Starting phenix.real_space_refine on Sat Mar 23 19:22:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbn_21594/03_2024/6wbn_21594_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbn_21594/03_2024/6wbn_21594.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbn_21594/03_2024/6wbn_21594.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbn_21594/03_2024/6wbn_21594.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbn_21594/03_2024/6wbn_21594_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbn_21594/03_2024/6wbn_21594_updated.pdb" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 42 5.49 5 S 154 5.16 5 C 25886 2.51 5 N 5726 2.21 5 O 6594 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 31": "OE1" <-> "OE2" Residue "A ARG 217": "NH1" <-> "NH2" Residue "A ARG 254": "NH1" <-> "NH2" Residue "A GLU 336": "OE1" <-> "OE2" Residue "B GLU 31": "OE1" <-> "OE2" Residue "B ARG 217": "NH1" <-> "NH2" Residue "B ARG 254": "NH1" <-> "NH2" Residue "B GLU 336": "OE1" <-> "OE2" Residue "C GLU 31": "OE1" <-> "OE2" Residue "C ARG 217": "NH1" <-> "NH2" Residue "C ARG 254": "NH1" <-> "NH2" Residue "C GLU 336": "OE1" <-> "OE2" Residue "D GLU 31": "OE1" <-> "OE2" Residue "D ARG 217": "NH1" <-> "NH2" Residue "D ARG 254": "NH1" <-> "NH2" Residue "D GLU 336": "OE1" <-> "OE2" Residue "E GLU 31": "OE1" <-> "OE2" Residue "E ARG 217": "NH1" <-> "NH2" Residue "E ARG 254": "NH1" <-> "NH2" Residue "E GLU 336": "OE1" <-> "OE2" Residue "F GLU 31": "OE1" <-> "OE2" Residue "F ARG 217": "NH1" <-> "NH2" Residue "F ARG 254": "NH1" <-> "NH2" Residue "F GLU 336": "OE1" <-> "OE2" Residue "G GLU 31": "OE1" <-> "OE2" Residue "G ARG 217": "NH1" <-> "NH2" Residue "G ARG 254": "NH1" <-> "NH2" Residue "G GLU 336": "OE1" <-> "OE2" Residue "H GLU 31": "OE1" <-> "OE2" Residue "H ARG 217": "NH1" <-> "NH2" Residue "H ARG 254": "NH1" <-> "NH2" Residue "H GLU 336": "OE1" <-> "OE2" Residue "I GLU 31": "OE1" <-> "OE2" Residue "I ARG 217": "NH1" <-> "NH2" Residue "I ARG 254": "NH1" <-> "NH2" Residue "I GLU 336": "OE1" <-> "OE2" Residue "J GLU 31": "OE1" <-> "OE2" Residue "J ARG 217": "NH1" <-> "NH2" Residue "J ARG 254": "NH1" <-> "NH2" Residue "J GLU 336": "OE1" <-> "OE2" Residue "K GLU 31": "OE1" <-> "OE2" Residue "K ARG 217": "NH1" <-> "NH2" Residue "K ARG 254": "NH1" <-> "NH2" Residue "K GLU 336": "OE1" <-> "OE2" Residue "L GLU 31": "OE1" <-> "OE2" Residue "L ARG 217": "NH1" <-> "NH2" Residue "L ARG 254": "NH1" <-> "NH2" Residue "L GLU 336": "OE1" <-> "OE2" Residue "M GLU 31": "OE1" <-> "OE2" Residue "M ARG 217": "NH1" <-> "NH2" Residue "M ARG 254": "NH1" <-> "NH2" Residue "M GLU 336": "OE1" <-> "OE2" Residue "N GLU 31": "OE1" <-> "OE2" Residue "N ARG 217": "NH1" <-> "NH2" Residue "N ARG 254": "NH1" <-> "NH2" Residue "N GLU 336": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 38402 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 2539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2539 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 15, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 8, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 93 Chain: "B" Number of atoms: 2539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2539 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 15, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 8, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 93 Chain: "C" Number of atoms: 2539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2539 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 15, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 8, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 93 Chain: "D" Number of atoms: 2539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2539 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 15, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 8, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 93 Chain: "E" Number of atoms: 2539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2539 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 15, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 8, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 93 Chain: "F" Number of atoms: 2539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2539 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 15, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 8, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 93 Chain: "G" Number of atoms: 2539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2539 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 15, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 8, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 93 Chain: "H" Number of atoms: 2539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2539 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 15, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 8, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 93 Chain: "I" Number of atoms: 2539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2539 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 15, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 8, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 93 Chain: "J" Number of atoms: 2539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2539 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 15, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 8, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 93 Chain: "K" Number of atoms: 2539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2539 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 15, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 8, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 93 Chain: "L" Number of atoms: 2539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2539 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 15, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 8, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 93 Chain: "M" Number of atoms: 2539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2539 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 15, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 8, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 93 Chain: "N" Number of atoms: 2539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2539 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 15, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 8, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 93 Chain: "A" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 229 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 2, 'PTY': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 66 Chain: "B" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 204 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'PTY': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 47 Chain: "C" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 204 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'PTY': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 47 Chain: "D" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 204 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'PTY': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 47 Chain: "E" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 204 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'PTY': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 47 Chain: "F" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 204 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'PTY': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 47 Chain: "G" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 179 Unusual residues: {'3PE': 1, 'CLR': 2, 'PTY': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 Chain: "H" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 204 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'PTY': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 47 Chain: "I" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 204 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'PTY': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 47 Chain: "J" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 204 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'PTY': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 47 Chain: "K" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 204 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'PTY': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 47 Chain: "L" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 204 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'PTY': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 47 Chain: "M" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 204 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'PTY': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 47 Chain: "N" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 204 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'PTY': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 47 Time building chain proxies: 20.16, per 1000 atoms: 0.52 Number of scatterers: 38402 At special positions: 0 Unit cell: (109.62, 107.996, 230.608, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 154 16.00 P 42 15.00 O 6594 8.00 N 5726 7.00 C 25886 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=28, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 265 " distance=2.03 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 265 " distance=2.03 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 246 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 265 " distance=2.03 Simple disulfide: pdb=" SG CYS C 84 " - pdb=" SG CYS C 246 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 265 " distance=2.03 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 246 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 265 " distance=2.03 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 246 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 265 " distance=2.03 Simple disulfide: pdb=" SG CYS F 84 " - pdb=" SG CYS F 246 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 265 " distance=2.03 Simple disulfide: pdb=" SG CYS G 84 " - pdb=" SG CYS G 246 " distance=2.03 Simple disulfide: pdb=" SG CYS H 66 " - pdb=" SG CYS H 265 " distance=2.03 Simple disulfide: pdb=" SG CYS H 84 " - pdb=" SG CYS H 246 " distance=2.03 Simple disulfide: pdb=" SG CYS I 66 " - pdb=" SG CYS I 265 " distance=2.03 Simple disulfide: pdb=" SG CYS I 84 " - pdb=" SG CYS I 246 " distance=2.03 Simple disulfide: pdb=" SG CYS J 66 " - pdb=" SG CYS J 265 " distance=2.03 Simple disulfide: pdb=" SG CYS J 84 " - pdb=" SG CYS J 246 " distance=2.03 Simple disulfide: pdb=" SG CYS K 66 " - pdb=" SG CYS K 265 " distance=2.03 Simple disulfide: pdb=" SG CYS K 84 " - pdb=" SG CYS K 246 " distance=2.03 Simple disulfide: pdb=" SG CYS L 66 " - pdb=" SG CYS L 265 " distance=2.03 Simple disulfide: pdb=" SG CYS L 84 " - pdb=" SG CYS L 246 " distance=2.03 Simple disulfide: pdb=" SG CYS M 66 " - pdb=" SG CYS M 265 " distance=2.03 Simple disulfide: pdb=" SG CYS M 84 " - pdb=" SG CYS M 246 " distance=2.03 Simple disulfide: pdb=" SG CYS N 66 " - pdb=" SG CYS N 265 " distance=2.03 Simple disulfide: pdb=" SG CYS N 84 " - pdb=" SG CYS N 246 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 16.53 Conformation dependent library (CDL) restraints added in 7.3 seconds 9436 Ramachandran restraints generated. 4718 Oldfield, 0 Emsley, 4718 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9240 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 210 helices and 14 sheets defined 64.5% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.65 Creating SS restraints... Processing helix chain 'A' and resid 3 through 11 Processing helix chain 'A' and resid 33 through 53 Proline residue: A 46 - end of helix Processing helix chain 'A' and resid 74 through 88 Processing helix chain 'A' and resid 101 through 107 Processing helix chain 'A' and resid 109 through 130 Proline residue: A 123 - end of helix Processing helix chain 'A' and resid 132 through 161 Processing helix chain 'A' and resid 195 through 203 Processing helix chain 'A' and resid 208 through 235 Processing helix chain 'A' and resid 251 through 254 Processing helix chain 'A' and resid 270 through 295 Proline residue: A 289 - end of helix Processing helix chain 'A' and resid 297 through 300 No H-bonds generated for 'chain 'A' and resid 297 through 300' Processing helix chain 'A' and resid 305 through 311 removed outlier: 3.773A pdb=" N TYR A 309 " --> pdb=" O VAL A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 341 removed outlier: 5.041A pdb=" N SER A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N GLU A 341 " --> pdb=" O GLU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 357 Processing helix chain 'A' and resid 362 through 369 Processing helix chain 'B' and resid 3 through 11 Processing helix chain 'B' and resid 33 through 53 Proline residue: B 46 - end of helix Processing helix chain 'B' and resid 74 through 88 Processing helix chain 'B' and resid 101 through 107 Processing helix chain 'B' and resid 109 through 130 Proline residue: B 123 - end of helix Processing helix chain 'B' and resid 132 through 161 Processing helix chain 'B' and resid 195 through 203 Processing helix chain 'B' and resid 208 through 235 Processing helix chain 'B' and resid 251 through 254 Processing helix chain 'B' and resid 270 through 295 Proline residue: B 289 - end of helix Processing helix chain 'B' and resid 297 through 300 No H-bonds generated for 'chain 'B' and resid 297 through 300' Processing helix chain 'B' and resid 305 through 311 removed outlier: 3.772A pdb=" N TYR B 309 " --> pdb=" O VAL B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 341 removed outlier: 5.041A pdb=" N SER B 340 " --> pdb=" O GLU B 336 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N GLU B 341 " --> pdb=" O GLU B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 357 Processing helix chain 'B' and resid 362 through 369 Processing helix chain 'C' and resid 3 through 11 Processing helix chain 'C' and resid 33 through 53 Proline residue: C 46 - end of helix Processing helix chain 'C' and resid 74 through 88 Processing helix chain 'C' and resid 101 through 107 Processing helix chain 'C' and resid 109 through 130 Proline residue: C 123 - end of helix Processing helix chain 'C' and resid 132 through 161 Processing helix chain 'C' and resid 195 through 203 Processing helix chain 'C' and resid 208 through 235 Processing helix chain 'C' and resid 251 through 254 Processing helix chain 'C' and resid 270 through 295 Proline residue: C 289 - end of helix Processing helix chain 'C' and resid 297 through 300 No H-bonds generated for 'chain 'C' and resid 297 through 300' Processing helix chain 'C' and resid 305 through 311 removed outlier: 3.773A pdb=" N TYR C 309 " --> pdb=" O VAL C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 341 removed outlier: 5.041A pdb=" N SER C 340 " --> pdb=" O GLU C 336 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N GLU C 341 " --> pdb=" O GLU C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 357 Processing helix chain 'C' and resid 362 through 369 Processing helix chain 'D' and resid 3 through 11 Processing helix chain 'D' and resid 33 through 53 Proline residue: D 46 - end of helix Processing helix chain 'D' and resid 74 through 88 Processing helix chain 'D' and resid 101 through 107 Processing helix chain 'D' and resid 109 through 130 Proline residue: D 123 - end of helix Processing helix chain 'D' and resid 132 through 161 Processing helix chain 'D' and resid 195 through 203 Processing helix chain 'D' and resid 208 through 235 Processing helix chain 'D' and resid 251 through 254 Processing helix chain 'D' and resid 270 through 295 Proline residue: D 289 - end of helix Processing helix chain 'D' and resid 297 through 300 No H-bonds generated for 'chain 'D' and resid 297 through 300' Processing helix chain 'D' and resid 305 through 311 removed outlier: 3.772A pdb=" N TYR D 309 " --> pdb=" O VAL D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 341 removed outlier: 5.041A pdb=" N SER D 340 " --> pdb=" O GLU D 336 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N GLU D 341 " --> pdb=" O GLU D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 357 Processing helix chain 'D' and resid 362 through 369 Processing helix chain 'E' and resid 3 through 11 Processing helix chain 'E' and resid 33 through 53 Proline residue: E 46 - end of helix Processing helix chain 'E' and resid 74 through 88 Processing helix chain 'E' and resid 101 through 107 Processing helix chain 'E' and resid 109 through 130 Proline residue: E 123 - end of helix Processing helix chain 'E' and resid 132 through 161 Processing helix chain 'E' and resid 195 through 203 Processing helix chain 'E' and resid 208 through 235 Processing helix chain 'E' and resid 251 through 254 Processing helix chain 'E' and resid 270 through 295 Proline residue: E 289 - end of helix Processing helix chain 'E' and resid 297 through 300 No H-bonds generated for 'chain 'E' and resid 297 through 300' Processing helix chain 'E' and resid 305 through 311 removed outlier: 3.772A pdb=" N TYR E 309 " --> pdb=" O VAL E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 341 removed outlier: 5.041A pdb=" N SER E 340 " --> pdb=" O GLU E 336 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N GLU E 341 " --> pdb=" O GLU E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 343 through 357 Processing helix chain 'E' and resid 362 through 369 Processing helix chain 'F' and resid 3 through 11 Processing helix chain 'F' and resid 33 through 53 Proline residue: F 46 - end of helix Processing helix chain 'F' and resid 74 through 88 Processing helix chain 'F' and resid 101 through 107 Processing helix chain 'F' and resid 109 through 130 Proline residue: F 123 - end of helix Processing helix chain 'F' and resid 132 through 161 Processing helix chain 'F' and resid 195 through 203 Processing helix chain 'F' and resid 208 through 235 Processing helix chain 'F' and resid 251 through 254 Processing helix chain 'F' and resid 270 through 295 Proline residue: F 289 - end of helix Processing helix chain 'F' and resid 297 through 300 No H-bonds generated for 'chain 'F' and resid 297 through 300' Processing helix chain 'F' and resid 305 through 311 removed outlier: 3.772A pdb=" N TYR F 309 " --> pdb=" O VAL F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 341 removed outlier: 5.042A pdb=" N SER F 340 " --> pdb=" O GLU F 336 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N GLU F 341 " --> pdb=" O GLU F 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 343 through 357 Processing helix chain 'F' and resid 362 through 369 Processing helix chain 'G' and resid 3 through 11 Processing helix chain 'G' and resid 33 through 53 Proline residue: G 46 - end of helix Processing helix chain 'G' and resid 74 through 88 Processing helix chain 'G' and resid 101 through 107 Processing helix chain 'G' and resid 109 through 130 Proline residue: G 123 - end of helix Processing helix chain 'G' and resid 132 through 161 Processing helix chain 'G' and resid 195 through 203 Processing helix chain 'G' and resid 208 through 235 Processing helix chain 'G' and resid 251 through 254 Processing helix chain 'G' and resid 270 through 295 Proline residue: G 289 - end of helix Processing helix chain 'G' and resid 297 through 300 No H-bonds generated for 'chain 'G' and resid 297 through 300' Processing helix chain 'G' and resid 305 through 311 removed outlier: 3.773A pdb=" N TYR G 309 " --> pdb=" O VAL G 305 " (cutoff:3.500A) Processing helix chain 'G' and resid 327 through 341 removed outlier: 5.042A pdb=" N SER G 340 " --> pdb=" O GLU G 336 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N GLU G 341 " --> pdb=" O GLU G 337 " (cutoff:3.500A) Processing helix chain 'G' and resid 343 through 357 Processing helix chain 'G' and resid 362 through 369 Processing helix chain 'H' and resid 3 through 11 Processing helix chain 'H' and resid 33 through 53 Proline residue: H 46 - end of helix Processing helix chain 'H' and resid 74 through 88 Processing helix chain 'H' and resid 101 through 107 Processing helix chain 'H' and resid 109 through 130 Proline residue: H 123 - end of helix Processing helix chain 'H' and resid 132 through 161 Processing helix chain 'H' and resid 195 through 203 Processing helix chain 'H' and resid 208 through 235 Processing helix chain 'H' and resid 251 through 254 Processing helix chain 'H' and resid 270 through 295 Proline residue: H 289 - end of helix Processing helix chain 'H' and resid 297 through 300 No H-bonds generated for 'chain 'H' and resid 297 through 300' Processing helix chain 'H' and resid 305 through 311 removed outlier: 3.773A pdb=" N TYR H 309 " --> pdb=" O VAL H 305 " (cutoff:3.500A) Processing helix chain 'H' and resid 327 through 341 removed outlier: 5.040A pdb=" N SER H 340 " --> pdb=" O GLU H 336 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N GLU H 341 " --> pdb=" O GLU H 337 " (cutoff:3.500A) Processing helix chain 'H' and resid 343 through 357 Processing helix chain 'H' and resid 362 through 369 Processing helix chain 'I' and resid 3 through 11 Processing helix chain 'I' and resid 33 through 53 Proline residue: I 46 - end of helix Processing helix chain 'I' and resid 74 through 88 Processing helix chain 'I' and resid 101 through 107 Processing helix chain 'I' and resid 109 through 130 Proline residue: I 123 - end of helix Processing helix chain 'I' and resid 132 through 161 Processing helix chain 'I' and resid 195 through 203 Processing helix chain 'I' and resid 208 through 235 Processing helix chain 'I' and resid 251 through 254 Processing helix chain 'I' and resid 270 through 295 Proline residue: I 289 - end of helix Processing helix chain 'I' and resid 297 through 300 No H-bonds generated for 'chain 'I' and resid 297 through 300' Processing helix chain 'I' and resid 305 through 311 removed outlier: 3.772A pdb=" N TYR I 309 " --> pdb=" O VAL I 305 " (cutoff:3.500A) Processing helix chain 'I' and resid 327 through 341 removed outlier: 5.041A pdb=" N SER I 340 " --> pdb=" O GLU I 336 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N GLU I 341 " --> pdb=" O GLU I 337 " (cutoff:3.500A) Processing helix chain 'I' and resid 343 through 357 Processing helix chain 'I' and resid 362 through 369 Processing helix chain 'J' and resid 3 through 11 Processing helix chain 'J' and resid 33 through 53 Proline residue: J 46 - end of helix Processing helix chain 'J' and resid 74 through 88 Processing helix chain 'J' and resid 101 through 107 Processing helix chain 'J' and resid 109 through 130 Proline residue: J 123 - end of helix Processing helix chain 'J' and resid 132 through 161 Processing helix chain 'J' and resid 195 through 203 Processing helix chain 'J' and resid 208 through 235 Processing helix chain 'J' and resid 251 through 254 Processing helix chain 'J' and resid 270 through 295 Proline residue: J 289 - end of helix Processing helix chain 'J' and resid 297 through 300 No H-bonds generated for 'chain 'J' and resid 297 through 300' Processing helix chain 'J' and resid 305 through 311 removed outlier: 3.772A pdb=" N TYR J 309 " --> pdb=" O VAL J 305 " (cutoff:3.500A) Processing helix chain 'J' and resid 327 through 341 removed outlier: 5.040A pdb=" N SER J 340 " --> pdb=" O GLU J 336 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N GLU J 341 " --> pdb=" O GLU J 337 " (cutoff:3.500A) Processing helix chain 'J' and resid 343 through 357 Processing helix chain 'J' and resid 362 through 369 Processing helix chain 'K' and resid 3 through 11 Processing helix chain 'K' and resid 33 through 53 Proline residue: K 46 - end of helix Processing helix chain 'K' and resid 74 through 88 Processing helix chain 'K' and resid 101 through 107 Processing helix chain 'K' and resid 109 through 130 Proline residue: K 123 - end of helix Processing helix chain 'K' and resid 132 through 161 Processing helix chain 'K' and resid 195 through 203 Processing helix chain 'K' and resid 208 through 235 Processing helix chain 'K' and resid 251 through 254 Processing helix chain 'K' and resid 270 through 295 Proline residue: K 289 - end of helix Processing helix chain 'K' and resid 297 through 300 No H-bonds generated for 'chain 'K' and resid 297 through 300' Processing helix chain 'K' and resid 305 through 311 removed outlier: 3.773A pdb=" N TYR K 309 " --> pdb=" O VAL K 305 " (cutoff:3.500A) Processing helix chain 'K' and resid 327 through 341 removed outlier: 5.041A pdb=" N SER K 340 " --> pdb=" O GLU K 336 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N GLU K 341 " --> pdb=" O GLU K 337 " (cutoff:3.500A) Processing helix chain 'K' and resid 343 through 357 Processing helix chain 'K' and resid 362 through 369 Processing helix chain 'L' and resid 3 through 11 Processing helix chain 'L' and resid 33 through 53 Proline residue: L 46 - end of helix Processing helix chain 'L' and resid 74 through 88 Processing helix chain 'L' and resid 101 through 107 Processing helix chain 'L' and resid 109 through 130 Proline residue: L 123 - end of helix Processing helix chain 'L' and resid 132 through 161 Processing helix chain 'L' and resid 195 through 203 Processing helix chain 'L' and resid 208 through 235 Processing helix chain 'L' and resid 251 through 254 Processing helix chain 'L' and resid 270 through 295 Proline residue: L 289 - end of helix Processing helix chain 'L' and resid 297 through 300 No H-bonds generated for 'chain 'L' and resid 297 through 300' Processing helix chain 'L' and resid 305 through 311 removed outlier: 3.773A pdb=" N TYR L 309 " --> pdb=" O VAL L 305 " (cutoff:3.500A) Processing helix chain 'L' and resid 327 through 341 removed outlier: 5.041A pdb=" N SER L 340 " --> pdb=" O GLU L 336 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N GLU L 341 " --> pdb=" O GLU L 337 " (cutoff:3.500A) Processing helix chain 'L' and resid 343 through 357 Processing helix chain 'L' and resid 362 through 369 Processing helix chain 'M' and resid 3 through 11 Processing helix chain 'M' and resid 33 through 53 Proline residue: M 46 - end of helix Processing helix chain 'M' and resid 74 through 88 Processing helix chain 'M' and resid 101 through 107 Processing helix chain 'M' and resid 109 through 130 Proline residue: M 123 - end of helix Processing helix chain 'M' and resid 132 through 161 Processing helix chain 'M' and resid 195 through 203 Processing helix chain 'M' and resid 208 through 235 Processing helix chain 'M' and resid 251 through 254 Processing helix chain 'M' and resid 270 through 295 Proline residue: M 289 - end of helix Processing helix chain 'M' and resid 297 through 300 No H-bonds generated for 'chain 'M' and resid 297 through 300' Processing helix chain 'M' and resid 305 through 311 removed outlier: 3.773A pdb=" N TYR M 309 " --> pdb=" O VAL M 305 " (cutoff:3.500A) Processing helix chain 'M' and resid 327 through 341 removed outlier: 5.041A pdb=" N SER M 340 " --> pdb=" O GLU M 336 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N GLU M 341 " --> pdb=" O GLU M 337 " (cutoff:3.500A) Processing helix chain 'M' and resid 343 through 357 Processing helix chain 'M' and resid 362 through 369 Processing helix chain 'N' and resid 3 through 11 Processing helix chain 'N' and resid 33 through 53 Proline residue: N 46 - end of helix Processing helix chain 'N' and resid 74 through 88 Processing helix chain 'N' and resid 101 through 107 Processing helix chain 'N' and resid 109 through 130 Proline residue: N 123 - end of helix Processing helix chain 'N' and resid 132 through 161 Processing helix chain 'N' and resid 195 through 203 Processing helix chain 'N' and resid 208 through 235 Processing helix chain 'N' and resid 251 through 254 Processing helix chain 'N' and resid 270 through 295 Proline residue: N 289 - end of helix Processing helix chain 'N' and resid 297 through 300 No H-bonds generated for 'chain 'N' and resid 297 through 300' Processing helix chain 'N' and resid 305 through 311 removed outlier: 3.773A pdb=" N TYR N 309 " --> pdb=" O VAL N 305 " (cutoff:3.500A) Processing helix chain 'N' and resid 327 through 341 removed outlier: 5.041A pdb=" N SER N 340 " --> pdb=" O GLU N 336 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N GLU N 341 " --> pdb=" O GLU N 337 " (cutoff:3.500A) Processing helix chain 'N' and resid 343 through 357 Processing helix chain 'N' and resid 362 through 369 Processing sheet with id= A, first strand: chain 'A' and resid 243 through 246 Processing sheet with id= B, first strand: chain 'B' and resid 243 through 246 Processing sheet with id= C, first strand: chain 'C' and resid 243 through 246 Processing sheet with id= D, first strand: chain 'D' and resid 243 through 246 Processing sheet with id= E, first strand: chain 'E' and resid 243 through 246 Processing sheet with id= F, first strand: chain 'F' and resid 243 through 246 Processing sheet with id= G, first strand: chain 'G' and resid 243 through 246 Processing sheet with id= H, first strand: chain 'H' and resid 243 through 246 Processing sheet with id= I, first strand: chain 'I' and resid 243 through 246 Processing sheet with id= J, first strand: chain 'J' and resid 243 through 246 Processing sheet with id= K, first strand: chain 'K' and resid 243 through 246 Processing sheet with id= L, first strand: chain 'L' and resid 243 through 246 Processing sheet with id= M, first strand: chain 'M' and resid 243 through 246 Processing sheet with id= N, first strand: chain 'N' and resid 243 through 246 2142 hydrogen bonds defined for protein. 6342 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: 12.33 Time building geometry restraints manager: 17.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5807 1.32 - 1.44: 9642 1.44 - 1.56: 23527 1.56 - 1.69: 84 1.69 - 1.81: 182 Bond restraints: 39242 Sorted by residual: bond pdb=" N ASP B 256 " pdb=" CA ASP B 256 " ideal model delta sigma weight residual 1.458 1.493 -0.036 1.25e-02 6.40e+03 8.23e+00 bond pdb=" N ASP H 256 " pdb=" CA ASP H 256 " ideal model delta sigma weight residual 1.458 1.493 -0.036 1.25e-02 6.40e+03 8.20e+00 bond pdb=" N ASP D 256 " pdb=" CA ASP D 256 " ideal model delta sigma weight residual 1.458 1.493 -0.036 1.25e-02 6.40e+03 8.20e+00 bond pdb=" N ASP M 256 " pdb=" CA ASP M 256 " ideal model delta sigma weight residual 1.458 1.493 -0.036 1.25e-02 6.40e+03 8.12e+00 bond pdb=" N ASP I 256 " pdb=" CA ASP I 256 " ideal model delta sigma weight residual 1.458 1.493 -0.036 1.25e-02 6.40e+03 8.11e+00 ... (remaining 39237 not shown) Histogram of bond angle deviations from ideal: 98.32 - 105.46: 891 105.46 - 112.61: 21285 112.61 - 119.75: 13452 119.75 - 126.89: 17262 126.89 - 134.03: 366 Bond angle restraints: 53256 Sorted by residual: angle pdb=" C THR G 258 " pdb=" N VAL G 259 " pdb=" CA VAL G 259 " ideal model delta sigma weight residual 122.59 125.27 -2.68 7.20e-01 1.93e+00 1.39e+01 angle pdb=" C THR I 258 " pdb=" N VAL I 259 " pdb=" CA VAL I 259 " ideal model delta sigma weight residual 122.59 125.26 -2.67 7.20e-01 1.93e+00 1.37e+01 angle pdb=" C THR D 258 " pdb=" N VAL D 259 " pdb=" CA VAL D 259 " ideal model delta sigma weight residual 122.59 125.25 -2.66 7.20e-01 1.93e+00 1.37e+01 angle pdb=" C THR H 258 " pdb=" N VAL H 259 " pdb=" CA VAL H 259 " ideal model delta sigma weight residual 122.59 125.25 -2.66 7.20e-01 1.93e+00 1.37e+01 angle pdb=" C THR E 258 " pdb=" N VAL E 259 " pdb=" CA VAL E 259 " ideal model delta sigma weight residual 122.59 125.24 -2.65 7.20e-01 1.93e+00 1.36e+01 ... (remaining 53251 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.84: 24164 33.84 - 67.67: 1050 67.67 - 101.51: 28 101.51 - 135.35: 28 135.35 - 169.19: 14 Dihedral angle restraints: 25284 sinusoidal: 11074 harmonic: 14210 Sorted by residual: dihedral pdb=" N1 PTY M 401 " pdb=" C2 PTY M 401 " pdb=" C3 PTY M 401 " pdb=" O11 PTY M 401 " ideal model delta sinusoidal sigma weight residual 65.33 -103.86 169.19 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" N1 PTY N 402 " pdb=" C2 PTY N 402 " pdb=" C3 PTY N 402 " pdb=" O11 PTY N 402 " ideal model delta sinusoidal sigma weight residual 65.33 -103.84 169.17 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" N1 PTY K 401 " pdb=" C2 PTY K 401 " pdb=" C3 PTY K 401 " pdb=" O11 PTY K 401 " ideal model delta sinusoidal sigma weight residual 65.33 -103.84 169.17 1 3.00e+01 1.11e-03 2.11e+01 ... (remaining 25281 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 3797 0.038 - 0.076: 1784 0.076 - 0.114: 584 0.114 - 0.152: 135 0.152 - 0.190: 14 Chirality restraints: 6314 Sorted by residual: chirality pdb=" CA LEU I 146 " pdb=" N LEU I 146 " pdb=" C LEU I 146 " pdb=" CB LEU I 146 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.05e-01 chirality pdb=" CA LEU D 146 " pdb=" N LEU D 146 " pdb=" C LEU D 146 " pdb=" CB LEU D 146 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.04e-01 chirality pdb=" CA LEU E 146 " pdb=" N LEU E 146 " pdb=" C LEU E 146 " pdb=" CB LEU E 146 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.99e-01 ... (remaining 6311 not shown) Planarity restraints: 6230 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU I 122 " 0.024 5.00e-02 4.00e+02 3.54e-02 2.01e+00 pdb=" N PRO I 123 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO I 123 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO I 123 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 122 " 0.024 5.00e-02 4.00e+02 3.53e-02 2.00e+00 pdb=" N PRO B 123 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 123 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 123 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 122 " -0.024 5.00e-02 4.00e+02 3.53e-02 1.99e+00 pdb=" N PRO D 123 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO D 123 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 123 " -0.020 5.00e-02 4.00e+02 ... (remaining 6227 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 314 2.64 - 3.20: 36529 3.20 - 3.77: 59898 3.77 - 4.33: 79638 4.33 - 4.90: 132976 Nonbonded interactions: 309355 Sorted by model distance: nonbonded pdb=" NZ LYS I 148 " pdb=" O ASN J 369 " model vdw 2.069 2.520 nonbonded pdb=" NZ LYS M 148 " pdb=" O ASN N 369 " model vdw 2.073 2.520 nonbonded pdb=" O ASN H 369 " pdb=" NZ LYS N 148 " model vdw 2.076 2.520 nonbonded pdb=" NZ LYS L 148 " pdb=" O ASN M 369 " model vdw 2.078 2.520 nonbonded pdb=" NZ LYS K 148 " pdb=" O ASN L 369 " model vdw 2.084 2.520 ... (remaining 309350 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 373 or resid 402 or resid 405)) selection = (chain 'B' and (resid 2 through 373 or resid 402 or resid 405)) selection = (chain 'C' and (resid 2 through 373 or resid 402 or resid 405)) selection = (chain 'D' and (resid 2 through 373 or resid 402 or resid 405)) selection = (chain 'E' and (resid 2 through 373 or resid 402 or resid 405)) selection = (chain 'F' and (resid 2 through 373 or resid 402 or resid 405)) selection = (chain 'G' and (resid 2 through 373 or resid 402 or resid 405)) selection = (chain 'H' and (resid 2 through 373 or resid 402 or resid 405)) selection = (chain 'I' and (resid 2 through 373 or resid 402 or resid 405)) selection = (chain 'J' and (resid 2 through 373 or resid 402 or resid 405)) selection = (chain 'K' and (resid 2 through 373 or resid 402 or resid 405)) selection = (chain 'L' and (resid 2 through 373 or resid 402 or resid 405)) selection = (chain 'M' and (resid 2 through 373 or resid 402 or resid 405)) selection = (chain 'N' and (resid 2 through 373 or (resid 402 and (name C1 or name C11 or na \ me C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 o \ r name C19 or name C2 or name C20 or name C21 or name C3 or name C30 or name C31 \ or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name \ C38 or name C39 or name C40 or name C41 or name C5 or name C6 or name C8 or nam \ e N1 or name O10 or name O11 or name O12 or name O13 or name O14 or name O30 or \ name O4 or name O7 or name P1 )) or resid 405)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.010 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: 0.040 Extract box with map and model: 14.760 Check model and map are aligned: 0.530 Set scattering table: 0.320 Process input model: 100.600 Find NCS groups from input model: 3.600 Set up NCS constraints: 0.420 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 138.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.049 39242 Z= 0.638 Angle : 0.876 10.199 53256 Z= 0.455 Chirality : 0.048 0.190 6314 Planarity : 0.004 0.035 6230 Dihedral : 16.955 169.187 15960 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.80 % Allowed : 11.41 % Favored : 87.79 % 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: -0.59 (0.12), residues: 4718 helix: 0.55 (0.09), residues: 3150 sheet: None (None), residues: 0 loop : -2.35 (0.16), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP F 104 HIS 0.004 0.001 HIS B 134 PHE 0.021 0.002 PHE M 67 TYR 0.021 0.002 TYR N 345 ARG 0.003 0.001 ARG M 29 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9436 Ramachandran restraints generated. 4718 Oldfield, 0 Emsley, 4718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9436 Ramachandran restraints generated. 4718 Oldfield, 0 Emsley, 4718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 4298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 377 time to evaluate : 3.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ARG cc_start: 0.8348 (mpt-90) cc_final: 0.8122 (mmm-85) REVERT: I 256 ASP cc_start: 0.8345 (t0) cc_final: 0.8038 (t0) REVERT: K 200 LEU cc_start: 0.7787 (tt) cc_final: 0.7572 (mp) REVERT: N 89 GLN cc_start: 0.8555 (mp10) cc_final: 0.7695 (mt0) REVERT: N 200 LEU cc_start: 0.7770 (tt) cc_final: 0.7538 (mp) outliers start: 28 outliers final: 10 residues processed: 405 average time/residue: 1.7369 time to fit residues: 831.4155 Evaluate side-chains 269 residues out of total 4298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 259 time to evaluate : 4.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain M residue 88 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 401 optimal weight: 20.0000 chunk 360 optimal weight: 0.8980 chunk 200 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 chunk 243 optimal weight: 0.9990 chunk 192 optimal weight: 0.0050 chunk 373 optimal weight: 7.9990 chunk 144 optimal weight: 0.9980 chunk 226 optimal weight: 1.9990 chunk 277 optimal weight: 0.8980 chunk 432 optimal weight: 0.7980 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 76 GLN A 89 GLN A 134 HIS A 208 ASN A 264 GLN B 76 GLN B 89 GLN B 134 HIS B 208 ASN B 264 GLN B 353 ASN C 76 GLN C 89 GLN C 134 HIS C 208 ASN C 353 ASN D 76 GLN D 89 GLN D 134 HIS D 208 ASN D 264 GLN D 353 ASN E 76 GLN E 89 GLN E 134 HIS E 208 ASN E 264 GLN E 353 ASN F 76 GLN F 89 GLN F 134 HIS F 208 ASN F 353 ASN G 76 GLN G 89 GLN G 134 HIS G 208 ASN G 353 ASN H 76 GLN H 134 HIS H 208 ASN H 264 GLN H 353 ASN I 76 GLN I 134 HIS I 208 ASN I 264 GLN J 76 GLN J 134 HIS J 208 ASN J 353 ASN K 76 GLN K 134 HIS K 208 ASN K 264 GLN L 76 GLN L 89 GLN L 134 HIS L 208 ASN L 353 ASN M 76 GLN M 89 GLN M 134 HIS M 208 ASN M 353 ASN N 76 GLN N 89 GLN N 134 HIS N 208 ASN N 264 GLN Total number of N/Q/H flips: 71 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 39242 Z= 0.160 Angle : 0.559 7.094 53256 Z= 0.275 Chirality : 0.040 0.122 6314 Planarity : 0.004 0.033 6230 Dihedral : 14.858 127.566 8704 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.79 % Allowed : 15.85 % Favored : 81.36 % 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: 0.74 (0.13), residues: 4718 helix: 1.59 (0.09), residues: 3206 sheet: None (None), residues: 0 loop : -2.01 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 104 HIS 0.003 0.002 HIS B 134 PHE 0.010 0.001 PHE E 129 TYR 0.017 0.001 TYR E 345 ARG 0.006 0.001 ARG F 254 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9436 Ramachandran restraints generated. 4718 Oldfield, 0 Emsley, 4718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9436 Ramachandran restraints generated. 4718 Oldfield, 0 Emsley, 4718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 4298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 312 time to evaluate : 3.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8045 (tm-30) cc_final: 0.7813 (tm-30) REVERT: A 140 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8222 (ptpp) REVERT: B 9 GLU cc_start: 0.8239 (tm-30) cc_final: 0.7975 (tm-30) REVERT: D 5 GLN cc_start: 0.8119 (tm-30) cc_final: 0.7870 (tm-30) REVERT: D 9 GLU cc_start: 0.8189 (tm-30) cc_final: 0.7961 (tm-30) REVERT: D 353 ASN cc_start: 0.9012 (OUTLIER) cc_final: 0.8586 (t0) REVERT: E 9 GLU cc_start: 0.8159 (tm-30) cc_final: 0.7881 (tm-30) REVERT: F 9 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7903 (tm-30) REVERT: G 5 GLN cc_start: 0.8231 (tm-30) cc_final: 0.8018 (tm-30) REVERT: G 9 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7893 (tm-30) REVERT: G 128 ARG cc_start: 0.8245 (tmm160) cc_final: 0.8045 (tmm160) REVERT: H 5 GLN cc_start: 0.7874 (tm-30) cc_final: 0.7604 (tm-30) REVERT: H 9 GLU cc_start: 0.8008 (tm-30) cc_final: 0.7734 (tm-30) REVERT: H 143 MET cc_start: 0.8736 (mtp) cc_final: 0.8532 (mtm) REVERT: I 9 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7781 (tm-30) REVERT: I 354 ILE cc_start: 0.8316 (mm) cc_final: 0.8100 (mt) REVERT: J 9 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7761 (tm-30) REVERT: J 354 ILE cc_start: 0.8264 (mm) cc_final: 0.8057 (mt) REVERT: K 9 GLU cc_start: 0.8106 (tm-30) cc_final: 0.7805 (tm-30) REVERT: K 200 LEU cc_start: 0.7867 (tt) cc_final: 0.7650 (mp) REVERT: L 9 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7727 (tm-30) REVERT: L 143 MET cc_start: 0.8542 (mtp) cc_final: 0.8214 (mtm) REVERT: M 5 GLN cc_start: 0.7885 (tm-30) cc_final: 0.7630 (tm-30) REVERT: M 9 GLU cc_start: 0.7984 (tm-30) cc_final: 0.7735 (tm-30) REVERT: M 354 ILE cc_start: 0.8197 (mm) cc_final: 0.7975 (mt) REVERT: N 9 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7809 (tm-30) REVERT: N 196 VAL cc_start: 0.6858 (OUTLIER) cc_final: 0.6196 (p) REVERT: N 200 LEU cc_start: 0.7759 (tt) cc_final: 0.7529 (mp) REVERT: N 354 ILE cc_start: 0.8162 (mm) cc_final: 0.7961 (mt) outliers start: 98 outliers final: 36 residues processed: 367 average time/residue: 1.5590 time to fit residues: 688.8043 Evaluate side-chains 306 residues out of total 4298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 267 time to evaluate : 4.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 140 LYS Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 353 ASN Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain H residue 31 GLU Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 246 CYS Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 246 CYS Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain J residue 246 CYS Chi-restraints excluded: chain K residue 31 GLU Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain K residue 246 CYS Chi-restraints excluded: chain L residue 31 GLU Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 246 CYS Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain M residue 246 CYS Chi-restraints excluded: chain N residue 31 GLU Chi-restraints excluded: chain N residue 196 VAL Chi-restraints excluded: chain N residue 246 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 240 optimal weight: 6.9990 chunk 134 optimal weight: 30.0000 chunk 359 optimal weight: 4.9990 chunk 294 optimal weight: 7.9990 chunk 119 optimal weight: 5.9990 chunk 433 optimal weight: 8.9990 chunk 467 optimal weight: 8.9990 chunk 385 optimal weight: 3.9990 chunk 429 optimal weight: 1.9990 chunk 147 optimal weight: 5.9990 chunk 347 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 89 GLN A 264 GLN B 264 GLN C 89 GLN D 264 GLN E 264 GLN F 89 GLN G 89 GLN H 264 GLN I 56 GLN I 89 GLN I 264 GLN I 353 ASN ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 5 GLN K 264 GLN K 353 ASN L 89 GLN ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 264 GLN N 353 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 39242 Z= 0.387 Angle : 0.629 7.414 53256 Z= 0.313 Chirality : 0.042 0.153 6314 Planarity : 0.004 0.035 6230 Dihedral : 13.802 100.170 8704 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 4.07 % Allowed : 17.62 % Favored : 78.32 % 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: 1.08 (0.13), residues: 4718 helix: 1.86 (0.09), residues: 3178 sheet: None (None), residues: 0 loop : -1.85 (0.16), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP G 104 HIS 0.003 0.001 HIS J 134 PHE 0.019 0.002 PHE J 67 TYR 0.023 0.002 TYR D 345 ARG 0.005 0.000 ARG B 254 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9436 Ramachandran restraints generated. 4718 Oldfield, 0 Emsley, 4718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9436 Ramachandran restraints generated. 4718 Oldfield, 0 Emsley, 4718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 4298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 278 time to evaluate : 3.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7831 (tm-30) REVERT: B 9 GLU cc_start: 0.8428 (tm-30) cc_final: 0.8026 (tm-30) REVERT: B 29 ARG cc_start: 0.8237 (mmm-85) cc_final: 0.7857 (mmm-85) REVERT: B 353 ASN cc_start: 0.9122 (OUTLIER) cc_final: 0.8612 (t0) REVERT: C 9 GLU cc_start: 0.8276 (tm-30) cc_final: 0.8061 (tm-30) REVERT: C 353 ASN cc_start: 0.9107 (OUTLIER) cc_final: 0.8678 (t0) REVERT: D 5 GLN cc_start: 0.8266 (tm-30) cc_final: 0.7993 (tm-30) REVERT: D 9 GLU cc_start: 0.8349 (tm-30) cc_final: 0.7973 (tm-30) REVERT: D 89 GLN cc_start: 0.9046 (OUTLIER) cc_final: 0.8567 (mt0) REVERT: E 5 GLN cc_start: 0.8292 (tm-30) cc_final: 0.8041 (tp40) REVERT: E 9 GLU cc_start: 0.8366 (tm-30) cc_final: 0.8019 (tm-30) REVERT: E 29 ARG cc_start: 0.8199 (mmm-85) cc_final: 0.7835 (mmm-85) REVERT: E 353 ASN cc_start: 0.9057 (OUTLIER) cc_final: 0.8647 (t0) REVERT: F 5 GLN cc_start: 0.8242 (tm-30) cc_final: 0.8008 (tp40) REVERT: F 9 GLU cc_start: 0.8398 (tm-30) cc_final: 0.8022 (tm-30) REVERT: F 29 ARG cc_start: 0.8270 (mmm-85) cc_final: 0.7907 (mmm-85) REVERT: F 353 ASN cc_start: 0.9071 (OUTLIER) cc_final: 0.8564 (t0) REVERT: G 5 GLN cc_start: 0.8369 (tm-30) cc_final: 0.8118 (tm-30) REVERT: G 9 GLU cc_start: 0.8326 (tm-30) cc_final: 0.7952 (tm-30) REVERT: G 353 ASN cc_start: 0.9059 (OUTLIER) cc_final: 0.8507 (t0) REVERT: H 5 GLN cc_start: 0.8051 (tm-30) cc_final: 0.7652 (tm-30) REVERT: H 9 GLU cc_start: 0.8215 (tm-30) cc_final: 0.7824 (tm-30) REVERT: H 89 GLN cc_start: 0.9100 (OUTLIER) cc_final: 0.8490 (mt0) REVERT: I 9 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7805 (tm-30) REVERT: I 197 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7537 (tm-30) REVERT: I 200 LEU cc_start: 0.8289 (mt) cc_final: 0.8079 (pp) REVERT: J 9 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7743 (tm-30) REVERT: K 9 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7740 (tm-30) REVERT: K 89 GLN cc_start: 0.9053 (OUTLIER) cc_final: 0.8369 (mt0) REVERT: K 200 LEU cc_start: 0.7821 (tt) cc_final: 0.7564 (mp) REVERT: L 9 GLU cc_start: 0.8174 (tm-30) cc_final: 0.7815 (tm-30) REVERT: L 143 MET cc_start: 0.8581 (mtp) cc_final: 0.8286 (mtm) REVERT: M 5 GLN cc_start: 0.8004 (tm-30) cc_final: 0.7662 (tm-30) REVERT: M 9 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7793 (tm-30) REVERT: N 9 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7799 (tm-30) REVERT: N 89 GLN cc_start: 0.9046 (OUTLIER) cc_final: 0.8710 (mt0) REVERT: N 200 LEU cc_start: 0.7820 (tt) cc_final: 0.7551 (mp) REVERT: N 354 ILE cc_start: 0.8143 (mm) cc_final: 0.7908 (mt) outliers start: 143 outliers final: 47 residues processed: 386 average time/residue: 1.4448 time to fit residues: 681.4404 Evaluate side-chains 299 residues out of total 4298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 243 time to evaluate : 4.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 353 ASN Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 353 ASN Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain E residue 353 ASN Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain F residue 353 ASN Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain G residue 353 ASN Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain H residue 89 GLN Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 246 CYS Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 246 CYS Chi-restraints excluded: chain I residue 254 ARG Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain J residue 88 VAL Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain J residue 246 CYS Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 89 GLN Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain K residue 246 CYS Chi-restraints excluded: chain L residue 57 GLU Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 246 CYS Chi-restraints excluded: chain M residue 57 GLU Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain M residue 246 CYS Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain N residue 196 VAL Chi-restraints excluded: chain N residue 246 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 427 optimal weight: 2.9990 chunk 325 optimal weight: 3.9990 chunk 224 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 206 optimal weight: 0.4980 chunk 290 optimal weight: 10.0000 chunk 434 optimal weight: 3.9990 chunk 460 optimal weight: 9.9990 chunk 227 optimal weight: 2.9990 chunk 411 optimal weight: 4.9990 chunk 123 optimal weight: 0.6980 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 353 ASN B 264 GLN C 89 GLN C 264 GLN D 264 GLN F 264 GLN G 264 GLN H 89 GLN ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 GLN M 89 GLN N 5 GLN ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 39242 Z= 0.227 Angle : 0.547 8.029 53256 Z= 0.272 Chirality : 0.040 0.142 6314 Planarity : 0.004 0.035 6230 Dihedral : 12.717 97.145 8704 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.47 % Allowed : 18.16 % Favored : 78.37 % 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: 1.41 (0.13), residues: 4718 helix: 2.10 (0.09), residues: 3178 sheet: None (None), residues: 0 loop : -1.69 (0.16), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 104 HIS 0.002 0.001 HIS M 134 PHE 0.015 0.001 PHE M 244 TYR 0.018 0.001 TYR F 345 ARG 0.002 0.000 ARG C 152 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9436 Ramachandran restraints generated. 4718 Oldfield, 0 Emsley, 4718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9436 Ramachandran restraints generated. 4718 Oldfield, 0 Emsley, 4718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 4298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 267 time to evaluate : 4.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8283 (tm-30) cc_final: 0.7858 (tm-30) REVERT: A 353 ASN cc_start: 0.9308 (OUTLIER) cc_final: 0.8882 (t0) REVERT: B 9 GLU cc_start: 0.8432 (tm-30) cc_final: 0.7981 (tm-30) REVERT: B 29 ARG cc_start: 0.8158 (mmm-85) cc_final: 0.7766 (mmm-85) REVERT: C 9 GLU cc_start: 0.8389 (tm-30) cc_final: 0.8072 (tm-30) REVERT: C 143 MET cc_start: 0.8930 (mtm) cc_final: 0.8711 (mtp) REVERT: D 5 GLN cc_start: 0.8300 (tm-30) cc_final: 0.7999 (tm-30) REVERT: D 9 GLU cc_start: 0.8379 (tm-30) cc_final: 0.7992 (tm-30) REVERT: E 5 GLN cc_start: 0.8290 (tm-30) cc_final: 0.8037 (tp40) REVERT: E 9 GLU cc_start: 0.8404 (tm-30) cc_final: 0.8029 (tm-30) REVERT: E 29 ARG cc_start: 0.8151 (mmm-85) cc_final: 0.7837 (mmm-85) REVERT: F 9 GLU cc_start: 0.8433 (tm-30) cc_final: 0.8025 (tm-30) REVERT: F 29 ARG cc_start: 0.8171 (mmm-85) cc_final: 0.7921 (mmm-85) REVERT: G 5 GLN cc_start: 0.8390 (tm-30) cc_final: 0.7998 (tm-30) REVERT: G 9 GLU cc_start: 0.8354 (tm-30) cc_final: 0.7930 (tm-30) REVERT: H 5 GLN cc_start: 0.8096 (tm-30) cc_final: 0.7718 (tm-30) REVERT: H 9 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7799 (tm-30) REVERT: I 9 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7783 (tm-30) REVERT: I 89 GLN cc_start: 0.9009 (OUTLIER) cc_final: 0.8372 (mt0) REVERT: I 197 GLU cc_start: 0.7909 (tm-30) cc_final: 0.7467 (tm-30) REVERT: I 200 LEU cc_start: 0.8121 (mt) cc_final: 0.7908 (pp) REVERT: J 9 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7701 (tm-30) REVERT: K 9 GLU cc_start: 0.8174 (tm-30) cc_final: 0.7713 (tm-30) REVERT: L 9 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7787 (tm-30) REVERT: L 143 MET cc_start: 0.8625 (mtp) cc_final: 0.8304 (mtm) REVERT: L 152 ARG cc_start: 0.7207 (OUTLIER) cc_final: 0.6554 (mtm110) REVERT: M 5 GLN cc_start: 0.8055 (tm-30) cc_final: 0.7681 (tm-30) REVERT: M 9 GLU cc_start: 0.8245 (tm-30) cc_final: 0.7824 (tm-30) REVERT: N 9 GLU cc_start: 0.8222 (tm-30) cc_final: 0.7819 (tm-30) REVERT: N 89 GLN cc_start: 0.8962 (OUTLIER) cc_final: 0.8648 (mt0) REVERT: N 354 ILE cc_start: 0.8024 (mm) cc_final: 0.7791 (mt) outliers start: 122 outliers final: 46 residues processed: 355 average time/residue: 1.4484 time to fit residues: 625.9471 Evaluate side-chains 293 residues out of total 4298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 243 time to evaluate : 4.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 353 ASN Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 246 CYS Chi-restraints excluded: chain I residue 31 GLU Chi-restraints excluded: chain I residue 37 MET Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 246 CYS Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain J residue 246 CYS Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain K residue 246 CYS Chi-restraints excluded: chain L residue 37 MET Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain L residue 146 LEU Chi-restraints excluded: chain L residue 152 ARG Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 246 CYS Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain M residue 246 CYS Chi-restraints excluded: chain N residue 37 MET Chi-restraints excluded: chain N residue 56 GLN Chi-restraints excluded: chain N residue 57 GLU Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain N residue 196 VAL Chi-restraints excluded: chain N residue 246 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 383 optimal weight: 9.9990 chunk 261 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 342 optimal weight: 3.9990 chunk 189 optimal weight: 1.9990 chunk 392 optimal weight: 9.9990 chunk 318 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 234 optimal weight: 10.0000 chunk 412 optimal weight: 2.9990 chunk 116 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 89 GLN C 264 GLN E 264 GLN I 89 GLN ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 GLN ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 39242 Z= 0.292 Angle : 0.576 8.359 53256 Z= 0.286 Chirality : 0.040 0.147 6314 Planarity : 0.004 0.034 6230 Dihedral : 12.510 93.718 8704 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 4.18 % Allowed : 18.07 % Favored : 77.75 % 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: 1.48 (0.13), residues: 4718 helix: 2.16 (0.09), residues: 3178 sheet: None (None), residues: 0 loop : -1.67 (0.16), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 104 HIS 0.003 0.001 HIS F 134 PHE 0.013 0.001 PHE J 67 TYR 0.018 0.001 TYR B 345 ARG 0.002 0.000 ARG A 29 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9436 Ramachandran restraints generated. 4718 Oldfield, 0 Emsley, 4718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9436 Ramachandran restraints generated. 4718 Oldfield, 0 Emsley, 4718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 4298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 242 time to evaluate : 4.157 Fit side-chains revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8333 (tm-30) cc_final: 0.7891 (tm-30) REVERT: A 31 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.8053 (mt-10) REVERT: B 9 GLU cc_start: 0.8464 (tm-30) cc_final: 0.8056 (tm-30) REVERT: B 29 ARG cc_start: 0.8194 (mmm-85) cc_final: 0.7916 (mmm-85) REVERT: C 9 GLU cc_start: 0.8423 (tm-30) cc_final: 0.8066 (tm-30) REVERT: C 89 GLN cc_start: 0.8995 (OUTLIER) cc_final: 0.8298 (mt0) REVERT: C 143 MET cc_start: 0.8987 (mtm) cc_final: 0.8750 (mtp) REVERT: D 5 GLN cc_start: 0.8354 (tm-30) cc_final: 0.8038 (tm-30) REVERT: D 9 GLU cc_start: 0.8401 (tm-30) cc_final: 0.8001 (tm-30) REVERT: E 5 GLN cc_start: 0.8351 (tm-30) cc_final: 0.8129 (tm-30) REVERT: E 9 GLU cc_start: 0.8439 (tm-30) cc_final: 0.8035 (tm-30) REVERT: E 29 ARG cc_start: 0.8201 (mmm-85) cc_final: 0.7842 (mmm-85) REVERT: F 5 GLN cc_start: 0.8203 (tp40) cc_final: 0.7921 (tp40) REVERT: F 9 GLU cc_start: 0.8478 (tm-30) cc_final: 0.8090 (tm-30) REVERT: F 29 ARG cc_start: 0.8186 (mmm-85) cc_final: 0.7852 (mmm-85) REVERT: G 5 GLN cc_start: 0.8422 (tm-30) cc_final: 0.8022 (tm-30) REVERT: G 9 GLU cc_start: 0.8381 (tm-30) cc_final: 0.7946 (tm-30) REVERT: H 5 GLN cc_start: 0.8146 (tm-30) cc_final: 0.7702 (tm-30) REVERT: H 9 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7816 (tm-30) REVERT: I 9 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7793 (tm-30) REVERT: I 197 GLU cc_start: 0.7838 (tm-30) cc_final: 0.7353 (tm-30) REVERT: I 200 LEU cc_start: 0.8075 (mt) cc_final: 0.7860 (pp) REVERT: J 9 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7748 (tm-30) REVERT: K 9 GLU cc_start: 0.8236 (tm-30) cc_final: 0.7750 (tm-30) REVERT: L 9 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7774 (tm-30) REVERT: L 143 MET cc_start: 0.8660 (mtp) cc_final: 0.8430 (mtm) REVERT: L 152 ARG cc_start: 0.7117 (OUTLIER) cc_final: 0.6470 (mtm110) REVERT: M 5 GLN cc_start: 0.8113 (tm-30) cc_final: 0.7698 (tm-30) REVERT: M 9 GLU cc_start: 0.8284 (tm-30) cc_final: 0.7822 (tm-30) REVERT: N 9 GLU cc_start: 0.8266 (tm-30) cc_final: 0.7845 (tm-30) outliers start: 147 outliers final: 67 residues processed: 350 average time/residue: 1.4299 time to fit residues: 613.2117 Evaluate side-chains 305 residues out of total 4298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 235 time to evaluate : 4.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 246 CYS Chi-restraints excluded: chain H residue 285 VAL Chi-restraints excluded: chain I residue 31 GLU Chi-restraints excluded: chain I residue 37 MET Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 246 CYS Chi-restraints excluded: chain I residue 285 VAL Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain J residue 246 CYS Chi-restraints excluded: chain J residue 285 VAL Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain K residue 246 CYS Chi-restraints excluded: chain K residue 285 VAL Chi-restraints excluded: chain L residue 37 MET Chi-restraints excluded: chain L residue 57 GLU Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain L residue 146 LEU Chi-restraints excluded: chain L residue 152 ARG Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 246 CYS Chi-restraints excluded: chain L residue 285 VAL Chi-restraints excluded: chain M residue 57 GLU Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain M residue 246 CYS Chi-restraints excluded: chain M residue 285 VAL Chi-restraints excluded: chain N residue 56 GLN Chi-restraints excluded: chain N residue 57 GLU Chi-restraints excluded: chain N residue 196 VAL Chi-restraints excluded: chain N residue 246 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 154 optimal weight: 0.9980 chunk 414 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 270 optimal weight: 30.0000 chunk 113 optimal weight: 1.9990 chunk 460 optimal weight: 6.9990 chunk 382 optimal weight: 2.9990 chunk 213 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 152 optimal weight: 7.9990 chunk 241 optimal weight: 8.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN B 264 GLN H 353 ASN I 5 GLN ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 39242 Z= 0.273 Angle : 0.564 8.704 53256 Z= 0.281 Chirality : 0.040 0.130 6314 Planarity : 0.004 0.034 6230 Dihedral : 12.172 92.097 8704 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 4.89 % Allowed : 17.47 % Favored : 77.63 % 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: 1.53 (0.13), residues: 4718 helix: 2.18 (0.09), residues: 3178 sheet: None (None), residues: 0 loop : -1.59 (0.16), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 104 HIS 0.002 0.001 HIS M 134 PHE 0.014 0.001 PHE K 141 TYR 0.023 0.001 TYR H 345 ARG 0.002 0.000 ARG A 254 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9436 Ramachandran restraints generated. 4718 Oldfield, 0 Emsley, 4718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9436 Ramachandran restraints generated. 4718 Oldfield, 0 Emsley, 4718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 4298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 246 time to evaluate : 3.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8362 (tm-30) cc_final: 0.7899 (tm-30) REVERT: B 9 GLU cc_start: 0.8498 (tm-30) cc_final: 0.8056 (tm-30) REVERT: B 29 ARG cc_start: 0.8231 (mmm-85) cc_final: 0.7949 (mmm-85) REVERT: C 9 GLU cc_start: 0.8434 (tm-30) cc_final: 0.8054 (tm-30) REVERT: C 31 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8249 (mt-10) REVERT: C 143 MET cc_start: 0.8983 (mtm) cc_final: 0.8719 (mtp) REVERT: D 5 GLN cc_start: 0.8383 (tm-30) cc_final: 0.8066 (tm-30) REVERT: D 9 GLU cc_start: 0.8423 (tm-30) cc_final: 0.8020 (tm-30) REVERT: E 5 GLN cc_start: 0.8369 (tm-30) cc_final: 0.8136 (tm-30) REVERT: E 9 GLU cc_start: 0.8443 (tm-30) cc_final: 0.8044 (tm-30) REVERT: E 29 ARG cc_start: 0.8205 (mmm-85) cc_final: 0.7825 (mmm-85) REVERT: E 37 MET cc_start: 0.8612 (OUTLIER) cc_final: 0.8108 (ttt) REVERT: F 5 GLN cc_start: 0.8276 (tp40) cc_final: 0.7953 (tp40) REVERT: F 9 GLU cc_start: 0.8492 (tm-30) cc_final: 0.8091 (tm-30) REVERT: F 29 ARG cc_start: 0.8160 (mmm-85) cc_final: 0.7920 (mmm-85) REVERT: G 5 GLN cc_start: 0.8418 (tm-30) cc_final: 0.8010 (tm-30) REVERT: G 9 GLU cc_start: 0.8415 (tm-30) cc_final: 0.7973 (tm-30) REVERT: G 31 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8239 (mt-10) REVERT: G 196 VAL cc_start: 0.8392 (OUTLIER) cc_final: 0.8142 (p) REVERT: G 200 LEU cc_start: 0.8103 (tt) cc_final: 0.7840 (mt) REVERT: H 5 GLN cc_start: 0.8167 (tm-30) cc_final: 0.7718 (tm-30) REVERT: H 9 GLU cc_start: 0.8282 (tm-30) cc_final: 0.7837 (tm-30) REVERT: H 352 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8421 (mp0) REVERT: I 9 GLU cc_start: 0.8261 (tm-30) cc_final: 0.7819 (tm-30) REVERT: I 200 LEU cc_start: 0.8019 (mt) cc_final: 0.7810 (pp) REVERT: J 9 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7715 (tm-30) REVERT: K 9 GLU cc_start: 0.8234 (tm-30) cc_final: 0.7737 (tm-30) REVERT: L 9 GLU cc_start: 0.8207 (tm-30) cc_final: 0.7760 (tm-30) REVERT: L 143 MET cc_start: 0.8683 (mtp) cc_final: 0.8457 (mtm) REVERT: L 152 ARG cc_start: 0.7181 (OUTLIER) cc_final: 0.6511 (mtm110) REVERT: M 5 GLN cc_start: 0.8127 (tm-30) cc_final: 0.7707 (tm-30) REVERT: M 9 GLU cc_start: 0.8297 (tm-30) cc_final: 0.7833 (tm-30) REVERT: M 57 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7790 (pm20) REVERT: N 9 GLU cc_start: 0.8288 (tm-30) cc_final: 0.7849 (tm-30) REVERT: N 89 GLN cc_start: 0.9027 (OUTLIER) cc_final: 0.8535 (mt0) REVERT: N 352 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8416 (mp0) outliers start: 172 outliers final: 72 residues processed: 381 average time/residue: 1.3354 time to fit residues: 631.1442 Evaluate side-chains 314 residues out of total 4298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 235 time to evaluate : 4.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 246 CYS Chi-restraints excluded: chain H residue 285 VAL Chi-restraints excluded: chain H residue 352 GLU Chi-restraints excluded: chain I residue 31 GLU Chi-restraints excluded: chain I residue 37 MET Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 246 CYS Chi-restraints excluded: chain I residue 254 ARG Chi-restraints excluded: chain I residue 285 VAL Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain J residue 246 CYS Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain K residue 246 CYS Chi-restraints excluded: chain K residue 285 VAL Chi-restraints excluded: chain L residue 37 MET Chi-restraints excluded: chain L residue 57 GLU Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain L residue 146 LEU Chi-restraints excluded: chain L residue 152 ARG Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 246 CYS Chi-restraints excluded: chain L residue 285 VAL Chi-restraints excluded: chain M residue 57 GLU Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain M residue 246 CYS Chi-restraints excluded: chain N residue 37 MET Chi-restraints excluded: chain N residue 56 GLN Chi-restraints excluded: chain N residue 57 GLU Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain N residue 146 LEU Chi-restraints excluded: chain N residue 196 VAL Chi-restraints excluded: chain N residue 246 CYS Chi-restraints excluded: chain N residue 352 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 444 optimal weight: 0.6980 chunk 51 optimal weight: 7.9990 chunk 262 optimal weight: 0.8980 chunk 336 optimal weight: 9.9990 chunk 260 optimal weight: 4.9990 chunk 387 optimal weight: 10.0000 chunk 257 optimal weight: 1.9990 chunk 458 optimal weight: 10.0000 chunk 287 optimal weight: 6.9990 chunk 279 optimal weight: 0.4980 chunk 211 optimal weight: 4.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 264 GLN H 353 ASN ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 39242 Z= 0.215 Angle : 0.559 9.008 53256 Z= 0.275 Chirality : 0.039 0.137 6314 Planarity : 0.004 0.034 6230 Dihedral : 11.829 88.044 8704 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.93 % Allowed : 18.27 % Favored : 77.80 % 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: 1.86 (0.13), residues: 4718 helix: 2.46 (0.09), residues: 3080 sheet: 0.20 (0.41), residues: 168 loop : -1.45 (0.17), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 104 HIS 0.002 0.001 HIS H 134 PHE 0.012 0.001 PHE K 141 TYR 0.022 0.001 TYR I 345 ARG 0.002 0.000 ARG G 152 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9436 Ramachandran restraints generated. 4718 Oldfield, 0 Emsley, 4718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9436 Ramachandran restraints generated. 4718 Oldfield, 0 Emsley, 4718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 4298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 248 time to evaluate : 4.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8385 (tm-30) cc_final: 0.7928 (tm-30) REVERT: B 9 GLU cc_start: 0.8483 (tm-30) cc_final: 0.8038 (tm-30) REVERT: B 29 ARG cc_start: 0.8204 (mmm-85) cc_final: 0.7979 (mmm-85) REVERT: B 37 MET cc_start: 0.8637 (OUTLIER) cc_final: 0.7984 (ttt) REVERT: C 9 GLU cc_start: 0.8444 (tm-30) cc_final: 0.7989 (tm-30) REVERT: C 31 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8236 (mt-10) REVERT: C 143 MET cc_start: 0.8990 (mtm) cc_final: 0.8745 (mtp) REVERT: D 5 GLN cc_start: 0.8398 (tm-30) cc_final: 0.8077 (tm-30) REVERT: D 9 GLU cc_start: 0.8413 (tm-30) cc_final: 0.8009 (tm-30) REVERT: E 5 GLN cc_start: 0.8364 (tm-30) cc_final: 0.8126 (tm-30) REVERT: E 9 GLU cc_start: 0.8448 (tm-30) cc_final: 0.8059 (tm-30) REVERT: E 29 ARG cc_start: 0.8170 (mmm-85) cc_final: 0.7873 (mmm-85) REVERT: E 37 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.8116 (ttt) REVERT: F 5 GLN cc_start: 0.8284 (tp40) cc_final: 0.7936 (tp40) REVERT: F 9 GLU cc_start: 0.8490 (tm-30) cc_final: 0.8090 (tm-30) REVERT: F 29 ARG cc_start: 0.8153 (mmm-85) cc_final: 0.7924 (mmm-85) REVERT: G 5 GLN cc_start: 0.8413 (tm-30) cc_final: 0.8009 (tm-30) REVERT: G 9 GLU cc_start: 0.8430 (tm-30) cc_final: 0.7999 (tm-30) REVERT: G 31 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8208 (mt-10) REVERT: G 200 LEU cc_start: 0.8076 (tt) cc_final: 0.7852 (mt) REVERT: H 5 GLN cc_start: 0.8146 (tm-30) cc_final: 0.7693 (tm-30) REVERT: H 9 GLU cc_start: 0.8303 (tm-30) cc_final: 0.7856 (tm-30) REVERT: I 9 GLU cc_start: 0.8280 (tm-30) cc_final: 0.7823 (tm-30) REVERT: J 9 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7720 (tm-30) REVERT: J 353 ASN cc_start: 0.8882 (OUTLIER) cc_final: 0.8676 (t0) REVERT: K 9 GLU cc_start: 0.8223 (tm-30) cc_final: 0.7733 (tm-30) REVERT: L 9 GLU cc_start: 0.8215 (tm-30) cc_final: 0.7775 (tm-30) REVERT: L 143 MET cc_start: 0.8655 (mtp) cc_final: 0.8439 (mtm) REVERT: M 5 GLN cc_start: 0.8125 (tm-30) cc_final: 0.7728 (tm-30) REVERT: M 9 GLU cc_start: 0.8317 (tm-30) cc_final: 0.7853 (tm-30) REVERT: M 352 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8626 (pm20) REVERT: M 353 ASN cc_start: 0.8899 (OUTLIER) cc_final: 0.8652 (t0) REVERT: N 9 GLU cc_start: 0.8308 (tm-30) cc_final: 0.7870 (tm-30) REVERT: N 89 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.8491 (mt0) REVERT: N 352 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8366 (mp0) outliers start: 138 outliers final: 72 residues processed: 357 average time/residue: 1.3993 time to fit residues: 624.4033 Evaluate side-chains 312 residues out of total 4298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 233 time to evaluate : 4.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 246 CYS Chi-restraints excluded: chain H residue 353 ASN Chi-restraints excluded: chain I residue 31 GLU Chi-restraints excluded: chain I residue 37 MET Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 246 CYS Chi-restraints excluded: chain I residue 278 VAL Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain J residue 246 CYS Chi-restraints excluded: chain J residue 353 ASN Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain K residue 246 CYS Chi-restraints excluded: chain K residue 278 VAL Chi-restraints excluded: chain L residue 37 MET Chi-restraints excluded: chain L residue 57 GLU Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain L residue 146 LEU Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 246 CYS Chi-restraints excluded: chain M residue 57 GLU Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain M residue 246 CYS Chi-restraints excluded: chain M residue 278 VAL Chi-restraints excluded: chain M residue 352 GLU Chi-restraints excluded: chain M residue 353 ASN Chi-restraints excluded: chain N residue 37 MET Chi-restraints excluded: chain N residue 57 GLU Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain N residue 196 VAL Chi-restraints excluded: chain N residue 246 CYS Chi-restraints excluded: chain N residue 352 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 283 optimal weight: 2.9990 chunk 183 optimal weight: 10.0000 chunk 274 optimal weight: 7.9990 chunk 138 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 88 optimal weight: 6.9990 chunk 291 optimal weight: 0.8980 chunk 312 optimal weight: 3.9990 chunk 226 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 360 optimal weight: 8.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 264 GLN H 353 ASN I 5 GLN I 353 ASN ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 353 ASN M 353 ASN N 353 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 39242 Z= 0.227 Angle : 0.562 8.912 53256 Z= 0.278 Chirality : 0.039 0.149 6314 Planarity : 0.004 0.034 6230 Dihedral : 11.610 82.051 8704 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.44 % Allowed : 18.67 % Favored : 77.89 % 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: 1.89 (0.13), residues: 4718 helix: 2.48 (0.09), residues: 3080 sheet: 0.20 (0.41), residues: 168 loop : -1.42 (0.17), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 74 HIS 0.002 0.001 HIS J 134 PHE 0.010 0.001 PHE L 54 TYR 0.017 0.001 TYR K 345 ARG 0.002 0.000 ARG A 29 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9436 Ramachandran restraints generated. 4718 Oldfield, 0 Emsley, 4718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9436 Ramachandran restraints generated. 4718 Oldfield, 0 Emsley, 4718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 4298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 241 time to evaluate : 4.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8441 (tm-30) cc_final: 0.7969 (tm-30) REVERT: B 9 GLU cc_start: 0.8475 (tm-30) cc_final: 0.8061 (tm-30) REVERT: B 29 ARG cc_start: 0.8221 (mmm-85) cc_final: 0.7992 (mmm-85) REVERT: C 9 GLU cc_start: 0.8462 (tm-30) cc_final: 0.8005 (tm-30) REVERT: C 31 GLU cc_start: 0.8463 (mt-10) cc_final: 0.8226 (mt-10) REVERT: C 89 GLN cc_start: 0.8998 (OUTLIER) cc_final: 0.8241 (mt0) REVERT: C 143 MET cc_start: 0.8981 (mtm) cc_final: 0.8734 (mtp) REVERT: D 5 GLN cc_start: 0.8413 (tm-30) cc_final: 0.8090 (tm-30) REVERT: D 9 GLU cc_start: 0.8425 (tm-30) cc_final: 0.8016 (tm-30) REVERT: D 200 LEU cc_start: 0.7936 (tt) cc_final: 0.7707 (mp) REVERT: E 5 GLN cc_start: 0.8386 (tm-30) cc_final: 0.8141 (tm-30) REVERT: E 9 GLU cc_start: 0.8461 (tm-30) cc_final: 0.8067 (tm-30) REVERT: E 29 ARG cc_start: 0.8185 (mmm-85) cc_final: 0.7890 (mmm-85) REVERT: E 37 MET cc_start: 0.8642 (OUTLIER) cc_final: 0.8123 (ttt) REVERT: E 200 LEU cc_start: 0.8048 (tt) cc_final: 0.7827 (mt) REVERT: F 5 GLN cc_start: 0.8305 (tp40) cc_final: 0.7948 (tp40) REVERT: F 9 GLU cc_start: 0.8514 (tm-30) cc_final: 0.8114 (tm-30) REVERT: F 29 ARG cc_start: 0.8123 (mmm-85) cc_final: 0.7908 (mmm-85) REVERT: G 5 GLN cc_start: 0.8432 (tm-30) cc_final: 0.8029 (tm-30) REVERT: G 9 GLU cc_start: 0.8440 (tm-30) cc_final: 0.8007 (tm-30) REVERT: G 31 GLU cc_start: 0.8463 (mt-10) cc_final: 0.8190 (mt-10) REVERT: G 143 MET cc_start: 0.8979 (mtp) cc_final: 0.8706 (mtp) REVERT: H 5 GLN cc_start: 0.8158 (tm-30) cc_final: 0.7703 (tm-30) REVERT: H 9 GLU cc_start: 0.8316 (tm-30) cc_final: 0.7897 (tm-30) REVERT: I 5 GLN cc_start: 0.8334 (tt0) cc_final: 0.8131 (tm-30) REVERT: I 9 GLU cc_start: 0.8297 (tm-30) cc_final: 0.7835 (tm-30) REVERT: J 9 GLU cc_start: 0.8237 (tm-30) cc_final: 0.7756 (tm-30) REVERT: J 254 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7848 (ttp-170) REVERT: K 9 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7751 (tm-30) REVERT: K 57 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8183 (pm20) REVERT: L 9 GLU cc_start: 0.8233 (tm-30) cc_final: 0.7795 (tm-30) REVERT: L 143 MET cc_start: 0.8658 (mtp) cc_final: 0.8434 (mtm) REVERT: M 5 GLN cc_start: 0.8137 (tm-30) cc_final: 0.7716 (tm-30) REVERT: M 9 GLU cc_start: 0.8320 (tm-30) cc_final: 0.7875 (tm-30) REVERT: N 9 GLU cc_start: 0.8326 (tm-30) cc_final: 0.7902 (tm-30) REVERT: N 89 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.8480 (mt0) REVERT: N 352 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8306 (mp0) outliers start: 121 outliers final: 77 residues processed: 339 average time/residue: 1.3749 time to fit residues: 575.0147 Evaluate side-chains 317 residues out of total 4298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 234 time to evaluate : 4.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 246 CYS Chi-restraints excluded: chain I residue 31 GLU Chi-restraints excluded: chain I residue 37 MET Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 246 CYS Chi-restraints excluded: chain I residue 254 ARG Chi-restraints excluded: chain I residue 278 VAL Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain J residue 246 CYS Chi-restraints excluded: chain J residue 254 ARG Chi-restraints excluded: chain J residue 278 VAL Chi-restraints excluded: chain J residue 285 VAL Chi-restraints excluded: chain K residue 57 GLU Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain K residue 246 CYS Chi-restraints excluded: chain K residue 278 VAL Chi-restraints excluded: chain L residue 37 MET Chi-restraints excluded: chain L residue 57 GLU Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain L residue 146 LEU Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 246 CYS Chi-restraints excluded: chain M residue 57 GLU Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain M residue 246 CYS Chi-restraints excluded: chain M residue 278 VAL Chi-restraints excluded: chain M residue 285 VAL Chi-restraints excluded: chain N residue 37 MET Chi-restraints excluded: chain N residue 56 GLN Chi-restraints excluded: chain N residue 57 GLU Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain N residue 196 VAL Chi-restraints excluded: chain N residue 246 CYS Chi-restraints excluded: chain N residue 352 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 417 optimal weight: 0.0270 chunk 439 optimal weight: 4.9990 chunk 401 optimal weight: 0.9990 chunk 427 optimal weight: 0.9990 chunk 257 optimal weight: 0.9980 chunk 186 optimal weight: 5.9990 chunk 335 optimal weight: 9.9990 chunk 131 optimal weight: 10.0000 chunk 386 optimal weight: 3.9990 chunk 404 optimal weight: 4.9990 chunk 426 optimal weight: 2.9990 overall best weight: 1.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN ** H 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 89 GLN K 89 GLN N 264 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 39242 Z= 0.173 Angle : 0.548 14.097 53256 Z= 0.271 Chirality : 0.039 0.253 6314 Planarity : 0.004 0.034 6230 Dihedral : 11.113 72.524 8704 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.22 % Allowed : 19.81 % Favored : 77.97 % 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: 1.98 (0.13), residues: 4718 helix: 2.56 (0.09), residues: 3080 sheet: -0.27 (0.41), residues: 182 loop : -1.34 (0.17), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 74 HIS 0.002 0.001 HIS H 134 PHE 0.009 0.001 PHE L 54 TYR 0.014 0.001 TYR H 345 ARG 0.002 0.000 ARG D 75 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9436 Ramachandran restraints generated. 4718 Oldfield, 0 Emsley, 4718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9436 Ramachandran restraints generated. 4718 Oldfield, 0 Emsley, 4718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 4298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 253 time to evaluate : 4.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8451 (tm-30) cc_final: 0.7964 (tm-30) REVERT: B 9 GLU cc_start: 0.8501 (tm-30) cc_final: 0.8064 (tm-30) REVERT: B 29 ARG cc_start: 0.8184 (mmm-85) cc_final: 0.7943 (mmm-85) REVERT: B 37 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.7907 (ttt) REVERT: B 200 LEU cc_start: 0.7982 (tt) cc_final: 0.7775 (mt) REVERT: C 9 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8009 (tm-30) REVERT: C 31 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8197 (mt-10) REVERT: C 143 MET cc_start: 0.8978 (mtm) cc_final: 0.8765 (mtp) REVERT: C 200 LEU cc_start: 0.8021 (tt) cc_final: 0.7815 (mt) REVERT: D 5 GLN cc_start: 0.8418 (tm-30) cc_final: 0.8101 (tm-30) REVERT: D 9 GLU cc_start: 0.8438 (tm-30) cc_final: 0.8025 (tm-30) REVERT: D 200 LEU cc_start: 0.7954 (tt) cc_final: 0.7730 (mp) REVERT: E 5 GLN cc_start: 0.8388 (tm-30) cc_final: 0.8124 (tm-30) REVERT: E 9 GLU cc_start: 0.8469 (tm-30) cc_final: 0.8076 (tm-30) REVERT: E 29 ARG cc_start: 0.8139 (mmm-85) cc_final: 0.7841 (mmm-85) REVERT: F 5 GLN cc_start: 0.8276 (tp40) cc_final: 0.7929 (tp40) REVERT: F 9 GLU cc_start: 0.8517 (tm-30) cc_final: 0.8113 (tm-30) REVERT: F 29 ARG cc_start: 0.8098 (mmm-85) cc_final: 0.7896 (mmm-85) REVERT: G 5 GLN cc_start: 0.8418 (tm-30) cc_final: 0.8022 (tm-30) REVERT: G 9 GLU cc_start: 0.8457 (tm-30) cc_final: 0.8025 (tm-30) REVERT: G 31 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8151 (mt-10) REVERT: H 5 GLN cc_start: 0.8159 (tm-30) cc_final: 0.7700 (tm-30) REVERT: H 9 GLU cc_start: 0.8321 (tm-30) cc_final: 0.7906 (tm-30) REVERT: I 9 GLU cc_start: 0.8311 (tm-30) cc_final: 0.7857 (tm-30) REVERT: I 56 GLN cc_start: 0.8487 (tp40) cc_final: 0.8286 (mm-40) REVERT: J 9 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7758 (tm-30) REVERT: K 9 GLU cc_start: 0.8246 (tm-30) cc_final: 0.7769 (tm-30) REVERT: K 57 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8149 (pm20) REVERT: K 352 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8504 (mp0) REVERT: L 9 GLU cc_start: 0.8239 (tm-30) cc_final: 0.7822 (tm-30) REVERT: L 143 MET cc_start: 0.8665 (mtp) cc_final: 0.8444 (mtm) REVERT: M 5 GLN cc_start: 0.8146 (tm-30) cc_final: 0.7720 (tm-30) REVERT: M 9 GLU cc_start: 0.8346 (tm-30) cc_final: 0.7910 (tm-30) REVERT: M 57 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7742 (pm20) REVERT: N 9 GLU cc_start: 0.8311 (tm-30) cc_final: 0.7890 (tm-30) REVERT: N 89 GLN cc_start: 0.8953 (OUTLIER) cc_final: 0.8462 (mt0) REVERT: N 200 LEU cc_start: 0.8064 (mp) cc_final: 0.7758 (pp) REVERT: N 352 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8209 (mp0) outliers start: 78 outliers final: 58 residues processed: 312 average time/residue: 1.4154 time to fit residues: 541.3085 Evaluate side-chains 303 residues out of total 4298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 239 time to evaluate : 3.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 246 CYS Chi-restraints excluded: chain H residue 278 VAL Chi-restraints excluded: chain I residue 31 GLU Chi-restraints excluded: chain I residue 37 MET Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 246 CYS Chi-restraints excluded: chain I residue 278 VAL Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain J residue 278 VAL Chi-restraints excluded: chain K residue 57 GLU Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain K residue 278 VAL Chi-restraints excluded: chain K residue 352 GLU Chi-restraints excluded: chain L residue 37 MET Chi-restraints excluded: chain L residue 57 GLU Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain L residue 146 LEU Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 246 CYS Chi-restraints excluded: chain M residue 57 GLU Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain M residue 246 CYS Chi-restraints excluded: chain M residue 278 VAL Chi-restraints excluded: chain N residue 37 MET Chi-restraints excluded: chain N residue 57 GLU Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain N residue 196 VAL Chi-restraints excluded: chain N residue 352 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 280 optimal weight: 0.9990 chunk 452 optimal weight: 3.9990 chunk 275 optimal weight: 7.9990 chunk 214 optimal weight: 0.7980 chunk 314 optimal weight: 2.9990 chunk 474 optimal weight: 5.9990 chunk 436 optimal weight: 5.9990 chunk 377 optimal weight: 2.9990 chunk 39 optimal weight: 0.0170 chunk 291 optimal weight: 7.9990 chunk 231 optimal weight: 40.0000 overall best weight: 1.5624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 ASN ** H 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 89 GLN K 89 GLN K 353 ASN ** N 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 39242 Z= 0.198 Angle : 0.560 11.881 53256 Z= 0.278 Chirality : 0.039 0.285 6314 Planarity : 0.004 0.034 6230 Dihedral : 10.963 63.632 8702 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.16 % Allowed : 19.95 % Favored : 77.89 % 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: 2.00 (0.13), residues: 4718 helix: 2.57 (0.09), residues: 3080 sheet: 0.24 (0.42), residues: 168 loop : -1.39 (0.17), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP H 74 HIS 0.001 0.001 HIS J 106 PHE 0.012 0.001 PHE H 141 TYR 0.015 0.001 TYR F 345 ARG 0.003 0.000 ARG N 75 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9436 Ramachandran restraints generated. 4718 Oldfield, 0 Emsley, 4718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9436 Ramachandran restraints generated. 4718 Oldfield, 0 Emsley, 4718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 4298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 242 time to evaluate : 4.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8465 (tm-30) cc_final: 0.7992 (tm-30) REVERT: B 9 GLU cc_start: 0.8526 (tm-30) cc_final: 0.8095 (tm-30) REVERT: B 29 ARG cc_start: 0.8212 (mmm-85) cc_final: 0.7976 (mmm-85) REVERT: B 37 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.7919 (ttt) REVERT: C 9 GLU cc_start: 0.8479 (tm-30) cc_final: 0.8021 (tm-30) REVERT: C 31 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8201 (mt-10) REVERT: C 143 MET cc_start: 0.8973 (mtm) cc_final: 0.8762 (mtp) REVERT: D 5 GLN cc_start: 0.8438 (tm-30) cc_final: 0.8124 (tm-30) REVERT: D 9 GLU cc_start: 0.8470 (tm-30) cc_final: 0.8064 (tm-30) REVERT: D 200 LEU cc_start: 0.8020 (tt) cc_final: 0.7818 (mp) REVERT: E 5 GLN cc_start: 0.8401 (tm-30) cc_final: 0.8115 (tm-30) REVERT: E 9 GLU cc_start: 0.8488 (tm-30) cc_final: 0.8089 (tm-30) REVERT: E 29 ARG cc_start: 0.8180 (mmm-85) cc_final: 0.7893 (mmm-85) REVERT: E 37 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.8087 (ttt) REVERT: F 5 GLN cc_start: 0.8287 (tp40) cc_final: 0.7937 (tp40) REVERT: F 9 GLU cc_start: 0.8533 (tm-30) cc_final: 0.8123 (tm-30) REVERT: G 5 GLN cc_start: 0.8420 (tm-30) cc_final: 0.8017 (tm-30) REVERT: G 9 GLU cc_start: 0.8469 (tm-30) cc_final: 0.8038 (tm-30) REVERT: G 31 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8148 (mt-10) REVERT: H 5 GLN cc_start: 0.8174 (tm-30) cc_final: 0.7719 (tm-30) REVERT: H 9 GLU cc_start: 0.8328 (tm-30) cc_final: 0.7917 (tm-30) REVERT: I 9 GLU cc_start: 0.8322 (tm-30) cc_final: 0.7868 (tm-30) REVERT: I 56 GLN cc_start: 0.8493 (tp40) cc_final: 0.8292 (mm-40) REVERT: J 9 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7776 (tm-30) REVERT: J 254 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7865 (ttp-170) REVERT: K 9 GLU cc_start: 0.8250 (tm-30) cc_final: 0.7805 (tm-30) REVERT: K 57 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8168 (pm20) REVERT: L 9 GLU cc_start: 0.8250 (tm-30) cc_final: 0.7836 (tm-30) REVERT: L 143 MET cc_start: 0.8688 (mtp) cc_final: 0.8470 (mtm) REVERT: M 5 GLN cc_start: 0.8149 (tm-30) cc_final: 0.7733 (tm-30) REVERT: M 9 GLU cc_start: 0.8369 (tm-30) cc_final: 0.7939 (tm-30) REVERT: N 9 GLU cc_start: 0.8335 (tm-30) cc_final: 0.7910 (tm-30) REVERT: N 89 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.8464 (mt0) REVERT: N 200 LEU cc_start: 0.8109 (mp) cc_final: 0.7801 (pp) REVERT: N 352 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8196 (mp0) outliers start: 76 outliers final: 57 residues processed: 299 average time/residue: 1.4580 time to fit residues: 531.7996 Evaluate side-chains 298 residues out of total 4298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 235 time to evaluate : 4.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 246 CYS Chi-restraints excluded: chain H residue 278 VAL Chi-restraints excluded: chain I residue 31 GLU Chi-restraints excluded: chain I residue 37 MET Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 246 CYS Chi-restraints excluded: chain I residue 278 VAL Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain J residue 254 ARG Chi-restraints excluded: chain J residue 278 VAL Chi-restraints excluded: chain K residue 57 GLU Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain K residue 278 VAL Chi-restraints excluded: chain L residue 37 MET Chi-restraints excluded: chain L residue 57 GLU Chi-restraints excluded: chain L residue 146 LEU Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 246 CYS Chi-restraints excluded: chain M residue 57 GLU Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain M residue 246 CYS Chi-restraints excluded: chain M residue 278 VAL Chi-restraints excluded: chain N residue 37 MET Chi-restraints excluded: chain N residue 57 GLU Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain N residue 196 VAL Chi-restraints excluded: chain N residue 352 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 299 optimal weight: 20.0000 chunk 402 optimal weight: 40.0000 chunk 115 optimal weight: 2.9990 chunk 348 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 104 optimal weight: 0.4980 chunk 378 optimal weight: 1.9990 chunk 158 optimal weight: 0.6980 chunk 388 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 5 GLN K 89 GLN ** N 353 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 = 0.3920 r_free = 0.3920 target = 0.105886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.069444 restraints weight = 85460.775| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.58 r_work: 0.2985 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 39242 Z= 0.176 Angle : 0.557 14.130 53256 Z= 0.276 Chirality : 0.039 0.267 6314 Planarity : 0.004 0.034 6230 Dihedral : 10.735 64.219 8699 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.16 % Allowed : 20.03 % Favored : 77.80 % 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: 2.04 (0.13), residues: 4718 helix: 2.62 (0.09), residues: 3066 sheet: 0.26 (0.42), residues: 168 loop : -1.39 (0.17), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP H 74 HIS 0.001 0.001 HIS H 134 PHE 0.013 0.001 PHE H 141 TYR 0.014 0.001 TYR F 345 ARG 0.004 0.000 ARG A 75 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11003.31 seconds wall clock time: 200 minutes 22.27 seconds (12022.27 seconds total)