Starting phenix.real_space_refine on Tue Apr 7 08:27:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7npf_12515/04_2026/7npf_12515_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7npf_12515/04_2026/7npf_12515.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7npf_12515/04_2026/7npf_12515.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7npf_12515/04_2026/7npf_12515.map" model { file = "/net/cci-nas-00/data/ceres_data/7npf_12515/04_2026/7npf_12515_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7npf_12515/04_2026/7npf_12515_neut.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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: 6 Type Number sf(0) Gaussians P 122 5.49 5 Mg 8 5.21 5 S 168 5.16 5 C 16504 2.51 5 N 4551 2.21 5 O 5420 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26773 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3070 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 404, 3065 Classifications: {'peptide': 404} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 17, 'TRANS': 386} Chain breaks: 1 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2, 'HIS:plan': 1, 'ARG:plan': 4, 'PHE:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 3, 'TRP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 88 Conformer: "B" Number of residues, atoms: 404, 3065 Classifications: {'peptide': 404} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 17, 'TRANS': 386} Chain breaks: 1 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2, 'HIS:plan': 1, 'ARG:plan': 4, 'PHE:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 3, 'TRP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 88 bond proxies already assigned to first conformer: 3118 Chain: "B" Number of atoms: 3057 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 402, 3052 Classifications: {'peptide': 402} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 17, 'TRANS': 384} Chain breaks: 1 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2, 'HIS:plan': 1, 'ARG:plan': 4, 'PHE:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 3, 'TRP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 88 Conformer: "B" Number of residues, atoms: 402, 3052 Classifications: {'peptide': 402} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 17, 'TRANS': 384} Chain breaks: 1 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2, 'HIS:plan': 1, 'ARG:plan': 4, 'PHE:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 3, 'TRP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 88 bond proxies already assigned to first conformer: 3105 Chain: "C" Number of atoms: 3070 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 404, 3065 Classifications: {'peptide': 404} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 17, 'TRANS': 386} Chain breaks: 1 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2, 'HIS:plan': 1, 'ARG:plan': 4, 'PHE:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 3, 'TRP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 88 Conformer: "B" Number of residues, atoms: 404, 3065 Classifications: {'peptide': 404} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 17, 'TRANS': 386} Chain breaks: 1 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2, 'HIS:plan': 1, 'ARG:plan': 4, 'PHE:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 3, 'TRP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 88 bond proxies already assigned to first conformer: 3118 Chain: "D" Number of atoms: 3057 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 402, 3052 Classifications: {'peptide': 402} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 17, 'TRANS': 384} Chain breaks: 1 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2, 'HIS:plan': 1, 'ARG:plan': 4, 'PHE:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 3, 'TRP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 88 Conformer: "B" Number of residues, atoms: 402, 3052 Classifications: {'peptide': 402} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 17, 'TRANS': 384} Chain breaks: 1 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2, 'HIS:plan': 1, 'ARG:plan': 4, 'PHE:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 3, 'TRP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 88 bond proxies already assigned to first conformer: 3105 Chain: "E" Number of atoms: 3070 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 404, 3065 Classifications: {'peptide': 404} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 17, 'TRANS': 386} Chain breaks: 1 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2, 'HIS:plan': 1, 'ARG:plan': 4, 'PHE:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 3, 'TRP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 88 Conformer: "B" Number of residues, atoms: 404, 3065 Classifications: {'peptide': 404} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 17, 'TRANS': 386} Chain breaks: 1 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2, 'HIS:plan': 1, 'ARG:plan': 4, 'PHE:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 3, 'TRP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 88 bond proxies already assigned to first conformer: 3118 Chain: "F" Number of atoms: 3057 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 402, 3052 Classifications: {'peptide': 402} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 17, 'TRANS': 384} Chain breaks: 1 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2, 'HIS:plan': 1, 'ARG:plan': 4, 'PHE:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 3, 'TRP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 88 Conformer: "B" Number of residues, atoms: 402, 3052 Classifications: {'peptide': 402} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 17, 'TRANS': 384} Chain breaks: 1 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2, 'HIS:plan': 1, 'ARG:plan': 4, 'PHE:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 3, 'TRP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 88 bond proxies already assigned to first conformer: 3105 Chain: "G" Number of atoms: 3070 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 404, 3065 Classifications: {'peptide': 404} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 17, 'TRANS': 386} Chain breaks: 1 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2, 'HIS:plan': 1, 'ARG:plan': 4, 'PHE:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 3, 'TRP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 88 Conformer: "B" Number of residues, atoms: 404, 3065 Classifications: {'peptide': 404} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 17, 'TRANS': 386} Chain breaks: 1 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2, 'HIS:plan': 1, 'ARG:plan': 4, 'PHE:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 3, 'TRP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 88 bond proxies already assigned to first conformer: 3118 Chain: "H" Number of atoms: 3057 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 402, 3052 Classifications: {'peptide': 402} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 17, 'TRANS': 384} Chain breaks: 1 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2, 'HIS:plan': 1, 'ARG:plan': 4, 'PHE:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 3, 'TRP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 88 Conformer: "B" Number of residues, atoms: 402, 3052 Classifications: {'peptide': 402} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 17, 'TRANS': 384} Chain breaks: 1 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2, 'HIS:plan': 1, 'ARG:plan': 4, 'PHE:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 3, 'TRP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 88 bond proxies already assigned to first conformer: 3105 Chain: "I" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 1029 Classifications: {'DNA': 49} Link IDs: {'rna3p': 48} Chain: "J" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 980 Classifications: {'DNA': 49} Link IDs: {'rna3p': 48} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N AALA A 272 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA A 272 " occ=0.50 residue: pdb=" N AALA B 272 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA B 272 " occ=0.50 residue: pdb=" N AALA C 272 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA C 272 " occ=0.50 residue: pdb=" N AALA D 272 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA D 272 " occ=0.50 residue: pdb=" N AALA E 272 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA E 272 " occ=0.50 residue: pdb=" N AALA F 272 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA F 272 " occ=0.50 residue: pdb=" N AALA G 272 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA G 272 " occ=0.50 residue: pdb=" N AALA H 272 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA H 272 " occ=0.50 Time building chain proxies: 10.61, per 1000 atoms: 0.40 Number of scatterers: 26773 At special positions: 0 Unit cell: (145.6, 141.44, 206.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 168 16.00 P 122 15.00 Mg 8 11.99 O 5420 8.00 N 4551 7.00 C 16504 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 - 3.00 Amino acid : True - 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.26 Conformation dependent library (CDL) restraints added in 2.1 seconds 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6248 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 12 sheets defined 55.7% alpha, 4.6% beta 26 base pairs and 88 stacking pairs defined. Time for finding SS restraints: 3.10 Creating SS restraints... Processing helix chain 'A' and resid 5 through 34 removed outlier: 4.719A pdb=" N GLN A 21 " --> pdb=" O GLN A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 51 Processing helix chain 'A' and resid 54 through 67 Processing helix chain 'A' and resid 83 through 93 Processing helix chain 'A' and resid 123 through 137 Processing helix chain 'A' and resid 174 through 181 Processing helix chain 'A' and resid 190 through 198 Processing helix chain 'A' and resid 213 through 216 Processing helix chain 'A' and resid 217 through 230 removed outlier: 3.838A pdb=" N ALA A 221 " --> pdb=" O ALA A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 243 removed outlier: 3.557A pdb=" N LEU A 238 " --> pdb=" O ASP A 234 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU A 239 " --> pdb=" O ILE A 235 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LYS A 240 " --> pdb=" O VAL A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 248 Processing helix chain 'A' and resid 263 through 273 removed outlier: 3.508A pdb=" N SER A 273 " --> pdb=" O ALA A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 304 Proline residue: A 298 - end of helix Processing helix chain 'A' and resid 325 through 339 Processing helix chain 'A' and resid 351 through 360 removed outlier: 3.674A pdb=" N GLU A 355 " --> pdb=" O SER A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 367 Processing helix chain 'A' and resid 375 through 400 Processing helix chain 'A' and resid 402 through 407 removed outlier: 3.798A pdb=" N GLN A 406 " --> pdb=" O SER A 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 34 removed outlier: 3.702A pdb=" N GLN B 21 " --> pdb=" O GLN B 17 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL B 22 " --> pdb=" O LEU B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 51 Processing helix chain 'B' and resid 54 through 66 Processing helix chain 'B' and resid 83 through 94 Processing helix chain 'B' and resid 123 through 137 removed outlier: 3.595A pdb=" N LEU B 137 " --> pdb=" O ALA B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 181 Processing helix chain 'B' and resid 190 through 198 Processing helix chain 'B' and resid 213 through 216 Processing helix chain 'B' and resid 217 through 230 removed outlier: 4.178A pdb=" N ALA B 221 " --> pdb=" O ALA B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 235 No H-bonds generated for 'chain 'B' and resid 233 through 235' Processing helix chain 'B' and resid 236 through 248 removed outlier: 4.299A pdb=" N LYS B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ASP B 245 " --> pdb=" O GLU B 241 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N LYS B 246 " --> pdb=" O LYS B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 251 No H-bonds generated for 'chain 'B' and resid 249 through 251' Processing helix chain 'B' and resid 263 through 273 Processing helix chain 'B' and resid 283 through 304 Proline residue: B 298 - end of helix Processing helix chain 'B' and resid 325 through 339 Processing helix chain 'B' and resid 351 through 360 removed outlier: 3.675A pdb=" N GLU B 355 " --> pdb=" O SER B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 372 Processing helix chain 'B' and resid 376 through 407 removed outlier: 4.862A pdb=" N SER B 403 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN B 406 " --> pdb=" O SER B 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 34 removed outlier: 4.719A pdb=" N GLN C 21 " --> pdb=" O GLN C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 51 Processing helix chain 'C' and resid 54 through 67 Processing helix chain 'C' and resid 83 through 93 Processing helix chain 'C' and resid 123 through 137 Processing helix chain 'C' and resid 174 through 181 Processing helix chain 'C' and resid 190 through 198 Processing helix chain 'C' and resid 213 through 216 Processing helix chain 'C' and resid 217 through 230 removed outlier: 3.838A pdb=" N ALA C 221 " --> pdb=" O ALA C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 243 removed outlier: 3.557A pdb=" N LEU C 238 " --> pdb=" O ASP C 234 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU C 239 " --> pdb=" O ILE C 235 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LYS C 240 " --> pdb=" O VAL C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 248 Processing helix chain 'C' and resid 263 through 273 removed outlier: 3.508A pdb=" N SER C 273 " --> pdb=" O ALA C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 304 Proline residue: C 298 - end of helix Processing helix chain 'C' and resid 325 through 339 Processing helix chain 'C' and resid 351 through 360 removed outlier: 3.675A pdb=" N GLU C 355 " --> pdb=" O SER C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 367 Processing helix chain 'C' and resid 375 through 400 Processing helix chain 'C' and resid 402 through 407 removed outlier: 3.798A pdb=" N GLN C 406 " --> pdb=" O SER C 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 34 removed outlier: 3.703A pdb=" N GLN D 21 " --> pdb=" O GLN D 17 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL D 22 " --> pdb=" O LEU D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 51 Processing helix chain 'D' and resid 54 through 66 Processing helix chain 'D' and resid 83 through 94 Processing helix chain 'D' and resid 123 through 137 removed outlier: 3.595A pdb=" N LEU D 137 " --> pdb=" O ALA D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 181 Processing helix chain 'D' and resid 190 through 198 Processing helix chain 'D' and resid 213 through 216 Processing helix chain 'D' and resid 217 through 230 removed outlier: 4.177A pdb=" N ALA D 221 " --> pdb=" O ALA D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 235 No H-bonds generated for 'chain 'D' and resid 233 through 235' Processing helix chain 'D' and resid 236 through 248 removed outlier: 4.299A pdb=" N LYS D 240 " --> pdb=" O VAL D 236 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ASP D 245 " --> pdb=" O GLU D 241 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N LYS D 246 " --> pdb=" O LYS D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 263 through 273 Processing helix chain 'D' and resid 283 through 304 Proline residue: D 298 - end of helix Processing helix chain 'D' and resid 325 through 339 Processing helix chain 'D' and resid 351 through 360 removed outlier: 3.674A pdb=" N GLU D 355 " --> pdb=" O SER D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 372 Processing helix chain 'D' and resid 376 through 407 removed outlier: 4.861A pdb=" N SER D 403 " --> pdb=" O SER D 399 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN D 406 " --> pdb=" O SER D 402 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 34 removed outlier: 4.719A pdb=" N GLN E 21 " --> pdb=" O GLN E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 51 Processing helix chain 'E' and resid 54 through 67 Processing helix chain 'E' and resid 83 through 93 Processing helix chain 'E' and resid 123 through 137 Processing helix chain 'E' and resid 174 through 181 Processing helix chain 'E' and resid 190 through 198 Processing helix chain 'E' and resid 213 through 216 Processing helix chain 'E' and resid 217 through 230 removed outlier: 3.839A pdb=" N ALA E 221 " --> pdb=" O ALA E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 243 removed outlier: 3.556A pdb=" N LEU E 238 " --> pdb=" O ASP E 234 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU E 239 " --> pdb=" O ILE E 235 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LYS E 240 " --> pdb=" O VAL E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 248 Processing helix chain 'E' and resid 263 through 273 removed outlier: 3.508A pdb=" N SER E 273 " --> pdb=" O ALA E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 304 Proline residue: E 298 - end of helix Processing helix chain 'E' and resid 325 through 339 Processing helix chain 'E' and resid 351 through 360 removed outlier: 3.674A pdb=" N GLU E 355 " --> pdb=" O SER E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 367 Processing helix chain 'E' and resid 375 through 400 Processing helix chain 'E' and resid 402 through 407 removed outlier: 3.798A pdb=" N GLN E 406 " --> pdb=" O SER E 402 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 34 removed outlier: 3.704A pdb=" N GLN F 21 " --> pdb=" O GLN F 17 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL F 22 " --> pdb=" O LEU F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 51 Processing helix chain 'F' and resid 54 through 66 Processing helix chain 'F' and resid 83 through 94 Processing helix chain 'F' and resid 123 through 137 removed outlier: 3.594A pdb=" N LEU F 137 " --> pdb=" O ALA F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 181 Processing helix chain 'F' and resid 190 through 198 Processing helix chain 'F' and resid 213 through 216 Processing helix chain 'F' and resid 217 through 230 removed outlier: 4.178A pdb=" N ALA F 221 " --> pdb=" O ALA F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 235 No H-bonds generated for 'chain 'F' and resid 233 through 235' Processing helix chain 'F' and resid 236 through 248 removed outlier: 4.299A pdb=" N LYS F 240 " --> pdb=" O VAL F 236 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ASP F 245 " --> pdb=" O GLU F 241 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N LYS F 246 " --> pdb=" O LYS F 242 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 251 No H-bonds generated for 'chain 'F' and resid 249 through 251' Processing helix chain 'F' and resid 263 through 273 Processing helix chain 'F' and resid 283 through 304 Proline residue: F 298 - end of helix Processing helix chain 'F' and resid 325 through 339 Processing helix chain 'F' and resid 351 through 360 removed outlier: 3.675A pdb=" N GLU F 355 " --> pdb=" O SER F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 372 Processing helix chain 'F' and resid 376 through 407 removed outlier: 4.861A pdb=" N SER F 403 " --> pdb=" O SER F 399 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN F 406 " --> pdb=" O SER F 402 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 34 removed outlier: 4.719A pdb=" N GLN G 21 " --> pdb=" O GLN G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 51 Processing helix chain 'G' and resid 54 through 67 Processing helix chain 'G' and resid 83 through 93 Processing helix chain 'G' and resid 123 through 137 Processing helix chain 'G' and resid 174 through 181 Processing helix chain 'G' and resid 190 through 198 Processing helix chain 'G' and resid 213 through 216 Processing helix chain 'G' and resid 217 through 230 removed outlier: 3.839A pdb=" N ALA G 221 " --> pdb=" O ALA G 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 243 removed outlier: 3.557A pdb=" N LEU G 238 " --> pdb=" O ASP G 234 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU G 239 " --> pdb=" O ILE G 235 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LYS G 240 " --> pdb=" O VAL G 236 " (cutoff:3.500A) Processing helix chain 'G' and resid 243 through 248 Processing helix chain 'G' and resid 263 through 273 removed outlier: 3.508A pdb=" N SER G 273 " --> pdb=" O ALA G 269 " (cutoff:3.500A) Processing helix chain 'G' and resid 283 through 304 Proline residue: G 298 - end of helix Processing helix chain 'G' and resid 325 through 339 Processing helix chain 'G' and resid 351 through 360 removed outlier: 3.674A pdb=" N GLU G 355 " --> pdb=" O SER G 351 " (cutoff:3.500A) Processing helix chain 'G' and resid 363 through 367 Processing helix chain 'G' and resid 375 through 400 Processing helix chain 'G' and resid 402 through 407 removed outlier: 3.798A pdb=" N GLN G 406 " --> pdb=" O SER G 402 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 34 removed outlier: 3.702A pdb=" N GLN H 21 " --> pdb=" O GLN H 17 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL H 22 " --> pdb=" O LEU H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 51 Processing helix chain 'H' and resid 54 through 66 Processing helix chain 'H' and resid 83 through 94 Processing helix chain 'H' and resid 123 through 137 removed outlier: 3.595A pdb=" N LEU H 137 " --> pdb=" O ALA H 133 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 181 Processing helix chain 'H' and resid 190 through 198 Processing helix chain 'H' and resid 213 through 216 Processing helix chain 'H' and resid 217 through 230 removed outlier: 4.178A pdb=" N ALA H 221 " --> pdb=" O ALA H 217 " (cutoff:3.500A) Processing helix chain 'H' and resid 233 through 235 No H-bonds generated for 'chain 'H' and resid 233 through 235' Processing helix chain 'H' and resid 236 through 248 removed outlier: 4.299A pdb=" N LYS H 240 " --> pdb=" O VAL H 236 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ASP H 245 " --> pdb=" O GLU H 241 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N LYS H 246 " --> pdb=" O LYS H 242 " (cutoff:3.500A) Processing helix chain 'H' and resid 249 through 251 No H-bonds generated for 'chain 'H' and resid 249 through 251' Processing helix chain 'H' and resid 263 through 273 Processing helix chain 'H' and resid 283 through 304 Proline residue: H 298 - end of helix Processing helix chain 'H' and resid 325 through 339 Processing helix chain 'H' and resid 351 through 360 removed outlier: 3.674A pdb=" N GLU H 355 " --> pdb=" O SER H 351 " (cutoff:3.500A) Processing helix chain 'H' and resid 368 through 372 Processing helix chain 'H' and resid 376 through 407 removed outlier: 4.861A pdb=" N SER H 403 " --> pdb=" O SER H 399 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN H 406 " --> pdb=" O SER H 402 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 111 through 115 removed outlier: 5.682A pdb=" N CYS A 146 " --> pdb=" O MET A 255 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ASP A 257 " --> pdb=" O CYS A 146 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ILE A 148 " --> pdb=" O ASP A 257 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ILE A 145 " --> pdb=" O LYS A 208 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ILE A 210 " --> pdb=" O ILE A 145 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU A 147 " --> pdb=" O ILE A 210 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 276 through 278 removed outlier: 3.842A pdb=" N ARG A 315 " --> pdb=" O LEU A 276 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 200 through 201 removed outlier: 4.401A pdb=" N LEU B 200 " --> pdb=" O THR B 209 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N THR B 209 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS B 208 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU B 147 " --> pdb=" O LYS B 208 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE B 210 " --> pdb=" O LEU B 147 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N CYS B 146 " --> pdb=" O MET B 255 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ASP B 257 " --> pdb=" O CYS B 146 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ILE B 148 " --> pdb=" O ASP B 257 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ILE B 112 " --> pdb=" O ALA B 275 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LEU B 277 " --> pdb=" O ILE B 112 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ASN B 114 " --> pdb=" O LEU B 277 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 111 through 115 removed outlier: 5.682A pdb=" N CYS C 146 " --> pdb=" O MET C 255 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ASP C 257 " --> pdb=" O CYS C 146 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ILE C 148 " --> pdb=" O ASP C 257 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N ILE C 145 " --> pdb=" O LYS C 208 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ILE C 210 " --> pdb=" O ILE C 145 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU C 147 " --> pdb=" O ILE C 210 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 276 through 278 removed outlier: 3.841A pdb=" N ARG C 315 " --> pdb=" O LEU C 276 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 200 through 201 removed outlier: 4.400A pdb=" N LEU D 200 " --> pdb=" O THR D 209 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N THR D 209 " --> pdb=" O LEU D 200 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LYS D 208 " --> pdb=" O ILE D 145 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU D 147 " --> pdb=" O LYS D 208 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE D 210 " --> pdb=" O LEU D 147 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N CYS D 146 " --> pdb=" O MET D 255 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ASP D 257 " --> pdb=" O CYS D 146 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE D 148 " --> pdb=" O ASP D 257 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ILE D 112 " --> pdb=" O ALA D 275 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LEU D 277 " --> pdb=" O ILE D 112 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ASN D 114 " --> pdb=" O LEU D 277 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 111 through 115 removed outlier: 5.682A pdb=" N CYS E 146 " --> pdb=" O MET E 255 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ASP E 257 " --> pdb=" O CYS E 146 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ILE E 148 " --> pdb=" O ASP E 257 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ILE E 145 " --> pdb=" O LYS E 208 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ILE E 210 " --> pdb=" O ILE E 145 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU E 147 " --> pdb=" O ILE E 210 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 276 through 278 removed outlier: 3.842A pdb=" N ARG E 315 " --> pdb=" O LEU E 276 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 200 through 201 removed outlier: 4.401A pdb=" N LEU F 200 " --> pdb=" O THR F 209 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N THR F 209 " --> pdb=" O LEU F 200 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS F 208 " --> pdb=" O ILE F 145 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU F 147 " --> pdb=" O LYS F 208 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE F 210 " --> pdb=" O LEU F 147 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N CYS F 146 " --> pdb=" O MET F 255 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ASP F 257 " --> pdb=" O CYS F 146 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ILE F 148 " --> pdb=" O ASP F 257 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ILE F 112 " --> pdb=" O ALA F 275 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LEU F 277 " --> pdb=" O ILE F 112 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ASN F 114 " --> pdb=" O LEU F 277 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 111 through 115 removed outlier: 5.683A pdb=" N CYS G 146 " --> pdb=" O MET G 255 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ASP G 257 " --> pdb=" O CYS G 146 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ILE G 148 " --> pdb=" O ASP G 257 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N ILE G 145 " --> pdb=" O LYS G 208 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ILE G 210 " --> pdb=" O ILE G 145 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU G 147 " --> pdb=" O ILE G 210 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 276 through 278 removed outlier: 3.842A pdb=" N ARG G 315 " --> pdb=" O LEU G 276 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 200 through 201 removed outlier: 4.401A pdb=" N LEU H 200 " --> pdb=" O THR H 209 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N THR H 209 " --> pdb=" O LEU H 200 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LYS H 208 " --> pdb=" O ILE H 145 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU H 147 " --> pdb=" O LYS H 208 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE H 210 " --> pdb=" O LEU H 147 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N CYS H 146 " --> pdb=" O MET H 255 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ASP H 257 " --> pdb=" O CYS H 146 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ILE H 148 " --> pdb=" O ASP H 257 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ILE H 112 " --> pdb=" O ALA H 275 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N LEU H 277 " --> pdb=" O ILE H 112 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ASN H 114 " --> pdb=" O LEU H 277 " (cutoff:3.500A) 1204 hydrogen bonds defined for protein. 3532 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 52 hydrogen bonds 104 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 88 stacking parallelities Total time for adding SS restraints: 4.78 Time building geometry restraints manager: 3.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 8927 1.36 - 1.50: 7561 1.50 - 1.65: 10720 1.65 - 1.80: 185 1.80 - 1.95: 111 Bond restraints: 27504 Sorted by residual: bond pdb=" C3' DT J 19 " pdb=" O3' DT J 19 " ideal model delta sigma weight residual 1.422 1.545 -0.123 3.00e-02 1.11e+03 1.68e+01 bond pdb=" C3' DA I 19 " pdb=" O3' DA I 19 " ideal model delta sigma weight residual 1.422 1.525 -0.103 3.00e-02 1.11e+03 1.19e+01 bond pdb=" C3' DA I 48 " pdb=" O3' DA I 48 " ideal model delta sigma weight residual 1.422 1.499 -0.077 3.00e-02 1.11e+03 6.66e+00 bond pdb=" C3' DT J 29 " pdb=" O3' DT J 29 " ideal model delta sigma weight residual 1.422 1.480 -0.058 3.00e-02 1.11e+03 3.73e+00 bond pdb=" C2' DA I 20 " pdb=" C1' DA I 20 " ideal model delta sigma weight residual 1.525 1.492 0.033 2.00e-02 2.50e+03 2.68e+00 ... (remaining 27499 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 37052 2.63 - 5.25: 851 5.25 - 7.88: 77 7.88 - 10.50: 1 10.50 - 13.13: 6 Bond angle restraints: 37987 Sorted by residual: angle pdb=" OP1 DT J 20 " pdb=" P DT J 20 " pdb=" O5' DT J 20 " ideal model delta sigma weight residual 109.00 95.87 13.13 3.00e+00 1.11e-01 1.92e+01 angle pdb=" N GLN F 383 " pdb=" CA GLN F 383 " pdb=" CB GLN F 383 " ideal model delta sigma weight residual 110.39 116.99 -6.60 1.66e+00 3.63e-01 1.58e+01 angle pdb=" N GLN D 383 " pdb=" CA GLN D 383 " pdb=" CB GLN D 383 " ideal model delta sigma weight residual 110.39 116.98 -6.59 1.66e+00 3.63e-01 1.57e+01 angle pdb=" N GLN H 383 " pdb=" CA GLN H 383 " pdb=" CB GLN H 383 " ideal model delta sigma weight residual 110.39 116.96 -6.57 1.66e+00 3.63e-01 1.57e+01 angle pdb=" N GLN B 383 " pdb=" CA GLN B 383 " pdb=" CB GLN B 383 " ideal model delta sigma weight residual 110.39 116.94 -6.55 1.66e+00 3.63e-01 1.56e+01 ... (remaining 37982 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.30: 15531 33.30 - 66.60: 828 66.60 - 99.90: 52 99.90 - 133.21: 1 133.21 - 166.51: 10 Dihedral angle restraints: 16422 sinusoidal: 6878 harmonic: 9544 Sorted by residual: dihedral pdb=" CA THR E 8 " pdb=" C THR E 8 " pdb=" N ILE E 9 " pdb=" CA ILE E 9 " ideal model delta harmonic sigma weight residual 180.00 141.40 38.60 0 5.00e+00 4.00e-02 5.96e+01 dihedral pdb=" CA THR C 8 " pdb=" C THR C 8 " pdb=" N ILE C 9 " pdb=" CA ILE C 9 " ideal model delta harmonic sigma weight residual 180.00 141.41 38.59 0 5.00e+00 4.00e-02 5.96e+01 dihedral pdb=" CA THR G 8 " pdb=" C THR G 8 " pdb=" N ILE G 9 " pdb=" CA ILE G 9 " ideal model delta harmonic sigma weight residual 180.00 141.44 38.56 0 5.00e+00 4.00e-02 5.95e+01 ... (remaining 16419 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 3663 0.065 - 0.130: 651 0.130 - 0.195: 95 0.195 - 0.260: 9 0.260 - 0.325: 10 Chirality restraints: 4428 Sorted by residual: chirality pdb=" C1' DA I 32 " pdb=" O4' DA I 32 " pdb=" C2' DA I 32 " pdb=" N9 DA I 32 " both_signs ideal model delta sigma weight residual False 2.42 2.09 0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" C1' DT J 31 " pdb=" O4' DT J 31 " pdb=" C2' DT J 31 " pdb=" N1 DT J 31 " both_signs ideal model delta sigma weight residual False 2.47 2.14 0.32 2.00e-01 2.50e+01 2.63e+00 chirality pdb=" P DA I 49 " pdb=" OP1 DA I 49 " pdb=" OP2 DA I 49 " pdb=" O5' DA I 49 " both_signs ideal model delta sigma weight residual True 2.35 -2.65 -0.31 2.00e-01 2.50e+01 2.34e+00 ... (remaining 4425 not shown) Planarity restraints: 4598 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 5 " -0.019 2.00e-02 2.50e+03 3.79e-02 1.44e+01 pdb=" C ARG A 5 " 0.066 2.00e-02 2.50e+03 pdb=" O ARG A 5 " -0.025 2.00e-02 2.50e+03 pdb=" N GLU A 6 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 5 " 0.019 2.00e-02 2.50e+03 3.79e-02 1.43e+01 pdb=" C ARG C 5 " -0.065 2.00e-02 2.50e+03 pdb=" O ARG C 5 " 0.025 2.00e-02 2.50e+03 pdb=" N GLU C 6 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG E 5 " 0.019 2.00e-02 2.50e+03 3.78e-02 1.43e+01 pdb=" C ARG E 5 " -0.065 2.00e-02 2.50e+03 pdb=" O ARG E 5 " 0.025 2.00e-02 2.50e+03 pdb=" N GLU E 6 " 0.021 2.00e-02 2.50e+03 ... (remaining 4595 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 475 2.58 - 3.16: 25293 3.16 - 3.74: 44797 3.74 - 4.32: 60407 4.32 - 4.90: 92976 Nonbonded interactions: 223948 Sorted by model distance: nonbonded pdb=" O VAL D 115 " pdb="MG MG D 501 " model vdw 1.998 2.170 nonbonded pdb=" O VAL F 115 " pdb="MG MG F 501 " model vdw 1.998 2.170 nonbonded pdb=" O VAL B 115 " pdb="MG MG B 501 " model vdw 1.999 2.170 nonbonded pdb=" O VAL H 115 " pdb="MG MG H 501 " model vdw 1.999 2.170 nonbonded pdb="MG MG A 501 " pdb=" O1B AGS A 502 " model vdw 2.021 2.170 ... (remaining 223943 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 271 or resid 273 through 372 or resid 375 throug \ h 502)) selection = (chain 'B' and (resid 4 through 271 or resid 273 through 502)) selection = (chain 'C' and (resid 4 through 271 or resid 273 through 372 or resid 375 throug \ h 502)) selection = (chain 'D' and (resid 4 through 271 or resid 273 through 502)) selection = (chain 'E' and (resid 4 through 271 or resid 273 through 372 or resid 375 throug \ h 502)) selection = (chain 'F' and (resid 4 through 271 or resid 273 through 502)) selection = (chain 'G' and (resid 4 through 271 or resid 273 through 372 or resid 375 throug \ h 502)) selection = (chain 'H' and (resid 4 through 271 or resid 273 through 502)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.200 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: 0.290 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 32.150 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.090 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6200 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.123 27508 Z= 0.197 Angle : 0.917 13.131 37987 Z= 0.505 Chirality : 0.053 0.325 4428 Planarity : 0.007 0.067 4598 Dihedral : 19.230 166.507 10174 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.87 % Favored : 91.01 % Rotamer: Outliers : 0.47 % Allowed : 1.66 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.00 (0.14), residues: 3216 helix: -1.85 (0.12), residues: 1572 sheet: -2.23 (0.29), residues: 268 loop : -1.93 (0.17), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.002 ARG C 26 TYR 0.010 0.001 TYR B 361 PHE 0.030 0.003 PHE G 304 TRP 0.050 0.004 TRP C 111 HIS 0.014 0.001 HIS B 398 Details of bonding type rmsd covalent geometry : bond 0.00432 (27504) covalent geometry : angle 0.91720 (37987) hydrogen bonds : bond 0.13935 ( 1256) hydrogen bonds : angle 8.09178 ( 3636) Misc. bond : bond 0.00293 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1048 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 1036 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 VAL cc_start: 0.8834 (t) cc_final: 0.8370 (p) REVERT: A 27 ILE cc_start: 0.7650 (mt) cc_final: 0.7416 (mt) REVERT: A 78 ASN cc_start: 0.8224 (m-40) cc_final: 0.7506 (t0) REVERT: A 206 ASN cc_start: 0.6923 (p0) cc_final: 0.6544 (p0) REVERT: A 226 TYR cc_start: 0.8573 (m-10) cc_final: 0.8143 (m-80) REVERT: A 250 ASP cc_start: 0.8506 (p0) cc_final: 0.8199 (p0) REVERT: A 355 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8468 (mt-10) REVERT: B 10 GLU cc_start: 0.8656 (mp0) cc_final: 0.7756 (pp20) REVERT: B 17 GLN cc_start: 0.8754 (tp-100) cc_final: 0.8330 (mm-40) REVERT: B 99 PHE cc_start: 0.6217 (t80) cc_final: 0.5987 (t80) REVERT: B 130 HIS cc_start: 0.7470 (m170) cc_final: 0.7038 (m90) REVERT: B 153 GLN cc_start: 0.8511 (mp10) cc_final: 0.8287 (mp10) REVERT: B 190 ASP cc_start: 0.7828 (t0) cc_final: 0.7287 (p0) REVERT: B 191 THR cc_start: 0.8521 (p) cc_final: 0.7908 (t) REVERT: B 192 GLU cc_start: 0.8711 (mt-10) cc_final: 0.8309 (mp0) REVERT: B 216 ASP cc_start: 0.6806 (m-30) cc_final: 0.6542 (m-30) REVERT: B 297 LEU cc_start: 0.7384 (mp) cc_final: 0.7077 (tp) REVERT: B 331 VAL cc_start: 0.8826 (t) cc_final: 0.8036 (t) REVERT: B 387 GLN cc_start: 0.7807 (tm-30) cc_final: 0.7307 (tm-30) REVERT: B 391 LEU cc_start: 0.9353 (mp) cc_final: 0.9106 (mp) REVERT: C 25 ASP cc_start: 0.8536 (m-30) cc_final: 0.8320 (t70) REVERT: C 84 LEU cc_start: 0.8981 (tt) cc_final: 0.8716 (tt) REVERT: C 126 MET cc_start: 0.7752 (tmm) cc_final: 0.6784 (tpp) REVERT: C 199 MET cc_start: 0.7367 (mmm) cc_final: 0.6986 (mmm) REVERT: C 216 ASP cc_start: 0.6686 (m-30) cc_final: 0.6243 (m-30) REVERT: C 226 TYR cc_start: 0.8599 (m-10) cc_final: 0.8054 (m-80) REVERT: C 297 LEU cc_start: 0.7348 (mp) cc_final: 0.7057 (mp) REVERT: C 379 LEU cc_start: 0.7660 (tt) cc_final: 0.7454 (tt) REVERT: C 398 HIS cc_start: 0.7965 (m170) cc_final: 0.7027 (m90) REVERT: D 42 MET cc_start: 0.8088 (mtt) cc_final: 0.6373 (mtp) REVERT: D 199 MET cc_start: 0.5002 (pmm) cc_final: 0.4708 (pmm) REVERT: D 225 GLN cc_start: 0.8568 (mm110) cc_final: 0.8365 (mm-40) REVERT: D 332 LEU cc_start: 0.9176 (tp) cc_final: 0.8874 (tp) REVERT: D 344 MET cc_start: 0.5422 (ttp) cc_final: 0.4680 (tpt) REVERT: E 200 LEU cc_start: 0.7143 (mt) cc_final: 0.6620 (tt) REVERT: E 250 ASP cc_start: 0.8336 (p0) cc_final: 0.8066 (p0) REVERT: E 294 PHE cc_start: 0.7182 (m-80) cc_final: 0.6957 (m-80) REVERT: E 398 HIS cc_start: 0.7701 (m170) cc_final: 0.7408 (m90) REVERT: F 20 GLN cc_start: 0.7627 (mt0) cc_final: 0.7335 (mt0) REVERT: F 25 ASP cc_start: 0.8550 (m-30) cc_final: 0.8291 (m-30) REVERT: F 29 ILE cc_start: 0.8862 (mt) cc_final: 0.8611 (mt) REVERT: F 157 ARG cc_start: 0.7404 (mtm110) cc_final: 0.7203 (mtp180) REVERT: F 225 GLN cc_start: 0.8623 (mm110) cc_final: 0.8370 (mm-40) REVERT: F 331 VAL cc_start: 0.9170 (t) cc_final: 0.8167 (t) REVERT: G 199 MET cc_start: 0.5543 (mmm) cc_final: 0.4891 (mmm) REVERT: G 218 MET cc_start: 0.8170 (tmm) cc_final: 0.7968 (tmm) REVERT: G 226 TYR cc_start: 0.8659 (m-10) cc_final: 0.8356 (m-80) REVERT: G 233 LEU cc_start: 0.7782 (mm) cc_final: 0.7480 (mm) REVERT: H 14 GLN cc_start: 0.7606 (tm-30) cc_final: 0.6984 (pp30) REVERT: H 32 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7489 (mm-30) REVERT: H 46 LEU cc_start: 0.9144 (mt) cc_final: 0.8908 (mt) REVERT: H 47 MET cc_start: 0.8434 (mmm) cc_final: 0.7997 (mmm) REVERT: H 73 THR cc_start: 0.7987 (t) cc_final: 0.7394 (t) REVERT: H 86 GLU cc_start: 0.7484 (mt-10) cc_final: 0.7214 (mt-10) REVERT: H 213 PHE cc_start: 0.7068 (m-80) cc_final: 0.6792 (m-80) REVERT: H 344 MET cc_start: 0.4111 (ttp) cc_final: 0.2748 (ttp) outliers start: 12 outliers final: 1 residues processed: 1040 average time/residue: 0.1574 time to fit residues: 262.9883 Evaluate side-chains 845 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 844 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 9.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 GLN A 398 HIS B 78 ASN ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 ASN ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 ASN C 7 GLN C 20 GLN C 79 HIS C 161 ASN C 398 HIS ** D 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 ASN ** D 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 398 HIS D 405 ASN E 108 ASN E 161 ASN E 342 GLN F 17 GLN ** F 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 383 GLN G 400 HIS H 21 GLN H 79 HIS ** H 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 225 GLN ** H 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 405 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.216348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.174217 restraints weight = 174023.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.183820 restraints weight = 92420.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.190724 restraints weight = 56198.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.195443 restraints weight = 37349.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.199084 restraints weight = 26708.918| |-----------------------------------------------------------------------------| r_work (final): 0.4339 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4341 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4341 r_free = 0.4341 target_work(ls_wunit_k1) = 0.199 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4341 r_free = 0.4341 target_work(ls_wunit_k1) = 0.199 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4341 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6440 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 27508 Z= 0.207 Angle : 0.853 12.662 37987 Z= 0.449 Chirality : 0.048 0.277 4428 Planarity : 0.006 0.097 4598 Dihedral : 20.633 167.836 4738 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 18.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 0.12 % Allowed : 3.24 % Favored : 96.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.14), residues: 3216 helix: -1.14 (0.12), residues: 1584 sheet: -2.01 (0.26), residues: 272 loop : -1.39 (0.17), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG H 35 TYR 0.024 0.002 TYR E 226 PHE 0.038 0.003 PHE E 293 TRP 0.032 0.003 TRP H 267 HIS 0.014 0.002 HIS A 100 Details of bonding type rmsd covalent geometry : bond 0.00449 (27504) covalent geometry : angle 0.85345 (37987) hydrogen bonds : bond 0.05607 ( 1256) hydrogen bonds : angle 6.59715 ( 3636) Misc. bond : bond 0.00025 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 935 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 932 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 THR cc_start: 0.5795 (m) cc_final: 0.5469 (m) REVERT: A 30 VAL cc_start: 0.8704 (t) cc_final: 0.8465 (t) REVERT: A 65 MET cc_start: 0.7968 (tpt) cc_final: 0.7650 (tpp) REVERT: A 78 ASN cc_start: 0.8719 (m-40) cc_final: 0.7954 (t0) REVERT: A 86 GLU cc_start: 0.8313 (mm-30) cc_final: 0.7774 (mm-30) REVERT: A 130 HIS cc_start: 0.6834 (m90) cc_final: 0.6496 (m90) REVERT: A 191 THR cc_start: 0.9514 (p) cc_final: 0.8958 (t) REVERT: A 206 ASN cc_start: 0.7451 (p0) cc_final: 0.7002 (p0) REVERT: A 207 LEU cc_start: 0.8235 (tp) cc_final: 0.7826 (tp) REVERT: A 226 TYR cc_start: 0.8556 (m-10) cc_final: 0.8295 (m-80) REVERT: A 348 ILE cc_start: 0.9101 (mm) cc_final: 0.8881 (mm) REVERT: A 394 GLU cc_start: 0.8192 (pp20) cc_final: 0.7899 (pp20) REVERT: A 398 HIS cc_start: 0.8256 (m-70) cc_final: 0.7775 (m-70) REVERT: A 400 HIS cc_start: 0.8925 (m90) cc_final: 0.8416 (m90) REVERT: B 5 ARG cc_start: 0.6968 (ttm170) cc_final: 0.6185 (ttm170) REVERT: B 10 GLU cc_start: 0.8788 (mp0) cc_final: 0.7932 (pp20) REVERT: B 17 GLN cc_start: 0.8999 (tp-100) cc_final: 0.8616 (mm-40) REVERT: B 18 LEU cc_start: 0.8536 (pp) cc_final: 0.7970 (pp) REVERT: B 22 VAL cc_start: 0.8315 (t) cc_final: 0.7383 (t) REVERT: B 99 PHE cc_start: 0.6372 (t80) cc_final: 0.6120 (t80) REVERT: B 139 LEU cc_start: 0.8139 (mp) cc_final: 0.7833 (mp) REVERT: B 153 GLN cc_start: 0.8598 (mp10) cc_final: 0.8252 (mp10) REVERT: B 156 LEU cc_start: 0.7958 (mp) cc_final: 0.7648 (mp) REVERT: B 215 GLU cc_start: 0.9174 (mp0) cc_final: 0.8868 (mp0) REVERT: B 216 ASP cc_start: 0.6710 (m-30) cc_final: 0.6441 (m-30) REVERT: B 293 PHE cc_start: 0.8238 (t80) cc_final: 0.7850 (t80) REVERT: B 297 LEU cc_start: 0.7682 (mp) cc_final: 0.7467 (tp) REVERT: B 314 VAL cc_start: 0.8388 (t) cc_final: 0.8112 (t) REVERT: B 331 VAL cc_start: 0.9093 (t) cc_final: 0.8353 (t) REVERT: B 341 ASP cc_start: 0.7472 (p0) cc_final: 0.5902 (m-30) REVERT: C 7 GLN cc_start: 0.6331 (OUTLIER) cc_final: 0.6120 (pm20) REVERT: C 47 MET cc_start: 0.7406 (tmm) cc_final: 0.7143 (tmm) REVERT: C 124 LYS cc_start: 0.7785 (ptpp) cc_final: 0.7345 (ptpp) REVERT: C 126 MET cc_start: 0.7979 (tmm) cc_final: 0.7069 (tpp) REVERT: C 179 MET cc_start: 0.7310 (mmp) cc_final: 0.7088 (mmp) REVERT: C 199 MET cc_start: 0.7707 (mmm) cc_final: 0.7448 (mmm) REVERT: C 216 ASP cc_start: 0.6631 (m-30) cc_final: 0.6397 (m-30) REVERT: C 226 TYR cc_start: 0.8481 (m-10) cc_final: 0.7988 (m-80) REVERT: C 232 SER cc_start: 0.8410 (p) cc_final: 0.8078 (p) REVERT: C 241 GLU cc_start: 0.8431 (mp0) cc_final: 0.7797 (mp0) REVERT: C 354 PHE cc_start: 0.9181 (m-80) cc_final: 0.8958 (m-80) REVERT: C 387 GLN cc_start: 0.8109 (tm-30) cc_final: 0.7525 (tm-30) REVERT: C 398 HIS cc_start: 0.7937 (m-70) cc_final: 0.7293 (m-70) REVERT: D 153 GLN cc_start: 0.7501 (mp10) cc_final: 0.7213 (mp10) REVERT: D 255 MET cc_start: 0.5129 (mtt) cc_final: 0.4597 (mtt) REVERT: D 296 HIS cc_start: 0.7904 (t-90) cc_final: 0.7573 (t-90) REVERT: D 297 LEU cc_start: 0.8227 (mp) cc_final: 0.7141 (mp) REVERT: E 91 MET cc_start: 0.6339 (mmp) cc_final: 0.6078 (mmp) REVERT: E 118 GLN cc_start: 0.8743 (pm20) cc_final: 0.8523 (mp10) REVERT: E 159 PHE cc_start: 0.7869 (t80) cc_final: 0.7392 (t80) REVERT: E 161 ASN cc_start: 0.7365 (m-40) cc_final: 0.7145 (m-40) REVERT: E 192 GLU cc_start: 0.8403 (mp0) cc_final: 0.8125 (mp0) REVERT: E 250 ASP cc_start: 0.8158 (p0) cc_final: 0.7819 (p0) REVERT: E 293 PHE cc_start: 0.8430 (t80) cc_final: 0.8196 (t80) REVERT: E 344 MET cc_start: 0.7004 (tpp) cc_final: 0.6718 (tpp) REVERT: F 25 ASP cc_start: 0.8420 (m-30) cc_final: 0.8183 (m-30) REVERT: F 84 LEU cc_start: 0.8941 (tp) cc_final: 0.8724 (tp) REVERT: F 195 ARG cc_start: 0.7585 (mtt90) cc_final: 0.7171 (tpp80) REVERT: F 255 MET cc_start: 0.5355 (mtt) cc_final: 0.5137 (mtt) REVERT: F 331 VAL cc_start: 0.8971 (t) cc_final: 0.7958 (t) REVERT: F 387 GLN cc_start: 0.8122 (tm-30) cc_final: 0.7797 (tm-30) REVERT: F 398 HIS cc_start: 0.7617 (m-70) cc_final: 0.6976 (m-70) REVERT: G 13 TYR cc_start: 0.8117 (t80) cc_final: 0.7824 (t80) REVERT: G 89 MET cc_start: 0.5644 (tmm) cc_final: 0.4402 (tmm) REVERT: G 218 MET cc_start: 0.8246 (tmm) cc_final: 0.8043 (tmm) REVERT: G 233 LEU cc_start: 0.7685 (mm) cc_final: 0.7425 (mm) REVERT: G 236 VAL cc_start: 0.7348 (m) cc_final: 0.6885 (m) REVERT: G 270 MET cc_start: 0.7717 (mmp) cc_final: 0.7444 (mmm) REVERT: G 320 MET cc_start: 0.6370 (tpt) cc_final: 0.6159 (tpt) REVERT: H 17 GLN cc_start: 0.8698 (mm-40) cc_final: 0.8017 (mt0) REVERT: H 32 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7574 (mm-30) REVERT: H 42 MET cc_start: 0.6664 (ttm) cc_final: 0.5363 (ttt) REVERT: H 47 MET cc_start: 0.8995 (mmm) cc_final: 0.8780 (mmm) REVERT: H 139 LEU cc_start: 0.8709 (mp) cc_final: 0.8228 (mm) REVERT: H 192 GLU cc_start: 0.8950 (tp30) cc_final: 0.8742 (tp30) REVERT: H 193 PHE cc_start: 0.8821 (t80) cc_final: 0.8460 (t80) REVERT: H 213 PHE cc_start: 0.7322 (m-80) cc_final: 0.6791 (m-80) REVERT: H 317 MET cc_start: 0.8674 (ttt) cc_final: 0.8373 (ttt) REVERT: H 344 MET cc_start: 0.4607 (ttp) cc_final: 0.3139 (ttp) REVERT: H 398 HIS cc_start: 0.8153 (m-70) cc_final: 0.7740 (m-70) outliers start: 3 outliers final: 1 residues processed: 934 average time/residue: 0.1565 time to fit residues: 239.1766 Evaluate side-chains 812 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 810 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 157 optimal weight: 5.9990 chunk 312 optimal weight: 20.0000 chunk 313 optimal weight: 20.0000 chunk 53 optimal weight: 8.9990 chunk 98 optimal weight: 40.0000 chunk 52 optimal weight: 20.0000 chunk 130 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 239 optimal weight: 6.9990 chunk 65 optimal weight: 20.0000 chunk 233 optimal weight: 1.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN A 118 GLN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 ASN B 116 GLN ** B 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 ASN B 225 GLN ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 383 GLN D 70 HIS ** D 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 GLN ** D 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 7 GLN E 342 GLN ** E 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 116 GLN F 225 GLN ** F 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 406 GLN G 383 GLN H 14 GLN ** H 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 116 GLN ** H 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 ASN H 225 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.216439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.176724 restraints weight = 172585.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.186398 restraints weight = 91008.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.192003 restraints weight = 55701.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.197827 restraints weight = 37339.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.200691 restraints weight = 24885.302| |-----------------------------------------------------------------------------| r_work (final): 0.4356 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4353 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4353 r_free = 0.4353 target_work(ls_wunit_k1) = 0.200 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4353 r_free = 0.4353 target_work(ls_wunit_k1) = 0.200 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4353 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6441 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 27508 Z= 0.175 Angle : 0.801 9.760 37987 Z= 0.420 Chirality : 0.046 0.261 4428 Planarity : 0.006 0.061 4598 Dihedral : 20.254 171.734 4738 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 0.12 % Allowed : 3.59 % Favored : 96.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.14), residues: 3216 helix: -0.61 (0.12), residues: 1600 sheet: -1.66 (0.26), residues: 268 loop : -1.07 (0.18), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 195 TYR 0.040 0.002 TYR E 226 PHE 0.042 0.002 PHE D 293 TRP 0.059 0.003 TRP C 401 HIS 0.011 0.002 HIS B 130 Details of bonding type rmsd covalent geometry : bond 0.00380 (27504) covalent geometry : angle 0.80067 (37987) hydrogen bonds : bond 0.04963 ( 1256) hydrogen bonds : angle 6.31694 ( 3636) Misc. bond : bond 0.00079 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 920 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 917 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 VAL cc_start: 0.8632 (t) cc_final: 0.8303 (t) REVERT: A 65 MET cc_start: 0.8166 (tpt) cc_final: 0.7945 (tmm) REVERT: A 78 ASN cc_start: 0.8674 (m-40) cc_final: 0.7911 (t0) REVERT: A 86 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8188 (mm-30) REVERT: A 130 HIS cc_start: 0.7067 (m90) cc_final: 0.6857 (m90) REVERT: A 192 GLU cc_start: 0.9470 (mp0) cc_final: 0.9191 (pm20) REVERT: A 206 ASN cc_start: 0.7621 (p0) cc_final: 0.7153 (p0) REVERT: A 207 LEU cc_start: 0.8470 (tp) cc_final: 0.8072 (tp) REVERT: A 226 TYR cc_start: 0.8587 (m-10) cc_final: 0.8295 (m-80) REVERT: A 234 ASP cc_start: 0.8426 (m-30) cc_final: 0.8159 (m-30) REVERT: A 348 ILE cc_start: 0.9100 (mm) cc_final: 0.8898 (mm) REVERT: A 400 HIS cc_start: 0.8914 (m90) cc_final: 0.8366 (m90) REVERT: B 5 ARG cc_start: 0.6916 (ttm170) cc_final: 0.6069 (ttm170) REVERT: B 10 GLU cc_start: 0.8710 (mp0) cc_final: 0.7764 (pp20) REVERT: B 18 LEU cc_start: 0.8534 (pp) cc_final: 0.7722 (pp) REVERT: B 130 HIS cc_start: 0.7274 (m170) cc_final: 0.6634 (m90) REVERT: B 153 GLN cc_start: 0.8550 (mp10) cc_final: 0.8234 (mp10) REVERT: B 156 LEU cc_start: 0.7780 (mp) cc_final: 0.7495 (mp) REVERT: B 192 GLU cc_start: 0.8954 (mt-10) cc_final: 0.8623 (mp0) REVERT: B 215 GLU cc_start: 0.9214 (mp0) cc_final: 0.8829 (mp0) REVERT: B 293 PHE cc_start: 0.8344 (t80) cc_final: 0.7917 (t80) REVERT: B 313 PHE cc_start: 0.7128 (p90) cc_final: 0.6349 (p90) REVERT: B 331 VAL cc_start: 0.9064 (t) cc_final: 0.8204 (t) REVERT: B 341 ASP cc_start: 0.7483 (p0) cc_final: 0.6127 (m-30) REVERT: B 387 GLN cc_start: 0.7997 (tm-30) cc_final: 0.7568 (tm-30) REVERT: B 391 LEU cc_start: 0.9307 (mp) cc_final: 0.8869 (mp) REVERT: C 32 GLU cc_start: 0.8158 (pt0) cc_final: 0.7794 (pp20) REVERT: C 47 MET cc_start: 0.7571 (tmm) cc_final: 0.7126 (tmm) REVERT: C 124 LYS cc_start: 0.7791 (ptpp) cc_final: 0.7334 (ptpp) REVERT: C 126 MET cc_start: 0.8041 (tmm) cc_final: 0.7180 (tpp) REVERT: C 179 MET cc_start: 0.7271 (mmp) cc_final: 0.6475 (mmt) REVERT: C 199 MET cc_start: 0.7732 (mmm) cc_final: 0.7452 (mmm) REVERT: C 208 LYS cc_start: 0.6241 (mppt) cc_final: 0.5782 (mppt) REVERT: C 216 ASP cc_start: 0.6671 (m-30) cc_final: 0.6367 (m-30) REVERT: C 226 TYR cc_start: 0.8478 (m-10) cc_final: 0.7918 (m-80) REVERT: C 241 GLU cc_start: 0.8471 (mp0) cc_final: 0.7942 (mp0) REVERT: D 84 LEU cc_start: 0.8711 (tp) cc_final: 0.7938 (tp) REVERT: D 153 GLN cc_start: 0.7446 (mp10) cc_final: 0.7080 (mp10) REVERT: D 255 MET cc_start: 0.4901 (mtt) cc_final: 0.4227 (mtt) REVERT: D 344 MET cc_start: 0.5811 (ttp) cc_final: 0.5268 (tpt) REVERT: E 192 GLU cc_start: 0.8587 (mp0) cc_final: 0.8352 (mp0) REVERT: E 241 GLU cc_start: 0.8707 (mp0) cc_final: 0.8451 (mp0) REVERT: E 250 ASP cc_start: 0.8137 (p0) cc_final: 0.7799 (p0) REVERT: F 195 ARG cc_start: 0.7659 (mtt90) cc_final: 0.7303 (tpp80) REVERT: F 255 MET cc_start: 0.5335 (mtt) cc_final: 0.4938 (mtp) REVERT: F 270 MET cc_start: 0.6224 (ttt) cc_final: 0.5425 (ttt) REVERT: F 320 MET cc_start: 0.6217 (mmp) cc_final: 0.5182 (mmp) REVERT: F 331 VAL cc_start: 0.8840 (t) cc_final: 0.8474 (t) REVERT: F 387 GLN cc_start: 0.8088 (tm-30) cc_final: 0.7740 (tm-30) REVERT: F 398 HIS cc_start: 0.7536 (m-70) cc_final: 0.6987 (m-70) REVERT: G 13 TYR cc_start: 0.8225 (t80) cc_final: 0.7914 (t80) REVERT: G 39 PHE cc_start: 0.4868 (m-80) cc_final: 0.4610 (m-80) REVERT: G 55 ARG cc_start: 0.7441 (mmt90) cc_final: 0.6949 (mmt90) REVERT: G 81 SER cc_start: 0.8560 (t) cc_final: 0.7866 (p) REVERT: G 89 MET cc_start: 0.5083 (tmm) cc_final: 0.3952 (tmm) REVERT: G 141 LYS cc_start: 0.3407 (mmmt) cc_final: 0.2881 (mmmt) REVERT: G 218 MET cc_start: 0.8239 (tmm) cc_final: 0.8014 (tmm) REVERT: G 226 TYR cc_start: 0.8417 (m-80) cc_final: 0.7892 (m-80) REVERT: G 233 LEU cc_start: 0.7649 (mm) cc_final: 0.7345 (mm) REVERT: H 14 GLN cc_start: 0.8206 (tm130) cc_final: 0.7623 (tm-30) REVERT: H 17 GLN cc_start: 0.8588 (mm-40) cc_final: 0.7225 (mt0) REVERT: H 21 GLN cc_start: 0.9043 (mp10) cc_final: 0.8709 (mp-120) REVERT: H 28 GLU cc_start: 0.9032 (tm-30) cc_final: 0.8089 (tm-30) REVERT: H 29 ILE cc_start: 0.9073 (mt) cc_final: 0.8791 (mt) REVERT: H 32 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7560 (mm-30) REVERT: H 192 GLU cc_start: 0.9070 (tp30) cc_final: 0.8797 (tp30) REVERT: H 344 MET cc_start: 0.4386 (ttp) cc_final: 0.3323 (ttp) REVERT: H 387 GLN cc_start: 0.8557 (tm-30) cc_final: 0.7924 (tm-30) REVERT: H 394 GLU cc_start: 0.9091 (tm-30) cc_final: 0.7361 (tm-30) REVERT: H 398 HIS cc_start: 0.8163 (m-70) cc_final: 0.7243 (m-70) outliers start: 3 outliers final: 1 residues processed: 919 average time/residue: 0.1525 time to fit residues: 230.1017 Evaluate side-chains 794 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 793 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 108 optimal weight: 4.9990 chunk 297 optimal weight: 20.0000 chunk 159 optimal weight: 6.9990 chunk 27 optimal weight: 20.0000 chunk 68 optimal weight: 4.9990 chunk 96 optimal weight: 0.8980 chunk 120 optimal weight: 20.0000 chunk 289 optimal weight: 40.0000 chunk 125 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 chunk 251 optimal weight: 10.0000 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN A 387 GLN B 78 ASN ** B 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 ASN ** C 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 ASN C 383 GLN D 17 GLN D 20 GLN ** D 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 ASN E 342 GLN E 398 HIS ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 398 HIS F 406 GLN G 383 GLN ** H 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 225 GLN ** H 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 405 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.213668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.174407 restraints weight = 168156.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.183482 restraints weight = 88744.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.189743 restraints weight = 53796.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.194308 restraints weight = 35853.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.197596 restraints weight = 25445.726| |-----------------------------------------------------------------------------| r_work (final): 0.4326 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4325 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4325 r_free = 0.4325 target_work(ls_wunit_k1) = 0.197 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4325 r_free = 0.4325 target_work(ls_wunit_k1) = 0.197 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4325 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6504 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 27508 Z= 0.196 Angle : 0.820 13.702 37987 Z= 0.427 Chirality : 0.047 0.256 4428 Planarity : 0.006 0.114 4598 Dihedral : 19.947 171.989 4738 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 18.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.55 % Favored : 93.42 % Rotamer: Outliers : 0.08 % Allowed : 2.84 % Favored : 97.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.14), residues: 3216 helix: -0.30 (0.12), residues: 1588 sheet: -1.69 (0.26), residues: 272 loop : -0.97 (0.18), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 195 TYR 0.027 0.002 TYR F 301 PHE 0.043 0.003 PHE C 293 TRP 0.036 0.003 TRP B 287 HIS 0.016 0.002 HIS E 398 Details of bonding type rmsd covalent geometry : bond 0.00428 (27504) covalent geometry : angle 0.82022 (37987) hydrogen bonds : bond 0.04882 ( 1256) hydrogen bonds : angle 6.21678 ( 3636) Misc. bond : bond 0.00059 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 907 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 905 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.8729 (mp0) cc_final: 0.8420 (mp0) REVERT: A 19 THR cc_start: 0.8256 (t) cc_final: 0.7337 (t) REVERT: A 22 VAL cc_start: 0.8765 (t) cc_final: 0.7925 (t) REVERT: A 30 VAL cc_start: 0.8650 (t) cc_final: 0.8361 (t) REVERT: A 78 ASN cc_start: 0.8745 (m-40) cc_final: 0.7915 (t0) REVERT: A 86 GLU cc_start: 0.8434 (mm-30) cc_final: 0.8143 (mm-30) REVERT: A 130 HIS cc_start: 0.7075 (m90) cc_final: 0.6784 (m90) REVERT: A 192 GLU cc_start: 0.9511 (mp0) cc_final: 0.9231 (pm20) REVERT: A 206 ASN cc_start: 0.7554 (p0) cc_final: 0.7099 (p0) REVERT: A 207 LEU cc_start: 0.8571 (tp) cc_final: 0.8205 (tp) REVERT: A 226 TYR cc_start: 0.8589 (m-10) cc_final: 0.8288 (m-80) REVERT: A 234 ASP cc_start: 0.8442 (m-30) cc_final: 0.8140 (m-30) REVERT: A 348 ILE cc_start: 0.9093 (mm) cc_final: 0.8886 (mm) REVERT: A 383 GLN cc_start: 0.8980 (pt0) cc_final: 0.8771 (pt0) REVERT: A 394 GLU cc_start: 0.8159 (pp20) cc_final: 0.7897 (pp20) REVERT: A 398 HIS cc_start: 0.8050 (m-70) cc_final: 0.7733 (m-70) REVERT: A 400 HIS cc_start: 0.8885 (m90) cc_final: 0.8300 (m90) REVERT: B 5 ARG cc_start: 0.7109 (ttm170) cc_final: 0.6098 (ttm170) REVERT: B 10 GLU cc_start: 0.8874 (mp0) cc_final: 0.8160 (pp20) REVERT: B 18 LEU cc_start: 0.8450 (pp) cc_final: 0.7835 (pp) REVERT: B 130 HIS cc_start: 0.7450 (m170) cc_final: 0.6792 (m90) REVERT: B 153 GLN cc_start: 0.8625 (mp10) cc_final: 0.8260 (mp10) REVERT: B 156 LEU cc_start: 0.7761 (mp) cc_final: 0.7455 (mp) REVERT: B 192 GLU cc_start: 0.8955 (mt-10) cc_final: 0.8645 (mp0) REVERT: B 215 GLU cc_start: 0.9236 (mp0) cc_final: 0.8830 (mp0) REVERT: B 297 LEU cc_start: 0.7912 (tp) cc_final: 0.6788 (tp) REVERT: B 304 PHE cc_start: 0.6895 (m-10) cc_final: 0.6140 (m-10) REVERT: B 313 PHE cc_start: 0.7095 (p90) cc_final: 0.6413 (p90) REVERT: B 317 MET cc_start: 0.8311 (tpp) cc_final: 0.7763 (tpt) REVERT: B 341 ASP cc_start: 0.7457 (p0) cc_final: 0.6189 (m-30) REVERT: B 387 GLN cc_start: 0.7934 (tm-30) cc_final: 0.7406 (tm-30) REVERT: B 391 LEU cc_start: 0.9365 (mp) cc_final: 0.8882 (mp) REVERT: C 9 ILE cc_start: 0.8038 (mt) cc_final: 0.7801 (mt) REVERT: C 65 MET cc_start: 0.9295 (ttp) cc_final: 0.8061 (tmm) REVERT: C 82 ILE cc_start: 0.8723 (pt) cc_final: 0.8052 (pt) REVERT: C 90 LEU cc_start: 0.7382 (tt) cc_final: 0.6557 (mm) REVERT: C 124 LYS cc_start: 0.7924 (ptpp) cc_final: 0.7475 (ptpp) REVERT: C 126 MET cc_start: 0.8078 (tmm) cc_final: 0.7233 (tpp) REVERT: C 179 MET cc_start: 0.7164 (mmp) cc_final: 0.6913 (mmp) REVERT: C 199 MET cc_start: 0.7892 (mmm) cc_final: 0.7622 (mmm) REVERT: C 208 LYS cc_start: 0.6471 (mppt) cc_final: 0.5876 (mppt) REVERT: C 216 ASP cc_start: 0.6782 (m-30) cc_final: 0.6498 (m-30) REVERT: C 226 TYR cc_start: 0.8618 (m-10) cc_final: 0.8129 (m-80) REVERT: C 241 GLU cc_start: 0.8509 (mp0) cc_final: 0.8112 (mp0) REVERT: C 308 TRP cc_start: 0.5137 (t-100) cc_final: 0.4861 (t-100) REVERT: C 361 TYR cc_start: 0.6890 (m-80) cc_final: 0.6506 (m-80) REVERT: D 84 LEU cc_start: 0.8686 (tp) cc_final: 0.8185 (tp) REVERT: D 89 MET cc_start: 0.6780 (ppp) cc_final: 0.6540 (ptt) REVERT: D 153 GLN cc_start: 0.7460 (mp10) cc_final: 0.6961 (mp10) REVERT: D 347 THR cc_start: 0.7345 (t) cc_final: 0.6999 (m) REVERT: E 192 GLU cc_start: 0.8512 (mp0) cc_final: 0.8297 (mp0) REVERT: E 250 ASP cc_start: 0.8169 (p0) cc_final: 0.7778 (p0) REVERT: F 84 LEU cc_start: 0.8910 (tp) cc_final: 0.8674 (tp) REVERT: F 176 VAL cc_start: 0.8745 (t) cc_final: 0.8520 (t) REVERT: F 195 ARG cc_start: 0.7666 (mtt90) cc_final: 0.7285 (tpp80) REVERT: F 255 MET cc_start: 0.5486 (mtt) cc_final: 0.5005 (mtp) REVERT: F 320 MET cc_start: 0.6392 (mmp) cc_final: 0.5504 (mmp) REVERT: F 331 VAL cc_start: 0.8867 (t) cc_final: 0.8537 (t) REVERT: F 383 GLN cc_start: 0.8853 (pm20) cc_final: 0.8443 (pm20) REVERT: F 387 GLN cc_start: 0.8143 (tm-30) cc_final: 0.7416 (tm-30) REVERT: F 391 LEU cc_start: 0.9195 (mp) cc_final: 0.8694 (mp) REVERT: G 28 GLU cc_start: 0.7623 (mp0) cc_final: 0.7346 (mp0) REVERT: G 39 PHE cc_start: 0.4846 (m-80) cc_final: 0.4482 (m-80) REVERT: G 65 MET cc_start: 0.7949 (tmm) cc_final: 0.7565 (tmm) REVERT: G 81 SER cc_start: 0.8616 (t) cc_final: 0.7891 (p) REVERT: G 89 MET cc_start: 0.5829 (tmm) cc_final: 0.5503 (tmm) REVERT: G 141 LYS cc_start: 0.3408 (mmmt) cc_final: 0.2924 (mmmt) REVERT: G 218 MET cc_start: 0.8326 (tmm) cc_final: 0.8093 (tmm) REVERT: G 226 TYR cc_start: 0.8511 (m-80) cc_final: 0.7554 (m-80) REVERT: G 233 LEU cc_start: 0.7659 (mm) cc_final: 0.7376 (mm) REVERT: G 320 MET cc_start: 0.6611 (tpt) cc_final: 0.6353 (tpt) REVERT: H 14 GLN cc_start: 0.7791 (pp30) cc_final: 0.6948 (pp30) REVERT: H 17 GLN cc_start: 0.8652 (mm-40) cc_final: 0.7865 (mt0) REVERT: H 28 GLU cc_start: 0.8986 (tm-30) cc_final: 0.8074 (tm-30) REVERT: H 29 ILE cc_start: 0.9005 (mt) cc_final: 0.8754 (mt) REVERT: H 32 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7494 (mm-30) REVERT: H 42 MET cc_start: 0.6836 (ttm) cc_final: 0.5302 (ttm) REVERT: H 64 LYS cc_start: 0.9121 (pttm) cc_final: 0.8785 (pttm) REVERT: H 192 GLU cc_start: 0.9132 (tp30) cc_final: 0.8844 (tp30) REVERT: H 193 PHE cc_start: 0.8705 (t80) cc_final: 0.8453 (t80) REVERT: H 230 ASN cc_start: 0.7444 (p0) cc_final: 0.7236 (p0) REVERT: H 339 LEU cc_start: 0.7887 (pt) cc_final: 0.7648 (pt) REVERT: H 344 MET cc_start: 0.4631 (ttp) cc_final: 0.3727 (ttp) REVERT: H 387 GLN cc_start: 0.8590 (tm-30) cc_final: 0.7939 (tm-30) REVERT: H 394 GLU cc_start: 0.9020 (tm-30) cc_final: 0.7673 (tm-30) REVERT: H 398 HIS cc_start: 0.8332 (m-70) cc_final: 0.7720 (m-70) REVERT: H 404 LEU cc_start: 0.8942 (mm) cc_final: 0.8554 (mm) outliers start: 2 outliers final: 0 residues processed: 907 average time/residue: 0.1532 time to fit residues: 228.5149 Evaluate side-chains 799 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 799 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 303 optimal weight: 30.0000 chunk 43 optimal weight: 2.9990 chunk 131 optimal weight: 7.9990 chunk 293 optimal weight: 5.9990 chunk 145 optimal weight: 5.9990 chunk 199 optimal weight: 0.9980 chunk 233 optimal weight: 7.9990 chunk 193 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 ASN B 225 GLN ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 398 HIS ** C 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 398 HIS ** D 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 ASN E 342 GLN ** E 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 225 GLN ** H 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 225 GLN H 405 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.213339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.173635 restraints weight = 170114.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.182685 restraints weight = 89753.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.189192 restraints weight = 54550.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.193838 restraints weight = 36354.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.196640 restraints weight = 25817.685| |-----------------------------------------------------------------------------| r_work (final): 0.4311 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4311 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4311 r_free = 0.4311 target_work(ls_wunit_k1) = 0.196 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4311 r_free = 0.4311 target_work(ls_wunit_k1) = 0.196 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4311 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6521 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 27508 Z= 0.184 Angle : 0.792 12.516 37987 Z= 0.416 Chirality : 0.046 0.257 4428 Planarity : 0.006 0.123 4598 Dihedral : 19.716 170.620 4738 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 18.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 0.04 % Allowed : 2.33 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.14), residues: 3216 helix: -0.18 (0.12), residues: 1580 sheet: -1.60 (0.26), residues: 296 loop : -0.98 (0.18), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 5 TYR 0.031 0.002 TYR G 226 PHE 0.049 0.003 PHE C 293 TRP 0.044 0.002 TRP H 287 HIS 0.015 0.002 HIS E 398 Details of bonding type rmsd covalent geometry : bond 0.00403 (27504) covalent geometry : angle 0.79219 (37987) hydrogen bonds : bond 0.04671 ( 1256) hydrogen bonds : angle 6.11470 ( 3636) Misc. bond : bond 0.00080 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 900 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 899 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.8935 (mp0) cc_final: 0.8706 (mp0) REVERT: A 19 THR cc_start: 0.8140 (t) cc_final: 0.7692 (t) REVERT: A 78 ASN cc_start: 0.8771 (m-40) cc_final: 0.7917 (t0) REVERT: A 192 GLU cc_start: 0.9530 (mp0) cc_final: 0.9261 (pm20) REVERT: A 206 ASN cc_start: 0.7578 (p0) cc_final: 0.7126 (p0) REVERT: A 207 LEU cc_start: 0.8612 (tp) cc_final: 0.8304 (tp) REVERT: A 226 TYR cc_start: 0.8550 (m-10) cc_final: 0.8244 (m-80) REVERT: A 234 ASP cc_start: 0.8422 (m-30) cc_final: 0.8177 (m-30) REVERT: A 361 TYR cc_start: 0.8513 (m-80) cc_final: 0.8203 (m-80) REVERT: A 394 GLU cc_start: 0.8116 (pp20) cc_final: 0.7843 (pp20) REVERT: A 398 HIS cc_start: 0.8068 (m-70) cc_final: 0.7823 (m-70) REVERT: A 400 HIS cc_start: 0.8916 (m90) cc_final: 0.8353 (m90) REVERT: B 5 ARG cc_start: 0.7149 (ttm170) cc_final: 0.6258 (ttm170) REVERT: B 10 GLU cc_start: 0.8824 (mp0) cc_final: 0.7772 (pp20) REVERT: B 18 LEU cc_start: 0.8341 (pp) cc_final: 0.7727 (pp) REVERT: B 130 HIS cc_start: 0.7382 (m170) cc_final: 0.6737 (m90) REVERT: B 153 GLN cc_start: 0.8635 (mp10) cc_final: 0.8264 (mp10) REVERT: B 156 LEU cc_start: 0.7824 (mp) cc_final: 0.7542 (mp) REVERT: B 192 GLU cc_start: 0.9002 (mt-10) cc_final: 0.8649 (mp0) REVERT: B 215 GLU cc_start: 0.9264 (mp0) cc_final: 0.8846 (mp0) REVERT: B 313 PHE cc_start: 0.7059 (p90) cc_final: 0.6370 (p90) REVERT: B 317 MET cc_start: 0.8437 (tpp) cc_final: 0.7879 (tpt) REVERT: B 331 VAL cc_start: 0.8991 (t) cc_final: 0.8096 (t) REVERT: B 332 LEU cc_start: 0.9131 (tp) cc_final: 0.8883 (tp) REVERT: B 341 ASP cc_start: 0.7856 (p0) cc_final: 0.6723 (m-30) REVERT: B 383 GLN cc_start: 0.9309 (pm20) cc_final: 0.9031 (pm20) REVERT: B 387 GLN cc_start: 0.7891 (tm-30) cc_final: 0.7330 (tm-30) REVERT: B 391 LEU cc_start: 0.9332 (mp) cc_final: 0.8798 (mp) REVERT: C 9 ILE cc_start: 0.7903 (mt) cc_final: 0.7367 (mt) REVERT: C 17 GLN cc_start: 0.8871 (mt0) cc_final: 0.8300 (mt0) REVERT: C 31 LEU cc_start: 0.8581 (mm) cc_final: 0.8312 (mm) REVERT: C 65 MET cc_start: 0.9339 (ttp) cc_final: 0.7915 (tmm) REVERT: C 90 LEU cc_start: 0.7391 (tt) cc_final: 0.6611 (mm) REVERT: C 124 LYS cc_start: 0.7951 (ptpp) cc_final: 0.7461 (ptpp) REVERT: C 126 MET cc_start: 0.7971 (tmm) cc_final: 0.7281 (tpp) REVERT: C 179 MET cc_start: 0.7198 (mmp) cc_final: 0.6736 (mmp) REVERT: C 199 MET cc_start: 0.7861 (mmm) cc_final: 0.7602 (mmm) REVERT: C 208 LYS cc_start: 0.6352 (mppt) cc_final: 0.5734 (mppt) REVERT: C 216 ASP cc_start: 0.6790 (m-30) cc_final: 0.6483 (m-30) REVERT: C 226 TYR cc_start: 0.8579 (m-10) cc_final: 0.8076 (m-80) REVERT: C 241 GLU cc_start: 0.8372 (mp0) cc_final: 0.7935 (mp0) REVERT: C 325 ASN cc_start: 0.6530 (t0) cc_final: 0.6173 (t0) REVERT: D 84 LEU cc_start: 0.8761 (tp) cc_final: 0.8210 (tp) REVERT: D 153 GLN cc_start: 0.7437 (mp10) cc_final: 0.6960 (mp10) REVERT: D 293 PHE cc_start: 0.8057 (t80) cc_final: 0.7856 (t80) REVERT: D 334 GLU cc_start: 0.8630 (tt0) cc_final: 0.8180 (tt0) REVERT: D 344 MET cc_start: 0.5643 (ttp) cc_final: 0.4885 (tpt) REVERT: E 192 GLU cc_start: 0.8607 (mp0) cc_final: 0.8404 (mp0) REVERT: E 241 GLU cc_start: 0.8680 (mp0) cc_final: 0.8291 (mp0) REVERT: E 250 ASP cc_start: 0.8172 (p0) cc_final: 0.7857 (p0) REVERT: F 10 GLU cc_start: 0.8611 (mm-30) cc_final: 0.8130 (pp20) REVERT: F 84 LEU cc_start: 0.8966 (tp) cc_final: 0.8764 (tp) REVERT: F 86 GLU cc_start: 0.7955 (mt-10) cc_final: 0.6800 (mt-10) REVERT: F 124 LYS cc_start: 0.8488 (mmtm) cc_final: 0.7937 (mmtm) REVERT: F 195 ARG cc_start: 0.7610 (mtt90) cc_final: 0.7164 (tpp80) REVERT: F 208 LYS cc_start: 0.5688 (mmtt) cc_final: 0.5053 (mmtm) REVERT: F 255 MET cc_start: 0.5396 (mtt) cc_final: 0.5030 (mtp) REVERT: F 331 VAL cc_start: 0.8818 (t) cc_final: 0.8412 (t) REVERT: F 387 GLN cc_start: 0.7955 (tm-30) cc_final: 0.7256 (tm-30) REVERT: F 391 LEU cc_start: 0.9099 (mp) cc_final: 0.8564 (mp) REVERT: F 394 GLU cc_start: 0.7428 (tm-30) cc_final: 0.6060 (tm-30) REVERT: F 398 HIS cc_start: 0.7161 (m90) cc_final: 0.6769 (m90) REVERT: G 39 PHE cc_start: 0.4770 (m-80) cc_final: 0.4303 (m-80) REVERT: G 65 MET cc_start: 0.7882 (tmm) cc_final: 0.7408 (tmm) REVERT: G 89 MET cc_start: 0.5912 (tmm) cc_final: 0.5527 (tmm) REVERT: G 218 MET cc_start: 0.8348 (tmm) cc_final: 0.8094 (tmm) REVERT: G 226 TYR cc_start: 0.8422 (m-80) cc_final: 0.7665 (m-80) REVERT: G 233 LEU cc_start: 0.7623 (mm) cc_final: 0.7406 (mm) REVERT: G 286 ASP cc_start: 0.8901 (m-30) cc_final: 0.8621 (m-30) REVERT: G 292 ASN cc_start: 0.7860 (m-40) cc_final: 0.7543 (m-40) REVERT: G 320 MET cc_start: 0.6618 (tpt) cc_final: 0.6357 (tpt) REVERT: H 14 GLN cc_start: 0.7863 (pp30) cc_final: 0.6975 (pp30) REVERT: H 17 GLN cc_start: 0.8670 (mm-40) cc_final: 0.7897 (mt0) REVERT: H 28 GLU cc_start: 0.9009 (tm-30) cc_final: 0.8063 (tm-30) REVERT: H 29 ILE cc_start: 0.9100 (mt) cc_final: 0.8796 (mt) REVERT: H 32 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7552 (mm-30) REVERT: H 42 MET cc_start: 0.7522 (ttm) cc_final: 0.6677 (ttm) REVERT: H 64 LYS cc_start: 0.9156 (pttm) cc_final: 0.8669 (pttm) REVERT: H 192 GLU cc_start: 0.9158 (tp30) cc_final: 0.8867 (tp30) REVERT: H 193 PHE cc_start: 0.8726 (t80) cc_final: 0.8442 (t80) REVERT: H 344 MET cc_start: 0.4847 (ttp) cc_final: 0.2635 (ttp) REVERT: H 387 GLN cc_start: 0.8472 (tm-30) cc_final: 0.7819 (tm-30) REVERT: H 393 LEU cc_start: 0.8652 (tp) cc_final: 0.8448 (tp) REVERT: H 394 GLU cc_start: 0.9039 (tm-30) cc_final: 0.8593 (tm-30) REVERT: H 404 LEU cc_start: 0.8954 (mm) cc_final: 0.8499 (mm) outliers start: 1 outliers final: 0 residues processed: 899 average time/residue: 0.1570 time to fit residues: 230.7495 Evaluate side-chains 805 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 805 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 133 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 265 optimal weight: 0.0870 chunk 290 optimal weight: 20.0000 chunk 270 optimal weight: 8.9990 chunk 160 optimal weight: 40.0000 chunk 324 optimal weight: 10.0000 chunk 113 optimal weight: 7.9990 chunk 112 optimal weight: 5.9990 chunk 210 optimal weight: 5.9990 chunk 161 optimal weight: 5.9990 overall best weight: 4.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 ASN ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 ASN ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 ASN D 398 HIS E 23 GLN ** E 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 79 HIS ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 225 GLN ** H 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 225 GLN ** H 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 398 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.212008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.171020 restraints weight = 194666.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.180560 restraints weight = 99432.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.187700 restraints weight = 60939.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.193155 restraints weight = 36407.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.196024 restraints weight = 24511.478| |-----------------------------------------------------------------------------| r_work (final): 0.4300 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4298 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4298 r_free = 0.4298 target_work(ls_wunit_k1) = 0.195 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4298 r_free = 0.4298 target_work(ls_wunit_k1) = 0.195 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4298 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6552 moved from start: 0.4441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 27508 Z= 0.194 Angle : 0.804 11.675 37987 Z= 0.422 Chirality : 0.047 0.420 4428 Planarity : 0.007 0.152 4598 Dihedral : 19.585 166.941 4738 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 19.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 0.08 % Allowed : 2.25 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.14), residues: 3216 helix: -0.17 (0.12), residues: 1588 sheet: -1.51 (0.26), residues: 296 loop : -0.97 (0.18), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.061 0.002 ARG H 50 TYR 0.022 0.002 TYR G 226 PHE 0.052 0.003 PHE E 293 TRP 0.052 0.003 TRP H 267 HIS 0.020 0.002 HIS E 261 Details of bonding type rmsd covalent geometry : bond 0.00420 (27504) covalent geometry : angle 0.80366 (37987) hydrogen bonds : bond 0.04669 ( 1256) hydrogen bonds : angle 6.08947 ( 3636) Misc. bond : bond 0.00074 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 896 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 894 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 THR cc_start: 0.7998 (t) cc_final: 0.7687 (t) REVERT: A 65 MET cc_start: 0.6770 (tmm) cc_final: 0.6434 (tmm) REVERT: A 78 ASN cc_start: 0.8843 (m-40) cc_final: 0.7947 (t0) REVERT: A 89 MET cc_start: 0.8672 (ptt) cc_final: 0.8288 (ppp) REVERT: A 130 HIS cc_start: 0.6901 (m90) cc_final: 0.6438 (m90) REVERT: A 192 GLU cc_start: 0.9546 (mp0) cc_final: 0.9277 (pm20) REVERT: A 206 ASN cc_start: 0.7794 (p0) cc_final: 0.7339 (p0) REVERT: A 209 THR cc_start: 0.7582 (t) cc_final: 0.7301 (t) REVERT: A 226 TYR cc_start: 0.8560 (m-10) cc_final: 0.8241 (m-80) REVERT: A 234 ASP cc_start: 0.8493 (m-30) cc_final: 0.8282 (m-30) REVERT: A 355 GLU cc_start: 0.8964 (mt-10) cc_final: 0.8637 (mt-10) REVERT: A 361 TYR cc_start: 0.8508 (m-80) cc_final: 0.8240 (m-80) REVERT: A 394 GLU cc_start: 0.8122 (pp20) cc_final: 0.7492 (pp20) REVERT: A 398 HIS cc_start: 0.8072 (m-70) cc_final: 0.7645 (m-70) REVERT: A 400 HIS cc_start: 0.8937 (m90) cc_final: 0.8372 (m90) REVERT: B 5 ARG cc_start: 0.7249 (ttm170) cc_final: 0.6349 (ttm170) REVERT: B 9 ILE cc_start: 0.9068 (pt) cc_final: 0.8829 (pt) REVERT: B 10 GLU cc_start: 0.8915 (mp0) cc_final: 0.7948 (pp20) REVERT: B 156 LEU cc_start: 0.7916 (mp) cc_final: 0.7578 (mp) REVERT: B 192 GLU cc_start: 0.9034 (mt-10) cc_final: 0.8694 (mp0) REVERT: B 215 GLU cc_start: 0.9212 (mp0) cc_final: 0.8771 (mp0) REVERT: B 297 LEU cc_start: 0.7793 (tp) cc_final: 0.6052 (tp) REVERT: B 313 PHE cc_start: 0.7094 (p90) cc_final: 0.6495 (p90) REVERT: B 317 MET cc_start: 0.8521 (tpp) cc_final: 0.7911 (tpt) REVERT: B 332 LEU cc_start: 0.9100 (tp) cc_final: 0.8744 (tp) REVERT: B 341 ASP cc_start: 0.7861 (p0) cc_final: 0.7113 (t0) REVERT: B 383 GLN cc_start: 0.9285 (pm20) cc_final: 0.9001 (pm20) REVERT: B 387 GLN cc_start: 0.7860 (tm-30) cc_final: 0.7350 (tm-30) REVERT: B 391 LEU cc_start: 0.9295 (mp) cc_final: 0.8710 (mp) REVERT: C 9 ILE cc_start: 0.7820 (mt) cc_final: 0.7292 (mt) REVERT: C 65 MET cc_start: 0.9379 (ttp) cc_final: 0.7977 (tmm) REVERT: C 90 LEU cc_start: 0.7386 (tt) cc_final: 0.6621 (mm) REVERT: C 124 LYS cc_start: 0.7972 (ptpp) cc_final: 0.7460 (ptpp) REVERT: C 179 MET cc_start: 0.7220 (mmp) cc_final: 0.6299 (mmt) REVERT: C 199 MET cc_start: 0.7849 (mmm) cc_final: 0.7497 (mmm) REVERT: C 208 LYS cc_start: 0.6382 (mppt) cc_final: 0.5464 (mppt) REVERT: C 216 ASP cc_start: 0.6877 (m-30) cc_final: 0.6537 (m-30) REVERT: C 226 TYR cc_start: 0.8832 (m-10) cc_final: 0.8180 (m-80) REVERT: C 241 GLU cc_start: 0.8492 (mp0) cc_final: 0.8066 (mp0) REVERT: C 311 LEU cc_start: 0.5484 (mp) cc_final: 0.5248 (mp) REVERT: C 325 ASN cc_start: 0.6727 (t0) cc_final: 0.6366 (t0) REVERT: D 84 LEU cc_start: 0.8706 (tp) cc_final: 0.8212 (tp) REVERT: D 153 GLN cc_start: 0.7400 (mp10) cc_final: 0.6926 (mp10) REVERT: D 334 GLU cc_start: 0.8657 (tt0) cc_final: 0.8412 (tt0) REVERT: D 344 MET cc_start: 0.5782 (ttp) cc_final: 0.5068 (tpt) REVERT: E 241 GLU cc_start: 0.8605 (mp0) cc_final: 0.8259 (mp0) REVERT: E 250 ASP cc_start: 0.8085 (p0) cc_final: 0.7812 (p0) REVERT: F 10 GLU cc_start: 0.8611 (mm-30) cc_final: 0.8197 (pp20) REVERT: F 25 ASP cc_start: 0.8467 (m-30) cc_final: 0.8264 (m-30) REVERT: F 84 LEU cc_start: 0.8909 (tp) cc_final: 0.8277 (tp) REVERT: F 86 GLU cc_start: 0.7944 (mt-10) cc_final: 0.6946 (mt-10) REVERT: F 157 ARG cc_start: 0.6643 (mtm180) cc_final: 0.6333 (mmp80) REVERT: F 195 ARG cc_start: 0.7612 (mtt90) cc_final: 0.7106 (tpp80) REVERT: F 208 LYS cc_start: 0.5755 (mmtt) cc_final: 0.4859 (mmtm) REVERT: F 215 GLU cc_start: 0.8848 (pm20) cc_final: 0.8624 (pm20) REVERT: F 261 HIS cc_start: 0.7585 (m-70) cc_final: 0.7249 (m-70) REVERT: F 331 VAL cc_start: 0.8808 (t) cc_final: 0.8489 (t) REVERT: F 387 GLN cc_start: 0.7862 (tm-30) cc_final: 0.7127 (tm-30) REVERT: F 391 LEU cc_start: 0.9069 (mp) cc_final: 0.8584 (mp) REVERT: F 394 GLU cc_start: 0.7430 (tm-30) cc_final: 0.5997 (tm-30) REVERT: F 398 HIS cc_start: 0.7213 (m90) cc_final: 0.6536 (m90) REVERT: G 28 GLU cc_start: 0.7559 (mp0) cc_final: 0.7325 (mp0) REVERT: G 65 MET cc_start: 0.7745 (tmm) cc_final: 0.7318 (tmm) REVERT: G 218 MET cc_start: 0.8372 (tmm) cc_final: 0.8092 (tmm) REVERT: G 225 GLN cc_start: 0.7213 (mp10) cc_final: 0.6923 (pp30) REVERT: G 226 TYR cc_start: 0.8391 (m-80) cc_final: 0.7475 (m-80) REVERT: G 233 LEU cc_start: 0.7609 (mm) cc_final: 0.7321 (mm) REVERT: G 255 MET cc_start: 0.5195 (ttm) cc_final: 0.4175 (tpt) REVERT: G 292 ASN cc_start: 0.7855 (m-40) cc_final: 0.7639 (m-40) REVERT: G 320 MET cc_start: 0.6763 (tpt) cc_final: 0.6345 (tpt) REVERT: H 14 GLN cc_start: 0.8099 (pp30) cc_final: 0.7362 (pp30) REVERT: H 28 GLU cc_start: 0.9031 (tm-30) cc_final: 0.8059 (tm-30) REVERT: H 29 ILE cc_start: 0.9170 (mt) cc_final: 0.8868 (mt) REVERT: H 32 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7608 (mm-30) REVERT: H 42 MET cc_start: 0.7382 (ttm) cc_final: 0.6969 (ttm) REVERT: H 46 LEU cc_start: 0.9350 (mt) cc_final: 0.9095 (mt) REVERT: H 62 ILE cc_start: 0.9438 (tt) cc_final: 0.8862 (tt) REVERT: H 64 LYS cc_start: 0.9147 (pttm) cc_final: 0.8611 (pttm) REVERT: H 157 ARG cc_start: 0.7877 (mtm180) cc_final: 0.7392 (mtt180) REVERT: H 192 GLU cc_start: 0.9216 (tp30) cc_final: 0.8883 (tp30) REVERT: H 193 PHE cc_start: 0.8743 (t80) cc_final: 0.8468 (t80) REVERT: H 225 GLN cc_start: 0.8893 (mp10) cc_final: 0.8610 (mp10) REVERT: H 344 MET cc_start: 0.4617 (ttp) cc_final: 0.2781 (ttp) REVERT: H 387 GLN cc_start: 0.8448 (tm-30) cc_final: 0.7392 (tm-30) REVERT: H 391 LEU cc_start: 0.9303 (mp) cc_final: 0.9098 (mp) REVERT: H 394 GLU cc_start: 0.9044 (tm-30) cc_final: 0.7620 (tm-30) REVERT: H 398 HIS cc_start: 0.8117 (m90) cc_final: 0.7412 (m90) REVERT: H 404 LEU cc_start: 0.8953 (mm) cc_final: 0.8562 (mm) outliers start: 2 outliers final: 0 residues processed: 894 average time/residue: 0.1565 time to fit residues: 228.3760 Evaluate side-chains 789 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 789 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 35 optimal weight: 3.9990 chunk 3 optimal weight: 30.0000 chunk 205 optimal weight: 20.0000 chunk 115 optimal weight: 10.0000 chunk 156 optimal weight: 0.0470 chunk 264 optimal weight: 10.0000 chunk 81 optimal weight: 20.0000 chunk 66 optimal weight: 10.0000 chunk 267 optimal weight: 6.9990 chunk 129 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 overall best weight: 3.6084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN A 105 ASN ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 GLN B 206 ASN B 225 GLN ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 328 GLN C 398 HIS ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 ASN ** E 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 225 GLN F 230 ASN H 116 GLN ** H 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 405 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.213506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.172667 restraints weight = 187187.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.182004 restraints weight = 96757.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.188446 restraints weight = 59828.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.194383 restraints weight = 37595.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.197422 restraints weight = 24539.169| |-----------------------------------------------------------------------------| r_work (final): 0.4314 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4314 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4314 r_free = 0.4314 target_work(ls_wunit_k1) = 0.197 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4314 r_free = 0.4314 target_work(ls_wunit_k1) = 0.197 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4314 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6529 moved from start: 0.4697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 27508 Z= 0.179 Angle : 0.816 14.419 37987 Z= 0.429 Chirality : 0.046 0.228 4428 Planarity : 0.006 0.107 4598 Dihedral : 19.459 168.565 4738 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 18.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 0.20 % Allowed : 1.50 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.14), residues: 3216 helix: -0.14 (0.12), residues: 1616 sheet: -1.34 (0.27), residues: 296 loop : -0.91 (0.18), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 50 TYR 0.033 0.002 TYR B 301 PHE 0.044 0.003 PHE D 293 TRP 0.076 0.004 TRP C 401 HIS 0.008 0.001 HIS B 130 Details of bonding type rmsd covalent geometry : bond 0.00393 (27504) covalent geometry : angle 0.81563 (37987) hydrogen bonds : bond 0.04602 ( 1256) hydrogen bonds : angle 6.13072 ( 3636) Misc. bond : bond 0.00078 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 881 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 876 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 THR cc_start: 0.7991 (t) cc_final: 0.7415 (t) REVERT: A 65 MET cc_start: 0.6786 (tmm) cc_final: 0.6411 (tmm) REVERT: A 78 ASN cc_start: 0.8836 (m-40) cc_final: 0.7939 (t0) REVERT: A 89 MET cc_start: 0.8678 (ptt) cc_final: 0.8345 (ppp) REVERT: A 130 HIS cc_start: 0.6892 (m90) cc_final: 0.6405 (m90) REVERT: A 192 GLU cc_start: 0.9529 (mp0) cc_final: 0.9276 (pm20) REVERT: A 206 ASN cc_start: 0.7829 (p0) cc_final: 0.7357 (p0) REVERT: A 209 THR cc_start: 0.7665 (t) cc_final: 0.7424 (t) REVERT: A 226 TYR cc_start: 0.8510 (m-10) cc_final: 0.8118 (m-80) REVERT: A 234 ASP cc_start: 0.8591 (m-30) cc_final: 0.8372 (m-30) REVERT: A 355 GLU cc_start: 0.9000 (mt-10) cc_final: 0.8639 (mt-10) REVERT: A 361 TYR cc_start: 0.8479 (m-80) cc_final: 0.8190 (m-80) REVERT: A 394 GLU cc_start: 0.8022 (pp20) cc_final: 0.7799 (pp20) REVERT: A 400 HIS cc_start: 0.8455 (m90) cc_final: 0.7992 (m90) REVERT: B 5 ARG cc_start: 0.7275 (ttm170) cc_final: 0.6396 (ttm170) REVERT: B 10 GLU cc_start: 0.8912 (mp0) cc_final: 0.7922 (pp20) REVERT: B 156 LEU cc_start: 0.8075 (mp) cc_final: 0.7764 (mp) REVERT: B 192 GLU cc_start: 0.9002 (mt-10) cc_final: 0.8677 (mp0) REVERT: B 215 GLU cc_start: 0.9231 (mp0) cc_final: 0.8688 (mp0) REVERT: B 297 LEU cc_start: 0.8050 (tp) cc_final: 0.7323 (tp) REVERT: B 313 PHE cc_start: 0.7050 (p90) cc_final: 0.6463 (p90) REVERT: B 331 VAL cc_start: 0.8936 (t) cc_final: 0.8071 (t) REVERT: B 332 LEU cc_start: 0.9110 (tp) cc_final: 0.8896 (tp) REVERT: B 341 ASP cc_start: 0.7685 (p0) cc_final: 0.6980 (t0) REVERT: B 387 GLN cc_start: 0.7848 (tm-30) cc_final: 0.7253 (tm-30) REVERT: B 391 LEU cc_start: 0.9295 (mp) cc_final: 0.8695 (mp) REVERT: C 65 MET cc_start: 0.9391 (ttp) cc_final: 0.8136 (tmm) REVERT: C 90 LEU cc_start: 0.7416 (tt) cc_final: 0.6658 (mm) REVERT: C 124 LYS cc_start: 0.7948 (ptpp) cc_final: 0.7407 (ptpp) REVERT: C 179 MET cc_start: 0.7230 (mmp) cc_final: 0.6436 (mmt) REVERT: C 199 MET cc_start: 0.7869 (mmm) cc_final: 0.7478 (mmm) REVERT: C 208 LYS cc_start: 0.6254 (mppt) cc_final: 0.5366 (mppt) REVERT: C 216 ASP cc_start: 0.6794 (m-30) cc_final: 0.6488 (m-30) REVERT: C 226 TYR cc_start: 0.8715 (m-10) cc_final: 0.8186 (m-80) REVERT: C 241 GLU cc_start: 0.8490 (mp0) cc_final: 0.7880 (mp0) REVERT: C 325 ASN cc_start: 0.6761 (t0) cc_final: 0.6405 (t0) REVERT: C 335 MET cc_start: 0.8571 (mtm) cc_final: 0.8333 (mtm) REVERT: C 391 LEU cc_start: 0.8776 (mp) cc_final: 0.8517 (mp) REVERT: D 84 LEU cc_start: 0.8792 (tp) cc_final: 0.8166 (tp) REVERT: D 153 GLN cc_start: 0.7333 (mp10) cc_final: 0.6847 (mp10) REVERT: D 232 SER cc_start: 0.8296 (p) cc_final: 0.8086 (p) REVERT: D 344 MET cc_start: 0.5680 (ttp) cc_final: 0.5173 (tpt) REVERT: E 241 GLU cc_start: 0.8609 (mp0) cc_final: 0.8266 (mp0) REVERT: E 250 ASP cc_start: 0.8035 (p0) cc_final: 0.7770 (p0) REVERT: F 25 ASP cc_start: 0.8442 (m-30) cc_final: 0.8233 (m-30) REVERT: F 84 LEU cc_start: 0.8904 (tp) cc_final: 0.8280 (tp) REVERT: F 86 GLU cc_start: 0.7985 (mt-10) cc_final: 0.6920 (mt-10) REVERT: F 124 LYS cc_start: 0.8350 (mmtp) cc_final: 0.7722 (mmtm) REVERT: F 157 ARG cc_start: 0.6658 (mtm180) cc_final: 0.6336 (mmp80) REVERT: F 195 ARG cc_start: 0.7557 (mtt90) cc_final: 0.7075 (tpp80) REVERT: F 208 LYS cc_start: 0.5792 (mmtt) cc_final: 0.5126 (mmtm) REVERT: F 255 MET cc_start: 0.5304 (mtt) cc_final: 0.5042 (mtp) REVERT: F 261 HIS cc_start: 0.7451 (m-70) cc_final: 0.7239 (m-70) REVERT: F 331 VAL cc_start: 0.8741 (t) cc_final: 0.8455 (t) REVERT: F 384 ASP cc_start: 0.8571 (m-30) cc_final: 0.8309 (m-30) REVERT: F 387 GLN cc_start: 0.7678 (tm-30) cc_final: 0.7035 (tm-30) REVERT: F 391 LEU cc_start: 0.9042 (mp) cc_final: 0.8381 (mp) REVERT: F 398 HIS cc_start: 0.7210 (m90) cc_final: 0.6700 (m90) REVERT: G 65 MET cc_start: 0.7668 (tmm) cc_final: 0.7223 (tmm) REVERT: G 218 MET cc_start: 0.8387 (tmm) cc_final: 0.8120 (tmm) REVERT: G 225 GLN cc_start: 0.7136 (mp10) cc_final: 0.6923 (pp30) REVERT: G 226 TYR cc_start: 0.8355 (m-80) cc_final: 0.7486 (m-80) REVERT: G 233 LEU cc_start: 0.7529 (mm) cc_final: 0.7265 (mm) REVERT: G 255 MET cc_start: 0.5232 (ttm) cc_final: 0.4145 (tpt) REVERT: G 292 ASN cc_start: 0.7866 (m-40) cc_final: 0.7604 (m-40) REVERT: G 320 MET cc_start: 0.6643 (tpt) cc_final: 0.6226 (tpt) REVERT: H 14 GLN cc_start: 0.8077 (pp30) cc_final: 0.7337 (pp30) REVERT: H 28 GLU cc_start: 0.9008 (tm-30) cc_final: 0.8008 (tm-30) REVERT: H 29 ILE cc_start: 0.9175 (mt) cc_final: 0.8906 (mt) REVERT: H 32 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7634 (mm-30) REVERT: H 42 MET cc_start: 0.7886 (ttm) cc_final: 0.7496 (ttm) REVERT: H 64 LYS cc_start: 0.9165 (pttm) cc_final: 0.8618 (pttm) REVERT: H 157 ARG cc_start: 0.7832 (mtm180) cc_final: 0.7394 (mtt180) REVERT: H 159 PHE cc_start: 0.7854 (t80) cc_final: 0.7050 (t80) REVERT: H 192 GLU cc_start: 0.9221 (tp30) cc_final: 0.8904 (tp30) REVERT: H 193 PHE cc_start: 0.8745 (t80) cc_final: 0.8467 (t80) REVERT: H 320 MET cc_start: 0.6301 (mpp) cc_final: 0.5527 (mpp) REVERT: H 344 MET cc_start: 0.4549 (ttp) cc_final: 0.3976 (ttp) REVERT: H 383 GLN cc_start: 0.8719 (pm20) cc_final: 0.8517 (pm20) REVERT: H 387 GLN cc_start: 0.8414 (tm-30) cc_final: 0.7337 (tm-30) REVERT: H 394 GLU cc_start: 0.9176 (tm-30) cc_final: 0.7880 (tm-30) REVERT: H 398 HIS cc_start: 0.8127 (m90) cc_final: 0.7527 (m90) REVERT: H 404 LEU cc_start: 0.9005 (mm) cc_final: 0.8439 (mm) outliers start: 5 outliers final: 1 residues processed: 880 average time/residue: 0.1542 time to fit residues: 222.2884 Evaluate side-chains 785 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 784 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 226 optimal weight: 3.9990 chunk 228 optimal weight: 6.9990 chunk 177 optimal weight: 20.0000 chunk 61 optimal weight: 8.9990 chunk 96 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 29 optimal weight: 20.0000 chunk 127 optimal weight: 8.9990 chunk 205 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 67 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 ASN A 116 GLN ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 17 GLN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 ASN E 14 GLN E 88 HIS ** E 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 17 GLN ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 400 HIS ** H 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 225 GLN ** H 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 398 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.210621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.171928 restraints weight = 181048.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.180941 restraints weight = 94515.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.187371 restraints weight = 58076.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.192844 restraints weight = 35527.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.195250 restraints weight = 23436.915| |-----------------------------------------------------------------------------| r_work (final): 0.4293 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4293 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4293 r_free = 0.4293 target_work(ls_wunit_k1) = 0.195 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4293 r_free = 0.4293 target_work(ls_wunit_k1) = 0.195 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4293 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6589 moved from start: 0.4993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 27508 Z= 0.203 Angle : 0.838 14.222 37987 Z= 0.442 Chirality : 0.047 0.244 4428 Planarity : 0.006 0.144 4598 Dihedral : 19.288 168.287 4738 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 19.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 0.12 % Allowed : 1.30 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.14), residues: 3216 helix: -0.20 (0.12), residues: 1616 sheet: -1.32 (0.28), residues: 296 loop : -0.88 (0.18), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 195 TYR 0.033 0.002 TYR F 301 PHE 0.045 0.003 PHE D 293 TRP 0.066 0.004 TRP C 401 HIS 0.012 0.002 HIS F 70 Details of bonding type rmsd covalent geometry : bond 0.00438 (27504) covalent geometry : angle 0.83765 (37987) hydrogen bonds : bond 0.04829 ( 1256) hydrogen bonds : angle 6.20482 ( 3636) Misc. bond : bond 0.00095 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 879 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 876 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 THR cc_start: 0.7974 (t) cc_final: 0.7394 (t) REVERT: A 65 MET cc_start: 0.6959 (tmm) cc_final: 0.6535 (tmm) REVERT: A 78 ASN cc_start: 0.8634 (m-40) cc_final: 0.7925 (t0) REVERT: A 130 HIS cc_start: 0.6912 (m90) cc_final: 0.6393 (m90) REVERT: A 147 LEU cc_start: 0.9415 (tp) cc_final: 0.9172 (tp) REVERT: A 192 GLU cc_start: 0.9540 (mp0) cc_final: 0.9298 (pm20) REVERT: A 206 ASN cc_start: 0.7756 (p0) cc_final: 0.7340 (p0) REVERT: A 226 TYR cc_start: 0.8509 (m-10) cc_final: 0.8117 (m-80) REVERT: A 234 ASP cc_start: 0.8623 (m-30) cc_final: 0.8377 (m-30) REVERT: A 241 GLU cc_start: 0.8565 (mp0) cc_final: 0.8313 (mp0) REVERT: A 255 MET cc_start: 0.7001 (ppp) cc_final: 0.6608 (ppp) REVERT: A 355 GLU cc_start: 0.9049 (mt-10) cc_final: 0.8672 (mt-10) REVERT: A 361 TYR cc_start: 0.8517 (m-80) cc_final: 0.8214 (m-80) REVERT: A 394 GLU cc_start: 0.7933 (pp20) cc_final: 0.7315 (pp20) REVERT: A 400 HIS cc_start: 0.8639 (m90) cc_final: 0.8139 (m90) REVERT: B 5 ARG cc_start: 0.7226 (ttm170) cc_final: 0.6285 (ttm170) REVERT: B 9 ILE cc_start: 0.9011 (pt) cc_final: 0.8790 (pt) REVERT: B 10 GLU cc_start: 0.8883 (mp0) cc_final: 0.7966 (pp20) REVERT: B 156 LEU cc_start: 0.8121 (mp) cc_final: 0.7823 (mp) REVERT: B 192 GLU cc_start: 0.8944 (mt-10) cc_final: 0.8666 (mp0) REVERT: B 215 GLU cc_start: 0.9255 (mp0) cc_final: 0.8671 (mp0) REVERT: B 297 LEU cc_start: 0.8123 (tp) cc_final: 0.7395 (tp) REVERT: B 313 PHE cc_start: 0.7185 (p90) cc_final: 0.6640 (p90) REVERT: B 317 MET cc_start: 0.8118 (tpt) cc_final: 0.7291 (tpt) REVERT: B 331 VAL cc_start: 0.8930 (t) cc_final: 0.8020 (t) REVERT: B 332 LEU cc_start: 0.9068 (tp) cc_final: 0.8835 (tp) REVERT: B 341 ASP cc_start: 0.7822 (p0) cc_final: 0.6970 (t0) REVERT: B 383 GLN cc_start: 0.9342 (pm20) cc_final: 0.9108 (pm20) REVERT: B 387 GLN cc_start: 0.7998 (tm-30) cc_final: 0.7762 (tm-30) REVERT: B 391 LEU cc_start: 0.9323 (mp) cc_final: 0.8735 (mp) REVERT: C 65 MET cc_start: 0.9348 (ttp) cc_final: 0.8003 (tmm) REVERT: C 90 LEU cc_start: 0.7484 (tt) cc_final: 0.6758 (mm) REVERT: C 117 ASN cc_start: 0.8246 (t0) cc_final: 0.8045 (t0) REVERT: C 124 LYS cc_start: 0.8026 (ptpp) cc_final: 0.7393 (ptpp) REVERT: C 159 PHE cc_start: 0.7398 (t80) cc_final: 0.7042 (t80) REVERT: C 179 MET cc_start: 0.7424 (mmp) cc_final: 0.6406 (mmt) REVERT: C 199 MET cc_start: 0.7996 (mmm) cc_final: 0.7618 (mmm) REVERT: C 208 LYS cc_start: 0.6209 (mppt) cc_final: 0.5269 (mppt) REVERT: C 216 ASP cc_start: 0.6828 (m-30) cc_final: 0.6539 (m-30) REVERT: C 226 TYR cc_start: 0.8822 (m-10) cc_final: 0.8285 (m-80) REVERT: C 241 GLU cc_start: 0.8539 (mp0) cc_final: 0.7881 (mp0) REVERT: C 325 ASN cc_start: 0.6788 (t0) cc_final: 0.6451 (t0) REVERT: C 386 VAL cc_start: 0.8856 (t) cc_final: 0.8579 (p) REVERT: D 84 LEU cc_start: 0.8747 (tp) cc_final: 0.8136 (tp) REVERT: D 153 GLN cc_start: 0.7384 (mp10) cc_final: 0.6870 (mp10) REVERT: D 344 MET cc_start: 0.5825 (ttp) cc_final: 0.5181 (tpt) REVERT: E 241 GLU cc_start: 0.8578 (mp0) cc_final: 0.8231 (mp0) REVERT: E 250 ASP cc_start: 0.8022 (p0) cc_final: 0.7748 (p0) REVERT: F 86 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7131 (mt-10) REVERT: F 124 LYS cc_start: 0.8590 (mmtp) cc_final: 0.8218 (mmtm) REVERT: F 157 ARG cc_start: 0.6806 (mtm180) cc_final: 0.6464 (mmp80) REVERT: F 195 ARG cc_start: 0.7528 (mtt90) cc_final: 0.7017 (tpp80) REVERT: F 208 LYS cc_start: 0.5681 (mmtt) cc_final: 0.5049 (mmtm) REVERT: F 255 MET cc_start: 0.5131 (mtt) cc_final: 0.4863 (mtp) REVERT: F 261 HIS cc_start: 0.7502 (m-70) cc_final: 0.7041 (m-70) REVERT: F 301 TYR cc_start: 0.8044 (m-80) cc_final: 0.7807 (m-80) REVERT: F 331 VAL cc_start: 0.8760 (t) cc_final: 0.8517 (t) REVERT: F 383 GLN cc_start: 0.8884 (pm20) cc_final: 0.8606 (pm20) REVERT: F 384 ASP cc_start: 0.8637 (m-30) cc_final: 0.8337 (m-30) REVERT: F 387 GLN cc_start: 0.7911 (tm-30) cc_final: 0.7233 (tm-30) REVERT: F 391 LEU cc_start: 0.9159 (mp) cc_final: 0.8468 (mp) REVERT: F 398 HIS cc_start: 0.7213 (m90) cc_final: 0.6781 (m90) REVERT: G 59 ASP cc_start: 0.8841 (m-30) cc_final: 0.8431 (m-30) REVERT: G 218 MET cc_start: 0.8385 (tmm) cc_final: 0.8089 (tmm) REVERT: G 226 TYR cc_start: 0.8391 (m-80) cc_final: 0.7603 (m-80) REVERT: G 233 LEU cc_start: 0.7539 (mm) cc_final: 0.7287 (mm) REVERT: G 292 ASN cc_start: 0.7847 (m-40) cc_final: 0.7603 (m-40) REVERT: H 14 GLN cc_start: 0.8058 (pp30) cc_final: 0.7275 (pp30) REVERT: H 28 GLU cc_start: 0.8954 (tm-30) cc_final: 0.8374 (tm-30) REVERT: H 29 ILE cc_start: 0.9174 (mt) cc_final: 0.8873 (mt) REVERT: H 64 LYS cc_start: 0.9081 (pttm) cc_final: 0.8522 (pttm) REVERT: H 159 PHE cc_start: 0.7965 (t80) cc_final: 0.7131 (t80) REVERT: H 192 GLU cc_start: 0.9232 (tp30) cc_final: 0.8928 (tp30) REVERT: H 193 PHE cc_start: 0.8759 (t80) cc_final: 0.8490 (t80) REVERT: H 225 GLN cc_start: 0.8961 (mp10) cc_final: 0.8698 (mp10) REVERT: H 320 MET cc_start: 0.6673 (mpp) cc_final: 0.5857 (mpp) REVERT: H 344 MET cc_start: 0.4846 (ttp) cc_final: 0.4266 (ttp) REVERT: H 383 GLN cc_start: 0.8831 (pm20) cc_final: 0.8579 (pm20) REVERT: H 387 GLN cc_start: 0.8609 (tm-30) cc_final: 0.7774 (tm-30) REVERT: H 391 LEU cc_start: 0.9402 (mp) cc_final: 0.9033 (mp) REVERT: H 394 GLU cc_start: 0.9332 (tm-30) cc_final: 0.8440 (tm-30) REVERT: H 398 HIS cc_start: 0.8412 (m-70) cc_final: 0.7439 (m-70) REVERT: H 404 LEU cc_start: 0.8818 (mm) cc_final: 0.8518 (mm) outliers start: 3 outliers final: 1 residues processed: 877 average time/residue: 0.1521 time to fit residues: 218.9412 Evaluate side-chains 786 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 785 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 133 optimal weight: 5.9990 chunk 189 optimal weight: 5.9990 chunk 249 optimal weight: 0.9990 chunk 155 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 306 optimal weight: 5.9990 chunk 246 optimal weight: 8.9990 chunk 254 optimal weight: 6.9990 chunk 22 optimal weight: 20.0000 chunk 301 optimal weight: 8.9990 chunk 325 optimal weight: 10.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN A 105 ASN ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 ASN D 405 ASN ** E 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 383 GLN ** F 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 398 HIS G 225 GLN ** H 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 405 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.212581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.172306 restraints weight = 189635.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.182283 restraints weight = 97790.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.188182 restraints weight = 58034.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.194526 restraints weight = 37687.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.197557 restraints weight = 23012.158| |-----------------------------------------------------------------------------| r_work (final): 0.4314 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4312 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4312 r_free = 0.4312 target_work(ls_wunit_k1) = 0.197 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4312 r_free = 0.4312 target_work(ls_wunit_k1) = 0.197 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4312 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6554 moved from start: 0.5178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 27508 Z= 0.180 Angle : 0.839 14.356 37987 Z= 0.437 Chirality : 0.047 0.237 4428 Planarity : 0.006 0.105 4598 Dihedral : 19.196 170.794 4738 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 18.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 0.12 % Allowed : 0.43 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.14), residues: 3216 helix: -0.19 (0.12), residues: 1620 sheet: -1.20 (0.29), residues: 296 loop : -0.89 (0.18), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG E 26 TYR 0.030 0.002 TYR F 301 PHE 0.048 0.002 PHE D 293 TRP 0.055 0.004 TRP F 267 HIS 0.013 0.002 HIS G 398 Details of bonding type rmsd covalent geometry : bond 0.00391 (27504) covalent geometry : angle 0.83897 (37987) hydrogen bonds : bond 0.04569 ( 1256) hydrogen bonds : angle 6.18037 ( 3636) Misc. bond : bond 0.00096 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 877 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 874 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8802 (m-40) cc_final: 0.8104 (t0) REVERT: A 130 HIS cc_start: 0.6871 (m90) cc_final: 0.6396 (m90) REVERT: A 147 LEU cc_start: 0.9384 (tp) cc_final: 0.9161 (tp) REVERT: A 192 GLU cc_start: 0.9538 (mp0) cc_final: 0.9321 (pm20) REVERT: A 206 ASN cc_start: 0.7721 (p0) cc_final: 0.7328 (p0) REVERT: A 226 TYR cc_start: 0.8493 (m-10) cc_final: 0.8072 (m-80) REVERT: A 234 ASP cc_start: 0.8615 (m-30) cc_final: 0.8370 (m-30) REVERT: A 241 GLU cc_start: 0.8513 (mp0) cc_final: 0.8229 (mp0) REVERT: A 255 MET cc_start: 0.6857 (ppp) cc_final: 0.6517 (ppp) REVERT: A 361 TYR cc_start: 0.8489 (m-80) cc_final: 0.8238 (m-80) REVERT: A 383 GLN cc_start: 0.8865 (pt0) cc_final: 0.8662 (pt0) REVERT: A 394 GLU cc_start: 0.8061 (pp20) cc_final: 0.7790 (pp20) REVERT: A 398 HIS cc_start: 0.8125 (m-70) cc_final: 0.7579 (m-70) REVERT: A 400 HIS cc_start: 0.8616 (m90) cc_final: 0.8088 (m90) REVERT: B 5 ARG cc_start: 0.7417 (ttm170) cc_final: 0.6376 (ttm170) REVERT: B 156 LEU cc_start: 0.8006 (mp) cc_final: 0.7727 (mp) REVERT: B 192 GLU cc_start: 0.8990 (mt-10) cc_final: 0.8708 (mp0) REVERT: B 215 GLU cc_start: 0.9212 (mp0) cc_final: 0.8710 (mp0) REVERT: B 255 MET cc_start: 0.3432 (mtt) cc_final: 0.3167 (mtt) REVERT: B 297 LEU cc_start: 0.7983 (tp) cc_final: 0.7386 (tp) REVERT: B 313 PHE cc_start: 0.6999 (p90) cc_final: 0.6448 (p90) REVERT: B 331 VAL cc_start: 0.9010 (t) cc_final: 0.7946 (t) REVERT: B 332 LEU cc_start: 0.9091 (tp) cc_final: 0.8874 (tp) REVERT: B 341 ASP cc_start: 0.7671 (p0) cc_final: 0.6885 (t0) REVERT: B 383 GLN cc_start: 0.9336 (pm20) cc_final: 0.9085 (pm20) REVERT: B 387 GLN cc_start: 0.8058 (tm-30) cc_final: 0.7740 (tm-30) REVERT: B 391 LEU cc_start: 0.9298 (mp) cc_final: 0.8690 (mp) REVERT: B 398 HIS cc_start: 0.6609 (m90) cc_final: 0.6245 (m90) REVERT: C 59 ASP cc_start: 0.8921 (m-30) cc_final: 0.8720 (m-30) REVERT: C 65 MET cc_start: 0.9343 (ttp) cc_final: 0.8054 (tmm) REVERT: C 124 LYS cc_start: 0.8051 (ptpp) cc_final: 0.7421 (ptpp) REVERT: C 126 MET cc_start: 0.7496 (tmm) cc_final: 0.6938 (tpp) REVERT: C 179 MET cc_start: 0.7247 (mmp) cc_final: 0.6256 (mmt) REVERT: C 199 MET cc_start: 0.7969 (mmm) cc_final: 0.7694 (mmm) REVERT: C 208 LYS cc_start: 0.6062 (mppt) cc_final: 0.5188 (mppt) REVERT: C 216 ASP cc_start: 0.6913 (m-30) cc_final: 0.6626 (m-30) REVERT: C 226 TYR cc_start: 0.8831 (m-10) cc_final: 0.8282 (m-80) REVERT: C 241 GLU cc_start: 0.8521 (mp0) cc_final: 0.7987 (mp0) REVERT: C 320 MET cc_start: 0.7275 (tpt) cc_final: 0.6545 (tpt) REVERT: C 325 ASN cc_start: 0.6732 (t0) cc_final: 0.6400 (t0) REVERT: C 335 MET cc_start: 0.8280 (mtm) cc_final: 0.8057 (mtm) REVERT: C 391 LEU cc_start: 0.8713 (mp) cc_final: 0.8498 (mp) REVERT: D 84 LEU cc_start: 0.8744 (tp) cc_final: 0.8001 (tp) REVERT: D 153 GLN cc_start: 0.7322 (mp10) cc_final: 0.6806 (mp10) REVERT: D 239 LEU cc_start: 0.9035 (tp) cc_final: 0.8823 (tp) REVERT: D 255 MET cc_start: 0.4358 (mtt) cc_final: 0.3696 (mtt) REVERT: D 328 GLN cc_start: 0.7262 (tp-100) cc_final: 0.6869 (tp-100) REVERT: D 332 LEU cc_start: 0.8977 (tp) cc_final: 0.8776 (tp) REVERT: D 344 MET cc_start: 0.5760 (ttp) cc_final: 0.5144 (tpt) REVERT: E 22 VAL cc_start: 0.7887 (t) cc_final: 0.7570 (p) REVERT: E 179 MET cc_start: 0.8625 (mmt) cc_final: 0.8031 (mmp) REVERT: E 250 ASP cc_start: 0.7923 (p0) cc_final: 0.7611 (p0) REVERT: E 363 THR cc_start: 0.8518 (m) cc_final: 0.8211 (m) REVERT: F 10 GLU cc_start: 0.8592 (mm-30) cc_final: 0.7964 (pp20) REVERT: F 25 ASP cc_start: 0.8492 (m-30) cc_final: 0.8288 (m-30) REVERT: F 84 LEU cc_start: 0.8875 (tp) cc_final: 0.8641 (tp) REVERT: F 124 LYS cc_start: 0.8633 (mmtp) cc_final: 0.8265 (mmtm) REVERT: F 157 ARG cc_start: 0.6724 (mtm180) cc_final: 0.6437 (mmp80) REVERT: F 215 GLU cc_start: 0.8844 (pm20) cc_final: 0.8144 (pm20) REVERT: F 216 ASP cc_start: 0.7020 (m-30) cc_final: 0.6792 (m-30) REVERT: F 255 MET cc_start: 0.5100 (mtt) cc_final: 0.4783 (mtp) REVERT: F 261 HIS cc_start: 0.7478 (m-70) cc_final: 0.7249 (m-70) REVERT: F 335 MET cc_start: 0.7548 (mpp) cc_final: 0.7158 (mpp) REVERT: F 383 GLN cc_start: 0.8871 (pm20) cc_final: 0.8583 (pm20) REVERT: F 384 ASP cc_start: 0.8614 (m-30) cc_final: 0.8314 (m-30) REVERT: F 387 GLN cc_start: 0.7849 (tm-30) cc_final: 0.7198 (tm-30) REVERT: F 391 LEU cc_start: 0.9199 (mp) cc_final: 0.8495 (mp) REVERT: F 398 HIS cc_start: 0.7333 (m-70) cc_final: 0.6705 (m-70) REVERT: G 32 GLU cc_start: 0.7817 (pp20) cc_final: 0.7128 (pp20) REVERT: G 65 MET cc_start: 0.7730 (tmm) cc_final: 0.7334 (tmm) REVERT: G 89 MET cc_start: 0.6089 (ttt) cc_final: 0.5371 (ttp) REVERT: G 218 MET cc_start: 0.8432 (tmm) cc_final: 0.8109 (tmm) REVERT: G 226 TYR cc_start: 0.8404 (m-80) cc_final: 0.7622 (m-80) REVERT: G 233 LEU cc_start: 0.7515 (mm) cc_final: 0.7302 (mm) REVERT: G 292 ASN cc_start: 0.7919 (m-40) cc_final: 0.7713 (m-40) REVERT: G 320 MET cc_start: 0.6514 (tpt) cc_final: 0.6314 (tpt) REVERT: G 342 GLN cc_start: 0.4985 (mm110) cc_final: 0.4780 (mm-40) REVERT: H 14 GLN cc_start: 0.8057 (pp30) cc_final: 0.7271 (pp30) REVERT: H 28 GLU cc_start: 0.8964 (tm-30) cc_final: 0.8401 (tm-30) REVERT: H 29 ILE cc_start: 0.9168 (mt) cc_final: 0.8875 (mt) REVERT: H 64 LYS cc_start: 0.9048 (pttm) cc_final: 0.8495 (pttm) REVERT: H 159 PHE cc_start: 0.7968 (t80) cc_final: 0.7157 (t80) REVERT: H 192 GLU cc_start: 0.9246 (tp30) cc_final: 0.8854 (tp30) REVERT: H 193 PHE cc_start: 0.8780 (t80) cc_final: 0.8573 (t80) REVERT: H 320 MET cc_start: 0.6629 (mpp) cc_final: 0.5827 (mpp) REVERT: H 344 MET cc_start: 0.4698 (ttp) cc_final: 0.4175 (ttp) REVERT: H 387 GLN cc_start: 0.8514 (tm-30) cc_final: 0.7573 (tm-30) REVERT: H 391 LEU cc_start: 0.9366 (mp) cc_final: 0.8960 (mp) REVERT: H 394 GLU cc_start: 0.8972 (tm-30) cc_final: 0.7762 (tm-30) REVERT: H 398 HIS cc_start: 0.8071 (m-70) cc_final: 0.6899 (m-70) REVERT: H 404 LEU cc_start: 0.8859 (mm) cc_final: 0.8516 (mm) outliers start: 3 outliers final: 1 residues processed: 876 average time/residue: 0.1545 time to fit residues: 220.1018 Evaluate side-chains 780 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 779 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 291 optimal weight: 20.0000 chunk 40 optimal weight: 10.0000 chunk 298 optimal weight: 10.0000 chunk 268 optimal weight: 8.9990 chunk 86 optimal weight: 30.0000 chunk 311 optimal weight: 6.9990 chunk 104 optimal weight: 9.9990 chunk 84 optimal weight: 0.7980 chunk 160 optimal weight: 30.0000 chunk 203 optimal weight: 0.0040 chunk 202 optimal weight: 8.9990 overall best weight: 5.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 ASN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 161 ASN B 225 GLN ** B 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 161 ASN D 230 ASN ** E 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 20 GLN ** F 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 225 GLN ** H 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.210905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.172615 restraints weight = 163260.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.182047 restraints weight = 86288.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.187742 restraints weight = 51656.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.193112 restraints weight = 33200.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.196034 restraints weight = 21494.541| |-----------------------------------------------------------------------------| r_work (final): 0.4295 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4297 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4297 r_free = 0.4297 target_work(ls_wunit_k1) = 0.195 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4297 r_free = 0.4297 target_work(ls_wunit_k1) = 0.195 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4297 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6591 moved from start: 0.5439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 27508 Z= 0.199 Angle : 0.850 13.752 37987 Z= 0.445 Chirality : 0.047 0.240 4428 Planarity : 0.006 0.093 4598 Dihedral : 19.149 170.765 4738 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 19.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 0.12 % Allowed : 0.32 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.14), residues: 3216 helix: -0.24 (0.12), residues: 1624 sheet: -1.19 (0.29), residues: 296 loop : -0.93 (0.18), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG E 26 TYR 0.026 0.002 TYR G 226 PHE 0.046 0.003 PHE D 293 TRP 0.066 0.004 TRP F 287 HIS 0.017 0.002 HIS E 398 Details of bonding type rmsd covalent geometry : bond 0.00435 (27504) covalent geometry : angle 0.84987 (37987) hydrogen bonds : bond 0.04762 ( 1256) hydrogen bonds : angle 6.20742 ( 3636) Misc. bond : bond 0.00085 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 878 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 875 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 THR cc_start: 0.7910 (t) cc_final: 0.7447 (t) REVERT: A 20 GLN cc_start: 0.8903 (mp10) cc_final: 0.8673 (pm20) REVERT: A 65 MET cc_start: 0.7326 (tmm) cc_final: 0.6702 (tmm) REVERT: A 78 ASN cc_start: 0.8754 (m-40) cc_final: 0.8055 (t0) REVERT: A 130 HIS cc_start: 0.6939 (m90) cc_final: 0.6534 (m90) REVERT: A 147 LEU cc_start: 0.9341 (tp) cc_final: 0.9128 (tp) REVERT: A 206 ASN cc_start: 0.7701 (p0) cc_final: 0.7300 (p0) REVERT: A 226 TYR cc_start: 0.8442 (m-10) cc_final: 0.8042 (m-80) REVERT: A 234 ASP cc_start: 0.8605 (m-30) cc_final: 0.8351 (m-30) REVERT: A 241 GLU cc_start: 0.8508 (mp0) cc_final: 0.8204 (mp0) REVERT: A 255 MET cc_start: 0.6888 (ppp) cc_final: 0.6490 (ppp) REVERT: A 355 GLU cc_start: 0.9081 (mt-10) cc_final: 0.8767 (mt-10) REVERT: A 361 TYR cc_start: 0.8471 (m-80) cc_final: 0.8163 (m-80) REVERT: A 383 GLN cc_start: 0.8888 (pt0) cc_final: 0.8669 (pt0) REVERT: A 394 GLU cc_start: 0.8060 (pp20) cc_final: 0.7839 (pp20) REVERT: A 400 HIS cc_start: 0.8563 (m90) cc_final: 0.8047 (m90) REVERT: B 5 ARG cc_start: 0.7278 (ttm170) cc_final: 0.6285 (ttm170) REVERT: B 10 GLU cc_start: 0.8839 (mp0) cc_final: 0.7732 (pp20) REVERT: B 156 LEU cc_start: 0.7965 (mp) cc_final: 0.7641 (mp) REVERT: B 192 GLU cc_start: 0.8951 (mt-10) cc_final: 0.8713 (mp0) REVERT: B 215 GLU cc_start: 0.9263 (mp0) cc_final: 0.8767 (mp0) REVERT: B 297 LEU cc_start: 0.8068 (tp) cc_final: 0.7496 (tp) REVERT: B 313 PHE cc_start: 0.7090 (p90) cc_final: 0.6590 (p90) REVERT: B 331 VAL cc_start: 0.9026 (t) cc_final: 0.8105 (t) REVERT: B 332 LEU cc_start: 0.9143 (tp) cc_final: 0.8869 (tp) REVERT: B 341 ASP cc_start: 0.7624 (p0) cc_final: 0.6755 (t0) REVERT: B 344 MET cc_start: 0.8132 (ttm) cc_final: 0.7358 (ttm) REVERT: B 383 GLN cc_start: 0.9310 (pm20) cc_final: 0.9060 (pm20) REVERT: B 387 GLN cc_start: 0.7980 (tm-30) cc_final: 0.7715 (tm-30) REVERT: B 391 LEU cc_start: 0.9279 (mp) cc_final: 0.8678 (mp) REVERT: B 398 HIS cc_start: 0.6556 (m90) cc_final: 0.6266 (m90) REVERT: C 59 ASP cc_start: 0.8879 (m-30) cc_final: 0.8672 (m-30) REVERT: C 65 MET cc_start: 0.9318 (ttp) cc_final: 0.7955 (tmm) REVERT: C 124 LYS cc_start: 0.8073 (ptpp) cc_final: 0.7429 (ptpp) REVERT: C 159 PHE cc_start: 0.7097 (t80) cc_final: 0.6891 (t80) REVERT: C 199 MET cc_start: 0.8064 (mmm) cc_final: 0.7742 (mmm) REVERT: C 208 LYS cc_start: 0.6173 (mppt) cc_final: 0.5246 (mppt) REVERT: C 226 TYR cc_start: 0.8843 (m-10) cc_final: 0.8319 (m-80) REVERT: C 320 MET cc_start: 0.7436 (tpt) cc_final: 0.7181 (tpt) REVERT: C 325 ASN cc_start: 0.6803 (t0) cc_final: 0.6546 (t0) REVERT: C 386 VAL cc_start: 0.8958 (t) cc_final: 0.8700 (p) REVERT: D 84 LEU cc_start: 0.8791 (tp) cc_final: 0.8121 (tp) REVERT: D 153 GLN cc_start: 0.7366 (mp10) cc_final: 0.6860 (mp10) REVERT: D 328 GLN cc_start: 0.7266 (tp-100) cc_final: 0.7060 (tp-100) REVERT: D 344 MET cc_start: 0.5653 (ttp) cc_final: 0.5307 (tpt) REVERT: E 179 MET cc_start: 0.8608 (mmt) cc_final: 0.8266 (mmt) REVERT: E 250 ASP cc_start: 0.7931 (p0) cc_final: 0.7647 (p0) REVERT: E 363 THR cc_start: 0.8605 (m) cc_final: 0.8339 (m) REVERT: F 10 GLU cc_start: 0.8628 (mm-30) cc_final: 0.7931 (pp20) REVERT: F 65 MET cc_start: 0.7481 (tmm) cc_final: 0.7113 (tmm) REVERT: F 124 LYS cc_start: 0.8689 (mmtp) cc_final: 0.8370 (mmtm) REVERT: F 157 ARG cc_start: 0.7146 (ttm170) cc_final: 0.6789 (mmp80) REVERT: F 215 GLU cc_start: 0.8820 (pm20) cc_final: 0.8130 (pm20) REVERT: F 216 ASP cc_start: 0.7017 (m-30) cc_final: 0.6793 (m-30) REVERT: F 255 MET cc_start: 0.5045 (mtt) cc_final: 0.4764 (mtp) REVERT: F 261 HIS cc_start: 0.7546 (m-70) cc_final: 0.7292 (m-70) REVERT: F 383 GLN cc_start: 0.8887 (pm20) cc_final: 0.8632 (pm20) REVERT: F 384 ASP cc_start: 0.8609 (m-30) cc_final: 0.8326 (m-30) REVERT: F 387 GLN cc_start: 0.7900 (tm-30) cc_final: 0.7269 (tm-30) REVERT: F 391 LEU cc_start: 0.9158 (mp) cc_final: 0.8457 (mp) REVERT: F 398 HIS cc_start: 0.7167 (m-70) cc_final: 0.6458 (m-70) REVERT: G 59 ASP cc_start: 0.8749 (m-30) cc_final: 0.8338 (m-30) REVERT: G 65 MET cc_start: 0.7626 (tmm) cc_final: 0.7214 (tmm) REVERT: G 89 MET cc_start: 0.6051 (ttt) cc_final: 0.5213 (ttp) REVERT: G 218 MET cc_start: 0.8527 (tmm) cc_final: 0.8199 (tmm) REVERT: G 226 TYR cc_start: 0.8302 (m-80) cc_final: 0.7558 (m-80) REVERT: G 292 ASN cc_start: 0.7906 (m-40) cc_final: 0.7656 (m-40) REVERT: G 320 MET cc_start: 0.6728 (tpt) cc_final: 0.6526 (tpt) REVERT: G 387 GLN cc_start: 0.6734 (tp-100) cc_final: 0.6508 (tp40) REVERT: G 396 VAL cc_start: 0.8268 (t) cc_final: 0.8056 (t) REVERT: H 14 GLN cc_start: 0.8024 (pp30) cc_final: 0.7262 (pp30) REVERT: H 28 GLU cc_start: 0.8964 (tm-30) cc_final: 0.8394 (tm-30) REVERT: H 29 ILE cc_start: 0.9187 (mt) cc_final: 0.8866 (mt) REVERT: H 64 LYS cc_start: 0.9023 (pttm) cc_final: 0.8495 (pttm) REVERT: H 124 LYS cc_start: 0.8185 (mptt) cc_final: 0.7430 (mmtm) REVERT: H 157 ARG cc_start: 0.7794 (mtt180) cc_final: 0.7486 (mtt180) REVERT: H 159 PHE cc_start: 0.8095 (t80) cc_final: 0.7313 (t80) REVERT: H 192 GLU cc_start: 0.9143 (tp30) cc_final: 0.8779 (tp30) REVERT: H 193 PHE cc_start: 0.8797 (t80) cc_final: 0.8567 (t80) REVERT: H 225 GLN cc_start: 0.8974 (mp10) cc_final: 0.8716 (mp10) REVERT: H 320 MET cc_start: 0.6651 (mpp) cc_final: 0.5868 (mpp) REVERT: H 344 MET cc_start: 0.4786 (ttp) cc_final: 0.4328 (ttp) REVERT: H 387 GLN cc_start: 0.8537 (tm-30) cc_final: 0.7648 (tm-30) REVERT: H 391 LEU cc_start: 0.9402 (mp) cc_final: 0.9014 (mp) REVERT: H 398 HIS cc_start: 0.8101 (m-70) cc_final: 0.7568 (m-70) REVERT: H 404 LEU cc_start: 0.8753 (mm) cc_final: 0.8449 (mm) outliers start: 3 outliers final: 0 residues processed: 878 average time/residue: 0.1527 time to fit residues: 219.1872 Evaluate side-chains 782 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 782 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 61 optimal weight: 0.0870 chunk 257 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 11 optimal weight: 7.9990 chunk 199 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 47 optimal weight: 30.0000 chunk 99 optimal weight: 20.0000 chunk 105 optimal weight: 9.9990 chunk 116 optimal weight: 6.9990 chunk 300 optimal weight: 10.0000 overall best weight: 5.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 ASN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 161 ASN ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 161 ASN D 230 ASN ** E 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 225 GLN G 225 GLN ** H 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 405 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.210320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.170117 restraints weight = 189730.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.179706 restraints weight = 95837.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.185762 restraints weight = 57858.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.191564 restraints weight = 36924.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.195383 restraints weight = 23115.471| |-----------------------------------------------------------------------------| r_work (final): 0.4289 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4290 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4290 r_free = 0.4290 target_work(ls_wunit_k1) = 0.195 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4290 r_free = 0.4290 target_work(ls_wunit_k1) = 0.195 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4290 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6607 moved from start: 0.5628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 27508 Z= 0.201 Angle : 0.861 13.087 37987 Z= 0.453 Chirality : 0.048 0.237 4428 Planarity : 0.006 0.093 4598 Dihedral : 19.090 171.729 4738 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 19.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 0.12 % Allowed : 0.20 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.14), residues: 3216 helix: -0.26 (0.12), residues: 1624 sheet: -1.13 (0.29), residues: 296 loop : -0.95 (0.18), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG E 26 TYR 0.028 0.002 TYR F 143 PHE 0.048 0.003 PHE F 159 TRP 0.058 0.004 TRP F 267 HIS 0.017 0.002 HIS C 398 Details of bonding type rmsd covalent geometry : bond 0.00437 (27504) covalent geometry : angle 0.86102 (37987) hydrogen bonds : bond 0.04780 ( 1256) hydrogen bonds : angle 6.21284 ( 3636) Misc. bond : bond 0.00086 ( 4) =============================================================================== Job complete usr+sys time: 5760.89 seconds wall clock time: 99 minutes 41.63 seconds (5981.63 seconds total)