Starting phenix.real_space_refine on Mon Feb 19 08:42:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cv0_7631/02_2024/6cv0_7631.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cv0_7631/02_2024/6cv0_7631.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cv0_7631/02_2024/6cv0_7631.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cv0_7631/02_2024/6cv0_7631.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cv0_7631/02_2024/6cv0_7631.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cv0_7631/02_2024/6cv0_7631.pdb" } resolution = 3.93 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= 0.006 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 126 5.16 5 C 15264 2.51 5 N 3960 2.21 5 O 4842 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 202": "NH1" <-> "NH2" Residue "A PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A ARG 512": "NH1" <-> "NH2" Residue "A PHE 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 972": "NH1" <-> "NH2" Residue "A PHE 975": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 987": "NH1" <-> "NH2" Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 202": "NH1" <-> "NH2" Residue "B PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 408": "NH1" <-> "NH2" Residue "B ARG 512": "NH1" <-> "NH2" Residue "B PHE 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 972": "NH1" <-> "NH2" Residue "B PHE 975": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 987": "NH1" <-> "NH2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 202": "NH1" <-> "NH2" Residue "C PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 408": "NH1" <-> "NH2" Residue "C ARG 512": "NH1" <-> "NH2" Residue "C PHE 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 972": "NH1" <-> "NH2" Residue "C PHE 975": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 987": "NH1" <-> "NH2" 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: 24192 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 7658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7658 Classifications: {'peptide': 993} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 37, 'TRANS': 955} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 7658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7658 Classifications: {'peptide': 993} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 37, 'TRANS': 955} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 7658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7658 Classifications: {'peptide': 993} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 37, 'TRANS': 955} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" 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: "E" 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: "F" 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: "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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 12.44, per 1000 atoms: 0.51 Number of scatterers: 24192 At special positions: 0 Unit cell: (135.66, 144.84, 168.3, 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 126 16.00 O 4842 8.00 N 3960 7.00 C 15264 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 98 " distance=2.03 Simple disulfide: pdb=" SG CYS A 102 " - pdb=" SG CYS A 160 " distance=2.02 Simple disulfide: pdb=" SG CYS A 114 " - pdb=" SG CYS A 120 " distance=2.02 Simple disulfide: pdb=" SG CYS A 221 " - pdb=" SG CYS A 231 " distance=2.02 Simple disulfide: pdb=" SG CYS A 329 " - pdb=" SG CYS A 369 " distance=2.03 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 370 " distance=2.03 Simple disulfide: pdb=" SG CYS A 381 " - pdb=" SG CYS A 395 " distance=2.01 Simple disulfide: pdb=" SG CYS A 431 " - pdb=" SG CYS A 491 " distance=2.04 Simple disulfide: pdb=" SG CYS A 546 " - pdb=" SG CYS A 555 " distance=2.03 Simple disulfide: pdb=" SG CYS A 610 " - pdb=" SG CYS A 632 " distance=2.04 Simple disulfide: pdb=" SG CYS A 615 " - pdb=" SG CYS A 621 " distance=2.03 Simple disulfide: pdb=" SG CYS A 715 " - pdb=" SG CYS A 728 " distance=2.03 Simple disulfide: pdb=" SG CYS A 905 " - pdb=" SG CYS A 916 " distance=2.05 Simple disulfide: pdb=" SG CYS A 955 " - pdb=" SG CYS A1006 " distance=2.04 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 98 " distance=2.03 Simple disulfide: pdb=" SG CYS B 102 " - pdb=" SG CYS B 160 " distance=2.02 Simple disulfide: pdb=" SG CYS B 114 " - pdb=" SG CYS B 120 " distance=2.02 Simple disulfide: pdb=" SG CYS B 221 " - pdb=" SG CYS B 231 " distance=2.02 Simple disulfide: pdb=" SG CYS B 329 " - pdb=" SG CYS B 369 " distance=2.03 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 370 " distance=2.03 Simple disulfide: pdb=" SG CYS B 381 " - pdb=" SG CYS B 395 " distance=2.01 Simple disulfide: pdb=" SG CYS B 431 " - pdb=" SG CYS B 491 " distance=2.04 Simple disulfide: pdb=" SG CYS B 546 " - pdb=" SG CYS B 555 " distance=2.03 Simple disulfide: pdb=" SG CYS B 610 " - pdb=" SG CYS B 632 " distance=2.04 Simple disulfide: pdb=" SG CYS B 615 " - pdb=" SG CYS B 621 " distance=2.03 Simple disulfide: pdb=" SG CYS B 715 " - pdb=" SG CYS B 728 " distance=2.03 Simple disulfide: pdb=" SG CYS B 905 " - pdb=" SG CYS B 916 " distance=2.05 Simple disulfide: pdb=" SG CYS B 955 " - pdb=" SG CYS B1006 " distance=2.04 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 98 " distance=2.03 Simple disulfide: pdb=" SG CYS C 102 " - pdb=" SG CYS C 160 " distance=2.02 Simple disulfide: pdb=" SG CYS C 114 " - pdb=" SG CYS C 120 " distance=2.02 Simple disulfide: pdb=" SG CYS C 221 " - pdb=" SG CYS C 231 " distance=2.02 Simple disulfide: pdb=" SG CYS C 329 " - pdb=" SG CYS C 369 " distance=2.03 Simple disulfide: pdb=" SG CYS C 358 " - pdb=" SG CYS C 370 " distance=2.03 Simple disulfide: pdb=" SG CYS C 381 " - pdb=" SG CYS C 395 " distance=2.01 Simple disulfide: pdb=" SG CYS C 431 " - pdb=" SG CYS C 491 " distance=2.04 Simple disulfide: pdb=" SG CYS C 546 " - pdb=" SG CYS C 555 " distance=2.03 Simple disulfide: pdb=" SG CYS C 610 " - pdb=" SG CYS C 632 " distance=2.04 Simple disulfide: pdb=" SG CYS C 615 " - pdb=" SG CYS C 621 " distance=2.03 Simple disulfide: pdb=" SG CYS C 715 " - pdb=" SG CYS C 728 " distance=2.03 Simple disulfide: pdb=" SG CYS C 905 " - pdb=" SG CYS C 916 " distance=2.05 Simple disulfide: pdb=" SG CYS C 955 " - pdb=" SG CYS C1006 " distance=2.04 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 D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " NAG H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " NAG I 3 " " 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 O 2 " - " NAG O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " NAG P 3 " " 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 V 2 " - " NAG V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " NAG W 3 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG A1201 " - " ASN A 676 " " NAG A1202 " - " ASN A 714 " " NAG A1203 " - " ASN A 669 " " NAG A1204 " - " ASN A 591 " " NAG A1207 " - " ASN A 947 " " NAG A1212 " - " ASN A 178 " " NAG A1213 " - " ASN A 163 " " NAG A1216 " - " ASN A 51 " " NAG A1217 " - " ASN A 247 " " NAG A1218 " - " ASN A 271 " " NAG A1219 " - " ASN A 306 " " NAG A1226 " - " ASN A 513 " " NAG A1229 " - " ASN A 77 " " NAG B1201 " - " ASN B 676 " " NAG B1202 " - " ASN B 714 " " NAG B1203 " - " ASN B 669 " " NAG B1204 " - " ASN B 591 " " NAG B1207 " - " ASN B 947 " " NAG B1212 " - " ASN B 178 " " NAG B1213 " - " ASN B 163 " " NAG B1216 " - " ASN B 51 " " NAG B1217 " - " ASN B 247 " " NAG B1218 " - " ASN B 271 " " NAG B1219 " - " ASN B 306 " " NAG B1226 " - " ASN B 513 " " NAG B1229 " - " ASN B 77 " " NAG C1201 " - " ASN C 676 " " NAG C1202 " - " ASN C 714 " " NAG C1203 " - " ASN C 669 " " NAG C1204 " - " ASN C 591 " " NAG C1207 " - " ASN C 947 " " NAG C1212 " - " ASN C 178 " " NAG C1213 " - " ASN C 163 " " NAG C1216 " - " ASN C 51 " " NAG C1217 " - " ASN C 247 " " NAG C1218 " - " ASN C 271 " " NAG C1219 " - " ASN C 306 " " NAG C1226 " - " ASN C 513 " " NAG C1229 " - " ASN C 77 " " NAG D 1 " - " ASN A 579 " " NAG E 1 " - " ASN A 237 " " NAG F 1 " - " ASN A 212 " " NAG G 1 " - " ASN A 144 " " NAG H 1 " - " ASN A 276 " " NAG I 1 " - " ASN A 447 " " NAG J 1 " - " ASN A 103 " " NAG K 1 " - " ASN B 579 " " NAG L 1 " - " ASN B 237 " " NAG M 1 " - " ASN B 212 " " NAG N 1 " - " ASN B 144 " " NAG O 1 " - " ASN B 276 " " NAG P 1 " - " ASN B 447 " " NAG Q 1 " - " ASN B 103 " " NAG R 1 " - " ASN C 579 " " NAG S 1 " - " ASN C 237 " " NAG T 1 " - " ASN C 212 " " NAG U 1 " - " ASN C 144 " " NAG V 1 " - " ASN C 276 " " NAG W 1 " - " ASN C 447 " " NAG X 1 " - " ASN C 103 " Time building additional restraints: 9.71 Conformation dependent library (CDL) restraints added in 4.4 seconds 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5508 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 42 sheets defined 20.1% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.78 Creating SS restraints... Processing helix chain 'A' and resid 163 through 165 No H-bonds generated for 'chain 'A' and resid 163 through 165' Processing helix chain 'A' and resid 224 through 234 removed outlier: 4.407A pdb=" N LEU A 229 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA A 230 " --> pdb=" O ARG A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 336 removed outlier: 3.978A pdb=" N ILE A 336 " --> pdb=" O LEU A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 362 removed outlier: 3.551A pdb=" N GLN A 360 " --> pdb=" O GLY A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 470 No H-bonds generated for 'chain 'A' and resid 468 through 470' Processing helix chain 'A' and resid 609 through 615 removed outlier: 3.687A pdb=" N CYS A 615 " --> pdb=" O LEU A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 626 Processing helix chain 'A' and resid 628 through 658 removed outlier: 4.024A pdb=" N CYS A 632 " --> pdb=" O TYR A 628 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP A 633 " --> pdb=" O GLY A 629 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL A 638 " --> pdb=" O ASN A 634 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL A 639 " --> pdb=" O ILE A 635 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU A 649 " --> pdb=" O LYS A 645 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU A 651 " --> pdb=" O ASP A 647 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR A 657 " --> pdb=" O PHE A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 699 Processing helix chain 'A' and resid 723 through 725 No H-bonds generated for 'chain 'A' and resid 723 through 725' Processing helix chain 'A' and resid 726 through 732 Processing helix chain 'A' and resid 749 through 761 Processing helix chain 'A' and resid 771 through 780 removed outlier: 3.652A pdb=" N LEU A 775 " --> pdb=" O PHE A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 811 removed outlier: 3.675A pdb=" N ALA A 797 " --> pdb=" O GLN A 793 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE A 811 " --> pdb=" O MET A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 833 removed outlier: 3.946A pdb=" N GLN A 820 " --> pdb=" O LEU A 816 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LEU A 832 " --> pdb=" O GLN A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 906 removed outlier: 3.830A pdb=" N ASN A 863 " --> pdb=" O ALA A 859 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N ALA A 864 " --> pdb=" O ILE A 860 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLN A 865 " --> pdb=" O GLN A 861 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL A 906 " --> pdb=" O ILE A 902 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 165 No H-bonds generated for 'chain 'B' and resid 163 through 165' Processing helix chain 'B' and resid 224 through 234 removed outlier: 4.407A pdb=" N LEU B 229 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA B 230 " --> pdb=" O ARG B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 336 removed outlier: 3.978A pdb=" N ILE B 336 " --> pdb=" O LEU B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 362 removed outlier: 3.550A pdb=" N GLN B 360 " --> pdb=" O GLY B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 470 No H-bonds generated for 'chain 'B' and resid 468 through 470' Processing helix chain 'B' and resid 609 through 615 removed outlier: 3.686A pdb=" N CYS B 615 " --> pdb=" O LEU B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 626 Processing helix chain 'B' and resid 628 through 658 removed outlier: 4.024A pdb=" N CYS B 632 " --> pdb=" O TYR B 628 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP B 633 " --> pdb=" O GLY B 629 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL B 638 " --> pdb=" O ASN B 634 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL B 639 " --> pdb=" O ILE B 635 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU B 649 " --> pdb=" O LYS B 645 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU B 651 " --> pdb=" O ASP B 647 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR B 657 " --> pdb=" O PHE B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 699 Processing helix chain 'B' and resid 723 through 725 No H-bonds generated for 'chain 'B' and resid 723 through 725' Processing helix chain 'B' and resid 726 through 732 Processing helix chain 'B' and resid 749 through 761 Processing helix chain 'B' and resid 771 through 780 removed outlier: 3.653A pdb=" N LEU B 775 " --> pdb=" O PHE B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 793 through 811 removed outlier: 3.675A pdb=" N ALA B 797 " --> pdb=" O GLN B 793 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE B 811 " --> pdb=" O MET B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 833 removed outlier: 3.946A pdb=" N GLN B 820 " --> pdb=" O LEU B 816 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LEU B 832 " --> pdb=" O GLN B 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 858 through 906 removed outlier: 3.830A pdb=" N ASN B 863 " --> pdb=" O ALA B 859 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ALA B 864 " --> pdb=" O ILE B 860 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLN B 865 " --> pdb=" O GLN B 861 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL B 906 " --> pdb=" O ILE B 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 165 No H-bonds generated for 'chain 'C' and resid 163 through 165' Processing helix chain 'C' and resid 224 through 234 removed outlier: 4.407A pdb=" N LEU C 229 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA C 230 " --> pdb=" O ARG C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 336 removed outlier: 3.977A pdb=" N ILE C 336 " --> pdb=" O LEU C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 362 removed outlier: 3.551A pdb=" N GLN C 360 " --> pdb=" O GLY C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 470 No H-bonds generated for 'chain 'C' and resid 468 through 470' Processing helix chain 'C' and resid 609 through 615 removed outlier: 3.686A pdb=" N CYS C 615 " --> pdb=" O LEU C 611 " (cutoff:3.500A) Processing helix chain 'C' and resid 621 through 626 Processing helix chain 'C' and resid 628 through 658 removed outlier: 4.024A pdb=" N CYS C 632 " --> pdb=" O TYR C 628 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP C 633 " --> pdb=" O GLY C 629 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL C 638 " --> pdb=" O ASN C 634 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N VAL C 639 " --> pdb=" O ILE C 635 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU C 649 " --> pdb=" O LYS C 645 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU C 651 " --> pdb=" O ASP C 647 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR C 657 " --> pdb=" O PHE C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 699 Processing helix chain 'C' and resid 723 through 725 No H-bonds generated for 'chain 'C' and resid 723 through 725' Processing helix chain 'C' and resid 726 through 732 Processing helix chain 'C' and resid 749 through 761 Processing helix chain 'C' and resid 771 through 780 removed outlier: 3.652A pdb=" N LEU C 775 " --> pdb=" O PHE C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 793 through 811 removed outlier: 3.675A pdb=" N ALA C 797 " --> pdb=" O GLN C 793 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE C 811 " --> pdb=" O MET C 807 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 833 removed outlier: 3.946A pdb=" N GLN C 820 " --> pdb=" O LEU C 816 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LEU C 832 " --> pdb=" O GLN C 828 " (cutoff:3.500A) Processing helix chain 'C' and resid 858 through 906 removed outlier: 3.830A pdb=" N ASN C 863 " --> pdb=" O ALA C 859 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ALA C 864 " --> pdb=" O ILE C 860 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLN C 865 " --> pdb=" O GLN C 861 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL C 906 " --> pdb=" O ILE C 902 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 45 removed outlier: 3.702A pdb=" N GLY A 39 " --> pdb=" O PHE A 210 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE A 210 " --> pdb=" O GLY A 39 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N HIS A 41 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA A 206 " --> pdb=" O HIS A 43 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASP A 217 " --> pdb=" O TYR A 209 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL A 211 " --> pdb=" O ALA A 215 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N ALA A 215 " --> pdb=" O VAL A 211 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 55 removed outlier: 5.030A pdb=" N ASN A 51 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N VAL A 200 " --> pdb=" O ASN A 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 74 through 78 removed outlier: 3.787A pdb=" N THR A 184 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER A 185 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL A 109 " --> pdb=" O CYS A 102 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL A 133 " --> pdb=" O LEU A 145 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU A 145 " --> pdb=" O VAL A 133 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA A 135 " --> pdb=" O TYR A 143 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N TYR A 143 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 241 through 245 removed outlier: 3.633A pdb=" N TYR A 243 " --> pdb=" O PHE A 498 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLN A 496 " --> pdb=" O PHE A 245 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY A 507 " --> pdb=" O VAL A 499 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N SER A 501 " --> pdb=" O LEU A 505 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N LEU A 505 " --> pdb=" O SER A 501 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN A 518 " --> pdb=" O TYR A 525 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 255 through 257 removed outlier: 6.728A pdb=" N PHE A 255 " --> pdb=" O ASN A 435 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR A 434 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE A 436 " --> pdb=" O ARG A 439 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS A 487 " --> pdb=" O THR A 446 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR A 484 " --> pdb=" O VAL A 477 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL A 477 " --> pdb=" O THR A 484 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ASP A 473 " --> pdb=" O VAL A 488 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE A 465 " --> pdb=" O ASP A 473 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 270 through 273 removed outlier: 6.456A pdb=" N HIS A 270 " --> pdb=" O ASN A 304 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N ASN A 306 " --> pdb=" O HIS A 270 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N PHE A 272 " --> pdb=" O ASN A 306 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLY A 301 " --> pdb=" O GLN A 410 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N GLY A 406 " --> pdb=" O SER A 344 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N SER A 344 " --> pdb=" O GLY A 406 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N PHE A 342 " --> pdb=" O ARG A 408 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N GLN A 410 " --> pdb=" O LEU A 340 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU A 340 " --> pdb=" O GLN A 410 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 314 through 315 Processing sheet with id=AA8, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA9, first strand: chain 'A' and resid 554 through 556 Processing sheet with id=AB1, first strand: chain 'A' and resid 584 through 587 removed outlier: 3.589A pdb=" N VAL A 948 " --> pdb=" O VAL A 584 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE A 586 " --> pdb=" O VAL A 946 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 594 through 600 removed outlier: 3.813A pdb=" N GLU A 597 " --> pdb=" O PHE A 935 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE A 599 " --> pdb=" O ILE A 933 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE A 933 " --> pdb=" O ILE A 599 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 605 through 608 removed outlier: 4.650A pdb=" N LYS A 605 " --> pdb=" O LEU A 738 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A 736 " --> pdb=" O GLN A 607 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 965 through 966 removed outlier: 3.583A pdb=" N LEU A1003 " --> pdb=" O ALA A 965 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 975 through 978 removed outlier: 3.718A pdb=" N VAL A 978 " --> pdb=" O SER A 981 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 39 through 45 removed outlier: 3.701A pdb=" N GLY B 39 " --> pdb=" O PHE B 210 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE B 210 " --> pdb=" O GLY B 39 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N HIS B 41 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA B 206 " --> pdb=" O HIS B 43 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASP B 217 " --> pdb=" O TYR B 209 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL B 211 " --> pdb=" O ALA B 215 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N ALA B 215 " --> pdb=" O VAL B 211 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 50 through 55 removed outlier: 5.030A pdb=" N ASN B 51 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N VAL B 200 " --> pdb=" O ASN B 51 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 74 through 78 removed outlier: 3.786A pdb=" N THR B 184 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER B 185 " --> pdb=" O ASN B 103 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL B 109 " --> pdb=" O CYS B 102 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL B 133 " --> pdb=" O LEU B 145 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU B 145 " --> pdb=" O VAL B 133 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA B 135 " --> pdb=" O TYR B 143 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N TYR B 143 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 241 through 245 removed outlier: 3.634A pdb=" N TYR B 243 " --> pdb=" O PHE B 498 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLN B 496 " --> pdb=" O PHE B 245 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY B 507 " --> pdb=" O VAL B 499 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N SER B 501 " --> pdb=" O LEU B 505 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N LEU B 505 " --> pdb=" O SER B 501 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN B 518 " --> pdb=" O TYR B 525 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 255 through 257 removed outlier: 6.727A pdb=" N PHE B 255 " --> pdb=" O ASN B 435 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR B 434 " --> pdb=" O GLY B 441 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE B 436 " --> pdb=" O ARG B 439 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS B 487 " --> pdb=" O THR B 446 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR B 484 " --> pdb=" O VAL B 477 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL B 477 " --> pdb=" O THR B 484 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ASP B 473 " --> pdb=" O VAL B 488 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILE B 465 " --> pdb=" O ASP B 473 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 270 through 273 removed outlier: 6.457A pdb=" N HIS B 270 " --> pdb=" O ASN B 304 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N ASN B 306 " --> pdb=" O HIS B 270 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N PHE B 272 " --> pdb=" O ASN B 306 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLY B 301 " --> pdb=" O GLN B 410 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N GLY B 406 " --> pdb=" O SER B 344 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N SER B 344 " --> pdb=" O GLY B 406 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N PHE B 342 " --> pdb=" O ARG B 408 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N GLN B 410 " --> pdb=" O LEU B 340 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU B 340 " --> pdb=" O GLN B 410 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 314 through 315 Processing sheet with id=AC4, first strand: chain 'B' and resid 347 through 350 Processing sheet with id=AC5, first strand: chain 'B' and resid 554 through 556 Processing sheet with id=AC6, first strand: chain 'B' and resid 584 through 587 removed outlier: 3.590A pdb=" N VAL B 948 " --> pdb=" O VAL B 584 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE B 586 " --> pdb=" O VAL B 946 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 594 through 600 removed outlier: 3.812A pdb=" N GLU B 597 " --> pdb=" O PHE B 935 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE B 599 " --> pdb=" O ILE B 933 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE B 933 " --> pdb=" O ILE B 599 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 605 through 608 removed outlier: 4.649A pdb=" N LYS B 605 " --> pdb=" O LEU B 738 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU B 736 " --> pdb=" O GLN B 607 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 965 through 966 removed outlier: 3.583A pdb=" N LEU B1003 " --> pdb=" O ALA B 965 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 975 through 978 removed outlier: 3.717A pdb=" N VAL B 978 " --> pdb=" O SER B 981 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 39 through 45 removed outlier: 3.701A pdb=" N GLY C 39 " --> pdb=" O PHE C 210 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE C 210 " --> pdb=" O GLY C 39 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N HIS C 41 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA C 206 " --> pdb=" O HIS C 43 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASP C 217 " --> pdb=" O TYR C 209 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL C 211 " --> pdb=" O ALA C 215 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ALA C 215 " --> pdb=" O VAL C 211 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 50 through 55 removed outlier: 5.029A pdb=" N ASN C 51 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N VAL C 200 " --> pdb=" O ASN C 51 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 74 through 78 removed outlier: 3.786A pdb=" N THR C 184 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER C 185 " --> pdb=" O ASN C 103 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL C 109 " --> pdb=" O CYS C 102 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL C 133 " --> pdb=" O LEU C 145 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU C 145 " --> pdb=" O VAL C 133 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA C 135 " --> pdb=" O TYR C 143 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N TYR C 143 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 241 through 245 removed outlier: 3.633A pdb=" N TYR C 243 " --> pdb=" O PHE C 498 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLN C 496 " --> pdb=" O PHE C 245 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY C 507 " --> pdb=" O VAL C 499 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N SER C 501 " --> pdb=" O LEU C 505 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LEU C 505 " --> pdb=" O SER C 501 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN C 518 " --> pdb=" O TYR C 525 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 255 through 257 removed outlier: 6.728A pdb=" N PHE C 255 " --> pdb=" O ASN C 435 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR C 434 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE C 436 " --> pdb=" O ARG C 439 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS C 487 " --> pdb=" O THR C 446 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR C 484 " --> pdb=" O VAL C 477 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL C 477 " --> pdb=" O THR C 484 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ASP C 473 " --> pdb=" O VAL C 488 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE C 465 " --> pdb=" O ASP C 473 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 270 through 273 removed outlier: 6.458A pdb=" N HIS C 270 " --> pdb=" O ASN C 304 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N ASN C 306 " --> pdb=" O HIS C 270 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N PHE C 272 " --> pdb=" O ASN C 306 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLY C 301 " --> pdb=" O GLN C 410 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N GLY C 406 " --> pdb=" O SER C 344 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N SER C 344 " --> pdb=" O GLY C 406 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N PHE C 342 " --> pdb=" O ARG C 408 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N GLN C 410 " --> pdb=" O LEU C 340 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU C 340 " --> pdb=" O GLN C 410 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 314 through 315 Processing sheet with id=AD9, first strand: chain 'C' and resid 347 through 350 Processing sheet with id=AE1, first strand: chain 'C' and resid 554 through 556 Processing sheet with id=AE2, first strand: chain 'C' and resid 584 through 587 removed outlier: 3.589A pdb=" N VAL C 948 " --> pdb=" O VAL C 584 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE C 586 " --> pdb=" O VAL C 946 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 594 through 600 removed outlier: 3.812A pdb=" N GLU C 597 " --> pdb=" O PHE C 935 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE C 599 " --> pdb=" O ILE C 933 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE C 933 " --> pdb=" O ILE C 599 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 605 through 608 removed outlier: 4.649A pdb=" N LYS C 605 " --> pdb=" O LEU C 738 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU C 736 " --> pdb=" O GLN C 607 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 965 through 966 removed outlier: 3.583A pdb=" N LEU C1003 " --> pdb=" O ALA C 965 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 975 through 978 removed outlier: 3.717A pdb=" N VAL C 978 " --> pdb=" O SER C 981 " (cutoff:3.500A) 594 hydrogen bonds defined for protein. 1638 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: 9.04 Time building geometry restraints manager: 10.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7550 1.34 - 1.46: 6133 1.46 - 1.58: 10836 1.58 - 1.71: 0 1.71 - 1.83: 168 Bond restraints: 24687 Sorted by residual: bond pdb=" C1 NAG A1213 " pdb=" O5 NAG A1213 " ideal model delta sigma weight residual 1.406 1.462 -0.056 2.00e-02 2.50e+03 7.88e+00 bond pdb=" CA LEU B 169 " pdb=" C LEU B 169 " ideal model delta sigma weight residual 1.524 1.558 -0.035 1.26e-02 6.30e+03 7.66e+00 bond pdb=" CA LEU C 169 " pdb=" C LEU C 169 " ideal model delta sigma weight residual 1.524 1.558 -0.034 1.26e-02 6.30e+03 7.25e+00 bond pdb=" CA LEU A 169 " pdb=" C LEU A 169 " ideal model delta sigma weight residual 1.524 1.557 -0.034 1.26e-02 6.30e+03 7.23e+00 bond pdb=" N ASN A 170 " pdb=" CA ASN A 170 " ideal model delta sigma weight residual 1.457 1.492 -0.034 1.29e-02 6.01e+03 7.08e+00 ... (remaining 24682 not shown) Histogram of bond angle deviations from ideal: 98.60 - 105.68: 448 105.68 - 112.77: 12807 112.77 - 119.85: 8459 119.85 - 126.93: 11668 126.93 - 134.02: 188 Bond angle restraints: 33570 Sorted by residual: angle pdb=" N LEU B 169 " pdb=" CA LEU B 169 " pdb=" C LEU B 169 " ideal model delta sigma weight residual 110.23 98.60 11.63 1.45e+00 4.76e-01 6.43e+01 angle pdb=" N LEU A 169 " pdb=" CA LEU A 169 " pdb=" C LEU A 169 " ideal model delta sigma weight residual 110.23 98.61 11.62 1.45e+00 4.76e-01 6.42e+01 angle pdb=" N LEU C 169 " pdb=" CA LEU C 169 " pdb=" C LEU C 169 " ideal model delta sigma weight residual 110.23 98.67 11.56 1.45e+00 4.76e-01 6.36e+01 angle pdb=" N MET B 746 " pdb=" CA MET B 746 " pdb=" C MET B 746 " ideal model delta sigma weight residual 114.75 106.43 8.32 1.26e+00 6.30e-01 4.36e+01 angle pdb=" N MET C 746 " pdb=" CA MET C 746 " pdb=" C MET C 746 " ideal model delta sigma weight residual 114.75 106.47 8.28 1.26e+00 6.30e-01 4.31e+01 ... (remaining 33565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.66: 14529 16.66 - 33.31: 901 33.31 - 49.97: 277 49.97 - 66.63: 43 66.63 - 83.29: 42 Dihedral angle restraints: 15792 sinusoidal: 7143 harmonic: 8649 Sorted by residual: dihedral pdb=" CB CYS A 715 " pdb=" SG CYS A 715 " pdb=" SG CYS A 728 " pdb=" CB CYS A 728 " ideal model delta sinusoidal sigma weight residual 93.00 176.29 -83.29 1 1.00e+01 1.00e-02 8.48e+01 dihedral pdb=" CB CYS B 715 " pdb=" SG CYS B 715 " pdb=" SG CYS B 728 " pdb=" CB CYS B 728 " ideal model delta sinusoidal sigma weight residual 93.00 176.28 -83.28 1 1.00e+01 1.00e-02 8.48e+01 dihedral pdb=" CB CYS C 715 " pdb=" SG CYS C 715 " pdb=" SG CYS C 728 " pdb=" CB CYS C 728 " ideal model delta sinusoidal sigma weight residual 93.00 176.26 -83.26 1 1.00e+01 1.00e-02 8.47e+01 ... (remaining 15789 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 3839 0.126 - 0.252: 201 0.252 - 0.378: 15 0.378 - 0.504: 3 0.504 - 0.630: 4 Chirality restraints: 4062 Sorted by residual: chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN A 103 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.77 -0.63 2.00e-01 2.50e+01 9.91e+00 chirality pdb=" C1 NAG X 1 " pdb=" ND2 ASN C 103 " pdb=" C2 NAG X 1 " pdb=" O5 NAG X 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.78 -0.62 2.00e-01 2.50e+01 9.70e+00 chirality pdb=" C1 NAG C1213 " pdb=" ND2 ASN C 163 " pdb=" C2 NAG C1213 " pdb=" O5 NAG C1213 " both_signs ideal model delta sigma weight residual False -2.40 -1.81 -0.59 2.00e-01 2.50e+01 8.85e+00 ... (remaining 4059 not shown) Planarity restraints: 4287 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 163 " -0.017 2.00e-02 2.50e+03 3.34e-02 1.12e+01 pdb=" C ASN A 163 " 0.058 2.00e-02 2.50e+03 pdb=" O ASN A 163 " -0.022 2.00e-02 2.50e+03 pdb=" N LEU A 164 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 163 " -0.017 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C ASN B 163 " 0.057 2.00e-02 2.50e+03 pdb=" O ASN B 163 " -0.022 2.00e-02 2.50e+03 pdb=" N LEU B 164 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 163 " 0.016 2.00e-02 2.50e+03 3.17e-02 1.01e+01 pdb=" C ASN C 163 " -0.055 2.00e-02 2.50e+03 pdb=" O ASN C 163 " 0.021 2.00e-02 2.50e+03 pdb=" N LEU C 164 " 0.018 2.00e-02 2.50e+03 ... (remaining 4284 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 977 2.70 - 3.25: 22494 3.25 - 3.80: 35779 3.80 - 4.35: 41708 4.35 - 4.90: 70315 Nonbonded interactions: 171273 Sorted by model distance: nonbonded pdb=" CD1 TYR A 28 " pdb=" N TYR A 29 " model vdw 2.150 3.420 nonbonded pdb=" CD1 TYR C 28 " pdb=" N TYR C 29 " model vdw 2.151 3.420 nonbonded pdb=" CD1 TYR B 28 " pdb=" N TYR B 29 " model vdw 2.155 3.420 nonbonded pdb=" OD1 ASN B 276 " pdb=" OH TYR B 351 " model vdw 2.256 2.440 nonbonded pdb=" OD1 ASN C 276 " pdb=" OH TYR C 351 " model vdw 2.256 2.440 ... (remaining 171268 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' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'X' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'O' selection = chain 'P' selection = chain 'V' selection = chain 'W' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.760 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: 8.470 Check model and map are aligned: 0.330 Set scattering table: 0.230 Process input model: 62.620 Find NCS groups from input model: 1.500 Set up NCS constraints: 0.310 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 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 : 0.007 0.056 24687 Z= 0.423 Angle : 1.095 11.628 33570 Z= 0.592 Chirality : 0.068 0.630 4062 Planarity : 0.007 0.072 4227 Dihedral : 12.099 76.297 10158 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.20 % Allowed : 13.31 % Favored : 86.48 % Rotamer: Outliers : 0.51 % Allowed : 6.95 % Favored : 92.54 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.95 (0.12), residues: 2967 helix: -2.43 (0.16), residues: 534 sheet: -3.73 (0.16), residues: 462 loop : -3.66 (0.11), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 40 HIS 0.013 0.003 HIS B 823 PHE 0.035 0.004 PHE A 975 TYR 0.029 0.002 TYR C 29 ARG 0.009 0.001 ARG A 890 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 596 time to evaluate : 2.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 THR cc_start: 0.8166 (p) cc_final: 0.7966 (p) REVERT: A 440 THR cc_start: 0.9165 (m) cc_final: 0.8888 (p) REVERT: A 493 ASP cc_start: 0.7564 (p0) cc_final: 0.7266 (p0) REVERT: A 508 ILE cc_start: 0.9507 (mp) cc_final: 0.9271 (mt) REVERT: A 732 TYR cc_start: 0.7460 (m-10) cc_final: 0.7229 (m-10) REVERT: A 941 THR cc_start: 0.8818 (m) cc_final: 0.8558 (p) REVERT: A 949 THR cc_start: 0.8392 (p) cc_final: 0.8068 (p) REVERT: A 974 ILE cc_start: 0.7882 (tp) cc_final: 0.7561 (mp) REVERT: B 184 THR cc_start: 0.8118 (t) cc_final: 0.7861 (m) REVERT: B 235 THR cc_start: 0.9432 (t) cc_final: 0.9153 (m) REVERT: B 371 TYR cc_start: 0.8550 (m-10) cc_final: 0.7865 (m-80) REVERT: B 440 THR cc_start: 0.9186 (m) cc_final: 0.8984 (p) REVERT: B 508 ILE cc_start: 0.9495 (mp) cc_final: 0.9223 (mt) REVERT: B 634 ASN cc_start: 0.8619 (t0) cc_final: 0.8246 (t0) REVERT: B 732 TYR cc_start: 0.7458 (m-10) cc_final: 0.7241 (m-10) REVERT: B 828 GLN cc_start: 0.7698 (mm110) cc_final: 0.7461 (tm-30) REVERT: B 941 THR cc_start: 0.8772 (m) cc_final: 0.8486 (p) REVERT: B 974 ILE cc_start: 0.7934 (tp) cc_final: 0.7634 (mp) REVERT: C 184 THR cc_start: 0.8003 (t) cc_final: 0.7736 (m) REVERT: C 201 MET cc_start: 0.7949 (ptp) cc_final: 0.7372 (ptt) REVERT: C 249 SER cc_start: 0.6832 (p) cc_final: 0.6573 (t) REVERT: C 253 GLN cc_start: 0.8089 (mt0) cc_final: 0.6927 (pm20) REVERT: C 440 THR cc_start: 0.9095 (m) cc_final: 0.8807 (p) REVERT: C 828 GLN cc_start: 0.7739 (mm110) cc_final: 0.7092 (tm-30) REVERT: C 846 ILE cc_start: 0.8861 (tp) cc_final: 0.8618 (tp) REVERT: C 941 THR cc_start: 0.8879 (m) cc_final: 0.8517 (p) REVERT: C 974 ILE cc_start: 0.7877 (tp) cc_final: 0.7580 (mp) REVERT: C 991 MET cc_start: 0.8288 (ttt) cc_final: 0.7963 (tpp) outliers start: 13 outliers final: 0 residues processed: 606 average time/residue: 0.3640 time to fit residues: 345.0772 Evaluate side-chains 344 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 344 time to evaluate : 2.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 250 optimal weight: 4.9990 chunk 225 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 151 optimal weight: 6.9990 chunk 120 optimal weight: 2.9990 chunk 232 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 141 optimal weight: 3.9990 chunk 173 optimal weight: 0.9980 chunk 269 optimal weight: 0.0070 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS A 129 ASN ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 289 ASN A 326 HIS A 355 GLN A 523 GLN A 774 GLN A 776 GLN A 822 GLN A 888 HIS A 900 GLN A 963 GLN ** A 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 GLN B 41 HIS B 96 GLN B 129 ASN B 216 GLN B 289 ASN B 326 HIS B 523 GLN B 626 GLN B 774 GLN B 776 GLN B 822 GLN B 888 HIS B 900 GLN B 963 GLN ** B 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 HIS C 43 HIS C 96 GLN C 129 ASN C 319 ASN C 326 HIS C 410 GLN C 523 GLN C 774 GLN C 822 GLN C 888 HIS ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 900 GLN C 963 GLN C 979 ASN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 24687 Z= 0.206 Angle : 0.729 8.122 33570 Z= 0.377 Chirality : 0.050 0.640 4062 Planarity : 0.005 0.059 4227 Dihedral : 8.326 58.933 5070 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.82 % Favored : 89.18 % Rotamer: Outliers : 3.57 % Allowed : 13.35 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.01 (0.13), residues: 2967 helix: -0.33 (0.23), residues: 507 sheet: -2.90 (0.19), residues: 477 loop : -3.49 (0.12), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 341 HIS 0.006 0.001 HIS B 921 PHE 0.022 0.002 PHE C 97 TYR 0.026 0.001 TYR A 983 ARG 0.006 0.001 ARG C 332 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 383 time to evaluate : 2.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.8183 (mpp) cc_final: 0.7893 (mtt) REVERT: A 113 HIS cc_start: 0.7598 (t-90) cc_final: 0.6949 (p-80) REVERT: A 184 THR cc_start: 0.7779 (t) cc_final: 0.7433 (m) REVERT: A 189 TYR cc_start: 0.6106 (m-10) cc_final: 0.5878 (m-10) REVERT: A 249 SER cc_start: 0.7029 (p) cc_final: 0.6820 (t) REVERT: A 253 GLN cc_start: 0.8226 (mt0) cc_final: 0.6922 (pm20) REVERT: A 508 ILE cc_start: 0.9502 (mp) cc_final: 0.9260 (mt) REVERT: A 512 ARG cc_start: 0.8020 (ptt90) cc_final: 0.7404 (ttp-110) REVERT: A 677 ILE cc_start: 0.8012 (OUTLIER) cc_final: 0.7557 (pp) REVERT: A 758 MET cc_start: 0.8967 (tmm) cc_final: 0.8704 (tmm) REVERT: A 784 ILE cc_start: 0.8394 (OUTLIER) cc_final: 0.7859 (pt) REVERT: A 814 THR cc_start: 0.8125 (t) cc_final: 0.7779 (m) REVERT: A 846 ILE cc_start: 0.8992 (tp) cc_final: 0.8742 (tp) REVERT: A 902 ILE cc_start: 0.8884 (mm) cc_final: 0.8668 (mt) REVERT: A 974 ILE cc_start: 0.8006 (tp) cc_final: 0.7745 (mp) REVERT: B 113 HIS cc_start: 0.7746 (t-90) cc_final: 0.6953 (p-80) REVERT: B 172 ASP cc_start: 0.8799 (p0) cc_final: 0.8572 (p0) REVERT: B 184 THR cc_start: 0.8033 (t) cc_final: 0.7767 (m) REVERT: B 256 ILE cc_start: 0.8727 (pt) cc_final: 0.8516 (pt) REVERT: B 371 TYR cc_start: 0.8602 (m-10) cc_final: 0.8114 (m-80) REVERT: B 508 ILE cc_start: 0.9476 (mp) cc_final: 0.9185 (mt) REVERT: B 512 ARG cc_start: 0.8234 (ptt180) cc_final: 0.7840 (ptt-90) REVERT: B 514 GLU cc_start: 0.4623 (tp30) cc_final: 0.4375 (tp30) REVERT: B 611 LEU cc_start: 0.9080 (tm) cc_final: 0.8689 (tp) REVERT: B 634 ASN cc_start: 0.8641 (t0) cc_final: 0.8210 (t0) REVERT: B 732 TYR cc_start: 0.7379 (m-10) cc_final: 0.7159 (m-10) REVERT: B 814 THR cc_start: 0.7904 (t) cc_final: 0.7602 (m) REVERT: B 828 GLN cc_start: 0.7881 (mm110) cc_final: 0.7594 (tm-30) REVERT: B 860 ILE cc_start: 0.7738 (pp) cc_final: 0.7402 (pt) REVERT: B 902 ILE cc_start: 0.8948 (mm) cc_final: 0.8717 (mt) REVERT: B 974 ILE cc_start: 0.7976 (tp) cc_final: 0.7694 (mp) REVERT: C 83 MET cc_start: 0.8286 (mpp) cc_final: 0.7910 (mtt) REVERT: C 184 THR cc_start: 0.8034 (t) cc_final: 0.7700 (m) REVERT: C 189 TYR cc_start: 0.6205 (m-10) cc_final: 0.5996 (m-10) REVERT: C 201 MET cc_start: 0.7985 (ptp) cc_final: 0.7648 (ptt) REVERT: C 253 GLN cc_start: 0.8151 (mt0) cc_final: 0.6941 (pm20) REVERT: C 371 TYR cc_start: 0.8614 (m-10) cc_final: 0.8366 (m-80) REVERT: C 389 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7356 (pp) REVERT: C 493 ASP cc_start: 0.7424 (p0) cc_final: 0.6928 (p0) REVERT: C 512 ARG cc_start: 0.8061 (ptt90) cc_final: 0.7510 (ttp80) REVERT: C 648 MET cc_start: 0.6721 (tmm) cc_final: 0.6486 (tmm) REVERT: C 677 ILE cc_start: 0.8016 (OUTLIER) cc_final: 0.7728 (pp) REVERT: C 726 LEU cc_start: 0.8107 (mm) cc_final: 0.7678 (tp) REVERT: C 746 MET cc_start: 0.8720 (tpp) cc_final: 0.7717 (ttp) REVERT: C 784 ILE cc_start: 0.8295 (OUTLIER) cc_final: 0.7858 (pt) REVERT: C 814 THR cc_start: 0.7886 (t) cc_final: 0.7568 (m) REVERT: C 828 GLN cc_start: 0.7619 (mm110) cc_final: 0.7412 (tm-30) REVERT: C 846 ILE cc_start: 0.9009 (tp) cc_final: 0.8703 (tp) REVERT: C 941 THR cc_start: 0.8733 (m) cc_final: 0.8510 (p) outliers start: 91 outliers final: 39 residues processed: 448 average time/residue: 0.3257 time to fit residues: 240.9484 Evaluate side-chains 353 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 309 time to evaluate : 2.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASN Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 201 MET Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 583 ASN Chi-restraints excluded: chain A residue 596 ASP Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 648 MET Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 677 ILE Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 921 HIS Chi-restraints excluded: chain B residue 51 ASN Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 583 ASN Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 908 SER Chi-restraints excluded: chain B residue 949 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 460 ASP Chi-restraints excluded: chain C residue 583 ASN Chi-restraints excluded: chain C residue 596 ASP Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 677 ILE Chi-restraints excluded: chain C residue 784 ILE Chi-restraints excluded: chain C residue 840 ASN Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 908 SER Chi-restraints excluded: chain C residue 949 THR Chi-restraints excluded: chain C residue 1018 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 149 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 224 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 270 optimal weight: 5.9990 chunk 291 optimal weight: 0.8980 chunk 240 optimal weight: 0.9980 chunk 267 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 chunk 216 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS A 96 GLN A 261 ASN A 863 ASN ** A 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 GLN ** B 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 GLN B 921 HIS ** B 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 GLN C 774 GLN C 894 GLN C 979 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24687 Z= 0.235 Angle : 0.689 7.239 33570 Z= 0.358 Chirality : 0.049 0.546 4062 Planarity : 0.005 0.050 4227 Dihedral : 7.442 59.826 5070 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.20 % Favored : 87.80 % Rotamer: Outliers : 3.93 % Allowed : 17.24 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.54 (0.14), residues: 2967 helix: 0.45 (0.24), residues: 510 sheet: -2.26 (0.23), residues: 444 loop : -3.39 (0.11), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 341 HIS 0.004 0.001 HIS B 823 PHE 0.023 0.002 PHE A 210 TYR 0.022 0.001 TYR B 983 ARG 0.004 0.001 ARG A 778 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 338 time to evaluate : 2.858 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.8209 (mpp) cc_final: 0.7829 (mtt) REVERT: A 184 THR cc_start: 0.8254 (t) cc_final: 0.7940 (m) REVERT: A 253 GLN cc_start: 0.8243 (mt0) cc_final: 0.6946 (pm20) REVERT: A 371 TYR cc_start: 0.8708 (m-80) cc_final: 0.8448 (m-80) REVERT: A 430 THR cc_start: 0.9124 (OUTLIER) cc_final: 0.8905 (m) REVERT: A 512 ARG cc_start: 0.8058 (ptt90) cc_final: 0.7387 (ttp-110) REVERT: A 677 ILE cc_start: 0.8068 (OUTLIER) cc_final: 0.7608 (pp) REVERT: A 758 MET cc_start: 0.9067 (tmm) cc_final: 0.8632 (tmm) REVERT: A 784 ILE cc_start: 0.8560 (OUTLIER) cc_final: 0.8204 (pt) REVERT: A 846 ILE cc_start: 0.9043 (tp) cc_final: 0.8811 (tp) REVERT: A 857 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8521 (pp) REVERT: A 911 ILE cc_start: 0.7933 (OUTLIER) cc_final: 0.7698 (tp) REVERT: A 974 ILE cc_start: 0.7857 (tp) cc_final: 0.7585 (mp) REVERT: B 172 ASP cc_start: 0.8885 (p0) cc_final: 0.8652 (p0) REVERT: B 184 THR cc_start: 0.8389 (t) cc_final: 0.8138 (m) REVERT: B 201 MET cc_start: 0.7970 (ptt) cc_final: 0.7549 (ptt) REVERT: B 253 GLN cc_start: 0.8148 (mt0) cc_final: 0.6978 (pm20) REVERT: B 256 ILE cc_start: 0.8961 (pt) cc_final: 0.8755 (pt) REVERT: B 261 ASN cc_start: 0.6299 (t0) cc_final: 0.5961 (t0) REVERT: B 371 TYR cc_start: 0.8669 (m-10) cc_final: 0.8024 (m-80) REVERT: B 430 THR cc_start: 0.9210 (OUTLIER) cc_final: 0.8901 (m) REVERT: B 508 ILE cc_start: 0.9487 (mp) cc_final: 0.9229 (mt) REVERT: B 512 ARG cc_start: 0.8173 (ptt180) cc_final: 0.7593 (ttp-170) REVERT: B 611 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8778 (tp) REVERT: B 634 ASN cc_start: 0.8612 (t0) cc_final: 0.8155 (t0) REVERT: B 732 TYR cc_start: 0.7505 (m-10) cc_final: 0.7245 (m-10) REVERT: B 828 GLN cc_start: 0.7972 (mm110) cc_final: 0.7715 (tm-30) REVERT: B 846 ILE cc_start: 0.9053 (tp) cc_final: 0.8850 (tp) REVERT: B 902 ILE cc_start: 0.8933 (mm) cc_final: 0.8651 (mt) REVERT: B 904 GLU cc_start: 0.6304 (tm-30) cc_final: 0.5967 (tm-30) REVERT: B 974 ILE cc_start: 0.8132 (tp) cc_final: 0.7703 (mp) REVERT: B 991 MET cc_start: 0.8060 (ttt) cc_final: 0.7787 (ttm) REVERT: C 83 MET cc_start: 0.8345 (mpp) cc_final: 0.7961 (mtt) REVERT: C 113 HIS cc_start: 0.7692 (t-90) cc_final: 0.6970 (p-80) REVERT: C 184 THR cc_start: 0.8264 (t) cc_final: 0.7941 (m) REVERT: C 201 MET cc_start: 0.8048 (ptp) cc_final: 0.7712 (ptt) REVERT: C 253 GLN cc_start: 0.8222 (mt0) cc_final: 0.6990 (pm20) REVERT: C 389 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7226 (pp) REVERT: C 512 ARG cc_start: 0.8111 (ptt90) cc_final: 0.7473 (ttp80) REVERT: C 648 MET cc_start: 0.6754 (tmm) cc_final: 0.6479 (tmm) REVERT: C 677 ILE cc_start: 0.8019 (OUTLIER) cc_final: 0.7651 (pp) REVERT: C 726 LEU cc_start: 0.8166 (mm) cc_final: 0.7778 (tp) REVERT: C 784 ILE cc_start: 0.8489 (OUTLIER) cc_final: 0.8080 (pt) REVERT: C 846 ILE cc_start: 0.9077 (tp) cc_final: 0.8859 (tp) REVERT: C 941 THR cc_start: 0.8814 (m) cc_final: 0.8577 (p) outliers start: 100 outliers final: 58 residues processed: 404 average time/residue: 0.3058 time to fit residues: 206.1415 Evaluate side-chains 370 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 302 time to evaluate : 2.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASN Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 201 MET Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 583 ASN Chi-restraints excluded: chain A residue 596 ASP Chi-restraints excluded: chain A residue 648 MET Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 677 ILE Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 921 HIS Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain B residue 51 ASN Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 232 GLN Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 460 ASP Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 583 ASN Chi-restraints excluded: chain B residue 596 ASP Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 908 SER Chi-restraints excluded: chain B residue 921 HIS Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 451 SER Chi-restraints excluded: chain C residue 460 ASP Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 583 ASN Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 677 ILE Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 784 ILE Chi-restraints excluded: chain C residue 908 SER Chi-restraints excluded: chain C residue 949 THR Chi-restraints excluded: chain C residue 985 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 266 optimal weight: 20.0000 chunk 203 optimal weight: 3.9990 chunk 140 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 181 optimal weight: 0.9980 chunk 271 optimal weight: 8.9990 chunk 287 optimal weight: 5.9990 chunk 141 optimal weight: 0.6980 chunk 256 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN A 774 GLN A 894 GLN ** A 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 GLN B 232 GLN ** B 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 863 ASN ** B 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 ASN C 410 GLN C 863 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 24687 Z= 0.275 Angle : 0.694 7.648 33570 Z= 0.358 Chirality : 0.050 0.520 4062 Planarity : 0.004 0.047 4227 Dihedral : 7.195 56.821 5070 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.44 % Favored : 87.56 % Rotamer: Outliers : 4.52 % Allowed : 18.41 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.39 (0.14), residues: 2967 helix: 0.81 (0.24), residues: 513 sheet: -2.17 (0.23), residues: 444 loop : -3.37 (0.11), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 341 HIS 0.019 0.001 HIS B 921 PHE 0.027 0.002 PHE C 210 TYR 0.016 0.001 TYR C 29 ARG 0.003 0.001 ARG A 895 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 306 time to evaluate : 3.154 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.8190 (mpp) cc_final: 0.7851 (mtt) REVERT: A 184 THR cc_start: 0.8336 (t) cc_final: 0.8045 (m) REVERT: A 189 TYR cc_start: 0.6317 (m-80) cc_final: 0.6078 (t80) REVERT: A 253 GLN cc_start: 0.8258 (mt0) cc_final: 0.6831 (pm20) REVERT: A 371 TYR cc_start: 0.8705 (m-80) cc_final: 0.8394 (m-80) REVERT: A 512 ARG cc_start: 0.8072 (ptt90) cc_final: 0.7329 (ttp-110) REVERT: A 677 ILE cc_start: 0.8189 (OUTLIER) cc_final: 0.7753 (pp) REVERT: A 746 MET cc_start: 0.8652 (tpt) cc_final: 0.8356 (tpp) REVERT: A 758 MET cc_start: 0.9152 (tmm) cc_final: 0.8639 (tmm) REVERT: A 784 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8197 (pt) REVERT: A 846 ILE cc_start: 0.9046 (tp) cc_final: 0.8821 (tp) REVERT: A 857 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8519 (pp) REVERT: A 911 ILE cc_start: 0.7912 (OUTLIER) cc_final: 0.7652 (tp) REVERT: A 974 ILE cc_start: 0.7867 (tp) cc_final: 0.7587 (mp) REVERT: B 113 HIS cc_start: 0.7922 (t-90) cc_final: 0.6858 (p90) REVERT: B 172 ASP cc_start: 0.8958 (p0) cc_final: 0.8695 (p0) REVERT: B 184 THR cc_start: 0.8448 (t) cc_final: 0.8183 (m) REVERT: B 253 GLN cc_start: 0.8183 (mt0) cc_final: 0.6946 (pm20) REVERT: B 321 MET cc_start: 0.8031 (mmm) cc_final: 0.7789 (tpt) REVERT: B 371 TYR cc_start: 0.8688 (m-80) cc_final: 0.8164 (m-80) REVERT: B 508 ILE cc_start: 0.9489 (mp) cc_final: 0.9256 (mt) REVERT: B 512 ARG cc_start: 0.8179 (ptt180) cc_final: 0.7548 (ttp-170) REVERT: B 611 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8832 (tp) REVERT: B 634 ASN cc_start: 0.8685 (t0) cc_final: 0.8321 (t0) REVERT: B 677 ILE cc_start: 0.8279 (OUTLIER) cc_final: 0.7860 (pp) REVERT: B 732 TYR cc_start: 0.7594 (m-10) cc_final: 0.7340 (m-10) REVERT: B 828 GLN cc_start: 0.8051 (mm110) cc_final: 0.7771 (tm-30) REVERT: B 902 ILE cc_start: 0.8936 (mm) cc_final: 0.8669 (mt) REVERT: B 974 ILE cc_start: 0.8108 (tp) cc_final: 0.7695 (mp) REVERT: C 83 MET cc_start: 0.8297 (mpp) cc_final: 0.7970 (mtt) REVERT: C 184 THR cc_start: 0.8275 (t) cc_final: 0.7963 (m) REVERT: C 201 MET cc_start: 0.8166 (ptp) cc_final: 0.7907 (ptt) REVERT: C 253 GLN cc_start: 0.8222 (mt0) cc_final: 0.6977 (pm20) REVERT: C 430 THR cc_start: 0.9156 (OUTLIER) cc_final: 0.8877 (m) REVERT: C 512 ARG cc_start: 0.8072 (ptt90) cc_final: 0.7459 (ttp80) REVERT: C 648 MET cc_start: 0.6718 (tmm) cc_final: 0.6430 (tmm) REVERT: C 677 ILE cc_start: 0.8085 (OUTLIER) cc_final: 0.7698 (pp) REVERT: C 726 LEU cc_start: 0.8187 (mm) cc_final: 0.7776 (tp) REVERT: C 746 MET cc_start: 0.8823 (tpp) cc_final: 0.7814 (ttp) REVERT: C 784 ILE cc_start: 0.8545 (OUTLIER) cc_final: 0.8175 (pt) REVERT: C 846 ILE cc_start: 0.9060 (tp) cc_final: 0.8845 (tp) REVERT: C 921 HIS cc_start: 0.8526 (p90) cc_final: 0.8177 (p90) REVERT: C 941 THR cc_start: 0.8852 (m) cc_final: 0.8629 (p) outliers start: 115 outliers final: 74 residues processed: 386 average time/residue: 0.2963 time to fit residues: 190.7078 Evaluate side-chains 375 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 292 time to evaluate : 2.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASN Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 201 MET Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 583 ASN Chi-restraints excluded: chain A residue 596 ASP Chi-restraints excluded: chain A residue 648 MET Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 677 ILE Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 921 HIS Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain B residue 51 ASN Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 322 TYR Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 460 ASP Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 583 ASN Chi-restraints excluded: chain B residue 596 ASP Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 677 ILE Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 792 ASN Chi-restraints excluded: chain B residue 814 THR Chi-restraints excluded: chain B residue 831 ILE Chi-restraints excluded: chain B residue 908 SER Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 451 SER Chi-restraints excluded: chain C residue 460 ASP Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 583 ASN Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 596 ASP Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 677 ILE Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 784 ILE Chi-restraints excluded: chain C residue 792 ASN Chi-restraints excluded: chain C residue 814 THR Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 908 SER Chi-restraints excluded: chain C residue 949 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 239 optimal weight: 0.9980 chunk 162 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 213 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 244 optimal weight: 3.9990 chunk 198 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 146 optimal weight: 0.1980 chunk 257 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 24687 Z= 0.242 Angle : 0.669 8.058 33570 Z= 0.344 Chirality : 0.049 0.519 4062 Planarity : 0.004 0.045 4227 Dihedral : 6.698 58.224 5070 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.00 % Favored : 88.00 % Rotamer: Outliers : 5.34 % Allowed : 18.69 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (0.14), residues: 2967 helix: 1.28 (0.24), residues: 510 sheet: -1.98 (0.21), residues: 531 loop : -3.37 (0.12), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 341 HIS 0.004 0.001 HIS A 937 PHE 0.027 0.002 PHE C 210 TYR 0.022 0.001 TYR C 29 ARG 0.003 0.000 ARG B 366 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 300 time to evaluate : 3.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.8138 (mpp) cc_final: 0.7903 (mtt) REVERT: A 113 HIS cc_start: 0.7920 (t-90) cc_final: 0.6807 (p-80) REVERT: A 169 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7953 (tp) REVERT: A 184 THR cc_start: 0.8328 (t) cc_final: 0.8048 (m) REVERT: A 253 GLN cc_start: 0.8286 (mt0) cc_final: 0.6874 (pm20) REVERT: A 371 TYR cc_start: 0.8691 (m-80) cc_final: 0.8418 (m-80) REVERT: A 512 ARG cc_start: 0.7980 (ptt90) cc_final: 0.7292 (ttp-110) REVERT: A 677 ILE cc_start: 0.8269 (OUTLIER) cc_final: 0.7819 (pp) REVERT: A 746 MET cc_start: 0.8627 (tpt) cc_final: 0.8342 (tpp) REVERT: A 784 ILE cc_start: 0.8529 (OUTLIER) cc_final: 0.8185 (pt) REVERT: A 846 ILE cc_start: 0.9035 (tp) cc_final: 0.8812 (tp) REVERT: A 857 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8636 (pp) REVERT: A 911 ILE cc_start: 0.7942 (OUTLIER) cc_final: 0.7686 (tp) REVERT: A 974 ILE cc_start: 0.7921 (tp) cc_final: 0.7657 (mp) REVERT: B 113 HIS cc_start: 0.7960 (t-90) cc_final: 0.6903 (p90) REVERT: B 172 ASP cc_start: 0.8993 (p0) cc_final: 0.8703 (p0) REVERT: B 184 THR cc_start: 0.8471 (t) cc_final: 0.8181 (m) REVERT: B 253 GLN cc_start: 0.8215 (mt0) cc_final: 0.6994 (pm20) REVERT: B 371 TYR cc_start: 0.8672 (m-80) cc_final: 0.8221 (m-80) REVERT: B 430 THR cc_start: 0.9245 (OUTLIER) cc_final: 0.8922 (m) REVERT: B 508 ILE cc_start: 0.9501 (mp) cc_final: 0.9282 (mt) REVERT: B 512 ARG cc_start: 0.8185 (ptt180) cc_final: 0.7565 (ttp-170) REVERT: B 611 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8876 (tp) REVERT: B 634 ASN cc_start: 0.8691 (t0) cc_final: 0.8371 (t0) REVERT: B 677 ILE cc_start: 0.8299 (OUTLIER) cc_final: 0.7850 (pp) REVERT: B 732 TYR cc_start: 0.7643 (m-10) cc_final: 0.7431 (m-10) REVERT: B 974 ILE cc_start: 0.7961 (tp) cc_final: 0.7612 (mp) REVERT: C 83 MET cc_start: 0.8258 (mpp) cc_final: 0.7953 (mtt) REVERT: C 97 PHE cc_start: 0.8343 (t80) cc_final: 0.8108 (t80) REVERT: C 184 THR cc_start: 0.8224 (t) cc_final: 0.7924 (m) REVERT: C 201 MET cc_start: 0.8138 (ptp) cc_final: 0.7900 (ptt) REVERT: C 253 GLN cc_start: 0.8254 (mt0) cc_final: 0.6984 (pm20) REVERT: C 269 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8118 (pp) REVERT: C 430 THR cc_start: 0.9175 (OUTLIER) cc_final: 0.8902 (m) REVERT: C 512 ARG cc_start: 0.8067 (ptt90) cc_final: 0.7614 (ttp-170) REVERT: C 635 ILE cc_start: 0.8995 (OUTLIER) cc_final: 0.8654 (tp) REVERT: C 648 MET cc_start: 0.6602 (tmm) cc_final: 0.6322 (tmm) REVERT: C 677 ILE cc_start: 0.8100 (OUTLIER) cc_final: 0.7713 (pp) REVERT: C 726 LEU cc_start: 0.8177 (mm) cc_final: 0.7819 (tp) REVERT: C 784 ILE cc_start: 0.8570 (OUTLIER) cc_final: 0.8242 (pt) REVERT: C 846 ILE cc_start: 0.9019 (tp) cc_final: 0.8790 (tp) REVERT: C 921 HIS cc_start: 0.8625 (p90) cc_final: 0.8285 (p90) REVERT: C 941 THR cc_start: 0.8862 (m) cc_final: 0.8651 (p) outliers start: 136 outliers final: 77 residues processed: 400 average time/residue: 0.3097 time to fit residues: 205.8812 Evaluate side-chains 369 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 279 time to evaluate : 2.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASN Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 201 MET Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 596 ASP Chi-restraints excluded: chain A residue 648 MET Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 677 ILE Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 921 HIS Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain B residue 51 ASN Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 460 ASP Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 596 ASP Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 677 ILE Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 792 ASN Chi-restraints excluded: chain B residue 814 THR Chi-restraints excluded: chain B residue 831 ILE Chi-restraints excluded: chain B residue 908 SER Chi-restraints excluded: chain B residue 911 ILE Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 451 SER Chi-restraints excluded: chain C residue 460 ASP Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 583 ASN Chi-restraints excluded: chain C residue 596 ASP Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 677 ILE Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 784 ILE Chi-restraints excluded: chain C residue 814 THR Chi-restraints excluded: chain C residue 857 LEU Chi-restraints excluded: chain C residue 908 SER Chi-restraints excluded: chain C residue 949 THR Chi-restraints excluded: chain C residue 984 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 96 optimal weight: 6.9990 chunk 258 optimal weight: 0.5980 chunk 56 optimal weight: 0.2980 chunk 168 optimal weight: 3.9990 chunk 70 optimal weight: 0.0770 chunk 287 optimal weight: 0.8980 chunk 238 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 150 optimal weight: 8.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 921 HIS ** B 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24687 Z= 0.176 Angle : 0.647 9.676 33570 Z= 0.328 Chirality : 0.048 0.518 4062 Planarity : 0.004 0.044 4227 Dihedral : 6.080 49.089 5070 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.55 % Favored : 89.45 % Rotamer: Outliers : 4.59 % Allowed : 19.67 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.15), residues: 2967 helix: 1.56 (0.24), residues: 522 sheet: -1.78 (0.22), residues: 522 loop : -3.30 (0.12), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 92 HIS 0.004 0.001 HIS C 823 PHE 0.017 0.001 PHE A 210 TYR 0.015 0.001 TYR C 29 ARG 0.005 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 300 time to evaluate : 2.767 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 HIS cc_start: 0.7676 (t-90) cc_final: 0.6744 (p-80) REVERT: A 184 THR cc_start: 0.8221 (t) cc_final: 0.7928 (m) REVERT: A 253 GLN cc_start: 0.8209 (mt0) cc_final: 0.6931 (pm20) REVERT: A 463 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8372 (mm) REVERT: A 512 ARG cc_start: 0.7893 (ptt90) cc_final: 0.7266 (ttp-110) REVERT: A 651 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8618 (tp) REVERT: A 677 ILE cc_start: 0.8097 (OUTLIER) cc_final: 0.7593 (pp) REVERT: A 746 MET cc_start: 0.8590 (tpt) cc_final: 0.8306 (tpp) REVERT: A 784 ILE cc_start: 0.8519 (OUTLIER) cc_final: 0.8222 (pt) REVERT: A 857 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8546 (pp) REVERT: A 911 ILE cc_start: 0.7904 (OUTLIER) cc_final: 0.7649 (tp) REVERT: A 974 ILE cc_start: 0.7863 (tp) cc_final: 0.7607 (mp) REVERT: B 113 HIS cc_start: 0.7823 (t-90) cc_final: 0.6930 (p-80) REVERT: B 172 ASP cc_start: 0.8968 (p0) cc_final: 0.8637 (p0) REVERT: B 184 THR cc_start: 0.8367 (t) cc_final: 0.8076 (m) REVERT: B 253 GLN cc_start: 0.8157 (mt0) cc_final: 0.6949 (pm20) REVERT: B 371 TYR cc_start: 0.8646 (m-80) cc_final: 0.8282 (m-80) REVERT: B 430 THR cc_start: 0.9281 (OUTLIER) cc_final: 0.8956 (m) REVERT: B 463 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8381 (mm) REVERT: B 508 ILE cc_start: 0.9455 (mp) cc_final: 0.9235 (mt) REVERT: B 512 ARG cc_start: 0.8166 (ptt180) cc_final: 0.7659 (ttp-170) REVERT: B 611 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8860 (tp) REVERT: B 634 ASN cc_start: 0.8631 (t0) cc_final: 0.8332 (t0) REVERT: B 677 ILE cc_start: 0.8236 (OUTLIER) cc_final: 0.7806 (pp) REVERT: B 836 MET cc_start: 0.8053 (tpp) cc_final: 0.7742 (tpp) REVERT: B 846 ILE cc_start: 0.8882 (tp) cc_final: 0.8423 (mt) REVERT: B 974 ILE cc_start: 0.7888 (tp) cc_final: 0.7571 (mp) REVERT: C 83 MET cc_start: 0.8190 (mpp) cc_final: 0.7936 (mtt) REVERT: C 184 THR cc_start: 0.8113 (t) cc_final: 0.7817 (m) REVERT: C 201 MET cc_start: 0.8041 (ptp) cc_final: 0.7795 (ptt) REVERT: C 253 GLN cc_start: 0.8144 (mt0) cc_final: 0.6950 (pm20) REVERT: C 430 THR cc_start: 0.9160 (OUTLIER) cc_final: 0.8895 (m) REVERT: C 512 ARG cc_start: 0.7970 (ptt90) cc_final: 0.7359 (ttp80) REVERT: C 635 ILE cc_start: 0.8988 (OUTLIER) cc_final: 0.8617 (tp) REVERT: C 648 MET cc_start: 0.6538 (tmm) cc_final: 0.6311 (tmm) REVERT: C 677 ILE cc_start: 0.8007 (OUTLIER) cc_final: 0.7606 (pp) REVERT: C 726 LEU cc_start: 0.8150 (mm) cc_final: 0.7685 (tp) REVERT: C 784 ILE cc_start: 0.8528 (OUTLIER) cc_final: 0.8209 (pt) REVERT: C 846 ILE cc_start: 0.9008 (tp) cc_final: 0.8767 (tp) REVERT: C 921 HIS cc_start: 0.8515 (p90) cc_final: 0.8184 (p90) outliers start: 117 outliers final: 68 residues processed: 384 average time/residue: 0.2929 time to fit residues: 189.2806 Evaluate side-chains 351 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 269 time to evaluate : 2.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASN Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 201 MET Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 648 MET Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 677 ILE Chi-restraints excluded: chain A residue 769 ILE Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 921 HIS Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain B residue 51 ASN Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 130 PHE Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 460 ASP Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 677 ILE Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain B residue 814 THR Chi-restraints excluded: chain B residue 908 SER Chi-restraints excluded: chain B residue 911 ILE Chi-restraints excluded: chain B residue 921 HIS Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 130 PHE Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 451 SER Chi-restraints excluded: chain C residue 460 ASP Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 677 ILE Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 784 ILE Chi-restraints excluded: chain C residue 792 ASN Chi-restraints excluded: chain C residue 814 THR Chi-restraints excluded: chain C residue 857 LEU Chi-restraints excluded: chain C residue 908 SER Chi-restraints excluded: chain C residue 949 THR Chi-restraints excluded: chain C residue 985 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 277 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 163 optimal weight: 10.0000 chunk 209 optimal weight: 7.9990 chunk 162 optimal weight: 3.9990 chunk 241 optimal weight: 0.9990 chunk 160 optimal weight: 0.7980 chunk 286 optimal weight: 6.9990 chunk 179 optimal weight: 4.9990 chunk 174 optimal weight: 0.8980 chunk 132 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN ** A 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 GLN B 234 ASN B 921 HIS ** B 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24687 Z= 0.195 Angle : 0.660 8.130 33570 Z= 0.334 Chirality : 0.049 0.557 4062 Planarity : 0.004 0.043 4227 Dihedral : 5.884 42.470 5070 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.49 % Favored : 88.51 % Rotamer: Outliers : 4.24 % Allowed : 20.49 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.15), residues: 2967 helix: 1.72 (0.24), residues: 522 sheet: -1.78 (0.22), residues: 525 loop : -3.26 (0.12), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 341 HIS 0.016 0.001 HIS B 921 PHE 0.028 0.001 PHE C 97 TYR 0.013 0.001 TYR A 983 ARG 0.004 0.000 ARG B 920 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 276 time to evaluate : 2.838 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 HIS cc_start: 0.7702 (t-90) cc_final: 0.6808 (p-80) REVERT: A 169 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7923 (tp) REVERT: A 184 THR cc_start: 0.8208 (t) cc_final: 0.7926 (m) REVERT: A 253 GLN cc_start: 0.8215 (mt0) cc_final: 0.6933 (pm20) REVERT: A 463 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8428 (mm) REVERT: A 512 ARG cc_start: 0.7882 (ptt90) cc_final: 0.7238 (ttp-110) REVERT: A 677 ILE cc_start: 0.8092 (OUTLIER) cc_final: 0.7578 (pp) REVERT: A 746 MET cc_start: 0.8573 (tpt) cc_final: 0.8284 (tpp) REVERT: A 784 ILE cc_start: 0.8502 (OUTLIER) cc_final: 0.8174 (pt) REVERT: A 857 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8624 (pp) REVERT: A 911 ILE cc_start: 0.7866 (OUTLIER) cc_final: 0.7642 (tp) REVERT: A 974 ILE cc_start: 0.7867 (tp) cc_final: 0.7634 (mp) REVERT: A 991 MET cc_start: 0.7901 (ttt) cc_final: 0.7657 (tpp) REVERT: B 113 HIS cc_start: 0.7872 (t-90) cc_final: 0.6927 (p90) REVERT: B 172 ASP cc_start: 0.8943 (p0) cc_final: 0.8657 (p0) REVERT: B 184 THR cc_start: 0.8361 (t) cc_final: 0.8070 (m) REVERT: B 253 GLN cc_start: 0.8138 (mt0) cc_final: 0.6947 (pm20) REVERT: B 371 TYR cc_start: 0.8611 (m-80) cc_final: 0.8266 (m-80) REVERT: B 430 THR cc_start: 0.9290 (OUTLIER) cc_final: 0.8969 (m) REVERT: B 463 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8433 (mm) REVERT: B 508 ILE cc_start: 0.9460 (mp) cc_final: 0.9237 (mt) REVERT: B 512 ARG cc_start: 0.8180 (ptt180) cc_final: 0.7292 (ttp-110) REVERT: B 611 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8882 (tp) REVERT: B 634 ASN cc_start: 0.8699 (t0) cc_final: 0.8438 (t0) REVERT: B 677 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7728 (pp) REVERT: B 846 ILE cc_start: 0.8678 (tp) cc_final: 0.8321 (mt) REVERT: B 974 ILE cc_start: 0.7883 (tp) cc_final: 0.7611 (mp) REVERT: C 83 MET cc_start: 0.8188 (mpp) cc_final: 0.7952 (mtt) REVERT: C 184 THR cc_start: 0.8141 (t) cc_final: 0.7835 (m) REVERT: C 201 MET cc_start: 0.8028 (ptp) cc_final: 0.7785 (ptt) REVERT: C 253 GLN cc_start: 0.8146 (mt0) cc_final: 0.6948 (pm20) REVERT: C 430 THR cc_start: 0.9161 (OUTLIER) cc_final: 0.8910 (m) REVERT: C 512 ARG cc_start: 0.7986 (ptt90) cc_final: 0.7360 (ttp80) REVERT: C 603 MET cc_start: 0.7827 (ptm) cc_final: 0.7458 (ptm) REVERT: C 635 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8638 (tp) REVERT: C 648 MET cc_start: 0.6643 (tmm) cc_final: 0.6357 (tmm) REVERT: C 677 ILE cc_start: 0.8001 (OUTLIER) cc_final: 0.7596 (pp) REVERT: C 726 LEU cc_start: 0.8226 (mm) cc_final: 0.7710 (tp) REVERT: C 846 ILE cc_start: 0.9003 (tp) cc_final: 0.8763 (tp) REVERT: C 921 HIS cc_start: 0.8497 (p90) cc_final: 0.8134 (p90) outliers start: 108 outliers final: 78 residues processed: 356 average time/residue: 0.2949 time to fit residues: 175.1362 Evaluate side-chains 354 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 263 time to evaluate : 2.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASN Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 201 MET Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 596 ASP Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 677 ILE Chi-restraints excluded: chain A residue 769 ILE Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 792 ASN Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 921 HIS Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain B residue 51 ASN Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 130 PHE Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 460 ASP Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 677 ILE Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 908 SER Chi-restraints excluded: chain B residue 911 ILE Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 130 PHE Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 460 ASP Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 677 ILE Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 784 ILE Chi-restraints excluded: chain C residue 788 LEU Chi-restraints excluded: chain C residue 792 ASN Chi-restraints excluded: chain C residue 814 THR Chi-restraints excluded: chain C residue 857 LEU Chi-restraints excluded: chain C residue 908 SER Chi-restraints excluded: chain C residue 949 THR Chi-restraints excluded: chain C residue 984 ILE Chi-restraints excluded: chain C residue 985 THR Chi-restraints excluded: chain C residue 1020 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 177 optimal weight: 0.8980 chunk 114 optimal weight: 0.0270 chunk 170 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 181 optimal weight: 0.9980 chunk 195 optimal weight: 5.9990 chunk 141 optimal weight: 0.3980 chunk 26 optimal weight: 4.9990 chunk 225 optimal weight: 0.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 626 GLN ** A 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24687 Z= 0.165 Angle : 0.646 9.863 33570 Z= 0.326 Chirality : 0.048 0.525 4062 Planarity : 0.004 0.043 4227 Dihedral : 5.713 71.821 5070 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.65 % Favored : 89.35 % Rotamer: Outliers : 4.00 % Allowed : 20.69 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.15), residues: 2967 helix: 2.14 (0.24), residues: 504 sheet: -1.53 (0.23), residues: 504 loop : -3.14 (0.12), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 40 HIS 0.010 0.001 HIS B 921 PHE 0.019 0.001 PHE C 97 TYR 0.014 0.001 TYR B 29 ARG 0.004 0.000 ARG B 920 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 279 time to evaluate : 2.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 HIS cc_start: 0.7667 (t-90) cc_final: 0.6822 (p-80) REVERT: A 184 THR cc_start: 0.8013 (t) cc_final: 0.7722 (m) REVERT: A 253 GLN cc_start: 0.8144 (mt0) cc_final: 0.6871 (pm20) REVERT: A 321 MET cc_start: 0.7153 (tpt) cc_final: 0.6942 (tpt) REVERT: A 463 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8367 (mm) REVERT: A 512 ARG cc_start: 0.7858 (ptt90) cc_final: 0.7250 (ttp-110) REVERT: A 651 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8702 (tp) REVERT: A 677 ILE cc_start: 0.8028 (OUTLIER) cc_final: 0.7511 (pp) REVERT: A 746 MET cc_start: 0.8532 (tpt) cc_final: 0.8243 (tpp) REVERT: A 846 ILE cc_start: 0.8991 (tp) cc_final: 0.8142 (tp) REVERT: A 911 ILE cc_start: 0.7877 (OUTLIER) cc_final: 0.7660 (tp) REVERT: A 974 ILE cc_start: 0.7776 (tp) cc_final: 0.7562 (mp) REVERT: B 113 HIS cc_start: 0.7781 (t-90) cc_final: 0.6927 (p90) REVERT: B 172 ASP cc_start: 0.8906 (p0) cc_final: 0.8604 (p0) REVERT: B 184 THR cc_start: 0.8292 (t) cc_final: 0.7990 (m) REVERT: B 253 GLN cc_start: 0.8100 (mt0) cc_final: 0.6904 (pm20) REVERT: B 330 ASN cc_start: 0.7911 (OUTLIER) cc_final: 0.7696 (m-40) REVERT: B 371 TYR cc_start: 0.8574 (m-80) cc_final: 0.8293 (m-80) REVERT: B 430 THR cc_start: 0.9294 (OUTLIER) cc_final: 0.8986 (m) REVERT: B 463 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8381 (mm) REVERT: B 508 ILE cc_start: 0.9438 (mp) cc_final: 0.9219 (mt) REVERT: B 512 ARG cc_start: 0.8087 (ptt180) cc_final: 0.7633 (ttp-170) REVERT: B 611 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8889 (tp) REVERT: B 677 ILE cc_start: 0.8118 (OUTLIER) cc_final: 0.7675 (pp) REVERT: B 974 ILE cc_start: 0.7804 (tp) cc_final: 0.7544 (mp) REVERT: C 83 MET cc_start: 0.8266 (mpp) cc_final: 0.7957 (mtt) REVERT: C 113 HIS cc_start: 0.7515 (t-90) cc_final: 0.6831 (p90) REVERT: C 184 THR cc_start: 0.8078 (t) cc_final: 0.7730 (m) REVERT: C 201 MET cc_start: 0.7946 (ptp) cc_final: 0.7684 (ptp) REVERT: C 253 GLN cc_start: 0.8056 (mt0) cc_final: 0.6900 (pm20) REVERT: C 330 ASN cc_start: 0.8015 (m-40) cc_final: 0.7741 (m-40) REVERT: C 430 THR cc_start: 0.9151 (OUTLIER) cc_final: 0.8908 (m) REVERT: C 635 ILE cc_start: 0.8989 (OUTLIER) cc_final: 0.8607 (tp) REVERT: C 648 MET cc_start: 0.6549 (tmm) cc_final: 0.6246 (tmm) REVERT: C 677 ILE cc_start: 0.7931 (OUTLIER) cc_final: 0.7503 (pp) REVERT: C 726 LEU cc_start: 0.8202 (mm) cc_final: 0.7666 (tp) REVERT: C 846 ILE cc_start: 0.8961 (tp) cc_final: 0.8483 (tp) REVERT: C 921 HIS cc_start: 0.8405 (p90) cc_final: 0.8098 (p90) outliers start: 102 outliers final: 72 residues processed: 352 average time/residue: 0.3062 time to fit residues: 178.9321 Evaluate side-chains 339 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 255 time to evaluate : 2.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASN Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 201 MET Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 677 ILE Chi-restraints excluded: chain A residue 769 ILE Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 921 HIS Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain A residue 951 ILE Chi-restraints excluded: chain B residue 29 TYR Chi-restraints excluded: chain B residue 51 ASN Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 130 PHE Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 460 ASP Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 677 ILE Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 792 ASN Chi-restraints excluded: chain B residue 908 SER Chi-restraints excluded: chain B residue 911 ILE Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 130 PHE Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 395 CYS Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 451 SER Chi-restraints excluded: chain C residue 460 ASP Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 677 ILE Chi-restraints excluded: chain C residue 679 LEU Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 784 ILE Chi-restraints excluded: chain C residue 814 THR Chi-restraints excluded: chain C residue 857 LEU Chi-restraints excluded: chain C residue 908 SER Chi-restraints excluded: chain C residue 949 THR Chi-restraints excluded: chain C residue 984 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 260 optimal weight: 0.9990 chunk 274 optimal weight: 6.9990 chunk 250 optimal weight: 6.9990 chunk 266 optimal weight: 0.0980 chunk 160 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 209 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 241 optimal weight: 0.5980 chunk 252 optimal weight: 1.9990 chunk 265 optimal weight: 0.5980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 ASN A 496 GLN ** A 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 ASN ** B 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 264 ASN ** C 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24687 Z= 0.173 Angle : 0.645 10.024 33570 Z= 0.326 Chirality : 0.047 0.515 4062 Planarity : 0.004 0.050 4227 Dihedral : 5.365 50.167 5070 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.92 % Favored : 89.08 % Rotamer: Outliers : 3.85 % Allowed : 21.04 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.15), residues: 2967 helix: 2.24 (0.24), residues: 504 sheet: -1.58 (0.21), residues: 555 loop : -3.17 (0.12), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 92 HIS 0.004 0.001 HIS C 101 PHE 0.014 0.001 PHE C 210 TYR 0.012 0.001 TYR B 29 ARG 0.004 0.000 ARG C 602 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 275 time to evaluate : 2.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 HIS cc_start: 0.7770 (t-90) cc_final: 0.6867 (p-80) REVERT: A 184 THR cc_start: 0.7982 (t) cc_final: 0.7681 (m) REVERT: A 253 GLN cc_start: 0.8164 (mt0) cc_final: 0.6740 (pm20) REVERT: A 463 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8363 (mm) REVERT: A 512 ARG cc_start: 0.7894 (ptt90) cc_final: 0.7261 (ttp-110) REVERT: A 651 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8745 (tp) REVERT: A 677 ILE cc_start: 0.8035 (OUTLIER) cc_final: 0.7511 (pp) REVERT: A 746 MET cc_start: 0.8508 (tpt) cc_final: 0.8229 (tpp) REVERT: A 846 ILE cc_start: 0.8983 (tp) cc_final: 0.8152 (tp) REVERT: A 911 ILE cc_start: 0.7868 (OUTLIER) cc_final: 0.7642 (tp) REVERT: A 974 ILE cc_start: 0.7758 (tp) cc_final: 0.7557 (mp) REVERT: B 113 HIS cc_start: 0.7770 (t-90) cc_final: 0.6955 (p90) REVERT: B 172 ASP cc_start: 0.8844 (p0) cc_final: 0.8596 (p0) REVERT: B 184 THR cc_start: 0.8295 (t) cc_final: 0.7979 (m) REVERT: B 330 ASN cc_start: 0.7944 (OUTLIER) cc_final: 0.7703 (m-40) REVERT: B 371 TYR cc_start: 0.8568 (m-80) cc_final: 0.8299 (m-80) REVERT: B 430 THR cc_start: 0.9294 (OUTLIER) cc_final: 0.8920 (m) REVERT: B 463 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8394 (mm) REVERT: B 508 ILE cc_start: 0.9438 (mp) cc_final: 0.9167 (mt) REVERT: B 512 ARG cc_start: 0.8143 (ptt180) cc_final: 0.7646 (ttp-170) REVERT: B 611 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8909 (tp) REVERT: B 974 ILE cc_start: 0.7779 (tp) cc_final: 0.7572 (mp) REVERT: B 985 THR cc_start: 0.8949 (t) cc_final: 0.8688 (p) REVERT: C 83 MET cc_start: 0.8261 (mpp) cc_final: 0.7964 (mtt) REVERT: C 184 THR cc_start: 0.8083 (t) cc_final: 0.7767 (m) REVERT: C 201 MET cc_start: 0.7935 (ptp) cc_final: 0.7700 (ptp) REVERT: C 253 GLN cc_start: 0.8023 (mt0) cc_final: 0.6885 (pm20) REVERT: C 330 ASN cc_start: 0.8068 (m-40) cc_final: 0.7792 (m-40) REVERT: C 430 THR cc_start: 0.9158 (OUTLIER) cc_final: 0.8934 (m) REVERT: C 512 ARG cc_start: 0.7973 (ptt90) cc_final: 0.7426 (ttp-170) REVERT: C 635 ILE cc_start: 0.8998 (OUTLIER) cc_final: 0.8589 (tp) REVERT: C 648 MET cc_start: 0.6688 (tmm) cc_final: 0.6348 (tmm) REVERT: C 677 ILE cc_start: 0.7890 (OUTLIER) cc_final: 0.7495 (pp) REVERT: C 726 LEU cc_start: 0.8200 (mm) cc_final: 0.7651 (tp) REVERT: C 846 ILE cc_start: 0.8981 (tp) cc_final: 0.8486 (tp) REVERT: C 991 MET cc_start: 0.7976 (ttt) cc_final: 0.7682 (tpp) outliers start: 98 outliers final: 77 residues processed: 343 average time/residue: 0.2959 time to fit residues: 170.0790 Evaluate side-chains 353 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 265 time to evaluate : 2.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASN Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 201 MET Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 677 ILE Chi-restraints excluded: chain A residue 769 ILE Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 921 HIS Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain A residue 951 ILE Chi-restraints excluded: chain B residue 29 TYR Chi-restraints excluded: chain B residue 51 ASN Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 130 PHE Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 460 ASP Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 662 PHE Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 792 ASN Chi-restraints excluded: chain B residue 908 SER Chi-restraints excluded: chain B residue 911 ILE Chi-restraints excluded: chain B residue 921 HIS Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 130 PHE Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 395 CYS Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 451 SER Chi-restraints excluded: chain C residue 460 ASP Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 677 ILE Chi-restraints excluded: chain C residue 679 LEU Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 784 ILE Chi-restraints excluded: chain C residue 792 ASN Chi-restraints excluded: chain C residue 814 THR Chi-restraints excluded: chain C residue 857 LEU Chi-restraints excluded: chain C residue 908 SER Chi-restraints excluded: chain C residue 934 VAL Chi-restraints excluded: chain C residue 949 THR Chi-restraints excluded: chain C residue 984 ILE Chi-restraints excluded: chain C residue 1020 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 175 optimal weight: 0.5980 chunk 282 optimal weight: 2.9990 chunk 172 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 chunk 196 optimal weight: 10.0000 chunk 295 optimal weight: 6.9990 chunk 272 optimal weight: 0.8980 chunk 235 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 181 optimal weight: 0.4980 chunk 144 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 496 GLN ** A 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 496 GLN ** B 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 24687 Z= 0.240 Angle : 0.687 10.106 33570 Z= 0.348 Chirality : 0.049 0.533 4062 Planarity : 0.004 0.054 4227 Dihedral : 5.572 37.449 5070 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.03 % Favored : 87.97 % Rotamer: Outliers : 3.69 % Allowed : 21.40 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.15), residues: 2967 helix: 1.91 (0.24), residues: 528 sheet: -1.70 (0.22), residues: 558 loop : -3.21 (0.12), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 40 HIS 0.005 0.001 HIS C 937 PHE 0.028 0.002 PHE C 444 TYR 0.013 0.001 TYR A 400 ARG 0.005 0.000 ARG C 920 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 276 time to evaluate : 2.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 TYR cc_start: 0.6977 (t80) cc_final: 0.6619 (t80) REVERT: A 172 ASP cc_start: 0.8504 (p0) cc_final: 0.8048 (t0) REVERT: A 184 THR cc_start: 0.8134 (t) cc_final: 0.7906 (m) REVERT: A 253 GLN cc_start: 0.8285 (mt0) cc_final: 0.7006 (pm20) REVERT: A 651 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8715 (tp) REVERT: A 677 ILE cc_start: 0.8104 (OUTLIER) cc_final: 0.7546 (pp) REVERT: A 746 MET cc_start: 0.8570 (tpt) cc_final: 0.8257 (tpp) REVERT: A 846 ILE cc_start: 0.8996 (tp) cc_final: 0.8140 (tp) REVERT: A 911 ILE cc_start: 0.7969 (OUTLIER) cc_final: 0.7684 (tp) REVERT: B 172 ASP cc_start: 0.8888 (p0) cc_final: 0.8642 (p0) REVERT: B 184 THR cc_start: 0.8316 (t) cc_final: 0.8076 (m) REVERT: B 253 GLN cc_start: 0.8165 (mt0) cc_final: 0.6934 (pm20) REVERT: B 371 TYR cc_start: 0.8598 (m-80) cc_final: 0.8293 (m-80) REVERT: B 430 THR cc_start: 0.9293 (OUTLIER) cc_final: 0.8975 (m) REVERT: B 463 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8431 (mm) REVERT: B 498 PHE cc_start: 0.8684 (p90) cc_final: 0.8438 (p90) REVERT: B 508 ILE cc_start: 0.9464 (mp) cc_final: 0.9262 (mt) REVERT: B 512 ARG cc_start: 0.8143 (ptt180) cc_final: 0.7613 (ttp-170) REVERT: B 611 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8948 (tp) REVERT: B 836 MET cc_start: 0.8560 (tpp) cc_final: 0.8298 (tpp) REVERT: B 974 ILE cc_start: 0.7754 (tp) cc_final: 0.7528 (mp) REVERT: B 985 THR cc_start: 0.8965 (t) cc_final: 0.8677 (p) REVERT: C 83 MET cc_start: 0.8291 (mpp) cc_final: 0.7965 (mtt) REVERT: C 184 THR cc_start: 0.8140 (t) cc_final: 0.7817 (m) REVERT: C 201 MET cc_start: 0.8008 (ptp) cc_final: 0.7772 (ptp) REVERT: C 253 GLN cc_start: 0.8147 (mt0) cc_final: 0.6959 (pm20) REVERT: C 330 ASN cc_start: 0.8106 (m-40) cc_final: 0.7820 (m-40) REVERT: C 430 THR cc_start: 0.9187 (OUTLIER) cc_final: 0.8935 (m) REVERT: C 512 ARG cc_start: 0.7999 (ptt90) cc_final: 0.7518 (ttp-170) REVERT: C 635 ILE cc_start: 0.9019 (OUTLIER) cc_final: 0.8653 (tp) REVERT: C 677 ILE cc_start: 0.8001 (OUTLIER) cc_final: 0.7558 (pp) REVERT: C 726 LEU cc_start: 0.8247 (mm) cc_final: 0.7771 (tp) REVERT: C 846 ILE cc_start: 0.8982 (tp) cc_final: 0.8726 (tp) REVERT: C 921 HIS cc_start: 0.8564 (p90) cc_final: 0.8344 (p90) REVERT: C 991 MET cc_start: 0.7938 (ttt) cc_final: 0.7669 (tpp) outliers start: 94 outliers final: 81 residues processed: 341 average time/residue: 0.2956 time to fit residues: 169.6586 Evaluate side-chains 354 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 264 time to evaluate : 2.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASN Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 201 MET Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 677 ILE Chi-restraints excluded: chain A residue 769 ILE Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 792 ASN Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 921 HIS Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain A residue 951 ILE Chi-restraints excluded: chain B residue 29 TYR Chi-restraints excluded: chain B residue 51 ASN Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 130 PHE Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 460 ASP Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 662 PHE Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 792 ASN Chi-restraints excluded: chain B residue 908 SER Chi-restraints excluded: chain B residue 911 ILE Chi-restraints excluded: chain B residue 921 HIS Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 130 PHE Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 395 CYS Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 451 SER Chi-restraints excluded: chain C residue 460 ASP Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 677 ILE Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 784 ILE Chi-restraints excluded: chain C residue 792 ASN Chi-restraints excluded: chain C residue 814 THR Chi-restraints excluded: chain C residue 857 LEU Chi-restraints excluded: chain C residue 908 SER Chi-restraints excluded: chain C residue 934 VAL Chi-restraints excluded: chain C residue 949 THR Chi-restraints excluded: chain C residue 984 ILE Chi-restraints excluded: chain C residue 1020 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 187 optimal weight: 4.9990 chunk 250 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 217 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 235 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 242 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 626 GLN ** A 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 496 GLN ** B 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.145121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.126952 restraints weight = 36356.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.126096 restraints weight = 35617.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.126046 restraints weight = 36518.152| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24687 Z= 0.209 Angle : 0.667 9.986 33570 Z= 0.338 Chirality : 0.048 0.521 4062 Planarity : 0.004 0.054 4227 Dihedral : 5.463 34.108 5070 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.49 % Favored : 88.51 % Rotamer: Outliers : 3.93 % Allowed : 21.32 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.15), residues: 2967 helix: 2.01 (0.24), residues: 525 sheet: -1.64 (0.22), residues: 552 loop : -3.21 (0.12), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 92 HIS 0.004 0.001 HIS C 101 PHE 0.021 0.001 PHE C 210 TYR 0.012 0.001 TYR B 29 ARG 0.003 0.000 ARG A 366 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4599.40 seconds wall clock time: 85 minutes 6.22 seconds (5106.22 seconds total)