Starting phenix.real_space_refine on Sun Aug 11 00:00:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvo_34134/08_2024/7yvo_34134.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvo_34134/08_2024/7yvo_34134.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvo_34134/08_2024/7yvo_34134.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvo_34134/08_2024/7yvo_34134.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvo_34134/08_2024/7yvo_34134.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvo_34134/08_2024/7yvo_34134.cif" } resolution = 3.3 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= -0.001 sd= 0.035 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 131 5.16 5 C 19336 2.51 5 N 5010 2.21 5 O 5808 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 34": "NH1" <-> "NH2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 44": "NH1" <-> "NH2" Residue "A ARG 102": "NH1" <-> "NH2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A ARG 346": "NH1" <-> "NH2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 454": "NH1" <-> "NH2" Residue "A ARG 457": "NH1" <-> "NH2" Residue "A ARG 466": "NH1" <-> "NH2" Residue "A ARG 498": "NH1" <-> "NH2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A ARG 577": "NH1" <-> "NH2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A GLU 654": "OE1" <-> "OE2" Residue "A GLU 702": "OE1" <-> "OE2" Residue "A ARG 765": "NH1" <-> "NH2" Residue "A GLU 773": "OE1" <-> "OE2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A ARG 905": "NH1" <-> "NH2" Residue "A ARG 983": "NH1" <-> "NH2" Residue "A ARG 995": "NH1" <-> "NH2" Residue "A ARG 1000": "NH1" <-> "NH2" Residue "A ARG 1014": "NH1" <-> "NH2" Residue "A GLU 1017": "OE1" <-> "OE2" Residue "A ARG 1019": "NH1" <-> "NH2" Residue "A ARG 1039": "NH1" <-> "NH2" Residue "A ARG 1091": "NH1" <-> "NH2" Residue "B ARG 34": "NH1" <-> "NH2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 44": "NH1" <-> "NH2" Residue "B ARG 102": "NH1" <-> "NH2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 273": "NH1" <-> "NH2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B ARG 454": "NH1" <-> "NH2" Residue "B ARG 457": "NH1" <-> "NH2" Residue "B ARG 567": "NH1" <-> "NH2" Residue "B ARG 577": "NH1" <-> "NH2" Residue "B GLU 583": "OE1" <-> "OE2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "B GLU 702": "OE1" <-> "OE2" Residue "B ARG 765": "NH1" <-> "NH2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B ARG 905": "NH1" <-> "NH2" Residue "B ARG 983": "NH1" <-> "NH2" Residue "B ARG 995": "NH1" <-> "NH2" Residue "B ARG 1000": "NH1" <-> "NH2" Residue "B ARG 1014": "NH1" <-> "NH2" Residue "B GLU 1017": "OE1" <-> "OE2" Residue "B ARG 1019": "NH1" <-> "NH2" Residue "B ARG 1039": "NH1" <-> "NH2" Residue "B ARG 1091": "NH1" <-> "NH2" Residue "C ARG 34": "NH1" <-> "NH2" Residue "C ARG 44": "NH1" <-> "NH2" Residue "C ARG 102": "NH1" <-> "NH2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C ARG 237": "NH1" <-> "NH2" Residue "C ARG 273": "NH1" <-> "NH2" Residue "C ARG 328": "NH1" <-> "NH2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "C ARG 346": "NH1" <-> "NH2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C ARG 454": "NH1" <-> "NH2" Residue "C ARG 457": "NH1" <-> "NH2" Residue "C ARG 466": "NH1" <-> "NH2" Residue "C ARG 498": "NH1" <-> "NH2" Residue "C ARG 567": "NH1" <-> "NH2" Residue "C ARG 577": "NH1" <-> "NH2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "C GLU 654": "OE1" <-> "OE2" Residue "C GLU 702": "OE1" <-> "OE2" Residue "C ARG 765": "NH1" <-> "NH2" Residue "C ARG 815": "NH1" <-> "NH2" Residue "C ARG 905": "NH1" <-> "NH2" Residue "C ARG 983": "NH1" <-> "NH2" Residue "C GLU 990": "OE1" <-> "OE2" Residue "C ARG 995": "NH1" <-> "NH2" Residue "C ARG 1000": "NH1" <-> "NH2" Residue "C ARG 1014": "NH1" <-> "NH2" Residue "C GLU 1017": "OE1" <-> "OE2" Residue "C ARG 1019": "NH1" <-> "NH2" Residue "C ARG 1039": "NH1" <-> "NH2" Residue "C ARG 1091": "NH1" <-> "NH2" Residue "C GLU 1092": "OE1" <-> "OE2" Residue "H GLU 1": "OE1" <-> "OE2" Residue "H ARG 18": "NH1" <-> "NH2" Residue "H ARG 24": "NH1" <-> "NH2" Residue "H ARG 45": "NH1" <-> "NH2" Residue "H ARG 54": "NH1" <-> "NH2" Residue "H ARG 61": "NH1" <-> "NH2" Residue "I GLU 1": "OE1" <-> "OE2" Residue "I ARG 19": "NH1" <-> "NH2" Residue "I ARG 38": "NH1" <-> "NH2" Residue "I ARG 66": "NH1" <-> "NH2" Residue "I ARG 86": "NH1" <-> "NH2" Residue "I GLU 88": "OE1" <-> "OE2" Residue "J ARG 18": "NH1" <-> "NH2" Residue "J ARG 24": "NH1" <-> "NH2" Residue "J ARG 45": "NH1" <-> "NH2" Residue "J ARG 54": "NH1" <-> "NH2" Residue "J ARG 61": "NH1" <-> "NH2" Residue "J GLU 81": "OE1" <-> "OE2" Residue "J GLU 107": "OE1" <-> "OE2" Residue "K GLU 1": "OE1" <-> "OE2" Residue "K ARG 19": "NH1" <-> "NH2" Residue "K ARG 38": "NH1" <-> "NH2" Residue "K ARG 66": "NH1" <-> "NH2" Residue "K ARG 86": "NH1" <-> "NH2" Residue "K GLU 88": "OE1" <-> "OE2" Residue "L ARG 26": "NH1" <-> "NH2" Residue "L ARG 55": "NH1" <-> "NH2" Residue "L ARG 62": "NH1" <-> "NH2" Residue "L ARG 80": "NH1" <-> "NH2" Residue "M GLU 6": "OE1" <-> "OE2" Residue "M ARG 13": "NH1" <-> "NH2" Residue "M ARG 40": "NH1" <-> "NH2" Residue "M ARG 60": "NH1" <-> "NH2" Residue "M ARG 66": "NH1" <-> "NH2" Residue "M ARG 68": "NH1" <-> "NH2" Residue "M ARG 100": "NH1" <-> "NH2" Residue "M GLU 111": "OE1" <-> "OE2" Residue "N ARG 26": "NH1" <-> "NH2" Residue "N ARG 55": "NH1" <-> "NH2" Residue "N ARG 62": "NH1" <-> "NH2" Residue "N ARG 80": "NH1" <-> "NH2" Residue "O GLU 6": "OE1" <-> "OE2" Residue "O ARG 13": "NH1" <-> "NH2" Residue "O ARG 40": "NH1" <-> "NH2" Residue "O ARG 60": "NH1" <-> "NH2" Residue "O ARG 66": "NH1" <-> "NH2" Residue "O ARG 68": "NH1" <-> "NH2" Residue "O ARG 100": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 30285 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 7725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7725 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 56, 'TRANS': 967} Chain breaks: 7 Unresolved non-hydrogen bonds: 285 Unresolved non-hydrogen angles: 350 Unresolved non-hydrogen dihedrals: 230 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 10, 'TYR:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 10, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 174 Chain: "B" Number of atoms: 7413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 987, 7413 Classifications: {'peptide': 987} Incomplete info: {'truncation_to_alanine': 89} Link IDs: {'PTRANS': 54, 'TRANS': 932} Chain breaks: 10 Unresolved non-hydrogen bonds: 316 Unresolved non-hydrogen angles: 388 Unresolved non-hydrogen dihedrals: 257 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 9, 'TYR:plan': 3, 'ASN:plan1': 7, 'ASP:plan': 11, 'PHE:plan': 2, 'GLU:plan': 10, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 198 Chain: "C" Number of atoms: 7719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7719 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PTRANS': 56, 'TRANS': 967} Chain breaks: 7 Unresolved non-hydrogen bonds: 292 Unresolved non-hydrogen angles: 359 Unresolved non-hydrogen dihedrals: 237 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 10, 'TYR:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 10, 'PHE:plan': 3, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 180 Chain: "H" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 818 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 101} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 865 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 115} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "J" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 818 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 101} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 865 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 115} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "L" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 816 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "M" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 956 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 7, 'TRANS': 114} Chain: "N" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 816 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "O" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 956 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 7, 'TRANS': 114} Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 17.77, per 1000 atoms: 0.59 Number of scatterers: 30285 At special positions: 0 Unit cell: (183.68, 151.7, 226.32, 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 131 16.00 O 5808 8.00 N 5010 7.00 C 19336 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.02 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.05 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.01 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.05 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.01 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.05 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.06 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.02 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.06 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.01 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.05 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.02 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.05 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.01 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.01 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 95 " distance=2.04 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 97 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 89 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 97 " distance=2.03 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: 11.49 Conformation dependent library (CDL) restraints added in 5.2 seconds 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7340 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 57 sheets defined 20.3% alpha, 29.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.25 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 349 through 353 removed outlier: 4.160A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 371 removed outlier: 3.653A pdb=" N ASN A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.510A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.542A pdb=" N GLN A 506 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 571 No H-bonds generated for 'chain 'A' and resid 569 through 571' Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.508A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.594A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.937A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 983 removed outlier: 3.505A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.053A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 4.163A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU A1145 " --> pdb=" O LEU A1141 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1140 through 1145' Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 345 removed outlier: 4.653A pdb=" N THR B 345 " --> pdb=" O VAL B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 569 through 571 No H-bonds generated for 'chain 'B' and resid 569 through 571' Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.609A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.882A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 983 removed outlier: 3.541A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.882A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 4.072A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU B1145 " --> pdb=" O LEU B1141 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1140 through 1145' Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 349 through 353 removed outlier: 4.082A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 371 removed outlier: 3.581A pdb=" N ASN C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.607A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 571 No H-bonds generated for 'chain 'C' and resid 569 through 571' Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.790A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 983 removed outlier: 3.558A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.889A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 3.829A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 83 removed outlier: 4.104A pdb=" N SER H 83 " --> pdb=" O SER H 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 73 through 75 No H-bonds generated for 'chain 'I' and resid 73 through 75' Processing helix chain 'I' and resid 86 through 90 removed outlier: 4.085A pdb=" N THR I 90 " --> pdb=" O ALA I 87 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 83 removed outlier: 4.053A pdb=" N SER J 83 " --> pdb=" O SER J 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 75 No H-bonds generated for 'chain 'K' and resid 73 through 75' Processing helix chain 'K' and resid 86 through 90 removed outlier: 3.954A pdb=" N THR K 90 " --> pdb=" O ALA K 87 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 66 Processing helix chain 'M' and resid 88 through 92 Processing helix chain 'O' and resid 63 through 66 Processing helix chain 'O' and resid 88 through 92 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 8.612A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.571A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASN C 542 " --> pdb=" O ILE C 326 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.875A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.537A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.004A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.723A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 357 through 358 removed outlier: 3.913A pdb=" N VAL A 433 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.345A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.985A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.801A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.801A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.371A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 789 removed outlier: 6.029A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.537A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 29 through 31 removed outlier: 8.704A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.900A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.879A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.376A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 324 through 328 removed outlier: 5.579A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.661A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.732A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.008A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE B 664 " --> pdb=" O ALA B 672 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.783A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.783A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.354A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.470A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 29 through 31 removed outlier: 8.787A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.839A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.785A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.958A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 357 through 358 removed outlier: 3.701A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE1, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.986A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.762A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.762A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.409A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 5 through 7 removed outlier: 3.755A pdb=" N GLU H 70 " --> pdb=" O SER H 67 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 53 through 54 removed outlier: 6.545A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AE8, first strand: chain 'I' and resid 10 through 12 removed outlier: 5.898A pdb=" N GLY I 10 " --> pdb=" O THR I 115 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N MET I 34 " --> pdb=" O VAL I 50 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 5 through 7 removed outlier: 3.684A pdb=" N GLU J 70 " --> pdb=" O SER J 67 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.067A pdb=" N LEU J 11 " --> pdb=" O GLU J 107 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AF3, first strand: chain 'K' and resid 10 through 12 removed outlier: 5.765A pdb=" N GLY K 10 " --> pdb=" O THR K 115 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 10 through 12 removed outlier: 5.765A pdb=" N GLY K 10 " --> pdb=" O THR K 115 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR K 107 " --> pdb=" O ARG K 97 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AF6, first strand: chain 'L' and resid 46 through 49 removed outlier: 5.263A pdb=" N LEU L 47 " --> pdb=" O HIS L 38 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N HIS L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'M' and resid 3 through 8 Processing sheet with id=AF8, first strand: chain 'M' and resid 59 through 61 removed outlier: 5.185A pdb=" N TRP M 49 " --> pdb=" O ARG M 40 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ARG M 40 " --> pdb=" O TRP M 49 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA M 51 " --> pdb=" O TRP M 38 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'N' and resid 18 through 23 Processing sheet with id=AG1, first strand: chain 'N' and resid 46 through 49 removed outlier: 6.751A pdb=" N TRP N 36 " --> pdb=" O LEU N 48 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'O' and resid 3 through 8 Processing sheet with id=AG3, first strand: chain 'O' and resid 11 through 12 removed outlier: 6.668A pdb=" N VAL O 36 " --> pdb=" O LEU O 52 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LEU O 52 " --> pdb=" O VAL O 36 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TRP O 38 " --> pdb=" O LEU O 50 " (cutoff:3.500A) 1241 hydrogen bonds defined for protein. 3297 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: 16.61 Time building geometry restraints manager: 12.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 8232 1.33 - 1.46: 9896 1.46 - 1.59: 12699 1.59 - 1.73: 6 1.73 - 1.86: 161 Bond restraints: 30994 Sorted by residual: bond pdb=" C LEU B 223 " pdb=" N GLU B 224 " ideal model delta sigma weight residual 1.331 1.213 0.118 2.07e-02 2.33e+03 3.25e+01 bond pdb=" CB TRP C 886 " pdb=" CG TRP C 886 " ideal model delta sigma weight residual 1.498 1.336 0.162 3.10e-02 1.04e+03 2.74e+01 bond pdb=" CB CYS C 649 " pdb=" SG CYS C 649 " ideal model delta sigma weight residual 1.808 1.648 0.160 3.30e-02 9.18e+02 2.34e+01 bond pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " ideal model delta sigma weight residual 1.808 1.664 0.144 3.30e-02 9.18e+02 1.90e+01 bond pdb=" CA SER B 884 " pdb=" CB SER B 884 " ideal model delta sigma weight residual 1.534 1.468 0.067 1.55e-02 4.16e+03 1.85e+01 ... (remaining 30989 not shown) Histogram of bond angle deviations from ideal: 93.90 - 102.09: 64 102.09 - 110.28: 9530 110.28 - 118.47: 15077 118.47 - 126.65: 17243 126.65 - 134.84: 398 Bond angle restraints: 42312 Sorted by residual: angle pdb=" C ILE C 326 " pdb=" N VAL C 327 " pdb=" CA VAL C 327 " ideal model delta sigma weight residual 121.97 134.84 -12.87 1.80e+00 3.09e-01 5.11e+01 angle pdb=" CA CYS B 432 " pdb=" CB CYS B 432 " pdb=" SG CYS B 432 " ideal model delta sigma weight residual 114.40 130.29 -15.89 2.30e+00 1.89e-01 4.77e+01 angle pdb=" C SER J 30 " pdb=" N SER J 31 " pdb=" CA SER J 31 " ideal model delta sigma weight residual 122.14 111.34 10.80 1.67e+00 3.59e-01 4.18e+01 angle pdb=" CA CYS A 538 " pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " ideal model delta sigma weight residual 114.40 128.70 -14.30 2.30e+00 1.89e-01 3.87e+01 angle pdb=" N PHE C 329 " pdb=" CA PHE C 329 " pdb=" C PHE C 329 " ideal model delta sigma weight residual 108.82 119.22 -10.40 1.69e+00 3.50e-01 3.79e+01 ... (remaining 42307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.32: 17615 22.32 - 44.64: 929 44.64 - 66.96: 168 66.96 - 89.28: 34 89.28 - 111.61: 3 Dihedral angle restraints: 18749 sinusoidal: 7321 harmonic: 11428 Sorted by residual: dihedral pdb=" CA PRO H 95 " pdb=" C PRO H 95 " pdb=" N PRO H 96 " pdb=" CA PRO H 96 " ideal model delta harmonic sigma weight residual -180.00 -68.39 -111.61 0 5.00e+00 4.00e-02 4.98e+02 dihedral pdb=" CA PRO J 95 " pdb=" C PRO J 95 " pdb=" N PRO J 96 " pdb=" CA PRO J 96 " ideal model delta harmonic sigma weight residual -180.00 -68.47 -111.53 0 5.00e+00 4.00e-02 4.98e+02 dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 760 " pdb=" CB CYS A 760 " ideal model delta sinusoidal sigma weight residual -86.00 -6.13 -79.87 1 1.00e+01 1.00e-02 7.91e+01 ... (remaining 18746 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 3632 0.080 - 0.161: 1148 0.161 - 0.241: 135 0.241 - 0.321: 22 0.321 - 0.401: 3 Chirality restraints: 4940 Sorted by residual: chirality pdb=" CA CYS C 649 " pdb=" N CYS C 649 " pdb=" C CYS C 649 " pdb=" CB CYS C 649 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" CA ASN A 709 " pdb=" N ASN A 709 " pdb=" C ASN A 709 " pdb=" CB ASN A 709 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" CA CYS C 617 " pdb=" N CYS C 617 " pdb=" C CYS C 617 " pdb=" CB CYS C 617 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.95e+00 ... (remaining 4937 not shown) Planarity restraints: 5409 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 94 " 0.036 2.00e-02 2.50e+03 2.48e-02 1.53e+01 pdb=" CG TRP H 94 " -0.066 2.00e-02 2.50e+03 pdb=" CD1 TRP H 94 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP H 94 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP H 94 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP H 94 " 0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP H 94 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 94 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 94 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP H 94 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY C 526 " -0.062 5.00e-02 4.00e+02 9.58e-02 1.47e+01 pdb=" N PRO C 527 " 0.166 5.00e-02 4.00e+02 pdb=" CA PRO C 527 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO C 527 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 380 " -0.035 2.00e-02 2.50e+03 2.51e-02 1.26e+01 pdb=" CG TYR B 380 " 0.061 2.00e-02 2.50e+03 pdb=" CD1 TYR B 380 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR B 380 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR B 380 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR B 380 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 380 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR B 380 " -0.003 2.00e-02 2.50e+03 ... (remaining 5406 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 448 2.56 - 3.15: 27503 3.15 - 3.73: 46195 3.73 - 4.32: 64140 4.32 - 4.90: 106871 Nonbonded interactions: 245157 Sorted by model distance: nonbonded pdb=" O TRP C 353 " pdb=" NH1 ARG C 466 " model vdw 1.977 3.120 nonbonded pdb=" OG1 THR N 5 " pdb=" OG SER N 23 " model vdw 1.993 3.040 nonbonded pdb=" O SER J 28 " pdb=" ND2 ASN J 92 " model vdw 2.057 3.120 nonbonded pdb=" O GLN N 1 " pdb=" ND2 ASN N 28 " model vdw 2.071 3.120 nonbonded pdb=" O VAL I 50 " pdb=" OG1 THR I 57 " model vdw 2.081 3.040 ... (remaining 245152 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 328 or (resid 329 and (name N or name CA or nam \ e C or name O or name CB )) or resid 330 through 368 or (resid 369 and (name N o \ r name CA or name C or name O or name CB )) or resid 370 through 402 or (resid 4 \ 03 and (name N or name CA or name C or name O or name CB )) or resid 404 through \ 405 or (resid 406 and (name N or name CA or name C or name O or name CB )) or r \ esid 407 through 423 or (resid 424 and (name N or name CA or name C or name O or \ name CB )) or resid 425 through 438 or (resid 439 and (name N or name CA or nam \ e C or name O or name CB )) or resid 440 through 441 or (resid 442 and (name N o \ r name CA or name C or name O or name CB )) or resid 443 or resid 451 through 46 \ 4 or (resid 465 and (name N or name CA or name C or name O or name CB )) or resi \ d 491 through 497 or resid 503 through 508 or (resid 509 and (name N or name CA \ or name C or name O or name CB )) or resid 510 through 1146 or resid 1301 throug \ h 1312)) selection = (chain 'B' and (resid 27 through 328 or (resid 329 and (name N or name CA or nam \ e C or name O or name CB )) or resid 330 through 1146 or resid 1301 through 1312 \ )) selection = (chain 'C' and (resid 27 through 368 or (resid 369 and (name N or name CA or nam \ e C or name O or name CB )) or resid 370 through 402 or (resid 403 and (name N o \ r name CA or name C or name O or name CB )) or resid 404 through 405 or (resid 4 \ 06 and (name N or name CA or name C or name O or name CB )) or resid 407 through \ 423 or (resid 424 and (name N or name CA or name C or name O or name CB )) or r \ esid 425 through 438 or (resid 439 and (name N or name CA or name C or name O or \ name CB )) or resid 440 through 441 or (resid 442 and (name N or name CA or nam \ e C or name O or name CB )) or resid 443 or resid 451 through 464 or (resid 465 \ and (name N or name CA or name C or name O or name CB )) or resid 491 through 49 \ 7 or resid 503 through 508 or (resid 509 and (name N or name CA or name C or nam \ e O or name CB )) or resid 510 through 1146 or resid 1301 through 1312)) } ncs_group { reference = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'M' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 21.920 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: 0.000 Extract box with map and model: 0.890 Check model and map are aligned: 0.210 Set scattering table: 0.280 Process input model: 87.110 Find NCS groups from input model: 1.840 Set up NCS constraints: 0.180 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: 0.020 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 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 : 0.020 0.163 30994 Z= 1.292 Angle : 1.435 16.524 42312 Z= 0.781 Chirality : 0.075 0.401 4940 Planarity : 0.007 0.096 5409 Dihedral : 13.558 111.605 11271 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 23.21 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.56 % Favored : 94.05 % Rotamer: Outliers : 1.33 % Allowed : 8.83 % Favored : 89.83 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.96 % 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: -2.52 (0.12), residues: 3883 helix: -0.09 (0.19), residues: 669 sheet: -1.43 (0.14), residues: 1066 loop : -2.40 (0.12), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.004 TRP H 94 HIS 0.009 0.003 HIS B 245 PHE 0.055 0.005 PHE B 559 TYR 0.061 0.004 TYR B 380 ARG 0.026 0.002 ARG O 100 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 3417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 253 time to evaluate : 3.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 PHE cc_start: 0.7461 (m-80) cc_final: 0.7205 (m-80) REVERT: A 238 PHE cc_start: 0.7227 (p90) cc_final: 0.6274 (p90) REVERT: A 776 LYS cc_start: 0.9031 (ttpp) cc_final: 0.8795 (ttpp) REVERT: B 128 ILE cc_start: 0.9043 (mt) cc_final: 0.8809 (mm) REVERT: B 129 LYS cc_start: 0.8142 (mtpt) cc_final: 0.7900 (pttp) REVERT: B 200 TYR cc_start: 0.8834 (m-80) cc_final: 0.8467 (m-80) REVERT: B 231 ILE cc_start: 0.6811 (mm) cc_final: 0.6581 (tt) REVERT: B 338 PHE cc_start: 0.9225 (m-80) cc_final: 0.8892 (m-80) REVERT: B 354 ASN cc_start: 0.7364 (t0) cc_final: 0.6959 (t0) REVERT: B 357 ARG cc_start: 0.7330 (mtt180) cc_final: 0.6498 (mtt180) REVERT: B 436 TRP cc_start: 0.5841 (m-10) cc_final: 0.5345 (m-10) REVERT: C 365 TYR cc_start: 0.8254 (m-80) cc_final: 0.8013 (m-80) REVERT: C 960 ASN cc_start: 0.8695 (t0) cc_final: 0.8273 (t0) REVERT: I 34 MET cc_start: 0.4810 (mmm) cc_final: 0.4119 (tpt) REVERT: J 94 TRP cc_start: 0.6931 (t-100) cc_final: 0.5614 (t-100) REVERT: K 34 MET cc_start: 0.5387 (mmm) cc_final: 0.4771 (mtm) REVERT: O 29 LEU cc_start: 0.6699 (tp) cc_final: 0.5533 (pp) outliers start: 42 outliers final: 16 residues processed: 286 average time/residue: 0.4112 time to fit residues: 190.1211 Evaluate side-chains 159 residues out of total 3417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 143 time to evaluate : 3.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain M residue 88 ASP Chi-restraints excluded: chain O residue 16 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 329 optimal weight: 10.0000 chunk 295 optimal weight: 0.8980 chunk 164 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 199 optimal weight: 5.9990 chunk 157 optimal weight: 0.9980 chunk 305 optimal weight: 8.9990 chunk 118 optimal weight: 8.9990 chunk 185 optimal weight: 0.8980 chunk 227 optimal weight: 2.9990 chunk 354 optimal weight: 7.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN A 505 HIS A 657 ASN A 955 ASN A1002 GLN A1134 ASN ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN B 437 ASN B 506 GLN B 955 ASN B1002 GLN B1074 ASN C 282 ASN C 448 ASN C 450 ASN ** C 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN C 657 ASN C 762 GLN C1002 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 GLN I 81 GLN J 79 GLN ** J 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 1 GLN L 6 GLN ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 50 HIS ** M 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 99 HIS N 6 GLN ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 50 HIS O 86 ASN ** O 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 105 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 30994 Z= 0.258 Angle : 0.685 10.613 42312 Z= 0.358 Chirality : 0.047 0.279 4940 Planarity : 0.005 0.109 5409 Dihedral : 7.431 60.495 5016 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.94 % Favored : 94.95 % Rotamer: Outliers : 2.13 % Allowed : 12.33 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 1.44 % 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: -1.38 (0.13), residues: 3883 helix: 1.35 (0.21), residues: 653 sheet: -0.51 (0.15), residues: 1094 loop : -1.95 (0.12), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 353 HIS 0.005 0.001 HIS M 99 PHE 0.016 0.002 PHE B 559 TYR 0.025 0.002 TYR J 98 ARG 0.005 0.001 ARG N 55 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 192 time to evaluate : 3.250 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 298 GLU cc_start: 0.8507 (tm-30) cc_final: 0.8253 (tm-30) REVERT: A 486 VAL cc_start: -0.2935 (OUTLIER) cc_final: -0.3191 (m) REVERT: B 200 TYR cc_start: 0.8694 (m-80) cc_final: 0.8333 (m-10) REVERT: B 231 ILE cc_start: 0.7066 (mm) cc_final: 0.6827 (tt) REVERT: B 354 ASN cc_start: 0.7213 (t0) cc_final: 0.6939 (t0) REVERT: B 402 ILE cc_start: 0.7257 (OUTLIER) cc_final: 0.6875 (tp) REVERT: B 436 TRP cc_start: 0.5752 (m-10) cc_final: 0.5435 (m-10) REVERT: B 577 ARG cc_start: 0.6660 (OUTLIER) cc_final: 0.6166 (ttm110) REVERT: C 298 GLU cc_start: 0.7996 (tt0) cc_final: 0.7735 (tt0) REVERT: C 365 TYR cc_start: 0.8167 (m-80) cc_final: 0.7808 (m-80) REVERT: C 524 VAL cc_start: 0.8031 (p) cc_final: 0.7367 (p) REVERT: C 752 LEU cc_start: 0.9466 (tp) cc_final: 0.9193 (tt) REVERT: C 960 ASN cc_start: 0.8533 (t0) cc_final: 0.8244 (t0) REVERT: H 4 MET cc_start: 0.2153 (mtp) cc_final: 0.1447 (mtt) REVERT: H 23 CYS cc_start: 0.2507 (OUTLIER) cc_final: 0.2182 (t) REVERT: H 71 PHE cc_start: 0.3564 (m-80) cc_final: 0.3206 (m-10) REVERT: I 34 MET cc_start: 0.4799 (mmm) cc_final: 0.4328 (tpt) REVERT: I 51 MET cc_start: 0.4389 (tmm) cc_final: 0.4109 (tmm) REVERT: J 4 MET cc_start: 0.2092 (mmm) cc_final: 0.1530 (mmp) REVERT: J 73 LEU cc_start: 0.2753 (tt) cc_final: 0.2513 (tp) REVERT: O 29 LEU cc_start: 0.6370 (tp) cc_final: 0.5272 (pp) outliers start: 67 outliers final: 21 residues processed: 246 average time/residue: 0.3981 time to fit residues: 163.0049 Evaluate side-chains 176 residues out of total 3417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 151 time to evaluate : 3.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 577 ARG Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain H residue 23 CYS Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 16 GLN Chi-restraints excluded: chain O residue 21 THR Chi-restraints excluded: chain O residue 80 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 196 optimal weight: 2.9990 chunk 109 optimal weight: 9.9990 chunk 294 optimal weight: 1.9990 chunk 241 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 354 optimal weight: 50.0000 chunk 383 optimal weight: 7.9990 chunk 315 optimal weight: 5.9990 chunk 351 optimal weight: 0.8980 chunk 120 optimal weight: 50.0000 chunk 284 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN A 450 ASN ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1134 ASN C 448 ASN ** C 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN ** C 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 89 GLN ** J 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 104 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 30994 Z= 0.286 Angle : 0.630 11.997 42312 Z= 0.330 Chirality : 0.045 0.201 4940 Planarity : 0.005 0.067 5409 Dihedral : 6.696 60.911 4998 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.84 % Favored : 95.08 % Rotamer: Outliers : 2.29 % Allowed : 13.35 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.96 % 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: -1.05 (0.13), residues: 3883 helix: 1.64 (0.21), residues: 669 sheet: -0.41 (0.15), residues: 1060 loop : -1.67 (0.12), residues: 2154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 353 HIS 0.004 0.001 HIS A1088 PHE 0.021 0.002 PHE B 342 TYR 0.025 0.001 TYR B 380 ARG 0.006 0.000 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 3417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 158 time to evaluate : 3.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7255 (p90) cc_final: 0.6549 (p90) REVERT: A 298 GLU cc_start: 0.8595 (tm-30) cc_final: 0.8329 (tm-30) REVERT: A 398 ASP cc_start: 0.0460 (OUTLIER) cc_final: 0.0232 (m-30) REVERT: A 486 VAL cc_start: -0.2996 (OUTLIER) cc_final: -0.3228 (m) REVERT: B 231 ILE cc_start: 0.7071 (mm) cc_final: 0.6788 (tt) REVERT: B 309 GLU cc_start: 0.7883 (mp0) cc_final: 0.7662 (pm20) REVERT: B 342 PHE cc_start: 0.8728 (m-80) cc_final: 0.8386 (m-80) REVERT: B 436 TRP cc_start: 0.5585 (m-10) cc_final: 0.5372 (m-10) REVERT: B 505 HIS cc_start: 0.7911 (OUTLIER) cc_final: 0.7664 (t-90) REVERT: B 1094 VAL cc_start: 0.8551 (OUTLIER) cc_final: 0.8296 (m) REVERT: C 135 PHE cc_start: 0.6315 (t80) cc_final: 0.6017 (t80) REVERT: C 365 TYR cc_start: 0.8140 (m-80) cc_final: 0.7812 (m-80) REVERT: C 369 TYR cc_start: 0.8580 (m-80) cc_final: 0.8240 (m-80) REVERT: C 524 VAL cc_start: 0.7976 (OUTLIER) cc_final: 0.7640 (p) REVERT: C 960 ASN cc_start: 0.8568 (t0) cc_final: 0.8255 (t0) REVERT: H 4 MET cc_start: 0.1776 (mtp) cc_final: 0.1165 (mtp) REVERT: H 23 CYS cc_start: 0.2632 (OUTLIER) cc_final: 0.1909 (t) REVERT: H 71 PHE cc_start: 0.3450 (m-80) cc_final: 0.3065 (m-10) REVERT: I 34 MET cc_start: 0.4844 (mmm) cc_final: 0.3955 (tpp) REVERT: I 51 MET cc_start: 0.4085 (tmm) cc_final: 0.3869 (tmm) REVERT: J 4 MET cc_start: 0.2318 (mmm) cc_final: 0.1733 (mmp) REVERT: J 24 ARG cc_start: 0.7922 (ttp-170) cc_final: 0.7615 (ttp80) REVERT: J 73 LEU cc_start: 0.2740 (tt) cc_final: 0.2500 (tp) REVERT: J 94 TRP cc_start: 0.5958 (t-100) cc_final: 0.4487 (t-100) REVERT: O 9 LEU cc_start: 0.0773 (OUTLIER) cc_final: 0.0199 (mp) REVERT: O 29 LEU cc_start: 0.6206 (tp) cc_final: 0.5187 (pp) outliers start: 72 outliers final: 37 residues processed: 221 average time/residue: 0.3713 time to fit residues: 141.9538 Evaluate side-chains 177 residues out of total 3417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 133 time to evaluate : 3.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 505 HIS Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 577 ARG Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain H residue 23 CYS Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain K residue 95 CYS Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 16 GLN Chi-restraints excluded: chain O residue 21 THR Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 80 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 350 optimal weight: 1.9990 chunk 266 optimal weight: 3.9990 chunk 184 optimal weight: 0.8980 chunk 39 optimal weight: 30.0000 chunk 169 optimal weight: 0.0980 chunk 238 optimal weight: 9.9990 chunk 356 optimal weight: 30.0000 chunk 376 optimal weight: 7.9990 chunk 186 optimal weight: 1.9990 chunk 337 optimal weight: 40.0000 chunk 101 optimal weight: 4.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 965 GLN ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1083 HIS C 448 ASN ** C 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 16 GLN ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 30994 Z= 0.281 Angle : 0.613 11.175 42312 Z= 0.321 Chirality : 0.045 0.203 4940 Planarity : 0.004 0.065 5409 Dihedral : 6.391 61.865 4998 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.97 % Favored : 94.98 % Rotamer: Outliers : 2.80 % Allowed : 14.30 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.96 % 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: -0.92 (0.13), residues: 3883 helix: 1.64 (0.21), residues: 670 sheet: -0.22 (0.15), residues: 1048 loop : -1.60 (0.12), residues: 2165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 886 HIS 0.004 0.001 HIS A 69 PHE 0.021 0.001 PHE B 342 TYR 0.022 0.001 TYR C1067 ARG 0.004 0.000 ARG C 498 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 3417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 149 time to evaluate : 3.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7260 (p90) cc_final: 0.6520 (p90) REVERT: A 298 GLU cc_start: 0.8644 (tm-30) cc_final: 0.8331 (tm-30) REVERT: A 398 ASP cc_start: 0.0050 (OUTLIER) cc_final: -0.0181 (m-30) REVERT: A 486 VAL cc_start: -0.2851 (OUTLIER) cc_final: -0.3090 (m) REVERT: B 231 ILE cc_start: 0.7544 (mm) cc_final: 0.7221 (tt) REVERT: B 309 GLU cc_start: 0.7967 (mp0) cc_final: 0.7717 (pm20) REVERT: B 342 PHE cc_start: 0.8733 (m-80) cc_final: 0.8442 (m-80) REVERT: B 436 TRP cc_start: 0.5450 (m-10) cc_final: 0.5228 (m-10) REVERT: B 505 HIS cc_start: 0.7943 (OUTLIER) cc_final: 0.7706 (t-90) REVERT: B 752 LEU cc_start: 0.9514 (OUTLIER) cc_final: 0.9288 (tt) REVERT: B 1094 VAL cc_start: 0.8610 (OUTLIER) cc_final: 0.8328 (m) REVERT: C 135 PHE cc_start: 0.6391 (t80) cc_final: 0.6045 (t80) REVERT: C 369 TYR cc_start: 0.8633 (m-80) cc_final: 0.8109 (m-80) REVERT: C 960 ASN cc_start: 0.8580 (t0) cc_final: 0.8250 (t0) REVERT: H 4 MET cc_start: 0.1702 (mtp) cc_final: 0.1253 (mtt) REVERT: H 23 CYS cc_start: 0.2824 (OUTLIER) cc_final: 0.2322 (t) REVERT: H 71 PHE cc_start: 0.3533 (m-80) cc_final: 0.3202 (m-10) REVERT: I 34 MET cc_start: 0.4736 (mmm) cc_final: 0.3841 (tpp) REVERT: J 4 MET cc_start: 0.2430 (mmm) cc_final: 0.1585 (mmp) REVERT: J 94 TRP cc_start: 0.5902 (t-100) cc_final: 0.4586 (t-100) REVERT: K 34 MET cc_start: 0.6315 (tpp) cc_final: 0.5237 (mmt) REVERT: M 2 ILE cc_start: 0.3142 (OUTLIER) cc_final: 0.2775 (pt) REVERT: M 52 LEU cc_start: -0.4162 (OUTLIER) cc_final: -0.4365 (mt) REVERT: O 9 LEU cc_start: 0.0675 (OUTLIER) cc_final: 0.0100 (mp) REVERT: O 29 LEU cc_start: 0.6120 (tp) cc_final: 0.5146 (pp) outliers start: 88 outliers final: 47 residues processed: 223 average time/residue: 0.3734 time to fit residues: 143.6431 Evaluate side-chains 182 residues out of total 3417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 126 time to evaluate : 3.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 505 HIS Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 577 ARG Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 542 ASN Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain H residue 23 CYS Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 43 THR Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 16 GLN Chi-restraints excluded: chain O residue 21 THR Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 80 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 313 optimal weight: 1.9990 chunk 213 optimal weight: 0.9990 chunk 5 optimal weight: 0.0070 chunk 280 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 321 optimal weight: 7.9990 chunk 260 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 192 optimal weight: 0.8980 chunk 338 optimal weight: 20.0000 chunk 95 optimal weight: 0.6980 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN B 354 ASN C 448 ASN ** C 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 90 GLN ** J 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 99 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 30994 Z= 0.166 Angle : 0.566 11.090 42312 Z= 0.294 Chirality : 0.043 0.228 4940 Planarity : 0.004 0.057 5409 Dihedral : 5.808 62.746 4996 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.82 % Favored : 95.13 % Rotamer: Outliers : 2.51 % Allowed : 15.54 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.96 % 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: -0.63 (0.13), residues: 3883 helix: 1.87 (0.21), residues: 661 sheet: -0.03 (0.15), residues: 1093 loop : -1.43 (0.13), residues: 2129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 436 HIS 0.005 0.001 HIS A 69 PHE 0.020 0.001 PHE A 92 TYR 0.022 0.001 TYR A1138 ARG 0.005 0.000 ARG J 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 164 time to evaluate : 3.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 PHE cc_start: 0.6735 (m-80) cc_final: 0.6523 (m-80) REVERT: A 238 PHE cc_start: 0.7131 (p90) cc_final: 0.6409 (p90) REVERT: A 298 GLU cc_start: 0.8599 (tm-30) cc_final: 0.8308 (tm-30) REVERT: A 486 VAL cc_start: -0.2932 (OUTLIER) cc_final: -0.3170 (m) REVERT: B 231 ILE cc_start: 0.7589 (mm) cc_final: 0.7256 (tt) REVERT: B 309 GLU cc_start: 0.7963 (mp0) cc_final: 0.7690 (pm20) REVERT: B 342 PHE cc_start: 0.8847 (m-80) cc_final: 0.7638 (m-80) REVERT: B 505 HIS cc_start: 0.7832 (OUTLIER) cc_final: 0.7575 (t-90) REVERT: B 752 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.9274 (tt) REVERT: B 1094 VAL cc_start: 0.8573 (OUTLIER) cc_final: 0.8294 (m) REVERT: C 135 PHE cc_start: 0.6456 (t80) cc_final: 0.6078 (t80) REVERT: C 369 TYR cc_start: 0.8713 (m-80) cc_final: 0.8364 (m-80) REVERT: C 451 TYR cc_start: 0.7933 (m-80) cc_final: 0.7693 (m-80) REVERT: C 960 ASN cc_start: 0.8502 (t0) cc_final: 0.8208 (t0) REVERT: C 983 ARG cc_start: 0.8961 (ptt180) cc_final: 0.8746 (ptt-90) REVERT: H 4 MET cc_start: 0.1881 (mtp) cc_final: 0.1646 (mtp) REVERT: H 23 CYS cc_start: 0.2471 (OUTLIER) cc_final: 0.2165 (t) REVERT: H 71 PHE cc_start: 0.3575 (m-80) cc_final: 0.3236 (m-10) REVERT: I 34 MET cc_start: 0.4540 (mmm) cc_final: 0.3571 (ptm) REVERT: I 51 MET cc_start: 0.4415 (tmm) cc_final: 0.4010 (tmm) REVERT: I 82 MET cc_start: -0.3107 (mpp) cc_final: -0.5241 (ttp) REVERT: J 94 TRP cc_start: 0.5657 (t-100) cc_final: 0.4437 (t-100) REVERT: M 2 ILE cc_start: 0.3191 (OUTLIER) cc_final: 0.2845 (pt) REVERT: N 77 SER cc_start: 0.5673 (m) cc_final: 0.5335 (t) REVERT: O 29 LEU cc_start: 0.5917 (tp) cc_final: 0.5124 (pp) REVERT: O 87 MET cc_start: -0.0628 (tpp) cc_final: -0.1241 (tpt) outliers start: 79 outliers final: 44 residues processed: 235 average time/residue: 0.3508 time to fit residues: 142.6425 Evaluate side-chains 187 residues out of total 3417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 137 time to evaluate : 2.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 505 HIS Chi-restraints excluded: chain B residue 577 ARG Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residu------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 448 ASN ** C 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 32 ASN ** O 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 30994 Z= 0.294 Angle : 0.599 9.415 42312 Z= 0.310 Chirality : 0.045 0.256 4940 Planarity : 0.004 0.058 5409 Dihedral : 5.844 62.318 4996 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.82 % Favored : 95.13 % Rotamer: Outliers : 2.57 % Allowed : 16.56 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.96 % 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: -0.65 (0.13), residues: 3883 helix: 1.68 (0.21), residues: 672 sheet: -0.11 (0.15), residues: 1108 loop : -1.35 (0.13), residues: 2103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP O 38 HIS 0.006 0.001 HIS O 99 PHE 0.017 0.001 PHE B 898 TYR 0.023 0.001 TYR C 170 ARG 0.003 0.000 ARG J 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 3417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 138 time to evaluate : 3.625 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 238 PHE cc_start: 0.7249 (p90) cc_final: 0.6890 (p90) REVERT: A 298 GLU cc_start: 0.8658 (tm-30) cc_final: 0.8318 (tm-30) REVERT: B 231 ILE cc_start: 0.7558 (mm) cc_final: 0.7166 (tt) REVERT: B 309 GLU cc_start: 0.8034 (mp0) cc_final: 0.7775 (pm20) REVERT: B 338 PHE cc_start: 0.9140 (OUTLIER) cc_final: 0.8855 (t80) REVERT: B 505 HIS cc_start: 0.7892 (OUTLIER) cc_final: 0.7657 (t-90) REVERT: B 752 LEU cc_start: 0.9515 (OUTLIER) cc_final: 0.9287 (tt) REVERT: C 135 PHE cc_start: 0.6466 (t80) cc_final: 0.6054 (t80) REVERT: C 369 TYR cc_start: 0.8820 (m-80) cc_final: 0.8313 (m-80) REVERT: C 451 TYR cc_start: 0.8017 (m-80) cc_final: 0.7784 (m-80) REVERT: C 902 MET cc_start: 0.9029 (mmm) cc_final: 0.8747 (tpt) REVERT: C 960 ASN cc_start: 0.8565 (t0) cc_final: 0.8217 (t0) REVERT: C 994 ASP cc_start: 0.8664 (OUTLIER) cc_final: 0.8349 (t0) REVERT: H 4 MET cc_start: 0.2271 (mtp) cc_final: 0.2003 (mtp) REVERT: H 23 CYS cc_start: 0.2637 (OUTLIER) cc_final: 0.2304 (t) REVERT: H 71 PHE cc_start: 0.3485 (m-80) cc_final: 0.3107 (m-10) REVERT: I 34 MET cc_start: 0.4485 (mmm) cc_final: 0.2743 (tpt) REVERT: I 61 ASP cc_start: 0.4937 (OUTLIER) cc_final: 0.4706 (p0) REVERT: I 82 MET cc_start: -0.3327 (mpp) cc_final: -0.5290 (ttp) REVERT: J 94 TRP cc_start: 0.5784 (t-100) cc_final: 0.4567 (t-100) REVERT: M 2 ILE cc_start: 0.3148 (OUTLIER) cc_final: 0.2783 (pt) REVERT: N 77 SER cc_start: 0.5634 (m) cc_final: 0.5280 (t) REVERT: O 29 LEU cc_start: 0.5940 (tp) cc_final: 0.5129 (pp) REVERT: O 53 ILE cc_start: 0.5735 (OUTLIER) cc_final: 0.5519 (pt) outliers start: 81 outliers final: 54 residues processed: 210 average time/residue: 0.3304 time to fit residues: 121.5253 Evaluate side-chains 189 residues out of total 3417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 127 time to evaluate : 3.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 505 HIS Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 577 ARG Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain C residue 542 ASN Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain H residue 23 CYS Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 43 THR Chi-restraints excluded: chain O residue 16 GLN Chi-restraints excluded: chain O residue 21 THR Chi-restraints excluded: chain O residue 53 ILE Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 80 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 363 optimal weight: 40.0000 chunk 42 optimal weight: 9.9990 chunk 214 optimal weight: 7.9990 chunk 275 optimal weight: 0.5980 chunk 213 optimal weight: 3.9990 chunk 317 optimal weight: 20.0000 chunk 210 optimal weight: 5.9990 chunk 375 optimal weight: 8.9990 chunk 235 optimal weight: 10.0000 chunk 229 optimal weight: 5.9990 chunk 173 optimal weight: 0.6980 overall best weight: 3.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -build -allalt -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: