Starting phenix.real_space_refine on Sat Dec 16 22:45:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqa_21346/12_2023/6vqa_21346_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqa_21346/12_2023/6vqa_21346.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqa_21346/12_2023/6vqa_21346.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqa_21346/12_2023/6vqa_21346.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqa_21346/12_2023/6vqa_21346_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqa_21346/12_2023/6vqa_21346_updated.pdb" } resolution = 3.7 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= 0.092 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 2 5.49 5 Mg 1 5.21 5 S 203 5.16 5 C 22864 2.51 5 N 6223 2.21 5 O 6821 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 104": "NH1" <-> "NH2" Residue "A TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 338": "NH1" <-> "NH2" Residue "A TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 388": "NH1" <-> "NH2" Residue "A ARG 400": "NH1" <-> "NH2" Residue "A PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 529": "OD1" <-> "OD2" Residue "A PHE 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 68": "OE1" <-> "OE2" Residue "B TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 279": "OE1" <-> "OE2" Residue "B TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 338": "NH1" <-> "NH2" Residue "B TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 388": "NH1" <-> "NH2" Residue "B ASP 419": "OD1" <-> "OD2" Residue "B PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 323": "NH1" <-> "NH2" Residue "C TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 338": "NH1" <-> "NH2" Residue "C TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 388": "NH1" <-> "NH2" Residue "C ARG 400": "NH1" <-> "NH2" Residue "C PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 90": "OE1" <-> "OE2" Residue "R PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 214": "OE1" <-> "OE2" Residue "S TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 36114 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 4651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4651 Classifications: {'peptide': 600} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 569} Chain: "B" Number of atoms: 4651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4651 Classifications: {'peptide': 600} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 569} Chain: "C" Number of atoms: 4651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4651 Classifications: {'peptide': 600} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 569} Chain: "D" Number of atoms: 3595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3595 Classifications: {'peptide': 459} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 431} Chain breaks: 1 Chain: "E" Number of atoms: 3595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3595 Classifications: {'peptide': 459} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 431} Chain breaks: 1 Chain: "F" Number of atoms: 3595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3595 Classifications: {'peptide': 459} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 431} Chain breaks: 1 Chain: "H" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 914 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 2, 'TRANS': 106} Chain breaks: 1 Chain: "I" Number of atoms: 1288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1288 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 5, 'TRANS': 155} Chain: "J" Number of atoms: 1288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1288 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 5, 'TRANS': 155} Chain: "K" Number of atoms: 1288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1288 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 5, 'TRANS': 155} Chain: "M" Number of atoms: 382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 382 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "N" Number of atoms: 382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 382 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "O" Number of atoms: 382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 382 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "Q" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1722 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 8, 'TRANS': 203} Chain: "R" Number of atoms: 1878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1878 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 222} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1824 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 9, 'TRANS': 214} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 17.99, per 1000 atoms: 0.50 Number of scatterers: 36114 At special positions: 0 Unit cell: (169.6, 171.72, 143.1, 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 203 16.00 P 2 15.00 Mg 1 11.99 O 6821 8.00 N 6223 7.00 C 22864 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.30 Conformation dependent library (CDL) restraints added in 6.4 seconds 9076 Ramachandran restraints generated. 4538 Oldfield, 0 Emsley, 4538 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8532 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 165 helices and 35 sheets defined 45.6% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.80 Creating SS restraints... Processing helix chain 'A' and resid 106 through 112 removed outlier: 3.656A pdb=" N SER A 111 " --> pdb=" O SER A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 254 No H-bonds generated for 'chain 'A' and resid 252 through 254' Processing helix chain 'A' and resid 257 through 266 Processing helix chain 'A' and resid 281 through 293 Proline residue: A 292 - end of helix Processing helix chain 'A' and resid 305 through 307 No H-bonds generated for 'chain 'A' and resid 305 through 307' Processing helix chain 'A' and resid 320 through 340 removed outlier: 4.513A pdb=" N ILE A 327 " --> pdb=" O ARG A 323 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N TYR A 328 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N MET A 340 " --> pdb=" O TYR A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 364 Processing helix chain 'A' and resid 371 through 373 No H-bonds generated for 'chain 'A' and resid 371 through 373' Processing helix chain 'A' and resid 378 through 388 removed outlier: 3.707A pdb=" N ARG A 388 " --> pdb=" O SER A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 415 No H-bonds generated for 'chain 'A' and resid 413 through 415' Processing helix chain 'A' and resid 420 through 426 Processing helix chain 'A' and resid 438 through 441 No H-bonds generated for 'chain 'A' and resid 438 through 441' Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 472 through 496 removed outlier: 4.595A pdb=" N GLU A 491 " --> pdb=" O GLU A 487 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ILE A 492 " --> pdb=" O ASP A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 518 Processing helix chain 'A' and resid 534 through 558 removed outlier: 3.832A pdb=" N THR A 558 " --> pdb=" O ALA A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 573 Processing helix chain 'A' and resid 575 through 586 removed outlier: 4.877A pdb=" N LYS A 585 " --> pdb=" O LEU A 581 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N PHE A 586 " --> pdb=" O SER A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 615 removed outlier: 3.994A pdb=" N LEU A 615 " --> pdb=" O ALA A 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 113 Processing helix chain 'B' and resid 256 through 265 Processing helix chain 'B' and resid 281 through 293 Proline residue: B 292 - end of helix Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 321 through 340 removed outlier: 3.558A pdb=" N SER B 326 " --> pdb=" O ARG B 323 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE B 331 " --> pdb=" O TYR B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 364 Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 376 through 388 removed outlier: 4.365A pdb=" N GLY B 379 " --> pdb=" O ALA B 376 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA B 383 " --> pdb=" O ALA B 380 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER B 384 " --> pdb=" O ARG B 381 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU B 387 " --> pdb=" O SER B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 415 No H-bonds generated for 'chain 'B' and resid 413 through 415' Processing helix chain 'B' and resid 420 through 426 Processing helix chain 'B' and resid 437 through 441 Processing helix chain 'B' and resid 458 through 468 removed outlier: 4.406A pdb=" N GLU B 463 " --> pdb=" O ARG B 459 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N TYR B 464 " --> pdb=" O ALA B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 496 removed outlier: 4.088A pdb=" N ILE B 492 " --> pdb=" O ASP B 488 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LEU B 495 " --> pdb=" O GLU B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 518 Processing helix chain 'B' and resid 534 through 556 Processing helix chain 'B' and resid 567 through 573 Processing helix chain 'B' and resid 575 through 585 removed outlier: 4.994A pdb=" N LYS B 585 " --> pdb=" O LEU B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 615 Processing helix chain 'C' and resid 106 through 113 Processing helix chain 'C' and resid 232 through 235 No H-bonds generated for 'chain 'C' and resid 232 through 235' Processing helix chain 'C' and resid 256 through 266 Processing helix chain 'C' and resid 281 through 291 Processing helix chain 'C' and resid 305 through 308 Processing helix chain 'C' and resid 320 through 340 removed outlier: 4.646A pdb=" N ILE C 327 " --> pdb=" O ARG C 323 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N TYR C 328 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N MET C 340 " --> pdb=" O TYR C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 364 Processing helix chain 'C' and resid 371 through 373 No H-bonds generated for 'chain 'C' and resid 371 through 373' Processing helix chain 'C' and resid 378 through 386 Processing helix chain 'C' and resid 420 through 426 Processing helix chain 'C' and resid 437 through 441 Processing helix chain 'C' and resid 458 through 468 removed outlier: 4.302A pdb=" N GLU C 463 " --> pdb=" O ARG C 459 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N TYR C 464 " --> pdb=" O ALA C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 496 removed outlier: 3.593A pdb=" N ILE C 492 " --> pdb=" O ASP C 488 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU C 495 " --> pdb=" O GLU C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 518 Processing helix chain 'C' and resid 534 through 557 Processing helix chain 'C' and resid 567 through 573 Processing helix chain 'C' and resid 575 through 587 removed outlier: 5.054A pdb=" N LYS C 585 " --> pdb=" O LEU C 581 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N PHE C 586 " --> pdb=" O SER C 582 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LYS C 587 " --> pdb=" O SER C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 615 Processing helix chain 'D' and resid 160 through 162 No H-bonds generated for 'chain 'D' and resid 160 through 162' Processing helix chain 'D' and resid 175 through 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' Processing helix chain 'D' and resid 199 through 209 Processing helix chain 'D' and resid 238 through 250 Processing helix chain 'D' and resid 253 through 256 Processing helix chain 'D' and resid 270 through 288 Proline residue: D 275 - end of helix Processing helix chain 'D' and resid 300 through 313 Processing helix chain 'D' and resid 320 through 322 No H-bonds generated for 'chain 'D' and resid 320 through 322' Processing helix chain 'D' and resid 327 through 335 Processing helix chain 'D' and resid 357 through 359 No H-bonds generated for 'chain 'D' and resid 357 through 359' Processing helix chain 'D' and resid 364 through 372 removed outlier: 3.906A pdb=" N ILE D 372 " --> pdb=" O LEU D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 385 No H-bonds generated for 'chain 'D' and resid 382 through 385' Processing helix chain 'D' and resid 402 through 405 No H-bonds generated for 'chain 'D' and resid 402 through 405' Processing helix chain 'D' and resid 415 through 439 removed outlier: 3.665A pdb=" N VAL D 438 " --> pdb=" O ALA D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 461 Processing helix chain 'D' and resid 473 through 486 removed outlier: 4.129A pdb=" N ILE D 486 " --> pdb=" O GLN D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 491 No H-bonds generated for 'chain 'D' and resid 489 through 491' Processing helix chain 'D' and resid 497 through 503 Processing helix chain 'E' and resid 125 through 127 No H-bonds generated for 'chain 'E' and resid 125 through 127' Processing helix chain 'E' and resid 175 through 178 No H-bonds generated for 'chain 'E' and resid 175 through 178' Processing helix chain 'E' and resid 199 through 209 removed outlier: 3.645A pdb=" N ARG E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 250 Processing helix chain 'E' and resid 254 through 256 No H-bonds generated for 'chain 'E' and resid 254 through 256' Processing helix chain 'E' and resid 270 through 272 No H-bonds generated for 'chain 'E' and resid 270 through 272' Processing helix chain 'E' and resid 274 through 287 Processing helix chain 'E' and resid 300 through 313 Processing helix chain 'E' and resid 327 through 335 Processing helix chain 'E' and resid 357 through 359 No H-bonds generated for 'chain 'E' and resid 357 through 359' Processing helix chain 'E' and resid 364 through 372 Processing helix chain 'E' and resid 381 through 386 removed outlier: 4.006A pdb=" N ARG E 386 " --> pdb=" O GLN E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 402 through 405 No H-bonds generated for 'chain 'E' and resid 402 through 405' Processing helix chain 'E' and resid 415 through 439 removed outlier: 4.358A pdb=" N VAL E 438 " --> pdb=" O ALA E 434 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 443 No H-bonds generated for 'chain 'E' and resid 441 through 443' Processing helix chain 'E' and resid 446 through 461 removed outlier: 4.374A pdb=" N TYR E 451 " --> pdb=" O ASP E 447 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS E 460 " --> pdb=" O GLN E 456 " (cutoff:3.500A) Processing helix chain 'E' and resid 473 through 486 removed outlier: 4.170A pdb=" N ILE E 486 " --> pdb=" O GLN E 482 " (cutoff:3.500A) Processing helix chain 'E' and resid 489 through 491 No H-bonds generated for 'chain 'E' and resid 489 through 491' Processing helix chain 'E' and resid 497 through 503 removed outlier: 4.956A pdb=" N GLU E 502 " --> pdb=" O SER E 498 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 127 No H-bonds generated for 'chain 'F' and resid 125 through 127' Processing helix chain 'F' and resid 175 through 178 No H-bonds generated for 'chain 'F' and resid 175 through 178' Processing helix chain 'F' and resid 199 through 209 Processing helix chain 'F' and resid 238 through 250 Processing helix chain 'F' and resid 254 through 256 No H-bonds generated for 'chain 'F' and resid 254 through 256' Processing helix chain 'F' and resid 270 through 287 removed outlier: 3.547A pdb=" N THR F 274 " --> pdb=" O ARG F 271 " (cutoff:3.500A) Proline residue: F 275 - end of helix removed outlier: 3.614A pdb=" N ALA F 278 " --> pdb=" O PRO F 275 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU F 279 " --> pdb=" O ARG F 276 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR F 280 " --> pdb=" O LEU F 277 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA F 286 " --> pdb=" O GLU F 283 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR F 287 " --> pdb=" O PHE F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 313 Processing helix chain 'F' and resid 320 through 322 No H-bonds generated for 'chain 'F' and resid 320 through 322' Processing helix chain 'F' and resid 327 through 335 removed outlier: 3.749A pdb=" N ILE F 334 " --> pdb=" O ASP F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 357 through 359 No H-bonds generated for 'chain 'F' and resid 357 through 359' Processing helix chain 'F' and resid 364 through 372 Processing helix chain 'F' and resid 382 through 385 No H-bonds generated for 'chain 'F' and resid 382 through 385' Processing helix chain 'F' and resid 400 through 403 removed outlier: 4.202A pdb=" N LYS F 403 " --> pdb=" O ARG F 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 400 through 403' Processing helix chain 'F' and resid 415 through 439 removed outlier: 4.093A pdb=" N VAL F 438 " --> pdb=" O ALA F 434 " (cutoff:3.500A) Processing helix chain 'F' and resid 441 through 443 No H-bonds generated for 'chain 'F' and resid 441 through 443' Processing helix chain 'F' and resid 446 through 461 Processing helix chain 'F' and resid 473 through 486 removed outlier: 3.805A pdb=" N ILE F 486 " --> pdb=" O GLN F 482 " (cutoff:3.500A) Processing helix chain 'F' and resid 489 through 491 No H-bonds generated for 'chain 'F' and resid 489 through 491' Processing helix chain 'F' and resid 497 through 503 Processing helix chain 'H' and resid 13 through 47 Processing helix chain 'H' and resid 156 through 174 Processing helix chain 'H' and resid 176 through 215 Processing helix chain 'I' and resid 67 through 106 Processing helix chain 'I' and resid 110 through 127 Processing helix chain 'I' and resid 138 through 159 Proline residue: I 142 - end of helix removed outlier: 3.744A pdb=" N LYS I 145 " --> pdb=" O PRO I 142 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS I 150 " --> pdb=" O ALA I 147 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ILE I 152 " --> pdb=" O GLN I 149 " (cutoff:3.500A) Proline residue: I 153 - end of helix removed outlier: 3.684A pdb=" N LYS I 156 " --> pdb=" O PRO I 153 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR I 159 " --> pdb=" O LYS I 156 " (cutoff:3.500A) Processing helix chain 'I' and resid 196 through 206 Processing helix chain 'I' and resid 208 through 216 Processing helix chain 'J' and resid 67 through 106 Processing helix chain 'J' and resid 109 through 127 removed outlier: 4.570A pdb=" N VAL J 114 " --> pdb=" O THR J 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 138 through 158 Proline residue: J 142 - end of helix removed outlier: 3.762A pdb=" N LYS J 145 " --> pdb=" O PRO J 142 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS J 150 " --> pdb=" O ALA J 147 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ILE J 152 " --> pdb=" O GLN J 149 " (cutoff:3.500A) Proline residue: J 153 - end of helix removed outlier: 3.622A pdb=" N LYS J 156 " --> pdb=" O PRO J 153 " (cutoff:3.500A) Processing helix chain 'J' and resid 196 through 216 removed outlier: 3.920A pdb=" N GLN J 206 " --> pdb=" O LEU J 202 " (cutoff:3.500A) Proline residue: J 209 - end of helix Processing helix chain 'K' and resid 67 through 106 Processing helix chain 'K' and resid 110 through 127 Processing helix chain 'K' and resid 138 through 159 Proline residue: K 142 - end of helix removed outlier: 3.740A pdb=" N LYS K 145 " --> pdb=" O PRO K 142 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ILE K 152 " --> pdb=" O GLN K 149 " (cutoff:3.500A) Proline residue: K 153 - end of helix removed outlier: 3.767A pdb=" N LYS K 156 " --> pdb=" O PRO K 153 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE K 157 " --> pdb=" O MET K 154 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR K 159 " --> pdb=" O LYS K 156 " (cutoff:3.500A) Processing helix chain 'K' and resid 196 through 204 Processing helix chain 'K' and resid 208 through 216 removed outlier: 3.631A pdb=" N GLY K 213 " --> pdb=" O PRO K 209 " (cutoff:3.500A) Processing helix chain 'M' and resid 71 through 90 Processing helix chain 'M' and resid 92 through 104 Processing helix chain 'N' and resid 71 through 90 removed outlier: 3.854A pdb=" N ARG N 90 " --> pdb=" O SER N 86 " (cutoff:3.500A) Processing helix chain 'N' and resid 92 through 104 Processing helix chain 'O' and resid 71 through 103 removed outlier: 3.608A pdb=" N ASN O 91 " --> pdb=" O SER O 87 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N GLU O 93 " --> pdb=" O GLN O 89 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N ARG O 94 " --> pdb=" O ARG O 90 " (cutoff:3.500A) Processing helix chain 'Q' and resid 15 through 36 Processing helix chain 'Q' and resid 43 through 53 removed outlier: 3.628A pdb=" N TYR Q 49 " --> pdb=" O ILE Q 45 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ASP Q 51 " --> pdb=" O GLU Q 47 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL Q 52 " --> pdb=" O ASP Q 48 " (cutoff:3.500A) Processing helix chain 'Q' and resid 63 through 71 Processing helix chain 'Q' and resid 78 through 98 removed outlier: 4.088A pdb=" N ILE Q 98 " --> pdb=" O LEU Q 94 " (cutoff:3.500A) Processing helix chain 'Q' and resid 105 through 116 Processing helix chain 'Q' and resid 121 through 123 No H-bonds generated for 'chain 'Q' and resid 121 through 123' Processing helix chain 'Q' and resid 125 through 142 removed outlier: 3.795A pdb=" N LEU Q 140 " --> pdb=" O LEU Q 136 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS Q 141 " --> pdb=" O THR Q 137 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ASN Q 142 " --> pdb=" O ASP Q 138 " (cutoff:3.500A) Processing helix chain 'Q' and resid 147 through 166 removed outlier: 3.552A pdb=" N GLN Q 165 " --> pdb=" O MET Q 161 " (cutoff:3.500A) Processing helix chain 'Q' and resid 173 through 186 Processing helix chain 'Q' and resid 194 through 206 Processing helix chain 'R' and resid 15 through 36 Processing helix chain 'R' and resid 43 through 48 Processing helix chain 'R' and resid 50 through 55 removed outlier: 4.942A pdb=" N TRP R 55 " --> pdb=" O ASP R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 70 Processing helix chain 'R' and resid 78 through 98 removed outlier: 3.895A pdb=" N LEU R 88 " --> pdb=" O ARG R 84 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU R 91 " --> pdb=" O ILE R 87 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE R 98 " --> pdb=" O LEU R 94 " (cutoff:3.500A) Processing helix chain 'R' and resid 105 through 116 Processing helix chain 'R' and resid 125 through 141 removed outlier: 3.547A pdb=" N LYS R 141 " --> pdb=" O THR R 137 " (cutoff:3.500A) Processing helix chain 'R' and resid 147 through 166 Processing helix chain 'R' and resid 173 through 187 Processing helix chain 'R' and resid 193 through 206 Processing helix chain 'R' and resid 219 through 232 removed outlier: 3.587A pdb=" N MET R 229 " --> pdb=" O LEU R 225 " (cutoff:3.500A) Processing helix chain 'S' and resid 15 through 36 Processing helix chain 'S' and resid 43 through 55 removed outlier: 3.610A pdb=" N TYR S 49 " --> pdb=" O ILE S 45 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ASP S 51 " --> pdb=" O GLU S 47 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL S 52 " --> pdb=" O ASP S 48 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N TRP S 55 " --> pdb=" O ASP S 51 " (cutoff:3.500A) Processing helix chain 'S' and resid 62 through 70 Processing helix chain 'S' and resid 78 through 96 Processing helix chain 'S' and resid 105 through 117 Processing helix chain 'S' and resid 121 through 123 No H-bonds generated for 'chain 'S' and resid 121 through 123' Processing helix chain 'S' and resid 125 through 142 removed outlier: 3.908A pdb=" N ASN S 142 " --> pdb=" O ASP S 138 " (cutoff:3.500A) Processing helix chain 'S' and resid 147 through 166 Processing helix chain 'S' and resid 173 through 186 Processing helix chain 'S' and resid 193 through 205 Processing helix chain 'S' and resid 219 through 234 Processing sheet with id= A, first strand: chain 'A' and resid 18 through 20 removed outlier: 3.500A pdb=" N LEU A 42 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N CYS A 32 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N VAL A 21 " --> pdb=" O CYS A 32 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 87 through 90 Processing sheet with id= C, first strand: chain 'A' and resid 183 through 185 removed outlier: 4.701A pdb=" N GLU A 134 " --> pdb=" O ASN A 157 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ILE A 166 " --> pdb=" O TYR A 153 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ILE A 155 " --> pdb=" O HIS A 164 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N HIS A 164 " --> pdb=" O ILE A 155 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 199 through 203 removed outlier: 6.238A pdb=" N GLU A 195 " --> pdb=" O VAL A 176 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N VAL A 176 " --> pdb=" O GLU A 195 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 309 through 312 removed outlier: 6.344A pdb=" N ILE A 272 " --> pdb=" O ALA A 310 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N VAL A 312 " --> pdb=" O ILE A 272 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TYR A 274 " --> pdb=" O VAL A 312 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N VAL A 344 " --> pdb=" O GLU A 401 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N SER A 403 " --> pdb=" O VAL A 344 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N MET A 346 " --> pdb=" O SER A 403 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N SER A 405 " --> pdb=" O MET A 346 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N ALA A 348 " --> pdb=" O SER A 405 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 295 through 297 Processing sheet with id= G, first strand: chain 'B' and resid 78 through 80 removed outlier: 6.508A pdb=" N THR B 30 " --> pdb=" O HIS B 22 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N VAL B 24 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N VAL B 28 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG B 56 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLN B 65 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ILE B 54 " --> pdb=" O GLN B 65 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLU B 41 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N LYS B 84 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N ARG B 44 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N THR B 82 " --> pdb=" O ARG B 44 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 87 through 90 Processing sheet with id= I, first strand: chain 'B' and resid 133 through 135 Processing sheet with id= J, first strand: chain 'B' and resid 200 through 203 removed outlier: 6.219A pdb=" N GLU B 195 " --> pdb=" O VAL B 176 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N VAL B 176 " --> pdb=" O GLU B 195 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 219 through 221 removed outlier: 4.283A pdb=" N ARG B 391 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 245 through 248 removed outlier: 6.423A pdb=" N ILE B 406 " --> pdb=" O THR B 246 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ILE B 248 " --> pdb=" O ILE B 406 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N GLY B 408 " --> pdb=" O ILE B 248 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'B' and resid 272 through 277 Processing sheet with id= N, first strand: chain 'C' and resid 18 through 20 removed outlier: 6.892A pdb=" N THR C 63 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU C 57 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N MET C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N CYS C 32 " --> pdb=" O VAL C 21 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N VAL C 21 " --> pdb=" O CYS C 32 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 87 through 90 Processing sheet with id= P, first strand: chain 'C' and resid 98 through 100 removed outlier: 6.807A pdb=" N LEU C 311 " --> pdb=" O PHE C 99 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'C' and resid 183 through 185 removed outlier: 6.945A pdb=" N ILE C 166 " --> pdb=" O TYR C 153 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ILE C 155 " --> pdb=" O HIS C 164 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N HIS C 164 " --> pdb=" O ILE C 155 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 199 through 203 removed outlier: 6.158A pdb=" N GLU C 195 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N VAL C 176 " --> pdb=" O GLU C 195 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 219 through 221 removed outlier: 4.098A pdb=" N ARG C 391 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 245 through 247 removed outlier: 8.359A pdb=" N THR C 246 " --> pdb=" O VAL C 404 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ILE C 406 " --> pdb=" O THR C 246 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL C 271 " --> pdb=" O SER C 345 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N MET C 347 " --> pdb=" O VAL C 271 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE C 273 " --> pdb=" O MET C 347 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 295 through 297 Processing sheet with id= V, first strand: chain 'D' and resid 50 through 54 removed outlier: 6.656A pdb=" N ILE D 59 " --> pdb=" O SER D 51 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N VAL D 53 " --> pdb=" O LEU D 57 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU D 57 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA D 94 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLN D 97 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL D 86 " --> pdb=" O GLN D 97 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 120 through 123 Processing sheet with id= X, first strand: chain 'D' and resid 131 through 133 removed outlier: 8.147A pdb=" N PHE D 132 " --> pdb=" O VAL D 257 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU D 259 " --> pdb=" O PHE D 132 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N CYS D 258 " --> pdb=" O PHE D 227 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE D 229 " --> pdb=" O CYS D 258 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N PHE D 260 " --> pdb=" O ILE D 229 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N PHE D 231 " --> pdb=" O PHE D 260 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N ASN D 262 " --> pdb=" O PHE D 231 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ALA D 233 " --> pdb=" O ASN D 262 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N HIS D 292 " --> pdb=" O ALA D 228 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N VAL D 230 " --> pdb=" O HIS D 292 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LEU D 294 " --> pdb=" O VAL D 230 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ALA D 232 " --> pdb=" O LEU D 294 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE D 296 " --> pdb=" O ALA D 232 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N MET D 234 " --> pdb=" O ILE D 296 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N THR D 298 " --> pdb=" O MET D 234 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL D 236 " --> pdb=" O THR D 298 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N SER D 347 " --> pdb=" O VAL D 293 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N VAL D 295 " --> pdb=" O SER D 347 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N THR D 349 " --> pdb=" O VAL D 295 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LEU D 297 " --> pdb=" O THR D 349 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'D' and resid 191 through 194 Processing sheet with id= Z, first strand: chain 'E' and resid 50 through 54 removed outlier: 6.799A pdb=" N ILE E 59 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL E 53 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU E 57 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU E 88 " --> pdb=" O VAL E 95 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLN E 97 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N VAL E 86 " --> pdb=" O GLN E 97 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 120 through 123 Processing sheet with id= AB, first strand: chain 'E' and resid 131 through 133 removed outlier: 8.101A pdb=" N PHE E 132 " --> pdb=" O VAL E 257 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU E 259 " --> pdb=" O PHE E 132 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ILE E 229 " --> pdb=" O CYS E 258 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N PHE E 260 " --> pdb=" O ILE E 229 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N PHE E 231 " --> pdb=" O PHE E 260 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ASN E 262 " --> pdb=" O PHE E 231 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ALA E 233 " --> pdb=" O ASN E 262 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N SER E 347 " --> pdb=" O VAL E 293 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N VAL E 295 " --> pdb=" O SER E 347 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N THR E 349 " --> pdb=" O VAL E 295 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N LEU E 297 " --> pdb=" O THR E 349 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ILE E 351 " --> pdb=" O LEU E 297 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 50 through 54 removed outlier: 6.742A pdb=" N ILE F 59 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N VAL F 53 " --> pdb=" O LEU F 57 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU F 57 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU F 88 " --> pdb=" O VAL F 95 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N GLN F 97 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N VAL F 86 " --> pdb=" O GLN F 97 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 120 through 123 Processing sheet with id= AE, first strand: chain 'F' and resid 130 through 133 removed outlier: 3.639A pdb=" N ARG F 130 " --> pdb=" O VAL F 257 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE F 229 " --> pdb=" O CYS F 258 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N PHE F 260 " --> pdb=" O ILE F 229 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N PHE F 231 " --> pdb=" O PHE F 260 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ASN F 262 " --> pdb=" O PHE F 231 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N ALA F 233 " --> pdb=" O ASN F 262 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N SER F 347 " --> pdb=" O VAL F 293 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N VAL F 295 " --> pdb=" O SER F 347 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N THR F 349 " --> pdb=" O VAL F 295 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N LEU F 297 " --> pdb=" O THR F 349 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'F' and resid 191 through 193 Processing sheet with id= AG, first strand: chain 'I' and resid 164 through 167 Processing sheet with id= AH, first strand: chain 'J' and resid 164 through 167 Processing sheet with id= AI, first strand: chain 'K' and resid 164 through 167 1587 hydrogen bonds defined for protein. 4491 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: 13.21 Time building geometry restraints manager: 14.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 6862 1.32 - 1.44: 8323 1.44 - 1.57: 21219 1.57 - 1.69: 3 1.69 - 1.81: 358 Bond restraints: 36765 Sorted by residual: bond pdb=" C ASP C 290 " pdb=" N PHE C 291 " ideal model delta sigma weight residual 1.334 1.216 0.119 1.26e-02 6.30e+03 8.85e+01 bond pdb=" N PRO D 391 " pdb=" CA PRO D 391 " ideal model delta sigma weight residual 1.469 1.531 -0.063 7.40e-03 1.83e+04 7.19e+01 bond pdb=" C TYR F 504 " pdb=" N PRO F 505 " ideal model delta sigma weight residual 1.337 1.406 -0.070 1.06e-02 8.90e+03 4.33e+01 bond pdb=" C ARG C 104 " pdb=" N PRO C 105 " ideal model delta sigma weight residual 1.333 1.393 -0.060 1.01e-02 9.80e+03 3.48e+01 bond pdb=" N PRO F 352 " pdb=" CA PRO F 352 " ideal model delta sigma weight residual 1.466 1.538 -0.072 1.24e-02 6.50e+03 3.32e+01 ... (remaining 36760 not shown) Histogram of bond angle deviations from ideal: 100.83 - 107.50: 1389 107.50 - 114.17: 20669 114.17 - 120.84: 17437 120.84 - 127.51: 9911 127.51 - 134.18: 270 Bond angle restraints: 49676 Sorted by residual: angle pdb=" C ILE D 189 " pdb=" N PRO D 190 " pdb=" CA PRO D 190 " ideal model delta sigma weight residual 119.85 129.30 -9.45 1.01e+00 9.80e-01 8.76e+01 angle pdb=" C ARG B 215 " pdb=" N PRO B 216 " pdb=" CA PRO B 216 " ideal model delta sigma weight residual 119.76 129.27 -9.51 1.03e+00 9.43e-01 8.53e+01 angle pdb=" C SER C 411 " pdb=" N PRO C 412 " pdb=" CA PRO C 412 " ideal model delta sigma weight residual 120.38 129.05 -8.67 1.03e+00 9.43e-01 7.09e+01 angle pdb=" C LEU D 395 " pdb=" N PRO D 396 " pdb=" CA PRO D 396 " ideal model delta sigma weight residual 120.04 128.53 -8.49 1.08e+00 8.57e-01 6.19e+01 angle pdb=" C ASN B 397 " pdb=" N PRO B 398 " pdb=" CA PRO B 398 " ideal model delta sigma weight residual 119.82 127.35 -7.53 9.80e-01 1.04e+00 5.91e+01 ... (remaining 49671 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.67: 22017 23.67 - 47.34: 413 47.34 - 71.01: 117 71.01 - 94.68: 31 94.68 - 118.35: 2 Dihedral angle restraints: 22580 sinusoidal: 9309 harmonic: 13271 Sorted by residual: dihedral pdb=" C5' ADP B 701 " pdb=" O5' ADP B 701 " pdb=" PA ADP B 701 " pdb=" O2A ADP B 701 " ideal model delta sinusoidal sigma weight residual -60.00 -178.34 118.35 1 2.00e+01 2.50e-03 3.54e+01 dihedral pdb=" O2A ADP B 701 " pdb=" O3A ADP B 701 " pdb=" PA ADP B 701 " pdb=" PB ADP B 701 " ideal model delta sinusoidal sigma weight residual -60.00 38.41 -98.41 1 2.00e+01 2.50e-03 2.75e+01 dihedral pdb=" CA VAL B 392 " pdb=" C VAL B 392 " pdb=" N LYS B 393 " pdb=" CA LYS B 393 " ideal model delta harmonic sigma weight residual 180.00 159.08 20.92 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 22577 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 3816 0.052 - 0.105: 1167 0.105 - 0.157: 482 0.157 - 0.209: 77 0.209 - 0.261: 33 Chirality restraints: 5575 Sorted by residual: chirality pdb=" CA VAL D 379 " pdb=" N VAL D 379 " pdb=" C VAL D 379 " pdb=" CB VAL D 379 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CA VAL C 404 " pdb=" N VAL C 404 " pdb=" C VAL C 404 " pdb=" CB VAL C 404 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA PRO F 352 " pdb=" N PRO F 352 " pdb=" C PRO F 352 " pdb=" CB PRO F 352 " both_signs ideal model delta sigma weight residual False 2.72 2.97 -0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 5572 not shown) Planarity restraints: 6440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO D 390 " 0.019 2.00e-02 2.50e+03 3.77e-02 1.42e+01 pdb=" C PRO D 390 " -0.065 2.00e-02 2.50e+03 pdb=" O PRO D 390 " 0.025 2.00e-02 2.50e+03 pdb=" N PRO D 391 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 584 " -0.016 2.00e-02 2.50e+03 3.41e-02 1.16e+01 pdb=" C MET B 584 " 0.059 2.00e-02 2.50e+03 pdb=" O MET B 584 " -0.022 2.00e-02 2.50e+03 pdb=" N LYS B 585 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 189 " -0.016 2.00e-02 2.50e+03 3.22e-02 1.03e+01 pdb=" C ILE D 189 " 0.056 2.00e-02 2.50e+03 pdb=" O ILE D 189 " -0.021 2.00e-02 2.50e+03 pdb=" N PRO D 190 " -0.018 2.00e-02 2.50e+03 ... (remaining 6437 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 10681 2.82 - 3.34: 35791 3.34 - 3.86: 60991 3.86 - 4.38: 72679 4.38 - 4.90: 120853 Nonbonded interactions: 300995 Sorted by model distance: nonbonded pdb=" OG SER B 269 " pdb=" OG SER B 345 " model vdw 2.302 2.440 nonbonded pdb=" NE ARG K 135 " pdb=" O ALA K 171 " model vdw 2.373 2.520 nonbonded pdb=" OG SER A 128 " pdb=" OD1 ASP A 130 " model vdw 2.374 2.440 nonbonded pdb=" OD1 ASP E 266 " pdb=" NZ LYS Q 9 " model vdw 2.380 2.520 nonbonded pdb=" OD1 ASP F 266 " pdb=" NZ LYS R 9 " model vdw 2.392 2.520 ... (remaining 300990 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' and resid 17 through 616) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' } ncs_group { reference = (chain 'Q' and resid 12 through 218) selection = (chain 'R' and resid 12 through 218) selection = (chain 'S' and resid 12 through 218) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 10.320 Check model and map are aligned: 0.570 Set scattering table: 0.320 Process input model: 92.030 Find NCS groups from input model: 2.260 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 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 : 0.010 0.119 36765 Z= 0.649 Angle : 0.895 10.671 49676 Z= 0.632 Chirality : 0.062 0.261 5575 Planarity : 0.004 0.038 6440 Dihedral : 10.831 118.347 14048 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.71 % Favored : 97.09 % Rotamer: Outliers : 0.05 % Allowed : 0.58 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % 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: 0.27 (0.12), residues: 4538 helix: 0.63 (0.10), residues: 2081 sheet: -0.24 (0.20), residues: 612 loop : -0.00 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 55 HIS 0.003 0.000 HIS D 199 PHE 0.010 0.000 PHE B 252 TYR 0.016 0.000 TYR E 389 ARG 0.004 0.000 ARG E 208 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9076 Ramachandran restraints generated. 4538 Oldfield, 0 Emsley, 4538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9076 Ramachandran restraints generated. 4538 Oldfield, 0 Emsley, 4538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1619 residues out of total 3955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1617 time to evaluate : 4.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 1618 average time/residue: 0.5396 time to fit residues: 1370.9711 Evaluate side-chains 857 residues out of total 3955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 857 time to evaluate : 4.665 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.7535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 380 optimal weight: 10.0000 chunk 341 optimal weight: 0.7980 chunk 189 optimal weight: 7.9990 chunk 116 optimal weight: 0.9980 chunk 230 optimal weight: 2.9990 chunk 182 optimal weight: 0.9990 chunk 353 optimal weight: 1.9990 chunk 136 optimal weight: 9.9990 chunk 214 optimal weight: 0.8980 chunk 263 optimal weight: 0.9980 chunk 409 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 573 HIS C 444 HIS C 468 HIS D 62 HIS D 181 ASN ** D 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 GLN ** D 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 ASN E 42 GLN ** E 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 251 ASN F 382 GLN H 27 GLN J 126 GLN ** K 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 77 ASN Q 40 ASN Q 50 GLN ** Q 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 162 GLN R 34 GLN R 134 ASN R 172 ASN S 198 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 36765 Z= 0.224 Angle : 0.642 9.295 49676 Z= 0.328 Chirality : 0.045 0.172 5575 Planarity : 0.005 0.044 6440 Dihedral : 4.850 113.301 5018 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.98 % Favored : 97.99 % Rotamer: Outliers : 2.86 % Allowed : 13.20 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % 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: 0.99 (0.12), residues: 4538 helix: 1.55 (0.11), residues: 2096 sheet: -0.27 (0.21), residues: 618 loop : 0.06 (0.15), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 567 HIS 0.005 0.001 HIS E 73 PHE 0.024 0.002 PHE E 231 TYR 0.039 0.002 TYR S 197 ARG 0.008 0.001 ARG A 476 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9076 Ramachandran restraints generated. 4538 Oldfield, 0 Emsley, 4538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9076 Ramachandran restraints generated. 4538 Oldfield, 0 Emsley, 4538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1055 residues out of total 3955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 942 time to evaluate : 4.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 113 outliers final: 66 residues processed: 1000 average time/residue: 0.4716 time to fit residues: 774.0211 Evaluate side-chains 834 residues out of total 3955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 768 time to evaluate : 4.168 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 0 residues processed: 66 average time/residue: 0.3367 time to fit residues: 47.7666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 227 optimal weight: 4.9990 chunk 127 optimal weight: 6.9990 chunk 340 optimal weight: 0.0170 chunk 278 optimal weight: 0.0770 chunk 112 optimal weight: 3.9990 chunk 410 optimal weight: 5.9990 chunk 443 optimal weight: 10.0000 chunk 365 optimal weight: 0.7980 chunk 406 optimal weight: 0.7980 chunk 139 optimal weight: 3.9990 chunk 329 optimal weight: 4.9990 overall best weight: 1.1378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 573 HIS C 65 GLN ** C 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 603 GLN ** D 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 GLN E 465 GLN F 181 ASN K 206 GLN ** M 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 111 GLN R 127 HIS ** R 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 198 HIS S 198 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.4094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 36765 Z= 0.212 Angle : 0.603 9.119 49676 Z= 0.302 Chirality : 0.044 0.172 5575 Planarity : 0.004 0.045 6440 Dihedral : 4.694 119.139 5018 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.80 % Allowed : 15.25 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % 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: 0.99 (0.12), residues: 4538 helix: 1.63 (0.11), residues: 2107 sheet: -0.30 (0.21), residues: 609 loop : -0.04 (0.15), residues: 1822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 567 HIS 0.008 0.001 HIS R 198 PHE 0.027 0.002 PHE R 200 TYR 0.032 0.002 TYR Q 112 ARG 0.010 0.001 ARG N 79 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9076 Ramachandran restraints generated. 4538 Oldfield, 0 Emsley, 4538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9076 Ramachandran restraints generated. 4538 Oldfield, 0 Emsley, 4538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 895 residues out of total 3955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 824 time to evaluate : 4.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 71 outliers final: 33 residues processed: 855 average time/residue: 0.4773 time to fit residues: 670.8022 Evaluate side-chains 762 residues out of total 3955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 729 time to evaluate : 4.232 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.3706 time to fit residues: 28.7506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 405 optimal weight: 0.4980 chunk 308 optimal weight: 0.9980 chunk 212 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 195 optimal weight: 2.9990 chunk 275 optimal weight: 0.9980 chunk 411 optimal weight: 10.0000 chunk 435 optimal weight: 5.9990 chunk 215 optimal weight: 1.9990 chunk 390 optimal weight: 6.9990 chunk 117 optimal weight: 7.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 HIS B 610 ASN ** D 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 251 ASN ** E 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 456 GLN ** O 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 134 ASN R 198 HIS S 198 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.4483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 36765 Z= 0.233 Angle : 0.600 13.445 49676 Z= 0.300 Chirality : 0.044 0.189 5575 Planarity : 0.004 0.045 6440 Dihedral : 4.664 128.391 5018 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.28 % Allowed : 15.63 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.13), residues: 4538 helix: 1.68 (0.11), residues: 2111 sheet: -0.19 (0.21), residues: 601 loop : -0.14 (0.15), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 450 HIS 0.008 0.001 HIS R 198 PHE 0.025 0.002 PHE R 200 TYR 0.033 0.002 TYR Q 112 ARG 0.010 0.001 ARG F 400 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9076 Ramachandran restraints generated. 4538 Oldfield, 0 Emsley, 4538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9076 Ramachandran restraints generated. 4538 Oldfield, 0 Emsley, 4538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 892 residues out of total 3955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 802 time to evaluate : 4.690 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 outliers start: 90 outliers final: 47 residues processed: 839 average time/residue: 0.4839 time to fit residues: 670.2562 Evaluate side-chains 763 residues out of total 3955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 716 time to evaluate : 4.258 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 0 residues processed: 47 average time/residue: 0.3461 time to fit residues: 36.1535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 363 optimal weight: 2.9990 chunk 247 optimal weight: 4.9990 chunk 6 optimal weight: 8.9990 chunk 324 optimal weight: 3.9990 chunk 179 optimal weight: 8.9990 chunk 372 optimal weight: 0.7980 chunk 301 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 222 optimal weight: 6.9990 chunk 391 optimal weight: 0.5980 chunk 110 optimal weight: 6.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN ** A 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 573 HIS B 610 ASN ** C 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 HIS ** D 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 GLN I 74 ASN K 122 GLN ** M 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 82 GLN O 88 GLN R 21 GLN R 127 HIS R 134 ASN S 198 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.4820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 36765 Z= 0.258 Angle : 0.596 9.996 49676 Z= 0.299 Chirality : 0.044 0.393 5575 Planarity : 0.004 0.045 6440 Dihedral : 4.649 133.525 5018 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.85 % Allowed : 17.32 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.13), residues: 4538 helix: 1.76 (0.11), residues: 2087 sheet: -0.24 (0.21), residues: 584 loop : -0.26 (0.14), residues: 1867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 450 HIS 0.004 0.001 HIS E 73 PHE 0.029 0.002 PHE R 200 TYR 0.040 0.002 TYR R 197 ARG 0.018 0.001 ARG N 78 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9076 Ramachandran restraints generated. 4538 Oldfield, 0 Emsley, 4538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9076 Ramachandran restraints generated. 4538 Oldfield, 0 Emsley, 4538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 829 residues out of total 3955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 756 time to evaluate : 4.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 73 outliers final: 35 residues processed: 787 average time/residue: 0.4918 time to fit residues: 642.2879 Evaluate side-chains 729 residues out of total 3955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 694 time to evaluate : 4.199 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.3312 time to fit residues: 26.2459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 146 optimal weight: 5.9990 chunk 392 optimal weight: 9.9990 chunk 86 optimal weight: 9.9990 chunk 255 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 436 optimal weight: 0.9980 chunk 362 optimal weight: 0.9990 chunk 202 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 144 optimal weight: 5.9990 chunk 229 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 HIS ** B 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 573 HIS B 610 ASN ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 181 ASN ** E 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 GLN I 74 ASN ** K 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 196 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.5031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 36765 Z= 0.242 Angle : 0.597 13.824 49676 Z= 0.298 Chirality : 0.043 0.302 5575 Planarity : 0.004 0.042 6440 Dihedral : 4.621 133.975 5018 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.75 % Allowed : 18.49 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % 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: 0.99 (0.13), residues: 4538 helix: 1.81 (0.11), residues: 2084 sheet: -0.34 (0.21), residues: 580 loop : -0.27 (0.14), residues: 1874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 450 HIS 0.004 0.001 HIS E 73 PHE 0.029 0.002 PHE R 200 TYR 0.051 0.001 TYR R 197 ARG 0.018 0.000 ARG N 78 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9076 Ramachandran restraints generated. 4538 Oldfield, 0 Emsley, 4538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9076 Ramachandran restraints generated. 4538 Oldfield, 0 Emsley, 4538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 803 residues out of total 3955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 734 time to evaluate : 4.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 69 outliers final: 34 residues processed: 761 average time/residue: 0.4850 time to fit residues: 609.7861 Evaluate side-chains 719 residues out of total 3955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 685 time to evaluate : 4.114 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.3774 time to fit residues: 28.8465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 420 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 248 optimal weight: 6.9990 chunk 318 optimal weight: 4.9990 chunk 246 optimal weight: 3.9990 chunk 367 optimal weight: 0.9990 chunk 243 optimal weight: 0.9980 chunk 434 optimal weight: 0.9990 chunk 272 optimal weight: 4.9990 chunk 265 optimal weight: 0.9980 chunk 200 optimal weight: 0.9980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 468 HIS B 164 HIS ** B 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 573 HIS B 610 ASN ** C 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 350 GLN ** E 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 421 GLN H 27 GLN K 122 GLN O 82 GLN ** O 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 127 HIS ** S 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.5224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 36765 Z= 0.199 Angle : 0.583 9.930 49676 Z= 0.291 Chirality : 0.043 0.274 5575 Planarity : 0.004 0.051 6440 Dihedral : 4.565 134.595 5018 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.29 % Allowed : 19.09 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.13), residues: 4538 helix: 1.83 (0.11), residues: 2082 sheet: -0.34 (0.22), residues: 565 loop : -0.31 (0.14), residues: 1891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 567 HIS 0.005 0.001 HIS R 127 PHE 0.031 0.002 PHE R 200 TYR 0.043 0.001 TYR R 197 ARG 0.011 0.000 ARG M 94 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9076 Ramachandran restraints generated. 4538 Oldfield, 0 Emsley, 4538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9076 Ramachandran restraints generated. 4538 Oldfield, 0 Emsley, 4538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 789 residues out of total 3955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 738 time to evaluate : 4.477 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 outliers start: 51 outliers final: 27 residues processed: 756 average time/residue: 0.4877 time to fit residues: 608.8062 Evaluate side-chains 720 residues out of total 3955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 693 time to evaluate : 4.047 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.3598 time to fit residues: 23.2013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 268 optimal weight: 2.9990 chunk 173 optimal weight: 9.9990 chunk 259 optimal weight: 1.9990 chunk 130 optimal weight: 9.9990 chunk 85 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 276 optimal weight: 5.9990 chunk 296 optimal weight: 0.5980 chunk 214 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 341 optimal weight: 0.8980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 610 ASN ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 HIS ** E 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 421 GLN H 27 GLN O 82 GLN ** O 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.5393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 36765 Z= 0.237 Angle : 0.621 15.856 49676 Z= 0.307 Chirality : 0.044 0.385 5575 Planarity : 0.004 0.056 6440 Dihedral : 4.571 134.191 5018 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.99 % Allowed : 19.68 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % 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: 0.91 (0.13), residues: 4538 helix: 1.80 (0.12), residues: 2087 sheet: -0.41 (0.22), residues: 555 loop : -0.37 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 450 HIS 0.009 0.001 HIS D 415 PHE 0.033 0.002 PHE R 200 TYR 0.038 0.001 TYR R 197 ARG 0.013 0.000 ARG M 94 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9076 Ramachandran restraints generated. 4538 Oldfield, 0 Emsley, 4538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9076 Ramachandran restraints generated. 4538 Oldfield, 0 Emsley, 4538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 762 residues out of total 3955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 723 time to evaluate : 4.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 20 residues processed: 741 average time/residue: 0.4856 time to fit residues: 597.0720 Evaluate side-chains 702 residues out of total 3955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 682 time to evaluate : 3.685 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.3140 time to fit residues: 17.3891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 395 optimal weight: 9.9990 chunk 416 optimal weight: 0.9980 chunk 379 optimal weight: 9.9990 chunk 405 optimal weight: 10.0000 chunk 243 optimal weight: 0.1980 chunk 176 optimal weight: 6.9990 chunk 318 optimal weight: 8.9990 chunk 124 optimal weight: 0.7980 chunk 366 optimal weight: 7.9990 chunk 383 optimal weight: 8.9990 chunk 403 optimal weight: 4.9990 overall best weight: 2.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 610 ASN C 444 HIS ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 74 ASN ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 127 HIS S 50 GLN ** S 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 198 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.5565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 36765 Z= 0.356 Angle : 0.677 13.345 49676 Z= 0.339 Chirality : 0.046 0.356 5575 Planarity : 0.004 0.055 6440 Dihedral : 4.732 134.340 5018 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.75 % Favored : 96.23 % Rotamer: Outliers : 0.96 % Allowed : 19.90 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % 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: 0.72 (0.13), residues: 4538 helix: 1.66 (0.12), residues: 2101 sheet: -0.60 (0.22), residues: 572 loop : -0.47 (0.14), residues: 1865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 567 HIS 0.008 0.001 HIS D 415 PHE 0.032 0.002 PHE R 200 TYR 0.033 0.002 TYR C 535 ARG 0.013 0.001 ARG M 78 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9076 Ramachandran restraints generated. 4538 Oldfield, 0 Emsley, 4538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9076 Ramachandran restraints generated. 4538 Oldfield, 0 Emsley, 4538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 3955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 698 time to evaluate : 4.784 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 outliers start: 38 outliers final: 24 residues processed: 714 average time/residue: 0.4495 time to fit residues: 535.5061 Evaluate side-chains 692 residues out of total 3955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 668 time to evaluate : 3.131 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.2740 time to fit residues: 16.8224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 266 optimal weight: 3.9990 chunk 428 optimal weight: 2.9990 chunk 261 optimal weight: 0.2980 chunk 203 optimal weight: 1.9990 chunk 297 optimal weight: 0.7980 chunk 449 optimal weight: 2.9990 chunk 413 optimal weight: 3.9990 chunk 357 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 276 optimal weight: 0.9980 chunk 219 optimal weight: 9.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 103 GLN ** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 610 ASN ** C 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 421 GLN H 27 GLN K 74 ASN ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 198 HIS S 207 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.5665 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: