Starting phenix.real_space_refine on Wed Feb 21 09:19:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvp_34135/02_2024/7yvp_34135.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvp_34135/02_2024/7yvp_34135.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvp_34135/02_2024/7yvp_34135.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvp_34135/02_2024/7yvp_34135.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvp_34135/02_2024/7yvp_34135.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvp_34135/02_2024/7yvp_34135.pdb" } resolution = 3.8 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= 0.029 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 19286 2.51 5 N 4950 2.21 5 O 5810 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "I PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 40": "NH1" <-> "NH2" Residue "I ASP 56": "OD1" <-> "OD2" Residue "I ASP 58": "OD1" <-> "OD2" Residue "I ARG 60": "NH1" <-> "NH2" Residue "I ARG 68": "NH1" <-> "NH2" Residue "I ASP 74": "OD1" <-> "OD2" Residue "I ASP 88": "OD1" <-> "OD2" Residue "J ARG 56": "NH1" <-> "NH2" Residue "J ARG 63": "NH1" <-> "NH2" Residue "J GLU 83": "OE1" <-> "OE2" Residue "J ASP 84": "OD1" <-> "OD2" Residue "L PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 40": "NH1" <-> "NH2" Residue "L ASP 56": "OD1" <-> "OD2" Residue "L ASP 57": "OD1" <-> "OD2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L GLU 66": "OE1" <-> "OE2" Residue "L ARG 68": "NH1" <-> "NH2" Residue "L ASP 88": "OD1" <-> "OD2" Residue "M GLU 52": "OE1" <-> "OE2" Residue "M ARG 56": "NH1" <-> "NH2" Residue "M ARG 63": "NH1" <-> "NH2" Residue "M ASP 85": "OD1" <-> "OD2" Residue "O GLU 17": "OE1" <-> "OE2" Residue "O ARG 18": "NH1" <-> "NH2" Residue "O ARG 24": "NH1" <-> "NH2" Residue "O ARG 45": "NH1" <-> "NH2" Residue "O ARG 54": "NH1" <-> "NH2" Residue "O ARG 61": "NH1" <-> "NH2" Residue "O ASP 82": "OD1" <-> "OD2" Residue "O GLU 107": "OE1" <-> "OE2" Residue "P ARG 19": "NH1" <-> "NH2" Residue "P ARG 38": "NH1" <-> "NH2" Residue "P ARG 66": "NH1" <-> "NH2" Residue "P ARG 86": "NH1" <-> "NH2" Residue "P ARG 97": "NH1" <-> "NH2" 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 ASP 339": "OD1" <-> "OD2" 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 GLU 471": "OE1" <-> "OE2" Residue "A ARG 498": "NH1" <-> "NH2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ASP 737": "OD1" <-> "OD2" Residue "A ARG 765": "NH1" <-> "NH2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A ARG 905": "NH1" <-> "NH2" Residue "A ASP 950": "OD1" <-> "OD2" Residue "A ASP 979": "OD1" <-> "OD2" Residue "A ARG 983": "NH1" <-> "NH2" Residue "A ASP 994": "OD1" <-> "OD2" 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 ASP 1041": "OD1" <-> "OD2" Residue "A ARG 1091": "NH1" <-> "NH2" Residue "A GLU 1092": "OE1" <-> "OE2" Residue "A ASP 1139": "OD1" <-> "OD2" Residue "A ASP 1146": "OD1" <-> "OD2" Residue "B ARG 34": "NH1" <-> "NH2" Residue "B TYR 38": "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 ARG 273": "NH1" <-> "NH2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B ASP 364": "OD1" <-> "OD2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 389": "OD1" <-> "OD2" Residue "B ASP 398": "OD1" <-> "OD2" Residue "B ARG 454": "NH1" <-> "NH2" Residue "B ARG 457": "NH1" <-> "NH2" Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ASP 745": "OD1" <-> "OD2" Residue "B ARG 765": "NH1" <-> "NH2" Residue "B GLU 780": "OE1" <-> "OE2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B ARG 905": "NH1" <-> "NH2" Residue "B ASP 979": "OD1" <-> "OD2" 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 "B ASP 1146": "OD1" <-> "OD2" Residue "C ARG 34": "NH1" <-> "NH2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 44": "NH1" <-> "NH2" Residue "C ARG 102": "NH1" <-> "NH2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C ASP 198": "OD1" <-> "OD2" Residue "C ASP 228": "OD1" <-> "OD2" Residue "C ARG 237": "NH1" <-> "NH2" Residue "C ARG 273": "NH1" <-> "NH2" Residue "C ARG 328": "NH1" <-> "NH2" 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 PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 GLU 780": "OE1" <-> "OE2" 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 ASP 994": "OD1" <-> "OD2" 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 ASP 1041": "OD1" <-> "OD2" Residue "C ARG 1091": "NH1" <-> "NH2" Residue "C GLU 1092": "OE1" <-> "OE2" Residue "C ASP 1118": "OD1" <-> "OD2" Residue "C ASP 1146": "OD1" <-> "OD2" 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 "H GLU 81": "OE1" <-> "OE2" Residue "K ARG 19": "NH1" <-> "NH2" Residue "K ARG 38": "NH1" <-> "NH2" Residue "K ARG 66": "NH1" <-> "NH2" Residue "K ASP 72": "OD1" <-> "OD2" Residue "K ARG 86": "NH1" <-> "NH2" Residue "K ASP 89": "OD1" <-> "OD2" Residue "K ARG 97": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 30177 Number of models: 1 Model: "" Number of chains: 14 Chain: "I" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 914 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 110} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 796 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "L" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 914 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 110} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 796 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "O" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 821 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 101} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "P" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 870 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: "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: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 821 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 101} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "K" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 870 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: "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: 18.49, per 1000 atoms: 0.61 Number of scatterers: 30177 At special positions: 0 Unit cell: (178.76, 148.42, 227.14, 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 5810 8.00 N 4950 7.00 C 19286 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, symmetry=0 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 97 " distance=2.02 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 90 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 97 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 90 " distance=2.02 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.04 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 95 " distance=2.04 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=1.99 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=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.02 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.06 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 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=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 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=2.04 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=2.02 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=2.04 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 95 " 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: 11.01 Conformation dependent library (CDL) restraints added in 5.3 seconds 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7332 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 63 sheets defined 20.3% alpha, 29.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.90 Creating SS restraints... Processing helix chain 'I' and resid 88 through 92 removed outlier: 3.661A pdb=" N THR I 92 " --> pdb=" O PRO I 89 " (cutoff:3.500A) Processing helix chain 'J' and resid 81 through 85 removed outlier: 3.678A pdb=" N ASP J 85 " --> pdb=" O ALA J 82 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 92 removed outlier: 3.846A pdb=" N THR L 92 " --> pdb=" O PRO L 89 " (cutoff:3.500A) Processing helix chain 'M' and resid 81 through 85 removed outlier: 3.714A pdb=" N ASP M 85 " --> pdb=" O ALA M 82 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 83 removed outlier: 4.024A pdb=" N SER O 83 " --> pdb=" O SER O 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 73 through 75 No H-bonds generated for 'chain 'P' and resid 73 through 75' Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 367 through 371 removed outlier: 3.576A pdb=" N ASN A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.885A pdb=" N GLU A 406 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.594A 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 801 through 805 removed outlier: 4.494A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.828A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.784A 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: 3.909A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.871A 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: 3.554A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.073A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 4.118A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.796A 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 344 Processing helix chain 'B' and resid 383 through 390 Processing helix chain 'B' and resid 403 through 407 removed outlier: 3.542A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) 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 758 through 783 Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.533A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.761A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.622A 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: 3.843A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.835A 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: 3.563A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.955A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) 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: 3.686A 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: 4.098A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 371 removed outlier: 3.557A pdb=" N ASN C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.579A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.642A 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 758 through 783 Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.638A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.721A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) 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: 3.850A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.830A 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: 3.716A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.891A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 3.774A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 83 removed outlier: 4.162A pdb=" N SER H 83 " --> pdb=" O SER H 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 72 through 75 Processing sheet with id=AA1, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'I' and resid 11 through 12 Processing sheet with id=AA3, first strand: chain 'I' and resid 59 through 61 removed outlier: 5.676A pdb=" N TRP I 49 " --> pdb=" O ARG I 40 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ARG I 40 " --> pdb=" O TRP I 49 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA I 51 " --> pdb=" O TRP I 38 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TYR I 108 " --> pdb=" O HIS I 99 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 59 through 61 removed outlier: 5.676A pdb=" N TRP I 49 " --> pdb=" O ARG I 40 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ARG I 40 " --> pdb=" O TRP I 49 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA I 51 " --> pdb=" O TRP I 38 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR I 95 " --> pdb=" O THR I 113 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'J' and resid 18 through 21 Processing sheet with id=AA6, first strand: chain 'J' and resid 47 through 50 removed outlier: 6.294A pdb=" N LEU J 48 " --> pdb=" O GLN J 39 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLN J 39 " --> pdb=" O LEU J 48 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE J 50 " --> pdb=" O TRP J 37 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 47 through 50 removed outlier: 6.294A pdb=" N LEU J 48 " --> pdb=" O GLN J 39 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLN J 39 " --> pdb=" O LEU J 48 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE J 50 " --> pdb=" O TRP J 37 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'L' and resid 11 through 12 Processing sheet with id=AB1, first strand: chain 'L' and resid 59 through 61 removed outlier: 5.461A pdb=" N TRP L 49 " --> pdb=" O ARG L 40 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N ARG L 40 " --> pdb=" O TRP L 49 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA L 51 " --> pdb=" O TRP L 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'M' and resid 9 through 10 removed outlier: 3.731A pdb=" N VAL M 10 " --> pdb=" O LYS M 105 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N GLN M 39 " --> pdb=" O LEU M 48 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N LEU M 48 " --> pdb=" O GLN M 39 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 9 through 10 removed outlier: 3.731A pdb=" N VAL M 10 " --> pdb=" O LYS M 105 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 18 through 20 Processing sheet with id=AB5, first strand: chain 'O' and resid 5 through 7 removed outlier: 3.739A pdb=" N GLU O 70 " --> pdb=" O SER O 67 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.102A pdb=" N LEU O 11 " --> pdb=" O GLU O 107 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL O 85 " --> pdb=" O GLN O 38 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N TRP O 35 " --> pdb=" O LEU O 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'P' and resid 3 through 7 removed outlier: 3.768A pdb=" N GLN P 3 " --> pdb=" O SER P 25 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'P' and resid 10 through 12 removed outlier: 6.245A pdb=" N GLY P 10 " --> pdb=" O THR P 115 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ARG P 38 " --> pdb=" O TRP P 47 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N TRP P 47 " --> pdb=" O ARG P 38 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.506A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.640A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.712A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.144A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.502A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.240A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR A 612 " --> pdb=" O CYS A 649 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.526A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.114A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.114A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL A 433 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.299A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.216A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE A 664 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AD3, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.206A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.206A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AD6, first strand: chain 'A' and resid 788 through 789 removed outlier: 6.059A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 5.621A pdb=" N VAL A1122 " --> pdb=" O PHE A1089 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N PHE A1089 " --> pdb=" O VAL A1122 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N GLY A1124 " --> pdb=" O ALA A1087 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 30 through 31 Processing sheet with id=AD9, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.942A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 63 through 66 removed outlier: 4.439A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.823A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.557A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 324 through 328 removed outlier: 5.514A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.649A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.617A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AE8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.267A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE B 664 " --> pdb=" O ALA B 672 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AF1, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.139A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.139A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 735 through 736 removed outlier: 3.637A pdb=" N SER B 735 " --> pdb=" O THR B 859 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.533A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 29 through 31 removed outlier: 8.585A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.641A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.714A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.079A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR C 612 " --> pdb=" O CYS C 649 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 357 through 358 removed outlier: 3.980A pdb=" N ARG C 509 " --> pdb=" O TRP C 436 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY C 431 " --> pdb=" O TYR C 380 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.079A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.598A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE C 664 " --> pdb=" O ALA C 672 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 711 through 728 removed outlier: 7.060A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 711 through 728 removed outlier: 7.060A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.396A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.486A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'H' and resid 5 through 7 removed outlier: 3.958A pdb=" N GLU H 70 " --> pdb=" O SER H 67 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.385A pdb=" N LEU H 11 " --> pdb=" O GLU H 107 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL H 85 " --> pdb=" O GLN H 38 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N LEU H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N TYR H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'K' and resid 3 through 7 removed outlier: 3.973A pdb=" N GLN K 3 " --> pdb=" O SER K 25 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.428A pdb=" N GLY K 10 " --> pdb=" O THR K 115 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N MET K 34 " --> pdb=" O VAL K 50 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N VAL K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) 1173 hydrogen bonds defined for protein. 3117 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: 16.68 Time building geometry restraints manager: 12.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 8697 1.33 - 1.46: 8369 1.46 - 1.59: 13642 1.59 - 1.72: 1 1.72 - 1.84: 167 Bond restraints: 30876 Sorted by residual: bond pdb=" C PRO B 862 " pdb=" O PRO B 862 " ideal model delta sigma weight residual 1.240 1.204 0.037 1.12e-02 7.97e+03 1.08e+01 bond pdb=" C PRO A 862 " pdb=" O PRO A 862 " ideal model delta sigma weight residual 1.240 1.204 0.037 1.12e-02 7.97e+03 1.07e+01 bond pdb=" N THR A 333 " pdb=" CA THR A 333 " ideal model delta sigma weight residual 1.459 1.486 -0.027 9.10e-03 1.21e+04 8.90e+00 bond pdb=" N LYS A 528 " pdb=" CA LYS A 528 " ideal model delta sigma weight residual 1.457 1.493 -0.035 1.29e-02 6.01e+03 7.53e+00 bond pdb=" N ILE A 332 " pdb=" CA ILE A 332 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.25e-02 6.40e+03 7.14e+00 ... (remaining 30871 not shown) Histogram of bond angle deviations from ideal: 96.76 - 104.27: 531 104.27 - 111.78: 14773 111.78 - 119.29: 10453 119.29 - 126.80: 16041 126.80 - 134.31: 360 Bond angle restraints: 42158 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 121.97 133.53 -11.56 1.80e+00 3.09e-01 4.12e+01 angle pdb=" C HIS A 519 " pdb=" N ALA A 520 " pdb=" CA ALA A 520 " ideal model delta sigma weight residual 121.59 101.44 20.15 3.54e+00 7.98e-02 3.24e+01 angle pdb=" N TYR J 51 " pdb=" CA TYR J 51 " pdb=" C TYR J 51 " ideal model delta sigma weight residual 109.52 101.20 8.32 1.55e+00 4.16e-01 2.88e+01 angle pdb=" CA CYS B 432 " pdb=" CB CYS B 432 " pdb=" SG CYS B 432 " ideal model delta sigma weight residual 114.40 126.37 -11.97 2.30e+00 1.89e-01 2.71e+01 angle pdb=" C CYS A 336 " pdb=" CA CYS A 336 " pdb=" CB CYS A 336 " ideal model delta sigma weight residual 110.17 100.05 10.12 1.97e+00 2.58e-01 2.64e+01 ... (remaining 42153 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.31: 17737 23.31 - 46.62: 802 46.62 - 69.94: 137 69.94 - 93.25: 24 93.25 - 116.56: 1 Dihedral angle restraints: 18701 sinusoidal: 7281 harmonic: 11420 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 -63.44 -116.56 0 5.00e+00 4.00e-02 5.43e+02 dihedral pdb=" CA PRO O 95 " pdb=" C PRO O 95 " pdb=" N PRO O 96 " pdb=" CA PRO O 96 " ideal model delta harmonic sigma weight residual 180.00 -122.32 -57.68 0 5.00e+00 4.00e-02 1.33e+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 -5.33 -80.67 1 1.00e+01 1.00e-02 8.04e+01 ... (remaining 18698 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 4516 0.098 - 0.196: 411 0.196 - 0.294: 18 0.294 - 0.391: 2 0.391 - 0.489: 1 Chirality restraints: 4948 Sorted by residual: chirality pdb=" CG LEU B 518 " pdb=" CB LEU B 518 " pdb=" CD1 LEU B 518 " pdb=" CD2 LEU B 518 " both_signs ideal model delta sigma weight residual False -2.59 -2.10 -0.49 2.00e-01 2.50e+01 5.98e+00 chirality pdb=" CA TRP H 94 " pdb=" N TRP H 94 " pdb=" C TRP H 94 " pdb=" CB TRP H 94 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" CA CYS A 617 " pdb=" N CYS A 617 " pdb=" C CYS A 617 " pdb=" CB CYS A 617 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.36 2.00e-01 2.50e+01 3.15e+00 ... (remaining 4945 not shown) Planarity restraints: 5371 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 526 " -0.062 5.00e-02 4.00e+02 9.51e-02 1.45e+01 pdb=" N PRO C 527 " 0.164 5.00e-02 4.00e+02 pdb=" CA PRO C 527 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO C 527 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE L 102 " -0.062 5.00e-02 4.00e+02 9.44e-02 1.43e+01 pdb=" N PRO L 103 " 0.163 5.00e-02 4.00e+02 pdb=" CA PRO L 103 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO L 103 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP H 94 " -0.060 5.00e-02 4.00e+02 8.91e-02 1.27e+01 pdb=" N PRO H 95 " 0.154 5.00e-02 4.00e+02 pdb=" CA PRO H 95 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO H 95 " -0.049 5.00e-02 4.00e+02 ... (remaining 5368 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 934 2.67 - 3.23: 30348 3.23 - 3.78: 45783 3.78 - 4.34: 59739 4.34 - 4.90: 99329 Nonbonded interactions: 236133 Sorted by model distance: nonbonded pdb=" O ILE L 105 " pdb=" OH TYR M 38 " model vdw 2.111 2.440 nonbonded pdb=" ND2 ASN A1098 " pdb=" O7 NAG A1309 " model vdw 2.139 2.520 nonbonded pdb=" NE2 GLN H 42 " pdb=" O ALA H 43 " model vdw 2.141 2.520 nonbonded pdb=" O THR B1076 " pdb=" OG SER B1097 " model vdw 2.149 2.440 nonbonded pdb=" O CYS P 22 " pdb=" OG1 THR P 77 " model vdw 2.150 2.440 ... (remaining 236128 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 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 'O' } ncs_group { reference = chain 'I' selection = chain 'L' } ncs_group { reference = chain 'J' selection = chain 'M' } ncs_group { reference = chain 'K' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 36.310 Check model and map are aligned: 0.450 Set scattering table: 0.290 Process input model: 86.080 Find NCS groups from input model: 2.520 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 141.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 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 : 0.009 0.117 30876 Z= 0.557 Angle : 1.032 20.146 42158 Z= 0.555 Chirality : 0.057 0.489 4948 Planarity : 0.006 0.095 5371 Dihedral : 13.186 116.559 11231 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.49 % Allowed : 5.45 % Favored : 94.06 % Rotamer: Outliers : 1.21 % Allowed : 8.08 % Favored : 90.71 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % 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: -2.70 (0.12), residues: 3871 helix: -0.02 (0.19), residues: 657 sheet: -1.71 (0.14), residues: 1030 loop : -2.47 (0.12), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.004 TRP H 94 HIS 0.008 0.002 HIS A1048 PHE 0.031 0.003 PHE B 194 TYR 0.031 0.003 TYR A 873 ARG 0.008 0.001 ARG C1000 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 225 time to evaluate : 3.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 77 LYS cc_start: 0.4591 (tttm) cc_final: 0.4160 (mttt) REVERT: I 96 TYR cc_start: 0.7344 (m-80) cc_final: 0.6710 (m-80) REVERT: L 54 TYR cc_start: 0.4346 (m-80) cc_final: 0.4146 (m-80) REVERT: M 52 GLU cc_start: 0.9097 (mt-10) cc_final: 0.8749 (mm-30) REVERT: B 200 TYR cc_start: 0.8994 (m-80) cc_final: 0.8640 (m-10) REVERT: B 773 GLU cc_start: 0.8865 (tp30) cc_final: 0.8532 (tp30) REVERT: B 780 GLU cc_start: 0.7960 (pt0) cc_final: 0.7517 (pt0) REVERT: C 129 LYS cc_start: 0.8555 (mtpt) cc_final: 0.8355 (mtpp) REVERT: C 229 LEU cc_start: 0.9121 (mt) cc_final: 0.8770 (pp) REVERT: C 365 TYR cc_start: 0.8584 (m-80) cc_final: 0.8172 (m-80) REVERT: C 960 ASN cc_start: 0.9388 (t0) cc_final: 0.9041 (t0) REVERT: C 1138 TYR cc_start: 0.8057 (m-80) cc_final: 0.7519 (m-10) REVERT: H 4 MET cc_start: 0.3606 (mmm) cc_final: 0.3326 (mtt) outliers start: 38 outliers final: 14 residues processed: 262 average time/residue: 0.4613 time to fit residues: 187.7727 Evaluate side-chains 146 residues out of total 3413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 132 time to evaluate : 3.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 538 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 325 optimal weight: 3.9990 chunk 292 optimal weight: 6.9990 chunk 162 optimal weight: 0.9980 chunk 99 optimal weight: 9.9990 chunk 197 optimal weight: 7.9990 chunk 156 optimal weight: 0.6980 chunk 302 optimal weight: 30.0000 chunk 117 optimal weight: 0.9980 chunk 183 optimal weight: 7.9990 chunk 225 optimal weight: 0.0170 chunk 350 optimal weight: 1.9990 overall best weight: 0.9420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 GLN L 16 GLN L 41 GLN M 6 GLN M 39 GLN ** O 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 81 GLN A 370 ASN ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN A 460 ASN ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN A 914 ASN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 ASN B 334 ASN B 388 ASN B 506 GLN B 709 ASN B1134 ASN C 370 ASN ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN C1134 ASN H 6 GLN ** H 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN ** K 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 30876 Z= 0.187 Angle : 0.652 10.758 42158 Z= 0.339 Chirality : 0.046 0.312 4948 Planarity : 0.005 0.107 5371 Dihedral : 7.141 59.935 4997 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.55 % Favored : 94.32 % Rotamer: Outliers : 2.10 % Allowed : 11.52 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.03 % 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: -1.57 (0.13), residues: 3871 helix: 1.27 (0.21), residues: 653 sheet: -0.81 (0.14), residues: 1137 loop : -2.00 (0.12), residues: 2081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP O 94 HIS 0.004 0.001 HIS B1088 PHE 0.023 0.001 PHE B 429 TYR 0.037 0.001 TYR P 107 ARG 0.007 0.001 ARG C 765 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 3413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 184 time to evaluate : 3.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 77 LYS cc_start: 0.5037 (tttm) cc_final: 0.4050 (mttt) REVERT: I 96 TYR cc_start: 0.6987 (m-80) cc_final: 0.6726 (m-80) REVERT: L 36 VAL cc_start: 0.8552 (t) cc_final: 0.8316 (t) REVERT: L 38 TRP cc_start: 0.5381 (m100) cc_final: 0.5138 (m100) REVERT: M 52 GLU cc_start: 0.9040 (mt-10) cc_final: 0.8676 (mm-30) REVERT: O 86 TYR cc_start: 0.5883 (m-80) cc_final: 0.5654 (m-80) REVERT: A 902 MET cc_start: 0.9050 (tpp) cc_final: 0.8819 (tpt) REVERT: A 1135 ASN cc_start: 0.8978 (t0) cc_final: 0.8507 (t0) REVERT: B 191 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8163 (mt-10) REVERT: B 200 TYR cc_start: 0.8917 (m-80) cc_final: 0.8709 (m-10) REVERT: B 1096 VAL cc_start: 0.9081 (OUTLIER) cc_final: 0.8820 (p) REVERT: C 129 LYS cc_start: 0.8355 (mtpt) cc_final: 0.7708 (mtpp) REVERT: C 229 LEU cc_start: 0.9226 (mt) cc_final: 0.8891 (pp) REVERT: C 365 TYR cc_start: 0.8290 (m-80) cc_final: 0.8003 (m-80) REVERT: C 902 MET cc_start: 0.9336 (tpp) cc_final: 0.8866 (tpt) REVERT: C 960 ASN cc_start: 0.9364 (t0) cc_final: 0.8989 (t0) REVERT: C 1138 TYR cc_start: 0.7947 (m-80) cc_final: 0.7406 (m-10) REVERT: H 4 MET cc_start: 0.3524 (mmm) cc_final: 0.2787 (mtt) REVERT: H 36 TYR cc_start: 0.3336 (m-80) cc_final: 0.3133 (m-80) REVERT: K 36 TRP cc_start: 0.4255 (m100) cc_final: 0.3984 (m100) REVERT: K 110 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.8005 (pm20) outliers start: 66 outliers final: 21 residues processed: 242 average time/residue: 0.4120 time to fit residues: 162.0065 Evaluate side-chains 165 residues out of total 3413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 142 time to evaluate : 3.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain K residue 110 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 194 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 291 optimal weight: 9.9990 chunk 238 optimal weight: 4.9990 chunk 96 optimal weight: 7.9990 chunk 351 optimal weight: 3.9990 chunk 379 optimal weight: 10.0000 chunk 312 optimal weight: 5.9990 chunk 348 optimal weight: 9.9990 chunk 119 optimal weight: 2.9990 chunk 281 optimal weight: 40.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 16 GLN ** O 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 81 ASN A 165 ASN ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 417 ASN ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN ** C 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 GLN ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 ASN ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 81 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 30876 Z= 0.348 Angle : 0.681 12.468 42158 Z= 0.351 Chirality : 0.046 0.368 4948 Planarity : 0.004 0.053 5371 Dihedral : 6.892 59.920 4986 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.35 % Favored : 93.57 % Rotamer: Outliers : 2.93 % Allowed : 13.14 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.03 % 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: -1.34 (0.13), residues: 3871 helix: 1.44 (0.21), residues: 645 sheet: -0.78 (0.15), residues: 1110 loop : -1.74 (0.12), residues: 2116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP L 109 HIS 0.006 0.001 HIS C1048 PHE 0.020 0.002 PHE A 92 TYR 0.023 0.002 TYR C1067 ARG 0.007 0.000 ARG L 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 143 time to evaluate : 3.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 77 LYS cc_start: 0.5056 (tttm) cc_final: 0.4216 (mttt) REVERT: L 48 GLU cc_start: 0.4348 (mp0) cc_final: 0.4065 (mp0) REVERT: M 52 GLU cc_start: 0.9170 (mt-10) cc_final: 0.8833 (mm-30) REVERT: O 45 ARG cc_start: 0.8593 (ttp-170) cc_final: 0.8356 (mpp80) REVERT: O 107 GLU cc_start: 0.7349 (mp0) cc_final: 0.7140 (tt0) REVERT: P 66 ARG cc_start: 0.5982 (ttp-170) cc_final: 0.5581 (ttp-170) REVERT: P 79 TYR cc_start: 0.8808 (m-80) cc_final: 0.8415 (m-80) REVERT: A 902 MET cc_start: 0.9201 (tpp) cc_final: 0.8944 (tpt) REVERT: A 904 TYR cc_start: 0.8487 (OUTLIER) cc_final: 0.7991 (m-10) REVERT: B 200 TYR cc_start: 0.9007 (m-80) cc_final: 0.8752 (m-10) REVERT: B 437 ASN cc_start: 0.8956 (m110) cc_final: 0.8392 (m-40) REVERT: B 904 TYR cc_start: 0.8166 (OUTLIER) cc_final: 0.7850 (m-10) REVERT: B 1139 ASP cc_start: 0.9078 (OUTLIER) cc_final: 0.8547 (p0) REVERT: C 229 LEU cc_start: 0.9233 (mt) cc_final: 0.8870 (pp) REVERT: C 365 TYR cc_start: 0.8388 (m-80) cc_final: 0.8080 (m-80) REVERT: C 422 ASN cc_start: 0.2663 (OUTLIER) cc_final: 0.2105 (p0) REVERT: C 904 TYR cc_start: 0.8627 (OUTLIER) cc_final: 0.8420 (m-10) REVERT: C 960 ASN cc_start: 0.9400 (t0) cc_final: 0.8994 (t0) REVERT: C 1002 GLN cc_start: 0.9238 (tp40) cc_final: 0.9006 (tp40) REVERT: C 1138 TYR cc_start: 0.8042 (m-80) cc_final: 0.7524 (m-10) REVERT: K 36 TRP cc_start: 0.4398 (m100) cc_final: 0.4151 (m100) outliers start: 92 outliers final: 45 residues processed: 224 average time/residue: 0.3922 time to fit residues: 143.8866 Evaluate side-chains 178 residues out of total 3413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 128 time to evaluate : 3.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain O residue 98 TYR Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 1139 ASP Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain K residue 77 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 346 optimal weight: 4.9990 chunk 264 optimal weight: 0.9980 chunk 182 optimal weight: 0.9980 chunk 38 optimal weight: 30.0000 chunk 167 optimal weight: 0.9990 chunk 235 optimal weight: 0.7980 chunk 352 optimal weight: 3.9990 chunk 373 optimal weight: 30.0000 chunk 184 optimal weight: 0.0470 chunk 334 optimal weight: 0.5980 chunk 100 optimal weight: 40.0000 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 3 GLN A 81 ASN ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1134 ASN B 81 ASN ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 90 GLN ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 30876 Z= 0.153 Angle : 0.583 12.315 42158 Z= 0.301 Chirality : 0.044 0.333 4948 Planarity : 0.004 0.059 5371 Dihedral : 6.251 59.446 4984 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.32 % Favored : 94.63 % Rotamer: Outliers : 2.51 % Allowed : 14.44 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.05 % 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: -0.99 (0.13), residues: 3871 helix: 1.80 (0.21), residues: 652 sheet: -0.52 (0.15), residues: 1111 loop : -1.58 (0.13), residues: 2108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP M 37 HIS 0.004 0.001 HIS A 69 PHE 0.014 0.001 PHE L 24 TYR 0.018 0.001 TYR K 79 ARG 0.008 0.000 ARG C 328 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 3413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 160 time to evaluate : 3.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 77 LYS cc_start: 0.4875 (tttm) cc_final: 0.3943 (mttt) REVERT: L 48 GLU cc_start: 0.4545 (mp0) cc_final: 0.4335 (mp0) REVERT: M 52 GLU cc_start: 0.9172 (mt-10) cc_final: 0.8769 (mm-30) REVERT: O 45 ARG cc_start: 0.8594 (ttp-170) cc_final: 0.8341 (mpp80) REVERT: P 59 TYR cc_start: 0.6496 (OUTLIER) cc_final: 0.6232 (t80) REVERT: A 900 MET cc_start: 0.9061 (OUTLIER) cc_final: 0.8793 (mtm) REVERT: A 1017 GLU cc_start: 0.8843 (mm-30) cc_final: 0.8565 (tp30) REVERT: A 1135 ASN cc_start: 0.9002 (t0) cc_final: 0.8377 (t0) REVERT: B 200 TYR cc_start: 0.8866 (m-80) cc_final: 0.8656 (m-80) REVERT: C 88 ASP cc_start: 0.8613 (OUTLIER) cc_final: 0.7882 (p0) REVERT: C 229 LEU cc_start: 0.9274 (mt) cc_final: 0.8931 (pp) REVERT: C 242 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8441 (mm) REVERT: C 365 TYR cc_start: 0.8278 (m-80) cc_final: 0.8027 (m-80) REVERT: C 422 ASN cc_start: 0.2178 (OUTLIER) cc_final: 0.1492 (p0) REVERT: C 546 LEU cc_start: 0.8830 (tp) cc_final: 0.8485 (pp) REVERT: C 780 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7723 (mt-10) REVERT: C 904 TYR cc_start: 0.8551 (OUTLIER) cc_final: 0.8149 (m-10) REVERT: C 960 ASN cc_start: 0.9362 (t0) cc_final: 0.8965 (t0) REVERT: C 1002 GLN cc_start: 0.9137 (tp40) cc_final: 0.8887 (tp40) REVERT: C 1138 TYR cc_start: 0.8023 (m-80) cc_final: 0.7505 (m-10) outliers start: 79 outliers final: 36 residues processed: 226 average time/residue: 0.3984 time to fit residues: 147.4423 Evaluate side-chains 184 residues out of total 3413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 142 time to evaluate : 3.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain O residue 98 TYR Chi-restraints excluded: chain P residue 59 TYR Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 105 THR Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain C residue 1139 ASP Chi-restraints excluded: chain H residue 98 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 310 optimal weight: 1.9990 chunk 211 optimal weight: 4.9990 chunk 5 optimal weight: 30.0000 chunk 277 optimal weight: 8.9990 chunk 153 optimal weight: 5.9990 chunk 318 optimal weight: 0.4980 chunk 257 optimal weight: 0.9990 chunk 0 optimal weight: 50.0000 chunk 190 optimal weight: 5.9990 chunk 334 optimal weight: 0.4980 chunk 94 optimal weight: 7.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 3 GLN A 81 ASN ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 GLN C 165 ASN ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 30876 Z= 0.216 Angle : 0.586 11.538 42158 Z= 0.302 Chirality : 0.044 0.309 4948 Planarity : 0.004 0.057 5371 Dihedral : 6.006 59.354 4983 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.68 % Favored : 94.29 % Rotamer: Outliers : 3.02 % Allowed : 15.43 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.05 % 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: -0.88 (0.13), residues: 3871 helix: 1.78 (0.21), residues: 652 sheet: -0.45 (0.15), residues: 1148 loop : -1.47 (0.13), residues: 2071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP K 36 HIS 0.004 0.001 HIS A 69 PHE 0.029 0.001 PHE B 429 TYR 0.021 0.001 TYR P 107 ARG 0.003 0.000 ARG K 97 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 3413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 147 time to evaluate : 3.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 77 LYS cc_start: 0.4866 (tttm) cc_final: 0.4034 (mttt) REVERT: L 41 GLN cc_start: 0.8223 (mp10) cc_final: 0.7830 (mp10) REVERT: L 48 GLU cc_start: 0.4691 (mp0) cc_final: 0.4437 (mp0) REVERT: M 52 GLU cc_start: 0.9161 (mt-10) cc_final: 0.8755 (mm-30) REVERT: O 45 ARG cc_start: 0.8600 (ttp-170) cc_final: 0.8353 (mpp80) REVERT: P 51 MET cc_start: 0.6772 (tpp) cc_final: 0.6560 (tpp) REVERT: A 791 THR cc_start: 0.9019 (OUTLIER) cc_final: 0.8710 (t) REVERT: A 1017 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8442 (tp30) REVERT: B 200 TYR cc_start: 0.8912 (m-80) cc_final: 0.8633 (m-80) REVERT: B 904 TYR cc_start: 0.8249 (OUTLIER) cc_final: 0.7950 (m-10) REVERT: C 88 ASP cc_start: 0.8797 (OUTLIER) cc_final: 0.8455 (p0) REVERT: C 229 LEU cc_start: 0.9194 (mt) cc_final: 0.8850 (pp) REVERT: C 242 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8421 (mm) REVERT: C 422 ASN cc_start: 0.2308 (OUTLIER) cc_final: 0.1595 (p0) REVERT: C 546 LEU cc_start: 0.8757 (tp) cc_final: 0.8441 (pp) REVERT: C 869 MET cc_start: 0.9217 (mtm) cc_final: 0.8924 (mtm) REVERT: C 904 TYR cc_start: 0.8575 (OUTLIER) cc_final: 0.8151 (m-10) REVERT: C 909 ILE cc_start: 0.9206 (OUTLIER) cc_final: 0.9000 (tp) REVERT: C 960 ASN cc_start: 0.9393 (t0) cc_final: 0.8990 (t0) REVERT: C 1002 GLN cc_start: 0.9177 (tp40) cc_final: 0.8923 (tp40) REVERT: C 1138 TYR cc_start: 0.8088 (m-80) cc_final: 0.7589 (m-10) outliers start: 95 outliers final: 55 residues processed: 225 average time/residue: 0.4216 time to fit residues: 155.7380 Evaluate side-chains 194 residues out of total 3413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 132 time to evaluate : 3.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain O residue 98 TYR Chi-restraints excluded: chain P residue 105 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 1139 ASP Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 77 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 125 optimal weight: 1.9990 chunk 336 optimal weight: 0.0770 chunk 73 optimal weight: 10.0000 chunk 219 optimal weight: 0.6980 chunk 92 optimal weight: 20.0000 chunk 373 optimal weight: 30.0000 chunk 310 optimal weight: 6.9990 chunk 172 optimal weight: 20.0000 chunk 31 optimal weight: 6.9990 chunk 123 optimal weight: 5.9990 chunk 196 optimal weight: 0.0470 overall best weight: 1.7640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 30 ASN A 81 ASN ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN B 960 ASN ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 542 ASN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 30876 Z= 0.210 Angle : 0.575 13.756 42158 Z= 0.295 Chirality : 0.043 0.264 4948 Planarity : 0.004 0.058 5371 Dihedral : 5.848 58.433 4983 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.99 % Allowed : 16.13 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.05 % 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: -0.80 (0.13), residues: 3871 helix: 1.85 (0.21), residues: 652 sheet: -0.41 (0.15), residues: 1124 loop : -1.41 (0.13), residues: 2095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP M 37 HIS 0.004 0.001 HIS A 69 PHE 0.022 0.001 PHE B 429 TYR 0.015 0.001 TYR C1067 ARG 0.002 0.000 ARG P 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 3413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 135 time to evaluate : 3.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 77 LYS cc_start: 0.4807 (tttm) cc_final: 0.3984 (mttt) REVERT: M 52 GLU cc_start: 0.9150 (mt-10) cc_final: 0.8748 (mm-30) REVERT: O 45 ARG cc_start: 0.8587 (ttp-170) cc_final: 0.8338 (mpp80) REVERT: A 979 ASP cc_start: 0.9393 (m-30) cc_final: 0.9081 (p0) REVERT: A 1017 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8442 (tp30) REVERT: B 200 TYR cc_start: 0.8886 (m-80) cc_final: 0.8584 (m-80) REVERT: B 904 TYR cc_start: 0.8298 (OUTLIER) cc_final: 0.8000 (m-10) REVERT: B 960 ASN cc_start: 0.9393 (OUTLIER) cc_final: 0.8868 (t0) REVERT: C 229 LEU cc_start: 0.9206 (mt) cc_final: 0.8842 (pp) REVERT: C 242 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8400 (mm) REVERT: C 422 ASN cc_start: 0.2364 (OUTLIER) cc_final: 0.1690 (p0) REVERT: C 524 VAL cc_start: 0.4896 (OUTLIER) cc_final: 0.4691 (p) REVERT: C 546 LEU cc_start: 0.8717 (tp) cc_final: 0.8361 (pp) REVERT: C 902 MET cc_start: 0.9405 (tpt) cc_final: 0.8995 (tpt) REVERT: C 904 TYR cc_start: 0.8553 (OUTLIER) cc_final: 0.8121 (m-10) REVERT: C 909 ILE cc_start: 0.9239 (OUTLIER) cc_final: 0.9013 (tp) REVERT: C 960 ASN cc_start: 0.9369 (t0) cc_final: 0.8966 (t0) REVERT: C 1002 GLN cc_start: 0.9158 (tp40) cc_final: 0.8915 (tp40) REVERT: C 1138 TYR cc_start: 0.8120 (m-80) cc_final: 0.7596 (m-10) outliers start: 94 outliers final: 58 residues processed: 217 average time/residue: 0.3849 time to fit residues: 140.3664 Evaluate side-chains 195 residues out of total 3413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 130 time to evaluate : 3.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 87 MET Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain O residue 98 TYR Chi-restraints excluded: chain P residue 105 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 1139 ASP Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 77 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 360 optimal weight: 1.9990 chunk 42 optimal weight: 40.0000 chunk 212 optimal weight: 10.0000 chunk 272 optimal weight: 30.0000 chunk 211 optimal weight: 2.9990 chunk 314 optimal weight: 10.0000 chunk 208 optimal weight: 9.9990 chunk 372 optimal weight: 50.0000 chunk 232 optimal weight: 0.0770 chunk 226 optimal weight: 2.9990 chunk 171 optimal weight: 0.3980 overall best weight: 1.6944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 81 ASN ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 30876 Z= 0.204 Angle : 0.571 12.709 42158 Z= 0.293 Chirality : 0.043 0.252 4948 Planarity : 0.004 0.058 5371 Dihedral : 5.705 56.850 4982 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 3.09 % Allowed : 16.29 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.05 % 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: -0.69 (0.13), residues: 3871 helix: 1.90 (0.21), residues: 652 sheet: -0.33 (0.15), residues: 1137 loop : -1.33 (0.13), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP M 37 HIS 0.006 0.001 HIS A 69 PHE 0.014 0.001 PHE B 515 TYR 0.015 0.001 TYR C1067 ARG 0.002 0.000 ARG A1091 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 3413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 139 time to evaluate : 3.277 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: I 77 LYS cc_start: 0.4822 (tttm) cc_final: 0.4056 (mttt) REVERT: L 41 GLN cc_start: 0.8217 (mp10) cc_final: 0.7931 (mp10) REVERT: M 52 GLU cc_start: 0.9157 (mt-10) cc_final: 0.8750 (mm-30) REVERT: O 45 ARG cc_start: 0.8575 (ttp-170) cc_final: 0.8320 (mpp80) REVERT: P 79 TYR cc_start: 0.8665 (m-80) cc_final: 0.8355 (m-80) REVERT: A 740 MET cc_start: 0.9371 (tpp) cc_final: 0.8687 (tpp) REVERT: A 791 THR cc_start: 0.9038 (OUTLIER) cc_final: 0.8740 (t) REVERT: A 979 ASP cc_start: 0.9408 (m-30) cc_final: 0.9074 (p0) REVERT: A 1017 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8439 (tp30) REVERT: B 200 TYR cc_start: 0.8907 (m-80) cc_final: 0.8589 (m-80) REVERT: B 904 TYR cc_start: 0.8295 (OUTLIER) cc_final: 0.7991 (m-10) REVERT: C 88 ASP cc_start: 0.8818 (OUTLIER) cc_final: 0.8392 (p0) REVERT: C 229 LEU cc_start: 0.9228 (mt) cc_final: 0.8848 (pp) REVERT: C 242 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8375 (mm) REVERT: C 422 ASN cc_start: 0.2363 (OUTLIER) cc_final: 0.1683 (p0) REVERT: C 501 TYR cc_start: 0.8380 (OUTLIER) cc_final: 0.8051 (m-10) REVERT: C 524 VAL cc_start: 0.4930 (OUTLIER) cc_final: 0.4724 (p) REVERT: C 546 LEU cc_start: 0.8734 (tp) cc_final: 0.8378 (pp) REVERT: C 773 GLU cc_start: 0.9050 (tt0) cc_final: 0.8643 (tt0) REVERT: C 902 MET cc_start: 0.9406 (tpt) cc_final: 0.9006 (tpt) REVERT: C 904 TYR cc_start: 0.8521 (OUTLIER) cc_final: 0.8020 (m-10) REVERT: C 909 ILE cc_start: 0.9240 (OUTLIER) cc_final: 0.9017 (tp) REVERT: C 960 ASN cc_start: 0.9368 (t0) cc_final: 0.8966 (t0) REVERT: C 1002 GLN cc_start: 0.9146 (tp40) cc_final: 0.8895 (tp40) REVERT: C 1138 TYR cc_start: 0.8124 (m-80) cc_final: 0.7632 (m-10) REVERT: H 4 MET cc_start: 0.3989 (mtt) cc_final: 0.1926 (mtt) outliers start: 97 outliers final: 63 residues processed: 222 average time/residue: 0.3867 time to fit residues: 143.8591 Evaluate side-chains 202 residues out of total 3413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 130 time to evaluate : 3.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 87 MET Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain O residue 92 ASN Chi-restraints excluded: chain O residue 98 TYR Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 105 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 1139 ASP Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 77 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 230 optimal weight: 0.0870 chunk 148 optimal weight: 0.1980 chunk 222 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 72 optimal weight: 20.0000 chunk 236 optimal weight: 1.9990 chunk 253 optimal weight: 4.9990 chunk 183 optimal weight: 50.0000 chunk 34 optimal weight: 50.0000 chunk 292 optimal weight: 10.0000 overall best weight: 2.2564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 ASN ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 960 ASN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 30876 Z= 0.253 Angle : 0.591 12.511 42158 Z= 0.304 Chirality : 0.043 0.225 4948 Planarity : 0.004 0.060 5371 Dihedral : 5.761 59.561 4982 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 2.96 % Allowed : 16.96 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.05 % 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: 3871 helix: 1.81 (0.21), residues: 652 sheet: -0.31 (0.15), residues: 1147 loop : -1.25 (0.13), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP M 37 HIS 0.004 0.001 HIS C1048 PHE 0.026 0.001 PHE C 888 TYR 0.016 0.001 TYR C1067 ARG 0.003 0.000 ARG A1091 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 3413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 141 time to evaluate : 3.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 77 LYS cc_start: 0.4835 (tttm) cc_final: 0.4062 (mttt) REVERT: L 48 GLU cc_start: 0.5154 (mp0) cc_final: 0.4949 (mp0) REVERT: M 52 GLU cc_start: 0.9151 (mt-10) cc_final: 0.8771 (mm-30) REVERT: O 45 ARG cc_start: 0.8594 (ttp-170) cc_final: 0.8335 (mpp80) REVERT: O 75 ILE cc_start: 0.7804 (tp) cc_final: 0.7512 (tp) REVERT: P 51 MET cc_start: 0.7135 (tpt) cc_final: 0.6728 (tpt) REVERT: P 79 TYR cc_start: 0.8692 (m-80) cc_final: 0.8388 (m-80) REVERT: A 740 MET cc_start: 0.9396 (tpp) cc_final: 0.8788 (tpp) REVERT: A 791 THR cc_start: 0.9064 (OUTLIER) cc_final: 0.8765 (t) REVERT: A 1017 GLU cc_start: 0.8888 (mm-30) cc_final: 0.8476 (tp30) REVERT: A 1138 TYR cc_start: 0.7600 (t80) cc_final: 0.7393 (t80) REVERT: B 200 TYR cc_start: 0.8923 (m-80) cc_final: 0.8601 (m-10) REVERT: B 904 TYR cc_start: 0.8308 (OUTLIER) cc_final: 0.8005 (m-10) REVERT: C 229 LEU cc_start: 0.9252 (mt) cc_final: 0.8850 (pp) REVERT: C 242 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8372 (mm) REVERT: C 422 ASN cc_start: 0.2578 (OUTLIER) cc_final: 0.1856 (p0) REVERT: C 501 TYR cc_start: 0.8323 (OUTLIER) cc_final: 0.7999 (m-10) REVERT: C 524 VAL cc_start: 0.4727 (OUTLIER) cc_final: 0.4509 (p) REVERT: C 546 LEU cc_start: 0.8707 (tp) cc_final: 0.8295 (pp) REVERT: C 904 TYR cc_start: 0.8531 (OUTLIER) cc_final: 0.8020 (m-10) REVERT: C 909 ILE cc_start: 0.9268 (OUTLIER) cc_final: 0.9057 (tp) REVERT: C 960 ASN cc_start: 0.9386 (t0) cc_final: 0.8993 (t0) REVERT: C 1002 GLN cc_start: 0.9179 (tp40) cc_final: 0.8930 (tp40) REVERT: C 1138 TYR cc_start: 0.8161 (m-80) cc_final: 0.7651 (m-10) REVERT: K 51 MET cc_start: 0.4735 (mpp) cc_final: 0.4342 (mpp) outliers start: 93 outliers final: 70 residues processed: 221 average time/residue: 0.4051 time to fit residues: 148.2916 Evaluate side-chains 212 residues out of total 3413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 134 time to evaluate : 3.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 87 MET Chi-restraints excluded: chain M residue 49 MET Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain O residue 92 ASN Chi-restraints excluded: chain O residue 98 TYR Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 105 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 1139 ASP Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 77 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 338 optimal weight: 0.6980 chunk 356 optimal weight: 0.7980 chunk 325 optimal weight: 4.9990 chunk 346 optimal weight: 4.9990 chunk 208 optimal weight: 8.9990 chunk 151 optimal weight: 0.6980 chunk 272 optimal weight: 9.9990 chunk 106 optimal weight: 30.0000 chunk 313 optimal weight: 0.8980 chunk 327 optimal weight: 8.9990 chunk 345 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 ASN A 481 ASN ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN B 81 ASN B 657 ASN C 542 ASN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 30876 Z= 0.146 Angle : 0.566 12.554 42158 Z= 0.290 Chirality : 0.043 0.231 4948 Planarity : 0.004 0.058 5371 Dihedral : 5.493 54.323 4982 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.55 % Allowed : 17.47 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.05 % 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: -0.49 (0.13), residues: 3871 helix: 2.00 (0.21), residues: 652 sheet: -0.16 (0.15), residues: 1136 loop : -1.21 (0.13), residues: 2083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP M 37 HIS 0.003 0.001 HIS A 69 PHE 0.024 0.001 PHE C 888 TYR 0.021 0.001 TYR P 107 ARG 0.003 0.000 ARG O 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 3413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 142 time to evaluate : 3.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 77 LYS cc_start: 0.4808 (tttm) cc_final: 0.4037 (mttt) REVERT: L 48 GLU cc_start: 0.5193 (mp0) cc_final: 0.4956 (mp0) REVERT: L 74 ASP cc_start: 0.7601 (t0) cc_final: 0.7295 (t0) REVERT: M 52 GLU cc_start: 0.9119 (mt-10) cc_final: 0.8727 (mm-30) REVERT: O 45 ARG cc_start: 0.8586 (ttp-170) cc_final: 0.8330 (mpp80) REVERT: P 79 TYR cc_start: 0.8679 (m-80) cc_final: 0.8371 (m-80) REVERT: A 740 MET cc_start: 0.9374 (tpp) cc_final: 0.8758 (tpp) REVERT: A 791 THR cc_start: 0.9054 (OUTLIER) cc_final: 0.8821 (p) REVERT: A 979 ASP cc_start: 0.9439 (m-30) cc_final: 0.9038 (p0) REVERT: B 200 TYR cc_start: 0.8876 (m-80) cc_final: 0.8565 (m-80) REVERT: B 904 TYR cc_start: 0.8316 (OUTLIER) cc_final: 0.7956 (m-10) REVERT: C 229 LEU cc_start: 0.9233 (mt) cc_final: 0.8829 (pp) REVERT: C 422 ASN cc_start: 0.2302 (OUTLIER) cc_final: 0.1565 (p0) REVERT: C 501 TYR cc_start: 0.8340 (OUTLIER) cc_final: 0.8025 (m-10) REVERT: C 524 VAL cc_start: 0.4602 (OUTLIER) cc_final: 0.4397 (p) REVERT: C 546 LEU cc_start: 0.8706 (tp) cc_final: 0.8338 (pp) REVERT: C 904 TYR cc_start: 0.8468 (OUTLIER) cc_final: 0.7950 (m-10) REVERT: C 960 ASN cc_start: 0.9323 (t0) cc_final: 0.8918 (t0) REVERT: C 1002 GLN cc_start: 0.9099 (tp40) cc_final: 0.8852 (tp40) REVERT: C 1138 TYR cc_start: 0.8115 (m-80) cc_final: 0.7591 (m-10) REVERT: K 51 MET cc_start: 0.4517 (mpp) cc_final: 0.4184 (mpp) outliers start: 80 outliers final: 65 residues processed: 210 average time/residue: 0.3961 time to fit residues: 138.4560 Evaluate side-chains 211 residues out of total 3413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 140 time to evaluate : 3.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 87 MET Chi-restraints excluded: chain M residue 49 MET Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain O residue 92 ASN Chi-restraints excluded: chain O residue 98 TYR Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 105 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain C residue 1139 ASP Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 77 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 227 optimal weight: 0.0050 chunk 366 optimal weight: 0.0670 chunk 223 optimal weight: 0.7980 chunk 173 optimal weight: 5.9990 chunk 254 optimal weight: 0.9980 chunk 384 optimal weight: 50.0000 chunk 353 optimal weight: 3.9990 chunk 306 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 236 optimal weight: 3.9990 chunk 187 optimal weight: 10.0000 overall best weight: 0.5532 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 ASN ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 960 ASN B1036 GLN C 165 ASN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 30876 Z= 0.132 Angle : 0.556 14.810 42158 Z= 0.281 Chirality : 0.043 0.200 4948 Planarity : 0.004 0.058 5371 Dihedral : 5.059 53.509 4981 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.26 % Allowed : 17.88 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.05 % 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: -0.38 (0.14), residues: 3871 helix: 2.04 (0.21), residues: 651 sheet: -0.01 (0.15), residues: 1130 loop : -1.16 (0.13), residues: 2090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 36 HIS 0.003 0.000 HIS A 69 PHE 0.024 0.001 PHE C 888 TYR 0.015 0.001 TYR O 49 ARG 0.002 0.000 ARG P 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 3413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 154 time to evaluate : 3.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 77 LYS cc_start: 0.4809 (tttm) cc_final: 0.4038 (mttt) REVERT: L 74 ASP cc_start: 0.7680 (t0) cc_final: 0.7397 (t0) REVERT: M 52 GLU cc_start: 0.9104 (mt-10) cc_final: 0.8739 (mm-30) REVERT: O 45 ARG cc_start: 0.8584 (ttp-170) cc_final: 0.8324 (mpp80) REVERT: P 79 TYR cc_start: 0.8703 (m-80) cc_final: 0.8397 (m-80) REVERT: A 791 THR cc_start: 0.9015 (OUTLIER) cc_final: 0.8789 (p) REVERT: A 979 ASP cc_start: 0.9454 (m-30) cc_final: 0.9075 (p0) REVERT: A 1017 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8609 (tp30) REVERT: B 200 TYR cc_start: 0.8858 (m-80) cc_final: 0.8570 (m-80) REVERT: B 387 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8414 (tp) REVERT: B 904 TYR cc_start: 0.8356 (OUTLIER) cc_final: 0.7991 (m-10) REVERT: B 960 ASN cc_start: 0.9336 (OUTLIER) cc_final: 0.8792 (t0) REVERT: C 229 LEU cc_start: 0.9215 (mt) cc_final: 0.8733 (pp) REVERT: C 422 ASN cc_start: 0.1967 (OUTLIER) cc_final: 0.1219 (p0) REVERT: C 501 TYR cc_start: 0.8364 (OUTLIER) cc_final: 0.8041 (m-10) REVERT: C 902 MET cc_start: 0.9394 (tpt) cc_final: 0.9053 (tpt) REVERT: C 904 TYR cc_start: 0.8423 (OUTLIER) cc_final: 0.7794 (m-10) REVERT: C 960 ASN cc_start: 0.9319 (t0) cc_final: 0.8910 (t0) REVERT: C 1002 GLN cc_start: 0.9051 (tp40) cc_final: 0.8799 (tp40) REVERT: C 1041 ASP cc_start: 0.8208 (t0) cc_final: 0.7868 (t0) REVERT: C 1138 TYR cc_start: 0.8101 (m-80) cc_final: 0.7579 (m-10) REVERT: K 51 MET cc_start: 0.4885 (mpp) cc_final: 0.4552 (mpp) outliers start: 71 outliers final: 54 residues processed: 214 average time/residue: 0.3913 time to fit residues: 139.5640 Evaluate side-chains 199 residues out of total 3413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 138 time to evaluate : 3.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 87 MET Chi-restraints excluded: chain M residue 49 MET Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain O residue 92 ASN Chi-restraints excluded: chain O residue 98 TYR Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 105 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain C residue 1139 ASP Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain K residue 68 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 243 optimal weight: 2.9990 chunk 326 optimal weight: 0.9980 chunk 93 optimal weight: 10.0000 chunk 282 optimal weight: 0.0570 chunk 45 optimal weight: 40.0000 chunk 85 optimal weight: 5.9990 chunk 306 optimal weight: 20.0000 chunk 128 optimal weight: 0.7980 chunk 314 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 overall best weight: 1.9702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 ASN ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN B1036 GLN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.103978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.065964 restraints weight = 137125.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.066598 restraints weight = 76795.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.066763 restraints weight = 46922.951| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 30876 Z= 0.227 Angle : 0.585 12.214 42158 Z= 0.296 Chirality : 0.043 0.193 4948 Planarity : 0.004 0.059 5371 Dihedral : 5.138 55.143 4980 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 2.29 % Allowed : 18.01 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.05 % 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: -0.42 (0.14), residues: 3871 helix: 1.93 (0.21), residues: 653 sheet: -0.05 (0.15), residues: 1130 loop : -1.15 (0.13), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP I 38 HIS 0.005 0.001 HIS C1048 PHE 0.023 0.001 PHE C 888 TYR 0.016 0.001 TYR H 36 ARG 0.006 0.000 ARG O 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6549.71 seconds wall clock time: 121 minutes 42.83 seconds (7302.83 seconds total)