Starting phenix.real_space_refine on Tue Mar 26 00:10:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jb1_9787/03_2024/6jb1_9787_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jb1_9787/03_2024/6jb1_9787.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jb1_9787/03_2024/6jb1_9787.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jb1_9787/03_2024/6jb1_9787.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jb1_9787/03_2024/6jb1_9787_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jb1_9787/03_2024/6jb1_9787_neut_updated.pdb" } resolution = 3.3 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= 0.095 sd= 0.834 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 72 5.49 5 S 244 5.16 5 C 33772 2.51 5 N 8628 2.21 5 O 9312 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 177": "NH1" <-> "NH2" Residue "A ARG 206": "NH1" <-> "NH2" Residue "A ARG 221": "NH1" <-> "NH2" Residue "A ARG 301": "NH1" <-> "NH2" Residue "A ARG 314": "NH1" <-> "NH2" Residue "A ARG 353": "NH1" <-> "NH2" Residue "B GLU 186": "OE1" <-> "OE2" Residue "B ARG 202": "NH1" <-> "NH2" Residue "B ARG 248": "NH1" <-> "NH2" Residue "B ARG 258": "NH1" <-> "NH2" Residue "B ARG 265": "NH1" <-> "NH2" Residue "B ARG 370": "NH1" <-> "NH2" Residue "B ARG 486": "NH1" <-> "NH2" Residue "B ARG 504": "NH1" <-> "NH2" Residue "B ARG 521": "NH1" <-> "NH2" Residue "B ARG 527": "NH1" <-> "NH2" Residue "B ARG 534": "NH1" <-> "NH2" Residue "B ARG 598": "NH1" <-> "NH2" Residue "B ARG 702": "NH1" <-> "NH2" Residue "B ARG 705": "NH1" <-> "NH2" Residue "B ARG 878": "NH1" <-> "NH2" Residue "B ARG 999": "NH1" <-> "NH2" Residue "B ARG 1099": "NH1" <-> "NH2" Residue "B ARG 1104": "NH1" <-> "NH2" Residue "B ARG 1111": "NH1" <-> "NH2" Residue "B ARG 1145": "NH1" <-> "NH2" Residue "B ARG 1183": "NH1" <-> "NH2" Residue "B ARG 1218": "NH1" <-> "NH2" Residue "B ARG 1300": "NH1" <-> "NH2" Residue "C ARG 177": "NH1" <-> "NH2" Residue "C ARG 206": "NH1" <-> "NH2" Residue "C ARG 221": "NH1" <-> "NH2" Residue "C ARG 301": "NH1" <-> "NH2" Residue "C ARG 314": "NH1" <-> "NH2" Residue "C ARG 353": "NH1" <-> "NH2" Residue "D GLU 186": "OE1" <-> "OE2" Residue "D ARG 202": "NH1" <-> "NH2" Residue "D ARG 248": "NH1" <-> "NH2" Residue "D ARG 258": "NH1" <-> "NH2" Residue "D ARG 265": "NH1" <-> "NH2" Residue "D ARG 370": "NH1" <-> "NH2" Residue "D ARG 486": "NH1" <-> "NH2" Residue "D ARG 504": "NH1" <-> "NH2" Residue "D ARG 521": "NH1" <-> "NH2" Residue "D ARG 527": "NH1" <-> "NH2" Residue "D ARG 534": "NH1" <-> "NH2" Residue "D ARG 598": "NH1" <-> "NH2" Residue "D ARG 702": "NH1" <-> "NH2" Residue "D ARG 705": "NH1" <-> "NH2" Residue "D ARG 878": "NH1" <-> "NH2" Residue "D ARG 999": "NH1" <-> "NH2" Residue "D ARG 1099": "NH1" <-> "NH2" Residue "D ARG 1104": "NH1" <-> "NH2" Residue "D ARG 1111": "NH1" <-> "NH2" Residue "D ARG 1145": "NH1" <-> "NH2" Residue "D ARG 1183": "NH1" <-> "NH2" Residue "D ARG 1218": "NH1" <-> "NH2" Residue "D ARG 1300": "NH1" <-> "NH2" Residue "E ARG 177": "NH1" <-> "NH2" Residue "E ARG 206": "NH1" <-> "NH2" Residue "E ARG 221": "NH1" <-> "NH2" Residue "E ARG 301": "NH1" <-> "NH2" Residue "E ARG 314": "NH1" <-> "NH2" Residue "E ARG 353": "NH1" <-> "NH2" Residue "F GLU 186": "OE1" <-> "OE2" Residue "F ARG 202": "NH1" <-> "NH2" Residue "F ARG 248": "NH1" <-> "NH2" Residue "F ARG 258": "NH1" <-> "NH2" Residue "F ARG 265": "NH1" <-> "NH2" Residue "F ARG 370": "NH1" <-> "NH2" Residue "F ARG 486": "NH1" <-> "NH2" Residue "F ARG 504": "NH1" <-> "NH2" Residue "F ARG 521": "NH1" <-> "NH2" Residue "F ARG 527": "NH1" <-> "NH2" Residue "F ARG 534": "NH1" <-> "NH2" Residue "F ARG 598": "NH1" <-> "NH2" Residue "F ARG 702": "NH1" <-> "NH2" Residue "F ARG 705": "NH1" <-> "NH2" Residue "F ARG 878": "NH1" <-> "NH2" Residue "F ARG 999": "NH1" <-> "NH2" Residue "F ARG 1099": "NH1" <-> "NH2" Residue "F ARG 1104": "NH1" <-> "NH2" Residue "F ARG 1111": "NH1" <-> "NH2" Residue "F ARG 1145": "NH1" <-> "NH2" Residue "F ARG 1183": "NH1" <-> "NH2" Residue "F ARG 1218": "NH1" <-> "NH2" Residue "F ARG 1300": "NH1" <-> "NH2" Residue "G ARG 177": "NH1" <-> "NH2" Residue "G ARG 206": "NH1" <-> "NH2" Residue "G ARG 221": "NH1" <-> "NH2" Residue "G ARG 301": "NH1" <-> "NH2" Residue "G ARG 314": "NH1" <-> "NH2" Residue "G ARG 353": "NH1" <-> "NH2" Residue "H GLU 186": "OE1" <-> "OE2" Residue "H ARG 202": "NH1" <-> "NH2" Residue "H ARG 248": "NH1" <-> "NH2" Residue "H ARG 258": "NH1" <-> "NH2" Residue "H ARG 265": "NH1" <-> "NH2" Residue "H ARG 370": "NH1" <-> "NH2" Residue "H ARG 486": "NH1" <-> "NH2" Residue "H ARG 504": "NH1" <-> "NH2" Residue "H ARG 521": "NH1" <-> "NH2" Residue "H ARG 527": "NH1" <-> "NH2" Residue "H ARG 534": "NH1" <-> "NH2" Residue "H ARG 598": "NH1" <-> "NH2" Residue "H ARG 702": "NH1" <-> "NH2" Residue "H ARG 705": "NH1" <-> "NH2" Residue "H ARG 878": "NH1" <-> "NH2" Residue "H ARG 999": "NH1" <-> "NH2" Residue "H ARG 1099": "NH1" <-> "NH2" Residue "H ARG 1104": "NH1" <-> "NH2" Residue "H ARG 1111": "NH1" <-> "NH2" Residue "H ARG 1145": "NH1" <-> "NH2" Residue "H ARG 1183": "NH1" <-> "NH2" Residue "H ARG 1218": "NH1" <-> "NH2" Residue "H ARG 1300": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 52028 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2543 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 13, 'TRANS': 313} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 9890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1366, 9890 Classifications: {'peptide': 1366} Incomplete info: {'truncation_to_alanine': 254} Link IDs: {'PTRANS': 46, 'TRANS': 1319} Chain breaks: 9 Unresolved non-hydrogen bonds: 925 Unresolved non-hydrogen angles: 1155 Unresolved non-hydrogen dihedrals: 741 Unresolved non-hydrogen chiralities: 85 Planarities with less than four sites: {'GLN:plan1': 20, 'ASP:plan': 26, 'TYR:plan': 2, 'ASN:plan1': 8, 'HIS:plan': 6, 'PHE:plan': 14, 'GLU:plan': 23, 'ARG:plan': 22} Unresolved non-hydrogen planarities: 512 Chain: "C" Number of atoms: 2543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2543 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 13, 'TRANS': 313} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 9890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1366, 9890 Classifications: {'peptide': 1366} Incomplete info: {'truncation_to_alanine': 254} Link IDs: {'PTRANS': 46, 'TRANS': 1319} Chain breaks: 9 Unresolved non-hydrogen bonds: 925 Unresolved non-hydrogen angles: 1155 Unresolved non-hydrogen dihedrals: 741 Unresolved non-hydrogen chiralities: 85 Planarities with less than four sites: {'GLN:plan1': 20, 'ASP:plan': 26, 'TYR:plan': 2, 'ASN:plan1': 8, 'HIS:plan': 6, 'PHE:plan': 14, 'GLU:plan': 23, 'ARG:plan': 22} Unresolved non-hydrogen planarities: 512 Chain: "E" Number of atoms: 2543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2543 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 13, 'TRANS': 313} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "F" Number of atoms: 9890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1366, 9890 Classifications: {'peptide': 1366} Incomplete info: {'truncation_to_alanine': 254} Link IDs: {'PTRANS': 46, 'TRANS': 1319} Chain breaks: 9 Unresolved non-hydrogen bonds: 925 Unresolved non-hydrogen angles: 1155 Unresolved non-hydrogen dihedrals: 741 Unresolved non-hydrogen chiralities: 85 Planarities with less than four sites: {'GLN:plan1': 20, 'ASP:plan': 26, 'TYR:plan': 2, 'ASN:plan1': 8, 'HIS:plan': 6, 'PHE:plan': 14, 'GLU:plan': 23, 'ARG:plan': 22} Unresolved non-hydrogen planarities: 512 Chain: "G" Number of atoms: 2543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2543 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 13, 'TRANS': 313} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "H" Number of atoms: 9890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1366, 9890 Classifications: {'peptide': 1366} Incomplete info: {'truncation_to_alanine': 254} Link IDs: {'PTRANS': 46, 'TRANS': 1319} Chain breaks: 9 Unresolved non-hydrogen bonds: 925 Unresolved non-hydrogen angles: 1155 Unresolved non-hydrogen dihedrals: 741 Unresolved non-hydrogen chiralities: 85 Planarities with less than four sites: {'GLN:plan1': 20, 'ASP:plan': 26, 'TYR:plan': 2, 'ASN:plan1': 8, 'HIS:plan': 6, 'PHE:plan': 14, 'GLU:plan': 23, 'ARG:plan': 22} Unresolved non-hydrogen planarities: 512 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'POV:plan-3': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 512 Unusual residues: {'AGS': 1, 'AJP': 1, 'BJX': 1, 'POV': 8, 'PTY': 4} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 254 Unresolved non-hydrogen angles: 270 Unresolved non-hydrogen dihedrals: 259 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-1': 4, 'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'POV:plan-3': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 512 Unusual residues: {'AGS': 1, 'AJP': 1, 'BJX': 1, 'POV': 8, 'PTY': 4} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 254 Unresolved non-hydrogen angles: 270 Unresolved non-hydrogen dihedrals: 259 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-1': 4, 'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 22 Chain: "E" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'POV:plan-3': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 512 Unusual residues: {'AGS': 1, 'AJP': 1, 'BJX': 1, 'POV': 8, 'PTY': 4} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 254 Unresolved non-hydrogen angles: 270 Unresolved non-hydrogen dihedrals: 259 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-1': 4, 'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 22 Chain: "G" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'POV:plan-3': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 512 Unusual residues: {'AGS': 1, 'AJP': 1, 'BJX': 1, 'POV': 8, 'PTY': 4} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 254 Unresolved non-hydrogen angles: 270 Unresolved non-hydrogen dihedrals: 259 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-1': 4, 'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 22 Time building chain proxies: 27.92, per 1000 atoms: 0.54 Number of scatterers: 52028 At special positions: 0 Unit cell: (242.292, 242.292, 141.668, 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 244 16.00 P 72 15.00 O 9312 8.00 N 8628 7.00 C 33772 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 142 " distance=2.05 Simple disulfide: pdb=" SG CYS B 6 " - pdb=" SG CYS B 26 " distance=2.03 Simple disulfide: pdb=" SG CYS C 110 " - pdb=" SG CYS C 142 " distance=2.05 Simple disulfide: pdb=" SG CYS D 6 " - pdb=" SG CYS D 26 " distance=2.03 Simple disulfide: pdb=" SG CYS E 110 " - pdb=" SG CYS E 142 " distance=2.05 Simple disulfide: pdb=" SG CYS F 6 " - pdb=" SG CYS F 26 " distance=2.03 Simple disulfide: pdb=" SG CYS G 110 " - pdb=" SG CYS G 142 " distance=2.05 Simple disulfide: pdb=" SG CYS H 6 " - pdb=" SG CYS H 26 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 20.59 Conformation dependent library (CDL) restraints added in 9.9 seconds 13368 Ramachandran restraints generated. 6684 Oldfield, 0 Emsley, 6684 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12776 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 216 helices and 32 sheets defined 57.4% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 13.21 Creating SS restraints... Processing helix chain 'A' and resid 54 through 57 No H-bonds generated for 'chain 'A' and resid 54 through 57' Processing helix chain 'A' and resid 59 through 65 Processing helix chain 'A' and resid 68 through 96 removed outlier: 3.732A pdb=" N SER A 82 " --> pdb=" O SER A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 128 Processing helix chain 'A' and resid 143 through 171 Processing helix chain 'A' and resid 330 through 332 No H-bonds generated for 'chain 'A' and resid 330 through 332' Processing helix chain 'A' and resid 346 through 357 Processing helix chain 'B' and resid 13 through 15 No H-bonds generated for 'chain 'B' and resid 13 through 15' Processing helix chain 'B' and resid 21 through 23 No H-bonds generated for 'chain 'B' and resid 21 through 23' Processing helix chain 'B' and resid 28 through 51 removed outlier: 3.642A pdb=" N ASN B 32 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL B 34 " --> pdb=" O ALA B 30 " (cutoff:3.500A) Proline residue: B 35 - end of helix Proline residue: B 45 - end of helix Processing helix chain 'B' and resid 71 through 95 Processing helix chain 'B' and resid 104 through 130 Proline residue: B 109 - end of helix removed outlier: 3.732A pdb=" N MET B 115 " --> pdb=" O GLY B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 160 removed outlier: 3.587A pdb=" N ILE B 141 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N TRP B 143 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N THR B 149 " --> pdb=" O ALA B 146 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE B 152 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL B 155 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS B 156 " --> pdb=" O LYS B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 192 Processing helix chain 'B' and resid 208 through 211 No H-bonds generated for 'chain 'B' and resid 208 through 211' Processing helix chain 'B' and resid 224 through 229 Processing helix chain 'B' and resid 232 through 242 Processing helix chain 'B' and resid 255 through 257 No H-bonds generated for 'chain 'B' and resid 255 through 257' Processing helix chain 'B' and resid 259 through 275 Processing helix chain 'B' and resid 284 through 328 removed outlier: 6.263A pdb=" N ARG B 297 " --> pdb=" O HIS B 293 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ARG B 298 " --> pdb=" O ALA B 294 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLY B 316 " --> pdb=" O LEU B 312 " (cutoff:3.500A) Proline residue: B 317 - end of helix Processing helix chain 'B' and resid 348 through 353 removed outlier: 3.542A pdb=" N GLY B 353 " --> pdb=" O GLN B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 401 removed outlier: 3.786A pdb=" N HIS B 401 " --> pdb=" O ASN B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 422 Processing helix chain 'B' and resid 424 through 456 Proline residue: B 436 - end of helix removed outlier: 3.556A pdb=" N TRP B 439 " --> pdb=" O CYS B 435 " (cutoff:3.500A) Proline residue: B 442 - end of helix Processing helix chain 'B' and resid 458 through 504 removed outlier: 3.617A pdb=" N ILE B 462 " --> pdb=" O VAL B 458 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU B 470 " --> pdb=" O VAL B 466 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ALA B 471 " --> pdb=" O ILE B 467 " (cutoff:3.500A) Proline residue: B 472 - end of helix removed outlier: 4.014A pdb=" N HIS B 491 " --> pdb=" O SER B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 512 Processing helix chain 'B' and resid 515 through 563 removed outlier: 3.868A pdb=" N ALA B 535 " --> pdb=" O THR B 531 " (cutoff:3.500A) Proline residue: B 551 - end of helix Processing helix chain 'B' and resid 573 through 615 removed outlier: 4.312A pdb=" N THR B 588 " --> pdb=" O HIS B 584 " (cutoff:3.500A) Proline residue: B 589 - end of helix removed outlier: 4.588A pdb=" N SER B 594 " --> pdb=" O LEU B 590 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N SER B 595 " --> pdb=" O PHE B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 726 Processing helix chain 'B' and resid 784 through 789 Processing helix chain 'B' and resid 797 through 806 Processing helix chain 'B' and resid 809 through 813 Processing helix chain 'B' and resid 832 through 845 Processing helix chain 'B' and resid 862 through 871 Processing helix chain 'B' and resid 914 through 918 Processing helix chain 'B' and resid 998 through 1006 Processing helix chain 'B' and resid 1010 through 1038 removed outlier: 3.796A pdb=" N ALA B1035 " --> pdb=" O ASP B1031 " (cutoff:3.500A) Processing helix chain 'B' and resid 1061 through 1106 Processing helix chain 'B' and resid 1110 through 1115 Processing helix chain 'B' and resid 1118 through 1126 removed outlier: 3.867A pdb=" N PHE B1125 " --> pdb=" O ILE B1121 " (cutoff:3.500A) Processing helix chain 'B' and resid 1128 through 1160 removed outlier: 4.487A pdb=" N ILE B1136 " --> pdb=" O ILE B1132 " (cutoff:3.500A) Proline residue: B1137 - end of helix Processing helix chain 'B' and resid 1164 through 1209 removed outlier: 3.858A pdb=" N LEU B1169 " --> pdb=" O LEU B1165 " (cutoff:3.500A) Proline residue: B1170 - end of helix removed outlier: 3.790A pdb=" N GLN B1197 " --> pdb=" O ASP B1193 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU B1198 " --> pdb=" O ASP B1194 " (cutoff:3.500A) Proline residue: B1199 - end of helix Processing helix chain 'B' and resid 1211 through 1216 Processing helix chain 'B' and resid 1220 through 1273 Processing helix chain 'B' and resid 1278 through 1320 removed outlier: 3.597A pdb=" N GLY B1282 " --> pdb=" O ALA B1278 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N SER B1292 " --> pdb=" O ALA B1288 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ASN B1293 " --> pdb=" O LEU B1289 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR B1294 " --> pdb=" O MET B1290 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE B1307 " --> pdb=" O ALA B1303 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN B1308 " --> pdb=" O ASP B1304 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA B1311 " --> pdb=" O ILE B1307 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL B1312 " --> pdb=" O GLN B1308 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS B1320 " --> pdb=" O HIS B1316 " (cutoff:3.500A) Processing helix chain 'B' and resid 1385 through 1393 Processing helix chain 'B' and resid 1415 through 1419 Processing helix chain 'B' and resid 1436 through 1440 Processing helix chain 'B' and resid 1448 through 1457 Processing helix chain 'B' and resid 1461 through 1465 Processing helix chain 'B' and resid 1484 through 1498 Processing helix chain 'B' and resid 1514 through 1527 removed outlier: 4.208A pdb=" N ILE B1519 " --> pdb=" O ALA B1515 " (cutoff:3.500A) Processing helix chain 'B' and resid 1540 through 1545 Processing helix chain 'B' and resid 1563 through 1569 removed outlier: 3.882A pdb=" N SER B1568 " --> pdb=" O GLU B1564 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 57 No H-bonds generated for 'chain 'C' and resid 54 through 57' Processing helix chain 'C' and resid 59 through 65 Processing helix chain 'C' and resid 68 through 96 removed outlier: 3.732A pdb=" N SER C 82 " --> pdb=" O SER C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 128 Processing helix chain 'C' and resid 143 through 171 Processing helix chain 'C' and resid 330 through 332 No H-bonds generated for 'chain 'C' and resid 330 through 332' Processing helix chain 'C' and resid 346 through 357 Processing helix chain 'D' and resid 13 through 15 No H-bonds generated for 'chain 'D' and resid 13 through 15' Processing helix chain 'D' and resid 21 through 23 No H-bonds generated for 'chain 'D' and resid 21 through 23' Processing helix chain 'D' and resid 28 through 51 removed outlier: 3.642A pdb=" N ASN D 32 " --> pdb=" O VAL D 28 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL D 33 " --> pdb=" O ASP D 29 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL D 34 " --> pdb=" O ALA D 30 " (cutoff:3.500A) Proline residue: D 35 - end of helix Proline residue: D 45 - end of helix Processing helix chain 'D' and resid 71 through 95 Processing helix chain 'D' and resid 104 through 130 Proline residue: D 109 - end of helix removed outlier: 3.732A pdb=" N MET D 115 " --> pdb=" O GLY D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 160 removed outlier: 3.587A pdb=" N ILE D 141 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N TRP D 143 " --> pdb=" O LEU D 140 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N THR D 149 " --> pdb=" O ALA D 146 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE D 152 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL D 155 " --> pdb=" O ILE D 152 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS D 156 " --> pdb=" O LYS D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 192 Processing helix chain 'D' and resid 208 through 211 No H-bonds generated for 'chain 'D' and resid 208 through 211' Processing helix chain 'D' and resid 224 through 229 Processing helix chain 'D' and resid 232 through 242 Processing helix chain 'D' and resid 255 through 257 No H-bonds generated for 'chain 'D' and resid 255 through 257' Processing helix chain 'D' and resid 259 through 275 Processing helix chain 'D' and resid 284 through 328 removed outlier: 6.263A pdb=" N ARG D 297 " --> pdb=" O HIS D 293 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ARG D 298 " --> pdb=" O ALA D 294 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLY D 316 " --> pdb=" O LEU D 312 " (cutoff:3.500A) Proline residue: D 317 - end of helix Processing helix chain 'D' and resid 348 through 353 removed outlier: 3.542A pdb=" N GLY D 353 " --> pdb=" O GLN D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 401 removed outlier: 3.786A pdb=" N HIS D 401 " --> pdb=" O ASN D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 422 Processing helix chain 'D' and resid 424 through 456 Proline residue: D 436 - end of helix removed outlier: 3.556A pdb=" N TRP D 439 " --> pdb=" O CYS D 435 " (cutoff:3.500A) Proline residue: D 442 - end of helix Processing helix chain 'D' and resid 458 through 504 removed outlier: 3.617A pdb=" N ILE D 462 " --> pdb=" O VAL D 458 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU D 470 " --> pdb=" O VAL D 466 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ALA D 471 " --> pdb=" O ILE D 467 " (cutoff:3.500A) Proline residue: D 472 - end of helix removed outlier: 4.014A pdb=" N HIS D 491 " --> pdb=" O SER D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 506 through 512 Processing helix chain 'D' and resid 515 through 563 removed outlier: 3.868A pdb=" N ALA D 535 " --> pdb=" O THR D 531 " (cutoff:3.500A) Proline residue: D 551 - end of helix Processing helix chain 'D' and resid 573 through 615 removed outlier: 4.312A pdb=" N THR D 588 " --> pdb=" O HIS D 584 " (cutoff:3.500A) Proline residue: D 589 - end of helix removed outlier: 4.588A pdb=" N SER D 594 " --> pdb=" O LEU D 590 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N SER D 595 " --> pdb=" O PHE D 591 " (cutoff:3.500A) Processing helix chain 'D' and resid 719 through 726 Processing helix chain 'D' and resid 784 through 789 Processing helix chain 'D' and resid 797 through 806 Processing helix chain 'D' and resid 809 through 813 Processing helix chain 'D' and resid 832 through 845 Processing helix chain 'D' and resid 862 through 871 Processing helix chain 'D' and resid 914 through 918 Processing helix chain 'D' and resid 998 through 1006 Processing helix chain 'D' and resid 1010 through 1038 removed outlier: 3.796A pdb=" N ALA D1035 " --> pdb=" O ASP D1031 " (cutoff:3.500A) Processing helix chain 'D' and resid 1061 through 1106 Processing helix chain 'D' and resid 1110 through 1115 Processing helix chain 'D' and resid 1118 through 1126 removed outlier: 3.867A pdb=" N PHE D1125 " --> pdb=" O ILE D1121 " (cutoff:3.500A) Processing helix chain 'D' and resid 1128 through 1160 removed outlier: 4.487A pdb=" N ILE D1136 " --> pdb=" O ILE D1132 " (cutoff:3.500A) Proline residue: D1137 - end of helix Processing helix chain 'D' and resid 1164 through 1209 removed outlier: 3.858A pdb=" N LEU D1169 " --> pdb=" O LEU D1165 " (cutoff:3.500A) Proline residue: D1170 - end of helix removed outlier: 3.790A pdb=" N GLN D1197 " --> pdb=" O ASP D1193 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU D1198 " --> pdb=" O ASP D1194 " (cutoff:3.500A) Proline residue: D1199 - end of helix Processing helix chain 'D' and resid 1211 through 1216 Processing helix chain 'D' and resid 1220 through 1273 Processing helix chain 'D' and resid 1278 through 1320 removed outlier: 3.597A pdb=" N GLY D1282 " --> pdb=" O ALA D1278 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N SER D1292 " --> pdb=" O ALA D1288 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ASN D1293 " --> pdb=" O LEU D1289 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR D1294 " --> pdb=" O MET D1290 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE D1307 " --> pdb=" O ALA D1303 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN D1308 " --> pdb=" O ASP D1304 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA D1311 " --> pdb=" O ILE D1307 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL D1312 " --> pdb=" O GLN D1308 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS D1320 " --> pdb=" O HIS D1316 " (cutoff:3.500A) Processing helix chain 'D' and resid 1385 through 1393 Processing helix chain 'D' and resid 1415 through 1419 Processing helix chain 'D' and resid 1436 through 1440 Processing helix chain 'D' and resid 1448 through 1457 Processing helix chain 'D' and resid 1461 through 1465 Processing helix chain 'D' and resid 1484 through 1498 Processing helix chain 'D' and resid 1514 through 1527 removed outlier: 4.208A pdb=" N ILE D1519 " --> pdb=" O ALA D1515 " (cutoff:3.500A) Processing helix chain 'D' and resid 1540 through 1545 Processing helix chain 'D' and resid 1563 through 1569 removed outlier: 3.882A pdb=" N SER D1568 " --> pdb=" O GLU D1564 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 57 No H-bonds generated for 'chain 'E' and resid 54 through 57' Processing helix chain 'E' and resid 59 through 65 Processing helix chain 'E' and resid 68 through 96 removed outlier: 3.732A pdb=" N SER E 82 " --> pdb=" O SER E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 128 Processing helix chain 'E' and resid 143 through 171 Processing helix chain 'E' and resid 330 through 332 No H-bonds generated for 'chain 'E' and resid 330 through 332' Processing helix chain 'E' and resid 346 through 357 Processing helix chain 'F' and resid 13 through 15 No H-bonds generated for 'chain 'F' and resid 13 through 15' Processing helix chain 'F' and resid 21 through 23 No H-bonds generated for 'chain 'F' and resid 21 through 23' Processing helix chain 'F' and resid 28 through 51 removed outlier: 3.642A pdb=" N ASN F 32 " --> pdb=" O VAL F 28 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL F 33 " --> pdb=" O ASP F 29 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL F 34 " --> pdb=" O ALA F 30 " (cutoff:3.500A) Proline residue: F 35 - end of helix Proline residue: F 45 - end of helix Processing helix chain 'F' and resid 71 through 95 Processing helix chain 'F' and resid 104 through 130 Proline residue: F 109 - end of helix removed outlier: 3.732A pdb=" N MET F 115 " --> pdb=" O GLY F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 160 removed outlier: 3.587A pdb=" N ILE F 141 " --> pdb=" O ALA F 138 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N TRP F 143 " --> pdb=" O LEU F 140 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N THR F 149 " --> pdb=" O ALA F 146 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE F 152 " --> pdb=" O THR F 149 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL F 155 " --> pdb=" O ILE F 152 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS F 156 " --> pdb=" O LYS F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 192 Processing helix chain 'F' and resid 208 through 211 No H-bonds generated for 'chain 'F' and resid 208 through 211' Processing helix chain 'F' and resid 224 through 229 Processing helix chain 'F' and resid 232 through 242 Processing helix chain 'F' and resid 255 through 257 No H-bonds generated for 'chain 'F' and resid 255 through 257' Processing helix chain 'F' and resid 259 through 275 Processing helix chain 'F' and resid 284 through 328 removed outlier: 6.263A pdb=" N ARG F 297 " --> pdb=" O HIS F 293 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ARG F 298 " --> pdb=" O ALA F 294 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLY F 316 " --> pdb=" O LEU F 312 " (cutoff:3.500A) Proline residue: F 317 - end of helix Processing helix chain 'F' and resid 348 through 353 removed outlier: 3.542A pdb=" N GLY F 353 " --> pdb=" O GLN F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 357 through 401 removed outlier: 3.786A pdb=" N HIS F 401 " --> pdb=" O ASN F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 422 Processing helix chain 'F' and resid 424 through 456 Proline residue: F 436 - end of helix removed outlier: 3.556A pdb=" N TRP F 439 " --> pdb=" O CYS F 435 " (cutoff:3.500A) Proline residue: F 442 - end of helix Processing helix chain 'F' and resid 458 through 504 removed outlier: 3.617A pdb=" N ILE F 462 " --> pdb=" O VAL F 458 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU F 470 " --> pdb=" O VAL F 466 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ALA F 471 " --> pdb=" O ILE F 467 " (cutoff:3.500A) Proline residue: F 472 - end of helix removed outlier: 4.014A pdb=" N HIS F 491 " --> pdb=" O SER F 487 " (cutoff:3.500A) Processing helix chain 'F' and resid 506 through 512 Processing helix chain 'F' and resid 515 through 563 removed outlier: 3.868A pdb=" N ALA F 535 " --> pdb=" O THR F 531 " (cutoff:3.500A) Proline residue: F 551 - end of helix Processing helix chain 'F' and resid 573 through 615 removed outlier: 4.312A pdb=" N THR F 588 " --> pdb=" O HIS F 584 " (cutoff:3.500A) Proline residue: F 589 - end of helix removed outlier: 4.588A pdb=" N SER F 594 " --> pdb=" O LEU F 590 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N SER F 595 " --> pdb=" O PHE F 591 " (cutoff:3.500A) Processing helix chain 'F' and resid 719 through 726 Processing helix chain 'F' and resid 784 through 789 Processing helix chain 'F' and resid 797 through 806 Processing helix chain 'F' and resid 809 through 813 Processing helix chain 'F' and resid 832 through 845 Processing helix chain 'F' and resid 862 through 871 Processing helix chain 'F' and resid 914 through 918 Processing helix chain 'F' and resid 998 through 1006 Processing helix chain 'F' and resid 1010 through 1038 removed outlier: 3.796A pdb=" N ALA F1035 " --> pdb=" O ASP F1031 " (cutoff:3.500A) Processing helix chain 'F' and resid 1061 through 1106 Processing helix chain 'F' and resid 1110 through 1115 Processing helix chain 'F' and resid 1118 through 1126 removed outlier: 3.867A pdb=" N PHE F1125 " --> pdb=" O ILE F1121 " (cutoff:3.500A) Processing helix chain 'F' and resid 1128 through 1160 removed outlier: 4.487A pdb=" N ILE F1136 " --> pdb=" O ILE F1132 " (cutoff:3.500A) Proline residue: F1137 - end of helix Processing helix chain 'F' and resid 1164 through 1209 removed outlier: 3.858A pdb=" N LEU F1169 " --> pdb=" O LEU F1165 " (cutoff:3.500A) Proline residue: F1170 - end of helix removed outlier: 3.790A pdb=" N GLN F1197 " --> pdb=" O ASP F1193 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU F1198 " --> pdb=" O ASP F1194 " (cutoff:3.500A) Proline residue: F1199 - end of helix Processing helix chain 'F' and resid 1211 through 1216 Processing helix chain 'F' and resid 1220 through 1273 Processing helix chain 'F' and resid 1278 through 1320 removed outlier: 3.597A pdb=" N GLY F1282 " --> pdb=" O ALA F1278 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N SER F1292 " --> pdb=" O ALA F1288 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ASN F1293 " --> pdb=" O LEU F1289 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR F1294 " --> pdb=" O MET F1290 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE F1307 " --> pdb=" O ALA F1303 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN F1308 " --> pdb=" O ASP F1304 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA F1311 " --> pdb=" O ILE F1307 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL F1312 " --> pdb=" O GLN F1308 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS F1320 " --> pdb=" O HIS F1316 " (cutoff:3.500A) Processing helix chain 'F' and resid 1385 through 1393 Processing helix chain 'F' and resid 1415 through 1419 Processing helix chain 'F' and resid 1436 through 1440 Processing helix chain 'F' and resid 1448 through 1457 Processing helix chain 'F' and resid 1461 through 1465 Processing helix chain 'F' and resid 1484 through 1498 Processing helix chain 'F' and resid 1514 through 1527 removed outlier: 4.208A pdb=" N ILE F1519 " --> pdb=" O ALA F1515 " (cutoff:3.500A) Processing helix chain 'F' and resid 1540 through 1545 Processing helix chain 'F' and resid 1563 through 1569 removed outlier: 3.882A pdb=" N SER F1568 " --> pdb=" O GLU F1564 " (cutoff:3.500A) Processing helix chain 'G' and resid 54 through 57 No H-bonds generated for 'chain 'G' and resid 54 through 57' Processing helix chain 'G' and resid 59 through 65 Processing helix chain 'G' and resid 68 through 96 removed outlier: 3.732A pdb=" N SER G 82 " --> pdb=" O SER G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 128 Processing helix chain 'G' and resid 143 through 171 Processing helix chain 'G' and resid 330 through 332 No H-bonds generated for 'chain 'G' and resid 330 through 332' Processing helix chain 'G' and resid 346 through 357 Processing helix chain 'H' and resid 13 through 15 No H-bonds generated for 'chain 'H' and resid 13 through 15' Processing helix chain 'H' and resid 21 through 23 No H-bonds generated for 'chain 'H' and resid 21 through 23' Processing helix chain 'H' and resid 28 through 51 removed outlier: 3.642A pdb=" N ASN H 32 " --> pdb=" O VAL H 28 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL H 33 " --> pdb=" O ASP H 29 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL H 34 " --> pdb=" O ALA H 30 " (cutoff:3.500A) Proline residue: H 35 - end of helix Proline residue: H 45 - end of helix Processing helix chain 'H' and resid 71 through 95 Processing helix chain 'H' and resid 104 through 130 Proline residue: H 109 - end of helix removed outlier: 3.732A pdb=" N MET H 115 " --> pdb=" O GLY H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 133 through 160 removed outlier: 3.587A pdb=" N ILE H 141 " --> pdb=" O ALA H 138 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N TRP H 143 " --> pdb=" O LEU H 140 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N THR H 149 " --> pdb=" O ALA H 146 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE H 152 " --> pdb=" O THR H 149 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL H 155 " --> pdb=" O ILE H 152 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS H 156 " --> pdb=" O LYS H 153 " (cutoff:3.500A) Processing helix chain 'H' and resid 167 through 192 Processing helix chain 'H' and resid 208 through 211 No H-bonds generated for 'chain 'H' and resid 208 through 211' Processing helix chain 'H' and resid 224 through 229 Processing helix chain 'H' and resid 232 through 242 Processing helix chain 'H' and resid 255 through 257 No H-bonds generated for 'chain 'H' and resid 255 through 257' Processing helix chain 'H' and resid 259 through 275 Processing helix chain 'H' and resid 284 through 328 removed outlier: 6.263A pdb=" N ARG H 297 " --> pdb=" O HIS H 293 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ARG H 298 " --> pdb=" O ALA H 294 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLY H 316 " --> pdb=" O LEU H 312 " (cutoff:3.500A) Proline residue: H 317 - end of helix Processing helix chain 'H' and resid 348 through 353 removed outlier: 3.542A pdb=" N GLY H 353 " --> pdb=" O GLN H 349 " (cutoff:3.500A) Processing helix chain 'H' and resid 357 through 401 removed outlier: 3.786A pdb=" N HIS H 401 " --> pdb=" O ASN H 397 " (cutoff:3.500A) Processing helix chain 'H' and resid 414 through 422 Processing helix chain 'H' and resid 424 through 456 Proline residue: H 436 - end of helix removed outlier: 3.556A pdb=" N TRP H 439 " --> pdb=" O CYS H 435 " (cutoff:3.500A) Proline residue: H 442 - end of helix Processing helix chain 'H' and resid 458 through 504 removed outlier: 3.617A pdb=" N ILE H 462 " --> pdb=" O VAL H 458 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU H 470 " --> pdb=" O VAL H 466 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ALA H 471 " --> pdb=" O ILE H 467 " (cutoff:3.500A) Proline residue: H 472 - end of helix removed outlier: 4.014A pdb=" N HIS H 491 " --> pdb=" O SER H 487 " (cutoff:3.500A) Processing helix chain 'H' and resid 506 through 512 Processing helix chain 'H' and resid 515 through 563 removed outlier: 3.868A pdb=" N ALA H 535 " --> pdb=" O THR H 531 " (cutoff:3.500A) Proline residue: H 551 - end of helix Processing helix chain 'H' and resid 573 through 615 removed outlier: 4.312A pdb=" N THR H 588 " --> pdb=" O HIS H 584 " (cutoff:3.500A) Proline residue: H 589 - end of helix removed outlier: 4.588A pdb=" N SER H 594 " --> pdb=" O LEU H 590 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N SER H 595 " --> pdb=" O PHE H 591 " (cutoff:3.500A) Processing helix chain 'H' and resid 719 through 726 Processing helix chain 'H' and resid 784 through 789 Processing helix chain 'H' and resid 797 through 806 Processing helix chain 'H' and resid 809 through 813 Processing helix chain 'H' and resid 832 through 845 Processing helix chain 'H' and resid 862 through 871 Processing helix chain 'H' and resid 914 through 918 Processing helix chain 'H' and resid 998 through 1006 Processing helix chain 'H' and resid 1010 through 1038 removed outlier: 3.796A pdb=" N ALA H1035 " --> pdb=" O ASP H1031 " (cutoff:3.500A) Processing helix chain 'H' and resid 1061 through 1106 Processing helix chain 'H' and resid 1110 through 1115 Processing helix chain 'H' and resid 1118 through 1126 removed outlier: 3.867A pdb=" N PHE H1125 " --> pdb=" O ILE H1121 " (cutoff:3.500A) Processing helix chain 'H' and resid 1128 through 1160 removed outlier: 4.487A pdb=" N ILE H1136 " --> pdb=" O ILE H1132 " (cutoff:3.500A) Proline residue: H1137 - end of helix Processing helix chain 'H' and resid 1164 through 1209 removed outlier: 3.858A pdb=" N LEU H1169 " --> pdb=" O LEU H1165 " (cutoff:3.500A) Proline residue: H1170 - end of helix removed outlier: 3.790A pdb=" N GLN H1197 " --> pdb=" O ASP H1193 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU H1198 " --> pdb=" O ASP H1194 " (cutoff:3.500A) Proline residue: H1199 - end of helix Processing helix chain 'H' and resid 1211 through 1216 Processing helix chain 'H' and resid 1220 through 1273 Processing helix chain 'H' and resid 1278 through 1320 removed outlier: 3.597A pdb=" N GLY H1282 " --> pdb=" O ALA H1278 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N SER H1292 " --> pdb=" O ALA H1288 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ASN H1293 " --> pdb=" O LEU H1289 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR H1294 " --> pdb=" O MET H1290 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE H1307 " --> pdb=" O ALA H1303 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN H1308 " --> pdb=" O ASP H1304 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA H1311 " --> pdb=" O ILE H1307 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL H1312 " --> pdb=" O GLN H1308 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS H1320 " --> pdb=" O HIS H1316 " (cutoff:3.500A) Processing helix chain 'H' and resid 1385 through 1393 Processing helix chain 'H' and resid 1415 through 1419 Processing helix chain 'H' and resid 1436 through 1440 Processing helix chain 'H' and resid 1448 through 1457 Processing helix chain 'H' and resid 1461 through 1465 Processing helix chain 'H' and resid 1484 through 1498 Processing helix chain 'H' and resid 1514 through 1527 removed outlier: 4.208A pdb=" N ILE H1519 " --> pdb=" O ALA H1515 " (cutoff:3.500A) Processing helix chain 'H' and resid 1540 through 1545 Processing helix chain 'H' and resid 1563 through 1569 removed outlier: 3.882A pdb=" N SER H1568 " --> pdb=" O GLU H1564 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 181 through 183 Processing sheet with id= B, first strand: chain 'A' and resid 188 through 192 Processing sheet with id= C, first strand: chain 'A' and resid 235 through 238 removed outlier: 3.551A pdb=" N VAL A 236 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N MET A 217 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 319 through 321 Processing sheet with id= E, first strand: chain 'B' and resid 701 through 703 Processing sheet with id= F, first strand: chain 'B' and resid 907 through 912 removed outlier: 7.154A pdb=" N ALA B 902 " --> pdb=" O GLN B 909 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N GLU B 911 " --> pdb=" O ILE B 900 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ILE B 900 " --> pdb=" O GLU B 911 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N TRP B 899 " --> pdb=" O LEU B 708 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 1367 through 1369 Processing sheet with id= H, first strand: chain 'B' and resid 1557 through 1560 removed outlier: 3.632A pdb=" N MET B1550 " --> pdb=" O GLY B1376 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N PHE B1503 " --> pdb=" O VAL B1534 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N ILE B1536 " --> pdb=" O PHE B1503 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N MET B1505 " --> pdb=" O ILE B1536 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 181 through 183 Processing sheet with id= J, first strand: chain 'C' and resid 188 through 192 Processing sheet with id= K, first strand: chain 'C' and resid 235 through 238 removed outlier: 3.551A pdb=" N VAL C 236 " --> pdb=" O VAL C 219 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N MET C 217 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 319 through 321 Processing sheet with id= M, first strand: chain 'D' and resid 701 through 703 Processing sheet with id= N, first strand: chain 'D' and resid 907 through 912 removed outlier: 7.154A pdb=" N ALA D 902 " --> pdb=" O GLN D 909 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N GLU D 911 " --> pdb=" O ILE D 900 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ILE D 900 " --> pdb=" O GLU D 911 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N TRP D 899 " --> pdb=" O LEU D 708 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 1367 through 1369 Processing sheet with id= P, first strand: chain 'D' and resid 1557 through 1560 removed outlier: 3.632A pdb=" N MET D1550 " --> pdb=" O GLY D1376 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N PHE D1503 " --> pdb=" O VAL D1534 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N ILE D1536 " --> pdb=" O PHE D1503 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N MET D1505 " --> pdb=" O ILE D1536 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 181 through 183 Processing sheet with id= R, first strand: chain 'E' and resid 188 through 192 Processing sheet with id= S, first strand: chain 'E' and resid 235 through 238 removed outlier: 3.551A pdb=" N VAL E 236 " --> pdb=" O VAL E 219 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N MET E 217 " --> pdb=" O ILE E 238 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 319 through 321 Processing sheet with id= U, first strand: chain 'F' and resid 701 through 703 Processing sheet with id= V, first strand: chain 'F' and resid 907 through 912 removed outlier: 7.154A pdb=" N ALA F 902 " --> pdb=" O GLN F 909 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N GLU F 911 " --> pdb=" O ILE F 900 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ILE F 900 " --> pdb=" O GLU F 911 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N TRP F 899 " --> pdb=" O LEU F 708 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 1367 through 1369 Processing sheet with id= X, first strand: chain 'F' and resid 1557 through 1560 removed outlier: 3.632A pdb=" N MET F1550 " --> pdb=" O GLY F1376 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N PHE F1503 " --> pdb=" O VAL F1534 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N ILE F1536 " --> pdb=" O PHE F1503 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N MET F1505 " --> pdb=" O ILE F1536 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'G' and resid 181 through 183 Processing sheet with id= Z, first strand: chain 'G' and resid 188 through 192 Processing sheet with id= AA, first strand: chain 'G' and resid 235 through 238 removed outlier: 3.551A pdb=" N VAL G 236 " --> pdb=" O VAL G 219 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N MET G 217 " --> pdb=" O ILE G 238 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'G' and resid 319 through 321 Processing sheet with id= AC, first strand: chain 'H' and resid 701 through 703 Processing sheet with id= AD, first strand: chain 'H' and resid 907 through 912 removed outlier: 7.154A pdb=" N ALA H 902 " --> pdb=" O GLN H 909 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N GLU H 911 " --> pdb=" O ILE H 900 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ILE H 900 " --> pdb=" O GLU H 911 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N TRP H 899 " --> pdb=" O LEU H 708 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'H' and resid 1367 through 1369 Processing sheet with id= AF, first strand: chain 'H' and resid 1557 through 1560 removed outlier: 3.632A pdb=" N MET H1550 " --> pdb=" O GLY H1376 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N PHE H1503 " --> pdb=" O VAL H1534 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N ILE H1536 " --> pdb=" O PHE H1503 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N MET H1505 " --> pdb=" O ILE H1536 " (cutoff:3.500A) 3044 hydrogen bonds defined for protein. 8652 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: 21.34 Time building geometry restraints manager: 22.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.39: 19880 1.39 - 1.56: 32660 1.56 - 1.73: 180 1.73 - 1.90: 364 1.90 - 2.08: 8 Bond restraints: 53092 Sorted by residual: bond pdb=" C4 AGS A 402 " pdb=" C5 AGS A 402 " ideal model delta sigma weight residual 1.386 1.470 -0.084 1.00e-02 1.00e+04 7.00e+01 bond pdb=" C4 AGS G 401 " pdb=" C5 AGS G 401 " ideal model delta sigma weight residual 1.386 1.470 -0.084 1.00e-02 1.00e+04 7.00e+01 bond pdb=" C4 AGS C 401 " pdb=" C5 AGS C 401 " ideal model delta sigma weight residual 1.386 1.470 -0.084 1.00e-02 1.00e+04 7.00e+01 bond pdb=" C4 AGS E 401 " pdb=" C5 AGS E 401 " ideal model delta sigma weight residual 1.386 1.470 -0.084 1.00e-02 1.00e+04 7.00e+01 bond pdb=" C4 AGS B1602 " pdb=" C5 AGS B1602 " ideal model delta sigma weight residual 1.386 1.469 -0.083 1.00e-02 1.00e+04 6.90e+01 ... (remaining 53087 not shown) Histogram of bond angle deviations from ideal: 95.69 - 103.79: 656 103.79 - 111.90: 28180 111.90 - 120.00: 20104 120.00 - 128.11: 22944 128.11 - 136.22: 468 Bond angle restraints: 72352 Sorted by residual: angle pdb=" C5 AGS H1602 " pdb=" C4 AGS H1602 " pdb=" N3 AGS H1602 " ideal model delta sigma weight residual 126.80 118.81 7.99 7.41e-01 1.82e+00 1.16e+02 angle pdb=" C5 AGS B1602 " pdb=" C4 AGS B1602 " pdb=" N3 AGS B1602 " ideal model delta sigma weight residual 126.80 118.81 7.99 7.41e-01 1.82e+00 1.16e+02 angle pdb=" C5 AGS F1602 " pdb=" C4 AGS F1602 " pdb=" N3 AGS F1602 " ideal model delta sigma weight residual 126.80 118.81 7.99 7.41e-01 1.82e+00 1.16e+02 angle pdb=" C5 AGS D1602 " pdb=" C4 AGS D1602 " pdb=" N3 AGS D1602 " ideal model delta sigma weight residual 126.80 118.81 7.99 7.41e-01 1.82e+00 1.16e+02 angle pdb=" C5 AGS A 402 " pdb=" C4 AGS A 402 " pdb=" N3 AGS A 402 " ideal model delta sigma weight residual 126.80 119.41 7.39 7.41e-01 1.82e+00 9.95e+01 ... (remaining 72347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.01: 30516 35.01 - 70.02: 1052 70.02 - 105.03: 252 105.03 - 140.04: 208 140.04 - 175.05: 56 Dihedral angle restraints: 32084 sinusoidal: 12420 harmonic: 19664 Sorted by residual: dihedral pdb=" CA SER E 113 " pdb=" C SER E 113 " pdb=" N ILE E 114 " pdb=" CA ILE E 114 " ideal model delta harmonic sigma weight residual 180.00 153.32 26.68 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA SER C 113 " pdb=" C SER C 113 " pdb=" N ILE C 114 " pdb=" CA ILE C 114 " ideal model delta harmonic sigma weight residual 180.00 153.32 26.68 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA SER G 113 " pdb=" C SER G 113 " pdb=" N ILE G 114 " pdb=" CA ILE G 114 " ideal model delta harmonic sigma weight residual 180.00 153.32 26.68 0 5.00e+00 4.00e-02 2.85e+01 ... (remaining 32081 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.189: 8568 1.189 - 2.378: 0 2.378 - 3.566: 0 3.566 - 4.755: 16 4.755 - 5.944: 100 Chirality restraints: 8684 Sorted by residual: chirality pdb=" C12 AJP H1601 " pdb=" C07 AJP H1601 " pdb=" C11 AJP H1601 " pdb=" C13 AJP H1601 " both_signs ideal model delta sigma weight residual False 3.01 -2.94 5.94 2.00e-01 2.50e+01 8.83e+02 chirality pdb=" C12 AJP F1601 " pdb=" C07 AJP F1601 " pdb=" C11 AJP F1601 " pdb=" C13 AJP F1601 " both_signs ideal model delta sigma weight residual False 3.01 -2.94 5.94 2.00e-01 2.50e+01 8.83e+02 chirality pdb=" C12 AJP B1601 " pdb=" C07 AJP B1601 " pdb=" C11 AJP B1601 " pdb=" C13 AJP B1601 " both_signs ideal model delta sigma weight residual False 3.01 -2.94 5.94 2.00e-01 2.50e+01 8.83e+02 ... (remaining 8681 not shown) Planarity restraints: 8792 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" O BJX F1603 " 0.011 2.00e-02 2.50e+03 5.13e-02 3.29e+01 pdb=" C16 BJX F1603 " 0.026 2.00e-02 2.50e+03 pdb=" C17 BJX F1603 " -0.050 2.00e-02 2.50e+03 pdb=" C5 BJX F1603 " -0.063 2.00e-02 2.50e+03 pdb=" N1 BJX F1603 " 0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" O BJX H1603 " 0.011 2.00e-02 2.50e+03 5.13e-02 3.29e+01 pdb=" C16 BJX H1603 " 0.026 2.00e-02 2.50e+03 pdb=" C17 BJX H1603 " -0.050 2.00e-02 2.50e+03 pdb=" C5 BJX H1603 " -0.063 2.00e-02 2.50e+03 pdb=" N1 BJX H1603 " 0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" O BJX D1603 " -0.011 2.00e-02 2.50e+03 5.13e-02 3.29e+01 pdb=" C16 BJX D1603 " -0.026 2.00e-02 2.50e+03 pdb=" C17 BJX D1603 " 0.050 2.00e-02 2.50e+03 pdb=" C5 BJX D1603 " 0.063 2.00e-02 2.50e+03 pdb=" N1 BJX D1603 " -0.076 2.00e-02 2.50e+03 ... (remaining 8789 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 11664 2.79 - 3.31: 51088 3.31 - 3.84: 87316 3.84 - 4.37: 98588 4.37 - 4.90: 169752 Nonbonded interactions: 418408 Sorted by model distance: nonbonded pdb=" OD2 ASP H1031 " pdb=" OH TYR H1287 " model vdw 2.257 2.440 nonbonded pdb=" OD2 ASP F1031 " pdb=" OH TYR F1287 " model vdw 2.257 2.440 nonbonded pdb=" OD2 ASP D1031 " pdb=" OH TYR D1287 " model vdw 2.257 2.440 nonbonded pdb=" OD2 ASP B1031 " pdb=" OH TYR B1287 " model vdw 2.257 2.440 nonbonded pdb=" OG1 THR B 548 " pdb=" NH1 ARG B1145 " model vdw 2.265 2.520 ... (remaining 418403 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 32 through 358) selection = (chain 'C' and resid 32 through 358) selection = (chain 'E' and resid 32 through 358) selection = (chain 'G' and resid 32 through 358) } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 6.410 Check model and map are aligned: 0.720 Set scattering table: 0.430 Process input model: 135.050 Find NCS groups from input model: 3.260 Set up NCS constraints: 0.330 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 149.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6547 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 : 0.008 0.147 53092 Z= 0.545 Angle : 1.063 20.172 72352 Z= 0.513 Chirality : 0.580 5.944 8684 Planarity : 0.004 0.051 8792 Dihedral : 23.676 175.047 19284 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 6.21 % Allowed : 10.52 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.09), residues: 6684 helix: -0.66 (0.07), residues: 4056 sheet: -1.76 (0.20), residues: 512 loop : -2.73 (0.12), residues: 2116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 65 HIS 0.004 0.001 HIS H 36 PHE 0.027 0.002 PHE G 75 TYR 0.016 0.002 TYR D 123 ARG 0.004 0.001 ARG G 136 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13368 Ramachandran restraints generated. 6684 Oldfield, 0 Emsley, 6684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13368 Ramachandran restraints generated. 6684 Oldfield, 0 Emsley, 6684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1716 residues out of total 5876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 300 poor density : 1416 time to evaluate : 5.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASP cc_start: 0.7216 (t0) cc_final: 0.6968 (t0) REVERT: A 67 LYS cc_start: 0.8093 (mttt) cc_final: 0.7569 (tptt) REVERT: A 77 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.8105 (mtp) REVERT: A 84 LEU cc_start: 0.9040 (mt) cc_final: 0.8694 (mt) REVERT: A 142 CYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7648 (p) REVERT: A 149 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8409 (tp) REVERT: A 177 ARG cc_start: 0.7607 (tpt90) cc_final: 0.6903 (tpt170) REVERT: A 185 LYS cc_start: 0.7980 (tttt) cc_final: 0.7411 (tmtt) REVERT: A 280 ASP cc_start: 0.8810 (t0) cc_final: 0.8442 (t0) REVERT: B 44 PHE cc_start: 0.8478 (m-10) cc_final: 0.8254 (m-10) REVERT: B 124 TYR cc_start: 0.8997 (t80) cc_final: 0.8616 (t80) REVERT: B 211 GLN cc_start: 0.7959 (mt0) cc_final: 0.7595 (mt0) REVERT: B 223 ASN cc_start: 0.8621 (OUTLIER) cc_final: 0.7892 (p0) REVERT: B 226 SER cc_start: 0.9103 (t) cc_final: 0.8376 (p) REVERT: B 229 THR cc_start: 0.9047 (OUTLIER) cc_final: 0.8830 (p) REVERT: B 289 ARG cc_start: 0.7326 (mtp180) cc_final: 0.6477 (mmt180) REVERT: B 340 PHE cc_start: 0.7986 (OUTLIER) cc_final: 0.7677 (t80) REVERT: B 354 ASN cc_start: 0.9254 (t0) cc_final: 0.8959 (t0) REVERT: B 454 TYR cc_start: 0.7203 (t80) cc_final: 0.6816 (m-80) REVERT: B 500 ASN cc_start: 0.7640 (t0) cc_final: 0.7361 (t0) REVERT: B 565 PHE cc_start: 0.7231 (t80) cc_final: 0.6733 (m-80) REVERT: B 1003 LYS cc_start: 0.6835 (mmtm) cc_final: 0.6322 (mttm) REVERT: B 1066 MET cc_start: 0.6854 (ttp) cc_final: 0.6529 (tpp) REVERT: B 1194 ASP cc_start: 0.8096 (m-30) cc_final: 0.7880 (m-30) REVERT: B 1197 GLN cc_start: 0.7747 (tt0) cc_final: 0.7327 (tp40) REVERT: B 1246 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.7389 (mmp-170) REVERT: B 1339 TRP cc_start: 0.5089 (t-100) cc_final: 0.4869 (t-100) REVERT: C 58 ASP cc_start: 0.7215 (t0) cc_final: 0.6969 (t0) REVERT: C 67 LYS cc_start: 0.8093 (mttt) cc_final: 0.7569 (tptt) REVERT: C 77 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.8108 (mtp) REVERT: C 84 LEU cc_start: 0.9040 (mt) cc_final: 0.8694 (mt) REVERT: C 142 CYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7647 (p) REVERT: C 149 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8407 (tp) REVERT: C 177 ARG cc_start: 0.7606 (tpt90) cc_final: 0.6903 (tpt170) REVERT: C 185 LYS cc_start: 0.7980 (tttt) cc_final: 0.7411 (tmtt) REVERT: C 280 ASP cc_start: 0.8807 (t0) cc_final: 0.8440 (t0) REVERT: D 44 PHE cc_start: 0.8478 (m-10) cc_final: 0.8253 (m-10) REVERT: D 124 TYR cc_start: 0.8997 (t80) cc_final: 0.8614 (t80) REVERT: D 211 GLN cc_start: 0.7959 (mt0) cc_final: 0.7595 (mt0) REVERT: D 223 ASN cc_start: 0.8620 (OUTLIER) cc_final: 0.7891 (p0) REVERT: D 226 SER cc_start: 0.9100 (t) cc_final: 0.8372 (p) REVERT: D 229 THR cc_start: 0.9046 (OUTLIER) cc_final: 0.8829 (p) REVERT: D 289 ARG cc_start: 0.7327 (mtp180) cc_final: 0.6477 (mmt180) REVERT: D 340 PHE cc_start: 0.7987 (OUTLIER) cc_final: 0.7678 (t80) REVERT: D 354 ASN cc_start: 0.9253 (t0) cc_final: 0.8958 (t0) REVERT: D 454 TYR cc_start: 0.7204 (t80) cc_final: 0.6817 (m-80) REVERT: D 500 ASN cc_start: 0.7640 (t0) cc_final: 0.7362 (t0) REVERT: D 565 PHE cc_start: 0.7232 (t80) cc_final: 0.6733 (m-80) REVERT: D 1003 LYS cc_start: 0.6838 (mmtm) cc_final: 0.6325 (mttm) REVERT: D 1066 MET cc_start: 0.6853 (ttp) cc_final: 0.6528 (tpp) REVERT: D 1194 ASP cc_start: 0.8098 (m-30) cc_final: 0.7880 (m-30) REVERT: D 1197 GLN cc_start: 0.7749 (tt0) cc_final: 0.7328 (tp40) REVERT: D 1246 ARG cc_start: 0.7629 (OUTLIER) cc_final: 0.7385 (mmp-170) REVERT: D 1339 TRP cc_start: 0.5091 (t-100) cc_final: 0.4870 (t-100) REVERT: E 58 ASP cc_start: 0.7215 (t0) cc_final: 0.6970 (t0) REVERT: E 67 LYS cc_start: 0.8093 (mttt) cc_final: 0.7569 (tptt) REVERT: E 77 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.8106 (mtp) REVERT: E 84 LEU cc_start: 0.9041 (mt) cc_final: 0.8695 (mt) REVERT: E 142 CYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7647 (p) REVERT: E 149 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8408 (tp) REVERT: E 177 ARG cc_start: 0.7609 (tpt90) cc_final: 0.6905 (tpt170) REVERT: E 185 LYS cc_start: 0.7978 (tttt) cc_final: 0.7409 (tmtt) REVERT: E 280 ASP cc_start: 0.8809 (t0) cc_final: 0.8440 (t0) REVERT: F 44 PHE cc_start: 0.8478 (m-10) cc_final: 0.8254 (m-10) REVERT: F 124 TYR cc_start: 0.8996 (t80) cc_final: 0.8614 (t80) REVERT: F 211 GLN cc_start: 0.7958 (mt0) cc_final: 0.7594 (mt0) REVERT: F 223 ASN cc_start: 0.8618 (OUTLIER) cc_final: 0.7888 (p0) REVERT: F 226 SER cc_start: 0.9099 (t) cc_final: 0.8372 (p) REVERT: F 229 THR cc_start: 0.9049 (OUTLIER) cc_final: 0.8832 (p) REVERT: F 289 ARG cc_start: 0.7327 (mtp180) cc_final: 0.6477 (mmt180) REVERT: F 340 PHE cc_start: 0.7987 (OUTLIER) cc_final: 0.7679 (t80) REVERT: F 354 ASN cc_start: 0.9253 (t0) cc_final: 0.8957 (t0) REVERT: F 454 TYR cc_start: 0.7203 (t80) cc_final: 0.6816 (m-80) REVERT: F 500 ASN cc_start: 0.7640 (t0) cc_final: 0.7360 (t0) REVERT: F 565 PHE cc_start: 0.7232 (t80) cc_final: 0.6733 (m-80) REVERT: F 1003 LYS cc_start: 0.6837 (mmtm) cc_final: 0.6323 (mttm) REVERT: F 1066 MET cc_start: 0.6852 (ttp) cc_final: 0.6527 (tpp) REVERT: F 1194 ASP cc_start: 0.8098 (m-30) cc_final: 0.7881 (m-30) REVERT: F 1197 GLN cc_start: 0.7746 (tt0) cc_final: 0.7327 (tp40) REVERT: F 1246 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.7383 (mmp-170) REVERT: F 1339 TRP cc_start: 0.5089 (t-100) cc_final: 0.4869 (t-100) REVERT: G 58 ASP cc_start: 0.7216 (t0) cc_final: 0.6969 (t0) REVERT: G 67 LYS cc_start: 0.8093 (mttt) cc_final: 0.7569 (tptt) REVERT: G 77 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.8107 (mtp) REVERT: G 84 LEU cc_start: 0.9040 (mt) cc_final: 0.8694 (mt) REVERT: G 142 CYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7650 (p) REVERT: G 149 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8407 (tp) REVERT: G 177 ARG cc_start: 0.7610 (tpt90) cc_final: 0.6907 (tpt170) REVERT: G 185 LYS cc_start: 0.7979 (tttt) cc_final: 0.7411 (tmtt) REVERT: G 280 ASP cc_start: 0.8808 (t0) cc_final: 0.8440 (t0) REVERT: H 44 PHE cc_start: 0.8479 (m-10) cc_final: 0.8254 (m-10) REVERT: H 124 TYR cc_start: 0.8997 (t80) cc_final: 0.8615 (t80) REVERT: H 211 GLN cc_start: 0.7959 (mt0) cc_final: 0.7595 (mt0) REVERT: H 223 ASN cc_start: 0.8618 (OUTLIER) cc_final: 0.7889 (p0) REVERT: H 226 SER cc_start: 0.9101 (t) cc_final: 0.8373 (p) REVERT: H 229 THR cc_start: 0.9047 (OUTLIER) cc_final: 0.8831 (p) REVERT: H 289 ARG cc_start: 0.7326 (mtp180) cc_final: 0.6475 (mmt180) REVERT: H 340 PHE cc_start: 0.7985 (OUTLIER) cc_final: 0.7675 (t80) REVERT: H 354 ASN cc_start: 0.9253 (t0) cc_final: 0.8957 (t0) REVERT: H 454 TYR cc_start: 0.7204 (t80) cc_final: 0.6817 (m-80) REVERT: H 500 ASN cc_start: 0.7641 (t0) cc_final: 0.7361 (t0) REVERT: H 565 PHE cc_start: 0.7231 (t80) cc_final: 0.6732 (m-80) REVERT: H 1003 LYS cc_start: 0.6836 (mmtm) cc_final: 0.6323 (mttm) REVERT: H 1066 MET cc_start: 0.6853 (ttp) cc_final: 0.6528 (tpp) REVERT: H 1194 ASP cc_start: 0.8098 (m-30) cc_final: 0.7881 (m-30) REVERT: H 1197 GLN cc_start: 0.7747 (tt0) cc_final: 0.7327 (tp40) REVERT: H 1246 ARG cc_start: 0.7627 (OUTLIER) cc_final: 0.7384 (mmp-170) REVERT: H 1339 TRP cc_start: 0.5088 (t-100) cc_final: 0.4868 (t-100) outliers start: 300 outliers final: 84 residues processed: 1612 average time/residue: 0.5824 time to fit residues: 1588.3463 Evaluate side-chains 1052 residues out of total 5876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 940 time to evaluate : 5.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 209 ASP Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 1139 THR Chi-restraints excluded: chain B residue 1240 PHE Chi-restraints excluded: chain B residue 1242 THR Chi-restraints excluded: chain B residue 1246 ARG Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 77 MET Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 142 CYS Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 26 CYS Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 209 ASP Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 223 ASN Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 340 PHE Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 1139 THR Chi-restraints excluded: chain D residue 1240 PHE Chi-restraints excluded: chain D residue 1242 THR Chi-restraints excluded: chain D residue 1246 ARG Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 77 MET Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 142 CYS Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 166 CYS Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 26 CYS Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 209 ASP Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 223 ASN Chi-restraints excluded: chain F residue 229 THR Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 340 PHE Chi-restraints excluded: chain F residue 531 THR Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain F residue 1139 THR Chi-restraints excluded: chain F residue 1240 PHE Chi-restraints excluded: chain F residue 1242 THR Chi-restraints excluded: chain F residue 1246 ARG Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 77 MET Chi-restraints excluded: chain G residue 131 ILE Chi-restraints excluded: chain G residue 142 CYS Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain G residue 166 CYS Chi-restraints excluded: chain G residue 167 ILE Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 296 ILE Chi-restraints excluded: chain G residue 309 ILE Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 26 CYS Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 209 ASP Chi-restraints excluded: chain H residue 218 LEU Chi-restraints excluded: chain H residue 223 ASN Chi-restraints excluded: chain H residue 229 THR Chi-restraints excluded: chain H residue 239 THR Chi-restraints excluded: chain H residue 340 PHE Chi-restraints excluded: chain H residue 531 THR Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 1139 THR Chi-restraints excluded: chain H residue 1240 PHE Chi-restraints excluded: chain H residue 1242 THR Chi-restraints excluded: chain H residue 1246 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 672 random chunks: chunk 567 optimal weight: 0.5980 chunk 509 optimal weight: 0.6980 chunk 282 optimal weight: 0.8980 chunk 173 optimal weight: 0.7980 chunk 343 optimal weight: 0.9980 chunk 272 optimal weight: 9.9990 chunk 526 optimal weight: 5.9990 chunk 203 optimal weight: 0.5980 chunk 320 optimal weight: 9.9990 chunk 392 optimal weight: 4.9990 chunk 610 optimal weight: 20.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN A 107 ASN A 335 ASN B 211 GLN B 219 GLN B 354 ASN B 437 ASN B 491 HIS B 547 ASN B 846 GLN ** B1316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 ASN C 335 ASN D 211 GLN D 219 GLN D 354 ASN D 437 ASN D 491 HIS D 547 ASN D 846 GLN D1020 GLN ** D1316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 ASN E 107 ASN E 335 ASN F 211 GLN F 219 GLN F 354 ASN F 437 ASN F 491 HIS F 547 ASN F 846 GLN ** F1316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 48 ASN G 107 ASN G 335 ASN H 211 GLN H 219 GLN H 354 ASN H 437 ASN H 491 HIS H 547 ASN H 846 GLN H1020 GLN ** H1316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6563 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 53092 Z= 0.197 Angle : 0.939 38.190 72352 Z= 0.383 Chirality : 0.081 2.184 8684 Planarity : 0.004 0.054 8792 Dihedral : 20.054 179.759 9584 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.87 % Allowed : 19.41 % Favored : 75.72 % 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: -0.52 (0.10), residues: 6684 helix: 0.77 (0.08), residues: 4068 sheet: -1.34 (0.21), residues: 524 loop : -2.29 (0.12), residues: 2092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 430 HIS 0.011 0.001 HIS H 896 PHE 0.017 0.001 PHE A 86 TYR 0.021 0.002 TYR D 195 ARG 0.005 0.000 ARG F1187 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13368 Ramachandran restraints generated. 6684 Oldfield, 0 Emsley, 6684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13368 Ramachandran restraints generated. 6684 Oldfield, 0 Emsley, 6684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1287 residues out of total 5876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 1052 time to evaluate : 5.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASP cc_start: 0.6994 (t0) cc_final: 0.6762 (t0) REVERT: A 67 LYS cc_start: 0.8098 (mttt) cc_final: 0.7567 (tptt) REVERT: A 84 LEU cc_start: 0.9067 (mt) cc_final: 0.8850 (mt) REVERT: A 124 SER cc_start: 0.9409 (t) cc_final: 0.8968 (p) REVERT: A 177 ARG cc_start: 0.7910 (tpt90) cc_final: 0.7254 (tpt170) REVERT: A 185 LYS cc_start: 0.7967 (tttt) cc_final: 0.7384 (tmtt) REVERT: A 237 ASP cc_start: 0.7438 (t70) cc_final: 0.7235 (t0) REVERT: A 280 ASP cc_start: 0.8786 (t0) cc_final: 0.8385 (t0) REVERT: A 332 LYS cc_start: 0.8040 (mtmm) cc_final: 0.7622 (mtmm) REVERT: A 335 ASN cc_start: 0.7990 (m-40) cc_final: 0.7777 (m110) REVERT: B 43 THR cc_start: 0.9077 (m) cc_final: 0.8657 (p) REVERT: B 65 TRP cc_start: 0.8898 (p90) cc_final: 0.8028 (p90) REVERT: B 66 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.7787 (pp) REVERT: B 91 GLU cc_start: 0.8360 (pp20) cc_final: 0.8059 (pp20) REVERT: B 216 ARG cc_start: 0.7675 (ttm110) cc_final: 0.7353 (mtt-85) REVERT: B 233 MET cc_start: 0.8216 (mmm) cc_final: 0.7613 (tpp) REVERT: B 289 ARG cc_start: 0.7317 (mtp180) cc_final: 0.6555 (mmt180) REVERT: B 340 PHE cc_start: 0.8215 (OUTLIER) cc_final: 0.7773 (t80) REVERT: B 354 ASN cc_start: 0.9173 (t0) cc_final: 0.8789 (t0) REVERT: B 454 TYR cc_start: 0.7175 (t80) cc_final: 0.6832 (m-80) REVERT: B 500 ASN cc_start: 0.7618 (t0) cc_final: 0.7287 (t0) REVERT: B 565 PHE cc_start: 0.7095 (t80) cc_final: 0.6497 (m-80) REVERT: B 567 LYS cc_start: 0.7433 (mttt) cc_final: 0.7209 (mttt) REVERT: B 689 THR cc_start: 0.4859 (OUTLIER) cc_final: 0.4575 (p) REVERT: B 1066 MET cc_start: 0.6985 (ttp) cc_final: 0.6645 (tpp) REVERT: B 1197 GLN cc_start: 0.7759 (tt0) cc_final: 0.7324 (tp40) REVERT: B 1276 LEU cc_start: 0.8887 (tp) cc_final: 0.8529 (tt) REVERT: B 1339 TRP cc_start: 0.5128 (t-100) cc_final: 0.4903 (t-100) REVERT: C 58 ASP cc_start: 0.6995 (t0) cc_final: 0.6765 (t0) REVERT: C 67 LYS cc_start: 0.8097 (mttt) cc_final: 0.7565 (tptt) REVERT: C 84 LEU cc_start: 0.9068 (mt) cc_final: 0.8850 (mt) REVERT: C 124 SER cc_start: 0.9407 (t) cc_final: 0.8966 (p) REVERT: C 177 ARG cc_start: 0.7910 (tpt90) cc_final: 0.7254 (tpt170) REVERT: C 185 LYS cc_start: 0.7968 (tttt) cc_final: 0.7384 (tmtt) REVERT: C 237 ASP cc_start: 0.7438 (t70) cc_final: 0.7235 (t0) REVERT: C 280 ASP cc_start: 0.8784 (t0) cc_final: 0.8384 (t0) REVERT: C 332 LYS cc_start: 0.8042 (mtmm) cc_final: 0.7623 (mtmm) REVERT: C 335 ASN cc_start: 0.7987 (m-40) cc_final: 0.7777 (m110) REVERT: D 43 THR cc_start: 0.9079 (m) cc_final: 0.8659 (p) REVERT: D 65 TRP cc_start: 0.8900 (p90) cc_final: 0.8029 (p90) REVERT: D 66 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.7786 (pp) REVERT: D 91 GLU cc_start: 0.8361 (pp20) cc_final: 0.8062 (pp20) REVERT: D 216 ARG cc_start: 0.7677 (ttm110) cc_final: 0.7355 (mtt-85) REVERT: D 233 MET cc_start: 0.8217 (mmm) cc_final: 0.7614 (tpp) REVERT: D 289 ARG cc_start: 0.7317 (mtp180) cc_final: 0.6555 (mmt180) REVERT: D 340 PHE cc_start: 0.8215 (OUTLIER) cc_final: 0.7775 (t80) REVERT: D 354 ASN cc_start: 0.9172 (t0) cc_final: 0.8787 (t0) REVERT: D 454 TYR cc_start: 0.7175 (t80) cc_final: 0.6832 (m-80) REVERT: D 500 ASN cc_start: 0.7617 (t0) cc_final: 0.7285 (t0) REVERT: D 565 PHE cc_start: 0.7096 (t80) cc_final: 0.6498 (m-80) REVERT: D 567 LYS cc_start: 0.7431 (mttt) cc_final: 0.7208 (mttt) REVERT: D 689 THR cc_start: 0.4861 (OUTLIER) cc_final: 0.4577 (p) REVERT: D 1066 MET cc_start: 0.6984 (ttp) cc_final: 0.6645 (tpp) REVERT: D 1197 GLN cc_start: 0.7759 (tt0) cc_final: 0.7325 (tp40) REVERT: D 1276 LEU cc_start: 0.8890 (tp) cc_final: 0.8532 (tt) REVERT: D 1339 TRP cc_start: 0.5126 (t-100) cc_final: 0.4901 (t-100) REVERT: E 58 ASP cc_start: 0.6994 (t0) cc_final: 0.6763 (t0) REVERT: E 67 LYS cc_start: 0.8098 (mttt) cc_final: 0.7565 (tptt) REVERT: E 84 LEU cc_start: 0.9069 (mt) cc_final: 0.8852 (mt) REVERT: E 124 SER cc_start: 0.9407 (t) cc_final: 0.8967 (p) REVERT: E 177 ARG cc_start: 0.7913 (tpt90) cc_final: 0.7256 (tpt170) REVERT: E 185 LYS cc_start: 0.7967 (tttt) cc_final: 0.7383 (tmtt) REVERT: E 237 ASP cc_start: 0.7439 (t70) cc_final: 0.7235 (t0) REVERT: E 280 ASP cc_start: 0.8785 (t0) cc_final: 0.8384 (t0) REVERT: E 332 LYS cc_start: 0.8040 (mtmm) cc_final: 0.7622 (mtmm) REVERT: E 335 ASN cc_start: 0.7986 (m-40) cc_final: 0.7776 (m110) REVERT: F 43 THR cc_start: 0.9078 (m) cc_final: 0.8658 (p) REVERT: F 65 TRP cc_start: 0.8900 (p90) cc_final: 0.8030 (p90) REVERT: F 66 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.7785 (pp) REVERT: F 91 GLU cc_start: 0.8360 (pp20) cc_final: 0.8062 (pp20) REVERT: F 216 ARG cc_start: 0.7679 (ttm110) cc_final: 0.7356 (mtt-85) REVERT: F 233 MET cc_start: 0.8219 (mmm) cc_final: 0.7615 (tpp) REVERT: F 289 ARG cc_start: 0.7317 (mtp180) cc_final: 0.6554 (mmt180) REVERT: F 340 PHE cc_start: 0.8215 (OUTLIER) cc_final: 0.7772 (t80) REVERT: F 354 ASN cc_start: 0.9171 (t0) cc_final: 0.8786 (t0) REVERT: F 454 TYR cc_start: 0.7175 (t80) cc_final: 0.6832 (m-80) REVERT: F 500 ASN cc_start: 0.7617 (t0) cc_final: 0.7287 (t0) REVERT: F 565 PHE cc_start: 0.7097 (t80) cc_final: 0.6498 (m-80) REVERT: F 567 LYS cc_start: 0.7430 (mttt) cc_final: 0.7207 (mttt) REVERT: F 689 THR cc_start: 0.4861 (OUTLIER) cc_final: 0.4576 (p) REVERT: F 1066 MET cc_start: 0.6983 (ttp) cc_final: 0.6643 (tpp) REVERT: F 1197 GLN cc_start: 0.7757 (tt0) cc_final: 0.7322 (tp40) REVERT: F 1276 LEU cc_start: 0.8890 (tp) cc_final: 0.8531 (tt) REVERT: F 1339 TRP cc_start: 0.5125 (t-100) cc_final: 0.4902 (t-100) REVERT: G 58 ASP cc_start: 0.6994 (t0) cc_final: 0.6763 (t0) REVERT: G 67 LYS cc_start: 0.8098 (mttt) cc_final: 0.7566 (tptt) REVERT: G 84 LEU cc_start: 0.9069 (mt) cc_final: 0.8852 (mt) REVERT: G 124 SER cc_start: 0.9408 (t) cc_final: 0.8965 (p) REVERT: G 177 ARG cc_start: 0.7913 (tpt90) cc_final: 0.7255 (tpt170) REVERT: G 185 LYS cc_start: 0.7966 (tttt) cc_final: 0.7383 (tmtt) REVERT: G 237 ASP cc_start: 0.7436 (t70) cc_final: 0.7235 (t0) REVERT: G 280 ASP cc_start: 0.8784 (t0) cc_final: 0.8383 (t0) REVERT: G 332 LYS cc_start: 0.8041 (mtmm) cc_final: 0.7623 (mtmm) REVERT: G 335 ASN cc_start: 0.7989 (m-40) cc_final: 0.7777 (m110) REVERT: H 43 THR cc_start: 0.9079 (m) cc_final: 0.8659 (p) REVERT: H 65 TRP cc_start: 0.8899 (p90) cc_final: 0.8028 (p90) REVERT: H 66 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.7783 (pp) REVERT: H 91 GLU cc_start: 0.8359 (pp20) cc_final: 0.8060 (pp20) REVERT: H 216 ARG cc_start: 0.7679 (ttm110) cc_final: 0.7356 (mtt-85) REVERT: H 233 MET cc_start: 0.8217 (mmm) cc_final: 0.7614 (tpp) REVERT: H 289 ARG cc_start: 0.7317 (mtp180) cc_final: 0.6555 (mmt180) REVERT: H 340 PHE cc_start: 0.8217 (OUTLIER) cc_final: 0.7773 (t80) REVERT: H 354 ASN cc_start: 0.9173 (t0) cc_final: 0.8787 (t0) REVERT: H 454 TYR cc_start: 0.7175 (t80) cc_final: 0.6832 (m-80) REVERT: H 500 ASN cc_start: 0.7617 (t0) cc_final: 0.7285 (t0) REVERT: H 565 PHE cc_start: 0.7096 (t80) cc_final: 0.6497 (m-80) REVERT: H 567 LYS cc_start: 0.7430 (mttt) cc_final: 0.7208 (mttt) REVERT: H 689 THR cc_start: 0.4861 (OUTLIER) cc_final: 0.4576 (p) REVERT: H 1066 MET cc_start: 0.6985 (ttp) cc_final: 0.6645 (tpp) REVERT: H 1197 GLN cc_start: 0.7758 (tt0) cc_final: 0.7323 (tp40) REVERT: H 1276 LEU cc_start: 0.8889 (tp) cc_final: 0.8531 (tt) REVERT: H 1339 TRP cc_start: 0.5125 (t-100) cc_final: 0.4900 (t-100) outliers start: 235 outliers final: 146 residues processed: 1211 average time/residue: 0.5570 time to fit residues: 1165.8348 Evaluate side-chains 1098 residues out of total 5876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 940 time to evaluate : 5.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 313 GLN Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain B residue 10 ASN Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 689 THR Chi-restraints excluded: chain B residue 1007 SER Chi-restraints excluded: chain B residue 1071 LEU Chi-restraints excluded: chain B residue 1089 THR Chi-restraints excluded: chain B residue 1097 LEU Chi-restraints excluded: chain B residue 1240 PHE Chi-restraints excluded: chain B residue 1246 ARG Chi-restraints excluded: chain B residue 1250 VAL Chi-restraints excluded: chain B residue 1298 MET Chi-restraints excluded: chain B residue 1320 LYS Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 313 GLN Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain D residue 10 ASN Chi-restraints excluded: chain D residue 26 CYS Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 340 PHE Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 371 THR Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 689 THR Chi-restraints excluded: chain D residue 1007 SER Chi-restraints excluded: chain D residue 1071 LEU Chi-restraints excluded: chain D residue 1089 THR Chi-restraints excluded: chain D residue 1097 LEU Chi-restraints excluded: chain D residue 1240 PHE Chi-restraints excluded: chain D residue 1246 ARG Chi-restraints excluded: chain D residue 1250 VAL Chi-restraints excluded: chain D residue 1298 MET Chi-restraints excluded: chain D residue 1320 LYS Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 78 SER Chi-restraints excluded: chain E residue 107 ASN Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 166 CYS Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 313 GLN Chi-restraints excluded: chain E residue 323 ASP Chi-restraints excluded: chain F residue 10 ASN Chi-restraints excluded: chain F residue 26 CYS Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 340 PHE Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain F residue 362 LEU Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 399 ILE Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain F residue 681 ILE Chi-restraints excluded: chain F residue 689 THR Chi-restraints excluded: chain F residue 1007 SER Chi-restraints excluded: chain F residue 1071 LEU Chi-restraints excluded: chain F residue 1089 THR Chi-restraints excluded: chain F residue 1097 LEU Chi-restraints excluded: chain F residue 1240 PHE Chi-restraints excluded: chain F residue 1246 ARG Chi-restraints excluded: chain F residue 1250 VAL Chi-restraints excluded: chain F residue 1298 MET Chi-restraints excluded: chain F residue 1320 LYS Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 107 ASN Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 166 CYS Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain G residue 296 ILE Chi-restraints excluded: chain G residue 309 ILE Chi-restraints excluded: chain G residue 313 GLN Chi-restraints excluded: chain G residue 323 ASP Chi-restraints excluded: chain H residue 10 ASN Chi-restraints excluded: chain H residue 26 CYS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 137 ILE Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 218 LEU Chi-restraints excluded: chain H residue 340 PHE Chi-restraints excluded: chain H residue 360 VAL Chi-restraints excluded: chain H residue 361 LEU Chi-restraints excluded: chain H residue 362 LEU Chi-restraints excluded: chain H residue 371 THR Chi-restraints excluded: chain H residue 399 ILE Chi-restraints excluded: chain H residue 452 LEU Chi-restraints excluded: chain H residue 681 ILE Chi-restraints excluded: chain H residue 689 THR Chi-restraints excluded: chain H residue 1007 SER Chi-restraints excluded: chain H residue 1071 LEU Chi-restraints excluded: chain H residue 1089 THR Chi-restraints excluded: chain H residue 1097 LEU Chi-restraints excluded: chain H residue 1240 PHE Chi-restraints excluded: chain H residue 1246 ARG Chi-restraints excluded: chain H residue 1250 VAL Chi-restraints excluded: chain H residue 1298 MET Chi-restraints excluded: chain H residue 1320 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 672 random chunks: chunk 339 optimal weight: 6.9990 chunk 189 optimal weight: 8.9990 chunk 507 optimal weight: 1.9990 chunk 415 optimal weight: 3.9990 chunk 168 optimal weight: 10.0000 chunk 611 optimal weight: 10.0000 chunk 660 optimal weight: 6.9990 chunk 544 optimal weight: 7.9990 chunk 606 optimal weight: 7.9990 chunk 208 optimal weight: 7.9990 chunk 490 optimal weight: 0.0060 overall best weight: 4.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 HIS A 153 ASN B 160 HIS B 211 GLN ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1020 GLN B1135 HIS B1203 HIS C 46 HIS C 153 ASN D 160 HIS D 211 GLN ** D 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1135 HIS D1203 HIS E 46 HIS E 153 ASN F 160 HIS F 211 GLN ** F 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1020 GLN F1135 HIS F1203 HIS G 46 HIS G 153 ASN H 160 HIS H 211 GLN ** H 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1135 HIS H1203 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6664 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 53092 Z= 0.433 Angle : 0.969 35.731 72352 Z= 0.418 Chirality : 0.081 2.057 8684 Planarity : 0.005 0.042 8792 Dihedral : 19.694 177.125 9498 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 8.60 % Allowed : 19.08 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.10), residues: 6684 helix: 0.98 (0.08), residues: 4040 sheet: -1.27 (0.21), residues: 508 loop : -1.97 (0.12), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H1247 HIS 0.011 0.001 HIS H 896 PHE 0.016 0.002 PHE G 75 TYR 0.018 0.002 TYR F 195 ARG 0.005 0.001 ARG D 102 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13368 Ramachandran restraints generated. 6684 Oldfield, 0 Emsley, 6684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13368 Ramachandran restraints generated. 6684 Oldfield, 0 Emsley, 6684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1272 residues out of total 5876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 415 poor density : 857 time to evaluate : 5.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASN cc_start: 0.8434 (t0) cc_final: 0.7996 (t0) REVERT: A 67 LYS cc_start: 0.8323 (mttt) cc_final: 0.7668 (tptt) REVERT: A 185 LYS cc_start: 0.8037 (tttt) cc_final: 0.7407 (tmtt) REVERT: A 237 ASP cc_start: 0.7680 (t70) cc_final: 0.7411 (t0) REVERT: A 313 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7387 (mt0) REVERT: A 332 LYS cc_start: 0.8184 (mtmm) cc_final: 0.7543 (mtmm) REVERT: A 335 ASN cc_start: 0.8070 (m-40) cc_final: 0.7555 (m110) REVERT: B 43 THR cc_start: 0.9130 (m) cc_final: 0.8749 (p) REVERT: B 91 GLU cc_start: 0.8394 (pp20) cc_final: 0.8136 (pp20) REVERT: B 124 TYR cc_start: 0.8918 (t80) cc_final: 0.8596 (t80) REVERT: B 289 ARG cc_start: 0.7416 (mtp180) cc_final: 0.6707 (mmt180) REVERT: B 340 PHE cc_start: 0.8402 (OUTLIER) cc_final: 0.7798 (t80) REVERT: B 354 ASN cc_start: 0.9319 (t0) cc_final: 0.8911 (t0) REVERT: B 367 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7762 (mp) REVERT: B 454 TYR cc_start: 0.6934 (t80) cc_final: 0.6420 (m-80) REVERT: B 500 ASN cc_start: 0.7760 (t0) cc_final: 0.7455 (t0) REVERT: B 565 PHE cc_start: 0.6774 (t80) cc_final: 0.6193 (m-80) REVERT: B 567 LYS cc_start: 0.7496 (mttt) cc_final: 0.7269 (mttt) REVERT: B 689 THR cc_start: 0.4559 (OUTLIER) cc_final: 0.4229 (p) REVERT: B 1066 MET cc_start: 0.6908 (ttp) cc_final: 0.6595 (tpp) REVERT: B 1197 GLN cc_start: 0.7915 (tt0) cc_final: 0.7537 (tp40) REVERT: B 1229 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7925 (mm-30) REVERT: B 1294 TYR cc_start: 0.7542 (m-10) cc_final: 0.7131 (m-10) REVERT: C 43 ASN cc_start: 0.8434 (t0) cc_final: 0.7996 (t0) REVERT: C 67 LYS cc_start: 0.8336 (mttt) cc_final: 0.7670 (tptt) REVERT: C 185 LYS cc_start: 0.8037 (tttt) cc_final: 0.7407 (tmtt) REVERT: C 237 ASP cc_start: 0.7681 (t70) cc_final: 0.7396 (t0) REVERT: C 280 ASP cc_start: 0.8718 (t0) cc_final: 0.8269 (t0) REVERT: C 313 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7386 (mt0) REVERT: C 332 LYS cc_start: 0.8185 (mtmm) cc_final: 0.7400 (mtmm) REVERT: C 335 ASN cc_start: 0.8071 (m-40) cc_final: 0.7582 (m110) REVERT: D 43 THR cc_start: 0.9132 (m) cc_final: 0.8751 (p) REVERT: D 91 GLU cc_start: 0.8394 (pp20) cc_final: 0.8136 (pp20) REVERT: D 124 TYR cc_start: 0.8918 (t80) cc_final: 0.8596 (t80) REVERT: D 289 ARG cc_start: 0.7416 (mtp180) cc_final: 0.6706 (mmt180) REVERT: D 340 PHE cc_start: 0.8401 (OUTLIER) cc_final: 0.7796 (t80) REVERT: D 354 ASN cc_start: 0.9320 (t0) cc_final: 0.8912 (t0) REVERT: D 367 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7762 (mp) REVERT: D 454 TYR cc_start: 0.6935 (t80) cc_final: 0.6420 (m-80) REVERT: D 500 ASN cc_start: 0.7758 (t0) cc_final: 0.7454 (t0) REVERT: D 565 PHE cc_start: 0.6777 (t80) cc_final: 0.6195 (m-80) REVERT: D 567 LYS cc_start: 0.7495 (mttt) cc_final: 0.7268 (mttt) REVERT: D 689 THR cc_start: 0.4555 (OUTLIER) cc_final: 0.4226 (p) REVERT: D 1066 MET cc_start: 0.6909 (ttp) cc_final: 0.6595 (tpp) REVERT: D 1197 GLN cc_start: 0.7914 (tt0) cc_final: 0.7536 (tp40) REVERT: D 1229 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7926 (mm-30) REVERT: D 1294 TYR cc_start: 0.7547 (m-10) cc_final: 0.7135 (m-10) REVERT: E 43 ASN cc_start: 0.8436 (t0) cc_final: 0.7998 (t0) REVERT: E 67 LYS cc_start: 0.8336 (mttt) cc_final: 0.7669 (tptt) REVERT: E 185 LYS cc_start: 0.8036 (tttt) cc_final: 0.7406 (tmtt) REVERT: E 237 ASP cc_start: 0.7682 (t70) cc_final: 0.7396 (t0) REVERT: E 280 ASP cc_start: 0.8718 (t0) cc_final: 0.8268 (t0) REVERT: E 313 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7389 (mt0) REVERT: E 332 LYS cc_start: 0.8181 (mtmm) cc_final: 0.7397 (mtmm) REVERT: E 335 ASN cc_start: 0.8071 (m-40) cc_final: 0.7583 (m110) REVERT: F 43 THR cc_start: 0.9132 (m) cc_final: 0.8750 (p) REVERT: F 91 GLU cc_start: 0.8392 (pp20) cc_final: 0.8136 (pp20) REVERT: F 124 TYR cc_start: 0.8917 (t80) cc_final: 0.8596 (t80) REVERT: F 289 ARG cc_start: 0.7415 (mtp180) cc_final: 0.6707 (mmt180) REVERT: F 340 PHE cc_start: 0.8403 (OUTLIER) cc_final: 0.7797 (t80) REVERT: F 354 ASN cc_start: 0.9320 (t0) cc_final: 0.8911 (t0) REVERT: F 367 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7762 (mp) REVERT: F 454 TYR cc_start: 0.6934 (t80) cc_final: 0.6420 (m-80) REVERT: F 500 ASN cc_start: 0.7759 (t0) cc_final: 0.7454 (t0) REVERT: F 565 PHE cc_start: 0.6777 (t80) cc_final: 0.6195 (m-80) REVERT: F 567 LYS cc_start: 0.7496 (mttt) cc_final: 0.7269 (mttt) REVERT: F 689 THR cc_start: 0.4559 (OUTLIER) cc_final: 0.4229 (p) REVERT: F 1066 MET cc_start: 0.6908 (ttp) cc_final: 0.6595 (tpp) REVERT: F 1197 GLN cc_start: 0.7914 (tt0) cc_final: 0.7537 (tp40) REVERT: F 1229 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7926 (mm-30) REVERT: F 1294 TYR cc_start: 0.7545 (m-10) cc_final: 0.7133 (m-10) REVERT: G 43 ASN cc_start: 0.8436 (t0) cc_final: 0.7999 (t0) REVERT: G 67 LYS cc_start: 0.8334 (mttt) cc_final: 0.7670 (tptt) REVERT: G 185 LYS cc_start: 0.8036 (tttt) cc_final: 0.7407 (tmtt) REVERT: G 237 ASP cc_start: 0.7680 (t70) cc_final: 0.7394 (t0) REVERT: G 280 ASP cc_start: 0.8718 (t0) cc_final: 0.8269 (t0) REVERT: G 313 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7387 (mt0) REVERT: G 332 LYS cc_start: 0.8184 (mtmm) cc_final: 0.7398 (mtmm) REVERT: G 335 ASN cc_start: 0.8073 (m-40) cc_final: 0.7583 (m110) REVERT: H 43 THR cc_start: 0.9132 (m) cc_final: 0.8751 (p) REVERT: H 91 GLU cc_start: 0.8395 (pp20) cc_final: 0.8137 (pp20) REVERT: H 124 TYR cc_start: 0.8917 (t80) cc_final: 0.8597 (t80) REVERT: H 289 ARG cc_start: 0.7415 (mtp180) cc_final: 0.6707 (mmt180) REVERT: H 340 PHE cc_start: 0.8401 (OUTLIER) cc_final: 0.7795 (t80) REVERT: H 354 ASN cc_start: 0.9320 (t0) cc_final: 0.8911 (t0) REVERT: H 367 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7761 (mp) REVERT: H 454 TYR cc_start: 0.6935 (t80) cc_final: 0.6421 (m-80) REVERT: H 500 ASN cc_start: 0.7761 (t0) cc_final: 0.7456 (t0) REVERT: H 565 PHE cc_start: 0.6776 (t80) cc_final: 0.6195 (m-80) REVERT: H 567 LYS cc_start: 0.7495 (mttt) cc_final: 0.7269 (mttt) REVERT: H 689 THR cc_start: 0.4560 (OUTLIER) cc_final: 0.4231 (p) REVERT: H 1066 MET cc_start: 0.6911 (ttp) cc_final: 0.6597 (tpp) REVERT: H 1197 GLN cc_start: 0.7916 (tt0) cc_final: 0.7538 (tp40) REVERT: H 1229 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7925 (mm-30) REVERT: H 1294 TYR cc_start: 0.7542 (m-10) cc_final: 0.7131 (m-10) outliers start: 415 outliers final: 272 residues processed: 1142 average time/residue: 0.5513 time to fit residues: 1102.3131 Evaluate side-chains 1112 residues out of total 5876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 288 poor density : 824 time to evaluate : 5.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 313 GLN Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 10 ASN Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 209 ASP Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 689 THR Chi-restraints excluded: chain B residue 770 VAL Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 848 THR Chi-restraints excluded: chain B residue 1007 SER Chi-restraints excluded: chain B residue 1039 ASP Chi-restraints excluded: chain B residue 1071 LEU Chi-restraints excluded: chain B residue 1082 THR Chi-restraints excluded: chain B residue 1084 VAL Chi-restraints excluded: chain B residue 1097 LEU Chi-restraints excluded: chain B residue 1105 ILE Chi-restraints excluded: chain B residue 1129 CYS Chi-restraints excluded: chain B residue 1147 THR Chi-restraints excluded: chain B residue 1155 THR Chi-restraints excluded: chain B residue 1220 GLU Chi-restraints excluded: chain B residue 1246 ARG Chi-restraints excluded: chain B residue 1259 VAL Chi-restraints excluded: chain B residue 1295 LEU Chi-restraints excluded: chain B residue 1298 MET Chi-restraints excluded: chain B residue 1549 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 77 MET Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 110 CYS Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 313 GLN Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 10 ASN Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 26 CYS Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 209 ASP Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 340 PHE Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 371 THR Chi-restraints excluded: chain D residue 391 ILE Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 446 ILE Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 575 VAL Chi-restraints excluded: chain D residue 579 SER Chi-restraints excluded: chain D residue 597 VAL Chi-restraints excluded: chain D residue 605 VAL Chi-restraints excluded: chain D residue 679 VAL Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 689 THR Chi-restraints excluded: chain D residue 770 VAL Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 848 THR Chi-restraints excluded: chain D residue 1007 SER Chi-restraints excluded: chain D residue 1039 ASP Chi-restraints excluded: chain D residue 1071 LEU Chi-restraints excluded: chain D residue 1082 THR Chi-restraints excluded: chain D residue 1084 VAL Chi-restraints excluded: chain D residue 1097 LEU Chi-restraints excluded: chain D residue 1105 ILE Chi-restraints excluded: chain D residue 1129 CYS Chi-restraints excluded: chain D residue 1147 THR Chi-restraints excluded: chain D residue 1155 THR Chi-restraints excluded: chain D residue 1220 GLU Chi-restraints excluded: chain D residue 1246 ARG Chi-restraints excluded: chain D residue 1259 VAL Chi-restraints excluded: chain D residue 1295 LEU Chi-restraints excluded: chain D residue 1298 MET Chi-restraints excluded: chain D residue 1549 VAL Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 77 MET Chi-restraints excluded: chain E residue 78 SER Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 313 GLN Chi-restraints excluded: chain E residue 323 ASP Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 10 ASN Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 26 CYS Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 209 ASP Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 234 ASN Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 304 THR Chi-restraints excluded: chain F residue 340 PHE Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 362 LEU Chi-restraints excluded: chain F residue 367 LEU Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 391 ILE Chi-restraints excluded: chain F residue 399 ILE Chi-restraints excluded: chain F residue 446 ILE Chi-restraints excluded: chain F residue 531 THR Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain F residue 556 LEU Chi-restraints excluded: chain F residue 575 VAL Chi-restraints excluded: chain F residue 579 SER Chi-restraints excluded: chain F residue 597 VAL Chi-restraints excluded: chain F residue 605 VAL Chi-restraints excluded: chain F residue 679 VAL Chi-restraints excluded: chain F residue 681 ILE Chi-restraints excluded: chain F residue 689 THR Chi-restraints excluded: chain F residue 770 VAL Chi-restraints excluded: chain F residue 779 LEU Chi-restraints excluded: chain F residue 848 THR Chi-restraints excluded: chain F residue 1007 SER Chi-restraints excluded: chain F residue 1039 ASP Chi-restraints excluded: chain F residue 1071 LEU Chi-restraints excluded: chain F residue 1082 THR Chi-restraints excluded: chain F residue 1084 VAL Chi-restraints excluded: chain F residue 1097 LEU Chi-restraints excluded: chain F residue 1105 ILE Chi-restraints excluded: chain F residue 1129 CYS Chi-restraints excluded: chain F residue 1147 THR Chi-restraints excluded: chain F residue 1155 THR Chi-restraints excluded: chain F residue 1220 GLU Chi-restraints excluded: chain F residue 1246 ARG Chi-restraints excluded: chain F residue 1259 VAL Chi-restraints excluded: chain F residue 1295 LEU Chi-restraints excluded: chain F residue 1298 MET Chi-restraints excluded: chain F residue 1549 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 77 MET Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 110 CYS Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 208 SER Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain G residue 296 ILE Chi-restraints excluded: chain G residue 309 ILE Chi-restraints excluded: chain G residue 313 GLN Chi-restraints excluded: chain G residue 323 ASP Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 10 ASN Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 26 CYS Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain H residue 137 ILE Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 189 VAL Chi-restraints excluded: chain H residue 209 ASP Chi-restraints excluded: chain H residue 213 LEU Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 218 LEU Chi-restraints excluded: chain H residue 234 ASN Chi-restraints excluded: chain H residue 239 THR Chi-restraints excluded: chain H residue 304 THR Chi-restraints excluded: chain H residue 340 PHE Chi-restraints excluded: chain H residue 360 VAL Chi-restraints excluded: chain H residue 362 LEU Chi-restraints excluded: chain H residue 367 LEU Chi-restraints excluded: chain H residue 371 THR Chi-restraints excluded: chain H residue 391 ILE Chi-restraints excluded: chain H residue 399 ILE Chi-restraints excluded: chain H residue 446 ILE Chi-restraints excluded: chain H residue 531 THR Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 556 LEU Chi-restraints excluded: chain H residue 575 VAL Chi-restraints excluded: chain H residue 579 SER Chi-restraints excluded: chain H residue 597 VAL Chi-restraints excluded: chain H residue 605 VAL Chi-restraints excluded: chain H residue 679 VAL Chi-restraints excluded: chain H residue 681 ILE Chi-restraints excluded: chain H residue 689 THR Chi-restraints excluded: chain H residue 770 VAL Chi-restraints excluded: chain H residue 779 LEU Chi-restraints excluded: chain H residue 848 THR Chi-restraints excluded: chain H residue 1007 SER Chi-restraints excluded: chain H residue 1039 ASP Chi-restraints excluded: chain H residue 1071 LEU Chi-restraints excluded: chain H residue 1082 THR Chi-restraints excluded: chain H residue 1084 VAL Chi-restraints excluded: chain H residue 1097 LEU Chi-restraints excluded: chain H residue 1105 ILE Chi-restraints excluded: chain H residue 1129 CYS Chi-restraints excluded: chain H residue 1147 THR Chi-restraints excluded: chain H residue 1155 THR Chi-restraints excluded: chain H residue 1220 GLU Chi-restraints excluded: chain H residue 1246 ARG Chi-restraints excluded: chain H residue 1259 VAL Chi-restraints excluded: chain H residue 1295 LEU Chi-restraints excluded: chain H residue 1298 MET Chi-restraints excluded: chain H residue 1549 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 672 random chunks: chunk 604 optimal weight: 10.0000 chunk 459 optimal weight: 0.9980 chunk 317 optimal weight: 8.9990 chunk 67 optimal weight: 0.9980 chunk 291 optimal weight: 0.9980 chunk 410 optimal weight: 4.9990 chunk 613 optimal weight: 20.0000 chunk 649 optimal weight: 20.0000 chunk 320 optimal weight: 0.6980 chunk 581 optimal weight: 0.8980 chunk 175 optimal weight: 0.0040 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 ASN B 24 ASN B 211 GLN ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1020 GLN C 153 ASN D 211 GLN ** D 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1020 GLN E 153 ASN F 24 ASN F 211 GLN ** F 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1020 GLN G 153 ASN H 24 ASN H 211 GLN ** H 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1020 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6601 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 53092 Z= 0.167 Angle : 0.869 34.810 72352 Z= 0.357 Chirality : 0.078 2.010 8684 Planarity : 0.004 0.043 8792 Dihedral : 19.304 179.776 9480 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 5.03 % Allowed : 23.30 % Favored : 71.67 % 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: 0.41 (0.10), residues: 6684 helix: 1.46 (0.08), residues: 4084 sheet: -1.02 (0.22), residues: 496 loop : -1.79 (0.13), residues: 2104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D1247 HIS 0.006 0.001 HIS B 562 PHE 0.017 0.001 PHE B1182 TYR 0.025 0.002 TYR B 263 ARG 0.005 0.000 ARG F 102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13368 Ramachandran restraints generated. 6684 Oldfield, 0 Emsley, 6684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13368 Ramachandran restraints generated. 6684 Oldfield, 0 Emsley, 6684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1158 residues out of total 5876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 243 poor density : 915 time to evaluate : 5.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASN cc_start: 0.8447 (t0) cc_final: 0.7903 (t0) REVERT: A 67 LYS cc_start: 0.8208 (mttt) cc_final: 0.7407 (tptt) REVERT: A 71 THR cc_start: 0.8961 (OUTLIER) cc_final: 0.8645 (m) REVERT: A 185 LYS cc_start: 0.8032 (tttt) cc_final: 0.7376 (tmtt) REVERT: A 237 ASP cc_start: 0.7586 (t70) cc_final: 0.7289 (t0) REVERT: A 280 ASP cc_start: 0.8797 (t0) cc_final: 0.8356 (t0) REVERT: A 282 GLU cc_start: 0.6920 (tt0) cc_final: 0.6648 (tt0) REVERT: A 304 TYR cc_start: 0.8691 (m-80) cc_final: 0.8423 (m-80) REVERT: A 313 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7351 (mt0) REVERT: A 335 ASN cc_start: 0.8072 (m-40) cc_final: 0.7790 (m110) REVERT: B 43 THR cc_start: 0.9038 (m) cc_final: 0.8639 (p) REVERT: B 91 GLU cc_start: 0.8537 (pp20) cc_final: 0.8291 (pp20) REVERT: B 96 ASP cc_start: 0.9192 (p0) cc_final: 0.8926 (p0) REVERT: B 198 PHE cc_start: 0.5442 (OUTLIER) cc_final: 0.5132 (m-80) REVERT: B 289 ARG cc_start: 0.7376 (mtp180) cc_final: 0.6682 (mmt180) REVERT: B 340 PHE cc_start: 0.8398 (OUTLIER) cc_final: 0.7685 (t80) REVERT: B 354 ASN cc_start: 0.9160 (t0) cc_final: 0.8845 (t0) REVERT: B 454 TYR cc_start: 0.6915 (t80) cc_final: 0.6384 (m-80) REVERT: B 500 ASN cc_start: 0.7853 (t0) cc_final: 0.7567 (t0) REVERT: B 565 PHE cc_start: 0.6736 (t80) cc_final: 0.6172 (m-80) REVERT: B 567 LYS cc_start: 0.7466 (mttt) cc_final: 0.7210 (mttt) REVERT: B 1066 MET cc_start: 0.7018 (ttp) cc_final: 0.6692 (tpp) REVERT: B 1110 MET cc_start: 0.5696 (tpp) cc_final: 0.5343 (mmt) REVERT: B 1197 GLN cc_start: 0.7830 (tt0) cc_final: 0.7422 (tp40) REVERT: B 1220 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.7790 (mp0) REVERT: B 1294 TYR cc_start: 0.7462 (m-10) cc_final: 0.7057 (m-10) REVERT: C 43 ASN cc_start: 0.8445 (t0) cc_final: 0.7902 (t0) REVERT: C 67 LYS cc_start: 0.8216 (mttt) cc_final: 0.7416 (tptt) REVERT: C 71 THR cc_start: 0.8970 (OUTLIER) cc_final: 0.8654 (m) REVERT: C 185 LYS cc_start: 0.8033 (tttt) cc_final: 0.7377 (tmtt) REVERT: C 237 ASP cc_start: 0.7591 (t70) cc_final: 0.7293 (t0) REVERT: C 280 ASP cc_start: 0.8797 (t0) cc_final: 0.8356 (t0) REVERT: C 282 GLU cc_start: 0.6916 (tt0) cc_final: 0.6647 (tt0) REVERT: C 304 TYR cc_start: 0.8690 (m-80) cc_final: 0.8423 (m-80) REVERT: C 313 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7350 (mt0) REVERT: C 335 ASN cc_start: 0.8070 (m-40) cc_final: 0.7789 (m110) REVERT: D 43 THR cc_start: 0.9040 (m) cc_final: 0.8641 (p) REVERT: D 91 GLU cc_start: 0.8538 (pp20) cc_final: 0.8292 (pp20) REVERT: D 96 ASP cc_start: 0.9192 (p0) cc_final: 0.8926 (p0) REVERT: D 198 PHE cc_start: 0.5442 (OUTLIER) cc_final: 0.5133 (m-80) REVERT: D 289 ARG cc_start: 0.7377 (mtp180) cc_final: 0.6682 (mmt180) REVERT: D 340 PHE cc_start: 0.8395 (OUTLIER) cc_final: 0.7686 (t80) REVERT: D 354 ASN cc_start: 0.9159 (t0) cc_final: 0.8845 (t0) REVERT: D 454 TYR cc_start: 0.6915 (t80) cc_final: 0.6384 (m-80) REVERT: D 500 ASN cc_start: 0.7853 (t0) cc_final: 0.7567 (t0) REVERT: D 565 PHE cc_start: 0.6737 (t80) cc_final: 0.6173 (m-80) REVERT: D 567 LYS cc_start: 0.7465 (mttt) cc_final: 0.7209 (mttt) REVERT: D 1066 MET cc_start: 0.7019 (ttp) cc_final: 0.6693 (tpp) REVERT: D 1110 MET cc_start: 0.5697 (tpp) cc_final: 0.5344 (mmt) REVERT: D 1197 GLN cc_start: 0.7828 (tt0) cc_final: 0.7420 (tp40) REVERT: D 1220 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.7791 (mp0) REVERT: D 1294 TYR cc_start: 0.7468 (m-10) cc_final: 0.7063 (m-10) REVERT: E 43 ASN cc_start: 0.8447 (t0) cc_final: 0.7904 (t0) REVERT: E 67 LYS cc_start: 0.8217 (mttt) cc_final: 0.7417 (tptt) REVERT: E 71 THR cc_start: 0.8970 (OUTLIER) cc_final: 0.8655 (m) REVERT: E 185 LYS cc_start: 0.8032 (tttt) cc_final: 0.7377 (tmtt) REVERT: E 237 ASP cc_start: 0.7590 (t70) cc_final: 0.7293 (t0) REVERT: E 280 ASP cc_start: 0.8797 (t0) cc_final: 0.8355 (t0) REVERT: E 282 GLU cc_start: 0.6919 (tt0) cc_final: 0.6646 (tt0) REVERT: E 304 TYR cc_start: 0.8688 (m-80) cc_final: 0.8420 (m-80) REVERT: E 313 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7349 (mt0) REVERT: E 335 ASN cc_start: 0.8071 (m-40) cc_final: 0.7790 (m110) REVERT: F 43 THR cc_start: 0.9039 (m) cc_final: 0.8640 (p) REVERT: F 91 GLU cc_start: 0.8537 (pp20) cc_final: 0.8292 (pp20) REVERT: F 96 ASP cc_start: 0.9192 (p0) cc_final: 0.8927 (p0) REVERT: F 198 PHE cc_start: 0.5442 (OUTLIER) cc_final: 0.5131 (m-80) REVERT: F 289 ARG cc_start: 0.7374 (mtp180) cc_final: 0.6681 (mmt180) REVERT: F 340 PHE cc_start: 0.8398 (OUTLIER) cc_final: 0.7686 (t80) REVERT: F 354 ASN cc_start: 0.9159 (t0) cc_final: 0.8845 (t0) REVERT: F 454 TYR cc_start: 0.6915 (t80) cc_final: 0.6384 (m-80) REVERT: F 500 ASN cc_start: 0.7851 (t0) cc_final: 0.7565 (t0) REVERT: F 565 PHE cc_start: 0.6739 (t80) cc_final: 0.6174 (m-80) REVERT: F 567 LYS cc_start: 0.7466 (mttt) cc_final: 0.7209 (mttt) REVERT: F 1066 MET cc_start: 0.7018 (ttp) cc_final: 0.6693 (tpp) REVERT: F 1110 MET cc_start: 0.5695 (tpp) cc_final: 0.5341 (mmt) REVERT: F 1197 GLN cc_start: 0.7828 (tt0) cc_final: 0.7421 (tp40) REVERT: F 1220 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.7790 (mp0) REVERT: F 1294 TYR cc_start: 0.7467 (m-10) cc_final: 0.7060 (m-10) REVERT: G 43 ASN cc_start: 0.8448 (t0) cc_final: 0.7905 (t0) REVERT: G 67 LYS cc_start: 0.8219 (mttt) cc_final: 0.7406 (tptt) REVERT: G 71 THR cc_start: 0.8978 (OUTLIER) cc_final: 0.8683 (m) REVERT: G 185 LYS cc_start: 0.8032 (tttt) cc_final: 0.7376 (tmtt) REVERT: G 237 ASP cc_start: 0.7588 (t70) cc_final: 0.7290 (t0) REVERT: G 280 ASP cc_start: 0.8797 (t0) cc_final: 0.8354 (t0) REVERT: G 282 GLU cc_start: 0.6918 (tt0) cc_final: 0.6647 (tt0) REVERT: G 304 TYR cc_start: 0.8689 (m-80) cc_final: 0.8422 (m-80) REVERT: G 313 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.7349 (mt0) REVERT: G 335 ASN cc_start: 0.8071 (m-40) cc_final: 0.7790 (m110) REVERT: H 43 THR cc_start: 0.9039 (m) cc_final: 0.8641 (p) REVERT: H 91 GLU cc_start: 0.8538 (pp20) cc_final: 0.8290 (pp20) REVERT: H 96 ASP cc_start: 0.9190 (p0) cc_final: 0.8924 (p0) REVERT: H 198 PHE cc_start: 0.5440 (OUTLIER) cc_final: 0.5130 (m-80) REVERT: H 289 ARG cc_start: 0.7374 (mtp180) cc_final: 0.6681 (mmt180) REVERT: H 340 PHE cc_start: 0.8396 (OUTLIER) cc_final: 0.7684 (t80) REVERT: H 354 ASN cc_start: 0.9162 (t0) cc_final: 0.8848 (t0) REVERT: H 454 TYR cc_start: 0.6916 (t80) cc_final: 0.6385 (m-80) REVERT: H 500 ASN cc_start: 0.7853 (t0) cc_final: 0.7566 (t0) REVERT: H 565 PHE cc_start: 0.6738 (t80) cc_final: 0.6173 (m-80) REVERT: H 567 LYS cc_start: 0.7466 (mttt) cc_final: 0.7209 (mttt) REVERT: H 1066 MET cc_start: 0.7018 (ttp) cc_final: 0.6692 (tpp) REVERT: H 1110 MET cc_start: 0.5694 (tpp) cc_final: 0.5340 (mmt) REVERT: H 1197 GLN cc_start: 0.7830 (tt0) cc_final: 0.7421 (tp40) REVERT: H 1220 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.7790 (mp0) REVERT: H 1294 TYR cc_start: 0.7463 (m-10) cc_final: 0.7059 (m-10) outliers start: 243 outliers final: 131 residues processed: 1070 average time/residue: 0.6233 time to fit residues: 1158.9549 Evaluate side-chains 980 residues out of total 5876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 829 time to evaluate : 5.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 313 GLN Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 209 ASP Chi-restraints excluded: chain B residue 211 GLN Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 1007 SER Chi-restraints excluded: chain B residue 1097 LEU Chi-restraints excluded: chain B residue 1147 THR Chi-restraints excluded: chain B residue 1220 GLU Chi-restraints excluded: chain B residue 1242 THR Chi-restraints excluded: chain B residue 1246 ARG Chi-restraints excluded: chain B residue 1249 GLU Chi-restraints excluded: chain B residue 1298 MET Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 313 GLN Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 26 CYS Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 198 PHE Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 209 ASP Chi-restraints excluded: chain D residue 211 GLN Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 340 PHE Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 1007 SER Chi-restraints excluded: chain D residue 1097 LEU Chi-restraints excluded: chain D residue 1147 THR Chi-restraints excluded: chain D residue 1220 GLU Chi-restraints excluded: chain D residue 1242 THR Chi-restraints excluded: chain D residue 1246 ARG Chi-restraints excluded: chain D residue 1249 GLU Chi-restraints excluded: chain D residue 1298 MET Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 313 GLN Chi-restraints excluded: chain E residue 323 ASP Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 26 CYS Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 198 PHE Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 209 ASP Chi-restraints excluded: chain F residue 211 GLN Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 340 PHE Chi-restraints excluded: chain F residue 362 LEU Chi-restraints excluded: chain F residue 399 ILE Chi-restraints excluded: chain F residue 556 LEU Chi-restraints excluded: chain F residue 681 ILE Chi-restraints excluded: chain F residue 1007 SER Chi-restraints excluded: chain F residue 1097 LEU Chi-restraints excluded: chain F residue 1147 THR Chi-restraints excluded: chain F residue 1220 GLU Chi-restraints excluded: chain F residue 1242 THR Chi-restraints excluded: chain F residue 1246 ARG Chi-restraints excluded: chain F residue 1249 GLU Chi-restraints excluded: chain F residue 1298 MET Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 261 ILE Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain G residue 309 ILE Chi-restraints excluded: chain G residue 313 GLN Chi-restraints excluded: chain G residue 323 ASP Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 26 CYS Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 137 ILE Chi-restraints excluded: chain H residue 198 PHE Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain H residue 209 ASP Chi-restraints excluded: chain H residue 211 GLN Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 218 LEU Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 340 PHE Chi-restraints excluded: chain H residue 362 LEU Chi-restraints excluded: chain H residue 399 ILE Chi-restraints excluded: chain H residue 556 LEU Chi-restraints excluded: chain H residue 681 ILE Chi-restraints excluded: chain H residue 1007 SER Chi-restraints excluded: chain H residue 1097 LEU Chi-restraints excluded: chain H residue 1147 THR Chi-restraints excluded: chain H residue 1220 GLU Chi-restraints excluded: chain H residue 1242 THR Chi-restraints excluded: chain H residue 1246 ARG Chi-restraints excluded: chain H residue 1249 GLU Chi-restraints excluded: chain H residue 1298 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 672 random chunks: chunk 540 optimal weight: 0.7980 chunk 368 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 483 optimal weight: 10.0000 chunk 268 optimal weight: 5.9990 chunk 554 optimal weight: 0.1980 chunk 448 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 331 optimal weight: 20.0000 chunk 583 optimal weight: 10.0000 chunk 163 optimal weight: 20.0000 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 211 GLN ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 211 GLN ** D 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 211 GLN ** F 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 211 GLN ** H 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6633 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 53092 Z= 0.253 Angle : 0.879 35.054 72352 Z= 0.365 Chirality : 0.079 1.998 8684 Planarity : 0.004 0.046 8792 Dihedral : 19.116 179.659 9464 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 6.05 % Allowed : 22.95 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.10), residues: 6684 helix: 1.59 (0.08), residues: 4060 sheet: -0.89 (0.22), residues: 480 loop : -1.57 (0.13), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H1247 HIS 0.005 0.001 HIS H 896 PHE 0.028 0.001 PHE A 168 TYR 0.016 0.002 TYR B 195 ARG 0.006 0.000 ARG D 102 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13368 Ramachandran restraints generated. 6684 Oldfield, 0 Emsley, 6684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13368 Ramachandran restraints generated. 6684 Oldfield, 0 Emsley, 6684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1133 residues out of total 5876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 292 poor density : 841 time to evaluate : 5.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASN cc_start: 0.8495 (t0) cc_final: 0.7866 (t0) REVERT: A 67 LYS cc_start: 0.8183 (mttt) cc_final: 0.7411 (tptt) REVERT: A 71 THR cc_start: 0.8911 (m) cc_final: 0.8604 (m) REVERT: A 185 LYS cc_start: 0.8052 (tttt) cc_final: 0.7413 (tmtt) REVERT: A 280 ASP cc_start: 0.8818 (t0) cc_final: 0.8381 (t0) REVERT: A 282 GLU cc_start: 0.6974 (tt0) cc_final: 0.6692 (tt0) REVERT: A 313 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7386 (mt0) REVERT: B 43 THR cc_start: 0.9063 (m) cc_final: 0.8683 (p) REVERT: B 91 GLU cc_start: 0.8526 (pp20) cc_final: 0.8286 (pp20) REVERT: B 96 ASP cc_start: 0.9189 (p0) cc_final: 0.8946 (p0) REVERT: B 198 PHE cc_start: 0.5817 (OUTLIER) cc_final: 0.5234 (m-80) REVERT: B 211 GLN cc_start: 0.7304 (OUTLIER) cc_final: 0.6885 (mp10) REVERT: B 289 ARG cc_start: 0.7379 (mtp180) cc_final: 0.6696 (mmt180) REVERT: B 340 PHE cc_start: 0.8426 (OUTLIER) cc_final: 0.7839 (t80) REVERT: B 354 ASN cc_start: 0.9232 (t0) cc_final: 0.8886 (t0) REVERT: B 454 TYR cc_start: 0.6861 (t80) cc_final: 0.6336 (m-80) REVERT: B 500 ASN cc_start: 0.7882 (t0) cc_final: 0.7560 (t0) REVERT: B 506 MET cc_start: 0.4303 (tpp) cc_final: 0.4100 (tpp) REVERT: B 565 PHE cc_start: 0.6698 (t80) cc_final: 0.6126 (m-80) REVERT: B 567 LYS cc_start: 0.7495 (mttt) cc_final: 0.7250 (mttt) REVERT: B 1066 MET cc_start: 0.7036 (ttp) cc_final: 0.6706 (tpp) REVERT: B 1197 GLN cc_start: 0.7924 (tt0) cc_final: 0.7520 (tp40) REVERT: B 1294 TYR cc_start: 0.7423 (m-10) cc_final: 0.7117 (m-10) REVERT: C 43 ASN cc_start: 0.8493 (t0) cc_final: 0.7865 (t0) REVERT: C 67 LYS cc_start: 0.8227 (mttt) cc_final: 0.7422 (tptt) REVERT: C 71 THR cc_start: 0.8930 (m) cc_final: 0.8633 (m) REVERT: C 185 LYS cc_start: 0.8054 (tttt) cc_final: 0.7413 (tmtt) REVERT: C 280 ASP cc_start: 0.8815 (t0) cc_final: 0.8378 (t0) REVERT: C 282 GLU cc_start: 0.6965 (tt0) cc_final: 0.6694 (tt0) REVERT: C 313 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7385 (mt0) REVERT: D 43 THR cc_start: 0.9065 (m) cc_final: 0.8684 (p) REVERT: D 91 GLU cc_start: 0.8525 (pp20) cc_final: 0.8285 (pp20) REVERT: D 96 ASP cc_start: 0.9189 (p0) cc_final: 0.8945 (p0) REVERT: D 198 PHE cc_start: 0.5819 (OUTLIER) cc_final: 0.5235 (m-80) REVERT: D 211 GLN cc_start: 0.7299 (OUTLIER) cc_final: 0.6876 (mp10) REVERT: D 289 ARG cc_start: 0.7381 (mtp180) cc_final: 0.6697 (mmt180) REVERT: D 340 PHE cc_start: 0.8424 (OUTLIER) cc_final: 0.7840 (t80) REVERT: D 354 ASN cc_start: 0.9232 (t0) cc_final: 0.8885 (t0) REVERT: D 454 TYR cc_start: 0.6860 (t80) cc_final: 0.6335 (m-80) REVERT: D 500 ASN cc_start: 0.7880 (t0) cc_final: 0.7558 (t0) REVERT: D 506 MET cc_start: 0.4303 (tpp) cc_final: 0.4102 (tpp) REVERT: D 565 PHE cc_start: 0.6701 (t80) cc_final: 0.6129 (m-80) REVERT: D 567 LYS cc_start: 0.7495 (mttt) cc_final: 0.7249 (mttt) REVERT: D 1066 MET cc_start: 0.7037 (ttp) cc_final: 0.6707 (tpp) REVERT: D 1197 GLN cc_start: 0.7924 (tt0) cc_final: 0.7520 (tp40) REVERT: D 1294 TYR cc_start: 0.7429 (m-10) cc_final: 0.7123 (m-10) REVERT: E 43 ASN cc_start: 0.8495 (t0) cc_final: 0.7867 (t0) REVERT: E 67 LYS cc_start: 0.8229 (mttt) cc_final: 0.7422 (tptt) REVERT: E 71 THR cc_start: 0.8926 (m) cc_final: 0.8632 (m) REVERT: E 185 LYS cc_start: 0.8053 (tttt) cc_final: 0.7413 (tmtt) REVERT: E 280 ASP cc_start: 0.8816 (t0) cc_final: 0.8379 (t0) REVERT: E 282 GLU cc_start: 0.6972 (tt0) cc_final: 0.6693 (tt0) REVERT: E 313 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7385 (mt0) REVERT: F 43 THR cc_start: 0.9065 (m) cc_final: 0.8684 (p) REVERT: F 91 GLU cc_start: 0.8524 (pp20) cc_final: 0.8285 (pp20) REVERT: F 96 ASP cc_start: 0.9189 (p0) cc_final: 0.8945 (p0) REVERT: F 198 PHE cc_start: 0.5818 (OUTLIER) cc_final: 0.5234 (m-80) REVERT: F 211 GLN cc_start: 0.7303 (OUTLIER) cc_final: 0.6885 (mp10) REVERT: F 289 ARG cc_start: 0.7379 (mtp180) cc_final: 0.6696 (mmt180) REVERT: F 340 PHE cc_start: 0.8427 (OUTLIER) cc_final: 0.7839 (t80) REVERT: F 354 ASN cc_start: 0.9231 (t0) cc_final: 0.8885 (t0) REVERT: F 454 TYR cc_start: 0.6862 (t80) cc_final: 0.6336 (m-80) REVERT: F 500 ASN cc_start: 0.7881 (t0) cc_final: 0.7558 (t0) REVERT: F 506 MET cc_start: 0.4306 (tpp) cc_final: 0.4103 (tpp) REVERT: F 565 PHE cc_start: 0.6702 (t80) cc_final: 0.6128 (m-80) REVERT: F 567 LYS cc_start: 0.7494 (mttt) cc_final: 0.7249 (mttt) REVERT: F 1066 MET cc_start: 0.7036 (ttp) cc_final: 0.6706 (tpp) REVERT: F 1197 GLN cc_start: 0.7922 (tt0) cc_final: 0.7518 (tp40) REVERT: F 1294 TYR cc_start: 0.7425 (m-10) cc_final: 0.7120 (m-10) REVERT: G 43 ASN cc_start: 0.8497 (t0) cc_final: 0.7870 (t0) REVERT: G 67 LYS cc_start: 0.8285 (mttt) cc_final: 0.7463 (tptt) REVERT: G 71 THR cc_start: 0.8936 (m) cc_final: 0.8643 (m) REVERT: G 185 LYS cc_start: 0.8054 (tttt) cc_final: 0.7415 (tmtt) REVERT: G 280 ASP cc_start: 0.8814 (t0) cc_final: 0.8378 (t0) REVERT: G 282 GLU cc_start: 0.6971 (tt0) cc_final: 0.6693 (tt0) REVERT: G 313 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7385 (mt0) REVERT: H 43 THR cc_start: 0.9063 (m) cc_final: 0.8683 (p) REVERT: H 91 GLU cc_start: 0.8525 (pp20) cc_final: 0.8286 (pp20) REVERT: H 96 ASP cc_start: 0.9189 (p0) cc_final: 0.8945 (p0) REVERT: H 198 PHE cc_start: 0.5815 (OUTLIER) cc_final: 0.5233 (m-80) REVERT: H 211 GLN cc_start: 0.7305 (OUTLIER) cc_final: 0.6885 (mp10) REVERT: H 289 ARG cc_start: 0.7380 (mtp180) cc_final: 0.6696 (mmt180) REVERT: H 340 PHE cc_start: 0.8426 (OUTLIER) cc_final: 0.7839 (t80) REVERT: H 354 ASN cc_start: 0.9233 (t0) cc_final: 0.8886 (t0) REVERT: H 454 TYR cc_start: 0.6862 (t80) cc_final: 0.6337 (m-80) REVERT: H 500 ASN cc_start: 0.7882 (t0) cc_final: 0.7560 (t0) REVERT: H 506 MET cc_start: 0.4301 (tpp) cc_final: 0.4099 (tpp) REVERT: H 565 PHE cc_start: 0.6701 (t80) cc_final: 0.6127 (m-80) REVERT: H 567 LYS cc_start: 0.7493 (mttt) cc_final: 0.7248 (mttt) REVERT: H 1066 MET cc_start: 0.7037 (ttp) cc_final: 0.6707 (tpp) REVERT: H 1197 GLN cc_start: 0.7923 (tt0) cc_final: 0.7519 (tp40) REVERT: H 1294 TYR cc_start: 0.7420 (m-10) cc_final: 0.7116 (m-10) outliers start: 292 outliers final: 199 residues processed: 1038 average time/residue: 0.5983 time to fit residues: 1081.5503 Evaluate side-chains 1047 residues out of total 5876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 832 time to evaluate : 5.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 313 GLN Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 10 ASN Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 209 ASP Chi-restraints excluded: chain B residue 211 GLN Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 794 PHE Chi-restraints excluded: chain B residue 848 THR Chi-restraints excluded: chain B residue 1007 SER Chi-restraints excluded: chain B residue 1084 VAL Chi-restraints excluded: chain B residue 1097 LEU Chi-restraints excluded: chain B residue 1147 THR Chi-restraints excluded: chain B residue 1220 GLU Chi-restraints excluded: chain B residue 1242 THR Chi-restraints excluded: chain B residue 1246 ARG Chi-restraints excluded: chain B residue 1249 GLU Chi-restraints excluded: chain B residue 1250 VAL Chi-restraints excluded: chain B residue 1259 VAL Chi-restraints excluded: chain B residue 1298 MET Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 313 GLN Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 10 ASN Chi-restraints excluded: chain D residue 26 CYS Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 198 PHE Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 209 ASP Chi-restraints excluded: chain D residue 211 GLN Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 340 PHE Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 371 THR Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 579 SER Chi-restraints excluded: chain D residue 605 VAL Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 794 PHE Chi-restraints excluded: chain D residue 848 THR Chi-restraints excluded: chain D residue 1007 SER Chi-restraints excluded: chain D residue 1084 VAL Chi-restraints excluded: chain D residue 1097 LEU Chi-restraints excluded: chain D residue 1147 THR Chi-restraints excluded: chain D residue 1220 GLU Chi-restraints excluded: chain D residue 1242 THR Chi-restraints excluded: chain D residue 1246 ARG Chi-restraints excluded: chain D residue 1249 GLU Chi-restraints excluded: chain D residue 1250 VAL Chi-restraints excluded: chain D residue 1259 VAL Chi-restraints excluded: chain D residue 1298 MET Chi-restraints excluded: chain E residue 78 SER Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 313 GLN Chi-restraints excluded: chain E residue 323 ASP Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 10 ASN Chi-restraints excluded: chain F residue 26 CYS Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 198 PHE Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 209 ASP Chi-restraints excluded: chain F residue 211 GLN Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 234 ASN Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 304 THR Chi-restraints excluded: chain F residue 340 PHE Chi-restraints excluded: chain F residue 362 LEU Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 399 ILE Chi-restraints excluded: chain F residue 531 THR Chi-restraints excluded: chain F residue 556 LEU Chi-restraints excluded: chain F residue 579 SER Chi-restraints excluded: chain F residue 605 VAL Chi-restraints excluded: chain F residue 681 ILE Chi-restraints excluded: chain F residue 794 PHE Chi-restraints excluded: chain F residue 848 THR Chi-restraints excluded: chain F residue 1007 SER Chi-restraints excluded: chain F residue 1084 VAL Chi-restraints excluded: chain F residue 1097 LEU Chi-restraints excluded: chain F residue 1147 THR Chi-restraints excluded: chain F residue 1220 GLU Chi-restraints excluded: chain F residue 1242 THR Chi-restraints excluded: chain F residue 1246 ARG Chi-restraints excluded: chain F residue 1249 GLU Chi-restraints excluded: chain F residue 1250 VAL Chi-restraints excluded: chain F residue 1259 VAL Chi-restraints excluded: chain F residue 1298 MET Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 261 ILE Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain G residue 309 ILE Chi-restraints excluded: chain G residue 313 GLN Chi-restraints excluded: chain G residue 323 ASP Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 10 ASN Chi-restraints excluded: chain H residue 26 CYS Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain H residue 137 ILE Chi-restraints excluded: chain H residue 189 VAL Chi-restraints excluded: chain H residue 198 PHE Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain H residue 209 ASP Chi-restraints excluded: chain H residue 211 GLN Chi-restraints excluded: chain H residue 213 LEU Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 218 LEU Chi-restraints excluded: chain H residue 234 ASN Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 304 THR Chi-restraints excluded: chain H residue 340 PHE Chi-restraints excluded: chain H residue 362 LEU Chi-restraints excluded: chain H residue 371 THR Chi-restraints excluded: chain H residue 399 ILE Chi-restraints excluded: chain H residue 531 THR Chi-restraints excluded: chain H residue 556 LEU Chi-restraints excluded: chain H residue 579 SER Chi-restraints excluded: chain H residue 605 VAL Chi-restraints excluded: chain H residue 681 ILE Chi-restraints excluded: chain H residue 794 PHE Chi-restraints excluded: chain H residue 848 THR Chi-restraints excluded: chain H residue 1007 SER Chi-restraints excluded: chain H residue 1084 VAL Chi-restraints excluded: chain H residue 1097 LEU Chi-restraints excluded: chain H residue 1147 THR Chi-restraints excluded: chain H residue 1220 GLU Chi-restraints excluded: chain H residue 1242 THR Chi-restraints excluded: chain H residue 1246 ARG Chi-restraints excluded: chain H residue 1249 GLU Chi-restraints excluded: chain H residue 1250 VAL Chi-restraints excluded: chain H residue 1259 VAL Chi-restraints excluded: chain H residue 1298 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 672 random chunks: chunk 218 optimal weight: 0.8980 chunk 584 optimal weight: 30.0000 chunk 128 optimal weight: 6.9990 chunk 381 optimal weight: 0.9980 chunk 160 optimal weight: 30.0000 chunk 650 optimal weight: 6.9990 chunk 539 optimal weight: 4.9990 chunk 301 optimal weight: 6.9990 chunk 54 optimal weight: 0.9980 chunk 215 optimal weight: 6.9990 chunk 341 optimal weight: 0.8980 overall best weight: 1.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN B 211 GLN ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 211 GLN ** D 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 547 ASN E 48 ASN F 211 GLN ** F 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 547 ASN G 48 ASN H 211 GLN ** H 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6629 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 53092 Z= 0.232 Angle : 0.869 35.069 72352 Z= 0.360 Chirality : 0.079 1.991 8684 Planarity : 0.004 0.046 8792 Dihedral : 19.007 179.453 9460 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 6.36 % Allowed : 22.10 % Favored : 71.54 % 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: 0.76 (0.11), residues: 6684 helix: 1.65 (0.08), residues: 4076 sheet: -0.83 (0.22), residues: 496 loop : -1.46 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP D 514 HIS 0.004 0.001 HIS H 896 PHE 0.015 0.001 PHE B1182 TYR 0.015 0.001 TYR B 195 ARG 0.008 0.000 ARG H 370 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13368 Ramachandran restraints generated. 6684 Oldfield, 0 Emsley, 6684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13368 Ramachandran restraints generated. 6684 Oldfield, 0 Emsley, 6684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1164 residues out of total 5876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 307 poor density : 857 time to evaluate : 5.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASN cc_start: 0.8514 (t0) cc_final: 0.7895 (t0) REVERT: A 67 LYS cc_start: 0.8176 (mttt) cc_final: 0.7384 (tptt) REVERT: A 71 THR cc_start: 0.8920 (m) cc_final: 0.8651 (m) REVERT: A 185 LYS cc_start: 0.7988 (tttt) cc_final: 0.7377 (tmtt) REVERT: A 237 ASP cc_start: 0.7638 (t70) cc_final: 0.7303 (t0) REVERT: A 280 ASP cc_start: 0.8839 (t0) cc_final: 0.8397 (t0) REVERT: A 313 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7393 (mt0) REVERT: B 43 THR cc_start: 0.9053 (m) cc_final: 0.8674 (p) REVERT: B 91 GLU cc_start: 0.8533 (pp20) cc_final: 0.8295 (pp20) REVERT: B 198 PHE cc_start: 0.5715 (OUTLIER) cc_final: 0.5063 (m-80) REVERT: B 211 GLN cc_start: 0.7137 (OUTLIER) cc_final: 0.6654 (mp10) REVERT: B 289 ARG cc_start: 0.7377 (mtp180) cc_final: 0.6691 (mmt180) REVERT: B 340 PHE cc_start: 0.8444 (OUTLIER) cc_final: 0.7811 (t80) REVERT: B 354 ASN cc_start: 0.9245 (t0) cc_final: 0.8857 (t0) REVERT: B 454 TYR cc_start: 0.6864 (t80) cc_final: 0.6329 (m-80) REVERT: B 500 ASN cc_start: 0.7902 (t0) cc_final: 0.7561 (t0) REVERT: B 506 MET cc_start: 0.4273 (tpp) cc_final: 0.4029 (tpp) REVERT: B 565 PHE cc_start: 0.6698 (t80) cc_final: 0.6124 (m-80) REVERT: B 567 LYS cc_start: 0.7500 (mttt) cc_final: 0.7249 (mttt) REVERT: B 1066 MET cc_start: 0.7030 (ttp) cc_final: 0.6698 (tpp) REVERT: B 1197 GLN cc_start: 0.7941 (tt0) cc_final: 0.7530 (tp40) REVERT: B 1229 GLU cc_start: 0.8254 (mm-30) cc_final: 0.8033 (mm-30) REVERT: B 1294 TYR cc_start: 0.7464 (m-10) cc_final: 0.7132 (m-10) REVERT: C 43 ASN cc_start: 0.8511 (t0) cc_final: 0.7890 (t0) REVERT: C 67 LYS cc_start: 0.8243 (mttt) cc_final: 0.7427 (tptt) REVERT: C 71 THR cc_start: 0.8933 (m) cc_final: 0.8658 (m) REVERT: C 185 LYS cc_start: 0.7989 (tttt) cc_final: 0.7379 (tmtt) REVERT: C 237 ASP cc_start: 0.7641 (t70) cc_final: 0.7306 (t0) REVERT: C 280 ASP cc_start: 0.8838 (t0) cc_final: 0.8397 (t0) REVERT: C 313 GLN cc_start: 0.8139 (OUTLIER) cc_final: 0.7391 (mt0) REVERT: C 332 LYS cc_start: 0.8101 (mtmm) cc_final: 0.7600 (mtmm) REVERT: C 335 ASN cc_start: 0.8115 (m-40) cc_final: 0.7851 (m110) REVERT: D 43 THR cc_start: 0.9055 (m) cc_final: 0.8677 (p) REVERT: D 91 GLU cc_start: 0.8531 (pp20) cc_final: 0.8296 (pp20) REVERT: D 198 PHE cc_start: 0.5719 (OUTLIER) cc_final: 0.5066 (m-80) REVERT: D 211 GLN cc_start: 0.7107 (OUTLIER) cc_final: 0.6628 (mp10) REVERT: D 289 ARG cc_start: 0.7379 (mtp180) cc_final: 0.6692 (mmt180) REVERT: D 340 PHE cc_start: 0.8442 (OUTLIER) cc_final: 0.7812 (t80) REVERT: D 354 ASN cc_start: 0.9245 (t0) cc_final: 0.8857 (t0) REVERT: D 454 TYR cc_start: 0.6864 (t80) cc_final: 0.6328 (m-80) REVERT: D 500 ASN cc_start: 0.7899 (t0) cc_final: 0.7560 (t0) REVERT: D 506 MET cc_start: 0.4269 (tpp) cc_final: 0.4026 (tpp) REVERT: D 565 PHE cc_start: 0.6699 (t80) cc_final: 0.6126 (m-80) REVERT: D 567 LYS cc_start: 0.7500 (mttt) cc_final: 0.7249 (mttt) REVERT: D 1066 MET cc_start: 0.7031 (ttp) cc_final: 0.6699 (tpp) REVERT: D 1197 GLN cc_start: 0.7941 (tt0) cc_final: 0.7529 (tp40) REVERT: D 1229 GLU cc_start: 0.8253 (mm-30) cc_final: 0.8033 (mm-30) REVERT: D 1294 TYR cc_start: 0.7468 (m-10) cc_final: 0.7135 (m-10) REVERT: E 43 ASN cc_start: 0.8514 (t0) cc_final: 0.7895 (t0) REVERT: E 67 LYS cc_start: 0.8244 (mttt) cc_final: 0.7426 (tptt) REVERT: E 71 THR cc_start: 0.8926 (m) cc_final: 0.8660 (m) REVERT: E 185 LYS cc_start: 0.7988 (tttt) cc_final: 0.7378 (tmtt) REVERT: E 237 ASP cc_start: 0.7639 (t70) cc_final: 0.7304 (t0) REVERT: E 280 ASP cc_start: 0.8839 (t0) cc_final: 0.8398 (t0) REVERT: E 313 GLN cc_start: 0.8139 (OUTLIER) cc_final: 0.7391 (mt0) REVERT: E 332 LYS cc_start: 0.8099 (mtmm) cc_final: 0.7598 (mtmm) REVERT: E 335 ASN cc_start: 0.8114 (m-40) cc_final: 0.7850 (m110) REVERT: F 43 THR cc_start: 0.9056 (m) cc_final: 0.8678 (p) REVERT: F 91 GLU cc_start: 0.8531 (pp20) cc_final: 0.8295 (pp20) REVERT: F 198 PHE cc_start: 0.5719 (OUTLIER) cc_final: 0.5064 (m-80) REVERT: F 211 GLN cc_start: 0.7136 (OUTLIER) cc_final: 0.6653 (mp10) REVERT: F 289 ARG cc_start: 0.7379 (mtp180) cc_final: 0.6691 (mmt180) REVERT: F 340 PHE cc_start: 0.8444 (OUTLIER) cc_final: 0.7811 (t80) REVERT: F 354 ASN cc_start: 0.9245 (t0) cc_final: 0.8857 (t0) REVERT: F 454 TYR cc_start: 0.6864 (t80) cc_final: 0.6329 (m-80) REVERT: F 500 ASN cc_start: 0.7898 (t0) cc_final: 0.7558 (t0) REVERT: F 506 MET cc_start: 0.4275 (tpp) cc_final: 0.4031 (tpp) REVERT: F 565 PHE cc_start: 0.6698 (t80) cc_final: 0.6124 (m-80) REVERT: F 567 LYS cc_start: 0.7499 (mttt) cc_final: 0.7249 (mttt) REVERT: F 1066 MET cc_start: 0.7029 (ttp) cc_final: 0.6698 (tpp) REVERT: F 1197 GLN cc_start: 0.7940 (tt0) cc_final: 0.7528 (tp40) REVERT: F 1229 GLU cc_start: 0.8252 (mm-30) cc_final: 0.8032 (mm-30) REVERT: F 1294 TYR cc_start: 0.7468 (m-10) cc_final: 0.7135 (m-10) REVERT: G 43 ASN cc_start: 0.8516 (t0) cc_final: 0.7896 (t0) REVERT: G 67 LYS cc_start: 0.8264 (mttt) cc_final: 0.7438 (tptt) REVERT: G 71 THR cc_start: 0.8929 (m) cc_final: 0.8674 (m) REVERT: G 185 LYS cc_start: 0.7988 (tttt) cc_final: 0.7378 (tmtt) REVERT: G 237 ASP cc_start: 0.7636 (t70) cc_final: 0.7302 (t0) REVERT: G 280 ASP cc_start: 0.8837 (t0) cc_final: 0.8396 (t0) REVERT: G 313 GLN cc_start: 0.8142 (OUTLIER) cc_final: 0.7393 (mt0) REVERT: G 332 LYS cc_start: 0.8099 (mtmm) cc_final: 0.7600 (mtmm) REVERT: G 335 ASN cc_start: 0.8117 (m-40) cc_final: 0.7848 (m110) REVERT: H 43 THR cc_start: 0.9056 (m) cc_final: 0.8678 (p) REVERT: H 91 GLU cc_start: 0.8531 (pp20) cc_final: 0.8294 (pp20) REVERT: H 198 PHE cc_start: 0.5716 (OUTLIER) cc_final: 0.5063 (m-80) REVERT: H 211 GLN cc_start: 0.7135 (OUTLIER) cc_final: 0.6652 (mp10) REVERT: H 289 ARG cc_start: 0.7378 (mtp180) cc_final: 0.6691 (mmt180) REVERT: H 340 PHE cc_start: 0.8442 (OUTLIER) cc_final: 0.7810 (t80) REVERT: H 354 ASN cc_start: 0.9246 (t0) cc_final: 0.8857 (t0) REVERT: H 454 TYR cc_start: 0.6865 (t80) cc_final: 0.6330 (m-80) REVERT: H 500 ASN cc_start: 0.7898 (t0) cc_final: 0.7559 (t0) REVERT: H 506 MET cc_start: 0.4272 (tpp) cc_final: 0.4028 (tpp) REVERT: H 565 PHE cc_start: 0.6698 (t80) cc_final: 0.6123 (m-80) REVERT: H 567 LYS cc_start: 0.7498 (mttt) cc_final: 0.7248 (mttt) REVERT: H 1066 MET cc_start: 0.7030 (ttp) cc_final: 0.6697 (tpp) REVERT: H 1197 GLN cc_start: 0.7939 (tt0) cc_final: 0.7528 (tp40) REVERT: H 1229 GLU cc_start: 0.8253 (mm-30) cc_final: 0.8032 (mm-30) REVERT: H 1294 TYR cc_start: 0.7461 (m-10) cc_final: 0.7129 (m-10) outliers start: 307 outliers final: 228 residues processed: 1069 average time/residue: 0.5526 time to fit residues: 1024.2024 Evaluate side-chains 1075 residues out of total 5876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 831 time to evaluate : 5.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 313 GLN Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 10 ASN Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 209 ASP Chi-restraints excluded: chain B residue 211 GLN Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 794 PHE Chi-restraints excluded: chain B residue 848 THR Chi-restraints excluded: chain B residue 1007 SER Chi-restraints excluded: chain B residue 1039 ASP Chi-restraints excluded: chain B residue 1084 VAL Chi-restraints excluded: chain B residue 1097 LEU Chi-restraints excluded: chain B residue 1147 THR Chi-restraints excluded: chain B residue 1220 GLU Chi-restraints excluded: chain B residue 1242 THR Chi-restraints excluded: chain B residue 1246 ARG Chi-restraints excluded: chain B residue 1249 GLU Chi-restraints excluded: chain B residue 1250 VAL Chi-restraints excluded: chain B residue 1259 VAL Chi-restraints excluded: chain B residue 1267 SER Chi-restraints excluded: chain B residue 1298 MET Chi-restraints excluded: chain B residue 1312 VAL Chi-restraints excluded: chain B residue 1424 ILE Chi-restraints excluded: chain B residue 1549 VAL Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 313 GLN Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 10 ASN Chi-restraints excluded: chain D residue 26 CYS Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 198 PHE Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 209 ASP Chi-restraints excluded: chain D residue 211 GLN Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 340 PHE Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 371 THR Chi-restraints excluded: chain D residue 391 ILE Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 547 ASN Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 579 SER Chi-restraints excluded: chain D residue 605 VAL Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 794 PHE Chi-restraints excluded: chain D residue 848 THR Chi-restraints excluded: chain D residue 1007 SER Chi-restraints excluded: chain D residue 1039 ASP Chi-restraints excluded: chain D residue 1084 VAL Chi-restraints excluded: chain D residue 1097 LEU Chi-restraints excluded: chain D residue 1147 THR Chi-restraints excluded: chain D residue 1220 GLU Chi-restraints excluded: chain D residue 1242 THR Chi-restraints excluded: chain D residue 1246 ARG Chi-restraints excluded: chain D residue 1249 GLU Chi-restraints excluded: chain D residue 1250 VAL Chi-restraints excluded: chain D residue 1259 VAL Chi-restraints excluded: chain D residue 1267 SER Chi-restraints excluded: chain D residue 1298 MET Chi-restraints excluded: chain D residue 1312 VAL Chi-restraints excluded: chain D residue 1424 ILE Chi-restraints excluded: chain D residue 1549 VAL Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 313 GLN Chi-restraints excluded: chain E residue 323 ASP Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 10 ASN Chi-restraints excluded: chain F residue 26 CYS Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 198 PHE Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 209 ASP Chi-restraints excluded: chain F residue 211 GLN Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 304 THR Chi-restraints excluded: chain F residue 340 PHE Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain F residue 362 LEU Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 391 ILE Chi-restraints excluded: chain F residue 399 ILE Chi-restraints excluded: chain F residue 531 THR Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain F residue 547 ASN Chi-restraints excluded: chain F residue 556 LEU Chi-restraints excluded: chain F residue 579 SER Chi-restraints excluded: chain F residue 605 VAL Chi-restraints excluded: chain F residue 681 ILE Chi-restraints excluded: chain F residue 794 PHE Chi-restraints excluded: chain F residue 848 THR Chi-restraints excluded: chain F residue 1007 SER Chi-restraints excluded: chain F residue 1039 ASP Chi-restraints excluded: chain F residue 1084 VAL Chi-restraints excluded: chain F residue 1097 LEU Chi-restraints excluded: chain F residue 1147 THR Chi-restraints excluded: chain F residue 1220 GLU Chi-restraints excluded: chain F residue 1242 THR Chi-restraints excluded: chain F residue 1246 ARG Chi-restraints excluded: chain F residue 1249 GLU Chi-restraints excluded: chain F residue 1250 VAL Chi-restraints excluded: chain F residue 1259 VAL Chi-restraints excluded: chain F residue 1267 SER Chi-restraints excluded: chain F residue 1298 MET Chi-restraints excluded: chain F residue 1312 VAL Chi-restraints excluded: chain F residue 1424 ILE Chi-restraints excluded: chain F residue 1549 VAL Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 261 ILE Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain G residue 309 ILE Chi-restraints excluded: chain G residue 313 GLN Chi-restraints excluded: chain G residue 323 ASP Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 10 ASN Chi-restraints excluded: chain H residue 26 CYS Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain H residue 137 ILE Chi-restraints excluded: chain H residue 189 VAL Chi-restraints excluded: chain H residue 198 PHE Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain H residue 209 ASP Chi-restraints excluded: chain H residue 211 GLN Chi-restraints excluded: chain H residue 213 LEU Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 218 LEU Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 304 THR Chi-restraints excluded: chain H residue 340 PHE Chi-restraints excluded: chain H residue 360 VAL Chi-restraints excluded: chain H residue 361 LEU Chi-restraints excluded: chain H residue 362 LEU Chi-restraints excluded: chain H residue 371 THR Chi-restraints excluded: chain H residue 391 ILE Chi-restraints excluded: chain H residue 399 ILE Chi-restraints excluded: chain H residue 531 THR Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 556 LEU Chi-restraints excluded: chain H residue 579 SER Chi-restraints excluded: chain H residue 605 VAL Chi-restraints excluded: chain H residue 681 ILE Chi-restraints excluded: chain H residue 794 PHE Chi-restraints excluded: chain H residue 848 THR Chi-restraints excluded: chain H residue 1007 SER Chi-restraints excluded: chain H residue 1039 ASP Chi-restraints excluded: chain H residue 1084 VAL Chi-restraints excluded: chain H residue 1097 LEU Chi-restraints excluded: chain H residue 1147 THR Chi-restraints excluded: chain H residue 1220 GLU Chi-restraints excluded: chain H residue 1242 THR Chi-restraints excluded: chain H residue 1246 ARG Chi-restraints excluded: chain H residue 1249 GLU Chi-restraints excluded: chain H residue 1250 VAL Chi-restraints excluded: chain H residue 1259 VAL Chi-restraints excluded: chain H residue 1267 SER Chi-restraints excluded: chain H residue 1298 MET Chi-restraints excluded: chain H residue 1312 VAL Chi-restraints excluded: chain H residue 1424 ILE Chi-restraints excluded: chain H residue 1549 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 672 random chunks: chunk 626 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 370 optimal weight: 0.0970 chunk 474 optimal weight: 10.0000 chunk 367 optimal weight: 0.5980 chunk 547 optimal weight: 0.9990 chunk 363 optimal weight: 0.9980 chunk 647 optimal weight: 1.9990 chunk 405 optimal weight: 2.9990 chunk 394 optimal weight: 10.0000 chunk 299 optimal weight: 7.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 211 GLN ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 547 ASN C 48 ASN D 211 GLN ** D 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 547 ASN F 125 HIS F 211 GLN ** F 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 547 ASN H 211 GLN ** H 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 547 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6614 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 53092 Z= 0.175 Angle : 0.856 34.890 72352 Z= 0.352 Chirality : 0.079 2.004 8684 Planarity : 0.004 0.045 8792 Dihedral : 18.887 179.792 9456 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.89 % Allowed : 24.57 % Favored : 70.55 % 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: 0.92 (0.11), residues: 6684 helix: 1.75 (0.08), residues: 4084 sheet: -0.72 (0.22), residues: 496 loop : -1.36 (0.13), residues: 2104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.001 TRP D 514 HIS 0.004 0.001 HIS H1024 PHE 0.016 0.001 PHE B1182 TYR 0.015 0.001 TYR D 195 ARG 0.011 0.000 ARG F 370 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13368 Ramachandran restraints generated. 6684 Oldfield, 0 Emsley, 6684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13368 Ramachandran restraints generated. 6684 Oldfield, 0 Emsley, 6684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1100 residues out of total 5876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 864 time to evaluate : 6.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASN cc_start: 0.8524 (t0) cc_final: 0.7884 (t0) REVERT: A 67 LYS cc_start: 0.8150 (mttt) cc_final: 0.7369 (tptt) REVERT: A 71 THR cc_start: 0.8887 (m) cc_final: 0.8629 (m) REVERT: A 185 LYS cc_start: 0.7966 (tttt) cc_final: 0.7447 (tttm) REVERT: A 280 ASP cc_start: 0.8874 (t0) cc_final: 0.8450 (t0) REVERT: A 282 GLU cc_start: 0.7050 (tt0) cc_final: 0.6829 (tt0) REVERT: A 313 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7386 (mt0) REVERT: A 332 LYS cc_start: 0.8116 (mtmm) cc_final: 0.7788 (mtmm) REVERT: B 43 THR cc_start: 0.9046 (m) cc_final: 0.8667 (p) REVERT: B 91 GLU cc_start: 0.8539 (pp20) cc_final: 0.8311 (pp20) REVERT: B 198 PHE cc_start: 0.5835 (OUTLIER) cc_final: 0.5161 (m-80) REVERT: B 289 ARG cc_start: 0.7450 (mtp180) cc_final: 0.6714 (mmt180) REVERT: B 340 PHE cc_start: 0.8443 (OUTLIER) cc_final: 0.7813 (t80) REVERT: B 354 ASN cc_start: 0.9207 (t0) cc_final: 0.8839 (t0) REVERT: B 454 TYR cc_start: 0.6859 (t80) cc_final: 0.6321 (m-80) REVERT: B 500 ASN cc_start: 0.7903 (t0) cc_final: 0.7613 (t0) REVERT: B 565 PHE cc_start: 0.6648 (t80) cc_final: 0.6099 (m-80) REVERT: B 567 LYS cc_start: 0.7497 (mttt) cc_final: 0.7246 (mttt) REVERT: B 1066 MET cc_start: 0.7104 (ttp) cc_final: 0.6787 (tpp) REVERT: B 1197 GLN cc_start: 0.8011 (tt0) cc_final: 0.7530 (tp40) REVERT: B 1220 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.7764 (mp0) REVERT: B 1229 GLU cc_start: 0.8240 (mm-30) cc_final: 0.8011 (mm-30) REVERT: B 1294 TYR cc_start: 0.7446 (m-10) cc_final: 0.7216 (m-10) REVERT: C 43 ASN cc_start: 0.8520 (t0) cc_final: 0.7880 (t0) REVERT: C 67 LYS cc_start: 0.8224 (mttt) cc_final: 0.7413 (tptt) REVERT: C 71 THR cc_start: 0.8921 (m) cc_final: 0.8652 (m) REVERT: C 185 LYS cc_start: 0.7969 (tttt) cc_final: 0.7448 (tttm) REVERT: C 280 ASP cc_start: 0.8875 (t0) cc_final: 0.8449 (t0) REVERT: C 282 GLU cc_start: 0.7043 (tt0) cc_final: 0.6822 (tt0) REVERT: C 313 GLN cc_start: 0.8139 (OUTLIER) cc_final: 0.7400 (mt0) REVERT: D 43 THR cc_start: 0.9044 (m) cc_final: 0.8667 (p) REVERT: D 91 GLU cc_start: 0.8537 (pp20) cc_final: 0.8308 (pp20) REVERT: D 198 PHE cc_start: 0.5838 (OUTLIER) cc_final: 0.5163 (m-80) REVERT: D 289 ARG cc_start: 0.7450 (mtp180) cc_final: 0.6714 (mmt180) REVERT: D 340 PHE cc_start: 0.8444 (OUTLIER) cc_final: 0.7816 (t80) REVERT: D 354 ASN cc_start: 0.9207 (t0) cc_final: 0.8838 (t0) REVERT: D 454 TYR cc_start: 0.6858 (t80) cc_final: 0.6320 (m-80) REVERT: D 500 ASN cc_start: 0.7901 (t0) cc_final: 0.7612 (t0) REVERT: D 565 PHE cc_start: 0.6649 (t80) cc_final: 0.6100 (m-80) REVERT: D 567 LYS cc_start: 0.7498 (mttt) cc_final: 0.7246 (mttt) REVERT: D 1066 MET cc_start: 0.7104 (ttp) cc_final: 0.6787 (tpp) REVERT: D 1197 GLN cc_start: 0.8012 (tt0) cc_final: 0.7530 (tp40) REVERT: D 1220 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7764 (mp0) REVERT: D 1229 GLU cc_start: 0.8241 (mm-30) cc_final: 0.8011 (mm-30) REVERT: D 1294 TYR cc_start: 0.7453 (m-10) cc_final: 0.7220 (m-10) REVERT: E 43 ASN cc_start: 0.8522 (t0) cc_final: 0.7883 (t0) REVERT: E 67 LYS cc_start: 0.8217 (mttt) cc_final: 0.7412 (tptt) REVERT: E 71 THR cc_start: 0.8899 (m) cc_final: 0.8650 (m) REVERT: E 185 LYS cc_start: 0.7966 (tttt) cc_final: 0.7446 (tttm) REVERT: E 280 ASP cc_start: 0.8875 (t0) cc_final: 0.8450 (t0) REVERT: E 282 GLU cc_start: 0.7048 (tt0) cc_final: 0.6825 (tt0) REVERT: E 313 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7401 (mt0) REVERT: F 43 THR cc_start: 0.9045 (m) cc_final: 0.8667 (p) REVERT: F 91 GLU cc_start: 0.8539 (pp20) cc_final: 0.8309 (pp20) REVERT: F 198 PHE cc_start: 0.5837 (OUTLIER) cc_final: 0.5162 (m-80) REVERT: F 289 ARG cc_start: 0.7449 (mtp180) cc_final: 0.6713 (mmt180) REVERT: F 340 PHE cc_start: 0.8444 (OUTLIER) cc_final: 0.7813 (t80) REVERT: F 354 ASN cc_start: 0.9207 (t0) cc_final: 0.8839 (t0) REVERT: F 454 TYR cc_start: 0.6860 (t80) cc_final: 0.6321 (m-80) REVERT: F 500 ASN cc_start: 0.7903 (t0) cc_final: 0.7613 (t0) REVERT: F 565 PHE cc_start: 0.6650 (t80) cc_final: 0.6099 (m-80) REVERT: F 567 LYS cc_start: 0.7496 (mttt) cc_final: 0.7245 (mttt) REVERT: F 1066 MET cc_start: 0.7105 (ttp) cc_final: 0.6789 (tpp) REVERT: F 1197 GLN cc_start: 0.8012 (tt0) cc_final: 0.7530 (tp40) REVERT: F 1220 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.7764 (mp0) REVERT: F 1229 GLU cc_start: 0.8239 (mm-30) cc_final: 0.8010 (mm-30) REVERT: F 1294 TYR cc_start: 0.7452 (m-10) cc_final: 0.7222 (m-10) REVERT: G 43 ASN cc_start: 0.8526 (t0) cc_final: 0.7886 (t0) REVERT: G 67 LYS cc_start: 0.8242 (mttt) cc_final: 0.7418 (tptt) REVERT: G 71 THR cc_start: 0.8906 (m) cc_final: 0.8623 (m) REVERT: G 185 LYS cc_start: 0.7965 (tttt) cc_final: 0.7445 (tttm) REVERT: G 280 ASP cc_start: 0.8875 (t0) cc_final: 0.8449 (t0) REVERT: G 282 GLU cc_start: 0.7045 (tt0) cc_final: 0.6823 (tt0) REVERT: G 313 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7400 (mt0) REVERT: H 43 THR cc_start: 0.9047 (m) cc_final: 0.8669 (p) REVERT: H 91 GLU cc_start: 0.8537 (pp20) cc_final: 0.8309 (pp20) REVERT: H 198 PHE cc_start: 0.5834 (OUTLIER) cc_final: 0.5162 (m-80) REVERT: H 289 ARG cc_start: 0.7448 (mtp180) cc_final: 0.6713 (mmt180) REVERT: H 340 PHE cc_start: 0.8443 (OUTLIER) cc_final: 0.7812 (t80) REVERT: H 354 ASN cc_start: 0.9209 (t0) cc_final: 0.8840 (t0) REVERT: H 454 TYR cc_start: 0.6860 (t80) cc_final: 0.6322 (m-80) REVERT: H 500 ASN cc_start: 0.7903 (t0) cc_final: 0.7613 (t0) REVERT: H 565 PHE cc_start: 0.6649 (t80) cc_final: 0.6099 (m-80) REVERT: H 567 LYS cc_start: 0.7495 (mttt) cc_final: 0.7244 (mttt) REVERT: H 1066 MET cc_start: 0.7105 (ttp) cc_final: 0.6787 (tpp) REVERT: H 1197 GLN cc_start: 0.8010 (tt0) cc_final: 0.7528 (tp40) REVERT: H 1220 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7764 (mp0) REVERT: H 1229 GLU cc_start: 0.8240 (mm-30) cc_final: 0.8011 (mm-30) REVERT: H 1294 TYR cc_start: 0.7445 (m-10) cc_final: 0.7214 (m-10) outliers start: 236 outliers final: 177 residues processed: 1038 average time/residue: 0.5664 time to fit residues: 1026.3572 Evaluate side-chains 1034 residues out of total 5876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 841 time to evaluate : 4.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 313 GLN Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 10 ASN Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 547 ASN Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 794 PHE Chi-restraints excluded: chain B residue 848 THR Chi-restraints excluded: chain B residue 1007 SER Chi-restraints excluded: chain B residue 1039 ASP Chi-restraints excluded: chain B residue 1097 LEU Chi-restraints excluded: chain B residue 1147 THR Chi-restraints excluded: chain B residue 1220 GLU Chi-restraints excluded: chain B residue 1242 THR Chi-restraints excluded: chain B residue 1246 ARG Chi-restraints excluded: chain B residue 1250 VAL Chi-restraints excluded: chain B residue 1267 SER Chi-restraints excluded: chain B residue 1298 MET Chi-restraints excluded: chain B residue 1312 VAL Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 313 GLN Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 10 ASN Chi-restraints excluded: chain D residue 26 CYS Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 198 PHE Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 340 PHE Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 371 THR Chi-restraints excluded: chain D residue 391 ILE Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 473 VAL Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 794 PHE Chi-restraints excluded: chain D residue 848 THR Chi-restraints excluded: chain D residue 1007 SER Chi-restraints excluded: chain D residue 1039 ASP Chi-restraints excluded: chain D residue 1097 LEU Chi-restraints excluded: chain D residue 1147 THR Chi-restraints excluded: chain D residue 1220 GLU Chi-restraints excluded: chain D residue 1242 THR Chi-restraints excluded: chain D residue 1246 ARG Chi-restraints excluded: chain D residue 1250 VAL Chi-restraints excluded: chain D residue 1267 SER Chi-restraints excluded: chain D residue 1298 MET Chi-restraints excluded: chain D residue 1312 VAL Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 163 MET Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 313 GLN Chi-restraints excluded: chain E residue 323 ASP Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 10 ASN Chi-restraints excluded: chain F residue 26 CYS Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 198 PHE Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 304 THR Chi-restraints excluded: chain F residue 340 PHE Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain F residue 362 LEU Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 391 ILE Chi-restraints excluded: chain F residue 399 ILE Chi-restraints excluded: chain F residue 473 VAL Chi-restraints excluded: chain F residue 556 LEU Chi-restraints excluded: chain F residue 681 ILE Chi-restraints excluded: chain F residue 794 PHE Chi-restraints excluded: chain F residue 848 THR Chi-restraints excluded: chain F residue 1007 SER Chi-restraints excluded: chain F residue 1039 ASP Chi-restraints excluded: chain F residue 1097 LEU Chi-restraints excluded: chain F residue 1147 THR Chi-restraints excluded: chain F residue 1220 GLU Chi-restraints excluded: chain F residue 1242 THR Chi-restraints excluded: chain F residue 1246 ARG Chi-restraints excluded: chain F residue 1250 VAL Chi-restraints excluded: chain F residue 1267 SER Chi-restraints excluded: chain F residue 1298 MET Chi-restraints excluded: chain F residue 1312 VAL Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 163 MET Chi-restraints excluded: chain G residue 167 ILE Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 261 ILE Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain G residue 309 ILE Chi-restraints excluded: chain G residue 313 GLN Chi-restraints excluded: chain G residue 323 ASP Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 10 ASN Chi-restraints excluded: chain H residue 26 CYS Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain H residue 137 ILE Chi-restraints excluded: chain H residue 198 PHE Chi-restraints excluded: chain H residue 213 LEU Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 218 LEU Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 304 THR Chi-restraints excluded: chain H residue 340 PHE Chi-restraints excluded: chain H residue 361 LEU Chi-restraints excluded: chain H residue 362 LEU Chi-restraints excluded: chain H residue 371 THR Chi-restraints excluded: chain H residue 391 ILE Chi-restraints excluded: chain H residue 399 ILE Chi-restraints excluded: chain H residue 547 ASN Chi-restraints excluded: chain H residue 556 LEU Chi-restraints excluded: chain H residue 681 ILE Chi-restraints excluded: chain H residue 794 PHE Chi-restraints excluded: chain H residue 848 THR Chi-restraints excluded: chain H residue 1007 SER Chi-restraints excluded: chain H residue 1039 ASP Chi-restraints excluded: chain H residue 1097 LEU Chi-restraints excluded: chain H residue 1147 THR Chi-restraints excluded: chain H residue 1220 GLU Chi-restraints excluded: chain H residue 1242 THR Chi-restraints excluded: chain H residue 1246 ARG Chi-restraints excluded: chain H residue 1250 VAL Chi-restraints excluded: chain H residue 1267 SER Chi-restraints excluded: chain H residue 1298 MET Chi-restraints excluded: chain H residue 1312 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 672 random chunks: chunk 400 optimal weight: 6.9990 chunk 258 optimal weight: 7.9990 chunk 386 optimal weight: 4.9990 chunk 195 optimal weight: 6.9990 chunk 127 optimal weight: 0.0980 chunk 125 optimal weight: 10.0000 chunk 411 optimal weight: 9.9990 chunk 441 optimal weight: 7.9990 chunk 320 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 509 optimal weight: 3.9990 overall best weight: 4.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 24 ASN ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 24 ASN ** F 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 562 HIS H 24 ASN ** H 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 562 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6681 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 53092 Z= 0.435 Angle : 0.965 35.359 72352 Z= 0.416 Chirality : 0.081 1.989 8684 Planarity : 0.005 0.049 8792 Dihedral : 19.067 179.000 9456 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 5.99 % Allowed : 23.94 % Favored : 70.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.10), residues: 6684 helix: 1.44 (0.08), residues: 4060 sheet: -0.85 (0.23), residues: 508 loop : -1.32 (0.14), residues: 2116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP B 514 HIS 0.007 0.001 HIS H 896 PHE 0.016 0.002 PHE C 75 TYR 0.018 0.002 TYR H 512 ARG 0.009 0.001 ARG B 370 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13368 Ramachandran restraints generated. 6684 Oldfield, 0 Emsley, 6684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13368 Ramachandran restraints generated. 6684 Oldfield, 0 Emsley, 6684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1122 residues out of total 5876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 289 poor density : 833 time to evaluate : 4.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASN cc_start: 0.8551 (t0) cc_final: 0.7873 (t0) REVERT: A 67 LYS cc_start: 0.8428 (mttt) cc_final: 0.7573 (tptt) REVERT: A 71 THR cc_start: 0.9017 (m) cc_final: 0.8737 (m) REVERT: A 185 LYS cc_start: 0.8005 (tttt) cc_final: 0.7536 (tttm) REVERT: A 237 ASP cc_start: 0.7751 (t70) cc_final: 0.7373 (t0) REVERT: A 280 ASP cc_start: 0.8836 (t0) cc_final: 0.8361 (t0) REVERT: A 313 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7474 (mt0) REVERT: A 332 LYS cc_start: 0.8149 (mtmm) cc_final: 0.7760 (mtmm) REVERT: B 42 ILE cc_start: 0.7978 (tt) cc_final: 0.7664 (tt) REVERT: B 43 THR cc_start: 0.9081 (m) cc_final: 0.8709 (p) REVERT: B 91 GLU cc_start: 0.8608 (pp20) cc_final: 0.8349 (pp20) REVERT: B 198 PHE cc_start: 0.5288 (OUTLIER) cc_final: 0.5029 (t80) REVERT: B 211 GLN cc_start: 0.6381 (pp30) cc_final: 0.6095 (pp30) REVERT: B 226 SER cc_start: 0.9048 (m) cc_final: 0.8775 (m) REVERT: B 289 ARG cc_start: 0.7462 (mtp180) cc_final: 0.6748 (mmt180) REVERT: B 340 PHE cc_start: 0.8536 (OUTLIER) cc_final: 0.7673 (t80) REVERT: B 354 ASN cc_start: 0.9338 (t0) cc_final: 0.8947 (t0) REVERT: B 454 TYR cc_start: 0.6863 (t80) cc_final: 0.6375 (m-80) REVERT: B 500 ASN cc_start: 0.7880 (t0) cc_final: 0.7591 (t0) REVERT: B 565 PHE cc_start: 0.6706 (t80) cc_final: 0.6142 (m-80) REVERT: B 1066 MET cc_start: 0.7058 (ttp) cc_final: 0.6731 (tpp) REVERT: B 1197 GLN cc_start: 0.8038 (tt0) cc_final: 0.7662 (tp40) REVERT: B 1220 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.7709 (mp0) REVERT: B 1294 TYR cc_start: 0.7469 (m-10) cc_final: 0.7130 (m-10) REVERT: C 43 ASN cc_start: 0.8552 (t0) cc_final: 0.7870 (t0) REVERT: C 67 LYS cc_start: 0.8320 (mttt) cc_final: 0.7481 (tptt) REVERT: C 71 THR cc_start: 0.8966 (m) cc_final: 0.8692 (m) REVERT: C 185 LYS cc_start: 0.8007 (tttt) cc_final: 0.7538 (tttm) REVERT: C 237 ASP cc_start: 0.7752 (t70) cc_final: 0.7374 (t0) REVERT: C 280 ASP cc_start: 0.8834 (t0) cc_final: 0.8359 (t0) REVERT: C 313 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7439 (mt0) REVERT: C 332 LYS cc_start: 0.8100 (mtmm) cc_final: 0.7757 (mtmm) REVERT: D 42 ILE cc_start: 0.7980 (tt) cc_final: 0.7666 (tt) REVERT: D 43 THR cc_start: 0.9082 (m) cc_final: 0.8711 (p) REVERT: D 91 GLU cc_start: 0.8608 (pp20) cc_final: 0.8348 (pp20) REVERT: D 198 PHE cc_start: 0.5291 (OUTLIER) cc_final: 0.5029 (t80) REVERT: D 226 SER cc_start: 0.9047 (m) cc_final: 0.8774 (m) REVERT: D 289 ARG cc_start: 0.7462 (mtp180) cc_final: 0.6747 (mmt180) REVERT: D 340 PHE cc_start: 0.8536 (OUTLIER) cc_final: 0.7675 (t80) REVERT: D 354 ASN cc_start: 0.9339 (t0) cc_final: 0.8946 (t0) REVERT: D 454 TYR cc_start: 0.6864 (t80) cc_final: 0.6375 (m-80) REVERT: D 500 ASN cc_start: 0.7878 (t0) cc_final: 0.7590 (t0) REVERT: D 565 PHE cc_start: 0.6708 (t80) cc_final: 0.6145 (m-80) REVERT: D 1066 MET cc_start: 0.7057 (ttp) cc_final: 0.6731 (tpp) REVERT: D 1197 GLN cc_start: 0.8039 (tt0) cc_final: 0.7662 (tp40) REVERT: D 1220 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.7708 (mp0) REVERT: D 1294 TYR cc_start: 0.7471 (m-10) cc_final: 0.7131 (m-10) REVERT: E 43 ASN cc_start: 0.8553 (t0) cc_final: 0.7875 (t0) REVERT: E 67 LYS cc_start: 0.8343 (mttt) cc_final: 0.7489 (tptt) REVERT: E 71 THR cc_start: 0.8963 (m) cc_final: 0.8689 (m) REVERT: E 185 LYS cc_start: 0.8006 (tttt) cc_final: 0.7536 (tttm) REVERT: E 237 ASP cc_start: 0.7753 (t70) cc_final: 0.7374 (t0) REVERT: E 280 ASP cc_start: 0.8834 (t0) cc_final: 0.8359 (t0) REVERT: E 313 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.7440 (mt0) REVERT: E 332 LYS cc_start: 0.8100 (mtmm) cc_final: 0.7755 (mtmm) REVERT: F 42 ILE cc_start: 0.7982 (tt) cc_final: 0.7669 (tt) REVERT: F 43 THR cc_start: 0.9081 (m) cc_final: 0.8711 (p) REVERT: F 91 GLU cc_start: 0.8609 (pp20) cc_final: 0.8351 (pp20) REVERT: F 198 PHE cc_start: 0.5288 (OUTLIER) cc_final: 0.5028 (t80) REVERT: F 211 GLN cc_start: 0.6379 (pp30) cc_final: 0.6094 (pp30) REVERT: F 226 SER cc_start: 0.9048 (m) cc_final: 0.8775 (m) REVERT: F 289 ARG cc_start: 0.7461 (mtp180) cc_final: 0.6746 (mmt180) REVERT: F 340 PHE cc_start: 0.8536 (OUTLIER) cc_final: 0.7674 (t80) REVERT: F 354 ASN cc_start: 0.9339 (t0) cc_final: 0.8947 (t0) REVERT: F 454 TYR cc_start: 0.6863 (t80) cc_final: 0.6374 (m-80) REVERT: F 500 ASN cc_start: 0.7879 (t0) cc_final: 0.7590 (t0) REVERT: F 565 PHE cc_start: 0.6708 (t80) cc_final: 0.6144 (m-80) REVERT: F 1066 MET cc_start: 0.7057 (ttp) cc_final: 0.6732 (tpp) REVERT: F 1197 GLN cc_start: 0.8039 (tt0) cc_final: 0.7662 (tp40) REVERT: F 1220 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.7708 (mp0) REVERT: F 1294 TYR cc_start: 0.7471 (m-10) cc_final: 0.7131 (m-10) REVERT: G 43 ASN cc_start: 0.8552 (t0) cc_final: 0.7874 (t0) REVERT: G 66 LEU cc_start: 0.9077 (mt) cc_final: 0.8634 (mt) REVERT: G 67 LYS cc_start: 0.8412 (mttt) cc_final: 0.7527 (tptt) REVERT: G 71 THR cc_start: 0.9031 (m) cc_final: 0.8750 (m) REVERT: G 185 LYS cc_start: 0.8003 (tttt) cc_final: 0.7534 (tttm) REVERT: G 237 ASP cc_start: 0.7753 (t70) cc_final: 0.7376 (t0) REVERT: G 280 ASP cc_start: 0.8835 (t0) cc_final: 0.8360 (t0) REVERT: G 313 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.7443 (mt0) REVERT: G 332 LYS cc_start: 0.8101 (mtmm) cc_final: 0.7756 (mtmm) REVERT: H 42 ILE cc_start: 0.7985 (tt) cc_final: 0.7672 (tt) REVERT: H 43 THR cc_start: 0.9083 (m) cc_final: 0.8713 (p) REVERT: H 91 GLU cc_start: 0.8608 (pp20) cc_final: 0.8349 (pp20) REVERT: H 198 PHE cc_start: 0.5288 (OUTLIER) cc_final: 0.5029 (t80) REVERT: H 211 GLN cc_start: 0.6380 (pp30) cc_final: 0.6096 (pp30) REVERT: H 226 SER cc_start: 0.9048 (m) cc_final: 0.8775 (m) REVERT: H 289 ARG cc_start: 0.7461 (mtp180) cc_final: 0.6747 (mmt180) REVERT: H 340 PHE cc_start: 0.8535 (OUTLIER) cc_final: 0.7674 (t80) REVERT: H 354 ASN cc_start: 0.9339 (t0) cc_final: 0.8947 (t0) REVERT: H 454 TYR cc_start: 0.6863 (t80) cc_final: 0.6376 (m-80) REVERT: H 500 ASN cc_start: 0.7879 (t0) cc_final: 0.7591 (t0) REVERT: H 565 PHE cc_start: 0.6708 (t80) cc_final: 0.6142 (m-80) REVERT: H 1066 MET cc_start: 0.7058 (ttp) cc_final: 0.6731 (tpp) REVERT: H 1197 GLN cc_start: 0.8038 (tt0) cc_final: 0.7662 (tp40) REVERT: H 1220 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.7708 (mp0) REVERT: H 1294 TYR cc_start: 0.7468 (m-10) cc_final: 0.7129 (m-10) outliers start: 289 outliers final: 225 residues processed: 1029 average time/residue: 0.4786 time to fit residues: 859.8221 Evaluate side-chains 1051 residues out of total 5876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 810 time to evaluate : 5.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 313 GLN Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 209 ASP Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 848 THR Chi-restraints excluded: chain B residue 1007 SER Chi-restraints excluded: chain B residue 1030 ILE Chi-restraints excluded: chain B residue 1039 ASP Chi-restraints excluded: chain B residue 1084 VAL Chi-restraints excluded: chain B residue 1097 LEU Chi-restraints excluded: chain B residue 1105 ILE Chi-restraints excluded: chain B residue 1147 THR Chi-restraints excluded: chain B residue 1220 GLU Chi-restraints excluded: chain B residue 1242 THR Chi-restraints excluded: chain B residue 1259 VAL Chi-restraints excluded: chain B residue 1267 SER Chi-restraints excluded: chain B residue 1298 MET Chi-restraints excluded: chain B residue 1312 VAL Chi-restraints excluded: chain C residue 77 MET Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 313 GLN Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 26 CYS Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 198 PHE Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 209 ASP Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 340 PHE Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 371 THR Chi-restraints excluded: chain D residue 391 ILE Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 473 VAL Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 579 SER Chi-restraints excluded: chain D residue 605 VAL Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 848 THR Chi-restraints excluded: chain D residue 1007 SER Chi-restraints excluded: chain D residue 1030 ILE Chi-restraints excluded: chain D residue 1039 ASP Chi-restraints excluded: chain D residue 1084 VAL Chi-restraints excluded: chain D residue 1097 LEU Chi-restraints excluded: chain D residue 1105 ILE Chi-restraints excluded: chain D residue 1147 THR Chi-restraints excluded: chain D residue 1220 GLU Chi-restraints excluded: chain D residue 1242 THR Chi-restraints excluded: chain D residue 1259 VAL Chi-restraints excluded: chain D residue 1267 SER Chi-restraints excluded: chain D residue 1298 MET Chi-restraints excluded: chain D residue 1312 VAL Chi-restraints excluded: chain E residue 77 MET Chi-restraints excluded: chain E residue 78 SER Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 313 GLN Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 323 ASP Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 26 CYS Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 198 PHE Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 209 ASP Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 234 ASN Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 304 THR Chi-restraints excluded: chain F residue 340 PHE Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 362 LEU Chi-restraints excluded: chain F residue 367 LEU Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 391 ILE Chi-restraints excluded: chain F residue 399 ILE Chi-restraints excluded: chain F residue 473 VAL Chi-restraints excluded: chain F residue 531 THR Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain F residue 579 SER Chi-restraints excluded: chain F residue 605 VAL Chi-restraints excluded: chain F residue 681 ILE Chi-restraints excluded: chain F residue 779 LEU Chi-restraints excluded: chain F residue 848 THR Chi-restraints excluded: chain F residue 1007 SER Chi-restraints excluded: chain F residue 1030 ILE Chi-restraints excluded: chain F residue 1039 ASP Chi-restraints excluded: chain F residue 1084 VAL Chi-restraints excluded: chain F residue 1097 LEU Chi-restraints excluded: chain F residue 1105 ILE Chi-restraints excluded: chain F residue 1147 THR Chi-restraints excluded: chain F residue 1220 GLU Chi-restraints excluded: chain F residue 1242 THR Chi-restraints excluded: chain F residue 1259 VAL Chi-restraints excluded: chain F residue 1267 SER Chi-restraints excluded: chain F residue 1298 MET Chi-restraints excluded: chain F residue 1312 VAL Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 261 ILE Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain G residue 309 ILE Chi-restraints excluded: chain G residue 313 GLN Chi-restraints excluded: chain G residue 316 VAL Chi-restraints excluded: chain G residue 323 ASP Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 26 CYS Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain H residue 137 ILE Chi-restraints excluded: chain H residue 189 VAL Chi-restraints excluded: chain H residue 198 PHE Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain H residue 209 ASP Chi-restraints excluded: chain H residue 213 LEU Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 218 LEU Chi-restraints excluded: chain H residue 234 ASN Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 304 THR Chi-restraints excluded: chain H residue 340 PHE Chi-restraints excluded: chain H residue 360 VAL Chi-restraints excluded: chain H residue 362 LEU Chi-restraints excluded: chain H residue 367 LEU Chi-restraints excluded: chain H residue 371 THR Chi-restraints excluded: chain H residue 391 ILE Chi-restraints excluded: chain H residue 399 ILE Chi-restraints excluded: chain H residue 473 VAL Chi-restraints excluded: chain H residue 531 THR Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 579 SER Chi-restraints excluded: chain H residue 605 VAL Chi-restraints excluded: chain H residue 681 ILE Chi-restraints excluded: chain H residue 779 LEU Chi-restraints excluded: chain H residue 848 THR Chi-restraints excluded: chain H residue 1007 SER Chi-restraints excluded: chain H residue 1030 ILE Chi-restraints excluded: chain H residue 1039 ASP Chi-restraints excluded: chain H residue 1084 VAL Chi-restraints excluded: chain H residue 1097 LEU Chi-restraints excluded: chain H residue 1105 ILE Chi-restraints excluded: chain H residue 1147 THR Chi-restraints excluded: chain H residue 1220 GLU Chi-restraints excluded: chain H residue 1242 THR Chi-restraints excluded: chain H residue 1259 VAL Chi-restraints excluded: chain H residue 1267 SER Chi-restraints excluded: chain H residue 1298 MET Chi-restraints excluded: chain H residue 1312 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 672 random chunks: chunk 589 optimal weight: 0.9980 chunk 620 optimal weight: 1.9990 chunk 566 optimal weight: 2.9990 chunk 603 optimal weight: 0.9990 chunk 363 optimal weight: 0.8980 chunk 262 optimal weight: 20.0000 chunk 473 optimal weight: 1.9990 chunk 185 optimal weight: 0.8980 chunk 545 optimal weight: 2.9990 chunk 570 optimal weight: 0.8980 chunk 601 optimal weight: 9.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 HIS ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 547 ASN B 562 HIS ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 HIS ** D 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 562 HIS ** E 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 419 ASN ** G 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 125 HIS ** H 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 547 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6623 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 53092 Z= 0.180 Angle : 0.875 34.726 72352 Z= 0.362 Chirality : 0.079 2.004 8684 Planarity : 0.004 0.047 8792 Dihedral : 18.878 178.820 9440 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.52 % Allowed : 25.37 % Favored : 70.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.11), residues: 6684 helix: 1.75 (0.08), residues: 4064 sheet: -0.84 (0.22), residues: 524 loop : -1.29 (0.13), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B 514 HIS 0.004 0.001 HIS D1024 PHE 0.018 0.001 PHE D1182 TYR 0.014 0.001 TYR B 195 ARG 0.007 0.000 ARG F 370 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13368 Ramachandran restraints generated. 6684 Oldfield, 0 Emsley, 6684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13368 Ramachandran restraints generated. 6684 Oldfield, 0 Emsley, 6684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1053 residues out of total 5876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 835 time to evaluate : 5.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASN cc_start: 0.8573 (t0) cc_final: 0.7780 (t0) REVERT: A 67 LYS cc_start: 0.8335 (mttt) cc_final: 0.7461 (tptt) REVERT: A 71 THR cc_start: 0.8959 (m) cc_final: 0.8696 (m) REVERT: A 185 LYS cc_start: 0.7997 (tttt) cc_final: 0.7525 (tttm) REVERT: A 237 ASP cc_start: 0.7651 (t70) cc_final: 0.7343 (t0) REVERT: A 280 ASP cc_start: 0.8887 (t0) cc_final: 0.8427 (t0) REVERT: A 282 GLU cc_start: 0.7067 (tt0) cc_final: 0.6807 (tt0) REVERT: A 313 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7279 (mt0) REVERT: A 335 ASN cc_start: 0.8111 (m110) cc_final: 0.7885 (m-40) REVERT: B 43 THR cc_start: 0.9060 (m) cc_final: 0.8707 (p) REVERT: B 91 GLU cc_start: 0.8709 (pp20) cc_final: 0.8484 (pp20) REVERT: B 198 PHE cc_start: 0.5584 (OUTLIER) cc_final: 0.4752 (m-80) REVERT: B 211 GLN cc_start: 0.6366 (pp30) cc_final: 0.6099 (pp30) REVERT: B 289 ARG cc_start: 0.7426 (mtp180) cc_final: 0.6748 (mmt180) REVERT: B 340 PHE cc_start: 0.8555 (OUTLIER) cc_final: 0.7740 (t80) REVERT: B 354 ASN cc_start: 0.9208 (t0) cc_final: 0.8845 (t0) REVERT: B 454 TYR cc_start: 0.6721 (t80) cc_final: 0.6356 (m-80) REVERT: B 500 ASN cc_start: 0.7920 (t0) cc_final: 0.7638 (t0) REVERT: B 565 PHE cc_start: 0.6600 (t80) cc_final: 0.6107 (m-80) REVERT: B 1066 MET cc_start: 0.7121 (ttp) cc_final: 0.6802 (tpp) REVERT: B 1197 GLN cc_start: 0.8030 (tt0) cc_final: 0.7565 (tp40) REVERT: B 1220 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7701 (mp0) REVERT: C 43 ASN cc_start: 0.8570 (t0) cc_final: 0.7912 (t0) REVERT: C 67 LYS cc_start: 0.8247 (mttt) cc_final: 0.7436 (tptt) REVERT: C 71 THR cc_start: 0.8900 (m) cc_final: 0.8640 (m) REVERT: C 185 LYS cc_start: 0.7998 (tttt) cc_final: 0.7526 (tttm) REVERT: C 237 ASP cc_start: 0.7654 (t70) cc_final: 0.7345 (t0) REVERT: C 280 ASP cc_start: 0.8887 (t0) cc_final: 0.8427 (t0) REVERT: C 282 GLU cc_start: 0.7060 (tt0) cc_final: 0.6805 (tt0) REVERT: C 313 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7284 (mt0) REVERT: C 332 LYS cc_start: 0.8099 (mtmm) cc_final: 0.7746 (mtmm) REVERT: D 43 THR cc_start: 0.9060 (m) cc_final: 0.8708 (p) REVERT: D 91 GLU cc_start: 0.8709 (pp20) cc_final: 0.8483 (pp20) REVERT: D 198 PHE cc_start: 0.5586 (OUTLIER) cc_final: 0.4752 (m-80) REVERT: D 289 ARG cc_start: 0.7426 (mtp180) cc_final: 0.6749 (mmt180) REVERT: D 340 PHE cc_start: 0.8554 (OUTLIER) cc_final: 0.7740 (t80) REVERT: D 354 ASN cc_start: 0.9208 (t0) cc_final: 0.8845 (t0) REVERT: D 454 TYR cc_start: 0.6721 (t80) cc_final: 0.6355 (m-80) REVERT: D 500 ASN cc_start: 0.7920 (t0) cc_final: 0.7638 (t0) REVERT: D 565 PHE cc_start: 0.6601 (t80) cc_final: 0.6107 (m-80) REVERT: D 1066 MET cc_start: 0.7035 (ttp) cc_final: 0.6699 (tpp) REVERT: D 1197 GLN cc_start: 0.8030 (tt0) cc_final: 0.7565 (tp40) REVERT: D 1220 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.7702 (mp0) REVERT: E 43 ASN cc_start: 0.8574 (t0) cc_final: 0.7782 (t0) REVERT: E 67 LYS cc_start: 0.8277 (mttt) cc_final: 0.7447 (tptt) REVERT: E 71 THR cc_start: 0.8891 (m) cc_final: 0.8635 (m) REVERT: E 185 LYS cc_start: 0.7994 (tttt) cc_final: 0.7522 (tttm) REVERT: E 237 ASP cc_start: 0.7655 (t70) cc_final: 0.7348 (t0) REVERT: E 280 ASP cc_start: 0.8885 (t0) cc_final: 0.8425 (t0) REVERT: E 282 GLU cc_start: 0.7060 (tt0) cc_final: 0.6799 (tt0) REVERT: E 313 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7286 (mt0) REVERT: E 332 LYS cc_start: 0.8097 (mtmm) cc_final: 0.7745 (mtmm) REVERT: F 43 THR cc_start: 0.9060 (m) cc_final: 0.8708 (p) REVERT: F 91 GLU cc_start: 0.8707 (pp20) cc_final: 0.8483 (pp20) REVERT: F 198 PHE cc_start: 0.5586 (OUTLIER) cc_final: 0.4754 (m-80) REVERT: F 211 GLN cc_start: 0.6364 (pp30) cc_final: 0.6098 (pp30) REVERT: F 289 ARG cc_start: 0.7424 (mtp180) cc_final: 0.6748 (mmt180) REVERT: F 340 PHE cc_start: 0.8555 (OUTLIER) cc_final: 0.7741 (t80) REVERT: F 354 ASN cc_start: 0.9207 (t0) cc_final: 0.8844 (t0) REVERT: F 454 TYR cc_start: 0.6722 (t80) cc_final: 0.6355 (m-80) REVERT: F 500 ASN cc_start: 0.7920 (t0) cc_final: 0.7638 (t0) REVERT: F 565 PHE cc_start: 0.6592 (t80) cc_final: 0.6098 (m-80) REVERT: F 1066 MET cc_start: 0.7037 (ttp) cc_final: 0.6700 (tpp) REVERT: F 1197 GLN cc_start: 0.8029 (tt0) cc_final: 0.7563 (tp40) REVERT: F 1220 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.7702 (mp0) REVERT: G 43 ASN cc_start: 0.8576 (t0) cc_final: 0.7783 (t0) REVERT: G 67 LYS cc_start: 0.8401 (mttt) cc_final: 0.7508 (tptt) REVERT: G 71 THR cc_start: 0.8980 (m) cc_final: 0.8703 (m) REVERT: G 185 LYS cc_start: 0.7995 (tttt) cc_final: 0.7523 (tttm) REVERT: G 237 ASP cc_start: 0.7653 (t70) cc_final: 0.7345 (t0) REVERT: G 280 ASP cc_start: 0.8884 (t0) cc_final: 0.8423 (t0) REVERT: G 282 GLU cc_start: 0.7065 (tt0) cc_final: 0.6803 (tt0) REVERT: G 313 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7285 (mt0) REVERT: G 332 LYS cc_start: 0.8096 (mtmm) cc_final: 0.7742 (mtmm) REVERT: H 43 THR cc_start: 0.9060 (m) cc_final: 0.8709 (p) REVERT: H 91 GLU cc_start: 0.8708 (pp20) cc_final: 0.8483 (pp20) REVERT: H 198 PHE cc_start: 0.5583 (OUTLIER) cc_final: 0.4751 (m-80) REVERT: H 211 GLN cc_start: 0.6367 (pp30) cc_final: 0.6102 (pp30) REVERT: H 289 ARG cc_start: 0.7426 (mtp180) cc_final: 0.6748 (mmt180) REVERT: H 340 PHE cc_start: 0.8553 (OUTLIER) cc_final: 0.7739 (t80) REVERT: H 354 ASN cc_start: 0.9208 (t0) cc_final: 0.8845 (t0) REVERT: H 454 TYR cc_start: 0.6721 (t80) cc_final: 0.6355 (m-80) REVERT: H 500 ASN cc_start: 0.7920 (t0) cc_final: 0.7638 (t0) REVERT: H 565 PHE cc_start: 0.6594 (t80) cc_final: 0.6100 (m-80) REVERT: H 1066 MET cc_start: 0.7121 (ttp) cc_final: 0.6801 (tpp) REVERT: H 1197 GLN cc_start: 0.8029 (tt0) cc_final: 0.7563 (tp40) REVERT: H 1220 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.7702 (mp0) outliers start: 218 outliers final: 181 residues processed: 1003 average time/residue: 0.4763 time to fit residues: 833.5537 Evaluate side-chains 1005 residues out of total 5876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 808 time to evaluate : 4.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 313 GLN Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 10 ASN Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 209 ASP Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 848 THR Chi-restraints excluded: chain B residue 1007 SER Chi-restraints excluded: chain B residue 1097 LEU Chi-restraints excluded: chain B residue 1147 THR Chi-restraints excluded: chain B residue 1220 GLU Chi-restraints excluded: chain B residue 1242 THR Chi-restraints excluded: chain B residue 1267 SER Chi-restraints excluded: chain B residue 1298 MET Chi-restraints excluded: chain B residue 1312 VAL Chi-restraints excluded: chain B residue 1424 ILE Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 313 GLN Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 10 ASN Chi-restraints excluded: chain D residue 26 CYS Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 198 PHE Chi-restraints excluded: chain D residue 209 ASP Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 340 PHE Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 371 THR Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 473 VAL Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 848 THR Chi-restraints excluded: chain D residue 1007 SER Chi-restraints excluded: chain D residue 1097 LEU Chi-restraints excluded: chain D residue 1147 THR Chi-restraints excluded: chain D residue 1220 GLU Chi-restraints excluded: chain D residue 1242 THR Chi-restraints excluded: chain D residue 1267 SER Chi-restraints excluded: chain D residue 1298 MET Chi-restraints excluded: chain D residue 1312 VAL Chi-restraints excluded: chain D residue 1424 ILE Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 163 MET Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 313 GLN Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 323 ASP Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 10 ASN Chi-restraints excluded: chain F residue 26 CYS Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 198 PHE Chi-restraints excluded: chain F residue 209 ASP Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 304 THR Chi-restraints excluded: chain F residue 340 PHE Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 362 LEU Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 399 ILE Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 473 VAL Chi-restraints excluded: chain F residue 531 THR Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain F residue 556 LEU Chi-restraints excluded: chain F residue 681 ILE Chi-restraints excluded: chain F residue 848 THR Chi-restraints excluded: chain F residue 1007 SER Chi-restraints excluded: chain F residue 1097 LEU Chi-restraints excluded: chain F residue 1147 THR Chi-restraints excluded: chain F residue 1220 GLU Chi-restraints excluded: chain F residue 1242 THR Chi-restraints excluded: chain F residue 1267 SER Chi-restraints excluded: chain F residue 1298 MET Chi-restraints excluded: chain F residue 1312 VAL Chi-restraints excluded: chain F residue 1424 ILE Chi-restraints excluded: chain G residue 77 MET Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 163 MET Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 261 ILE Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain G residue 309 ILE Chi-restraints excluded: chain G residue 313 GLN Chi-restraints excluded: chain G residue 316 VAL Chi-restraints excluded: chain G residue 323 ASP Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 10 ASN Chi-restraints excluded: chain H residue 26 CYS Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain H residue 137 ILE Chi-restraints excluded: chain H residue 198 PHE Chi-restraints excluded: chain H residue 209 ASP Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 218 LEU Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 304 THR Chi-restraints excluded: chain H residue 340 PHE Chi-restraints excluded: chain H residue 360 VAL Chi-restraints excluded: chain H residue 362 LEU Chi-restraints excluded: chain H residue 371 THR Chi-restraints excluded: chain H residue 399 ILE Chi-restraints excluded: chain H residue 423 ILE Chi-restraints excluded: chain H residue 473 VAL Chi-restraints excluded: chain H residue 531 THR Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 550 ILE Chi-restraints excluded: chain H residue 556 LEU Chi-restraints excluded: chain H residue 681 ILE Chi-restraints excluded: chain H residue 848 THR Chi-restraints excluded: chain H residue 1007 SER Chi-restraints excluded: chain H residue 1097 LEU Chi-restraints excluded: chain H residue 1147 THR Chi-restraints excluded: chain H residue 1220 GLU Chi-restraints excluded: chain H residue 1242 THR Chi-restraints excluded: chain H residue 1267 SER Chi-restraints excluded: chain H residue 1298 MET Chi-restraints excluded: chain H residue 1312 VAL Chi-restraints excluded: chain H residue 1424 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 672 random chunks: chunk 396 optimal weight: 4.9990 chunk 638 optimal weight: 0.9980 chunk 389 optimal weight: 0.6980 chunk 302 optimal weight: 0.8980 chunk 443 optimal weight: 9.9990 chunk 669 optimal weight: 40.0000 chunk 616 optimal weight: 8.9990 chunk 533 optimal weight: 6.9990 chunk 55 optimal weight: 0.0670 chunk 411 optimal weight: 9.9990 chunk 326 optimal weight: 20.0000 overall best weight: 1.5320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 GLN ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 ASN D 219 GLN ** E 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 219 GLN ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 219 GLN ** H 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6634 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 53092 Z= 0.218 Angle : 0.875 34.792 72352 Z= 0.363 Chirality : 0.079 1.996 8684 Planarity : 0.004 0.047 8792 Dihedral : 18.749 179.416 9440 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 4.39 % Allowed : 26.04 % Favored : 69.57 % 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: 1.00 (0.11), residues: 6684 helix: 1.80 (0.08), residues: 4048 sheet: -0.70 (0.23), residues: 496 loop : -1.23 (0.13), residues: 2140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 514 HIS 0.004 0.001 HIS H1024 PHE 0.017 0.001 PHE D1182 TYR 0.016 0.001 TYR B 123 ARG 0.006 0.000 ARG H 370 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13368 Ramachandran restraints generated. 6684 Oldfield, 0 Emsley, 6684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13368 Ramachandran restraints generated. 6684 Oldfield, 0 Emsley, 6684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1020 residues out of total 5876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 808 time to evaluate : 4.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASN cc_start: 0.8587 (t0) cc_final: 0.7792 (t0) REVERT: A 67 LYS cc_start: 0.8422 (mttt) cc_final: 0.7547 (tptt) REVERT: A 71 THR cc_start: 0.8975 (m) cc_final: 0.8706 (m) REVERT: A 185 LYS cc_start: 0.8012 (tttt) cc_final: 0.7555 (tttm) REVERT: A 237 ASP cc_start: 0.7661 (t70) cc_final: 0.7296 (t0) REVERT: A 280 ASP cc_start: 0.8877 (t0) cc_final: 0.8397 (t0) REVERT: A 313 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7356 (mt0) REVERT: A 335 ASN cc_start: 0.8128 (m110) cc_final: 0.7904 (m-40) REVERT: B 43 THR cc_start: 0.9046 (m) cc_final: 0.8679 (p) REVERT: B 91 GLU cc_start: 0.8696 (pp20) cc_final: 0.8460 (pp20) REVERT: B 198 PHE cc_start: 0.5518 (OUTLIER) cc_final: 0.4783 (m-80) REVERT: B 211 GLN cc_start: 0.6373 (pp30) cc_final: 0.6076 (pp30) REVERT: B 264 GLN cc_start: 0.9070 (tt0) cc_final: 0.8659 (tm-30) REVERT: B 289 ARG cc_start: 0.7433 (mtp180) cc_final: 0.6772 (mmt180) REVERT: B 340 PHE cc_start: 0.8529 (OUTLIER) cc_final: 0.7655 (t80) REVERT: B 354 ASN cc_start: 0.9240 (t0) cc_final: 0.8871 (t0) REVERT: B 454 TYR cc_start: 0.6841 (t80) cc_final: 0.6353 (m-80) REVERT: B 500 ASN cc_start: 0.7918 (t0) cc_final: 0.7625 (t0) REVERT: B 565 PHE cc_start: 0.6534 (t80) cc_final: 0.6110 (m-80) REVERT: B 1066 MET cc_start: 0.7121 (ttp) cc_final: 0.6805 (tpp) REVERT: B 1197 GLN cc_start: 0.7788 (tt0) cc_final: 0.7345 (tp40) REVERT: B 1220 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.7714 (mp0) REVERT: C 43 ASN cc_start: 0.8584 (t0) cc_final: 0.7788 (t0) REVERT: C 67 LYS cc_start: 0.8262 (mttt) cc_final: 0.7448 (tptt) REVERT: C 71 THR cc_start: 0.8903 (m) cc_final: 0.8647 (m) REVERT: C 185 LYS cc_start: 0.8014 (tttt) cc_final: 0.7556 (tttm) REVERT: C 237 ASP cc_start: 0.7664 (t70) cc_final: 0.7298 (t0) REVERT: C 280 ASP cc_start: 0.8878 (t0) cc_final: 0.8399 (t0) REVERT: C 313 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7335 (mt0) REVERT: C 332 LYS cc_start: 0.8024 (mtmm) cc_final: 0.7799 (mtmm) REVERT: C 335 ASN cc_start: 0.8160 (m110) cc_final: 0.7945 (m-40) REVERT: D 43 THR cc_start: 0.9053 (m) cc_final: 0.8687 (p) REVERT: D 91 GLU cc_start: 0.8696 (pp20) cc_final: 0.8461 (pp20) REVERT: D 198 PHE cc_start: 0.5520 (OUTLIER) cc_final: 0.4785 (m-80) REVERT: D 264 GLN cc_start: 0.9093 (tt0) cc_final: 0.8679 (tm-30) REVERT: D 289 ARG cc_start: 0.7433 (mtp180) cc_final: 0.6772 (mmt180) REVERT: D 340 PHE cc_start: 0.8529 (OUTLIER) cc_final: 0.7657 (t80) REVERT: D 354 ASN cc_start: 0.9239 (t0) cc_final: 0.8869 (t0) REVERT: D 454 TYR cc_start: 0.6841 (t80) cc_final: 0.6351 (m-80) REVERT: D 500 ASN cc_start: 0.7918 (t0) cc_final: 0.7625 (t0) REVERT: D 565 PHE cc_start: 0.6535 (t80) cc_final: 0.6110 (m-80) REVERT: D 1066 MET cc_start: 0.7120 (ttp) cc_final: 0.6804 (tpp) REVERT: D 1197 GLN cc_start: 0.7788 (tt0) cc_final: 0.7345 (tp40) REVERT: D 1220 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.7715 (mp0) REVERT: E 43 ASN cc_start: 0.8587 (t0) cc_final: 0.7793 (t0) REVERT: E 67 LYS cc_start: 0.8300 (mttt) cc_final: 0.7461 (tptt) REVERT: E 71 THR cc_start: 0.8893 (m) cc_final: 0.8640 (m) REVERT: E 185 LYS cc_start: 0.8010 (tttt) cc_final: 0.7552 (tttm) REVERT: E 237 ASP cc_start: 0.7666 (t70) cc_final: 0.7300 (t0) REVERT: E 280 ASP cc_start: 0.8876 (t0) cc_final: 0.8397 (t0) REVERT: E 313 GLN cc_start: 0.8065 (OUTLIER) cc_final: 0.7335 (mt0) REVERT: E 332 LYS cc_start: 0.8023 (mtmm) cc_final: 0.7798 (mtmm) REVERT: E 335 ASN cc_start: 0.8160 (m110) cc_final: 0.7945 (m-40) REVERT: F 43 THR cc_start: 0.9052 (m) cc_final: 0.8687 (p) REVERT: F 91 GLU cc_start: 0.8696 (pp20) cc_final: 0.8463 (pp20) REVERT: F 198 PHE cc_start: 0.5519 (OUTLIER) cc_final: 0.4785 (m-80) REVERT: F 211 GLN cc_start: 0.6371 (pp30) cc_final: 0.6077 (pp30) REVERT: F 264 GLN cc_start: 0.9069 (tt0) cc_final: 0.8658 (tm-30) REVERT: F 289 ARG cc_start: 0.7432 (mtp180) cc_final: 0.6771 (mmt180) REVERT: F 340 PHE cc_start: 0.8529 (OUTLIER) cc_final: 0.7655 (t80) REVERT: F 354 ASN cc_start: 0.9239 (t0) cc_final: 0.8870 (t0) REVERT: F 454 TYR cc_start: 0.6842 (t80) cc_final: 0.6353 (m-80) REVERT: F 500 ASN cc_start: 0.7917 (t0) cc_final: 0.7623 (t0) REVERT: F 565 PHE cc_start: 0.6535 (t80) cc_final: 0.6110 (m-80) REVERT: F 1066 MET cc_start: 0.7121 (ttp) cc_final: 0.6805 (tpp) REVERT: F 1197 GLN cc_start: 0.7787 (tt0) cc_final: 0.7344 (tp40) REVERT: F 1220 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.7712 (mp0) REVERT: G 43 ASN cc_start: 0.8588 (t0) cc_final: 0.7793 (t0) REVERT: G 66 LEU cc_start: 0.9197 (mt) cc_final: 0.8711 (mt) REVERT: G 67 LYS cc_start: 0.8426 (mttt) cc_final: 0.7526 (tptt) REVERT: G 71 THR cc_start: 0.9007 (m) cc_final: 0.8733 (m) REVERT: G 185 LYS cc_start: 0.8012 (tttt) cc_final: 0.7554 (tttm) REVERT: G 237 ASP cc_start: 0.7664 (t70) cc_final: 0.7298 (t0) REVERT: G 280 ASP cc_start: 0.8876 (t0) cc_final: 0.8397 (t0) REVERT: G 313 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7332 (mt0) REVERT: G 332 LYS cc_start: 0.8020 (mtmm) cc_final: 0.7795 (mtmm) REVERT: G 335 ASN cc_start: 0.8161 (m110) cc_final: 0.7947 (m-40) REVERT: H 43 THR cc_start: 0.9055 (m) cc_final: 0.8690 (p) REVERT: H 91 GLU cc_start: 0.8695 (pp20) cc_final: 0.8460 (pp20) REVERT: H 198 PHE cc_start: 0.5519 (OUTLIER) cc_final: 0.4784 (m-80) REVERT: H 211 GLN cc_start: 0.6372 (pp30) cc_final: 0.6076 (pp30) REVERT: H 264 GLN cc_start: 0.9071 (tt0) cc_final: 0.8659 (tm-30) REVERT: H 289 ARG cc_start: 0.7432 (mtp180) cc_final: 0.6771 (mmt180) REVERT: H 340 PHE cc_start: 0.8527 (OUTLIER) cc_final: 0.7654 (t80) REVERT: H 354 ASN cc_start: 0.9239 (t0) cc_final: 0.8868 (t0) REVERT: H 454 TYR cc_start: 0.6841 (t80) cc_final: 0.6352 (m-80) REVERT: H 500 ASN cc_start: 0.7918 (t0) cc_final: 0.7625 (t0) REVERT: H 565 PHE cc_start: 0.6537 (t80) cc_final: 0.6112 (m-80) REVERT: H 1066 MET cc_start: 0.7121 (ttp) cc_final: 0.6805 (tpp) REVERT: H 1197 GLN cc_start: 0.7787 (tt0) cc_final: 0.7344 (tp40) REVERT: H 1220 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.7714 (mp0) outliers start: 212 outliers final: 178 residues processed: 966 average time/residue: 0.4489 time to fit residues: 754.6389 Evaluate side-chains 992 residues out of total 5876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 798 time to evaluate : 4.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 313 GLN Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 10 ASN Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 209 ASP Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 848 THR Chi-restraints excluded: chain B residue 1007 SER Chi-restraints excluded: chain B residue 1097 LEU Chi-restraints excluded: chain B residue 1147 THR Chi-restraints excluded: chain B residue 1220 GLU Chi-restraints excluded: chain B residue 1267 SER Chi-restraints excluded: chain B residue 1298 MET Chi-restraints excluded: chain B residue 1312 VAL Chi-restraints excluded: chain B residue 1424 ILE Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 313 GLN Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 10 ASN Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 26 CYS Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 198 PHE Chi-restraints excluded: chain D residue 209 ASP Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 340 PHE Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 371 THR Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 473 VAL Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 550 ILE Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 848 THR Chi-restraints excluded: chain D residue 1007 SER Chi-restraints excluded: chain D residue 1097 LEU Chi-restraints excluded: chain D residue 1147 THR Chi-restraints excluded: chain D residue 1220 GLU Chi-restraints excluded: chain D residue 1267 SER Chi-restraints excluded: chain D residue 1298 MET Chi-restraints excluded: chain D residue 1312 VAL Chi-restraints excluded: chain D residue 1424 ILE Chi-restraints excluded: chain E residue 77 MET Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 163 MET Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 313 GLN Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 323 ASP Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 10 ASN Chi-restraints excluded: chain F residue 26 CYS Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 198 PHE Chi-restraints excluded: chain F residue 209 ASP Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 304 THR Chi-restraints excluded: chain F residue 340 PHE Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 362 LEU Chi-restraints excluded: chain F residue 367 LEU Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 399 ILE Chi-restraints excluded: chain F residue 473 VAL Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain F residue 550 ILE Chi-restraints excluded: chain F residue 556 LEU Chi-restraints excluded: chain F residue 681 ILE Chi-restraints excluded: chain F residue 848 THR Chi-restraints excluded: chain F residue 1007 SER Chi-restraints excluded: chain F residue 1097 LEU Chi-restraints excluded: chain F residue 1147 THR Chi-restraints excluded: chain F residue 1220 GLU Chi-restraints excluded: chain F residue 1267 SER Chi-restraints excluded: chain F residue 1298 MET Chi-restraints excluded: chain F residue 1312 VAL Chi-restraints excluded: chain F residue 1424 ILE Chi-restraints excluded: chain G residue 77 MET Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 167 ILE Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 261 ILE Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain G residue 309 ILE Chi-restraints excluded: chain G residue 313 GLN Chi-restraints excluded: chain G residue 316 VAL Chi-restraints excluded: chain G residue 323 ASP Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 10 ASN Chi-restraints excluded: chain H residue 26 CYS Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain H residue 137 ILE Chi-restraints excluded: chain H residue 198 PHE Chi-restraints excluded: chain H residue 209 ASP Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 218 LEU Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 304 THR Chi-restraints excluded: chain H residue 340 PHE Chi-restraints excluded: chain H residue 360 VAL Chi-restraints excluded: chain H residue 362 LEU Chi-restraints excluded: chain H residue 367 LEU Chi-restraints excluded: chain H residue 371 THR Chi-restraints excluded: chain H residue 399 ILE Chi-restraints excluded: chain H residue 473 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 556 LEU Chi-restraints excluded: chain H residue 681 ILE Chi-restraints excluded: chain H residue 848 THR Chi-restraints excluded: chain H residue 1007 SER Chi-restraints excluded: chain H residue 1097 LEU Chi-restraints excluded: chain H residue 1147 THR Chi-restraints excluded: chain H residue 1220 GLU Chi-restraints excluded: chain H residue 1267 SER Chi-restraints excluded: chain H residue 1298 MET Chi-restraints excluded: chain H residue 1312 VAL Chi-restraints excluded: chain H residue 1424 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 672 random chunks: chunk 423 optimal weight: 0.9990 chunk 567 optimal weight: 7.9990 chunk 163 optimal weight: 30.0000 chunk 491 optimal weight: 0.0970 chunk 78 optimal weight: 6.9990 chunk 148 optimal weight: 9.9990 chunk 533 optimal weight: 5.9990 chunk 223 optimal weight: 0.6980 chunk 548 optimal weight: 0.0770 chunk 67 optimal weight: 4.9990 chunk 98 optimal weight: 0.0970 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 547 ASN ** E 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.149515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.117246 restraints weight = 95305.358| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.71 r_work: 0.3293 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 53092 Z= 0.158 Angle : 0.852 34.434 72352 Z= 0.351 Chirality : 0.079 2.013 8684 Planarity : 0.004 0.044 8792 Dihedral : 18.498 179.220 9440 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.38 % Allowed : 26.80 % Favored : 69.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.11), residues: 6684 helix: 1.97 (0.08), residues: 4032 sheet: -0.64 (0.23), residues: 492 loop : -1.15 (0.13), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 514 HIS 0.006 0.001 HIS D1024 PHE 0.017 0.001 PHE D1182 TYR 0.013 0.001 TYR B 123 ARG 0.007 0.000 ARG B 258 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15898.96 seconds wall clock time: 280 minutes 34.76 seconds (16834.76 seconds total)