Starting phenix.real_space_refine on Thu Mar 5 14:55:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kgf_22868/03_2026/7kgf_22868.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kgf_22868/03_2026/7kgf_22868.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7kgf_22868/03_2026/7kgf_22868.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kgf_22868/03_2026/7kgf_22868.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7kgf_22868/03_2026/7kgf_22868.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kgf_22868/03_2026/7kgf_22868.map" } resolution = 3.42 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 ------------------------------------------------------------------------------- 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= 0.139 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: 4 Type Number sf(0) Gaussians S 135 5.16 5 C 15120 2.51 5 N 3792 2.21 5 O 4308 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 129 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23355 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1020, 7785 Classifications: {'peptide': 1020} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 973} Chain breaks: 1 Restraints were copied for chains: B, C Time building chain proxies: 7.94, per 1000 atoms: 0.34 Number of scatterers: 23355 At special positions: 0 Unit cell: (119.88, 123.12, 140.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 135 16.00 O 4308 8.00 N 3792 7.00 C 15120 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.95 Conformation dependent library (CDL) restraints added in 931.1 milliseconds 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5706 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 24 sheets defined 61.6% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 3 through 8 Processing helix chain 'A' and resid 8 through 30 removed outlier: 4.289A pdb=" N ALA A 12 " --> pdb=" O ARG A 8 " (cutoff:3.500A) Proline residue: A 28 - end of helix Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 61 through 70 removed outlier: 3.777A pdb=" N ARG A 67 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLU A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 116 removed outlier: 4.290A pdb=" N ALA A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 126 removed outlier: 3.626A pdb=" N GLN A 125 " --> pdb=" O VAL A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 161 Processing helix chain 'A' and resid 161 through 169 removed outlier: 3.545A pdb=" N ARG A 168 " --> pdb=" O GLU A 164 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL A 169 " --> pdb=" O GLU A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 197 removed outlier: 3.652A pdb=" N LEU A 193 " --> pdb=" O ASP A 189 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 194 " --> pdb=" O PRO A 190 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER A 195 " --> pdb=" O ASN A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 211 Processing helix chain 'A' and resid 242 through 248 removed outlier: 3.615A pdb=" N PHE A 246 " --> pdb=" O SER A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 265 No H-bonds generated for 'chain 'A' and resid 262 through 265' Processing helix chain 'A' and resid 298 through 314 Processing helix chain 'A' and resid 329 through 360 removed outlier: 3.915A pdb=" N VAL A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LYS A 334 " --> pdb=" O ALA A 330 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE A 335 " --> pdb=" O PRO A 331 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET A 355 " --> pdb=" O VAL A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 387 removed outlier: 4.064A pdb=" N ILE A 367 " --> pdb=" O ARG A 363 " (cutoff:3.500A) Proline residue: A 368 - end of helix removed outlier: 3.852A pdb=" N VAL A 371 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA A 372 " --> pdb=" O PRO A 368 " (cutoff:3.500A) Proline residue: A 373 - end of helix Processing helix chain 'A' and resid 391 through 406 removed outlier: 4.498A pdb=" N GLY A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL A 406 " --> pdb=" O ILE A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 424 Processing helix chain 'A' and resid 426 through 453 removed outlier: 5.326A pdb=" N SER A 440 " --> pdb=" O LYS A 436 " (cutoff:3.500A) Proline residue: A 441 - end of helix removed outlier: 4.319A pdb=" N PHE A 453 " --> pdb=" O LEU A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 458 removed outlier: 3.630A pdb=" N ALA A 457 " --> pdb=" O PHE A 453 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE A 458 " --> pdb=" O LEU A 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 453 through 458' Processing helix chain 'A' and resid 460 through 497 removed outlier: 3.571A pdb=" N GLY A 464 " --> pdb=" O SER A 460 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR A 473 " --> pdb=" O GLN A 469 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N THR A 489 " --> pdb=" O ALA A 485 " (cutoff:3.500A) Proline residue: A 490 - end of helix Processing helix chain 'A' and resid 509 through 534 Processing helix chain 'A' and resid 535 through 556 Processing helix chain 'A' and resid 580 through 597 removed outlier: 3.609A pdb=" N THR A 584 " --> pdb=" O THR A 580 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASP A 597 " --> pdb=" O ASN A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 632 Processing helix chain 'A' and resid 635 through 650 Processing helix chain 'A' and resid 683 through 701 removed outlier: 3.681A pdb=" N LYS A 700 " --> pdb=" O ALA A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 730 Processing helix chain 'A' and resid 733 through 743 removed outlier: 3.651A pdb=" N VAL A 737 " --> pdb=" O LYS A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 771 removed outlier: 3.567A pdb=" N ARG A 771 " --> pdb=" O ALA A 768 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 768 through 771' Processing helix chain 'A' and resid 773 through 779 removed outlier: 3.879A pdb=" N ILE A 777 " --> pdb=" O GLN A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 841 removed outlier: 3.783A pdb=" N LYS A 841 " --> pdb=" O GLN A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 862 Processing helix chain 'A' and resid 863 through 884 Processing helix chain 'A' and resid 886 through 894 Processing helix chain 'A' and resid 895 through 911 Processing helix chain 'A' and resid 915 through 947 removed outlier: 3.807A pdb=" N ILE A 936 " --> pdb=" O ASN A 932 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N PHE A 939 " --> pdb=" O LEU A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 949 through 981 removed outlier: 5.016A pdb=" N ARG A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) Proline residue: A 964 - end of helix Proline residue: A 978 - end of helix Processing helix chain 'A' and resid 986 through 1027 removed outlier: 4.802A pdb=" N GLY A 996 " --> pdb=" O ALA A 992 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N VAL A 997 " --> pdb=" O LEU A 993 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N PHE A1010 " --> pdb=" O ILE A1006 " (cutoff:3.500A) Proline residue: A1013 - end of helix Processing helix chain 'B' and resid 3 through 8 Processing helix chain 'B' and resid 8 through 30 removed outlier: 4.289A pdb=" N ALA B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Proline residue: B 28 - end of helix Processing helix chain 'B' and resid 53 through 61 Processing helix chain 'B' and resid 61 through 70 removed outlier: 3.777A pdb=" N ARG B 67 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLU B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 116 removed outlier: 4.291A pdb=" N ALA B 116 " --> pdb=" O LYS B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 126 removed outlier: 3.626A pdb=" N GLN B 125 " --> pdb=" O VAL B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 161 Processing helix chain 'B' and resid 161 through 169 removed outlier: 3.546A pdb=" N ARG B 168 " --> pdb=" O GLU B 164 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL B 169 " --> pdb=" O GLU B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 197 removed outlier: 3.651A pdb=" N LEU B 193 " --> pdb=" O ASP B 189 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL B 194 " --> pdb=" O PRO B 190 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER B 195 " --> pdb=" O ASN B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 211 Processing helix chain 'B' and resid 242 through 248 removed outlier: 3.614A pdb=" N PHE B 246 " --> pdb=" O SER B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 265 No H-bonds generated for 'chain 'B' and resid 262 through 265' Processing helix chain 'B' and resid 298 through 314 Processing helix chain 'B' and resid 329 through 360 removed outlier: 3.914A pdb=" N VAL B 333 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LYS B 334 " --> pdb=" O ALA B 330 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE B 335 " --> pdb=" O PRO B 331 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET B 355 " --> pdb=" O VAL B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 387 removed outlier: 4.064A pdb=" N ILE B 367 " --> pdb=" O ARG B 363 " (cutoff:3.500A) Proline residue: B 368 - end of helix removed outlier: 3.851A pdb=" N VAL B 371 " --> pdb=" O ILE B 367 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA B 372 " --> pdb=" O PRO B 368 " (cutoff:3.500A) Proline residue: B 373 - end of helix Processing helix chain 'B' and resid 391 through 406 removed outlier: 4.498A pdb=" N GLY B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL B 406 " --> pdb=" O ILE B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 424 Processing helix chain 'B' and resid 426 through 453 removed outlier: 5.325A pdb=" N SER B 440 " --> pdb=" O LYS B 436 " (cutoff:3.500A) Proline residue: B 441 - end of helix removed outlier: 4.319A pdb=" N PHE B 453 " --> pdb=" O LEU B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 458 removed outlier: 3.629A pdb=" N ALA B 457 " --> pdb=" O PHE B 453 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE B 458 " --> pdb=" O LEU B 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 453 through 458' Processing helix chain 'B' and resid 460 through 497 removed outlier: 3.572A pdb=" N GLY B 464 " --> pdb=" O SER B 460 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR B 473 " --> pdb=" O GLN B 469 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N THR B 489 " --> pdb=" O ALA B 485 " (cutoff:3.500A) Proline residue: B 490 - end of helix Processing helix chain 'B' and resid 509 through 534 Processing helix chain 'B' and resid 535 through 556 Processing helix chain 'B' and resid 580 through 597 removed outlier: 3.609A pdb=" N THR B 584 " --> pdb=" O THR B 580 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASP B 597 " --> pdb=" O ASN B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 632 Processing helix chain 'B' and resid 635 through 650 Processing helix chain 'B' and resid 683 through 701 removed outlier: 3.683A pdb=" N LYS B 700 " --> pdb=" O ALA B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 730 Processing helix chain 'B' and resid 733 through 743 removed outlier: 3.652A pdb=" N VAL B 737 " --> pdb=" O LYS B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 771 removed outlier: 3.567A pdb=" N ARG B 771 " --> pdb=" O ALA B 768 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 768 through 771' Processing helix chain 'B' and resid 773 through 779 removed outlier: 3.880A pdb=" N ILE B 777 " --> pdb=" O GLN B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 841 removed outlier: 3.782A pdb=" N LYS B 841 " --> pdb=" O GLN B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 852 through 862 Processing helix chain 'B' and resid 863 through 884 Processing helix chain 'B' and resid 886 through 894 Processing helix chain 'B' and resid 895 through 911 Processing helix chain 'B' and resid 915 through 947 removed outlier: 3.807A pdb=" N ILE B 936 " --> pdb=" O ASN B 932 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N PHE B 939 " --> pdb=" O LEU B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 949 through 981 removed outlier: 5.016A pdb=" N ARG B 963 " --> pdb=" O LYS B 959 " (cutoff:3.500A) Proline residue: B 964 - end of helix Proline residue: B 978 - end of helix Processing helix chain 'B' and resid 986 through 1027 removed outlier: 4.802A pdb=" N GLY B 996 " --> pdb=" O ALA B 992 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N VAL B 997 " --> pdb=" O LEU B 993 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N PHE B1010 " --> pdb=" O ILE B1006 " (cutoff:3.500A) Proline residue: B1013 - end of helix Processing helix chain 'C' and resid 3 through 8 Processing helix chain 'C' and resid 8 through 30 removed outlier: 4.288A pdb=" N ALA C 12 " --> pdb=" O ARG C 8 " (cutoff:3.500A) Proline residue: C 28 - end of helix Processing helix chain 'C' and resid 53 through 61 Processing helix chain 'C' and resid 61 through 70 removed outlier: 3.777A pdb=" N ARG C 67 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLU C 68 " --> pdb=" O LEU C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 116 removed outlier: 4.291A pdb=" N ALA C 116 " --> pdb=" O LYS C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 126 removed outlier: 3.627A pdb=" N GLN C 125 " --> pdb=" O VAL C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 161 Processing helix chain 'C' and resid 161 through 169 removed outlier: 3.546A pdb=" N ARG C 168 " --> pdb=" O GLU C 164 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL C 169 " --> pdb=" O GLU C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 197 removed outlier: 3.652A pdb=" N LEU C 193 " --> pdb=" O ASP C 189 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL C 194 " --> pdb=" O PRO C 190 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER C 195 " --> pdb=" O ASN C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 211 Processing helix chain 'C' and resid 242 through 248 removed outlier: 3.614A pdb=" N PHE C 246 " --> pdb=" O SER C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 265 No H-bonds generated for 'chain 'C' and resid 262 through 265' Processing helix chain 'C' and resid 298 through 314 Processing helix chain 'C' and resid 329 through 360 removed outlier: 3.914A pdb=" N VAL C 333 " --> pdb=" O THR C 329 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LYS C 334 " --> pdb=" O ALA C 330 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE C 335 " --> pdb=" O PRO C 331 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET C 355 " --> pdb=" O VAL C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 387 removed outlier: 4.063A pdb=" N ILE C 367 " --> pdb=" O ARG C 363 " (cutoff:3.500A) Proline residue: C 368 - end of helix removed outlier: 3.850A pdb=" N VAL C 371 " --> pdb=" O ILE C 367 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA C 372 " --> pdb=" O PRO C 368 " (cutoff:3.500A) Proline residue: C 373 - end of helix Processing helix chain 'C' and resid 391 through 406 removed outlier: 4.498A pdb=" N GLY C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL C 406 " --> pdb=" O ILE C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 424 Processing helix chain 'C' and resid 426 through 453 removed outlier: 5.326A pdb=" N SER C 440 " --> pdb=" O LYS C 436 " (cutoff:3.500A) Proline residue: C 441 - end of helix removed outlier: 4.319A pdb=" N PHE C 453 " --> pdb=" O LEU C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 458 removed outlier: 3.629A pdb=" N ALA C 457 " --> pdb=" O PHE C 453 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE C 458 " --> pdb=" O LEU C 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 453 through 458' Processing helix chain 'C' and resid 460 through 497 removed outlier: 3.571A pdb=" N GLY C 464 " --> pdb=" O SER C 460 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR C 473 " --> pdb=" O GLN C 469 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N THR C 489 " --> pdb=" O ALA C 485 " (cutoff:3.500A) Proline residue: C 490 - end of helix Processing helix chain 'C' and resid 509 through 534 Processing helix chain 'C' and resid 535 through 556 Processing helix chain 'C' and resid 580 through 597 removed outlier: 3.609A pdb=" N THR C 584 " --> pdb=" O THR C 580 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASP C 597 " --> pdb=" O ASN C 593 " (cutoff:3.500A) Processing helix chain 'C' and resid 628 through 632 Processing helix chain 'C' and resid 635 through 650 Processing helix chain 'C' and resid 683 through 701 removed outlier: 3.681A pdb=" N LYS C 700 " --> pdb=" O ALA C 696 " (cutoff:3.500A) Processing helix chain 'C' and resid 723 through 730 Processing helix chain 'C' and resid 733 through 743 removed outlier: 3.651A pdb=" N VAL C 737 " --> pdb=" O LYS C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 771 removed outlier: 3.568A pdb=" N ARG C 771 " --> pdb=" O ALA C 768 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 768 through 771' Processing helix chain 'C' and resid 773 through 779 removed outlier: 3.879A pdb=" N ILE C 777 " --> pdb=" O GLN C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 827 through 841 removed outlier: 3.782A pdb=" N LYS C 841 " --> pdb=" O GLN C 837 " (cutoff:3.500A) Processing helix chain 'C' and resid 852 through 862 Processing helix chain 'C' and resid 863 through 884 Processing helix chain 'C' and resid 886 through 894 Processing helix chain 'C' and resid 895 through 911 Processing helix chain 'C' and resid 915 through 946 removed outlier: 3.807A pdb=" N ILE C 936 " --> pdb=" O ASN C 932 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N PHE C 939 " --> pdb=" O LEU C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 949 through 981 removed outlier: 5.017A pdb=" N ARG C 963 " --> pdb=" O LYS C 959 " (cutoff:3.500A) Proline residue: C 964 - end of helix Proline residue: C 978 - end of helix Processing helix chain 'C' and resid 986 through 1027 removed outlier: 4.803A pdb=" N GLY C 996 " --> pdb=" O ALA C 992 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N VAL C 997 " --> pdb=" O LEU C 993 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N PHE C1010 " --> pdb=" O ILE C1006 " (cutoff:3.500A) Proline residue: C1013 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 127 through 132 removed outlier: 3.715A pdb=" N SER A 132 " --> pdb=" O GLN A 42 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLN A 42 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N THR A 87 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N THR A 82 " --> pdb=" O THR A 87 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLU A 89 " --> pdb=" O ALA A 80 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ALA A 80 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N THR A 91 " --> pdb=" O TYR A 78 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TYR A 78 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N THR A 93 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASN A 808 " --> pdb=" O SER A 815 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N MET A 706 " --> pdb=" O ILE A 821 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 127 through 132 removed outlier: 3.715A pdb=" N SER A 132 " --> pdb=" O GLN A 42 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLN A 42 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N THR A 87 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N THR A 82 " --> pdb=" O THR A 87 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLU A 89 " --> pdb=" O ALA A 80 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ALA A 80 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N THR A 91 " --> pdb=" O TYR A 78 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TYR A 78 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N THR A 93 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASN A 808 " --> pdb=" O SER A 815 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 177 removed outlier: 3.603A pdb=" N LYS A 174 " --> pdb=" O GLN A 292 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR A 287 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET A 138 " --> pdb=" O ILE A 291 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LEU A 139 " --> pdb=" O PRO A 326 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 172 through 177 removed outlier: 3.603A pdb=" N LYS A 174 " --> pdb=" O GLN A 292 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA A 286 " --> pdb=" O ILE A 279 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ILE A 279 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER A 603 " --> pdb=" O THR A 625 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU A 654 " --> pdb=" O GLN A 574 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 266 through 272 removed outlier: 7.656A pdb=" N LYS A 182 " --> pdb=" O GLN A 761 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N ILE A 763 " --> pdb=" O LYS A 182 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N MET A 184 " --> pdb=" O ILE A 763 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N GLN A 765 " --> pdb=" O MET A 184 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ILE A 186 " --> pdb=" O GLN A 765 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ARG A 758 " --> pdb=" O PRO A 754 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N GLN A 760 " --> pdb=" O ASP A 752 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ASP A 752 " --> pdb=" O GLN A 760 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL A 762 " --> pdb=" O ILE A 750 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 217 through 218 removed outlier: 4.073A pdb=" N ILE C 722 " --> pdb=" O GLN A 237 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS C 721 " --> pdb=" O THR C 797 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 250 through 252 Processing sheet with id=AA8, first strand: chain 'A' and resid 796 through 803 removed outlier: 3.692A pdb=" N LYS A 721 " --> pdb=" O THR A 797 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ASP A 716 " --> pdb=" O PRO B 233 " (cutoff:3.500A) removed outlier: 8.654A pdb=" N SER B 235 " --> pdb=" O ASP A 716 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ILE A 718 " --> pdb=" O SER B 235 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N GLN B 237 " --> pdb=" O ILE A 718 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU A 720 " --> pdb=" O GLN B 237 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 781 through 783 Processing sheet with id=AB1, first strand: chain 'B' and resid 127 through 132 removed outlier: 3.714A pdb=" N SER B 132 " --> pdb=" O GLN B 42 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLN B 42 " --> pdb=" O SER B 132 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N THR B 87 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N THR B 82 " --> pdb=" O THR B 87 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLU B 89 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ALA B 80 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N THR B 91 " --> pdb=" O TYR B 78 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TYR B 78 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N THR B 93 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASN B 808 " --> pdb=" O SER B 815 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N MET B 706 " --> pdb=" O ILE B 821 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 127 through 132 removed outlier: 3.714A pdb=" N SER B 132 " --> pdb=" O GLN B 42 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLN B 42 " --> pdb=" O SER B 132 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N THR B 87 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N THR B 82 " --> pdb=" O THR B 87 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLU B 89 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ALA B 80 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N THR B 91 " --> pdb=" O TYR B 78 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TYR B 78 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N THR B 93 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASN B 808 " --> pdb=" O SER B 815 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 172 through 177 removed outlier: 3.604A pdb=" N LYS B 174 " --> pdb=" O GLN B 292 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR B 287 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N MET B 138 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N LEU B 139 " --> pdb=" O PRO B 326 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 172 through 177 removed outlier: 3.604A pdb=" N LYS B 174 " --> pdb=" O GLN B 292 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA B 286 " --> pdb=" O ILE B 279 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE B 279 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER B 603 " --> pdb=" O THR B 625 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU B 654 " --> pdb=" O GLN B 574 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 266 through 272 removed outlier: 7.656A pdb=" N LYS B 182 " --> pdb=" O GLN B 761 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N ILE B 763 " --> pdb=" O LYS B 182 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N MET B 184 " --> pdb=" O ILE B 763 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N GLN B 765 " --> pdb=" O MET B 184 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ILE B 186 " --> pdb=" O GLN B 765 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ARG B 758 " --> pdb=" O PRO B 754 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N GLN B 760 " --> pdb=" O ASP B 752 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ASP B 752 " --> pdb=" O GLN B 760 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL B 762 " --> pdb=" O ILE B 750 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 250 through 252 Processing sheet with id=AB7, first strand: chain 'B' and resid 796 through 803 removed outlier: 3.693A pdb=" N LYS B 721 " --> pdb=" O THR B 797 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ASP B 716 " --> pdb=" O PRO C 233 " (cutoff:3.500A) removed outlier: 8.649A pdb=" N SER C 235 " --> pdb=" O ASP B 716 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ILE B 718 " --> pdb=" O SER C 235 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N GLN C 237 " --> pdb=" O ILE B 718 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU B 720 " --> pdb=" O GLN C 237 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 781 through 783 Processing sheet with id=AB9, first strand: chain 'C' and resid 127 through 132 removed outlier: 3.715A pdb=" N SER C 132 " --> pdb=" O GLN C 42 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLN C 42 " --> pdb=" O SER C 132 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N THR C 87 " --> pdb=" O THR C 82 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N THR C 82 " --> pdb=" O THR C 87 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLU C 89 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ALA C 80 " --> pdb=" O GLU C 89 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N THR C 91 " --> pdb=" O TYR C 78 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TYR C 78 " --> pdb=" O THR C 91 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N THR C 93 " --> pdb=" O LEU C 76 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASN C 808 " --> pdb=" O SER C 815 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N MET C 706 " --> pdb=" O ILE C 821 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 127 through 132 removed outlier: 3.715A pdb=" N SER C 132 " --> pdb=" O GLN C 42 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLN C 42 " --> pdb=" O SER C 132 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N THR C 87 " --> pdb=" O THR C 82 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N THR C 82 " --> pdb=" O THR C 87 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLU C 89 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ALA C 80 " --> pdb=" O GLU C 89 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N THR C 91 " --> pdb=" O TYR C 78 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TYR C 78 " --> pdb=" O THR C 91 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N THR C 93 " --> pdb=" O LEU C 76 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASN C 808 " --> pdb=" O SER C 815 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 172 through 177 removed outlier: 3.603A pdb=" N LYS C 174 " --> pdb=" O GLN C 292 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR C 287 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET C 138 " --> pdb=" O ILE C 291 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LEU C 139 " --> pdb=" O PRO C 326 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 172 through 177 removed outlier: 3.603A pdb=" N LYS C 174 " --> pdb=" O GLN C 292 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA C 286 " --> pdb=" O ILE C 279 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE C 279 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER C 603 " --> pdb=" O THR C 625 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU C 654 " --> pdb=" O GLN C 574 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 266 through 272 removed outlier: 7.656A pdb=" N LYS C 182 " --> pdb=" O GLN C 761 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N ILE C 763 " --> pdb=" O LYS C 182 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N MET C 184 " --> pdb=" O ILE C 763 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N GLN C 765 " --> pdb=" O MET C 184 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ILE C 186 " --> pdb=" O GLN C 765 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ARG C 758 " --> pdb=" O PRO C 754 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N GLN C 760 " --> pdb=" O ASP C 752 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ASP C 752 " --> pdb=" O GLN C 760 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL C 762 " --> pdb=" O ILE C 750 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 250 through 252 Processing sheet with id=AC6, first strand: chain 'C' and resid 781 through 783 1563 hydrogen bonds defined for protein. 4581 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: 4.60 Time building geometry restraints manager: 2.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.06 - 1.21: 33 1.21 - 1.36: 7431 1.36 - 1.52: 7083 1.52 - 1.67: 8970 1.67 - 1.82: 264 Bond restraints: 23781 Sorted by residual: bond pdb=" C SER A 817 " pdb=" O SER A 817 " ideal model delta sigma weight residual 1.236 1.062 0.173 1.22e-02 6.72e+03 2.02e+02 bond pdb=" C SER B 817 " pdb=" O SER B 817 " ideal model delta sigma weight residual 1.236 1.063 0.173 1.22e-02 6.72e+03 2.02e+02 bond pdb=" C SER C 817 " pdb=" O SER C 817 " ideal model delta sigma weight residual 1.236 1.063 0.173 1.22e-02 6.72e+03 2.01e+02 bond pdb=" C ILE C 57 " pdb=" O ILE C 57 " ideal model delta sigma weight residual 1.237 1.124 0.113 1.29e-02 6.01e+03 7.65e+01 bond pdb=" C ILE A 57 " pdb=" O ILE A 57 " ideal model delta sigma weight residual 1.237 1.124 0.113 1.29e-02 6.01e+03 7.64e+01 ... (remaining 23776 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 31672 2.62 - 5.24: 483 5.24 - 7.86: 80 7.86 - 10.48: 9 10.48 - 13.10: 6 Bond angle restraints: 32250 Sorted by residual: angle pdb=" CA SER B 817 " pdb=" C SER B 817 " pdb=" O SER B 817 " ideal model delta sigma weight residual 120.36 107.26 13.10 1.07e+00 8.73e-01 1.50e+02 angle pdb=" CA SER C 817 " pdb=" C SER C 817 " pdb=" O SER C 817 " ideal model delta sigma weight residual 120.36 107.30 13.06 1.07e+00 8.73e-01 1.49e+02 angle pdb=" CA SER A 817 " pdb=" C SER A 817 " pdb=" O SER A 817 " ideal model delta sigma weight residual 120.36 107.34 13.02 1.07e+00 8.73e-01 1.48e+02 angle pdb=" CA MET A 835 " pdb=" C MET A 835 " pdb=" O MET A 835 " ideal model delta sigma weight residual 120.42 112.80 7.62 1.06e+00 8.90e-01 5.17e+01 angle pdb=" CA MET B 835 " pdb=" C MET B 835 " pdb=" O MET B 835 " ideal model delta sigma weight residual 120.42 112.80 7.62 1.06e+00 8.90e-01 5.16e+01 ... (remaining 32245 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 13020 18.00 - 35.99: 1083 35.99 - 53.99: 234 53.99 - 71.98: 42 71.98 - 89.98: 30 Dihedral angle restraints: 14409 sinusoidal: 5592 harmonic: 8817 Sorted by residual: dihedral pdb=" CA ASN A 161 " pdb=" C ASN A 161 " pdb=" N VAL A 162 " pdb=" CA VAL A 162 " ideal model delta harmonic sigma weight residual -180.00 -161.62 -18.38 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA ASN B 161 " pdb=" C ASN B 161 " pdb=" N VAL B 162 " pdb=" CA VAL B 162 " ideal model delta harmonic sigma weight residual -180.00 -161.65 -18.35 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA ASN C 161 " pdb=" C ASN C 161 " pdb=" N VAL C 162 " pdb=" CA VAL C 162 " ideal model delta harmonic sigma weight residual -180.00 -161.69 -18.31 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 14406 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.341: 3864 0.341 - 0.682: 0 0.682 - 1.024: 0 1.024 - 1.365: 0 1.365 - 1.706: 6 Chirality restraints: 3870 Sorted by residual: chirality pdb=" CG LEU B 962 " pdb=" CB LEU B 962 " pdb=" CD1 LEU B 962 " pdb=" CD2 LEU B 962 " both_signs ideal model delta sigma weight residual False -2.59 -0.88 -1.71 2.00e-01 2.50e+01 7.28e+01 chirality pdb=" CG LEU C 962 " pdb=" CB LEU C 962 " pdb=" CD1 LEU C 962 " pdb=" CD2 LEU C 962 " both_signs ideal model delta sigma weight residual False -2.59 -0.89 -1.70 2.00e-01 2.50e+01 7.24e+01 chirality pdb=" CG LEU A 962 " pdb=" CB LEU A 962 " pdb=" CD1 LEU A 962 " pdb=" CD2 LEU A 962 " both_signs ideal model delta sigma weight residual False -2.59 -0.89 -1.70 2.00e-01 2.50e+01 7.24e+01 ... (remaining 3867 not shown) Planarity restraints: 4056 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET C 656 " -0.016 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C MET C 656 " 0.056 2.00e-02 2.50e+03 pdb=" O MET C 656 " -0.021 2.00e-02 2.50e+03 pdb=" N ALA C 657 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 338 " -0.016 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C GLU C 338 " 0.056 2.00e-02 2.50e+03 pdb=" O GLU C 338 " -0.020 2.00e-02 2.50e+03 pdb=" N LYS C 339 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 656 " -0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C MET A 656 " 0.056 2.00e-02 2.50e+03 pdb=" O MET A 656 " -0.021 2.00e-02 2.50e+03 pdb=" N ALA A 657 " -0.020 2.00e-02 2.50e+03 ... (remaining 4053 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 132 2.55 - 3.14: 19551 3.14 - 3.73: 36108 3.73 - 4.31: 50279 4.31 - 4.90: 84808 Nonbonded interactions: 190878 Sorted by model distance: nonbonded pdb=" O ARG B 67 " pdb=" OG SER B 70 " model vdw 1.967 3.040 nonbonded pdb=" O ARG C 67 " pdb=" OG SER C 70 " model vdw 1.968 3.040 nonbonded pdb=" O ARG A 67 " pdb=" OG SER A 70 " model vdw 1.968 3.040 nonbonded pdb=" OD1 ASN B 143 " pdb=" N SER B 144 " model vdw 2.099 3.120 nonbonded pdb=" OD1 ASN A 143 " pdb=" N SER A 144 " model vdw 2.099 3.120 ... (remaining 190873 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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 individual isotropic 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: 0.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 24.110 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 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 : 0.005 0.173 23781 Z= 0.367 Angle : 0.801 13.102 32250 Z= 0.517 Chirality : 0.080 1.706 3870 Planarity : 0.005 0.061 4056 Dihedral : 14.605 89.978 8703 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.94 % Allowed : 1.33 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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 are not related in a simple way. whole: 1.47 (0.15), residues: 3048 helix: 1.76 (0.13), residues: 1647 sheet: 0.30 (0.24), residues: 429 loop : 0.05 (0.21), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 724 TYR 0.009 0.001 TYR C 705 PHE 0.018 0.001 PHE C 569 TRP 0.004 0.001 TRP B 187 HIS 0.003 0.001 HIS C 360 Details of bonding type rmsd covalent geometry : bond 0.00517 (23781) covalent geometry : angle 0.80121 (32250) hydrogen bonds : bond 0.15644 ( 1500) hydrogen bonds : angle 6.25676 ( 4581) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 514 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 192 LYS cc_start: 0.5992 (OUTLIER) cc_final: 0.5779 (mttm) REVERT: A 322 GLU cc_start: 0.7114 (tt0) cc_final: 0.6676 (tp30) REVERT: A 335 ILE cc_start: 0.8231 (tp) cc_final: 0.8028 (tp) REVERT: A 578 ASP cc_start: 0.7145 (OUTLIER) cc_final: 0.6887 (p0) REVERT: A 632 ARG cc_start: 0.6560 (mtm-85) cc_final: 0.5875 (mtm-85) REVERT: A 740 ILE cc_start: 0.6898 (tt) cc_final: 0.6630 (tt) REVERT: A 759 MET cc_start: 0.7595 (mmm) cc_final: 0.7267 (mmp) REVERT: A 783 MET cc_start: 0.6422 (tpp) cc_final: 0.6168 (tpt) REVERT: A 967 MET cc_start: 0.6128 (mtp) cc_final: 0.5904 (mmt) REVERT: B 192 LYS cc_start: 0.6015 (OUTLIER) cc_final: 0.5705 (mttm) REVERT: B 304 GLU cc_start: 0.5796 (mm-30) cc_final: 0.5543 (mm-30) REVERT: B 322 GLU cc_start: 0.6987 (tt0) cc_final: 0.6555 (tp30) REVERT: B 578 ASP cc_start: 0.7373 (OUTLIER) cc_final: 0.7075 (p0) REVERT: B 638 LYS cc_start: 0.7299 (mtpp) cc_final: 0.6681 (mtpp) REVERT: B 759 MET cc_start: 0.7508 (mmm) cc_final: 0.7225 (mmp) REVERT: C 35 PHE cc_start: 0.8568 (m-80) cc_final: 0.8244 (m-10) REVERT: C 192 LYS cc_start: 0.6286 (OUTLIER) cc_final: 0.5934 (mttm) REVERT: C 226 LYS cc_start: 0.7268 (mtpp) cc_final: 0.7011 (ttmm) REVERT: C 322 GLU cc_start: 0.7157 (tt0) cc_final: 0.6854 (tp30) REVERT: C 481 SER cc_start: 0.7568 (t) cc_final: 0.7294 (t) REVERT: C 578 ASP cc_start: 0.7179 (OUTLIER) cc_final: 0.6905 (p0) REVERT: C 632 ARG cc_start: 0.6569 (mtm-85) cc_final: 0.6073 (mtm-85) REVERT: C 638 LYS cc_start: 0.7412 (mtpp) cc_final: 0.6988 (mtpp) REVERT: C 656 MET cc_start: 0.7616 (mmm) cc_final: 0.7367 (tpt) REVERT: C 844 LYS cc_start: 0.7738 (ptmm) cc_final: 0.7359 (tmtt) REVERT: C 857 GLU cc_start: 0.8262 (tt0) cc_final: 0.7964 (tt0) REVERT: C 908 MET cc_start: 0.7204 (mtm) cc_final: 0.6915 (mtp) REVERT: C 942 MET cc_start: 0.5588 (mtp) cc_final: 0.5349 (mtt) REVERT: C 967 MET cc_start: 0.6163 (mtp) cc_final: 0.5962 (mmt) outliers start: 24 outliers final: 0 residues processed: 532 average time/residue: 0.1406 time to fit residues: 119.4682 Evaluate side-chains 439 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 433 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain C residue 192 LYS Chi-restraints excluded: chain C residue 578 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 ASN ** A 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 161 ASN ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN B 714 GLN B 760 GLN C 161 ASN ** C 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 ASN C 691 GLN ** C 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.185608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.151883 restraints weight = 25671.313| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.52 r_work: 0.3252 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 23781 Z= 0.181 Angle : 0.646 7.951 32250 Z= 0.340 Chirality : 0.044 0.172 3870 Planarity : 0.005 0.057 4056 Dihedral : 4.913 56.783 3216 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.38 % Allowed : 9.90 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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 are not related in a simple way. whole: 1.46 (0.15), residues: 3048 helix: 1.75 (0.12), residues: 1707 sheet: -0.01 (0.22), residues: 489 loop : 0.13 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 632 TYR 0.017 0.002 TYR A 848 PHE 0.028 0.002 PHE A 824 TRP 0.006 0.001 TRP C 556 HIS 0.008 0.002 HIS B 360 Details of bonding type rmsd covalent geometry : bond 0.00411 (23781) covalent geometry : angle 0.64595 (32250) hydrogen bonds : bond 0.05166 ( 1500) hydrogen bonds : angle 4.76154 ( 4581) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 489 time to evaluate : 0.741 Fit side-chains REVERT: A 32 ILE cc_start: 0.7551 (pt) cc_final: 0.7337 (pt) REVERT: A 115 GLU cc_start: 0.5889 (tp30) cc_final: 0.5614 (pt0) REVERT: A 213 GLU cc_start: 0.7624 (tp30) cc_final: 0.6941 (tt0) REVERT: A 269 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7471 (mt-10) REVERT: A 311 GLU cc_start: 0.6850 (mm-30) cc_final: 0.6561 (mm-30) REVERT: A 631 GLU cc_start: 0.6756 (mm-30) cc_final: 0.6002 (mm-30) REVERT: A 632 ARG cc_start: 0.6681 (mtm-85) cc_final: 0.4734 (mtm-85) REVERT: A 656 MET cc_start: 0.8034 (mmm) cc_final: 0.7798 (tpt) REVERT: A 722 ILE cc_start: 0.8404 (mp) cc_final: 0.8109 (mp) REVERT: A 723 ASP cc_start: 0.7463 (t0) cc_final: 0.6807 (t70) REVERT: A 783 MET cc_start: 0.6895 (tpp) cc_final: 0.6599 (tpp) REVERT: A 832 MET cc_start: 0.8090 (mtp) cc_final: 0.7762 (mtp) REVERT: A 834 GLU cc_start: 0.7090 (mt-10) cc_final: 0.6675 (mm-30) REVERT: A 893 MET cc_start: 0.7288 (mmt) cc_final: 0.6864 (mmt) REVERT: A 942 MET cc_start: 0.6111 (mtp) cc_final: 0.5827 (mtt) REVERT: A 967 MET cc_start: 0.6912 (mtp) cc_final: 0.6221 (mmt) REVERT: B 192 LYS cc_start: 0.5865 (OUTLIER) cc_final: 0.5639 (mttm) REVERT: B 213 GLU cc_start: 0.7668 (tp30) cc_final: 0.7093 (tt0) REVERT: B 304 GLU cc_start: 0.6708 (mm-30) cc_final: 0.6159 (mm-30) REVERT: B 322 GLU cc_start: 0.7453 (tt0) cc_final: 0.6769 (tp30) REVERT: B 334 LYS cc_start: 0.8168 (mmmm) cc_final: 0.7889 (mmmm) REVERT: B 339 LYS cc_start: 0.7687 (mmmm) cc_final: 0.7415 (tptp) REVERT: B 435 MET cc_start: 0.8083 (mmm) cc_final: 0.7205 (mtt) REVERT: B 632 ARG cc_start: 0.6876 (mtm-85) cc_final: 0.6292 (mtm-85) REVERT: B 656 MET cc_start: 0.7672 (mmm) cc_final: 0.7234 (tpp) REVERT: B 700 LYS cc_start: 0.7581 (ptpt) cc_final: 0.7232 (mttt) REVERT: B 772 MET cc_start: 0.7931 (mmp) cc_final: 0.7714 (mmp) REVERT: B 835 MET cc_start: 0.8719 (tpt) cc_final: 0.8516 (tpt) REVERT: B 967 MET cc_start: 0.7132 (mmt) cc_final: 0.6927 (mmp) REVERT: C 32 ILE cc_start: 0.7367 (pt) cc_final: 0.6986 (pt) REVERT: C 192 LYS cc_start: 0.5701 (OUTLIER) cc_final: 0.5441 (mttm) REVERT: C 226 LYS cc_start: 0.7522 (mtpp) cc_final: 0.7319 (ttmm) REVERT: C 322 GLU cc_start: 0.7758 (tt0) cc_final: 0.7040 (tp30) REVERT: C 334 LYS cc_start: 0.8241 (mmmm) cc_final: 0.8035 (mmmm) REVERT: C 339 LYS cc_start: 0.7608 (mmmm) cc_final: 0.7283 (tptp) REVERT: C 561 MET cc_start: 0.7162 (mmm) cc_final: 0.6788 (mmm) REVERT: C 632 ARG cc_start: 0.6771 (mtm-85) cc_final: 0.6191 (mtm-85) REVERT: C 638 LYS cc_start: 0.7904 (mtpp) cc_final: 0.7418 (mtpp) REVERT: C 857 GLU cc_start: 0.8459 (tt0) cc_final: 0.8252 (tt0) REVERT: C 893 MET cc_start: 0.7359 (mmm) cc_final: 0.7002 (mmt) REVERT: C 967 MET cc_start: 0.7219 (mtp) cc_final: 0.6397 (mmt) outliers start: 61 outliers final: 39 residues processed: 516 average time/residue: 0.1337 time to fit residues: 110.5504 Evaluate side-chains 502 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 460 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 161 ASN Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 527 MET Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 564 GLU Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 827 SER Chi-restraints excluded: chain B residue 846 ILE Chi-restraints excluded: chain B residue 909 SER Chi-restraints excluded: chain B residue 936 ILE Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 192 LYS Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 604 ASN Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 687 LEU Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 909 SER Chi-restraints excluded: chain C residue 936 ILE Chi-restraints excluded: chain C residue 977 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 293 optimal weight: 0.9980 chunk 252 optimal weight: 9.9990 chunk 260 optimal weight: 3.9990 chunk 177 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 220 optimal weight: 5.9990 chunk 180 optimal weight: 7.9990 chunk 143 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 162 optimal weight: 0.4980 chunk 104 optimal weight: 0.4980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 799 GLN ** A 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.186417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.150081 restraints weight = 25526.741| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.58 r_work: 0.3251 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23781 Z= 0.136 Angle : 0.571 11.312 32250 Z= 0.300 Chirality : 0.042 0.186 3870 Planarity : 0.004 0.046 4056 Dihedral : 4.608 59.575 3210 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.11 % Allowed : 13.14 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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 are not related in a simple way. whole: 1.48 (0.15), residues: 3048 helix: 1.78 (0.12), residues: 1704 sheet: 0.01 (0.22), residues: 489 loop : 0.10 (0.22), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 168 TYR 0.013 0.001 TYR A 848 PHE 0.022 0.001 PHE B 824 TRP 0.007 0.001 TRP A 556 HIS 0.005 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00295 (23781) covalent geometry : angle 0.57098 (32250) hydrogen bonds : bond 0.04437 ( 1500) hydrogen bonds : angle 4.53121 ( 4581) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 472 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ILE cc_start: 0.7614 (pt) cc_final: 0.7312 (pt) REVERT: A 269 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7776 (mt-10) REVERT: A 311 GLU cc_start: 0.7008 (mm-30) cc_final: 0.6708 (mm-30) REVERT: A 631 GLU cc_start: 0.6882 (mm-30) cc_final: 0.6190 (mm-30) REVERT: A 632 ARG cc_start: 0.6883 (mtm-85) cc_final: 0.4797 (mtm-85) REVERT: A 647 MET cc_start: 0.7087 (mmt) cc_final: 0.6605 (mmm) REVERT: A 656 MET cc_start: 0.8168 (mmm) cc_final: 0.7850 (tpt) REVERT: A 723 ASP cc_start: 0.7537 (t0) cc_final: 0.6912 (t70) REVERT: A 783 MET cc_start: 0.6947 (tpp) cc_final: 0.6623 (tpp) REVERT: A 834 GLU cc_start: 0.7395 (mt-10) cc_final: 0.7066 (mm-30) REVERT: A 893 MET cc_start: 0.7482 (mmt) cc_final: 0.6985 (mmt) REVERT: A 967 MET cc_start: 0.7073 (mtp) cc_final: 0.6258 (mmt) REVERT: B 49 TYR cc_start: 0.6772 (t80) cc_final: 0.6542 (t80) REVERT: B 213 GLU cc_start: 0.7855 (tp30) cc_final: 0.7033 (tt0) REVERT: B 304 GLU cc_start: 0.7094 (mm-30) cc_final: 0.6478 (mm-30) REVERT: B 322 GLU cc_start: 0.7718 (tt0) cc_final: 0.6989 (tp30) REVERT: B 334 LYS cc_start: 0.8200 (mmmm) cc_final: 0.7911 (mmmm) REVERT: B 339 LYS cc_start: 0.7791 (mmmm) cc_final: 0.7433 (tptp) REVERT: B 345 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8126 (mm) REVERT: B 435 MET cc_start: 0.8078 (mmm) cc_final: 0.7454 (mmm) REVERT: B 632 ARG cc_start: 0.6848 (mtm-85) cc_final: 0.6299 (mtm-85) REVERT: B 656 MET cc_start: 0.7791 (mmm) cc_final: 0.7575 (mmm) REVERT: B 700 LYS cc_start: 0.7595 (ptpt) cc_final: 0.7264 (mtmt) REVERT: B 723 ASP cc_start: 0.7687 (t0) cc_final: 0.7172 (t70) REVERT: B 835 MET cc_start: 0.8678 (tpt) cc_final: 0.8054 (tpt) REVERT: B 967 MET cc_start: 0.7145 (mmt) cc_final: 0.6820 (mmp) REVERT: C 32 ILE cc_start: 0.7511 (pt) cc_final: 0.7058 (pt) REVERT: C 226 LYS cc_start: 0.7643 (mtpp) cc_final: 0.7441 (ttmm) REVERT: C 322 GLU cc_start: 0.8105 (tt0) cc_final: 0.7330 (tp30) REVERT: C 339 LYS cc_start: 0.7724 (mmmm) cc_final: 0.7464 (tptt) REVERT: C 538 MET cc_start: 0.8469 (mmp) cc_final: 0.8239 (mmm) REVERT: C 632 ARG cc_start: 0.6846 (mtm-85) cc_final: 0.6115 (mtm-85) REVERT: C 638 LYS cc_start: 0.8028 (mtpp) cc_final: 0.7519 (mtpp) REVERT: C 772 MET cc_start: 0.8080 (mmp) cc_final: 0.7690 (mmp) REVERT: C 967 MET cc_start: 0.7261 (mtp) cc_final: 0.6306 (mmt) outliers start: 54 outliers final: 36 residues processed: 497 average time/residue: 0.1342 time to fit residues: 107.6536 Evaluate side-chains 486 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 448 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 527 MET Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 437 GLU Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 827 SER Chi-restraints excluded: chain B residue 846 ILE Chi-restraints excluded: chain B residue 936 ILE Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 437 GLU Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 687 LEU Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 908 MET Chi-restraints excluded: chain C residue 936 ILE Chi-restraints excluded: chain C residue 977 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 186 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 168 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 293 optimal weight: 9.9990 chunk 235 optimal weight: 0.0470 chunk 23 optimal weight: 6.9990 chunk 52 optimal weight: 20.0000 chunk 105 optimal weight: 4.9990 chunk 169 optimal weight: 1.9990 chunk 50 optimal weight: 30.0000 overall best weight: 1.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 ASN A 594 ASN ** A 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 808 ASN ** C 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 598 ASN C 799 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.185789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.150686 restraints weight = 25548.610| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.57 r_work: 0.3251 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23781 Z= 0.131 Angle : 0.557 8.626 32250 Z= 0.289 Chirality : 0.041 0.190 3870 Planarity : 0.004 0.045 4056 Dihedral : 4.181 40.795 3200 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.50 % Allowed : 15.09 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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 are not related in a simple way. whole: 1.55 (0.15), residues: 3048 helix: 1.85 (0.12), residues: 1704 sheet: 0.05 (0.22), residues: 489 loop : 0.09 (0.22), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 168 TYR 0.012 0.001 TYR A 848 PHE 0.019 0.001 PHE B 901 TRP 0.007 0.001 TRP C 556 HIS 0.005 0.001 HIS B 360 Details of bonding type rmsd covalent geometry : bond 0.00290 (23781) covalent geometry : angle 0.55660 (32250) hydrogen bonds : bond 0.04069 ( 1500) hydrogen bonds : angle 4.36690 ( 4581) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 456 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ILE cc_start: 0.7624 (pt) cc_final: 0.7285 (pt) REVERT: A 311 GLU cc_start: 0.7004 (mm-30) cc_final: 0.6729 (mm-30) REVERT: A 339 LYS cc_start: 0.7687 (mmmm) cc_final: 0.7216 (tptt) REVERT: A 592 GLU cc_start: 0.7751 (pt0) cc_final: 0.7011 (tp30) REVERT: A 631 GLU cc_start: 0.6969 (mm-30) cc_final: 0.6300 (mm-30) REVERT: A 656 MET cc_start: 0.8202 (mmm) cc_final: 0.7909 (tpt) REVERT: A 723 ASP cc_start: 0.7467 (t0) cc_final: 0.6894 (t70) REVERT: A 749 TYR cc_start: 0.8236 (t80) cc_final: 0.7863 (t80) REVERT: A 783 MET cc_start: 0.6843 (tpp) cc_final: 0.6559 (tpp) REVERT: A 834 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7121 (mm-30) REVERT: A 837 GLN cc_start: 0.7488 (mm-40) cc_final: 0.7153 (mp10) REVERT: A 872 MET cc_start: 0.7046 (OUTLIER) cc_final: 0.6657 (mtp) REVERT: A 893 MET cc_start: 0.7517 (mmt) cc_final: 0.7208 (mmt) REVERT: A 967 MET cc_start: 0.7028 (mtp) cc_final: 0.6163 (mmt) REVERT: B 213 GLU cc_start: 0.7839 (tp30) cc_final: 0.7019 (tt0) REVERT: B 304 GLU cc_start: 0.7120 (mm-30) cc_final: 0.6488 (mm-30) REVERT: B 334 LYS cc_start: 0.8166 (mmmm) cc_final: 0.7873 (mmmm) REVERT: B 339 LYS cc_start: 0.7739 (mmmm) cc_final: 0.7348 (tptp) REVERT: B 345 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8103 (mm) REVERT: B 435 MET cc_start: 0.8081 (mmm) cc_final: 0.7498 (mmm) REVERT: B 632 ARG cc_start: 0.6797 (mtm-85) cc_final: 0.6170 (mtm-85) REVERT: B 700 LYS cc_start: 0.7649 (ptpt) cc_final: 0.7329 (mtmt) REVERT: B 723 ASP cc_start: 0.7619 (t0) cc_final: 0.7102 (t70) REVERT: B 772 MET cc_start: 0.7890 (mmp) cc_final: 0.7562 (mmp) REVERT: B 835 MET cc_start: 0.8656 (tpt) cc_final: 0.8062 (tpt) REVERT: B 849 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7801 (tp30) REVERT: B 872 MET cc_start: 0.7177 (mmm) cc_final: 0.6965 (mmm) REVERT: B 967 MET cc_start: 0.7153 (mmt) cc_final: 0.6815 (mmp) REVERT: C 32 ILE cc_start: 0.7523 (pt) cc_final: 0.7053 (pt) REVERT: C 226 LYS cc_start: 0.7664 (mtpp) cc_final: 0.7440 (ttmm) REVERT: C 322 GLU cc_start: 0.8108 (tt0) cc_final: 0.7268 (tp30) REVERT: C 339 LYS cc_start: 0.7701 (mmmm) cc_final: 0.7389 (tptt) REVERT: C 538 MET cc_start: 0.8560 (mmp) cc_final: 0.8335 (mmm) REVERT: C 561 MET cc_start: 0.7224 (mmm) cc_final: 0.6948 (mmm) REVERT: C 632 ARG cc_start: 0.6823 (mtm-85) cc_final: 0.6037 (mtm-85) REVERT: C 638 LYS cc_start: 0.7988 (mtpp) cc_final: 0.7462 (mtpp) REVERT: C 723 ASP cc_start: 0.7813 (t0) cc_final: 0.7292 (t70) REVERT: C 834 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7119 (mm-30) REVERT: C 849 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7324 (tp30) REVERT: C 872 MET cc_start: 0.7447 (OUTLIER) cc_final: 0.7204 (mtm) REVERT: C 893 MET cc_start: 0.7561 (mmp) cc_final: 0.7236 (mmt) REVERT: C 967 MET cc_start: 0.7178 (mtp) cc_final: 0.6188 (mmt) outliers start: 64 outliers final: 33 residues processed: 489 average time/residue: 0.1400 time to fit residues: 111.1089 Evaluate side-chains 480 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 442 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 527 MET Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 437 GLU Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 827 SER Chi-restraints excluded: chain B residue 846 ILE Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 896 VAL Chi-restraints excluded: chain B residue 936 ILE Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 437 GLU Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 687 LEU Chi-restraints excluded: chain C residue 849 GLU Chi-restraints excluded: chain C residue 872 MET Chi-restraints excluded: chain C residue 936 ILE Chi-restraints excluded: chain C residue 977 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 86 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 chunk 234 optimal weight: 6.9990 chunk 167 optimal weight: 0.3980 chunk 50 optimal weight: 40.0000 chunk 246 optimal weight: 50.0000 chunk 30 optimal weight: 0.6980 chunk 25 optimal weight: 10.0000 chunk 171 optimal weight: 9.9990 chunk 186 optimal weight: 5.9990 chunk 252 optimal weight: 8.9990 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 598 ASN ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 799 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 808 ASN ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 598 ASN ** C 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 714 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.180776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.144606 restraints weight = 25218.525| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.65 r_work: 0.3158 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 23781 Z= 0.214 Angle : 0.656 13.632 32250 Z= 0.337 Chirality : 0.044 0.181 3870 Planarity : 0.005 0.051 4056 Dihedral : 4.458 24.154 3198 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.85 % Allowed : 16.22 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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 are not related in a simple way. whole: 1.20 (0.15), residues: 3048 helix: 1.62 (0.12), residues: 1698 sheet: -0.13 (0.22), residues: 483 loop : -0.13 (0.22), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 185 TYR 0.019 0.002 TYR C 77 PHE 0.039 0.002 PHE B 824 TRP 0.006 0.001 TRP B 568 HIS 0.005 0.001 HIS B 360 Details of bonding type rmsd covalent geometry : bond 0.00513 (23781) covalent geometry : angle 0.65588 (32250) hydrogen bonds : bond 0.04790 ( 1500) hydrogen bonds : angle 4.56890 ( 4581) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 459 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ILE cc_start: 0.7669 (pt) cc_final: 0.7437 (pt) REVERT: A 304 GLU cc_start: 0.6905 (mm-30) cc_final: 0.6626 (mm-30) REVERT: A 631 GLU cc_start: 0.6898 (mm-30) cc_final: 0.6205 (mm-30) REVERT: A 656 MET cc_start: 0.8042 (mmm) cc_final: 0.7738 (tpt) REVERT: A 695 MET cc_start: 0.7805 (mmp) cc_final: 0.7587 (mmp) REVERT: A 723 ASP cc_start: 0.7584 (t0) cc_final: 0.7024 (t70) REVERT: A 783 MET cc_start: 0.6783 (tpp) cc_final: 0.6471 (tpt) REVERT: A 834 GLU cc_start: 0.7375 (mt-10) cc_final: 0.7063 (mm-30) REVERT: A 849 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7883 (mt-10) REVERT: A 890 LEU cc_start: 0.6237 (OUTLIER) cc_final: 0.6016 (tp) REVERT: A 893 MET cc_start: 0.7506 (mmt) cc_final: 0.7201 (mmt) REVERT: A 938 GLU cc_start: 0.6508 (mm-30) cc_final: 0.5809 (mm-30) REVERT: A 967 MET cc_start: 0.6923 (mtp) cc_final: 0.6120 (mmt) REVERT: A 1001 MET cc_start: 0.7195 (tpt) cc_final: 0.6850 (tpt) REVERT: B 49 TYR cc_start: 0.6771 (t80) cc_final: 0.6451 (t80) REVERT: B 213 GLU cc_start: 0.7861 (tp30) cc_final: 0.7084 (tt0) REVERT: B 304 GLU cc_start: 0.7030 (mm-30) cc_final: 0.6793 (mm-30) REVERT: B 334 LYS cc_start: 0.8101 (mmmm) cc_final: 0.7777 (mmmm) REVERT: B 339 LYS cc_start: 0.7721 (mmmm) cc_final: 0.7357 (tptp) REVERT: B 345 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8122 (mm) REVERT: B 383 MET cc_start: 0.8181 (mtp) cc_final: 0.7961 (mtp) REVERT: B 435 MET cc_start: 0.7954 (mmm) cc_final: 0.7404 (mmm) REVERT: B 632 ARG cc_start: 0.6776 (mtm-85) cc_final: 0.6018 (mtm-85) REVERT: B 656 MET cc_start: 0.7660 (mmm) cc_final: 0.6808 (tpt) REVERT: B 684 MET cc_start: 0.7458 (tpt) cc_final: 0.7205 (tpt) REVERT: B 700 LYS cc_start: 0.7601 (ptpt) cc_final: 0.7232 (ptpt) REVERT: B 723 ASP cc_start: 0.7621 (t0) cc_final: 0.7090 (t70) REVERT: B 772 MET cc_start: 0.7797 (mmp) cc_final: 0.7519 (mmt) REVERT: B 835 MET cc_start: 0.8698 (tpt) cc_final: 0.8459 (tpt) REVERT: B 872 MET cc_start: 0.7252 (mmm) cc_final: 0.7022 (mmm) REVERT: B 967 MET cc_start: 0.7028 (mmt) cc_final: 0.6732 (mmp) REVERT: C 32 ILE cc_start: 0.7656 (pt) cc_final: 0.7322 (pt) REVERT: C 117 ARG cc_start: 0.4063 (mpp80) cc_final: 0.3584 (mtt180) REVERT: C 226 LYS cc_start: 0.7639 (mtpp) cc_final: 0.7421 (ttmm) REVERT: C 248 ASN cc_start: 0.6129 (t0) cc_final: 0.5925 (t0) REVERT: C 301 LYS cc_start: 0.7569 (mtpp) cc_final: 0.7360 (mtpp) REVERT: C 322 GLU cc_start: 0.7997 (tt0) cc_final: 0.7222 (tp30) REVERT: C 339 LYS cc_start: 0.7749 (mmmm) cc_final: 0.7277 (tptp) REVERT: C 420 MET cc_start: 0.8282 (tpp) cc_final: 0.8026 (tpp) REVERT: C 538 MET cc_start: 0.8540 (mmp) cc_final: 0.8325 (mmm) REVERT: C 561 MET cc_start: 0.7320 (mmm) cc_final: 0.7044 (mmm) REVERT: C 632 ARG cc_start: 0.6822 (mtm-85) cc_final: 0.5988 (mtm-85) REVERT: C 638 LYS cc_start: 0.8009 (mtpp) cc_final: 0.7803 (mtpp) REVERT: C 723 ASP cc_start: 0.7762 (t0) cc_final: 0.7263 (t70) REVERT: C 834 GLU cc_start: 0.7464 (mt-10) cc_final: 0.6767 (mm-30) REVERT: C 837 GLN cc_start: 0.7585 (OUTLIER) cc_final: 0.6916 (mp10) REVERT: C 849 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7541 (tp30) REVERT: C 857 GLU cc_start: 0.8523 (tt0) cc_final: 0.8293 (tt0) REVERT: C 872 MET cc_start: 0.7411 (OUTLIER) cc_final: 0.7091 (mtm) REVERT: C 893 MET cc_start: 0.7367 (mmp) cc_final: 0.7096 (mmt) REVERT: C 967 MET cc_start: 0.7139 (mtp) cc_final: 0.6093 (mmt) outliers start: 73 outliers final: 49 residues processed: 499 average time/residue: 0.1384 time to fit residues: 110.3637 Evaluate side-chains 506 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 451 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 527 MET Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 437 GLU Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 826 THR Chi-restraints excluded: chain B residue 827 SER Chi-restraints excluded: chain B residue 846 ILE Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 896 VAL Chi-restraints excluded: chain B residue 904 ILE Chi-restraints excluded: chain B residue 912 LEU Chi-restraints excluded: chain B residue 936 ILE Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 437 GLU Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 837 GLN Chi-restraints excluded: chain C residue 849 GLU Chi-restraints excluded: chain C residue 872 MET Chi-restraints excluded: chain C residue 875 VAL Chi-restraints excluded: chain C residue 896 VAL Chi-restraints excluded: chain C residue 908 MET Chi-restraints excluded: chain C residue 909 SER Chi-restraints excluded: chain C residue 936 ILE Chi-restraints excluded: chain C residue 977 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 118 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 190 optimal weight: 8.9990 chunk 160 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 287 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 232 optimal weight: 0.9990 chunk 169 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 chunk 305 optimal weight: 20.0000 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 ASN A 714 GLN ** A 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B 837 GLN ** C 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.183499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.146507 restraints weight = 25277.532| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.67 r_work: 0.3186 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 23781 Z= 0.138 Angle : 0.573 8.515 32250 Z= 0.299 Chirality : 0.042 0.206 3870 Planarity : 0.004 0.044 4056 Dihedral : 4.276 24.232 3198 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.14 % Allowed : 18.52 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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 are not related in a simple way. whole: 1.36 (0.15), residues: 3048 helix: 1.72 (0.12), residues: 1725 sheet: 0.16 (0.23), residues: 429 loop : -0.23 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 185 TYR 0.016 0.001 TYR A 848 PHE 0.029 0.001 PHE B 824 TRP 0.008 0.001 TRP B 556 HIS 0.007 0.001 HIS B 360 Details of bonding type rmsd covalent geometry : bond 0.00312 (23781) covalent geometry : angle 0.57308 (32250) hydrogen bonds : bond 0.04133 ( 1500) hydrogen bonds : angle 4.42799 ( 4581) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 445 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ILE cc_start: 0.7617 (pt) cc_final: 0.7352 (pt) REVERT: A 115 GLU cc_start: 0.5805 (tp30) cc_final: 0.5292 (pt0) REVERT: A 376 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7429 (mp) REVERT: A 631 GLU cc_start: 0.6928 (mm-30) cc_final: 0.6239 (mm-30) REVERT: A 656 MET cc_start: 0.8071 (mmm) cc_final: 0.7782 (tpt) REVERT: A 723 ASP cc_start: 0.7483 (t0) cc_final: 0.6919 (t70) REVERT: A 783 MET cc_start: 0.6676 (tpp) cc_final: 0.6411 (tpt) REVERT: A 834 GLU cc_start: 0.7317 (mt-10) cc_final: 0.7025 (mm-30) REVERT: A 849 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7824 (mt-10) REVERT: A 890 LEU cc_start: 0.6323 (OUTLIER) cc_final: 0.6085 (tp) REVERT: A 893 MET cc_start: 0.7669 (mmt) cc_final: 0.7340 (mmt) REVERT: A 938 GLU cc_start: 0.6386 (mm-30) cc_final: 0.6023 (mm-30) REVERT: A 967 MET cc_start: 0.6872 (mtp) cc_final: 0.6042 (mmt) REVERT: A 1001 MET cc_start: 0.7142 (tpt) cc_final: 0.6682 (tpt) REVERT: B 29 LYS cc_start: 0.7160 (mttt) cc_final: 0.6401 (mmmm) REVERT: B 49 TYR cc_start: 0.6723 (t80) cc_final: 0.6437 (t80) REVERT: B 186 ILE cc_start: 0.8312 (OUTLIER) cc_final: 0.8012 (mm) REVERT: B 213 GLU cc_start: 0.7739 (tp30) cc_final: 0.6999 (tt0) REVERT: B 304 GLU cc_start: 0.6895 (mm-30) cc_final: 0.6690 (mm-30) REVERT: B 334 LYS cc_start: 0.8063 (mmmm) cc_final: 0.7745 (mmmm) REVERT: B 339 LYS cc_start: 0.7723 (mmmm) cc_final: 0.7368 (tptp) REVERT: B 345 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8131 (mm) REVERT: B 435 MET cc_start: 0.7892 (mmm) cc_final: 0.7368 (mmm) REVERT: B 632 ARG cc_start: 0.6767 (mtm-85) cc_final: 0.5907 (mtm-85) REVERT: B 638 LYS cc_start: 0.7912 (mtpp) cc_final: 0.7529 (ttmm) REVERT: B 656 MET cc_start: 0.7560 (mmm) cc_final: 0.6890 (tpt) REVERT: B 723 ASP cc_start: 0.7631 (t0) cc_final: 0.7145 (t70) REVERT: B 967 MET cc_start: 0.7013 (mmt) cc_final: 0.6730 (mmp) REVERT: C 32 ILE cc_start: 0.7556 (pt) cc_final: 0.7169 (pt) REVERT: C 125 GLN cc_start: 0.7738 (OUTLIER) cc_final: 0.6768 (tm-30) REVERT: C 226 LYS cc_start: 0.7525 (mtpp) cc_final: 0.7278 (ttmm) REVERT: C 322 GLU cc_start: 0.7989 (tt0) cc_final: 0.7215 (tp30) REVERT: C 339 LYS cc_start: 0.7750 (mmmm) cc_final: 0.7315 (tptp) REVERT: C 469 GLN cc_start: 0.7872 (OUTLIER) cc_final: 0.7562 (mp10) REVERT: C 538 MET cc_start: 0.8508 (mmp) cc_final: 0.8290 (mmm) REVERT: C 561 MET cc_start: 0.7025 (mmm) cc_final: 0.6771 (mmm) REVERT: C 632 ARG cc_start: 0.6883 (mtm-85) cc_final: 0.5998 (mtm-85) REVERT: C 723 ASP cc_start: 0.7690 (t0) cc_final: 0.7222 (t70) REVERT: C 834 GLU cc_start: 0.7421 (mt-10) cc_final: 0.6771 (mm-30) REVERT: C 837 GLN cc_start: 0.7587 (OUTLIER) cc_final: 0.6905 (mp10) REVERT: C 849 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7503 (tp30) REVERT: C 872 MET cc_start: 0.7310 (OUTLIER) cc_final: 0.7018 (mtm) REVERT: C 893 MET cc_start: 0.7406 (OUTLIER) cc_final: 0.7128 (mmt) REVERT: C 967 MET cc_start: 0.7199 (mtp) cc_final: 0.6105 (mmt) outliers start: 55 outliers final: 34 residues processed: 470 average time/residue: 0.1354 time to fit residues: 102.6430 Evaluate side-chains 480 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 435 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 527 MET Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 437 GLU Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 827 SER Chi-restraints excluded: chain B residue 846 ILE Chi-restraints excluded: chain B residue 896 VAL Chi-restraints excluded: chain B residue 912 LEU Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 437 GLU Chi-restraints excluded: chain C residue 469 GLN Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 837 GLN Chi-restraints excluded: chain C residue 849 GLU Chi-restraints excluded: chain C residue 872 MET Chi-restraints excluded: chain C residue 893 MET Chi-restraints excluded: chain C residue 896 VAL Chi-restraints excluded: chain C residue 936 ILE Chi-restraints excluded: chain C residue 977 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 180 optimal weight: 4.9990 chunk 230 optimal weight: 0.0770 chunk 253 optimal weight: 8.9990 chunk 140 optimal weight: 9.9990 chunk 262 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 286 optimal weight: 6.9990 chunk 214 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 ASN A 801 ASN ** A 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 594 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.182806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.147373 restraints weight = 25341.894| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.62 r_work: 0.3186 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 23781 Z= 0.151 Angle : 0.572 10.058 32250 Z= 0.299 Chirality : 0.042 0.189 3870 Planarity : 0.004 0.043 4056 Dihedral : 4.247 23.780 3198 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.50 % Allowed : 18.48 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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 are not related in a simple way. whole: 1.28 (0.15), residues: 3048 helix: 1.70 (0.12), residues: 1725 sheet: -0.21 (0.22), residues: 465 loop : -0.16 (0.22), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 185 TYR 0.018 0.001 TYR A 848 PHE 0.027 0.001 PHE B 824 TRP 0.008 0.001 TRP B 556 HIS 0.007 0.001 HIS B 360 Details of bonding type rmsd covalent geometry : bond 0.00352 (23781) covalent geometry : angle 0.57241 (32250) hydrogen bonds : bond 0.04137 ( 1500) hydrogen bonds : angle 4.39096 ( 4581) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 444 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ILE cc_start: 0.7637 (pt) cc_final: 0.7388 (pt) REVERT: A 115 GLU cc_start: 0.5768 (tp30) cc_final: 0.5233 (pt0) REVERT: A 304 GLU cc_start: 0.6870 (mm-30) cc_final: 0.6594 (mm-30) REVERT: A 376 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7383 (mp) REVERT: A 631 GLU cc_start: 0.6933 (mm-30) cc_final: 0.6259 (mm-30) REVERT: A 656 MET cc_start: 0.8106 (mmm) cc_final: 0.7821 (tpt) REVERT: A 723 ASP cc_start: 0.7531 (t0) cc_final: 0.6957 (t70) REVERT: A 783 MET cc_start: 0.6719 (tpp) cc_final: 0.6401 (tpt) REVERT: A 834 GLU cc_start: 0.7262 (mt-10) cc_final: 0.6980 (mm-30) REVERT: A 849 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7798 (mt-10) REVERT: A 890 LEU cc_start: 0.6311 (OUTLIER) cc_final: 0.6094 (tp) REVERT: A 893 MET cc_start: 0.7593 (mmt) cc_final: 0.7388 (mpp) REVERT: A 967 MET cc_start: 0.7092 (mtp) cc_final: 0.6182 (mmt) REVERT: A 1001 MET cc_start: 0.7151 (tpt) cc_final: 0.6645 (tpt) REVERT: B 29 LYS cc_start: 0.7240 (mttt) cc_final: 0.6501 (mmmm) REVERT: B 186 ILE cc_start: 0.8296 (OUTLIER) cc_final: 0.7999 (mm) REVERT: B 213 GLU cc_start: 0.7769 (tp30) cc_final: 0.7061 (tt0) REVERT: B 304 GLU cc_start: 0.6981 (mm-30) cc_final: 0.6763 (mm-30) REVERT: B 334 LYS cc_start: 0.8105 (mmmm) cc_final: 0.7786 (mmmm) REVERT: B 339 LYS cc_start: 0.7742 (mmmm) cc_final: 0.7361 (tptp) REVERT: B 345 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.8075 (mm) REVERT: B 435 MET cc_start: 0.7879 (mmm) cc_final: 0.7353 (mmm) REVERT: B 632 ARG cc_start: 0.6794 (mtm-85) cc_final: 0.5745 (mtm-85) REVERT: B 638 LYS cc_start: 0.7999 (mtpp) cc_final: 0.7556 (ttmm) REVERT: B 656 MET cc_start: 0.7600 (mmm) cc_final: 0.6901 (tpt) REVERT: B 723 ASP cc_start: 0.7652 (t0) cc_final: 0.7146 (t70) REVERT: B 833 ARG cc_start: 0.6759 (ttm110) cc_final: 0.6471 (ttm110) REVERT: B 872 MET cc_start: 0.7393 (mmm) cc_final: 0.6950 (mmm) REVERT: B 967 MET cc_start: 0.7019 (mmt) cc_final: 0.6734 (mmp) REVERT: C 32 ILE cc_start: 0.7558 (pt) cc_final: 0.7173 (pt) REVERT: C 117 ARG cc_start: 0.3965 (mpp80) cc_final: 0.3631 (mtt180) REVERT: C 226 LYS cc_start: 0.7511 (mtpp) cc_final: 0.7238 (ttmm) REVERT: C 322 GLU cc_start: 0.8020 (tt0) cc_final: 0.7234 (tp30) REVERT: C 339 LYS cc_start: 0.7765 (mmmm) cc_final: 0.7310 (tptp) REVERT: C 469 GLN cc_start: 0.7833 (OUTLIER) cc_final: 0.7417 (mp10) REVERT: C 538 MET cc_start: 0.8384 (mmp) cc_final: 0.8158 (mmm) REVERT: C 561 MET cc_start: 0.6992 (mmm) cc_final: 0.6760 (mmm) REVERT: C 632 ARG cc_start: 0.6900 (mtm-85) cc_final: 0.5894 (mtm-85) REVERT: C 638 LYS cc_start: 0.7961 (mtpp) cc_final: 0.7268 (mtpp) REVERT: C 723 ASP cc_start: 0.7713 (t0) cc_final: 0.7220 (t70) REVERT: C 834 GLU cc_start: 0.7441 (mt-10) cc_final: 0.6869 (mm-30) REVERT: C 837 GLN cc_start: 0.7596 (OUTLIER) cc_final: 0.7015 (mp10) REVERT: C 849 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7500 (tp30) REVERT: C 872 MET cc_start: 0.7273 (OUTLIER) cc_final: 0.6933 (mtm) REVERT: C 896 VAL cc_start: 0.7805 (OUTLIER) cc_final: 0.7277 (t) REVERT: C 967 MET cc_start: 0.7164 (mtp) cc_final: 0.6107 (mmt) outliers start: 64 outliers final: 39 residues processed: 473 average time/residue: 0.1408 time to fit residues: 107.0012 Evaluate side-chains 489 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 440 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 641 SER Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 437 GLU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 827 SER Chi-restraints excluded: chain B residue 846 ILE Chi-restraints excluded: chain B residue 896 VAL Chi-restraints excluded: chain B residue 909 SER Chi-restraints excluded: chain B residue 912 LEU Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 437 GLU Chi-restraints excluded: chain C residue 469 GLN Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 748 MET Chi-restraints excluded: chain C residue 837 GLN Chi-restraints excluded: chain C residue 849 GLU Chi-restraints excluded: chain C residue 872 MET Chi-restraints excluded: chain C residue 875 VAL Chi-restraints excluded: chain C residue 896 VAL Chi-restraints excluded: chain C residue 936 ILE Chi-restraints excluded: chain C residue 977 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 303 optimal weight: 1.9990 chunk 9 optimal weight: 9.9990 chunk 141 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 184 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 252 optimal weight: 9.9990 chunk 54 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 ASN ** A 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 ASN ** C 210 ASN ** 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 = 0.3844 r_free = 0.3844 target = 0.182630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.147231 restraints weight = 25296.203| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.56 r_work: 0.3191 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 23781 Z= 0.163 Angle : 0.588 10.820 32250 Z= 0.309 Chirality : 0.042 0.192 3870 Planarity : 0.004 0.043 4056 Dihedral : 4.282 23.866 3198 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.77 % Allowed : 18.71 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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 are not related in a simple way. whole: 1.25 (0.15), residues: 3048 helix: 1.67 (0.12), residues: 1725 sheet: 0.03 (0.24), residues: 423 loop : -0.30 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 185 TYR 0.017 0.001 TYR A 848 PHE 0.025 0.001 PHE B 824 TRP 0.006 0.001 TRP B 556 HIS 0.007 0.001 HIS B 360 Details of bonding type rmsd covalent geometry : bond 0.00382 (23781) covalent geometry : angle 0.58814 (32250) hydrogen bonds : bond 0.04192 ( 1500) hydrogen bonds : angle 4.41084 ( 4581) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 442 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ILE cc_start: 0.7803 (pt) cc_final: 0.7488 (pt) REVERT: A 115 GLU cc_start: 0.6035 (tp30) cc_final: 0.5310 (pt0) REVERT: A 304 GLU cc_start: 0.7212 (mm-30) cc_final: 0.6886 (mm-30) REVERT: A 376 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7446 (mp) REVERT: A 631 GLU cc_start: 0.6967 (mm-30) cc_final: 0.6345 (mm-30) REVERT: A 656 MET cc_start: 0.8259 (mmm) cc_final: 0.7967 (tpt) REVERT: A 723 ASP cc_start: 0.7598 (t0) cc_final: 0.6943 (t70) REVERT: A 783 MET cc_start: 0.6846 (tpp) cc_final: 0.6485 (tpt) REVERT: A 832 MET cc_start: 0.8540 (mtp) cc_final: 0.8121 (mtp) REVERT: A 834 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7326 (mm-30) REVERT: A 846 ILE cc_start: 0.8471 (mm) cc_final: 0.8270 (mm) REVERT: A 849 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.8000 (mt-10) REVERT: A 967 MET cc_start: 0.7144 (mtp) cc_final: 0.6196 (mmt) REVERT: A 1001 MET cc_start: 0.7259 (tpt) cc_final: 0.6763 (tpt) REVERT: B 29 LYS cc_start: 0.7402 (mttt) cc_final: 0.6713 (mmmm) REVERT: B 158 LEU cc_start: 0.8528 (tt) cc_final: 0.8228 (tt) REVERT: B 186 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.8042 (mm) REVERT: B 213 GLU cc_start: 0.7969 (tp30) cc_final: 0.7212 (tt0) REVERT: B 304 GLU cc_start: 0.7193 (mm-30) cc_final: 0.6969 (mm-30) REVERT: B 334 LYS cc_start: 0.8202 (mmmm) cc_final: 0.7903 (mmmm) REVERT: B 339 LYS cc_start: 0.7820 (mmmm) cc_final: 0.7356 (tptp) REVERT: B 345 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.8050 (mm) REVERT: B 435 MET cc_start: 0.7947 (mmm) cc_final: 0.7416 (mmm) REVERT: B 632 ARG cc_start: 0.6910 (mtm-85) cc_final: 0.5678 (mtm-85) REVERT: B 638 LYS cc_start: 0.8114 (mtpp) cc_final: 0.7728 (ttmm) REVERT: B 656 MET cc_start: 0.7745 (mmm) cc_final: 0.7063 (tpt) REVERT: B 723 ASP cc_start: 0.7791 (t0) cc_final: 0.7241 (t70) REVERT: B 772 MET cc_start: 0.7712 (mmt) cc_final: 0.7342 (mmp) REVERT: B 849 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7943 (mt-10) REVERT: B 967 MET cc_start: 0.7122 (mmt) cc_final: 0.6827 (mmp) REVERT: C 32 ILE cc_start: 0.7728 (pt) cc_final: 0.7319 (pt) REVERT: C 117 ARG cc_start: 0.4083 (mpp80) cc_final: 0.3762 (mtt180) REVERT: C 226 LYS cc_start: 0.7688 (mtpp) cc_final: 0.7409 (ttmm) REVERT: C 301 LYS cc_start: 0.7602 (mtpp) cc_final: 0.7211 (mttm) REVERT: C 322 GLU cc_start: 0.8193 (tt0) cc_final: 0.7371 (tp30) REVERT: C 339 LYS cc_start: 0.7820 (mmmm) cc_final: 0.7255 (tptp) REVERT: C 376 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7465 (mp) REVERT: C 469 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7647 (mp10) REVERT: C 538 MET cc_start: 0.8384 (mmp) cc_final: 0.8155 (mmm) REVERT: C 632 ARG cc_start: 0.6982 (mtm-85) cc_final: 0.6193 (mtm-85) REVERT: C 638 LYS cc_start: 0.8105 (mtpp) cc_final: 0.7434 (mtpp) REVERT: C 723 ASP cc_start: 0.7789 (t0) cc_final: 0.7266 (t70) REVERT: C 834 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7165 (mm-30) REVERT: C 837 GLN cc_start: 0.7807 (OUTLIER) cc_final: 0.7260 (mp10) REVERT: C 849 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7601 (tp30) REVERT: C 872 MET cc_start: 0.7389 (OUTLIER) cc_final: 0.7071 (mtm) REVERT: C 896 VAL cc_start: 0.7960 (OUTLIER) cc_final: 0.7424 (t) REVERT: C 967 MET cc_start: 0.7314 (mtp) cc_final: 0.6280 (mmt) outliers start: 71 outliers final: 50 residues processed: 477 average time/residue: 0.1354 time to fit residues: 104.0363 Evaluate side-chains 503 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 442 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 527 MET Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 641 SER Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 437 GLU Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 827 SER Chi-restraints excluded: chain B residue 844 LYS Chi-restraints excluded: chain B residue 846 ILE Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 896 VAL Chi-restraints excluded: chain B residue 909 SER Chi-restraints excluded: chain B residue 912 LEU Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 469 GLN Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 748 MET Chi-restraints excluded: chain C residue 797 THR Chi-restraints excluded: chain C residue 837 GLN Chi-restraints excluded: chain C residue 849 GLU Chi-restraints excluded: chain C residue 872 MET Chi-restraints excluded: chain C residue 875 VAL Chi-restraints excluded: chain C residue 896 VAL Chi-restraints excluded: chain C residue 908 MET Chi-restraints excluded: chain C residue 909 SER Chi-restraints excluded: chain C residue 936 ILE Chi-restraints excluded: chain C residue 977 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 145 optimal weight: 6.9990 chunk 250 optimal weight: 0.9980 chunk 266 optimal weight: 7.9990 chunk 257 optimal weight: 5.9990 chunk 104 optimal weight: 7.9990 chunk 222 optimal weight: 3.9990 chunk 170 optimal weight: 4.9990 chunk 160 optimal weight: 2.9990 chunk 188 optimal weight: 5.9990 chunk 280 optimal weight: 5.9990 chunk 265 optimal weight: 0.0770 overall best weight: 2.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 ASN ** A 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 ASN B 594 ASN ** C 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.182448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.145977 restraints weight = 25336.260| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.56 r_work: 0.3195 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 23781 Z= 0.157 Angle : 0.588 11.490 32250 Z= 0.308 Chirality : 0.042 0.181 3870 Planarity : 0.004 0.043 4056 Dihedral : 4.261 23.783 3198 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.57 % Allowed : 19.22 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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 are not related in a simple way. whole: 1.26 (0.15), residues: 3048 helix: 1.69 (0.12), residues: 1725 sheet: 0.01 (0.24), residues: 423 loop : -0.31 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 185 TYR 0.018 0.001 TYR A 848 PHE 0.024 0.001 PHE B 824 TRP 0.005 0.001 TRP B 556 HIS 0.006 0.001 HIS B 360 Details of bonding type rmsd covalent geometry : bond 0.00369 (23781) covalent geometry : angle 0.58750 (32250) hydrogen bonds : bond 0.04150 ( 1500) hydrogen bonds : angle 4.41298 ( 4581) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 436 time to evaluate : 0.788 Fit side-chains revert: symmetry clash REVERT: A 32 ILE cc_start: 0.7825 (pt) cc_final: 0.7501 (pt) REVERT: A 376 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7413 (mp) REVERT: A 656 MET cc_start: 0.8247 (mmm) cc_final: 0.7948 (tpt) REVERT: A 723 ASP cc_start: 0.7588 (t0) cc_final: 0.6930 (t70) REVERT: A 783 MET cc_start: 0.6838 (tpp) cc_final: 0.6537 (tpt) REVERT: A 832 MET cc_start: 0.8506 (mtp) cc_final: 0.8082 (mtp) REVERT: A 834 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7336 (mm-30) REVERT: A 837 GLN cc_start: 0.7395 (mm-40) cc_final: 0.7103 (mp10) REVERT: A 849 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.8008 (mt-10) REVERT: A 893 MET cc_start: 0.7773 (mmt) cc_final: 0.7543 (mpp) REVERT: A 967 MET cc_start: 0.7173 (mtp) cc_final: 0.6179 (mmt) REVERT: A 1001 MET cc_start: 0.7339 (tpt) cc_final: 0.6812 (tpt) REVERT: B 29 LYS cc_start: 0.7420 (mttt) cc_final: 0.6742 (mmmm) REVERT: B 158 LEU cc_start: 0.8550 (tt) cc_final: 0.8284 (tt) REVERT: B 186 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.8050 (mm) REVERT: B 304 GLU cc_start: 0.7197 (mm-30) cc_final: 0.6995 (mm-30) REVERT: B 334 LYS cc_start: 0.8207 (mmmm) cc_final: 0.7909 (mmmm) REVERT: B 339 LYS cc_start: 0.7837 (mmmm) cc_final: 0.7363 (tptp) REVERT: B 345 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.8055 (mm) REVERT: B 435 MET cc_start: 0.7920 (mmm) cc_final: 0.7395 (mmm) REVERT: B 632 ARG cc_start: 0.6885 (mtm-85) cc_final: 0.5649 (mtm-85) REVERT: B 656 MET cc_start: 0.7746 (mmm) cc_final: 0.7018 (tpt) REVERT: B 723 ASP cc_start: 0.7794 (t0) cc_final: 0.7256 (t70) REVERT: B 849 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.7946 (mt-10) REVERT: B 872 MET cc_start: 0.7673 (mmm) cc_final: 0.7175 (mmm) REVERT: B 967 MET cc_start: 0.7059 (mmt) cc_final: 0.6768 (mmp) REVERT: C 32 ILE cc_start: 0.7717 (pt) cc_final: 0.7293 (pt) REVERT: C 117 ARG cc_start: 0.4109 (mpp80) cc_final: 0.3764 (mtt180) REVERT: C 226 LYS cc_start: 0.7673 (mtpp) cc_final: 0.7374 (ttmm) REVERT: C 322 GLU cc_start: 0.8225 (tt0) cc_final: 0.7361 (tp30) REVERT: C 339 LYS cc_start: 0.7812 (mmmm) cc_final: 0.7247 (tptp) REVERT: C 376 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7418 (mp) REVERT: C 469 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7656 (mp10) REVERT: C 538 MET cc_start: 0.8401 (mmp) cc_final: 0.8176 (mmm) REVERT: C 632 ARG cc_start: 0.7055 (mtm-85) cc_final: 0.6159 (mtm-85) REVERT: C 638 LYS cc_start: 0.8100 (mtpp) cc_final: 0.7423 (mtpp) REVERT: C 723 ASP cc_start: 0.7788 (t0) cc_final: 0.7257 (t70) REVERT: C 834 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7168 (mm-30) REVERT: C 837 GLN cc_start: 0.7802 (OUTLIER) cc_final: 0.7255 (mp10) REVERT: C 849 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7602 (tp30) REVERT: C 872 MET cc_start: 0.7476 (OUTLIER) cc_final: 0.7182 (mtm) REVERT: C 896 VAL cc_start: 0.8015 (OUTLIER) cc_final: 0.7528 (t) REVERT: C 967 MET cc_start: 0.7280 (mtp) cc_final: 0.6247 (mmt) outliers start: 66 outliers final: 45 residues processed: 467 average time/residue: 0.1364 time to fit residues: 102.7752 Evaluate side-chains 491 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 435 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 527 MET Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 641 SER Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 652 GLU Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 437 GLU Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 658 VAL Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 827 SER Chi-restraints excluded: chain B residue 844 LYS Chi-restraints excluded: chain B residue 846 ILE Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 896 VAL Chi-restraints excluded: chain B residue 909 SER Chi-restraints excluded: chain B residue 912 LEU Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 469 GLN Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 748 MET Chi-restraints excluded: chain C residue 797 THR Chi-restraints excluded: chain C residue 837 GLN Chi-restraints excluded: chain C residue 849 GLU Chi-restraints excluded: chain C residue 872 MET Chi-restraints excluded: chain C residue 875 VAL Chi-restraints excluded: chain C residue 896 VAL Chi-restraints excluded: chain C residue 936 ILE Chi-restraints excluded: chain C residue 977 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 172 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 264 optimal weight: 7.9990 chunk 190 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 chunk 77 optimal weight: 9.9990 chunk 287 optimal weight: 1.9990 chunk 243 optimal weight: 7.9990 chunk 268 optimal weight: 0.6980 chunk 297 optimal weight: 7.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 ASN A 799 GLN A 805 GLN ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 ASN ** C 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.180558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.144841 restraints weight = 25404.064| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.62 r_work: 0.3163 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 23781 Z= 0.209 Angle : 0.637 8.767 32250 Z= 0.333 Chirality : 0.044 0.192 3870 Planarity : 0.004 0.045 4056 Dihedral : 4.443 23.905 3198 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.38 % Allowed : 19.61 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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 are not related in a simple way. whole: 1.03 (0.15), residues: 3048 helix: 1.54 (0.12), residues: 1722 sheet: -0.40 (0.22), residues: 477 loop : -0.27 (0.22), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 185 TYR 0.019 0.002 TYR C 77 PHE 0.027 0.002 PHE B 824 TRP 0.007 0.001 TRP A 556 HIS 0.006 0.001 HIS B 360 Details of bonding type rmsd covalent geometry : bond 0.00504 (23781) covalent geometry : angle 0.63664 (32250) hydrogen bonds : bond 0.04534 ( 1500) hydrogen bonds : angle 4.53922 ( 4581) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 437 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ILE cc_start: 0.7840 (pt) cc_final: 0.7557 (pt) REVERT: A 304 GLU cc_start: 0.7270 (mm-30) cc_final: 0.6954 (mm-30) REVERT: A 376 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7494 (mp) REVERT: A 478 ILE cc_start: 0.7720 (mp) cc_final: 0.7421 (mp) REVERT: A 631 GLU cc_start: 0.7085 (mm-30) cc_final: 0.6361 (mm-30) REVERT: A 647 MET cc_start: 0.7503 (mmp) cc_final: 0.7144 (mmm) REVERT: A 656 MET cc_start: 0.8109 (mmm) cc_final: 0.7754 (tpt) REVERT: A 723 ASP cc_start: 0.7656 (t0) cc_final: 0.7002 (t70) REVERT: A 783 MET cc_start: 0.6887 (tpp) cc_final: 0.6684 (tpp) REVERT: A 834 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7348 (mm-30) REVERT: A 849 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.8013 (mt-10) REVERT: A 967 MET cc_start: 0.7202 (mtp) cc_final: 0.6228 (mmt) REVERT: A 1001 MET cc_start: 0.7310 (tpt) cc_final: 0.6798 (tpt) REVERT: B 29 LYS cc_start: 0.7406 (mttt) cc_final: 0.6739 (mmmm) REVERT: B 186 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.8050 (mm) REVERT: B 304 GLU cc_start: 0.7268 (mm-30) cc_final: 0.6961 (mm-30) REVERT: B 334 LYS cc_start: 0.8234 (mmmm) cc_final: 0.7925 (mmmm) REVERT: B 339 LYS cc_start: 0.7833 (mmmm) cc_final: 0.7366 (tptp) REVERT: B 435 MET cc_start: 0.7907 (mmm) cc_final: 0.7382 (mmm) REVERT: B 632 ARG cc_start: 0.6825 (mtm-85) cc_final: 0.5449 (mtm-85) REVERT: B 722 ILE cc_start: 0.8752 (OUTLIER) cc_final: 0.8345 (mp) REVERT: B 723 ASP cc_start: 0.7833 (t0) cc_final: 0.7226 (t70) REVERT: B 849 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8021 (mt-10) REVERT: B 872 MET cc_start: 0.7724 (mmm) cc_final: 0.7178 (mmm) REVERT: B 967 MET cc_start: 0.7091 (mmt) cc_final: 0.6787 (mmp) REVERT: C 32 ILE cc_start: 0.7768 (pt) cc_final: 0.7390 (pt) REVERT: C 117 ARG cc_start: 0.4296 (mpp80) cc_final: 0.3675 (mtt180) REVERT: C 226 LYS cc_start: 0.7739 (mtpp) cc_final: 0.7448 (ttmm) REVERT: C 269 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7759 (mt-10) REVERT: C 322 GLU cc_start: 0.8241 (tt0) cc_final: 0.7397 (tp30) REVERT: C 339 LYS cc_start: 0.7866 (mmmm) cc_final: 0.7282 (tptp) REVERT: C 408 ASP cc_start: 0.6506 (m-30) cc_final: 0.6291 (m-30) REVERT: C 469 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7687 (mp10) REVERT: C 538 MET cc_start: 0.8397 (mmp) cc_final: 0.8175 (mmm) REVERT: C 632 ARG cc_start: 0.7112 (mtm-85) cc_final: 0.6186 (mtm-85) REVERT: C 723 ASP cc_start: 0.7796 (t0) cc_final: 0.7264 (t70) REVERT: C 834 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7197 (mm-30) REVERT: C 837 GLN cc_start: 0.7804 (OUTLIER) cc_final: 0.7269 (mp10) REVERT: C 849 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7604 (tp30) REVERT: C 872 MET cc_start: 0.7512 (OUTLIER) cc_final: 0.7199 (mtm) REVERT: C 896 VAL cc_start: 0.7995 (OUTLIER) cc_final: 0.7500 (t) REVERT: C 967 MET cc_start: 0.7312 (mtp) cc_final: 0.6290 (mmt) outliers start: 61 outliers final: 43 residues processed: 471 average time/residue: 0.1401 time to fit residues: 105.9325 Evaluate side-chains 488 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 435 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 527 MET Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 797 THR Chi-restraints excluded: chain A residue 805 GLN Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 437 GLU Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 658 VAL Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 827 SER Chi-restraints excluded: chain B residue 844 LYS Chi-restraints excluded: chain B residue 846 ILE Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 896 VAL Chi-restraints excluded: chain B residue 909 SER Chi-restraints excluded: chain B residue 912 LEU Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 469 GLN Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 748 MET Chi-restraints excluded: chain C residue 797 THR Chi-restraints excluded: chain C residue 837 GLN Chi-restraints excluded: chain C residue 849 GLU Chi-restraints excluded: chain C residue 872 MET Chi-restraints excluded: chain C residue 875 VAL Chi-restraints excluded: chain C residue 896 VAL Chi-restraints excluded: chain C residue 909 SER Chi-restraints excluded: chain C residue 936 ILE Chi-restraints excluded: chain C residue 977 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 65 optimal weight: 8.9990 chunk 118 optimal weight: 8.9990 chunk 247 optimal weight: 7.9990 chunk 217 optimal weight: 0.0070 chunk 130 optimal weight: 2.9990 chunk 282 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 chunk 257 optimal weight: 5.9990 chunk 146 optimal weight: 7.9990 chunk 100 optimal weight: 10.0000 chunk 45 optimal weight: 0.9990 overall best weight: 2.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 ASN A 805 GLN ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 ASN ** C 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.181423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.147794 restraints weight = 25320.381| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.56 r_work: 0.3173 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.189 23781 Z= 0.217 Angle : 0.773 59.191 32250 Z= 0.429 Chirality : 0.045 0.762 3870 Planarity : 0.004 0.045 4056 Dihedral : 4.438 23.897 3198 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.38 % Allowed : 19.69 % Favored : 77.93 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.17 % 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 are not related in a simple way. whole: 1.02 (0.15), residues: 3048 helix: 1.54 (0.12), residues: 1722 sheet: -0.41 (0.22), residues: 477 loop : -0.29 (0.22), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 185 TYR 0.019 0.002 TYR C 77 PHE 0.026 0.002 PHE B 824 TRP 0.005 0.001 TRP B 568 HIS 0.006 0.001 HIS B 360 Details of bonding type rmsd covalent geometry : bond 0.00502 (23781) covalent geometry : angle 0.77302 (32250) hydrogen bonds : bond 0.04496 ( 1500) hydrogen bonds : angle 4.53774 ( 4581) =============================================================================== Job complete usr+sys time: 4959.04 seconds wall clock time: 85 minutes 49.29 seconds (5149.29 seconds total)