Starting phenix.real_space_refine on Tue Feb 20 06:47:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z9q_14575/02_2024/7z9q_14575.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z9q_14575/02_2024/7z9q_14575.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z9q_14575/02_2024/7z9q_14575.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z9q_14575/02_2024/7z9q_14575.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z9q_14575/02_2024/7z9q_14575.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z9q_14575/02_2024/7z9q_14575.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 117 5.16 5 C 17225 2.51 5 N 4462 2.21 5 O 5261 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1107": "NH1" <-> "NH2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1019": "NH1" <-> "NH2" Residue "D TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 27065 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 7646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 987, 7646 Classifications: {'peptide': 987} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 49, 'TRANS': 937} Chain breaks: 9 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ASN:plan1': 4, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 51 Chain: "B" Number of atoms: 7677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 7677 Classifications: {'peptide': 992} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 49, 'TRANS': 942} Chain breaks: 8 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 3, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 55 Chain: "C" Number of atoms: 7659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 990, 7659 Classifications: {'peptide': 990} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 49, 'TRANS': 940} Chain breaks: 7 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 48 Chain: "D" Number of atoms: 1053 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 134, 1049 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 131} Conformer: "B" Number of residues, atoms: 134, 1049 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 131} bond proxies already assigned to first conformer: 1073 Chain: "E" Number of atoms: 1053 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 134, 1049 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 131} Conformer: "B" Number of residues, atoms: 134, 1049 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 131} bond proxies already assigned to first conformer: 1073 Chain: "F" Number of atoms: 1053 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 134, 1049 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 131} Conformer: "B" Number of residues, atoms: 134, 1049 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 131} bond proxies already assigned to first conformer: 1073 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 14.82, per 1000 atoms: 0.55 Number of scatterers: 27065 At special positions: 0 Unit cell: (131.44, 137.8, 227.9, 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 117 16.00 O 5261 8.00 N 4462 7.00 C 17225 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.05 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.05 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.05 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.07 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " 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=2.05 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.01 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.06 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.00 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.00 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.00 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 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 603 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 657 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A 165 " " NAG A1308 " - " ASN A 343 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B1074 " " NAG B1310 " - " ASN B 343 " " NAG C1401 " - " ASN C 343 " " NAG C1402 " - " ASN C 61 " " NAG C1403 " - " ASN C 234 " " NAG C1404 " - " ASN C 331 " " NAG C1405 " - " ASN C 603 " " NAG C1406 " - " ASN C 616 " " NAG C1407 " - " ASN C 657 " " NAG C1408 " - " ASN C 165 " " NAG G 1 " - " ASN A 122 " " NAG H 1 " - " ASN A 234 " " NAG I 1 " - " ASN A 282 " " NAG J 1 " - " ASN A 331 " " NAG K 1 " - " ASN A 717 " " NAG L 1 " - " ASN A 801 " " NAG M 1 " - " ASN A1098 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN B 717 " " NAG P 1 " - " ASN B 801 " " NAG Q 1 " - " ASN B1098 " " NAG R 1 " - " ASN B1134 " " NAG S 1 " - " ASN C 122 " " NAG T 1 " - " ASN C 282 " " NAG U 1 " - " ASN C 709 " " NAG V 1 " - " ASN C 717 " " NAG W 1 " - " ASN C 801 " " NAG X 1 " - " ASN C1074 " " NAG Y 1 " - " ASN C1098 " " NAG Z 1 " - " ASN C1134 " Time building additional restraints: 10.86 Conformation dependent library (CDL) restraints added in 5.6 seconds 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6290 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 54 sheets defined 24.6% alpha, 28.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.74 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.964A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 384 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.261A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.646A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.098A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.674A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) 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 984 removed outlier: 3.668A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.407A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.093A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 4.028A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 384 through 389 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.262A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.675A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.644A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.112A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.695A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) 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 984 removed outlier: 3.637A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.411A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.091A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 4.022A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 384 through 389 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.280A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.642A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.106A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.664A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) 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 984 removed outlier: 3.637A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.332A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.086A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 111 Processing helix chain 'E' and resid 105 through 111 Processing helix chain 'F' and resid 105 through 111 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.647A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 8.820A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.564A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.571A pdb=" N ASN A 125 " --> pdb=" O ASN A 122 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.555A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 324 through 327 removed outlier: 6.660A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.497A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.561A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.863A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.969A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.195A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.705A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.376A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.654A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 8.879A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.571A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 83 through 85 Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.588A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.130A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.482A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 653 through 655 removed outlier: 6.556A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.860A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.978A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.195A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 788 through 790 removed outlier: 5.788A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.378A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.652A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 8.827A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.876A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.583A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.133A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.493A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'C' and resid 653 through 655 removed outlier: 6.561A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.864A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.968A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.188A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.379A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AF2, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.198A pdb=" N GLY D 10 " --> pdb=" O THR D 124 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N SER D 126 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N MET D 12 " --> pdb=" O SER D 126 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA D 33 " --> pdb=" O PHE D 99 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ARG D 38 " --> pdb=" O PHE D 47 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N PHE D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.198A pdb=" N GLY D 10 " --> pdb=" O THR D 124 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N SER D 126 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N MET D 12 " --> pdb=" O SER D 126 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AF5, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.198A pdb=" N GLY E 10 " --> pdb=" O THR E 124 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N SER E 126 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N MET E 12 " --> pdb=" O SER E 126 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA E 33 " --> pdb=" O PHE E 99 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ARG E 38 " --> pdb=" O PHE E 47 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N PHE E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.198A pdb=" N GLY E 10 " --> pdb=" O THR E 124 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N SER E 126 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N MET E 12 " --> pdb=" O SER E 126 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AF8, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.198A pdb=" N GLY F 10 " --> pdb=" O THR F 124 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N SER F 126 " --> pdb=" O GLY F 10 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N MET F 12 " --> pdb=" O SER F 126 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA F 33 " --> pdb=" O PHE F 99 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ARG F 38 " --> pdb=" O PHE F 47 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N PHE F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.198A pdb=" N GLY F 10 " --> pdb=" O THR F 124 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N SER F 126 " --> pdb=" O GLY F 10 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N MET F 12 " --> pdb=" O SER F 126 " (cutoff:3.500A) 1172 hydrogen bonds defined for protein. 3129 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.61 Time building geometry restraints manager: 11.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4489 1.32 - 1.44: 7761 1.44 - 1.57: 15271 1.57 - 1.69: 0 1.69 - 1.82: 150 Bond restraints: 27671 Sorted by residual: bond pdb=" C TRP F 117 " pdb=" O TRP F 117 " ideal model delta sigma weight residual 1.234 1.290 -0.056 1.22e-02 6.72e+03 2.13e+01 bond pdb=" C TRP D 117 " pdb=" O TRP D 117 " ideal model delta sigma weight residual 1.234 1.290 -0.056 1.22e-02 6.72e+03 2.11e+01 bond pdb=" C TRP E 117 " pdb=" O TRP E 117 " ideal model delta sigma weight residual 1.234 1.290 -0.056 1.22e-02 6.72e+03 2.09e+01 bond pdb=" C VAL D 125 " pdb=" O VAL D 125 " ideal model delta sigma weight residual 1.237 1.192 0.046 1.10e-02 8.26e+03 1.71e+01 bond pdb=" C VAL F 125 " pdb=" O VAL F 125 " ideal model delta sigma weight residual 1.237 1.192 0.045 1.10e-02 8.26e+03 1.70e+01 ... (remaining 27666 not shown) Histogram of bond angle deviations from ideal: 95.91 - 103.71: 314 103.71 - 111.52: 10515 111.52 - 119.32: 12987 119.32 - 127.13: 13679 127.13 - 134.93: 151 Bond angle restraints: 37646 Sorted by residual: angle pdb=" C LYS A 113 " pdb=" CA LYS A 113 " pdb=" CB LYS A 113 " ideal model delta sigma weight residual 109.83 116.61 -6.78 9.90e-01 1.02e+00 4.69e+01 angle pdb=" C PRO C 600 " pdb=" CA PRO C 600 " pdb=" CB PRO C 600 " ideal model delta sigma weight residual 111.44 102.60 8.84 1.51e+00 4.39e-01 3.42e+01 angle pdb=" CA ASP F 115 " pdb=" CB ASP F 115 " pdb=" CG ASP F 115 " ideal model delta sigma weight residual 112.60 118.40 -5.80 1.00e+00 1.00e+00 3.37e+01 angle pdb=" CA ASP D 115 " pdb=" CB ASP D 115 " pdb=" CG ASP D 115 " ideal model delta sigma weight residual 112.60 118.40 -5.80 1.00e+00 1.00e+00 3.36e+01 angle pdb=" CA ASP E 115 " pdb=" CB ASP E 115 " pdb=" CG ASP E 115 " ideal model delta sigma weight residual 112.60 118.38 -5.78 1.00e+00 1.00e+00 3.34e+01 ... (remaining 37641 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 15900 17.53 - 35.05: 1059 35.05 - 52.58: 218 52.58 - 70.10: 41 70.10 - 87.63: 26 Dihedral angle restraints: 17244 sinusoidal: 7451 harmonic: 9793 Sorted by residual: dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual 93.00 -179.37 -87.63 1 1.00e+01 1.00e-02 9.20e+01 dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual 93.00 -179.68 -87.32 1 1.00e+01 1.00e-02 9.15e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 -179.76 -87.24 1 1.00e+01 1.00e-02 9.14e+01 ... (remaining 17241 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 3869 0.126 - 0.252: 560 0.252 - 0.378: 23 0.378 - 0.504: 2 0.504 - 0.630: 1 Chirality restraints: 4455 Sorted by residual: chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.31 -0.09 2.00e-02 2.50e+03 1.93e+01 chirality pdb=" C1 NAG B1305 " pdb=" ND2 ASN B 603 " pdb=" C2 NAG B1305 " pdb=" O5 NAG B1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.77 -0.63 2.00e-01 2.50e+01 9.92e+00 chirality pdb=" C1 NAG Y 2 " pdb=" O4 NAG Y 1 " pdb=" C2 NAG Y 2 " pdb=" O5 NAG Y 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.34 -0.06 2.00e-02 2.50e+03 9.92e+00 ... (remaining 4452 not shown) Planarity restraints: 4810 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 80 " 0.044 2.00e-02 2.50e+03 4.00e-02 3.20e+01 pdb=" CG TYR D 80 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR D 80 " -0.075 2.00e-02 2.50e+03 pdb=" CD2 TYR D 80 " -0.020 2.00e-02 2.50e+03 pdb=" CE1 TYR D 80 " 0.038 2.00e-02 2.50e+03 pdb=" CE2 TYR D 80 " -0.016 2.00e-02 2.50e+03 pdb=" CZ TYR D 80 " 0.053 2.00e-02 2.50e+03 pdb=" OH TYR D 80 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 80 " 0.045 2.00e-02 2.50e+03 3.99e-02 3.18e+01 pdb=" CG TYR F 80 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR F 80 " -0.075 2.00e-02 2.50e+03 pdb=" CD2 TYR F 80 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 TYR F 80 " 0.039 2.00e-02 2.50e+03 pdb=" CE2 TYR F 80 " -0.015 2.00e-02 2.50e+03 pdb=" CZ TYR F 80 " 0.052 2.00e-02 2.50e+03 pdb=" OH TYR F 80 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 80 " -0.044 2.00e-02 2.50e+03 3.99e-02 3.18e+01 pdb=" CG TYR E 80 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR E 80 " 0.075 2.00e-02 2.50e+03 pdb=" CD2 TYR E 80 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 TYR E 80 " -0.039 2.00e-02 2.50e+03 pdb=" CE2 TYR E 80 " 0.016 2.00e-02 2.50e+03 pdb=" CZ TYR E 80 " -0.052 2.00e-02 2.50e+03 pdb=" OH TYR E 80 " 0.014 2.00e-02 2.50e+03 ... (remaining 4807 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 80 2.56 - 3.14: 21144 3.14 - 3.73: 40222 3.73 - 4.31: 60934 4.31 - 4.90: 97995 Nonbonded interactions: 220375 Sorted by model distance: nonbonded pdb=" O ASN A 81 " pdb=" NE2 GLN A 239 " model vdw 1.974 2.520 nonbonded pdb=" NH1 ARG C 328 " pdb=" OD2 ASP C 578 " model vdw 2.204 2.520 nonbonded pdb=" OH TYR B 200 " pdb=" OE1 GLU C 516 " model vdw 2.207 2.440 nonbonded pdb=" OH TYR B 200 " pdb=" OH TYR C 396 " model vdw 2.215 2.440 nonbonded pdb=" NE2 GLN C 804 " pdb=" OE1 GLN C 935 " model vdw 2.279 2.520 ... (remaining 220370 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 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 66 or resid 82 through 96 or (resi \ d 97 and (name N or name CA or name C or name O or name CB )) or resid 98 or (re \ sid 99 and (name N or name CA or name C or name O or name CB )) or resid 100 thr \ ough 110 or (resid 111 through 113 and (name N or name CA or name C or name O or \ name CB )) or resid 116 through 128 or (resid 129 and (name N or name CA or nam \ e C or name O or name CB )) or resid 130 through 134 or (resid 135 through 138 a \ nd (name N or name CA or name C or name O or name CB )) or resid 139 through 140 \ or resid 166 through 168 or (resid 169 and (name N or name CA or name C or name \ O or name CB )) or resid 170 through 172 or resid 187 or (resid 188 and (name N \ or name CA or name C or name O or name CB )) or resid 189 through 210 or (resid \ 211 through 215 and (name N or name CA or name C or name O or name CB )) or res \ id 216 through 241 or (resid 242 through 263 and (name N or name CA or name C or \ name O or name CB )) or resid 265 through 280 or (resid 281 and (name N or name \ CA or name C or name O or name CB )) or resid 282 through 567 or (resid 568 and \ (name N or name CA or name C or name O or name CB )) or resid 569 through 570 o \ r (resid 571 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 72 through 581 or (resid 582 through 583 and (name N or name CA or name C or nam \ e O or name CB )) or resid 584 through 585 or (resid 586 and (name N or name CA \ or name C or name O or name CB )) or resid 587 through 660 or (resid 661 and (na \ me N or name CA or name C or name O or name CB )) or resid 662 through 676 or re \ sid 690 through 747 or (resid 748 and (name N or name CA or name C or name O or \ name CB )) or resid 749 through 810 or (resid 811 and (name N or name CA or name \ C or name O or name CB )) or resid 812 through 827 or resid 856 through 939 or \ (resid 940 and (name N or name CA or name C or name O or name CB )) or resid 941 \ through 984 or (resid 985 and (name N or name CA or name C or name O or name CB \ )) or resid 986 through 1143 or (resid 1144 through 1146 and (name N or name CA \ or name C or name O or name CB )) or resid 1147 or resid 1301 through 1308)) selection = (chain 'B' and (resid 27 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 52 or (resid 53 and (name N or nam \ e CA or name C or name O or name CB )) or resid 54 through 66 or resid 82 throug \ h 95 or (resid 96 through 97 and (name N or name CA or name C or name O or name \ CB )) or resid 98 through 111 or (resid 112 through 113 and (name N or name CA o \ r name C or name O or name CB )) or resid 116 through 124 or (resid 125 and (nam \ e N or name CA or name C or name O or name CB )) or resid 126 through 131 or (re \ sid 132 and (name N or name CA or name C or name O or name CB )) or resid 133 or \ (resid 134 through 138 and (name N or name CA or name C or name O or name CB )) \ or resid 139 through 140 or resid 166 through 168 or (resid 169 and (name N or \ name CA or name C or name O or name CB )) or resid 170 through 171 or (resid 172 \ and (name N or name CA or name C or name O or name CB )) or resid 187 through 1 \ 96 or resid 200 through 210 or (resid 211 and (name N or name CA or name C or na \ me O or name CB )) or (resid 215 and (name N or name CA or name C or name O or n \ ame CB )) or resid 216 through 263 or resid 265 through 528 or (resid 529 and (n \ ame N or name CA or name C or name O or name CB )) or resid 530 through 660 or ( \ resid 661 and (name N or name CA or name C or name O or name CB )) or resid 662 \ through 747 or (resid 748 and (name N or name CA or name C or name O or name CB \ )) or resid 749 through 810 or (resid 811 and (name N or name CA or name C or na \ me O or name CB )) or resid 812 through 827 or resid 856 through 939 or (resid 9 \ 40 and (name N or name CA or name C or name O or name CB )) or resid 941 through \ 984 or (resid 985 and (name N or name CA or name C or name O or name CB )) or r \ esid 986 through 1141 or (resid 1142 and (name N or name CA or name C or name O \ or name CB )) or resid 1143 through 1144 or (resid 1145 through 1146 and (name N \ or name CA or name C or name O or name CB )) or resid 1147 or resid 1301 throug \ h 1308)) selection = (chain 'C' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 95 or (resi \ d 96 through 97 and (name N or name CA or name C or name O or name CB )) or resi \ d 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or re \ sid 100 through 110 or (resid 111 through 113 and (name N or name CA or name C o \ r name O or name CB )) or resid 116 through 124 or (resid 125 and (name N or nam \ e CA or name C or name O or name CB )) or resid 126 through 128 or (resid 129 an \ d (name N or name CA or name C or name O or name CB )) or resid 130 through 133 \ or (resid 134 through 138 and (name N or name CA or name C or name O or name CB \ )) or resid 139 through 140 or resid 166 through 187 or (resid 188 and (name N o \ r name CA or name C or name O or name CB )) or resid 189 through 196 or resid 20 \ 0 through 211 or (resid 215 and (name N or name CA or name C or name O or name C \ B )) or resid 216 through 528 or (resid 529 and (name N or name CA or name C or \ name O or name CB )) or resid 530 through 567 or (resid 568 and (name N or name \ CA or name C or name O or name CB )) or resid 569 through 570 or (resid 571 and \ (name N or name CA or name C or name O or name CB )) or resid 572 through 581 or \ (resid 582 through 583 and (name N or name CA or name C or name O or name CB )) \ or resid 584 through 585 or (resid 586 and (name N or name CA or name C or name \ O or name CB )) or resid 587 through 1141 or (resid 1142 and (name N or name CA \ or name C or name O or name CB )) or resid 1143 or (resid 1144 through 1146 and \ (name N or name CA or name C or name O or name CB )) or resid 1147 or resid 140 \ 1 through 1408)) } ncs_group { reference = (chain 'D' and (resid 1 through 4 or resid 6 through 134)) selection = (chain 'E' and (resid 1 through 4 or resid 6 through 134)) selection = (chain 'F' and (resid 1 through 4 or resid 6 through 134)) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } 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=0.50 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: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.100 Check model and map are aligned: 0.350 Set scattering table: 0.220 Process input model: 76.560 Find NCS groups from input model: 2.190 Set up NCS constraints: 0.360 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4577 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 : 0.010 0.056 27671 Z= 0.666 Angle : 1.542 10.138 37646 Z= 1.047 Chirality : 0.087 0.630 4455 Planarity : 0.007 0.053 4764 Dihedral : 12.573 85.484 10828 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.44 % Favored : 96.25 % Rotamer: Outliers : 0.88 % Allowed : 5.15 % Favored : 93.98 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.07 (0.13), residues: 3314 helix: -0.61 (0.18), residues: 671 sheet: 0.11 (0.17), residues: 799 loop : -1.11 (0.13), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.007 TRP F 112 HIS 0.062 0.003 HIS C 655 PHE 0.036 0.006 PHE B 565 TYR 0.075 0.008 TYR E 80 ARG 0.024 0.003 ARG B 328 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 2914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 625 time to evaluate : 2.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 HIS cc_start: 0.5015 (t70) cc_final: 0.4799 (t-170) REVERT: A 64 TRP cc_start: 0.5818 (t60) cc_final: 0.5548 (t60) REVERT: A 170 TYR cc_start: 0.5195 (t80) cc_final: 0.4960 (t80) REVERT: A 218 GLN cc_start: 0.7287 (tt0) cc_final: 0.6901 (tm-30) REVERT: A 307 THR cc_start: 0.7977 (m) cc_final: 0.7652 (t) REVERT: A 316 SER cc_start: 0.4937 (t) cc_final: 0.4424 (p) REVERT: A 369 TYR cc_start: 0.6862 (p90) cc_final: 0.6219 (p90) REVERT: A 554 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7983 (mp0) REVERT: A 568 ASP cc_start: 0.6020 (t0) cc_final: 0.5685 (m-30) REVERT: A 591 SER cc_start: 0.6413 (t) cc_final: 0.6170 (p) REVERT: A 666 ILE cc_start: 0.7531 (mt) cc_final: 0.7188 (mp) REVERT: A 693 ILE cc_start: 0.6297 (pt) cc_final: 0.5895 (pt) REVERT: A 702 GLU cc_start: 0.7713 (pt0) cc_final: 0.7306 (mp0) REVERT: A 758 SER cc_start: 0.5122 (m) cc_final: 0.4845 (t) REVERT: A 804 GLN cc_start: 0.6830 (mm-40) cc_final: 0.6506 (mt0) REVERT: A 968 SER cc_start: 0.7296 (m) cc_final: 0.6792 (t) REVERT: B 54 LEU cc_start: 0.7836 (mt) cc_final: 0.7610 (mt) REVERT: B 290 ASP cc_start: 0.5856 (t0) cc_final: 0.5651 (t0) REVERT: B 320 VAL cc_start: 0.5679 (t) cc_final: 0.4743 (m) REVERT: B 358 ILE cc_start: 0.6547 (mm) cc_final: 0.6239 (mp) REVERT: B 359 SER cc_start: 0.6548 (p) cc_final: 0.6291 (t) REVERT: B 389 ASP cc_start: 0.8250 (m-30) cc_final: 0.7515 (t70) REVERT: B 400 PHE cc_start: 0.5290 (p90) cc_final: 0.4967 (p90) REVERT: B 409 GLN cc_start: 0.4909 (mt0) cc_final: 0.4680 (mt0) REVERT: B 465 GLU cc_start: 0.4787 (tt0) cc_final: 0.4399 (tt0) REVERT: B 468 ILE cc_start: 0.5543 (pp) cc_final: 0.5153 (mp) REVERT: B 492 LEU cc_start: 0.3638 (mt) cc_final: 0.3309 (mt) REVERT: B 497 PHE cc_start: 0.3858 (m-80) cc_final: 0.3617 (m-80) REVERT: B 508 TYR cc_start: 0.6093 (m-80) cc_final: 0.5487 (m-80) REVERT: B 534 VAL cc_start: 0.6403 (t) cc_final: 0.6102 (p) REVERT: B 574 ASP cc_start: 0.6189 (OUTLIER) cc_final: 0.5980 (p0) REVERT: B 646 ARG cc_start: 0.6710 (tpp80) cc_final: 0.5906 (tpt90) REVERT: B 912 THR cc_start: 0.7500 (OUTLIER) cc_final: 0.7171 (p) REVERT: B 973 ILE cc_start: 0.6821 (pt) cc_final: 0.6506 (pt) REVERT: B 977 LEU cc_start: 0.5435 (tp) cc_final: 0.5233 (tp) REVERT: B 990 GLU cc_start: 0.5034 (mt-10) cc_final: 0.4829 (tt0) REVERT: C 48 LEU cc_start: 0.6680 (mt) cc_final: 0.6082 (mt) REVERT: C 189 LEU cc_start: 0.5832 (tp) cc_final: 0.5129 (tp) REVERT: C 191 GLU cc_start: 0.5942 (mt-10) cc_final: 0.5610 (mp0) REVERT: C 306 PHE cc_start: 0.3737 (m-80) cc_final: 0.2833 (m-80) REVERT: C 314 GLN cc_start: 0.7042 (tt0) cc_final: 0.6836 (tm-30) REVERT: C 317 ASN cc_start: 0.6428 (m-40) cc_final: 0.6018 (t160) REVERT: C 319 ARG cc_start: 0.5624 (mtp85) cc_final: 0.5371 (mtp85) REVERT: C 385 THR cc_start: 0.6944 (p) cc_final: 0.6705 (p) REVERT: C 605 SER cc_start: 0.6048 (t) cc_final: 0.5565 (p) REVERT: C 607 GLN cc_start: 0.6725 (tt0) cc_final: 0.6206 (pt0) REVERT: C 740 MET cc_start: 0.6916 (ttt) cc_final: 0.6515 (ttm) REVERT: C 751 ASN cc_start: 0.7638 (m-40) cc_final: 0.7426 (m110) REVERT: C 791 THR cc_start: 0.7730 (OUTLIER) cc_final: 0.7522 (t) REVERT: C 973 ILE cc_start: 0.7384 (tt) cc_final: 0.6968 (pt) REVERT: C 1017 GLU cc_start: 0.6721 (tt0) cc_final: 0.6472 (tm-30) REVERT: C 1045 LYS cc_start: 0.7222 (tttt) cc_final: 0.6838 (tttt) REVERT: C 1125 ASN cc_start: 0.6483 (p0) cc_final: 0.6262 (p0) REVERT: C 1144 GLU cc_start: 0.7110 (mm-30) cc_final: 0.6572 (mp0) REVERT: F 51 ILE cc_start: 0.3968 (tt) cc_final: 0.1185 (tt) REVERT: F 71 SER cc_start: 0.5285 (p) cc_final: 0.5052 (t) REVERT: F 78 THR cc_start: 0.4483 (m) cc_final: 0.4113 (m) REVERT: F 83 MET cc_start: 0.2778 (mtp) cc_final: 0.1958 (ptp) outliers start: 25 outliers final: 3 residues processed: 645 average time/residue: 0.3954 time to fit residues: 398.6280 Evaluate side-chains 313 residues out of total 2914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 307 time to evaluate : 2.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain E residue 2 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 282 optimal weight: 0.6980 chunk 253 optimal weight: 0.9980 chunk 140 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 chunk 171 optimal weight: 2.9990 chunk 135 optimal weight: 7.9990 chunk 262 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 159 optimal weight: 0.9990 chunk 195 optimal weight: 1.9990 chunk 304 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 784 GLN A 804 GLN A 935 GLN A 955 ASN A 957 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN B 675 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 978 ASN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN C 607 GLN C 784 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN C1023 ASN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4603 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 27671 Z= 0.215 Angle : 0.636 11.458 37646 Z= 0.328 Chirality : 0.045 0.243 4455 Planarity : 0.003 0.032 4764 Dihedral : 6.226 62.687 5018 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.03 % Allowed : 10.54 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.14), residues: 3314 helix: 1.04 (0.20), residues: 678 sheet: 0.27 (0.17), residues: 812 loop : -0.58 (0.14), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 436 HIS 0.006 0.001 HIS C 519 PHE 0.026 0.002 PHE B 541 TYR 0.033 0.002 TYR D 116 ARG 0.004 0.001 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 362 time to evaluate : 2.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.6836 (OUTLIER) cc_final: 0.6593 (m) REVERT: A 49 HIS cc_start: 0.5124 (t70) cc_final: 0.4825 (t-170) REVERT: A 64 TRP cc_start: 0.5794 (t60) cc_final: 0.5540 (t60) REVERT: A 129 LYS cc_start: 0.5938 (pttt) cc_final: 0.5708 (ptpp) REVERT: A 218 GLN cc_start: 0.7209 (tt0) cc_final: 0.6874 (tm-30) REVERT: A 305 SER cc_start: 0.7070 (t) cc_final: 0.6865 (t) REVERT: A 316 SER cc_start: 0.5365 (t) cc_final: 0.5017 (p) REVERT: A 554 GLU cc_start: 0.8446 (mt-10) cc_final: 0.8192 (mp0) REVERT: A 591 SER cc_start: 0.6598 (t) cc_final: 0.6339 (p) REVERT: A 699 LEU cc_start: 0.7575 (mt) cc_final: 0.7024 (mt) REVERT: A 702 GLU cc_start: 0.7653 (pt0) cc_final: 0.7299 (mp0) REVERT: A 758 SER cc_start: 0.4935 (m) cc_final: 0.4690 (t) REVERT: A 804 GLN cc_start: 0.6890 (mm110) cc_final: 0.6563 (mt0) REVERT: A 808 ASP cc_start: 0.5540 (t0) cc_final: 0.5089 (m-30) REVERT: A 957 GLN cc_start: 0.6149 (mt0) cc_final: 0.5915 (tm-30) REVERT: A 968 SER cc_start: 0.7378 (m) cc_final: 0.6555 (p) REVERT: A 1010 GLN cc_start: 0.5775 (mm-40) cc_final: 0.5542 (mt0) REVERT: A 1107 ARG cc_start: 0.6556 (mtm180) cc_final: 0.6018 (mtm-85) REVERT: B 54 LEU cc_start: 0.7858 (mt) cc_final: 0.7638 (mt) REVERT: B 357 ARG cc_start: 0.7869 (ttt180) cc_final: 0.7657 (ttm110) REVERT: B 358 ILE cc_start: 0.6626 (mm) cc_final: 0.6134 (mp) REVERT: B 389 ASP cc_start: 0.8130 (m-30) cc_final: 0.7469 (t70) REVERT: B 409 GLN cc_start: 0.4553 (mt0) cc_final: 0.3999 (mt0) REVERT: B 646 ARG cc_start: 0.6798 (tpp80) cc_final: 0.5862 (tpt90) REVERT: B 671 CYS cc_start: 0.5673 (m) cc_final: 0.5241 (m) REVERT: B 912 THR cc_start: 0.6988 (OUTLIER) cc_final: 0.6679 (p) REVERT: C 189 LEU cc_start: 0.5666 (tp) cc_final: 0.5463 (tp) REVERT: C 314 GLN cc_start: 0.7171 (tt0) cc_final: 0.6920 (tm-30) REVERT: C 317 ASN cc_start: 0.5940 (m-40) cc_final: 0.5706 (t0) REVERT: C 557 LYS cc_start: 0.7375 (mttm) cc_final: 0.7081 (mttt) REVERT: C 605 SER cc_start: 0.5659 (t) cc_final: 0.5304 (p) REVERT: C 607 GLN cc_start: 0.6521 (tt0) cc_final: 0.6058 (pt0) REVERT: C 740 MET cc_start: 0.6835 (ttt) cc_final: 0.6519 (ttm) REVERT: C 751 ASN cc_start: 0.7531 (m-40) cc_final: 0.7274 (m110) REVERT: C 804 GLN cc_start: 0.7369 (mm-40) cc_final: 0.7096 (mt0) REVERT: C 856 ASN cc_start: 0.3611 (OUTLIER) cc_final: 0.3249 (m110) REVERT: C 973 ILE cc_start: 0.7423 (tt) cc_final: 0.7007 (pt) REVERT: C 1045 LYS cc_start: 0.7049 (tttt) cc_final: 0.6812 (tptm) REVERT: C 1125 ASN cc_start: 0.6329 (p0) cc_final: 0.6075 (p0) REVERT: C 1144 GLU cc_start: 0.7275 (mm-30) cc_final: 0.6739 (mp0) REVERT: F 34 MET cc_start: 0.3047 (OUTLIER) cc_final: 0.2724 (ptp) REVERT: F 47 PHE cc_start: 0.4039 (t80) cc_final: 0.3308 (t80) REVERT: F 83 MET cc_start: 0.2781 (mtp) cc_final: 0.1956 (ptp) outliers start: 58 outliers final: 28 residues processed: 405 average time/residue: 0.3680 time to fit residues: 241.1610 Evaluate side-chains 311 residues out of total 2914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 279 time to evaluate : 2.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain F residue 34 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 169 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 253 optimal weight: 2.9990 chunk 207 optimal weight: 0.0980 chunk 83 optimal weight: 3.9990 chunk 304 optimal weight: 2.9990 chunk 329 optimal weight: 10.0000 chunk 271 optimal weight: 1.9990 chunk 302 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 chunk 244 optimal weight: 8.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 207 HIS A 450 ASN A 644 GLN A1048 HIS B 613 GLN B 655 HIS B 675 GLN B 901 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1048 HIS C 125 ASN C 450 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN C1005 GLN C1048 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4633 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 : 0.004 0.078 27671 Z= 0.247 Angle : 0.607 10.519 37646 Z= 0.311 Chirality : 0.045 0.312 4455 Planarity : 0.004 0.062 4764 Dihedral : 5.811 57.687 5014 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.29 % Favored : 96.65 % Rotamer: Outliers : 2.84 % Allowed : 11.38 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.12 (0.14), residues: 3314 helix: 1.36 (0.20), residues: 685 sheet: 0.27 (0.17), residues: 848 loop : -0.49 (0.14), residues: 1781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 436 HIS 0.012 0.001 HIS C 519 PHE 0.032 0.002 PHE A 32 TYR 0.028 0.002 TYR A 369 ARG 0.004 0.000 ARG C 567 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 303 time to evaluate : 2.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.6954 (m) cc_final: 0.6730 (m) REVERT: A 48 LEU cc_start: 0.7487 (mt) cc_final: 0.7273 (mp) REVERT: A 49 HIS cc_start: 0.5105 (t70) cc_final: 0.4680 (t-170) REVERT: A 64 TRP cc_start: 0.5804 (t60) cc_final: 0.5568 (t60) REVERT: A 129 LYS cc_start: 0.5987 (OUTLIER) cc_final: 0.5706 (pttp) REVERT: A 316 SER cc_start: 0.6010 (t) cc_final: 0.5651 (p) REVERT: A 554 GLU cc_start: 0.8333 (mt-10) cc_final: 0.8119 (mm-30) REVERT: A 591 SER cc_start: 0.6643 (t) cc_final: 0.6376 (p) REVERT: A 702 GLU cc_start: 0.7676 (pt0) cc_final: 0.7287 (mp0) REVERT: A 758 SER cc_start: 0.5260 (m) cc_final: 0.4961 (t) REVERT: A 804 GLN cc_start: 0.6988 (mm110) cc_final: 0.6638 (mp10) REVERT: A 808 ASP cc_start: 0.5377 (t0) cc_final: 0.5058 (m-30) REVERT: A 854 LYS cc_start: 0.7387 (tttt) cc_final: 0.6697 (tptt) REVERT: A 855 PHE cc_start: 0.6735 (m-10) cc_final: 0.6469 (m-10) REVERT: A 957 GLN cc_start: 0.6016 (mt0) cc_final: 0.5770 (tm-30) REVERT: A 1010 GLN cc_start: 0.5889 (mm-40) cc_final: 0.5579 (mt0) REVERT: B 241 LEU cc_start: 0.8050 (mt) cc_final: 0.7786 (pp) REVERT: B 278 LYS cc_start: 0.5074 (tttt) cc_final: 0.4859 (ptmt) REVERT: B 358 ILE cc_start: 0.6370 (mm) cc_final: 0.6116 (mp) REVERT: B 389 ASP cc_start: 0.8290 (m-30) cc_final: 0.7641 (t70) REVERT: B 409 GLN cc_start: 0.4795 (mt0) cc_final: 0.4262 (mt0) REVERT: B 508 TYR cc_start: 0.6284 (m-80) cc_final: 0.5550 (m-80) REVERT: B 538 CYS cc_start: 0.5208 (m) cc_final: 0.4105 (t) REVERT: B 646 ARG cc_start: 0.6810 (tpp80) cc_final: 0.5901 (tpt90) REVERT: B 671 CYS cc_start: 0.5528 (m) cc_final: 0.5188 (m) REVERT: C 314 GLN cc_start: 0.6811 (tt0) cc_final: 0.6470 (tm-30) REVERT: C 565 PHE cc_start: 0.4914 (p90) cc_final: 0.4676 (p90) REVERT: C 605 SER cc_start: 0.5716 (t) cc_final: 0.5240 (p) REVERT: C 607 GLN cc_start: 0.6265 (tt0) cc_final: 0.5682 (pt0) REVERT: C 740 MET cc_start: 0.6690 (ttt) cc_final: 0.6427 (ttm) REVERT: C 751 ASN cc_start: 0.7434 (m-40) cc_final: 0.7197 (m110) REVERT: C 804 GLN cc_start: 0.7446 (mm110) cc_final: 0.7239 (mt0) REVERT: C 856 ASN cc_start: 0.3998 (OUTLIER) cc_final: 0.3666 (m110) REVERT: C 973 ILE cc_start: 0.7248 (tt) cc_final: 0.6789 (pt) REVERT: C 1045 LYS cc_start: 0.6937 (tttt) cc_final: 0.6700 (tptm) REVERT: C 1125 ASN cc_start: 0.6215 (p0) cc_final: 0.5957 (p0) REVERT: C 1144 GLU cc_start: 0.7257 (mm-30) cc_final: 0.6709 (mp0) REVERT: F 34 MET cc_start: 0.3260 (ptt) cc_final: 0.2984 (ptp) outliers start: 78 outliers final: 57 residues processed: 366 average time/residue: 0.3538 time to fit residues: 213.4063 Evaluate side-chains 308 residues out of total 2914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 249 time to evaluate : 2.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 107 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 301 optimal weight: 9.9990 chunk 229 optimal weight: 30.0000 chunk 158 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 145 optimal weight: 5.9990 chunk 204 optimal weight: 5.9990 chunk 305 optimal weight: 10.0000 chunk 323 optimal weight: 0.8980 chunk 159 optimal weight: 1.9990 chunk 289 optimal weight: 0.7980 chunk 87 optimal weight: 0.0870 overall best weight: 1.5562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS B 30 ASN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 439 ASN B 675 GLN ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN C 762 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4650 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 27671 Z= 0.254 Angle : 0.600 13.311 37646 Z= 0.307 Chirality : 0.048 0.954 4455 Planarity : 0.004 0.043 4764 Dihedral : 5.710 58.090 5014 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.11 % Favored : 96.83 % Rotamer: Outliers : 3.40 % Allowed : 12.75 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.18 (0.14), residues: 3314 helix: 1.57 (0.20), residues: 672 sheet: 0.33 (0.17), residues: 814 loop : -0.50 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 104 HIS 0.008 0.001 HIS C 519 PHE 0.024 0.002 PHE B 541 TYR 0.026 0.002 TYR A 369 ARG 0.003 0.000 ARG C 328 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 285 time to evaluate : 3.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.7574 (mt) cc_final: 0.7373 (mp) REVERT: A 49 HIS cc_start: 0.4951 (t70) cc_final: 0.4494 (t-170) REVERT: A 129 LYS cc_start: 0.6030 (OUTLIER) cc_final: 0.5728 (pttp) REVERT: A 316 SER cc_start: 0.6260 (t) cc_final: 0.5856 (p) REVERT: A 554 GLU cc_start: 0.8301 (mt-10) cc_final: 0.8067 (mm-30) REVERT: A 591 SER cc_start: 0.6725 (t) cc_final: 0.6445 (p) REVERT: A 702 GLU cc_start: 0.7620 (pt0) cc_final: 0.7253 (mp0) REVERT: A 758 SER cc_start: 0.5351 (m) cc_final: 0.5124 (t) REVERT: A 804 GLN cc_start: 0.7054 (mm110) cc_final: 0.6702 (mp10) REVERT: A 808 ASP cc_start: 0.5253 (t0) cc_final: 0.4992 (m-30) REVERT: A 957 GLN cc_start: 0.6000 (mt0) cc_final: 0.5673 (tm-30) REVERT: A 1010 GLN cc_start: 0.5740 (mm-40) cc_final: 0.5370 (mt0) REVERT: A 1107 ARG cc_start: 0.7052 (mtm180) cc_final: 0.6681 (mtm180) REVERT: B 241 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.8032 (pp) REVERT: B 278 LYS cc_start: 0.5382 (tttt) cc_final: 0.5158 (ptmt) REVERT: B 357 ARG cc_start: 0.7671 (ttt180) cc_final: 0.7390 (ttm110) REVERT: B 358 ILE cc_start: 0.6278 (mm) cc_final: 0.5972 (mp) REVERT: B 389 ASP cc_start: 0.8430 (m-30) cc_final: 0.7822 (t70) REVERT: B 409 GLN cc_start: 0.4885 (mt0) cc_final: 0.4284 (mm-40) REVERT: B 508 TYR cc_start: 0.6298 (m-80) cc_final: 0.5584 (m-80) REVERT: B 590 CYS cc_start: 0.3865 (OUTLIER) cc_final: 0.3598 (t) REVERT: B 646 ARG cc_start: 0.6788 (tpp80) cc_final: 0.5955 (tpt90) REVERT: B 671 CYS cc_start: 0.6000 (m) cc_final: 0.5559 (m) REVERT: B 808 ASP cc_start: 0.6777 (t0) cc_final: 0.6563 (t70) REVERT: C 554 GLU cc_start: 0.7522 (mp0) cc_final: 0.7087 (pm20) REVERT: C 605 SER cc_start: 0.5787 (t) cc_final: 0.5471 (p) REVERT: C 740 MET cc_start: 0.6746 (ttt) cc_final: 0.6483 (ttm) REVERT: C 751 ASN cc_start: 0.7376 (m-40) cc_final: 0.7099 (m110) REVERT: C 791 THR cc_start: 0.7423 (OUTLIER) cc_final: 0.7191 (m) REVERT: C 796 ASP cc_start: 0.4625 (t0) cc_final: 0.4334 (t0) REVERT: C 973 ILE cc_start: 0.7184 (tt) cc_final: 0.6724 (pt) REVERT: C 977 LEU cc_start: 0.5518 (OUTLIER) cc_final: 0.5292 (mp) REVERT: C 1045 LYS cc_start: 0.6897 (tttt) cc_final: 0.6678 (tptm) REVERT: C 1144 GLU cc_start: 0.7205 (mm-30) cc_final: 0.6668 (mp0) REVERT: F 34 MET cc_start: 0.2973 (ptt) cc_final: 0.2641 (ptp) outliers start: 94 outliers final: 60 residues processed: 362 average time/residue: 0.3568 time to fit residues: 213.3755 Evaluate side-chains 327 residues out of total 2914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 262 time to evaluate : 3.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 107 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 269 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 241 optimal weight: 0.5980 chunk 133 optimal weight: 10.0000 chunk 276 optimal weight: 3.9990 chunk 223 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 165 optimal weight: 2.9990 chunk 290 optimal weight: 0.4980 chunk 81 optimal weight: 4.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1071 GLN B 196 ASN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN B 564 GLN ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4663 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 27671 Z= 0.307 Angle : 0.612 10.109 37646 Z= 0.313 Chirality : 0.046 0.263 4455 Planarity : 0.004 0.048 4764 Dihedral : 5.645 59.925 5014 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.65 % Favored : 96.29 % Rotamer: Outliers : 3.33 % Allowed : 13.66 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 0.02 (0.14), residues: 3314 helix: 1.39 (0.20), residues: 677 sheet: 0.29 (0.17), residues: 829 loop : -0.63 (0.14), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 104 HIS 0.008 0.001 HIS C 519 PHE 0.024 0.002 PHE B 541 TYR 0.025 0.002 TYR A 369 ARG 0.011 0.001 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 277 time to evaluate : 2.924 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.7620 (mt) cc_final: 0.7410 (mp) REVERT: A 129 LYS cc_start: 0.5995 (OUTLIER) cc_final: 0.5711 (pttp) REVERT: A 316 SER cc_start: 0.6528 (t) cc_final: 0.6104 (p) REVERT: A 554 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7898 (mm-30) REVERT: A 591 SER cc_start: 0.6976 (t) cc_final: 0.6701 (p) REVERT: A 702 GLU cc_start: 0.7788 (pt0) cc_final: 0.7342 (mp0) REVERT: A 758 SER cc_start: 0.5203 (m) cc_final: 0.4926 (t) REVERT: A 773 GLU cc_start: 0.5099 (tt0) cc_final: 0.4609 (tt0) REVERT: A 804 GLN cc_start: 0.6788 (mm110) cc_final: 0.6494 (mp10) REVERT: A 808 ASP cc_start: 0.5289 (t0) cc_final: 0.5070 (m-30) REVERT: A 931 ILE cc_start: 0.5999 (mm) cc_final: 0.5766 (mm) REVERT: A 957 GLN cc_start: 0.5959 (mt0) cc_final: 0.5711 (tm-30) REVERT: A 1010 GLN cc_start: 0.5746 (mm-40) cc_final: 0.5373 (mt0) REVERT: A 1107 ARG cc_start: 0.6888 (mtm180) cc_final: 0.6555 (mtm180) REVERT: B 241 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.8014 (pp) REVERT: B 278 LYS cc_start: 0.5592 (tttt) cc_final: 0.5369 (ptmt) REVERT: B 346 ARG cc_start: 0.6802 (ptt-90) cc_final: 0.6522 (ttm-80) REVERT: B 357 ARG cc_start: 0.7669 (ttt180) cc_final: 0.7415 (ttm110) REVERT: B 358 ILE cc_start: 0.6304 (mm) cc_final: 0.6056 (mp) REVERT: B 387 LEU cc_start: 0.7316 (mt) cc_final: 0.7108 (mt) REVERT: B 389 ASP cc_start: 0.8385 (m-30) cc_final: 0.7928 (p0) REVERT: B 646 ARG cc_start: 0.6807 (tpp80) cc_final: 0.5957 (tpt90) REVERT: B 671 CYS cc_start: 0.6111 (m) cc_final: 0.5643 (m) REVERT: B 808 ASP cc_start: 0.6519 (t0) cc_final: 0.6302 (t70) REVERT: C 48 LEU cc_start: 0.7448 (mt) cc_final: 0.7115 (mt) REVERT: C 554 GLU cc_start: 0.7525 (mp0) cc_final: 0.7087 (pm20) REVERT: C 605 SER cc_start: 0.5644 (t) cc_final: 0.5104 (p) REVERT: C 607 GLN cc_start: 0.6189 (tt0) cc_final: 0.5623 (pt0) REVERT: C 740 MET cc_start: 0.6790 (ttt) cc_final: 0.6530 (ttm) REVERT: C 796 ASP cc_start: 0.5119 (t0) cc_final: 0.4764 (t0) REVERT: C 973 ILE cc_start: 0.7140 (tt) cc_final: 0.6701 (pt) REVERT: C 1045 LYS cc_start: 0.6735 (tttt) cc_final: 0.6533 (tptm) REVERT: C 1144 GLU cc_start: 0.7243 (mm-30) cc_final: 0.6733 (mp0) outliers start: 92 outliers final: 67 residues processed: 351 average time/residue: 0.3476 time to fit residues: 201.6645 Evaluate side-chains 316 residues out of total 2914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 247 time to evaluate : 3.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 107 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 108 optimal weight: 1.9990 chunk 291 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 190 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 324 optimal weight: 7.9990 chunk 269 optimal weight: 0.7980 chunk 150 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 170 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 207 HIS ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS C 751 ASN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4661 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 27671 Z= 0.224 Angle : 0.561 10.171 37646 Z= 0.287 Chirality : 0.044 0.233 4455 Planarity : 0.004 0.078 4764 Dihedral : 5.344 56.759 5014 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.99 % Favored : 96.95 % Rotamer: Outliers : 2.80 % Allowed : 14.57 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.14 (0.14), residues: 3314 helix: 1.65 (0.20), residues: 674 sheet: 0.33 (0.17), residues: 822 loop : -0.60 (0.14), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 104 HIS 0.010 0.001 HIS A 49 PHE 0.043 0.002 PHE B 140 TYR 0.022 0.001 TYR A 369 ARG 0.013 0.000 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 279 time to evaluate : 3.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.7578 (mt) cc_final: 0.7360 (mp) REVERT: A 129 LYS cc_start: 0.5961 (OUTLIER) cc_final: 0.5683 (pttp) REVERT: A 316 SER cc_start: 0.6363 (t) cc_final: 0.5942 (p) REVERT: A 554 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7851 (mm-30) REVERT: A 591 SER cc_start: 0.6946 (t) cc_final: 0.6664 (p) REVERT: A 702 GLU cc_start: 0.7783 (pt0) cc_final: 0.7345 (mp0) REVERT: A 758 SER cc_start: 0.5420 (m) cc_final: 0.5151 (t) REVERT: A 804 GLN cc_start: 0.6805 (mm110) cc_final: 0.6505 (mp10) REVERT: A 808 ASP cc_start: 0.5321 (t0) cc_final: 0.5093 (m-30) REVERT: A 931 ILE cc_start: 0.6025 (mm) cc_final: 0.5805 (mm) REVERT: A 957 GLN cc_start: 0.5959 (mt0) cc_final: 0.5697 (tm-30) REVERT: A 1010 GLN cc_start: 0.5890 (mm-40) cc_final: 0.5494 (mt0) REVERT: A 1107 ARG cc_start: 0.6862 (mtm180) cc_final: 0.6391 (mtm180) REVERT: B 278 LYS cc_start: 0.5740 (tttt) cc_final: 0.5474 (ptmt) REVERT: B 346 ARG cc_start: 0.6843 (ptt-90) cc_final: 0.6450 (ttm-80) REVERT: B 347 PHE cc_start: 0.2676 (m-10) cc_final: 0.2423 (m-80) REVERT: B 389 ASP cc_start: 0.8303 (m-30) cc_final: 0.7776 (t70) REVERT: B 646 ARG cc_start: 0.6737 (tpp80) cc_final: 0.5869 (tpt90) REVERT: B 671 CYS cc_start: 0.6083 (m) cc_final: 0.5607 (m) REVERT: B 808 ASP cc_start: 0.6397 (t0) cc_final: 0.6191 (t70) REVERT: B 817 PHE cc_start: 0.5985 (t80) cc_final: 0.5779 (t80) REVERT: B 988 GLU cc_start: 0.6461 (OUTLIER) cc_final: 0.6150 (pt0) REVERT: C 48 LEU cc_start: 0.7150 (mt) cc_final: 0.6756 (mt) REVERT: C 554 GLU cc_start: 0.7600 (mp0) cc_final: 0.7068 (pm20) REVERT: C 562 PHE cc_start: 0.6764 (p90) cc_final: 0.6501 (p90) REVERT: C 605 SER cc_start: 0.5596 (t) cc_final: 0.5174 (p) REVERT: C 740 MET cc_start: 0.6731 (ttt) cc_final: 0.6490 (ttm) REVERT: C 791 THR cc_start: 0.7337 (OUTLIER) cc_final: 0.7063 (m) REVERT: C 796 ASP cc_start: 0.5104 (t0) cc_final: 0.4727 (t0) REVERT: C 973 ILE cc_start: 0.7308 (tt) cc_final: 0.6866 (pt) REVERT: C 1144 GLU cc_start: 0.7309 (mm-30) cc_final: 0.6798 (mp0) outliers start: 77 outliers final: 59 residues processed: 342 average time/residue: 0.3611 time to fit residues: 204.7041 Evaluate side-chains 317 residues out of total 2914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 255 time to evaluate : 2.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 107 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 312 optimal weight: 9.9990 chunk 36 optimal weight: 8.9990 chunk 184 optimal weight: 4.9990 chunk 236 optimal weight: 9.9990 chunk 183 optimal weight: 0.9990 chunk 272 optimal weight: 0.9990 chunk 180 optimal weight: 0.0970 chunk 322 optimal weight: 8.9990 chunk 202 optimal weight: 9.9990 chunk 196 optimal weight: 2.9990 chunk 149 optimal weight: 0.6980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN B 675 GLN ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4666 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 27671 Z= 0.206 Angle : 0.554 10.228 37646 Z= 0.283 Chirality : 0.044 0.214 4455 Planarity : 0.004 0.052 4764 Dihedral : 5.173 57.882 5014 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.62 % Favored : 96.32 % Rotamer: Outliers : 2.87 % Allowed : 15.13 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.21 (0.14), residues: 3314 helix: 1.77 (0.20), residues: 676 sheet: 0.33 (0.17), residues: 826 loop : -0.56 (0.14), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 104 HIS 0.003 0.001 HIS C 207 PHE 0.025 0.001 PHE B 541 TYR 0.028 0.001 TYR C 904 ARG 0.014 0.000 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 272 time to evaluate : 3.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.7569 (mt) cc_final: 0.7357 (mt) REVERT: A 90 VAL cc_start: 0.7193 (OUTLIER) cc_final: 0.6693 (m) REVERT: A 102 ARG cc_start: 0.4820 (mmt90) cc_final: 0.3414 (mtp180) REVERT: A 129 LYS cc_start: 0.5938 (OUTLIER) cc_final: 0.5665 (pttp) REVERT: A 316 SER cc_start: 0.6496 (t) cc_final: 0.6074 (p) REVERT: A 554 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7843 (mm-30) REVERT: A 591 SER cc_start: 0.6894 (t) cc_final: 0.6616 (p) REVERT: A 654 GLU cc_start: 0.5560 (mp0) cc_final: 0.5302 (mp0) REVERT: A 702 GLU cc_start: 0.7752 (pt0) cc_final: 0.7308 (mp0) REVERT: A 804 GLN cc_start: 0.6830 (mm110) cc_final: 0.6440 (mp10) REVERT: A 808 ASP cc_start: 0.5319 (t0) cc_final: 0.5095 (m-30) REVERT: A 931 ILE cc_start: 0.6042 (mm) cc_final: 0.5807 (mm) REVERT: A 957 GLN cc_start: 0.5928 (mt0) cc_final: 0.5690 (tm-30) REVERT: A 1010 GLN cc_start: 0.5895 (mm-40) cc_final: 0.5496 (mt0) REVERT: A 1107 ARG cc_start: 0.7482 (mtm180) cc_final: 0.7208 (mtm180) REVERT: B 278 LYS cc_start: 0.5669 (tttt) cc_final: 0.5399 (ptmt) REVERT: B 346 ARG cc_start: 0.6959 (ptt-90) cc_final: 0.6614 (ttm-80) REVERT: B 347 PHE cc_start: 0.2763 (m-10) cc_final: 0.2351 (m-80) REVERT: B 357 ARG cc_start: 0.7756 (ttt180) cc_final: 0.7437 (ttm110) REVERT: B 389 ASP cc_start: 0.8274 (m-30) cc_final: 0.7782 (t70) REVERT: B 564 GLN cc_start: 0.4234 (mt0) cc_final: 0.4014 (mt0) REVERT: B 646 ARG cc_start: 0.6673 (tpp80) cc_final: 0.5837 (tpt90) REVERT: B 671 CYS cc_start: 0.6085 (m) cc_final: 0.5588 (m) REVERT: B 808 ASP cc_start: 0.6336 (t0) cc_final: 0.6112 (t70) REVERT: B 817 PHE cc_start: 0.6058 (t80) cc_final: 0.5837 (t80) REVERT: B 988 GLU cc_start: 0.6578 (OUTLIER) cc_final: 0.6277 (pt0) REVERT: C 48 LEU cc_start: 0.7174 (mt) cc_final: 0.6789 (mt) REVERT: C 453 TYR cc_start: 0.4297 (p90) cc_final: 0.3929 (p90) REVERT: C 554 GLU cc_start: 0.7693 (mp0) cc_final: 0.7092 (pm20) REVERT: C 562 PHE cc_start: 0.6863 (p90) cc_final: 0.6604 (p90) REVERT: C 740 MET cc_start: 0.6582 (ttt) cc_final: 0.6355 (ttm) REVERT: C 791 THR cc_start: 0.7339 (OUTLIER) cc_final: 0.7065 (m) REVERT: C 973 ILE cc_start: 0.7294 (tt) cc_final: 0.6817 (pt) REVERT: C 1144 GLU cc_start: 0.7289 (mm-30) cc_final: 0.6745 (mp0) REVERT: D 53 TRP cc_start: 0.4369 (t-100) cc_final: 0.4150 (t-100) REVERT: F 34 MET cc_start: 0.2819 (ptt) cc_final: 0.2477 (ptp) outliers start: 79 outliers final: 60 residues processed: 337 average time/residue: 0.3590 time to fit residues: 197.9365 Evaluate side-chains 313 residues out of total 2914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 249 time to evaluate : 2.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 107 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 199 optimal weight: 8.9990 chunk 128 optimal weight: 3.9990 chunk 192 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 205 optimal weight: 0.9980 chunk 219 optimal weight: 6.9990 chunk 159 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 253 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 901 GLN B 414 GLN ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 122 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4680 moved from start: 0.4844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 27671 Z= 0.351 Angle : 0.637 10.849 37646 Z= 0.323 Chirality : 0.046 0.238 4455 Planarity : 0.004 0.058 4764 Dihedral : 5.764 59.110 5014 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.17 % Favored : 95.77 % Rotamer: Outliers : 3.29 % Allowed : 14.92 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.09 (0.14), residues: 3314 helix: 1.45 (0.20), residues: 677 sheet: 0.20 (0.17), residues: 811 loop : -0.75 (0.14), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 64 HIS 0.004 0.001 HIS B1064 PHE 0.024 0.002 PHE C 65 TYR 0.030 0.002 TYR C 904 ARG 0.015 0.001 ARG F 103 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 254 time to evaluate : 3.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 VAL cc_start: 0.7357 (OUTLIER) cc_final: 0.6915 (m) REVERT: A 129 LYS cc_start: 0.5591 (OUTLIER) cc_final: 0.5368 (pttp) REVERT: A 316 SER cc_start: 0.6652 (t) cc_final: 0.6142 (p) REVERT: A 546 LEU cc_start: 0.7181 (OUTLIER) cc_final: 0.6970 (mp) REVERT: A 554 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7858 (mm-30) REVERT: A 591 SER cc_start: 0.6898 (t) cc_final: 0.6609 (p) REVERT: A 702 GLU cc_start: 0.7779 (pt0) cc_final: 0.7341 (mp0) REVERT: A 773 GLU cc_start: 0.5205 (tt0) cc_final: 0.4821 (tt0) REVERT: A 804 GLN cc_start: 0.6641 (mm110) cc_final: 0.6276 (mp10) REVERT: A 808 ASP cc_start: 0.5245 (t0) cc_final: 0.5032 (m-30) REVERT: A 931 ILE cc_start: 0.6075 (mm) cc_final: 0.5832 (mm) REVERT: A 957 GLN cc_start: 0.5852 (mt0) cc_final: 0.5588 (tm-30) REVERT: A 1010 GLN cc_start: 0.5931 (mm-40) cc_final: 0.5555 (mt0) REVERT: A 1107 ARG cc_start: 0.6924 (mtm180) cc_final: 0.6663 (mtm180) REVERT: B 138 ASP cc_start: 0.7739 (t0) cc_final: 0.7331 (m-30) REVERT: B 278 LYS cc_start: 0.5769 (tttt) cc_final: 0.5471 (ptmt) REVERT: B 346 ARG cc_start: 0.7178 (ptt-90) cc_final: 0.6813 (ttm-80) REVERT: B 357 ARG cc_start: 0.7487 (ttt180) cc_final: 0.7222 (ttm110) REVERT: B 389 ASP cc_start: 0.8284 (m-30) cc_final: 0.7951 (p0) REVERT: B 646 ARG cc_start: 0.6888 (tpp80) cc_final: 0.6065 (tpt90) REVERT: B 671 CYS cc_start: 0.6178 (m) cc_final: 0.5689 (m) REVERT: B 808 ASP cc_start: 0.6365 (t0) cc_final: 0.6152 (t70) REVERT: B 988 GLU cc_start: 0.6515 (OUTLIER) cc_final: 0.6196 (pt0) REVERT: B 1139 ASP cc_start: 0.6718 (t0) cc_final: 0.6446 (t0) REVERT: C 48 LEU cc_start: 0.7110 (mt) cc_final: 0.6705 (mt) REVERT: C 554 GLU cc_start: 0.7636 (mp0) cc_final: 0.7113 (pm20) REVERT: C 562 PHE cc_start: 0.6638 (p90) cc_final: 0.6332 (p90) REVERT: C 740 MET cc_start: 0.6664 (ttt) cc_final: 0.6389 (ttm) REVERT: C 791 THR cc_start: 0.7325 (OUTLIER) cc_final: 0.7043 (m) REVERT: C 973 ILE cc_start: 0.7084 (tt) cc_final: 0.6512 (pt) outliers start: 91 outliers final: 66 residues processed: 328 average time/residue: 0.3724 time to fit residues: 200.6876 Evaluate side-chains 312 residues out of total 2914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 241 time to evaluate : 2.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 107 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 293 optimal weight: 0.0070 chunk 309 optimal weight: 7.9990 chunk 282 optimal weight: 0.5980 chunk 300 optimal weight: 0.0370 chunk 181 optimal weight: 0.0570 chunk 131 optimal weight: 3.9990 chunk 236 optimal weight: 8.9990 chunk 92 optimal weight: 3.9990 chunk 271 optimal weight: 0.6980 chunk 284 optimal weight: 0.6980 chunk 299 optimal weight: 5.9990 overall best weight: 0.2794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 784 GLN A 955 ASN B 30 ASN B 414 GLN B 460 ASN ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN C 388 ASN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4664 moved from start: 0.4901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 27671 Z= 0.142 Angle : 0.542 10.712 37646 Z= 0.276 Chirality : 0.043 0.244 4455 Planarity : 0.004 0.055 4764 Dihedral : 5.043 53.775 5014 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.60 % Favored : 97.34 % Rotamer: Outliers : 1.96 % Allowed : 16.32 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.26 (0.14), residues: 3314 helix: 1.86 (0.20), residues: 681 sheet: 0.27 (0.17), residues: 819 loop : -0.51 (0.14), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 104 HIS 0.003 0.000 HIS A 49 PHE 0.027 0.001 PHE C 133 TYR 0.023 0.001 TYR B 200 ARG 0.010 0.000 ARG F 103 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 281 time to evaluate : 2.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.7536 (mt) cc_final: 0.7163 (mp) REVERT: A 90 VAL cc_start: 0.7215 (OUTLIER) cc_final: 0.6731 (m) REVERT: A 102 ARG cc_start: 0.4913 (mmt90) cc_final: 0.3647 (mtp180) REVERT: A 316 SER cc_start: 0.6310 (t) cc_final: 0.5898 (p) REVERT: A 554 GLU cc_start: 0.8285 (mt-10) cc_final: 0.7907 (mm-30) REVERT: A 591 SER cc_start: 0.6680 (t) cc_final: 0.6393 (p) REVERT: A 702 GLU cc_start: 0.7769 (pt0) cc_final: 0.7324 (mp0) REVERT: A 804 GLN cc_start: 0.6712 (mm110) cc_final: 0.6222 (mp10) REVERT: A 957 GLN cc_start: 0.5921 (mt0) cc_final: 0.5654 (tm-30) REVERT: A 1010 GLN cc_start: 0.5955 (mm-40) cc_final: 0.5530 (mt0) REVERT: A 1107 ARG cc_start: 0.7395 (mtm180) cc_final: 0.7149 (mtm180) REVERT: B 138 ASP cc_start: 0.7679 (t0) cc_final: 0.7300 (m-30) REVERT: B 278 LYS cc_start: 0.5773 (tttt) cc_final: 0.5487 (ptmt) REVERT: B 346 ARG cc_start: 0.7092 (ptt-90) cc_final: 0.6744 (ttm-80) REVERT: B 357 ARG cc_start: 0.7686 (ttt180) cc_final: 0.7391 (ttm110) REVERT: B 389 ASP cc_start: 0.8044 (m-30) cc_final: 0.7825 (p0) REVERT: B 646 ARG cc_start: 0.6770 (tpp80) cc_final: 0.5811 (tpt90) REVERT: B 671 CYS cc_start: 0.5982 (m) cc_final: 0.5494 (m) REVERT: B 808 ASP cc_start: 0.6414 (t0) cc_final: 0.6193 (t70) REVERT: B 912 THR cc_start: 0.6618 (OUTLIER) cc_final: 0.6252 (p) REVERT: B 988 GLU cc_start: 0.6563 (OUTLIER) cc_final: 0.6264 (pt0) REVERT: C 48 LEU cc_start: 0.7248 (mt) cc_final: 0.6875 (mt) REVERT: C 554 GLU cc_start: 0.7631 (mp0) cc_final: 0.6988 (pm20) REVERT: C 562 PHE cc_start: 0.6801 (p90) cc_final: 0.6516 (p90) REVERT: C 740 MET cc_start: 0.6440 (ttt) cc_final: 0.5774 (ttm) REVERT: C 791 THR cc_start: 0.7405 (OUTLIER) cc_final: 0.7126 (m) REVERT: C 973 ILE cc_start: 0.7118 (tt) cc_final: 0.6604 (pt) REVERT: D 53 TRP cc_start: 0.4215 (t-100) cc_final: 0.3971 (t-100) outliers start: 53 outliers final: 43 residues processed: 325 average time/residue: 0.3477 time to fit residues: 186.5664 Evaluate side-chains 299 residues out of total 2914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 252 time to evaluate : 2.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 983 ARG Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 107 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 197 optimal weight: 10.0000 chunk 318 optimal weight: 30.0000 chunk 194 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 221 optimal weight: 0.8980 chunk 333 optimal weight: 10.0000 chunk 307 optimal weight: 6.9990 chunk 265 optimal weight: 0.2980 chunk 27 optimal weight: 8.9990 chunk 205 optimal weight: 6.9990 chunk 162 optimal weight: 1.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 784 GLN A 901 GLN B 564 GLN B 675 GLN ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4684 moved from start: 0.5060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 27671 Z= 0.293 Angle : 0.597 9.935 37646 Z= 0.304 Chirality : 0.045 0.298 4455 Planarity : 0.004 0.056 4764 Dihedral : 5.353 59.284 5014 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.02 % Favored : 95.92 % Rotamer: Outliers : 2.03 % Allowed : 16.78 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.08 (0.14), residues: 3314 helix: 1.67 (0.20), residues: 680 sheet: 0.26 (0.17), residues: 837 loop : -0.67 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 104 HIS 0.003 0.001 HIS C1064 PHE 0.024 0.002 PHE C 65 TYR 0.025 0.002 TYR C 904 ARG 0.012 0.000 ARG C 190 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 264 time to evaluate : 3.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.7350 (mt) cc_final: 0.7065 (mt) REVERT: A 90 VAL cc_start: 0.7351 (OUTLIER) cc_final: 0.6924 (m) REVERT: A 102 ARG cc_start: 0.4987 (mmt90) cc_final: 0.3654 (mtp180) REVERT: A 316 SER cc_start: 0.6543 (t) cc_final: 0.6101 (p) REVERT: A 554 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7868 (mm-30) REVERT: A 591 SER cc_start: 0.6910 (t) cc_final: 0.6615 (p) REVERT: A 702 GLU cc_start: 0.7725 (pt0) cc_final: 0.7315 (mp0) REVERT: A 773 GLU cc_start: 0.5233 (tt0) cc_final: 0.4746 (tt0) REVERT: A 804 GLN cc_start: 0.6628 (mm110) cc_final: 0.6277 (mp10) REVERT: A 957 GLN cc_start: 0.5903 (mt0) cc_final: 0.5636 (tm-30) REVERT: A 1010 GLN cc_start: 0.5925 (mm-40) cc_final: 0.5535 (mt0) REVERT: A 1107 ARG cc_start: 0.7206 (mtm180) cc_final: 0.6985 (mtm180) REVERT: B 138 ASP cc_start: 0.7721 (t0) cc_final: 0.7367 (m-30) REVERT: B 278 LYS cc_start: 0.5781 (tttt) cc_final: 0.5493 (ptmt) REVERT: B 346 ARG cc_start: 0.7238 (ptt-90) cc_final: 0.6857 (ttm-80) REVERT: B 357 ARG cc_start: 0.7540 (ttt180) cc_final: 0.7256 (ttm110) REVERT: B 389 ASP cc_start: 0.8080 (m-30) cc_final: 0.7770 (t70) REVERT: B 454 ARG cc_start: 0.5988 (ttm-80) cc_final: 0.5126 (tpt-90) REVERT: B 646 ARG cc_start: 0.6905 (tpp80) cc_final: 0.6004 (tpt90) REVERT: B 671 CYS cc_start: 0.6162 (m) cc_final: 0.5764 (m) REVERT: B 808 ASP cc_start: 0.6368 (t0) cc_final: 0.6146 (t0) REVERT: B 988 GLU cc_start: 0.6595 (OUTLIER) cc_final: 0.6300 (pt0) REVERT: B 1139 ASP cc_start: 0.6718 (t0) cc_final: 0.6446 (t0) REVERT: C 48 LEU cc_start: 0.7194 (mt) cc_final: 0.6800 (mt) REVERT: C 554 GLU cc_start: 0.7600 (mp0) cc_final: 0.6945 (pm20) REVERT: C 562 PHE cc_start: 0.6705 (p90) cc_final: 0.6495 (p90) REVERT: C 740 MET cc_start: 0.6602 (ttt) cc_final: 0.6308 (ttm) REVERT: C 791 THR cc_start: 0.7304 (OUTLIER) cc_final: 0.7020 (m) REVERT: C 973 ILE cc_start: 0.7059 (tt) cc_final: 0.6515 (pt) outliers start: 55 outliers final: 45 residues processed: 310 average time/residue: 0.3774 time to fit residues: 190.1561 Evaluate side-chains 301 residues out of total 2914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 253 time to evaluate : 2.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 107 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 211 optimal weight: 10.0000 chunk 283 optimal weight: 0.8980 chunk 81 optimal weight: 0.0970 chunk 245 optimal weight: 0.0030 chunk 39 optimal weight: 5.9990 chunk 73 optimal weight: 0.4980 chunk 266 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 273 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 901 GLN B 564 GLN ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN C 935 GLN C1005 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.171569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.115068 restraints weight = 61203.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.118974 restraints weight = 32734.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.120288 restraints weight = 18581.614| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3447 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3447 r_free = 0.3447 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3447 r_free = 0.3447 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3447 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.5136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 27671 Z= 0.156 Angle : 0.539 10.455 37646 Z= 0.274 Chirality : 0.043 0.275 4455 Planarity : 0.004 0.056 4764 Dihedral : 4.901 54.522 5014 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.78 % Favored : 97.16 % Rotamer: Outliers : 1.75 % Allowed : 17.41 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.26 (0.15), residues: 3314 helix: 1.93 (0.20), residues: 682 sheet: 0.24 (0.17), residues: 842 loop : -0.53 (0.14), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 104 HIS 0.003 0.001 HIS A1048 PHE 0.028 0.001 PHE C 133 TYR 0.024 0.001 TYR B 200 ARG 0.014 0.000 ARG F 103 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5441.18 seconds wall clock time: 100 minutes 16.65 seconds (6016.65 seconds total)