Starting phenix.real_space_refine on Sat Feb 17 05:56:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7un9_26617/02_2024/7un9_26617_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7un9_26617/02_2024/7un9_26617.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7un9_26617/02_2024/7un9_26617_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7un9_26617/02_2024/7un9_26617_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7un9_26617/02_2024/7un9_26617_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7un9_26617/02_2024/7un9_26617.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7un9_26617/02_2024/7un9_26617.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7un9_26617/02_2024/7un9_26617_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7un9_26617/02_2024/7un9_26617_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.061 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 73 5.16 5 C 11233 2.51 5 N 2947 2.21 5 O 3410 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 182": "OE1" <-> "OE2" Residue "A ASP 194": "OD1" <-> "OD2" Residue "A GLU 269": "OE1" <-> "OE2" Residue "A TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 259": "OD1" <-> "OD2" Residue "B GLU 269": "OE1" <-> "OE2" Residue "B ASP 285": "OD1" <-> "OD2" Residue "B PHE 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 79": "OD1" <-> "OD2" Residue "G GLU 171": "OE1" <-> "OE2" Residue "G GLU 177": "OE1" <-> "OE2" Residue "G ASP 203": "OD1" <-> "OD2" Residue "G TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 254": "OD1" <-> "OD2" Residue "H GLU 84": "OE1" <-> "OE2" Residue "H TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 172": "OE1" <-> "OE2" Residue "H GLU 180": "OE1" <-> "OE2" Residue "H ASP 194": "OD1" <-> "OD2" Residue "H GLU 199": "OE1" <-> "OE2" Residue "H PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 254": "OD1" <-> "OD2" Residue "H ASP 283": "OD1" <-> "OD2" Residue "C GLU 172": "OE1" <-> "OE2" Residue "C PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 287": "OD1" <-> "OD2" Residue "C TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 259": "OD1" <-> "OD2" Residue "D GLU 269": "OE1" <-> "OE2" Residue "D PHE 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 182": "OE1" <-> "OE2" Residue "I TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 259": "OD1" <-> "OD2" Residue "I GLU 269": "OE1" <-> "OE2" Residue "I ASP 283": "OD1" <-> "OD2" Residue "I PHE 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 172": "OE1" <-> "OE2" Residue "J GLU 180": "OE1" <-> "OE2" Residue "J PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 283": "OD1" <-> "OD2" Residue "J ASP 287": "OD1" <-> "OD2" Residue "J GLU 295": "OE1" <-> "OE2" Residue "E GLU 177": "OE1" <-> "OE2" Residue "E ASP 203": "OD1" <-> "OD2" Residue "E PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 259": "OD1" <-> "OD2" Residue "E TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 269": "OE1" <-> "OE2" Residue "K GLU 171": "OE1" <-> "OE2" Residue "K ASP 202": "OD1" <-> "OD2" Residue "K PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 199": "OE1" <-> "OE2" Residue "L PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 243": "OD1" <-> "OD2" Residue "L PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17675 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 1345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1345 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 7, 'TRANS': 163} Chain breaks: 2 Chain: "B" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1388 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 9, 'TRANS': 167} Chain: "G" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1740 Classifications: {'peptide': 241} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 9, 'TRANS': 231} Chain breaks: 9 Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'UNK:plan-1': 55} Unresolved non-hydrogen planarities: 55 Chain: "H" Number of atoms: 1980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 1980 Classifications: {'peptide': 261} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain breaks: 7 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'UNK:plan-1': 28} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 1345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1345 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 7, 'TRANS': 163} Chain breaks: 2 Chain: "D" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1388 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 9, 'TRANS': 167} Chain: "I" Number of atoms: 1352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1352 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 8, 'TRANS': 163} Chain breaks: 1 Chain: "J" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1388 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 9, 'TRANS': 167} Chain: "E" Number of atoms: 1345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1345 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 7, 'TRANS': 163} Chain breaks: 2 Chain: "F" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1388 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 9, 'TRANS': 167} Chain: "K" Number of atoms: 1352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1352 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 8, 'TRANS': 163} Chain breaks: 1 Chain: "L" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1388 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 9, 'TRANS': 167} Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'C2E': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'C2E': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'C2E': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'C2E': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'C2E': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'C2E': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.53, per 1000 atoms: 0.54 Number of scatterers: 17675 At special positions: 0 Unit cell: (113.025, 136.95, 137.775, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 73 16.00 P 12 15.00 O 3410 8.00 N 2947 7.00 C 11233 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: 7.03 Conformation dependent library (CDL) restraints added in 3.1 seconds 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4194 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 70 helices and 27 sheets defined 42.1% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.05 Creating SS restraints... Processing helix chain 'A' and resid 155 through 164 Processing helix chain 'A' and resid 166 through 176 Processing helix chain 'A' and resid 207 through 216 Processing helix chain 'A' and resid 262 through 274 Processing helix chain 'A' and resid 284 through 305 Processing helix chain 'B' and resid 154 through 164 Processing helix chain 'B' and resid 166 through 176 Processing helix chain 'B' and resid 207 through 216 removed outlier: 3.701A pdb=" N LYS B 215 " --> pdb=" O THR B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 274 removed outlier: 4.185A pdb=" N LYS B 272 " --> pdb=" O GLU B 269 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR B 274 " --> pdb=" O LEU B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 306 Processing helix chain 'G' and resid 14 through 22 Processing helix chain 'G' and resid 45 through 52 Processing helix chain 'G' and resid 74 through 85 Processing helix chain 'G' and resid 134 through 143 Processing helix chain 'G' and resid 154 through 164 Processing helix chain 'G' and resid 166 through 176 Processing helix chain 'G' and resid 206 through 217 Processing helix chain 'G' and resid 262 through 274 removed outlier: 4.185A pdb=" N LYS G 272 " --> pdb=" O GLU G 269 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU G 273 " --> pdb=" O SER G 270 " (cutoff:3.500A) Processing helix chain 'G' and resid 284 through 307 Processing helix chain 'G' and resid 309 through 311 No H-bonds generated for 'chain 'G' and resid 309 through 311' Processing helix chain 'H' and resid 15 through 22 Processing helix chain 'H' and resid 45 through 50 Processing helix chain 'H' and resid 75 through 87 Processing helix chain 'H' and resid 129 through 144 removed outlier: 3.578A pdb=" N SER H 135 " --> pdb=" O LYS H 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 154 through 164 Processing helix chain 'H' and resid 166 through 176 Processing helix chain 'H' and resid 207 through 216 Processing helix chain 'H' and resid 262 through 274 removed outlier: 4.358A pdb=" N LEU H 271 " --> pdb=" O VAL H 268 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LYS H 272 " --> pdb=" O GLU H 269 " (cutoff:3.500A) Processing helix chain 'H' and resid 284 through 306 Processing helix chain 'C' and resid 154 through 164 Processing helix chain 'C' and resid 166 through 176 Processing helix chain 'C' and resid 207 through 216 Processing helix chain 'C' and resid 262 through 274 Processing helix chain 'C' and resid 284 through 306 Processing helix chain 'D' and resid 154 through 164 Processing helix chain 'D' and resid 166 through 176 Processing helix chain 'D' and resid 207 through 216 removed outlier: 3.704A pdb=" N LYS D 215 " --> pdb=" O THR D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 274 removed outlier: 4.077A pdb=" N LYS D 272 " --> pdb=" O GLU D 269 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR D 274 " --> pdb=" O LEU D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 307 Processing helix chain 'I' and resid 154 through 164 Processing helix chain 'I' and resid 166 through 176 Processing helix chain 'I' and resid 206 through 216 Processing helix chain 'I' and resid 262 through 274 removed outlier: 4.041A pdb=" N LYS I 272 " --> pdb=" O GLU I 269 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU I 273 " --> pdb=" O SER I 270 " (cutoff:3.500A) Processing helix chain 'I' and resid 284 through 307 Processing helix chain 'I' and resid 309 through 311 No H-bonds generated for 'chain 'I' and resid 309 through 311' Processing helix chain 'J' and resid 154 through 164 Processing helix chain 'J' and resid 166 through 176 Processing helix chain 'J' and resid 207 through 216 Processing helix chain 'J' and resid 262 through 274 removed outlier: 4.166A pdb=" N LEU J 271 " --> pdb=" O VAL J 268 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS J 272 " --> pdb=" O GLU J 269 " (cutoff:3.500A) Processing helix chain 'J' and resid 284 through 307 Processing helix chain 'E' and resid 155 through 164 Processing helix chain 'E' and resid 166 through 176 Processing helix chain 'E' and resid 207 through 216 Processing helix chain 'E' and resid 262 through 274 Processing helix chain 'E' and resid 284 through 305 Processing helix chain 'F' and resid 154 through 164 Processing helix chain 'F' and resid 166 through 176 Processing helix chain 'F' and resid 207 through 216 Processing helix chain 'F' and resid 262 through 274 removed outlier: 4.243A pdb=" N LYS F 272 " --> pdb=" O GLU F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 307 Processing helix chain 'K' and resid 154 through 164 Processing helix chain 'K' and resid 166 through 176 Processing helix chain 'K' and resid 207 through 216 Processing helix chain 'K' and resid 262 through 274 removed outlier: 4.080A pdb=" N LYS K 272 " --> pdb=" O GLU K 269 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU K 273 " --> pdb=" O SER K 270 " (cutoff:3.500A) Processing helix chain 'K' and resid 284 through 307 Processing helix chain 'L' and resid 154 through 164 Processing helix chain 'L' and resid 166 through 176 Processing helix chain 'L' and resid 207 through 216 Processing helix chain 'L' and resid 262 through 274 removed outlier: 3.976A pdb=" N LEU L 271 " --> pdb=" O VAL L 268 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LYS L 272 " --> pdb=" O GLU L 269 " (cutoff:3.500A) Processing helix chain 'L' and resid 284 through 307 Processing sheet with id= A, first strand: chain 'A' and resid 178 through 181 Processing sheet with id= B, first strand: chain 'A' and resid 220 through 222 removed outlier: 4.138A pdb=" N HIS A 239 " --> pdb=" O LEU A 258 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 184 through 187 Processing sheet with id= D, first strand: chain 'B' and resid 255 through 259 Processing sheet with id= E, first strand: chain 'G' and resid 58 through 61 removed outlier: 6.702A pdb=" N UNK G 98 " --> pdb=" O UNK G 59 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N UNK G 61 " --> pdb=" O UNK G 98 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N UNK G 100 " --> pdb=" O UNK G 61 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'G' and resid 178 through 181 Processing sheet with id= G, first strand: chain 'G' and resid 220 through 222 removed outlier: 4.276A pdb=" N HIS G 239 " --> pdb=" O LEU G 258 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'H' and resid 59 through 61 Processing sheet with id= I, first strand: chain 'H' and resid 178 through 181 Processing sheet with id= J, first strand: chain 'H' and resid 220 through 222 removed outlier: 4.167A pdb=" N HIS H 239 " --> pdb=" O LEU H 258 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 178 through 181 Processing sheet with id= L, first strand: chain 'C' and resid 255 through 260 Processing sheet with id= M, first strand: chain 'C' and resid 220 through 222 Processing sheet with id= N, first strand: chain 'D' and resid 178 through 181 Processing sheet with id= O, first strand: chain 'D' and resid 315 through 318 removed outlier: 8.900A pdb=" N ASN D 316 " --> pdb=" O PHE D 191 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL D 193 " --> pdb=" O ASN D 316 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N LEU D 318 " --> pdb=" O VAL D 193 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N VAL D 195 " --> pdb=" O LEU D 318 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE D 255 " --> pdb=" O ARG D 192 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ASP D 194 " --> pdb=" O ILE D 255 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU D 257 " --> pdb=" O ASP D 194 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL D 196 " --> pdb=" O LEU D 257 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ASP D 259 " --> pdb=" O VAL D 196 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N HIS D 239 " --> pdb=" O LEU D 258 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'I' and resid 178 through 181 Processing sheet with id= Q, first strand: chain 'I' and resid 220 through 222 removed outlier: 4.303A pdb=" N HIS I 239 " --> pdb=" O LEU I 258 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'J' and resid 178 through 181 Processing sheet with id= S, first strand: chain 'J' and resid 220 through 223 removed outlier: 9.119A pdb=" N ILE J 260 " --> pdb=" O PRO J 237 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N HIS J 239 " --> pdb=" O LEU J 258 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 178 through 181 Processing sheet with id= U, first strand: chain 'E' and resid 220 through 222 removed outlier: 3.926A pdb=" N HIS E 239 " --> pdb=" O LEU E 258 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 178 through 181 Processing sheet with id= W, first strand: chain 'F' and resid 315 through 318 removed outlier: 8.819A pdb=" N ASN F 316 " --> pdb=" O PHE F 191 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL F 193 " --> pdb=" O ASN F 316 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N LEU F 318 " --> pdb=" O VAL F 193 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N VAL F 195 " --> pdb=" O LEU F 318 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE F 255 " --> pdb=" O ARG F 192 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ASP F 194 " --> pdb=" O ILE F 255 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU F 257 " --> pdb=" O ASP F 194 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL F 196 " --> pdb=" O LEU F 257 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ASP F 259 " --> pdb=" O VAL F 196 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N HIS F 239 " --> pdb=" O LEU F 258 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'K' and resid 178 through 181 Processing sheet with id= Y, first strand: chain 'K' and resid 220 through 223 removed outlier: 4.165A pdb=" N HIS K 239 " --> pdb=" O LEU K 258 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'L' and resid 178 through 181 Processing sheet with id= AA, first strand: chain 'L' and resid 220 through 222 removed outlier: 3.976A pdb=" N HIS L 239 " --> pdb=" O LEU L 258 " (cutoff:3.500A) 852 hydrogen bonds defined for protein. 2154 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: 5.05 Time building geometry restraints manager: 7.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3449 1.33 - 1.45: 4098 1.45 - 1.57: 10315 1.57 - 1.69: 42 1.69 - 1.81: 109 Bond restraints: 18013 Sorted by residual: bond pdb=" C3A C2E F 401 " pdb=" C4A C2E F 401 " ideal model delta sigma weight residual 1.223 1.641 -0.418 2.00e-02 2.50e+03 4.38e+02 bond pdb=" C3A C2E K 401 " pdb=" C4A C2E K 401 " ideal model delta sigma weight residual 1.223 1.641 -0.418 2.00e-02 2.50e+03 4.37e+02 bond pdb=" C3A C2E C 401 " pdb=" C4A C2E C 401 " ideal model delta sigma weight residual 1.223 1.641 -0.418 2.00e-02 2.50e+03 4.37e+02 bond pdb=" C3A C2E A 401 " pdb=" C4A C2E A 401 " ideal model delta sigma weight residual 1.223 1.641 -0.418 2.00e-02 2.50e+03 4.36e+02 bond pdb=" C3A C2E I 401 " pdb=" C4A C2E I 401 " ideal model delta sigma weight residual 1.223 1.640 -0.417 2.00e-02 2.50e+03 4.35e+02 ... (remaining 18008 not shown) Histogram of bond angle deviations from ideal: 100.20 - 106.86: 568 106.86 - 113.51: 10073 113.51 - 120.17: 6089 120.17 - 126.82: 7565 126.82 - 133.48: 152 Bond angle restraints: 24447 Sorted by residual: angle pdb=" C1' C2E G 401 " pdb=" N9 C2E G 401 " pdb=" C4 C2E G 401 " ideal model delta sigma weight residual 152.55 125.04 27.51 3.00e+00 1.11e-01 8.41e+01 angle pdb=" C1' C2E C 401 " pdb=" N9 C2E C 401 " pdb=" C8 C2E C 401 " ideal model delta sigma weight residual 98.76 126.25 -27.49 3.00e+00 1.11e-01 8.39e+01 angle pdb=" C1' C2E C 401 " pdb=" N9 C2E C 401 " pdb=" C4 C2E C 401 " ideal model delta sigma weight residual 152.55 125.10 27.45 3.00e+00 1.11e-01 8.37e+01 angle pdb=" C1' C2E G 401 " pdb=" N9 C2E G 401 " pdb=" C8 C2E G 401 " ideal model delta sigma weight residual 98.76 126.19 -27.43 3.00e+00 1.11e-01 8.36e+01 angle pdb=" C1' C2E I 401 " pdb=" N9 C2E I 401 " pdb=" C4 C2E I 401 " ideal model delta sigma weight residual 152.55 125.24 27.31 3.00e+00 1.11e-01 8.29e+01 ... (remaining 24442 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.34: 10391 29.34 - 58.67: 341 58.67 - 88.01: 40 88.01 - 117.35: 13 117.35 - 146.68: 18 Dihedral angle restraints: 10803 sinusoidal: 4303 harmonic: 6500 Sorted by residual: dihedral pdb=" CA ASP F 243 " pdb=" C ASP F 243 " pdb=" N PRO F 244 " pdb=" CA PRO F 244 " ideal model delta harmonic sigma weight residual 180.00 156.26 23.74 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" O4' C2E F 401 " pdb=" C4' C2E F 401 " pdb=" C5' C2E F 401 " pdb=" O5' C2E F 401 " ideal model delta sinusoidal sigma weight residual 169.91 -43.41 -146.68 1 3.00e+01 1.11e-03 1.96e+01 dihedral pdb=" O4' C2E C 401 " pdb=" C4' C2E C 401 " pdb=" C5' C2E C 401 " pdb=" O5' C2E C 401 " ideal model delta sinusoidal sigma weight residual 169.91 -45.09 -145.00 1 3.00e+01 1.11e-03 1.94e+01 ... (remaining 10800 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2397 0.052 - 0.103: 343 0.103 - 0.155: 100 0.155 - 0.207: 0 0.207 - 0.258: 1 Chirality restraints: 2841 Sorted by residual: chirality pdb=" CA ASP A 243 " pdb=" N ASP A 243 " pdb=" C ASP A 243 " pdb=" CB ASP A 243 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA ILE H 260 " pdb=" N ILE H 260 " pdb=" C ILE H 260 " pdb=" CB ILE H 260 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.93e-01 chirality pdb=" CA ILE L 260 " pdb=" N ILE L 260 " pdb=" C ILE L 260 " pdb=" CB ILE L 260 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.64e-01 ... (remaining 2838 not shown) Planarity restraints: 3073 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER K 251 " -0.075 5.00e-02 4.00e+02 1.12e-01 2.00e+01 pdb=" N PRO K 252 " 0.193 5.00e-02 4.00e+02 pdb=" CA PRO K 252 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO K 252 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP K 243 " 0.055 5.00e-02 4.00e+02 8.32e-02 1.11e+01 pdb=" N PRO K 244 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO K 244 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO K 244 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP F 243 " 0.048 5.00e-02 4.00e+02 7.27e-02 8.46e+00 pdb=" N PRO F 244 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO F 244 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO F 244 " 0.040 5.00e-02 4.00e+02 ... (remaining 3070 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 69 2.46 - 3.07: 12496 3.07 - 3.68: 26187 3.68 - 4.29: 39530 4.29 - 4.90: 66380 Nonbonded interactions: 144662 Sorted by model distance: nonbonded pdb=" OG SER H 154 " pdb=" OE1 GLU H 293 " model vdw 1.849 2.440 nonbonded pdb=" OG SER J 154 " pdb=" OE1 GLU J 293 " model vdw 1.912 2.440 nonbonded pdb=" OG SER C 154 " pdb=" OE1 GLU C 293 " model vdw 1.912 2.440 nonbonded pdb=" OH TYR I 162 " pdb=" OG1 THR I 311 " model vdw 2.054 2.440 nonbonded pdb=" OG SER A 190 " pdb=" OD1 ASP A 254 " model vdw 2.062 2.440 ... (remaining 144657 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 146 through 322) selection = (chain 'B' and (resid 146 through 226 or resid 232 through 275 or resid 277 thro \ ugh 322)) selection = (chain 'C' and resid 146 through 322) selection = (chain 'D' and (resid 146 through 226 or resid 232 through 275 or resid 277 thro \ ugh 322)) selection = chain 'E' selection = (chain 'F' and (resid 146 through 226 or resid 232 through 275 or resid 277 thro \ ugh 322)) selection = (chain 'I' and (resid 146 through 275 or resid 277 through 322)) selection = (chain 'J' and (resid 146 through 226 or resid 232 through 275 or resid 277 thro \ ugh 322)) selection = (chain 'K' and (resid 146 through 275 or resid 277 through 322)) selection = (chain 'L' and (resid 146 through 226 or resid 232 through 275 or resid 277 thro \ ugh 322)) } ncs_group { reference = (chain 'G' and (resid 13 through 56 or resid 74 through 86 or resid 146 through \ 322)) selection = (chain 'H' and (resid 7 through 51 or resid 74 through 86 or resid 146 through 2 \ 26 or resid 232 through 322)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.550 Check model and map are aligned: 0.250 Set scattering table: 0.160 Process input model: 46.490 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.070 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:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 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 : 0.017 0.418 18013 Z= 1.121 Angle : 0.897 27.508 24447 Z= 0.379 Chirality : 0.041 0.258 2841 Planarity : 0.005 0.112 3073 Dihedral : 16.414 146.683 6609 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.05 % Allowed : 0.10 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.18), residues: 2111 helix: 1.90 (0.17), residues: 885 sheet: -0.10 (0.26), residues: 372 loop : -0.57 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 256 PHE 0.013 0.001 PHE J 191 TYR 0.024 0.001 TYR J 162 ARG 0.009 0.001 ARG F 168 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 445 time to evaluate : 2.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 LYS cc_start: 0.8191 (pptt) cc_final: 0.7594 (ptpt) REVERT: A 293 GLU cc_start: 0.7575 (mm-30) cc_final: 0.7035 (mm-30) REVERT: B 177 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7418 (mt-10) REVERT: B 291 MET cc_start: 0.7425 (ppp) cc_final: 0.7123 (ttt) REVERT: H 63 LYS cc_start: 0.3431 (pttp) cc_final: 0.1994 (mtmm) REVERT: H 230 LEU cc_start: 0.7541 (mm) cc_final: 0.7285 (mm) REVERT: H 287 ASP cc_start: 0.7129 (m-30) cc_final: 0.6546 (m-30) REVERT: D 154 SER cc_start: 0.8808 (p) cc_final: 0.8600 (m) REVERT: D 192 ARG cc_start: 0.7909 (ptm160) cc_final: 0.7449 (ptm160) REVERT: D 225 CYS cc_start: 0.7228 (m) cc_final: 0.6710 (m) REVERT: D 259 ASP cc_start: 0.8135 (t70) cc_final: 0.7725 (t70) REVERT: D 287 ASP cc_start: 0.7915 (m-30) cc_final: 0.7684 (m-30) REVERT: I 187 LYS cc_start: 0.7281 (mmtm) cc_final: 0.6926 (mmtm) REVERT: I 211 THR cc_start: 0.8481 (m) cc_final: 0.8279 (m) REVERT: I 290 GLU cc_start: 0.8232 (tt0) cc_final: 0.7725 (tt0) REVERT: J 148 GLN cc_start: 0.8578 (pt0) cc_final: 0.8281 (pt0) REVERT: J 256 HIS cc_start: 0.8110 (t-170) cc_final: 0.7876 (t-170) REVERT: J 291 MET cc_start: 0.6898 (mmt) cc_final: 0.6232 (mmm) REVERT: E 257 LEU cc_start: 0.8719 (mp) cc_final: 0.8511 (mp) REVERT: E 262 SER cc_start: 0.8508 (m) cc_final: 0.8085 (t) REVERT: E 287 ASP cc_start: 0.7639 (t0) cc_final: 0.7395 (t0) REVERT: F 210 THR cc_start: 0.8722 (m) cc_final: 0.8502 (m) REVERT: F 290 GLU cc_start: 0.8225 (tt0) cc_final: 0.8014 (tt0) REVERT: K 214 ASN cc_start: 0.8881 (m-40) cc_final: 0.8402 (m-40) REVERT: K 285 ASP cc_start: 0.8355 (m-30) cc_final: 0.8064 (m-30) REVERT: L 269 GLU cc_start: 0.7523 (tp30) cc_final: 0.7320 (tp30) outliers start: 1 outliers final: 0 residues processed: 445 average time/residue: 0.3101 time to fit residues: 206.1834 Evaluate side-chains 344 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 344 time to evaluate : 1.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 0.0000 chunk 148 optimal weight: 1.9990 chunk 82 optimal weight: 0.0000 chunk 50 optimal weight: 6.9990 chunk 100 optimal weight: 7.9990 chunk 79 optimal weight: 0.7980 chunk 153 optimal weight: 0.0670 chunk 59 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 114 optimal weight: 4.9990 chunk 177 optimal weight: 0.9980 overall best weight: 0.3526 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 ASN G 148 GLN G 278 ASN H 163 ASN H 320 ASN ** C 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 320 ASN D 163 ASN D 278 ASN D 296 ASN ** I 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 163 ASN ** J 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 ASN E 320 ASN F 214 ASN L 163 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 18013 Z= 0.161 Angle : 0.506 9.300 24447 Z= 0.251 Chirality : 0.041 0.152 2841 Planarity : 0.004 0.068 3073 Dihedral : 15.099 145.935 2478 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.56 % Allowed : 7.66 % Favored : 90.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.18), residues: 2111 helix: 1.98 (0.17), residues: 888 sheet: -0.25 (0.26), residues: 396 loop : -0.45 (0.21), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 239 PHE 0.021 0.001 PHE K 209 TYR 0.019 0.001 TYR J 162 ARG 0.006 0.000 ARG I 292 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 390 time to evaluate : 2.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7399 (mt-10) REVERT: H 63 LYS cc_start: 0.3612 (pttp) cc_final: 0.2289 (mtmm) REVERT: C 146 MET cc_start: 0.6839 (tpp) cc_final: 0.6348 (tpp) REVERT: D 192 ARG cc_start: 0.7804 (ptm160) cc_final: 0.7578 (ptm160) REVERT: D 225 CYS cc_start: 0.7256 (m) cc_final: 0.6650 (m) REVERT: D 259 ASP cc_start: 0.8155 (t70) cc_final: 0.7750 (t70) REVERT: D 287 ASP cc_start: 0.7848 (m-30) cc_final: 0.7130 (m-30) REVERT: I 184 LYS cc_start: 0.6928 (mtpp) cc_final: 0.5919 (ttpp) REVERT: I 187 LYS cc_start: 0.7386 (mmtm) cc_final: 0.6983 (mmtm) REVERT: I 199 GLU cc_start: 0.6284 (pt0) cc_final: 0.5902 (pt0) REVERT: I 290 GLU cc_start: 0.8111 (tt0) cc_final: 0.7551 (tt0) REVERT: J 291 MET cc_start: 0.7005 (mmt) cc_final: 0.6581 (mmm) REVERT: E 262 SER cc_start: 0.8371 (m) cc_final: 0.7942 (t) REVERT: K 285 ASP cc_start: 0.8306 (m-30) cc_final: 0.8021 (m-30) REVERT: L 269 GLU cc_start: 0.7552 (tp30) cc_final: 0.7316 (tp30) outliers start: 30 outliers final: 26 residues processed: 405 average time/residue: 0.2978 time to fit residues: 183.2815 Evaluate side-chains 372 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 346 time to evaluate : 1.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain G residue 200 THR Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 233 THR Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 278 ASN Chi-restraints excluded: chain I residue 223 THR Chi-restraints excluded: chain I residue 224 THR Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain J residue 193 VAL Chi-restraints excluded: chain E residue 148 GLN Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain K residue 200 THR Chi-restraints excluded: chain K residue 301 LEU Chi-restraints excluded: chain K residue 319 THR Chi-restraints excluded: chain L residue 212 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 148 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 178 optimal weight: 3.9990 chunk 192 optimal weight: 6.9990 chunk 158 optimal weight: 4.9990 chunk 176 optimal weight: 0.6980 chunk 60 optimal weight: 0.0770 chunk 143 optimal weight: 0.9980 overall best weight: 0.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 GLN ** H 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 163 ASN ** J 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18013 Z= 0.177 Angle : 0.496 9.785 24447 Z= 0.244 Chirality : 0.040 0.174 2841 Planarity : 0.004 0.056 3073 Dihedral : 14.398 133.453 2478 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.93 % Allowed : 10.00 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.18), residues: 2111 helix: 1.97 (0.17), residues: 891 sheet: -0.03 (0.26), residues: 381 loop : -0.49 (0.20), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS J 256 PHE 0.017 0.001 PHE I 240 TYR 0.016 0.001 TYR J 303 ARG 0.006 0.000 ARG I 292 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 372 time to evaluate : 2.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7365 (mt-10) REVERT: G 204 ASN cc_start: 0.7976 (t0) cc_final: 0.7740 (t0) REVERT: C 146 MET cc_start: 0.6875 (tpp) cc_final: 0.6377 (tpp) REVERT: D 192 ARG cc_start: 0.7792 (ptm160) cc_final: 0.7592 (ptm160) REVERT: D 287 ASP cc_start: 0.7611 (m-30) cc_final: 0.7190 (m-30) REVERT: I 184 LYS cc_start: 0.6668 (mtpp) cc_final: 0.6435 (tttt) REVERT: I 199 GLU cc_start: 0.6234 (pt0) cc_final: 0.5873 (pt0) REVERT: I 290 GLU cc_start: 0.8147 (tt0) cc_final: 0.7612 (tt0) REVERT: J 269 GLU cc_start: 0.6051 (mt-10) cc_final: 0.5829 (mt-10) REVERT: J 291 MET cc_start: 0.7019 (mmt) cc_final: 0.6401 (mmm) REVERT: E 262 SER cc_start: 0.8366 (m) cc_final: 0.7909 (t) REVERT: K 214 ASN cc_start: 0.9011 (m-40) cc_final: 0.8459 (m-40) REVERT: K 285 ASP cc_start: 0.8309 (m-30) cc_final: 0.8026 (m-30) REVERT: L 286 MET cc_start: 0.7981 (tpp) cc_final: 0.7633 (tpp) outliers start: 37 outliers final: 34 residues processed: 394 average time/residue: 0.2897 time to fit residues: 173.2252 Evaluate side-chains 380 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 346 time to evaluate : 1.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain G residue 200 THR Chi-restraints excluded: chain G residue 220 SER Chi-restraints excluded: chain G residue 254 ASP Chi-restraints excluded: chain G residue 285 ASP Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 291 MET Chi-restraints excluded: chain I residue 224 THR Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain J residue 193 VAL Chi-restraints excluded: chain E residue 148 GLN Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain K residue 301 LEU Chi-restraints excluded: chain K residue 319 THR Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 212 LEU Chi-restraints excluded: chain L residue 223 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 0.7980 chunk 134 optimal weight: 3.9990 chunk 92 optimal weight: 0.2980 chunk 19 optimal weight: 0.7980 chunk 85 optimal weight: 0.0970 chunk 119 optimal weight: 5.9990 chunk 178 optimal weight: 4.9990 chunk 189 optimal weight: 0.2980 chunk 93 optimal weight: 0.8980 chunk 169 optimal weight: 0.0470 chunk 51 optimal weight: 3.9990 overall best weight: 0.3076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 GLN H 125 GLN ** C 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 214 ASN J 163 ASN ** J 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 18013 Z= 0.130 Angle : 0.466 9.958 24447 Z= 0.231 Chirality : 0.040 0.178 2841 Planarity : 0.004 0.052 3073 Dihedral : 13.658 125.982 2478 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.98 % Allowed : 11.41 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.18), residues: 2111 helix: 2.03 (0.17), residues: 889 sheet: -0.15 (0.26), residues: 386 loop : -0.47 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS J 256 PHE 0.020 0.001 PHE I 240 TYR 0.013 0.001 TYR E 314 ARG 0.006 0.000 ARG I 292 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 388 time to evaluate : 2.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 ARG cc_start: 0.7320 (ttp-110) cc_final: 0.6908 (ttp-170) REVERT: B 177 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7378 (mt-10) REVERT: G 204 ASN cc_start: 0.8034 (t0) cc_final: 0.7758 (t0) REVERT: H 283 ASP cc_start: 0.8072 (t0) cc_final: 0.7594 (t0) REVERT: H 287 ASP cc_start: 0.7153 (m-30) cc_final: 0.6649 (m-30) REVERT: C 172 GLU cc_start: 0.7190 (mm-30) cc_final: 0.6883 (mm-30) REVERT: C 194 ASP cc_start: 0.7093 (m-30) cc_final: 0.6838 (m-30) REVERT: D 211 THR cc_start: 0.9224 (t) cc_final: 0.9012 (m) REVERT: D 287 ASP cc_start: 0.7531 (m-30) cc_final: 0.7101 (m-30) REVERT: I 199 GLU cc_start: 0.6209 (pt0) cc_final: 0.5848 (pt0) REVERT: I 215 LYS cc_start: 0.8191 (mtpp) cc_final: 0.7967 (mtpp) REVERT: I 290 GLU cc_start: 0.8123 (tt0) cc_final: 0.7614 (tt0) REVERT: J 287 ASP cc_start: 0.7980 (m-30) cc_final: 0.7571 (m-30) REVERT: J 291 MET cc_start: 0.7042 (mmt) cc_final: 0.6449 (mmm) REVERT: F 291 MET cc_start: 0.7499 (ttt) cc_final: 0.7176 (ttm) REVERT: K 285 ASP cc_start: 0.8265 (m-30) cc_final: 0.7978 (m-30) REVERT: L 286 MET cc_start: 0.7955 (tpp) cc_final: 0.7541 (tpp) outliers start: 38 outliers final: 25 residues processed: 409 average time/residue: 0.2973 time to fit residues: 183.8377 Evaluate side-chains 383 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 358 time to evaluate : 2.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain G residue 220 SER Chi-restraints excluded: chain G residue 285 ASP Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 291 MET Chi-restraints excluded: chain I residue 223 THR Chi-restraints excluded: chain I residue 224 THR Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain J residue 151 LEU Chi-restraints excluded: chain J residue 193 VAL Chi-restraints excluded: chain E residue 148 GLN Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain K residue 200 THR Chi-restraints excluded: chain K residue 301 LEU Chi-restraints excluded: chain K residue 319 THR Chi-restraints excluded: chain L residue 212 LEU Chi-restraints excluded: chain L residue 221 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 2 optimal weight: 0.5980 chunk 141 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 161 optimal weight: 0.4980 chunk 130 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 96 optimal weight: 0.0870 chunk 170 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 overall best weight: 1.2360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN G 320 ASN H 174 HIS C 174 HIS C 320 ASN I 214 ASN J 163 ASN ** J 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18013 Z= 0.226 Angle : 0.510 9.974 24447 Z= 0.250 Chirality : 0.041 0.242 2841 Planarity : 0.004 0.063 3073 Dihedral : 13.651 126.262 2478 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.81 % Allowed : 12.60 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.18), residues: 2111 helix: 2.01 (0.17), residues: 888 sheet: -0.04 (0.26), residues: 384 loop : -0.38 (0.21), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 239 PHE 0.024 0.001 PHE J 238 TYR 0.020 0.001 TYR J 303 ARG 0.007 0.000 ARG I 292 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 350 time to evaluate : 2.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 LYS cc_start: 0.8167 (pptt) cc_final: 0.7700 (ptpt) REVERT: B 177 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7517 (mt-10) REVERT: G 204 ASN cc_start: 0.8087 (t0) cc_final: 0.7849 (t0) REVERT: G 285 ASP cc_start: 0.7924 (OUTLIER) cc_final: 0.7580 (m-30) REVERT: H 287 ASP cc_start: 0.7209 (m-30) cc_final: 0.6726 (m-30) REVERT: C 146 MET cc_start: 0.6948 (tpp) cc_final: 0.6447 (tpp) REVERT: D 287 ASP cc_start: 0.7473 (m-30) cc_final: 0.7011 (m-30) REVERT: I 199 GLU cc_start: 0.6236 (pt0) cc_final: 0.5938 (pt0) REVERT: I 215 LYS cc_start: 0.8204 (mtpp) cc_final: 0.7974 (mtpp) REVERT: I 290 GLU cc_start: 0.8203 (tt0) cc_final: 0.7682 (tt0) REVERT: J 291 MET cc_start: 0.7031 (mmt) cc_final: 0.6420 (mmm) REVERT: K 214 ASN cc_start: 0.9101 (m-40) cc_final: 0.8553 (m-40) REVERT: K 241 LYS cc_start: 0.7902 (OUTLIER) cc_final: 0.7499 (pttt) REVERT: K 285 ASP cc_start: 0.8323 (m-30) cc_final: 0.8024 (m-30) REVERT: K 305 ILE cc_start: 0.8583 (mt) cc_final: 0.8351 (mp) REVERT: L 286 MET cc_start: 0.7985 (tpp) cc_final: 0.7753 (tpp) outliers start: 54 outliers final: 41 residues processed: 384 average time/residue: 0.3436 time to fit residues: 197.9897 Evaluate side-chains 384 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 341 time to evaluate : 1.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain G residue 200 THR Chi-restraints excluded: chain G residue 220 SER Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 254 ASP Chi-restraints excluded: chain G residue 285 ASP Chi-restraints excluded: chain G residue 290 GLU Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 233 THR Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain C residue 316 ASN Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain I residue 181 LEU Chi-restraints excluded: chain I residue 223 THR Chi-restraints excluded: chain I residue 224 THR Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain J residue 193 VAL Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain E residue 148 GLN Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain K residue 200 THR Chi-restraints excluded: chain K residue 241 LYS Chi-restraints excluded: chain K residue 301 LEU Chi-restraints excluded: chain K residue 319 THR Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 212 LEU Chi-restraints excluded: chain L residue 221 LYS Chi-restraints excluded: chain L residue 223 THR Chi-restraints excluded: chain L residue 268 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 5.9990 chunk 170 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 chunk 46 optimal weight: 7.9990 chunk 189 optimal weight: 4.9990 chunk 157 optimal weight: 1.9990 chunk 87 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 99 optimal weight: 0.9980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN H 125 GLN D 278 ASN I 163 ASN I 214 ASN ** J 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 214 ASN E 174 HIS E 208 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 18013 Z= 0.359 Angle : 0.599 10.097 24447 Z= 0.293 Chirality : 0.044 0.182 2841 Planarity : 0.004 0.063 3073 Dihedral : 14.326 138.934 2478 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.59 % Allowed : 13.02 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.18), residues: 2111 helix: 1.67 (0.17), residues: 889 sheet: -0.08 (0.27), residues: 372 loop : -0.34 (0.21), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 239 PHE 0.028 0.002 PHE K 209 TYR 0.023 0.002 TYR E 162 ARG 0.009 0.001 ARG I 292 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 351 time to evaluate : 2.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 LYS cc_start: 0.8212 (pptt) cc_final: 0.7766 (ptpt) REVERT: A 192 ARG cc_start: 0.7566 (ttp-110) cc_final: 0.6854 (ttp80) REVERT: B 177 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7605 (mt-10) REVERT: B 291 MET cc_start: 0.7275 (ttt) cc_final: 0.7012 (ttp) REVERT: G 204 ASN cc_start: 0.8151 (t0) cc_final: 0.7921 (t0) REVERT: G 214 ASN cc_start: 0.8578 (m-40) cc_final: 0.8331 (m-40) REVERT: G 285 ASP cc_start: 0.7924 (OUTLIER) cc_final: 0.7645 (m-30) REVERT: H 287 ASP cc_start: 0.7271 (m-30) cc_final: 0.6797 (m-30) REVERT: C 199 GLU cc_start: 0.7071 (tp30) cc_final: 0.6835 (tp30) REVERT: C 320 ASN cc_start: 0.8136 (m110) cc_final: 0.7935 (m-40) REVERT: D 190 SER cc_start: 0.8566 (p) cc_final: 0.8318 (p) REVERT: D 287 ASP cc_start: 0.7431 (m-30) cc_final: 0.6942 (m-30) REVERT: I 187 LYS cc_start: 0.7531 (mmtm) cc_final: 0.6875 (ptpp) REVERT: I 199 GLU cc_start: 0.6362 (pt0) cc_final: 0.6057 (pt0) REVERT: I 208 ASN cc_start: 0.8639 (m110) cc_final: 0.8317 (m-40) REVERT: I 215 LYS cc_start: 0.8184 (mtpp) cc_final: 0.7910 (mtpp) REVERT: I 290 GLU cc_start: 0.8332 (tt0) cc_final: 0.7828 (tt0) REVERT: E 287 ASP cc_start: 0.7658 (t0) cc_final: 0.7379 (t0) REVERT: K 241 LYS cc_start: 0.7931 (OUTLIER) cc_final: 0.7586 (pttt) REVERT: K 285 ASP cc_start: 0.8387 (m-30) cc_final: 0.8090 (m-30) REVERT: L 269 GLU cc_start: 0.7769 (tp30) cc_final: 0.7551 (tp30) REVERT: L 302 LYS cc_start: 0.8050 (mttt) cc_final: 0.7666 (mttm) outliers start: 69 outliers final: 50 residues processed: 393 average time/residue: 0.3028 time to fit residues: 176.6119 Evaluate side-chains 391 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 339 time to evaluate : 2.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain G residue 176 SER Chi-restraints excluded: chain G residue 200 THR Chi-restraints excluded: chain G residue 220 SER Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 254 ASP Chi-restraints excluded: chain G residue 285 ASP Chi-restraints excluded: chain G residue 290 GLU Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 233 THR Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 316 ASN Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 223 THR Chi-restraints excluded: chain I residue 224 THR Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain J residue 151 LEU Chi-restraints excluded: chain J residue 193 VAL Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain E residue 148 GLN Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 180 GLU Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 200 THR Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain K residue 200 THR Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 241 LYS Chi-restraints excluded: chain K residue 319 THR Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 200 THR Chi-restraints excluded: chain L residue 221 LYS Chi-restraints excluded: chain L residue 223 THR Chi-restraints excluded: chain L residue 268 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 108 optimal weight: 0.8980 chunk 138 optimal weight: 0.3980 chunk 107 optimal weight: 0.9990 chunk 159 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 188 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 115 optimal weight: 7.9990 chunk 87 optimal weight: 7.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN H 125 GLN I 214 ASN E 208 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18013 Z= 0.179 Angle : 0.497 10.224 24447 Z= 0.247 Chirality : 0.041 0.216 2841 Planarity : 0.004 0.069 3073 Dihedral : 13.871 128.190 2478 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.28 % Allowed : 13.80 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.18), residues: 2111 helix: 1.88 (0.17), residues: 888 sheet: -0.14 (0.27), residues: 384 loop : -0.41 (0.21), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 256 PHE 0.024 0.001 PHE J 191 TYR 0.023 0.001 TYR E 162 ARG 0.008 0.000 ARG I 292 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 355 time to evaluate : 2.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 LYS cc_start: 0.8199 (pptt) cc_final: 0.7754 (ptpt) REVERT: A 192 ARG cc_start: 0.7557 (ttp-110) cc_final: 0.6920 (ttp80) REVERT: B 177 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7556 (mt-10) REVERT: B 291 MET cc_start: 0.7221 (ttt) cc_final: 0.6967 (ttp) REVERT: G 204 ASN cc_start: 0.8057 (t0) cc_final: 0.7834 (t0) REVERT: G 285 ASP cc_start: 0.7903 (OUTLIER) cc_final: 0.7625 (m-30) REVERT: H 283 ASP cc_start: 0.8244 (t0) cc_final: 0.7684 (t0) REVERT: H 287 ASP cc_start: 0.7232 (m-30) cc_final: 0.6780 (m-30) REVERT: C 199 GLU cc_start: 0.6930 (tp30) cc_final: 0.6722 (tp30) REVERT: C 320 ASN cc_start: 0.8163 (m110) cc_final: 0.7935 (m-40) REVERT: D 190 SER cc_start: 0.8609 (p) cc_final: 0.8370 (p) REVERT: D 287 ASP cc_start: 0.7440 (m-30) cc_final: 0.6954 (m-30) REVERT: I 180 GLU cc_start: 0.7056 (tp30) cc_final: 0.6855 (tp30) REVERT: I 187 LYS cc_start: 0.7509 (mmtm) cc_final: 0.6833 (ptpp) REVERT: I 199 GLU cc_start: 0.6320 (pt0) cc_final: 0.6049 (pt0) REVERT: I 215 LYS cc_start: 0.8118 (mtpp) cc_final: 0.7834 (mtpp) REVERT: I 290 GLU cc_start: 0.8270 (tt0) cc_final: 0.7839 (tt0) REVERT: J 291 MET cc_start: 0.6986 (mmt) cc_final: 0.6394 (mmm) REVERT: F 192 ARG cc_start: 0.8202 (ttp-170) cc_final: 0.7801 (ptt-90) REVERT: F 291 MET cc_start: 0.7553 (ttt) cc_final: 0.7251 (ttm) REVERT: K 285 ASP cc_start: 0.8334 (m-30) cc_final: 0.8036 (m-30) REVERT: L 275 LEU cc_start: 0.8785 (mp) cc_final: 0.8542 (mt) outliers start: 63 outliers final: 49 residues processed: 392 average time/residue: 0.3068 time to fit residues: 180.3057 Evaluate side-chains 395 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 345 time to evaluate : 1.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain G residue 176 SER Chi-restraints excluded: chain G residue 200 THR Chi-restraints excluded: chain G residue 220 SER Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 254 ASP Chi-restraints excluded: chain G residue 285 ASP Chi-restraints excluded: chain G residue 290 GLU Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 233 THR Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain H residue 293 GLU Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 291 MET Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 223 THR Chi-restraints excluded: chain I residue 224 THR Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain J residue 151 LEU Chi-restraints excluded: chain J residue 193 VAL Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 265 SER Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain K residue 200 THR Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 241 LYS Chi-restraints excluded: chain K residue 301 LEU Chi-restraints excluded: chain K residue 319 THR Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 200 THR Chi-restraints excluded: chain L residue 221 LYS Chi-restraints excluded: chain L residue 223 THR Chi-restraints excluded: chain L residue 268 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 112 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 chunk 120 optimal weight: 1.9990 chunk 128 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 chunk 17 optimal weight: 0.0030 chunk 148 optimal weight: 0.5980 overall best weight: 0.8592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 GLN H 122 ASN H 125 GLN ** C 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 HIS D 278 ASN I 214 ASN K 279 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18013 Z= 0.186 Angle : 0.498 10.449 24447 Z= 0.246 Chirality : 0.041 0.243 2841 Planarity : 0.004 0.064 3073 Dihedral : 13.618 128.099 2478 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.02 % Allowed : 14.48 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.18), residues: 2111 helix: 1.92 (0.17), residues: 888 sheet: -0.14 (0.27), residues: 384 loop : -0.39 (0.21), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 256 PHE 0.031 0.001 PHE J 191 TYR 0.027 0.001 TYR E 162 ARG 0.009 0.000 ARG I 292 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 348 time to evaluate : 2.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 LYS cc_start: 0.8188 (pptt) cc_final: 0.7754 (ptpt) REVERT: B 177 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7569 (mt-10) REVERT: B 291 MET cc_start: 0.7238 (ttt) cc_final: 0.6981 (ttp) REVERT: G 204 ASN cc_start: 0.8028 (t0) cc_final: 0.7819 (t0) REVERT: G 285 ASP cc_start: 0.7904 (OUTLIER) cc_final: 0.7623 (m-30) REVERT: H 283 ASP cc_start: 0.8232 (t0) cc_final: 0.7700 (t0) REVERT: H 287 ASP cc_start: 0.7269 (m-30) cc_final: 0.6804 (m-30) REVERT: C 146 MET cc_start: 0.6773 (tpp) cc_final: 0.6279 (tpp) REVERT: C 172 GLU cc_start: 0.7223 (mm-30) cc_final: 0.6937 (mm-30) REVERT: C 320 ASN cc_start: 0.8175 (m110) cc_final: 0.7905 (m-40) REVERT: D 190 SER cc_start: 0.8634 (p) cc_final: 0.8422 (p) REVERT: D 287 ASP cc_start: 0.7445 (m-30) cc_final: 0.6982 (m-30) REVERT: I 187 LYS cc_start: 0.7465 (mmtm) cc_final: 0.6859 (ptpp) REVERT: I 199 GLU cc_start: 0.6295 (pt0) cc_final: 0.5966 (pt0) REVERT: I 215 LYS cc_start: 0.8102 (mtpp) cc_final: 0.7891 (mtpp) REVERT: I 290 GLU cc_start: 0.8286 (tt0) cc_final: 0.7847 (tt0) REVERT: J 291 MET cc_start: 0.7021 (mmt) cc_final: 0.6433 (mmm) REVERT: E 172 GLU cc_start: 0.7374 (mp0) cc_final: 0.7119 (mp0) REVERT: F 192 ARG cc_start: 0.8171 (ttp-170) cc_final: 0.7779 (ptt-90) REVERT: F 291 MET cc_start: 0.7545 (ttt) cc_final: 0.7245 (ttm) REVERT: K 214 ASN cc_start: 0.9098 (m-40) cc_final: 0.8536 (m-40) REVERT: K 241 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7559 (pttt) REVERT: K 279 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.7625 (mm110) REVERT: K 285 ASP cc_start: 0.8344 (m-30) cc_final: 0.8038 (m-30) REVERT: L 275 LEU cc_start: 0.8754 (mp) cc_final: 0.8506 (mt) outliers start: 58 outliers final: 46 residues processed: 387 average time/residue: 0.3009 time to fit residues: 174.1409 Evaluate side-chains 391 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 342 time to evaluate : 1.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain G residue 200 THR Chi-restraints excluded: chain G residue 220 SER Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 254 ASP Chi-restraints excluded: chain G residue 265 SER Chi-restraints excluded: chain G residue 285 ASP Chi-restraints excluded: chain G residue 290 GLU Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 233 THR Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 291 MET Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 223 THR Chi-restraints excluded: chain I residue 224 THR Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain J residue 151 LEU Chi-restraints excluded: chain J residue 193 VAL Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 265 SER Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 180 GLU Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain K residue 200 THR Chi-restraints excluded: chain K residue 241 LYS Chi-restraints excluded: chain K residue 279 GLN Chi-restraints excluded: chain K residue 301 LEU Chi-restraints excluded: chain K residue 319 THR Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 200 THR Chi-restraints excluded: chain L residue 221 LYS Chi-restraints excluded: chain L residue 223 THR Chi-restraints excluded: chain L residue 268 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 0.5980 chunk 180 optimal weight: 1.9990 chunk 165 optimal weight: 5.9990 chunk 176 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 76 optimal weight: 0.1980 chunk 138 optimal weight: 0.3980 chunk 54 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 chunk 175 optimal weight: 3.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 GLN ** H 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18013 Z= 0.182 Angle : 0.497 10.201 24447 Z= 0.246 Chirality : 0.041 0.216 2841 Planarity : 0.004 0.066 3073 Dihedral : 13.476 128.934 2478 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.76 % Allowed : 14.95 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.18), residues: 2111 helix: 1.98 (0.17), residues: 883 sheet: -0.13 (0.27), residues: 384 loop : -0.37 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 256 PHE 0.034 0.001 PHE J 191 TYR 0.020 0.001 TYR E 162 ARG 0.008 0.000 ARG I 292 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 350 time to evaluate : 2.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 LYS cc_start: 0.8215 (pptt) cc_final: 0.7782 (ptpt) REVERT: B 177 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7547 (mt-10) REVERT: B 291 MET cc_start: 0.7222 (ttt) cc_final: 0.6974 (ttp) REVERT: G 204 ASN cc_start: 0.8025 (t0) cc_final: 0.7818 (t0) REVERT: G 285 ASP cc_start: 0.7894 (OUTLIER) cc_final: 0.7624 (m-30) REVERT: H 283 ASP cc_start: 0.8251 (t0) cc_final: 0.7682 (t0) REVERT: H 287 ASP cc_start: 0.7242 (m-30) cc_final: 0.6806 (m-30) REVERT: C 146 MET cc_start: 0.6806 (tpp) cc_final: 0.6313 (tpp) REVERT: C 172 GLU cc_start: 0.7258 (mm-30) cc_final: 0.6972 (mm-30) REVERT: D 287 ASP cc_start: 0.7456 (m-30) cc_final: 0.7037 (m-30) REVERT: I 187 LYS cc_start: 0.7541 (mmtm) cc_final: 0.6944 (ptpp) REVERT: I 199 GLU cc_start: 0.6335 (pt0) cc_final: 0.6023 (pt0) REVERT: I 290 GLU cc_start: 0.8279 (tt0) cc_final: 0.7854 (tt0) REVERT: J 238 PHE cc_start: 0.8293 (p90) cc_final: 0.8078 (p90) REVERT: J 291 MET cc_start: 0.6997 (mmt) cc_final: 0.6414 (mmm) REVERT: F 192 ARG cc_start: 0.8142 (ttp-170) cc_final: 0.7775 (ptt-90) REVERT: F 291 MET cc_start: 0.7545 (ttt) cc_final: 0.7239 (ttm) REVERT: K 241 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7573 (pttt) REVERT: K 285 ASP cc_start: 0.8335 (m-30) cc_final: 0.8027 (m-30) REVERT: L 184 LYS cc_start: 0.7515 (tttp) cc_final: 0.7299 (tmtt) REVERT: L 275 LEU cc_start: 0.8733 (mp) cc_final: 0.8484 (mt) outliers start: 53 outliers final: 46 residues processed: 385 average time/residue: 0.2991 time to fit residues: 172.6011 Evaluate side-chains 390 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 342 time to evaluate : 1.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain G residue 200 THR Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 254 ASP Chi-restraints excluded: chain G residue 285 ASP Chi-restraints excluded: chain G residue 290 GLU Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain G residue 321 VAL Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 233 THR Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 291 MET Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 223 THR Chi-restraints excluded: chain I residue 224 THR Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain J residue 151 LEU Chi-restraints excluded: chain J residue 193 VAL Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 265 SER Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 180 GLU Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain K residue 200 THR Chi-restraints excluded: chain K residue 241 LYS Chi-restraints excluded: chain K residue 301 LEU Chi-restraints excluded: chain K residue 319 THR Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 200 THR Chi-restraints excluded: chain L residue 221 LYS Chi-restraints excluded: chain L residue 223 THR Chi-restraints excluded: chain L residue 268 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 8.9990 chunk 186 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 88 optimal weight: 0.2980 chunk 129 optimal weight: 6.9990 chunk 195 optimal weight: 1.9990 chunk 179 optimal weight: 0.0020 chunk 155 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 overall best weight: 1.2392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 122 ASN ** H 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 320 ASN I 214 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18013 Z= 0.226 Angle : 0.522 10.024 24447 Z= 0.257 Chirality : 0.041 0.286 2841 Planarity : 0.004 0.066 3073 Dihedral : 13.505 128.912 2478 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.76 % Allowed : 15.10 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.18), residues: 2111 helix: 1.92 (0.17), residues: 883 sheet: -0.07 (0.28), residues: 375 loop : -0.31 (0.21), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 256 PHE 0.035 0.001 PHE J 191 TYR 0.033 0.001 TYR E 162 ARG 0.009 0.000 ARG I 292 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 344 time to evaluate : 1.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 LYS cc_start: 0.8228 (pptt) cc_final: 0.7784 (ptpt) REVERT: B 177 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7569 (mt-10) REVERT: B 291 MET cc_start: 0.7247 (ttt) cc_final: 0.6991 (ttp) REVERT: G 204 ASN cc_start: 0.8030 (t0) cc_final: 0.7819 (t0) REVERT: G 285 ASP cc_start: 0.7905 (OUTLIER) cc_final: 0.7620 (m-30) REVERT: H 283 ASP cc_start: 0.8266 (t0) cc_final: 0.7685 (t0) REVERT: H 287 ASP cc_start: 0.7261 (m-30) cc_final: 0.6834 (m-30) REVERT: D 287 ASP cc_start: 0.7450 (m-30) cc_final: 0.7021 (m-30) REVERT: I 168 ARG cc_start: 0.7962 (mmm-85) cc_final: 0.7749 (mmm160) REVERT: I 187 LYS cc_start: 0.7550 (mmtm) cc_final: 0.6921 (ptpp) REVERT: I 199 GLU cc_start: 0.6353 (pt0) cc_final: 0.6046 (pt0) REVERT: I 290 GLU cc_start: 0.8315 (tt0) cc_final: 0.7890 (tt0) REVERT: F 192 ARG cc_start: 0.8153 (ttp-170) cc_final: 0.7791 (ptt-90) REVERT: F 291 MET cc_start: 0.7535 (ttt) cc_final: 0.7234 (ttm) REVERT: K 241 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7632 (pttt) REVERT: K 285 ASP cc_start: 0.8362 (m-30) cc_final: 0.8061 (m-30) REVERT: L 275 LEU cc_start: 0.8745 (mp) cc_final: 0.8500 (mt) REVERT: L 302 LYS cc_start: 0.8018 (mttt) cc_final: 0.7658 (mttm) outliers start: 53 outliers final: 49 residues processed: 381 average time/residue: 0.3165 time to fit residues: 178.5794 Evaluate side-chains 391 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 340 time to evaluate : 2.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain G residue 176 SER Chi-restraints excluded: chain G residue 200 THR Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 254 ASP Chi-restraints excluded: chain G residue 265 SER Chi-restraints excluded: chain G residue 285 ASP Chi-restraints excluded: chain G residue 290 GLU Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain G residue 321 VAL Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 233 THR Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 223 THR Chi-restraints excluded: chain I residue 224 THR Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain J residue 151 LEU Chi-restraints excluded: chain J residue 193 VAL Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 265 SER Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 180 GLU Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain K residue 200 THR Chi-restraints excluded: chain K residue 241 LYS Chi-restraints excluded: chain K residue 301 LEU Chi-restraints excluded: chain K residue 319 THR Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 200 THR Chi-restraints excluded: chain L residue 221 LYS Chi-restraints excluded: chain L residue 223 THR Chi-restraints excluded: chain L residue 268 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 3.9990 chunk 165 optimal weight: 0.0470 chunk 47 optimal weight: 0.9990 chunk 143 optimal weight: 7.9990 chunk 22 optimal weight: 0.4980 chunk 43 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 chunk 65 optimal weight: 0.4980 chunk 159 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 278 ASN I 214 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.156361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.127052 restraints weight = 21642.720| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.81 r_work: 0.3259 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 18013 Z= 0.157 Angle : 0.491 10.554 24447 Z= 0.242 Chirality : 0.040 0.271 2841 Planarity : 0.004 0.064 3073 Dihedral : 13.205 129.795 2478 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.50 % Allowed : 15.52 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.18), residues: 2111 helix: 2.05 (0.17), residues: 883 sheet: -0.10 (0.27), residues: 384 loop : -0.33 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS I 256 PHE 0.032 0.001 PHE J 191 TYR 0.031 0.001 TYR E 162 ARG 0.008 0.000 ARG I 292 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4428.32 seconds wall clock time: 81 minutes 26.79 seconds (4886.79 seconds total)