Starting phenix.real_space_refine on Fri Apr 12 19:40:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d60_30586/04_2024/7d60_30586_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d60_30586/04_2024/7d60_30586.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d60_30586/04_2024/7d60_30586_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d60_30586/04_2024/7d60_30586_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d60_30586/04_2024/7d60_30586_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d60_30586/04_2024/7d60_30586.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d60_30586/04_2024/7d60_30586.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d60_30586/04_2024/7d60_30586_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d60_30586/04_2024/7d60_30586_updated.pdb" } resolution = 2.61 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 55 5.49 5 S 220 5.16 5 C 17303 2.51 5 N 4224 2.21 5 O 4862 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 46": "OE1" <-> "OE2" Residue "A TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 46": "OE1" <-> "OE2" Residue "B TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 46": "OE1" <-> "OE2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 46": "OE1" <-> "OE2" Residue "D TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 46": "OE1" <-> "OE2" Residue "E TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 46": "OE1" <-> "OE2" Residue "F TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 46": "OE1" <-> "OE2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 46": "OE1" <-> "OE2" Residue "I TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 46": "OE1" <-> "OE2" Residue "J TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 46": "OE1" <-> "OE2" Residue "K TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 26664 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2305 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 276} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2305 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 276} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2305 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 276} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2305 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 276} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2305 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 276} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2305 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 276} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2305 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 276} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2305 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 276} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2305 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 276} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2305 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 276} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2305 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 276} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 119 Unusual residues: {'PA8': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "B" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 119 Unusual residues: {'PA8': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "C" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 119 Unusual residues: {'PA8': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "D" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 119 Unusual residues: {'PA8': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "E" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 119 Unusual residues: {'PA8': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "F" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 119 Unusual residues: {'PA8': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "G" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 119 Unusual residues: {'PA8': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "H" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 119 Unusual residues: {'PA8': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "I" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 119 Unusual residues: {'PA8': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "J" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 119 Unusual residues: {'PA8': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "K" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 119 Unusual residues: {'PA8': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Time building chain proxies: 13.32, per 1000 atoms: 0.50 Number of scatterers: 26664 At special positions: 0 Unit cell: (155.1, 156.2, 105.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 220 16.00 P 55 15.00 O 4862 8.00 N 4224 7.00 C 17303 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 127 " distance=2.04 Simple disulfide: pdb=" SG CYS A 43 " - pdb=" SG CYS A 158 " distance=2.03 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 149 " distance=2.04 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 127 " distance=2.04 Simple disulfide: pdb=" SG CYS B 43 " - pdb=" SG CYS B 158 " distance=2.03 Simple disulfide: pdb=" SG CYS B 142 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS C 41 " - pdb=" SG CYS C 127 " distance=2.04 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 158 " distance=2.03 Simple disulfide: pdb=" SG CYS C 142 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 127 " distance=2.04 Simple disulfide: pdb=" SG CYS D 43 " - pdb=" SG CYS D 158 " distance=2.03 Simple disulfide: pdb=" SG CYS D 142 " - pdb=" SG CYS D 149 " distance=2.04 Simple disulfide: pdb=" SG CYS E 41 " - pdb=" SG CYS E 127 " distance=2.04 Simple disulfide: pdb=" SG CYS E 43 " - pdb=" SG CYS E 158 " distance=2.03 Simple disulfide: pdb=" SG CYS E 142 " - pdb=" SG CYS E 149 " distance=2.03 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 127 " distance=2.04 Simple disulfide: pdb=" SG CYS F 43 " - pdb=" SG CYS F 158 " distance=2.03 Simple disulfide: pdb=" SG CYS F 142 " - pdb=" SG CYS F 149 " distance=2.04 Simple disulfide: pdb=" SG CYS G 41 " - pdb=" SG CYS G 127 " distance=2.04 Simple disulfide: pdb=" SG CYS G 43 " - pdb=" SG CYS G 158 " distance=2.03 Simple disulfide: pdb=" SG CYS G 142 " - pdb=" SG CYS G 149 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 127 " distance=2.04 Simple disulfide: pdb=" SG CYS H 43 " - pdb=" SG CYS H 158 " distance=2.03 Simple disulfide: pdb=" SG CYS H 142 " - pdb=" SG CYS H 149 " distance=2.04 Simple disulfide: pdb=" SG CYS I 41 " - pdb=" SG CYS I 127 " distance=2.04 Simple disulfide: pdb=" SG CYS I 43 " - pdb=" SG CYS I 158 " distance=2.03 Simple disulfide: pdb=" SG CYS I 142 " - pdb=" SG CYS I 149 " distance=2.03 Simple disulfide: pdb=" SG CYS J 41 " - pdb=" SG CYS J 127 " distance=2.04 Simple disulfide: pdb=" SG CYS J 43 " - pdb=" SG CYS J 158 " distance=2.03 Simple disulfide: pdb=" SG CYS J 142 " - pdb=" SG CYS J 149 " distance=2.04 Simple disulfide: pdb=" SG CYS K 41 " - pdb=" SG CYS K 127 " distance=2.04 Simple disulfide: pdb=" SG CYS K 43 " - pdb=" SG CYS K 158 " distance=2.03 Simple disulfide: pdb=" SG CYS K 142 " - pdb=" SG CYS K 149 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.19 Conformation dependent library (CDL) restraints added in 5.3 seconds 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6006 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 176 helices and 0 sheets defined 68.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.42 Creating SS restraints... Processing helix chain 'A' and resid 3 through 8 Processing helix chain 'A' and resid 10 through 13 No H-bonds generated for 'chain 'A' and resid 10 through 13' Processing helix chain 'A' and resid 15 through 37 removed outlier: 3.956A pdb=" N TYR A 20 " --> pdb=" O THR A 16 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA A 24 " --> pdb=" O TYR A 20 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU A 33 " --> pdb=" O GLY A 29 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A 36 " --> pdb=" O ARG A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 68 removed outlier: 3.618A pdb=" N PHE A 54 " --> pdb=" O TYR A 50 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 55 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) Proline residue: A 58 - end of helix removed outlier: 3.562A pdb=" N PHE A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 77 removed outlier: 3.613A pdb=" N LEU A 76 " --> pdb=" O ARG A 72 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE A 77 " --> pdb=" O SER A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 86 No H-bonds generated for 'chain 'A' and resid 84 through 86' Processing helix chain 'A' and resid 95 through 106 Processing helix chain 'A' and resid 109 through 120 removed outlier: 3.648A pdb=" N VAL A 117 " --> pdb=" O MET A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 130 Processing helix chain 'A' and resid 138 through 141 No H-bonds generated for 'chain 'A' and resid 138 through 141' Processing helix chain 'A' and resid 147 through 149 No H-bonds generated for 'chain 'A' and resid 147 through 149' Processing helix chain 'A' and resid 153 through 155 No H-bonds generated for 'chain 'A' and resid 153 through 155' Processing helix chain 'A' and resid 168 through 203 removed outlier: 3.778A pdb=" N LEU A 173 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER A 174 " --> pdb=" O GLU A 170 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN A 176 " --> pdb=" O LYS A 172 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN A 180 " --> pdb=" O GLN A 176 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A 182 " --> pdb=" O GLN A 178 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE A 187 " --> pdb=" O GLY A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 246 removed outlier: 3.559A pdb=" N LYS A 221 " --> pdb=" O THR A 217 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS A 223 " --> pdb=" O ALA A 219 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU A 224 " --> pdb=" O GLN A 220 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN A 225 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASN A 235 " --> pdb=" O LEU A 231 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS A 236 " --> pdb=" O ASP A 232 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 266 removed outlier: 3.763A pdb=" N SER A 266 " --> pdb=" O TRP A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 287 Processing helix chain 'B' and resid 3 through 8 Processing helix chain 'B' and resid 10 through 13 No H-bonds generated for 'chain 'B' and resid 10 through 13' Processing helix chain 'B' and resid 15 through 37 removed outlier: 3.957A pdb=" N TYR B 20 " --> pdb=" O THR B 16 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA B 24 " --> pdb=" O TYR B 20 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL B 36 " --> pdb=" O ARG B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 68 removed outlier: 3.617A pdb=" N PHE B 54 " --> pdb=" O TYR B 50 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU B 55 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE B 56 " --> pdb=" O LEU B 52 " (cutoff:3.500A) Proline residue: B 58 - end of helix removed outlier: 3.561A pdb=" N PHE B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 77 removed outlier: 3.613A pdb=" N LEU B 76 " --> pdb=" O ARG B 72 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE B 77 " --> pdb=" O SER B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 86 No H-bonds generated for 'chain 'B' and resid 84 through 86' Processing helix chain 'B' and resid 95 through 106 Processing helix chain 'B' and resid 109 through 120 removed outlier: 3.648A pdb=" N VAL B 117 " --> pdb=" O MET B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 130 Processing helix chain 'B' and resid 138 through 141 No H-bonds generated for 'chain 'B' and resid 138 through 141' Processing helix chain 'B' and resid 147 through 149 No H-bonds generated for 'chain 'B' and resid 147 through 149' Processing helix chain 'B' and resid 153 through 155 No H-bonds generated for 'chain 'B' and resid 153 through 155' Processing helix chain 'B' and resid 168 through 203 removed outlier: 3.778A pdb=" N LEU B 173 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER B 174 " --> pdb=" O GLU B 170 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B 175 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN B 176 " --> pdb=" O LYS B 172 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN B 178 " --> pdb=" O SER B 174 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN B 180 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU B 182 " --> pdb=" O GLN B 178 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE B 187 " --> pdb=" O GLY B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 246 removed outlier: 3.559A pdb=" N LYS B 221 " --> pdb=" O THR B 217 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS B 223 " --> pdb=" O ALA B 219 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU B 224 " --> pdb=" O GLN B 220 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN B 235 " --> pdb=" O LEU B 231 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS B 236 " --> pdb=" O ASP B 232 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE B 245 " --> pdb=" O ASN B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 266 removed outlier: 3.764A pdb=" N SER B 266 " --> pdb=" O TRP B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 287 Processing helix chain 'C' and resid 3 through 8 Processing helix chain 'C' and resid 10 through 13 No H-bonds generated for 'chain 'C' and resid 10 through 13' Processing helix chain 'C' and resid 15 through 37 removed outlier: 3.956A pdb=" N TYR C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA C 24 " --> pdb=" O TYR C 20 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU C 33 " --> pdb=" O GLY C 29 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL C 36 " --> pdb=" O ARG C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 68 removed outlier: 3.618A pdb=" N PHE C 54 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU C 55 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE C 56 " --> pdb=" O LEU C 52 " (cutoff:3.500A) Proline residue: C 58 - end of helix removed outlier: 3.561A pdb=" N PHE C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 77 removed outlier: 3.613A pdb=" N LEU C 76 " --> pdb=" O ARG C 72 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE C 77 " --> pdb=" O SER C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 86 No H-bonds generated for 'chain 'C' and resid 84 through 86' Processing helix chain 'C' and resid 95 through 106 Processing helix chain 'C' and resid 109 through 120 removed outlier: 3.647A pdb=" N VAL C 117 " --> pdb=" O MET C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 130 Processing helix chain 'C' and resid 138 through 141 No H-bonds generated for 'chain 'C' and resid 138 through 141' Processing helix chain 'C' and resid 147 through 149 No H-bonds generated for 'chain 'C' and resid 147 through 149' Processing helix chain 'C' and resid 153 through 155 No H-bonds generated for 'chain 'C' and resid 153 through 155' Processing helix chain 'C' and resid 168 through 203 removed outlier: 3.777A pdb=" N LEU C 173 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER C 174 " --> pdb=" O GLU C 170 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU C 175 " --> pdb=" O LEU C 171 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN C 176 " --> pdb=" O LYS C 172 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN C 178 " --> pdb=" O SER C 174 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN C 180 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU C 182 " --> pdb=" O GLN C 178 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE C 187 " --> pdb=" O GLY C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 246 removed outlier: 3.560A pdb=" N LYS C 221 " --> pdb=" O THR C 217 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS C 223 " --> pdb=" O ALA C 219 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU C 224 " --> pdb=" O GLN C 220 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN C 225 " --> pdb=" O LYS C 221 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN C 235 " --> pdb=" O LEU C 231 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS C 236 " --> pdb=" O ASP C 232 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE C 245 " --> pdb=" O ASN C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 266 removed outlier: 3.764A pdb=" N SER C 266 " --> pdb=" O TRP C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 287 Processing helix chain 'D' and resid 3 through 8 Processing helix chain 'D' and resid 10 through 13 No H-bonds generated for 'chain 'D' and resid 10 through 13' Processing helix chain 'D' and resid 15 through 37 removed outlier: 3.956A pdb=" N TYR D 20 " --> pdb=" O THR D 16 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA D 24 " --> pdb=" O TYR D 20 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU D 33 " --> pdb=" O GLY D 29 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL D 36 " --> pdb=" O ARG D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 68 removed outlier: 3.618A pdb=" N PHE D 54 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU D 55 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE D 56 " --> pdb=" O LEU D 52 " (cutoff:3.500A) Proline residue: D 58 - end of helix removed outlier: 3.561A pdb=" N PHE D 67 " --> pdb=" O LEU D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 77 removed outlier: 3.613A pdb=" N LEU D 76 " --> pdb=" O ARG D 72 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE D 77 " --> pdb=" O SER D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 86 No H-bonds generated for 'chain 'D' and resid 84 through 86' Processing helix chain 'D' and resid 95 through 106 Processing helix chain 'D' and resid 109 through 120 removed outlier: 3.647A pdb=" N VAL D 117 " --> pdb=" O MET D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 130 Processing helix chain 'D' and resid 138 through 141 No H-bonds generated for 'chain 'D' and resid 138 through 141' Processing helix chain 'D' and resid 147 through 149 No H-bonds generated for 'chain 'D' and resid 147 through 149' Processing helix chain 'D' and resid 153 through 155 No H-bonds generated for 'chain 'D' and resid 153 through 155' Processing helix chain 'D' and resid 168 through 203 removed outlier: 3.778A pdb=" N LEU D 173 " --> pdb=" O GLU D 169 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER D 174 " --> pdb=" O GLU D 170 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU D 175 " --> pdb=" O LEU D 171 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN D 176 " --> pdb=" O LYS D 172 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN D 178 " --> pdb=" O SER D 174 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN D 180 " --> pdb=" O GLN D 176 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU D 182 " --> pdb=" O GLN D 178 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE D 187 " --> pdb=" O GLY D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 246 removed outlier: 3.560A pdb=" N LYS D 221 " --> pdb=" O THR D 217 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS D 223 " --> pdb=" O ALA D 219 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU D 224 " --> pdb=" O GLN D 220 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN D 225 " --> pdb=" O LYS D 221 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN D 235 " --> pdb=" O LEU D 231 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS D 236 " --> pdb=" O ASP D 232 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE D 245 " --> pdb=" O ASN D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 266 removed outlier: 3.765A pdb=" N SER D 266 " --> pdb=" O TRP D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 287 Processing helix chain 'E' and resid 3 through 8 Processing helix chain 'E' and resid 10 through 13 No H-bonds generated for 'chain 'E' and resid 10 through 13' Processing helix chain 'E' and resid 15 through 37 removed outlier: 3.957A pdb=" N TYR E 20 " --> pdb=" O THR E 16 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA E 24 " --> pdb=" O TYR E 20 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU E 33 " --> pdb=" O GLY E 29 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL E 36 " --> pdb=" O ARG E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 68 removed outlier: 3.618A pdb=" N PHE E 54 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU E 55 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE E 56 " --> pdb=" O LEU E 52 " (cutoff:3.500A) Proline residue: E 58 - end of helix removed outlier: 3.562A pdb=" N PHE E 67 " --> pdb=" O LEU E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 77 removed outlier: 3.613A pdb=" N LEU E 76 " --> pdb=" O ARG E 72 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE E 77 " --> pdb=" O SER E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 86 No H-bonds generated for 'chain 'E' and resid 84 through 86' Processing helix chain 'E' and resid 95 through 106 Processing helix chain 'E' and resid 109 through 120 removed outlier: 3.648A pdb=" N VAL E 117 " --> pdb=" O MET E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 130 Processing helix chain 'E' and resid 138 through 141 No H-bonds generated for 'chain 'E' and resid 138 through 141' Processing helix chain 'E' and resid 147 through 149 No H-bonds generated for 'chain 'E' and resid 147 through 149' Processing helix chain 'E' and resid 153 through 155 No H-bonds generated for 'chain 'E' and resid 153 through 155' Processing helix chain 'E' and resid 168 through 203 removed outlier: 3.778A pdb=" N LEU E 173 " --> pdb=" O GLU E 169 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER E 174 " --> pdb=" O GLU E 170 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU E 175 " --> pdb=" O LEU E 171 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN E 176 " --> pdb=" O LYS E 172 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN E 178 " --> pdb=" O SER E 174 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN E 180 " --> pdb=" O GLN E 176 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU E 182 " --> pdb=" O GLN E 178 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE E 187 " --> pdb=" O GLY E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 246 removed outlier: 3.560A pdb=" N LYS E 221 " --> pdb=" O THR E 217 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS E 223 " --> pdb=" O ALA E 219 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU E 224 " --> pdb=" O GLN E 220 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN E 225 " --> pdb=" O LYS E 221 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN E 235 " --> pdb=" O LEU E 231 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS E 236 " --> pdb=" O ASP E 232 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE E 245 " --> pdb=" O ASN E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 266 removed outlier: 3.763A pdb=" N SER E 266 " --> pdb=" O TRP E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 287 Processing helix chain 'F' and resid 3 through 8 Processing helix chain 'F' and resid 10 through 13 No H-bonds generated for 'chain 'F' and resid 10 through 13' Processing helix chain 'F' and resid 15 through 37 removed outlier: 3.956A pdb=" N TYR F 20 " --> pdb=" O THR F 16 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA F 24 " --> pdb=" O TYR F 20 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU F 33 " --> pdb=" O GLY F 29 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL F 36 " --> pdb=" O ARG F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 68 removed outlier: 3.618A pdb=" N PHE F 54 " --> pdb=" O TYR F 50 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU F 55 " --> pdb=" O GLY F 51 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE F 56 " --> pdb=" O LEU F 52 " (cutoff:3.500A) Proline residue: F 58 - end of helix removed outlier: 3.561A pdb=" N PHE F 67 " --> pdb=" O LEU F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 77 removed outlier: 3.613A pdb=" N LEU F 76 " --> pdb=" O ARG F 72 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE F 77 " --> pdb=" O SER F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 86 No H-bonds generated for 'chain 'F' and resid 84 through 86' Processing helix chain 'F' and resid 95 through 106 Processing helix chain 'F' and resid 109 through 120 removed outlier: 3.647A pdb=" N VAL F 117 " --> pdb=" O MET F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 130 Processing helix chain 'F' and resid 138 through 141 No H-bonds generated for 'chain 'F' and resid 138 through 141' Processing helix chain 'F' and resid 147 through 149 No H-bonds generated for 'chain 'F' and resid 147 through 149' Processing helix chain 'F' and resid 153 through 155 No H-bonds generated for 'chain 'F' and resid 153 through 155' Processing helix chain 'F' and resid 168 through 203 removed outlier: 3.778A pdb=" N LEU F 173 " --> pdb=" O GLU F 169 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER F 174 " --> pdb=" O GLU F 170 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU F 175 " --> pdb=" O LEU F 171 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN F 176 " --> pdb=" O LYS F 172 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN F 178 " --> pdb=" O SER F 174 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN F 180 " --> pdb=" O GLN F 176 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU F 182 " --> pdb=" O GLN F 178 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE F 187 " --> pdb=" O GLY F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 246 removed outlier: 3.560A pdb=" N LYS F 221 " --> pdb=" O THR F 217 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS F 223 " --> pdb=" O ALA F 219 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU F 224 " --> pdb=" O GLN F 220 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN F 225 " --> pdb=" O LYS F 221 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN F 235 " --> pdb=" O LEU F 231 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS F 236 " --> pdb=" O ASP F 232 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE F 245 " --> pdb=" O ASN F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 266 removed outlier: 3.763A pdb=" N SER F 266 " --> pdb=" O TRP F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 287 Processing helix chain 'G' and resid 3 through 8 Processing helix chain 'G' and resid 10 through 13 No H-bonds generated for 'chain 'G' and resid 10 through 13' Processing helix chain 'G' and resid 15 through 37 removed outlier: 3.957A pdb=" N TYR G 20 " --> pdb=" O THR G 16 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA G 24 " --> pdb=" O TYR G 20 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU G 33 " --> pdb=" O GLY G 29 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL G 36 " --> pdb=" O ARG G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 68 removed outlier: 3.618A pdb=" N PHE G 54 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU G 55 " --> pdb=" O GLY G 51 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE G 56 " --> pdb=" O LEU G 52 " (cutoff:3.500A) Proline residue: G 58 - end of helix removed outlier: 3.561A pdb=" N PHE G 67 " --> pdb=" O LEU G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 77 removed outlier: 3.613A pdb=" N LEU G 76 " --> pdb=" O ARG G 72 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE G 77 " --> pdb=" O SER G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 86 No H-bonds generated for 'chain 'G' and resid 84 through 86' Processing helix chain 'G' and resid 95 through 106 Processing helix chain 'G' and resid 109 through 120 removed outlier: 3.647A pdb=" N VAL G 117 " --> pdb=" O MET G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 130 Processing helix chain 'G' and resid 138 through 141 No H-bonds generated for 'chain 'G' and resid 138 through 141' Processing helix chain 'G' and resid 147 through 149 No H-bonds generated for 'chain 'G' and resid 147 through 149' Processing helix chain 'G' and resid 153 through 155 No H-bonds generated for 'chain 'G' and resid 153 through 155' Processing helix chain 'G' and resid 168 through 203 removed outlier: 3.778A pdb=" N LEU G 173 " --> pdb=" O GLU G 169 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER G 174 " --> pdb=" O GLU G 170 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU G 175 " --> pdb=" O LEU G 171 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN G 176 " --> pdb=" O LYS G 172 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN G 178 " --> pdb=" O SER G 174 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN G 180 " --> pdb=" O GLN G 176 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU G 182 " --> pdb=" O GLN G 178 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE G 187 " --> pdb=" O GLY G 183 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 246 removed outlier: 3.559A pdb=" N LYS G 221 " --> pdb=" O THR G 217 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS G 223 " --> pdb=" O ALA G 219 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU G 224 " --> pdb=" O GLN G 220 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN G 225 " --> pdb=" O LYS G 221 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN G 235 " --> pdb=" O LEU G 231 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS G 236 " --> pdb=" O ASP G 232 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE G 245 " --> pdb=" O ASN G 241 " (cutoff:3.500A) Processing helix chain 'G' and resid 259 through 266 removed outlier: 3.764A pdb=" N SER G 266 " --> pdb=" O TRP G 262 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 287 Processing helix chain 'H' and resid 3 through 8 Processing helix chain 'H' and resid 10 through 13 No H-bonds generated for 'chain 'H' and resid 10 through 13' Processing helix chain 'H' and resid 15 through 37 removed outlier: 3.956A pdb=" N TYR H 20 " --> pdb=" O THR H 16 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA H 24 " --> pdb=" O TYR H 20 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU H 33 " --> pdb=" O GLY H 29 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL H 36 " --> pdb=" O ARG H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 68 removed outlier: 3.618A pdb=" N PHE H 54 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU H 55 " --> pdb=" O GLY H 51 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE H 56 " --> pdb=" O LEU H 52 " (cutoff:3.500A) Proline residue: H 58 - end of helix removed outlier: 3.561A pdb=" N PHE H 67 " --> pdb=" O LEU H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 77 removed outlier: 3.613A pdb=" N LEU H 76 " --> pdb=" O ARG H 72 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE H 77 " --> pdb=" O SER H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 84 through 86 No H-bonds generated for 'chain 'H' and resid 84 through 86' Processing helix chain 'H' and resid 95 through 106 Processing helix chain 'H' and resid 109 through 120 removed outlier: 3.648A pdb=" N VAL H 117 " --> pdb=" O MET H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 123 through 130 Processing helix chain 'H' and resid 138 through 141 No H-bonds generated for 'chain 'H' and resid 138 through 141' Processing helix chain 'H' and resid 147 through 149 No H-bonds generated for 'chain 'H' and resid 147 through 149' Processing helix chain 'H' and resid 153 through 155 No H-bonds generated for 'chain 'H' and resid 153 through 155' Processing helix chain 'H' and resid 168 through 203 removed outlier: 3.778A pdb=" N LEU H 173 " --> pdb=" O GLU H 169 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER H 174 " --> pdb=" O GLU H 170 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU H 175 " --> pdb=" O LEU H 171 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN H 176 " --> pdb=" O LYS H 172 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN H 178 " --> pdb=" O SER H 174 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN H 180 " --> pdb=" O GLN H 176 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU H 182 " --> pdb=" O GLN H 178 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE H 187 " --> pdb=" O GLY H 183 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 246 removed outlier: 3.560A pdb=" N LYS H 221 " --> pdb=" O THR H 217 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS H 223 " --> pdb=" O ALA H 219 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU H 224 " --> pdb=" O GLN H 220 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN H 225 " --> pdb=" O LYS H 221 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN H 235 " --> pdb=" O LEU H 231 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS H 236 " --> pdb=" O ASP H 232 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE H 245 " --> pdb=" O ASN H 241 " (cutoff:3.500A) Processing helix chain 'H' and resid 259 through 266 removed outlier: 3.764A pdb=" N SER H 266 " --> pdb=" O TRP H 262 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 287 Processing helix chain 'I' and resid 3 through 8 Processing helix chain 'I' and resid 10 through 13 No H-bonds generated for 'chain 'I' and resid 10 through 13' Processing helix chain 'I' and resid 15 through 37 removed outlier: 3.956A pdb=" N TYR I 20 " --> pdb=" O THR I 16 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA I 24 " --> pdb=" O TYR I 20 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU I 33 " --> pdb=" O GLY I 29 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL I 36 " --> pdb=" O ARG I 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 68 removed outlier: 3.618A pdb=" N PHE I 54 " --> pdb=" O TYR I 50 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU I 55 " --> pdb=" O GLY I 51 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE I 56 " --> pdb=" O LEU I 52 " (cutoff:3.500A) Proline residue: I 58 - end of helix removed outlier: 3.561A pdb=" N PHE I 67 " --> pdb=" O LEU I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 77 removed outlier: 3.612A pdb=" N LEU I 76 " --> pdb=" O ARG I 72 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE I 77 " --> pdb=" O SER I 73 " (cutoff:3.500A) Processing helix chain 'I' and resid 84 through 86 No H-bonds generated for 'chain 'I' and resid 84 through 86' Processing helix chain 'I' and resid 95 through 106 Processing helix chain 'I' and resid 109 through 120 removed outlier: 3.647A pdb=" N VAL I 117 " --> pdb=" O MET I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 123 through 130 Processing helix chain 'I' and resid 138 through 141 No H-bonds generated for 'chain 'I' and resid 138 through 141' Processing helix chain 'I' and resid 147 through 149 No H-bonds generated for 'chain 'I' and resid 147 through 149' Processing helix chain 'I' and resid 153 through 155 No H-bonds generated for 'chain 'I' and resid 153 through 155' Processing helix chain 'I' and resid 168 through 203 removed outlier: 3.777A pdb=" N LEU I 173 " --> pdb=" O GLU I 169 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER I 174 " --> pdb=" O GLU I 170 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU I 175 " --> pdb=" O LEU I 171 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN I 176 " --> pdb=" O LYS I 172 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN I 178 " --> pdb=" O SER I 174 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN I 180 " --> pdb=" O GLN I 176 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU I 182 " --> pdb=" O GLN I 178 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE I 187 " --> pdb=" O GLY I 183 " (cutoff:3.500A) Processing helix chain 'I' and resid 209 through 246 removed outlier: 3.559A pdb=" N LYS I 221 " --> pdb=" O THR I 217 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS I 223 " --> pdb=" O ALA I 219 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU I 224 " --> pdb=" O GLN I 220 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN I 225 " --> pdb=" O LYS I 221 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASN I 235 " --> pdb=" O LEU I 231 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS I 236 " --> pdb=" O ASP I 232 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE I 245 " --> pdb=" O ASN I 241 " (cutoff:3.500A) Processing helix chain 'I' and resid 259 through 266 removed outlier: 3.765A pdb=" N SER I 266 " --> pdb=" O TRP I 262 " (cutoff:3.500A) Processing helix chain 'I' and resid 280 through 287 Processing helix chain 'J' and resid 3 through 8 Processing helix chain 'J' and resid 10 through 13 No H-bonds generated for 'chain 'J' and resid 10 through 13' Processing helix chain 'J' and resid 15 through 37 removed outlier: 3.956A pdb=" N TYR J 20 " --> pdb=" O THR J 16 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA J 24 " --> pdb=" O TYR J 20 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU J 33 " --> pdb=" O GLY J 29 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL J 36 " --> pdb=" O ARG J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 47 through 68 removed outlier: 3.618A pdb=" N PHE J 54 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU J 55 " --> pdb=" O GLY J 51 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE J 56 " --> pdb=" O LEU J 52 " (cutoff:3.500A) Proline residue: J 58 - end of helix removed outlier: 3.561A pdb=" N PHE J 67 " --> pdb=" O LEU J 63 " (cutoff:3.500A) Processing helix chain 'J' and resid 71 through 77 removed outlier: 3.613A pdb=" N LEU J 76 " --> pdb=" O ARG J 72 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE J 77 " --> pdb=" O SER J 73 " (cutoff:3.500A) Processing helix chain 'J' and resid 84 through 86 No H-bonds generated for 'chain 'J' and resid 84 through 86' Processing helix chain 'J' and resid 95 through 106 Processing helix chain 'J' and resid 109 through 120 removed outlier: 3.647A pdb=" N VAL J 117 " --> pdb=" O MET J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 123 through 130 Processing helix chain 'J' and resid 138 through 141 No H-bonds generated for 'chain 'J' and resid 138 through 141' Processing helix chain 'J' and resid 147 through 149 No H-bonds generated for 'chain 'J' and resid 147 through 149' Processing helix chain 'J' and resid 153 through 155 No H-bonds generated for 'chain 'J' and resid 153 through 155' Processing helix chain 'J' and resid 168 through 203 removed outlier: 3.777A pdb=" N LEU J 173 " --> pdb=" O GLU J 169 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER J 174 " --> pdb=" O GLU J 170 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU J 175 " --> pdb=" O LEU J 171 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN J 176 " --> pdb=" O LYS J 172 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN J 178 " --> pdb=" O SER J 174 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN J 180 " --> pdb=" O GLN J 176 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU J 182 " --> pdb=" O GLN J 178 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE J 187 " --> pdb=" O GLY J 183 " (cutoff:3.500A) Processing helix chain 'J' and resid 209 through 246 removed outlier: 3.559A pdb=" N LYS J 221 " --> pdb=" O THR J 217 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS J 223 " --> pdb=" O ALA J 219 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU J 224 " --> pdb=" O GLN J 220 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN J 225 " --> pdb=" O LYS J 221 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASN J 235 " --> pdb=" O LEU J 231 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS J 236 " --> pdb=" O ASP J 232 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE J 245 " --> pdb=" O ASN J 241 " (cutoff:3.500A) Processing helix chain 'J' and resid 259 through 266 removed outlier: 3.764A pdb=" N SER J 266 " --> pdb=" O TRP J 262 " (cutoff:3.500A) Processing helix chain 'J' and resid 280 through 287 Processing helix chain 'K' and resid 3 through 8 Processing helix chain 'K' and resid 10 through 13 No H-bonds generated for 'chain 'K' and resid 10 through 13' Processing helix chain 'K' and resid 15 through 37 removed outlier: 3.957A pdb=" N TYR K 20 " --> pdb=" O THR K 16 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA K 24 " --> pdb=" O TYR K 20 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU K 33 " --> pdb=" O GLY K 29 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL K 36 " --> pdb=" O ARG K 32 " (cutoff:3.500A) Processing helix chain 'K' and resid 47 through 68 removed outlier: 3.618A pdb=" N PHE K 54 " --> pdb=" O TYR K 50 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU K 55 " --> pdb=" O GLY K 51 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE K 56 " --> pdb=" O LEU K 52 " (cutoff:3.500A) Proline residue: K 58 - end of helix removed outlier: 3.561A pdb=" N PHE K 67 " --> pdb=" O LEU K 63 " (cutoff:3.500A) Processing helix chain 'K' and resid 71 through 77 removed outlier: 3.613A pdb=" N LEU K 76 " --> pdb=" O ARG K 72 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE K 77 " --> pdb=" O SER K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 84 through 86 No H-bonds generated for 'chain 'K' and resid 84 through 86' Processing helix chain 'K' and resid 95 through 106 Processing helix chain 'K' and resid 109 through 120 removed outlier: 3.647A pdb=" N VAL K 117 " --> pdb=" O MET K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 123 through 130 Processing helix chain 'K' and resid 138 through 141 No H-bonds generated for 'chain 'K' and resid 138 through 141' Processing helix chain 'K' and resid 147 through 149 No H-bonds generated for 'chain 'K' and resid 147 through 149' Processing helix chain 'K' and resid 153 through 155 No H-bonds generated for 'chain 'K' and resid 153 through 155' Processing helix chain 'K' and resid 168 through 203 removed outlier: 3.778A pdb=" N LEU K 173 " --> pdb=" O GLU K 169 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER K 174 " --> pdb=" O GLU K 170 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU K 175 " --> pdb=" O LEU K 171 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN K 176 " --> pdb=" O LYS K 172 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN K 178 " --> pdb=" O SER K 174 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN K 180 " --> pdb=" O GLN K 176 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU K 182 " --> pdb=" O GLN K 178 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE K 187 " --> pdb=" O GLY K 183 " (cutoff:3.500A) Processing helix chain 'K' and resid 209 through 246 removed outlier: 3.560A pdb=" N LYS K 221 " --> pdb=" O THR K 217 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS K 223 " --> pdb=" O ALA K 219 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU K 224 " --> pdb=" O GLN K 220 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN K 225 " --> pdb=" O LYS K 221 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN K 235 " --> pdb=" O LEU K 231 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS K 236 " --> pdb=" O ASP K 232 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE K 245 " --> pdb=" O ASN K 241 " (cutoff:3.500A) Processing helix chain 'K' and resid 259 through 266 removed outlier: 3.764A pdb=" N SER K 266 " --> pdb=" O TRP K 262 " (cutoff:3.500A) Processing helix chain 'K' and resid 280 through 287 1166 hydrogen bonds defined for protein. 3498 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: 7.36 Time building geometry restraints manager: 9.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3960 1.31 - 1.43: 7954 1.43 - 1.56: 15047 1.56 - 1.69: 55 1.69 - 1.82: 286 Bond restraints: 27302 Sorted by residual: bond pdb=" CB PRO C 111 " pdb=" CG PRO C 111 " ideal model delta sigma weight residual 1.492 1.422 0.070 5.00e-02 4.00e+02 1.94e+00 bond pdb=" CB PRO D 111 " pdb=" CG PRO D 111 " ideal model delta sigma weight residual 1.492 1.422 0.070 5.00e-02 4.00e+02 1.94e+00 bond pdb=" CB PRO K 111 " pdb=" CG PRO K 111 " ideal model delta sigma weight residual 1.492 1.422 0.070 5.00e-02 4.00e+02 1.93e+00 bond pdb=" CB PRO J 111 " pdb=" CG PRO J 111 " ideal model delta sigma weight residual 1.492 1.423 0.069 5.00e-02 4.00e+02 1.93e+00 bond pdb=" CB PRO I 111 " pdb=" CG PRO I 111 " ideal model delta sigma weight residual 1.492 1.423 0.069 5.00e-02 4.00e+02 1.93e+00 ... (remaining 27297 not shown) Histogram of bond angle deviations from ideal: 100.39 - 107.13: 686 107.13 - 113.88: 15299 113.88 - 120.63: 12093 120.63 - 127.37: 8379 127.37 - 134.12: 316 Bond angle restraints: 36773 Sorted by residual: angle pdb=" N ILE A 87 " pdb=" CA ILE A 87 " pdb=" C ILE A 87 " ideal model delta sigma weight residual 113.42 107.17 6.25 1.17e+00 7.31e-01 2.85e+01 angle pdb=" N ILE K 87 " pdb=" CA ILE K 87 " pdb=" C ILE K 87 " ideal model delta sigma weight residual 113.42 107.20 6.22 1.17e+00 7.31e-01 2.83e+01 angle pdb=" N ILE D 87 " pdb=" CA ILE D 87 " pdb=" C ILE D 87 " ideal model delta sigma weight residual 113.42 107.20 6.22 1.17e+00 7.31e-01 2.82e+01 angle pdb=" N ILE H 87 " pdb=" CA ILE H 87 " pdb=" C ILE H 87 " ideal model delta sigma weight residual 113.42 107.20 6.22 1.17e+00 7.31e-01 2.82e+01 angle pdb=" N ILE G 87 " pdb=" CA ILE G 87 " pdb=" C ILE G 87 " ideal model delta sigma weight residual 113.42 107.21 6.21 1.17e+00 7.31e-01 2.82e+01 ... (remaining 36768 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.88: 13571 16.88 - 33.77: 1972 33.77 - 50.65: 385 50.65 - 67.54: 143 67.54 - 84.42: 44 Dihedral angle restraints: 16115 sinusoidal: 6853 harmonic: 9262 Sorted by residual: dihedral pdb=" CA LYS D 221 " pdb=" C LYS D 221 " pdb=" N GLU D 222 " pdb=" CA GLU D 222 " ideal model delta harmonic sigma weight residual 180.00 151.81 28.19 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA LYS E 221 " pdb=" C LYS E 221 " pdb=" N GLU E 222 " pdb=" CA GLU E 222 " ideal model delta harmonic sigma weight residual 180.00 151.81 28.19 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA LYS C 221 " pdb=" C LYS C 221 " pdb=" N GLU C 222 " pdb=" CA GLU C 222 " ideal model delta harmonic sigma weight residual 180.00 151.82 28.18 0 5.00e+00 4.00e-02 3.18e+01 ... (remaining 16112 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2389 0.041 - 0.082: 1262 0.082 - 0.123: 220 0.123 - 0.164: 23 0.164 - 0.205: 22 Chirality restraints: 3916 Sorted by residual: chirality pdb=" CA PRO D 165 " pdb=" N PRO D 165 " pdb=" C PRO D 165 " pdb=" CB PRO D 165 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA PRO K 165 " pdb=" N PRO K 165 " pdb=" C PRO K 165 " pdb=" CB PRO K 165 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA PRO E 165 " pdb=" N PRO E 165 " pdb=" C PRO E 165 " pdb=" CB PRO E 165 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 3913 not shown) Planarity restraints: 4499 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA J 110 " -0.048 5.00e-02 4.00e+02 7.16e-02 8.21e+00 pdb=" N PRO J 111 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO J 111 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO J 111 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 110 " 0.048 5.00e-02 4.00e+02 7.16e-02 8.21e+00 pdb=" N PRO C 111 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO C 111 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 111 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA G 110 " -0.048 5.00e-02 4.00e+02 7.16e-02 8.21e+00 pdb=" N PRO G 111 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO G 111 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO G 111 " -0.040 5.00e-02 4.00e+02 ... (remaining 4496 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.90: 9644 2.90 - 3.40: 22563 3.40 - 3.90: 39595 3.90 - 4.40: 47842 4.40 - 4.90: 82005 Nonbonded interactions: 201649 Sorted by model distance: nonbonded pdb=" O LEU A 231 " pdb=" NZ LYS K 221 " model vdw 2.395 2.520 nonbonded pdb=" NZ LYS B 221 " pdb=" O LEU C 231 " model vdw 2.401 2.520 nonbonded pdb=" NZ LYS A 221 " pdb=" O LEU B 231 " model vdw 2.404 2.520 nonbonded pdb=" NZ LYS E 221 " pdb=" O LEU F 231 " model vdw 2.405 2.520 nonbonded pdb=" NZ LYS I 221 " pdb=" O LEU J 231 " model vdw 2.409 2.520 ... (remaining 201644 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' selection = chain 'I' selection = chain 'J' selection = chain 'K' } 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: 1.930 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: 0.030 Extract box with map and model: 9.660 Check model and map are aligned: 0.380 Set scattering table: 0.240 Process input model: 66.580 Find NCS groups from input model: 1.870 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 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 : 0.006 0.070 27302 Z= 0.385 Angle : 0.885 10.774 36773 Z= 0.453 Chirality : 0.048 0.205 3916 Planarity : 0.007 0.072 4499 Dihedral : 16.885 84.422 10010 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % 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: -6.95 (0.08), residues: 3146 helix: -4.81 (0.03), residues: 2409 sheet: None (None), residues: 0 loop : -2.59 (0.19), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 262 HIS 0.004 0.001 HIS B 282 PHE 0.017 0.002 PHE B 68 TYR 0.012 0.002 TYR E 209 ARG 0.003 0.001 ARG F 204 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 721 time to evaluate : 3.016 Fit side-chains revert: symmetry clash REVERT: A 22 PHE cc_start: 0.8483 (t80) cc_final: 0.8202 (t80) REVERT: A 32 ARG cc_start: 0.8503 (mmm160) cc_final: 0.8098 (mmp80) REVERT: A 283 ARG cc_start: 0.8291 (ttp80) cc_final: 0.8082 (ttp-110) REVERT: B 8 LEU cc_start: 0.7319 (mt) cc_final: 0.6916 (tt) REVERT: B 32 ARG cc_start: 0.8358 (mmm160) cc_final: 0.7941 (mmp80) REVERT: B 88 PHE cc_start: 0.7083 (m-80) cc_final: 0.6772 (m-80) REVERT: C 8 LEU cc_start: 0.7197 (mt) cc_final: 0.6860 (tt) REVERT: C 32 ARG cc_start: 0.8411 (mmm160) cc_final: 0.8167 (mmp80) REVERT: C 88 PHE cc_start: 0.7154 (m-80) cc_final: 0.6933 (m-80) REVERT: C 169 GLU cc_start: 0.7655 (tp30) cc_final: 0.7396 (tm-30) REVERT: C 276 GLN cc_start: 0.8050 (pt0) cc_final: 0.7676 (mt0) REVERT: C 283 ARG cc_start: 0.8321 (ttp80) cc_final: 0.8100 (ttp-170) REVERT: D 88 PHE cc_start: 0.6987 (m-80) cc_final: 0.6750 (m-80) REVERT: D 267 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7867 (mt-10) REVERT: E 32 ARG cc_start: 0.8375 (mmm160) cc_final: 0.8071 (mmp80) REVERT: E 88 PHE cc_start: 0.7209 (m-80) cc_final: 0.6876 (m-80) REVERT: E 169 GLU cc_start: 0.7695 (tp30) cc_final: 0.7478 (tm-30) REVERT: E 202 ARG cc_start: 0.7820 (mmm-85) cc_final: 0.7580 (mmt180) REVERT: E 283 ARG cc_start: 0.8343 (ttp80) cc_final: 0.8121 (ttp-170) REVERT: F 202 ARG cc_start: 0.7962 (mmm-85) cc_final: 0.7707 (mmt180) REVERT: F 233 TYR cc_start: 0.8795 (m-80) cc_final: 0.8578 (m-80) REVERT: F 267 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7835 (mt-10) REVERT: G 8 LEU cc_start: 0.6958 (mt) cc_final: 0.6530 (tt) REVERT: G 30 SER cc_start: 0.8812 (t) cc_final: 0.8605 (m) REVERT: G 169 GLU cc_start: 0.7673 (tp30) cc_final: 0.7426 (tm-30) REVERT: H 95 ARG cc_start: 0.7314 (ttt90) cc_final: 0.7083 (ttt90) REVERT: H 220 GLN cc_start: 0.7937 (tm-30) cc_final: 0.7724 (tp-100) REVERT: H 283 ARG cc_start: 0.8415 (ttp80) cc_final: 0.8166 (ttp-170) REVERT: I 8 LEU cc_start: 0.6954 (mt) cc_final: 0.6535 (tt) REVERT: I 88 PHE cc_start: 0.7097 (m-80) cc_final: 0.6829 (m-80) REVERT: I 97 PHE cc_start: 0.8449 (m-80) cc_final: 0.8194 (m-80) REVERT: I 202 ARG cc_start: 0.7906 (mmm-85) cc_final: 0.7568 (mmt180) REVERT: I 233 TYR cc_start: 0.8754 (m-80) cc_final: 0.8542 (m-80) REVERT: I 283 ARG cc_start: 0.8276 (ttp80) cc_final: 0.8006 (ttp-170) REVERT: J 46 GLU cc_start: 0.7260 (pt0) cc_final: 0.6969 (pp20) REVERT: J 283 ARG cc_start: 0.8242 (ttp80) cc_final: 0.7993 (ttp-170) REVERT: K 8 LEU cc_start: 0.7135 (mt) cc_final: 0.6725 (tt) REVERT: K 88 PHE cc_start: 0.7077 (m-80) cc_final: 0.6838 (m-80) REVERT: K 169 GLU cc_start: 0.7592 (tp30) cc_final: 0.7344 (tm-30) REVERT: K 220 GLN cc_start: 0.8062 (tm-30) cc_final: 0.7847 (tp-100) REVERT: K 276 GLN cc_start: 0.8205 (pt0) cc_final: 0.7951 (mt0) REVERT: K 283 ARG cc_start: 0.8318 (ttp80) cc_final: 0.8061 (ttp-170) outliers start: 0 outliers final: 0 residues processed: 721 average time/residue: 1.7709 time to fit residues: 1433.0879 Evaluate side-chains 491 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 491 time to evaluate : 2.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 260 optimal weight: 5.9990 chunk 233 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 157 optimal weight: 0.7980 chunk 124 optimal weight: 0.6980 chunk 241 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 146 optimal weight: 2.9990 chunk 179 optimal weight: 0.5980 chunk 279 optimal weight: 7.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN A 178 GLN A 225 GLN A 248 ASN B 83 ASN B 168 ASN B 248 ASN B 276 GLN C 225 GLN C 248 ASN C 287 ASN D 83 ASN D 248 ASN E 102 GLN E 248 ASN E 276 GLN F 168 ASN F 225 GLN F 248 ASN G 102 GLN G 178 GLN G 220 GLN G 248 ASN H 83 ASN H 276 GLN I 83 ASN I 248 ASN I 273 GLN I 276 GLN J 83 ASN ** J 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 248 ASN K 83 ASN K 178 GLN K 248 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 27302 Z= 0.155 Angle : 0.548 7.983 36773 Z= 0.290 Chirality : 0.036 0.125 3916 Planarity : 0.005 0.045 4499 Dihedral : 12.662 59.655 4092 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.29 % Allowed : 13.06 % Favored : 84.65 % 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: -3.56 (0.13), residues: 3146 helix: -2.31 (0.08), residues: 2387 sheet: None (None), residues: 0 loop : -1.70 (0.22), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 60 HIS 0.002 0.000 HIS C 282 PHE 0.016 0.001 PHE C 214 TYR 0.015 0.001 TYR A 98 ARG 0.007 0.000 ARG F 95 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 481 time to evaluate : 2.834 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 SER cc_start: 0.8436 (t) cc_final: 0.8146 (m) REVERT: B 88 PHE cc_start: 0.7291 (m-80) cc_final: 0.7047 (m-80) REVERT: C 169 GLU cc_start: 0.7562 (tp30) cc_final: 0.6915 (tp30) REVERT: C 276 GLN cc_start: 0.7919 (pt0) cc_final: 0.7558 (mt0) REVERT: D 88 PHE cc_start: 0.7405 (m-80) cc_final: 0.7203 (m-80) REVERT: D 200 TYR cc_start: 0.7868 (t80) cc_final: 0.7655 (t80) REVERT: E 88 PHE cc_start: 0.7201 (m-80) cc_final: 0.6930 (m-80) REVERT: E 169 GLU cc_start: 0.7544 (tp30) cc_final: 0.7104 (tm-30) REVERT: F 169 GLU cc_start: 0.7353 (tm-30) cc_final: 0.7122 (tp30) REVERT: F 267 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7751 (mt-10) REVERT: G 12 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7726 (mm) REVERT: G 95 ARG cc_start: 0.7264 (ttt90) cc_final: 0.6743 (ttp80) REVERT: G 169 GLU cc_start: 0.7517 (tp30) cc_final: 0.7201 (tm-30) REVERT: I 97 PHE cc_start: 0.8320 (m-80) cc_final: 0.8078 (m-80) REVERT: J 32 ARG cc_start: 0.8170 (mmp-170) cc_final: 0.7915 (mmp80) REVERT: J 169 GLU cc_start: 0.7384 (tm-30) cc_final: 0.7156 (tm-30) REVERT: K 88 PHE cc_start: 0.7237 (m-80) cc_final: 0.7021 (m-80) REVERT: K 129 MET cc_start: 0.8590 (tpp) cc_final: 0.8323 (mmt) REVERT: K 169 GLU cc_start: 0.7567 (tp30) cc_final: 0.7190 (tm-30) REVERT: K 224 GLU cc_start: 0.7116 (mt-10) cc_final: 0.6914 (mt-10) REVERT: K 276 GLN cc_start: 0.8148 (pt0) cc_final: 0.7856 (mt0) outliers start: 64 outliers final: 28 residues processed: 519 average time/residue: 1.5611 time to fit residues: 927.1394 Evaluate side-chains 438 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 409 time to evaluate : 2.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 256 MET Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 256 MET Chi-restraints excluded: chain I residue 13 ASN Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 149 CYS Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 231 LEU Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 44 SER Chi-restraints excluded: chain K residue 152 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 155 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 232 optimal weight: 4.9990 chunk 190 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 280 optimal weight: 4.9990 chunk 302 optimal weight: 0.8980 chunk 249 optimal weight: 8.9990 chunk 277 optimal weight: 7.9990 chunk 95 optimal weight: 0.5980 chunk 224 optimal weight: 6.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 102 GLN C 83 ASN E 176 GLN F 176 GLN F 273 GLN G 102 GLN G 220 GLN G 276 GLN H 102 GLN H 168 ASN H 276 GLN I 273 GLN I 276 GLN J 168 ASN J 176 GLN J 220 GLN ** J 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 27302 Z= 0.230 Angle : 0.579 7.947 36773 Z= 0.299 Chirality : 0.039 0.141 3916 Planarity : 0.004 0.038 4499 Dihedral : 12.313 59.798 4092 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.40 % Allowed : 16.00 % Favored : 80.60 % 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: -1.82 (0.14), residues: 3146 helix: -0.93 (0.10), residues: 2409 sheet: None (None), residues: 0 loop : -1.59 (0.23), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 262 HIS 0.002 0.001 HIS H 154 PHE 0.016 0.001 PHE A 214 TYR 0.012 0.001 TYR A 278 ARG 0.005 0.000 ARG F 95 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 411 time to evaluate : 3.070 Fit side-chains revert: symmetry clash REVERT: A 30 SER cc_start: 0.8602 (t) cc_final: 0.8387 (p) REVERT: A 102 GLN cc_start: 0.7988 (mt0) cc_final: 0.7687 (mt0) REVERT: B 88 PHE cc_start: 0.7451 (m-80) cc_final: 0.7245 (m-80) REVERT: B 273 GLN cc_start: 0.7855 (mt0) cc_final: 0.7620 (mt0) REVERT: C 276 GLN cc_start: 0.7905 (pt0) cc_final: 0.7524 (mt0) REVERT: E 88 PHE cc_start: 0.7327 (m-80) cc_final: 0.7114 (m-80) REVERT: E 95 ARG cc_start: 0.7596 (OUTLIER) cc_final: 0.6363 (ttm-80) REVERT: E 169 GLU cc_start: 0.7617 (tp30) cc_final: 0.7170 (tm-30) REVERT: F 26 LEU cc_start: 0.8720 (mt) cc_final: 0.8462 (mp) REVERT: F 169 GLU cc_start: 0.7408 (tm-30) cc_final: 0.7059 (tp30) REVERT: F 267 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7755 (mt-10) REVERT: I 97 PHE cc_start: 0.8275 (m-80) cc_final: 0.8021 (m-80) REVERT: I 163 MET cc_start: 0.7388 (ttp) cc_final: 0.6935 (ttm) REVERT: K 129 MET cc_start: 0.8549 (tpp) cc_final: 0.8341 (mmt) REVERT: K 169 GLU cc_start: 0.7509 (tp30) cc_final: 0.7186 (tm-30) REVERT: K 224 GLU cc_start: 0.7133 (mt-10) cc_final: 0.6905 (mt-10) REVERT: K 276 GLN cc_start: 0.8121 (pt0) cc_final: 0.7890 (mt0) outliers start: 95 outliers final: 53 residues processed: 468 average time/residue: 1.5668 time to fit residues: 836.7951 Evaluate side-chains 451 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 397 time to evaluate : 2.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 231 LEU Chi-restraints excluded: chain G residue 232 ASP Chi-restraints excluded: chain G residue 256 MET Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 231 LEU Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 231 LEU Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 44 SER Chi-restraints excluded: chain K residue 152 GLU Chi-restraints excluded: chain K residue 256 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 276 optimal weight: 0.9980 chunk 210 optimal weight: 0.6980 chunk 145 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 133 optimal weight: 0.7980 chunk 188 optimal weight: 4.9990 chunk 281 optimal weight: 0.0970 chunk 297 optimal weight: 0.6980 chunk 146 optimal weight: 2.9990 chunk 266 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN B 102 GLN C 102 GLN D 176 GLN E 102 GLN E 176 GLN E 273 GLN E 276 GLN F 102 GLN F 176 GLN F 273 GLN ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 220 GLN G 273 GLN H 102 GLN H 273 GLN H 276 GLN I 102 GLN I 273 GLN J 176 GLN J 178 GLN J 220 GLN ** J 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 70 ASN K 176 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 27302 Z= 0.129 Angle : 0.474 8.004 36773 Z= 0.244 Chirality : 0.035 0.130 3916 Planarity : 0.003 0.040 4499 Dihedral : 11.485 59.981 4092 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.10 % Favored : 97.87 % Rotamer: Outliers : 3.61 % Allowed : 16.32 % Favored : 80.06 % 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: -0.63 (0.15), residues: 3146 helix: -0.06 (0.11), residues: 2376 sheet: None (None), residues: 0 loop : -1.16 (0.23), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 60 HIS 0.002 0.000 HIS C 282 PHE 0.012 0.001 PHE A 214 TYR 0.012 0.001 TYR A 98 ARG 0.008 0.000 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 409 time to evaluate : 3.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7615 (mm) REVERT: A 30 SER cc_start: 0.8633 (t) cc_final: 0.8325 (m) REVERT: A 102 GLN cc_start: 0.8046 (mt0) cc_final: 0.7822 (mt0) REVERT: A 149 CYS cc_start: 0.6424 (t) cc_final: 0.5640 (t) REVERT: B 88 PHE cc_start: 0.7353 (m-80) cc_final: 0.7152 (m-80) REVERT: B 133 ARG cc_start: 0.7770 (tpp-160) cc_final: 0.7481 (tpp-160) REVERT: B 273 GLN cc_start: 0.7922 (mt0) cc_final: 0.7693 (mt0) REVERT: C 149 CYS cc_start: 0.5821 (OUTLIER) cc_final: 0.5523 (t) REVERT: C 276 GLN cc_start: 0.7859 (pt0) cc_final: 0.7529 (mt0) REVERT: D 12 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7675 (mm) REVERT: D 139 GLU cc_start: 0.7112 (pm20) cc_final: 0.6658 (mm-30) REVERT: D 200 TYR cc_start: 0.7956 (t80) cc_final: 0.7739 (t80) REVERT: E 12 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7627 (mm) REVERT: E 88 PHE cc_start: 0.7277 (m-80) cc_final: 0.7063 (m-80) REVERT: E 95 ARG cc_start: 0.7529 (OUTLIER) cc_final: 0.6395 (ttm-80) REVERT: E 169 GLU cc_start: 0.7498 (tp30) cc_final: 0.7190 (tm-30) REVERT: F 12 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7664 (mm) REVERT: F 26 LEU cc_start: 0.8745 (mt) cc_final: 0.8487 (mp) REVERT: F 169 GLU cc_start: 0.7419 (tm-30) cc_final: 0.7077 (tp30) REVERT: F 267 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7743 (mt-10) REVERT: H 169 GLU cc_start: 0.7328 (tp30) cc_final: 0.7109 (tp30) REVERT: I 12 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7557 (mm) REVERT: I 25 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7655 (mt) REVERT: I 97 PHE cc_start: 0.8292 (m-80) cc_final: 0.8040 (m-80) REVERT: I 163 MET cc_start: 0.7463 (ttp) cc_final: 0.7036 (ttm) REVERT: J 12 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7568 (mm) REVERT: J 169 GLU cc_start: 0.7425 (tm-30) cc_final: 0.7176 (tp30) REVERT: J 276 GLN cc_start: 0.7784 (pt0) cc_final: 0.7552 (mt0) REVERT: K 12 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7659 (mm) REVERT: K 70 ASN cc_start: 0.8575 (OUTLIER) cc_final: 0.8347 (t0) REVERT: K 129 MET cc_start: 0.8529 (tpp) cc_final: 0.8327 (mmt) REVERT: K 169 GLU cc_start: 0.7466 (tp30) cc_final: 0.6821 (tp30) REVERT: K 276 GLN cc_start: 0.8100 (pt0) cc_final: 0.7815 (mt0) outliers start: 101 outliers final: 45 residues processed: 476 average time/residue: 1.4972 time to fit residues: 817.7200 Evaluate side-chains 432 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 376 time to evaluate : 2.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 256 MET Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 149 CYS Chi-restraints excluded: chain H residue 256 MET Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 148 GLU Chi-restraints excluded: chain I residue 149 CYS Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 132 THR Chi-restraints excluded: chain J residue 149 CYS Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 70 ASN Chi-restraints excluded: chain K residue 149 CYS Chi-restraints excluded: chain K residue 152 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 247 optimal weight: 4.9990 chunk 168 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 221 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 254 optimal weight: 3.9990 chunk 205 optimal weight: 0.0570 chunk 0 optimal weight: 20.0000 chunk 152 optimal weight: 4.9990 chunk 267 optimal weight: 0.3980 chunk 75 optimal weight: 0.7980 overall best weight: 1.4502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 102 GLN C 178 GLN E 102 GLN E 176 GLN F 176 GLN F 273 GLN ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 273 GLN H 102 GLN H 273 GLN H 276 GLN I 273 GLN J 176 GLN J 220 GLN ** J 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 176 GLN K 273 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 27302 Z= 0.204 Angle : 0.530 7.924 36773 Z= 0.272 Chirality : 0.038 0.144 3916 Planarity : 0.003 0.040 4499 Dihedral : 11.553 59.824 4092 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.79 % Allowed : 16.93 % Favored : 79.28 % 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: -0.39 (0.15), residues: 3146 helix: 0.27 (0.11), residues: 2321 sheet: None (None), residues: 0 loop : -1.54 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 262 HIS 0.001 0.000 HIS I 282 PHE 0.014 0.001 PHE D 214 TYR 0.018 0.001 TYR K 98 ARG 0.007 0.000 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 395 time to evaluate : 3.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7616 (mm) REVERT: A 30 SER cc_start: 0.8692 (t) cc_final: 0.8392 (m) REVERT: A 102 GLN cc_start: 0.7988 (mt0) cc_final: 0.7693 (mt0) REVERT: A 149 CYS cc_start: 0.6476 (t) cc_final: 0.5709 (t) REVERT: B 12 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7591 (mm) REVERT: B 273 GLN cc_start: 0.7918 (mt0) cc_final: 0.7621 (mt0) REVERT: C 12 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7474 (mm) REVERT: C 276 GLN cc_start: 0.7872 (pt0) cc_final: 0.7584 (mt0) REVERT: D 12 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7656 (mm) REVERT: D 220 GLN cc_start: 0.7755 (tm-30) cc_final: 0.7542 (tm-30) REVERT: E 12 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7509 (mm) REVERT: E 95 ARG cc_start: 0.7575 (OUTLIER) cc_final: 0.6397 (ttm-80) REVERT: E 169 GLU cc_start: 0.7490 (tp30) cc_final: 0.7180 (tm-30) REVERT: F 12 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7672 (mm) REVERT: F 169 GLU cc_start: 0.7416 (tm-30) cc_final: 0.7065 (tp30) REVERT: H 12 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7452 (mm) REVERT: H 23 MET cc_start: 0.8365 (OUTLIER) cc_final: 0.7988 (ttp) REVERT: H 169 GLU cc_start: 0.7433 (tp30) cc_final: 0.7033 (tp30) REVERT: I 12 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7564 (mm) REVERT: I 25 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.7721 (mt) REVERT: I 97 PHE cc_start: 0.8262 (m-80) cc_final: 0.7995 (m-80) REVERT: I 149 CYS cc_start: 0.5706 (OUTLIER) cc_final: 0.5359 (t) REVERT: I 163 MET cc_start: 0.7460 (ttp) cc_final: 0.7026 (ttm) REVERT: J 12 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7577 (mm) REVERT: J 169 GLU cc_start: 0.7427 (tm-30) cc_final: 0.7219 (tm-30) REVERT: K 12 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7667 (mm) REVERT: K 129 MET cc_start: 0.8555 (tpp) cc_final: 0.8325 (mmt) REVERT: K 169 GLU cc_start: 0.7436 (tp30) cc_final: 0.6833 (tp30) REVERT: K 224 GLU cc_start: 0.7124 (mt-10) cc_final: 0.6896 (mt-10) REVERT: K 276 GLN cc_start: 0.8015 (pt0) cc_final: 0.7809 (mt0) outliers start: 106 outliers final: 64 residues processed: 464 average time/residue: 1.5259 time to fit residues: 810.7837 Evaluate side-chains 460 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 382 time to evaluate : 2.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 176 GLN Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 231 LEU Chi-restraints excluded: chain G residue 256 MET Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 23 MET Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 40 LYS Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 149 CYS Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 149 CYS Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 149 CYS Chi-restraints excluded: chain J residue 227 GLU Chi-restraints excluded: chain J residue 231 LEU Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 44 SER Chi-restraints excluded: chain K residue 149 CYS Chi-restraints excluded: chain K residue 256 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 100 optimal weight: 0.0060 chunk 268 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 174 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 298 optimal weight: 2.9990 chunk 247 optimal weight: 0.9980 chunk 137 optimal weight: 6.9990 chunk 24 optimal weight: 0.5980 chunk 98 optimal weight: 0.9980 chunk 156 optimal weight: 0.0470 overall best weight: 0.5094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 102 GLN C 168 ASN D 176 GLN D 273 GLN E 102 GLN E 176 GLN F 176 GLN F 273 GLN ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 GLN G 273 GLN H 102 GLN H 273 GLN H 276 GLN I 102 GLN I 273 GLN J 176 GLN ** J 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 176 GLN K 273 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 27302 Z= 0.119 Angle : 0.456 8.529 36773 Z= 0.233 Chirality : 0.034 0.127 3916 Planarity : 0.003 0.032 4499 Dihedral : 10.898 59.848 4092 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.40 % Allowed : 17.79 % Favored : 78.81 % 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: 0.15 (0.16), residues: 3146 helix: 0.67 (0.11), residues: 2332 sheet: None (None), residues: 0 loop : -1.41 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 60 HIS 0.002 0.000 HIS D 282 PHE 0.012 0.001 PHE D 88 TYR 0.017 0.001 TYR I 98 ARG 0.006 0.000 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 402 time to evaluate : 2.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7517 (mm) REVERT: A 30 SER cc_start: 0.8614 (t) cc_final: 0.8321 (m) REVERT: A 149 CYS cc_start: 0.6432 (t) cc_final: 0.5701 (t) REVERT: B 12 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7553 (mm) REVERT: B 273 GLN cc_start: 0.7923 (mt0) cc_final: 0.7620 (mt0) REVERT: C 12 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7466 (mm) REVERT: C 72 ARG cc_start: 0.7991 (ttp80) cc_final: 0.7743 (mtp180) REVERT: C 276 GLN cc_start: 0.7915 (pt0) cc_final: 0.7580 (mt0) REVERT: D 12 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7637 (mm) REVERT: D 200 TYR cc_start: 0.8006 (t80) cc_final: 0.7712 (t80) REVERT: E 12 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7564 (mm) REVERT: E 95 ARG cc_start: 0.7443 (OUTLIER) cc_final: 0.6140 (ttm-80) REVERT: E 133 ARG cc_start: 0.7779 (tpp-160) cc_final: 0.7535 (tpp-160) REVERT: E 169 GLU cc_start: 0.7380 (tp30) cc_final: 0.6724 (tp30) REVERT: F 169 GLU cc_start: 0.7374 (tm-30) cc_final: 0.7042 (tp30) REVERT: F 276 GLN cc_start: 0.7950 (pt0) cc_final: 0.7705 (mt0) REVERT: H 12 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7521 (mm) REVERT: H 169 GLU cc_start: 0.7418 (tp30) cc_final: 0.7023 (tp30) REVERT: I 25 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7675 (mt) REVERT: I 97 PHE cc_start: 0.8252 (m-80) cc_final: 0.8000 (m-80) REVERT: I 163 MET cc_start: 0.7441 (ttp) cc_final: 0.7122 (ttm) REVERT: I 169 GLU cc_start: 0.7340 (tm-30) cc_final: 0.7038 (tp30) REVERT: J 12 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7482 (mm) REVERT: J 169 GLU cc_start: 0.7318 (tm-30) cc_final: 0.7040 (tp30) REVERT: K 169 GLU cc_start: 0.7319 (tp30) cc_final: 0.6716 (tp30) REVERT: K 276 GLN cc_start: 0.8040 (pt0) cc_final: 0.7791 (mt0) outliers start: 95 outliers final: 48 residues processed: 465 average time/residue: 1.5177 time to fit residues: 807.7323 Evaluate side-chains 427 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 370 time to evaluate : 2.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 246 PHE Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 231 LEU Chi-restraints excluded: chain G residue 256 MET Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 40 LYS Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 148 GLU Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 132 THR Chi-restraints excluded: chain J residue 149 CYS Chi-restraints excluded: chain J residue 231 LEU Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 44 SER Chi-restraints excluded: chain K residue 149 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 287 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 169 optimal weight: 0.9990 chunk 217 optimal weight: 0.7980 chunk 168 optimal weight: 0.0040 chunk 250 optimal weight: 3.9990 chunk 166 optimal weight: 0.0970 chunk 296 optimal weight: 5.9990 chunk 185 optimal weight: 0.5980 chunk 180 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN A 273 GLN D 273 GLN E 102 GLN E 273 GLN F 176 GLN F 273 GLN ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 273 GLN H 273 GLN I 102 GLN I 273 GLN J 176 GLN ** J 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 276 GLN K 273 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 27302 Z= 0.115 Angle : 0.451 8.405 36773 Z= 0.230 Chirality : 0.034 0.131 3916 Planarity : 0.003 0.031 4499 Dihedral : 10.589 59.890 4092 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.76 % Allowed : 19.11 % Favored : 78.13 % 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: 0.53 (0.16), residues: 3146 helix: 0.96 (0.11), residues: 2332 sheet: None (None), residues: 0 loop : -1.31 (0.23), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 60 HIS 0.002 0.000 HIS D 282 PHE 0.012 0.001 PHE D 88 TYR 0.018 0.001 TYR A 98 ARG 0.006 0.000 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 386 time to evaluate : 3.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7504 (mm) REVERT: A 30 SER cc_start: 0.8650 (t) cc_final: 0.8409 (p) REVERT: A 149 CYS cc_start: 0.6460 (t) cc_final: 0.5741 (t) REVERT: B 12 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7493 (mm) REVERT: B 273 GLN cc_start: 0.7949 (mt0) cc_final: 0.7630 (mt0) REVERT: C 12 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7491 (mm) REVERT: C 25 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.7896 (mt) REVERT: C 72 ARG cc_start: 0.7953 (ttp80) cc_final: 0.7707 (mtp180) REVERT: C 276 GLN cc_start: 0.7894 (pt0) cc_final: 0.7582 (mt0) REVERT: D 12 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7623 (mm) REVERT: D 200 TYR cc_start: 0.7990 (t80) cc_final: 0.7741 (t80) REVERT: E 12 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7433 (mm) REVERT: E 95 ARG cc_start: 0.7434 (OUTLIER) cc_final: 0.6074 (ttm-80) REVERT: E 133 ARG cc_start: 0.7782 (tpp-160) cc_final: 0.7534 (tpp-160) REVERT: E 169 GLU cc_start: 0.7326 (tp30) cc_final: 0.6675 (tp30) REVERT: F 12 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7626 (mm) REVERT: F 169 GLU cc_start: 0.7324 (tm-30) cc_final: 0.7017 (tp30) REVERT: F 276 GLN cc_start: 0.7948 (pt0) cc_final: 0.7737 (mt0) REVERT: H 12 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7496 (mm) REVERT: H 169 GLU cc_start: 0.7309 (tp30) cc_final: 0.6963 (tp30) REVERT: I 12 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7475 (mm) REVERT: I 25 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7601 (mt) REVERT: I 163 MET cc_start: 0.7493 (ttp) cc_final: 0.7185 (ttm) REVERT: I 169 GLU cc_start: 0.7381 (tm-30) cc_final: 0.7041 (OUTLIER) REVERT: J 12 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7392 (mm) REVERT: J 149 CYS cc_start: 0.5767 (OUTLIER) cc_final: 0.5560 (t) REVERT: J 169 GLU cc_start: 0.7196 (tm-30) cc_final: 0.6904 (tp30) REVERT: J 220 GLN cc_start: 0.7633 (tp-100) cc_final: 0.7383 (tm-30) REVERT: K 12 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7569 (mm) REVERT: K 169 GLU cc_start: 0.7327 (tp30) cc_final: 0.6718 (tp30) REVERT: K 276 GLN cc_start: 0.8043 (pt0) cc_final: 0.7833 (mt0) outliers start: 77 outliers final: 42 residues processed: 439 average time/residue: 1.5297 time to fit residues: 769.0423 Evaluate side-chains 431 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 376 time to evaluate : 3.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 40 LYS Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 176 GLN Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 231 LEU Chi-restraints excluded: chain G residue 256 MET Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 40 LYS Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 256 MET Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 149 CYS Chi-restraints excluded: chain J residue 231 LEU Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 44 SER Chi-restraints excluded: chain K residue 149 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 183 optimal weight: 10.0000 chunk 118 optimal weight: 0.0980 chunk 177 optimal weight: 0.5980 chunk 89 optimal weight: 0.9990 chunk 58 optimal weight: 0.0170 chunk 57 optimal weight: 1.9990 chunk 188 optimal weight: 5.9990 chunk 202 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 27 optimal weight: 0.0770 chunk 233 optimal weight: 8.9990 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN A 273 GLN D 273 GLN F 176 GLN F 273 GLN G 273 GLN H 273 GLN I 102 GLN I 248 ASN I 273 GLN ** J 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 276 GLN K 273 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 27302 Z= 0.105 Angle : 0.442 9.094 36773 Z= 0.223 Chirality : 0.034 0.129 3916 Planarity : 0.003 0.030 4499 Dihedral : 10.265 59.966 4092 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.18 % Allowed : 20.04 % Favored : 77.77 % 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: 0.98 (0.16), residues: 3146 helix: 1.26 (0.12), residues: 2321 sheet: None (None), residues: 0 loop : -1.01 (0.23), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 60 HIS 0.003 0.000 HIS D 282 PHE 0.010 0.001 PHE D 88 TYR 0.015 0.001 TYR A 98 ARG 0.005 0.000 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 391 time to evaluate : 3.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7488 (mm) REVERT: A 30 SER cc_start: 0.8648 (t) cc_final: 0.8408 (p) REVERT: A 149 CYS cc_start: 0.6556 (t) cc_final: 0.5953 (t) REVERT: B 12 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7494 (mm) REVERT: B 273 GLN cc_start: 0.7921 (mt0) cc_final: 0.7649 (mt0) REVERT: C 12 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7496 (mm) REVERT: C 72 ARG cc_start: 0.7855 (ttp80) cc_final: 0.7599 (mtp180) REVERT: C 276 GLN cc_start: 0.7881 (pt0) cc_final: 0.7615 (mt0) REVERT: D 200 TYR cc_start: 0.7961 (t80) cc_final: 0.7695 (t80) REVERT: E 133 ARG cc_start: 0.7729 (tpp-160) cc_final: 0.7482 (tpp-160) REVERT: E 169 GLU cc_start: 0.7280 (tp30) cc_final: 0.6636 (tp30) REVERT: F 12 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7593 (mm) REVERT: F 169 GLU cc_start: 0.7369 (tm-30) cc_final: 0.7059 (tp30) REVERT: F 276 GLN cc_start: 0.7926 (pt0) cc_final: 0.7669 (mt0) REVERT: G 169 GLU cc_start: 0.7367 (tm-30) cc_final: 0.7090 (tp30) REVERT: H 12 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7482 (mm) REVERT: H 169 GLU cc_start: 0.7163 (tp30) cc_final: 0.6816 (tp30) REVERT: I 12 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7464 (mm) REVERT: I 25 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7619 (mt) REVERT: I 163 MET cc_start: 0.7399 (ttp) cc_final: 0.7096 (ttm) REVERT: I 169 GLU cc_start: 0.7324 (tm-30) cc_final: 0.6933 (tp30) REVERT: I 283 ARG cc_start: 0.8285 (ttp80) cc_final: 0.7982 (ttp-170) REVERT: J 12 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7348 (mm) REVERT: J 220 GLN cc_start: 0.7638 (tp-100) cc_final: 0.7412 (tm-30) REVERT: K 12 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7578 (mm) REVERT: K 169 GLU cc_start: 0.7266 (tp30) cc_final: 0.6616 (tp30) outliers start: 61 outliers final: 32 residues processed: 428 average time/residue: 1.5164 time to fit residues: 743.8419 Evaluate side-chains 417 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 376 time to evaluate : 2.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 231 LEU Chi-restraints excluded: chain G residue 256 MET Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 256 MET Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 231 LEU Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 44 SER Chi-restraints excluded: chain K residue 149 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 270 optimal weight: 2.9990 chunk 284 optimal weight: 2.9990 chunk 259 optimal weight: 3.9990 chunk 276 optimal weight: 2.9990 chunk 166 optimal weight: 0.9990 chunk 120 optimal weight: 0.7980 chunk 217 optimal weight: 0.7980 chunk 84 optimal weight: 0.4980 chunk 249 optimal weight: 0.6980 chunk 261 optimal weight: 0.5980 chunk 275 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN A 273 GLN D 273 GLN E 273 GLN F 176 GLN F 273 GLN G 273 GLN H 273 GLN I 273 GLN ** J 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 273 GLN K 276 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 27302 Z= 0.129 Angle : 0.464 8.658 36773 Z= 0.234 Chirality : 0.035 0.138 3916 Planarity : 0.003 0.032 4499 Dihedral : 10.216 59.869 4092 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.29 % Allowed : 20.15 % Favored : 77.56 % 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: 0.94 (0.16), residues: 3146 helix: 1.25 (0.12), residues: 2343 sheet: None (None), residues: 0 loop : -1.16 (0.23), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 60 HIS 0.002 0.000 HIS D 282 PHE 0.011 0.001 PHE D 88 TYR 0.019 0.001 TYR E 98 ARG 0.005 0.000 ARG E 32 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 382 time to evaluate : 3.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7426 (mm) REVERT: A 30 SER cc_start: 0.8666 (t) cc_final: 0.8430 (p) REVERT: B 12 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7493 (mm) REVERT: B 273 GLN cc_start: 0.7912 (mt0) cc_final: 0.7628 (mt0) REVERT: C 12 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7481 (mm) REVERT: C 25 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.7847 (mt) REVERT: C 72 ARG cc_start: 0.7848 (ttp80) cc_final: 0.7594 (mtp180) REVERT: C 276 GLN cc_start: 0.7897 (pt0) cc_final: 0.7625 (mt0) REVERT: D 12 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7550 (mm) REVERT: D 200 TYR cc_start: 0.7979 (t80) cc_final: 0.7729 (t80) REVERT: E 12 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7500 (mm) REVERT: E 23 MET cc_start: 0.8213 (ttm) cc_final: 0.7960 (ttm) REVERT: E 95 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.6201 (ttm-80) REVERT: E 169 GLU cc_start: 0.7281 (tp30) cc_final: 0.6643 (tp30) REVERT: F 12 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7614 (mm) REVERT: F 169 GLU cc_start: 0.7333 (tm-30) cc_final: 0.7008 (tp30) REVERT: F 276 GLN cc_start: 0.7902 (pt0) cc_final: 0.7654 (mt0) REVERT: G 25 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.7854 (mt) REVERT: H 12 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7452 (mm) REVERT: H 169 GLU cc_start: 0.7158 (tp30) cc_final: 0.6773 (tp30) REVERT: I 12 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7454 (mm) REVERT: I 25 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7630 (mt) REVERT: I 163 MET cc_start: 0.7411 (ttp) cc_final: 0.7090 (ttm) REVERT: I 169 GLU cc_start: 0.7293 (tm-30) cc_final: 0.6975 (tp30) REVERT: J 12 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7326 (mm) REVERT: J 220 GLN cc_start: 0.7656 (tp-100) cc_final: 0.7422 (tm-30) REVERT: K 12 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7508 (mm) REVERT: K 72 ARG cc_start: 0.7890 (ttp80) cc_final: 0.7668 (mtp180) REVERT: K 169 GLU cc_start: 0.7310 (tp30) cc_final: 0.6694 (tp30) outliers start: 64 outliers final: 41 residues processed: 421 average time/residue: 1.5446 time to fit residues: 754.4722 Evaluate side-chains 428 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 373 time to evaluate : 3.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 231 LEU Chi-restraints excluded: chain G residue 256 MET Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 256 MET Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 231 LEU Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 44 SER Chi-restraints excluded: chain K residue 94 CYS Chi-restraints excluded: chain K residue 149 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 181 optimal weight: 0.2980 chunk 292 optimal weight: 4.9990 chunk 178 optimal weight: 4.9990 chunk 138 optimal weight: 0.9990 chunk 203 optimal weight: 4.9990 chunk 306 optimal weight: 2.9990 chunk 282 optimal weight: 0.9980 chunk 244 optimal weight: 4.9990 chunk 25 optimal weight: 0.0010 chunk 188 optimal weight: 0.9980 chunk 149 optimal weight: 0.6980 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN A 273 GLN D 102 GLN D 273 GLN F 176 GLN F 273 GLN G 220 GLN G 273 GLN H 273 GLN I 102 GLN I 273 GLN ** J 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 273 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 27302 Z= 0.121 Angle : 0.458 9.008 36773 Z= 0.231 Chirality : 0.035 0.139 3916 Planarity : 0.003 0.031 4499 Dihedral : 10.054 59.939 4092 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.25 % Allowed : 20.08 % Favored : 77.67 % 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: 1.05 (0.16), residues: 3146 helix: 1.33 (0.12), residues: 2343 sheet: None (None), residues: 0 loop : -1.14 (0.23), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 60 HIS 0.002 0.000 HIS D 282 PHE 0.011 0.001 PHE D 88 TYR 0.019 0.001 TYR K 98 ARG 0.005 0.000 ARG E 32 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 385 time to evaluate : 3.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7462 (mm) REVERT: A 30 SER cc_start: 0.8669 (t) cc_final: 0.8430 (p) REVERT: B 12 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7464 (mm) REVERT: B 273 GLN cc_start: 0.7907 (mt0) cc_final: 0.7544 (mt0) REVERT: C 12 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7417 (mm) REVERT: C 72 ARG cc_start: 0.7832 (ttp80) cc_final: 0.7577 (mtp180) REVERT: C 276 GLN cc_start: 0.7926 (pt0) cc_final: 0.7579 (mt0) REVERT: D 12 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7557 (mm) REVERT: D 200 TYR cc_start: 0.7949 (t80) cc_final: 0.7702 (t80) REVERT: E 12 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7516 (mm) REVERT: E 95 ARG cc_start: 0.7426 (OUTLIER) cc_final: 0.6124 (ttm-80) REVERT: E 169 GLU cc_start: 0.7260 (tp30) cc_final: 0.6639 (tp30) REVERT: F 12 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7614 (mm) REVERT: F 169 GLU cc_start: 0.7327 (tm-30) cc_final: 0.6999 (tp30) REVERT: F 276 GLN cc_start: 0.7915 (pt0) cc_final: 0.7675 (mt0) REVERT: G 25 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.7848 (mt) REVERT: G 169 GLU cc_start: 0.7369 (tm-30) cc_final: 0.7089 (tp30) REVERT: H 12 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7470 (mm) REVERT: H 23 MET cc_start: 0.8234 (ttp) cc_final: 0.7839 (ttp) REVERT: H 72 ARG cc_start: 0.7902 (ttp-170) cc_final: 0.7613 (mtp180) REVERT: H 169 GLU cc_start: 0.7064 (tp30) cc_final: 0.6754 (tp30) REVERT: I 12 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7456 (mm) REVERT: I 25 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7622 (mt) REVERT: I 163 MET cc_start: 0.7397 (ttp) cc_final: 0.7108 (ttm) REVERT: I 169 GLU cc_start: 0.7289 (tm-30) cc_final: 0.6984 (tp30) REVERT: J 12 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7379 (mm) REVERT: J 220 GLN cc_start: 0.7666 (tp-100) cc_final: 0.7423 (tm-30) REVERT: K 12 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7505 (mm) REVERT: K 72 ARG cc_start: 0.7880 (ttp80) cc_final: 0.7665 (mtp180) REVERT: K 169 GLU cc_start: 0.7331 (tp30) cc_final: 0.6723 (tp30) outliers start: 63 outliers final: 42 residues processed: 425 average time/residue: 1.4946 time to fit residues: 729.4678 Evaluate side-chains 430 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 375 time to evaluate : 2.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 176 GLN Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 231 LEU Chi-restraints excluded: chain G residue 256 MET Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 256 MET Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 231 LEU Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 44 SER Chi-restraints excluded: chain K residue 94 CYS Chi-restraints excluded: chain K residue 149 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 194 optimal weight: 1.9990 chunk 260 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 225 optimal weight: 3.9990 chunk 36 optimal weight: 0.0670 chunk 67 optimal weight: 0.9990 chunk 244 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 251 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 overall best weight: 1.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN A 273 GLN C 168 ASN D 102 GLN D 273 GLN F 176 GLN F 273 GLN G 220 GLN G 273 GLN H 168 ASN H 273 GLN I 102 GLN I 273 GLN ** J 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 273 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.158057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.115326 restraints weight = 27680.778| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.86 r_work: 0.3161 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 27302 Z= 0.157 Angle : 0.493 12.079 36773 Z= 0.249 Chirality : 0.037 0.142 3916 Planarity : 0.003 0.031 4499 Dihedral : 10.178 59.940 4092 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.25 % Allowed : 20.40 % Favored : 77.34 % 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: 0.91 (0.16), residues: 3146 helix: 1.23 (0.12), residues: 2354 sheet: None (None), residues: 0 loop : -1.22 (0.24), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 262 HIS 0.001 0.000 HIS K 277 PHE 0.012 0.001 PHE D 214 TYR 0.018 0.001 TYR F 98 ARG 0.005 0.000 ARG E 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12094.20 seconds wall clock time: 216 minutes 9.67 seconds (12969.67 seconds total)