Starting phenix.real_space_refine on Fri Jul 26 19:05:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k9a_36982/07_2024/8k9a_36982.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k9a_36982/07_2024/8k9a_36982.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k9a_36982/07_2024/8k9a_36982.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k9a_36982/07_2024/8k9a_36982.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k9a_36982/07_2024/8k9a_36982.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k9a_36982/07_2024/8k9a_36982.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 130 5.16 5 C 22033 2.51 5 N 5506 2.21 5 O 6366 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 139": "OD1" <-> "OD2" Residue "A GLU 155": "OE1" <-> "OE2" Residue "A PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 839": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 916": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 943": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 962": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 368": "OD1" <-> "OD2" Residue "B GLU 379": "OE1" <-> "OE2" Residue "B TYR 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 525": "OD1" <-> "OD2" Residue "B TYR 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 633": "OE1" <-> "OE2" Residue "B GLU 648": "OE1" <-> "OE2" Residue "B PHE 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 743": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 744": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 329": "OD1" <-> "OD2" Residue "C ASP 435": "OD1" <-> "OD2" Residue "C ASP 630": "OD1" <-> "OD2" Residue "C TYR 650": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 662": "OD1" <-> "OD2" Residue "C PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 933": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 951": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 369": "OE1" <-> "OE2" Residue "D ASP 547": "OD1" <-> "OD2" Residue "D PHE 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 811": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 812": "OE1" <-> "OE2" Residue "D GLU 880": "OE1" <-> "OE2" Residue "D TYR 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 962": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 30": "OD1" <-> "OD2" Residue "F ASP 26": "OD1" <-> "OD2" Residue "F GLU 28": "OE1" <-> "OE2" Residue "F TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 97": "OE1" <-> "OE2" Residue "F PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 34035 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 970, 8081 Classifications: {'peptide': 970} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 950} Chain breaks: 5 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 8057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 969, 8057 Classifications: {'peptide': 969} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 949} Chain breaks: 3 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 8091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 971, 8091 Classifications: {'peptide': 971} Link IDs: {'CIS': 1, 'PTRANS': 19, 'TRANS': 950} Chain breaks: 3 Chain: "D" Number of atoms: 8093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 8093 Classifications: {'peptide': 972} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 952} Chain breaks: 5 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 855 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 3, 'TRANS': 107} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "F" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 858 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 3, 'TRANS': 107} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 31 Time building chain proxies: 17.76, per 1000 atoms: 0.52 Number of scatterers: 34035 At special positions: 0 Unit cell: (102, 130.05, 275.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 130 16.00 O 6366 8.00 N 5506 7.00 C 22033 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 - 3.50 Amino acid : False - 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: 11.26 Conformation dependent library (CDL) restraints added in 5.7 seconds 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7830 Finding SS restraints... Secondary structure from input PDB file: 225 helices and 16 sheets defined 65.4% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.90 Creating SS restraints... Processing helix chain 'A' and resid 9 through 20 removed outlier: 4.447A pdb=" N GLU A 13 " --> pdb=" O LYS A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 40 Processing helix chain 'A' and resid 48 through 53 removed outlier: 3.580A pdb=" N THR A 52 " --> pdb=" O ALA A 48 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU A 53 " --> pdb=" O GLY A 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 48 through 53' Processing helix chain 'A' and resid 58 through 72 removed outlier: 3.659A pdb=" N LEU A 62 " --> pdb=" O GLN A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 95 Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 96 through 108 removed outlier: 3.543A pdb=" N PHE A 100 " --> pdb=" O GLY A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 124 removed outlier: 3.710A pdb=" N ASP A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 146 Processing helix chain 'A' and resid 155 through 159 removed outlier: 3.548A pdb=" N VAL A 158 " --> pdb=" O GLU A 155 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA A 159 " --> pdb=" O GLU A 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 155 through 159' Processing helix chain 'A' and resid 186 through 192 Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 197 through 211 Processing helix chain 'A' and resid 222 through 234 removed outlier: 3.991A pdb=" N LYS A 234 " --> pdb=" O ASN A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 265 Processing helix chain 'A' and resid 271 through 275 removed outlier: 3.610A pdb=" N ILE A 275 " --> pdb=" O ALA A 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 271 through 275' Processing helix chain 'A' and resid 282 through 299 removed outlier: 3.632A pdb=" N TYR A 286 " --> pdb=" O TYR A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 317 Processing helix chain 'A' and resid 318 through 322 removed outlier: 3.703A pdb=" N ALA A 321 " --> pdb=" O PRO A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 334 removed outlier: 3.723A pdb=" N LEU A 330 " --> pdb=" O ARG A 326 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS A 331 " --> pdb=" O LYS A 327 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N HIS A 332 " --> pdb=" O ILE A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 366 Processing helix chain 'A' and resid 374 through 392 Processing helix chain 'A' and resid 411 through 416 removed outlier: 3.934A pdb=" N HIS A 415 " --> pdb=" O SER A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 427 removed outlier: 3.661A pdb=" N GLU A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU A 427 " --> pdb=" O LYS A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 445 Processing helix chain 'A' and resid 447 through 462 Processing helix chain 'A' and resid 467 through 493 removed outlier: 3.856A pdb=" N TYR A 471 " --> pdb=" O ASN A 467 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU A 473 " --> pdb=" O CYS A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 532 through 539 Processing helix chain 'A' and resid 540 through 547 removed outlier: 4.357A pdb=" N PHE A 544 " --> pdb=" O ILE A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 558 Processing helix chain 'A' and resid 559 through 563 Processing helix chain 'A' and resid 579 through 598 removed outlier: 3.623A pdb=" N ASN A 598 " --> pdb=" O PHE A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 604 removed outlier: 3.772A pdb=" N VAL A 603 " --> pdb=" O LEU A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 634 Processing helix chain 'A' and resid 648 through 659 Processing helix chain 'A' and resid 660 through 671 Processing helix chain 'A' and resid 680 through 702 removed outlier: 3.653A pdb=" N ILE A 684 " --> pdb=" O GLU A 680 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN A 702 " --> pdb=" O GLN A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 723 removed outlier: 3.956A pdb=" N SER A 714 " --> pdb=" O THR A 710 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N GLU A 715 " --> pdb=" O GLN A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 726 No H-bonds generated for 'chain 'A' and resid 724 through 726' Processing helix chain 'A' and resid 729 through 742 removed outlier: 3.623A pdb=" N PHE A 742 " --> pdb=" O LYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 763 removed outlier: 3.729A pdb=" N LYS A 763 " --> pdb=" O GLU A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 786 removed outlier: 3.804A pdb=" N ILE A 772 " --> pdb=" O PRO A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 812 removed outlier: 3.745A pdb=" N GLY A 805 " --> pdb=" O SER A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 826 removed outlier: 3.654A pdb=" N SER A 821 " --> pdb=" O SER A 817 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N CYS A 826 " --> pdb=" O GLU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 841 Processing helix chain 'A' and resid 846 through 855 removed outlier: 3.749A pdb=" N SER A 855 " --> pdb=" O SER A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 872 removed outlier: 3.693A pdb=" N ILE A 871 " --> pdb=" O ASN A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 896 Processing helix chain 'A' and resid 913 through 922 Processing helix chain 'A' and resid 929 through 933 removed outlier: 3.685A pdb=" N PHE A 933 " --> pdb=" O MET A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 945 removed outlier: 3.575A pdb=" N ASP A 941 " --> pdb=" O ASP A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 961 removed outlier: 4.025A pdb=" N TRP A 958 " --> pdb=" O ILE A 955 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS A 960 " --> pdb=" O SER A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 972 Processing helix chain 'A' and resid 977 through 991 Processing helix chain 'A' and resid 993 through 1005 removed outlier: 3.958A pdb=" N ILE A1005 " --> pdb=" O MET A1001 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 39 Processing helix chain 'B' and resid 48 through 54 removed outlier: 3.776A pdb=" N SER B 54 " --> pdb=" O VAL B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 71 removed outlier: 3.890A pdb=" N LEU B 62 " --> pdb=" O GLN B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 96 Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 97 through 109 Processing helix chain 'B' and resid 115 through 123 Processing helix chain 'B' and resid 136 through 141 Processing helix chain 'B' and resid 155 through 159 removed outlier: 3.506A pdb=" N ALA B 159 " --> pdb=" O GLU B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 183 removed outlier: 3.667A pdb=" N ASN B 182 " --> pdb=" O LYS B 179 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL B 183 " --> pdb=" O GLY B 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 179 through 183' Processing helix chain 'B' and resid 186 through 192 Processing helix chain 'B' and resid 192 through 197 Processing helix chain 'B' and resid 197 through 211 Processing helix chain 'B' and resid 222 through 235 removed outlier: 3.814A pdb=" N LYS B 234 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU B 235 " --> pdb=" O TRP B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 265 Processing helix chain 'B' and resid 282 through 299 removed outlier: 3.567A pdb=" N TYR B 286 " --> pdb=" O TYR B 282 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLU B 298 " --> pdb=" O ILE B 294 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN B 299 " --> pdb=" O GLU B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 317 Processing helix chain 'B' and resid 318 through 322 removed outlier: 3.513A pdb=" N ALA B 321 " --> pdb=" O PRO B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 334 Processing helix chain 'B' and resid 355 through 366 Processing helix chain 'B' and resid 368 through 373 removed outlier: 3.558A pdb=" N LEU B 373 " --> pdb=" O ARG B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 392 Processing helix chain 'B' and resid 411 through 416 Processing helix chain 'B' and resid 417 through 427 removed outlier: 3.913A pdb=" N MET B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLU B 427 " --> pdb=" O LYS B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 445 Processing helix chain 'B' and resid 447 through 461 Processing helix chain 'B' and resid 468 through 492 Processing helix chain 'B' and resid 508 through 519 removed outlier: 3.796A pdb=" N ALA B 513 " --> pdb=" O ASP B 509 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU B 516 " --> pdb=" O LEU B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 531 removed outlier: 3.656A pdb=" N MET B 531 " --> pdb=" O PHE B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 539 Processing helix chain 'B' and resid 540 through 547 Processing helix chain 'B' and resid 548 through 572 removed outlier: 3.792A pdb=" N TYR B 552 " --> pdb=" O ASN B 548 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASP B 553 " --> pdb=" O GLN B 549 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ASP B 554 " --> pdb=" O PHE B 550 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LYS B 557 " --> pdb=" O ASP B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 597 removed outlier: 3.973A pdb=" N VAL B 584 " --> pdb=" O SER B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 604 removed outlier: 4.116A pdb=" N VAL B 603 " --> pdb=" O LEU B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 628 removed outlier: 3.897A pdb=" N HIS B 609 " --> pdb=" O PHE B 605 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N THR B 628 " --> pdb=" O GLU B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 639 Processing helix chain 'B' and resid 648 through 659 Processing helix chain 'B' and resid 660 through 671 Processing helix chain 'B' and resid 680 through 701 removed outlier: 4.565A pdb=" N ALA B 701 " --> pdb=" O LYS B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 723 removed outlier: 4.421A pdb=" N SER B 714 " --> pdb=" O THR B 710 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N GLU B 715 " --> pdb=" O GLN B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 726 No H-bonds generated for 'chain 'B' and resid 724 through 726' Processing helix chain 'B' and resid 729 through 742 Processing helix chain 'B' and resid 750 through 765 removed outlier: 4.279A pdb=" N CYS B 764 " --> pdb=" O ARG B 760 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ASN B 765 " --> pdb=" O LEU B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 786 Processing helix chain 'B' and resid 801 through 812 removed outlier: 3.584A pdb=" N GLY B 805 " --> pdb=" O SER B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 826 removed outlier: 3.783A pdb=" N GLU B 822 " --> pdb=" O LYS B 818 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE B 823 " --> pdb=" O ARG B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 840 Processing helix chain 'B' and resid 841 through 845 removed outlier: 3.600A pdb=" N LEU B 844 " --> pdb=" O LEU B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 846 through 855 removed outlier: 3.937A pdb=" N SER B 855 " --> pdb=" O SER B 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 872 removed outlier: 3.523A pdb=" N MET B 866 " --> pdb=" O ILE B 862 " (cutoff:3.500A) Processing helix chain 'B' and resid 878 through 896 Processing helix chain 'B' and resid 911 through 922 Processing helix chain 'B' and resid 928 through 933 Processing helix chain 'B' and resid 937 through 945 Processing helix chain 'B' and resid 950 through 954 removed outlier: 3.694A pdb=" N LYS B 953 " --> pdb=" O ASP B 950 " (cutoff:3.500A) Processing helix chain 'B' and resid 955 through 962 removed outlier: 4.257A pdb=" N TRP B 958 " --> pdb=" O ILE B 955 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS B 960 " --> pdb=" O SER B 957 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR B 962 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 973 Processing helix chain 'B' and resid 976 through 991 removed outlier: 4.241A pdb=" N GLU B 982 " --> pdb=" O HIS B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 994 through 1003 removed outlier: 3.772A pdb=" N TYR B1003 " --> pdb=" O ILE B 999 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 39 Processing helix chain 'C' and resid 48 through 54 removed outlier: 3.650A pdb=" N SER C 54 " --> pdb=" O VAL C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 71 removed outlier: 3.638A pdb=" N LEU C 62 " --> pdb=" O GLN C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 96 Proline residue: C 88 - end of helix Processing helix chain 'C' and resid 97 through 109 Processing helix chain 'C' and resid 115 through 123 Processing helix chain 'C' and resid 136 through 145 removed outlier: 3.792A pdb=" N CYS C 142 " --> pdb=" O ILE C 138 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG C 145 " --> pdb=" O ALA C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 192 Processing helix chain 'C' and resid 192 through 197 Processing helix chain 'C' and resid 197 through 211 Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 254 through 265 Processing helix chain 'C' and resid 282 through 296 removed outlier: 4.045A pdb=" N VAL C 289 " --> pdb=" O ARG C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 317 Processing helix chain 'C' and resid 318 through 322 removed outlier: 3.848A pdb=" N ALA C 321 " --> pdb=" O PRO C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 328 No H-bonds generated for 'chain 'C' and resid 326 through 328' Processing helix chain 'C' and resid 329 through 334 removed outlier: 3.689A pdb=" N VAL C 333 " --> pdb=" O ASP C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 366 Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.605A pdb=" N SER C 371 " --> pdb=" O ASP C 368 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU C 373 " --> pdb=" O ARG C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 392 Processing helix chain 'C' and resid 411 through 416 removed outlier: 3.580A pdb=" N HIS C 415 " --> pdb=" O SER C 411 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY C 416 " --> pdb=" O LEU C 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 411 through 416' Processing helix chain 'C' and resid 417 through 427 removed outlier: 4.002A pdb=" N MET C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 445 Processing helix chain 'C' and resid 447 through 462 Processing helix chain 'C' and resid 468 through 496 Processing helix chain 'C' and resid 508 through 520 Processing helix chain 'C' and resid 532 through 539 Processing helix chain 'C' and resid 540 through 547 removed outlier: 3.734A pdb=" N PHE C 544 " --> pdb=" O ILE C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 571 removed outlier: 3.723A pdb=" N TYR C 552 " --> pdb=" O ASN C 548 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ASP C 553 " --> pdb=" O GLN C 549 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ASP C 554 " --> pdb=" O PHE C 550 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LYS C 557 " --> pdb=" O ASP C 553 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU C 558 " --> pdb=" O ASP C 554 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER C 567 " --> pdb=" O ASN C 563 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU C 571 " --> pdb=" O SER C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 598 removed outlier: 3.766A pdb=" N ASN C 598 " --> pdb=" O PHE C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 628 removed outlier: 3.626A pdb=" N HIS C 609 " --> pdb=" O PHE C 605 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N THR C 628 " --> pdb=" O GLU C 624 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 639 Processing helix chain 'C' and resid 648 through 658 Processing helix chain 'C' and resid 660 through 671 Processing helix chain 'C' and resid 672 through 676 removed outlier: 3.500A pdb=" N LYS C 675 " --> pdb=" O SER C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 680 through 701 removed outlier: 3.743A pdb=" N ALA C 701 " --> pdb=" O LYS C 697 " (cutoff:3.500A) Processing helix chain 'C' and resid 705 through 711 removed outlier: 4.040A pdb=" N GLN C 711 " --> pdb=" O VAL C 707 " (cutoff:3.500A) Processing helix chain 'C' and resid 712 through 723 Processing helix chain 'C' and resid 724 through 726 No H-bonds generated for 'chain 'C' and resid 724 through 726' Processing helix chain 'C' and resid 729 through 742 Processing helix chain 'C' and resid 750 through 763 removed outlier: 3.579A pdb=" N LYS C 763 " --> pdb=" O GLU C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 786 removed outlier: 3.580A pdb=" N ILE C 772 " --> pdb=" O PRO C 768 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 812 removed outlier: 4.020A pdb=" N GLY C 805 " --> pdb=" O SER C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 826 removed outlier: 3.764A pdb=" N CYS C 826 " --> pdb=" O GLU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 831 through 840 removed outlier: 3.633A pdb=" N ILE C 835 " --> pdb=" O LYS C 831 " (cutoff:3.500A) Processing helix chain 'C' and resid 841 through 845 Processing helix chain 'C' and resid 846 through 854 Processing helix chain 'C' and resid 862 through 872 removed outlier: 3.739A pdb=" N ASN C 867 " --> pdb=" O ASN C 863 " (cutoff:3.500A) Processing helix chain 'C' and resid 878 through 896 Processing helix chain 'C' and resid 911 through 922 Processing helix chain 'C' and resid 929 through 933 removed outlier: 3.981A pdb=" N PHE C 933 " --> pdb=" O MET C 930 " (cutoff:3.500A) Processing helix chain 'C' and resid 937 through 945 removed outlier: 3.700A pdb=" N ASP C 941 " --> pdb=" O ASP C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 957 through 962 removed outlier: 3.704A pdb=" N LYS C 960 " --> pdb=" O SER C 957 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TYR C 962 " --> pdb=" O LEU C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 963 through 973 Processing helix chain 'C' and resid 976 through 991 removed outlier: 4.712A pdb=" N GLU C 982 " --> pdb=" O HIS C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 994 through 1003 Processing helix chain 'D' and resid 9 through 20 removed outlier: 3.979A pdb=" N GLU D 13 " --> pdb=" O LYS D 9 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS D 16 " --> pdb=" O GLY D 12 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU D 20 " --> pdb=" O LYS D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 39 Processing helix chain 'D' and resid 48 through 53 removed outlier: 3.639A pdb=" N THR D 52 " --> pdb=" O ALA D 48 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU D 53 " --> pdb=" O GLY D 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 48 through 53' Processing helix chain 'D' and resid 58 through 72 removed outlier: 3.641A pdb=" N LEU D 62 " --> pdb=" O GLN D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 96 removed outlier: 3.854A pdb=" N TYR D 84 " --> pdb=" O SER D 80 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU D 85 " --> pdb=" O SER D 81 " (cutoff:3.500A) Proline residue: D 88 - end of helix Processing helix chain 'D' and resid 96 through 108 removed outlier: 3.531A pdb=" N PHE D 100 " --> pdb=" O GLY D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 124 removed outlier: 3.718A pdb=" N ASP D 119 " --> pdb=" O ASN D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 145 Processing helix chain 'D' and resid 186 through 192 Processing helix chain 'D' and resid 192 through 197 Processing helix chain 'D' and resid 197 through 211 Processing helix chain 'D' and resid 222 through 235 removed outlier: 3.644A pdb=" N LYS D 234 " --> pdb=" O ASN D 230 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU D 235 " --> pdb=" O TRP D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 265 Processing helix chain 'D' and resid 282 through 298 Processing helix chain 'D' and resid 304 through 317 Processing helix chain 'D' and resid 318 through 322 Processing helix chain 'D' and resid 326 through 334 removed outlier: 3.824A pdb=" N LYS D 331 " --> pdb=" O LYS D 327 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N HIS D 332 " --> pdb=" O ILE D 328 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE D 334 " --> pdb=" O LEU D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 365 removed outlier: 3.502A pdb=" N GLU D 365 " --> pdb=" O PHE D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 373 removed outlier: 3.943A pdb=" N LEU D 373 " --> pdb=" O GLU D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 392 Processing helix chain 'D' and resid 417 through 427 removed outlier: 3.857A pdb=" N GLU D 426 " --> pdb=" O LYS D 422 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU D 427 " --> pdb=" O LYS D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 446 Processing helix chain 'D' and resid 447 through 462 Processing helix chain 'D' and resid 468 through 493 removed outlier: 3.842A pdb=" N ASN D 477 " --> pdb=" O LEU D 473 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN D 491 " --> pdb=" O GLN D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 519 removed outlier: 3.786A pdb=" N ARG D 514 " --> pdb=" O GLU D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 539 Processing helix chain 'D' and resid 540 through 547 removed outlier: 4.494A pdb=" N PHE D 544 " --> pdb=" O ILE D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 551 through 558 Processing helix chain 'D' and resid 559 through 563 removed outlier: 3.639A pdb=" N ASN D 563 " --> pdb=" O GLU D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 598 removed outlier: 3.679A pdb=" N ASN D 598 " --> pdb=" O PHE D 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 604 removed outlier: 3.770A pdb=" N VAL D 603 " --> pdb=" O LEU D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 634 removed outlier: 3.599A pdb=" N HIS D 609 " --> pdb=" O PHE D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 659 Processing helix chain 'D' and resid 660 through 671 Processing helix chain 'D' and resid 681 through 701 Processing helix chain 'D' and resid 705 through 723 removed outlier: 3.765A pdb=" N GLN D 711 " --> pdb=" O VAL D 707 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER D 714 " --> pdb=" O THR D 710 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU D 715 " --> pdb=" O GLN D 711 " (cutoff:3.500A) Processing helix chain 'D' and resid 729 through 742 Processing helix chain 'D' and resid 750 through 762 Processing helix chain 'D' and resid 768 through 785 removed outlier: 3.513A pdb=" N ILE D 772 " --> pdb=" O PRO D 768 " (cutoff:3.500A) Processing helix chain 'D' and resid 800 through 812 removed outlier: 3.922A pdb=" N TYR D 804 " --> pdb=" O TYR D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 817 through 826 removed outlier: 3.651A pdb=" N CYS D 826 " --> pdb=" O GLU D 822 " (cutoff:3.500A) Processing helix chain 'D' and resid 831 through 841 removed outlier: 3.535A pdb=" N ILE D 835 " --> pdb=" O LYS D 831 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU D 841 " --> pdb=" O PHE D 837 " (cutoff:3.500A) Processing helix chain 'D' and resid 842 through 845 Processing helix chain 'D' and resid 846 through 855 removed outlier: 3.534A pdb=" N SER D 855 " --> pdb=" O SER D 851 " (cutoff:3.500A) Processing helix chain 'D' and resid 862 through 871 removed outlier: 4.067A pdb=" N MET D 866 " --> pdb=" O ILE D 862 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLY D 868 " --> pdb=" O ASP D 864 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ILE D 869 " --> pdb=" O LEU D 865 " (cutoff:3.500A) Processing helix chain 'D' and resid 878 through 896 Processing helix chain 'D' and resid 912 through 922 removed outlier: 3.596A pdb=" N PHE D 916 " --> pdb=" O TYR D 912 " (cutoff:3.500A) Processing helix chain 'D' and resid 928 through 934 removed outlier: 3.825A pdb=" N GLU D 931 " --> pdb=" O SER D 928 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE D 934 " --> pdb=" O GLU D 931 " (cutoff:3.500A) Processing helix chain 'D' and resid 937 through 945 Processing helix chain 'D' and resid 955 through 961 removed outlier: 3.506A pdb=" N TRP D 958 " --> pdb=" O ILE D 955 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS D 960 " --> pdb=" O SER D 957 " (cutoff:3.500A) Processing helix chain 'D' and resid 963 through 972 Processing helix chain 'D' and resid 977 through 991 Processing helix chain 'D' and resid 993 through 1003 Processing helix chain 'E' and resid 95 through 104 Processing helix chain 'F' and resid 10 through 13 removed outlier: 3.554A pdb=" N ASP F 13 " --> pdb=" O ALA F 10 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 10 through 13' Processing helix chain 'F' and resid 95 through 106 Processing sheet with id=AA1, first strand: chain 'A' and resid 150 through 152 removed outlier: 6.281A pdb=" N SER A 150 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LYS A 169 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE A 152 " --> pdb=" O LYS A 169 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N PHE A 44 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE A 213 " --> pdb=" O PHE A 244 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ILE A 246 " --> pdb=" O ILE A 213 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N PHE A 215 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N PHE A 245 " --> pdb=" O ILE A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 338 through 341 removed outlier: 3.675A pdb=" N THR A 345 " --> pdb=" O GLU A 341 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 150 through 152 removed outlier: 6.306A pdb=" N SER B 150 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LYS B 169 " --> pdb=" O SER B 150 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE B 152 " --> pdb=" O LYS B 169 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N HIS B 128 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE B 246 " --> pdb=" O PHE B 215 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N PHE B 245 " --> pdb=" O ILE B 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 338 through 340 Processing sheet with id=AA5, first strand: chain 'B' and resid 574 through 575 Processing sheet with id=AA6, first strand: chain 'C' and resid 150 through 152 removed outlier: 6.171A pdb=" N SER C 150 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LYS C 169 " --> pdb=" O SER C 150 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE C 152 " --> pdb=" O LYS C 169 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU C 42 " --> pdb=" O HIS C 128 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N ILE C 130 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N PHE C 44 " --> pdb=" O ILE C 130 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE C 246 " --> pdb=" O PHE C 215 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N PHE C 245 " --> pdb=" O ILE C 269 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 338 through 340 Processing sheet with id=AA8, first strand: chain 'C' and resid 573 through 575 removed outlier: 6.348A pdb=" N PHE F 23 " --> pdb=" O VAL F 113 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 150 through 152 removed outlier: 5.938A pdb=" N PHE D 44 " --> pdb=" O ILE D 130 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE D 213 " --> pdb=" O PHE D 244 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ILE D 246 " --> pdb=" O ILE D 213 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N PHE D 215 " --> pdb=" O ILE D 246 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N PHE D 245 " --> pdb=" O ILE D 269 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 338 through 340 Processing sheet with id=AB2, first strand: chain 'E' and resid 23 through 24 removed outlier: 6.279A pdb=" N PHE E 23 " --> pdb=" O VAL E 113 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'E' and resid 28 through 29 Processing sheet with id=AB4, first strand: chain 'E' and resid 32 through 33 Processing sheet with id=AB5, first strand: chain 'E' and resid 71 through 72 removed outlier: 8.831A pdb=" N VAL E 117 " --> pdb=" O PHE E 44 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LYS E 46 " --> pdb=" O VAL E 117 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 29 through 32 removed outlier: 4.169A pdb=" N ILE F 31 " --> pdb=" O ASN F 40 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ASN F 40 " --> pdb=" O ILE F 31 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 29 through 32 removed outlier: 4.169A pdb=" N ILE F 31 " --> pdb=" O ASN F 40 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ASN F 40 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU F 115 " --> pdb=" O PHE F 44 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS F 46 " --> pdb=" O GLU F 115 " (cutoff:3.500A) 1726 hydrogen bonds defined for protein. 4977 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.03 Time building geometry restraints manager: 12.58 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: 10786 1.34 - 1.46: 8697 1.46 - 1.58: 15115 1.58 - 1.70: 0 1.70 - 1.82: 214 Bond restraints: 34812 Sorted by residual: bond pdb=" N VAL C 859 " pdb=" CA VAL C 859 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.00e+01 bond pdb=" C VAL C 859 " pdb=" N GLU C 860 " ideal model delta sigma weight residual 1.331 1.289 0.041 1.31e-02 5.83e+03 1.00e+01 bond pdb=" N ILE C 138 " pdb=" CA ILE C 138 " ideal model delta sigma weight residual 1.462 1.495 -0.032 1.06e-02 8.90e+03 9.27e+00 bond pdb=" N VAL E 99 " pdb=" CA VAL E 99 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.17e-02 7.31e+03 8.74e+00 bond pdb=" N ILE B 138 " pdb=" CA ILE B 138 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.41e-02 5.03e+03 8.01e+00 ... (remaining 34807 not shown) Histogram of bond angle deviations from ideal: 97.25 - 104.74: 267 104.74 - 112.23: 16374 112.23 - 119.72: 12952 119.72 - 127.21: 17072 127.21 - 134.70: 234 Bond angle restraints: 46899 Sorted by residual: angle pdb=" N THR E 11 " pdb=" CA THR E 11 " pdb=" C THR E 11 " ideal model delta sigma weight residual 113.37 107.26 6.11 1.38e+00 5.25e-01 1.96e+01 angle pdb=" N TYR C 650 " pdb=" CA TYR C 650 " pdb=" C TYR C 650 " ideal model delta sigma weight residual 111.71 106.66 5.05 1.15e+00 7.56e-01 1.93e+01 angle pdb=" N ILE C 138 " pdb=" CA ILE C 138 " pdb=" C ILE C 138 " ideal model delta sigma weight residual 112.98 107.76 5.22 1.25e+00 6.40e-01 1.75e+01 angle pdb=" N THR C 555 " pdb=" CA THR C 555 " pdb=" C THR C 555 " ideal model delta sigma weight residual 112.90 107.59 5.31 1.31e+00 5.83e-01 1.64e+01 angle pdb=" CA THR C 555 " pdb=" CB THR C 555 " pdb=" OG1 THR C 555 " ideal model delta sigma weight residual 109.60 103.56 6.04 1.50e+00 4.44e-01 1.62e+01 ... (remaining 46894 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 17358 17.86 - 35.72: 2530 35.72 - 53.59: 683 53.59 - 71.45: 125 71.45 - 89.31: 41 Dihedral angle restraints: 20737 sinusoidal: 8568 harmonic: 12169 Sorted by residual: dihedral pdb=" CA MET C 647 " pdb=" C MET C 647 " pdb=" N GLU C 648 " pdb=" CA GLU C 648 " ideal model delta harmonic sigma weight residual -180.00 -160.50 -19.50 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA ASN B 705 " pdb=" C ASN B 705 " pdb=" N VAL B 706 " pdb=" CA VAL B 706 " ideal model delta harmonic sigma weight residual -180.00 -160.69 -19.31 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA LYS B 505 " pdb=" C LYS B 505 " pdb=" N PRO B 506 " pdb=" CA PRO B 506 " ideal model delta harmonic sigma weight residual 180.00 -161.23 -18.77 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 20734 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 4171 0.055 - 0.110: 736 0.110 - 0.164: 83 0.164 - 0.219: 10 0.219 - 0.274: 3 Chirality restraints: 5003 Sorted by residual: chirality pdb=" CG LEU D 922 " pdb=" CB LEU D 922 " pdb=" CD1 LEU D 922 " pdb=" CD2 LEU D 922 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CB VAL C 859 " pdb=" CA VAL C 859 " pdb=" CG1 VAL C 859 " pdb=" CG2 VAL C 859 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CB ILE C 661 " pdb=" CA ILE C 661 " pdb=" CG1 ILE C 661 " pdb=" CG2 ILE C 661 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 5000 not shown) Planarity restraints: 5976 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 462 " -0.014 2.00e-02 2.50e+03 2.83e-02 8.00e+00 pdb=" C SER B 462 " 0.049 2.00e-02 2.50e+03 pdb=" O SER B 462 " -0.018 2.00e-02 2.50e+03 pdb=" N ILE B 463 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 660 " 0.013 2.00e-02 2.50e+03 2.61e-02 6.82e+00 pdb=" C LYS D 660 " -0.045 2.00e-02 2.50e+03 pdb=" O LYS D 660 " 0.017 2.00e-02 2.50e+03 pdb=" N ILE D 661 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 458 " 0.013 2.00e-02 2.50e+03 2.52e-02 6.34e+00 pdb=" C ILE B 458 " -0.044 2.00e-02 2.50e+03 pdb=" O ILE B 458 " 0.016 2.00e-02 2.50e+03 pdb=" N ILE B 459 " 0.015 2.00e-02 2.50e+03 ... (remaining 5973 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 397 2.63 - 3.19: 31273 3.19 - 3.76: 52758 3.76 - 4.33: 68558 4.33 - 4.90: 112387 Nonbonded interactions: 265373 Sorted by model distance: nonbonded pdb=" OH TYR C 687 " pdb=" OE2 GLU C 715 " model vdw 2.057 2.440 nonbonded pdb=" O GLU C 516 " pdb=" OG1 THR C 520 " model vdw 2.127 2.440 nonbonded pdb=" O ILE C 458 " pdb=" OG SER C 462 " model vdw 2.137 2.440 nonbonded pdb=" OH TYR B 414 " pdb=" OD1 ASN B 654 " model vdw 2.138 2.440 nonbonded pdb=" OD1 ASP C 630 " pdb=" OG SER D 991 " model vdw 2.147 2.440 ... (remaining 265368 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 22 through 142 or resid 145 through 463 or resid 465 throu \ gh 498 or resid 503 through 747 or resid 749 through 753 or (resid 754 and (name \ N or name CA or name C or name O or name CB )) or resid 755 through 787 or resi \ d 794 through 896 or resid 910 through 1005)) selection = (chain 'B' and (resid 22 through 463 or resid 465 through 566 or resid 578 throu \ gh 747 or resid 749 through 759 or (resid 760 and (name N or name CA or name C o \ r name O or name CB )) or resid 761 through 787 or resid 794 through 857 or resi \ d 861 through 896 or resid 910 through 911 or (resid 912 and (name N or name CA \ or name C or name O or name CB )) or resid 913 through 974 or resid 976 through \ 1005)) selection = (chain 'C' and (resid 22 through 142 or resid 145 through 463 or resid 465 throu \ gh 498 or resid 503 through 504 or (resid 505 and (name N or name CA or name C o \ r name O or name CB )) or resid 506 through 566 or resid 578 through 753 or (res \ id 754 and (name N or name CA or name C or name O or name CB )) or resid 755 thr \ ough 759 or (resid 760 and (name N or name CA or name C or name O or name CB )) \ or resid 761 through 787 or resid 794 through 857 or resid 861 through 896 or re \ sid 910 through 911 or (resid 912 and (name N or name CA or name C or name O or \ name CB )) or resid 913 through 974 or resid 976 through 1005)) selection = (chain 'D' and (resid 22 through 142 or resid 145 through 498 or resid 503 throu \ gh 504 or (resid 505 and (name N or name CA or name C or name O or name CB )) or \ resid 506 through 747 or resid 749 through 753 or (resid 754 and (name N or nam \ e CA or name C or name O or name CB )) or resid 755 through 759 or (resid 760 an \ d (name N or name CA or name C or name O or name CB )) or resid 761 through 787 \ or resid 794 through 857 or resid 861 through 896 or resid 910 through 1005)) } ncs_group { reference = chain 'E' selection = (chain 'F' and (resid 10 through 25 or (resid 26 and (name N or name CA or name \ C or name O or name CB )) or resid 27 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.410 Check model and map are aligned: 0.250 Set scattering table: 0.330 Process input model: 84.040 Find NCS groups from input model: 2.180 Set up NCS constraints: 0.160 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: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 34812 Z= 0.191 Angle : 0.639 11.761 46899 Z= 0.344 Chirality : 0.042 0.274 5003 Planarity : 0.004 0.059 5976 Dihedral : 17.913 89.311 12907 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.14 % Favored : 95.76 % Rotamer: Outliers : 2.33 % Allowed : 29.78 % Favored : 67.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.13), residues: 4060 helix: 0.97 (0.11), residues: 2380 sheet: -1.59 (0.35), residues: 214 loop : -1.17 (0.16), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 757 HIS 0.005 0.001 HIS C 979 PHE 0.038 0.001 PHE C 778 TYR 0.037 0.001 TYR D 888 ARG 0.013 0.000 ARG A 669 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 246 time to evaluate : 3.774 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: A 811 PHE cc_start: 0.8006 (OUTLIER) cc_final: 0.7738 (t80) REVERT: B 647 MET cc_start: 0.8087 (pmm) cc_final: 0.7751 (pmm) REVERT: C 651 ASP cc_start: 0.8686 (t70) cc_final: 0.8413 (t0) REVERT: C 751 ILE cc_start: 0.8529 (mp) cc_final: 0.8205 (tp) REVERT: D 519 MET cc_start: 0.8287 (mtm) cc_final: 0.7929 (mpp) outliers start: 87 outliers final: 68 residues processed: 316 average time/residue: 0.4025 time to fit residues: 216.9555 Evaluate side-chains 291 residues out of total 3775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 222 time to evaluate : 4.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 554 ASP Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 651 ASP Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 757 TRP Chi-restraints excluded: chain A residue 776 ASP Chi-restraints excluded: chain A residue 811 PHE Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 936 MET Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 992 ASN Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 604 SER Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 406 SER Chi-restraints excluded: chain C residue 467 ASN Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 584 VAL Chi-restraints excluded: chain C residue 713 ILE Chi-restraints excluded: chain C residue 964 ASP Chi-restraints excluded: chain C residue 988 VAL Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain D residue 367 CYS Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 395 CYS Chi-restraints excluded: chain D residue 431 SER Chi-restraints excluded: chain D residue 490 THR Chi-restraints excluded: chain D residue 492 PHE Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 786 HIS Chi-restraints excluded: chain D residue 797 ASN Chi-restraints excluded: chain D residue 828 THR Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain D residue 922 LEU Chi-restraints excluded: chain D residue 1004 PHE Chi-restraints excluded: chain E residue 13 ASP Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 110 PHE Chi-restraints excluded: chain F residue 107 SER Chi-restraints excluded: chain F residue 110 PHE Chi-restraints excluded: chain F residue 119 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 345 optimal weight: 5.9990 chunk 310 optimal weight: 2.9990 chunk 172 optimal weight: 8.9990 chunk 105 optimal weight: 0.2980 chunk 209 optimal weight: 0.9980 chunk 165 optimal weight: 8.9990 chunk 320 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 194 optimal weight: 1.9990 chunk 238 optimal weight: 2.9990 chunk 371 optimal weight: 0.0980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 765 ASN A 867 ASN ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 GLN B 382 ASN B 391 ASN B 415 HIS ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 529 ASN B 702 ASN B 782 GLN B 867 ASN B 990 ASN C 58 GLN C 115 ASN ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 HIS ** C 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 848 ASN C 867 ASN C 895 ASN D 224 ASN D 477 ASN D 521 ASN D 789 GLN D 832 GLN F 54 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.0764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 34812 Z= 0.157 Angle : 0.521 10.064 46899 Z= 0.269 Chirality : 0.039 0.167 5003 Planarity : 0.003 0.053 5976 Dihedral : 5.875 58.212 4613 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.11 % Favored : 95.81 % Rotamer: Outliers : 3.56 % Allowed : 27.59 % Favored : 68.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.14), residues: 4060 helix: 1.32 (0.11), residues: 2417 sheet: -1.46 (0.36), residues: 198 loop : -1.09 (0.16), residues: 1445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 143 HIS 0.004 0.001 HIS D 503 PHE 0.016 0.001 PHE A 916 TYR 0.028 0.001 TYR D 888 ARG 0.005 0.000 ARG D 669 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 3775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 252 time to evaluate : 3.905 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: A 22 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7619 (mt) REVERT: A 143 TRP cc_start: 0.7848 (t-100) cc_final: 0.7550 (t-100) REVERT: A 744 PHE cc_start: 0.8960 (OUTLIER) cc_final: 0.8227 (t80) REVERT: B 115 ASN cc_start: 0.6697 (OUTLIER) cc_final: 0.6462 (m-40) REVERT: B 342 VAL cc_start: 0.8180 (OUTLIER) cc_final: 0.7894 (t) REVERT: B 517 ARG cc_start: 0.8140 (ptt-90) cc_final: 0.7550 (ttp80) REVERT: B 599 CYS cc_start: 0.9091 (m) cc_final: 0.8881 (m) REVERT: B 647 MET cc_start: 0.8220 (pmm) cc_final: 0.7723 (pmm) REVERT: B 838 LEU cc_start: 0.6009 (OUTLIER) cc_final: 0.5726 (mm) REVERT: C 124 MET cc_start: 0.9244 (mmm) cc_final: 0.8976 (mmm) REVERT: C 396 MET cc_start: 0.7888 (OUTLIER) cc_final: 0.7522 (mmt) REVERT: C 599 CYS cc_start: 0.7716 (t) cc_final: 0.7044 (t) REVERT: C 651 ASP cc_start: 0.8670 (t70) cc_final: 0.8398 (t0) REVERT: C 741 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8692 (mm) REVERT: C 936 MET cc_start: 0.6358 (mmp) cc_final: 0.6053 (mmp) REVERT: C 993 ASP cc_start: 0.9079 (OUTLIER) cc_final: 0.8764 (t0) REVERT: D 825 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.7386 (mm) REVERT: D 940 TYR cc_start: 0.7512 (t80) cc_final: 0.7304 (t80) REVERT: E 110 PHE cc_start: 0.6916 (OUTLIER) cc_final: 0.6410 (p90) REVERT: F 47 CYS cc_start: 0.7811 (t) cc_final: 0.7387 (t) outliers start: 133 outliers final: 55 residues processed: 356 average time/residue: 0.4061 time to fit residues: 245.3953 Evaluate side-chains 297 residues out of total 3775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 232 time to evaluate : 3.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 554 ASP Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 776 ASP Chi-restraints excluded: chain A residue 786 HIS Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 926 ASN Chi-restraints excluded: chain A residue 936 MET Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 521 ASN Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 761 LEU Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 992 ASN Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 467 ASN Chi-restraints excluded: chain C residue 666 ASN Chi-restraints excluded: chain C residue 706 VAL Chi-restraints excluded: chain C residue 713 ILE Chi-restraints excluded: chain C residue 741 LEU Chi-restraints excluded: chain C residue 978 HIS Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 993 ASP Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 616 MET Chi-restraints excluded: chain D residue 786 HIS Chi-restraints excluded: chain D residue 797 ASN Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 828 THR Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 25 TRP Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 110 PHE Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 110 PHE Chi-restraints excluded: chain F residue 119 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 206 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 309 optimal weight: 0.5980 chunk 252 optimal weight: 2.9990 chunk 102 optimal weight: 8.9990 chunk 372 optimal weight: 5.9990 chunk 401 optimal weight: 9.9990 chunk 331 optimal weight: 3.9990 chunk 368 optimal weight: 0.8980 chunk 126 optimal weight: 2.9990 chunk 298 optimal weight: 1.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 521 ASN ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 HIS ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 848 ASN D 224 ASN ** F 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 34812 Z= 0.243 Angle : 0.533 8.323 46899 Z= 0.277 Chirality : 0.040 0.282 5003 Planarity : 0.003 0.050 5976 Dihedral : 4.993 57.713 4544 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.46 % Favored : 95.47 % Rotamer: Outliers : 4.06 % Allowed : 27.21 % Favored : 68.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.14), residues: 4060 helix: 1.37 (0.11), residues: 2414 sheet: -1.33 (0.37), residues: 188 loop : -1.12 (0.16), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 143 HIS 0.005 0.001 HIS F 88 PHE 0.037 0.001 PHE D 839 TYR 0.020 0.001 TYR D 888 ARG 0.003 0.000 ARG C 760 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 3775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 250 time to evaluate : 3.842 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: A 9 LYS cc_start: 0.9035 (mmmt) cc_final: 0.8594 (tptp) REVERT: A 22 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7559 (mt) REVERT: A 143 TRP cc_start: 0.7842 (t-100) cc_final: 0.7552 (t-100) REVERT: A 412 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7443 (tm) REVERT: A 711 GLN cc_start: 0.9351 (mt0) cc_final: 0.8625 (tm-30) REVERT: A 744 PHE cc_start: 0.8956 (OUTLIER) cc_final: 0.8086 (t80) REVERT: B 342 VAL cc_start: 0.8241 (OUTLIER) cc_final: 0.7942 (t) REVERT: B 460 LEU cc_start: 0.8762 (mm) cc_final: 0.8521 (pp) REVERT: B 517 ARG cc_start: 0.8127 (ptt-90) cc_final: 0.7563 (ttp80) REVERT: B 599 CYS cc_start: 0.9117 (m) cc_final: 0.8899 (m) REVERT: B 647 MET cc_start: 0.8119 (pmm) cc_final: 0.7678 (pmm) REVERT: B 838 LEU cc_start: 0.6027 (OUTLIER) cc_final: 0.5746 (mm) REVERT: B 913 MET cc_start: 0.5036 (mpp) cc_final: 0.4539 (mpp) REVERT: B 921 PHE cc_start: 0.4127 (t80) cc_final: 0.3913 (t80) REVERT: B 936 MET cc_start: 0.3796 (OUTLIER) cc_final: 0.3424 (mmt) REVERT: C 124 MET cc_start: 0.9234 (mmm) cc_final: 0.8960 (mmm) REVERT: C 134 TYR cc_start: 0.8910 (OUTLIER) cc_final: 0.8078 (p90) REVERT: C 247 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7784 (ttt180) REVERT: C 279 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7740 (tm-30) REVERT: C 396 MET cc_start: 0.8033 (OUTLIER) cc_final: 0.7654 (mmm) REVERT: C 651 ASP cc_start: 0.8737 (t70) cc_final: 0.8453 (t0) REVERT: C 936 MET cc_start: 0.6511 (mmp) cc_final: 0.6289 (mmp) REVERT: D 428 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.8399 (tp40) REVERT: D 825 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7391 (mm) REVERT: D 940 TYR cc_start: 0.7503 (t80) cc_final: 0.7182 (t80) REVERT: E 67 PHE cc_start: 0.8122 (m-80) cc_final: 0.7673 (m-80) REVERT: F 47 CYS cc_start: 0.7881 (t) cc_final: 0.7614 (t) outliers start: 152 outliers final: 78 residues processed: 371 average time/residue: 0.4127 time to fit residues: 259.9769 Evaluate side-chains 317 residues out of total 3775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 227 time to evaluate : 3.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 554 ASP Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 651 ASP Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 776 ASP Chi-restraints excluded: chain A residue 786 HIS Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 926 ASN Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 915 THR Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain B residue 992 ASN Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 502 ARG Chi-restraints excluded: chain C residue 504 TYR Chi-restraints excluded: chain C residue 666 ASN Chi-restraints excluded: chain C residue 706 VAL Chi-restraints excluded: chain C residue 713 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 428 GLN Chi-restraints excluded: chain D residue 432 ILE Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 492 PHE Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 616 MET Chi-restraints excluded: chain D residue 797 ASN Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 828 THR Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain D residue 848 ASN Chi-restraints excluded: chain D residue 988 VAL Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 25 TRP Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 110 PHE Chi-restraints excluded: chain F residue 112 ILE Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 119 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 367 optimal weight: 9.9990 chunk 279 optimal weight: 9.9990 chunk 193 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 177 optimal weight: 20.0000 chunk 249 optimal weight: 0.5980 chunk 373 optimal weight: 10.0000 chunk 395 optimal weight: 9.9990 chunk 195 optimal weight: 3.9990 chunk 353 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 483 GLN ** A 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 521 ASN ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 HIS B 765 ASN ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 391 ASN ** C 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 ASN D 224 ASN ** D 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 17 HIS ** F 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 34812 Z= 0.352 Angle : 0.592 13.768 46899 Z= 0.306 Chirality : 0.042 0.186 5003 Planarity : 0.004 0.050 5976 Dihedral : 5.002 57.423 4533 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.02 % Favored : 94.90 % Rotamer: Outliers : 4.73 % Allowed : 26.97 % Favored : 68.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.13), residues: 4060 helix: 1.22 (0.11), residues: 2429 sheet: -1.56 (0.36), residues: 188 loop : -1.20 (0.16), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 143 HIS 0.007 0.001 HIS B 67 PHE 0.041 0.002 PHE A 839 TYR 0.024 0.002 TYR D 888 ARG 0.004 0.000 ARG C 760 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 3775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 239 time to evaluate : 3.787 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: A 9 LYS cc_start: 0.9042 (mmmt) cc_final: 0.8615 (tptp) REVERT: A 22 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7513 (mt) REVERT: A 412 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7525 (tm) REVERT: A 711 GLN cc_start: 0.9360 (tt0) cc_final: 0.8662 (tm-30) REVERT: A 744 PHE cc_start: 0.8903 (OUTLIER) cc_final: 0.8143 (t80) REVERT: A 802 ARG cc_start: 0.8510 (ptt90) cc_final: 0.7911 (tmt-80) REVERT: B 599 CYS cc_start: 0.9128 (m) cc_final: 0.8853 (m) REVERT: B 838 LEU cc_start: 0.6050 (OUTLIER) cc_final: 0.5774 (mm) REVERT: B 921 PHE cc_start: 0.3959 (t80) cc_final: 0.3737 (t80) REVERT: B 954 PHE cc_start: 0.5544 (t80) cc_final: 0.5229 (t80) REVERT: C 124 MET cc_start: 0.9224 (mmm) cc_final: 0.8945 (mmm) REVERT: C 134 TYR cc_start: 0.9013 (OUTLIER) cc_final: 0.8140 (p90) REVERT: C 247 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7767 (ttt180) REVERT: C 347 VAL cc_start: 0.8887 (OUTLIER) cc_final: 0.8548 (m) REVERT: C 651 ASP cc_start: 0.8682 (t70) cc_final: 0.8377 (t0) REVERT: C 738 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8662 (tptt) REVERT: C 751 ILE cc_start: 0.8615 (mp) cc_final: 0.8316 (tp) REVERT: C 825 LEU cc_start: 0.6753 (OUTLIER) cc_final: 0.6225 (mt) REVERT: C 1005 ILE cc_start: 0.7794 (mm) cc_final: 0.7182 (pt) REVERT: D 200 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8343 (mm) REVERT: D 358 GLU cc_start: 0.9254 (OUTLIER) cc_final: 0.8976 (mp0) REVERT: D 396 MET cc_start: 0.6933 (OUTLIER) cc_final: 0.6423 (mmt) REVERT: D 399 ASP cc_start: 0.7755 (OUTLIER) cc_final: 0.7224 (t0) REVERT: D 797 ASN cc_start: 0.8259 (OUTLIER) cc_final: 0.7904 (p0) REVERT: D 825 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7434 (mm) REVERT: D 940 TYR cc_start: 0.7535 (t80) cc_final: 0.7218 (t80) REVERT: E 67 PHE cc_start: 0.8107 (m-80) cc_final: 0.7717 (m-80) REVERT: F 47 CYS cc_start: 0.7808 (t) cc_final: 0.7602 (t) outliers start: 177 outliers final: 111 residues processed: 385 average time/residue: 0.4207 time to fit residues: 272.8002 Evaluate side-chains 351 residues out of total 3775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 225 time to evaluate : 3.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 521 ASN Chi-restraints excluded: chain A residue 554 ASP Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 646 PHE Chi-restraints excluded: chain A residue 651 ASP Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 776 ASP Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 926 ASN Chi-restraints excluded: chain A residue 936 MET Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 992 ASN Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 145 ARG Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 521 ASN Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 643 SER Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 765 ASN Chi-restraints excluded: chain B residue 802 ARG Chi-restraints excluded: chain B residue 814 ASN Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain B residue 992 ASN Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 467 ASN Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 504 TYR Chi-restraints excluded: chain C residue 579 SER Chi-restraints excluded: chain C residue 648 GLU Chi-restraints excluded: chain C residue 666 ASN Chi-restraints excluded: chain C residue 706 VAL Chi-restraints excluded: chain C residue 713 ILE Chi-restraints excluded: chain C residue 738 LYS Chi-restraints excluded: chain C residue 755 TYR Chi-restraints excluded: chain C residue 825 LEU Chi-restraints excluded: chain C residue 953 LYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 358 GLU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 395 CYS Chi-restraints excluded: chain D residue 396 MET Chi-restraints excluded: chain D residue 399 ASP Chi-restraints excluded: chain D residue 432 ILE Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 492 PHE Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 584 VAL Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 736 ILE Chi-restraints excluded: chain D residue 797 ASN Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 828 THR Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain D residue 848 ASN Chi-restraints excluded: chain D residue 938 ASP Chi-restraints excluded: chain D residue 988 VAL Chi-restraints excluded: chain E residue 42 CYS Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 112 ILE Chi-restraints excluded: chain F residue 119 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 329 optimal weight: 8.9990 chunk 224 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 294 optimal weight: 4.9990 chunk 163 optimal weight: 2.9990 chunk 337 optimal weight: 0.8980 chunk 273 optimal weight: 0.0170 chunk 0 optimal weight: 10.0000 chunk 201 optimal weight: 1.9990 chunk 354 optimal weight: 0.6980 chunk 99 optimal weight: 0.9980 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 521 ASN ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 765 ASN ** B 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 391 ASN ** C 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 829 GLN ** D 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 34812 Z= 0.139 Angle : 0.508 11.232 46899 Z= 0.262 Chirality : 0.039 0.163 5003 Planarity : 0.003 0.050 5976 Dihedral : 4.681 56.496 4529 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.67 % Favored : 96.26 % Rotamer: Outliers : 3.26 % Allowed : 28.44 % Favored : 68.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.14), residues: 4060 helix: 1.43 (0.11), residues: 2423 sheet: -1.43 (0.36), residues: 196 loop : -1.11 (0.16), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 143 HIS 0.005 0.001 HIS F 88 PHE 0.021 0.001 PHE D 839 TYR 0.021 0.001 TYR D 888 ARG 0.004 0.000 ARG C 502 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 3775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 264 time to evaluate : 3.875 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: A 9 LYS cc_start: 0.9064 (mmmt) cc_final: 0.8635 (tptp) REVERT: A 22 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7700 (mt) REVERT: A 143 TRP cc_start: 0.7805 (t-100) cc_final: 0.7550 (t-100) REVERT: A 188 ASP cc_start: 0.9037 (OUTLIER) cc_final: 0.8754 (m-30) REVERT: A 412 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7504 (tm) REVERT: A 744 PHE cc_start: 0.8957 (OUTLIER) cc_final: 0.8243 (t80) REVERT: A 802 ARG cc_start: 0.8506 (ptt90) cc_final: 0.7900 (tmt-80) REVERT: A 936 MET cc_start: 0.4692 (OUTLIER) cc_final: 0.4221 (ptp) REVERT: B 326 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.8084 (ptt180) REVERT: B 599 CYS cc_start: 0.9132 (m) cc_final: 0.8829 (m) REVERT: B 647 MET cc_start: 0.8337 (pmm) cc_final: 0.7799 (pmm) REVERT: B 648 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7583 (mp0) REVERT: B 753 LYS cc_start: 0.8728 (mmtm) cc_final: 0.8525 (mmtt) REVERT: B 838 LEU cc_start: 0.6092 (OUTLIER) cc_final: 0.5829 (mm) REVERT: B 954 PHE cc_start: 0.5465 (t80) cc_final: 0.5148 (t80) REVERT: C 124 MET cc_start: 0.9248 (mmm) cc_final: 0.8955 (mmm) REVERT: C 134 TYR cc_start: 0.8950 (OUTLIER) cc_final: 0.7936 (p90) REVERT: C 247 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7741 (ttt180) REVERT: C 279 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7654 (tm-30) REVERT: C 396 MET cc_start: 0.8028 (OUTLIER) cc_final: 0.7702 (mmm) REVERT: C 421 MET cc_start: 0.8599 (pmt) cc_final: 0.8066 (pmt) REVERT: C 599 CYS cc_start: 0.7883 (t) cc_final: 0.7224 (t) REVERT: C 651 ASP cc_start: 0.8646 (t70) cc_final: 0.8362 (t0) REVERT: C 825 LEU cc_start: 0.6681 (OUTLIER) cc_final: 0.6173 (mt) REVERT: C 1005 ILE cc_start: 0.7666 (mm) cc_final: 0.6987 (pt) REVERT: D 147 LYS cc_start: 0.5325 (tptp) cc_final: 0.4992 (tptt) REVERT: D 188 ASP cc_start: 0.8699 (t0) cc_final: 0.8247 (t0) REVERT: D 358 GLU cc_start: 0.9223 (OUTLIER) cc_final: 0.8953 (mp0) REVERT: D 396 MET cc_start: 0.6423 (OUTLIER) cc_final: 0.5981 (mtt) REVERT: D 825 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.7442 (mm) REVERT: D 940 TYR cc_start: 0.7475 (t80) cc_final: 0.7080 (t80) REVERT: E 16 TYR cc_start: 0.7108 (t80) cc_final: 0.6729 (t80) REVERT: E 47 CYS cc_start: 0.6397 (OUTLIER) cc_final: 0.5501 (t) REVERT: E 67 PHE cc_start: 0.8065 (m-80) cc_final: 0.7750 (m-80) outliers start: 122 outliers final: 59 residues processed: 357 average time/residue: 0.4273 time to fit residues: 258.0638 Evaluate side-chains 315 residues out of total 3775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 239 time to evaluate : 3.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 554 ASP Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 926 ASN Chi-restraints excluded: chain A residue 936 MET Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 326 ARG Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 435 ASP Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 802 ARG Chi-restraints excluded: chain B residue 814 ASN Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 940 TYR Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 467 ASN Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 504 TYR Chi-restraints excluded: chain C residue 666 ASN Chi-restraints excluded: chain C residue 825 LEU Chi-restraints excluded: chain C residue 953 LYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 358 GLU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain D residue 396 MET Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 647 MET Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 828 THR Chi-restraints excluded: chain D residue 838 LEU Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain D residue 848 ASN Chi-restraints excluded: chain D residue 938 ASP Chi-restraints excluded: chain D residue 988 VAL Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 42 CYS Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 119 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 133 optimal weight: 6.9990 chunk 356 optimal weight: 0.9990 chunk 78 optimal weight: 8.9990 chunk 232 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 395 optimal weight: 3.9990 chunk 328 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 130 optimal weight: 0.6980 chunk 207 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 483 GLN ** A 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 351 ASN ** C 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 GLN D 786 HIS ** D 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 34812 Z= 0.244 Angle : 0.535 10.903 46899 Z= 0.277 Chirality : 0.040 0.183 5003 Planarity : 0.003 0.050 5976 Dihedral : 4.460 59.661 4517 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.66 % Favored : 95.27 % Rotamer: Outliers : 4.12 % Allowed : 27.83 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.14), residues: 4060 helix: 1.38 (0.11), residues: 2430 sheet: -1.35 (0.37), residues: 186 loop : -1.14 (0.16), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 919 HIS 0.005 0.001 HIS B 67 PHE 0.021 0.001 PHE D 839 TYR 0.025 0.001 TYR D 888 ARG 0.009 0.000 ARG D 819 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 236 time to evaluate : 3.897 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: A 9 LYS cc_start: 0.9091 (mmmt) cc_final: 0.8644 (tptp) REVERT: A 19 PHE cc_start: 0.8705 (OUTLIER) cc_final: 0.8470 (t80) REVERT: A 143 TRP cc_start: 0.7829 (t-100) cc_final: 0.7547 (t-100) REVERT: A 412 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7576 (tm) REVERT: A 744 PHE cc_start: 0.8936 (OUTLIER) cc_final: 0.8234 (t80) REVERT: A 802 ARG cc_start: 0.8474 (ptt90) cc_final: 0.7884 (tmt-80) REVERT: A 936 MET cc_start: 0.4890 (OUTLIER) cc_final: 0.3859 (ptm) REVERT: B 283 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8197 (tt) REVERT: B 326 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.7638 (ptm160) REVERT: B 460 LEU cc_start: 0.8630 (mm) cc_final: 0.8339 (pp) REVERT: B 517 ARG cc_start: 0.8128 (ptt-90) cc_final: 0.7541 (ttp80) REVERT: B 599 CYS cc_start: 0.9127 (m) cc_final: 0.8847 (m) REVERT: B 648 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7562 (mp0) REVERT: B 838 LEU cc_start: 0.6032 (OUTLIER) cc_final: 0.5747 (mm) REVERT: B 921 PHE cc_start: 0.3964 (t80) cc_final: 0.3701 (t80) REVERT: C 124 MET cc_start: 0.9235 (mmm) cc_final: 0.8934 (mmm) REVERT: C 134 TYR cc_start: 0.8965 (OUTLIER) cc_final: 0.8007 (p90) REVERT: C 247 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7563 (ttt180) REVERT: C 279 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7699 (tm-30) REVERT: C 396 MET cc_start: 0.8071 (OUTLIER) cc_final: 0.7804 (mmm) REVERT: C 421 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.8318 (pmt) REVERT: C 651 ASP cc_start: 0.8710 (t70) cc_final: 0.8390 (t0) REVERT: C 738 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8682 (tptt) REVERT: C 825 LEU cc_start: 0.6645 (OUTLIER) cc_final: 0.6147 (mt) REVERT: C 1005 ILE cc_start: 0.7734 (mm) cc_final: 0.7046 (pt) REVERT: D 188 ASP cc_start: 0.8751 (OUTLIER) cc_final: 0.8380 (t0) REVERT: D 358 GLU cc_start: 0.9240 (OUTLIER) cc_final: 0.8989 (mp0) REVERT: D 396 MET cc_start: 0.6658 (OUTLIER) cc_final: 0.6102 (mmt) REVERT: D 543 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7320 (tp30) REVERT: D 797 ASN cc_start: 0.8238 (OUTLIER) cc_final: 0.7989 (p0) REVERT: D 825 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7369 (mm) REVERT: D 940 TYR cc_start: 0.7532 (t80) cc_final: 0.7137 (t80) REVERT: E 67 PHE cc_start: 0.8135 (m-80) cc_final: 0.7813 (m-80) REVERT: F 51 TYR cc_start: 0.8817 (m-10) cc_final: 0.8494 (m-10) REVERT: F 73 LEU cc_start: 0.8053 (mt) cc_final: 0.7834 (mp) outliers start: 154 outliers final: 90 residues processed: 360 average time/residue: 0.4306 time to fit residues: 261.6766 Evaluate side-chains 339 residues out of total 3775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 228 time to evaluate : 4.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 554 ASP Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 651 ASP Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 926 ASN Chi-restraints excluded: chain A residue 936 MET Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 145 ARG Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 326 ARG Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 435 ASP Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 521 ASN Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 643 SER Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 802 ARG Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 464 ASP Chi-restraints excluded: chain C residue 467 ASN Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 504 TYR Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 584 VAL Chi-restraints excluded: chain C residue 666 ASN Chi-restraints excluded: chain C residue 738 LYS Chi-restraints excluded: chain C residue 755 TYR Chi-restraints excluded: chain C residue 787 ILE Chi-restraints excluded: chain C residue 825 LEU Chi-restraints excluded: chain C residue 953 LYS Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain D residue 188 ASP Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 358 GLU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 396 MET Chi-restraints excluded: chain D residue 492 PHE Chi-restraints excluded: chain D residue 543 GLU Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 647 MET Chi-restraints excluded: chain D residue 797 ASN Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 828 THR Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain D residue 848 ASN Chi-restraints excluded: chain D residue 938 ASP Chi-restraints excluded: chain D residue 988 VAL Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 42 CYS Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 112 ILE Chi-restraints excluded: chain F residue 119 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 381 optimal weight: 0.1980 chunk 44 optimal weight: 0.7980 chunk 225 optimal weight: 3.9990 chunk 288 optimal weight: 4.9990 chunk 223 optimal weight: 0.8980 chunk 333 optimal weight: 0.5980 chunk 220 optimal weight: 1.9990 chunk 394 optimal weight: 50.0000 chunk 246 optimal weight: 0.8980 chunk 240 optimal weight: 0.0070 chunk 182 optimal weight: 1.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 ASN ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 961 ASN ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 351 ASN C 591 ASN D 786 HIS F 54 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 34812 Z= 0.131 Angle : 0.513 10.890 46899 Z= 0.261 Chirality : 0.039 0.237 5003 Planarity : 0.003 0.050 5976 Dihedral : 4.222 48.631 4515 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.79 % Favored : 96.11 % Rotamer: Outliers : 3.15 % Allowed : 28.55 % Favored : 68.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.14), residues: 4060 helix: 1.48 (0.11), residues: 2421 sheet: -1.40 (0.37), residues: 184 loop : -1.06 (0.16), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 143 HIS 0.005 0.001 HIS D 786 PHE 0.022 0.001 PHE F 59 TYR 0.026 0.001 TYR D 888 ARG 0.005 0.000 ARG A 247 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 247 time to evaluate : 3.820 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: A 9 LYS cc_start: 0.9065 (mmmt) cc_final: 0.8636 (tptp) REVERT: A 22 LEU cc_start: 0.7725 (mt) cc_final: 0.7491 (mt) REVERT: A 143 TRP cc_start: 0.7798 (t-100) cc_final: 0.7529 (t-100) REVERT: A 188 ASP cc_start: 0.9045 (OUTLIER) cc_final: 0.8754 (m-30) REVERT: A 223 TYR cc_start: 0.7561 (t80) cc_final: 0.7308 (t80) REVERT: A 412 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7559 (tm) REVERT: A 678 PHE cc_start: 0.8391 (OUTLIER) cc_final: 0.8060 (t80) REVERT: A 744 PHE cc_start: 0.8941 (OUTLIER) cc_final: 0.8243 (t80) REVERT: A 802 ARG cc_start: 0.8479 (ptt90) cc_final: 0.7822 (ttt180) REVERT: A 936 MET cc_start: 0.5079 (OUTLIER) cc_final: 0.3927 (ptm) REVERT: A 1004 PHE cc_start: 0.7172 (OUTLIER) cc_final: 0.6891 (t80) REVERT: B 283 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8121 (tt) REVERT: B 326 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.7640 (ptm160) REVERT: B 342 VAL cc_start: 0.8204 (OUTLIER) cc_final: 0.7907 (t) REVERT: B 460 LEU cc_start: 0.8711 (mm) cc_final: 0.8423 (pp) REVERT: B 517 ARG cc_start: 0.8024 (ptt-90) cc_final: 0.7483 (ttp80) REVERT: B 599 CYS cc_start: 0.9123 (m) cc_final: 0.8831 (m) REVERT: B 621 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8123 (pt0) REVERT: B 647 MET cc_start: 0.8225 (pmm) cc_final: 0.7657 (pmm) REVERT: B 648 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7535 (mp0) REVERT: B 838 LEU cc_start: 0.6103 (OUTLIER) cc_final: 0.5840 (mm) REVERT: B 921 PHE cc_start: 0.4073 (t80) cc_final: 0.3775 (t80) REVERT: C 124 MET cc_start: 0.9254 (mmm) cc_final: 0.8942 (mmm) REVERT: C 134 TYR cc_start: 0.8949 (OUTLIER) cc_final: 0.8057 (p90) REVERT: C 247 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7775 (ttt180) REVERT: C 279 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7602 (tm-30) REVERT: C 396 MET cc_start: 0.8073 (OUTLIER) cc_final: 0.7723 (mmm) REVERT: C 421 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.8368 (pmm) REVERT: C 599 CYS cc_start: 0.7907 (t) cc_final: 0.7236 (t) REVERT: C 651 ASP cc_start: 0.8651 (t70) cc_final: 0.8334 (t0) REVERT: C 825 LEU cc_start: 0.6670 (OUTLIER) cc_final: 0.6190 (mt) REVERT: C 892 ARG cc_start: 0.8287 (mmp-170) cc_final: 0.7486 (ptp-170) REVERT: D 147 LYS cc_start: 0.5375 (tptp) cc_final: 0.5045 (tptt) REVERT: D 188 ASP cc_start: 0.8689 (OUTLIER) cc_final: 0.8201 (t0) REVERT: D 358 GLU cc_start: 0.9218 (OUTLIER) cc_final: 0.8960 (mp0) REVERT: D 396 MET cc_start: 0.6329 (OUTLIER) cc_final: 0.5892 (mtt) REVERT: D 825 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7438 (mm) REVERT: D 930 MET cc_start: 0.8201 (pmm) cc_final: 0.7741 (pmm) REVERT: D 940 TYR cc_start: 0.7501 (t80) cc_final: 0.7077 (t80) REVERT: E 16 TYR cc_start: 0.7016 (t80) cc_final: 0.6667 (t80) REVERT: E 47 CYS cc_start: 0.6425 (OUTLIER) cc_final: 0.5508 (t) REVERT: E 67 PHE cc_start: 0.8114 (m-80) cc_final: 0.7900 (m-80) REVERT: F 51 TYR cc_start: 0.8805 (m-10) cc_final: 0.8518 (m-10) outliers start: 118 outliers final: 70 residues processed: 340 average time/residue: 0.4372 time to fit residues: 249.4764 Evaluate side-chains 328 residues out of total 3775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 236 time to evaluate : 3.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 554 ASP Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 678 PHE Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 810 HIS Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 926 ASN Chi-restraints excluded: chain A residue 936 MET Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 1004 PHE Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 145 ARG Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 326 ARG Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 435 ASP Chi-restraints excluded: chain B residue 469 CYS Chi-restraints excluded: chain B residue 521 ASN Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 802 ARG Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 464 ASP Chi-restraints excluded: chain C residue 467 ASN Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 504 TYR Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 584 VAL Chi-restraints excluded: chain C residue 666 ASN Chi-restraints excluded: chain C residue 755 TYR Chi-restraints excluded: chain C residue 825 LEU Chi-restraints excluded: chain C residue 953 LYS Chi-restraints excluded: chain D residue 188 ASP Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 358 GLU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 396 MET Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 647 MET Chi-restraints excluded: chain D residue 786 HIS Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 828 THR Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain D residue 848 ASN Chi-restraints excluded: chain D residue 938 ASP Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 42 CYS Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 119 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 243 optimal weight: 2.9990 chunk 157 optimal weight: 9.9990 chunk 235 optimal weight: 0.6980 chunk 118 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 250 optimal weight: 0.7980 chunk 268 optimal weight: 7.9990 chunk 194 optimal weight: 0.0010 chunk 36 optimal weight: 6.9990 chunk 309 optimal weight: 1.9990 overall best weight: 1.0990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 ASN ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 810 HIS ** D 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34812 Z= 0.169 Angle : 0.522 10.790 46899 Z= 0.264 Chirality : 0.039 0.285 5003 Planarity : 0.003 0.051 5976 Dihedral : 4.160 48.089 4513 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.24 % Favored : 95.67 % Rotamer: Outliers : 3.29 % Allowed : 28.63 % Favored : 68.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.14), residues: 4060 helix: 1.51 (0.11), residues: 2421 sheet: -1.37 (0.37), residues: 176 loop : -1.06 (0.16), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 919 HIS 0.014 0.001 HIS D 786 PHE 0.030 0.001 PHE B 949 TYR 0.026 0.001 TYR D 888 ARG 0.003 0.000 ARG C 760 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 3775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 240 time to evaluate : 3.795 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: A 9 LYS cc_start: 0.9073 (mmmt) cc_final: 0.8638 (tptp) REVERT: A 22 LEU cc_start: 0.7652 (mt) cc_final: 0.7376 (mt) REVERT: A 143 TRP cc_start: 0.7794 (t-100) cc_final: 0.7515 (t-100) REVERT: A 188 ASP cc_start: 0.9055 (OUTLIER) cc_final: 0.8765 (m-30) REVERT: A 223 TYR cc_start: 0.7651 (t80) cc_final: 0.7388 (t80) REVERT: A 412 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7590 (tm) REVERT: A 678 PHE cc_start: 0.8412 (OUTLIER) cc_final: 0.8128 (t80) REVERT: A 744 PHE cc_start: 0.8940 (OUTLIER) cc_final: 0.8277 (t80) REVERT: A 936 MET cc_start: 0.4888 (OUTLIER) cc_final: 0.3816 (ptm) REVERT: A 1004 PHE cc_start: 0.7138 (OUTLIER) cc_final: 0.6870 (t80) REVERT: B 283 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8147 (tt) REVERT: B 326 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.7604 (ptm160) REVERT: B 460 LEU cc_start: 0.8724 (mm) cc_final: 0.8446 (pp) REVERT: B 599 CYS cc_start: 0.9120 (m) cc_final: 0.8827 (m) REVERT: B 621 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8133 (pt0) REVERT: B 647 MET cc_start: 0.8177 (pmm) cc_final: 0.7088 (pmm) REVERT: B 648 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7703 (mm-30) REVERT: B 838 LEU cc_start: 0.6075 (OUTLIER) cc_final: 0.5813 (mm) REVERT: C 124 MET cc_start: 0.9256 (mmm) cc_final: 0.8952 (mmm) REVERT: C 134 TYR cc_start: 0.8955 (OUTLIER) cc_final: 0.8066 (p90) REVERT: C 247 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7759 (ttt180) REVERT: C 279 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7560 (tm-30) REVERT: C 396 MET cc_start: 0.8053 (OUTLIER) cc_final: 0.7719 (mmm) REVERT: C 421 MET cc_start: 0.8660 (OUTLIER) cc_final: 0.8369 (pmm) REVERT: C 578 MET cc_start: 0.8727 (tpp) cc_final: 0.8366 (tpp) REVERT: C 599 CYS cc_start: 0.8083 (t) cc_final: 0.7405 (t) REVERT: C 651 ASP cc_start: 0.8685 (t70) cc_final: 0.8400 (t0) REVERT: C 825 LEU cc_start: 0.6677 (OUTLIER) cc_final: 0.6196 (mt) REVERT: C 892 ARG cc_start: 0.8275 (mmp-170) cc_final: 0.7523 (ptp-170) REVERT: D 147 LYS cc_start: 0.5444 (tptp) cc_final: 0.5099 (tptt) REVERT: D 188 ASP cc_start: 0.8709 (OUTLIER) cc_final: 0.8238 (t0) REVERT: D 358 GLU cc_start: 0.9228 (OUTLIER) cc_final: 0.8978 (mp0) REVERT: D 396 MET cc_start: 0.6352 (OUTLIER) cc_final: 0.5911 (mtt) REVERT: D 786 HIS cc_start: 0.7056 (OUTLIER) cc_final: 0.5972 (t-90) REVERT: D 797 ASN cc_start: 0.8142 (OUTLIER) cc_final: 0.7900 (p0) REVERT: D 825 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7438 (mm) REVERT: D 930 MET cc_start: 0.8251 (pmm) cc_final: 0.7818 (pmm) REVERT: D 940 TYR cc_start: 0.7452 (t80) cc_final: 0.7001 (t80) REVERT: E 16 TYR cc_start: 0.7051 (t80) cc_final: 0.6678 (t80) REVERT: E 67 PHE cc_start: 0.8163 (m-80) cc_final: 0.7961 (m-80) REVERT: F 51 TYR cc_start: 0.8834 (m-10) cc_final: 0.8540 (m-10) REVERT: F 73 LEU cc_start: 0.8122 (mt) cc_final: 0.7858 (mp) outliers start: 123 outliers final: 82 residues processed: 340 average time/residue: 0.4337 time to fit residues: 248.5837 Evaluate side-chains 336 residues out of total 3775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 232 time to evaluate : 3.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 554 ASP Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 678 PHE Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 810 HIS Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 926 ASN Chi-restraints excluded: chain A residue 936 MET Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 1004 PHE Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 145 ARG Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 326 ARG Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 435 ASP Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 521 ASN Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 643 SER Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 802 ARG Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 961 ASN Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 464 ASP Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 504 TYR Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 579 SER Chi-restraints excluded: chain C residue 584 VAL Chi-restraints excluded: chain C residue 666 ASN Chi-restraints excluded: chain C residue 755 TYR Chi-restraints excluded: chain C residue 787 ILE Chi-restraints excluded: chain C residue 825 LEU Chi-restraints excluded: chain C residue 953 LYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain D residue 188 ASP Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 358 GLU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 395 CYS Chi-restraints excluded: chain D residue 396 MET Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 786 HIS Chi-restraints excluded: chain D residue 797 ASN Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 828 THR Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain D residue 848 ASN Chi-restraints excluded: chain D residue 938 ASP Chi-restraints excluded: chain D residue 988 VAL Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 42 CYS Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 119 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 358 optimal weight: 6.9990 chunk 377 optimal weight: 20.0000 chunk 344 optimal weight: 0.7980 chunk 367 optimal weight: 6.9990 chunk 221 optimal weight: 0.9980 chunk 160 optimal weight: 4.9990 chunk 288 optimal weight: 0.9980 chunk 112 optimal weight: 0.0980 chunk 331 optimal weight: 0.7980 chunk 347 optimal weight: 0.9980 chunk 366 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 ASN ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 810 HIS D 786 HIS ** D 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 34812 Z= 0.143 Angle : 0.522 15.408 46899 Z= 0.261 Chirality : 0.038 0.231 5003 Planarity : 0.003 0.050 5976 Dihedral : 4.096 48.193 4513 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.87 % Favored : 96.03 % Rotamer: Outliers : 3.13 % Allowed : 28.90 % Favored : 67.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.14), residues: 4060 helix: 1.55 (0.11), residues: 2417 sheet: -1.37 (0.37), residues: 176 loop : -1.01 (0.16), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 143 HIS 0.007 0.001 HIS D 786 PHE 0.021 0.001 PHE F 59 TYR 0.026 0.001 TYR D 888 ARG 0.004 0.000 ARG B 517 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 241 time to evaluate : 3.700 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: A 9 LYS cc_start: 0.9075 (mmmt) cc_final: 0.8642 (tptp) REVERT: A 22 LEU cc_start: 0.7683 (mt) cc_final: 0.7386 (mt) REVERT: A 143 TRP cc_start: 0.7766 (t-100) cc_final: 0.7502 (t-100) REVERT: A 188 ASP cc_start: 0.9024 (OUTLIER) cc_final: 0.8749 (m-30) REVERT: A 223 TYR cc_start: 0.7636 (t80) cc_final: 0.7371 (t80) REVERT: A 412 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7601 (tm) REVERT: A 678 PHE cc_start: 0.8363 (OUTLIER) cc_final: 0.8080 (t80) REVERT: A 744 PHE cc_start: 0.8940 (OUTLIER) cc_final: 0.8276 (t80) REVERT: A 936 MET cc_start: 0.5055 (OUTLIER) cc_final: 0.4204 (ptm) REVERT: A 1004 PHE cc_start: 0.7081 (OUTLIER) cc_final: 0.6816 (t80) REVERT: B 283 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8152 (tt) REVERT: B 326 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.7603 (ptm160) REVERT: B 460 LEU cc_start: 0.8672 (mm) cc_final: 0.8393 (pp) REVERT: B 517 ARG cc_start: 0.8065 (ptt-90) cc_final: 0.7559 (ttp80) REVERT: B 599 CYS cc_start: 0.9119 (m) cc_final: 0.8814 (m) REVERT: B 621 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8138 (pt0) REVERT: B 647 MET cc_start: 0.8172 (pmm) cc_final: 0.7645 (pmm) REVERT: B 648 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7644 (mp0) REVERT: B 838 LEU cc_start: 0.6068 (OUTLIER) cc_final: 0.5807 (mm) REVERT: B 919 TRP cc_start: 0.7541 (m-10) cc_final: 0.7319 (m-10) REVERT: B 930 MET cc_start: 0.2950 (ptt) cc_final: 0.2537 (mmt) REVERT: C 124 MET cc_start: 0.9258 (mmm) cc_final: 0.8962 (mmm) REVERT: C 134 TYR cc_start: 0.8945 (OUTLIER) cc_final: 0.8026 (p90) REVERT: C 247 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7739 (ttt180) REVERT: C 279 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7565 (tm-30) REVERT: C 396 MET cc_start: 0.8089 (OUTLIER) cc_final: 0.7741 (mmm) REVERT: C 421 MET cc_start: 0.8652 (OUTLIER) cc_final: 0.8360 (pmm) REVERT: C 460 LEU cc_start: 0.8854 (mt) cc_final: 0.8624 (mm) REVERT: C 578 MET cc_start: 0.8637 (tpp) cc_final: 0.8286 (tpp) REVERT: C 599 CYS cc_start: 0.8010 (t) cc_final: 0.7331 (t) REVERT: C 651 ASP cc_start: 0.8683 (t70) cc_final: 0.8386 (t0) REVERT: C 825 LEU cc_start: 0.6645 (OUTLIER) cc_final: 0.6164 (mt) REVERT: C 892 ARG cc_start: 0.8299 (mmp-170) cc_final: 0.7579 (ptp-170) REVERT: D 147 LYS cc_start: 0.5444 (tptp) cc_final: 0.5107 (tptt) REVERT: D 188 ASP cc_start: 0.8694 (OUTLIER) cc_final: 0.8217 (t0) REVERT: D 358 GLU cc_start: 0.9200 (OUTLIER) cc_final: 0.8956 (mp0) REVERT: D 396 MET cc_start: 0.6317 (OUTLIER) cc_final: 0.5886 (mtt) REVERT: D 825 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7581 (mm) REVERT: D 930 MET cc_start: 0.8215 (pmm) cc_final: 0.7775 (pmm) REVERT: D 940 TYR cc_start: 0.7496 (t80) cc_final: 0.7048 (t80) REVERT: E 16 TYR cc_start: 0.7061 (t80) cc_final: 0.6694 (t80) REVERT: F 51 TYR cc_start: 0.8843 (m-10) cc_final: 0.8561 (m-10) outliers start: 117 outliers final: 83 residues processed: 334 average time/residue: 0.4391 time to fit residues: 246.1310 Evaluate side-chains 338 residues out of total 3775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 235 time to evaluate : 3.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 678 PHE Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 810 HIS Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 926 ASN Chi-restraints excluded: chain A residue 936 MET Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 1004 PHE Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 145 ARG Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 326 ARG Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 435 ASP Chi-restraints excluded: chain B residue 469 CYS Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 521 ASN Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 643 SER Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 709 TYR Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 802 ARG Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 961 ASN Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 464 ASP Chi-restraints excluded: chain C residue 467 ASN Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 504 TYR Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 584 VAL Chi-restraints excluded: chain C residue 666 ASN Chi-restraints excluded: chain C residue 825 LEU Chi-restraints excluded: chain C residue 953 LYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain D residue 188 ASP Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 358 GLU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 395 CYS Chi-restraints excluded: chain D residue 396 MET Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 786 HIS Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 828 THR Chi-restraints excluded: chain D residue 848 ASN Chi-restraints excluded: chain D residue 885 ILE Chi-restraints excluded: chain D residue 938 ASP Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 42 CYS Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 119 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 241 optimal weight: 4.9990 chunk 388 optimal weight: 30.0000 chunk 237 optimal weight: 3.9990 chunk 184 optimal weight: 20.0000 chunk 270 optimal weight: 7.9990 chunk 407 optimal weight: 3.9990 chunk 375 optimal weight: 5.9990 chunk 324 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 250 optimal weight: 0.9980 chunk 198 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 521 ASN ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 ASN ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 351 ASN ** C 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 810 HIS ** D 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 34812 Z= 0.232 Angle : 0.558 14.632 46899 Z= 0.281 Chirality : 0.040 0.201 5003 Planarity : 0.003 0.053 5976 Dihedral : 4.177 47.389 4509 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.83 % Favored : 95.07 % Rotamer: Outliers : 3.15 % Allowed : 29.06 % Favored : 67.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.14), residues: 4060 helix: 1.48 (0.11), residues: 2430 sheet: -1.31 (0.38), residues: 166 loop : -1.08 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 919 HIS 0.012 0.001 HIS D 786 PHE 0.019 0.001 PHE F 59 TYR 0.027 0.001 TYR D 888 ARG 0.003 0.000 ARG C 760 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 3775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 236 time to evaluate : 4.037 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: A 9 LYS cc_start: 0.9073 (mmmt) cc_final: 0.8640 (tptp) REVERT: A 22 LEU cc_start: 0.7699 (mt) cc_final: 0.7405 (mt) REVERT: A 143 TRP cc_start: 0.7783 (t-100) cc_final: 0.7487 (t-100) REVERT: A 188 ASP cc_start: 0.9084 (OUTLIER) cc_final: 0.8809 (m-30) REVERT: A 412 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7612 (tm) REVERT: A 744 PHE cc_start: 0.8942 (OUTLIER) cc_final: 0.8232 (t80) REVERT: A 802 ARG cc_start: 0.8494 (ptt90) cc_final: 0.7940 (tmt-80) REVERT: A 936 MET cc_start: 0.5272 (OUTLIER) cc_final: 0.4265 (ptm) REVERT: A 1004 PHE cc_start: 0.6867 (OUTLIER) cc_final: 0.6622 (t80) REVERT: B 283 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8191 (tt) REVERT: B 326 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.7630 (ptm160) REVERT: B 460 LEU cc_start: 0.8777 (mm) cc_final: 0.8519 (pp) REVERT: B 517 ARG cc_start: 0.7982 (ptt-90) cc_final: 0.7496 (ttp80) REVERT: B 599 CYS cc_start: 0.9112 (m) cc_final: 0.8819 (m) REVERT: B 621 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8120 (pt0) REVERT: B 648 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7671 (mm-30) REVERT: B 838 LEU cc_start: 0.6075 (OUTLIER) cc_final: 0.5811 (mm) REVERT: B 930 MET cc_start: 0.2936 (ptt) cc_final: 0.2542 (mmt) REVERT: B 936 MET cc_start: 0.4458 (mpp) cc_final: 0.1859 (ttt) REVERT: C 124 MET cc_start: 0.9250 (mmm) cc_final: 0.8949 (mmm) REVERT: C 134 TYR cc_start: 0.8972 (OUTLIER) cc_final: 0.8094 (p90) REVERT: C 247 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7686 (ttt180) REVERT: C 279 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7662 (tm-30) REVERT: C 396 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7827 (mmm) REVERT: C 421 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.8295 (pmt) REVERT: C 651 ASP cc_start: 0.8734 (t70) cc_final: 0.8406 (t0) REVERT: C 738 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8595 (tptp) REVERT: C 825 LEU cc_start: 0.6571 (OUTLIER) cc_final: 0.6070 (mt) REVERT: C 892 ARG cc_start: 0.8302 (mmp-170) cc_final: 0.7598 (ptp-170) REVERT: D 147 LYS cc_start: 0.5569 (tptp) cc_final: 0.5222 (tptt) REVERT: D 188 ASP cc_start: 0.8769 (OUTLIER) cc_final: 0.8355 (t0) REVERT: D 358 GLU cc_start: 0.9243 (OUTLIER) cc_final: 0.8998 (mp0) REVERT: D 396 MET cc_start: 0.6481 (OUTLIER) cc_final: 0.6008 (mmt) REVERT: D 543 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7245 (tp30) REVERT: D 786 HIS cc_start: 0.6848 (OUTLIER) cc_final: 0.5873 (t-90) REVERT: D 825 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7611 (mm) REVERT: D 940 TYR cc_start: 0.7599 (t80) cc_final: 0.7124 (t80) REVERT: D 1001 MET cc_start: 0.8610 (tpp) cc_final: 0.7875 (mpp) REVERT: E 16 TYR cc_start: 0.7109 (t80) cc_final: 0.6738 (t80) REVERT: E 47 CYS cc_start: 0.6483 (OUTLIER) cc_final: 0.5589 (t) REVERT: E 67 PHE cc_start: 0.8374 (m-80) cc_final: 0.7949 (m-80) REVERT: F 13 ASP cc_start: 0.8591 (t70) cc_final: 0.8165 (t0) REVERT: F 51 TYR cc_start: 0.8865 (m-10) cc_final: 0.8587 (m-10) outliers start: 118 outliers final: 85 residues processed: 330 average time/residue: 0.4220 time to fit residues: 233.0420 Evaluate side-chains 337 residues out of total 3775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 229 time to evaluate : 4.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 521 ASN Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 810 HIS Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 926 ASN Chi-restraints excluded: chain A residue 936 MET Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 1004 PHE Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 145 ARG Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 326 ARG Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 435 ASP Chi-restraints excluded: chain B residue 469 CYS Chi-restraints excluded: chain B residue 521 ASN Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 643 SER Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 802 ARG Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 961 ASN Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 464 ASP Chi-restraints excluded: chain C residue 467 ASN Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 504 TYR Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 579 SER Chi-restraints excluded: chain C residue 584 VAL Chi-restraints excluded: chain C residue 666 ASN Chi-restraints excluded: chain C residue 738 LYS Chi-restraints excluded: chain C residue 755 TYR Chi-restraints excluded: chain C residue 825 LEU Chi-restraints excluded: chain C residue 953 LYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain D residue 188 ASP Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 358 GLU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 395 CYS Chi-restraints excluded: chain D residue 396 MET Chi-restraints excluded: chain D residue 543 GLU Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 647 MET Chi-restraints excluded: chain D residue 786 HIS Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 828 THR Chi-restraints excluded: chain D residue 848 ASN Chi-restraints excluded: chain D residue 885 ILE Chi-restraints excluded: chain D residue 938 ASP Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 42 CYS Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 119 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 257 optimal weight: 0.8980 chunk 345 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 299 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 90 optimal weight: 9.9990 chunk 324 optimal weight: 0.0770 chunk 136 optimal weight: 8.9990 chunk 333 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 overall best weight: 0.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 521 ASN ** A1002 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 ASN ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 782 GLN ** B 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 351 ASN C 810 HIS D 786 HIS ** D 789 GLN ** 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 = 0.3740 r_free = 0.3740 target = 0.105911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.075437 restraints weight = 93118.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.073023 restraints weight = 72628.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.073918 restraints weight = 79591.005| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 34812 Z= 0.153 Angle : 0.536 15.230 46899 Z= 0.267 Chirality : 0.039 0.222 5003 Planarity : 0.003 0.051 5976 Dihedral : 4.096 47.708 4509 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.89 % Favored : 96.01 % Rotamer: Outliers : 2.97 % Allowed : 29.24 % Favored : 67.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.14), residues: 4060 helix: 1.54 (0.11), residues: 2423 sheet: -1.40 (0.37), residues: 176 loop : -1.05 (0.16), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 919 HIS 0.004 0.001 HIS B 128 PHE 0.022 0.001 PHE A 301 TYR 0.027 0.001 TYR D 888 ARG 0.003 0.000 ARG C 326 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6041.14 seconds wall clock time: 110 minutes 48.57 seconds (6648.57 seconds total)