Starting phenix.real_space_refine (version: 1.21rc1) on Wed Oct 18 17:03:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbn_21594/10_2023/6wbn_21594_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbn_21594/10_2023/6wbn_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_21594/10_2023/6wbn_21594.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbn_21594/10_2023/6wbn_21594.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbn_21594/10_2023/6wbn_21594_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbn_21594/10_2023/6wbn_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: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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: 19.66, per 1000 atoms: 0.51 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: 15.78 Conformation dependent library (CDL) restraints added in 5.4 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: 5.96 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: 12.04 Time building geometry restraints manager: 16.88 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: 22288 33.84 - 67.67: 882 67.67 - 101.51: 28 101.51 - 135.35: 28 135.35 - 169.19: 14 Dihedral angle restraints: 23240 sinusoidal: 9030 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 23237 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: 3.090 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: 14.820 Check model and map are aligned: 0.600 Set scattering table: 0.380 Process input model: 95.110 Find NCS groups from input model: 3.230 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 130.190 ------------------------------------------------------------------------------- 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 : 17.116 169.187 13916 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 *********************** 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 : 4.412 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 outliers start: 28 outliers final: 10 residues processed: 405 average time/residue: 1.7499 time to fit residues: 839.8316 Evaluate side-chains 266 residues out of total 4298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 256 time to evaluate : 4.662 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 10 residues processed: 0 time to fit residues: 5.8073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 overall best weight: 0.7594 ------------------------------------------------------------------------------- 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 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 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 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 134 HIS N 208 ASN N 264 GLN Total number of N/Q/H flips: 67 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 39242 Z= 0.164 Angle : 0.562 7.155 53256 Z= 0.278 Chirality : 0.040 0.124 6314 Planarity : 0.004 0.039 6230 Dihedral : 14.325 134.714 6650 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.76 % Allowed : 15.91 % Favored : 81.33 % 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: 0.66 (0.13), residues: 4718 helix: 1.55 (0.09), residues: 3192 sheet: None (None), residues: 0 loop : -2.06 (0.16), residues: 1526 *********************** 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 402 residues out of total 4298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 305 time to evaluate : 4.490 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 outliers start: 97 outliers final: 44 residues processed: 361 average time/residue: 1.6091 time to fit residues: 699.5016 Evaluate side-chains 305 residues out of total 4298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 261 time to evaluate : 4.384 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 28 residues processed: 16 average time/residue: 1.0681 time to fit residues: 27.6037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 240 optimal weight: 0.3980 chunk 134 optimal weight: 30.0000 chunk 359 optimal weight: 4.9990 chunk 294 optimal weight: 0.9990 chunk 119 optimal weight: 4.9990 chunk 433 optimal weight: 8.9990 chunk 467 optimal weight: 6.9990 chunk 385 optimal weight: 3.9990 chunk 429 optimal weight: 0.9990 chunk 147 optimal weight: 5.9990 chunk 347 optimal weight: 3.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- 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 C 89 GLN D 89 GLN D 264 GLN E 264 GLN F 89 GLN H 264 GLN I 56 GLN I 89 GLN I 264 GLN ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 5 GLN L 89 GLN N 353 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 39242 Z= 0.245 Angle : 0.561 7.292 53256 Z= 0.281 Chirality : 0.040 0.144 6314 Planarity : 0.004 0.034 6230 Dihedral : 11.763 101.176 6650 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.56 % Allowed : 16.96 % Favored : 79.48 % 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: 1.22 (0.13), residues: 4718 helix: 1.98 (0.09), residues: 3178 sheet: None (None), residues: 0 loop : -1.83 (0.16), residues: 1540 *********************** 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 413 residues out of total 4298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 288 time to evaluate : 4.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 125 outliers final: 45 residues processed: 379 average time/residue: 1.4468 time to fit residues: 673.5181 Evaluate side-chains 291 residues out of total 4298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 246 time to evaluate : 4.458 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 35 residues processed: 10 average time/residue: 0.7679 time to fit residues: 16.4874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 427 optimal weight: 1.9990 chunk 325 optimal weight: 3.9990 chunk 224 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 206 optimal weight: 4.9990 chunk 290 optimal weight: 9.9990 chunk 434 optimal weight: 3.9990 chunk 460 optimal weight: 7.9990 chunk 227 optimal weight: 1.9990 chunk 411 optimal weight: 7.9990 chunk 123 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN C 89 GLN C 264 GLN D 353 ASN I 89 GLN I 353 ASN ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 353 ASN L 89 GLN M 89 GLN N 5 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 39242 Z= 0.227 Angle : 0.548 8.188 53256 Z= 0.274 Chirality : 0.039 0.139 6314 Planarity : 0.004 0.034 6230 Dihedral : 10.912 96.388 6650 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.99 % Allowed : 19.01 % Favored : 78.00 % 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: 1.43 (0.13), residues: 4718 helix: 2.14 (0.09), residues: 3178 sheet: None (None), residues: 0 loop : -1.73 (0.16), residues: 1540 *********************** 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 373 residues out of total 4298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 268 time to evaluate : 4.377 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 105 outliers final: 57 residues processed: 334 average time/residue: 1.4754 time to fit residues: 602.6812 Evaluate side-chains 303 residues out of total 4298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 246 time to evaluate : 4.062 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 38 residues processed: 19 average time/residue: 1.0879 time to fit residues: 31.3990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 383 optimal weight: 8.9990 chunk 261 optimal weight: 0.7980 chunk 6 optimal weight: 5.9990 chunk 342 optimal weight: 0.0570 chunk 189 optimal weight: 2.9990 chunk 392 optimal weight: 10.0000 chunk 318 optimal weight: 0.1980 chunk 0 optimal weight: 10.0000 chunk 234 optimal weight: 9.9990 chunk 412 optimal weight: 0.7980 chunk 116 optimal weight: 7.9990 overall best weight: 0.9700 ------------------------------------------------------------------------------- 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 A 353 ASN B 264 GLN C 264 GLN D 264 GLN E 264 GLN F 264 GLN G 264 GLN I 89 GLN ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 39242 Z= 0.160 Angle : 0.527 8.635 53256 Z= 0.264 Chirality : 0.038 0.150 6314 Planarity : 0.004 0.034 6230 Dihedral : 10.295 91.680 6650 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.85 % Allowed : 19.01 % Favored : 78.14 % 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: 1.58 (0.13), residues: 4718 helix: 2.25 (0.09), residues: 3206 sheet: None (None), residues: 0 loop : -1.75 (0.16), residues: 1512 *********************** 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 362 residues out of total 4298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 262 time to evaluate : 4.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 100 outliers final: 53 residues processed: 331 average time/residue: 1.4477 time to fit residues: 590.3393 Evaluate side-chains 301 residues out of total 4298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 248 time to evaluate : 4.125 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 41 residues processed: 12 average time/residue: 1.5892 time to fit residues: 28.7790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 154 optimal weight: 7.9990 chunk 414 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 270 optimal weight: 40.0000 chunk 113 optimal weight: 0.7980 chunk 460 optimal weight: 9.9990 chunk 382 optimal weight: 4.9990 chunk 213 optimal weight: 10.0000 chunk 38 optimal weight: 0.6980 chunk 152 optimal weight: 20.0000 chunk 241 optimal weight: 4.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN C 264 GLN I 89 GLN ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2891 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= 0.233 Angle : 0.555 8.667 53256 Z= 0.277 Chirality : 0.039 0.126 6314 Planarity : 0.004 0.033 6230 Dihedral : 10.173 86.506 6650 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.53 % Allowed : 18.53 % Favored : 77.95 % 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: 1.70 (0.13), residues: 4718 helix: 2.35 (0.09), residues: 3178 sheet: None (None), residues: 0 loop : -1.65 (0.16), residues: 1540 *********************** 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 391 residues out of total 4298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 267 time to evaluate : 4.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 124 outliers final: 60 residues processed: 353 average time/residue: 1.4066 time to fit residues: 613.3181 Evaluate side-chains 304 residues out of total 4298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 244 time to evaluate : 4.978 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 50 residues processed: 10 average time/residue: 1.6139 time to fit residues: 25.1929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 444 optimal weight: 0.0040 chunk 51 optimal weight: 9.9990 chunk 262 optimal weight: 0.9990 chunk 336 optimal weight: 10.0000 chunk 260 optimal weight: 5.9990 chunk 387 optimal weight: 0.8980 chunk 257 optimal weight: 2.9990 chunk 458 optimal weight: 20.0000 chunk 287 optimal weight: 5.9990 chunk 279 optimal weight: 0.4980 chunk 211 optimal weight: 0.8980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 332 ASN A 353 ASN I 89 GLN ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 332 ASN L 353 ASN N 332 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 39242 Z= 0.153 Angle : 0.549 8.971 53256 Z= 0.271 Chirality : 0.038 0.123 6314 Planarity : 0.004 0.034 6230 Dihedral : 9.689 83.478 6650 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.50 % Allowed : 19.86 % 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: 1.80 (0.13), residues: 4718 helix: 2.44 (0.09), residues: 3178 sheet: None (None), residues: 0 loop : -1.61 (0.16), residues: 1540 *********************** 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 353 residues out of total 4298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 265 time to evaluate : 4.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 88 outliers final: 60 residues processed: 331 average time/residue: 1.4175 time to fit residues: 580.6900 Evaluate side-chains 305 residues out of total 4298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 245 time to evaluate : 4.501 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 50 residues processed: 10 average time/residue: 1.1917 time to fit residues: 20.7180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 283 optimal weight: 4.9990 chunk 183 optimal weight: 0.7980 chunk 274 optimal weight: 7.9990 chunk 138 optimal weight: 0.0570 chunk 90 optimal weight: 0.0000 chunk 88 optimal weight: 6.9990 chunk 291 optimal weight: 4.9990 chunk 312 optimal weight: 0.5980 chunk 226 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 360 optimal weight: 6.9990 overall best weight: 1.0904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN H 5 GLN I 89 GLN I 332 ASN ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 353 ASN L 332 ASN M 353 ASN N 5 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3274 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= 0.172 Angle : 0.552 9.180 53256 Z= 0.273 Chirality : 0.038 0.140 6314 Planarity : 0.004 0.034 6230 Dihedral : 9.474 80.286 6650 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.19 % Allowed : 20.12 % Favored : 77.69 % 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: 2.49 (0.09), residues: 3164 sheet: None (None), residues: 0 loop : -1.56 (0.15), residues: 1554 *********************** 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 335 residues out of total 4298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 258 time to evaluate : 4.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 77 outliers final: 56 residues processed: 319 average time/residue: 1.4713 time to fit residues: 576.7889 Evaluate side-chains 297 residues out of total 4298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 241 time to evaluate : 4.622 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 49 residues processed: 7 average time/residue: 1.4264 time to fit residues: 18.1184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 417 optimal weight: 0.7980 chunk 439 optimal weight: 9.9990 chunk 401 optimal weight: 20.0000 chunk 427 optimal weight: 3.9990 chunk 257 optimal weight: 3.9990 chunk 186 optimal weight: 10.0000 chunk 335 optimal weight: 20.0000 chunk 131 optimal weight: 10.0000 chunk 386 optimal weight: 0.9980 chunk 404 optimal weight: 5.9990 chunk 426 optimal weight: 1.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 264 GLN I 89 GLN J 89 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 39242 Z= 0.263 Angle : 0.600 9.872 53256 Z= 0.299 Chirality : 0.040 0.186 6314 Planarity : 0.004 0.034 6230 Dihedral : 9.774 79.790 6650 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.31 % Allowed : 20.23 % Favored : 77.46 % 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: 2.63 (0.09), residues: 3080 sheet: 0.47 (0.40), residues: 168 loop : -1.48 (0.17), residues: 1470 *********************** 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 326 residues out of total 4298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 245 time to evaluate : 4.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 81 outliers final: 58 residues processed: 310 average time/residue: 1.4820 time to fit residues: 566.2283 Evaluate side-chains 287 residues out of total 4298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 229 time to evaluate : 4.413 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 50 residues processed: 8 average time/residue: 1.6629 time to fit residues: 21.4504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 280 optimal weight: 0.9980 chunk 452 optimal weight: 1.9990 chunk 275 optimal weight: 7.9990 chunk 214 optimal weight: 0.4980 chunk 314 optimal weight: 2.9990 chunk 474 optimal weight: 0.0870 chunk 436 optimal weight: 50.0000 chunk 377 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 291 optimal weight: 2.9990 chunk 231 optimal weight: 30.0000 overall best weight: 1.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 353 ASN I 89 GLN I 353 ASN J 332 ASN K 353 ASN M 332 ASN N 5 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 39242 Z= 0.173 Angle : 0.568 9.990 53256 Z= 0.281 Chirality : 0.039 0.190 6314 Planarity : 0.004 0.034 6230 Dihedral : 9.370 77.951 6650 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.74 % Allowed : 20.52 % 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: 2.12 (0.13), residues: 4718 helix: 2.71 (0.09), residues: 3066 sheet: 0.47 (0.40), residues: 168 loop : -1.44 (0.17), residues: 1484 ********************** 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 303 residues out of total 4298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 242 time to evaluate : 4.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 52 residues processed: 299 average time/residue: 1.4458 time to fit residues: 533.8067 Evaluate side-chains 282 residues out of total 4298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 230 time to evaluate : 4.687 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 50 residues processed: 2 average time/residue: 1.6750 time to fit residues: 9.5006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 299 optimal weight: 30.0000 chunk 402 optimal weight: 30.0000 chunk 115 optimal weight: 0.9980 chunk 348 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 104 optimal weight: 0.4980 chunk 378 optimal weight: 1.9990 chunk 158 optimal weight: 0.0470 chunk 388 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 overall best weight: 0.9080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 332 ASN D 332 ASN G 332 ASN H 332 ASN I 89 GLN N 353 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.106761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.070544 restraints weight = 85533.469| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.59 r_work: 0.3016 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 39242 Z= 0.163 Angle : 0.569 14.701 53256 Z= 0.283 Chirality : 0.039 0.354 6314 Planarity : 0.004 0.035 6230 Dihedral : 9.063 75.823 6650 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.82 % Allowed : 20.60 % Favored : 77.58 % 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: 2.17 (0.13), residues: 4718 helix: 2.75 (0.09), residues: 3066 sheet: 0.46 (0.40), residues: 168 loop : -1.42 (0.17), residues: 1484 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10764.44 seconds wall clock time: 199 minutes 14.50 seconds (11954.50 seconds total)