Starting phenix.real_space_refine on Sun Feb 25 10:15:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i49_35165/02_2024/8i49_35165_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i49_35165/02_2024/8i49_35165.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i49_35165/02_2024/8i49_35165.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i49_35165/02_2024/8i49_35165.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i49_35165/02_2024/8i49_35165_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i49_35165/02_2024/8i49_35165_trim_updated.pdb" } resolution = 2.41 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.112 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 18 5.49 5 S 108 5.16 5 C 16302 2.51 5 N 4266 2.21 5 O 4812 1.98 5 H 25248 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 100": "OE1" <-> "OE2" Residue "A ASP 111": "OD1" <-> "OD2" Residue "A ASP 112": "OD1" <-> "OD2" Residue "A TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 252": "OD1" <-> "OD2" Residue "A GLU 335": "OE1" <-> "OE2" Residue "A GLU 365": "OE1" <-> "OE2" Residue "A ASP 373": "OD1" <-> "OD2" Residue "A TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 429": "OD1" <-> "OD2" Residue "A GLU 468": "OE1" <-> "OE2" Residue "A ASP 524": "OD1" <-> "OD2" Residue "D TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 100": "OE1" <-> "OE2" Residue "D ASP 111": "OD1" <-> "OD2" Residue "D ASP 112": "OD1" <-> "OD2" Residue "D TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 252": "OD1" <-> "OD2" Residue "D GLU 335": "OE1" <-> "OE2" Residue "D GLU 365": "OE1" <-> "OE2" Residue "D ASP 373": "OD1" <-> "OD2" Residue "D TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 429": "OD1" <-> "OD2" Residue "D GLU 468": "OE1" <-> "OE2" Residue "D ASP 524": "OD1" <-> "OD2" Residue "E TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 100": "OE1" <-> "OE2" Residue "E ASP 111": "OD1" <-> "OD2" Residue "E ASP 112": "OD1" <-> "OD2" Residue "E TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 252": "OD1" <-> "OD2" Residue "E GLU 335": "OE1" <-> "OE2" Residue "E GLU 365": "OE1" <-> "OE2" Residue "E ASP 373": "OD1" <-> "OD2" Residue "E TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 429": "OD1" <-> "OD2" Residue "E GLU 468": "OE1" <-> "OE2" Residue "E ASP 524": "OD1" <-> "OD2" Residue "F TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 100": "OE1" <-> "OE2" Residue "F ASP 111": "OD1" <-> "OD2" Residue "F ASP 112": "OD1" <-> "OD2" Residue "F TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 252": "OD1" <-> "OD2" Residue "F GLU 335": "OE1" <-> "OE2" Residue "F GLU 365": "OE1" <-> "OE2" Residue "F ASP 373": "OD1" <-> "OD2" Residue "F TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 429": "OD1" <-> "OD2" Residue "F GLU 468": "OE1" <-> "OE2" Residue "F ASP 524": "OD1" <-> "OD2" Residue "C TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 100": "OE1" <-> "OE2" Residue "C ASP 111": "OD1" <-> "OD2" Residue "C ASP 112": "OD1" <-> "OD2" Residue "C TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 252": "OD1" <-> "OD2" Residue "C GLU 335": "OE1" <-> "OE2" Residue "C GLU 365": "OE1" <-> "OE2" Residue "C ASP 373": "OD1" <-> "OD2" Residue "C TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 429": "OD1" <-> "OD2" Residue "C GLU 468": "OE1" <-> "OE2" Residue "C ASP 524": "OD1" <-> "OD2" Residue "B TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 100": "OE1" <-> "OE2" Residue "B ASP 111": "OD1" <-> "OD2" Residue "B ASP 112": "OD1" <-> "OD2" Residue "B TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 252": "OD1" <-> "OD2" Residue "B GLU 335": "OE1" <-> "OE2" Residue "B GLU 365": "OE1" <-> "OE2" Residue "B ASP 373": "OD1" <-> "OD2" Residue "B TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 429": "OD1" <-> "OD2" Residue "B GLU 468": "OE1" <-> "OE2" Residue "B ASP 524": "OD1" <-> "OD2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 50754 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 8428 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 506} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 8428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 8428 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 506} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 8428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 8428 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 506} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 8428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 8428 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 506} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 8428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 8428 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 506} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 8428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 8428 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 506} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 21.74, per 1000 atoms: 0.43 Number of scatterers: 50754 At special positions: 0 Unit cell: (169.338, 158.184, 96.33, 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 108 16.00 P 18 15.00 O 4812 8.00 N 4266 7.00 C 16302 6.00 H 25248 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 39.91 Conformation dependent library (CDL) restraints added in 4.9 seconds 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5964 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 120 helices and 48 sheets defined 31.9% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.69 Creating SS restraints... Processing helix chain 'A' and resid 15 through 20 Processing helix chain 'A' and resid 41 through 57 Processing helix chain 'A' and resid 74 through 85 removed outlier: 3.681A pdb=" N PHE A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE A 83 " --> pdb=" O CYS A 79 " (cutoff:3.500A) Proline residue: A 84 - end of helix Processing helix chain 'A' and resid 99 through 109 Processing helix chain 'A' and resid 118 through 126 Proline residue: A 122 - end of helix Processing helix chain 'A' and resid 128 through 130 No H-bonds generated for 'chain 'A' and resid 128 through 130' Processing helix chain 'A' and resid 147 through 153 Processing helix chain 'A' and resid 189 through 203 Processing helix chain 'A' and resid 229 through 239 Proline residue: A 233 - end of helix removed outlier: 3.683A pdb=" N ALA A 236 " --> pdb=" O PRO A 233 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET A 238 " --> pdb=" O MET A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 261 Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 281 through 284 removed outlier: 3.996A pdb=" N ALA A 284 " --> pdb=" O LYS A 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 281 through 284' Processing helix chain 'A' and resid 301 through 308 Processing helix chain 'A' and resid 336 through 338 No H-bonds generated for 'chain 'A' and resid 336 through 338' Processing helix chain 'A' and resid 341 through 348 Processing helix chain 'A' and resid 396 through 401 Processing helix chain 'A' and resid 403 through 405 No H-bonds generated for 'chain 'A' and resid 403 through 405' Processing helix chain 'A' and resid 440 through 449 Processing helix chain 'A' and resid 484 through 492 Processing helix chain 'A' and resid 525 through 531 Processing helix chain 'D' and resid 15 through 20 Processing helix chain 'D' and resid 41 through 57 Processing helix chain 'D' and resid 74 through 85 removed outlier: 3.681A pdb=" N PHE D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE D 83 " --> pdb=" O CYS D 79 " (cutoff:3.500A) Proline residue: D 84 - end of helix Processing helix chain 'D' and resid 99 through 109 Processing helix chain 'D' and resid 118 through 126 Proline residue: D 122 - end of helix Processing helix chain 'D' and resid 128 through 130 No H-bonds generated for 'chain 'D' and resid 128 through 130' Processing helix chain 'D' and resid 147 through 153 Processing helix chain 'D' and resid 189 through 203 Processing helix chain 'D' and resid 229 through 239 Proline residue: D 233 - end of helix removed outlier: 3.683A pdb=" N ALA D 236 " --> pdb=" O PRO D 233 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET D 238 " --> pdb=" O MET D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 261 Processing helix chain 'D' and resid 270 through 278 Processing helix chain 'D' and resid 281 through 284 removed outlier: 3.996A pdb=" N ALA D 284 " --> pdb=" O LYS D 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 281 through 284' Processing helix chain 'D' and resid 301 through 308 Processing helix chain 'D' and resid 336 through 338 No H-bonds generated for 'chain 'D' and resid 336 through 338' Processing helix chain 'D' and resid 341 through 348 Processing helix chain 'D' and resid 396 through 401 Processing helix chain 'D' and resid 403 through 405 No H-bonds generated for 'chain 'D' and resid 403 through 405' Processing helix chain 'D' and resid 440 through 449 Processing helix chain 'D' and resid 484 through 492 Processing helix chain 'D' and resid 525 through 531 Processing helix chain 'E' and resid 15 through 20 Processing helix chain 'E' and resid 41 through 57 Processing helix chain 'E' and resid 74 through 85 removed outlier: 3.681A pdb=" N PHE E 81 " --> pdb=" O LEU E 77 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE E 83 " --> pdb=" O CYS E 79 " (cutoff:3.500A) Proline residue: E 84 - end of helix Processing helix chain 'E' and resid 99 through 109 Processing helix chain 'E' and resid 118 through 126 Proline residue: E 122 - end of helix Processing helix chain 'E' and resid 128 through 130 No H-bonds generated for 'chain 'E' and resid 128 through 130' Processing helix chain 'E' and resid 147 through 153 Processing helix chain 'E' and resid 189 through 203 Processing helix chain 'E' and resid 229 through 239 Proline residue: E 233 - end of helix removed outlier: 3.683A pdb=" N ALA E 236 " --> pdb=" O PRO E 233 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET E 238 " --> pdb=" O MET E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 261 Processing helix chain 'E' and resid 270 through 278 Processing helix chain 'E' and resid 281 through 284 removed outlier: 3.996A pdb=" N ALA E 284 " --> pdb=" O LYS E 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 281 through 284' Processing helix chain 'E' and resid 301 through 308 Processing helix chain 'E' and resid 336 through 338 No H-bonds generated for 'chain 'E' and resid 336 through 338' Processing helix chain 'E' and resid 341 through 348 Processing helix chain 'E' and resid 396 through 401 Processing helix chain 'E' and resid 403 through 405 No H-bonds generated for 'chain 'E' and resid 403 through 405' Processing helix chain 'E' and resid 440 through 449 Processing helix chain 'E' and resid 484 through 492 Processing helix chain 'E' and resid 525 through 531 Processing helix chain 'F' and resid 15 through 20 Processing helix chain 'F' and resid 41 through 57 Processing helix chain 'F' and resid 74 through 85 removed outlier: 3.680A pdb=" N PHE F 81 " --> pdb=" O LEU F 77 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE F 83 " --> pdb=" O CYS F 79 " (cutoff:3.500A) Proline residue: F 84 - end of helix Processing helix chain 'F' and resid 99 through 109 Processing helix chain 'F' and resid 118 through 126 Proline residue: F 122 - end of helix Processing helix chain 'F' and resid 128 through 130 No H-bonds generated for 'chain 'F' and resid 128 through 130' Processing helix chain 'F' and resid 147 through 153 Processing helix chain 'F' and resid 189 through 203 Processing helix chain 'F' and resid 229 through 239 Proline residue: F 233 - end of helix removed outlier: 3.683A pdb=" N ALA F 236 " --> pdb=" O PRO F 233 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET F 238 " --> pdb=" O MET F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 261 Processing helix chain 'F' and resid 270 through 278 Processing helix chain 'F' and resid 281 through 284 removed outlier: 3.996A pdb=" N ALA F 284 " --> pdb=" O LYS F 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 281 through 284' Processing helix chain 'F' and resid 301 through 308 Processing helix chain 'F' and resid 336 through 338 No H-bonds generated for 'chain 'F' and resid 336 through 338' Processing helix chain 'F' and resid 341 through 348 Processing helix chain 'F' and resid 396 through 401 Processing helix chain 'F' and resid 403 through 405 No H-bonds generated for 'chain 'F' and resid 403 through 405' Processing helix chain 'F' and resid 440 through 449 Processing helix chain 'F' and resid 484 through 492 Processing helix chain 'F' and resid 525 through 531 Processing helix chain 'C' and resid 15 through 20 Processing helix chain 'C' and resid 41 through 57 Processing helix chain 'C' and resid 74 through 85 removed outlier: 3.680A pdb=" N PHE C 81 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE C 83 " --> pdb=" O CYS C 79 " (cutoff:3.500A) Proline residue: C 84 - end of helix Processing helix chain 'C' and resid 99 through 109 Processing helix chain 'C' and resid 118 through 126 Proline residue: C 122 - end of helix Processing helix chain 'C' and resid 128 through 130 No H-bonds generated for 'chain 'C' and resid 128 through 130' Processing helix chain 'C' and resid 147 through 153 Processing helix chain 'C' and resid 189 through 203 Processing helix chain 'C' and resid 229 through 239 Proline residue: C 233 - end of helix removed outlier: 3.682A pdb=" N ALA C 236 " --> pdb=" O PRO C 233 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET C 238 " --> pdb=" O MET C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 261 Processing helix chain 'C' and resid 270 through 278 Processing helix chain 'C' and resid 281 through 284 removed outlier: 3.996A pdb=" N ALA C 284 " --> pdb=" O LYS C 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 281 through 284' Processing helix chain 'C' and resid 301 through 308 Processing helix chain 'C' and resid 336 through 338 No H-bonds generated for 'chain 'C' and resid 336 through 338' Processing helix chain 'C' and resid 341 through 348 Processing helix chain 'C' and resid 396 through 401 Processing helix chain 'C' and resid 403 through 405 No H-bonds generated for 'chain 'C' and resid 403 through 405' Processing helix chain 'C' and resid 440 through 449 Processing helix chain 'C' and resid 484 through 492 Processing helix chain 'C' and resid 525 through 531 Processing helix chain 'B' and resid 15 through 20 Processing helix chain 'B' and resid 41 through 57 Processing helix chain 'B' and resid 74 through 85 removed outlier: 3.681A pdb=" N PHE B 81 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE B 83 " --> pdb=" O CYS B 79 " (cutoff:3.500A) Proline residue: B 84 - end of helix Processing helix chain 'B' and resid 99 through 109 Processing helix chain 'B' and resid 118 through 126 Proline residue: B 122 - end of helix Processing helix chain 'B' and resid 128 through 130 No H-bonds generated for 'chain 'B' and resid 128 through 130' Processing helix chain 'B' and resid 147 through 153 Processing helix chain 'B' and resid 189 through 203 Processing helix chain 'B' and resid 229 through 239 Proline residue: B 233 - end of helix removed outlier: 3.683A pdb=" N ALA B 236 " --> pdb=" O PRO B 233 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET B 238 " --> pdb=" O MET B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 261 Processing helix chain 'B' and resid 270 through 278 Processing helix chain 'B' and resid 281 through 284 removed outlier: 3.996A pdb=" N ALA B 284 " --> pdb=" O LYS B 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 281 through 284' Processing helix chain 'B' and resid 301 through 308 Processing helix chain 'B' and resid 336 through 338 No H-bonds generated for 'chain 'B' and resid 336 through 338' Processing helix chain 'B' and resid 341 through 348 Processing helix chain 'B' and resid 396 through 401 Processing helix chain 'B' and resid 403 through 405 No H-bonds generated for 'chain 'B' and resid 403 through 405' Processing helix chain 'B' and resid 440 through 449 Processing helix chain 'B' and resid 484 through 492 Processing helix chain 'B' and resid 525 through 531 Processing sheet with id= A, first strand: chain 'A' and resid 30 through 33 Processing sheet with id= B, first strand: chain 'A' and resid 89 through 92 removed outlier: 6.387A pdb=" N ILE A 113 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N MET A 69 " --> pdb=" O ILE A 113 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU A 115 " --> pdb=" O MET A 69 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ARG A 136 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ILE A 116 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N VAL A 138 " --> pdb=" O ILE A 116 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 266 through 268 Processing sheet with id= D, first strand: chain 'A' and resid 361 through 363 Processing sheet with id= E, first strand: chain 'A' and resid 169 through 175 removed outlier: 6.808A pdb=" N PHE A 187 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N THR A 172 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL A 185 " --> pdb=" O THR A 172 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N TYR A 174 " --> pdb=" O LYS A 183 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N LYS A 183 " --> pdb=" O TYR A 174 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 317 through 319 Processing sheet with id= G, first strand: chain 'A' and resid 411 through 415 removed outlier: 6.665A pdb=" N HIS A 414 " --> pdb=" O ILE A 423 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ILE A 423 " --> pdb=" O HIS A 414 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 453 through 462 removed outlier: 6.874A pdb=" N THR A 475 " --> pdb=" O SER A 454 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL A 456 " --> pdb=" O LEU A 473 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU A 473 " --> pdb=" O VAL A 456 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL A 458 " --> pdb=" O LEU A 471 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU A 471 " --> pdb=" O VAL A 458 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N GLY A 460 " --> pdb=" O VAL A 469 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N VAL A 469 " --> pdb=" O GLY A 460 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 30 through 33 Processing sheet with id= J, first strand: chain 'D' and resid 89 through 92 removed outlier: 6.387A pdb=" N ILE D 113 " --> pdb=" O ALA D 67 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N MET D 69 " --> pdb=" O ILE D 113 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU D 115 " --> pdb=" O MET D 69 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ARG D 136 " --> pdb=" O ILE D 114 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ILE D 116 " --> pdb=" O ARG D 136 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N VAL D 138 " --> pdb=" O ILE D 116 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 266 through 268 Processing sheet with id= L, first strand: chain 'D' and resid 361 through 363 Processing sheet with id= M, first strand: chain 'D' and resid 169 through 175 removed outlier: 6.807A pdb=" N PHE D 187 " --> pdb=" O ALA D 170 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N THR D 172 " --> pdb=" O VAL D 185 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL D 185 " --> pdb=" O THR D 172 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N TYR D 174 " --> pdb=" O LYS D 183 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N LYS D 183 " --> pdb=" O TYR D 174 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 317 through 319 Processing sheet with id= O, first strand: chain 'D' and resid 411 through 415 removed outlier: 6.664A pdb=" N HIS D 414 " --> pdb=" O ILE D 423 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ILE D 423 " --> pdb=" O HIS D 414 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 453 through 462 removed outlier: 6.874A pdb=" N THR D 475 " --> pdb=" O SER D 454 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL D 456 " --> pdb=" O LEU D 473 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU D 473 " --> pdb=" O VAL D 456 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL D 458 " --> pdb=" O LEU D 471 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU D 471 " --> pdb=" O VAL D 458 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N GLY D 460 " --> pdb=" O VAL D 469 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N VAL D 469 " --> pdb=" O GLY D 460 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 30 through 33 Processing sheet with id= R, first strand: chain 'E' and resid 89 through 92 removed outlier: 6.387A pdb=" N ILE E 113 " --> pdb=" O ALA E 67 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N MET E 69 " --> pdb=" O ILE E 113 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU E 115 " --> pdb=" O MET E 69 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ARG E 136 " --> pdb=" O ILE E 114 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ILE E 116 " --> pdb=" O ARG E 136 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N VAL E 138 " --> pdb=" O ILE E 116 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 266 through 268 Processing sheet with id= T, first strand: chain 'E' and resid 361 through 363 Processing sheet with id= U, first strand: chain 'E' and resid 169 through 175 removed outlier: 6.808A pdb=" N PHE E 187 " --> pdb=" O ALA E 170 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N THR E 172 " --> pdb=" O VAL E 185 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL E 185 " --> pdb=" O THR E 172 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N TYR E 174 " --> pdb=" O LYS E 183 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N LYS E 183 " --> pdb=" O TYR E 174 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 317 through 319 Processing sheet with id= W, first strand: chain 'E' and resid 411 through 415 removed outlier: 6.665A pdb=" N HIS E 414 " --> pdb=" O ILE E 423 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ILE E 423 " --> pdb=" O HIS E 414 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 453 through 462 removed outlier: 6.873A pdb=" N THR E 475 " --> pdb=" O SER E 454 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL E 456 " --> pdb=" O LEU E 473 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU E 473 " --> pdb=" O VAL E 456 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL E 458 " --> pdb=" O LEU E 471 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU E 471 " --> pdb=" O VAL E 458 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N GLY E 460 " --> pdb=" O VAL E 469 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N VAL E 469 " --> pdb=" O GLY E 460 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'F' and resid 30 through 33 Processing sheet with id= Z, first strand: chain 'F' and resid 89 through 92 removed outlier: 6.387A pdb=" N ILE F 113 " --> pdb=" O ALA F 67 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N MET F 69 " --> pdb=" O ILE F 113 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU F 115 " --> pdb=" O MET F 69 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ARG F 136 " --> pdb=" O ILE F 114 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ILE F 116 " --> pdb=" O ARG F 136 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N VAL F 138 " --> pdb=" O ILE F 116 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'F' and resid 266 through 268 Processing sheet with id= AB, first strand: chain 'F' and resid 361 through 363 Processing sheet with id= AC, first strand: chain 'F' and resid 169 through 175 removed outlier: 6.808A pdb=" N PHE F 187 " --> pdb=" O ALA F 170 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N THR F 172 " --> pdb=" O VAL F 185 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL F 185 " --> pdb=" O THR F 172 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N TYR F 174 " --> pdb=" O LYS F 183 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N LYS F 183 " --> pdb=" O TYR F 174 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 317 through 319 Processing sheet with id= AE, first strand: chain 'F' and resid 411 through 415 removed outlier: 6.664A pdb=" N HIS F 414 " --> pdb=" O ILE F 423 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ILE F 423 " --> pdb=" O HIS F 414 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'F' and resid 453 through 462 removed outlier: 6.874A pdb=" N THR F 475 " --> pdb=" O SER F 454 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL F 456 " --> pdb=" O LEU F 473 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU F 473 " --> pdb=" O VAL F 456 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL F 458 " --> pdb=" O LEU F 471 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU F 471 " --> pdb=" O VAL F 458 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLY F 460 " --> pdb=" O VAL F 469 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N VAL F 469 " --> pdb=" O GLY F 460 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'C' and resid 30 through 33 Processing sheet with id= AH, first strand: chain 'C' and resid 89 through 92 removed outlier: 6.386A pdb=" N ILE C 113 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N MET C 69 " --> pdb=" O ILE C 113 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU C 115 " --> pdb=" O MET C 69 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ARG C 136 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ILE C 116 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N VAL C 138 " --> pdb=" O ILE C 116 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'C' and resid 266 through 268 Processing sheet with id= AJ, first strand: chain 'C' and resid 361 through 363 Processing sheet with id= AK, first strand: chain 'C' and resid 169 through 175 removed outlier: 6.808A pdb=" N PHE C 187 " --> pdb=" O ALA C 170 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N THR C 172 " --> pdb=" O VAL C 185 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL C 185 " --> pdb=" O THR C 172 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N TYR C 174 " --> pdb=" O LYS C 183 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N LYS C 183 " --> pdb=" O TYR C 174 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'C' and resid 317 through 319 Processing sheet with id= AM, first strand: chain 'C' and resid 411 through 415 removed outlier: 6.665A pdb=" N HIS C 414 " --> pdb=" O ILE C 423 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N ILE C 423 " --> pdb=" O HIS C 414 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'C' and resid 453 through 462 removed outlier: 6.874A pdb=" N THR C 475 " --> pdb=" O SER C 454 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL C 456 " --> pdb=" O LEU C 473 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU C 473 " --> pdb=" O VAL C 456 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL C 458 " --> pdb=" O LEU C 471 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU C 471 " --> pdb=" O VAL C 458 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N GLY C 460 " --> pdb=" O VAL C 469 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N VAL C 469 " --> pdb=" O GLY C 460 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'B' and resid 30 through 33 Processing sheet with id= AP, first strand: chain 'B' and resid 89 through 92 removed outlier: 6.387A pdb=" N ILE B 113 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N MET B 69 " --> pdb=" O ILE B 113 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU B 115 " --> pdb=" O MET B 69 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ARG B 136 " --> pdb=" O ILE B 114 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ILE B 116 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N VAL B 138 " --> pdb=" O ILE B 116 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'B' and resid 266 through 268 Processing sheet with id= AR, first strand: chain 'B' and resid 361 through 363 Processing sheet with id= AS, first strand: chain 'B' and resid 169 through 175 removed outlier: 6.808A pdb=" N PHE B 187 " --> pdb=" O ALA B 170 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N THR B 172 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL B 185 " --> pdb=" O THR B 172 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N TYR B 174 " --> pdb=" O LYS B 183 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N LYS B 183 " --> pdb=" O TYR B 174 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'B' and resid 317 through 319 Processing sheet with id= AU, first strand: chain 'B' and resid 411 through 415 removed outlier: 6.665A pdb=" N HIS B 414 " --> pdb=" O ILE B 423 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N ILE B 423 " --> pdb=" O HIS B 414 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'B' and resid 453 through 462 removed outlier: 6.873A pdb=" N THR B 475 " --> pdb=" O SER B 454 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL B 456 " --> pdb=" O LEU B 473 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU B 473 " --> pdb=" O VAL B 456 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL B 458 " --> pdb=" O LEU B 471 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU B 471 " --> pdb=" O VAL B 458 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N GLY B 460 " --> pdb=" O VAL B 469 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N VAL B 469 " --> pdb=" O GLY B 460 " (cutoff:3.500A) 606 hydrogen bonds defined for protein. 1656 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 20.41 Time building geometry restraints manager: 41.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.01: 25224 1.01 - 1.21: 381 1.21 - 1.41: 10372 1.41 - 1.61: 15131 1.61 - 1.81: 228 Bond restraints: 51336 Sorted by residual: bond pdb=" C6 ATP D1101 " pdb=" N6 ATP D1101 " ideal model delta sigma weight residual 1.337 1.466 -0.129 1.10e-02 8.26e+03 1.37e+02 bond pdb=" C6 ATP B1101 " pdb=" N6 ATP B1101 " ideal model delta sigma weight residual 1.337 1.466 -0.129 1.10e-02 8.26e+03 1.37e+02 bond pdb=" C6 ATP A1101 " pdb=" N6 ATP A1101 " ideal model delta sigma weight residual 1.337 1.465 -0.128 1.10e-02 8.26e+03 1.36e+02 bond pdb=" C6 ATP C1101 " pdb=" N6 ATP C1101 " ideal model delta sigma weight residual 1.337 1.465 -0.128 1.10e-02 8.26e+03 1.36e+02 bond pdb=" C6 ATP E1101 " pdb=" N6 ATP E1101 " ideal model delta sigma weight residual 1.337 1.465 -0.128 1.10e-02 8.26e+03 1.36e+02 ... (remaining 51331 not shown) Histogram of bond angle deviations from ideal: 98.68 - 107.99: 11372 107.99 - 117.29: 57285 117.29 - 126.60: 23810 126.60 - 135.90: 587 135.90 - 145.21: 6 Bond angle restraints: 93060 Sorted by residual: angle pdb=" PB ATP B1101 " pdb=" O3B ATP B1101 " pdb=" PG ATP B1101 " ideal model delta sigma weight residual 139.87 125.06 14.81 1.00e+00 1.00e+00 2.19e+02 angle pdb=" PB ATP D1101 " pdb=" O3B ATP D1101 " pdb=" PG ATP D1101 " ideal model delta sigma weight residual 139.87 125.08 14.79 1.00e+00 1.00e+00 2.19e+02 angle pdb=" PB ATP F1101 " pdb=" O3B ATP F1101 " pdb=" PG ATP F1101 " ideal model delta sigma weight residual 139.87 125.09 14.78 1.00e+00 1.00e+00 2.19e+02 angle pdb=" PB ATP A1101 " pdb=" O3B ATP A1101 " pdb=" PG ATP A1101 " ideal model delta sigma weight residual 139.87 125.09 14.78 1.00e+00 1.00e+00 2.18e+02 angle pdb=" PB ATP C1101 " pdb=" O3B ATP C1101 " pdb=" PG ATP C1101 " ideal model delta sigma weight residual 139.87 125.10 14.77 1.00e+00 1.00e+00 2.18e+02 ... (remaining 93055 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.32: 21599 17.32 - 34.64: 1549 34.64 - 51.96: 720 51.96 - 69.28: 206 69.28 - 86.60: 88 Dihedral angle restraints: 24162 sinusoidal: 13200 harmonic: 10962 Sorted by residual: dihedral pdb=" CA GLY C 324 " pdb=" C GLY C 324 " pdb=" N PRO C 325 " pdb=" CA PRO C 325 " ideal model delta harmonic sigma weight residual 0.00 27.26 -27.26 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA GLY E 324 " pdb=" C GLY E 324 " pdb=" N PRO E 325 " pdb=" CA PRO E 325 " ideal model delta harmonic sigma weight residual 0.00 27.21 -27.21 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA GLY A 324 " pdb=" C GLY A 324 " pdb=" N PRO A 325 " pdb=" CA PRO A 325 " ideal model delta harmonic sigma weight residual 0.00 27.20 -27.20 0 5.00e+00 4.00e-02 2.96e+01 ... (remaining 24159 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.125: 3605 0.125 - 0.251: 298 0.251 - 0.376: 74 0.376 - 0.501: 19 0.501 - 0.627: 6 Chirality restraints: 4002 Sorted by residual: chirality pdb=" CA LYS D 62 " pdb=" N LYS D 62 " pdb=" C LYS D 62 " pdb=" CB LYS D 62 " both_signs ideal model delta sigma weight residual False 2.51 1.88 0.63 2.00e-01 2.50e+01 9.81e+00 chirality pdb=" CA LYS E 62 " pdb=" N LYS E 62 " pdb=" C LYS E 62 " pdb=" CB LYS E 62 " both_signs ideal model delta sigma weight residual False 2.51 1.88 0.63 2.00e-01 2.50e+01 9.81e+00 chirality pdb=" CA LYS F 62 " pdb=" N LYS F 62 " pdb=" C LYS F 62 " pdb=" CB LYS F 62 " both_signs ideal model delta sigma weight residual False 2.51 1.88 0.63 2.00e-01 2.50e+01 9.78e+00 ... (remaining 3999 not shown) Planarity restraints: 7518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN F 464 " -0.227 2.00e-02 2.50e+03 4.66e-01 3.25e+03 pdb=" CG ASN F 464 " 0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN F 464 " 0.224 2.00e-02 2.50e+03 pdb=" ND2 ASN F 464 " 0.000 2.00e-02 2.50e+03 pdb="HD21 ASN F 464 " -0.782 2.00e-02 2.50e+03 pdb="HD22 ASN F 464 " 0.767 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 464 " 0.227 2.00e-02 2.50e+03 4.66e-01 3.25e+03 pdb=" CG ASN B 464 " -0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN B 464 " -0.225 2.00e-02 2.50e+03 pdb=" ND2 ASN B 464 " -0.000 2.00e-02 2.50e+03 pdb="HD21 ASN B 464 " 0.782 2.00e-02 2.50e+03 pdb="HD22 ASN B 464 " -0.766 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 464 " 0.227 2.00e-02 2.50e+03 4.66e-01 3.25e+03 pdb=" CG ASN A 464 " -0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN A 464 " -0.225 2.00e-02 2.50e+03 pdb=" ND2 ASN A 464 " -0.000 2.00e-02 2.50e+03 pdb="HD21 ASN A 464 " 0.782 2.00e-02 2.50e+03 pdb="HD22 ASN A 464 " -0.766 2.00e-02 2.50e+03 ... (remaining 7515 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.07: 901 2.07 - 2.70: 84636 2.70 - 3.33: 145203 3.33 - 3.97: 198372 3.97 - 4.60: 307775 Nonbonded interactions: 736887 Sorted by model distance: nonbonded pdb=" HD2 HIS C 108 " pdb=" HH TYR C 174 " model vdw 1.437 2.100 nonbonded pdb=" HD2 HIS E 108 " pdb=" HH TYR E 174 " model vdw 1.437 2.100 nonbonded pdb=" HD2 HIS B 108 " pdb=" HH TYR B 174 " model vdw 1.437 2.100 nonbonded pdb=" HD2 HIS A 108 " pdb=" HH TYR A 174 " model vdw 1.437 2.100 nonbonded pdb=" HD2 HIS D 108 " pdb=" HH TYR D 174 " model vdw 1.437 2.100 ... (remaining 736882 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.700 Extract box with map and model: 9.730 Check model and map are aligned: 0.720 Set scattering table: 0.420 Process input model: 157.180 Find NCS groups from input model: 2.390 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 186.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 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 : 0.015 0.129 26088 Z= 1.001 Angle : 1.456 14.809 35430 Z= 0.957 Chirality : 0.090 0.627 4002 Planarity : 0.008 0.065 4482 Dihedral : 16.837 86.598 9762 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.06 % Favored : 93.75 % Rotamer: Outliers : 0.43 % Allowed : 11.32 % Favored : 88.25 % Cbeta Deviations : 0.97 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.14), residues: 3168 helix: -0.25 (0.15), residues: 1092 sheet: -0.81 (0.21), residues: 540 loop : -1.60 (0.14), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.004 TRP F 466 HIS 0.010 0.002 HIS C 45 PHE 0.027 0.004 PHE F 315 TYR 0.028 0.004 TYR C 148 ARG 0.005 0.001 ARG E 136 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Evaluate side-chains 234 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 222 time to evaluate : 3.908 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: A 235 MET cc_start: 0.9421 (mtt) cc_final: 0.9130 (mtt) REVERT: D 175 THR cc_start: 0.8964 (t) cc_final: 0.8711 (t) REVERT: D 425 ASP cc_start: 0.7792 (t0) cc_final: 0.7553 (t70) REVERT: E 175 THR cc_start: 0.8971 (t) cc_final: 0.8733 (t) REVERT: B 235 MET cc_start: 0.9397 (mtt) cc_final: 0.9113 (mtt) outliers start: 12 outliers final: 8 residues processed: 234 average time/residue: 2.8955 time to fit residues: 792.6105 Evaluate side-chains 188 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 180 time to evaluate : 4.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain E residue 499 ILE Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain F residue 499 ILE Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain B residue 499 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 0.8980 chunk 241 optimal weight: 0.9980 chunk 133 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 162 optimal weight: 0.6980 chunk 128 optimal weight: 1.9990 chunk 249 optimal weight: 2.9990 chunk 96 optimal weight: 7.9990 chunk 151 optimal weight: 1.9990 chunk 185 optimal weight: 0.5980 chunk 288 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 26088 Z= 0.180 Angle : 0.591 7.795 35430 Z= 0.309 Chirality : 0.045 0.160 4002 Planarity : 0.004 0.052 4482 Dihedral : 9.048 59.177 3646 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.04 % Favored : 95.77 % Rotamer: Outliers : 0.83 % Allowed : 13.05 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.14), residues: 3168 helix: 0.51 (0.16), residues: 1092 sheet: -0.69 (0.21), residues: 552 loop : -1.36 (0.15), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 437 HIS 0.005 0.001 HIS A 228 PHE 0.010 0.001 PHE D 120 TYR 0.012 0.001 TYR D 148 ARG 0.007 0.000 ARG D 150 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Evaluate side-chains 216 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 193 time to evaluate : 4.539 Fit side-chains revert: symmetry clash REVERT: D 175 THR cc_start: 0.8924 (t) cc_final: 0.8604 (t) REVERT: D 425 ASP cc_start: 0.7659 (t0) cc_final: 0.7430 (t70) REVERT: E 28 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7683 (mp0) REVERT: E 175 THR cc_start: 0.8920 (t) cc_final: 0.8647 (t) REVERT: F 235 MET cc_start: 0.9266 (mtt) cc_final: 0.8834 (mtt) REVERT: C 235 MET cc_start: 0.9280 (mtt) cc_final: 0.8847 (mtt) REVERT: B 235 MET cc_start: 0.9216 (mtt) cc_final: 0.8942 (mtt) outliers start: 23 outliers final: 5 residues processed: 211 average time/residue: 3.0819 time to fit residues: 754.6199 Evaluate side-chains 186 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 180 time to evaluate : 3.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 158 GLU Chi-restraints excluded: chain F residue 375 GLU Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 488 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 160 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 240 optimal weight: 3.9990 chunk 196 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 289 optimal weight: 3.9990 chunk 312 optimal weight: 2.9990 chunk 257 optimal weight: 0.9990 chunk 286 optimal weight: 0.7980 chunk 98 optimal weight: 9.9990 chunk 232 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 108 HIS E 108 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 26088 Z= 0.280 Angle : 0.594 8.377 35430 Z= 0.314 Chirality : 0.046 0.161 4002 Planarity : 0.004 0.050 4482 Dihedral : 9.039 56.847 3634 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.36 % Favored : 95.45 % Rotamer: Outliers : 0.94 % Allowed : 12.33 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.14), residues: 3168 helix: 0.61 (0.16), residues: 1092 sheet: -0.70 (0.21), residues: 552 loop : -1.22 (0.15), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 230 HIS 0.006 0.001 HIS C 108 PHE 0.011 0.002 PHE A 173 TYR 0.015 0.002 TYR D 80 ARG 0.009 0.001 ARG C 150 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Evaluate side-chains 208 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 182 time to evaluate : 4.228 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 331 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7632 (mt0) REVERT: D 175 THR cc_start: 0.8926 (t) cc_final: 0.8674 (t) REVERT: D 425 ASP cc_start: 0.7794 (t0) cc_final: 0.7505 (t70) REVERT: E 175 THR cc_start: 0.8902 (t) cc_final: 0.8671 (t) REVERT: E 425 ASP cc_start: 0.7882 (t0) cc_final: 0.7512 (t70) REVERT: F 235 MET cc_start: 0.9355 (mtt) cc_final: 0.8927 (mtt) REVERT: F 331 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7229 (mt0) REVERT: C 235 MET cc_start: 0.9348 (mtt) cc_final: 0.8930 (mtt) REVERT: B 150 ARG cc_start: 0.7971 (mpt-90) cc_final: 0.7705 (mtm110) REVERT: B 331 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7488 (mt0) REVERT: B 375 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7244 (pm20) outliers start: 26 outliers final: 9 residues processed: 198 average time/residue: 2.8405 time to fit residues: 662.6885 Evaluate side-chains 185 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 172 time to evaluate : 4.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain D residue 158 GLU Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 331 GLN Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 331 GLN Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain B residue 375 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 285 optimal weight: 3.9990 chunk 217 optimal weight: 4.9990 chunk 150 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 290 optimal weight: 4.9990 chunk 307 optimal weight: 0.2980 chunk 151 optimal weight: 7.9990 chunk 275 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 26088 Z= 0.294 Angle : 0.594 8.467 35430 Z= 0.313 Chirality : 0.046 0.156 4002 Planarity : 0.004 0.052 4482 Dihedral : 8.743 60.582 3634 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.20 % Favored : 95.61 % Rotamer: Outliers : 1.16 % Allowed : 12.29 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.14), residues: 3168 helix: 0.63 (0.16), residues: 1092 sheet: -0.75 (0.21), residues: 552 loop : -1.13 (0.15), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 230 HIS 0.006 0.001 HIS A 228 PHE 0.011 0.002 PHE A 187 TYR 0.013 0.002 TYR F 148 ARG 0.009 0.001 ARG C 150 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Evaluate side-chains 212 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 180 time to evaluate : 3.962 Fit side-chains REVERT: A 331 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7570 (mt0) REVERT: D 175 THR cc_start: 0.8870 (t) cc_final: 0.8628 (t) REVERT: E 175 THR cc_start: 0.8841 (t) cc_final: 0.8611 (t) REVERT: E 375 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.6937 (pp20) REVERT: E 425 ASP cc_start: 0.7877 (t0) cc_final: 0.7633 (t70) REVERT: F 235 MET cc_start: 0.9363 (mtt) cc_final: 0.8922 (mtt) REVERT: F 331 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7204 (mt0) REVERT: C 197 MET cc_start: 0.9025 (mmp) cc_final: 0.8817 (mmm) REVERT: B 331 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.7557 (mt0) REVERT: B 375 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7254 (pm20) outliers start: 32 outliers final: 15 residues processed: 203 average time/residue: 2.9753 time to fit residues: 704.5864 Evaluate side-chains 192 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 172 time to evaluate : 3.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain D residue 158 GLU Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain E residue 222 THR Chi-restraints excluded: chain E residue 375 GLU Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 331 GLN Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain B residue 375 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 255 optimal weight: 10.0000 chunk 174 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 228 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 262 optimal weight: 10.0000 chunk 212 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 156 optimal weight: 7.9990 chunk 275 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 HIS F 108 HIS C 108 HIS B 108 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 26088 Z= 0.311 Angle : 0.596 8.780 35430 Z= 0.315 Chirality : 0.046 0.157 4002 Planarity : 0.004 0.060 4482 Dihedral : 8.746 65.574 3634 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.20 % Favored : 95.61 % Rotamer: Outliers : 1.27 % Allowed : 12.18 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.14), residues: 3168 helix: 0.63 (0.16), residues: 1092 sheet: -0.77 (0.21), residues: 552 loop : -1.05 (0.15), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 230 HIS 0.005 0.001 HIS B 228 PHE 0.011 0.002 PHE A 187 TYR 0.016 0.002 TYR D 148 ARG 0.012 0.001 ARG A 150 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Evaluate side-chains 210 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 175 time to evaluate : 3.974 Fit side-chains REVERT: A 331 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7585 (mt0) REVERT: D 175 THR cc_start: 0.8825 (t) cc_final: 0.8600 (t) REVERT: E 175 THR cc_start: 0.8813 (t) cc_final: 0.8602 (t) REVERT: E 425 ASP cc_start: 0.7895 (t0) cc_final: 0.7652 (t70) REVERT: F 235 MET cc_start: 0.9372 (mtt) cc_final: 0.8939 (mtt) REVERT: F 331 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7186 (mt0) REVERT: C 235 MET cc_start: 0.9368 (mtt) cc_final: 0.8928 (mtt) REVERT: C 331 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7045 (mm110) REVERT: B 331 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7573 (mt0) REVERT: B 375 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7336 (pm20) outliers start: 35 outliers final: 17 residues processed: 201 average time/residue: 2.9582 time to fit residues: 698.1244 Evaluate side-chains 192 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 170 time to evaluate : 3.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 136 ARG Chi-restraints excluded: chain E residue 222 THR Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 331 GLN Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 331 GLN Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain B residue 375 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 103 optimal weight: 1.9990 chunk 276 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 180 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 307 optimal weight: 0.7980 chunk 255 optimal weight: 9.9990 chunk 142 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 101 optimal weight: 0.7980 chunk 161 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 26088 Z= 0.163 Angle : 0.532 8.387 35430 Z= 0.277 Chirality : 0.043 0.151 4002 Planarity : 0.004 0.066 4482 Dihedral : 8.157 64.768 3634 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.88 % Favored : 95.93 % Rotamer: Outliers : 0.65 % Allowed : 12.94 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.15), residues: 3168 helix: 0.68 (0.16), residues: 1128 sheet: -0.67 (0.21), residues: 552 loop : -0.87 (0.15), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 230 HIS 0.005 0.001 HIS B 228 PHE 0.008 0.001 PHE B 187 TYR 0.011 0.001 TYR A 148 ARG 0.009 0.000 ARG C 150 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Evaluate side-chains 199 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 181 time to evaluate : 3.993 Fit side-chains REVERT: D 175 THR cc_start: 0.8793 (t) cc_final: 0.8576 (t) REVERT: E 175 THR cc_start: 0.8785 (t) cc_final: 0.8585 (t) REVERT: E 425 ASP cc_start: 0.7895 (t0) cc_final: 0.7687 (t70) REVERT: F 235 MET cc_start: 0.9341 (mtt) cc_final: 0.8946 (mtt) REVERT: C 197 MET cc_start: 0.9019 (mmp) cc_final: 0.8781 (mmm) REVERT: C 235 MET cc_start: 0.9339 (mtt) cc_final: 0.8938 (mtt) outliers start: 18 outliers final: 12 residues processed: 196 average time/residue: 3.0299 time to fit residues: 691.7357 Evaluate side-chains 186 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 174 time to evaluate : 3.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain E residue 222 THR Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain B residue 222 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 296 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 175 optimal weight: 3.9990 chunk 224 optimal weight: 0.3980 chunk 174 optimal weight: 1.9990 chunk 259 optimal weight: 7.9990 chunk 171 optimal weight: 0.5980 chunk 306 optimal weight: 3.9990 chunk 191 optimal weight: 3.9990 chunk 186 optimal weight: 3.9990 chunk 141 optimal weight: 0.0170 overall best weight: 1.0022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 26088 Z= 0.163 Angle : 0.521 8.445 35430 Z= 0.270 Chirality : 0.043 0.148 4002 Planarity : 0.004 0.084 4482 Dihedral : 7.878 65.077 3634 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.14 % Favored : 95.68 % Rotamer: Outliers : 0.65 % Allowed : 13.02 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.15), residues: 3168 helix: 0.91 (0.16), residues: 1098 sheet: -0.55 (0.22), residues: 552 loop : -0.61 (0.16), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 230 HIS 0.004 0.001 HIS B 228 PHE 0.007 0.001 PHE D 187 TYR 0.012 0.001 TYR D 148 ARG 0.010 0.000 ARG C 150 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Evaluate side-chains 195 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 177 time to evaluate : 4.404 Fit side-chains REVERT: A 136 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.8433 (ttt180) REVERT: A 331 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7590 (mt0) REVERT: D 175 THR cc_start: 0.8768 (t) cc_final: 0.8563 (t) REVERT: E 175 THR cc_start: 0.8775 (t) cc_final: 0.8571 (t) REVERT: F 235 MET cc_start: 0.9328 (mtt) cc_final: 0.8948 (mtt) REVERT: C 235 MET cc_start: 0.9333 (mtt) cc_final: 0.8971 (mtt) outliers start: 18 outliers final: 10 residues processed: 193 average time/residue: 3.2007 time to fit residues: 718.7588 Evaluate side-chains 184 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 172 time to evaluate : 3.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ARG Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain E residue 222 THR Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain B residue 222 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 189 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 194 optimal weight: 2.9990 chunk 208 optimal weight: 9.9990 chunk 151 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 240 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 26088 Z= 0.437 Angle : 0.652 9.096 35430 Z= 0.346 Chirality : 0.049 0.159 4002 Planarity : 0.005 0.053 4482 Dihedral : 8.641 76.891 3634 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.70 % Favored : 95.11 % Rotamer: Outliers : 0.94 % Allowed : 12.87 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.14), residues: 3168 helix: 0.44 (0.16), residues: 1128 sheet: -0.79 (0.21), residues: 552 loop : -0.85 (0.15), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 230 HIS 0.008 0.001 HIS A 228 PHE 0.014 0.002 PHE D 187 TYR 0.018 0.003 TYR F 148 ARG 0.009 0.001 ARG C 150 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Evaluate side-chains 199 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 173 time to evaluate : 4.295 Fit side-chains REVERT: A 136 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.8326 (ttt180) REVERT: A 331 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.7632 (mt0) REVERT: D 175 THR cc_start: 0.8785 (t) cc_final: 0.8573 (t) REVERT: E 259 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7852 (tm-30) REVERT: F 235 MET cc_start: 0.9384 (mtt) cc_final: 0.8928 (mtt) REVERT: C 235 MET cc_start: 0.9388 (mtt) cc_final: 0.8969 (mtt) REVERT: C 375 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7221 (pm20) REVERT: B 331 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7477 (mt0) outliers start: 26 outliers final: 15 residues processed: 196 average time/residue: 2.9374 time to fit residues: 673.0781 Evaluate side-chains 192 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 172 time to evaluate : 4.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ARG Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain E residue 222 THR Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 259 GLU Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 375 GLU Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 331 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 278 optimal weight: 3.9990 chunk 293 optimal weight: 2.9990 chunk 267 optimal weight: 0.6980 chunk 285 optimal weight: 0.5980 chunk 171 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 224 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 258 optimal weight: 9.9990 chunk 270 optimal weight: 2.9990 chunk 284 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 26088 Z= 0.153 Angle : 0.525 8.254 35430 Z= 0.274 Chirality : 0.043 0.148 4002 Planarity : 0.004 0.078 4482 Dihedral : 7.829 79.500 3634 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.20 % Favored : 95.61 % Rotamer: Outliers : 0.51 % Allowed : 13.23 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.15), residues: 3168 helix: 0.88 (0.16), residues: 1092 sheet: -0.63 (0.21), residues: 552 loop : -0.58 (0.15), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 230 HIS 0.005 0.001 HIS A 228 PHE 0.007 0.001 PHE D 225 TYR 0.010 0.001 TYR D 148 ARG 0.012 0.001 ARG A 150 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Evaluate side-chains 190 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 176 time to evaluate : 3.817 Fit side-chains REVERT: A 136 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.8376 (ttt180) REVERT: D 175 THR cc_start: 0.8759 (t) cc_final: 0.8550 (t) REVERT: F 235 MET cc_start: 0.9343 (mtt) cc_final: 0.8935 (mtt) REVERT: F 365 GLU cc_start: 0.7527 (mp0) cc_final: 0.7151 (pm20) REVERT: C 235 MET cc_start: 0.9343 (mtt) cc_final: 0.8956 (mtt) REVERT: B 365 GLU cc_start: 0.7488 (mp0) cc_final: 0.7113 (pm20) outliers start: 14 outliers final: 10 residues processed: 188 average time/residue: 3.0166 time to fit residues: 665.0245 Evaluate side-chains 181 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 170 time to evaluate : 3.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ARG Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain E residue 222 THR Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain B residue 222 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 187 optimal weight: 3.9990 chunk 302 optimal weight: 2.9990 chunk 184 optimal weight: 0.8980 chunk 143 optimal weight: 0.0980 chunk 209 optimal weight: 8.9990 chunk 316 optimal weight: 8.9990 chunk 291 optimal weight: 0.0870 chunk 252 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 194 optimal weight: 0.1980 chunk 154 optimal weight: 9.9990 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 26088 Z= 0.156 Angle : 0.511 7.737 35430 Z= 0.265 Chirality : 0.043 0.148 4002 Planarity : 0.004 0.099 4482 Dihedral : 7.613 83.873 3634 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.67 % Favored : 95.14 % Rotamer: Outliers : 0.51 % Allowed : 13.34 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.15), residues: 3168 helix: 1.01 (0.17), residues: 1098 sheet: -0.52 (0.22), residues: 552 loop : -0.48 (0.16), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 230 HIS 0.004 0.001 HIS E 228 PHE 0.007 0.001 PHE D 187 TYR 0.011 0.001 TYR B 148 ARG 0.012 0.000 ARG B 150 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Evaluate side-chains 191 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 177 time to evaluate : 3.976 Fit side-chains REVERT: A 136 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.8430 (ttt180) REVERT: D 175 THR cc_start: 0.8712 (t) cc_final: 0.8507 (t) REVERT: F 235 MET cc_start: 0.9338 (mtt) cc_final: 0.8978 (mtt) REVERT: F 365 GLU cc_start: 0.7641 (mp0) cc_final: 0.7248 (pm20) REVERT: C 235 MET cc_start: 0.9345 (mtt) cc_final: 0.8981 (mtt) REVERT: B 365 GLU cc_start: 0.7496 (mp0) cc_final: 0.7099 (pm20) outliers start: 14 outliers final: 10 residues processed: 191 average time/residue: 2.9349 time to fit residues: 654.2420 Evaluate side-chains 183 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 172 time to evaluate : 3.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ARG Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain E residue 222 THR Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain B residue 222 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 200 optimal weight: 4.9990 chunk 268 optimal weight: 4.9990 chunk 77 optimal weight: 0.4980 chunk 232 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 70 optimal weight: 0.3980 chunk 252 optimal weight: 4.9990 chunk 105 optimal weight: 10.0000 chunk 259 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.156579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.105430 restraints weight = 75098.834| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.12 r_work: 0.3092 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 26088 Z= 0.187 Angle : 0.523 7.225 35430 Z= 0.273 Chirality : 0.043 0.148 4002 Planarity : 0.004 0.080 4482 Dihedral : 7.630 88.292 3634 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.51 % Favored : 95.30 % Rotamer: Outliers : 0.40 % Allowed : 13.45 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.15), residues: 3168 helix: 0.98 (0.16), residues: 1098 sheet: -0.56 (0.22), residues: 552 loop : -0.46 (0.16), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 230 HIS 0.005 0.001 HIS A 228 PHE 0.009 0.001 PHE E 187 TYR 0.012 0.001 TYR D 148 ARG 0.011 0.000 ARG C 150 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13845.07 seconds wall clock time: 244 minutes 38.49 seconds (14678.49 seconds total)