Starting phenix.real_space_refine (version: 1.21rc1) on Sun Aug 20 09:36:20 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlo_24535/08_2023/7rlo_24535.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlo_24535/08_2023/7rlo_24535.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlo_24535/08_2023/7rlo_24535.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlo_24535/08_2023/7rlo_24535.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlo_24535/08_2023/7rlo_24535.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlo_24535/08_2023/7rlo_24535.pdb" } resolution = 2.6 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= 0.002 sd= 0.066 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 170 5.16 5 C 18281 2.51 5 N 4997 2.21 5 O 5259 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 54": "NH1" <-> "NH2" Residue "A ASP 137": "OD1" <-> "OD2" Residue "A ARG 145": "NH1" <-> "NH2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A GLU 167": "OE1" <-> "OE2" Residue "A ARG 171": "NH1" <-> "NH2" Residue "A GLU 187": "OE1" <-> "OE2" Residue "A GLU 198": "OE1" <-> "OE2" Residue "A ASP 199": "OD1" <-> "OD2" Residue "A PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 270": "OD1" <-> "OD2" Residue "A GLU 418": "OE1" <-> "OE2" Residue "A ARG 428": "NH1" <-> "NH2" Residue "B ASP 53": "OD1" <-> "OD2" Residue "B ARG 54": "NH1" <-> "NH2" Residue "B ASP 147": "OD1" <-> "OD2" Residue "B ARG 171": "NH1" <-> "NH2" Residue "B PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 199": "OD1" <-> "OD2" Residue "B PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 262": "OD1" <-> "OD2" Residue "B ASP 387": "OD1" <-> "OD2" Residue "B ARG 428": "NH1" <-> "NH2" Residue "C GLU 13": "OE1" <-> "OE2" Residue "C GLU 20": "OE1" <-> "OE2" Residue "C ARG 29": "NH1" <-> "NH2" Residue "C GLU 37": "OE1" <-> "OE2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C ARG 63": "NH1" <-> "NH2" Residue "C ARG 67": "NH1" <-> "NH2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "C ASP 121": "OD1" <-> "OD2" Residue "C PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 135": "OE1" <-> "OE2" Residue "C GLU 139": "OE1" <-> "OE2" Residue "C GLU 143": "OE1" <-> "OE2" Residue "C GLU 145": "OE1" <-> "OE2" Residue "C GLU 163": "OE1" <-> "OE2" Residue "C ARG 183": "NH1" <-> "NH2" Residue "C ARG 338": "NH1" <-> "NH2" Residue "D GLU 13": "OE1" <-> "OE2" Residue "D GLU 20": "OE1" <-> "OE2" Residue "D ARG 29": "NH1" <-> "NH2" Residue "D GLU 37": "OE1" <-> "OE2" Residue "D ARG 43": "NH1" <-> "NH2" Residue "D ARG 63": "NH1" <-> "NH2" Residue "D ARG 67": "NH1" <-> "NH2" Residue "D GLU 92": "OE1" <-> "OE2" Residue "D ASP 121": "OD1" <-> "OD2" Residue "D PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 135": "OE1" <-> "OE2" Residue "D GLU 139": "OE1" <-> "OE2" Residue "D GLU 143": "OE1" <-> "OE2" Residue "D GLU 145": "OE1" <-> "OE2" Residue "D GLU 163": "OE1" <-> "OE2" Residue "D ARG 183": "NH1" <-> "NH2" Residue "D ARG 338": "NH1" <-> "NH2" Residue "E ARG 170": "NH1" <-> "NH2" Residue "E GLU 283": "OE1" <-> "OE2" Residue "E GLU 294": "OE1" <-> "OE2" Residue "E GLU 295": "OE1" <-> "OE2" Residue "E ARG 321": "NH1" <-> "NH2" Residue "E ARG 321": "NH1" <-> "NH2" Residue "E ARG 374": "NH1" <-> "NH2" Residue "E ARG 417": "NH1" <-> "NH2" Residue "E GLU 439": "OE1" <-> "OE2" Residue "E ARG 467": "NH1" <-> "NH2" Residue "E ARG 467": "NH1" <-> "NH2" Residue "F ARG 170": "NH1" <-> "NH2" Residue "F GLU 246": "OE1" <-> "OE2" Residue "F ASP 251": "OD1" <-> "OD2" Residue "F GLU 294": "OE1" <-> "OE2" Residue "F ARG 321": "NH1" <-> "NH2" Residue "F ARG 321": "NH1" <-> "NH2" Residue "F ARG 374": "NH1" <-> "NH2" Residue "F ARG 417": "NH1" <-> "NH2" Residue "F GLU 439": "OE1" <-> "OE2" Residue "F ARG 467": "NH1" <-> "NH2" Residue "F ARG 467": "NH1" <-> "NH2" Residue "F GLU 469": "OE1" <-> "OE2" Residue "G GLU 5": "OE1" <-> "OE2" Residue "G GLU 54": "OE1" <-> "OE2" Residue "G ARG 74": "NH1" <-> "NH2" Residue "G ARG 108": "NH1" <-> "NH2" Residue "G ASP 121": "OD1" <-> "OD2" Residue "G ARG 132": "NH1" <-> "NH2" Residue "G ARG 136": "NH1" <-> "NH2" Residue "H GLU 8": "OE1" <-> "OE2" Residue "H GLU 16": "OE1" <-> "OE2" Residue "H ASP 17": "OD1" <-> "OD2" Residue "H ASP 19": "OD1" <-> "OD2" Residue "H ARG 74": "NH1" <-> "NH2" Residue "H GLU 98": "OE1" <-> "OE2" Residue "H ARG 108": "NH1" <-> "NH2" Residue "H ARG 132": "NH1" <-> "NH2" Residue "H ARG 136": "NH1" <-> "NH2" Residue "I PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 307": "OE1" <-> "OE2" Residue "I ARG 324": "NH1" <-> "NH2" Residue "J GLU 44": "OE1" <-> "OE2" Residue "J ASP 100": "OD1" <-> "OD2" Residue "J ASP 111": "OD1" <-> "OD2" Residue "J GLU 116": "OE1" <-> "OE2" Residue "J ASP 156": "OD1" <-> "OD2" Residue "J GLU 173": "OE1" <-> "OE2" Residue "J GLU 179": "OE1" <-> "OE2" Residue "J PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 213": "OD1" <-> "OD2" Residue "J GLU 217": "OE1" <-> "OE2" Residue "J ARG 324": "NH1" <-> "NH2" Residue "K ARG 20": "NH1" <-> "NH2" Residue "K TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 58": "NH1" <-> "NH2" Residue "K ASP 96": "OD1" <-> "OD2" Residue "K ARG 143": "NH1" <-> "NH2" Residue "K GLU 173": "OE1" <-> "OE2" Residue "K ARG 176": "NH1" <-> "NH2" Residue "K ASP 181": "OD1" <-> "OD2" Residue "K GLU 182": "OE1" <-> "OE2" Residue "K GLU 192": "OE1" <-> "OE2" Residue "K ARG 200": "NH1" <-> "NH2" Residue "K ASP 208": "OD1" <-> "OD2" Residue "L ARG 17": "NH1" <-> "NH2" Residue "L ARG 20": "NH1" <-> "NH2" Residue "L TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 58": "NH1" <-> "NH2" Residue "L ASP 96": "OD1" <-> "OD2" Residue "L GLU 127": "OE1" <-> "OE2" Residue "L ARG 143": "NH1" <-> "NH2" Residue "L GLU 173": "OE1" <-> "OE2" Residue "L ARG 176": "NH1" <-> "NH2" Residue "L ASP 181": "OD1" <-> "OD2" Residue "L GLU 192": "OE1" <-> "OE2" Residue "L ARG 200": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 28707 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3210 Classifications: {'peptide': 414} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 395} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 3202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3202 Classifications: {'peptide': 414} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 395} Chain breaks: 1 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "C" Number of atoms: 2604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2604 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 318} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 2604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2604 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 318} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 2772 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 353, 2750 Classifications: {'peptide': 353} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 334} Conformer: "B" Number of residues, atoms: 353, 2750 Classifications: {'peptide': 353} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 334} bond proxies already assigned to first conformer: 2778 Chain: "F" Number of atoms: 2772 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 353, 2750 Classifications: {'peptide': 353} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 334} Conformer: "B" Number of residues, atoms: 353, 2750 Classifications: {'peptide': 353} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 334} bond proxies already assigned to first conformer: 2778 Chain: "G" Number of atoms: 2205 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 284, 2194 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 274} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 284, 2194 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 274} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 2218 Chain: "H" Number of atoms: 2205 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 284, 2194 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 274} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 284, 2194 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 274} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 2218 Chain: "I" Number of atoms: 1867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1867 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 11, 'TRANS': 226} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 21 Chain: "J" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1789 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 217} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 18 Chain: "K" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1741 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 9, 'TRANS': 208} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 22 Chain: "L" Number of atoms: 1736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1736 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 9, 'TRANS': 208} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 22 Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N AARG E 321 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG E 321 " occ=0.50 residue: pdb=" N AARG E 467 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG E 467 " occ=0.50 residue: pdb=" N AARG F 321 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG F 321 " occ=0.50 residue: pdb=" N AARG F 467 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG F 467 " occ=0.50 residue: pdb=" N AARG G 132 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG G 132 " occ=0.50 residue: pdb=" N AARG H 132 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG H 132 " occ=0.50 Time building chain proxies: 17.95, per 1000 atoms: 0.63 Number of scatterers: 28707 At special positions: 0 Unit cell: (131.095, 136.94, 162.825, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 170 16.00 O 5259 8.00 N 4997 7.00 C 18281 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 10.55 Conformation dependent library (CDL) restraints added in 5.3 seconds 7244 Ramachandran restraints generated. 3622 Oldfield, 0 Emsley, 3622 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6976 Finding SS restraints... Secondary structure from input PDB file: 157 helices and 35 sheets defined 44.8% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.91 Creating SS restraints... Processing helix chain 'A' and resid 56 through 61 Processing helix chain 'A' and resid 64 through 68 Processing helix chain 'A' and resid 74 through 87 removed outlier: 3.622A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 108 removed outlier: 3.688A pdb=" N ILE A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 142 Processing helix chain 'A' and resid 162 through 175 removed outlier: 3.524A pdb=" N GLU A 175 " --> pdb=" O ARG A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 196 removed outlier: 4.045A pdb=" N CYS A 196 " --> pdb=" O PRO A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 233 removed outlier: 4.221A pdb=" N GLY A 233 " --> pdb=" O LEU A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 263 removed outlier: 4.162A pdb=" N ALA A 257 " --> pdb=" O SER A 253 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN A 258 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 278 removed outlier: 3.897A pdb=" N VAL A 278 " --> pdb=" O ARG A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 315 Processing helix chain 'B' and resid 74 through 87 removed outlier: 3.839A pdb=" N TYR B 78 " --> pdb=" O ALA B 74 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR B 79 " --> pdb=" O LEU B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 107 removed outlier: 3.551A pdb=" N ILE B 102 " --> pdb=" O LYS B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 142 removed outlier: 3.641A pdb=" N LEU B 135 " --> pdb=" O LEU B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 175 removed outlier: 3.643A pdb=" N LYS B 173 " --> pdb=" O ARG B 169 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU B 174 " --> pdb=" O LEU B 170 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU B 175 " --> pdb=" O ARG B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 234 removed outlier: 3.654A pdb=" N SER B 234 " --> pdb=" O LEU B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 263 removed outlier: 3.994A pdb=" N ALA B 257 " --> pdb=" O SER B 253 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE B 260 " --> pdb=" O VAL B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 279 removed outlier: 3.670A pdb=" N PHE B 272 " --> pdb=" O THR B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 315 Processing helix chain 'B' and resid 330 through 334 removed outlier: 3.554A pdb=" N GLN B 333 " --> pdb=" O SER B 330 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER B 334 " --> pdb=" O THR B 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 330 through 334' Processing helix chain 'C' and resid 9 through 25 removed outlier: 3.577A pdb=" N GLY C 25 " --> pdb=" O THR C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 48 Processing helix chain 'C' and resid 53 through 72 removed outlier: 3.881A pdb=" N LEU C 57 " --> pdb=" O ASN C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 98 removed outlier: 4.359A pdb=" N GLY C 79 " --> pdb=" O GLU C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 114 Processing helix chain 'C' and resid 128 through 153 removed outlier: 3.797A pdb=" N GLU C 145 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY C 146 " --> pdb=" O VAL C 142 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N MET C 148 " --> pdb=" O LEU C 144 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N GLU C 149 " --> pdb=" O GLU C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 182 Processing helix chain 'C' and resid 199 through 209 removed outlier: 3.617A pdb=" N MET C 203 " --> pdb=" O GLN C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 229 removed outlier: 3.591A pdb=" N VAL C 229 " --> pdb=" O MET C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 261 Processing helix chain 'C' and resid 270 through 274 removed outlier: 3.732A pdb=" N LYS C 273 " --> pdb=" O PRO C 270 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU C 274 " --> pdb=" O MET C 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 270 through 274' Processing helix chain 'C' and resid 296 through 304 removed outlier: 3.695A pdb=" N GLU C 299 " --> pdb=" O PRO C 296 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLY C 300 " --> pdb=" O PHE C 297 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ASP C 301 " --> pdb=" O THR C 298 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N ILE C 302 " --> pdb=" O GLU C 299 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU C 303 " --> pdb=" O GLY C 300 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU C 304 " --> pdb=" O ASP C 301 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 296 through 304' Processing helix chain 'C' and resid 317 through 321 removed outlier: 3.544A pdb=" N LEU C 320 " --> pdb=" O PRO C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 334 No H-bonds generated for 'chain 'C' and resid 332 through 334' Processing helix chain 'C' and resid 335 through 342 removed outlier: 3.585A pdb=" N LEU C 339 " --> pdb=" O TYR C 335 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER C 341 " --> pdb=" O TYR C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 349 removed outlier: 3.771A pdb=" N HIS C 349 " --> pdb=" O PRO C 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 25 removed outlier: 3.578A pdb=" N GLY D 25 " --> pdb=" O THR D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 48 Processing helix chain 'D' and resid 53 through 72 removed outlier: 3.881A pdb=" N LEU D 57 " --> pdb=" O ASN D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 98 removed outlier: 4.359A pdb=" N GLY D 79 " --> pdb=" O GLU D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 114 Processing helix chain 'D' and resid 128 through 153 removed outlier: 3.798A pdb=" N GLU D 145 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY D 146 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N MET D 148 " --> pdb=" O LEU D 144 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N GLU D 149 " --> pdb=" O GLU D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 182 Processing helix chain 'D' and resid 199 through 209 removed outlier: 3.617A pdb=" N MET D 203 " --> pdb=" O GLN D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 229 removed outlier: 3.592A pdb=" N VAL D 229 " --> pdb=" O MET D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 261 Processing helix chain 'D' and resid 270 through 274 removed outlier: 3.731A pdb=" N LYS D 273 " --> pdb=" O PRO D 270 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU D 274 " --> pdb=" O MET D 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 270 through 274' Processing helix chain 'D' and resid 296 through 304 removed outlier: 3.695A pdb=" N GLU D 299 " --> pdb=" O PRO D 296 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLY D 300 " --> pdb=" O PHE D 297 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ASP D 301 " --> pdb=" O THR D 298 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N ILE D 302 " --> pdb=" O GLU D 299 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU D 303 " --> pdb=" O GLY D 300 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU D 304 " --> pdb=" O ASP D 301 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 296 through 304' Processing helix chain 'D' and resid 317 through 321 removed outlier: 3.544A pdb=" N LEU D 320 " --> pdb=" O PRO D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 334 No H-bonds generated for 'chain 'D' and resid 332 through 334' Processing helix chain 'D' and resid 335 through 342 removed outlier: 3.585A pdb=" N LEU D 339 " --> pdb=" O TYR D 335 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER D 341 " --> pdb=" O TYR D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 349 removed outlier: 3.771A pdb=" N HIS D 349 " --> pdb=" O PRO D 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 196 removed outlier: 3.548A pdb=" N MET E 196 " --> pdb=" O THR E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 216 Processing helix chain 'E' and resid 222 through 239 Processing helix chain 'E' and resid 247 through 267 removed outlier: 3.861A pdb=" N VAL E 253 " --> pdb=" O SER E 249 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS E 257 " --> pdb=" O VAL E 253 " (cutoff:3.500A) Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 270 through 286 Processing helix chain 'E' and resid 292 through 312 Processing helix chain 'E' and resid 312 through 323 removed outlier: 3.571A pdb=" N GLN E 317 " --> pdb=" O VAL E 313 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA E 318 " --> pdb=" O LEU E 314 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE E 319 " --> pdb=" O ALA E 315 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 353 Processing helix chain 'E' and resid 369 through 378 removed outlier: 3.665A pdb=" N SER E 375 " --> pdb=" O HIS E 371 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS E 378 " --> pdb=" O ARG E 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 390 through 395 removed outlier: 3.853A pdb=" N VAL E 394 " --> pdb=" O ALA E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 398 No H-bonds generated for 'chain 'E' and resid 396 through 398' Processing helix chain 'E' and resid 420 through 429 removed outlier: 3.542A pdb=" N ALA E 429 " --> pdb=" O LEU E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 443 removed outlier: 3.623A pdb=" N PHE E 443 " --> pdb=" O THR E 440 " (cutoff:3.500A) Processing helix chain 'E' and resid 459 through 464 removed outlier: 3.600A pdb=" N LEU E 463 " --> pdb=" O PRO E 460 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN E 464 " --> pdb=" O ASP E 461 " (cutoff:3.500A) Processing helix chain 'E' and resid 493 through 497 Processing helix chain 'E' and resid 511 through 519 Processing helix chain 'F' and resid 192 through 196 Processing helix chain 'F' and resid 204 through 216 Processing helix chain 'F' and resid 221 through 239 Processing helix chain 'F' and resid 247 through 267 removed outlier: 3.986A pdb=" N VAL F 253 " --> pdb=" O SER F 249 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS F 257 " --> pdb=" O VAL F 253 " (cutoff:3.500A) Proline residue: F 258 - end of helix Processing helix chain 'F' and resid 270 through 286 Processing helix chain 'F' and resid 292 through 312 removed outlier: 3.893A pdb=" N SER F 298 " --> pdb=" O GLU F 294 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE F 312 " --> pdb=" O VAL F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 325 removed outlier: 4.064A pdb=" N GLN F 325 " --> pdb=" O AARG F 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 353 Processing helix chain 'F' and resid 369 through 379 removed outlier: 3.772A pdb=" N SER F 375 " --> pdb=" O HIS F 371 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N HIS F 378 " --> pdb=" O ARG F 374 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA F 379 " --> pdb=" O SER F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 390 through 395 removed outlier: 3.563A pdb=" N VAL F 394 " --> pdb=" O ALA F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 398 No H-bonds generated for 'chain 'F' and resid 396 through 398' Processing helix chain 'F' and resid 420 through 429 removed outlier: 3.591A pdb=" N ALA F 429 " --> pdb=" O LEU F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 443 removed outlier: 3.568A pdb=" N PHE F 443 " --> pdb=" O THR F 440 " (cutoff:3.500A) Processing helix chain 'F' and resid 459 through 464 Processing helix chain 'F' and resid 475 through 479 Processing helix chain 'F' and resid 493 through 497 Processing helix chain 'F' and resid 511 through 519 Processing helix chain 'G' and resid 7 through 15 Processing helix chain 'G' and resid 21 through 36 Processing helix chain 'G' and resid 41 through 60 removed outlier: 3.573A pdb=" N VAL G 59 " --> pdb=" O THR G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 80 removed outlier: 3.869A pdb=" N SER G 66 " --> pdb=" O SER G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 105 Processing helix chain 'G' and resid 106 through 116 removed outlier: 3.637A pdb=" N LEU G 114 " --> pdb=" O LYS G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 119 No H-bonds generated for 'chain 'G' and resid 117 through 119' Processing helix chain 'G' and resid 131 through 143 removed outlier: 3.539A pdb=" N ALA G 143 " --> pdb=" O GLU G 139 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 171 Processing helix chain 'G' and resid 179 through 181 No H-bonds generated for 'chain 'G' and resid 179 through 181' Processing helix chain 'G' and resid 182 through 187 Processing helix chain 'G' and resid 188 through 190 No H-bonds generated for 'chain 'G' and resid 188 through 190' Processing helix chain 'G' and resid 212 through 222 Processing helix chain 'G' and resid 247 through 252 removed outlier: 3.592A pdb=" N LYS G 251 " --> pdb=" O PRO G 247 " (cutoff:3.500A) Processing helix chain 'G' and resid 277 through 281 Processing helix chain 'G' and resid 295 through 304 Processing helix chain 'H' and resid 6 through 15 removed outlier: 3.555A pdb=" N LYS H 15 " --> pdb=" O LYS H 11 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 36 Processing helix chain 'H' and resid 41 through 60 Processing helix chain 'H' and resid 62 through 81 removed outlier: 3.821A pdb=" N SER H 66 " --> pdb=" O SER H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 105 Processing helix chain 'H' and resid 106 through 116 removed outlier: 3.682A pdb=" N LYS H 110 " --> pdb=" O LEU H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 119 No H-bonds generated for 'chain 'H' and resid 117 through 119' Processing helix chain 'H' and resid 131 through 143 Processing helix chain 'H' and resid 159 through 170 removed outlier: 3.905A pdb=" N LYS H 163 " --> pdb=" O LEU H 159 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS H 170 " --> pdb=" O LYS H 166 " (cutoff:3.500A) Processing helix chain 'H' and resid 179 through 183 removed outlier: 3.776A pdb=" N VAL H 183 " --> pdb=" O ASP H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 212 through 221 removed outlier: 3.644A pdb=" N CYS H 218 " --> pdb=" O GLN H 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 252 Processing helix chain 'H' and resid 277 through 281 Processing helix chain 'H' and resid 294 through 304 removed outlier: 3.917A pdb=" N ASP H 298 " --> pdb=" O SER H 294 " (cutoff:3.500A) Processing helix chain 'I' and resid 24 through 28 removed outlier: 3.502A pdb=" N LEU I 27 " --> pdb=" O PRO I 24 " (cutoff:3.500A) Processing helix chain 'I' and resid 36 through 44 Processing helix chain 'I' and resid 85 through 91 Processing helix chain 'I' and resid 93 through 97 Processing helix chain 'I' and resid 114 through 123 removed outlier: 4.334A pdb=" N LEU I 120 " --> pdb=" O GLU I 116 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE I 121 " --> pdb=" O VAL I 117 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA I 123 " --> pdb=" O ASP I 119 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 190 Processing helix chain 'I' and resid 208 through 218 removed outlier: 4.016A pdb=" N VAL I 212 " --> pdb=" O LYS I 208 " (cutoff:3.500A) Processing helix chain 'I' and resid 223 through 234 removed outlier: 5.005A pdb=" N ILE I 229 " --> pdb=" O ARG I 225 " (cutoff:3.500A) Proline residue: I 230 - end of helix Processing helix chain 'I' and resid 262 through 267 removed outlier: 3.922A pdb=" N PHE I 266 " --> pdb=" O ASP I 262 " (cutoff:3.500A) Processing helix chain 'I' and resid 315 through 334 Proline residue: I 327 - end of helix Processing helix chain 'J' and resid 24 through 28 removed outlier: 3.783A pdb=" N LEU J 28 " --> pdb=" O LYS J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 43 Processing helix chain 'J' and resid 86 through 92 removed outlier: 3.527A pdb=" N LEU J 90 " --> pdb=" O THR J 86 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 123 removed outlier: 4.448A pdb=" N LEU J 120 " --> pdb=" O GLU J 116 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE J 121 " --> pdb=" O VAL J 117 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA J 123 " --> pdb=" O ASP J 119 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 190 Processing helix chain 'J' and resid 209 through 218 Processing helix chain 'J' and resid 227 through 234 removed outlier: 3.823A pdb=" N TYR J 231 " --> pdb=" O GLU J 227 " (cutoff:3.500A) Processing helix chain 'J' and resid 315 through 334 removed outlier: 3.530A pdb=" N TYR J 319 " --> pdb=" O THR J 315 " (cutoff:3.500A) Proline residue: J 327 - end of helix Processing helix chain 'K' and resid 1 through 5 removed outlier: 3.516A pdb=" N TYR K 5 " --> pdb=" O ASN K 2 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 66 Processing helix chain 'K' and resid 90 through 97 Processing helix chain 'K' and resid 101 through 107 removed outlier: 3.514A pdb=" N PHE K 105 " --> pdb=" O ASP K 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 117 Processing helix chain 'K' and resid 126 through 132 removed outlier: 4.147A pdb=" N SER K 130 " --> pdb=" O CYS K 126 " (cutoff:3.500A) Processing helix chain 'K' and resid 142 through 152 Processing helix chain 'K' and resid 158 through 177 Processing helix chain 'K' and resid 180 through 184 Processing helix chain 'K' and resid 188 through 205 Processing helix chain 'K' and resid 206 through 208 No H-bonds generated for 'chain 'K' and resid 206 through 208' Processing helix chain 'K' and resid 218 through 224 Processing helix chain 'L' and resid 1 through 5 removed outlier: 3.594A pdb=" N TYR L 5 " --> pdb=" O ASN L 2 " (cutoff:3.500A) Processing helix chain 'L' and resid 61 through 66 Processing helix chain 'L' and resid 90 through 97 Processing helix chain 'L' and resid 98 through 100 No H-bonds generated for 'chain 'L' and resid 98 through 100' Processing helix chain 'L' and resid 102 through 107 Processing helix chain 'L' and resid 111 through 117 removed outlier: 3.617A pdb=" N ALA L 116 " --> pdb=" O ASN L 112 " (cutoff:3.500A) Processing helix chain 'L' and resid 126 through 132 removed outlier: 3.957A pdb=" N SER L 130 " --> pdb=" O CYS L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 142 through 153 removed outlier: 3.644A pdb=" N MET L 153 " --> pdb=" O TYR L 149 " (cutoff:3.500A) Processing helix chain 'L' and resid 158 through 177 Processing helix chain 'L' and resid 188 through 205 Processing helix chain 'L' and resid 206 through 208 No H-bonds generated for 'chain 'L' and resid 206 through 208' Processing helix chain 'L' and resid 218 through 224 Processing sheet with id=AA1, first strand: chain 'A' and resid 119 through 124 removed outlier: 3.542A pdb=" N CYS A 95 " --> pdb=" O ILE A 123 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ALA A 45 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N PHE A 94 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LEU A 47 " --> pdb=" O PHE A 94 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 151 " --> pdb=" O VAL A 46 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N TYR A 152 " --> pdb=" O HIS A 248 " (cutoff:3.500A) removed outlier: 9.137A pdb=" N HIS A 248 " --> pdb=" O TYR A 152 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N CYS A 247 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ILE A 184 " --> pdb=" O CYS A 247 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ILE A 249 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N THR A 182 " --> pdb=" O ILE A 249 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 155 through 157 Processing sheet with id=AA3, first strand: chain 'A' and resid 212 through 217 removed outlier: 6.283A pdb=" N ALA A 204 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N PHE A 215 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N VAL A 202 " --> pdb=" O PHE A 215 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL A 238 " --> pdb=" O PHE I 195 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ASP I 161 " --> pdb=" O LEU I 167 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N LEU I 167 " --> pdb=" O ASP I 161 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 223 through 227 Processing sheet with id=AA5, first strand: chain 'A' and resid 336 through 338 removed outlier: 5.965A pdb=" N LEU A 361 " --> pdb=" O ILE A 379 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N VAL A 378 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N TYR A 395 " --> pdb=" O LEU A 413 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU A 412 " --> pdb=" O LEU A 431 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL A 430 " --> pdb=" O ILE A 449 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 355 through 356 removed outlier: 6.240A pdb=" N ILE A 355 " --> pdb=" O ILE A 374 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLN A 407 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N THR A 424 " --> pdb=" O LEU A 443 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 384 through 385 removed outlier: 6.239A pdb=" N HIS A 384 " --> pdb=" O VAL A 402 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ARG A 401 " --> pdb=" O VAL A 419 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N GLU A 418 " --> pdb=" O VAL A 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 119 through 124 removed outlier: 6.599A pdb=" N THR B 91 " --> pdb=" O ARG B 121 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ILE B 123 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N VAL B 93 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ALA B 45 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N PHE B 94 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LEU B 47 " --> pdb=" O PHE B 94 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER B 250 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N TYR B 152 " --> pdb=" O HIS B 248 " (cutoff:3.500A) removed outlier: 9.567A pdb=" N HIS B 248 " --> pdb=" O TYR B 152 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ILE B 184 " --> pdb=" O CYS B 247 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE B 249 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N THR B 182 " --> pdb=" O ILE B 249 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N MET B 181 " --> pdb=" O HIS B 288 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N HIS B 290 " --> pdb=" O MET B 181 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N MET B 183 " --> pdb=" O HIS B 290 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N THR B 292 " --> pdb=" O MET B 183 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N PHE B 185 " --> pdb=" O THR B 292 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 155 through 157 Processing sheet with id=AB1, first strand: chain 'B' and resid 212 through 217 removed outlier: 6.721A pdb=" N VAL B 212 " --> pdb=" O ASP B 206 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ASP B 206 " --> pdb=" O VAL B 212 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL B 238 " --> pdb=" O PHE J 195 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 223 through 226 Processing sheet with id=AB3, first strand: chain 'B' and resid 336 through 337 removed outlier: 3.595A pdb=" N ARG B 344 " --> pdb=" O THR B 336 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LEU B 361 " --> pdb=" O ILE B 379 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N VAL B 378 " --> pdb=" O LEU B 396 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N TYR B 395 " --> pdb=" O LEU B 413 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU B 412 " --> pdb=" O LEU B 431 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL B 430 " --> pdb=" O ILE B 449 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 355 through 356 removed outlier: 7.095A pdb=" N ILE B 355 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL B 390 " --> pdb=" O ILE B 408 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 367 through 368 removed outlier: 6.369A pdb=" N VAL B 367 " --> pdb=" O ILE B 385 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N HIS B 384 " --> pdb=" O VAL B 402 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ARG B 401 " --> pdb=" O VAL B 419 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N GLU B 418 " --> pdb=" O VAL B 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 423 through 425 removed outlier: 7.163A pdb=" N THR B 424 " --> pdb=" O LEU B 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 329 through 331 removed outlier: 6.690A pdb=" N LEU C 265 " --> pdb=" O LEU C 323 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ILE C 325 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL C 267 " --> pdb=" O ILE C 325 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL C 232 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N CYS C 268 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE C 234 " --> pdb=" O CYS C 268 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N VAL C 164 " --> pdb=" O LYS C 231 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ILE C 233 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N MET C 166 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N THR C 214 " --> pdb=" O ARG F 483 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 238 through 239 removed outlier: 3.703A pdb=" N THR C 238 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 306 through 308 removed outlier: 6.109A pdb=" N SER C 307 " --> pdb=" O TYR F 385 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N LEU F 387 " --> pdb=" O SER C 307 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE F 333 " --> pdb=" O VAL F 359 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N VAL F 361 " --> pdb=" O ILE F 333 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL F 335 " --> pdb=" O VAL F 361 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N VAL F 332 " --> pdb=" O LYS F 400 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N LEU F 402 " --> pdb=" O VAL F 332 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N LEU F 334 " --> pdb=" O LEU F 402 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N GLY F 404 " --> pdb=" O LEU F 334 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N TYR F 336 " --> pdb=" O GLY F 404 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N VAL F 401 " --> pdb=" O LEU F 435 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N CYS F 437 " --> pdb=" O VAL F 401 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU F 403 " --> pdb=" O CYS F 437 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL F 434 " --> pdb=" O LEU F 499 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N ILE F 501 " --> pdb=" O VAL F 434 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N VAL F 436 " --> pdb=" O ILE F 501 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 329 through 331 removed outlier: 6.690A pdb=" N LEU D 265 " --> pdb=" O LEU D 323 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ILE D 325 " --> pdb=" O LEU D 265 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL D 267 " --> pdb=" O ILE D 325 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL D 232 " --> pdb=" O ILE D 266 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N CYS D 268 " --> pdb=" O VAL D 232 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE D 234 " --> pdb=" O CYS D 268 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N VAL D 164 " --> pdb=" O LYS D 231 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N ILE D 233 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N MET D 166 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N THR D 214 " --> pdb=" O ARG E 483 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 238 through 239 removed outlier: 3.703A pdb=" N THR D 238 " --> pdb=" O ARG D 246 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 306 through 308 removed outlier: 6.215A pdb=" N SER D 307 " --> pdb=" O TYR E 385 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N LEU E 387 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE E 333 " --> pdb=" O VAL E 359 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N VAL E 361 " --> pdb=" O ILE E 333 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL E 335 " --> pdb=" O VAL E 361 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N TYR E 336 " --> pdb=" O LEU E 402 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N GLY E 404 " --> pdb=" O TYR E 336 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL E 401 " --> pdb=" O LEU E 435 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N CYS E 437 " --> pdb=" O VAL E 401 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU E 403 " --> pdb=" O CYS E 437 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL E 434 " --> pdb=" O LEU E 499 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N ILE E 501 " --> pdb=" O VAL E 434 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL E 436 " --> pdb=" O ILE E 501 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 407 through 408 Processing sheet with id=AC5, first strand: chain 'F' and resid 407 through 408 Processing sheet with id=AC6, first strand: chain 'G' and resid 175 through 178 removed outlier: 8.709A pdb=" N THR G 176 " --> pdb=" O PHE G 148 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL G 150 " --> pdb=" O THR G 176 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N VAL G 178 " --> pdb=" O VAL G 150 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N VAL G 152 " --> pdb=" O VAL G 178 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N VAL G 193 " --> pdb=" O TYR G 227 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N VAL G 229 " --> pdb=" O VAL G 193 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL G 195 " --> pdb=" O VAL G 229 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N PHE G 226 " --> pdb=" O LEU G 283 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N PHE G 285 " --> pdb=" O PHE G 226 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL G 228 " --> pdb=" O PHE G 285 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 199 through 200 Processing sheet with id=AC8, first strand: chain 'H' and resid 175 through 178 removed outlier: 6.741A pdb=" N VAL H 150 " --> pdb=" O THR H 176 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N VAL H 178 " --> pdb=" O VAL H 150 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N VAL H 152 " --> pdb=" O VAL H 178 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N THR H 124 " --> pdb=" O LEU H 192 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N ILE H 194 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N LEU H 126 " --> pdb=" O ILE H 194 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL H 193 " --> pdb=" O TYR H 227 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N VAL H 229 " --> pdb=" O VAL H 193 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL H 195 " --> pdb=" O VAL H 229 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU H 283 " --> pdb=" O PHE H 226 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 199 through 200 Processing sheet with id=AD1, first strand: chain 'I' and resid 73 through 77 removed outlier: 4.039A pdb=" N MET I 8 " --> pdb=" O LEU I 104 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N SER I 105 " --> pdb=" O HIS I 203 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N HIS I 203 " --> pdb=" O SER I 105 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LEU I 131 " --> pdb=" O ALA I 202 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU I 204 " --> pdb=" O ALA I 129 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ALA I 129 " --> pdb=" O LEU I 204 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 51 through 54 removed outlier: 9.115A pdb=" N ILE J 52 " --> pdb=" O PHE J 3 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA J 5 " --> pdb=" O ILE J 52 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N VAL J 54 " --> pdb=" O ALA J 5 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL J 7 " --> pdb=" O VAL J 54 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N SER J 105 " --> pdb=" O HIS J 203 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N HIS J 203 " --> pdb=" O SER J 105 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ALA J 202 " --> pdb=" O ARG J 133 " (cutoff:3.500A) removed outlier: 8.680A pdb=" N ARG J 133 " --> pdb=" O ALA J 202 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N LEU J 204 " --> pdb=" O LEU J 131 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 8 through 13 removed outlier: 3.548A pdb=" N SER K 26 " --> pdb=" O ALA K 11 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 37 through 40 removed outlier: 4.452A pdb=" N ASP K 37 " --> pdb=" O LEU K 48 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 52 through 54 Processing sheet with id=AD6, first strand: chain 'L' and resid 8 through 13 removed outlier: 3.846A pdb=" N SER L 26 " --> pdb=" O ALA L 11 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN L 13 " --> pdb=" O SER L 24 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER L 24 " --> pdb=" O ASN L 13 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 37 through 40 removed outlier: 4.461A pdb=" N ASP L 37 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 52 through 54 1171 hydrogen bonds defined for protein. 3317 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: 9.88 Time building geometry restraints manager: 11.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9455 1.34 - 1.46: 5715 1.46 - 1.58: 13829 1.58 - 1.69: 0 1.69 - 1.81: 258 Bond restraints: 29257 Sorted by residual: bond pdb=" C LYS I 25 " pdb=" N PRO I 26 " ideal model delta sigma weight residual 1.336 1.361 -0.025 1.08e-02 8.57e+03 5.53e+00 bond pdb=" C VAL I 326 " pdb=" N PRO I 327 " ideal model delta sigma weight residual 1.334 1.376 -0.042 2.34e-02 1.83e+03 3.24e+00 bond pdb=" C LEU F 395 " pdb=" N PRO F 396 " ideal model delta sigma weight residual 1.335 1.356 -0.021 1.19e-02 7.06e+03 3.20e+00 bond pdb=" C VAL J 326 " pdb=" N PRO J 327 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.99e+00 bond pdb=" CA ILE L 14 " pdb=" CB ILE L 14 " ideal model delta sigma weight residual 1.528 1.546 -0.019 1.34e-02 5.57e+03 1.91e+00 ... (remaining 29252 not shown) Histogram of bond angle deviations from ideal: 100.11 - 106.88: 860 106.88 - 113.65: 16421 113.65 - 120.43: 11067 120.43 - 127.20: 11000 127.20 - 133.98: 301 Bond angle restraints: 39649 Sorted by residual: angle pdb=" N ARG K 17 " pdb=" CA ARG K 17 " pdb=" C ARG K 17 " ideal model delta sigma weight residual 113.18 106.06 7.12 1.33e+00 5.65e-01 2.87e+01 angle pdb=" C VAL J 76 " pdb=" N CYS J 77 " pdb=" CA CYS J 77 " ideal model delta sigma weight residual 121.56 128.99 -7.43 1.56e+00 4.11e-01 2.27e+01 angle pdb=" N ARG L 17 " pdb=" CA ARG L 17 " pdb=" C ARG L 17 " ideal model delta sigma weight residual 112.72 107.20 5.52 1.28e+00 6.10e-01 1.86e+01 angle pdb=" N CYS J 77 " pdb=" CA CYS J 77 " pdb=" C CYS J 77 " ideal model delta sigma weight residual 110.42 116.59 -6.17 1.46e+00 4.69e-01 1.78e+01 angle pdb=" N VAL J 326 " pdb=" CA VAL J 326 " pdb=" C VAL J 326 " ideal model delta sigma weight residual 108.88 117.30 -8.42 2.16e+00 2.14e-01 1.52e+01 ... (remaining 39644 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 16246 17.94 - 35.88: 1106 35.88 - 53.81: 316 53.81 - 71.75: 59 71.75 - 89.69: 33 Dihedral angle restraints: 17760 sinusoidal: 7018 harmonic: 10742 Sorted by residual: dihedral pdb=" CA VAL K 16 " pdb=" C VAL K 16 " pdb=" N ARG K 17 " pdb=" CA ARG K 17 " ideal model delta harmonic sigma weight residual 180.00 152.84 27.16 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA VAL L 16 " pdb=" C VAL L 16 " pdb=" N ARG L 17 " pdb=" CA ARG L 17 " ideal model delta harmonic sigma weight residual 180.00 154.74 25.26 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA PRO A 453 " pdb=" C PRO A 453 " pdb=" N PRO A 454 " pdb=" CA PRO A 454 " ideal model delta harmonic sigma weight residual 180.00 -157.39 -22.61 0 5.00e+00 4.00e-02 2.04e+01 ... (remaining 17757 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 3156 0.034 - 0.069: 984 0.069 - 0.103: 335 0.103 - 0.138: 150 0.138 - 0.172: 3 Chirality restraints: 4628 Sorted by residual: chirality pdb=" CG LEU K 201 " pdb=" CB LEU K 201 " pdb=" CD1 LEU K 201 " pdb=" CD2 LEU K 201 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.43e-01 chirality pdb=" CA PRO I 327 " pdb=" N PRO I 327 " pdb=" C PRO I 327 " pdb=" CB PRO I 327 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.35e-01 chirality pdb=" CA VAL J 46 " pdb=" N VAL J 46 " pdb=" C VAL J 46 " pdb=" CB VAL J 46 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.01e-01 ... (remaining 4625 not shown) Planarity restraints: 5049 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 395 " -0.026 5.00e-02 4.00e+02 3.87e-02 2.39e+00 pdb=" N PRO E 396 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO E 396 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO E 396 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 395 " 0.024 5.00e-02 4.00e+02 3.62e-02 2.10e+00 pdb=" N PRO F 396 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO F 396 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO F 396 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL J 326 " -0.007 2.00e-02 2.50e+03 1.42e-02 2.03e+00 pdb=" C VAL J 326 " 0.025 2.00e-02 2.50e+03 pdb=" O VAL J 326 " -0.009 2.00e-02 2.50e+03 pdb=" N PRO J 327 " -0.008 2.00e-02 2.50e+03 ... (remaining 5046 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 583 2.69 - 3.24: 26830 3.24 - 3.79: 44153 3.79 - 4.35: 60674 4.35 - 4.90: 100723 Nonbonded interactions: 232963 Sorted by model distance: nonbonded pdb=" OD2 ASP G 85 " pdb=" OG SER G 87 " model vdw 2.132 2.440 nonbonded pdb=" OD1 ASP C 121 " pdb=" OG SER C 123 " model vdw 2.199 2.440 nonbonded pdb=" OD1 ASP D 121 " pdb=" OG SER D 123 " model vdw 2.200 2.440 nonbonded pdb=" O SER G 80 " pdb=" OG SER G 80 " model vdw 2.250 2.440 nonbonded pdb=" OE1 GLU A 198 " pdb=" NE2 GLN A 219 " model vdw 2.273 2.520 ... (remaining 232958 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 41 through 433 or (resid 434 and (name N or name CA or nam \ e C or name O or name CB )) or resid 435 through 456 or (resid 457 and (name N o \ r name CA or name C or name O or name CB )) or resid 458 through 459)) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = (chain 'E' and (resid 167 through 320 or resid 322 through 466 or resid 468 thro \ ugh 519)) selection = (chain 'F' and (resid 167 through 320 or resid 322 through 466 or resid 468 thro \ ugh 519)) } ncs_group { reference = (chain 'G' and (resid 5 through 131 or resid 133 through 305)) selection = (chain 'H' and (resid 5 through 131 or resid 133 through 305)) } ncs_group { reference = (chain 'I' and (resid 1 through 78 or resid 84 through 235 or resid 297 through \ 334)) selection = (chain 'J' and (resid 1 through 77 or (resid 78 and (name N or name CA or name C \ or name O or name CB )) or resid 84 through 334)) } ncs_group { reference = (chain 'K' and (resid 1 through 220 or (resid 221 through 226 and (name N or nam \ e CA or name C or name O or name CB )))) selection = chain 'L' } 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=0.50 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: 5.070 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: 0.020 Extract box with map and model: 16.490 Check model and map are aligned: 0.460 Set scattering table: 0.280 Process input model: 74.770 Find NCS groups from input model: 1.630 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 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 : 0.002 0.047 29257 Z= 0.129 Angle : 0.489 8.511 39649 Z= 0.282 Chirality : 0.041 0.172 4628 Planarity : 0.003 0.039 5049 Dihedral : 14.087 89.691 10784 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.36 % Favored : 95.59 % Rotamer Outliers : 3.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % 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: -2.08 (0.13), residues: 3622 helix: -0.59 (0.13), residues: 1409 sheet: -1.62 (0.23), residues: 474 loop : -1.95 (0.13), residues: 1739 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7244 Ramachandran restraints generated. 3622 Oldfield, 0 Emsley, 3622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7244 Ramachandran restraints generated. 3622 Oldfield, 0 Emsley, 3622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 3218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 405 time to evaluate : 3.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 94 outliers final: 32 residues processed: 487 average time/residue: 1.5071 time to fit residues: 849.1621 Evaluate side-chains 277 residues out of total 3218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 245 time to evaluate : 3.610 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 32 residues processed: 0 time to fit residues: 4.7078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 304 optimal weight: 10.0000 chunk 273 optimal weight: 4.9990 chunk 151 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 184 optimal weight: 0.0020 chunk 146 optimal weight: 0.0670 chunk 282 optimal weight: 7.9990 chunk 109 optimal weight: 0.5980 chunk 172 optimal weight: 4.9990 chunk 210 optimal weight: 2.9990 chunk 327 optimal weight: 7.9990 overall best weight: 0.9328 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN A 89 GLN A 160 ASN A 255 GLN A 337 HIS A 359 ASN A 376 ASN A 393 GLN B 44 GLN B 72 ASN B 219 GLN B 290 HIS B 337 HIS B 359 ASN B 393 GLN B 398 GLN B 416 ASN C 80 ASN C 130 GLN C 158 HIS C 160 HIS C 277 GLN D 80 ASN D 106 GLN D 130 GLN D 158 HIS D 160 HIS E 194 GLN E 213 GLN E 235 GLN E 281 ASN E 325 GLN E 430 HIS E 448 GLN E 464 GLN F 213 GLN F 245 ASN F 281 ASN F 371 HIS F 411 ASN F 430 HIS F 448 GLN F 455 ASN F 464 GLN F 470 HIS G 109 ASN G 243 GLN G 244 GLN H 109 ASN H 222 GLN H 243 GLN I 41 ASN I 297 GLN I 323 ASN I 325 GLN J 32 ASN J 136 GLN J 190 HIS J 218 ASN J 325 GLN K 19 HIS K 59 ASN K 112 ASN K 145 GLN L 91 GLN L 112 ASN L 145 GLN Total number of N/Q/H flips: 67 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 29257 Z= 0.185 Angle : 0.533 11.254 39649 Z= 0.269 Chirality : 0.043 0.212 4628 Planarity : 0.004 0.043 5049 Dihedral : 3.767 24.988 3990 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer Outliers : 3.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % 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: -0.65 (0.14), residues: 3622 helix: 0.77 (0.14), residues: 1446 sheet: -0.84 (0.25), residues: 440 loop : -1.35 (0.14), residues: 1736 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7244 Ramachandran restraints generated. 3622 Oldfield, 0 Emsley, 3622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7244 Ramachandran restraints generated. 3622 Oldfield, 0 Emsley, 3622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 258 time to evaluate : 3.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 116 outliers final: 56 residues processed: 350 average time/residue: 1.3926 time to fit residues: 572.7872 Evaluate side-chains 277 residues out of total 3218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 221 time to evaluate : 3.595 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 51 residues processed: 5 average time/residue: 0.8574 time to fit residues: 10.2066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 182 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 chunk 272 optimal weight: 0.8980 chunk 223 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 chunk 328 optimal weight: 9.9990 chunk 354 optimal weight: 10.0000 chunk 292 optimal weight: 0.0570 chunk 325 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 263 optimal weight: 0.6980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN C 160 HIS C 277 GLN D 106 GLN G 244 GLN I 297 GLN J 325 GLN L 34 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.046 29257 Z= 0.152 Angle : 0.496 8.742 39649 Z= 0.250 Chirality : 0.042 0.150 4628 Planarity : 0.003 0.045 5049 Dihedral : 3.702 24.952 3990 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.16 % Favored : 95.81 % Rotamer Outliers : 3.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % 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: -0.04 (0.14), residues: 3622 helix: 1.31 (0.14), residues: 1458 sheet: -0.58 (0.26), residues: 442 loop : -1.04 (0.15), residues: 1722 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7244 Ramachandran restraints generated. 3622 Oldfield, 0 Emsley, 3622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7244 Ramachandran restraints generated. 3622 Oldfield, 0 Emsley, 3622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 244 time to evaluate : 3.785 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 122 outliers final: 61 residues processed: 349 average time/residue: 1.3333 time to fit residues: 552.3213 Evaluate side-chains 285 residues out of total 3218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 224 time to evaluate : 3.547 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 57 residues processed: 4 average time/residue: 1.0051 time to fit residues: 10.0388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 324 optimal weight: 7.9990 chunk 246 optimal weight: 7.9990 chunk 170 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 220 optimal weight: 4.9990 chunk 329 optimal weight: 0.9990 chunk 348 optimal weight: 6.9990 chunk 172 optimal weight: 2.9990 chunk 312 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 ASN C 277 GLN D 230 ASN E 422 GLN ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 422 GLN F 431 ASN F 470 HIS G 244 GLN J 218 ASN L 36 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.069 29257 Z= 0.275 Angle : 0.557 8.516 39649 Z= 0.282 Chirality : 0.045 0.165 4628 Planarity : 0.004 0.046 5049 Dihedral : 4.059 29.604 3990 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.52 % Favored : 95.42 % Rotamer Outliers : 4.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.14), residues: 3622 helix: 1.45 (0.14), residues: 1462 sheet: -0.52 (0.25), residues: 452 loop : -0.90 (0.15), residues: 1708 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7244 Ramachandran restraints generated. 3622 Oldfield, 0 Emsley, 3622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7244 Ramachandran restraints generated. 3622 Oldfield, 0 Emsley, 3622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 3218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 244 time to evaluate : 3.420 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 129 outliers final: 74 residues processed: 354 average time/residue: 1.3711 time to fit residues: 572.2668 Evaluate side-chains 294 residues out of total 3218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 220 time to evaluate : 3.434 Switching outliers to nearest non-outliers outliers start: 74 outliers final: 71 residues processed: 3 average time/residue: 0.6425 time to fit residues: 7.2390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 290 optimal weight: 0.9990 chunk 198 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 259 optimal weight: 3.9990 chunk 143 optimal weight: 0.8980 chunk 297 optimal weight: 10.0000 chunk 241 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 178 optimal weight: 3.9990 chunk 313 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 ASN C 277 GLN ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 244 GLN J 218 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 29257 Z= 0.176 Angle : 0.517 8.542 39649 Z= 0.261 Chirality : 0.043 0.147 4628 Planarity : 0.003 0.048 5049 Dihedral : 3.932 27.847 3990 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer Outliers : 3.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % 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 (0.15), residues: 3622 helix: 1.67 (0.14), residues: 1463 sheet: -0.28 (0.26), residues: 447 loop : -0.79 (0.15), residues: 1712 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7244 Ramachandran restraints generated. 3622 Oldfield, 0 Emsley, 3622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7244 Ramachandran restraints generated. 3622 Oldfield, 0 Emsley, 3622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 3218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 243 time to evaluate : 3.381 Fit side-chains revert: symmetry clash outliers start: 116 outliers final: 71 residues processed: 341 average time/residue: 1.3057 time to fit residues: 529.8683 Evaluate side-chains 295 residues out of total 3218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 224 time to evaluate : 3.459 Switching outliers to nearest non-outliers outliers start: 71 outliers final: 68 residues processed: 3 average time/residue: 0.7477 time to fit residues: 7.3667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 117 optimal weight: 6.9990 chunk 314 optimal weight: 10.0000 chunk 68 optimal weight: 0.9980 chunk 204 optimal weight: 0.8980 chunk 86 optimal weight: 9.9990 chunk 349 optimal weight: 10.0000 chunk 289 optimal weight: 4.9990 chunk 161 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 115 optimal weight: 8.9990 chunk 183 optimal weight: 9.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 ASN B 376 ASN C 277 GLN E 470 HIS F 470 HIS G 244 GLN K 36 HIS L 59 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.104 29257 Z= 0.463 Angle : 0.660 9.057 39649 Z= 0.335 Chirality : 0.049 0.204 4628 Planarity : 0.005 0.051 5049 Dihedral : 4.584 33.271 3990 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.13 % Favored : 94.81 % Rotamer Outliers : 4.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.14 (0.14), residues: 3622 helix: 1.35 (0.14), residues: 1477 sheet: -0.60 (0.24), residues: 485 loop : -0.80 (0.15), residues: 1660 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7244 Ramachandran restraints generated. 3622 Oldfield, 0 Emsley, 3622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7244 Ramachandran restraints generated. 3622 Oldfield, 0 Emsley, 3622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 230 time to evaluate : 3.476 Fit side-chains outliers start: 126 outliers final: 76 residues processed: 338 average time/residue: 1.3436 time to fit residues: 538.5660 Evaluate side-chains 301 residues out of total 3218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 225 time to evaluate : 3.395 Switching outliers to nearest non-outliers outliers start: 76 outliers final: 71 residues processed: 6 average time/residue: 0.7245 time to fit residues: 10.2436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 336 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 199 optimal weight: 0.9980 chunk 255 optimal weight: 2.9990 chunk 197 optimal weight: 1.9990 chunk 294 optimal weight: 0.8980 chunk 195 optimal weight: 10.0000 chunk 347 optimal weight: 7.9990 chunk 217 optimal weight: 0.8980 chunk 212 optimal weight: 0.9990 chunk 160 optimal weight: 10.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 ASN C 277 GLN E 347 GLN ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 244 GLN ** I 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 145 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 29257 Z= 0.204 Angle : 0.543 9.741 39649 Z= 0.275 Chirality : 0.044 0.158 4628 Planarity : 0.004 0.053 5049 Dihedral : 4.221 32.575 3990 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.50 % Favored : 95.45 % Rotamer Outliers : 3.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.46 (0.14), residues: 3622 helix: 1.65 (0.14), residues: 1466 sheet: -0.22 (0.25), residues: 444 loop : -0.72 (0.15), residues: 1712 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7244 Ramachandran restraints generated. 3622 Oldfield, 0 Emsley, 3622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7244 Ramachandran restraints generated. 3622 Oldfield, 0 Emsley, 3622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 235 time to evaluate : 3.752 Fit side-chains revert: symmetry clash outliers start: 104 outliers final: 77 residues processed: 324 average time/residue: 1.3053 time to fit residues: 502.7454 Evaluate side-chains 301 residues out of total 3218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 224 time to evaluate : 3.507 Switching outliers to nearest non-outliers outliers start: 77 outliers final: 71 residues processed: 6 average time/residue: 1.0543 time to fit residues: 12.1307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 215 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 chunk 207 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 221 optimal weight: 7.9990 chunk 237 optimal weight: 0.8980 chunk 172 optimal weight: 0.5980 chunk 32 optimal weight: 6.9990 chunk 273 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN C 277 GLN ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 470 HIS ** I 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 59 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 29257 Z= 0.174 Angle : 0.539 11.002 39649 Z= 0.271 Chirality : 0.043 0.171 4628 Planarity : 0.004 0.053 5049 Dihedral : 4.058 31.276 3990 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.36 % Favored : 95.59 % Rotamer Outliers : 2.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.65 (0.15), residues: 3622 helix: 1.79 (0.14), residues: 1466 sheet: -0.06 (0.26), residues: 444 loop : -0.62 (0.15), residues: 1712 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7244 Ramachandran restraints generated. 3622 Oldfield, 0 Emsley, 3622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7244 Ramachandran restraints generated. 3622 Oldfield, 0 Emsley, 3622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 3218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 234 time to evaluate : 3.568 Fit side-chains revert: symmetry clash outliers start: 90 outliers final: 72 residues processed: 317 average time/residue: 1.3482 time to fit residues: 508.4722 Evaluate side-chains 296 residues out of total 3218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 224 time to evaluate : 3.617 Switching outliers to nearest non-outliers outliers start: 72 outliers final: 71 residues processed: 1 average time/residue: 0.4257 time to fit residues: 5.5680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 316 optimal weight: 6.9990 chunk 333 optimal weight: 3.9990 chunk 304 optimal weight: 5.9990 chunk 324 optimal weight: 7.9990 chunk 195 optimal weight: 10.0000 chunk 141 optimal weight: 5.9990 chunk 254 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 chunk 292 optimal weight: 0.9980 chunk 306 optimal weight: 4.9990 chunk 323 optimal weight: 0.9980 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 GLN E 347 GLN ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 470 HIS ** I 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 218 ASN L 59 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 29257 Z= 0.248 Angle : 0.583 14.914 39649 Z= 0.292 Chirality : 0.045 0.171 4628 Planarity : 0.004 0.053 5049 Dihedral : 4.184 32.559 3990 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.72 % Favored : 95.23 % Rotamer Outliers : 2.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.62 (0.15), residues: 3622 helix: 1.76 (0.14), residues: 1466 sheet: -0.13 (0.25), residues: 448 loop : -0.61 (0.15), residues: 1708 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7244 Ramachandran restraints generated. 3622 Oldfield, 0 Emsley, 3622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7244 Ramachandran restraints generated. 3622 Oldfield, 0 Emsley, 3622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 3218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 236 time to evaluate : 3.927 Fit side-chains revert: symmetry clash outliers start: 85 outliers final: 76 residues processed: 315 average time/residue: 1.3659 time to fit residues: 508.0153 Evaluate side-chains 307 residues out of total 3218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 231 time to evaluate : 3.603 Switching outliers to nearest non-outliers outliers start: 76 outliers final: 74 residues processed: 2 average time/residue: 1.5864 time to fit residues: 8.3800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 212 optimal weight: 4.9990 chunk 342 optimal weight: 6.9990 chunk 209 optimal weight: 0.6980 chunk 162 optimal weight: 1.9990 chunk 238 optimal weight: 0.9990 chunk 359 optimal weight: 10.0000 chunk 331 optimal weight: 0.9980 chunk 286 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 221 optimal weight: 3.9990 chunk 175 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 GLN E 347 GLN ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 470 HIS ** I 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 59 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 29257 Z= 0.180 Angle : 0.561 15.208 39649 Z= 0.280 Chirality : 0.044 0.182 4628 Planarity : 0.004 0.053 5049 Dihedral : 4.070 30.927 3990 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.50 % Favored : 95.48 % Rotamer Outliers : 2.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.75 (0.15), residues: 3622 helix: 1.87 (0.14), residues: 1465 sheet: 0.05 (0.26), residues: 434 loop : -0.57 (0.15), residues: 1723 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7244 Ramachandran restraints generated. 3622 Oldfield, 0 Emsley, 3622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7244 Ramachandran restraints generated. 3622 Oldfield, 0 Emsley, 3622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 3218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 237 time to evaluate : 3.486 Fit side-chains revert: symmetry clash outliers start: 79 outliers final: 76 residues processed: 313 average time/residue: 1.3840 time to fit residues: 513.1727 Evaluate side-chains 306 residues out of total 3218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 230 time to evaluate : 3.836 Switching outliers to nearest non-outliers outliers start: 76 outliers final: 74 residues processed: 2 average time/residue: 0.4834 time to fit residues: 6.4264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 227 optimal weight: 5.9990 chunk 305 optimal weight: 9.9990 chunk 87 optimal weight: 5.9990 chunk 264 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 79 optimal weight: 8.9990 chunk 286 optimal weight: 2.9990 chunk 120 optimal weight: 6.9990 chunk 294 optimal weight: 0.8980 chunk 36 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 GLN E 347 GLN E 470 HIS ** I 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 218 ASN L 59 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.107923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.071453 restraints weight = 117784.624| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 3.59 r_work: 0.2828 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2838 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2838 r_free = 0.2838 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2838 r_free = 0.2838 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2838 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.103 29257 Z= 0.457 Angle : 0.674 12.744 39649 Z= 0.341 Chirality : 0.049 0.195 4628 Planarity : 0.004 0.055 5049 Dihedral : 4.572 34.875 3990 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.16 % Favored : 94.78 % Rotamer Outliers : 2.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.36 (0.14), residues: 3622 helix: 1.48 (0.14), residues: 1478 sheet: -0.26 (0.25), residues: 454 loop : -0.70 (0.15), residues: 1690 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9759.53 seconds wall clock time: 175 minutes 6.98 seconds (10506.98 seconds total)