Starting phenix.real_space_refine on Fri Feb 16 06:48:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lyg_30016/02_2024/6lyg_30016.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lyg_30016/02_2024/6lyg_30016.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lyg_30016/02_2024/6lyg_30016.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lyg_30016/02_2024/6lyg_30016.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lyg_30016/02_2024/6lyg_30016.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lyg_30016/02_2024/6lyg_30016.pdb" } resolution = 3.1 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 9552 2.51 5 N 2384 2.21 5 O 2632 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 83": "NH1" <-> "NH2" Residue "A GLU 140": "OE1" <-> "OE2" Residue "A GLU 164": "OE1" <-> "OE2" Residue "A GLU 167": "OE1" <-> "OE2" Residue "A ARG 171": "NH1" <-> "NH2" Residue "A GLU 172": "OE1" <-> "OE2" Residue "A ARG 176": "NH1" <-> "NH2" Residue "A ARG 179": "NH1" <-> "NH2" Residue "A ARG 201": "NH1" <-> "NH2" Residue "B ARG 83": "NH1" <-> "NH2" Residue "B GLU 140": "OE1" <-> "OE2" Residue "B GLU 164": "OE1" <-> "OE2" Residue "B GLU 167": "OE1" <-> "OE2" Residue "B ARG 171": "NH1" <-> "NH2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B ARG 176": "NH1" <-> "NH2" Residue "B ARG 179": "NH1" <-> "NH2" Residue "B ARG 201": "NH1" <-> "NH2" Residue "C ARG 83": "NH1" <-> "NH2" Residue "C GLU 140": "OE1" <-> "OE2" Residue "C GLU 164": "OE1" <-> "OE2" Residue "C GLU 167": "OE1" <-> "OE2" Residue "C ARG 171": "NH1" <-> "NH2" Residue "C GLU 172": "OE1" <-> "OE2" Residue "C ARG 176": "NH1" <-> "NH2" Residue "C ARG 179": "NH1" <-> "NH2" Residue "C ARG 201": "NH1" <-> "NH2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D GLU 140": "OE1" <-> "OE2" Residue "D GLU 164": "OE1" <-> "OE2" Residue "D GLU 167": "OE1" <-> "OE2" Residue "D ARG 171": "NH1" <-> "NH2" Residue "D GLU 172": "OE1" <-> "OE2" Residue "D ARG 176": "NH1" <-> "NH2" Residue "D ARG 179": "NH1" <-> "NH2" Residue "D ARG 201": "NH1" <-> "NH2" Residue "E ARG 83": "NH1" <-> "NH2" Residue "E GLU 140": "OE1" <-> "OE2" Residue "E GLU 164": "OE1" <-> "OE2" Residue "E GLU 167": "OE1" <-> "OE2" Residue "E ARG 171": "NH1" <-> "NH2" Residue "E GLU 172": "OE1" <-> "OE2" Residue "E ARG 176": "NH1" <-> "NH2" Residue "E ARG 179": "NH1" <-> "NH2" Residue "E ARG 201": "NH1" <-> "NH2" Residue "F ARG 83": "NH1" <-> "NH2" Residue "F GLU 140": "OE1" <-> "OE2" Residue "F GLU 164": "OE1" <-> "OE2" Residue "F GLU 167": "OE1" <-> "OE2" Residue "F ARG 171": "NH1" <-> "NH2" Residue "F GLU 172": "OE1" <-> "OE2" Residue "F ARG 176": "NH1" <-> "NH2" Residue "F ARG 179": "NH1" <-> "NH2" Residue "F ARG 201": "NH1" <-> "NH2" Residue "G ARG 83": "NH1" <-> "NH2" Residue "G GLU 140": "OE1" <-> "OE2" Residue "G GLU 164": "OE1" <-> "OE2" Residue "G GLU 167": "OE1" <-> "OE2" Residue "G ARG 171": "NH1" <-> "NH2" Residue "G GLU 172": "OE1" <-> "OE2" Residue "G ARG 176": "NH1" <-> "NH2" Residue "G ARG 179": "NH1" <-> "NH2" Residue "G ARG 201": "NH1" <-> "NH2" Residue "H ARG 83": "NH1" <-> "NH2" Residue "H GLU 140": "OE1" <-> "OE2" Residue "H GLU 164": "OE1" <-> "OE2" Residue "H GLU 167": "OE1" <-> "OE2" Residue "H ARG 171": "NH1" <-> "NH2" Residue "H GLU 172": "OE1" <-> "OE2" Residue "H ARG 176": "NH1" <-> "NH2" Residue "H ARG 179": "NH1" <-> "NH2" Residue "H ARG 201": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14688 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1822 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 9, 'TRANS': 222} Chain breaks: 3 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'PHE:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "B" Number of atoms: 1822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1822 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 9, 'TRANS': 222} Chain breaks: 3 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'PHE:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "C" Number of atoms: 1822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1822 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 9, 'TRANS': 222} Chain breaks: 3 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'PHE:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "D" Number of atoms: 1822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1822 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 9, 'TRANS': 222} Chain breaks: 3 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'PHE:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "E" Number of atoms: 1822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1822 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 9, 'TRANS': 222} Chain breaks: 3 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'PHE:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "F" Number of atoms: 1822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1822 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 9, 'TRANS': 222} Chain breaks: 3 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'PHE:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "G" Number of atoms: 1822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1822 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 9, 'TRANS': 222} Chain breaks: 3 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'PHE:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "H" Number of atoms: 1822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1822 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 9, 'TRANS': 222} Chain breaks: 3 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'PHE:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.94, per 1000 atoms: 0.54 Number of scatterers: 14688 At special positions: 0 Unit cell: (122.694, 122.694, 102.414, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 2632 8.00 N 2384 7.00 C 9552 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 43 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 43 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 41 " - pdb=" SG CYS C 126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 159 " distance=2.03 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 43 " - pdb=" SG CYS D 159 " distance=2.03 Simple disulfide: pdb=" SG CYS E 41 " - pdb=" SG CYS E 126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 43 " - pdb=" SG CYS E 159 " distance=2.03 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 43 " - pdb=" SG CYS F 159 " distance=2.03 Simple disulfide: pdb=" SG CYS G 41 " - pdb=" SG CYS G 126 " distance=2.03 Simple disulfide: pdb=" SG CYS G 43 " - pdb=" SG CYS G 159 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 43 " - pdb=" SG CYS H 159 " 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 Links applied NAG-ASN " NAG A1001 " - " ASN A 139 " " NAG B1001 " - " ASN B 139 " " NAG C1001 " - " ASN C 139 " " NAG D1001 " - " ASN D 139 " " NAG E1001 " - " ASN E 139 " " NAG F1001 " - " ASN F 139 " " NAG G1001 " - " ASN G 139 " " NAG H1001 " - " ASN H 139 " Time building additional restraints: 6.22 Conformation dependent library (CDL) restraints added in 3.0 seconds 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3600 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 0 sheets defined 78.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 5 through 18 Processing helix chain 'A' and resid 25 through 36 Processing helix chain 'A' and resid 47 through 70 Proline residue: A 59 - end of helix Processing helix chain 'A' and resid 73 through 83 removed outlier: 3.628A pdb=" N LEU A 77 " --> pdb=" O ASN A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 107 Processing helix chain 'A' and resid 107 through 120 removed outlier: 3.688A pdb=" N ALA A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 129 Processing helix chain 'A' and resid 146 through 156 removed outlier: 4.037A pdb=" N LYS A 152 " --> pdb=" O LYS A 148 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE A 153 " --> pdb=" O GLU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 204 Processing helix chain 'A' and resid 209 through 246 removed outlier: 3.565A pdb=" N LEU A 213 " --> pdb=" O GLN A 209 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER A 239 " --> pdb=" O GLU A 235 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N PHE A 240 " --> pdb=" O HIS A 236 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN A 246 " --> pdb=" O LYS A 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 18 Processing helix chain 'B' and resid 25 through 36 Processing helix chain 'B' and resid 47 through 70 Proline residue: B 59 - end of helix Processing helix chain 'B' and resid 73 through 83 removed outlier: 3.629A pdb=" N LEU B 77 " --> pdb=" O ASN B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 107 Processing helix chain 'B' and resid 107 through 120 removed outlier: 3.688A pdb=" N ALA B 111 " --> pdb=" O LEU B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 129 Processing helix chain 'B' and resid 146 through 156 removed outlier: 4.037A pdb=" N LYS B 152 " --> pdb=" O LYS B 148 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE B 153 " --> pdb=" O GLU B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 204 Processing helix chain 'B' and resid 209 through 246 removed outlier: 3.565A pdb=" N LEU B 213 " --> pdb=" O GLN B 209 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER B 239 " --> pdb=" O GLU B 235 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N PHE B 240 " --> pdb=" O HIS B 236 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN B 246 " --> pdb=" O LYS B 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 18 Processing helix chain 'C' and resid 25 through 36 Processing helix chain 'C' and resid 47 through 70 Proline residue: C 59 - end of helix Processing helix chain 'C' and resid 73 through 83 removed outlier: 3.628A pdb=" N LEU C 77 " --> pdb=" O ASN C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 107 removed outlier: 4.232A pdb=" N ARG C 96 " --> pdb=" O PRO C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 120 removed outlier: 3.688A pdb=" N ALA C 111 " --> pdb=" O LEU C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 129 Processing helix chain 'C' and resid 146 through 156 removed outlier: 4.037A pdb=" N LYS C 152 " --> pdb=" O LYS C 148 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE C 153 " --> pdb=" O GLU C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 204 Processing helix chain 'C' and resid 209 through 246 removed outlier: 3.565A pdb=" N LEU C 213 " --> pdb=" O GLN C 209 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER C 239 " --> pdb=" O GLU C 235 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N PHE C 240 " --> pdb=" O HIS C 236 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN C 246 " --> pdb=" O LYS C 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 18 Processing helix chain 'D' and resid 25 through 36 Processing helix chain 'D' and resid 47 through 70 Proline residue: D 59 - end of helix Processing helix chain 'D' and resid 73 through 83 removed outlier: 3.628A pdb=" N LEU D 77 " --> pdb=" O ASN D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 107 removed outlier: 4.232A pdb=" N ARG D 96 " --> pdb=" O PRO D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 120 removed outlier: 3.688A pdb=" N ALA D 111 " --> pdb=" O LEU D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 129 Processing helix chain 'D' and resid 146 through 156 removed outlier: 4.037A pdb=" N LYS D 152 " --> pdb=" O LYS D 148 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE D 153 " --> pdb=" O GLU D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 204 Processing helix chain 'D' and resid 209 through 246 removed outlier: 3.565A pdb=" N LEU D 213 " --> pdb=" O GLN D 209 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER D 239 " --> pdb=" O GLU D 235 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N PHE D 240 " --> pdb=" O HIS D 236 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN D 246 " --> pdb=" O LYS D 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 18 Processing helix chain 'E' and resid 25 through 36 Processing helix chain 'E' and resid 47 through 70 Proline residue: E 59 - end of helix Processing helix chain 'E' and resid 73 through 83 removed outlier: 3.628A pdb=" N LEU E 77 " --> pdb=" O ASN E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 107 removed outlier: 4.232A pdb=" N ARG E 96 " --> pdb=" O PRO E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 120 removed outlier: 3.688A pdb=" N ALA E 111 " --> pdb=" O LEU E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 129 Processing helix chain 'E' and resid 146 through 156 removed outlier: 4.037A pdb=" N LYS E 152 " --> pdb=" O LYS E 148 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE E 153 " --> pdb=" O GLU E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 204 Processing helix chain 'E' and resid 209 through 246 removed outlier: 3.565A pdb=" N LEU E 213 " --> pdb=" O GLN E 209 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER E 239 " --> pdb=" O GLU E 235 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N PHE E 240 " --> pdb=" O HIS E 236 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN E 246 " --> pdb=" O LYS E 242 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 18 Processing helix chain 'F' and resid 25 through 36 Processing helix chain 'F' and resid 47 through 70 Proline residue: F 59 - end of helix Processing helix chain 'F' and resid 73 through 83 removed outlier: 3.629A pdb=" N LEU F 77 " --> pdb=" O ASN F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 107 removed outlier: 4.232A pdb=" N ARG F 96 " --> pdb=" O PRO F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 120 removed outlier: 3.688A pdb=" N ALA F 111 " --> pdb=" O LEU F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 129 Processing helix chain 'F' and resid 146 through 156 removed outlier: 4.037A pdb=" N LYS F 152 " --> pdb=" O LYS F 148 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE F 153 " --> pdb=" O GLU F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 170 through 204 Processing helix chain 'F' and resid 209 through 246 removed outlier: 3.565A pdb=" N LEU F 213 " --> pdb=" O GLN F 209 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER F 239 " --> pdb=" O GLU F 235 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N PHE F 240 " --> pdb=" O HIS F 236 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN F 246 " --> pdb=" O LYS F 242 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 18 Processing helix chain 'G' and resid 25 through 36 Processing helix chain 'G' and resid 47 through 70 Proline residue: G 59 - end of helix Processing helix chain 'G' and resid 73 through 83 removed outlier: 3.628A pdb=" N LEU G 77 " --> pdb=" O ASN G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 107 removed outlier: 4.232A pdb=" N ARG G 96 " --> pdb=" O PRO G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 120 removed outlier: 3.688A pdb=" N ALA G 111 " --> pdb=" O LEU G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 129 Processing helix chain 'G' and resid 146 through 156 removed outlier: 4.037A pdb=" N LYS G 152 " --> pdb=" O LYS G 148 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE G 153 " --> pdb=" O GLU G 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 170 through 204 Processing helix chain 'G' and resid 209 through 246 removed outlier: 3.565A pdb=" N LEU G 213 " --> pdb=" O GLN G 209 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER G 239 " --> pdb=" O GLU G 235 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N PHE G 240 " --> pdb=" O HIS G 236 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN G 246 " --> pdb=" O LYS G 242 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 18 Processing helix chain 'H' and resid 25 through 36 Processing helix chain 'H' and resid 47 through 70 Proline residue: H 59 - end of helix Processing helix chain 'H' and resid 73 through 83 removed outlier: 3.628A pdb=" N LEU H 77 " --> pdb=" O ASN H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 107 removed outlier: 4.232A pdb=" N ARG H 96 " --> pdb=" O PRO H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 120 removed outlier: 3.688A pdb=" N ALA H 111 " --> pdb=" O LEU H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 129 Processing helix chain 'H' and resid 146 through 156 removed outlier: 4.037A pdb=" N LYS H 152 " --> pdb=" O LYS H 148 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE H 153 " --> pdb=" O GLU H 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 170 through 204 Processing helix chain 'H' and resid 209 through 246 removed outlier: 3.565A pdb=" N LEU H 213 " --> pdb=" O GLN H 209 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER H 239 " --> pdb=" O GLU H 235 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N PHE H 240 " --> pdb=" O HIS H 236 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN H 246 " --> pdb=" O LYS H 242 " (cutoff:3.500A) 1049 hydrogen bonds defined for protein. 3147 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: 4.06 Time building geometry restraints manager: 6.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4495 1.34 - 1.46: 3261 1.46 - 1.58: 7092 1.58 - 1.69: 0 1.69 - 1.81: 176 Bond restraints: 15024 Sorted by residual: bond pdb=" N ALA G 93 " pdb=" CA ALA G 93 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.23e-02 6.61e+03 4.81e+00 bond pdb=" N ALA B 93 " pdb=" CA ALA B 93 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.27e-02 6.20e+03 4.65e+00 bond pdb=" N ALA E 93 " pdb=" CA ALA E 93 " ideal model delta sigma weight residual 1.459 1.486 -0.026 1.23e-02 6.61e+03 4.62e+00 bond pdb=" N ALA C 93 " pdb=" CA ALA C 93 " ideal model delta sigma weight residual 1.459 1.486 -0.026 1.23e-02 6.61e+03 4.62e+00 bond pdb=" N ALA H 93 " pdb=" CA ALA H 93 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.23e-02 6.61e+03 4.60e+00 ... (remaining 15019 not shown) Histogram of bond angle deviations from ideal: 100.41 - 107.13: 450 107.13 - 113.85: 8460 113.85 - 120.57: 6378 120.57 - 127.29: 4896 127.29 - 134.01: 168 Bond angle restraints: 20352 Sorted by residual: angle pdb=" N ALA H 93 " pdb=" CA ALA H 93 " pdb=" C ALA H 93 " ideal model delta sigma weight residual 111.36 118.96 -7.60 1.09e+00 8.42e-01 4.86e+01 angle pdb=" N ALA D 93 " pdb=" CA ALA D 93 " pdb=" C ALA D 93 " ideal model delta sigma weight residual 111.36 118.96 -7.60 1.09e+00 8.42e-01 4.86e+01 angle pdb=" N ALA E 93 " pdb=" CA ALA E 93 " pdb=" C ALA E 93 " ideal model delta sigma weight residual 111.36 118.95 -7.59 1.09e+00 8.42e-01 4.85e+01 angle pdb=" N ALA C 93 " pdb=" CA ALA C 93 " pdb=" C ALA C 93 " ideal model delta sigma weight residual 111.36 118.95 -7.59 1.09e+00 8.42e-01 4.85e+01 angle pdb=" N ALA F 93 " pdb=" CA ALA F 93 " pdb=" C ALA F 93 " ideal model delta sigma weight residual 111.36 118.95 -7.59 1.09e+00 8.42e-01 4.85e+01 ... (remaining 20347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.00: 8231 17.00 - 34.00: 661 34.00 - 51.00: 140 51.00 - 67.99: 48 67.99 - 84.99: 24 Dihedral angle restraints: 9104 sinusoidal: 3600 harmonic: 5504 Sorted by residual: dihedral pdb=" CB CYS B 43 " pdb=" SG CYS B 43 " pdb=" SG CYS B 159 " pdb=" CB CYS B 159 " ideal model delta sinusoidal sigma weight residual 93.00 119.90 -26.90 1 1.00e+01 1.00e-02 1.04e+01 dihedral pdb=" CB CYS F 43 " pdb=" SG CYS F 43 " pdb=" SG CYS F 159 " pdb=" CB CYS F 159 " ideal model delta sinusoidal sigma weight residual 93.00 119.90 -26.90 1 1.00e+01 1.00e-02 1.04e+01 dihedral pdb=" CB CYS C 43 " pdb=" SG CYS C 43 " pdb=" SG CYS C 159 " pdb=" CB CYS C 159 " ideal model delta sinusoidal sigma weight residual 93.00 119.89 -26.89 1 1.00e+01 1.00e-02 1.04e+01 ... (remaining 9101 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2068 0.059 - 0.118: 250 0.118 - 0.178: 3 0.178 - 0.237: 9 0.237 - 0.296: 6 Chirality restraints: 2336 Sorted by residual: chirality pdb=" CA ALA F 93 " pdb=" N ALA F 93 " pdb=" C ALA F 93 " pdb=" CB ALA F 93 " both_signs ideal model delta sigma weight residual False 2.48 2.19 0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" CA ALA D 93 " pdb=" N ALA D 93 " pdb=" C ALA D 93 " pdb=" CB ALA D 93 " both_signs ideal model delta sigma weight residual False 2.48 2.19 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CA ALA G 93 " pdb=" N ALA G 93 " pdb=" C ALA G 93 " pdb=" CB ALA G 93 " both_signs ideal model delta sigma weight residual False 2.48 2.19 0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 2333 not shown) Planarity restraints: 2512 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO D 59 " -0.030 5.00e-02 4.00e+02 4.57e-02 3.34e+00 pdb=" N PRO D 60 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO D 60 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 60 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 59 " 0.030 5.00e-02 4.00e+02 4.56e-02 3.33e+00 pdb=" N PRO B 60 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 60 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 60 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 59 " 0.030 5.00e-02 4.00e+02 4.55e-02 3.32e+00 pdb=" N PRO A 60 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 60 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 60 " 0.026 5.00e-02 4.00e+02 ... (remaining 2509 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 4363 2.82 - 3.34: 14844 3.34 - 3.86: 23737 3.86 - 4.38: 24593 4.38 - 4.90: 45157 Nonbonded interactions: 112694 Sorted by model distance: nonbonded pdb=" OH TYR H 68 " pdb=" OG1 THR H 103 " model vdw 2.299 2.440 nonbonded pdb=" OH TYR F 68 " pdb=" OG1 THR F 103 " model vdw 2.299 2.440 nonbonded pdb=" OH TYR B 68 " pdb=" OG1 THR B 103 " model vdw 2.299 2.440 nonbonded pdb=" OH TYR A 68 " pdb=" OG1 THR A 103 " model vdw 2.300 2.440 nonbonded pdb=" OH TYR G 68 " pdb=" OG1 THR G 103 " model vdw 2.300 2.440 ... (remaining 112689 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 1.040 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: 0.010 Extract box with map and model: 4.510 Check model and map are aligned: 0.210 Set scattering table: 0.140 Process input model: 40.320 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 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 : 0.004 0.039 15024 Z= 0.233 Angle : 0.580 7.601 20352 Z= 0.358 Chirality : 0.042 0.296 2336 Planarity : 0.004 0.046 2504 Dihedral : 14.338 84.992 5456 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.00 % Allowed : 17.89 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.19), residues: 1792 helix: 0.79 (0.13), residues: 1416 sheet: None (None), residues: 0 loop : -3.07 (0.27), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 62 HIS 0.002 0.000 HIS H 220 PHE 0.007 0.001 PHE H 64 TYR 0.008 0.001 TYR H 177 ARG 0.002 0.000 ARG B 201 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 509 time to evaluate : 1.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.5776 (tm-30) cc_final: 0.5486 (tp40) REVERT: A 46 ASP cc_start: 0.8746 (m-30) cc_final: 0.8390 (m-30) REVERT: A 71 ASN cc_start: 0.8435 (t0) cc_final: 0.8185 (t0) REVERT: A 79 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7484 (tp30) REVERT: A 82 LYS cc_start: 0.8306 (tttt) cc_final: 0.8049 (ttmt) REVERT: A 105 ARG cc_start: 0.7954 (mpt180) cc_final: 0.7695 (tpp-160) REVERT: A 148 LYS cc_start: 0.8429 (mppt) cc_final: 0.7630 (ttmm) REVERT: A 165 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7096 (mp0) REVERT: A 238 LYS cc_start: 0.6739 (mtmm) cc_final: 0.6464 (mtmt) REVERT: B 38 GLU cc_start: 0.8027 (tp30) cc_final: 0.7704 (tp30) REVERT: B 46 ASP cc_start: 0.8770 (m-30) cc_final: 0.8161 (m-30) REVERT: B 73 ASN cc_start: 0.8313 (p0) cc_final: 0.8043 (p0) REVERT: B 79 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7530 (tp30) REVERT: B 82 LYS cc_start: 0.8451 (tttt) cc_final: 0.7891 (tptp) REVERT: B 105 ARG cc_start: 0.7935 (mpt180) cc_final: 0.7673 (tpp-160) REVERT: B 165 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7219 (mp0) REVERT: B 220 HIS cc_start: 0.7986 (m-70) cc_final: 0.7698 (m170) REVERT: C 32 GLN cc_start: 0.5774 (tm-30) cc_final: 0.5486 (tp40) REVERT: C 46 ASP cc_start: 0.8746 (m-30) cc_final: 0.8390 (m-30) REVERT: C 71 ASN cc_start: 0.8436 (t0) cc_final: 0.8181 (t0) REVERT: C 79 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7491 (tp30) REVERT: C 82 LYS cc_start: 0.8308 (tttt) cc_final: 0.8050 (ttmt) REVERT: C 105 ARG cc_start: 0.7953 (mpt180) cc_final: 0.7694 (tpp-160) REVERT: C 148 LYS cc_start: 0.8431 (mppt) cc_final: 0.7633 (ttmm) REVERT: C 165 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7096 (mp0) REVERT: C 238 LYS cc_start: 0.6740 (mtmm) cc_final: 0.6469 (mtmt) REVERT: D 38 GLU cc_start: 0.8028 (tp30) cc_final: 0.7704 (tp30) REVERT: D 46 ASP cc_start: 0.8771 (m-30) cc_final: 0.8156 (m-30) REVERT: D 73 ASN cc_start: 0.8333 (p0) cc_final: 0.8087 (p0) REVERT: D 79 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7535 (tp30) REVERT: D 82 LYS cc_start: 0.8450 (tttt) cc_final: 0.7885 (tptp) REVERT: D 105 ARG cc_start: 0.7933 (mpt180) cc_final: 0.7672 (tpp-160) REVERT: D 165 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7012 (mt-10) REVERT: D 220 HIS cc_start: 0.7989 (m-70) cc_final: 0.7690 (m170) REVERT: E 32 GLN cc_start: 0.5774 (tm-30) cc_final: 0.5486 (tp40) REVERT: E 46 ASP cc_start: 0.8746 (m-30) cc_final: 0.8391 (m-30) REVERT: E 71 ASN cc_start: 0.8437 (t0) cc_final: 0.8183 (t0) REVERT: E 79 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7496 (tp30) REVERT: E 82 LYS cc_start: 0.8308 (tttt) cc_final: 0.8046 (ttmt) REVERT: E 105 ARG cc_start: 0.7953 (mpt180) cc_final: 0.7696 (tpp-160) REVERT: E 148 LYS cc_start: 0.8429 (mppt) cc_final: 0.7631 (ttmm) REVERT: E 165 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7096 (mp0) REVERT: E 238 LYS cc_start: 0.6739 (mtmm) cc_final: 0.6467 (mtmt) REVERT: F 38 GLU cc_start: 0.8023 (tp30) cc_final: 0.7698 (tp30) REVERT: F 46 ASP cc_start: 0.8761 (m-30) cc_final: 0.8157 (m-30) REVERT: F 73 ASN cc_start: 0.8333 (p0) cc_final: 0.8084 (p0) REVERT: F 79 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7539 (tp30) REVERT: F 82 LYS cc_start: 0.8450 (tttt) cc_final: 0.7886 (tptp) REVERT: F 105 ARG cc_start: 0.7921 (mpt180) cc_final: 0.7661 (tpp-160) REVERT: F 148 LYS cc_start: 0.8462 (mppt) cc_final: 0.7848 (tttt) REVERT: F 165 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7020 (mt-10) REVERT: G 32 GLN cc_start: 0.5776 (tm-30) cc_final: 0.5485 (tp40) REVERT: G 46 ASP cc_start: 0.8745 (m-30) cc_final: 0.8389 (m-30) REVERT: G 71 ASN cc_start: 0.8438 (t0) cc_final: 0.8183 (t0) REVERT: G 79 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7494 (tp30) REVERT: G 82 LYS cc_start: 0.8307 (tttt) cc_final: 0.8049 (ttmt) REVERT: G 105 ARG cc_start: 0.7953 (mpt180) cc_final: 0.7696 (tpp-160) REVERT: G 148 LYS cc_start: 0.8430 (mppt) cc_final: 0.7631 (ttmm) REVERT: G 165 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7097 (mp0) REVERT: G 238 LYS cc_start: 0.6740 (mtmm) cc_final: 0.6470 (mtmt) REVERT: H 38 GLU cc_start: 0.8023 (tp30) cc_final: 0.7703 (tp30) REVERT: H 46 ASP cc_start: 0.8760 (m-30) cc_final: 0.8155 (m-30) REVERT: H 73 ASN cc_start: 0.8330 (p0) cc_final: 0.8083 (p0) REVERT: H 79 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7538 (tp30) REVERT: H 82 LYS cc_start: 0.8448 (tttt) cc_final: 0.7885 (tptp) REVERT: H 105 ARG cc_start: 0.7922 (mpt180) cc_final: 0.7663 (tpp-160) REVERT: H 148 LYS cc_start: 0.8463 (mppt) cc_final: 0.7850 (tttt) REVERT: H 165 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7017 (mt-10) outliers start: 0 outliers final: 0 residues processed: 509 average time/residue: 0.3397 time to fit residues: 233.0542 Evaluate side-chains 339 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 339 time to evaluate : 1.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 1.9990 chunk 139 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 144 optimal weight: 0.3980 chunk 55 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 167 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 HIS B 236 HIS C 236 HIS E 236 HIS F 236 HIS G 236 HIS H 236 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15024 Z= 0.219 Angle : 0.509 5.498 20352 Z= 0.267 Chirality : 0.037 0.126 2336 Planarity : 0.004 0.044 2504 Dihedral : 4.348 23.429 2144 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.58 % Allowed : 20.99 % Favored : 77.43 % 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: 1.87 (0.20), residues: 1792 helix: 2.11 (0.14), residues: 1408 sheet: None (None), residues: 0 loop : -2.24 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 62 HIS 0.005 0.002 HIS A 236 PHE 0.007 0.001 PHE D 124 TYR 0.008 0.001 TYR F 142 ARG 0.001 0.000 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 343 time to evaluate : 1.748 Fit side-chains REVERT: A 32 GLN cc_start: 0.5763 (tm-30) cc_final: 0.5432 (tp40) REVERT: A 46 ASP cc_start: 0.8757 (m-30) cc_final: 0.8405 (m-30) REVERT: A 71 ASN cc_start: 0.8599 (t0) cc_final: 0.8153 (t0) REVERT: A 105 ARG cc_start: 0.7872 (mpt180) cc_final: 0.7634 (tpp-160) REVERT: A 143 GLN cc_start: 0.7507 (mm110) cc_final: 0.7279 (mm110) REVERT: A 148 LYS cc_start: 0.8383 (mppt) cc_final: 0.7727 (ttmt) REVERT: A 165 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7163 (mp0) REVERT: B 38 GLU cc_start: 0.8101 (tp30) cc_final: 0.7727 (tp30) REVERT: B 46 ASP cc_start: 0.8771 (m-30) cc_final: 0.8165 (m-30) REVERT: B 71 ASN cc_start: 0.8741 (t0) cc_final: 0.8521 (t0) REVERT: B 73 ASN cc_start: 0.8688 (p0) cc_final: 0.8359 (p0) REVERT: B 105 ARG cc_start: 0.7969 (mpt180) cc_final: 0.7652 (tpp-160) REVERT: B 148 LYS cc_start: 0.8455 (mmtm) cc_final: 0.7898 (tttt) REVERT: B 165 GLU cc_start: 0.7737 (mt-10) cc_final: 0.6962 (mt-10) REVERT: C 32 GLN cc_start: 0.5764 (tm-30) cc_final: 0.5432 (tp40) REVERT: C 46 ASP cc_start: 0.8756 (m-30) cc_final: 0.8404 (m-30) REVERT: C 71 ASN cc_start: 0.8594 (t0) cc_final: 0.8149 (t0) REVERT: C 105 ARG cc_start: 0.7866 (mpt180) cc_final: 0.7630 (tpp-160) REVERT: C 143 GLN cc_start: 0.7508 (mm110) cc_final: 0.7280 (mm110) REVERT: C 148 LYS cc_start: 0.8386 (mppt) cc_final: 0.7729 (ttmt) REVERT: C 165 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7163 (mp0) REVERT: D 38 GLU cc_start: 0.8100 (tp30) cc_final: 0.7726 (tp30) REVERT: D 46 ASP cc_start: 0.8770 (m-30) cc_final: 0.8163 (m-30) REVERT: D 71 ASN cc_start: 0.8738 (t0) cc_final: 0.8517 (t0) REVERT: D 73 ASN cc_start: 0.8684 (p0) cc_final: 0.8362 (p0) REVERT: D 105 ARG cc_start: 0.7968 (mpt180) cc_final: 0.7650 (tpp-160) REVERT: D 148 LYS cc_start: 0.8378 (mmtm) cc_final: 0.7822 (tttt) REVERT: D 165 GLU cc_start: 0.7742 (mt-10) cc_final: 0.6965 (mt-10) REVERT: E 32 GLN cc_start: 0.5758 (tm-30) cc_final: 0.5429 (tp40) REVERT: E 46 ASP cc_start: 0.8754 (m-30) cc_final: 0.8403 (m-30) REVERT: E 71 ASN cc_start: 0.8594 (t0) cc_final: 0.8149 (t0) REVERT: E 105 ARG cc_start: 0.7870 (mpt180) cc_final: 0.7632 (tpp-160) REVERT: E 143 GLN cc_start: 0.7509 (mm110) cc_final: 0.7279 (mm110) REVERT: E 148 LYS cc_start: 0.8384 (mppt) cc_final: 0.7728 (ttmt) REVERT: E 165 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7165 (mp0) REVERT: F 46 ASP cc_start: 0.8773 (m-30) cc_final: 0.8169 (m-30) REVERT: F 71 ASN cc_start: 0.8741 (t0) cc_final: 0.8520 (t0) REVERT: F 73 ASN cc_start: 0.8684 (p0) cc_final: 0.8362 (p0) REVERT: F 105 ARG cc_start: 0.7965 (mpt180) cc_final: 0.7649 (tpp-160) REVERT: F 148 LYS cc_start: 0.8339 (mppt) cc_final: 0.7909 (tttt) REVERT: F 165 GLU cc_start: 0.7740 (mt-10) cc_final: 0.6964 (mt-10) REVERT: F 220 HIS cc_start: 0.7913 (m-70) cc_final: 0.7682 (m170) REVERT: G 32 GLN cc_start: 0.5760 (tm-30) cc_final: 0.5430 (tp40) REVERT: G 46 ASP cc_start: 0.8756 (m-30) cc_final: 0.8404 (m-30) REVERT: G 71 ASN cc_start: 0.8596 (t0) cc_final: 0.8149 (t0) REVERT: G 105 ARG cc_start: 0.7886 (mpt180) cc_final: 0.7648 (tpp-160) REVERT: G 143 GLN cc_start: 0.7510 (mm110) cc_final: 0.7281 (mm110) REVERT: G 148 LYS cc_start: 0.8384 (mppt) cc_final: 0.7727 (ttmt) REVERT: G 165 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7165 (mp0) REVERT: H 38 GLU cc_start: 0.8101 (tp30) cc_final: 0.7573 (tp30) REVERT: H 46 ASP cc_start: 0.8772 (m-30) cc_final: 0.8167 (m-30) REVERT: H 71 ASN cc_start: 0.8742 (t0) cc_final: 0.8520 (t0) REVERT: H 73 ASN cc_start: 0.8685 (p0) cc_final: 0.8360 (p0) REVERT: H 105 ARG cc_start: 0.7971 (mpt180) cc_final: 0.7652 (tpp-160) REVERT: H 148 LYS cc_start: 0.8343 (mppt) cc_final: 0.7916 (tttt) REVERT: H 165 GLU cc_start: 0.7734 (mt-10) cc_final: 0.6957 (mt-10) REVERT: H 220 HIS cc_start: 0.7908 (m-70) cc_final: 0.7676 (m170) outliers start: 24 outliers final: 10 residues processed: 353 average time/residue: 0.2947 time to fit residues: 146.3545 Evaluate side-chains 340 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 330 time to evaluate : 1.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 181 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 139 optimal weight: 7.9990 chunk 113 optimal weight: 1.9990 chunk 46 optimal weight: 9.9990 chunk 167 optimal weight: 0.4980 chunk 180 optimal weight: 3.9990 chunk 149 optimal weight: 0.0980 chunk 165 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 134 optimal weight: 9.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN C 71 ASN E 71 ASN G 71 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15024 Z= 0.164 Angle : 0.472 5.498 20352 Z= 0.247 Chirality : 0.036 0.122 2336 Planarity : 0.004 0.044 2504 Dihedral : 3.800 19.359 2144 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.92 % Allowed : 20.86 % Favored : 78.22 % 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: 2.61 (0.21), residues: 1792 helix: 2.62 (0.14), residues: 1416 sheet: None (None), residues: 0 loop : -2.02 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 62 HIS 0.003 0.001 HIS B 220 PHE 0.006 0.001 PHE G 64 TYR 0.022 0.001 TYR A 142 ARG 0.001 0.000 ARG B 226 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 407 time to evaluate : 2.204 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.5934 (tm-30) cc_final: 0.5618 (tp40) REVERT: A 46 ASP cc_start: 0.8812 (m-30) cc_final: 0.8474 (m-30) REVERT: A 71 ASN cc_start: 0.8611 (OUTLIER) cc_final: 0.8299 (t0) REVERT: A 79 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7431 (tp30) REVERT: A 105 ARG cc_start: 0.7852 (mpt180) cc_final: 0.7615 (tpp-160) REVERT: A 143 GLN cc_start: 0.7899 (mm110) cc_final: 0.7477 (mm110) REVERT: A 148 LYS cc_start: 0.8287 (mppt) cc_final: 0.7728 (ttmm) REVERT: A 165 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7121 (mp0) REVERT: B 46 ASP cc_start: 0.8772 (m-30) cc_final: 0.8282 (m-30) REVERT: B 71 ASN cc_start: 0.8719 (t0) cc_final: 0.8440 (t0) REVERT: B 73 ASN cc_start: 0.8722 (p0) cc_final: 0.8351 (p0) REVERT: B 79 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7483 (tp30) REVERT: B 105 ARG cc_start: 0.7961 (mpt180) cc_final: 0.7649 (tpp-160) REVERT: B 148 LYS cc_start: 0.8309 (mmtm) cc_final: 0.7899 (tttt) REVERT: B 165 GLU cc_start: 0.7642 (mt-10) cc_final: 0.6941 (mt-10) REVERT: B 167 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7420 (mp0) REVERT: B 220 HIS cc_start: 0.7971 (m-70) cc_final: 0.7764 (m170) REVERT: C 32 GLN cc_start: 0.5936 (tm-30) cc_final: 0.5620 (tp40) REVERT: C 46 ASP cc_start: 0.8813 (m-30) cc_final: 0.8474 (m-30) REVERT: C 71 ASN cc_start: 0.8610 (OUTLIER) cc_final: 0.8300 (t0) REVERT: C 79 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7440 (tp30) REVERT: C 105 ARG cc_start: 0.7848 (mpt180) cc_final: 0.7611 (tpp-160) REVERT: C 143 GLN cc_start: 0.7899 (mm110) cc_final: 0.7476 (mm110) REVERT: C 148 LYS cc_start: 0.8291 (mppt) cc_final: 0.7731 (ttmm) REVERT: C 165 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7123 (mp0) REVERT: D 46 ASP cc_start: 0.8770 (m-30) cc_final: 0.8277 (m-30) REVERT: D 71 ASN cc_start: 0.8715 (t0) cc_final: 0.8435 (t0) REVERT: D 73 ASN cc_start: 0.8713 (p0) cc_final: 0.8350 (p0) REVERT: D 79 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7491 (tp30) REVERT: D 105 ARG cc_start: 0.7945 (mpt180) cc_final: 0.7631 (tpp-160) REVERT: D 148 LYS cc_start: 0.8311 (mmtm) cc_final: 0.7828 (tttt) REVERT: D 165 GLU cc_start: 0.7652 (mt-10) cc_final: 0.6947 (mt-10) REVERT: D 167 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7365 (mp0) REVERT: D 220 HIS cc_start: 0.7966 (m-70) cc_final: 0.7752 (m170) REVERT: E 32 GLN cc_start: 0.5933 (tm-30) cc_final: 0.5619 (tp40) REVERT: E 46 ASP cc_start: 0.8812 (m-30) cc_final: 0.8473 (m-30) REVERT: E 71 ASN cc_start: 0.8610 (OUTLIER) cc_final: 0.8299 (t0) REVERT: E 79 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7443 (tp30) REVERT: E 105 ARG cc_start: 0.7850 (mpt180) cc_final: 0.7612 (tpp-160) REVERT: E 143 GLN cc_start: 0.7899 (mm110) cc_final: 0.7475 (mm110) REVERT: E 148 LYS cc_start: 0.8288 (mppt) cc_final: 0.7729 (ttmm) REVERT: E 165 GLU cc_start: 0.7551 (mt-10) cc_final: 0.7125 (mp0) REVERT: F 46 ASP cc_start: 0.8774 (m-30) cc_final: 0.8284 (m-30) REVERT: F 71 ASN cc_start: 0.8717 (t0) cc_final: 0.8436 (t0) REVERT: F 73 ASN cc_start: 0.8714 (p0) cc_final: 0.8349 (p0) REVERT: F 79 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7494 (tp30) REVERT: F 105 ARG cc_start: 0.7947 (mpt180) cc_final: 0.7632 (tpp-160) REVERT: F 147 GLN cc_start: 0.7498 (mm110) cc_final: 0.7166 (mm-40) REVERT: F 148 LYS cc_start: 0.8279 (mppt) cc_final: 0.7896 (tttt) REVERT: F 165 GLU cc_start: 0.7654 (mt-10) cc_final: 0.6950 (mt-10) REVERT: F 167 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7439 (mp0) REVERT: F 220 HIS cc_start: 0.7971 (m-70) cc_final: 0.7741 (m170) REVERT: G 32 GLN cc_start: 0.5934 (tm-30) cc_final: 0.5619 (tp40) REVERT: G 46 ASP cc_start: 0.8810 (m-30) cc_final: 0.8471 (m-30) REVERT: G 71 ASN cc_start: 0.8612 (OUTLIER) cc_final: 0.7943 (t0) REVERT: G 79 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7444 (tp30) REVERT: G 105 ARG cc_start: 0.7849 (mpt180) cc_final: 0.7608 (tpp-160) REVERT: G 143 GLN cc_start: 0.7899 (mm110) cc_final: 0.7476 (mm110) REVERT: G 148 LYS cc_start: 0.8283 (mppt) cc_final: 0.7716 (ttmm) REVERT: G 165 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7121 (mp0) REVERT: H 46 ASP cc_start: 0.8771 (m-30) cc_final: 0.8283 (m-30) REVERT: H 71 ASN cc_start: 0.8718 (t0) cc_final: 0.8437 (t0) REVERT: H 73 ASN cc_start: 0.8715 (p0) cc_final: 0.8349 (p0) REVERT: H 79 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7542 (tp30) REVERT: H 105 ARG cc_start: 0.7962 (mpt180) cc_final: 0.7647 (tpp-160) REVERT: H 147 GLN cc_start: 0.7609 (mm110) cc_final: 0.7288 (mm-40) REVERT: H 148 LYS cc_start: 0.8279 (mppt) cc_final: 0.7900 (tttt) REVERT: H 165 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7325 (mt-10) REVERT: H 167 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7470 (mp0) REVERT: H 220 HIS cc_start: 0.7969 (m-70) cc_final: 0.7743 (m170) outliers start: 14 outliers final: 5 residues processed: 407 average time/residue: 0.2907 time to fit residues: 168.4003 Evaluate side-chains 365 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 356 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 71 ASN Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 71 ASN Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 71 ASN Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 71 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 112 optimal weight: 8.9990 chunk 167 optimal weight: 0.5980 chunk 177 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15024 Z= 0.239 Angle : 0.496 5.626 20352 Z= 0.260 Chirality : 0.037 0.126 2336 Planarity : 0.004 0.046 2504 Dihedral : 3.639 15.899 2144 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.97 % Allowed : 19.74 % Favored : 78.29 % 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: 2.81 (0.20), residues: 1792 helix: 2.72 (0.13), residues: 1416 sheet: None (None), residues: 0 loop : -1.77 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 62 HIS 0.005 0.001 HIS A 220 PHE 0.006 0.001 PHE F 124 TYR 0.021 0.001 TYR A 142 ARG 0.001 0.000 ARG A 204 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 358 time to evaluate : 1.817 Fit side-chains revert: symmetry clash REVERT: A 32 GLN cc_start: 0.5796 (tm-30) cc_final: 0.5523 (tp40) REVERT: A 46 ASP cc_start: 0.8828 (m-30) cc_final: 0.8491 (m-30) REVERT: A 79 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7456 (tp30) REVERT: A 105 ARG cc_start: 0.7869 (mpt180) cc_final: 0.7626 (tpp-160) REVERT: A 143 GLN cc_start: 0.7971 (mm110) cc_final: 0.7545 (mm110) REVERT: A 148 LYS cc_start: 0.8170 (mppt) cc_final: 0.7607 (ttmm) REVERT: A 164 GLU cc_start: 0.7660 (pm20) cc_final: 0.7092 (pm20) REVERT: A 165 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7123 (mp0) REVERT: B 38 GLU cc_start: 0.8180 (tp30) cc_final: 0.7814 (tp30) REVERT: B 46 ASP cc_start: 0.8781 (m-30) cc_final: 0.8284 (m-30) REVERT: B 71 ASN cc_start: 0.8631 (t0) cc_final: 0.8314 (t0) REVERT: B 73 ASN cc_start: 0.8748 (p0) cc_final: 0.8379 (p0) REVERT: B 105 ARG cc_start: 0.8049 (mpt180) cc_final: 0.7753 (tpp-160) REVERT: B 147 GLN cc_start: 0.7706 (mm110) cc_final: 0.7325 (mm-40) REVERT: B 148 LYS cc_start: 0.8210 (mmtm) cc_final: 0.7852 (tttt) REVERT: B 165 GLU cc_start: 0.7679 (mt-10) cc_final: 0.6937 (mt-10) REVERT: B 220 HIS cc_start: 0.7955 (m-70) cc_final: 0.7725 (m170) REVERT: C 32 GLN cc_start: 0.5798 (tm-30) cc_final: 0.5523 (tp40) REVERT: C 46 ASP cc_start: 0.8826 (m-30) cc_final: 0.8493 (m-30) REVERT: C 79 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7485 (tp30) REVERT: C 105 ARG cc_start: 0.7864 (mpt180) cc_final: 0.7623 (tpp-160) REVERT: C 143 GLN cc_start: 0.7971 (mm110) cc_final: 0.7544 (mm110) REVERT: C 148 LYS cc_start: 0.8174 (mppt) cc_final: 0.7608 (ttmm) REVERT: C 164 GLU cc_start: 0.7661 (pm20) cc_final: 0.7092 (pm20) REVERT: C 165 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7125 (mp0) REVERT: D 38 GLU cc_start: 0.8181 (tp30) cc_final: 0.7815 (tp30) REVERT: D 46 ASP cc_start: 0.8778 (m-30) cc_final: 0.8282 (m-30) REVERT: D 71 ASN cc_start: 0.8628 (t0) cc_final: 0.8312 (t0) REVERT: D 73 ASN cc_start: 0.8738 (p0) cc_final: 0.8378 (p0) REVERT: D 79 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7482 (tp30) REVERT: D 105 ARG cc_start: 0.8026 (mpt180) cc_final: 0.7730 (tpp-160) REVERT: D 147 GLN cc_start: 0.7730 (mm110) cc_final: 0.7322 (mm-40) REVERT: D 148 LYS cc_start: 0.8246 (mmtm) cc_final: 0.7798 (tttt) REVERT: D 164 GLU cc_start: 0.7770 (pm20) cc_final: 0.7024 (pm20) REVERT: D 165 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7087 (mp0) REVERT: D 220 HIS cc_start: 0.7948 (m-70) cc_final: 0.7715 (m170) REVERT: E 32 GLN cc_start: 0.5795 (tm-30) cc_final: 0.5523 (tp40) REVERT: E 46 ASP cc_start: 0.8826 (m-30) cc_final: 0.8491 (m-30) REVERT: E 79 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7489 (tp30) REVERT: E 105 ARG cc_start: 0.7868 (mpt180) cc_final: 0.7624 (tpp-160) REVERT: E 143 GLN cc_start: 0.7970 (mm110) cc_final: 0.7544 (mm110) REVERT: E 148 LYS cc_start: 0.8171 (mppt) cc_final: 0.7606 (ttmm) REVERT: E 164 GLU cc_start: 0.7659 (pm20) cc_final: 0.7092 (pm20) REVERT: E 165 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7127 (mp0) REVERT: F 38 GLU cc_start: 0.7961 (tp30) cc_final: 0.7749 (tp30) REVERT: F 46 ASP cc_start: 0.8781 (m-30) cc_final: 0.8286 (m-30) REVERT: F 71 ASN cc_start: 0.8630 (t0) cc_final: 0.8313 (t0) REVERT: F 73 ASN cc_start: 0.8738 (p0) cc_final: 0.8376 (p0) REVERT: F 79 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7445 (tp30) REVERT: F 105 ARG cc_start: 0.8028 (mpt180) cc_final: 0.7731 (tpp-160) REVERT: F 147 GLN cc_start: 0.7641 (mm110) cc_final: 0.7324 (mm-40) REVERT: F 148 LYS cc_start: 0.8216 (mppt) cc_final: 0.7876 (tttt) REVERT: F 164 GLU cc_start: 0.7768 (pm20) cc_final: 0.7018 (pm20) REVERT: F 165 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7079 (mp0) REVERT: F 220 HIS cc_start: 0.7964 (m-70) cc_final: 0.7719 (m170) REVERT: G 32 GLN cc_start: 0.5798 (tm-30) cc_final: 0.5523 (tp40) REVERT: G 46 ASP cc_start: 0.8823 (m-30) cc_final: 0.8487 (m-30) REVERT: G 79 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7488 (tp30) REVERT: G 105 ARG cc_start: 0.7872 (mpt180) cc_final: 0.7632 (tpp-160) REVERT: G 143 GLN cc_start: 0.7970 (mm110) cc_final: 0.7545 (mm110) REVERT: G 148 LYS cc_start: 0.8171 (mppt) cc_final: 0.7607 (ttmm) REVERT: G 164 GLU cc_start: 0.7663 (pm20) cc_final: 0.7093 (pm20) REVERT: G 165 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7125 (mp0) REVERT: H 38 GLU cc_start: 0.8180 (tp30) cc_final: 0.7814 (tp30) REVERT: H 46 ASP cc_start: 0.8779 (m-30) cc_final: 0.8285 (m-30) REVERT: H 71 ASN cc_start: 0.8630 (t0) cc_final: 0.8313 (t0) REVERT: H 73 ASN cc_start: 0.8739 (p0) cc_final: 0.8375 (p0) REVERT: H 105 ARG cc_start: 0.8027 (mpt180) cc_final: 0.7730 (tpp-160) REVERT: H 147 GLN cc_start: 0.7644 (mm110) cc_final: 0.7332 (mm-40) REVERT: H 148 LYS cc_start: 0.8214 (mppt) cc_final: 0.7880 (tttt) REVERT: H 164 GLU cc_start: 0.7768 (pm20) cc_final: 0.6919 (pm20) REVERT: H 165 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7131 (mp0) REVERT: H 220 HIS cc_start: 0.7953 (m-70) cc_final: 0.7712 (m170) outliers start: 30 outliers final: 13 residues processed: 372 average time/residue: 0.2942 time to fit residues: 153.9414 Evaluate side-chains 368 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 355 time to evaluate : 1.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 181 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 chunk 0 optimal weight: 60.0000 chunk 90 optimal weight: 0.6980 chunk 159 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN C 71 ASN E 71 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15024 Z= 0.191 Angle : 0.472 5.534 20352 Z= 0.248 Chirality : 0.036 0.124 2336 Planarity : 0.004 0.045 2504 Dihedral : 3.512 16.304 2144 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.05 % Allowed : 20.20 % Favored : 78.75 % 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: 3.07 (0.20), residues: 1792 helix: 2.91 (0.13), residues: 1416 sheet: None (None), residues: 0 loop : -1.68 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 62 HIS 0.004 0.001 HIS A 220 PHE 0.005 0.001 PHE B 124 TYR 0.015 0.001 TYR A 142 ARG 0.001 0.000 ARG E 204 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 388 time to evaluate : 1.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.5820 (tm-30) cc_final: 0.5572 (tp40) REVERT: A 46 ASP cc_start: 0.8827 (m-30) cc_final: 0.8496 (m-30) REVERT: A 71 ASN cc_start: 0.8474 (OUTLIER) cc_final: 0.7805 (t0) REVERT: A 79 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7446 (tp30) REVERT: A 105 ARG cc_start: 0.7996 (mpt180) cc_final: 0.7737 (tpp-160) REVERT: A 143 GLN cc_start: 0.7969 (mm110) cc_final: 0.7557 (mm110) REVERT: A 148 LYS cc_start: 0.8164 (mppt) cc_final: 0.7630 (ttmm) REVERT: A 164 GLU cc_start: 0.7679 (pm20) cc_final: 0.6980 (pm20) REVERT: A 165 GLU cc_start: 0.7627 (mt-10) cc_final: 0.6996 (mp0) REVERT: B 38 GLU cc_start: 0.8169 (tp30) cc_final: 0.7796 (tp30) REVERT: B 46 ASP cc_start: 0.8779 (m-30) cc_final: 0.8287 (m-30) REVERT: B 71 ASN cc_start: 0.8556 (t0) cc_final: 0.8215 (t0) REVERT: B 73 ASN cc_start: 0.8767 (p0) cc_final: 0.8451 (p0) REVERT: B 79 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7467 (tp30) REVERT: B 105 ARG cc_start: 0.8028 (mpt180) cc_final: 0.7709 (tpp-160) REVERT: B 147 GLN cc_start: 0.7778 (mm110) cc_final: 0.7389 (mm-40) REVERT: B 148 LYS cc_start: 0.8179 (mmtm) cc_final: 0.7811 (tttt) REVERT: B 164 GLU cc_start: 0.7756 (pm20) cc_final: 0.7006 (pm20) REVERT: B 165 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7041 (mp0) REVERT: B 220 HIS cc_start: 0.7953 (m-70) cc_final: 0.7717 (m170) REVERT: C 32 GLN cc_start: 0.5823 (tm-30) cc_final: 0.5574 (tp40) REVERT: C 46 ASP cc_start: 0.8826 (m-30) cc_final: 0.8495 (m-30) REVERT: C 71 ASN cc_start: 0.8477 (OUTLIER) cc_final: 0.7811 (t0) REVERT: C 79 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7453 (tp30) REVERT: C 105 ARG cc_start: 0.7981 (mpt180) cc_final: 0.7725 (tpp-160) REVERT: C 143 GLN cc_start: 0.7969 (mm110) cc_final: 0.7556 (mm110) REVERT: C 148 LYS cc_start: 0.8167 (mppt) cc_final: 0.7631 (ttmm) REVERT: C 164 GLU cc_start: 0.7679 (pm20) cc_final: 0.6978 (pm20) REVERT: C 165 GLU cc_start: 0.7629 (mt-10) cc_final: 0.6997 (mp0) REVERT: D 46 ASP cc_start: 0.8778 (m-30) cc_final: 0.8285 (m-30) REVERT: D 71 ASN cc_start: 0.8554 (t0) cc_final: 0.8214 (t0) REVERT: D 73 ASN cc_start: 0.8754 (p0) cc_final: 0.8445 (p0) REVERT: D 79 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7472 (tp30) REVERT: D 105 ARG cc_start: 0.8025 (mpt180) cc_final: 0.7705 (tpp-160) REVERT: D 147 GLN cc_start: 0.7789 (mm110) cc_final: 0.7375 (mm-40) REVERT: D 148 LYS cc_start: 0.8214 (mmtm) cc_final: 0.7773 (tttt) REVERT: D 164 GLU cc_start: 0.7666 (pm20) cc_final: 0.7001 (pm20) REVERT: D 165 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7089 (mp0) REVERT: D 167 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7412 (mp0) REVERT: D 220 HIS cc_start: 0.7950 (m-70) cc_final: 0.7713 (m170) REVERT: E 32 GLN cc_start: 0.5822 (tm-30) cc_final: 0.5574 (tp40) REVERT: E 46 ASP cc_start: 0.8825 (m-30) cc_final: 0.8494 (m-30) REVERT: E 71 ASN cc_start: 0.8475 (OUTLIER) cc_final: 0.7809 (t0) REVERT: E 79 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7458 (tp30) REVERT: E 105 ARG cc_start: 0.7985 (mpt180) cc_final: 0.7727 (tpp-160) REVERT: E 143 GLN cc_start: 0.7970 (mm110) cc_final: 0.7557 (mm110) REVERT: E 148 LYS cc_start: 0.8163 (mppt) cc_final: 0.7627 (ttmm) REVERT: E 164 GLU cc_start: 0.7679 (pm20) cc_final: 0.6979 (pm20) REVERT: E 165 GLU cc_start: 0.7630 (mt-10) cc_final: 0.6998 (mp0) REVERT: F 38 GLU cc_start: 0.7915 (tp30) cc_final: 0.7688 (tp30) REVERT: F 46 ASP cc_start: 0.8780 (m-30) cc_final: 0.8289 (m-30) REVERT: F 71 ASN cc_start: 0.8556 (t0) cc_final: 0.8214 (t0) REVERT: F 73 ASN cc_start: 0.8755 (p0) cc_final: 0.8444 (p0) REVERT: F 79 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7468 (tp30) REVERT: F 105 ARG cc_start: 0.8051 (mpt180) cc_final: 0.7731 (tpp-160) REVERT: F 147 GLN cc_start: 0.7658 (mm110) cc_final: 0.7369 (mm-40) REVERT: F 148 LYS cc_start: 0.8249 (mppt) cc_final: 0.7895 (tttt) REVERT: F 164 GLU cc_start: 0.7686 (pm20) cc_final: 0.6980 (pm20) REVERT: F 165 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7055 (mp0) REVERT: F 220 HIS cc_start: 0.7933 (m-70) cc_final: 0.7685 (m170) REVERT: G 32 GLN cc_start: 0.5822 (tm-30) cc_final: 0.5574 (tp40) REVERT: G 46 ASP cc_start: 0.8824 (m-30) cc_final: 0.8490 (m-30) REVERT: G 79 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7478 (tp30) REVERT: G 105 ARG cc_start: 0.7991 (mpt180) cc_final: 0.7732 (tpp-160) REVERT: G 143 GLN cc_start: 0.7971 (mm110) cc_final: 0.7559 (mm110) REVERT: G 148 LYS cc_start: 0.8163 (mppt) cc_final: 0.7629 (ttmm) REVERT: G 164 GLU cc_start: 0.7683 (pm20) cc_final: 0.6984 (pm20) REVERT: G 165 GLU cc_start: 0.7627 (mt-10) cc_final: 0.6996 (mp0) REVERT: H 46 ASP cc_start: 0.8779 (m-30) cc_final: 0.8287 (m-30) REVERT: H 71 ASN cc_start: 0.8555 (t0) cc_final: 0.8214 (t0) REVERT: H 73 ASN cc_start: 0.8757 (p0) cc_final: 0.8445 (p0) REVERT: H 79 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7542 (tp30) REVERT: H 105 ARG cc_start: 0.8038 (mpt180) cc_final: 0.7716 (tpp-160) REVERT: H 147 GLN cc_start: 0.7659 (mm110) cc_final: 0.7375 (mm-40) REVERT: H 148 LYS cc_start: 0.8248 (mppt) cc_final: 0.7900 (tttt) REVERT: H 164 GLU cc_start: 0.7664 (pm20) cc_final: 0.7002 (pm20) REVERT: H 165 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7069 (mp0) REVERT: H 167 GLU cc_start: 0.7675 (mm-30) cc_final: 0.7360 (mp0) REVERT: H 220 HIS cc_start: 0.7935 (m-70) cc_final: 0.7689 (m170) outliers start: 16 outliers final: 5 residues processed: 391 average time/residue: 0.2971 time to fit residues: 163.1110 Evaluate side-chains 389 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 381 time to evaluate : 1.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 71 ASN Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 71 ASN Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 71 ASN Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 161 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 0.5980 chunk 160 optimal weight: 10.0000 chunk 35 optimal weight: 0.7980 chunk 104 optimal weight: 0.7980 chunk 43 optimal weight: 9.9990 chunk 178 optimal weight: 1.9990 chunk 147 optimal weight: 0.8980 chunk 82 optimal weight: 10.0000 chunk 14 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15024 Z= 0.172 Angle : 0.463 5.470 20352 Z= 0.243 Chirality : 0.036 0.123 2336 Planarity : 0.004 0.045 2504 Dihedral : 3.420 16.410 2144 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 0.99 % Allowed : 19.87 % Favored : 79.14 % 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: 3.19 (0.20), residues: 1792 helix: 2.98 (0.13), residues: 1416 sheet: None (None), residues: 0 loop : -1.58 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 62 HIS 0.004 0.001 HIS A 220 PHE 0.005 0.001 PHE B 124 TYR 0.016 0.001 TYR A 142 ARG 0.000 0.000 ARG A 204 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 380 time to evaluate : 1.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.5812 (tm-30) cc_final: 0.5572 (tp40) REVERT: A 46 ASP cc_start: 0.8826 (m-30) cc_final: 0.8500 (m-30) REVERT: A 79 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7458 (tp30) REVERT: A 105 ARG cc_start: 0.7999 (mpt180) cc_final: 0.7742 (tpp-160) REVERT: A 143 GLN cc_start: 0.7971 (mm110) cc_final: 0.7542 (mm110) REVERT: A 148 LYS cc_start: 0.8149 (mppt) cc_final: 0.7616 (ttmm) REVERT: A 164 GLU cc_start: 0.7700 (pm20) cc_final: 0.6996 (pm20) REVERT: A 165 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7021 (mp0) REVERT: B 38 GLU cc_start: 0.8141 (tp30) cc_final: 0.7754 (tp30) REVERT: B 46 ASP cc_start: 0.8778 (m-30) cc_final: 0.8287 (m-30) REVERT: B 71 ASN cc_start: 0.8558 (t0) cc_final: 0.8211 (t0) REVERT: B 73 ASN cc_start: 0.8778 (p0) cc_final: 0.8431 (p0) REVERT: B 79 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7448 (tp30) REVERT: B 105 ARG cc_start: 0.8053 (mpt180) cc_final: 0.7719 (tpp-160) REVERT: B 124 PHE cc_start: 0.8292 (OUTLIER) cc_final: 0.7563 (t80) REVERT: B 147 GLN cc_start: 0.7779 (mm110) cc_final: 0.7388 (mm-40) REVERT: B 148 LYS cc_start: 0.8181 (mmtm) cc_final: 0.7883 (tttt) REVERT: B 164 GLU cc_start: 0.7687 (pm20) cc_final: 0.6997 (pm20) REVERT: B 165 GLU cc_start: 0.7645 (mt-10) cc_final: 0.7051 (mp0) REVERT: B 220 HIS cc_start: 0.7971 (m-70) cc_final: 0.7732 (m170) REVERT: C 32 GLN cc_start: 0.5812 (tm-30) cc_final: 0.5572 (tp40) REVERT: C 46 ASP cc_start: 0.8826 (m-30) cc_final: 0.8498 (m-30) REVERT: C 79 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7466 (tp30) REVERT: C 105 ARG cc_start: 0.7995 (mpt180) cc_final: 0.7740 (tpp-160) REVERT: C 143 GLN cc_start: 0.7970 (mm110) cc_final: 0.7539 (mm110) REVERT: C 148 LYS cc_start: 0.8153 (mppt) cc_final: 0.7618 (ttmm) REVERT: C 164 GLU cc_start: 0.7699 (pm20) cc_final: 0.6995 (pm20) REVERT: C 165 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7021 (mp0) REVERT: D 46 ASP cc_start: 0.8775 (m-30) cc_final: 0.8285 (m-30) REVERT: D 71 ASN cc_start: 0.8556 (t0) cc_final: 0.8209 (t0) REVERT: D 73 ASN cc_start: 0.8769 (p0) cc_final: 0.8427 (p0) REVERT: D 79 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7457 (tp30) REVERT: D 105 ARG cc_start: 0.8050 (mpt180) cc_final: 0.7715 (tpp-160) REVERT: D 124 PHE cc_start: 0.8291 (OUTLIER) cc_final: 0.7564 (t80) REVERT: D 147 GLN cc_start: 0.7767 (mm110) cc_final: 0.7355 (mm-40) REVERT: D 148 LYS cc_start: 0.8180 (mmtm) cc_final: 0.7801 (tttt) REVERT: D 164 GLU cc_start: 0.7694 (pm20) cc_final: 0.7038 (pm20) REVERT: D 165 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7086 (mp0) REVERT: D 167 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7366 (mp0) REVERT: D 220 HIS cc_start: 0.7969 (m-70) cc_final: 0.7730 (m170) REVERT: E 32 GLN cc_start: 0.5811 (tm-30) cc_final: 0.5571 (tp40) REVERT: E 46 ASP cc_start: 0.8824 (m-30) cc_final: 0.8498 (m-30) REVERT: E 79 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7471 (tp30) REVERT: E 105 ARG cc_start: 0.7999 (mpt180) cc_final: 0.7741 (tpp-160) REVERT: E 143 GLN cc_start: 0.7971 (mm110) cc_final: 0.7542 (mm110) REVERT: E 148 LYS cc_start: 0.8149 (mppt) cc_final: 0.7616 (ttmm) REVERT: E 164 GLU cc_start: 0.7699 (pm20) cc_final: 0.6994 (pm20) REVERT: E 165 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7024 (mp0) REVERT: F 38 GLU cc_start: 0.7922 (tp30) cc_final: 0.7695 (tp30) REVERT: F 46 ASP cc_start: 0.8778 (m-30) cc_final: 0.8289 (m-30) REVERT: F 71 ASN cc_start: 0.8560 (t0) cc_final: 0.8214 (t0) REVERT: F 73 ASN cc_start: 0.8769 (p0) cc_final: 0.8427 (p0) REVERT: F 79 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7453 (tp30) REVERT: F 105 ARG cc_start: 0.8054 (mpt180) cc_final: 0.7717 (tpp-160) REVERT: F 124 PHE cc_start: 0.8292 (OUTLIER) cc_final: 0.7564 (t80) REVERT: F 147 GLN cc_start: 0.7687 (mm110) cc_final: 0.7414 (mm-40) REVERT: F 148 LYS cc_start: 0.8213 (mppt) cc_final: 0.7876 (tttt) REVERT: F 164 GLU cc_start: 0.7692 (pm20) cc_final: 0.7071 (pm20) REVERT: F 165 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7042 (mp0) REVERT: F 220 HIS cc_start: 0.7952 (m-70) cc_final: 0.7701 (m170) REVERT: G 32 GLN cc_start: 0.5812 (tm-30) cc_final: 0.5573 (tp40) REVERT: G 46 ASP cc_start: 0.8825 (m-30) cc_final: 0.8495 (m-30) REVERT: G 79 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7468 (tp30) REVERT: G 105 ARG cc_start: 0.7999 (mpt180) cc_final: 0.7739 (tpp-160) REVERT: G 143 GLN cc_start: 0.7971 (mm110) cc_final: 0.7541 (mm110) REVERT: G 148 LYS cc_start: 0.8149 (mppt) cc_final: 0.7615 (ttmm) REVERT: G 164 GLU cc_start: 0.7703 (pm20) cc_final: 0.6997 (pm20) REVERT: G 165 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7019 (mp0) REVERT: H 46 ASP cc_start: 0.8777 (m-30) cc_final: 0.8286 (m-30) REVERT: H 71 ASN cc_start: 0.8557 (t0) cc_final: 0.8209 (t0) REVERT: H 73 ASN cc_start: 0.8771 (p0) cc_final: 0.8428 (p0) REVERT: H 79 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7518 (tp30) REVERT: H 105 ARG cc_start: 0.8054 (mpt180) cc_final: 0.7717 (tpp-160) REVERT: H 124 PHE cc_start: 0.8293 (OUTLIER) cc_final: 0.7566 (t80) REVERT: H 147 GLN cc_start: 0.7689 (mm110) cc_final: 0.7419 (mm-40) REVERT: H 148 LYS cc_start: 0.8235 (mppt) cc_final: 0.7913 (tttt) REVERT: H 164 GLU cc_start: 0.7692 (pm20) cc_final: 0.7036 (pm20) REVERT: H 165 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7073 (mp0) REVERT: H 167 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7324 (mp0) REVERT: H 220 HIS cc_start: 0.7937 (m-70) cc_final: 0.7690 (m170) outliers start: 15 outliers final: 11 residues processed: 384 average time/residue: 0.2968 time to fit residues: 159.4032 Evaluate side-chains 391 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 376 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain F residue 124 PHE Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 124 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 101 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 chunk 99 optimal weight: 6.9990 chunk 177 optimal weight: 0.5980 chunk 110 optimal weight: 0.7980 chunk 108 optimal weight: 0.8980 chunk 81 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15024 Z= 0.169 Angle : 0.462 5.491 20352 Z= 0.242 Chirality : 0.036 0.122 2336 Planarity : 0.004 0.046 2504 Dihedral : 3.342 16.228 2144 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.25 % Allowed : 19.54 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.38 (0.20), residues: 1792 helix: 3.05 (0.13), residues: 1432 sheet: None (None), residues: 0 loop : -1.43 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 62 HIS 0.004 0.001 HIS A 220 PHE 0.005 0.001 PHE F 124 TYR 0.016 0.001 TYR A 142 ARG 0.001 0.000 ARG E 204 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 378 time to evaluate : 1.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.5830 (tm-30) cc_final: 0.5576 (tp40) REVERT: A 46 ASP cc_start: 0.8827 (m-30) cc_final: 0.8505 (m-30) REVERT: A 79 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7487 (tp30) REVERT: A 105 ARG cc_start: 0.8020 (mpt180) cc_final: 0.7754 (tpp-160) REVERT: A 143 GLN cc_start: 0.7977 (mm110) cc_final: 0.7651 (mm-40) REVERT: A 148 LYS cc_start: 0.8116 (mppt) cc_final: 0.7604 (ttmm) REVERT: A 164 GLU cc_start: 0.7686 (pm20) cc_final: 0.6777 (pm20) REVERT: A 165 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7323 (mp0) REVERT: B 46 ASP cc_start: 0.8770 (m-30) cc_final: 0.8292 (m-30) REVERT: B 73 ASN cc_start: 0.8773 (p0) cc_final: 0.8506 (p0) REVERT: B 79 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7455 (tp30) REVERT: B 105 ARG cc_start: 0.8052 (mpt180) cc_final: 0.7720 (tpp-160) REVERT: B 124 PHE cc_start: 0.8275 (OUTLIER) cc_final: 0.7551 (t80) REVERT: B 147 GLN cc_start: 0.7819 (mm110) cc_final: 0.7423 (mm-40) REVERT: B 148 LYS cc_start: 0.8117 (mmtm) cc_final: 0.7836 (tttt) REVERT: B 164 GLU cc_start: 0.7701 (pm20) cc_final: 0.6995 (pm20) REVERT: B 165 GLU cc_start: 0.7634 (mt-10) cc_final: 0.7180 (mp0) REVERT: B 167 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7360 (mp0) REVERT: B 220 HIS cc_start: 0.7958 (m-70) cc_final: 0.7720 (m170) REVERT: C 32 GLN cc_start: 0.5831 (tm-30) cc_final: 0.5576 (tp40) REVERT: C 46 ASP cc_start: 0.8826 (m-30) cc_final: 0.8503 (m-30) REVERT: C 79 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7494 (tp30) REVERT: C 105 ARG cc_start: 0.8009 (mpt180) cc_final: 0.7745 (tpp-160) REVERT: C 143 GLN cc_start: 0.7978 (mm110) cc_final: 0.7651 (mm-40) REVERT: C 148 LYS cc_start: 0.8118 (mppt) cc_final: 0.7604 (ttmm) REVERT: C 164 GLU cc_start: 0.7684 (pm20) cc_final: 0.6777 (pm20) REVERT: C 165 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7322 (mp0) REVERT: D 46 ASP cc_start: 0.8768 (m-30) cc_final: 0.8290 (m-30) REVERT: D 71 ASN cc_start: 0.8518 (OUTLIER) cc_final: 0.8184 (t0) REVERT: D 73 ASN cc_start: 0.8762 (p0) cc_final: 0.8350 (p0) REVERT: D 79 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7472 (tp30) REVERT: D 105 ARG cc_start: 0.8054 (mpt180) cc_final: 0.7712 (tpp-160) REVERT: D 124 PHE cc_start: 0.8274 (OUTLIER) cc_final: 0.7551 (t80) REVERT: D 147 GLN cc_start: 0.7816 (mm110) cc_final: 0.7406 (mm-40) REVERT: D 148 LYS cc_start: 0.8092 (mmtm) cc_final: 0.7757 (tttt) REVERT: D 164 GLU cc_start: 0.7727 (pm20) cc_final: 0.7022 (pm20) REVERT: D 165 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7203 (mp0) REVERT: D 167 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7361 (mp0) REVERT: D 220 HIS cc_start: 0.7958 (m-70) cc_final: 0.7724 (m170) REVERT: E 32 GLN cc_start: 0.5830 (tm-30) cc_final: 0.5574 (tp40) REVERT: E 46 ASP cc_start: 0.8826 (m-30) cc_final: 0.8504 (m-30) REVERT: E 79 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7499 (tp30) REVERT: E 105 ARG cc_start: 0.8013 (mpt180) cc_final: 0.7748 (tpp-160) REVERT: E 143 GLN cc_start: 0.7978 (mm110) cc_final: 0.7651 (mm-40) REVERT: E 148 LYS cc_start: 0.8114 (mppt) cc_final: 0.7601 (ttmm) REVERT: E 164 GLU cc_start: 0.7685 (pm20) cc_final: 0.6778 (pm20) REVERT: E 165 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7322 (mp0) REVERT: F 38 GLU cc_start: 0.7976 (tp30) cc_final: 0.7712 (tp30) REVERT: F 46 ASP cc_start: 0.8770 (m-30) cc_final: 0.8294 (m-30) REVERT: F 71 ASN cc_start: 0.8530 (OUTLIER) cc_final: 0.8195 (t0) REVERT: F 73 ASN cc_start: 0.8762 (p0) cc_final: 0.8352 (p0) REVERT: F 79 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7451 (tp30) REVERT: F 105 ARG cc_start: 0.8062 (mpt180) cc_final: 0.7737 (tpp-160) REVERT: F 124 PHE cc_start: 0.8274 (OUTLIER) cc_final: 0.7551 (t80) REVERT: F 143 GLN cc_start: 0.8160 (mt0) cc_final: 0.7887 (mm110) REVERT: F 147 GLN cc_start: 0.7718 (mm110) cc_final: 0.7460 (mm-40) REVERT: F 148 LYS cc_start: 0.8223 (mppt) cc_final: 0.7849 (tttt) REVERT: F 164 GLU cc_start: 0.7722 (pm20) cc_final: 0.7003 (pm20) REVERT: F 165 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7160 (mp0) REVERT: F 220 HIS cc_start: 0.7957 (m-70) cc_final: 0.7708 (m170) REVERT: G 32 GLN cc_start: 0.5831 (tm-30) cc_final: 0.5574 (tp40) REVERT: G 46 ASP cc_start: 0.8826 (m-30) cc_final: 0.8500 (m-30) REVERT: G 79 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7497 (tp30) REVERT: G 105 ARG cc_start: 0.8020 (mpt180) cc_final: 0.7752 (tpp-160) REVERT: G 143 GLN cc_start: 0.7977 (mm110) cc_final: 0.7651 (mm-40) REVERT: G 148 LYS cc_start: 0.8115 (mppt) cc_final: 0.7603 (ttmm) REVERT: G 164 GLU cc_start: 0.7708 (pm20) cc_final: 0.6812 (pm20) REVERT: G 165 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7323 (mp0) REVERT: H 46 ASP cc_start: 0.8778 (m-30) cc_final: 0.8287 (m-30) REVERT: H 71 ASN cc_start: 0.8528 (OUTLIER) cc_final: 0.8192 (t0) REVERT: H 73 ASN cc_start: 0.8765 (p0) cc_final: 0.8350 (p0) REVERT: H 79 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7460 (tp30) REVERT: H 105 ARG cc_start: 0.8063 (mpt180) cc_final: 0.7737 (tpp-160) REVERT: H 124 PHE cc_start: 0.8276 (OUTLIER) cc_final: 0.7552 (t80) REVERT: H 147 GLN cc_start: 0.7703 (mm110) cc_final: 0.7444 (mm-40) REVERT: H 148 LYS cc_start: 0.8222 (mppt) cc_final: 0.7879 (tttt) REVERT: H 164 GLU cc_start: 0.7723 (pm20) cc_final: 0.7020 (pm20) REVERT: H 165 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7184 (mp0) REVERT: H 167 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7352 (mp0) REVERT: H 220 HIS cc_start: 0.7941 (m-70) cc_final: 0.7695 (m170) outliers start: 19 outliers final: 11 residues processed: 382 average time/residue: 0.2923 time to fit residues: 156.7013 Evaluate side-chains 392 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 374 time to evaluate : 1.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 71 ASN Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain F residue 71 ASN Chi-restraints excluded: chain F residue 124 PHE Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 71 ASN Chi-restraints excluded: chain H residue 124 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 3.9990 chunk 70 optimal weight: 0.0770 chunk 105 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 34 optimal weight: 0.0870 chunk 112 optimal weight: 7.9990 chunk 120 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 161 optimal weight: 70.0000 overall best weight: 1.0322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15024 Z= 0.206 Angle : 0.476 5.567 20352 Z= 0.250 Chirality : 0.037 0.124 2336 Planarity : 0.004 0.046 2504 Dihedral : 3.345 16.067 2144 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.25 % Allowed : 19.34 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.25 (0.20), residues: 1792 helix: 3.02 (0.13), residues: 1424 sheet: None (None), residues: 0 loop : -1.66 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 62 HIS 0.005 0.001 HIS C 220 PHE 0.006 0.001 PHE F 124 TYR 0.017 0.001 TYR A 142 ARG 0.001 0.000 ARG F 171 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 373 time to evaluate : 1.920 Fit side-chains revert: symmetry clash REVERT: A 32 GLN cc_start: 0.5776 (tm-30) cc_final: 0.5507 (tp40) REVERT: A 46 ASP cc_start: 0.8831 (m-30) cc_final: 0.8505 (m-30) REVERT: A 79 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7489 (tp30) REVERT: A 105 ARG cc_start: 0.8054 (mpt180) cc_final: 0.7849 (tpp-160) REVERT: A 124 PHE cc_start: 0.8233 (OUTLIER) cc_final: 0.7985 (t80) REVERT: A 143 GLN cc_start: 0.7991 (mm110) cc_final: 0.7667 (mm110) REVERT: A 148 LYS cc_start: 0.8137 (mppt) cc_final: 0.7629 (ttmm) REVERT: A 164 GLU cc_start: 0.7665 (pm20) cc_final: 0.7160 (pm20) REVERT: A 165 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7110 (mp0) REVERT: B 46 ASP cc_start: 0.8773 (m-30) cc_final: 0.8288 (m-30) REVERT: B 71 ASN cc_start: 0.8705 (t0) cc_final: 0.8464 (t0) REVERT: B 73 ASN cc_start: 0.8775 (p0) cc_final: 0.8384 (p0) REVERT: B 79 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7474 (tp30) REVERT: B 105 ARG cc_start: 0.8087 (mpt180) cc_final: 0.7520 (ttm-80) REVERT: B 124 PHE cc_start: 0.8342 (OUTLIER) cc_final: 0.7614 (t80) REVERT: B 143 GLN cc_start: 0.8130 (mt0) cc_final: 0.7901 (mm110) REVERT: B 147 GLN cc_start: 0.7812 (mm110) cc_final: 0.7431 (mm-40) REVERT: B 148 LYS cc_start: 0.8083 (mmtm) cc_final: 0.7831 (tttt) REVERT: B 165 GLU cc_start: 0.7640 (mt-10) cc_final: 0.6969 (mt-10) REVERT: B 167 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7364 (mp0) REVERT: B 220 HIS cc_start: 0.7961 (m-70) cc_final: 0.7722 (m170) REVERT: C 32 GLN cc_start: 0.5776 (tm-30) cc_final: 0.5507 (tp40) REVERT: C 46 ASP cc_start: 0.8832 (m-30) cc_final: 0.8506 (m-30) REVERT: C 79 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7492 (tp30) REVERT: C 105 ARG cc_start: 0.8051 (mpt180) cc_final: 0.7754 (tpp-160) REVERT: C 124 PHE cc_start: 0.8232 (OUTLIER) cc_final: 0.7983 (t80) REVERT: C 143 GLN cc_start: 0.7992 (mm110) cc_final: 0.7669 (mm110) REVERT: C 148 LYS cc_start: 0.8140 (mppt) cc_final: 0.7628 (ttmm) REVERT: C 164 GLU cc_start: 0.7665 (pm20) cc_final: 0.6762 (pm20) REVERT: C 165 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7379 (mp0) REVERT: D 46 ASP cc_start: 0.8773 (m-30) cc_final: 0.8288 (m-30) REVERT: D 73 ASN cc_start: 0.8760 (p0) cc_final: 0.8479 (p0) REVERT: D 79 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7507 (tp30) REVERT: D 105 ARG cc_start: 0.8081 (mpt180) cc_final: 0.7520 (ttm-80) REVERT: D 124 PHE cc_start: 0.8344 (OUTLIER) cc_final: 0.7616 (t80) REVERT: D 147 GLN cc_start: 0.7828 (mm110) cc_final: 0.7431 (mm-40) REVERT: D 148 LYS cc_start: 0.8077 (mmtm) cc_final: 0.7773 (tttt) REVERT: D 165 GLU cc_start: 0.7646 (mt-10) cc_final: 0.6963 (mt-10) REVERT: D 167 GLU cc_start: 0.7713 (mm-30) cc_final: 0.7387 (mp0) REVERT: D 220 HIS cc_start: 0.7962 (m-70) cc_final: 0.7726 (m170) REVERT: E 32 GLN cc_start: 0.5760 (tm-30) cc_final: 0.5529 (tp40) REVERT: E 46 ASP cc_start: 0.8831 (m-30) cc_final: 0.8505 (m-30) REVERT: E 79 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7498 (tp30) REVERT: E 105 ARG cc_start: 0.8054 (mpt180) cc_final: 0.7756 (tpp-160) REVERT: E 124 PHE cc_start: 0.8232 (OUTLIER) cc_final: 0.7984 (t80) REVERT: E 143 GLN cc_start: 0.7993 (mm110) cc_final: 0.7669 (mm110) REVERT: E 148 LYS cc_start: 0.8136 (mppt) cc_final: 0.7626 (ttmm) REVERT: E 164 GLU cc_start: 0.7667 (pm20) cc_final: 0.6763 (pm20) REVERT: E 165 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7380 (mp0) REVERT: F 38 GLU cc_start: 0.7994 (tp30) cc_final: 0.7730 (tp30) REVERT: F 46 ASP cc_start: 0.8773 (m-30) cc_final: 0.8289 (m-30) REVERT: F 73 ASN cc_start: 0.8757 (p0) cc_final: 0.8481 (p0) REVERT: F 79 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7456 (tp30) REVERT: F 105 ARG cc_start: 0.8084 (mpt180) cc_final: 0.7513 (ttm-80) REVERT: F 124 PHE cc_start: 0.8343 (OUTLIER) cc_final: 0.7614 (t80) REVERT: F 143 GLN cc_start: 0.8163 (mt0) cc_final: 0.7897 (mm110) REVERT: F 147 GLN cc_start: 0.7754 (mm110) cc_final: 0.7403 (mm110) REVERT: F 148 LYS cc_start: 0.8207 (mppt) cc_final: 0.7825 (tttt) REVERT: F 165 GLU cc_start: 0.7640 (mt-10) cc_final: 0.6917 (mt-10) REVERT: F 220 HIS cc_start: 0.7962 (m-70) cc_final: 0.7711 (m170) REVERT: G 32 GLN cc_start: 0.5778 (tm-30) cc_final: 0.5507 (tp40) REVERT: G 46 ASP cc_start: 0.8831 (m-30) cc_final: 0.8505 (m-30) REVERT: G 79 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7498 (tp30) REVERT: G 105 ARG cc_start: 0.8055 (mpt180) cc_final: 0.7757 (tpp-160) REVERT: G 124 PHE cc_start: 0.8233 (OUTLIER) cc_final: 0.7985 (t80) REVERT: G 143 GLN cc_start: 0.7993 (mm110) cc_final: 0.7668 (mm110) REVERT: G 148 LYS cc_start: 0.8137 (mppt) cc_final: 0.7628 (ttmm) REVERT: G 164 GLU cc_start: 0.7685 (pm20) cc_final: 0.7188 (pm20) REVERT: G 165 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7110 (mp0) REVERT: H 46 ASP cc_start: 0.8772 (m-30) cc_final: 0.8285 (m-30) REVERT: H 73 ASN cc_start: 0.8762 (p0) cc_final: 0.8483 (p0) REVERT: H 79 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7514 (tp30) REVERT: H 105 ARG cc_start: 0.8085 (mpt180) cc_final: 0.7524 (ttm-80) REVERT: H 124 PHE cc_start: 0.8345 (OUTLIER) cc_final: 0.7614 (t80) REVERT: H 140 GLU cc_start: 0.7398 (pp20) cc_final: 0.7150 (pp20) REVERT: H 143 GLN cc_start: 0.8190 (mt0) cc_final: 0.7917 (mm110) REVERT: H 147 GLN cc_start: 0.7756 (mm110) cc_final: 0.7405 (mm110) REVERT: H 148 LYS cc_start: 0.8202 (mppt) cc_final: 0.7824 (tttt) REVERT: H 165 GLU cc_start: 0.7639 (mt-10) cc_final: 0.6957 (mt-10) REVERT: H 167 GLU cc_start: 0.7656 (mm-30) cc_final: 0.7373 (mp0) REVERT: H 220 HIS cc_start: 0.7961 (m-70) cc_final: 0.7718 (m170) outliers start: 19 outliers final: 11 residues processed: 381 average time/residue: 0.2863 time to fit residues: 154.1840 Evaluate side-chains 370 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 351 time to evaluate : 1.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 124 PHE Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain F residue 124 PHE Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 124 PHE Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 124 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 0.6980 chunk 155 optimal weight: 0.9980 chunk 165 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 129 optimal weight: 0.4980 chunk 50 optimal weight: 2.9990 chunk 149 optimal weight: 0.2980 chunk 156 optimal weight: 0.9980 chunk 164 optimal weight: 0.4980 chunk 108 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 236 HIS D 236 HIS F 236 HIS H 236 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15024 Z= 0.155 Angle : 0.456 5.421 20352 Z= 0.238 Chirality : 0.036 0.120 2336 Planarity : 0.004 0.045 2504 Dihedral : 3.287 16.441 2144 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.12 % Allowed : 20.07 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.42 (0.20), residues: 1792 helix: 3.09 (0.13), residues: 1440 sheet: None (None), residues: 0 loop : -1.60 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 62 HIS 0.005 0.001 HIS C 220 PHE 0.005 0.001 PHE G 64 TYR 0.016 0.001 TYR A 142 ARG 0.000 0.000 ARG E 204 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 345 time to evaluate : 1.657 Fit side-chains revert: symmetry clash REVERT: A 32 GLN cc_start: 0.5849 (tm-30) cc_final: 0.5597 (tp40) REVERT: A 46 ASP cc_start: 0.8829 (m-30) cc_final: 0.8506 (m-30) REVERT: A 73 ASN cc_start: 0.8110 (p0) cc_final: 0.7789 (p0) REVERT: A 79 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7481 (tp30) REVERT: A 105 ARG cc_start: 0.8076 (mpt180) cc_final: 0.7764 (tpp-160) REVERT: A 143 GLN cc_start: 0.7937 (mm110) cc_final: 0.7671 (mm-40) REVERT: A 147 GLN cc_start: 0.7624 (mm110) cc_final: 0.7260 (mm110) REVERT: A 148 LYS cc_start: 0.8105 (mppt) cc_final: 0.7571 (ttmm) REVERT: A 164 GLU cc_start: 0.7679 (pm20) cc_final: 0.7093 (pm20) REVERT: A 165 GLU cc_start: 0.7508 (mt-10) cc_final: 0.6870 (mp0) REVERT: B 46 ASP cc_start: 0.8770 (m-30) cc_final: 0.8291 (m-30) REVERT: B 71 ASN cc_start: 0.8705 (t0) cc_final: 0.8469 (t0) REVERT: B 73 ASN cc_start: 0.8734 (p0) cc_final: 0.8308 (p0) REVERT: B 79 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7465 (tp30) REVERT: B 105 ARG cc_start: 0.8074 (mpt180) cc_final: 0.7575 (ttm-80) REVERT: B 124 PHE cc_start: 0.8245 (OUTLIER) cc_final: 0.7518 (t80) REVERT: B 147 GLN cc_start: 0.7816 (mm110) cc_final: 0.7353 (mm110) REVERT: B 148 LYS cc_start: 0.8066 (mmtm) cc_final: 0.7835 (tttt) REVERT: B 165 GLU cc_start: 0.7608 (mt-10) cc_final: 0.6924 (mt-10) REVERT: B 167 GLU cc_start: 0.7625 (mm-30) cc_final: 0.7374 (mp0) REVERT: B 220 HIS cc_start: 0.7970 (m-70) cc_final: 0.7739 (m170) REVERT: C 32 GLN cc_start: 0.5850 (tm-30) cc_final: 0.5596 (tp40) REVERT: C 46 ASP cc_start: 0.8829 (m-30) cc_final: 0.8506 (m-30) REVERT: C 73 ASN cc_start: 0.8112 (p0) cc_final: 0.7793 (p0) REVERT: C 79 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7485 (tp30) REVERT: C 105 ARG cc_start: 0.8073 (mpt180) cc_final: 0.7759 (tpp-160) REVERT: C 143 GLN cc_start: 0.7939 (mm110) cc_final: 0.7671 (mm-40) REVERT: C 147 GLN cc_start: 0.7622 (mm110) cc_final: 0.7257 (mm110) REVERT: C 148 LYS cc_start: 0.8106 (mppt) cc_final: 0.7571 (ttmm) REVERT: C 164 GLU cc_start: 0.7661 (pm20) cc_final: 0.7066 (pm20) REVERT: C 165 GLU cc_start: 0.7509 (mt-10) cc_final: 0.6871 (mp0) REVERT: D 38 GLU cc_start: 0.8113 (tp30) cc_final: 0.7682 (tp30) REVERT: D 46 ASP cc_start: 0.8770 (m-30) cc_final: 0.8291 (m-30) REVERT: D 71 ASN cc_start: 0.8678 (t0) cc_final: 0.8434 (t0) REVERT: D 73 ASN cc_start: 0.8768 (p0) cc_final: 0.8419 (p0) REVERT: D 79 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7464 (tp30) REVERT: D 105 ARG cc_start: 0.8068 (mpt180) cc_final: 0.7521 (ttm-80) REVERT: D 124 PHE cc_start: 0.8246 (OUTLIER) cc_final: 0.7520 (t80) REVERT: D 143 GLN cc_start: 0.8220 (mt0) cc_final: 0.7824 (mm-40) REVERT: D 147 GLN cc_start: 0.7831 (mm110) cc_final: 0.7452 (mm-40) REVERT: D 148 LYS cc_start: 0.8095 (mmtm) cc_final: 0.7800 (tttt) REVERT: D 164 GLU cc_start: 0.7596 (pm20) cc_final: 0.7088 (pm20) REVERT: D 165 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7280 (mp0) REVERT: D 220 HIS cc_start: 0.7986 (m-70) cc_final: 0.7756 (m170) REVERT: E 32 GLN cc_start: 0.5846 (tm-30) cc_final: 0.5595 (tp40) REVERT: E 46 ASP cc_start: 0.8829 (m-30) cc_final: 0.8507 (m-30) REVERT: E 73 ASN cc_start: 0.8104 (p0) cc_final: 0.7787 (p0) REVERT: E 79 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7490 (tp30) REVERT: E 105 ARG cc_start: 0.8076 (mpt180) cc_final: 0.7761 (tpp-160) REVERT: E 143 GLN cc_start: 0.7938 (mm110) cc_final: 0.7672 (mm-40) REVERT: E 147 GLN cc_start: 0.7621 (mm110) cc_final: 0.7258 (mm110) REVERT: E 148 LYS cc_start: 0.8103 (mppt) cc_final: 0.7569 (ttmm) REVERT: E 164 GLU cc_start: 0.7671 (pm20) cc_final: 0.7077 (pm20) REVERT: E 165 GLU cc_start: 0.7511 (mt-10) cc_final: 0.6871 (mp0) REVERT: F 38 GLU cc_start: 0.7965 (tp30) cc_final: 0.7700 (tp30) REVERT: F 46 ASP cc_start: 0.8769 (m-30) cc_final: 0.8292 (m-30) REVERT: F 71 ASN cc_start: 0.8686 (t0) cc_final: 0.8435 (t0) REVERT: F 73 ASN cc_start: 0.8788 (p0) cc_final: 0.8427 (p0) REVERT: F 79 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7441 (tp30) REVERT: F 105 ARG cc_start: 0.8067 (mpt180) cc_final: 0.7524 (ttm-80) REVERT: F 124 PHE cc_start: 0.8246 (OUTLIER) cc_final: 0.7520 (t80) REVERT: F 143 GLN cc_start: 0.8129 (mt0) cc_final: 0.7927 (mm110) REVERT: F 147 GLN cc_start: 0.7762 (mm110) cc_final: 0.7432 (mm110) REVERT: F 148 LYS cc_start: 0.8192 (mppt) cc_final: 0.7836 (tttt) REVERT: F 164 GLU cc_start: 0.7594 (pm20) cc_final: 0.7088 (pm20) REVERT: F 165 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7273 (mp0) REVERT: F 220 HIS cc_start: 0.7983 (m-70) cc_final: 0.7742 (m170) REVERT: G 32 GLN cc_start: 0.5887 (tm-30) cc_final: 0.5635 (tp40) REVERT: G 46 ASP cc_start: 0.8828 (m-30) cc_final: 0.8503 (m-30) REVERT: G 73 ASN cc_start: 0.8074 (p0) cc_final: 0.7707 (p0) REVERT: G 79 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7488 (tp30) REVERT: G 105 ARG cc_start: 0.8065 (mpt180) cc_final: 0.7751 (tpp-160) REVERT: G 143 GLN cc_start: 0.7938 (mm110) cc_final: 0.7679 (mm-40) REVERT: G 147 GLN cc_start: 0.7622 (mm110) cc_final: 0.7259 (mm110) REVERT: G 148 LYS cc_start: 0.8104 (mppt) cc_final: 0.7570 (ttmm) REVERT: G 164 GLU cc_start: 0.7685 (pm20) cc_final: 0.7100 (pm20) REVERT: G 165 GLU cc_start: 0.7512 (mt-10) cc_final: 0.6872 (mp0) REVERT: H 38 GLU cc_start: 0.8112 (tp30) cc_final: 0.7681 (tp30) REVERT: H 46 ASP cc_start: 0.8770 (m-30) cc_final: 0.8292 (m-30) REVERT: H 71 ASN cc_start: 0.8688 (t0) cc_final: 0.8436 (t0) REVERT: H 73 ASN cc_start: 0.8790 (p0) cc_final: 0.8447 (p0) REVERT: H 79 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7503 (tp30) REVERT: H 105 ARG cc_start: 0.8067 (mpt180) cc_final: 0.7522 (ttm-80) REVERT: H 124 PHE cc_start: 0.8247 (OUTLIER) cc_final: 0.7520 (t80) REVERT: H 143 GLN cc_start: 0.8157 (mt0) cc_final: 0.7944 (mm110) REVERT: H 147 GLN cc_start: 0.7765 (mm110) cc_final: 0.7436 (mm110) REVERT: H 148 LYS cc_start: 0.8186 (mppt) cc_final: 0.7825 (tttt) REVERT: H 164 GLU cc_start: 0.7612 (pm20) cc_final: 0.7112 (pm20) REVERT: H 165 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7257 (mp0) REVERT: H 220 HIS cc_start: 0.7964 (m-70) cc_final: 0.7729 (m170) outliers start: 17 outliers final: 12 residues processed: 349 average time/residue: 0.3002 time to fit residues: 146.2146 Evaluate side-chains 348 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 332 time to evaluate : 1.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 142 TYR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain F residue 124 PHE Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 124 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 10.0000 chunk 106 optimal weight: 1.9990 chunk 82 optimal weight: 9.9990 chunk 121 optimal weight: 1.9990 chunk 183 optimal weight: 5.9990 chunk 168 optimal weight: 1.9990 chunk 145 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 112 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 chunk 115 optimal weight: 70.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 236 HIS D 32 GLN D 236 HIS F 32 GLN F 236 HIS G 71 ASN H 32 GLN H 236 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 15024 Z= 0.476 Angle : 0.594 5.920 20352 Z= 0.310 Chirality : 0.042 0.151 2336 Planarity : 0.004 0.049 2504 Dihedral : 3.603 17.916 2144 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.78 % Allowed : 19.47 % Favored : 78.75 % 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: 2.94 (0.20), residues: 1792 helix: 2.79 (0.13), residues: 1424 sheet: None (None), residues: 0 loop : -1.71 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 81 HIS 0.006 0.002 HIS G 220 PHE 0.012 0.002 PHE B 124 TYR 0.018 0.002 TYR G 142 ARG 0.002 0.001 ARG G 179 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 346 time to evaluate : 1.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.5918 (tm-30) cc_final: 0.5623 (tp40) REVERT: A 46 ASP cc_start: 0.8771 (m-30) cc_final: 0.8431 (m-30) REVERT: A 79 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7511 (tp30) REVERT: A 105 ARG cc_start: 0.8107 (mpt180) cc_final: 0.7888 (tpp-160) REVERT: A 124 PHE cc_start: 0.8419 (OUTLIER) cc_final: 0.8175 (t80) REVERT: A 147 GLN cc_start: 0.7713 (mm110) cc_final: 0.7369 (mm110) REVERT: A 148 LYS cc_start: 0.8198 (mppt) cc_final: 0.7689 (ttmm) REVERT: A 164 GLU cc_start: 0.7654 (pm20) cc_final: 0.6936 (pm20) REVERT: A 165 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7124 (mp0) REVERT: B 38 GLU cc_start: 0.8177 (tp30) cc_final: 0.7766 (tp30) REVERT: B 46 ASP cc_start: 0.8793 (m-30) cc_final: 0.8239 (m-30) REVERT: B 71 ASN cc_start: 0.8766 (t0) cc_final: 0.8513 (t0) REVERT: B 73 ASN cc_start: 0.8708 (p0) cc_final: 0.8213 (p0) REVERT: B 79 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7604 (tp30) REVERT: B 105 ARG cc_start: 0.8040 (mpt180) cc_final: 0.7522 (ttm-80) REVERT: B 124 PHE cc_start: 0.8436 (OUTLIER) cc_final: 0.7715 (t80) REVERT: B 147 GLN cc_start: 0.7954 (mm110) cc_final: 0.7496 (mm110) REVERT: B 148 LYS cc_start: 0.8137 (mmtm) cc_final: 0.7864 (tttt) REVERT: B 165 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7438 (mp0) REVERT: C 32 GLN cc_start: 0.5921 (tm-30) cc_final: 0.5624 (tp40) REVERT: C 46 ASP cc_start: 0.8771 (m-30) cc_final: 0.8429 (m-30) REVERT: C 79 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7512 (tp30) REVERT: C 105 ARG cc_start: 0.8101 (mpt180) cc_final: 0.7884 (tpp-160) REVERT: C 124 PHE cc_start: 0.8419 (OUTLIER) cc_final: 0.8175 (t80) REVERT: C 147 GLN cc_start: 0.7710 (mm110) cc_final: 0.7366 (mm110) REVERT: C 148 LYS cc_start: 0.8198 (mppt) cc_final: 0.7689 (ttmm) REVERT: C 164 GLU cc_start: 0.7654 (pm20) cc_final: 0.6936 (pm20) REVERT: C 165 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7122 (mp0) REVERT: D 38 GLU cc_start: 0.8178 (tp30) cc_final: 0.7768 (tp30) REVERT: D 46 ASP cc_start: 0.8793 (m-30) cc_final: 0.8239 (m-30) REVERT: D 71 ASN cc_start: 0.8742 (t0) cc_final: 0.8492 (t0) REVERT: D 73 ASN cc_start: 0.8700 (p0) cc_final: 0.8252 (p0) REVERT: D 79 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7602 (tp30) REVERT: D 105 ARG cc_start: 0.8042 (mpt180) cc_final: 0.7627 (ttm-80) REVERT: D 124 PHE cc_start: 0.8436 (OUTLIER) cc_final: 0.7717 (t80) REVERT: D 143 GLN cc_start: 0.8299 (mt0) cc_final: 0.7865 (mm110) REVERT: D 147 GLN cc_start: 0.7968 (mm110) cc_final: 0.7483 (mm110) REVERT: D 148 LYS cc_start: 0.8091 (mmtm) cc_final: 0.7805 (tttt) REVERT: D 165 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7419 (mp0) REVERT: D 220 HIS cc_start: 0.7931 (m-70) cc_final: 0.7678 (m170) REVERT: E 32 GLN cc_start: 0.5918 (tm-30) cc_final: 0.5623 (tp40) REVERT: E 46 ASP cc_start: 0.8771 (m-30) cc_final: 0.8430 (m-30) REVERT: E 79 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7516 (tp30) REVERT: E 105 ARG cc_start: 0.8094 (mpt180) cc_final: 0.7881 (tpp-160) REVERT: E 124 PHE cc_start: 0.8420 (OUTLIER) cc_final: 0.8177 (t80) REVERT: E 147 GLN cc_start: 0.7710 (mm110) cc_final: 0.7367 (mm110) REVERT: E 148 LYS cc_start: 0.8196 (mppt) cc_final: 0.7688 (ttmm) REVERT: E 164 GLU cc_start: 0.7656 (pm20) cc_final: 0.6936 (pm20) REVERT: E 165 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7124 (mp0) REVERT: F 38 GLU cc_start: 0.8061 (tp30) cc_final: 0.7782 (tp30) REVERT: F 46 ASP cc_start: 0.8794 (m-30) cc_final: 0.8239 (m-30) REVERT: F 71 ASN cc_start: 0.8749 (t0) cc_final: 0.8498 (t0) REVERT: F 73 ASN cc_start: 0.8703 (p0) cc_final: 0.8260 (p0) REVERT: F 79 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7559 (tp30) REVERT: F 105 ARG cc_start: 0.8042 (mpt180) cc_final: 0.7623 (ttm-80) REVERT: F 124 PHE cc_start: 0.8434 (OUTLIER) cc_final: 0.7714 (t80) REVERT: F 143 GLN cc_start: 0.8227 (mt0) cc_final: 0.7870 (mm110) REVERT: F 147 GLN cc_start: 0.7834 (mm110) cc_final: 0.7521 (mm110) REVERT: F 148 LYS cc_start: 0.8238 (mppt) cc_final: 0.7866 (tttt) REVERT: F 165 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7441 (mp0) REVERT: G 32 GLN cc_start: 0.5919 (tm-30) cc_final: 0.5622 (tp40) REVERT: G 46 ASP cc_start: 0.8771 (m-30) cc_final: 0.8427 (m-30) REVERT: G 71 ASN cc_start: 0.8423 (OUTLIER) cc_final: 0.7831 (t0) REVERT: G 79 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7516 (tp30) REVERT: G 105 ARG cc_start: 0.8109 (mpt180) cc_final: 0.7887 (tpp-160) REVERT: G 124 PHE cc_start: 0.8421 (OUTLIER) cc_final: 0.8177 (t80) REVERT: G 147 GLN cc_start: 0.7711 (mm110) cc_final: 0.7365 (mm110) REVERT: G 148 LYS cc_start: 0.8196 (mppt) cc_final: 0.7687 (ttmm) REVERT: G 165 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7422 (mp0) REVERT: H 38 GLU cc_start: 0.8178 (tp30) cc_final: 0.7769 (tp30) REVERT: H 46 ASP cc_start: 0.8792 (m-30) cc_final: 0.8237 (m-30) REVERT: H 71 ASN cc_start: 0.8747 (t0) cc_final: 0.8495 (t0) REVERT: H 73 ASN cc_start: 0.8701 (p0) cc_final: 0.8246 (p0) REVERT: H 79 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7650 (tp30) REVERT: H 105 ARG cc_start: 0.8043 (mpt180) cc_final: 0.7623 (ttm-80) REVERT: H 124 PHE cc_start: 0.8436 (OUTLIER) cc_final: 0.7715 (t80) REVERT: H 143 GLN cc_start: 0.8248 (mt0) cc_final: 0.7886 (mm110) REVERT: H 147 GLN cc_start: 0.7834 (mm110) cc_final: 0.7526 (mm110) REVERT: H 148 LYS cc_start: 0.8233 (mppt) cc_final: 0.7864 (tttt) REVERT: H 165 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7444 (mp0) outliers start: 27 outliers final: 18 residues processed: 357 average time/residue: 0.3201 time to fit residues: 159.0475 Evaluate side-chains 352 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 325 time to evaluate : 1.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 142 TYR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 124 PHE Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 124 PHE Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 71 ASN Chi-restraints excluded: chain G residue 124 PHE Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 124 PHE Chi-restraints excluded: chain H residue 181 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 134 optimal weight: 8.9990 chunk 21 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 146 optimal weight: 0.9980 chunk 61 optimal weight: 0.2980 chunk 150 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 236 HIS D 32 GLN D 236 HIS F 32 GLN F 236 HIS G 71 ASN H 32 GLN H 236 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.159425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.100782 restraints weight = 18099.382| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.35 r_work: 0.2888 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 15024 Z= 0.312 Angle : 0.797 59.181 20352 Z= 0.458 Chirality : 0.040 0.463 2336 Planarity : 0.004 0.049 2504 Dihedral : 3.634 21.935 2144 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.04 % Allowed : 20.13 % Favored : 77.83 % Cbeta Deviations : 0.06 % 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: 2.99 (0.20), residues: 1792 helix: 2.83 (0.13), residues: 1424 sheet: None (None), residues: 0 loop : -1.71 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 81 HIS 0.005 0.001 HIS G 220 PHE 0.010 0.001 PHE B 124 TYR 0.017 0.001 TYR G 142 ARG 0.001 0.000 ARG B 171 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3920.70 seconds wall clock time: 71 minutes 52.75 seconds (4312.75 seconds total)