ASP B 183 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 193 through 199
    Processing helix  chain 'B' and resid 230 through 238
      removed outlier: 4.074A  pdb=" N   ILE B 235 " --> pdb=" O   ARG B 232 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   PHE B 238 " --> pdb=" O   ILE B 235 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 264 through 278
    Processing helix  chain 'B' and resid 293 through 304
    Processing helix  chain 'B' and resid 313 through 318
      removed outlier: 4.349A  pdb=" N   ARG B 317 " --> pdb=" O   PRO B 313 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 331 through 352
      removed outlier: 4.261A  pdb=" N   SER B 352 " --> pdb=" O   ILE B 348 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 368 through 388
      removed outlier: 3.741A  pdb=" N   ILE B 372 " --> pdb=" O   ASP B 368 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 410 through 417
      removed outlier: 5.356A  pdb=" N   ARG A 411 " --> pdb=" O   CYS A 519 " (cutoff:3.500A)
      removed outlier: 6.723A  pdb=" N   CYS A 519 " --> pdb=" O   ARG A 411 " (cutoff:3.500A)
      removed outlier: 5.453A  pdb=" N   GLU A 413 " --> pdb=" O   VAL A 517 " (cutoff:3.500A)
      removed outlier: 6.910A  pdb=" N   VAL A 517 " --> pdb=" O   GLU A 413 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 420 through 422
    Processing sheet with id=AA3, first strand: chain 'A' and resid 462 through 463
    Processing sheet with id=AA4, first strand: chain 'A' and resid 976 through 979
      removed outlier: 4.287A  pdb=" N   TYR A 976 " --> pdb=" O   VAL A1102 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1032 through 1038
      removed outlier: 7.467A  pdb=" N   MET A1043 " --> pdb=" O   ILE A1035 " (cutoff:3.500A)
      removed outlier: 4.546A  pdb=" N   THR A1037 " --> pdb=" O   THR A1041 " (cutoff:3.500A)
      removed outlier: 6.176A  pdb=" N   THR A1041 " --> pdb=" O   THR A1037 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   ILE A1091 " --> pdb=" O   GLN A1133 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   ILE A1132 " --> pdb=" O   GLN A1163 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 208 through 214
      removed outlier: 6.424A  pdb=" N   HIS B  41 " --> pdb=" O   HIS B 220 " (cutoff:3.500A)
      removed outlier: 7.859A  pdb=" N   PHE B 222 " --> pdb=" O   HIS B  41 " (cutoff:3.500A)
      removed outlier: 7.074A  pdb=" N   LEU B  43 " --> pdb=" O   PHE B 222 " (cutoff:3.500A)
      removed outlier: 6.696A  pdb=" N   ARG B  42 " --> pdb=" O   ALA B 243 " (cutoff:3.500A)
      removed outlier: 7.549A  pdb=" N   ILE B 245 " --> pdb=" O   ARG B  42 " (cutoff:3.500A)
      removed outlier: 6.258A  pdb=" N   LEU B  44 " --> pdb=" O   ILE B 245 " (cutoff:3.500A)
      removed outlier: 7.049A  pdb=" N   VAL B 247 " --> pdb=" O   LEU B  44 " (cutoff:3.500A)
      removed outlier: 5.821A  pdb=" N   ILE B 244 " --> pdb=" O   ILE B 288 " (cutoff:3.500A)
      removed outlier: 6.854A  pdb=" N   PHE B 290 " --> pdb=" O   ILE B 244 " (cutoff:3.500A)
      removed outlier: 6.210A  pdb=" N   PHE B 246 " --> pdb=" O   PHE B 290 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   ASN B 292 " --> pdb=" O   PHE B 246 " (cutoff:3.500A)
      removed outlier: 6.246A  pdb=" N   VAL B 248 " --> pdb=" O   ASN B 292 " (cutoff:3.500A)

    580 hydrogen bonds defined for protein.
    1698 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.56

  Time building geometry restraints manager: 0.97 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.20 -     1.32: 1642
        1.32 -     1.45: 2690
        1.45 -     1.57: 5688
        1.57 -     1.69: 5
        1.69 -     1.82: 95
  Bond restraints: 10120
  Sorted by residual:
  bond pdb=" N   VAL A 253 "
       pdb=" CA  VAL A 253 "
    ideal  model  delta    sigma   weight residual
    1.461  1.493 -0.032 1.19e-02 7.06e+03 7.21e+00
  bond pdb=" N   MET A 255 "
       pdb=" CA  MET A 255 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.23e-02 6.61e+03 5.65e+00
  bond pdb=" N   THR A 256 "
       pdb=" CA  THR A 256 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.21e-02 6.83e+03 5.64e+00
  bond pdb=" N   TRP A 252 "
       pdb=" CA  TRP A 252 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.028 1.19e-02 7.06e+03 5.62e+00
  bond pdb=" N   THR A 257 "
       pdb=" CA  THR A 257 "
    ideal  model  delta    sigma   weight residual
    1.459  1.487 -0.028 1.21e-02 6.83e+03 5.40e+00
  ... (remaining 10115 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.48: 13531
        2.48 -     4.95: 150
        4.95 -     7.43: 20
        7.43 -     9.91: 2
        9.91 -    12.38: 2
  Bond angle restraints: 13705
  Sorted by residual:
  angle pdb=" CA  LEU A 418 "
        pdb=" CB  LEU A 418 "
        pdb=" CG  LEU A 418 "
      ideal   model   delta    sigma   weight residual
     116.30  128.68  -12.38 3.50e+00 8.16e-02 1.25e+01
  angle pdb=" CB  MET A 741 "
        pdb=" CG  MET A 741 "
        pdb=" SD  MET A 741 "
      ideal   model   delta    sigma   weight residual
     112.70  122.84  -10.14 3.00e+00 1.11e-01 1.14e+01
  angle pdb=" C   ASN B 239 "
        pdb=" N   ASP B 240 "
        pdb=" CA  ASP B 240 "
      ideal   model   delta    sigma   weight residual
     121.54  127.68   -6.14 1.91e+00 2.74e-01 1.03e+01
  angle pdb=" CA  GLN A1145 "
        pdb=" CB  GLN A1145 "
        pdb=" CG  GLN A1145 "
      ideal   model   delta    sigma   weight residual
     114.10  120.33   -6.23 2.00e+00 2.50e-01 9.72e+00
  angle pdb=" CA  GLU A 950 "
        pdb=" CB  GLU A 950 "
        pdb=" CG  GLU A 950 "
      ideal   model   delta    sigma   weight residual
     114.10  120.29   -6.19 2.00e+00 2.50e-01 9.58e+00
  ... (remaining 13700 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.56: 5226
       17.56 -    35.12: 653
       35.12 -    52.68: 206
       52.68 -    70.24: 31
       70.24 -    87.80: 15
  Dihedral angle restraints: 6131
    sinusoidal: 2551
      harmonic: 3580
  Sorted by residual:
  dihedral pdb=" CA  CYS A 469 "
           pdb=" C   CYS A 469 "
           pdb=" N   VAL A 470 "
           pdb=" CA  VAL A 470 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.82   25.18     0      5.00e+00 4.00e-02 2.54e+01
  dihedral pdb=" CA  MET A1002 "
           pdb=" C   MET A1002 "
           pdb=" N   ASN A1003 "
           pdb=" CA  ASN A1003 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.01   19.99     0      5.00e+00 4.00e-02 1.60e+01
  dihedral pdb=" CA  CYS A 457 "
           pdb=" C   CYS A 457 "
           pdb=" N   LEU A 458 "
           pdb=" CA  LEU A 458 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.54   18.46     0      5.00e+00 4.00e-02 1.36e+01
  ... (remaining 6128 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 1265
       0.050 -    0.101: 242
       0.101 -    0.151: 41
       0.151 -    0.202: 6
       0.202 -    0.252: 1
  Chirality restraints: 1555
  Sorted by residual:
  chirality pdb=" C8  FOK A1301 "
            pdb=" C7  FOK A1301 "
            pdb=" C9  FOK A1301 "
            pdb=" O1  FOK A1301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.90    2.65    0.25 2.00e-01 2.50e+01 1.59e+00
  chirality pdb=" C6  FOK A1301 "
            pdb=" C5  FOK A1301 "
            pdb=" C7  FOK A1301 "
            pdb=" O3  FOK A1301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.28   -2.48    0.20 2.00e-01 2.50e+01 1.02e+00
  chirality pdb=" C7  FOK A1301 "
            pdb=" C6  FOK A1301 "
            pdb=" C8  FOK A1301 "
            pdb=" O4  FOK A1301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.45   -2.64    0.18 2.00e-01 2.50e+01 8.37e-01
  ... (remaining 1552 not shown)

  Planarity restraints: 1733
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 931 "   -0.020 2.00e-02 2.50e+03   1.59e-02 6.35e+00
        pdb=" CG  TRP A 931 "    0.043 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 931 "   -0.017 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 931 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 931 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 931 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 931 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 931 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 931 "   -0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 931 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 834 "    0.032 5.00e-02 4.00e+02   4.89e-02 3.83e+00
        pdb=" N   PRO A 835 "   -0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO A 835 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 835 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B 121 "   -0.031 5.00e-02 4.00e+02   4.81e-02 3.70e+00
        pdb=" N   PRO B 122 "    0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO B 122 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO B 122 "   -0.027 5.00e-02 4.00e+02
  ... (remaining 1730 not shown)

  Histogram of nonbonded interaction distances:
        1.92 -     2.51: 72
        2.51 -     3.11: 7486
        3.11 -     3.71: 15997
        3.71 -     4.30: 21502
        4.30 -     4.90: 35140
  Nonbonded interactions: 80197
  Sorted by model distance:
  nonbonded pdb=" O2B GSP B 501 "
            pdb="MG    MG B 502 "
     model   vdw
     1.915 2.170
  nonbonded pdb=" O2G GSP B 501 "
            pdb="MG    MG B 502 "
     model   vdw
     2.018 2.170
  nonbonded pdb=" O   VAL A 758 "
            pdb=" OG1 THR A 762 "
     model   vdw
     2.211 3.040
  nonbonded pdb=" O   ASP A 191 "
            pdb=" OG1 THR A 194 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" OG1 THR A1000 "
            pdb=" OD1 ASN A1003 "
     model   vdw
     2.252 3.040
  ... (remaining 80192 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.800
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.750
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.250
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7491
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10122  Z= 0.142
  Angle     :  0.620  12.382  13709  Z= 0.312
  Chirality :  0.041   0.252   1555
  Planarity :  0.003   0.049   1733
  Dihedral  : 17.226  87.803   3807
  Min Nonbonded Distance : 1.915

Molprobity Statistics.
  All-atom Clashscore : 11.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  : 27.73 %
    Favored  : 71.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.41 (0.24), residues: 1211
  helix:  1.23 (0.20), residues: 690
  sheet: -0.13 (0.48), residues: 108
  loop : -1.23 (0.31), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 496 
 TYR   0.020   0.001   TYR A 468 
 PHE   0.031   0.002   PHE A 448 
 TRP   0.043   0.001   TRP A 931 
 HIS   0.009   0.001   HIS A 399 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 (10120)
  covalent geometry    : angle       0.61992 (13705)
  SS BOND              : bond        0.00570 (    2)
  SS BOND              : angle       1.16833 (    4)
  hydrogen bonds       : bond        0.21678 (  580)
  hydrogen bonds       : angle       6.74466 ( 1698)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2422 Ramachandran restraints generated.
    1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2422 Ramachandran restraints generated.
    1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 132
  time to evaluate  : 0.402 
Fit side-chains
REVERT: A  418 LEU cc_start: 0.8741 (tt) cc_final: 0.8387 (tp)
REVERT: B  387 HIS cc_start: 0.5764 (OUTLIER) cc_final: 0.4721 (t70)
  outliers start: 5
  outliers final: 3
  residues processed: 135
  average time/residue: 0.0717
  time to fit residues: 14.5628
Evaluate side-chains
  129 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 125
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  442 ASN
Chi-restraints excluded: chain A residue  679 LEU
Chi-restraints excluded: chain B residue  291 LEU
Chi-restraints excluded: chain B residue  387 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    0.9980
   chunk 113 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.2980
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    0.0870
   chunk 117 optimal weight:    0.7980
   overall best weight:    0.5358

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 403 GLN
A 888 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.162144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.130754 restraints weight = 18998.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.132414 restraints weight = 10979.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.132805 restraints weight = 9152.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.133178 restraints weight = 7005.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.133510 restraints weight = 6643.205|
|-----------------------------------------------------------------------------|
r_work (final): 0.3806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7451
moved from start:          0.1162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10122  Z= 0.136
  Angle     :  0.592   9.108  13709  Z= 0.305
  Chirality :  0.041   0.176   1555
  Planarity :  0.004   0.044   1733
  Dihedral  :  5.289  48.205   1439
  Min Nonbonded Distance : 1.928

Molprobity Statistics.
  All-atom Clashscore : 9.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 24.49 %
    Favored  : 71.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.72 (0.24), residues: 1211
  helix:  1.42 (0.19), residues: 722
  sheet:  0.04 (0.47), residues: 101
  loop : -1.18 (0.33), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 127 
 TYR   0.016   0.001   TYR A 468 
 PHE   0.015   0.001   PHE A 176 
 TRP   0.021   0.001   TRP A 931 
 HIS   0.004   0.001   HIS B 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 (10120)
  covalent geometry    : angle       0.59201 (13705)
  SS BOND              : bond        0.00403 (    2)
  SS BOND              : angle       0.85404 (    4)
  hydrogen bonds       : bond        0.05512 (  580)
  hydrogen bonds       : angle       4.53034 ( 1698)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2422 Ramachandran restraints generated.
    1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2422 Ramachandran restraints generated.
    1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 139
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
REVERT: A  428 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8375 (mp)
REVERT: A  856 ASN cc_start: 0.7349 (t0) cc_final: 0.6966 (t0)
REVERT: B  194 ASP cc_start: 0.8190 (p0) cc_final: 0.7707 (t0)
  outliers start: 41
  outliers final: 13
  residues processed: 170
  average time/residue: 0.0730
  time to fit residues: 18.4823
Evaluate side-chains
  140 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 126
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  402 HIS
Chi-restraints excluded: chain A residue  426 THR
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  457 CYS
Chi-restraints excluded: chain A residue  727 PHE
Chi-restraints excluded: chain A residue  783 THR
Chi-restraints excluded: chain A residue  804 LEU
Chi-restraints excluded: chain A residue  865 LEU
Chi-restraints excluded: chain A residue 1046 SER
Chi-restraints excluded: chain A residue 1138 THR
Chi-restraints excluded: chain A residue 1151 TYR
Chi-restraints excluded: chain B residue   57 VAL
Chi-restraints excluded: chain B residue  107 VAL
Chi-restraints excluded: chain B residue  191 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 97 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   chunk 94 optimal weight:    3.9990
   chunk 22 optimal weight:    0.1980
   chunk 90 optimal weight:    0.9990
   chunk 14 optimal weight:    0.0980
   chunk 80 optimal weight:    0.9980
   chunk 106 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   chunk 100 optimal weight:    4.9990
   overall best weight:    0.6584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 213 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.161031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.128994 restraints weight = 19213.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.131116 restraints weight = 10657.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.131467 restraints weight = 8132.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.131737 restraints weight = 6623.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.131759 restraints weight = 6506.432|
|-----------------------------------------------------------------------------|
r_work (final): 0.3778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7508
moved from start:          0.1568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10122  Z= 0.130
  Angle     :  0.577   8.502  13709  Z= 0.295
  Chirality :  0.041   0.175   1555
  Planarity :  0.003   0.040   1733
  Dihedral  :  4.476  28.349   1431
  Min Nonbonded Distance : 1.903

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 25.14 %
    Favored  : 70.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.85 (0.24), residues: 1211
  helix:  1.55 (0.19), residues: 724
  sheet: -0.04 (0.46), residues: 107
  loop : -1.17 (0.33), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 127 
 TYR   0.019   0.001   TYR A 468 
 PHE   0.027   0.001   PHE A 176 
 TRP   0.013   0.001   TRP A 931 
 HIS   0.005   0.001   HIS B 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 (10120)
  covalent geometry    : angle       0.57634 (13705)
  SS BOND              : bond        0.00404 (    2)
  SS BOND              : angle       1.05470 (    4)
  hydrogen bonds       : bond        0.05003 (  580)
  hydrogen bonds       : angle       4.28036 ( 1698)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2422 Ramachandran restraints generated.
    1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2422 Ramachandran restraints generated.
    1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 143
  time to evaluate  : 0.249 
Fit side-chains
REVERT: A  406 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.7909 (ptm-80)
REVERT: A  787 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.6990 (ptp-170)
REVERT: A  861 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7645 (tt)
REVERT: A  879 TYR cc_start: 0.6001 (m-80) cc_final: 0.5082 (m-80)
REVERT: B  194 ASP cc_start: 0.8146 (p0) cc_final: 0.7761 (t0)
REVERT: B  255 MET cc_start: 0.8764 (mpp) cc_final: 0.8502 (mpp)
  outliers start: 42
  outliers final: 23
  residues processed: 174
  average time/residue: 0.0756
  time to fit residues: 19.4584
Evaluate side-chains
  151 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 125
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  363 LEU
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain A residue  402 HIS
Chi-restraints excluded: chain A residue  406 ARG
Chi-restraints excluded: chain A residue  426 THR
Chi-restraints excluded: chain A residue  457 CYS
Chi-restraints excluded: chain A residue  489 LEU
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain A residue  718 LEU
Chi-restraints excluded: chain A residue  727 PHE
Chi-restraints excluded: chain A residue  783 THR
Chi-restraints excluded: chain A residue  787 ARG
Chi-restraints excluded: chain A residue  804 LEU
Chi-restraints excluded: chain A residue  861 LEU
Chi-restraints excluded: chain A residue 1046 SER
Chi-restraints excluded: chain A residue 1138 THR
Chi-restraints excluded: chain A residue 1151 TYR
Chi-restraints excluded: chain A residue 1161 SER
Chi-restraints excluded: chain B residue   57 VAL
Chi-restraints excluded: chain B residue  107 VAL
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  203 LEU
Chi-restraints excluded: chain B residue  287 VAL
Chi-restraints excluded: chain B residue  294 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 78 optimal weight:    0.5980
   chunk 62 optimal weight:    6.9990
   chunk 39 optimal weight:    0.5980
   chunk 23 optimal weight:    1.9990
   chunk 110 optimal weight:    0.6980
   chunk 88 optimal weight:    2.9990
   chunk 83 optimal weight:    1.9990
   chunk 10 optimal weight:    4.9990
   chunk 59 optimal weight:    1.9990
   chunk 44 optimal weight:    0.3980
   chunk 52 optimal weight:    0.8980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 258 GLN
** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 582 HIS
A 781 ASN
A 949 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.160804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.129528 restraints weight = 19134.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.130478 restraints weight = 11282.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.131045 restraints weight = 9658.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.131421 restraints weight = 7365.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.131579 restraints weight = 7188.095|
|-----------------------------------------------------------------------------|
r_work (final): 0.3787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7495
moved from start:          0.1939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10122  Z= 0.125
  Angle     :  0.567   7.181  13709  Z= 0.289
  Chirality :  0.041   0.175   1555
  Planarity :  0.003   0.038   1733
  Dihedral  :  4.414  25.123   1431
  Min Nonbonded Distance : 1.919

Molprobity Statistics.
  All-atom Clashscore : 9.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 25.14 %
    Favored  : 70.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.90 (0.24), residues: 1211
  helix:  1.62 (0.19), residues: 726
  sheet:  0.17 (0.50), residues: 92
  loop : -1.25 (0.32), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 127 
 TYR   0.018   0.001   TYR A 468 
 PHE   0.026   0.001   PHE A 799 
 TRP   0.012   0.001   TRP A 931 
 HIS   0.005   0.001   HIS A 399 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 (10120)
  covalent geometry    : angle       0.56647 (13705)
  SS BOND              : bond        0.00482 (    2)
  SS BOND              : angle       1.05719 (    4)
  hydrogen bonds       : bond        0.04704 (  580)
  hydrogen bonds       : angle       4.10749 ( 1698)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2422 Ramachandran restraints generated.
    1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2422 Ramachandran restraints generated.
    1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 140
  time to evaluate  : 0.283 
Fit side-chains
REVERT: A  406 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.7916 (ptm-80)
REVERT: A  787 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7308 (ptp-170)
REVERT: A  861 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7729 (tt)
REVERT: A  879 TYR cc_start: 0.5917 (m-80) cc_final: 0.4981 (m-80)
REVERT: A  952 MET cc_start: 0.7611 (OUTLIER) cc_final: 0.7209 (ttm)
  outliers start: 42
  outliers final: 25
  residues processed: 172
  average time/residue: 0.0672
  time to fit residues: 17.5992
Evaluate side-chains
  154 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 125
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 PHE
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain A residue  402 HIS
Chi-restraints excluded: chain A residue  406 ARG
Chi-restraints excluded: chain A residue  409 ILE
Chi-restraints excluded: chain A residue  426 THR
Chi-restraints excluded: chain A residue  457 CYS
Chi-restraints excluded: chain A residue  463 LEU
Chi-restraints excluded: chain A residue  489 LEU
Chi-restraints excluded: chain A residue  718 LEU
Chi-restraints excluded: chain A residue  783 THR
Chi-restraints excluded: chain A residue  787 ARG
Chi-restraints excluded: chain A residue  804 LEU
Chi-restraints excluded: chain A residue  861 LEU
Chi-restraints excluded: chain A residue  927 LEU
Chi-restraints excluded: chain A residue  928 ASP
Chi-restraints excluded: chain A residue  947 GLU
Chi-restraints excluded: chain A residue  952 MET
Chi-restraints excluded: chain A residue 1046 SER
Chi-restraints excluded: chain A residue 1138 THR
Chi-restraints excluded: chain A residue 1151 TYR
Chi-restraints excluded: chain A residue 1161 SER
Chi-restraints excluded: chain B residue   57 VAL
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  287 VAL
Chi-restraints excluded: chain B residue  294 GLN
Chi-restraints excluded: chain B residue  379 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 78 optimal weight:    0.7980
   chunk 16 optimal weight:    0.7980
   chunk 95 optimal weight:    0.8980
   chunk 15 optimal weight:    0.0870
   chunk 0 optimal weight:    8.9990
   chunk 32 optimal weight:    0.7980
   chunk 14 optimal weight:    4.9990
   chunk 42 optimal weight:    0.0970
   chunk 87 optimal weight:    6.9990
   chunk 113 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9990
   overall best weight:    0.5156

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.160947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.124377 restraints weight = 19610.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.128110 restraints weight = 10159.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.130548 restraints weight = 6816.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.131999 restraints weight = 5353.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.132759 restraints weight = 4625.246|
|-----------------------------------------------------------------------------|
r_work (final): 0.3799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7503
moved from start:          0.2102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10122  Z= 0.119
  Angle     :  0.561   8.089  13709  Z= 0.284
  Chirality :  0.041   0.175   1555
  Planarity :  0.003   0.037   1733
  Dihedral  :  4.374  24.490   1431
  Min Nonbonded Distance : 1.937

Molprobity Statistics.
  All-atom Clashscore : 9.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 25.42 %
    Favored  : 70.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.93 (0.24), residues: 1211
  helix:  1.65 (0.19), residues: 726
  sheet:  0.14 (0.50), residues: 92
  loop : -1.23 (0.32), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 127 
 TYR   0.017   0.001   TYR A 468 
 PHE   0.026   0.001   PHE A 799 
 TRP   0.010   0.001   TRP A 931 
 HIS   0.004   0.001   HIS B 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 (10120)
  covalent geometry    : angle       0.56068 (13705)
  SS BOND              : bond        0.00475 (    2)
  SS BOND              : angle       1.16552 (    4)
  hydrogen bonds       : bond        0.04542 (  580)
  hydrogen bonds       : angle       4.01962 ( 1698)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2422 Ramachandran restraints generated.
    1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2422 Ramachandran restraints generated.
    1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 131
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
REVERT: A  406 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.7922 (ptm-80)
REVERT: A  709 MET cc_start: 0.6063 (tpp) cc_final: 0.5839 (tpt)
REVERT: A  787 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7292 (ptp-170)
REVERT: A  952 MET cc_start: 0.7568 (OUTLIER) cc_final: 0.7147 (ttm)
REVERT: B  387 HIS cc_start: 0.5743 (OUTLIER) cc_final: 0.4867 (t70)
  outliers start: 45
  outliers final: 28
  residues processed: 166
  average time/residue: 0.0724
  time to fit residues: 18.2282
Evaluate side-chains
  155 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 123
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 PHE
Chi-restraints excluded: chain A residue  301 THR
Chi-restraints excluded: chain A residue  354 GLU
Chi-restraints excluded: chain A residue  363 LEU
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain A residue  402 HIS
Chi-restraints excluded: chain A residue  406 ARG
Chi-restraints excluded: chain A residue  409 ILE
Chi-restraints excluded: chain A residue  426 THR
Chi-restraints excluded: chain A residue  457 CYS
Chi-restraints excluded: chain A residue  463 LEU
Chi-restraints excluded: chain A residue  489 LEU
Chi-restraints excluded: chain A residue  783 THR
Chi-restraints excluded: chain A residue  785 LEU
Chi-restraints excluded: chain A residue  787 ARG
Chi-restraints excluded: chain A residue  804 LEU
Chi-restraints excluded: chain A residue  871 TYR
Chi-restraints excluded: chain A residue  927 LEU
Chi-restraints excluded: chain A residue  952 MET
Chi-restraints excluded: chain A residue 1038 ILE
Chi-restraints excluded: chain A residue 1046 SER
Chi-restraints excluded: chain A residue 1138 THR
Chi-restraints excluded: chain A residue 1151 TYR
Chi-restraints excluded: chain A residue 1161 SER
Chi-restraints excluded: chain B residue   57 VAL
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  203 LEU
Chi-restraints excluded: chain B residue  287 VAL
Chi-restraints excluded: chain B residue  294 GLN
Chi-restraints excluded: chain B residue  379 CYS
Chi-restraints excluded: chain B residue  387 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 99 optimal weight:    4.9990
   chunk 50 optimal weight:    4.9990
   chunk 14 optimal weight:    0.9990
   chunk 23 optimal weight:    4.9990
   chunk 117 optimal weight:    0.7980
   chunk 21 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9980
   chunk 55 optimal weight:    0.5980
   chunk 100 optimal weight:    4.9990
   chunk 89 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9980
   overall best weight:    0.8782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 326 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.156644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.120134 restraints weight = 19679.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.123471 restraints weight = 10409.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.125667 restraints weight = 7117.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.127080 restraints weight = 5645.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.127739 restraints weight = 4902.570|
|-----------------------------------------------------------------------------|
r_work (final): 0.3724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7534
moved from start:          0.2297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10122  Z= 0.139
  Angle     :  0.594   9.397  13709  Z= 0.300
  Chirality :  0.041   0.174   1555
  Planarity :  0.003   0.036   1733
  Dihedral  :  4.481  26.027   1431
  Min Nonbonded Distance : 1.876

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 24.95 %
    Favored  : 70.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.86 (0.24), residues: 1211
  helix:  1.61 (0.19), residues: 723
  sheet: -0.11 (0.46), residues: 107
  loop : -1.24 (0.33), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 317 
 TYR   0.020   0.001   TYR A 468 
 PHE   0.028   0.002   PHE A 799 
 TRP   0.008   0.001   TRP A 931 
 HIS   0.004   0.001   HIS A 402 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 (10120)
  covalent geometry    : angle       0.59325 (13705)
  SS BOND              : bond        0.00747 (    2)
  SS BOND              : angle       1.16637 (    4)
  hydrogen bonds       : bond        0.04719 (  580)
  hydrogen bonds       : angle       4.04696 ( 1698)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2422 Ramachandran restraints generated.
    1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2422 Ramachandran restraints generated.
    1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 122
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
REVERT: A  406 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.7905 (ptm-80)
REVERT: A  787 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7358 (ptp-170)
REVERT: A  879 TYR cc_start: 0.6022 (m-80) cc_final: 0.5069 (m-80)
REVERT: A  952 MET cc_start: 0.7587 (OUTLIER) cc_final: 0.7257 (ttm)
REVERT: A 1139 TYR cc_start: 0.5934 (OUTLIER) cc_final: 0.5245 (p90)
REVERT: B  387 HIS cc_start: 0.5903 (OUTLIER) cc_final: 0.5012 (t70)
  outliers start: 50
  outliers final: 34
  residues processed: 160
  average time/residue: 0.0730
  time to fit residues: 17.7156
Evaluate side-chains
  159 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 120
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  301 THR
Chi-restraints excluded: chain A residue  354 GLU
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain A residue  402 HIS
Chi-restraints excluded: chain A residue  406 ARG
Chi-restraints excluded: chain A residue  409 ILE
Chi-restraints excluded: chain A residue  426 THR
Chi-restraints excluded: chain A residue  432 LEU
Chi-restraints excluded: chain A residue  457 CYS
Chi-restraints excluded: chain A residue  458 LEU
Chi-restraints excluded: chain A residue  463 LEU
Chi-restraints excluded: chain A residue  489 LEU
Chi-restraints excluded: chain A residue  679 LEU
Chi-restraints excluded: chain A residue  783 THR
Chi-restraints excluded: chain A residue  787 ARG
Chi-restraints excluded: chain A residue  804 LEU
Chi-restraints excluded: chain A residue  871 TYR
Chi-restraints excluded: chain A residue  927 LEU
Chi-restraints excluded: chain A residue  928 ASP
Chi-restraints excluded: chain A residue  933 VAL
Chi-restraints excluded: chain A residue  947 GLU
Chi-restraints excluded: chain A residue  952 MET
Chi-restraints excluded: chain A residue 1038 ILE
Chi-restraints excluded: chain A residue 1046 SER
Chi-restraints excluded: chain A residue 1103 ILE
Chi-restraints excluded: chain A residue 1138 THR
Chi-restraints excluded: chain A residue 1139 TYR
Chi-restraints excluded: chain A residue 1151 TYR
Chi-restraints excluded: chain A residue 1161 SER
Chi-restraints excluded: chain B residue   57 VAL
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  203 LEU
Chi-restraints excluded: chain B residue  287 VAL
Chi-restraints excluded: chain B residue  294 GLN
Chi-restraints excluded: chain B residue  387 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 2 optimal weight:    0.8980
   chunk 109 optimal weight:    0.7980
   chunk 63 optimal weight:    0.6980
   chunk 106 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0670
   chunk 54 optimal weight:    2.9990
   chunk 41 optimal weight:    0.0010
   chunk 24 optimal weight:    1.9990
   chunk 73 optimal weight:    1.9990
   chunk 39 optimal weight:    5.9990
   chunk 76 optimal weight:    0.7980
   overall best weight:    0.4724

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.158749 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.124425 restraints weight = 19532.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.125533 restraints weight = 10722.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.126304 restraints weight = 7627.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.126667 restraints weight = 7476.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.126957 restraints weight = 6653.526|
|-----------------------------------------------------------------------------|
r_work (final): 0.3708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7565
moved from start:          0.2490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  10122  Z= 0.116
  Angle     :  0.570   8.297  13709  Z= 0.286
  Chirality :  0.041   0.195   1555
  Planarity :  0.003   0.035   1733
  Dihedral  :  4.362  25.153   1431
  Min Nonbonded Distance : 1.968

Molprobity Statistics.
  All-atom Clashscore : 9.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 26.16 %
    Favored  : 69.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.02 (0.25), residues: 1211
  helix:  1.73 (0.19), residues: 727
  sheet: -0.02 (0.47), residues: 102
  loop : -1.20 (0.33), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 926 
 TYR   0.016   0.001   TYR A 468 
 PHE   0.029   0.001   PHE A 799 
 TRP   0.009   0.001   TRP A 931 
 HIS   0.004   0.001   HIS A 402 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 (10120)
  covalent geometry    : angle       0.56982 (13705)
  SS BOND              : bond        0.00637 (    2)
  SS BOND              : angle       0.76943 (    4)
  hydrogen bonds       : bond        0.04375 (  580)
  hydrogen bonds       : angle       3.95413 ( 1698)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2422 Ramachandran restraints generated.
    1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2422 Ramachandran restraints generated.
    1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 137
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
REVERT: A  406 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.7887 (ptm-80)
REVERT: A  709 MET cc_start: 0.6063 (tpp) cc_final: 0.5780 (tpt)
REVERT: A  741 MET cc_start: 0.6418 (mmm) cc_final: 0.4328 (tmm)
REVERT: A  787 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7254 (ptp-170)
REVERT: A  879 TYR cc_start: 0.5998 (m-80) cc_final: 0.5392 (m-80)
REVERT: A  952 MET cc_start: 0.7538 (OUTLIER) cc_final: 0.7136 (ttm)
REVERT: B  387 HIS cc_start: 0.5942 (OUTLIER) cc_final: 0.5098 (t70)
  outliers start: 42
  outliers final: 29
  residues processed: 167
  average time/residue: 0.0737
  time to fit residues: 18.3949
Evaluate side-chains
  159 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 126
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 PHE
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  301 THR
Chi-restraints excluded: chain A residue  354 GLU
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain A residue  402 HIS
Chi-restraints excluded: chain A residue  406 ARG
Chi-restraints excluded: chain A residue  409 ILE
Chi-restraints excluded: chain A residue  426 THR
Chi-restraints excluded: chain A residue  432 LEU
Chi-restraints excluded: chain A residue  457 CYS
Chi-restraints excluded: chain A residue  463 LEU
Chi-restraints excluded: chain A residue  727 PHE
Chi-restraints excluded: chain A residue  783 THR
Chi-restraints excluded: chain A residue  787 ARG
Chi-restraints excluded: chain A residue  804 LEU
Chi-restraints excluded: chain A residue  858 VAL
Chi-restraints excluded: chain A residue  871 TYR
Chi-restraints excluded: chain A residue  927 LEU
Chi-restraints excluded: chain A residue  928 ASP
Chi-restraints excluded: chain A residue  952 MET
Chi-restraints excluded: chain A residue 1038 ILE
Chi-restraints excluded: chain A residue 1046 SER
Chi-restraints excluded: chain A residue 1138 THR
Chi-restraints excluded: chain A residue 1151 TYR
Chi-restraints excluded: chain A residue 1161 SER
Chi-restraints excluded: chain B residue  107 VAL
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  203 LEU
Chi-restraints excluded: chain B residue  287 VAL
Chi-restraints excluded: chain B residue  294 GLN
Chi-restraints excluded: chain B residue  387 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 105 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9980
   chunk 57 optimal weight:    1.9990
   chunk 56 optimal weight:    0.8980
   chunk 90 optimal weight:    0.4980
   chunk 58 optimal weight:    0.5980
   chunk 115 optimal weight:    3.9990
   chunk 84 optimal weight:    1.9990
   chunk 92 optimal weight:    0.9990
   chunk 67 optimal weight:    3.9990
   chunk 16 optimal weight:    0.7980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.157251 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.125032 restraints weight = 19503.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.126692 restraints weight = 11307.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.127142 restraints weight = 8780.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.127415 restraints weight = 6981.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.127579 restraints weight = 6862.978|
|-----------------------------------------------------------------------------|
r_work (final): 0.3726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7533
moved from start:          0.2556

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10122  Z= 0.132
  Angle     :  0.588   7.136  13709  Z= 0.296
  Chirality :  0.041   0.190   1555
  Planarity :  0.003   0.037   1733
  Dihedral  :  4.415  25.858   1431
  Min Nonbonded Distance : 1.897

Molprobity Statistics.
  All-atom Clashscore : 10.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 26.52 %
    Favored  : 69.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.96 (0.25), residues: 1211
  helix:  1.69 (0.19), residues: 727
  sheet: -0.14 (0.46), residues: 107
  loop : -1.21 (0.33), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 127 
 TYR   0.019   0.001   TYR A 468 
 PHE   0.029   0.002   PHE A 799 
 TRP   0.008   0.001   TRP A 931 
 HIS   0.004   0.001   HIS A 480 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 (10120)
  covalent geometry    : angle       0.58803 (13705)
  SS BOND              : bond        0.00551 (    2)
  SS BOND              : angle       1.10072 (    4)
  hydrogen bonds       : bond        0.04508 (  580)
  hydrogen bonds       : angle       3.97883 ( 1698)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2422 Ramachandran restraints generated.
    1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2422 Ramachandran restraints generated.
    1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 130
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
REVERT: A  373 GLU cc_start: 0.7576 (tm-30) cc_final: 0.7369 (tm-30)
REVERT: A  406 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.7872 (ptm-80)
REVERT: A  709 MET cc_start: 0.6274 (tpp) cc_final: 0.6073 (tpt)
REVERT: A  741 MET cc_start: 0.6357 (mmm) cc_final: 0.4213 (tmm)
REVERT: A  787 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.7475 (ptp-170)
REVERT: A  795 ILE cc_start: 0.8149 (tt) cc_final: 0.7946 (tt)
REVERT: A  952 MET cc_start: 0.7597 (OUTLIER) cc_final: 0.7242 (ttm)
REVERT: B  387 HIS cc_start: 0.5957 (OUTLIER) cc_final: 0.5095 (t70)
  outliers start: 41
  outliers final: 31
  residues processed: 163
  average time/residue: 0.0712
  time to fit residues: 17.5392
Evaluate side-chains
  158 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 123
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 PHE
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  301 THR
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain A residue  402 HIS
Chi-restraints excluded: chain A residue  406 ARG
Chi-restraints excluded: chain A residue  409 ILE
Chi-restraints excluded: chain A residue  426 THR
Chi-restraints excluded: chain A residue  432 LEU
Chi-restraints excluded: chain A residue  457 CYS
Chi-restraints excluded: chain A residue  463 LEU
Chi-restraints excluded: chain A residue  489 LEU
Chi-restraints excluded: chain A residue  783 THR
Chi-restraints excluded: chain A residue  787 ARG
Chi-restraints excluded: chain A residue  796 LEU
Chi-restraints excluded: chain A residue  804 LEU
Chi-restraints excluded: chain A residue  849 CYS
Chi-restraints excluded: chain A residue  858 VAL
Chi-restraints excluded: chain A residue  871 TYR
Chi-restraints excluded: chain A residue  927 LEU
Chi-restraints excluded: chain A residue  928 ASP
Chi-restraints excluded: chain A residue  933 VAL
Chi-restraints excluded: chain A residue  952 MET
Chi-restraints excluded: chain A residue 1038 ILE
Chi-restraints excluded: chain A residue 1046 SER
Chi-restraints excluded: chain A residue 1138 THR
Chi-restraints excluded: chain A residue 1151 TYR
Chi-restraints excluded: chain A residue 1161 SER
Chi-restraints excluded: chain B residue  107 VAL
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  287 VAL
Chi-restraints excluded: chain B residue  294 GLN
Chi-restraints excluded: chain B residue  387 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 103 optimal weight:    5.9990
   chunk 30 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9980
   chunk 97 optimal weight:    0.9980
   chunk 41 optimal weight:    3.9990
   chunk 119 optimal weight:    0.9990
   chunk 84 optimal weight:    1.9990
   chunk 50 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9980
   chunk 62 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   overall best weight:    1.1984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 403 GLN
A 781 ASN
** A1145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.154471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.118009 restraints weight = 19450.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.121302 restraints weight = 10352.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.123446 restraints weight = 7090.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.124747 restraints weight = 5652.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.125365 restraints weight = 4934.206|
|-----------------------------------------------------------------------------|
r_work (final): 0.3695
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7595
moved from start:          0.2751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  10122  Z= 0.164
  Angle     :  0.633   7.622  13709  Z= 0.322
  Chirality :  0.043   0.184   1555
  Planarity :  0.004   0.037   1733
  Dihedral  :  4.661  29.037   1431
  Min Nonbonded Distance : 1.841

Molprobity Statistics.
  All-atom Clashscore : 11.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 25.79 %
    Favored  : 69.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.69 (0.24), residues: 1211
  helix:  1.48 (0.19), residues: 729
  sheet: -0.03 (0.46), residues: 112
  loop : -1.44 (0.32), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 439 
 TYR   0.022   0.001   TYR A 468 
 PHE   0.030   0.002   PHE A 799 
 TRP   0.007   0.001   TRP A1113 
 HIS   0.005   0.001   HIS A 402 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 (10120)
  covalent geometry    : angle       0.63296 (13705)
  SS BOND              : bond        0.00566 (    2)
  SS BOND              : angle       1.31635 (    4)
  hydrogen bonds       : bond        0.04983 (  580)
  hydrogen bonds       : angle       4.09454 ( 1698)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2422 Ramachandran restraints generated.
    1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2422 Ramachandran restraints generated.
    1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 126
  time to evaluate  : 0.300 
Fit side-chains
REVERT: A  406 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.7832 (ptm-80)
REVERT: A  741 MET cc_start: 0.6370 (mmm) cc_final: 0.4294 (tmm)
REVERT: A  787 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7453 (ptp-170)
REVERT: A  952 MET cc_start: 0.7647 (OUTLIER) cc_final: 0.7304 (ttm)
REVERT: A 1139 TYR cc_start: 0.6198 (OUTLIER) cc_final: 0.5341 (p90)
REVERT: B  387 HIS cc_start: 0.5994 (OUTLIER) cc_final: 0.5117 (t70)
  outliers start: 46
  outliers final: 32
  residues processed: 160
  average time/residue: 0.0783
  time to fit residues: 18.3291
Evaluate side-chains
  159 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 122
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  301 THR
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  402 HIS
Chi-restraints excluded: chain A residue  406 ARG
Chi-restraints excluded: chain A residue  409 ILE
Chi-restraints excluded: chain A residue  426 THR
Chi-restraints excluded: chain A residue  432 LEU
Chi-restraints excluded: chain A residue  457 CYS
Chi-restraints excluded: chain A residue  463 LEU
Chi-restraints excluded: chain A residue  489 LEU
Chi-restraints excluded: chain A residue  783 THR
Chi-restraints excluded: chain A residue  787 ARG
Chi-restraints excluded: chain A residue  796 LEU
Chi-restraints excluded: chain A residue  804 LEU
Chi-restraints excluded: chain A residue  858 VAL
Chi-restraints excluded: chain A residue  871 TYR
Chi-restraints excluded: chain A residue  927 LEU
Chi-restraints excluded: chain A residue  928 ASP
Chi-restraints excluded: chain A residue  933 VAL
Chi-restraints excluded: chain A residue  952 MET
Chi-restraints excluded: chain A residue 1038 ILE
Chi-restraints excluded: chain A residue 1046 SER
Chi-restraints excluded: chain A residue 1103 ILE
Chi-restraints excluded: chain A residue 1138 THR
Chi-restraints excluded: chain A residue 1139 TYR
Chi-restraints excluded: chain A residue 1147 PHE
Chi-restraints excluded: chain A residue 1151 TYR
Chi-restraints excluded: chain A residue 1161 SER
Chi-restraints excluded: chain B residue  107 VAL
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  203 LEU
Chi-restraints excluded: chain B residue  287 VAL
Chi-restraints excluded: chain B residue  294 GLN
Chi-restraints excluded: chain B residue  387 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 31 optimal weight:    0.6980
   chunk 59 optimal weight:    0.2980
   chunk 65 optimal weight:    1.9990
   chunk 84 optimal weight:    0.8980
   chunk 15 optimal weight:    0.8980
   chunk 108 optimal weight:    0.0270
   chunk 66 optimal weight:    0.8980
   chunk 93 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9990
   chunk 14 optimal weight:    5.9990
   chunk 22 optimal weight:    0.9980
   overall best weight:    0.5638

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 403 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.157154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.122722 restraints weight = 19379.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.123785 restraints weight = 10783.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.124612 restraints weight = 7716.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.124960 restraints weight = 7505.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.125238 restraints weight = 6680.649|
|-----------------------------------------------------------------------------|
r_work (final): 0.3685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7600
moved from start:          0.2849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  10122  Z= 0.126
  Angle     :  0.611  10.351  13709  Z= 0.306
  Chirality :  0.042   0.204   1555
  Planarity :  0.003   0.038   1733
  Dihedral  :  4.509  27.792   1431
  Min Nonbonded Distance : 1.948

Molprobity Statistics.
  All-atom Clashscore : 10.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 27.45 %
    Favored  : 69.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.91 (0.25), residues: 1211
  helix:  1.63 (0.19), residues: 728
  sheet: -0.03 (0.45), residues: 112
  loop : -1.26 (0.33), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 356 
 TYR   0.017   0.001   TYR A 468 
 PHE   0.032   0.002   PHE A 799 
 TRP   0.013   0.001   TRP A 808 
 HIS   0.010   0.001   HIS A 399 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 (10120)
  covalent geometry    : angle       0.61052 (13705)
  SS BOND              : bond        0.00610 (    2)
  SS BOND              : angle       1.05022 (    4)
  hydrogen bonds       : bond        0.04535 (  580)
  hydrogen bonds       : angle       4.04525 ( 1698)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2422 Ramachandran restraints generated.
    1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2422 Ramachandran restraints generated.
    1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 130
  time to evaluate  : 0.346 
Fit side-chains
REVERT: A  255 MET cc_start: 0.8334 (mmm) cc_final: 0.7589 (mmt)
REVERT: A  406 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.7811 (ptm-80)
REVERT: A  741 MET cc_start: 0.6312 (mmm) cc_final: 0.4287 (tmm)
REVERT: A  952 MET cc_start: 0.7583 (OUTLIER) cc_final: 0.7205 (ttm)
REVERT: B  387 HIS cc_start: 0.5970 (OUTLIER) cc_final: 0.5153 (t70)
  outliers start: 32
  outliers final: 25
  residues processed: 153
  average time/residue: 0.0713
  time to fit residues: 16.7691
Evaluate side-chains
  152 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 124
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  301 THR
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  406 ARG
Chi-restraints excluded: chain A residue  409 ILE
Chi-restraints excluded: chain A residue  426 THR
Chi-restraints excluded: chain A residue  432 LEU
Chi-restraints excluded: chain A residue  457 CYS
Chi-restraints excluded: chain A residue  463 LEU
Chi-restraints excluded: chain A residue  489 LEU
Chi-restraints excluded: chain A residue  783 THR
Chi-restraints excluded: chain A residue  804 LEU
Chi-restraints excluded: chain A residue  858 VAL
Chi-restraints excluded: chain A residue  871 TYR
Chi-restraints excluded: chain A residue  927 LEU
Chi-restraints excluded: chain A residue  928 ASP
Chi-restraints excluded: chain A residue  933 VAL
Chi-restraints excluded: chain A residue  952 MET
Chi-restraints excluded: chain A residue 1038 ILE
Chi-restraints excluded: chain A residue 1046 SER
Chi-restraints excluded: chain A residue 1103 ILE
Chi-restraints excluded: chain A residue 1138 THR
Chi-restraints excluded: chain A residue 1151 TYR
Chi-restraints excluded: chain A residue 1161 SER
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  287 VAL
Chi-restraints excluded: chain B residue  294 GLN
Chi-restraints excluded: chain B residue  387 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 117 optimal weight:    0.5980
   chunk 50 optimal weight:    3.9990
   chunk 47 optimal weight:    0.7980
   chunk 37 optimal weight:    0.0870
   chunk 6 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9990
   chunk 87 optimal weight:    0.7980
   chunk 107 optimal weight:    2.9990
   chunk 14 optimal weight:    6.9990
   chunk 70 optimal weight:    4.9990
   overall best weight:    0.6560

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.157125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.122784 restraints weight = 19494.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.123721 restraints weight = 10874.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.124344 restraints weight = 7822.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.124820 restraints weight = 7521.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.125090 restraints weight = 6791.286|
|-----------------------------------------------------------------------------|
r_work (final): 0.3687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
moved from start:          0.2907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  10122  Z= 0.131
  Angle     :  0.617   9.947  13709  Z= 0.312
  Chirality :  0.042   0.203   1555
  Planarity :  0.003   0.038   1733
  Dihedral  :  4.512  27.331   1431
  Min Nonbonded Distance : 1.910

Molprobity Statistics.
  All-atom Clashscore : 10.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 27.63 %
    Favored  : 69.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.88 (0.25), residues: 1211
  helix:  1.61 (0.19), residues: 727
  sheet: -0.05 (0.45), residues: 112
  loop : -1.28 (0.33), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 356 
 TYR   0.018   0.001   TYR A 468 
 PHE   0.032   0.002   PHE A 799 
 TRP   0.017   0.001   TRP A 808 
 HIS   0.008   0.001   HIS A 399 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 (10120)
  covalent geometry    : angle       0.61651 (13705)
  SS BOND              : bond        0.00581 (    2)
  SS BOND              : angle       1.09809 (    4)
  hydrogen bonds       : bond        0.04556 (  580)
  hydrogen bonds       : angle       4.07061 ( 1698)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1684.98 seconds
wall clock time: 29 minutes 41.80 seconds (1781.80 seconds total)