Starting phenix.real_space_refine on Tue Sep 15 17:44:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/23il_68999/09_2026/23il_68999.cif Found real_map, /net/cci-nas-00/data/ceres_data/23il_68999/09_2026/23il_68999.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/23il_68999/09_2026/23il_68999.cif" } default_model = "/net/cci-nas-00/data/ceres_data/23il_68999/09_2026/23il_68999.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/23il_68999/09_2026/23il_68999.map" default_real_map = "/net/cci-nas-00/data/ceres_data/23il_68999/09_2026/23il_68999.map" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.041 sd= 1.431 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: 5 Type Number sf(0) Gaussians P 270 5.49 5 S 152 5.16 5 C 25397 2.51 5 N 7527 2.21 5 O 8280 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 122 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 41626 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 744 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "B" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 733 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 4, 'TRANS': 90} Chain: "D" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 685 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 2, 'TRANS': 85} Chain: "E" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 744 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "F" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 614 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "G" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 734 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 4, 'TRANS': 90} Chain: "H" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 703 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "K" Number of atoms: 6611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 801, 6611 Classifications: {'peptide': 801} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 25, 'TRANS': 775} Chain breaks: 5 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 3374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3374 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 27, 'TRANS': 390} Chain breaks: 4 Chain: "M" Number of atoms: 3327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3327 Classifications: {'peptide': 425} Link IDs: {'PTRANS': 31, 'TRANS': 393} Chain breaks: 1 Chain: "N" Number of atoms: 2739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2739 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 16, 'TRANS': 330} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "O" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2611 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 309} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "P" Number of atoms: 2439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2439 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 292} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "Q" Number of atoms: 1333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1333 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 5, 'TRANS': 162} Chain breaks: 1 Chain: "R" Number of atoms: 3718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3718 Classifications: {'peptide': 477} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 35, 'TRANS': 441} Chain breaks: 1 Chain: "S" Number of atoms: 3173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3173 Classifications: {'peptide': 388} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 25, 'TRANS': 362} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "T" Number of atoms: 542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 542 Classifications: {'peptide': 66} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 58} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "U" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 633 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 9, 'TRANS': 65} Chain breaks: 2 Chain: "I" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2734 Classifications: {'DNA': 134} Link IDs: {'rna3p': 133} Chain: "J" Number of atoms: 2760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2760 Classifications: {'DNA': 134} Link IDs: {'rna3p': 133} Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.83, per 1000 atoms: 0.21 Number of scatterers: 41626 At special positions: 0 Unit cell: (135.68, 219.42, 228.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 152 16.00 P 270 15.00 O 8280 8.00 N 7527 7.00 C 25397 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: 3.85 Conformation dependent library (CDL) restraints added in 1.7 seconds 8852 Ramachandran restraints generated. 4426 Oldfield, 0 Emsley, 4426 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8516 Finding SS restraints... Secondary structure from input PDB file: 189 helices and 29 sheets defined 58.3% alpha, 5.9% beta 128 base pairs and 229 stacking pairs defined. Time for finding SS restraints: 5.31 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 4.087A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.605A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.731A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.897A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.515A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG B 92 " --> pdb=" O TYR B 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.378A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 removed outlier: 4.004A pdb=" N LEU C 96 " --> pdb=" O GLU C 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 120 removed outlier: 3.685A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 removed outlier: 3.506A pdb=" N ILE E 51 " --> pdb=" O ALA E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.748A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.697A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASN F 64 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL F 65 " --> pdb=" O PHE F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.558A pdb=" N ARG F 92 " --> pdb=" O TYR F 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.358A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 35 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 120 removed outlier: 3.558A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 287 through 292 Processing helix chain 'K' and resid 300 through 304 Processing helix chain 'K' and resid 309 through 335 removed outlier: 3.506A pdb=" N LYS K 333 " --> pdb=" O TYR K 329 " (cutoff:3.500A) Processing helix chain 'K' and resid 354 through 366 removed outlier: 4.493A pdb=" N ILE K 361 " --> pdb=" O ARG K 357 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLU K 362 " --> pdb=" O LYS K 358 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS K 364 " --> pdb=" O ILE K 360 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU K 366 " --> pdb=" O GLU K 362 " (cutoff:3.500A) Processing helix chain 'K' and resid 370 through 388 removed outlier: 3.721A pdb=" N ALA K 374 " --> pdb=" O SER K 370 " (cutoff:3.500A) Processing helix chain 'K' and resid 389 through 394 removed outlier: 3.566A pdb=" N THR K 392 " --> pdb=" O LEU K 389 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR K 393 " --> pdb=" O ALA K 390 " (cutoff:3.500A) Processing helix chain 'K' and resid 405 through 488 removed outlier: 3.516A pdb=" N GLU K 427 " --> pdb=" O ARG K 423 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER K 457 " --> pdb=" O ARG K 453 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS K 458 " --> pdb=" O LEU K 454 " (cutoff:3.500A) Processing helix chain 'K' and resid 506 through 538 Processing helix chain 'K' and resid 562 through 568 Processing helix chain 'K' and resid 587 through 603 Processing helix chain 'K' and resid 616 through 631 Processing helix chain 'K' and resid 643 through 658 removed outlier: 4.218A pdb=" N THR K 648 " --> pdb=" O LEU K 644 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ASN K 649 " --> pdb=" O SER K 645 " (cutoff:3.500A) Processing helix chain 'K' and resid 669 through 683 removed outlier: 3.588A pdb=" N LYS K 679 " --> pdb=" O MET K 675 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY K 683 " --> pdb=" O LYS K 679 " (cutoff:3.500A) Processing helix chain 'K' and resid 691 through 698 Processing helix chain 'K' and resid 698 through 703 removed outlier: 3.523A pdb=" N LEU K 702 " --> pdb=" O ASP K 698 " (cutoff:3.500A) Processing helix chain 'K' and resid 715 through 719 Processing helix chain 'K' and resid 723 through 733 Processing helix chain 'K' and resid 750 through 761 Processing helix chain 'K' and resid 768 through 776 removed outlier: 3.508A pdb=" N GLU K 773 " --> pdb=" O LYS K 769 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N TRP K 774 " --> pdb=" O THR K 770 " (cutoff:3.500A) Processing helix chain 'K' and resid 791 through 807 Processing helix chain 'K' and resid 814 through 819 removed outlier: 4.015A pdb=" N VAL K 818 " --> pdb=" O LEU K 814 " (cutoff:3.500A) Processing helix chain 'K' and resid 835 through 849 removed outlier: 3.537A pdb=" N ALA K 839 " --> pdb=" O SER K 835 " (cutoff:3.500A) Processing helix chain 'K' and resid 869 through 879 Processing helix chain 'K' and resid 880 through 882 No H-bonds generated for 'chain 'K' and resid 880 through 882' Processing helix chain 'K' and resid 883 through 891 Processing helix chain 'K' and resid 897 through 901 Processing helix chain 'K' and resid 904 through 921 Proline residue: K 915 - end of helix Processing helix chain 'K' and resid 930 through 945 removed outlier: 4.176A pdb=" N MET K 934 " --> pdb=" O MET K 930 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP K 935 " --> pdb=" O THR K 931 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP K 939 " --> pdb=" O ASP K 935 " (cutoff:3.500A) Processing helix chain 'K' and resid 956 through 969 Processing helix chain 'K' and resid 981 through 985 removed outlier: 3.930A pdb=" N GLY K 985 " --> pdb=" O THR K 981 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 981 through 985' Processing helix chain 'K' and resid 1004 through 1016 removed outlier: 3.840A pdb=" N ASP K1008 " --> pdb=" O ASN K1004 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN K1012 " --> pdb=" O ASP K1008 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG K1014 " --> pdb=" O GLN K1010 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ALA K1015 " --> pdb=" O ALA K1011 " (cutoff:3.500A) Processing helix chain 'K' and resid 1035 through 1053 removed outlier: 3.992A pdb=" N ILE K1039 " --> pdb=" O VAL K1035 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP K1050 " --> pdb=" O LYS K1046 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY K1051 " --> pdb=" O LEU K1047 " (cutoff:3.500A) Processing helix chain 'K' and resid 1054 through 1058 removed outlier: 3.866A pdb=" N ARG K1058 " --> pdb=" O GLN K1055 " (cutoff:3.500A) Processing helix chain 'K' and resid 1064 through 1071 removed outlier: 3.949A pdb=" N ARG K1068 " --> pdb=" O SER K1064 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N MET K1071 " --> pdb=" O ASP K1067 " (cutoff:3.500A) Processing helix chain 'K' and resid 1091 through 1100 removed outlier: 3.820A pdb=" N MET K1097 " --> pdb=" O GLU K1093 " (cutoff:3.500A) Processing helix chain 'K' and resid 1102 through 1118 Processing helix chain 'K' and resid 1136 through 1140 Processing helix chain 'K' and resid 1141 through 1146 removed outlier: 3.518A pdb=" N HIS K1146 " --> pdb=" O GLU K1142 " (cutoff:3.500A) Processing helix chain 'L' and resid 99 through 115 Processing helix chain 'L' and resid 132 through 146 Processing helix chain 'L' and resid 157 through 166 Processing helix chain 'L' and resid 212 through 225 removed outlier: 4.056A pdb=" N PHE L 216 " --> pdb=" O GLY L 212 " (cutoff:3.500A) Processing helix chain 'L' and resid 226 through 228 No H-bonds generated for 'chain 'L' and resid 226 through 228' Processing helix chain 'L' and resid 230 through 240 removed outlier: 3.657A pdb=" N LEU L 237 " --> pdb=" O MET L 233 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS L 238 " --> pdb=" O ALA L 234 " (cutoff:3.500A) Processing helix chain 'L' and resid 494 through 499 Processing helix chain 'L' and resid 501 through 519 removed outlier: 3.816A pdb=" N ILE L 519 " --> pdb=" O ALA L 515 " (cutoff:3.500A) Processing helix chain 'L' and resid 524 through 530 Processing helix chain 'L' and resid 536 through 540 Processing helix chain 'L' and resid 543 through 557 removed outlier: 3.534A pdb=" N ASN L 547 " --> pdb=" O GLY L 543 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU L 557 " --> pdb=" O THR L 553 " (cutoff:3.500A) Processing helix chain 'L' and resid 663 through 670 removed outlier: 4.132A pdb=" N SER L 667 " --> pdb=" O LEU L 663 " (cutoff:3.500A) Processing helix chain 'L' and resid 673 through 688 removed outlier: 3.763A pdb=" N LEU L 677 " --> pdb=" O GLU L 673 " (cutoff:3.500A) Processing helix chain 'L' and resid 693 through 703 removed outlier: 4.111A pdb=" N GLU L 698 " --> pdb=" O ALA L 694 " (cutoff:3.500A) Processing helix chain 'L' and resid 707 through 714 Processing helix chain 'L' and resid 717 through 722 Processing helix chain 'M' and resid 60 through 66 removed outlier: 3.701A pdb=" N VAL M 66 " --> pdb=" O GLU M 63 " (cutoff:3.500A) Processing helix chain 'M' and resid 86 through 97 Processing helix chain 'M' and resid 139 through 144 removed outlier: 3.716A pdb=" N THR M 142 " --> pdb=" O LYS M 139 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU M 143 " --> pdb=" O PRO M 140 " (cutoff:3.500A) Processing helix chain 'M' and resid 155 through 168 Processing helix chain 'M' and resid 180 through 189 Processing helix chain 'M' and resid 224 through 239 Processing helix chain 'M' and resid 247 through 251 Processing helix chain 'M' and resid 275 through 294 removed outlier: 3.581A pdb=" N ARG M 279 " --> pdb=" O HIS M 275 " (cutoff:3.500A) Processing helix chain 'M' and resid 308 through 316 Processing helix chain 'M' and resid 333 through 340 Processing helix chain 'M' and resid 341 through 343 No H-bonds generated for 'chain 'M' and resid 341 through 343' Processing helix chain 'M' and resid 360 through 363 Processing helix chain 'M' and resid 364 through 375 Processing helix chain 'M' and resid 380 through 386 Processing helix chain 'M' and resid 392 through 397 removed outlier: 3.832A pdb=" N LEU M 396 " --> pdb=" O SER M 393 " (cutoff:3.500A) Processing helix chain 'M' and resid 400 through 412 removed outlier: 3.649A pdb=" N LEU M 404 " --> pdb=" O PHE M 400 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N HIS M 406 " --> pdb=" O ASP M 402 " (cutoff:3.500A) Processing helix chain 'M' and resid 424 through 430 removed outlier: 3.519A pdb=" N ARG M 429 " --> pdb=" O THR M 425 " (cutoff:3.500A) Processing helix chain 'M' and resid 430 through 442 Processing helix chain 'M' and resid 443 through 449 removed outlier: 3.564A pdb=" N GLN M 447 " --> pdb=" O THR M 444 " (cutoff:3.500A) Processing helix chain 'M' and resid 451 through 459 Processing helix chain 'M' and resid 461 through 466 removed outlier: 3.857A pdb=" N LYS M 465 " --> pdb=" O GLY M 461 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG M 466 " --> pdb=" O ILE M 462 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 461 through 466' Processing helix chain 'N' and resid 121 through 123 No H-bonds generated for 'chain 'N' and resid 121 through 123' Processing helix chain 'N' and resid 131 through 138 Processing helix chain 'N' and resid 150 through 168 removed outlier: 4.025A pdb=" N ASN N 168 " --> pdb=" O ALA N 164 " (cutoff:3.500A) Processing helix chain 'N' and resid 174 through 182 Processing helix chain 'N' and resid 185 through 199 Processing helix chain 'N' and resid 385 through 399 removed outlier: 3.798A pdb=" N LEU N 390 " --> pdb=" O ASP N 386 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG N 391 " --> pdb=" O ALA N 387 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU N 396 " --> pdb=" O LEU N 392 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N GLU N 397 " --> pdb=" O LEU N 393 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG N 398 " --> pdb=" O GLU N 394 " (cutoff:3.500A) Processing helix chain 'N' and resid 402 through 411 Processing helix chain 'N' and resid 416 through 423 removed outlier: 3.778A pdb=" N LEU N 420 " --> pdb=" O GLU N 416 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN N 421 " --> pdb=" O GLU N 417 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE N 422 " --> pdb=" O CYS N 418 " (cutoff:3.500A) Processing helix chain 'N' and resid 460 through 472 Processing helix chain 'N' and resid 474 through 480 removed outlier: 3.712A pdb=" N ALA N 480 " --> pdb=" O ALA N 476 " (cutoff:3.500A) Processing helix chain 'N' and resid 488 through 496 removed outlier: 4.127A pdb=" N ASN N 492 " --> pdb=" O ILE N 488 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU N 493 " --> pdb=" O LEU N 489 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG N 494 " --> pdb=" O LYS N 490 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS N 496 " --> pdb=" O ASN N 492 " (cutoff:3.500A) Processing helix chain 'N' and resid 547 through 631 removed outlier: 3.798A pdb=" N LEU N 551 " --> pdb=" O ALA N 547 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS N 587 " --> pdb=" O LYS N 583 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR N 590 " --> pdb=" O LEU N 586 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET N 597 " --> pdb=" O GLU N 593 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG N 603 " --> pdb=" O GLN N 599 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU N 612 " --> pdb=" O ALA N 608 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLU N 628 " --> pdb=" O ARG N 624 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL N 629 " --> pdb=" O GLU N 625 " (cutoff:3.500A) Processing helix chain 'N' and resid 641 through 654 removed outlier: 3.598A pdb=" N GLU N 647 " --> pdb=" O ARG N 643 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N VAL N 648 " --> pdb=" O MET N 644 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU N 649 " --> pdb=" O ALA N 645 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA N 652 " --> pdb=" O VAL N 648 " (cutoff:3.500A) Processing helix chain 'O' and resid 134 through 139 Processing helix chain 'O' and resid 140 through 143 Processing helix chain 'O' and resid 147 through 150 Processing helix chain 'O' and resid 151 through 168 removed outlier: 3.762A pdb=" N PHE O 161 " --> pdb=" O ASP O 157 " (cutoff:3.500A) Processing helix chain 'O' and resid 175 through 181 Processing helix chain 'O' and resid 186 through 201 removed outlier: 3.530A pdb=" N TRP O 200 " --> pdb=" O PHE O 196 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY O 201 " --> pdb=" O LEU O 197 " (cutoff:3.500A) Processing helix chain 'O' and resid 385 through 400 Processing helix chain 'O' and resid 403 through 411 removed outlier: 3.518A pdb=" N TYR O 409 " --> pdb=" O GLN O 405 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY O 411 " --> pdb=" O ALA O 407 " (cutoff:3.500A) Processing helix chain 'O' and resid 414 through 424 removed outlier: 3.538A pdb=" N CYS O 418 " --> pdb=" O THR O 414 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N VAL O 419 " --> pdb=" O ARG O 415 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N LEU O 420 " --> pdb=" O GLU O 416 " (cutoff:3.500A) Processing helix chain 'O' and resid 427 through 432 removed outlier: 4.090A pdb=" N TYR O 431 " --> pdb=" O ILE O 427 " (cutoff:3.500A) Processing helix chain 'O' and resid 462 through 472 removed outlier: 4.553A pdb=" N PHE O 468 " --> pdb=" O SER O 464 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU O 472 " --> pdb=" O PHE O 468 " (cutoff:3.500A) Processing helix chain 'O' and resid 474 through 498 Processing helix chain 'O' and resid 563 through 635 removed outlier: 3.515A pdb=" N GLN O 627 " --> pdb=" O VAL O 623 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU O 630 " --> pdb=" O VAL O 626 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARG O 631 " --> pdb=" O GLN O 627 " (cutoff:3.500A) Processing helix chain 'P' and resid 48 through 70 removed outlier: 3.647A pdb=" N ASN P 52 " --> pdb=" O ALA P 48 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLN P 53 " --> pdb=" O ALA P 49 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN P 54 " --> pdb=" O GLN P 50 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG P 70 " --> pdb=" O LYS P 66 " (cutoff:3.500A) Processing helix chain 'P' and resid 80 through 85 Processing helix chain 'P' and resid 90 through 120 removed outlier: 3.516A pdb=" N LYS P 112 " --> pdb=" O THR P 108 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASP P 115 " --> pdb=" O ARG P 111 " (cutoff:3.500A) Processing helix chain 'P' and resid 303 through 308 Processing helix chain 'P' and resid 313 through 329 removed outlier: 3.627A pdb=" N MET P 319 " --> pdb=" O GLN P 315 " (cutoff:3.500A) Processing helix chain 'P' and resid 355 through 362 removed outlier: 3.689A pdb=" N GLU P 361 " --> pdb=" O PRO P 357 " (cutoff:3.500A) Processing helix chain 'P' and resid 402 through 407 removed outlier: 3.931A pdb=" N THR P 406 " --> pdb=" O ASP P 402 " (cutoff:3.500A) Processing helix chain 'P' and resid 415 through 418 Processing helix chain 'P' and resid 419 through 459 Processing helix chain 'P' and resid 459 through 479 removed outlier: 3.589A pdb=" N ILE P 478 " --> pdb=" O ASP P 474 " (cutoff:3.500A) Processing helix chain 'P' and resid 517 through 528 removed outlier: 3.856A pdb=" N SER P 526 " --> pdb=" O ASN P 522 " (cutoff:3.500A) Processing helix chain 'Q' and resid 298 through 318 removed outlier: 3.579A pdb=" N HIS Q 311 " --> pdb=" O TYR Q 307 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU Q 312 " --> pdb=" O GLN Q 308 " (cutoff:3.500A) Processing helix chain 'Q' and resid 339 through 343 removed outlier: 4.050A pdb=" N ALA Q 342 " --> pdb=" O GLU Q 339 " (cutoff:3.500A) Processing helix chain 'Q' and resid 353 through 358 removed outlier: 4.360A pdb=" N GLN Q 357 " --> pdb=" O PHE Q 353 " (cutoff:3.500A) Processing helix chain 'Q' and resid 373 through 419 removed outlier: 3.550A pdb=" N VAL Q 380 " --> pdb=" O PHE Q 376 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA Q 414 " --> pdb=" O VAL Q 410 " (cutoff:3.500A) Processing helix chain 'Q' and resid 453 through 464 removed outlier: 3.713A pdb=" N VAL Q 459 " --> pdb=" O ILE Q 455 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL Q 463 " --> pdb=" O VAL Q 459 " (cutoff:3.500A) Processing helix chain 'R' and resid 753 through 761 removed outlier: 3.526A pdb=" N LYS R 759 " --> pdb=" O ASN R 755 " (cutoff:3.500A) Processing helix chain 'R' and resid 762 through 767 removed outlier: 3.695A pdb=" N GLN R 765 " --> pdb=" O GLU R 762 " (cutoff:3.500A) Processing helix chain 'R' and resid 782 through 791 Processing helix chain 'R' and resid 793 through 808 Processing helix chain 'R' and resid 831 through 852 removed outlier: 4.271A pdb=" N VAL R 835 " --> pdb=" O CYS R 831 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU R 836 " --> pdb=" O GLU R 832 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLU R 844 " --> pdb=" O GLU R 840 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N GLN R 845 " --> pdb=" O CYS R 841 " (cutoff:3.500A) Processing helix chain 'R' and resid 864 through 877 removed outlier: 3.669A pdb=" N ILE R 874 " --> pdb=" O ARG R 870 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N PHE R 877 " --> pdb=" O LYS R 873 " (cutoff:3.500A) Processing helix chain 'R' and resid 887 through 910 Processing helix chain 'R' and resid 911 through 916 removed outlier: 6.283A pdb=" N GLU R 914 " --> pdb=" O CYS R 911 " (cutoff:3.500A) Processing helix chain 'R' and resid 917 through 920 Processing helix chain 'R' and resid 921 through 938 Processing helix chain 'R' and resid 944 through 963 removed outlier: 3.689A pdb=" N THR R 957 " --> pdb=" O LYS R 953 " (cutoff:3.500A) Processing helix chain 'R' and resid 964 through 966 No H-bonds generated for 'chain 'R' and resid 964 through 966' Processing helix chain 'R' and resid 970 through 982 Processing helix chain 'R' and resid 983 through 985 No H-bonds generated for 'chain 'R' and resid 983 through 985' Processing helix chain 'R' and resid 1009 through 1023 removed outlier: 3.964A pdb=" N ARG R1023 " --> pdb=" O LYS R1019 " (cutoff:3.500A) Processing helix chain 'R' and resid 1027 through 1036 removed outlier: 3.697A pdb=" N PHE R1035 " --> pdb=" O TYR R1031 " (cutoff:3.500A) Processing helix chain 'R' and resid 1047 through 1059 Processing helix chain 'R' and resid 1074 through 1079 Processing helix chain 'R' and resid 1079 through 1096 removed outlier: 3.527A pdb=" N LEU R1096 " --> pdb=" O ILE R1092 " (cutoff:3.500A) Processing helix chain 'R' and resid 1103 through 1110 removed outlier: 3.977A pdb=" N ALA R1107 " --> pdb=" O GLY R1103 " (cutoff:3.500A) Processing helix chain 'R' and resid 1114 through 1133 Processing helix chain 'R' and resid 1156 through 1175 removed outlier: 3.713A pdb=" N LEU R1160 " --> pdb=" O ASP R1156 " (cutoff:3.500A) Processing helix chain 'R' and resid 1176 through 1178 No H-bonds generated for 'chain 'R' and resid 1176 through 1178' Processing helix chain 'R' and resid 1195 through 1201 Processing helix chain 'R' and resid 1214 through 1232 removed outlier: 3.530A pdb=" N VAL R1232 " --> pdb=" O GLU R1228 " (cutoff:3.500A) Processing helix chain 'S' and resid 69 through 90 Processing helix chain 'S' and resid 91 through 115 Processing helix chain 'S' and resid 166 through 173 Processing helix chain 'S' and resid 208 through 220 Processing helix chain 'S' and resid 228 through 245 removed outlier: 3.740A pdb=" N GLU S 241 " --> pdb=" O GLN S 237 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN S 242 " --> pdb=" O GLN S 238 " (cutoff:3.500A) Processing helix chain 'S' and resid 262 through 267 Processing helix chain 'S' and resid 300 through 312 removed outlier: 3.610A pdb=" N ALA S 306 " --> pdb=" O GLU S 302 " (cutoff:3.500A) Processing helix chain 'S' and resid 315 through 340 removed outlier: 3.681A pdb=" N THR S 319 " --> pdb=" O SER S 315 " (cutoff:3.500A) Processing helix chain 'S' and resid 353 through 358 removed outlier: 4.021A pdb=" N ALA S 357 " --> pdb=" O ASP S 353 " (cutoff:3.500A) Processing helix chain 'S' and resid 369 through 373 Processing helix chain 'S' and resid 384 through 404 removed outlier: 4.065A pdb=" N GLU S 389 " --> pdb=" O GLU S 385 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ARG S 390 " --> pdb=" O ALA S 386 " (cutoff:3.500A) Processing helix chain 'T' and resid 364 through 396 removed outlier: 3.878A pdb=" N ALA T 368 " --> pdb=" O THR T 364 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N HIS T 371 " --> pdb=" O HIS T 367 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N THR T 379 " --> pdb=" O GLU T 375 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TYR T 390 " --> pdb=" O MET T 386 " (cutoff:3.500A) Processing helix chain 'U' and resid 75 through 84 removed outlier: 3.957A pdb=" N LEU U 79 " --> pdb=" O SER U 75 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.175A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.423A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.277A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 101 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.249A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.415A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'K' and resid 663 through 665 removed outlier: 6.938A pdb=" N VAL K 664 " --> pdb=" O LEU K 689 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU K 639 " --> pdb=" O ILE K 711 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ASP K 713 " --> pdb=" O LEU K 639 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE K 641 " --> pdb=" O ASP K 713 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU K 811 " --> pdb=" O ILE K 608 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 825 through 832 removed outlier: 6.560A pdb=" N THR K 826 " --> pdb=" O ILE K1026 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N ARG K1028 " --> pdb=" O THR K 826 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N LYS K 828 " --> pdb=" O ARG K1028 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ILE K1030 " --> pdb=" O LYS K 828 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE K 830 " --> pdb=" O ILE K1030 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N LEU K 925 " --> pdb=" O ILE K 997 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL K 924 " --> pdb=" O PHE K 977 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N LEU K 979 " --> pdb=" O VAL K 924 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N MET K 926 " --> pdb=" O LEU K 979 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU K 949 " --> pdb=" O LEU K 978 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N SER K 980 " --> pdb=" O LEU K 949 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N LEU K 951 " --> pdb=" O SER K 980 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 37 through 40 removed outlier: 4.357A pdb=" N ARG L 37 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ALA L 25 " --> pdb=" O ARG L 37 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN L 26 " --> pdb=" O VAL L 15 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU L 14 " --> pdb=" O LEU L 124 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N MET L 126 " --> pdb=" O LEU L 14 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N ILE L 16 " --> pdb=" O MET L 126 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 44 through 45 Processing sheet with id=AB5, first strand: chain 'L' and resid 57 through 61 Processing sheet with id=AB6, first strand: chain 'L' and resid 92 through 93 Processing sheet with id=AB7, first strand: chain 'L' and resid 189 through 190 removed outlier: 3.578A pdb=" N VAL L 180 " --> pdb=" O VAL L 196 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL L 196 " --> pdb=" O VAL L 180 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 189 through 190 removed outlier: 8.075A pdb=" N VAL L 533 " --> pdb=" O ASN L 169 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N THR L 171 " --> pdb=" O VAL L 533 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N VAL L 535 " --> pdb=" O THR L 171 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N VAL L 173 " --> pdb=" O VAL L 535 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 351 through 363 Processing sheet with id=AC1, first strand: chain 'M' and resid 45 through 48 removed outlier: 6.175A pdb=" N LEU M 24 " --> pdb=" O LEU M 147 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N THR M 149 " --> pdb=" O LEU M 24 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N LEU M 26 " --> pdb=" O THR M 149 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N LEU M 146 " --> pdb=" O TRP M 176 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N SER M 178 " --> pdb=" O LEU M 146 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N MET M 148 " --> pdb=" O SER M 178 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'M' and resid 50 through 53 Processing sheet with id=AC3, first strand: chain 'M' and resid 212 through 221 removed outlier: 9.398A pdb=" N LYS M 215 " --> pdb=" O HIS M 209 " (cutoff:3.500A) removed outlier: 11.267A pdb=" N HIS M 209 " --> pdb=" O LYS M 215 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N SER M 217 " --> pdb=" O ALA M 207 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N VAL M 388 " --> pdb=" O HIS M 420 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'M' and resid 319 through 322 Processing sheet with id=AC5, first strand: chain 'N' and resid 116 through 119 Processing sheet with id=AC6, first strand: chain 'R' and resid 779 through 781 removed outlier: 6.580A pdb=" N VAL R 780 " --> pdb=" O ILE S 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'R' and resid 812 through 816 removed outlier: 5.997A pdb=" N TRP R 814 " --> pdb=" O PHE R 821 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N PHE R 821 " --> pdb=" O TRP R 814 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ALA R 816 " --> pdb=" O HIS R 819 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'S' and resid 180 through 189 Processing sheet with id=AC9, first strand: chain 'S' and resid 272 through 273 Processing sheet with id=AD1, first strand: chain 'S' and resid 379 through 382 removed outlier: 3.600A pdb=" N HIS S 284 " --> pdb=" O ILE S 281 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'U' and resid 34 through 40 1863 hydrogen bonds defined for protein. 5403 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 333 hydrogen bonds 666 hydrogen bond angles 0 basepair planarities 128 basepair parallelities 229 stacking parallelities Total time for adding SS restraints: 12.13 Time building geometry restraints manager: 5.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12772 1.34 - 1.46: 8423 1.46 - 1.58: 20998 1.58 - 1.70: 537 1.70 - 1.82: 270 Bond restraints: 43000 Sorted by residual: bond pdb=" C4 ADP K3000 " pdb=" C5 ADP K3000 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" C5 ADP K3000 " pdb=" C6 ADP K3000 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" C3' DT J 50 " pdb=" C2' DT J 50 " ideal model delta sigma weight residual 1.516 1.549 -0.033 8.00e-03 1.56e+04 1.66e+01 bond pdb=" C3' DG I 99 " pdb=" C2' DG I 99 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.16e+01 bond pdb=" C3' DG J 136 " pdb=" C2' DG J 136 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 ... (remaining 42995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 57874 2.44 - 4.88: 1154 4.88 - 7.32: 184 7.32 - 9.75: 51 9.75 - 12.19: 13 Bond angle restraints: 59276 Sorted by residual: angle pdb=" C PRO U 30 " pdb=" N VAL U 31 " pdb=" CA VAL U 31 " ideal model delta sigma weight residual 121.97 132.29 -10.32 1.80e+00 3.09e-01 3.28e+01 angle pdb=" N VAL O 465 " pdb=" CA VAL O 465 " pdb=" C VAL O 465 " ideal model delta sigma weight residual 112.96 107.80 5.16 1.00e+00 1.00e+00 2.66e+01 angle pdb=" CA ARG Q 377 " pdb=" CB ARG Q 377 " pdb=" CG ARG Q 377 " ideal model delta sigma weight residual 114.10 124.30 -10.20 2.00e+00 2.50e-01 2.60e+01 angle pdb=" O4' DA I 20 " pdb=" C4' DA I 20 " pdb=" C3' DA I 20 " ideal model delta sigma weight residual 106.00 102.95 3.05 6.00e-01 2.78e+00 2.58e+01 angle pdb=" C SER S 123 " pdb=" CA SER S 123 " pdb=" CB SER S 123 " ideal model delta sigma weight residual 115.79 109.82 5.97 1.19e+00 7.06e-01 2.51e+01 ... (remaining 59271 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.68: 23280 33.68 - 67.36: 2129 67.36 - 101.04: 78 101.04 - 134.71: 4 134.71 - 168.39: 3 Dihedral angle restraints: 25494 sinusoidal: 12370 harmonic: 13124 Sorted by residual: dihedral pdb=" C2' ADP K3000 " pdb=" C1' ADP K3000 " pdb=" N9 ADP K3000 " pdb=" C4 ADP K3000 " ideal model delta sinusoidal sigma weight residual 91.55 -47.61 139.16 1 2.00e+01 2.50e-03 4.22e+01 dihedral pdb=" O1B ADP K3000 " pdb=" O3A ADP K3000 " pdb=" PB ADP K3000 " pdb=" PA ADP K3000 " ideal model delta sinusoidal sigma weight residual 300.00 178.77 121.23 1 2.00e+01 2.50e-03 3.64e+01 dihedral pdb=" CA LEU M 59 " pdb=" C LEU M 59 " pdb=" N PHE M 60 " pdb=" CA PHE M 60 " ideal model delta harmonic sigma weight residual -180.00 -151.22 -28.78 0 5.00e+00 4.00e-02 3.31e+01 ... (remaining 25491 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 6424 0.114 - 0.228: 114 0.228 - 0.342: 4 0.342 - 0.457: 1 0.457 - 0.571: 10 Chirality restraints: 6553 Sorted by residual: chirality pdb=" P DG I 34 " pdb=" OP1 DG I 34 " pdb=" OP2 DG I 34 " pdb=" O5' DG I 34 " both_signs ideal model delta sigma weight residual True 2.34 -2.91 -0.57 2.00e-01 2.50e+01 8.14e+00 chirality pdb=" P DG I 33 " pdb=" OP1 DG I 33 " pdb=" OP2 DG I 33 " pdb=" O5' DG I 33 " both_signs ideal model delta sigma weight residual True 2.34 -2.89 -0.56 2.00e-01 2.50e+01 7.82e+00 chirality pdb=" P DT I 115 " pdb=" OP1 DT I 115 " pdb=" OP2 DT I 115 " pdb=" O5' DT I 115 " both_signs ideal model delta sigma weight residual True 2.34 -2.88 -0.54 2.00e-01 2.50e+01 7.30e+00 ... (remaining 6550 not shown) Planarity restraints: 6756 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU D 110 " 0.012 2.00e-02 2.50e+03 2.50e-02 6.23e+00 pdb=" CD GLU D 110 " -0.043 2.00e-02 2.50e+03 pdb=" OE1 GLU D 110 " 0.015 2.00e-02 2.50e+03 pdb=" OE2 GLU D 110 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA M 151 " 0.040 5.00e-02 4.00e+02 6.09e-02 5.93e+00 pdb=" N PRO M 152 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO M 152 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO M 152 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN S 72 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.89e+00 pdb=" CG ASN S 72 " -0.042 2.00e-02 2.50e+03 pdb=" OD1 ASN S 72 " 0.016 2.00e-02 2.50e+03 pdb=" ND2 ASN S 72 " 0.014 2.00e-02 2.50e+03 ... (remaining 6753 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 10476 2.80 - 3.33: 42805 3.33 - 3.85: 75071 3.85 - 4.38: 88230 4.38 - 4.90: 134067 Nonbonded interactions: 350649 Sorted by model distance: nonbonded pdb=" O ASN S 244 " pdb=" ND2 ASN S 244 " model vdw 2.278 3.120 nonbonded pdb=" O GLN Q 309 " pdb=" OE1 GLN Q 309 " model vdw 2.432 3.040 nonbonded pdb=" OD1 ASN M 78 " pdb=" N MET M 82 " model vdw 2.452 3.120 nonbonded pdb=" N GLN R 825 " pdb=" OE1 GLN R 825 " model vdw 2.478 3.120 nonbonded pdb=" N GLU O 565 " pdb=" OE1 GLU O 565 " model vdw 2.483 3.120 ... (remaining 350644 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 25 through 101) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 16 through 109) selection = (chain 'G' and resid 16 through 109) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 33 through 120) } 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: 5.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.810 Check model and map are aligned: 0.160 Set scattering table: 0.120 Process input model: 45.650 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.120 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 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 0.109 43000 Z= 0.321 Angle : 0.850 12.193 59276 Z= 0.519 Chirality : 0.050 0.571 6553 Planarity : 0.005 0.087 6756 Dihedral : 21.274 168.393 16978 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.95 % Favored : 94.94 % Rotamer: Outliers : 2.95 % Allowed : 23.55 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.12), residues: 4426 helix: -0.30 (0.10), residues: 2362 sheet: -0.73 (0.34), residues: 224 loop : -1.18 (0.15), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG M 429 TYR 0.035 0.002 TYR L 355 PHE 0.037 0.002 PHE M 60 TRP 0.041 0.002 TRP L 131 HIS 0.011 0.001 HIS R 809 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.32 (43000) covalent geometry : angle 0.85024 / 0.52 (59276) hydrogen bonds : bond 0.19466 / 12.85 ( 2194) hydrogen bonds : angle 7.33227 / 5.24 ( 6069) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8852 Ramachandran restraints generated. 4426 Oldfield, 0 Emsley, 4426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8852 Ramachandran restraints generated. 4426 Oldfield, 0 Emsley, 4426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1220 residues out of total 3875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 1106 time to evaluate : 1.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ARG cc_start: 0.8460 (ttm110) cc_final: 0.8069 (ttp80) REVERT: A 50 GLU cc_start: 0.8303 (pt0) cc_final: 0.8084 (pt0) REVERT: A 53 ARG cc_start: 0.7747 (mtp-110) cc_final: 0.7285 (ttp-110) REVERT: C 20 ARG cc_start: 0.8354 (mtp-110) cc_final: 0.7961 (ptm-80) REVERT: C 71 ARG cc_start: 0.8500 (ttp80) cc_final: 0.8261 (ttp80) REVERT: C 81 ARG cc_start: 0.9101 (tpt90) cc_final: 0.8886 (tpt170) REVERT: E 106 ASP cc_start: 0.8570 (m-30) cc_final: 0.8291 (m-30) REVERT: E 120 MET cc_start: 0.8986 (OUTLIER) cc_final: 0.7982 (mpp) REVERT: F 25 ASN cc_start: 0.8601 (t0) cc_final: 0.8071 (t0) REVERT: F 77 LYS cc_start: 0.8698 (mttp) cc_final: 0.8448 (mttp) REVERT: G 25 PHE cc_start: 0.8692 (m-80) cc_final: 0.8390 (m-80) REVERT: G 65 LEU cc_start: 0.9468 (OUTLIER) cc_final: 0.9237 (mm) REVERT: H 65 ASP cc_start: 0.8767 (t0) cc_final: 0.8452 (t0) REVERT: H 73 GLU cc_start: 0.8620 (tp30) cc_final: 0.8267 (tp30) REVERT: H 76 ARG cc_start: 0.8373 (ttm-80) cc_final: 0.8037 (mtm-85) REVERT: H 89 ARG cc_start: 0.8922 (mtp85) cc_final: 0.8488 (mtp85) REVERT: K 316 ASP cc_start: 0.7357 (t0) cc_final: 0.7118 (t0) REVERT: K 363 MET cc_start: 0.8017 (tpp) cc_final: 0.7371 (mmt) REVERT: K 401 MET cc_start: 0.8367 (mpp) cc_final: 0.7906 (mpp) REVERT: K 411 ILE cc_start: 0.8554 (mt) cc_final: 0.8301 (mm) REVERT: K 416 GLU cc_start: 0.8491 (mm-30) cc_final: 0.7715 (mp0) REVERT: K 446 LEU cc_start: 0.8489 (mt) cc_final: 0.8197 (pp) REVERT: K 463 MET cc_start: 0.8677 (mmm) cc_final: 0.8392 (mmm) REVERT: K 710 MET cc_start: 0.6987 (mpp) cc_final: 0.6704 (mpp) REVERT: K 713 ASP cc_start: 0.8100 (t70) cc_final: 0.7080 (p0) REVERT: K 756 MET cc_start: 0.9185 (mmm) cc_final: 0.8896 (mmm) REVERT: K 811 LEU cc_start: 0.7513 (tp) cc_final: 0.7173 (mp) REVERT: K 1048 ASP cc_start: 0.7531 (t70) cc_final: 0.7097 (p0) REVERT: L 529 TRP cc_start: 0.6789 (m-90) cc_final: 0.6524 (m-10) REVERT: M 25 VAL cc_start: 0.7484 (t) cc_final: 0.6944 (m) REVERT: M 42 MET cc_start: 0.6925 (mmm) cc_final: 0.6687 (mmm) REVERT: M 58 ASP cc_start: 0.7953 (m-30) cc_final: 0.7611 (t0) REVERT: M 74 ARG cc_start: 0.7341 (ptp-170) cc_final: 0.7101 (ptp-110) REVERT: M 76 TYR cc_start: 0.8220 (p90) cc_final: 0.7795 (p90) REVERT: M 85 ASP cc_start: 0.7971 (t0) cc_final: 0.6837 (t0) REVERT: M 92 VAL cc_start: 0.8457 (p) cc_final: 0.8235 (m) REVERT: M 153 TRP cc_start: 0.7390 (p90) cc_final: 0.7180 (p90) REVERT: M 411 MET cc_start: 0.6565 (mtt) cc_final: 0.5992 (mtp) REVERT: N 182 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8542 (mt) REVERT: N 417 GLU cc_start: 0.8211 (pt0) cc_final: 0.7920 (tm-30) REVERT: N 545 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.8260 (pm20) REVERT: N 566 GLU cc_start: 0.8435 (pt0) cc_final: 0.7704 (tt0) REVERT: N 585 GLU cc_start: 0.8323 (pm20) cc_final: 0.7922 (pm20) REVERT: N 589 LYS cc_start: 0.8646 (mtmm) cc_final: 0.8353 (mtmm) REVERT: N 599 GLN cc_start: 0.8460 (mm-40) cc_final: 0.8108 (mm-40) REVERT: N 602 ARG cc_start: 0.7975 (ttp80) cc_final: 0.7713 (ttp80) REVERT: N 610 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7462 (mp10) REVERT: O 135 GLU cc_start: 0.6430 (mp0) cc_final: 0.6225 (mp0) REVERT: O 142 PHE cc_start: 0.7999 (OUTLIER) cc_final: 0.7600 (t80) REVERT: O 143 PHE cc_start: 0.8691 (m-80) cc_final: 0.8415 (m-10) REVERT: O 159 ARG cc_start: 0.8014 (ttm170) cc_final: 0.7737 (ttt180) REVERT: O 188 CYS cc_start: 0.8443 (t) cc_final: 0.8094 (t) REVERT: O 212 ARG cc_start: 0.7595 (mpp-170) cc_final: 0.7342 (mtm-85) REVERT: O 225 LYS cc_start: 0.8937 (mmmt) cc_final: 0.8470 (mmmt) REVERT: O 394 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7612 (mp0) REVERT: O 405 GLN cc_start: 0.8211 (mp10) cc_final: 0.7643 (mp10) REVERT: O 435 GLU cc_start: 0.1893 (OUTLIER) cc_final: 0.1627 (tm-30) REVERT: O 474 ASP cc_start: 0.8094 (t0) cc_final: 0.7807 (t0) REVERT: O 494 ARG cc_start: 0.8089 (mmm160) cc_final: 0.7737 (mmm160) REVERT: O 566 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7210 (mm-30) REVERT: O 571 ARG cc_start: 0.7879 (tpt170) cc_final: 0.7627 (tpt170) REVERT: O 595 GLU cc_start: 0.8403 (tm-30) cc_final: 0.8088 (tm-30) REVERT: O 602 ARG cc_start: 0.8236 (ttm-80) cc_final: 0.7538 (mmm-85) REVERT: O 604 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7395 (tm-30) REVERT: O 606 GLU cc_start: 0.8423 (mt-10) cc_final: 0.7783 (mt-10) REVERT: P 58 GLN cc_start: 0.7884 (mm-40) cc_final: 0.7612 (mm-40) REVERT: P 74 ASP cc_start: 0.7893 (t0) cc_final: 0.7693 (t0) REVERT: P 120 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8635 (mp) REVERT: P 435 GLN cc_start: 0.7863 (mp10) cc_final: 0.7419 (mp10) REVERT: P 472 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8297 (tttp) REVERT: P 483 ASN cc_start: 0.7505 (t0) cc_final: 0.6978 (t0) REVERT: P 508 GLU cc_start: 0.6930 (tt0) cc_final: 0.6596 (pm20) REVERT: P 524 ARG cc_start: 0.6838 (OUTLIER) cc_final: 0.6616 (ttt-90) REVERT: P 526 SER cc_start: 0.8854 (OUTLIER) cc_final: 0.8575 (m) REVERT: Q 353 PHE cc_start: 0.7344 (OUTLIER) cc_final: 0.6856 (m-80) REVERT: Q 381 GLU cc_start: 0.8277 (mm-30) cc_final: 0.8040 (mm-30) REVERT: Q 390 GLU cc_start: 0.7929 (tm-30) cc_final: 0.7603 (tp30) REVERT: Q 401 MET cc_start: 0.8356 (tmm) cc_final: 0.7905 (tmm) REVERT: Q 402 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.7681 (mmm) REVERT: Q 419 ARG cc_start: 0.7481 (OUTLIER) cc_final: 0.7238 (ppt-90) REVERT: R 810 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.7985 (mtmm) REVERT: R 814 TRP cc_start: 0.7855 (m100) cc_final: 0.7592 (m100) REVERT: R 891 ASP cc_start: 0.8227 (m-30) cc_final: 0.7695 (p0) REVERT: R 926 LYS cc_start: 0.8886 (mmmt) cc_final: 0.8529 (mtmt) REVERT: R 930 VAL cc_start: 0.8956 (OUTLIER) cc_final: 0.8751 (p) REVERT: R 942 MET cc_start: 0.8985 (mmm) cc_final: 0.8643 (mmm) REVERT: R 1028 ARG cc_start: 0.8409 (mmm-85) cc_final: 0.8069 (mmm-85) REVERT: R 1108 TRP cc_start: 0.8214 (OUTLIER) cc_final: 0.7390 (m100) REVERT: S 128 GLU cc_start: 0.7416 (pt0) cc_final: 0.7024 (pp20) REVERT: S 167 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8034 (tmmt) REVERT: S 171 LYS cc_start: 0.8287 (mtmm) cc_final: 0.7970 (mtmm) REVERT: S 179 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7494 (tp30) REVERT: S 219 ASP cc_start: 0.8015 (t0) cc_final: 0.7482 (t0) REVERT: S 241 GLU cc_start: 0.8058 (pm20) cc_final: 0.7748 (pm20) REVERT: S 246 PHE cc_start: 0.8554 (t80) cc_final: 0.8314 (t80) REVERT: S 310 ARG cc_start: 0.7255 (tpt170) cc_final: 0.6803 (tpp-160) REVERT: S 335 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7844 (ttp-110) REVERT: S 374 LYS cc_start: 0.9151 (mmmt) cc_final: 0.8866 (mmmt) REVERT: S 381 TYR cc_start: 0.8288 (p90) cc_final: 0.7984 (p90) REVERT: S 389 GLU cc_start: 0.8535 (mp0) cc_final: 0.7720 (pm20) REVERT: S 390 ARG cc_start: 0.8564 (mmm160) cc_final: 0.8260 (mmm160) REVERT: S 392 GLU cc_start: 0.8631 (pp20) cc_final: 0.8098 (pp20) REVERT: S 422 ARG cc_start: 0.8090 (mtm110) cc_final: 0.7277 (ptt90) REVERT: S 441 GLU cc_start: 0.8501 (mp0) cc_final: 0.8153 (pm20) REVERT: S 442 GLU cc_start: 0.8417 (mp0) cc_final: 0.7701 (mp0) REVERT: S 444 ARG cc_start: 0.8178 (ttm-80) cc_final: 0.7747 (tpt170) REVERT: T 377 ASN cc_start: 0.8539 (t0) cc_final: 0.8320 (t0) REVERT: T 382 GLN cc_start: 0.8888 (mm110) cc_final: 0.8477 (mm-40) REVERT: T 386 MET cc_start: 0.7940 (mmp) cc_final: 0.7729 (mmp) REVERT: U 76 GLN cc_start: 0.8592 (mp10) cc_final: 0.7800 (mp10) REVERT: U 80 ARG cc_start: 0.8305 (tpm170) cc_final: 0.7982 (tpm170) REVERT: U 129 ARG cc_start: 0.7245 (OUTLIER) cc_final: 0.6797 (ttm170) outliers start: 114 outliers final: 74 residues processed: 1149 average time/residue: 0.3174 time to fit residues: 560.1170 Evaluate side-chains 1185 residues out of total 3875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 1089 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain K residue 310 PHE Chi-restraints excluded: chain K residue 311 GLU Chi-restraints excluded: chain K residue 360 ILE Chi-restraints excluded: chain K residue 441 HIS Chi-restraints excluded: chain K residue 613 MET Chi-restraints excluded: chain K residue 718 MET Chi-restraints excluded: chain K residue 737 PHE Chi-restraints excluded: chain K residue 759 PHE Chi-restraints excluded: chain K residue 837 LEU Chi-restraints excluded: chain K residue 1040 LEU Chi-restraints excluded: chain K residue 1090 MET Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 131 TRP Chi-restraints excluded: chain L residue 133 ARG Chi-restraints excluded: chain L residue 159 LEU Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 358 LEU Chi-restraints excluded: chain L residue 519 ILE Chi-restraints excluded: chain L residue 554 HIS Chi-restraints excluded: chain L residue 654 ILE Chi-restraints excluded: chain L residue 681 VAL Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain M residue 202 ASN Chi-restraints excluded: chain M residue 228 LEU Chi-restraints excluded: chain M residue 290 PHE Chi-restraints excluded: chain M residue 355 ASP Chi-restraints excluded: chain M residue 406 HIS Chi-restraints excluded: chain M residue 442 LEU Chi-restraints excluded: chain N residue 133 ILE Chi-restraints excluded: chain N residue 182 LEU Chi-restraints excluded: chain N residue 226 ILE Chi-restraints excluded: chain N residue 400 ASP Chi-restraints excluded: chain N residue 545 GLN Chi-restraints excluded: chain N residue 610 GLN Chi-restraints excluded: chain N residue 629 VAL Chi-restraints excluded: chain O residue 142 PHE Chi-restraints excluded: chain O residue 147 ASN Chi-restraints excluded: chain O residue 191 MET Chi-restraints excluded: chain O residue 394 GLU Chi-restraints excluded: chain O residue 417 GLU Chi-restraints excluded: chain O residue 435 GLU Chi-restraints excluded: chain O residue 466 VAL Chi-restraints excluded: chain O residue 472 LEU Chi-restraints excluded: chain O residue 484 LYS Chi-restraints excluded: chain O residue 491 GLN Chi-restraints excluded: chain O residue 568 GLU Chi-restraints excluded: chain O residue 604 GLU Chi-restraints excluded: chain P residue 112 LYS Chi-restraints excluded: chain P residue 120 LEU Chi-restraints excluded: chain P residue 366 HIS Chi-restraints excluded: chain P residue 472 LYS Chi-restraints excluded: chain P residue 477 ILE Chi-restraints excluded: chain P residue 490 VAL Chi-restraints excluded: chain P residue 524 ARG Chi-restraints excluded: chain P residue 526 SER Chi-restraints excluded: chain P residue 529 VAL Chi-restraints excluded: chain Q residue 301 GLU Chi-restraints excluded: chain Q residue 353 PHE Chi-restraints excluded: chain Q residue 402 MET Chi-restraints excluded: chain Q residue 404 LYS Chi-restraints excluded: chain Q residue 405 PHE Chi-restraints excluded: chain Q residue 419 ARG Chi-restraints excluded: chain R residue 810 LYS Chi-restraints excluded: chain R residue 930 VAL Chi-restraints excluded: chain R residue 939 GLU Chi-restraints excluded: chain R residue 1065 THR Chi-restraints excluded: chain R residue 1108 TRP Chi-restraints excluded: chain R residue 1165 LEU Chi-restraints excluded: chain S residue 167 LYS Chi-restraints excluded: chain S residue 181 VAL Chi-restraints excluded: chain S residue 225 MET Chi-restraints excluded: chain S residue 325 CYS Chi-restraints excluded: chain S residue 335 ARG Chi-restraints excluded: chain S residue 421 GLN Chi-restraints excluded: chain T residue 366 LEU Chi-restraints excluded: chain T residue 383 GLN Chi-restraints excluded: chain U residue 119 PHE Chi-restraints excluded: chain U residue 129 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 432 optimal weight: 2.9990 chunk 197 optimal weight: 0.0470 chunk 388 optimal weight: 0.9980 chunk 455 optimal weight: 50.0000 chunk 215 optimal weight: 0.3980 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 0.7980 chunk 401 optimal weight: 2.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN B 93 GLN D 44 GLN ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 GLN K 418 GLN ** K 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 730 GLN ** L 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 323 GLN S 72 ASN S 244 ASN T 347 GLN ** T 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 399 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.176657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.138080 restraints weight = 102500.537| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 3.92 r_work: 0.3598 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.0943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 43000 Z= 0.164 Angle : 0.731 12.007 59276 Z= 0.384 Chirality : 0.045 0.371 6553 Planarity : 0.005 0.061 6756 Dihedral : 22.193 167.789 8113 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.95 % Favored : 94.94 % Rotamer: Outliers : 3.49 % Allowed : 21.58 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.13), residues: 4426 helix: 0.34 (0.10), residues: 2439 sheet: -0.41 (0.35), residues: 229 loop : -1.20 (0.15), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG O 181 TYR 0.034 0.002 TYR S 111 PHE 0.033 0.002 PHE K 654 TRP 0.028 0.002 TRP L 529 HIS 0.011 0.001 HIS K 462 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.16 (43000) covalent geometry : angle 0.73066 / 0.38 (59276) hydrogen bonds : bond 0.05826 / 3.86 ( 2194) hydrogen bonds : angle 5.06716 / 3.61 ( 6069) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8852 Ramachandran restraints generated. 4426 Oldfield, 0 Emsley, 4426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8852 Ramachandran restraints generated. 4426 Oldfield, 0 Emsley, 4426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1257 residues out of total 3875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 1122 time to evaluate : 1.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ARG cc_start: 0.8673 (ttm110) cc_final: 0.8311 (ttp80) REVERT: A 53 ARG cc_start: 0.7962 (mtp-110) cc_final: 0.7672 (ttp-110) REVERT: A 54 TYR cc_start: 0.8235 (m-10) cc_final: 0.8017 (m-10) REVERT: B 59 LYS cc_start: 0.8735 (tppp) cc_final: 0.8388 (ttmm) REVERT: C 20 ARG cc_start: 0.8559 (mtp-110) cc_final: 0.8201 (ptm-80) REVERT: C 74 LYS cc_start: 0.8802 (mppt) cc_final: 0.8602 (mppt) REVERT: C 91 GLU cc_start: 0.8249 (tp30) cc_final: 0.7934 (tp30) REVERT: E 106 ASP cc_start: 0.8424 (m-30) cc_final: 0.8038 (m-30) REVERT: E 125 GLN cc_start: 0.8511 (mt0) cc_final: 0.7883 (mp10) REVERT: F 25 ASN cc_start: 0.8545 (t0) cc_final: 0.7983 (t0) REVERT: F 35 ARG cc_start: 0.8798 (mtp85) cc_final: 0.8509 (mtp85) REVERT: G 25 PHE cc_start: 0.8510 (m-80) cc_final: 0.8178 (m-80) REVERT: H 65 ASP cc_start: 0.8820 (t0) cc_final: 0.8480 (t0) REVERT: H 73 GLU cc_start: 0.8755 (tp30) cc_final: 0.8359 (tp30) REVERT: H 76 ARG cc_start: 0.8972 (ttm-80) cc_final: 0.8603 (ttm-80) REVERT: H 113 LYS cc_start: 0.8643 (pttt) cc_final: 0.8140 (pttt) REVERT: K 316 ASP cc_start: 0.7457 (t0) cc_final: 0.7213 (t0) REVERT: K 356 LYS cc_start: 0.8337 (tppt) cc_final: 0.8008 (tppt) REVERT: K 360 ILE cc_start: 0.8018 (OUTLIER) cc_final: 0.7198 (tp) REVERT: K 363 MET cc_start: 0.8158 (tpp) cc_final: 0.7438 (mtt) REVERT: K 401 MET cc_start: 0.8557 (mpp) cc_final: 0.8078 (mpp) REVERT: K 411 ILE cc_start: 0.8454 (mt) cc_final: 0.8170 (mm) REVERT: K 416 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7450 (mm-30) REVERT: K 430 LYS cc_start: 0.9066 (mmtm) cc_final: 0.8749 (mmtt) REVERT: K 446 LEU cc_start: 0.8516 (mt) cc_final: 0.8215 (pp) REVERT: K 453 ARG cc_start: 0.8104 (ppt170) cc_final: 0.7599 (ppt170) REVERT: K 714 GLU cc_start: 0.7178 (tp30) cc_final: 0.6425 (tp30) REVERT: K 756 MET cc_start: 0.9131 (mmm) cc_final: 0.8787 (mmm) REVERT: K 914 LEU cc_start: 0.9281 (tp) cc_final: 0.8827 (pp) REVERT: K 1048 ASP cc_start: 0.7501 (t70) cc_final: 0.7115 (p0) REVERT: L 121 THR cc_start: 0.7606 (OUTLIER) cc_final: 0.7388 (p) REVERT: L 126 MET cc_start: 0.5941 (ppp) cc_final: 0.5677 (ppp) REVERT: L 130 GLN cc_start: 0.8336 (mp10) cc_final: 0.8084 (mp10) REVERT: L 707 ARG cc_start: 0.8300 (ttt180) cc_final: 0.8003 (ptt180) REVERT: M 41 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7477 (pp20) REVERT: M 74 ARG cc_start: 0.7619 (ptp-170) cc_final: 0.7325 (ptp-110) REVERT: M 76 TYR cc_start: 0.8511 (p90) cc_final: 0.8210 (p90) REVERT: M 85 ASP cc_start: 0.7406 (t0) cc_final: 0.7205 (t0) REVERT: M 285 ARG cc_start: 0.7937 (ptm160) cc_final: 0.7675 (ptt-90) REVERT: M 408 LEU cc_start: 0.9238 (mt) cc_final: 0.8804 (tp) REVERT: M 411 MET cc_start: 0.6691 (mtt) cc_final: 0.6237 (mtp) REVERT: N 147 ARG cc_start: 0.8583 (ptm-80) cc_final: 0.8328 (ptt90) REVERT: N 182 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8477 (mt) REVERT: N 417 GLU cc_start: 0.8598 (pt0) cc_final: 0.8099 (tm-30) REVERT: N 462 VAL cc_start: 0.8354 (t) cc_final: 0.8110 (p) REVERT: N 474 ASP cc_start: 0.7508 (p0) cc_final: 0.7261 (p0) REVERT: N 568 GLU cc_start: 0.8684 (tm-30) cc_final: 0.8372 (tm-30) REVERT: N 589 LYS cc_start: 0.8669 (mtmm) cc_final: 0.8456 (mtmm) REVERT: N 595 GLU cc_start: 0.8575 (pt0) cc_final: 0.8302 (pt0) REVERT: N 599 GLN cc_start: 0.8618 (mm-40) cc_final: 0.8256 (mm-40) REVERT: N 619 PHE cc_start: 0.8732 (t80) cc_final: 0.8526 (t80) REVERT: O 142 PHE cc_start: 0.8040 (OUTLIER) cc_final: 0.7584 (t80) REVERT: O 143 PHE cc_start: 0.8550 (m-80) cc_final: 0.8347 (m-10) REVERT: O 198 GLU cc_start: 0.8482 (tp30) cc_final: 0.8107 (tp30) REVERT: O 225 LYS cc_start: 0.9043 (mmmt) cc_final: 0.8612 (mmmt) REVERT: O 237 TRP cc_start: 0.7871 (t60) cc_final: 0.7463 (t60) REVERT: O 405 GLN cc_start: 0.8362 (mp10) cc_final: 0.7868 (mp10) REVERT: O 453 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8405 (mp) REVERT: O 474 ASP cc_start: 0.8191 (t0) cc_final: 0.7875 (t0) REVERT: O 494 ARG cc_start: 0.8077 (mmm160) cc_final: 0.7822 (mmm160) REVERT: O 566 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7387 (mm-30) REVERT: O 571 ARG cc_start: 0.8442 (tpt170) cc_final: 0.8151 (tpt170) REVERT: O 597 MET cc_start: 0.7959 (ppp) cc_final: 0.7725 (ppp) REVERT: O 598 LEU cc_start: 0.8526 (mm) cc_final: 0.8077 (mm) REVERT: O 601 GLU cc_start: 0.8344 (pp20) cc_final: 0.7886 (pp20) REVERT: O 602 ARG cc_start: 0.8680 (ttm-80) cc_final: 0.8022 (mmm-85) REVERT: O 604 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7803 (tm-30) REVERT: O 606 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8030 (mt-10) REVERT: P 58 GLN cc_start: 0.7951 (mm-40) cc_final: 0.7656 (mm-40) REVERT: P 303 LEU cc_start: 0.6755 (OUTLIER) cc_final: 0.6513 (tt) REVERT: P 422 TYR cc_start: 0.8402 (t80) cc_final: 0.8066 (t80) REVERT: P 432 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8494 (mm) REVERT: P 435 GLN cc_start: 0.7947 (mt0) cc_final: 0.7689 (mp10) REVERT: P 483 ASN cc_start: 0.7248 (t0) cc_final: 0.6794 (t0) REVERT: P 508 GLU cc_start: 0.7102 (tt0) cc_final: 0.6590 (pm20) REVERT: Q 316 GLU cc_start: 0.7845 (pt0) cc_final: 0.7589 (pt0) REVERT: Q 326 GLN cc_start: 0.7636 (tp-100) cc_final: 0.7415 (tm-30) REVERT: Q 328 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7311 (pm20) REVERT: Q 364 TYR cc_start: 0.8025 (t80) cc_final: 0.6746 (t80) REVERT: Q 381 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8198 (mm-30) REVERT: Q 390 GLU cc_start: 0.8274 (tm-30) cc_final: 0.7932 (tm-30) REVERT: Q 395 LYS cc_start: 0.9068 (mmmt) cc_final: 0.8845 (mmmm) REVERT: Q 401 MET cc_start: 0.8621 (tmm) cc_final: 0.7785 (tmm) REVERT: Q 402 MET cc_start: 0.8287 (mmt) cc_final: 0.7634 (mmm) REVERT: R 781 ASP cc_start: 0.8368 (p0) cc_final: 0.8012 (p0) REVERT: R 810 LYS cc_start: 0.8425 (ptpt) cc_final: 0.8041 (ptpt) REVERT: R 845 GLN cc_start: 0.8248 (mp10) cc_final: 0.7588 (mp10) REVERT: R 926 LYS cc_start: 0.8912 (mmmt) cc_final: 0.8653 (mtpt) REVERT: R 945 TYR cc_start: 0.8846 (m-80) cc_final: 0.8564 (m-80) REVERT: R 972 GLU cc_start: 0.7924 (pm20) cc_final: 0.7379 (pp20) REVERT: R 973 GLN cc_start: 0.8714 (mm-40) cc_final: 0.8124 (mp10) REVERT: R 1025 GLU cc_start: 0.8647 (mp0) cc_final: 0.8397 (mp0) REVERT: R 1063 ASP cc_start: 0.7634 (p0) cc_final: 0.6635 (p0) REVERT: S 128 GLU cc_start: 0.7534 (pt0) cc_final: 0.7184 (pp20) REVERT: S 151 GLN cc_start: 0.8197 (pm20) cc_final: 0.7811 (pm20) REVERT: S 158 ARG cc_start: 0.7649 (mmm160) cc_final: 0.7377 (mmm160) REVERT: S 167 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8181 (tmmt) REVERT: S 179 GLU cc_start: 0.8328 (mm-30) cc_final: 0.8034 (tp30) REVERT: S 193 LYS cc_start: 0.7879 (tmtt) cc_final: 0.7619 (tmtt) REVERT: S 201 ASN cc_start: 0.9003 (t0) cc_final: 0.8773 (t0) REVERT: S 219 ASP cc_start: 0.8192 (t0) cc_final: 0.7774 (t0) REVERT: S 234 GLN cc_start: 0.8938 (tt0) cc_final: 0.8660 (tt0) REVERT: S 242 GLN cc_start: 0.8525 (mm110) cc_final: 0.8020 (mt0) REVERT: S 244 ASN cc_start: 0.8026 (t0) cc_final: 0.7818 (t0) REVERT: S 289 GLN cc_start: 0.8354 (pt0) cc_final: 0.7872 (pt0) REVERT: S 310 ARG cc_start: 0.7334 (tpt170) cc_final: 0.6962 (tpp-160) REVERT: S 335 ARG cc_start: 0.8386 (mtm110) cc_final: 0.8162 (ttp-110) REVERT: S 374 LYS cc_start: 0.9100 (mmmt) cc_final: 0.8819 (mmmt) REVERT: S 389 GLU cc_start: 0.8560 (mp0) cc_final: 0.8077 (pm20) REVERT: S 390 ARG cc_start: 0.8659 (mmm160) cc_final: 0.8324 (mmm160) REVERT: S 398 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.7895 (pt0) REVERT: S 402 GLN cc_start: 0.8295 (pm20) cc_final: 0.8086 (pm20) REVERT: S 422 ARG cc_start: 0.8552 (mtm110) cc_final: 0.7689 (ptt90) REVERT: S 441 GLU cc_start: 0.8666 (mp0) cc_final: 0.8449 (mp0) REVERT: S 442 GLU cc_start: 0.8725 (mp0) cc_final: 0.8449 (mp0) REVERT: S 444 ARG cc_start: 0.8740 (ttm-80) cc_final: 0.8382 (tpt170) REVERT: T 347 GLN cc_start: 0.7425 (OUTLIER) cc_final: 0.6986 (pm20) REVERT: T 377 ASN cc_start: 0.8531 (t0) cc_final: 0.8231 (t0) REVERT: T 380 LEU cc_start: 0.8799 (tp) cc_final: 0.8544 (tt) REVERT: T 382 GLN cc_start: 0.9019 (mm110) cc_final: 0.8681 (mm-40) REVERT: T 386 MET cc_start: 0.8449 (mmp) cc_final: 0.8238 (mmp) REVERT: U 22 GLU cc_start: 0.8141 (tp30) cc_final: 0.7315 (tp30) REVERT: U 80 ARG cc_start: 0.8412 (tpm170) cc_final: 0.8029 (tpm170) outliers start: 135 outliers final: 75 residues processed: 1192 average time/residue: 0.3100 time to fit residues: 568.9189 Evaluate side-chains 1167 residues out of total 3875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 1079 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain K residue 310 PHE Chi-restraints excluded: chain K residue 311 GLU Chi-restraints excluded: chain K residue 360 ILE Chi-restraints excluded: chain K residue 441 HIS Chi-restraints excluded: chain K residue 468 PHE Chi-restraints excluded: chain K residue 470 ILE Chi-restraints excluded: chain K residue 837 LEU Chi-restraints excluded: chain K residue 890 MET Chi-restraints excluded: chain L residue 120 ASN Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain L residue 133 ARG Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 159 LEU Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 359 VAL Chi-restraints excluded: chain L residue 541 ILE Chi-restraints excluded: chain L residue 542 ARG Chi-restraints excluded: chain L residue 554 HIS Chi-restraints excluded: chain M residue 26 LEU Chi-restraints excluded: chain M residue 31 CYS Chi-restraints excluded: chain M residue 41 GLU Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 202 ASN Chi-restraints excluded: chain M residue 228 LEU Chi-restraints excluded: chain M residue 289 GLU Chi-restraints excluded: chain M residue 290 PHE Chi-restraints excluded: chain M residue 406 HIS Chi-restraints excluded: chain N residue 182 LEU Chi-restraints excluded: chain N residue 205 GLN Chi-restraints excluded: chain N residue 226 ILE Chi-restraints excluded: chain N residue 389 ILE Chi-restraints excluded: chain N residue 400 ASP Chi-restraints excluded: chain N residue 554 MET Chi-restraints excluded: chain N residue 584 LEU Chi-restraints excluded: chain O residue 142 PHE Chi-restraints excluded: chain O residue 393 LEU Chi-restraints excluded: chain O residue 394 GLU Chi-restraints excluded: chain O residue 453 LEU Chi-restraints excluded: chain O residue 564 HIS Chi-restraints excluded: chain O residue 568 GLU Chi-restraints excluded: chain O residue 604 GLU Chi-restraints excluded: chain O residue 619 PHE Chi-restraints excluded: chain O residue 636 THR Chi-restraints excluded: chain P residue 86 ILE Chi-restraints excluded: chain P residue 303 LEU Chi-restraints excluded: chain P residue 432 LEU Chi-restraints excluded: chain P residue 477 ILE Chi-restraints excluded: chain P residue 490 VAL Chi-restraints excluded: chain P residue 503 VAL Chi-restraints excluded: chain P residue 529 VAL Chi-restraints excluded: chain Q residue 328 GLU Chi-restraints excluded: chain Q residue 353 PHE Chi-restraints excluded: chain Q residue 378 LYS Chi-restraints excluded: chain Q residue 392 GLU Chi-restraints excluded: chain Q residue 404 LYS Chi-restraints excluded: chain Q residue 405 PHE Chi-restraints excluded: chain Q residue 419 ARG Chi-restraints excluded: chain R residue 835 VAL Chi-restraints excluded: chain R residue 850 VAL Chi-restraints excluded: chain R residue 1165 LEU Chi-restraints excluded: chain S residue 167 LYS Chi-restraints excluded: chain S residue 181 VAL Chi-restraints excluded: chain S residue 202 LEU Chi-restraints excluded: chain S residue 398 GLU Chi-restraints excluded: chain T residue 347 GLN Chi-restraints excluded: chain T residue 379 THR Chi-restraints excluded: chain T residue 383 GLN Chi-restraints excluded: chain U residue 25 ASP Chi-restraints excluded: chain U residue 56 TRP Chi-restraints excluded: chain U residue 127 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 174 optimal weight: 0.8980 chunk 153 optimal weight: 1.9990 chunk 307 optimal weight: 6.9990 chunk 163 optimal weight: 2.9990 chunk 286 optimal weight: 3.9990 chunk 278 optimal weight: 0.9990 chunk 149 optimal weight: 0.9990 chunk 334 optimal weight: 1.9990 chunk 106 optimal weight: 0.3980 chunk 102 optimal weight: 40.0000 chunk 82 optimal weight: 4.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 HIS ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 144 ASN ** O 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 599 GLN ** P 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 323 GLN S 238 GLN S 284 HIS ** S 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 331 GLN T 347 GLN ** T 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 399 HIS ** U 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.175176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.136397 restraints weight = 102644.598| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 3.94 r_work: 0.3570 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 43000 Z= 0.189 Angle : 0.719 12.106 59276 Z= 0.379 Chirality : 0.046 0.366 6553 Planarity : 0.005 0.072 6756 Dihedral : 22.155 167.165 7974 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.15 % Favored : 94.76 % Rotamer: Outliers : 4.35 % Allowed : 21.64 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.13), residues: 4426 helix: 0.54 (0.10), residues: 2441 sheet: -0.31 (0.35), residues: 224 loop : -1.20 (0.15), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG P 113 TYR 0.035 0.002 TYR H 80 PHE 0.039 0.002 PHE K 654 TRP 0.053 0.002 TRP M 153 HIS 0.009 0.001 HIS P 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.19 (43000) covalent geometry : angle 0.71919 / 0.38 (59276) hydrogen bonds : bond 0.05205 / 3.46 ( 2194) hydrogen bonds : angle 4.80983 / 3.43 ( 6069) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8852 Ramachandran restraints generated. 4426 Oldfield, 0 Emsley, 4426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8852 Ramachandran restraints generated. 4426 Oldfield, 0 Emsley, 4426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1279 residues out of total 3875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 1111 time to evaluate : 1.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8319 (pt0) cc_final: 0.8053 (pt0) REVERT: A 53 ARG cc_start: 0.7942 (mtp-110) cc_final: 0.7596 (ttp-110) REVERT: A 54 TYR cc_start: 0.8255 (m-10) cc_final: 0.7816 (m-10) REVERT: A 78 PHE cc_start: 0.7927 (m-10) cc_final: 0.7683 (m-80) REVERT: C 91 GLU cc_start: 0.8253 (tp30) cc_final: 0.7897 (tp30) REVERT: E 106 ASP cc_start: 0.8448 (m-30) cc_final: 0.7969 (m-30) REVERT: F 35 ARG cc_start: 0.8819 (mtp85) cc_final: 0.8539 (mtp85) REVERT: G 25 PHE cc_start: 0.8590 (m-80) cc_final: 0.7671 (m-80) REVERT: G 56 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8194 (mm-30) REVERT: G 74 LYS cc_start: 0.8761 (mppt) cc_final: 0.8549 (mppt) REVERT: H 41 VAL cc_start: 0.8766 (m) cc_final: 0.8566 (t) REVERT: H 65 ASP cc_start: 0.8816 (t0) cc_final: 0.8409 (t0) REVERT: H 73 GLU cc_start: 0.8849 (tp30) cc_final: 0.8500 (tp30) REVERT: H 76 ARG cc_start: 0.8931 (ttm-80) cc_final: 0.8696 (ttm-80) REVERT: H 113 LYS cc_start: 0.8627 (pttt) cc_final: 0.8236 (pttt) REVERT: K 316 ASP cc_start: 0.7477 (t0) cc_final: 0.7229 (t0) REVERT: K 323 ASN cc_start: 0.8411 (t0) cc_final: 0.8107 (t0) REVERT: K 331 GLU cc_start: 0.8644 (pp20) cc_final: 0.8239 (pp20) REVERT: K 333 LYS cc_start: 0.8559 (pttt) cc_final: 0.8282 (pttp) REVERT: K 401 MET cc_start: 0.8559 (mpp) cc_final: 0.8098 (mpp) REVERT: K 411 ILE cc_start: 0.8474 (mt) cc_final: 0.8178 (mm) REVERT: K 416 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7412 (mm-30) REVERT: K 430 LYS cc_start: 0.9078 (mmtm) cc_final: 0.8749 (mmtt) REVERT: K 446 LEU cc_start: 0.8522 (mt) cc_final: 0.8183 (pp) REVERT: K 453 ARG cc_start: 0.8093 (ppt170) cc_final: 0.7438 (tmt170) REVERT: K 710 MET cc_start: 0.7347 (mpp) cc_final: 0.6963 (mpp) REVERT: K 713 ASP cc_start: 0.8244 (t70) cc_final: 0.7341 (p0) REVERT: K 756 MET cc_start: 0.9166 (mmm) cc_final: 0.8794 (mmm) REVERT: K 1012 GLN cc_start: 0.8157 (OUTLIER) cc_final: 0.7865 (pp30) REVERT: L 121 THR cc_start: 0.7712 (OUTLIER) cc_final: 0.7491 (p) REVERT: L 159 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8215 (tp) REVERT: L 189 ARG cc_start: 0.8255 (mtt180) cc_final: 0.7955 (mtt180) REVERT: L 655 LYS cc_start: 0.8171 (ptmm) cc_final: 0.7959 (ptmm) REVERT: L 698 GLU cc_start: 0.8691 (pm20) cc_final: 0.8448 (pm20) REVERT: L 707 ARG cc_start: 0.8372 (ttt180) cc_final: 0.7975 (ptt180) REVERT: L 709 ASP cc_start: 0.8015 (m-30) cc_final: 0.7716 (p0) REVERT: M 24 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7733 (mt) REVERT: M 41 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7502 (pp20) REVERT: M 76 TYR cc_start: 0.8570 (p90) cc_final: 0.8101 (p90) REVERT: M 153 TRP cc_start: 0.8345 (p90) cc_final: 0.8023 (p90) REVERT: M 177 LEU cc_start: 0.8615 (tp) cc_final: 0.8304 (tp) REVERT: M 408 LEU cc_start: 0.9297 (mt) cc_final: 0.8864 (tp) REVERT: M 411 MET cc_start: 0.6794 (mtt) cc_final: 0.6317 (mtp) REVERT: N 147 ARG cc_start: 0.8614 (ptm-80) cc_final: 0.8322 (ptt90) REVERT: N 182 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8477 (mt) REVERT: N 417 GLU cc_start: 0.8629 (pt0) cc_final: 0.8129 (tm-30) REVERT: N 462 VAL cc_start: 0.8380 (t) cc_final: 0.8148 (p) REVERT: N 472 LEU cc_start: 0.8585 (mp) cc_final: 0.7992 (mm) REVERT: N 474 ASP cc_start: 0.7570 (p0) cc_final: 0.7335 (p0) REVERT: N 545 GLN cc_start: 0.8684 (mp10) cc_final: 0.8454 (pm20) REVERT: N 568 GLU cc_start: 0.8674 (tm-30) cc_final: 0.8435 (tm-30) REVERT: N 585 GLU cc_start: 0.8515 (pm20) cc_final: 0.8042 (pm20) REVERT: N 589 LYS cc_start: 0.8714 (mtmm) cc_final: 0.8503 (mtmm) REVERT: N 597 MET cc_start: 0.8050 (tmm) cc_final: 0.7518 (tmm) REVERT: N 599 GLN cc_start: 0.8677 (mm-40) cc_final: 0.8285 (mm-40) REVERT: N 619 PHE cc_start: 0.8671 (t80) cc_final: 0.8370 (t80) REVERT: N 625 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7922 (tp30) REVERT: O 130 THR cc_start: 0.8707 (t) cc_final: 0.8440 (p) REVERT: O 142 PHE cc_start: 0.8138 (OUTLIER) cc_final: 0.7653 (t80) REVERT: O 198 GLU cc_start: 0.8502 (tp30) cc_final: 0.8108 (tp30) REVERT: O 225 LYS cc_start: 0.9043 (mmmt) cc_final: 0.8632 (mmmt) REVERT: O 237 TRP cc_start: 0.8041 (t60) cc_final: 0.7540 (t60) REVERT: O 405 GLN cc_start: 0.8402 (mp10) cc_final: 0.7505 (mp10) REVERT: O 416 GLU cc_start: 0.7625 (mm-30) cc_final: 0.7408 (mm-30) REVERT: O 431 TYR cc_start: 0.7730 (m-80) cc_final: 0.7525 (m-80) REVERT: O 435 GLU cc_start: 0.1832 (OUTLIER) cc_final: 0.1563 (tm-30) REVERT: O 453 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8369 (mp) REVERT: O 474 ASP cc_start: 0.8144 (t0) cc_final: 0.7811 (t0) REVERT: O 566 GLU cc_start: 0.8556 (mm-30) cc_final: 0.7313 (mm-30) REVERT: O 571 ARG cc_start: 0.8500 (tpt170) cc_final: 0.8257 (tpt170) REVERT: O 597 MET cc_start: 0.7989 (ppp) cc_final: 0.7629 (ppp) REVERT: O 598 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8180 (mm) REVERT: O 601 GLU cc_start: 0.8324 (pp20) cc_final: 0.7872 (pp20) REVERT: O 602 ARG cc_start: 0.8738 (ttm-80) cc_final: 0.8117 (mmm-85) REVERT: O 604 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7792 (tm-30) REVERT: O 606 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8077 (mt-10) REVERT: O 611 GLN cc_start: 0.8032 (tp-100) cc_final: 0.7278 (tp-100) REVERT: O 612 LEU cc_start: 0.8554 (tp) cc_final: 0.8308 (tt) REVERT: O 621 ARG cc_start: 0.8803 (mmm160) cc_final: 0.8567 (mmm160) REVERT: P 58 GLN cc_start: 0.7976 (mm-40) cc_final: 0.7671 (mm-40) REVERT: P 305 GLU cc_start: 0.8212 (mp0) cc_final: 0.7983 (pm20) REVERT: P 368 ARG cc_start: 0.7661 (mtt-85) cc_final: 0.6869 (mtt-85) REVERT: P 432 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8498 (mm) REVERT: P 435 GLN cc_start: 0.8089 (mt0) cc_final: 0.7774 (mp10) REVERT: P 483 ASN cc_start: 0.7326 (t0) cc_final: 0.7096 (t0) REVERT: P 508 GLU cc_start: 0.7082 (tt0) cc_final: 0.6615 (pm20) REVERT: Q 316 GLU cc_start: 0.7849 (pt0) cc_final: 0.7636 (pt0) REVERT: Q 328 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7373 (pm20) REVERT: Q 381 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8258 (mm-30) REVERT: Q 390 GLU cc_start: 0.8343 (tm-30) cc_final: 0.8121 (tm-30) REVERT: Q 395 LYS cc_start: 0.9115 (mmmt) cc_final: 0.8913 (mmmm) REVERT: Q 401 MET cc_start: 0.8590 (tmm) cc_final: 0.7544 (tmm) REVERT: Q 402 MET cc_start: 0.8368 (mmt) cc_final: 0.7663 (mmm) REVERT: Q 419 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7427 (ppt-90) REVERT: R 810 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.7959 (ptpt) REVERT: R 845 GLN cc_start: 0.8232 (mp10) cc_final: 0.7699 (mp10) REVERT: R 852 ASN cc_start: 0.8956 (m-40) cc_final: 0.8753 (m110) REVERT: R 926 LYS cc_start: 0.8875 (mmmt) cc_final: 0.8625 (mtpt) REVERT: R 1025 GLU cc_start: 0.8705 (mp0) cc_final: 0.8457 (mp0) REVERT: R 1093 MET cc_start: 0.8472 (ttp) cc_final: 0.8240 (ttp) REVERT: S 100 ASP cc_start: 0.8482 (t0) cc_final: 0.8086 (t0) REVERT: S 158 ARG cc_start: 0.7757 (mmm160) cc_final: 0.7495 (mmm160) REVERT: S 167 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8034 (tmmt) REVERT: S 171 LYS cc_start: 0.8313 (mtmm) cc_final: 0.7986 (mtmm) REVERT: S 172 LYS cc_start: 0.8396 (pttt) cc_final: 0.7834 (pttt) REVERT: S 179 GLU cc_start: 0.8317 (mm-30) cc_final: 0.7983 (tp30) REVERT: S 193 LYS cc_start: 0.7885 (tmtt) cc_final: 0.7362 (tmtt) REVERT: S 205 ARG cc_start: 0.8394 (mtp180) cc_final: 0.7993 (mtp-110) REVERT: S 219 ASP cc_start: 0.8254 (t0) cc_final: 0.8017 (t0) REVERT: S 289 GLN cc_start: 0.8408 (pt0) cc_final: 0.7966 (pt0) REVERT: S 335 ARG cc_start: 0.8444 (mtm110) cc_final: 0.8111 (ttp80) REVERT: S 374 LYS cc_start: 0.9104 (mmmt) cc_final: 0.8795 (mmmt) REVERT: S 389 GLU cc_start: 0.8617 (mp0) cc_final: 0.8392 (mp0) REVERT: S 390 ARG cc_start: 0.8681 (mmm160) cc_final: 0.8455 (mmm160) REVERT: S 441 GLU cc_start: 0.8671 (mp0) cc_final: 0.8440 (mp0) REVERT: S 442 GLU cc_start: 0.8687 (mp0) cc_final: 0.8367 (mp0) REVERT: S 444 ARG cc_start: 0.8720 (ttm-80) cc_final: 0.8132 (tpt170) REVERT: T 377 ASN cc_start: 0.8518 (t0) cc_final: 0.8107 (t0) REVERT: T 380 LEU cc_start: 0.8816 (tp) cc_final: 0.8563 (tt) REVERT: T 385 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8130 (mm-30) REVERT: T 386 MET cc_start: 0.8546 (mmp) cc_final: 0.8308 (mmp) REVERT: U 80 ARG cc_start: 0.8517 (tpm170) cc_final: 0.7971 (tpm170) REVERT: U 129 ARG cc_start: 0.7292 (OUTLIER) cc_final: 0.6787 (ttm170) outliers start: 168 outliers final: 100 residues processed: 1193 average time/residue: 0.3068 time to fit residues: 564.9245 Evaluate side-chains 1216 residues out of total 3875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 1097 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 310 PHE Chi-restraints excluded: chain K residue 311 GLU Chi-restraints excluded: chain K residue 394 ASN Chi-restraints excluded: chain K residue 441 HIS Chi-restraints excluded: chain K residue 737 PHE Chi-restraints excluded: chain K residue 764 ILE Chi-restraints excluded: chain K residue 837 LEU Chi-restraints excluded: chain K residue 890 MET Chi-restraints excluded: chain K residue 926 MET Chi-restraints excluded: chain K residue 937 MET Chi-restraints excluded: chain K residue 1012 GLN Chi-restraints excluded: chain K residue 1090 MET Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain L residue 131 TRP Chi-restraints excluded: chain L residue 133 ARG Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 159 LEU Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 358 LEU Chi-restraints excluded: chain L residue 359 VAL Chi-restraints excluded: chain L residue 519 ILE Chi-restraints excluded: chain L residue 542 ARG Chi-restraints excluded: chain L residue 554 HIS Chi-restraints excluded: chain L residue 706 THR Chi-restraints excluded: chain M residue 24 LEU Chi-restraints excluded: chain M residue 31 CYS Chi-restraints excluded: chain M residue 41 GLU Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain M residue 202 ASN Chi-restraints excluded: chain M residue 228 LEU Chi-restraints excluded: chain M residue 289 GLU Chi-restraints excluded: chain M residue 290 PHE Chi-restraints excluded: chain M residue 355 ASP Chi-restraints excluded: chain M residue 406 HIS Chi-restraints excluded: chain N residue 155 LYS Chi-restraints excluded: chain N residue 182 LEU Chi-restraints excluded: chain N residue 205 GLN Chi-restraints excluded: chain N residue 226 ILE Chi-restraints excluded: chain N residue 400 ASP Chi-restraints excluded: chain N residue 423 LEU Chi-restraints excluded: chain N residue 554 MET Chi-restraints excluded: chain N residue 584 LEU Chi-restraints excluded: chain N residue 625 GLU Chi-restraints excluded: chain N residue 629 VAL Chi-restraints excluded: chain O residue 129 ASN Chi-restraints excluded: chain O residue 142 PHE Chi-restraints excluded: chain O residue 393 LEU Chi-restraints excluded: chain O residue 394 GLU Chi-restraints excluded: chain O residue 435 GLU Chi-restraints excluded: chain O residue 453 LEU Chi-restraints excluded: chain O residue 466 VAL Chi-restraints excluded: chain O residue 472 LEU Chi-restraints excluded: chain O residue 564 HIS Chi-restraints excluded: chain O residue 568 GLU Chi-restraints excluded: chain O residue 598 LEU Chi-restraints excluded: chain O residue 604 GLU Chi-restraints excluded: chain O residue 620 LYS Chi-restraints excluded: chain O residue 636 THR Chi-restraints excluded: chain P residue 86 ILE Chi-restraints excluded: chain P residue 348 ILE Chi-restraints excluded: chain P residue 366 HIS Chi-restraints excluded: chain P residue 367 LEU Chi-restraints excluded: chain P residue 432 LEU Chi-restraints excluded: chain P residue 490 VAL Chi-restraints excluded: chain P residue 529 VAL Chi-restraints excluded: chain Q residue 328 GLU Chi-restraints excluded: chain Q residue 353 PHE Chi-restraints excluded: chain Q residue 392 GLU Chi-restraints excluded: chain Q residue 404 LYS Chi-restraints excluded: chain Q residue 405 PHE Chi-restraints excluded: chain Q residue 419 ARG Chi-restraints excluded: chain R residue 810 LYS Chi-restraints excluded: chain R residue 835 VAL Chi-restraints excluded: chain R residue 850 VAL Chi-restraints excluded: chain R residue 1065 THR Chi-restraints excluded: chain R residue 1108 TRP Chi-restraints excluded: chain R residue 1165 LEU Chi-restraints excluded: chain S residue 111 TYR Chi-restraints excluded: chain S residue 167 LYS Chi-restraints excluded: chain S residue 181 VAL Chi-restraints excluded: chain S residue 202 LEU Chi-restraints excluded: chain S residue 240 HIS Chi-restraints excluded: chain S residue 287 VAL Chi-restraints excluded: chain T residue 379 THR Chi-restraints excluded: chain T residue 383 GLN Chi-restraints excluded: chain T residue 394 ILE Chi-restraints excluded: chain U residue 25 ASP Chi-restraints excluded: chain U residue 56 TRP Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 129 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 113 optimal weight: 9.9990 chunk 48 optimal weight: 0.4980 chunk 384 optimal weight: 0.9980 chunk 205 optimal weight: 0.9990 chunk 405 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 432 optimal weight: 1.9990 chunk 202 optimal weight: 0.9980 chunk 230 optimal weight: 0.5980 chunk 95 optimal weight: 9.9990 chunk 383 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 HIS ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 106 HIS K 388 ASN ** K 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 848 HIS ** L 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 323 GLN ** R 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R1085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 72 ASN ** S 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 399 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.175325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.136895 restraints weight = 102019.794| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 3.90 r_work: 0.3577 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 43000 Z= 0.171 Angle : 0.711 12.343 59276 Z= 0.371 Chirality : 0.045 0.365 6553 Planarity : 0.005 0.062 6756 Dihedral : 22.150 166.877 7967 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.22 % Favored : 94.69 % Rotamer: Outliers : 3.96 % Allowed : 23.11 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.13), residues: 4426 helix: 0.59 (0.10), residues: 2451 sheet: -0.14 (0.36), residues: 212 loop : -1.19 (0.15), residues: 1763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG M 34 TYR 0.042 0.002 TYR H 80 PHE 0.039 0.002 PHE K 654 TRP 0.028 0.002 TRP L 131 HIS 0.008 0.001 HIS K 462 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.17 (43000) covalent geometry : angle 0.71104 / 0.37 (59276) hydrogen bonds : bond 0.04803 / 3.19 ( 2194) hydrogen bonds : angle 4.69804 / 3.35 ( 6069) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8852 Ramachandran restraints generated. 4426 Oldfield, 0 Emsley, 4426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8852 Ramachandran restraints generated. 4426 Oldfield, 0 Emsley, 4426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1271 residues out of total 3875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 1118 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8277 (pt0) cc_final: 0.7990 (pt0) REVERT: A 53 ARG cc_start: 0.7892 (mtp-110) cc_final: 0.7543 (ttp-110) REVERT: A 54 TYR cc_start: 0.8188 (m-10) cc_final: 0.7700 (m-10) REVERT: A 78 PHE cc_start: 0.7771 (m-10) cc_final: 0.7475 (m-80) REVERT: C 91 GLU cc_start: 0.8151 (tp30) cc_final: 0.7768 (tp30) REVERT: E 94 GLU cc_start: 0.8349 (mm-30) cc_final: 0.8058 (mm-30) REVERT: E 106 ASP cc_start: 0.8410 (m-30) cc_final: 0.7992 (m-30) REVERT: F 35 ARG cc_start: 0.8834 (mtp85) cc_final: 0.8608 (mtp85) REVERT: G 25 PHE cc_start: 0.8562 (m-80) cc_final: 0.7969 (m-80) REVERT: G 74 LYS cc_start: 0.8787 (mppt) cc_final: 0.8543 (mppt) REVERT: H 65 ASP cc_start: 0.8745 (t0) cc_final: 0.8391 (t0) REVERT: H 73 GLU cc_start: 0.8847 (tp30) cc_final: 0.8588 (tp30) REVERT: H 76 ARG cc_start: 0.8931 (ttm-80) cc_final: 0.8535 (ttm-80) REVERT: H 113 LYS cc_start: 0.8615 (pttt) cc_final: 0.8220 (pttt) REVERT: K 316 ASP cc_start: 0.7475 (t0) cc_final: 0.7222 (t0) REVERT: K 323 ASN cc_start: 0.8385 (t0) cc_final: 0.8056 (t0) REVERT: K 331 GLU cc_start: 0.8649 (pp20) cc_final: 0.8248 (pp20) REVERT: K 333 LYS cc_start: 0.8580 (pttt) cc_final: 0.8267 (pttp) REVERT: K 356 LYS cc_start: 0.8385 (tppt) cc_final: 0.8152 (tmmt) REVERT: K 401 MET cc_start: 0.8574 (mpp) cc_final: 0.8135 (mpp) REVERT: K 411 ILE cc_start: 0.8500 (mt) cc_final: 0.8195 (mm) REVERT: K 416 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7435 (mm-30) REVERT: K 430 LYS cc_start: 0.9065 (mmtm) cc_final: 0.8720 (mmtt) REVERT: K 453 ARG cc_start: 0.8182 (ppt170) cc_final: 0.7678 (ppt170) REVERT: K 713 ASP cc_start: 0.8233 (t70) cc_final: 0.7372 (p0) REVERT: K 756 MET cc_start: 0.9153 (mmm) cc_final: 0.8785 (mmm) REVERT: K 804 LYS cc_start: 0.8040 (tppt) cc_final: 0.7833 (tptt) REVERT: K 1048 ASP cc_start: 0.7719 (t0) cc_final: 0.7335 (p0) REVERT: L 114 MET cc_start: 0.7391 (ppp) cc_final: 0.7152 (ppp) REVERT: L 121 THR cc_start: 0.7650 (OUTLIER) cc_final: 0.7426 (p) REVERT: L 159 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8135 (tp) REVERT: L 245 VAL cc_start: 0.8278 (m) cc_final: 0.7994 (p) REVERT: L 655 LYS cc_start: 0.8225 (ptmm) cc_final: 0.7990 (ptmm) REVERT: L 707 ARG cc_start: 0.8431 (ttt180) cc_final: 0.8042 (ptt180) REVERT: L 709 ASP cc_start: 0.8038 (m-30) cc_final: 0.7687 (p0) REVERT: M 42 MET cc_start: 0.6858 (mmm) cc_final: 0.6623 (mmm) REVERT: M 76 TYR cc_start: 0.8555 (p90) cc_final: 0.8099 (p90) REVERT: M 77 MET cc_start: 0.7803 (mmm) cc_final: 0.7600 (mmm) REVERT: M 85 ASP cc_start: 0.6724 (OUTLIER) cc_final: 0.6391 (t70) REVERT: M 408 LEU cc_start: 0.9301 (mt) cc_final: 0.8880 (tp) REVERT: M 411 MET cc_start: 0.6745 (mtt) cc_final: 0.6290 (mtp) REVERT: N 147 ARG cc_start: 0.8628 (ptm-80) cc_final: 0.8360 (ptt90) REVERT: N 182 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8412 (mt) REVERT: N 400 ASP cc_start: 0.6877 (OUTLIER) cc_final: 0.6401 (m-30) REVERT: N 417 GLU cc_start: 0.8600 (pt0) cc_final: 0.8085 (tm-30) REVERT: N 474 ASP cc_start: 0.7502 (p0) cc_final: 0.7186 (p0) REVERT: N 545 GLN cc_start: 0.8654 (mp10) cc_final: 0.8390 (pm20) REVERT: N 568 GLU cc_start: 0.8684 (tm-30) cc_final: 0.8439 (tm-30) REVERT: N 585 GLU cc_start: 0.8469 (pm20) cc_final: 0.7973 (pm20) REVERT: N 589 LYS cc_start: 0.8713 (mtmm) cc_final: 0.8511 (mtmm) REVERT: N 597 MET cc_start: 0.7971 (tmm) cc_final: 0.7365 (tmm) REVERT: N 599 GLN cc_start: 0.8681 (mm-40) cc_final: 0.8368 (mm-40) REVERT: N 610 GLN cc_start: 0.8211 (mp10) cc_final: 0.7866 (mp10) REVERT: N 619 PHE cc_start: 0.8667 (t80) cc_final: 0.8392 (t80) REVERT: N 625 GLU cc_start: 0.8117 (tp30) cc_final: 0.7890 (tp30) REVERT: O 142 PHE cc_start: 0.7817 (OUTLIER) cc_final: 0.7408 (t80) REVERT: O 198 GLU cc_start: 0.8437 (tp30) cc_final: 0.8026 (tp30) REVERT: O 212 ARG cc_start: 0.7974 (mpp-170) cc_final: 0.7683 (mtm-85) REVERT: O 225 LYS cc_start: 0.9047 (mmmt) cc_final: 0.8625 (mmmt) REVERT: O 405 GLN cc_start: 0.8413 (mp10) cc_final: 0.7828 (mp10) REVERT: O 431 TYR cc_start: 0.7737 (m-10) cc_final: 0.7490 (m-80) REVERT: O 435 GLU cc_start: 0.1792 (OUTLIER) cc_final: 0.1530 (tm-30) REVERT: O 453 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8391 (mp) REVERT: O 474 ASP cc_start: 0.8132 (t0) cc_final: 0.7735 (t0) REVERT: O 566 GLU cc_start: 0.8405 (mm-30) cc_final: 0.7733 (mm-30) REVERT: O 571 ARG cc_start: 0.8533 (tpt170) cc_final: 0.8282 (tpt170) REVERT: O 597 MET cc_start: 0.8025 (ppp) cc_final: 0.7780 (ppp) REVERT: O 598 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.7880 (mm) REVERT: O 601 GLU cc_start: 0.8291 (pp20) cc_final: 0.8069 (pp20) REVERT: O 602 ARG cc_start: 0.8730 (ttm-80) cc_final: 0.8148 (mmm-85) REVERT: O 604 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7800 (tm-30) REVERT: O 606 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8085 (mt-10) REVERT: O 607 ARG cc_start: 0.8534 (mmp80) cc_final: 0.8055 (mmp80) REVERT: O 611 GLN cc_start: 0.8031 (tp-100) cc_final: 0.7255 (tp-100) REVERT: P 58 GLN cc_start: 0.7964 (mm-40) cc_final: 0.7624 (mm-40) REVERT: P 305 GLU cc_start: 0.8229 (mp0) cc_final: 0.7974 (pm20) REVERT: P 368 ARG cc_start: 0.7653 (mtt-85) cc_final: 0.6831 (mtt-85) REVERT: P 428 GLU cc_start: 0.7906 (tp30) cc_final: 0.7696 (tp30) REVERT: P 429 ILE cc_start: 0.8636 (pt) cc_final: 0.8420 (pt) REVERT: P 432 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8492 (mm) REVERT: P 435 GLN cc_start: 0.8122 (mt0) cc_final: 0.7749 (mp10) REVERT: P 474 ASP cc_start: 0.7738 (t0) cc_final: 0.7473 (t0) REVERT: P 483 ASN cc_start: 0.7301 (t0) cc_final: 0.7069 (t0) REVERT: P 508 GLU cc_start: 0.7107 (tt0) cc_final: 0.6613 (pm20) REVERT: Q 316 GLU cc_start: 0.7850 (pt0) cc_final: 0.7528 (pt0) REVERT: Q 328 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7308 (pm20) REVERT: Q 343 LEU cc_start: 0.8606 (tt) cc_final: 0.8393 (tt) REVERT: Q 390 GLU cc_start: 0.8322 (tm-30) cc_final: 0.7997 (tp30) REVERT: Q 395 LYS cc_start: 0.9133 (mmmt) cc_final: 0.8889 (tppt) REVERT: Q 401 MET cc_start: 0.8591 (tmm) cc_final: 0.7514 (tmm) REVERT: Q 402 MET cc_start: 0.8363 (mmt) cc_final: 0.7645 (mmm) REVERT: Q 419 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7687 (ptt-90) REVERT: R 781 ASP cc_start: 0.8495 (p0) cc_final: 0.8096 (p0) REVERT: R 810 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.7990 (ptpt) REVERT: R 845 GLN cc_start: 0.8135 (mp10) cc_final: 0.7631 (mp10) REVERT: R 852 ASN cc_start: 0.8955 (m-40) cc_final: 0.8693 (m110) REVERT: R 950 ASP cc_start: 0.7853 (t0) cc_final: 0.7400 (t0) REVERT: R 954 ASP cc_start: 0.7835 (m-30) cc_final: 0.7187 (m-30) REVERT: R 1025 GLU cc_start: 0.8709 (mp0) cc_final: 0.8462 (mp0) REVERT: R 1093 MET cc_start: 0.8444 (ttp) cc_final: 0.8228 (ttp) REVERT: S 102 LYS cc_start: 0.7757 (mttm) cc_final: 0.7262 (tttt) REVERT: S 135 ASN cc_start: 0.9019 (m110) cc_final: 0.8789 (m110) REVERT: S 151 GLN cc_start: 0.8179 (pm20) cc_final: 0.7924 (pm20) REVERT: S 167 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.7896 (tmmt) REVERT: S 171 LYS cc_start: 0.8283 (mtmm) cc_final: 0.7442 (mtmm) REVERT: S 179 GLU cc_start: 0.8299 (mm-30) cc_final: 0.7997 (tp30) REVERT: S 193 LYS cc_start: 0.7879 (tmtt) cc_final: 0.7340 (tmtt) REVERT: S 201 ASN cc_start: 0.9019 (t0) cc_final: 0.8815 (t0) REVERT: S 234 GLN cc_start: 0.8987 (tt0) cc_final: 0.8671 (tt0) REVERT: S 238 GLN cc_start: 0.8665 (tt0) cc_final: 0.8457 (tt0) REVERT: S 242 GLN cc_start: 0.8567 (mm110) cc_final: 0.8065 (mt0) REVERT: S 244 ASN cc_start: 0.8164 (t0) cc_final: 0.7902 (t0) REVERT: S 335 ARG cc_start: 0.8447 (mtm110) cc_final: 0.8135 (ttp-110) REVERT: S 374 LYS cc_start: 0.9074 (mmmt) cc_final: 0.8734 (mmmt) REVERT: S 389 GLU cc_start: 0.8628 (mp0) cc_final: 0.8081 (mp0) REVERT: S 392 GLU cc_start: 0.8743 (pp20) cc_final: 0.8138 (pp20) REVERT: S 441 GLU cc_start: 0.8663 (mp0) cc_final: 0.8445 (mp0) REVERT: S 444 ARG cc_start: 0.8784 (ttm-80) cc_final: 0.8281 (tpt170) REVERT: T 347 GLN cc_start: 0.7680 (pm20) cc_final: 0.7138 (pm20) REVERT: T 377 ASN cc_start: 0.8446 (t0) cc_final: 0.8091 (t0) REVERT: T 380 LEU cc_start: 0.8813 (tp) cc_final: 0.8558 (tt) REVERT: T 385 GLU cc_start: 0.8459 (mm-30) cc_final: 0.8110 (mm-30) REVERT: T 386 MET cc_start: 0.8514 (mmp) cc_final: 0.8238 (mmp) REVERT: U 80 ARG cc_start: 0.8530 (tpm170) cc_final: 0.7975 (tpm170) REVERT: U 129 ARG cc_start: 0.7272 (OUTLIER) cc_final: 0.6757 (ttm170) outliers start: 153 outliers final: 106 residues processed: 1189 average time/residue: 0.3057 time to fit residues: 561.3409 Evaluate side-chains 1234 residues out of total 3875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 1112 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 310 PHE Chi-restraints excluded: chain K residue 311 GLU Chi-restraints excluded: chain K residue 394 ASN Chi-restraints excluded: chain K residue 441 HIS Chi-restraints excluded: chain K residue 468 PHE Chi-restraints excluded: chain K residue 764 ILE Chi-restraints excluded: chain K residue 837 LEU Chi-restraints excluded: chain K residue 890 MET Chi-restraints excluded: chain K residue 937 MET Chi-restraints excluded: chain K residue 1012 GLN Chi-restraints excluded: chain K residue 1049 MET Chi-restraints excluded: chain K residue 1090 MET Chi-restraints excluded: chain L residue 120 ASN Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain L residue 133 ARG Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 159 LEU Chi-restraints excluded: chain L residue 187 ASP Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 226 SER Chi-restraints excluded: chain L residue 359 VAL Chi-restraints excluded: chain L residue 519 ILE Chi-restraints excluded: chain L residue 542 ARG Chi-restraints excluded: chain L residue 544 LEU Chi-restraints excluded: chain L residue 554 HIS Chi-restraints excluded: chain L residue 654 ILE Chi-restraints excluded: chain L residue 706 THR Chi-restraints excluded: chain M residue 24 LEU Chi-restraints excluded: chain M residue 31 CYS Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 85 ASP Chi-restraints excluded: chain M residue 202 ASN Chi-restraints excluded: chain M residue 289 GLU Chi-restraints excluded: chain M residue 290 PHE Chi-restraints excluded: chain M residue 406 HIS Chi-restraints excluded: chain N residue 182 LEU Chi-restraints excluded: chain N residue 205 GLN Chi-restraints excluded: chain N residue 226 ILE Chi-restraints excluded: chain N residue 392 LEU Chi-restraints excluded: chain N residue 400 ASP Chi-restraints excluded: chain N residue 423 LEU Chi-restraints excluded: chain N residue 554 MET Chi-restraints excluded: chain N residue 584 LEU Chi-restraints excluded: chain N residue 629 VAL Chi-restraints excluded: chain O residue 142 PHE Chi-restraints excluded: chain O residue 393 LEU Chi-restraints excluded: chain O residue 435 GLU Chi-restraints excluded: chain O residue 453 LEU Chi-restraints excluded: chain O residue 466 VAL Chi-restraints excluded: chain O residue 472 LEU Chi-restraints excluded: chain O residue 491 GLN Chi-restraints excluded: chain O residue 564 HIS Chi-restraints excluded: chain O residue 568 GLU Chi-restraints excluded: chain O residue 598 LEU Chi-restraints excluded: chain O residue 604 GLU Chi-restraints excluded: chain O residue 636 THR Chi-restraints excluded: chain P residue 73 THR Chi-restraints excluded: chain P residue 86 ILE Chi-restraints excluded: chain P residue 112 LYS Chi-restraints excluded: chain P residue 348 ILE Chi-restraints excluded: chain P residue 366 HIS Chi-restraints excluded: chain P residue 432 LEU Chi-restraints excluded: chain P residue 440 MET Chi-restraints excluded: chain P residue 458 ARG Chi-restraints excluded: chain P residue 477 ILE Chi-restraints excluded: chain P residue 490 VAL Chi-restraints excluded: chain P residue 503 VAL Chi-restraints excluded: chain P residue 529 VAL Chi-restraints excluded: chain Q residue 328 GLU Chi-restraints excluded: chain Q residue 353 PHE Chi-restraints excluded: chain Q residue 392 GLU Chi-restraints excluded: chain Q residue 404 LYS Chi-restraints excluded: chain Q residue 405 PHE Chi-restraints excluded: chain Q residue 419 ARG Chi-restraints excluded: chain R residue 810 LYS Chi-restraints excluded: chain R residue 835 VAL Chi-restraints excluded: chain R residue 850 VAL Chi-restraints excluded: chain R residue 1108 TRP Chi-restraints excluded: chain R residue 1165 LEU Chi-restraints excluded: chain S residue 111 TYR Chi-restraints excluded: chain S residue 167 LYS Chi-restraints excluded: chain S residue 181 VAL Chi-restraints excluded: chain S residue 202 LEU Chi-restraints excluded: chain S residue 240 HIS Chi-restraints excluded: chain S residue 286 LEU Chi-restraints excluded: chain S residue 287 VAL Chi-restraints excluded: chain S residue 421 GLN Chi-restraints excluded: chain S residue 429 VAL Chi-restraints excluded: chain T residue 379 THR Chi-restraints excluded: chain T residue 383 GLN Chi-restraints excluded: chain T residue 393 SER Chi-restraints excluded: chain T residue 394 ILE Chi-restraints excluded: chain U residue 31 VAL Chi-restraints excluded: chain U residue 56 TRP Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 129 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 287 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 180 optimal weight: 0.3980 chunk 369 optimal weight: 0.3980 chunk 34 optimal weight: 4.9990 chunk 263 optimal weight: 0.7980 chunk 225 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 114 optimal weight: 0.0040 chunk 395 optimal weight: 3.9990 chunk 382 optimal weight: 0.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN G 84 GLN H 44 GLN ** K 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 102 GLN M 202 ASN ** M 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 275 HIS ** N 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 323 GLN ** R 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R1085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 343 ASN ** T 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 399 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.176090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.137829 restraints weight = 102147.671| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 3.91 r_work: 0.3592 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 43000 Z= 0.148 Angle : 0.710 12.267 59276 Z= 0.368 Chirality : 0.045 0.363 6553 Planarity : 0.005 0.059 6756 Dihedral : 22.114 167.146 7962 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.31 % Favored : 94.60 % Rotamer: Outliers : 3.86 % Allowed : 24.12 % Favored : 72.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.13), residues: 4426 helix: 0.64 (0.10), residues: 2453 sheet: -0.19 (0.37), residues: 219 loop : -1.16 (0.15), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG Q 377 TYR 0.031 0.002 TYR S 111 PHE 0.041 0.002 PHE K 654 TRP 0.040 0.002 TRP L 529 HIS 0.008 0.001 HIS R 809 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.15 (43000) covalent geometry : angle 0.71032 / 0.37 (59276) hydrogen bonds : bond 0.04590 / 3.04 ( 2194) hydrogen bonds : angle 4.57606 / 3.26 ( 6069) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8852 Ramachandran restraints generated. 4426 Oldfield, 0 Emsley, 4426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8852 Ramachandran restraints generated. 4426 Oldfield, 0 Emsley, 4426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1265 residues out of total 3875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 1116 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8296 (pt0) cc_final: 0.8026 (pt0) REVERT: A 53 ARG cc_start: 0.7868 (mtp-110) cc_final: 0.7522 (ttp-110) REVERT: A 54 TYR cc_start: 0.8141 (m-10) cc_final: 0.7696 (m-10) REVERT: A 87 SER cc_start: 0.9202 (p) cc_final: 0.8932 (t) REVERT: C 56 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.7786 (tp30) REVERT: C 91 GLU cc_start: 0.8124 (tp30) cc_final: 0.7736 (tp30) REVERT: E 94 GLU cc_start: 0.8344 (mm-30) cc_final: 0.8083 (mm-30) REVERT: E 106 ASP cc_start: 0.8423 (m-30) cc_final: 0.8159 (m-30) REVERT: E 120 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.7703 (mpp) REVERT: F 35 ARG cc_start: 0.8833 (mtp85) cc_final: 0.8062 (mtp85) REVERT: G 25 PHE cc_start: 0.8408 (m-80) cc_final: 0.7912 (m-80) REVERT: G 74 LYS cc_start: 0.8838 (mppt) cc_final: 0.8545 (mppt) REVERT: H 59 MET cc_start: 0.8909 (mmm) cc_final: 0.8651 (mmm) REVERT: H 65 ASP cc_start: 0.8745 (t0) cc_final: 0.8394 (t0) REVERT: H 73 GLU cc_start: 0.8826 (tp30) cc_final: 0.8613 (tp30) REVERT: H 76 ARG cc_start: 0.8939 (ttm-80) cc_final: 0.8532 (tpp80) REVERT: H 113 LYS cc_start: 0.8616 (pttt) cc_final: 0.8261 (pttt) REVERT: K 316 ASP cc_start: 0.7486 (t0) cc_final: 0.7229 (t0) REVERT: K 323 ASN cc_start: 0.8375 (t0) cc_final: 0.8057 (t0) REVERT: K 331 GLU cc_start: 0.8621 (pp20) cc_final: 0.8152 (pp20) REVERT: K 333 LYS cc_start: 0.8589 (pttt) cc_final: 0.8330 (pttt) REVERT: K 356 LYS cc_start: 0.8420 (tppt) cc_final: 0.8183 (tmmt) REVERT: K 362 GLU cc_start: 0.7722 (mp0) cc_final: 0.6895 (pm20) REVERT: K 401 MET cc_start: 0.8611 (mpp) cc_final: 0.8196 (mpp) REVERT: K 411 ILE cc_start: 0.8563 (mt) cc_final: 0.8261 (mm) REVERT: K 416 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7448 (mm-30) REVERT: K 430 LYS cc_start: 0.9089 (mmtm) cc_final: 0.8734 (mmtt) REVERT: K 446 LEU cc_start: 0.8521 (mt) cc_final: 0.8267 (pp) REVERT: K 453 ARG cc_start: 0.8162 (ppt170) cc_final: 0.7616 (ppt170) REVERT: K 710 MET cc_start: 0.7378 (mpp) cc_final: 0.6843 (mpp) REVERT: K 713 ASP cc_start: 0.8244 (t70) cc_final: 0.7374 (p0) REVERT: K 756 MET cc_start: 0.9144 (mmm) cc_final: 0.8762 (mmm) REVERT: K 804 LYS cc_start: 0.7966 (tppt) cc_final: 0.7736 (tptt) REVERT: K 1048 ASP cc_start: 0.7707 (t0) cc_final: 0.7334 (p0) REVERT: L 121 THR cc_start: 0.7545 (OUTLIER) cc_final: 0.7314 (p) REVERT: L 159 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7993 (tp) REVERT: L 189 ARG cc_start: 0.8132 (mtt180) cc_final: 0.7914 (mtt180) REVERT: L 245 VAL cc_start: 0.8304 (OUTLIER) cc_final: 0.8041 (p) REVERT: L 655 LYS cc_start: 0.8218 (ptmm) cc_final: 0.7975 (ptmm) REVERT: L 709 ASP cc_start: 0.8055 (m-30) cc_final: 0.7714 (p0) REVERT: M 25 VAL cc_start: 0.7401 (t) cc_final: 0.6881 (m) REVERT: M 42 MET cc_start: 0.6908 (mmm) cc_final: 0.6657 (mmm) REVERT: M 74 ARG cc_start: 0.7312 (ptp-170) cc_final: 0.6871 (ptp90) REVERT: M 76 TYR cc_start: 0.8498 (p90) cc_final: 0.8101 (p90) REVERT: M 408 LEU cc_start: 0.9287 (mt) cc_final: 0.8876 (tp) REVERT: M 411 MET cc_start: 0.6743 (mtt) cc_final: 0.6309 (mtp) REVERT: N 147 ARG cc_start: 0.8581 (ptm-80) cc_final: 0.8338 (ptt90) REVERT: N 182 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8352 (mt) REVERT: N 400 ASP cc_start: 0.6798 (OUTLIER) cc_final: 0.6373 (m-30) REVERT: N 417 GLU cc_start: 0.8598 (pt0) cc_final: 0.7980 (tp30) REVERT: N 545 GLN cc_start: 0.8673 (mp10) cc_final: 0.8440 (pm20) REVERT: N 568 GLU cc_start: 0.8673 (tm-30) cc_final: 0.8438 (tm-30) REVERT: N 585 GLU cc_start: 0.8471 (pm20) cc_final: 0.7936 (pm20) REVERT: N 597 MET cc_start: 0.7920 (tmm) cc_final: 0.7302 (tmm) REVERT: N 599 GLN cc_start: 0.8698 (mm-40) cc_final: 0.8370 (mm-40) REVERT: N 610 GLN cc_start: 0.8200 (mp10) cc_final: 0.7529 (mp10) REVERT: N 625 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7791 (tp30) REVERT: O 135 GLU cc_start: 0.6546 (mp0) cc_final: 0.6335 (mp0) REVERT: O 142 PHE cc_start: 0.7736 (OUTLIER) cc_final: 0.7298 (t80) REVERT: O 198 GLU cc_start: 0.8430 (tp30) cc_final: 0.8027 (tp30) REVERT: O 212 ARG cc_start: 0.7872 (mpp-170) cc_final: 0.7614 (mtm-85) REVERT: O 225 LYS cc_start: 0.9060 (mmmt) cc_final: 0.8614 (mmtt) REVERT: O 237 TRP cc_start: 0.8113 (t60) cc_final: 0.7625 (t60) REVERT: O 405 GLN cc_start: 0.8443 (mp10) cc_final: 0.7871 (mp10) REVERT: O 435 GLU cc_start: 0.1771 (OUTLIER) cc_final: 0.1503 (tm-30) REVERT: O 453 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8394 (mp) REVERT: O 474 ASP cc_start: 0.8130 (t0) cc_final: 0.7678 (t70) REVERT: O 566 GLU cc_start: 0.8623 (mm-30) cc_final: 0.7194 (mm-30) REVERT: O 571 ARG cc_start: 0.8570 (tpt170) cc_final: 0.8289 (tpt170) REVERT: O 594 MET cc_start: 0.8418 (tpp) cc_final: 0.7886 (tpp) REVERT: O 597 MET cc_start: 0.8029 (ppp) cc_final: 0.7825 (ppp) REVERT: O 598 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.7875 (mm) REVERT: O 601 GLU cc_start: 0.8230 (pp20) cc_final: 0.7960 (pp20) REVERT: O 602 ARG cc_start: 0.8724 (ttm-80) cc_final: 0.8181 (mmm-85) REVERT: O 604 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7768 (tm-30) REVERT: O 606 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8096 (mt-10) REVERT: O 607 ARG cc_start: 0.8544 (mmp80) cc_final: 0.8006 (mmp80) REVERT: O 611 GLN cc_start: 0.7926 (tp-100) cc_final: 0.6709 (tp-100) REVERT: P 58 GLN cc_start: 0.7965 (mm-40) cc_final: 0.7581 (mm-40) REVERT: P 345 LEU cc_start: 0.8156 (mt) cc_final: 0.7764 (mt) REVERT: P 348 ILE cc_start: 0.3372 (OUTLIER) cc_final: 0.2015 (tt) REVERT: P 368 ARG cc_start: 0.7583 (mtt-85) cc_final: 0.6775 (mtt-85) REVERT: P 428 GLU cc_start: 0.7889 (tp30) cc_final: 0.7637 (tp30) REVERT: P 429 ILE cc_start: 0.8654 (pt) cc_final: 0.8431 (pt) REVERT: P 432 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8444 (mm) REVERT: P 435 GLN cc_start: 0.8027 (mt0) cc_final: 0.7619 (mp10) REVERT: P 474 ASP cc_start: 0.7789 (t0) cc_final: 0.7426 (t0) REVERT: P 483 ASN cc_start: 0.7225 (t0) cc_final: 0.7016 (t0) REVERT: P 508 GLU cc_start: 0.7015 (tt0) cc_final: 0.6587 (pm20) REVERT: P 525 GLU cc_start: 0.8327 (mm-30) cc_final: 0.8098 (mm-30) REVERT: P 531 LEU cc_start: 0.5373 (OUTLIER) cc_final: 0.5168 (pp) REVERT: Q 316 GLU cc_start: 0.7613 (pt0) cc_final: 0.7358 (pt0) REVERT: Q 328 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7271 (pm20) REVERT: Q 390 GLU cc_start: 0.8282 (tm-30) cc_final: 0.7965 (tp30) REVERT: Q 395 LYS cc_start: 0.9105 (mmmt) cc_final: 0.8877 (tppt) REVERT: Q 401 MET cc_start: 0.8570 (tmm) cc_final: 0.7324 (tmm) REVERT: Q 402 MET cc_start: 0.8319 (mmt) cc_final: 0.7575 (mmm) REVERT: R 810 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.7998 (ptpt) REVERT: R 833 GLU cc_start: 0.8011 (pm20) cc_final: 0.7737 (pm20) REVERT: R 836 GLU cc_start: 0.8377 (pp20) cc_final: 0.8145 (pp20) REVERT: R 845 GLN cc_start: 0.8045 (mp10) cc_final: 0.7585 (mp10) REVERT: R 850 VAL cc_start: 0.7805 (OUTLIER) cc_final: 0.7586 (m) REVERT: R 940 MET cc_start: 0.8125 (tpp) cc_final: 0.7740 (tpt) REVERT: R 1025 GLU cc_start: 0.8715 (mp0) cc_final: 0.8475 (mp0) REVERT: R 1032 LYS cc_start: 0.8455 (ttmm) cc_final: 0.8164 (ttmm) REVERT: R 1072 MET cc_start: 0.7424 (mmp) cc_final: 0.7102 (mmp) REVERT: R 1085 GLN cc_start: 0.8402 (mm-40) cc_final: 0.8192 (mm-40) REVERT: R 1106 ARG cc_start: 0.8717 (tpp-160) cc_final: 0.8094 (mmt180) REVERT: S 100 ASP cc_start: 0.8418 (t0) cc_final: 0.7959 (t0) REVERT: S 102 LYS cc_start: 0.7663 (mttm) cc_final: 0.7186 (tttt) REVERT: S 128 GLU cc_start: 0.7584 (pt0) cc_final: 0.6950 (pp20) REVERT: S 135 ASN cc_start: 0.9009 (m110) cc_final: 0.8640 (m110) REVERT: S 151 GLN cc_start: 0.8145 (pm20) cc_final: 0.7866 (pm20) REVERT: S 158 ARG cc_start: 0.7677 (mmm160) cc_final: 0.7456 (mmm160) REVERT: S 179 GLU cc_start: 0.8279 (mm-30) cc_final: 0.7990 (tp30) REVERT: S 193 LYS cc_start: 0.7846 (tmtt) cc_final: 0.7346 (tmtt) REVERT: S 219 ASP cc_start: 0.8303 (t0) cc_final: 0.8006 (t0) REVERT: S 238 GLN cc_start: 0.8569 (tt0) cc_final: 0.8350 (tt0) REVERT: S 242 GLN cc_start: 0.8539 (mm110) cc_final: 0.8066 (mt0) REVERT: S 244 ASN cc_start: 0.8209 (t0) cc_final: 0.7969 (t0) REVERT: S 335 ARG cc_start: 0.8440 (mtm110) cc_final: 0.8140 (ttp-110) REVERT: S 389 GLU cc_start: 0.8546 (mp0) cc_final: 0.7888 (pm20) REVERT: S 392 GLU cc_start: 0.8747 (pp20) cc_final: 0.8119 (pp20) REVERT: S 441 GLU cc_start: 0.8671 (mp0) cc_final: 0.8380 (mp0) REVERT: S 444 ARG cc_start: 0.8744 (ttm-80) cc_final: 0.8293 (tpt170) REVERT: T 347 GLN cc_start: 0.7660 (pm20) cc_final: 0.7128 (pm20) REVERT: T 377 ASN cc_start: 0.8428 (t0) cc_final: 0.8046 (t0) REVERT: T 378 ARG cc_start: 0.8322 (tpp80) cc_final: 0.8056 (tpp80) REVERT: T 380 LEU cc_start: 0.8818 (tp) cc_final: 0.8539 (tt) REVERT: T 385 GLU cc_start: 0.8453 (mm-30) cc_final: 0.8072 (mm-30) REVERT: T 386 MET cc_start: 0.8540 (mmp) cc_final: 0.8265 (mmp) REVERT: U 80 ARG cc_start: 0.8560 (tpm170) cc_final: 0.8017 (tpm170) REVERT: U 129 ARG cc_start: 0.7248 (OUTLIER) cc_final: 0.6743 (ttm170) outliers start: 149 outliers final: 99 residues processed: 1184 average time/residue: 0.3088 time to fit residues: 565.2060 Evaluate side-chains 1214 residues out of total 3875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 1095 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 310 PHE Chi-restraints excluded: chain K residue 311 GLU Chi-restraints excluded: chain K residue 394 ASN Chi-restraints excluded: chain K residue 441 HIS Chi-restraints excluded: chain K residue 468 PHE Chi-restraints excluded: chain K residue 764 ILE Chi-restraints excluded: chain K residue 837 LEU Chi-restraints excluded: chain K residue 890 MET Chi-restraints excluded: chain K residue 937 MET Chi-restraints excluded: chain K residue 1012 GLN Chi-restraints excluded: chain K residue 1049 MET Chi-restraints excluded: chain K residue 1090 MET Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 120 ASN Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain L residue 133 ARG Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 159 LEU Chi-restraints excluded: chain L residue 177 TYR Chi-restraints excluded: chain L residue 187 ASP Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 226 SER Chi-restraints excluded: chain L residue 245 VAL Chi-restraints excluded: chain L residue 358 LEU Chi-restraints excluded: chain L residue 359 VAL Chi-restraints excluded: chain L residue 519 ILE Chi-restraints excluded: chain L residue 542 ARG Chi-restraints excluded: chain L residue 544 LEU Chi-restraints excluded: chain L residue 554 HIS Chi-restraints excluded: chain L residue 654 ILE Chi-restraints excluded: chain L residue 677 LEU Chi-restraints excluded: chain L residue 706 THR Chi-restraints excluded: chain M residue 24 LEU Chi-restraints excluded: chain M residue 31 CYS Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 289 GLU Chi-restraints excluded: chain M residue 290 PHE Chi-restraints excluded: chain M residue 406 HIS Chi-restraints excluded: chain N residue 133 ILE Chi-restraints excluded: chain N residue 155 LYS Chi-restraints excluded: chain N residue 182 LEU Chi-restraints excluded: chain N residue 205 GLN Chi-restraints excluded: chain N residue 400 ASP Chi-restraints excluded: chain N residue 423 LEU Chi-restraints excluded: chain N residue 554 MET Chi-restraints excluded: chain N residue 584 LEU Chi-restraints excluded: chain N residue 625 GLU Chi-restraints excluded: chain N residue 629 VAL Chi-restraints excluded: chain N residue 643 ARG Chi-restraints excluded: chain O residue 142 PHE Chi-restraints excluded: chain O residue 202 LEU Chi-restraints excluded: chain O residue 393 LEU Chi-restraints excluded: chain O residue 435 GLU Chi-restraints excluded: chain O residue 453 LEU Chi-restraints excluded: chain O residue 466 VAL Chi-restraints excluded: chain O residue 472 LEU Chi-restraints excluded: chain O residue 491 GLN Chi-restraints excluded: chain O residue 564 HIS Chi-restraints excluded: chain O residue 568 GLU Chi-restraints excluded: chain O residue 598 LEU Chi-restraints excluded: chain O residue 604 GLU Chi-restraints excluded: chain O residue 636 THR Chi-restraints excluded: chain P residue 86 ILE Chi-restraints excluded: chain P residue 120 LEU Chi-restraints excluded: chain P residue 348 ILE Chi-restraints excluded: chain P residue 366 HIS Chi-restraints excluded: chain P residue 432 LEU Chi-restraints excluded: chain P residue 440 MET Chi-restraints excluded: chain P residue 490 VAL Chi-restraints excluded: chain P residue 503 VAL Chi-restraints excluded: chain P residue 529 VAL Chi-restraints excluded: chain P residue 531 LEU Chi-restraints excluded: chain Q residue 328 GLU Chi-restraints excluded: chain Q residue 353 PHE Chi-restraints excluded: chain Q residue 404 LYS Chi-restraints excluded: chain Q residue 419 ARG Chi-restraints excluded: chain Q residue 463 VAL Chi-restraints excluded: chain R residue 810 LYS Chi-restraints excluded: chain R residue 835 VAL Chi-restraints excluded: chain R residue 850 VAL Chi-restraints excluded: chain R residue 887 THR Chi-restraints excluded: chain R residue 1108 TRP Chi-restraints excluded: chain R residue 1165 LEU Chi-restraints excluded: chain S residue 111 TYR Chi-restraints excluded: chain S residue 181 VAL Chi-restraints excluded: chain S residue 202 LEU Chi-restraints excluded: chain S residue 240 HIS Chi-restraints excluded: chain S residue 286 LEU Chi-restraints excluded: chain S residue 287 VAL Chi-restraints excluded: chain S residue 429 VAL Chi-restraints excluded: chain T residue 379 THR Chi-restraints excluded: chain T residue 390 TYR Chi-restraints excluded: chain T residue 394 ILE Chi-restraints excluded: chain U residue 31 VAL Chi-restraints excluded: chain U residue 39 VAL Chi-restraints excluded: chain U residue 56 TRP Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 129 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 139 optimal weight: 30.0000 chunk 463 optimal weight: 5.9990 chunk 316 optimal weight: 0.6980 chunk 335 optimal weight: 2.9990 chunk 461 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 237 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 175 optimal weight: 0.8980 chunk 127 optimal weight: 40.0000 chunk 466 optimal weight: 20.0000 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN H 44 GLN ** K 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 682 GLN ** L 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 275 HIS ** N 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 599 GLN P 441 GLN ** P 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 323 GLN R 852 ASN ** R 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R1085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 80 GLN ** S 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 347 GLN ** T 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 399 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.173018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.134491 restraints weight = 101770.060| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 3.86 r_work: 0.3537 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 43000 Z= 0.231 Angle : 0.749 12.683 59276 Z= 0.392 Chirality : 0.047 0.361 6553 Planarity : 0.005 0.060 6756 Dihedral : 22.207 164.791 7947 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.56 % Favored : 94.33 % Rotamer: Outliers : 4.30 % Allowed : 24.61 % Favored : 71.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.13), residues: 4426 helix: 0.61 (0.10), residues: 2459 sheet: -0.39 (0.35), residues: 234 loop : -1.24 (0.15), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG M 34 TYR 0.053 0.002 TYR H 80 PHE 0.045 0.002 PHE K 654 TRP 0.063 0.002 TRP M 153 HIS 0.012 0.001 HIS L 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.23 (43000) covalent geometry : angle 0.74917 / 0.39 (59276) hydrogen bonds : bond 0.04789 / 3.19 ( 2194) hydrogen bonds : angle 4.62188 / 3.29 ( 6069) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8852 Ramachandran restraints generated. 4426 Oldfield, 0 Emsley, 4426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8852 Ramachandran restraints generated. 4426 Oldfield, 0 Emsley, 4426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1281 residues out of total 3875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 1115 time to evaluate : 1.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8336 (pt0) cc_final: 0.8086 (pt0) REVERT: A 53 ARG cc_start: 0.7922 (mtp-110) cc_final: 0.7560 (ttp-110) REVERT: A 87 SER cc_start: 0.9224 (p) cc_final: 0.8972 (t) REVERT: A 131 ARG cc_start: 0.8827 (mtm180) cc_final: 0.8552 (mtp85) REVERT: C 56 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.7781 (tp30) REVERT: C 91 GLU cc_start: 0.8107 (tp30) cc_final: 0.7731 (tp30) REVERT: E 106 ASP cc_start: 0.8469 (m-30) cc_final: 0.7961 (m-30) REVERT: E 120 MET cc_start: 0.8890 (OUTLIER) cc_final: 0.7755 (mpp) REVERT: G 74 LYS cc_start: 0.8769 (mppt) cc_final: 0.8514 (mppt) REVERT: H 65 ASP cc_start: 0.8724 (t0) cc_final: 0.8396 (t0) REVERT: H 73 GLU cc_start: 0.8865 (tp30) cc_final: 0.8600 (tp30) REVERT: H 76 ARG cc_start: 0.8940 (ttm-80) cc_final: 0.8675 (ttm110) REVERT: H 113 LYS cc_start: 0.8657 (pttt) cc_final: 0.8315 (pttt) REVERT: K 316 ASP cc_start: 0.7509 (t0) cc_final: 0.7268 (t0) REVERT: K 323 ASN cc_start: 0.8426 (t0) cc_final: 0.8099 (t0) REVERT: K 331 GLU cc_start: 0.8645 (pp20) cc_final: 0.8165 (pp20) REVERT: K 333 LYS cc_start: 0.8626 (pttt) cc_final: 0.8307 (pttp) REVERT: K 401 MET cc_start: 0.8610 (mpp) cc_final: 0.8193 (mpp) REVERT: K 411 ILE cc_start: 0.8512 (mt) cc_final: 0.8236 (mm) REVERT: K 416 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7464 (mm-30) REVERT: K 418 GLN cc_start: 0.8657 (mm110) cc_final: 0.8155 (mm-40) REVERT: K 446 LEU cc_start: 0.8544 (mt) cc_final: 0.8238 (pp) REVERT: K 453 ARG cc_start: 0.8236 (ppt170) cc_final: 0.7705 (ppt170) REVERT: K 461 ARG cc_start: 0.8423 (ttp80) cc_final: 0.7959 (tmm160) REVERT: K 713 ASP cc_start: 0.8259 (t70) cc_final: 0.7333 (p0) REVERT: K 714 GLU cc_start: 0.7339 (tp30) cc_final: 0.6370 (tp30) REVERT: K 756 MET cc_start: 0.9161 (mmm) cc_final: 0.8771 (mmm) REVERT: K 804 LYS cc_start: 0.7965 (tppt) cc_final: 0.7715 (tptt) REVERT: L 80 GLU cc_start: 0.6548 (OUTLIER) cc_final: 0.5649 (pm20) REVERT: L 121 THR cc_start: 0.7757 (OUTLIER) cc_final: 0.7519 (p) REVERT: L 159 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8088 (tp) REVERT: L 189 ARG cc_start: 0.8133 (mtt180) cc_final: 0.7786 (mtt180) REVERT: L 507 ARG cc_start: 0.8461 (mtp180) cc_final: 0.8235 (ptm-80) REVERT: L 655 LYS cc_start: 0.8338 (ptmm) cc_final: 0.8088 (ptmm) REVERT: M 42 MET cc_start: 0.6923 (mmm) cc_final: 0.6685 (mmm) REVERT: M 74 ARG cc_start: 0.7425 (ptp-170) cc_final: 0.7192 (ptp-110) REVERT: M 76 TYR cc_start: 0.8613 (p90) cc_final: 0.8118 (p90) REVERT: M 144 ASN cc_start: 0.7729 (m110) cc_final: 0.7522 (m110) REVERT: M 153 TRP cc_start: 0.8375 (p90) cc_final: 0.7741 (p90) REVERT: M 408 LEU cc_start: 0.9309 (mt) cc_final: 0.8916 (tp) REVERT: M 411 MET cc_start: 0.6762 (mtt) cc_final: 0.6339 (mtp) REVERT: N 147 ARG cc_start: 0.8622 (ptm-80) cc_final: 0.8379 (ptt90) REVERT: N 182 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8434 (mt) REVERT: N 400 ASP cc_start: 0.7092 (OUTLIER) cc_final: 0.2903 (p0) REVERT: N 417 GLU cc_start: 0.8583 (pt0) cc_final: 0.7939 (tp30) REVERT: N 545 GLN cc_start: 0.8660 (mp10) cc_final: 0.8456 (mp10) REVERT: N 568 GLU cc_start: 0.8677 (tm-30) cc_final: 0.8433 (tm-30) REVERT: N 583 LYS cc_start: 0.8944 (tptt) cc_final: 0.8690 (tptt) REVERT: N 589 LYS cc_start: 0.8713 (mtmm) cc_final: 0.7919 (mtmm) REVERT: N 597 MET cc_start: 0.8116 (tmm) cc_final: 0.7376 (tmm) REVERT: N 599 GLN cc_start: 0.8798 (mm-40) cc_final: 0.8535 (mm-40) REVERT: N 610 GLN cc_start: 0.8134 (mp10) cc_final: 0.7504 (mp10) REVERT: N 625 GLU cc_start: 0.8176 (tp30) cc_final: 0.7924 (tp30) REVERT: N 646 GLN cc_start: 0.8888 (tp40) cc_final: 0.8377 (tp40) REVERT: O 142 PHE cc_start: 0.7788 (OUTLIER) cc_final: 0.7408 (t80) REVERT: O 198 GLU cc_start: 0.8463 (tp30) cc_final: 0.8035 (tp30) REVERT: O 225 LYS cc_start: 0.9035 (mmmt) cc_final: 0.8556 (mmmt) REVERT: O 237 TRP cc_start: 0.8176 (t60) cc_final: 0.7650 (t60) REVERT: O 405 GLN cc_start: 0.8523 (mp10) cc_final: 0.7962 (mp10) REVERT: O 435 GLU cc_start: 0.1769 (OUTLIER) cc_final: 0.1495 (tm-30) REVERT: O 453 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8396 (mp) REVERT: O 474 ASP cc_start: 0.8088 (t0) cc_final: 0.7625 (t70) REVERT: O 566 GLU cc_start: 0.8516 (mm-30) cc_final: 0.7424 (mm-30) REVERT: O 571 ARG cc_start: 0.8623 (tpt170) cc_final: 0.8362 (tpt170) REVERT: O 597 MET cc_start: 0.8084 (ppp) cc_final: 0.7843 (ppp) REVERT: O 598 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.7861 (mm) REVERT: O 602 ARG cc_start: 0.8777 (ttm-80) cc_final: 0.8381 (ttm-80) REVERT: O 606 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8204 (mt-10) REVERT: O 607 ARG cc_start: 0.8603 (mmp80) cc_final: 0.8049 (mmp80) REVERT: O 611 GLN cc_start: 0.8041 (tp-100) cc_final: 0.7085 (tp-100) REVERT: O 615 ASP cc_start: 0.7264 (p0) cc_final: 0.6729 (p0) REVERT: P 58 GLN cc_start: 0.7968 (mm-40) cc_final: 0.7548 (mm-40) REVERT: P 109 MET cc_start: 0.8536 (mtp) cc_final: 0.8265 (mtt) REVERT: P 305 GLU cc_start: 0.8219 (mp0) cc_final: 0.7997 (pm20) REVERT: P 368 ARG cc_start: 0.7683 (mtt-85) cc_final: 0.6900 (mtt-85) REVERT: P 428 GLU cc_start: 0.7893 (tp30) cc_final: 0.7576 (tp30) REVERT: P 429 ILE cc_start: 0.8700 (pt) cc_final: 0.8431 (pt) REVERT: P 432 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8425 (mm) REVERT: P 435 GLN cc_start: 0.8079 (mt0) cc_final: 0.7634 (mp10) REVERT: P 474 ASP cc_start: 0.7967 (t0) cc_final: 0.7547 (t0) REVERT: P 483 ASN cc_start: 0.7424 (t0) cc_final: 0.7223 (t0) REVERT: P 508 GLU cc_start: 0.7165 (tt0) cc_final: 0.6724 (pm20) REVERT: P 531 LEU cc_start: 0.5415 (OUTLIER) cc_final: 0.5204 (pp) REVERT: Q 316 GLU cc_start: 0.7793 (pt0) cc_final: 0.7487 (pt0) REVERT: Q 328 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7437 (pm20) REVERT: Q 381 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8169 (mm-30) REVERT: Q 388 LYS cc_start: 0.8888 (mtpp) cc_final: 0.8672 (mtpp) REVERT: Q 390 GLU cc_start: 0.8302 (tm-30) cc_final: 0.8026 (tm-30) REVERT: Q 395 LYS cc_start: 0.9238 (mmmt) cc_final: 0.9001 (tppt) REVERT: Q 419 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7686 (ptt-90) REVERT: Q 465 LYS cc_start: 0.8413 (mmtt) cc_final: 0.7742 (tmtt) REVERT: R 781 ASP cc_start: 0.8472 (p0) cc_final: 0.8117 (p0) REVERT: R 810 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7990 (ptpt) REVERT: R 814 TRP cc_start: 0.8057 (m100) cc_final: 0.7789 (m100) REVERT: R 845 GLN cc_start: 0.8202 (mp10) cc_final: 0.7575 (mp10) REVERT: R 851 GLU cc_start: 0.8679 (tm-30) cc_final: 0.8411 (tm-30) REVERT: R 854 GLU cc_start: 0.8408 (pt0) cc_final: 0.7899 (pm20) REVERT: R 950 ASP cc_start: 0.7868 (t0) cc_final: 0.7380 (t0) REVERT: R 954 ASP cc_start: 0.7898 (m-30) cc_final: 0.7185 (m-30) REVERT: R 972 GLU cc_start: 0.7706 (pm20) cc_final: 0.7223 (pp20) REVERT: R 1025 GLU cc_start: 0.8734 (mp0) cc_final: 0.8510 (mp0) REVERT: R 1032 LYS cc_start: 0.8544 (ttmm) cc_final: 0.8218 (ttmm) REVERT: R 1072 MET cc_start: 0.7409 (mmp) cc_final: 0.7065 (mmp) REVERT: R 1160 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8684 (tp) REVERT: S 100 ASP cc_start: 0.8502 (t0) cc_final: 0.8078 (t0) REVERT: S 102 LYS cc_start: 0.7797 (mttm) cc_final: 0.7335 (tttt) REVERT: S 115 LYS cc_start: 0.8826 (mptt) cc_final: 0.8535 (mptt) REVERT: S 135 ASN cc_start: 0.9036 (m110) cc_final: 0.8674 (m110) REVERT: S 151 GLN cc_start: 0.8174 (pm20) cc_final: 0.7865 (pm20) REVERT: S 179 GLU cc_start: 0.8383 (mm-30) cc_final: 0.8111 (tp30) REVERT: S 219 ASP cc_start: 0.8197 (t0) cc_final: 0.7879 (t0) REVERT: S 234 GLN cc_start: 0.9000 (tt0) cc_final: 0.8614 (tt0) REVERT: S 238 GLN cc_start: 0.8639 (tt0) cc_final: 0.8221 (tt0) REVERT: S 241 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7883 (pm20) REVERT: S 297 PRO cc_start: 0.7774 (Cg_exo) cc_final: 0.7558 (Cg_endo) REVERT: S 335 ARG cc_start: 0.8513 (mtm110) cc_final: 0.8144 (ttp-110) REVERT: S 389 GLU cc_start: 0.8555 (mp0) cc_final: 0.7924 (pm20) REVERT: S 392 GLU cc_start: 0.8770 (pp20) cc_final: 0.8128 (pp20) REVERT: S 441 GLU cc_start: 0.8606 (mp0) cc_final: 0.8369 (mp0) REVERT: S 444 ARG cc_start: 0.8775 (ttm-80) cc_final: 0.8348 (tpt170) REVERT: T 372 HIS cc_start: 0.7712 (t-90) cc_final: 0.7425 (t-90) REVERT: T 377 ASN cc_start: 0.8454 (t0) cc_final: 0.8147 (t0) REVERT: T 378 ARG cc_start: 0.8427 (tpp80) cc_final: 0.8136 (tpp80) REVERT: T 380 LEU cc_start: 0.8819 (tp) cc_final: 0.8585 (tt) REVERT: T 385 GLU cc_start: 0.8488 (mm-30) cc_final: 0.8093 (mm-30) REVERT: T 386 MET cc_start: 0.8531 (mmp) cc_final: 0.8253 (mmp) REVERT: U 80 ARG cc_start: 0.8632 (tpm170) cc_final: 0.8099 (tpm170) REVERT: U 129 ARG cc_start: 0.7245 (OUTLIER) cc_final: 0.6726 (ttm170) outliers start: 166 outliers final: 109 residues processed: 1192 average time/residue: 0.3028 time to fit residues: 558.0702 Evaluate side-chains 1231 residues out of total 3875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 1103 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 310 PHE Chi-restraints excluded: chain K residue 311 GLU Chi-restraints excluded: chain K residue 441 HIS Chi-restraints excluded: chain K residue 468 PHE Chi-restraints excluded: chain K residue 710 MET Chi-restraints excluded: chain K residue 837 LEU Chi-restraints excluded: chain K residue 890 MET Chi-restraints excluded: chain K residue 937 MET Chi-restraints excluded: chain K residue 1049 MET Chi-restraints excluded: chain K residue 1090 MET Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 80 GLU Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 159 LEU Chi-restraints excluded: chain L residue 177 TYR Chi-restraints excluded: chain L residue 182 VAL Chi-restraints excluded: chain L residue 187 ASP Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 358 LEU Chi-restraints excluded: chain L residue 359 VAL Chi-restraints excluded: chain L residue 519 ILE Chi-restraints excluded: chain L residue 542 ARG Chi-restraints excluded: chain L residue 544 LEU Chi-restraints excluded: chain L residue 554 HIS Chi-restraints excluded: chain L residue 654 ILE Chi-restraints excluded: chain L residue 677 LEU Chi-restraints excluded: chain L residue 706 THR Chi-restraints excluded: chain M residue 24 LEU Chi-restraints excluded: chain M residue 31 CYS Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 180 THR Chi-restraints excluded: chain M residue 289 GLU Chi-restraints excluded: chain M residue 290 PHE Chi-restraints excluded: chain M residue 311 ASP Chi-restraints excluded: chain M residue 406 HIS Chi-restraints excluded: chain N residue 133 ILE Chi-restraints excluded: chain N residue 136 LYS Chi-restraints excluded: chain N residue 155 LYS Chi-restraints excluded: chain N residue 182 LEU Chi-restraints excluded: chain N residue 205 GLN Chi-restraints excluded: chain N residue 226 ILE Chi-restraints excluded: chain N residue 392 LEU Chi-restraints excluded: chain N residue 400 ASP Chi-restraints excluded: chain N residue 423 LEU Chi-restraints excluded: chain N residue 554 MET Chi-restraints excluded: chain N residue 584 LEU Chi-restraints excluded: chain N residue 629 VAL Chi-restraints excluded: chain N residue 643 ARG Chi-restraints excluded: chain O residue 142 PHE Chi-restraints excluded: chain O residue 393 LEU Chi-restraints excluded: chain O residue 435 GLU Chi-restraints excluded: chain O residue 453 LEU Chi-restraints excluded: chain O residue 466 VAL Chi-restraints excluded: chain O residue 472 LEU Chi-restraints excluded: chain O residue 564 HIS Chi-restraints excluded: chain O residue 568 GLU Chi-restraints excluded: chain O residue 598 LEU Chi-restraints excluded: chain O residue 636 THR Chi-restraints excluded: chain P residue 86 ILE Chi-restraints excluded: chain P residue 112 LYS Chi-restraints excluded: chain P residue 120 LEU Chi-restraints excluded: chain P residue 348 ILE Chi-restraints excluded: chain P residue 366 HIS Chi-restraints excluded: chain P residue 432 LEU Chi-restraints excluded: chain P residue 458 ARG Chi-restraints excluded: chain P residue 477 ILE Chi-restraints excluded: chain P residue 490 VAL Chi-restraints excluded: chain P residue 529 VAL Chi-restraints excluded: chain P residue 531 LEU Chi-restraints excluded: chain Q residue 328 GLU Chi-restraints excluded: chain Q residue 353 PHE Chi-restraints excluded: chain Q residue 392 GLU Chi-restraints excluded: chain Q residue 404 LYS Chi-restraints excluded: chain Q residue 405 PHE Chi-restraints excluded: chain Q residue 411 ILE Chi-restraints excluded: chain Q residue 419 ARG Chi-restraints excluded: chain R residue 796 GLU Chi-restraints excluded: chain R residue 810 LYS Chi-restraints excluded: chain R residue 835 VAL Chi-restraints excluded: chain R residue 850 VAL Chi-restraints excluded: chain R residue 887 THR Chi-restraints excluded: chain R residue 1108 TRP Chi-restraints excluded: chain R residue 1160 LEU Chi-restraints excluded: chain R residue 1165 LEU Chi-restraints excluded: chain S residue 111 TYR Chi-restraints excluded: chain S residue 181 VAL Chi-restraints excluded: chain S residue 202 LEU Chi-restraints excluded: chain S residue 225 MET Chi-restraints excluded: chain S residue 241 GLU Chi-restraints excluded: chain S residue 286 LEU Chi-restraints excluded: chain S residue 287 VAL Chi-restraints excluded: chain S residue 429 VAL Chi-restraints excluded: chain T residue 390 TYR Chi-restraints excluded: chain T residue 393 SER Chi-restraints excluded: chain T residue 394 ILE Chi-restraints excluded: chain U residue 31 VAL Chi-restraints excluded: chain U residue 39 VAL Chi-restraints excluded: chain U residue 56 TRP Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 129 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 60 optimal weight: 0.5980 chunk 365 optimal weight: 0.9990 chunk 462 optimal weight: 6.9990 chunk 86 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 318 optimal weight: 0.7980 chunk 458 optimal weight: 10.0000 chunk 105 optimal weight: 20.0000 chunk 12 optimal weight: 0.7980 chunk 209 optimal weight: 3.9990 chunk 168 optimal weight: 0.1980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN H 44 GLN ** K 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 469 ASN ** K 620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 682 GLN K1012 GLN ** L 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 275 HIS ** N 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 323 GLN Q 398 HIS R 880 GLN ** S 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.174699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.136820 restraints weight = 101218.755| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 3.86 r_work: 0.3572 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 43000 Z= 0.158 Angle : 0.737 15.291 59276 Z= 0.380 Chirality : 0.045 0.354 6553 Planarity : 0.005 0.059 6756 Dihedral : 22.146 166.068 7940 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.33 % Favored : 94.58 % Rotamer: Outliers : 3.83 % Allowed : 25.23 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.13), residues: 4426 helix: 0.65 (0.10), residues: 2452 sheet: -0.32 (0.35), residues: 234 loop : -1.19 (0.15), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG N 621 TYR 0.047 0.002 TYR H 80 PHE 0.048 0.002 PHE K 654 TRP 0.050 0.002 TRP L 529 HIS 0.009 0.001 HIS R 809 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.16 (43000) covalent geometry : angle 0.73700 / 0.38 (59276) hydrogen bonds : bond 0.04476 / 2.97 ( 2194) hydrogen bonds : angle 4.52876 / 3.23 ( 6069) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8852 Ramachandran restraints generated. 4426 Oldfield, 0 Emsley, 4426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8852 Ramachandran restraints generated. 4426 Oldfield, 0 Emsley, 4426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1261 residues out of total 3875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 1113 time to evaluate : 1.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ARG cc_start: 0.7886 (mtp-110) cc_final: 0.7616 (ttp-110) REVERT: A 87 SER cc_start: 0.9215 (p) cc_final: 0.8966 (t) REVERT: A 131 ARG cc_start: 0.8854 (mtm180) cc_final: 0.8588 (mtp85) REVERT: C 56 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.7803 (tp30) REVERT: C 91 GLU cc_start: 0.8118 (tp30) cc_final: 0.7754 (tp30) REVERT: C 92 GLU cc_start: 0.8290 (tp30) cc_final: 0.8010 (mm-30) REVERT: E 106 ASP cc_start: 0.8420 (m-30) cc_final: 0.8043 (m-30) REVERT: E 120 MET cc_start: 0.8885 (OUTLIER) cc_final: 0.7744 (mpp) REVERT: F 35 ARG cc_start: 0.8842 (mtp85) cc_final: 0.8549 (mtp85) REVERT: F 67 ARG cc_start: 0.8724 (ttm-80) cc_final: 0.8315 (ttm-80) REVERT: G 25 PHE cc_start: 0.8493 (m-80) cc_final: 0.8060 (m-80) REVERT: G 74 LYS cc_start: 0.8791 (mppt) cc_final: 0.8521 (mppt) REVERT: H 65 ASP cc_start: 0.8730 (t0) cc_final: 0.8379 (t0) REVERT: H 73 GLU cc_start: 0.8845 (tp30) cc_final: 0.8591 (tp30) REVERT: H 113 LYS cc_start: 0.8622 (pttt) cc_final: 0.8284 (pttt) REVERT: K 316 ASP cc_start: 0.7475 (t0) cc_final: 0.7198 (t0) REVERT: K 317 ARG cc_start: 0.7987 (ptm160) cc_final: 0.7177 (ttt180) REVERT: K 323 ASN cc_start: 0.8385 (t0) cc_final: 0.8062 (t0) REVERT: K 331 GLU cc_start: 0.8624 (pp20) cc_final: 0.8154 (pp20) REVERT: K 333 LYS cc_start: 0.8634 (pttt) cc_final: 0.8308 (pttp) REVERT: K 356 LYS cc_start: 0.8376 (tppt) cc_final: 0.8067 (tmmt) REVERT: K 362 GLU cc_start: 0.7676 (mp0) cc_final: 0.6936 (pm20) REVERT: K 401 MET cc_start: 0.8583 (mpp) cc_final: 0.8173 (mpp) REVERT: K 411 ILE cc_start: 0.8484 (mt) cc_final: 0.8162 (mm) REVERT: K 416 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7473 (mm-30) REVERT: K 418 GLN cc_start: 0.8636 (mm110) cc_final: 0.8194 (mm110) REVERT: K 446 LEU cc_start: 0.8524 (mt) cc_final: 0.8210 (pp) REVERT: K 453 ARG cc_start: 0.8212 (ppt170) cc_final: 0.7684 (ppt170) REVERT: K 710 MET cc_start: 0.7425 (OUTLIER) cc_final: 0.6979 (mpp) REVERT: K 713 ASP cc_start: 0.8261 (t70) cc_final: 0.7339 (p0) REVERT: K 714 GLU cc_start: 0.7330 (tp30) cc_final: 0.6368 (tp30) REVERT: K 756 MET cc_start: 0.9141 (mmm) cc_final: 0.8744 (mmm) REVERT: K 976 MET cc_start: 0.7366 (tpt) cc_final: 0.6924 (tpt) REVERT: L 80 GLU cc_start: 0.6543 (OUTLIER) cc_final: 0.5463 (pp20) REVERT: L 121 THR cc_start: 0.7596 (OUTLIER) cc_final: 0.7365 (p) REVERT: L 159 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8046 (tp) REVERT: L 189 ARG cc_start: 0.8126 (mtt180) cc_final: 0.7883 (mtt180) REVERT: L 195 ASN cc_start: 0.8098 (t0) cc_final: 0.7719 (t0) REVERT: L 245 VAL cc_start: 0.8565 (m) cc_final: 0.8232 (p) REVERT: L 507 ARG cc_start: 0.8422 (mtp180) cc_final: 0.8196 (ptm160) REVERT: L 655 LYS cc_start: 0.8279 (ptmm) cc_final: 0.8023 (ptmm) REVERT: L 709 ASP cc_start: 0.8099 (m-30) cc_final: 0.7755 (p0) REVERT: M 24 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7778 (mt) REVERT: M 25 VAL cc_start: 0.7363 (t) cc_final: 0.6803 (m) REVERT: M 42 MET cc_start: 0.6959 (mmm) cc_final: 0.6708 (mmm) REVERT: M 76 TYR cc_start: 0.8548 (OUTLIER) cc_final: 0.8101 (p90) REVERT: M 144 ASN cc_start: 0.7667 (m110) cc_final: 0.7434 (m110) REVERT: M 153 TRP cc_start: 0.8000 (p90) cc_final: 0.7688 (p90) REVERT: M 408 LEU cc_start: 0.9296 (mt) cc_final: 0.8872 (tp) REVERT: M 411 MET cc_start: 0.6742 (mtt) cc_final: 0.6330 (mtp) REVERT: N 147 ARG cc_start: 0.8587 (ptm-80) cc_final: 0.8350 (ptt90) REVERT: N 182 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8366 (mt) REVERT: N 400 ASP cc_start: 0.6939 (OUTLIER) cc_final: 0.6072 (m-30) REVERT: N 417 GLU cc_start: 0.8581 (pt0) cc_final: 0.7902 (tp30) REVERT: N 545 GLN cc_start: 0.8679 (mp10) cc_final: 0.8445 (mp10) REVERT: N 568 GLU cc_start: 0.8674 (tm-30) cc_final: 0.8428 (tm-30) REVERT: N 583 LYS cc_start: 0.8917 (tptt) cc_final: 0.8565 (tptt) REVERT: N 587 LYS cc_start: 0.8779 (mmmm) cc_final: 0.8128 (mmmm) REVERT: N 589 LYS cc_start: 0.8651 (mtmm) cc_final: 0.8393 (mtmm) REVERT: N 597 MET cc_start: 0.8005 (tmm) cc_final: 0.7262 (tmm) REVERT: N 599 GLN cc_start: 0.8762 (mm-40) cc_final: 0.8519 (mm-40) REVERT: N 610 GLN cc_start: 0.8078 (mp10) cc_final: 0.7416 (mp10) REVERT: N 625 GLU cc_start: 0.8069 (tp30) cc_final: 0.7793 (tp30) REVERT: N 646 GLN cc_start: 0.8876 (tp40) cc_final: 0.8374 (tp40) REVERT: O 142 PHE cc_start: 0.7707 (OUTLIER) cc_final: 0.7330 (t80) REVERT: O 198 GLU cc_start: 0.8433 (tp30) cc_final: 0.8007 (tp30) REVERT: O 212 ARG cc_start: 0.7939 (mpp-170) cc_final: 0.7652 (mtm-85) REVERT: O 225 LYS cc_start: 0.9052 (mmmt) cc_final: 0.8563 (mmmt) REVERT: O 237 TRP cc_start: 0.8174 (t60) cc_final: 0.7632 (t60) REVERT: O 405 GLN cc_start: 0.8505 (mp10) cc_final: 0.7954 (mp10) REVERT: O 424 GLN cc_start: 0.7977 (mt0) cc_final: 0.7771 (mt0) REVERT: O 435 GLU cc_start: 0.1691 (OUTLIER) cc_final: 0.1451 (tm-30) REVERT: O 453 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8421 (mp) REVERT: O 474 ASP cc_start: 0.8058 (t0) cc_final: 0.7576 (t0) REVERT: O 566 GLU cc_start: 0.8588 (mm-30) cc_final: 0.6655 (mm-30) REVERT: O 567 ARG cc_start: 0.8101 (mmt90) cc_final: 0.7758 (mmt90) REVERT: O 571 ARG cc_start: 0.8583 (tpt170) cc_final: 0.8329 (tpt170) REVERT: O 594 MET cc_start: 0.8569 (tpp) cc_final: 0.7827 (tpp) REVERT: O 597 MET cc_start: 0.8095 (ppp) cc_final: 0.7853 (ppp) REVERT: O 598 LEU cc_start: 0.8546 (mm) cc_final: 0.8184 (mm) REVERT: O 601 GLU cc_start: 0.8287 (pp20) cc_final: 0.7996 (pp20) REVERT: O 602 ARG cc_start: 0.8738 (ttm-80) cc_final: 0.8356 (ttm-80) REVERT: O 606 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8056 (mt-10) REVERT: O 607 ARG cc_start: 0.8573 (mmp80) cc_final: 0.8027 (mmp80) REVERT: O 611 GLN cc_start: 0.7870 (tp-100) cc_final: 0.7062 (tp-100) REVERT: O 612 LEU cc_start: 0.8503 (tp) cc_final: 0.8090 (tt) REVERT: P 58 GLN cc_start: 0.7975 (mm-40) cc_final: 0.7571 (mm-40) REVERT: P 74 ASP cc_start: 0.7605 (t0) cc_final: 0.7404 (t0) REVERT: P 428 GLU cc_start: 0.7870 (tp30) cc_final: 0.7523 (tp30) REVERT: P 429 ILE cc_start: 0.8678 (pt) cc_final: 0.8396 (pt) REVERT: P 432 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8450 (mm) REVERT: P 435 GLN cc_start: 0.8097 (mt0) cc_final: 0.7613 (mp10) REVERT: P 474 ASP cc_start: 0.8049 (OUTLIER) cc_final: 0.7521 (t0) REVERT: P 483 ASN cc_start: 0.7252 (t0) cc_final: 0.7018 (t0) REVERT: P 508 GLU cc_start: 0.7105 (tt0) cc_final: 0.6681 (pm20) REVERT: P 531 LEU cc_start: 0.5391 (OUTLIER) cc_final: 0.5181 (pp) REVERT: Q 316 GLU cc_start: 0.7790 (pt0) cc_final: 0.7558 (pt0) REVERT: Q 328 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7341 (pm20) REVERT: Q 364 TYR cc_start: 0.8435 (t80) cc_final: 0.7450 (t80) REVERT: Q 381 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8258 (mm-30) REVERT: Q 388 LYS cc_start: 0.8832 (mtpp) cc_final: 0.8602 (mtpp) REVERT: Q 390 GLU cc_start: 0.8335 (tm-30) cc_final: 0.8004 (tm-30) REVERT: Q 395 LYS cc_start: 0.9209 (mmmt) cc_final: 0.8943 (tppt) REVERT: Q 465 LYS cc_start: 0.8351 (mmtt) cc_final: 0.7784 (tmtt) REVERT: R 781 ASP cc_start: 0.8480 (p0) cc_final: 0.8149 (p0) REVERT: R 810 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.7931 (ptpt) REVERT: R 836 GLU cc_start: 0.8363 (pp20) cc_final: 0.8148 (pp20) REVERT: R 845 GLN cc_start: 0.8122 (mp10) cc_final: 0.7645 (mp10) REVERT: R 847 ASP cc_start: 0.8130 (m-30) cc_final: 0.7604 (m-30) REVERT: R 854 GLU cc_start: 0.8345 (pt0) cc_final: 0.7822 (pm20) REVERT: R 883 THR cc_start: 0.8548 (p) cc_final: 0.8295 (p) REVERT: R 1025 GLU cc_start: 0.8705 (mp0) cc_final: 0.8480 (mp0) REVERT: R 1032 LYS cc_start: 0.8497 (ttmm) cc_final: 0.8186 (ttmm) REVERT: R 1072 MET cc_start: 0.7381 (mmp) cc_final: 0.7038 (mmp) REVERT: R 1160 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8665 (tp) REVERT: S 100 ASP cc_start: 0.8482 (t0) cc_final: 0.7983 (t0) REVERT: S 102 LYS cc_start: 0.7738 (mttm) cc_final: 0.7345 (tttt) REVERT: S 104 MET cc_start: 0.6888 (mmp) cc_final: 0.6553 (mmp) REVERT: S 115 LYS cc_start: 0.8809 (mptt) cc_final: 0.8506 (mptt) REVERT: S 128 GLU cc_start: 0.7632 (pt0) cc_final: 0.6998 (pp20) REVERT: S 135 ASN cc_start: 0.9039 (m110) cc_final: 0.8720 (m110) REVERT: S 151 GLN cc_start: 0.8164 (pm20) cc_final: 0.7884 (pm20) REVERT: S 179 GLU cc_start: 0.8349 (mm-30) cc_final: 0.7977 (mm-30) REVERT: S 219 ASP cc_start: 0.8085 (t0) cc_final: 0.7842 (t0) REVERT: S 234 GLN cc_start: 0.8957 (tt0) cc_final: 0.8577 (tt0) REVERT: S 238 GLN cc_start: 0.8669 (tt0) cc_final: 0.8363 (tt0) REVERT: S 241 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7890 (pm20) REVERT: S 242 GLN cc_start: 0.8586 (mm-40) cc_final: 0.7981 (mt0) REVERT: S 286 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8562 (tt) REVERT: S 335 ARG cc_start: 0.8462 (mtm110) cc_final: 0.8156 (ttp-110) REVERT: S 389 GLU cc_start: 0.8551 (mp0) cc_final: 0.7841 (pm20) REVERT: S 392 GLU cc_start: 0.8749 (pp20) cc_final: 0.8076 (pp20) REVERT: S 444 ARG cc_start: 0.8761 (ttm-80) cc_final: 0.8354 (tpt170) REVERT: T 372 HIS cc_start: 0.7589 (t-90) cc_final: 0.7288 (t-90) REVERT: T 377 ASN cc_start: 0.8427 (t0) cc_final: 0.8137 (t0) REVERT: T 378 ARG cc_start: 0.8423 (tpp80) cc_final: 0.8121 (tpp80) REVERT: T 380 LEU cc_start: 0.8789 (tp) cc_final: 0.8548 (tt) REVERT: T 385 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8086 (mm-30) REVERT: T 386 MET cc_start: 0.8564 (mmp) cc_final: 0.8279 (mmp) REVERT: T 393 SER cc_start: 0.9302 (p) cc_final: 0.9010 (p) REVERT: U 27 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.6908 (mm-30) REVERT: U 80 ARG cc_start: 0.8580 (tpm170) cc_final: 0.8066 (tpm170) REVERT: U 129 ARG cc_start: 0.7155 (OUTLIER) cc_final: 0.6627 (ttm170) outliers start: 148 outliers final: 105 residues processed: 1185 average time/residue: 0.3020 time to fit residues: 553.7610 Evaluate side-chains 1231 residues out of total 3875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 1103 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 310 PHE Chi-restraints excluded: chain K residue 311 GLU Chi-restraints excluded: chain K residue 441 HIS Chi-restraints excluded: chain K residue 468 PHE Chi-restraints excluded: chain K residue 710 MET Chi-restraints excluded: chain K residue 837 LEU Chi-restraints excluded: chain K residue 890 MET Chi-restraints excluded: chain K residue 937 MET Chi-restraints excluded: chain K residue 1012 GLN Chi-restraints excluded: chain K residue 1049 MET Chi-restraints excluded: chain K residue 1090 MET Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 80 GLU Chi-restraints excluded: chain L residue 120 ASN Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain L residue 131 TRP Chi-restraints excluded: chain L residue 133 ARG Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 159 LEU Chi-restraints excluded: chain L residue 172 VAL Chi-restraints excluded: chain L residue 177 TYR Chi-restraints excluded: chain L residue 187 ASP Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 226 SER Chi-restraints excluded: chain L residue 358 LEU Chi-restraints excluded: chain L residue 359 VAL Chi-restraints excluded: chain L residue 519 ILE Chi-restraints excluded: chain L residue 542 ARG Chi-restraints excluded: chain L residue 544 LEU Chi-restraints excluded: chain L residue 554 HIS Chi-restraints excluded: chain L residue 654 ILE Chi-restraints excluded: chain L residue 706 THR Chi-restraints excluded: chain M residue 24 LEU Chi-restraints excluded: chain M residue 31 CYS Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 76 TYR Chi-restraints excluded: chain M residue 180 THR Chi-restraints excluded: chain M residue 289 GLU Chi-restraints excluded: chain M residue 290 PHE Chi-restraints excluded: chain M residue 406 HIS Chi-restraints excluded: chain N residue 133 ILE Chi-restraints excluded: chain N residue 155 LYS Chi-restraints excluded: chain N residue 182 LEU Chi-restraints excluded: chain N residue 205 GLN Chi-restraints excluded: chain N residue 226 ILE Chi-restraints excluded: chain N residue 392 LEU Chi-restraints excluded: chain N residue 400 ASP Chi-restraints excluded: chain N residue 423 LEU Chi-restraints excluded: chain N residue 554 MET Chi-restraints excluded: chain N residue 584 LEU Chi-restraints excluded: chain N residue 629 VAL Chi-restraints excluded: chain N residue 643 ARG Chi-restraints excluded: chain O residue 142 PHE Chi-restraints excluded: chain O residue 393 LEU Chi-restraints excluded: chain O residue 435 GLU Chi-restraints excluded: chain O residue 453 LEU Chi-restraints excluded: chain O residue 466 VAL Chi-restraints excluded: chain O residue 472 LEU Chi-restraints excluded: chain O residue 564 HIS Chi-restraints excluded: chain O residue 568 GLU Chi-restraints excluded: chain O residue 636 THR Chi-restraints excluded: chain P residue 86 ILE Chi-restraints excluded: chain P residue 120 LEU Chi-restraints excluded: chain P residue 348 ILE Chi-restraints excluded: chain P residue 366 HIS Chi-restraints excluded: chain P residue 432 LEU Chi-restraints excluded: chain P residue 440 MET Chi-restraints excluded: chain P residue 474 ASP Chi-restraints excluded: chain P residue 490 VAL Chi-restraints excluded: chain P residue 529 VAL Chi-restraints excluded: chain P residue 531 LEU Chi-restraints excluded: chain Q residue 328 GLU Chi-restraints excluded: chain Q residue 353 PHE Chi-restraints excluded: chain Q residue 357 GLN Chi-restraints excluded: chain Q residue 392 GLU Chi-restraints excluded: chain Q residue 404 LYS Chi-restraints excluded: chain Q residue 405 PHE Chi-restraints excluded: chain Q residue 419 ARG Chi-restraints excluded: chain Q residue 463 VAL Chi-restraints excluded: chain R residue 796 GLU Chi-restraints excluded: chain R residue 810 LYS Chi-restraints excluded: chain R residue 835 VAL Chi-restraints excluded: chain R residue 850 VAL Chi-restraints excluded: chain R residue 887 THR Chi-restraints excluded: chain R residue 1108 TRP Chi-restraints excluded: chain R residue 1160 LEU Chi-restraints excluded: chain R residue 1165 LEU Chi-restraints excluded: chain S residue 111 TYR Chi-restraints excluded: chain S residue 167 LYS Chi-restraints excluded: chain S residue 181 VAL Chi-restraints excluded: chain S residue 202 LEU Chi-restraints excluded: chain S residue 241 GLU Chi-restraints excluded: chain S residue 286 LEU Chi-restraints excluded: chain S residue 287 VAL Chi-restraints excluded: chain S residue 429 VAL Chi-restraints excluded: chain T residue 379 THR Chi-restraints excluded: chain T residue 390 TYR Chi-restraints excluded: chain T residue 394 ILE Chi-restraints excluded: chain U residue 27 GLU Chi-restraints excluded: chain U residue 31 VAL Chi-restraints excluded: chain U residue 39 VAL Chi-restraints excluded: chain U residue 56 TRP Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 129 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 136 optimal weight: 20.0000 chunk 391 optimal weight: 6.9990 chunk 55 optimal weight: 0.2980 chunk 328 optimal weight: 0.7980 chunk 99 optimal weight: 8.9990 chunk 75 optimal weight: 1.9990 chunk 430 optimal weight: 0.0370 chunk 17 optimal weight: 1.9990 chunk 316 optimal weight: 3.9990 chunk 458 optimal weight: 9.9990 chunk 231 optimal weight: 4.9990 overall best weight: 1.0262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN H 44 GLN ** K 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1012 GLN ** L 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 275 HIS ** N 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 599 GLN ** P 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 323 GLN ** R1085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.174060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.135541 restraints weight = 101887.393| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 3.89 r_work: 0.3555 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 43000 Z= 0.186 Angle : 0.756 15.330 59276 Z= 0.389 Chirality : 0.046 0.355 6553 Planarity : 0.005 0.060 6756 Dihedral : 22.152 165.518 7938 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.58 % Favored : 94.31 % Rotamer: Outliers : 4.04 % Allowed : 25.75 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.13), residues: 4426 helix: 0.66 (0.10), residues: 2451 sheet: -0.36 (0.35), residues: 234 loop : -1.21 (0.15), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG N 621 TYR 0.048 0.002 TYR H 80 PHE 0.046 0.002 PHE K 654 TRP 0.053 0.002 TRP L 529 HIS 0.010 0.001 HIS R 809 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.19 (43000) covalent geometry : angle 0.75617 / 0.39 (59276) hydrogen bonds : bond 0.04507 / 2.99 ( 2194) hydrogen bonds : angle 4.55713 / 3.25 ( 6069) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8852 Ramachandran restraints generated. 4426 Oldfield, 0 Emsley, 4426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8852 Ramachandran restraints generated. 4426 Oldfield, 0 Emsley, 4426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1259 residues out of total 3875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 1103 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ARG cc_start: 0.7903 (mtp-110) cc_final: 0.7644 (ttp-110) REVERT: A 87 SER cc_start: 0.9217 (p) cc_final: 0.8996 (t) REVERT: A 131 ARG cc_start: 0.8809 (mtm180) cc_final: 0.8422 (mtp85) REVERT: C 56 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.7822 (tp30) REVERT: C 91 GLU cc_start: 0.8133 (tp30) cc_final: 0.7760 (tp30) REVERT: C 92 GLU cc_start: 0.8267 (tp30) cc_final: 0.7992 (mm-30) REVERT: D 68 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7970 (mm-30) REVERT: E 50 GLU cc_start: 0.8354 (pt0) cc_final: 0.8116 (pt0) REVERT: E 106 ASP cc_start: 0.8423 (m-30) cc_final: 0.8145 (m-30) REVERT: E 120 MET cc_start: 0.8895 (OUTLIER) cc_final: 0.7759 (mpp) REVERT: F 35 ARG cc_start: 0.8873 (mtp85) cc_final: 0.8592 (mtp85) REVERT: G 74 LYS cc_start: 0.8773 (mppt) cc_final: 0.8499 (mppt) REVERT: H 65 ASP cc_start: 0.8701 (t0) cc_final: 0.8358 (t0) REVERT: H 73 GLU cc_start: 0.8849 (tp30) cc_final: 0.8568 (tp30) REVERT: H 113 LYS cc_start: 0.8646 (pttt) cc_final: 0.8333 (pttt) REVERT: K 316 ASP cc_start: 0.7484 (t0) cc_final: 0.7259 (t0) REVERT: K 317 ARG cc_start: 0.8009 (ptm160) cc_final: 0.6918 (ptm160) REVERT: K 323 ASN cc_start: 0.8420 (t0) cc_final: 0.8097 (t0) REVERT: K 331 GLU cc_start: 0.8647 (pp20) cc_final: 0.8179 (pp20) REVERT: K 333 LYS cc_start: 0.8643 (pttt) cc_final: 0.8311 (pttp) REVERT: K 356 LYS cc_start: 0.8376 (tppt) cc_final: 0.8073 (tmmt) REVERT: K 362 GLU cc_start: 0.7720 (mp0) cc_final: 0.6975 (pm20) REVERT: K 364 LYS cc_start: 0.8507 (pttt) cc_final: 0.8208 (pttt) REVERT: K 401 MET cc_start: 0.8611 (mpp) cc_final: 0.8207 (mpp) REVERT: K 411 ILE cc_start: 0.8486 (mt) cc_final: 0.8187 (mm) REVERT: K 416 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7479 (mm-30) REVERT: K 418 GLN cc_start: 0.8638 (mm110) cc_final: 0.8207 (mm110) REVERT: K 446 LEU cc_start: 0.8524 (mt) cc_final: 0.8159 (pp) REVERT: K 453 ARG cc_start: 0.8287 (ppt170) cc_final: 0.7737 (ppt170) REVERT: K 710 MET cc_start: 0.7477 (OUTLIER) cc_final: 0.7041 (mpp) REVERT: K 713 ASP cc_start: 0.8277 (t70) cc_final: 0.7396 (p0) REVERT: K 714 GLU cc_start: 0.7352 (tp30) cc_final: 0.6413 (tp30) REVERT: K 756 MET cc_start: 0.9140 (mmm) cc_final: 0.8758 (mmm) REVERT: L 80 GLU cc_start: 0.6612 (OUTLIER) cc_final: 0.5553 (pp20) REVERT: L 121 THR cc_start: 0.7639 (OUTLIER) cc_final: 0.7409 (p) REVERT: L 159 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8107 (tp) REVERT: L 195 ASN cc_start: 0.8240 (t0) cc_final: 0.7791 (t0) REVERT: L 239 ARG cc_start: 0.2414 (OUTLIER) cc_final: -0.1160 (ttm110) REVERT: L 507 ARG cc_start: 0.8478 (mtp180) cc_final: 0.8223 (ptm-80) REVERT: L 655 LYS cc_start: 0.8306 (ptmm) cc_final: 0.8062 (ptmm) REVERT: L 709 ASP cc_start: 0.8160 (m-30) cc_final: 0.7770 (p0) REVERT: M 25 VAL cc_start: 0.7451 (t) cc_final: 0.6883 (m) REVERT: M 42 MET cc_start: 0.7047 (mmm) cc_final: 0.6797 (mmm) REVERT: M 74 ARG cc_start: 0.7419 (ptp-170) cc_final: 0.7078 (ptp90) REVERT: M 76 TYR cc_start: 0.8616 (p90) cc_final: 0.8199 (p90) REVERT: M 153 TRP cc_start: 0.7964 (p90) cc_final: 0.7634 (p90) REVERT: M 408 LEU cc_start: 0.9314 (mt) cc_final: 0.8917 (tp) REVERT: M 411 MET cc_start: 0.6810 (mtt) cc_final: 0.6412 (mtp) REVERT: N 147 ARG cc_start: 0.8629 (ptm-80) cc_final: 0.8366 (ptt90) REVERT: N 182 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8348 (mt) REVERT: N 417 GLU cc_start: 0.8585 (pt0) cc_final: 0.7907 (tp30) REVERT: N 545 GLN cc_start: 0.8675 (mp10) cc_final: 0.8449 (mp10) REVERT: N 568 GLU cc_start: 0.8686 (tm-30) cc_final: 0.8430 (tm-30) REVERT: N 583 LYS cc_start: 0.8926 (tptt) cc_final: 0.8567 (tptt) REVERT: N 585 GLU cc_start: 0.8526 (pp20) cc_final: 0.7978 (pp20) REVERT: N 587 LYS cc_start: 0.8805 (mmmm) cc_final: 0.8155 (mmmm) REVERT: N 589 LYS cc_start: 0.8680 (mtmm) cc_final: 0.8225 (mtmm) REVERT: N 597 MET cc_start: 0.8073 (tmm) cc_final: 0.7314 (tmm) REVERT: N 599 GLN cc_start: 0.8797 (mm-40) cc_final: 0.8569 (mm-40) REVERT: N 602 ARG cc_start: 0.8114 (ttp80) cc_final: 0.7620 (ttp80) REVERT: N 625 GLU cc_start: 0.8119 (tp30) cc_final: 0.7831 (tp30) REVERT: N 646 GLN cc_start: 0.8905 (tp40) cc_final: 0.8431 (tp40) REVERT: O 142 PHE cc_start: 0.7760 (OUTLIER) cc_final: 0.7333 (t80) REVERT: O 147 ASN cc_start: 0.7560 (t0) cc_final: 0.7348 (t0) REVERT: O 198 GLU cc_start: 0.8420 (tp30) cc_final: 0.7997 (tp30) REVERT: O 212 ARG cc_start: 0.7958 (mpp-170) cc_final: 0.7718 (mtm-85) REVERT: O 225 LYS cc_start: 0.9074 (mmmt) cc_final: 0.8535 (mmmt) REVERT: O 237 TRP cc_start: 0.8209 (t60) cc_final: 0.7661 (t60) REVERT: O 405 GLN cc_start: 0.8519 (mp10) cc_final: 0.7963 (mp10) REVERT: O 435 GLU cc_start: 0.1705 (OUTLIER) cc_final: 0.1463 (tm-30) REVERT: O 453 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8427 (mp) REVERT: O 474 ASP cc_start: 0.8051 (t0) cc_final: 0.7568 (t0) REVERT: O 566 GLU cc_start: 0.8598 (mm-30) cc_final: 0.6658 (mm-30) REVERT: O 567 ARG cc_start: 0.8148 (mmt90) cc_final: 0.7786 (mmt90) REVERT: O 571 ARG cc_start: 0.8613 (tpt170) cc_final: 0.8365 (tpt170) REVERT: O 594 MET cc_start: 0.8523 (tpp) cc_final: 0.7790 (tpp) REVERT: O 597 MET cc_start: 0.8118 (ppp) cc_final: 0.7870 (ppp) REVERT: O 598 LEU cc_start: 0.8550 (mm) cc_final: 0.8132 (mm) REVERT: O 601 GLU cc_start: 0.8297 (pp20) cc_final: 0.8001 (pp20) REVERT: O 602 ARG cc_start: 0.8782 (ttm-80) cc_final: 0.8382 (ttm-80) REVERT: O 606 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8086 (mt-10) REVERT: O 607 ARG cc_start: 0.8591 (mmp80) cc_final: 0.8010 (mmp80) REVERT: O 611 GLN cc_start: 0.7915 (tp-100) cc_final: 0.6824 (tp-100) REVERT: O 612 LEU cc_start: 0.8483 (tp) cc_final: 0.7976 (tt) REVERT: O 615 ASP cc_start: 0.7140 (p0) cc_final: 0.6808 (p0) REVERT: P 58 GLN cc_start: 0.7988 (mm-40) cc_final: 0.7553 (mm-40) REVERT: P 74 ASP cc_start: 0.7602 (t0) cc_final: 0.7360 (t0) REVERT: P 428 GLU cc_start: 0.7894 (tp30) cc_final: 0.7522 (tp30) REVERT: P 429 ILE cc_start: 0.8684 (pt) cc_final: 0.8406 (pt) REVERT: P 432 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8450 (mm) REVERT: P 435 GLN cc_start: 0.8093 (mt0) cc_final: 0.7595 (mp10) REVERT: P 474 ASP cc_start: 0.8119 (OUTLIER) cc_final: 0.7591 (t0) REVERT: P 483 ASN cc_start: 0.7364 (t0) cc_final: 0.7092 (t0) REVERT: P 501 GLU cc_start: 0.8372 (mp0) cc_final: 0.8060 (mp0) REVERT: P 508 GLU cc_start: 0.7145 (tt0) cc_final: 0.6707 (pm20) REVERT: Q 316 GLU cc_start: 0.7835 (pt0) cc_final: 0.7586 (pt0) REVERT: Q 328 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7366 (pm20) REVERT: Q 364 TYR cc_start: 0.8397 (t80) cc_final: 0.7556 (t80) REVERT: Q 381 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8271 (mm-30) REVERT: Q 388 LYS cc_start: 0.8845 (mtpp) cc_final: 0.8614 (mtpp) REVERT: Q 390 GLU cc_start: 0.8343 (tm-30) cc_final: 0.8032 (tm-30) REVERT: Q 395 LYS cc_start: 0.9262 (mmmt) cc_final: 0.8995 (tppt) REVERT: Q 402 MET cc_start: 0.8443 (mmt) cc_final: 0.8082 (mmm) REVERT: Q 465 LYS cc_start: 0.8325 (mmtt) cc_final: 0.7907 (tmtt) REVERT: R 781 ASP cc_start: 0.8481 (p0) cc_final: 0.8077 (p0) REVERT: R 810 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.7971 (ptpt) REVERT: R 845 GLN cc_start: 0.8154 (mp10) cc_final: 0.7637 (mp10) REVERT: R 847 ASP cc_start: 0.8112 (m-30) cc_final: 0.7580 (m-30) REVERT: R 851 GLU cc_start: 0.8675 (tm-30) cc_final: 0.8400 (tm-30) REVERT: R 854 GLU cc_start: 0.8359 (pt0) cc_final: 0.7854 (pm20) REVERT: R 883 THR cc_start: 0.8532 (p) cc_final: 0.8285 (p) REVERT: R 950 ASP cc_start: 0.7923 (t0) cc_final: 0.7465 (t0) REVERT: R 954 ASP cc_start: 0.7848 (m-30) cc_final: 0.7158 (m-30) REVERT: R 1032 LYS cc_start: 0.8482 (ttmm) cc_final: 0.8174 (ttmm) REVERT: R 1072 MET cc_start: 0.7397 (mmp) cc_final: 0.7053 (mmp) REVERT: R 1160 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8654 (tp) REVERT: S 100 ASP cc_start: 0.8506 (t0) cc_final: 0.8125 (t0) REVERT: S 102 LYS cc_start: 0.7786 (mttm) cc_final: 0.7432 (tttt) REVERT: S 115 LYS cc_start: 0.8824 (mptt) cc_final: 0.8509 (mptt) REVERT: S 128 GLU cc_start: 0.7656 (pt0) cc_final: 0.7082 (pp20) REVERT: S 135 ASN cc_start: 0.9050 (m110) cc_final: 0.8710 (m110) REVERT: S 151 GLN cc_start: 0.8152 (pm20) cc_final: 0.7883 (pm20) REVERT: S 179 GLU cc_start: 0.8337 (mm-30) cc_final: 0.7978 (mm-30) REVERT: S 219 ASP cc_start: 0.8076 (t0) cc_final: 0.7810 (t0) REVERT: S 234 GLN cc_start: 0.8974 (tt0) cc_final: 0.8601 (tt0) REVERT: S 238 GLN cc_start: 0.8667 (tt0) cc_final: 0.8218 (tt0) REVERT: S 241 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7750 (pm20) REVERT: S 242 GLN cc_start: 0.8625 (mm-40) cc_final: 0.7979 (mt0) REVERT: S 335 ARG cc_start: 0.8473 (mtm110) cc_final: 0.7952 (ttp-110) REVERT: S 389 GLU cc_start: 0.8542 (mp0) cc_final: 0.7884 (pm20) REVERT: S 392 GLU cc_start: 0.8790 (pp20) cc_final: 0.8188 (pp20) REVERT: S 441 GLU cc_start: 0.8540 (mp0) cc_final: 0.8321 (mp0) REVERT: S 444 ARG cc_start: 0.8790 (ttm-80) cc_final: 0.8397 (tpt170) REVERT: T 372 HIS cc_start: 0.7658 (t-90) cc_final: 0.7338 (t-90) REVERT: T 377 ASN cc_start: 0.8406 (t0) cc_final: 0.8173 (t0) REVERT: T 378 ARG cc_start: 0.8459 (tpp80) cc_final: 0.8165 (tpp80) REVERT: T 380 LEU cc_start: 0.8790 (tp) cc_final: 0.8547 (tt) REVERT: T 385 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8093 (mm-30) REVERT: T 386 MET cc_start: 0.8588 (mmp) cc_final: 0.8305 (mmp) REVERT: T 393 SER cc_start: 0.9316 (OUTLIER) cc_final: 0.9027 (p) REVERT: U 27 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.6957 (mm-30) REVERT: U 80 ARG cc_start: 0.8578 (tpm170) cc_final: 0.8091 (tpm170) REVERT: U 129 ARG cc_start: 0.7169 (OUTLIER) cc_final: 0.6648 (ttm170) outliers start: 156 outliers final: 115 residues processed: 1177 average time/residue: 0.3097 time to fit residues: 562.1155 Evaluate side-chains 1234 residues out of total 3875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 1099 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 310 PHE Chi-restraints excluded: chain K residue 311 GLU Chi-restraints excluded: chain K residue 394 ASN Chi-restraints excluded: chain K residue 441 HIS Chi-restraints excluded: chain K residue 468 PHE Chi-restraints excluded: chain K residue 702 LEU Chi-restraints excluded: chain K residue 710 MET Chi-restraints excluded: chain K residue 718 MET Chi-restraints excluded: chain K residue 837 LEU Chi-restraints excluded: chain K residue 890 MET Chi-restraints excluded: chain K residue 937 MET Chi-restraints excluded: chain K residue 1012 GLN Chi-restraints excluded: chain K residue 1049 MET Chi-restraints excluded: chain K residue 1090 MET Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 80 GLU Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain L residue 131 TRP Chi-restraints excluded: chain L residue 133 ARG Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 159 LEU Chi-restraints excluded: chain L residue 172 VAL Chi-restraints excluded: chain L residue 177 TYR Chi-restraints excluded: chain L residue 182 VAL Chi-restraints excluded: chain L residue 187 ASP Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 226 SER Chi-restraints excluded: chain L residue 239 ARG Chi-restraints excluded: chain L residue 358 LEU Chi-restraints excluded: chain L residue 359 VAL Chi-restraints excluded: chain L residue 519 ILE Chi-restraints excluded: chain L residue 542 ARG Chi-restraints excluded: chain L residue 544 LEU Chi-restraints excluded: chain L residue 554 HIS Chi-restraints excluded: chain L residue 654 ILE Chi-restraints excluded: chain L residue 706 THR Chi-restraints excluded: chain M residue 24 LEU Chi-restraints excluded: chain M residue 31 CYS Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 180 THR Chi-restraints excluded: chain M residue 289 GLU Chi-restraints excluded: chain M residue 290 PHE Chi-restraints excluded: chain M residue 406 HIS Chi-restraints excluded: chain N residue 133 ILE Chi-restraints excluded: chain N residue 155 LYS Chi-restraints excluded: chain N residue 182 LEU Chi-restraints excluded: chain N residue 205 GLN Chi-restraints excluded: chain N residue 226 ILE Chi-restraints excluded: chain N residue 392 LEU Chi-restraints excluded: chain N residue 400 ASP Chi-restraints excluded: chain N residue 423 LEU Chi-restraints excluded: chain N residue 554 MET Chi-restraints excluded: chain N residue 584 LEU Chi-restraints excluded: chain N residue 629 VAL Chi-restraints excluded: chain N residue 643 ARG Chi-restraints excluded: chain O residue 142 PHE Chi-restraints excluded: chain O residue 393 LEU Chi-restraints excluded: chain O residue 435 GLU Chi-restraints excluded: chain O residue 453 LEU Chi-restraints excluded: chain O residue 466 VAL Chi-restraints excluded: chain O residue 472 LEU Chi-restraints excluded: chain O residue 491 GLN Chi-restraints excluded: chain O residue 564 HIS Chi-restraints excluded: chain O residue 636 THR Chi-restraints excluded: chain P residue 86 ILE Chi-restraints excluded: chain P residue 112 LYS Chi-restraints excluded: chain P residue 120 LEU Chi-restraints excluded: chain P residue 348 ILE Chi-restraints excluded: chain P residue 366 HIS Chi-restraints excluded: chain P residue 432 LEU Chi-restraints excluded: chain P residue 458 ARG Chi-restraints excluded: chain P residue 474 ASP Chi-restraints excluded: chain P residue 477 ILE Chi-restraints excluded: chain P residue 490 VAL Chi-restraints excluded: chain P residue 529 VAL Chi-restraints excluded: chain Q residue 328 GLU Chi-restraints excluded: chain Q residue 353 PHE Chi-restraints excluded: chain Q residue 357 GLN Chi-restraints excluded: chain Q residue 392 GLU Chi-restraints excluded: chain Q residue 404 LYS Chi-restraints excluded: chain Q residue 405 PHE Chi-restraints excluded: chain Q residue 419 ARG Chi-restraints excluded: chain Q residue 463 VAL Chi-restraints excluded: chain R residue 796 GLU Chi-restraints excluded: chain R residue 810 LYS Chi-restraints excluded: chain R residue 835 VAL Chi-restraints excluded: chain R residue 850 VAL Chi-restraints excluded: chain R residue 887 THR Chi-restraints excluded: chain R residue 1108 TRP Chi-restraints excluded: chain R residue 1160 LEU Chi-restraints excluded: chain R residue 1165 LEU Chi-restraints excluded: chain S residue 111 TYR Chi-restraints excluded: chain S residue 167 LYS Chi-restraints excluded: chain S residue 181 VAL Chi-restraints excluded: chain S residue 202 LEU Chi-restraints excluded: chain S residue 225 MET Chi-restraints excluded: chain S residue 241 GLU Chi-restraints excluded: chain S residue 287 VAL Chi-restraints excluded: chain S residue 429 VAL Chi-restraints excluded: chain T residue 379 THR Chi-restraints excluded: chain T residue 390 TYR Chi-restraints excluded: chain T residue 393 SER Chi-restraints excluded: chain T residue 394 ILE Chi-restraints excluded: chain U residue 27 GLU Chi-restraints excluded: chain U residue 31 VAL Chi-restraints excluded: chain U residue 39 VAL Chi-restraints excluded: chain U residue 56 TRP Chi-restraints excluded: chain U residue 129 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 402 optimal weight: 2.9990 chunk 140 optimal weight: 40.0000 chunk 203 optimal weight: 1.9990 chunk 139 optimal weight: 5.9990 chunk 102 optimal weight: 7.9990 chunk 202 optimal weight: 0.9980 chunk 228 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 439 optimal weight: 6.9990 chunk 446 optimal weight: 7.9990 chunk 270 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN ** K 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 275 HIS ** N 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 528 ASN ** Q 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 323 GLN ** R1085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 399 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.172262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.133544 restraints weight = 101149.600| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 3.88 r_work: 0.3521 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 43000 Z= 0.238 Angle : 0.805 14.933 59276 Z= 0.414 Chirality : 0.048 0.352 6553 Planarity : 0.005 0.075 6756 Dihedral : 22.226 164.213 7935 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.76 % Favored : 94.13 % Rotamer: Outliers : 4.14 % Allowed : 26.16 % Favored : 69.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.13), residues: 4426 helix: 0.55 (0.10), residues: 2467 sheet: -0.45 (0.35), residues: 230 loop : -1.29 (0.15), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG N 621 TYR 0.060 0.002 TYR H 80 PHE 0.048 0.002 PHE K 654 TRP 0.058 0.002 TRP L 529 HIS 0.010 0.001 HIS L 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.24 (43000) covalent geometry : angle 0.80537 / 0.41 (59276) hydrogen bonds : bond 0.04702 / 3.13 ( 2194) hydrogen bonds : angle 4.64233 / 3.31 ( 6069) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8852 Ramachandran restraints generated. 4426 Oldfield, 0 Emsley, 4426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8852 Ramachandran restraints generated. 4426 Oldfield, 0 Emsley, 4426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1261 residues out of total 3875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 1101 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ARG cc_start: 0.7920 (mtp-110) cc_final: 0.7609 (ttp-110) REVERT: A 87 SER cc_start: 0.9219 (p) cc_final: 0.9008 (t) REVERT: A 131 ARG cc_start: 0.8819 (mtm180) cc_final: 0.8403 (mtp85) REVERT: C 56 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.7832 (tp30) REVERT: C 77 ARG cc_start: 0.8459 (ttp80) cc_final: 0.8251 (ttp80) REVERT: C 91 GLU cc_start: 0.8152 (tp30) cc_final: 0.7774 (tp30) REVERT: C 92 GLU cc_start: 0.8233 (tp30) cc_final: 0.7962 (mm-30) REVERT: D 68 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7973 (mm-30) REVERT: E 50 GLU cc_start: 0.8306 (pt0) cc_final: 0.8085 (pt0) REVERT: E 106 ASP cc_start: 0.8405 (m-30) cc_final: 0.7983 (m-30) REVERT: E 120 MET cc_start: 0.8897 (OUTLIER) cc_final: 0.7790 (mpp) REVERT: E 131 ARG cc_start: 0.8780 (mtp180) cc_final: 0.8578 (mtp85) REVERT: G 74 LYS cc_start: 0.8780 (mppt) cc_final: 0.8501 (mppt) REVERT: H 65 ASP cc_start: 0.8708 (t0) cc_final: 0.8383 (t0) REVERT: H 73 GLU cc_start: 0.8850 (tp30) cc_final: 0.8571 (tp30) REVERT: H 113 LYS cc_start: 0.8666 (pttt) cc_final: 0.8337 (pttt) REVERT: K 316 ASP cc_start: 0.7523 (t0) cc_final: 0.7287 (t0) REVERT: K 317 ARG cc_start: 0.8101 (ptm160) cc_final: 0.6939 (ptm160) REVERT: K 323 ASN cc_start: 0.8443 (t0) cc_final: 0.8133 (t0) REVERT: K 331 GLU cc_start: 0.8677 (pp20) cc_final: 0.8202 (pp20) REVERT: K 356 LYS cc_start: 0.8439 (tppt) cc_final: 0.8131 (tmmt) REVERT: K 362 GLU cc_start: 0.7761 (mp0) cc_final: 0.7010 (pm20) REVERT: K 364 LYS cc_start: 0.8535 (pttt) cc_final: 0.8211 (pttt) REVERT: K 401 MET cc_start: 0.8583 (mpp) cc_final: 0.8179 (mpp) REVERT: K 411 ILE cc_start: 0.8516 (mt) cc_final: 0.8233 (mm) REVERT: K 416 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7452 (mm-30) REVERT: K 446 LEU cc_start: 0.8548 (mt) cc_final: 0.8192 (pp) REVERT: K 453 ARG cc_start: 0.8353 (ppt170) cc_final: 0.7835 (ppt170) REVERT: K 710 MET cc_start: 0.7503 (OUTLIER) cc_final: 0.7069 (mpp) REVERT: K 713 ASP cc_start: 0.8294 (t70) cc_final: 0.7382 (p0) REVERT: K 714 GLU cc_start: 0.7343 (tp30) cc_final: 0.6379 (tp30) REVERT: K 756 MET cc_start: 0.9137 (mmm) cc_final: 0.8753 (mmm) REVERT: L 80 GLU cc_start: 0.6647 (OUTLIER) cc_final: 0.4438 (pm20) REVERT: L 121 THR cc_start: 0.7744 (OUTLIER) cc_final: 0.7508 (p) REVERT: L 159 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.7817 (tp) REVERT: L 163 TYR cc_start: 0.8506 (m-80) cc_final: 0.7947 (m-80) REVERT: L 195 ASN cc_start: 0.8202 (t0) cc_final: 0.7830 (t0) REVERT: L 239 ARG cc_start: 0.2399 (OUTLIER) cc_final: -0.0194 (mtp85) REVERT: L 507 ARG cc_start: 0.8500 (mtp180) cc_final: 0.8256 (ptm-80) REVERT: L 554 HIS cc_start: 0.7582 (OUTLIER) cc_final: 0.6796 (p90) REVERT: L 655 LYS cc_start: 0.8371 (ptmm) cc_final: 0.8106 (ptmm) REVERT: L 707 ARG cc_start: 0.8471 (ttt180) cc_final: 0.8196 (ptt180) REVERT: M 25 VAL cc_start: 0.7630 (t) cc_final: 0.7111 (m) REVERT: M 42 MET cc_start: 0.7159 (mmm) cc_final: 0.6860 (mmm) REVERT: M 74 ARG cc_start: 0.7476 (ptp-170) cc_final: 0.7087 (ptp90) REVERT: M 76 TYR cc_start: 0.8673 (OUTLIER) cc_final: 0.8169 (p90) REVERT: M 153 TRP cc_start: 0.7955 (p90) cc_final: 0.7629 (p90) REVERT: M 408 LEU cc_start: 0.9330 (mt) cc_final: 0.8952 (tp) REVERT: M 411 MET cc_start: 0.6796 (mtt) cc_final: 0.6382 (mtp) REVERT: N 147 ARG cc_start: 0.8661 (ptm-80) cc_final: 0.8370 (ptt90) REVERT: N 417 GLU cc_start: 0.8573 (pt0) cc_final: 0.7915 (tp30) REVERT: N 545 GLN cc_start: 0.8692 (mp10) cc_final: 0.8442 (mp10) REVERT: N 568 GLU cc_start: 0.8704 (tm-30) cc_final: 0.8442 (tm-30) REVERT: N 583 LYS cc_start: 0.8983 (tptt) cc_final: 0.8658 (tptt) REVERT: N 585 GLU cc_start: 0.8464 (pp20) cc_final: 0.7878 (pp20) REVERT: N 587 LYS cc_start: 0.8794 (mmmm) cc_final: 0.8142 (mmmm) REVERT: N 589 LYS cc_start: 0.8719 (mtmm) cc_final: 0.8227 (mtmm) REVERT: N 597 MET cc_start: 0.8178 (tmm) cc_final: 0.7375 (tmm) REVERT: N 602 ARG cc_start: 0.8144 (ttp80) cc_final: 0.7695 (ttp80) REVERT: N 624 ARG cc_start: 0.7160 (OUTLIER) cc_final: 0.6330 (mmt180) REVERT: N 625 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7904 (tp30) REVERT: N 646 GLN cc_start: 0.8972 (tp40) cc_final: 0.8507 (tp40) REVERT: O 142 PHE cc_start: 0.7788 (OUTLIER) cc_final: 0.7378 (t80) REVERT: O 198 GLU cc_start: 0.8409 (tp30) cc_final: 0.7997 (tp30) REVERT: O 212 ARG cc_start: 0.8055 (mpp-170) cc_final: 0.7839 (mtm-85) REVERT: O 225 LYS cc_start: 0.9061 (mmmt) cc_final: 0.8789 (mmmm) REVERT: O 237 TRP cc_start: 0.8246 (t60) cc_final: 0.7992 (t60) REVERT: O 405 GLN cc_start: 0.8528 (mp10) cc_final: 0.7946 (mp10) REVERT: O 435 GLU cc_start: 0.1773 (OUTLIER) cc_final: 0.1503 (tm-30) REVERT: O 453 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8443 (mp) REVERT: O 474 ASP cc_start: 0.8044 (t0) cc_final: 0.7557 (t0) REVERT: O 566 GLU cc_start: 0.8596 (mm-30) cc_final: 0.6799 (mm-30) REVERT: O 567 ARG cc_start: 0.8239 (mmt90) cc_final: 0.7897 (mmt90) REVERT: O 571 ARG cc_start: 0.8656 (tpt170) cc_final: 0.8403 (tpt170) REVERT: O 597 MET cc_start: 0.8112 (ppp) cc_final: 0.7822 (ppp) REVERT: O 598 LEU cc_start: 0.8569 (mm) cc_final: 0.8190 (mm) REVERT: O 601 GLU cc_start: 0.8337 (pp20) cc_final: 0.8042 (pp20) REVERT: O 602 ARG cc_start: 0.8806 (ttm-80) cc_final: 0.8405 (ttm-80) REVERT: O 606 GLU cc_start: 0.8738 (mt-10) cc_final: 0.8164 (mt-10) REVERT: O 607 ARG cc_start: 0.8623 (mmp80) cc_final: 0.8059 (mmp80) REVERT: O 611 GLN cc_start: 0.7968 (tp-100) cc_final: 0.6921 (tp-100) REVERT: O 612 LEU cc_start: 0.8398 (tp) cc_final: 0.7976 (tt) REVERT: O 615 ASP cc_start: 0.7164 (p0) cc_final: 0.6780 (p0) REVERT: P 58 GLN cc_start: 0.7992 (mm-40) cc_final: 0.7531 (mm-40) REVERT: P 428 GLU cc_start: 0.7884 (tp30) cc_final: 0.7505 (tp30) REVERT: P 429 ILE cc_start: 0.8749 (pt) cc_final: 0.8466 (pt) REVERT: P 432 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8430 (mm) REVERT: P 435 GLN cc_start: 0.8127 (mt0) cc_final: 0.7439 (mt0) REVERT: P 474 ASP cc_start: 0.8170 (OUTLIER) cc_final: 0.7558 (t0) REVERT: P 483 ASN cc_start: 0.7259 (t0) cc_final: 0.7054 (t0) REVERT: P 508 GLU cc_start: 0.7208 (tt0) cc_final: 0.6747 (pm20) REVERT: Q 316 GLU cc_start: 0.7716 (pt0) cc_final: 0.7452 (pt0) REVERT: Q 328 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7534 (pm20) REVERT: Q 364 TYR cc_start: 0.8376 (t80) cc_final: 0.7483 (t80) REVERT: Q 381 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8355 (mm-30) REVERT: Q 388 LYS cc_start: 0.8880 (mtpp) cc_final: 0.8648 (mtpp) REVERT: Q 390 GLU cc_start: 0.8338 (tm-30) cc_final: 0.8001 (tm-30) REVERT: Q 395 LYS cc_start: 0.9277 (mmmt) cc_final: 0.9047 (tppt) REVERT: Q 402 MET cc_start: 0.8459 (mmt) cc_final: 0.8083 (mmm) REVERT: Q 419 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7742 (ptt-90) REVERT: Q 453 ASP cc_start: 0.7881 (t70) cc_final: 0.7644 (t70) REVERT: Q 465 LYS cc_start: 0.8310 (mmtt) cc_final: 0.7943 (tmtt) REVERT: R 781 ASP cc_start: 0.8427 (p0) cc_final: 0.8072 (p0) REVERT: R 810 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.8029 (ptpt) REVERT: R 845 GLN cc_start: 0.8175 (mp10) cc_final: 0.7951 (mm-40) REVERT: R 854 GLU cc_start: 0.8408 (pt0) cc_final: 0.7909 (pm20) REVERT: R 883 THR cc_start: 0.8549 (p) cc_final: 0.8296 (p) REVERT: R 1032 LYS cc_start: 0.8478 (ttmm) cc_final: 0.8161 (ttmm) REVERT: R 1072 MET cc_start: 0.7447 (mmp) cc_final: 0.7087 (mmp) REVERT: R 1093 MET cc_start: 0.8520 (ttp) cc_final: 0.8316 (ttp) REVERT: R 1160 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8684 (tp) REVERT: S 92 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7218 (pm20) REVERT: S 100 ASP cc_start: 0.8511 (t0) cc_final: 0.8175 (t0) REVERT: S 102 LYS cc_start: 0.7852 (mttm) cc_final: 0.7507 (tttt) REVERT: S 104 MET cc_start: 0.6956 (mmp) cc_final: 0.6709 (mmp) REVERT: S 115 LYS cc_start: 0.8880 (mptt) cc_final: 0.8557 (mptt) REVERT: S 128 GLU cc_start: 0.7646 (pt0) cc_final: 0.7087 (pp20) REVERT: S 135 ASN cc_start: 0.9078 (m110) cc_final: 0.8716 (m110) REVERT: S 151 GLN cc_start: 0.8147 (pm20) cc_final: 0.7855 (pm20) REVERT: S 167 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8187 (tmmt) REVERT: S 179 GLU cc_start: 0.8392 (mm-30) cc_final: 0.8157 (tp30) REVERT: S 234 GLN cc_start: 0.8984 (tt0) cc_final: 0.8617 (tt0) REVERT: S 241 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7934 (pm20) REVERT: S 242 GLN cc_start: 0.8613 (mm-40) cc_final: 0.7998 (mt0) REVERT: S 335 ARG cc_start: 0.8528 (mtm110) cc_final: 0.8050 (ttp-110) REVERT: S 389 GLU cc_start: 0.8548 (mp0) cc_final: 0.7917 (pm20) REVERT: S 392 GLU cc_start: 0.8798 (pp20) cc_final: 0.8206 (pp20) REVERT: S 441 GLU cc_start: 0.8555 (mp0) cc_final: 0.8350 (mp0) REVERT: S 444 ARG cc_start: 0.8824 (ttm-80) cc_final: 0.8428 (tpt170) REVERT: T 372 HIS cc_start: 0.7669 (t-90) cc_final: 0.7338 (t-90) REVERT: T 377 ASN cc_start: 0.8465 (t0) cc_final: 0.8244 (t0) REVERT: T 378 ARG cc_start: 0.8515 (tpp80) cc_final: 0.8211 (tpp80) REVERT: T 380 LEU cc_start: 0.8804 (tp) cc_final: 0.8555 (tt) REVERT: T 385 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8113 (mm-30) REVERT: T 386 MET cc_start: 0.8598 (mmp) cc_final: 0.8332 (mmp) REVERT: T 393 SER cc_start: 0.9307 (OUTLIER) cc_final: 0.8987 (p) REVERT: T 396 ARG cc_start: 0.7985 (tpm170) cc_final: 0.7721 (tpm170) REVERT: U 27 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.6966 (mm-30) REVERT: U 80 ARG cc_start: 0.8589 (tpm170) cc_final: 0.8112 (tpm170) REVERT: U 129 ARG cc_start: 0.7232 (OUTLIER) cc_final: 0.6700 (ttm170) outliers start: 160 outliers final: 115 residues processed: 1174 average time/residue: 0.3137 time to fit residues: 566.0506 Evaluate side-chains 1240 residues out of total 3875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 1099 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 310 PHE Chi-restraints excluded: chain K residue 311 GLU Chi-restraints excluded: chain K residue 441 HIS Chi-restraints excluded: chain K residue 468 PHE Chi-restraints excluded: chain K residue 702 LEU Chi-restraints excluded: chain K residue 710 MET Chi-restraints excluded: chain K residue 718 MET Chi-restraints excluded: chain K residue 837 LEU Chi-restraints excluded: chain K residue 890 MET Chi-restraints excluded: chain K residue 937 MET Chi-restraints excluded: chain K residue 1012 GLN Chi-restraints excluded: chain K residue 1049 MET Chi-restraints excluded: chain K residue 1090 MET Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 80 GLU Chi-restraints excluded: chain L residue 120 ASN Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain L residue 131 TRP Chi-restraints excluded: chain L residue 133 ARG Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 159 LEU Chi-restraints excluded: chain L residue 172 VAL Chi-restraints excluded: chain L residue 177 TYR Chi-restraints excluded: chain L residue 182 VAL Chi-restraints excluded: chain L residue 187 ASP Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 239 ARG Chi-restraints excluded: chain L residue 358 LEU Chi-restraints excluded: chain L residue 359 VAL Chi-restraints excluded: chain L residue 519 ILE Chi-restraints excluded: chain L residue 542 ARG Chi-restraints excluded: chain L residue 544 LEU Chi-restraints excluded: chain L residue 554 HIS Chi-restraints excluded: chain L residue 654 ILE Chi-restraints excluded: chain L residue 706 THR Chi-restraints excluded: chain M residue 24 LEU Chi-restraints excluded: chain M residue 31 CYS Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 76 TYR Chi-restraints excluded: chain M residue 180 THR Chi-restraints excluded: chain M residue 275 HIS Chi-restraints excluded: chain M residue 289 GLU Chi-restraints excluded: chain M residue 406 HIS Chi-restraints excluded: chain N residue 133 ILE Chi-restraints excluded: chain N residue 155 LYS Chi-restraints excluded: chain N residue 182 LEU Chi-restraints excluded: chain N residue 205 GLN Chi-restraints excluded: chain N residue 226 ILE Chi-restraints excluded: chain N residue 392 LEU Chi-restraints excluded: chain N residue 400 ASP Chi-restraints excluded: chain N residue 423 LEU Chi-restraints excluded: chain N residue 554 MET Chi-restraints excluded: chain N residue 584 LEU Chi-restraints excluded: chain N residue 624 ARG Chi-restraints excluded: chain N residue 625 GLU Chi-restraints excluded: chain N residue 629 VAL Chi-restraints excluded: chain N residue 643 ARG Chi-restraints excluded: chain O residue 142 PHE Chi-restraints excluded: chain O residue 393 LEU Chi-restraints excluded: chain O residue 394 GLU Chi-restraints excluded: chain O residue 435 GLU Chi-restraints excluded: chain O residue 453 LEU Chi-restraints excluded: chain O residue 466 VAL Chi-restraints excluded: chain O residue 472 LEU Chi-restraints excluded: chain O residue 491 GLN Chi-restraints excluded: chain O residue 564 HIS Chi-restraints excluded: chain O residue 636 THR Chi-restraints excluded: chain P residue 73 THR Chi-restraints excluded: chain P residue 86 ILE Chi-restraints excluded: chain P residue 112 LYS Chi-restraints excluded: chain P residue 120 LEU Chi-restraints excluded: chain P residue 348 ILE Chi-restraints excluded: chain P residue 366 HIS Chi-restraints excluded: chain P residue 432 LEU Chi-restraints excluded: chain P residue 458 ARG Chi-restraints excluded: chain P residue 474 ASP Chi-restraints excluded: chain P residue 477 ILE Chi-restraints excluded: chain P residue 490 VAL Chi-restraints excluded: chain P residue 529 VAL Chi-restraints excluded: chain Q residue 328 GLU Chi-restraints excluded: chain Q residue 353 PHE Chi-restraints excluded: chain Q residue 357 GLN Chi-restraints excluded: chain Q residue 392 GLU Chi-restraints excluded: chain Q residue 404 LYS Chi-restraints excluded: chain Q residue 405 PHE Chi-restraints excluded: chain Q residue 419 ARG Chi-restraints excluded: chain Q residue 463 VAL Chi-restraints excluded: chain R residue 796 GLU Chi-restraints excluded: chain R residue 810 LYS Chi-restraints excluded: chain R residue 835 VAL Chi-restraints excluded: chain R residue 850 VAL Chi-restraints excluded: chain R residue 887 THR Chi-restraints excluded: chain R residue 1108 TRP Chi-restraints excluded: chain R residue 1160 LEU Chi-restraints excluded: chain R residue 1165 LEU Chi-restraints excluded: chain R residue 1172 LYS Chi-restraints excluded: chain S residue 92 GLU Chi-restraints excluded: chain S residue 111 TYR Chi-restraints excluded: chain S residue 167 LYS Chi-restraints excluded: chain S residue 181 VAL Chi-restraints excluded: chain S residue 202 LEU Chi-restraints excluded: chain S residue 225 MET Chi-restraints excluded: chain S residue 241 GLU Chi-restraints excluded: chain S residue 287 VAL Chi-restraints excluded: chain S residue 429 VAL Chi-restraints excluded: chain T residue 379 THR Chi-restraints excluded: chain T residue 390 TYR Chi-restraints excluded: chain T residue 393 SER Chi-restraints excluded: chain T residue 394 ILE Chi-restraints excluded: chain U residue 27 GLU Chi-restraints excluded: chain U residue 31 VAL Chi-restraints excluded: chain U residue 39 VAL Chi-restraints excluded: chain U residue 56 TRP Chi-restraints excluded: chain U residue 129 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 270 optimal weight: 0.9980 chunk 292 optimal weight: 0.6980 chunk 87 optimal weight: 10.0000 chunk 4 optimal weight: 0.5980 chunk 272 optimal weight: 0.9990 chunk 411 optimal weight: 0.9980 chunk 351 optimal weight: 0.7980 chunk 211 optimal weight: 0.8980 chunk 162 optimal weight: 3.9990 chunk 337 optimal weight: 0.5980 chunk 282 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN H 44 GLN ** K 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1012 GLN ** L 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 231 GLN M 275 HIS ** N 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 441 GLN ** P 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 323 GLN ** Q 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R1085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 359 GLN ** T 399 HIS ** 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 = 0.4362 r_free = 0.4362 target = 0.174125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.135598 restraints weight = 101484.577| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 3.88 r_work: 0.3557 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 43000 Z= 0.167 Angle : 0.797 16.341 59276 Z= 0.407 Chirality : 0.047 0.348 6553 Planarity : 0.005 0.060 6756 Dihedral : 22.163 165.290 7933 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.42 % Favored : 94.46 % Rotamer: Outliers : 3.62 % Allowed : 26.76 % Favored : 69.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.27 (0.13), residues: 4426 helix: 0.61 (0.10), residues: 2458 sheet: -0.37 (0.36), residues: 231 loop : -1.25 (0.15), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG N 621 TYR 0.032 0.002 TYR S 111 PHE 0.047 0.002 PHE K 654 TRP 0.059 0.002 TRP L 529 HIS 0.030 0.001 HIS M 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.17 (43000) covalent geometry : angle 0.79728 / 0.41 (59276) hydrogen bonds : bond 0.04446 / 2.95 ( 2194) hydrogen bonds : angle 4.56046 / 3.26 ( 6069) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8852 Ramachandran restraints generated. 4426 Oldfield, 0 Emsley, 4426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8852 Ramachandran restraints generated. 4426 Oldfield, 0 Emsley, 4426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1249 residues out of total 3875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 1109 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.9075 (mt) cc_final: 0.8774 (mm) REVERT: A 53 ARG cc_start: 0.7925 (mtp-110) cc_final: 0.7698 (mtm110) REVERT: A 87 SER cc_start: 0.9206 (p) cc_final: 0.8998 (t) REVERT: A 131 ARG cc_start: 0.8848 (mtm180) cc_final: 0.8441 (mtp85) REVERT: C 56 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.7917 (tp30) REVERT: C 77 ARG cc_start: 0.8424 (ttp80) cc_final: 0.8049 (ttp80) REVERT: C 91 GLU cc_start: 0.8117 (tp30) cc_final: 0.7756 (tp30) REVERT: C 92 GLU cc_start: 0.8235 (tp30) cc_final: 0.8001 (mm-30) REVERT: D 106 HIS cc_start: 0.8851 (m-70) cc_final: 0.8496 (m-70) REVERT: E 50 GLU cc_start: 0.8279 (pt0) cc_final: 0.8058 (pt0) REVERT: E 106 ASP cc_start: 0.8345 (m-30) cc_final: 0.7948 (m-30) REVERT: E 120 MET cc_start: 0.8883 (OUTLIER) cc_final: 0.7784 (mpp) REVERT: E 131 ARG cc_start: 0.8734 (mtp180) cc_final: 0.8526 (mtp85) REVERT: G 25 PHE cc_start: 0.8465 (m-80) cc_final: 0.8084 (m-80) REVERT: G 74 LYS cc_start: 0.8754 (mppt) cc_final: 0.8476 (mppt) REVERT: H 65 ASP cc_start: 0.8687 (t0) cc_final: 0.8368 (t0) REVERT: H 73 GLU cc_start: 0.8812 (tp30) cc_final: 0.8576 (tp30) REVERT: H 113 LYS cc_start: 0.8648 (pttt) cc_final: 0.8357 (pttt) REVERT: K 316 ASP cc_start: 0.7503 (t0) cc_final: 0.7240 (t0) REVERT: K 317 ARG cc_start: 0.8122 (ptm160) cc_final: 0.6674 (ttp80) REVERT: K 323 ASN cc_start: 0.8420 (t0) cc_final: 0.8090 (t0) REVERT: K 331 GLU cc_start: 0.8670 (pp20) cc_final: 0.8153 (pp20) REVERT: K 333 LYS cc_start: 0.8568 (pttt) cc_final: 0.8347 (pttt) REVERT: K 356 LYS cc_start: 0.8433 (tppt) cc_final: 0.8101 (tmmt) REVERT: K 362 GLU cc_start: 0.7731 (mp0) cc_final: 0.6976 (pm20) REVERT: K 364 LYS cc_start: 0.8515 (pttt) cc_final: 0.8165 (pttt) REVERT: K 401 MET cc_start: 0.8591 (mpp) cc_final: 0.8193 (mpp) REVERT: K 411 ILE cc_start: 0.8497 (mt) cc_final: 0.8233 (mm) REVERT: K 416 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7467 (mm-30) REVERT: K 418 GLN cc_start: 0.8628 (mm110) cc_final: 0.8216 (mm110) REVERT: K 446 LEU cc_start: 0.8508 (mt) cc_final: 0.8188 (pp) REVERT: K 453 ARG cc_start: 0.8335 (ppt170) cc_final: 0.7790 (ppt170) REVERT: K 710 MET cc_start: 0.7501 (OUTLIER) cc_final: 0.7090 (mpp) REVERT: K 713 ASP cc_start: 0.8263 (t70) cc_final: 0.7344 (p0) REVERT: K 714 GLU cc_start: 0.7363 (tp30) cc_final: 0.6419 (tp30) REVERT: K 756 MET cc_start: 0.9133 (mmm) cc_final: 0.8734 (mmm) REVERT: L 80 GLU cc_start: 0.6555 (OUTLIER) cc_final: 0.4499 (pm20) REVERT: L 92 MET cc_start: 0.8526 (tmm) cc_final: 0.8240 (tmm) REVERT: L 121 THR cc_start: 0.7598 (OUTLIER) cc_final: 0.7359 (p) REVERT: L 159 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.7602 (tp) REVERT: L 163 TYR cc_start: 0.8483 (m-80) cc_final: 0.7900 (m-80) REVERT: L 195 ASN cc_start: 0.8261 (t0) cc_final: 0.7838 (t0) REVERT: L 507 ARG cc_start: 0.8419 (mtp180) cc_final: 0.8204 (ptm160) REVERT: L 554 HIS cc_start: 0.7489 (OUTLIER) cc_final: 0.6783 (p90) REVERT: L 655 LYS cc_start: 0.8291 (ptmm) cc_final: 0.8018 (ptmm) REVERT: L 709 ASP cc_start: 0.8186 (m-30) cc_final: 0.7887 (p0) REVERT: M 25 VAL cc_start: 0.6994 (t) cc_final: 0.6498 (m) REVERT: M 42 MET cc_start: 0.7175 (mmm) cc_final: 0.6913 (mmm) REVERT: M 60 PHE cc_start: 0.7292 (m-80) cc_final: 0.6919 (t80) REVERT: M 74 ARG cc_start: 0.7368 (ptp-170) cc_final: 0.6947 (ptp90) REVERT: M 76 TYR cc_start: 0.8567 (OUTLIER) cc_final: 0.8095 (p90) REVERT: M 86 TRP cc_start: 0.8058 (t60) cc_final: 0.7745 (t60) REVERT: M 153 TRP cc_start: 0.7763 (p90) cc_final: 0.7508 (p90) REVERT: M 289 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8265 (mp0) REVERT: M 404 LEU cc_start: 0.7978 (tp) cc_final: 0.7420 (pp) REVERT: M 408 LEU cc_start: 0.9309 (mt) cc_final: 0.8902 (tp) REVERT: M 411 MET cc_start: 0.6733 (mtt) cc_final: 0.6365 (mtp) REVERT: N 147 ARG cc_start: 0.8610 (ptm-80) cc_final: 0.8337 (ptt90) REVERT: N 403 TRP cc_start: 0.8692 (m100) cc_final: 0.7985 (m100) REVERT: N 417 GLU cc_start: 0.8564 (pt0) cc_final: 0.7896 (tp30) REVERT: N 545 GLN cc_start: 0.8718 (mp10) cc_final: 0.8453 (mp10) REVERT: N 568 GLU cc_start: 0.8641 (tm-30) cc_final: 0.8384 (tm-30) REVERT: N 583 LYS cc_start: 0.8943 (tptt) cc_final: 0.8539 (tptt) REVERT: N 585 GLU cc_start: 0.8497 (pp20) cc_final: 0.7891 (pp20) REVERT: N 587 LYS cc_start: 0.8761 (mmmm) cc_final: 0.8027 (mmmm) REVERT: N 589 LYS cc_start: 0.8670 (mtmm) cc_final: 0.8163 (mtmm) REVERT: N 597 MET cc_start: 0.8027 (tmm) cc_final: 0.7248 (tmm) REVERT: N 602 ARG cc_start: 0.8094 (ttp80) cc_final: 0.7630 (ttp80) REVERT: N 624 ARG cc_start: 0.7057 (OUTLIER) cc_final: 0.6197 (mmt180) REVERT: N 625 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7750 (tp30) REVERT: N 646 GLN cc_start: 0.8918 (tp40) cc_final: 0.8685 (tp40) REVERT: N 663 PHE cc_start: 0.6590 (m-80) cc_final: 0.6274 (m-80) REVERT: O 142 PHE cc_start: 0.7774 (OUTLIER) cc_final: 0.7428 (t80) REVERT: O 198 GLU cc_start: 0.8393 (tp30) cc_final: 0.7956 (tp30) REVERT: O 225 LYS cc_start: 0.9056 (mmmt) cc_final: 0.8726 (mmmm) REVERT: O 237 TRP cc_start: 0.8230 (t60) cc_final: 0.7980 (t60) REVERT: O 405 GLN cc_start: 0.8518 (mp10) cc_final: 0.7939 (mp10) REVERT: O 426 ASP cc_start: 0.7638 (m-30) cc_final: 0.7014 (p0) REVERT: O 435 GLU cc_start: 0.1784 (OUTLIER) cc_final: 0.1508 (tm-30) REVERT: O 453 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8442 (mp) REVERT: O 463 MET cc_start: 0.8348 (ttt) cc_final: 0.8099 (ttm) REVERT: O 474 ASP cc_start: 0.8021 (t0) cc_final: 0.7548 (t0) REVERT: O 566 GLU cc_start: 0.8608 (mm-30) cc_final: 0.6969 (mm-30) REVERT: O 567 ARG cc_start: 0.8246 (mmt90) cc_final: 0.7740 (mmt90) REVERT: O 571 ARG cc_start: 0.8607 (tpt170) cc_final: 0.8362 (tpt170) REVERT: O 597 MET cc_start: 0.8099 (ppp) cc_final: 0.7795 (ppp) REVERT: O 598 LEU cc_start: 0.8594 (mm) cc_final: 0.8146 (mm) REVERT: O 601 GLU cc_start: 0.8193 (pp20) cc_final: 0.7909 (pp20) REVERT: O 606 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8119 (mt-10) REVERT: O 607 ARG cc_start: 0.8584 (mmp80) cc_final: 0.8014 (mmp80) REVERT: O 611 GLN cc_start: 0.7878 (tp-100) cc_final: 0.7077 (tp-100) REVERT: O 612 LEU cc_start: 0.8427 (tp) cc_final: 0.8092 (tt) REVERT: P 58 GLN cc_start: 0.7999 (mm-40) cc_final: 0.7534 (mm-40) REVERT: P 428 GLU cc_start: 0.7862 (tp30) cc_final: 0.7599 (tp30) REVERT: P 429 ILE cc_start: 0.8727 (pt) cc_final: 0.8465 (pt) REVERT: P 432 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8482 (mm) REVERT: P 435 GLN cc_start: 0.8097 (mt0) cc_final: 0.7463 (mt0) REVERT: P 471 GLN cc_start: 0.8308 (mm110) cc_final: 0.7916 (mm110) REVERT: P 474 ASP cc_start: 0.8131 (OUTLIER) cc_final: 0.7494 (t0) REVERT: P 483 ASN cc_start: 0.7341 (t0) cc_final: 0.7123 (t0) REVERT: P 508 GLU cc_start: 0.7151 (tt0) cc_final: 0.6661 (pm20) REVERT: P 528 ASN cc_start: 0.8874 (t0) cc_final: 0.8621 (t0) REVERT: Q 316 GLU cc_start: 0.7605 (pt0) cc_final: 0.7380 (pt0) REVERT: Q 326 GLN cc_start: 0.7589 (tm-30) cc_final: 0.6965 (tm-30) REVERT: Q 328 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7443 (pm20) REVERT: Q 364 TYR cc_start: 0.8337 (t80) cc_final: 0.7484 (t80) REVERT: Q 388 LYS cc_start: 0.8804 (mtpp) cc_final: 0.8564 (mtpp) REVERT: Q 390 GLU cc_start: 0.8321 (tm-30) cc_final: 0.7923 (tm-30) REVERT: Q 395 LYS cc_start: 0.9248 (mmmt) cc_final: 0.9027 (tppt) REVERT: Q 402 MET cc_start: 0.8440 (mmt) cc_final: 0.8082 (mmm) REVERT: Q 453 ASP cc_start: 0.7820 (t70) cc_final: 0.7570 (t70) REVERT: Q 458 ARG cc_start: 0.8397 (ptm160) cc_final: 0.8168 (ptm160) REVERT: R 753 GLU cc_start: 0.7308 (tm-30) cc_final: 0.6962 (tm-30) REVERT: R 758 TRP cc_start: 0.8564 (t60) cc_final: 0.8291 (t60) REVERT: R 810 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.8022 (ptpt) REVERT: R 845 GLN cc_start: 0.8171 (mp10) cc_final: 0.7650 (mp10) REVERT: R 854 GLU cc_start: 0.8343 (pt0) cc_final: 0.7863 (pm20) REVERT: R 883 THR cc_start: 0.8509 (p) cc_final: 0.8249 (p) REVERT: R 950 ASP cc_start: 0.7921 (t0) cc_final: 0.7421 (t0) REVERT: R 954 ASP cc_start: 0.7835 (m-30) cc_final: 0.7080 (m-30) REVERT: R 1032 LYS cc_start: 0.8421 (ttmm) cc_final: 0.8111 (ttmm) REVERT: R 1085 GLN cc_start: 0.8445 (mm-40) cc_final: 0.8243 (mm-40) REVERT: R 1093 MET cc_start: 0.8461 (ttp) cc_final: 0.8247 (ttp) REVERT: R 1160 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8620 (tp) REVERT: S 92 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7242 (pm20) REVERT: S 100 ASP cc_start: 0.8536 (t0) cc_final: 0.8141 (t0) REVERT: S 102 LYS cc_start: 0.7832 (mttm) cc_final: 0.7491 (tttt) REVERT: S 104 MET cc_start: 0.6967 (mmp) cc_final: 0.6707 (mmp) REVERT: S 115 LYS cc_start: 0.8834 (mptt) cc_final: 0.8498 (mptt) REVERT: S 128 GLU cc_start: 0.7599 (pt0) cc_final: 0.7031 (pp20) REVERT: S 135 ASN cc_start: 0.9047 (m110) cc_final: 0.8676 (m110) REVERT: S 151 GLN cc_start: 0.8117 (pm20) cc_final: 0.7860 (pm20) REVERT: S 167 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8020 (tmmt) REVERT: S 171 LYS cc_start: 0.8298 (mtmm) cc_final: 0.7627 (mtmm) REVERT: S 179 GLU cc_start: 0.8300 (mm-30) cc_final: 0.7812 (mm-30) REVERT: S 203 HIS cc_start: 0.8862 (m90) cc_final: 0.8402 (m-70) REVERT: S 234 GLN cc_start: 0.8951 (tt0) cc_final: 0.8602 (tt0) REVERT: S 241 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7833 (pm20) REVERT: S 242 GLN cc_start: 0.8574 (mm-40) cc_final: 0.7948 (mt0) REVERT: S 310 ARG cc_start: 0.7741 (tpt170) cc_final: 0.7107 (tpp-160) REVERT: S 335 ARG cc_start: 0.8505 (mtm110) cc_final: 0.8009 (ttp-110) REVERT: S 389 GLU cc_start: 0.8530 (mp0) cc_final: 0.8190 (pm20) REVERT: S 444 ARG cc_start: 0.8775 (ttm-80) cc_final: 0.8398 (tpt170) REVERT: T 372 HIS cc_start: 0.7612 (t-90) cc_final: 0.7272 (t-90) REVERT: T 378 ARG cc_start: 0.8459 (tpp80) cc_final: 0.8158 (tpp80) REVERT: T 380 LEU cc_start: 0.8755 (tp) cc_final: 0.8493 (tt) REVERT: T 384 ARG cc_start: 0.8443 (ttt180) cc_final: 0.8211 (ttt180) REVERT: T 385 GLU cc_start: 0.8431 (mm-30) cc_final: 0.8045 (mm-30) REVERT: T 386 MET cc_start: 0.8604 (mmp) cc_final: 0.8341 (mmp) REVERT: T 393 SER cc_start: 0.9276 (p) cc_final: 0.8951 (p) REVERT: T 396 ARG cc_start: 0.7971 (tpm170) cc_final: 0.7707 (tpm170) REVERT: U 27 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.6940 (mm-30) REVERT: U 80 ARG cc_start: 0.8564 (tpm170) cc_final: 0.8114 (tpm170) REVERT: U 129 ARG cc_start: 0.7170 (OUTLIER) cc_final: 0.6639 (ttm170) outliers start: 140 outliers final: 104 residues processed: 1172 average time/residue: 0.2995 time to fit residues: 540.0340 Evaluate side-chains 1231 residues out of total 3875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 1103 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 310 PHE Chi-restraints excluded: chain K residue 311 GLU Chi-restraints excluded: chain K residue 394 ASN Chi-restraints excluded: chain K residue 441 HIS Chi-restraints excluded: chain K residue 468 PHE Chi-restraints excluded: chain K residue 702 LEU Chi-restraints excluded: chain K residue 710 MET Chi-restraints excluded: chain K residue 718 MET Chi-restraints excluded: chain K residue 837 LEU Chi-restraints excluded: chain K residue 890 MET Chi-restraints excluded: chain K residue 937 MET Chi-restraints excluded: chain K residue 1012 GLN Chi-restraints excluded: chain K residue 1049 MET Chi-restraints excluded: chain K residue 1090 MET Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 80 GLU Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain L residue 131 TRP Chi-restraints excluded: chain L residue 133 ARG Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 159 LEU Chi-restraints excluded: chain L residue 161 THR Chi-restraints excluded: chain L residue 172 VAL Chi-restraints excluded: chain L residue 177 TYR Chi-restraints excluded: chain L residue 182 VAL Chi-restraints excluded: chain L residue 187 ASP Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 358 LEU Chi-restraints excluded: chain L residue 359 VAL Chi-restraints excluded: chain L residue 519 ILE Chi-restraints excluded: chain L residue 542 ARG Chi-restraints excluded: chain L residue 544 LEU Chi-restraints excluded: chain L residue 554 HIS Chi-restraints excluded: chain L residue 654 ILE Chi-restraints excluded: chain L residue 706 THR Chi-restraints excluded: chain M residue 24 LEU Chi-restraints excluded: chain M residue 31 CYS Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 76 TYR Chi-restraints excluded: chain M residue 180 THR Chi-restraints excluded: chain M residue 275 HIS Chi-restraints excluded: chain M residue 289 GLU Chi-restraints excluded: chain M residue 406 HIS Chi-restraints excluded: chain N residue 133 ILE Chi-restraints excluded: chain N residue 155 LYS Chi-restraints excluded: chain N residue 182 LEU Chi-restraints excluded: chain N residue 205 GLN Chi-restraints excluded: chain N residue 226 ILE Chi-restraints excluded: chain N residue 400 ASP Chi-restraints excluded: chain N residue 423 LEU Chi-restraints excluded: chain N residue 554 MET Chi-restraints excluded: chain N residue 584 LEU Chi-restraints excluded: chain N residue 624 ARG Chi-restraints excluded: chain N residue 625 GLU Chi-restraints excluded: chain N residue 629 VAL Chi-restraints excluded: chain N residue 643 ARG Chi-restraints excluded: chain O residue 142 PHE Chi-restraints excluded: chain O residue 394 GLU Chi-restraints excluded: chain O residue 435 GLU Chi-restraints excluded: chain O residue 453 LEU Chi-restraints excluded: chain O residue 466 VAL Chi-restraints excluded: chain O residue 472 LEU Chi-restraints excluded: chain O residue 491 GLN Chi-restraints excluded: chain O residue 564 HIS Chi-restraints excluded: chain O residue 605 LEU Chi-restraints excluded: chain O residue 636 THR Chi-restraints excluded: chain P residue 86 ILE Chi-restraints excluded: chain P residue 112 LYS Chi-restraints excluded: chain P residue 120 LEU Chi-restraints excluded: chain P residue 348 ILE Chi-restraints excluded: chain P residue 432 LEU Chi-restraints excluded: chain P residue 474 ASP Chi-restraints excluded: chain P residue 490 VAL Chi-restraints excluded: chain P residue 529 VAL Chi-restraints excluded: chain Q residue 328 GLU Chi-restraints excluded: chain Q residue 404 LYS Chi-restraints excluded: chain Q residue 405 PHE Chi-restraints excluded: chain Q residue 419 ARG Chi-restraints excluded: chain Q residue 463 VAL Chi-restraints excluded: chain R residue 810 LYS Chi-restraints excluded: chain R residue 835 VAL Chi-restraints excluded: chain R residue 850 VAL Chi-restraints excluded: chain R residue 887 THR Chi-restraints excluded: chain R residue 1160 LEU Chi-restraints excluded: chain R residue 1165 LEU Chi-restraints excluded: chain R residue 1171 ARG Chi-restraints excluded: chain S residue 92 GLU Chi-restraints excluded: chain S residue 111 TYR Chi-restraints excluded: chain S residue 167 LYS Chi-restraints excluded: chain S residue 181 VAL Chi-restraints excluded: chain S residue 202 LEU Chi-restraints excluded: chain S residue 241 GLU Chi-restraints excluded: chain S residue 287 VAL Chi-restraints excluded: chain S residue 429 VAL Chi-restraints excluded: chain T residue 359 GLN Chi-restraints excluded: chain T residue 390 TYR Chi-restraints excluded: chain T residue 394 ILE Chi-restraints excluded: chain U residue 27 GLU Chi-restraints excluded: chain U residue 31 VAL Chi-restraints excluded: chain U residue 39 VAL Chi-restraints excluded: chain U residue 56 TRP Chi-restraints excluded: chain U residue 129 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 432 optimal weight: 2.9990 chunk 239 optimal weight: 1.9990 chunk 373 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 453 optimal weight: 90.0000 chunk 371 optimal weight: 0.8980 chunk 352 optimal weight: 2.9990 chunk 337 optimal weight: 0.9990 chunk 235 optimal weight: 0.5980 chunk 465 optimal weight: 7.9990 chunk 290 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN ** K 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 114 HIS ** N 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 366 HIS ** P 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 323 GLN ** Q 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R1085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R1117 GLN ** S 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 359 GLN ** T 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.173937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.136000 restraints weight = 101446.614| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 3.87 r_work: 0.3561 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.253 43000 Z= 0.221 Angle : 0.896 59.194 59276 Z= 0.488 Chirality : 0.048 0.614 6553 Planarity : 0.006 0.167 6756 Dihedral : 22.156 165.279 7930 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 18.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.42 % Favored : 94.49 % Rotamer: Outliers : 3.47 % Allowed : 27.07 % Favored : 69.46 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.13), residues: 4426 helix: 0.62 (0.10), residues: 2458 sheet: -0.37 (0.36), residues: 231 loop : -1.25 (0.15), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG P 113 TYR 0.032 0.002 TYR S 111 PHE 0.045 0.002 PHE K 654 TRP 0.053 0.002 TRP L 529 HIS 0.165 0.002 HIS M 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.22 (43000) covalent geometry : angle 0.89565 / 0.49 (59276) hydrogen bonds : bond 0.04453 / 2.95 ( 2194) hydrogen bonds : angle 4.56640 / 3.27 ( 6069) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15793.93 seconds wall clock time: 269 minutes 34.27 seconds (16174.27 seconds total)