Starting phenix.real_space_refine on Tue Apr 16 01:51:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqa_21346/04_2024/6vqa_21346_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqa_21346/04_2024/6vqa_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_21346/04_2024/6vqa_21346.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqa_21346/04_2024/6vqa_21346.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqa_21346/04_2024/6vqa_21346_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqa_21346/04_2024/6vqa_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: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 17.68, per 1000 atoms: 0.49 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: 14.19 Conformation dependent library (CDL) restraints added in 6.0 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: 6.98 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: 13.56 Time building geometry restraints manager: 15.32 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: 2.970 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: 10.410 Check model and map are aligned: 0.570 Set scattering table: 0.360 Process input model: 93.200 Find NCS groups from input model: 2.010 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.820 ------------------------------------------------------------------------------- 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 : 4.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 THR cc_start: 0.7946 (m) cc_final: 0.7408 (p) REVERT: A 61 MET cc_start: 0.8166 (mtp) cc_final: 0.7416 (ttm) REVERT: A 142 ARG cc_start: 0.7368 (mmt-90) cc_final: 0.6968 (mmt180) REVERT: A 171 ARG cc_start: 0.8335 (mtt180) cc_final: 0.7774 (mtm180) REVERT: A 224 ASN cc_start: 0.8830 (p0) cc_final: 0.8459 (p0) REVERT: A 254 CYS cc_start: 0.7018 (p) cc_final: 0.6797 (p) REVERT: A 303 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7451 (mt-10) REVERT: A 306 MET cc_start: 0.8866 (mmm) cc_final: 0.8643 (tpp) REVERT: A 324 GLU cc_start: 0.8935 (tm-30) cc_final: 0.8591 (tm-30) REVERT: A 356 GLU cc_start: 0.8700 (tp30) cc_final: 0.8132 (tp30) REVERT: A 417 PHE cc_start: 0.7968 (m-80) cc_final: 0.7742 (m-10) REVERT: A 436 ASP cc_start: 0.8227 (t0) cc_final: 0.7839 (t70) REVERT: A 443 LYS cc_start: 0.9032 (mttt) cc_final: 0.8351 (tptp) REVERT: A 447 SER cc_start: 0.7433 (m) cc_final: 0.6666 (t) REVERT: A 550 MET cc_start: 0.8883 (mmm) cc_final: 0.7914 (mtm) REVERT: A 567 TRP cc_start: 0.8684 (t-100) cc_final: 0.8388 (t-100) REVERT: A 584 MET cc_start: 0.7426 (mtp) cc_final: 0.7050 (mtp) REVERT: A 597 ILE cc_start: 0.8449 (mt) cc_final: 0.8135 (mm) REVERT: A 605 LEU cc_start: 0.8933 (tp) cc_final: 0.8683 (tt) REVERT: A 608 MET cc_start: 0.8454 (mtm) cc_final: 0.8101 (ttp) REVERT: B 30 THR cc_start: 0.8142 (m) cc_final: 0.7724 (p) REVERT: B 77 ASP cc_start: 0.7484 (m-30) cc_final: 0.7039 (m-30) REVERT: B 116 ILE cc_start: 0.8681 (pt) cc_final: 0.8464 (pt) REVERT: B 130 ASP cc_start: 0.8279 (m-30) cc_final: 0.8047 (p0) REVERT: B 219 GLU cc_start: 0.7355 (tt0) cc_final: 0.7078 (tp30) REVERT: B 229 THR cc_start: 0.8968 (m) cc_final: 0.8716 (m) REVERT: B 231 GLN cc_start: 0.7812 (mm-40) cc_final: 0.7410 (mm-40) REVERT: B 254 CYS cc_start: 0.8651 (m) cc_final: 0.8163 (m) REVERT: B 296 MET cc_start: 0.7931 (ttm) cc_final: 0.7482 (ppp) REVERT: B 298 VAL cc_start: 0.8507 (t) cc_final: 0.8171 (t) REVERT: B 349 ASP cc_start: 0.7779 (t0) cc_final: 0.7450 (t0) REVERT: B 360 GLU cc_start: 0.8015 (tt0) cc_final: 0.7793 (tp30) REVERT: B 387 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7805 (tp30) REVERT: B 447 SER cc_start: 0.8374 (p) cc_final: 0.7865 (p) REVERT: B 463 GLU cc_start: 0.8689 (tt0) cc_final: 0.8081 (tt0) REVERT: B 488 ASP cc_start: 0.7400 (m-30) cc_final: 0.6972 (m-30) REVERT: B 530 ARG cc_start: 0.7413 (ptm160) cc_final: 0.7040 (ttp80) REVERT: C 50 LEU cc_start: 0.8570 (mt) cc_final: 0.8349 (mt) REVERT: C 55 ILE cc_start: 0.8090 (mm) cc_final: 0.7802 (mm) REVERT: C 74 SER cc_start: 0.7799 (m) cc_final: 0.7064 (p) REVERT: C 77 ASP cc_start: 0.7614 (m-30) cc_final: 0.7259 (m-30) REVERT: C 168 LEU cc_start: 0.8507 (tp) cc_final: 0.8089 (tp) REVERT: C 173 ARG cc_start: 0.6831 (pmt170) cc_final: 0.6454 (pmt170) REVERT: C 206 VAL cc_start: 0.9243 (t) cc_final: 0.8931 (m) REVERT: C 213 GLN cc_start: 0.6655 (mm-40) cc_final: 0.6227 (mt0) REVERT: C 218 THR cc_start: 0.8783 (m) cc_final: 0.8286 (p) REVERT: C 235 ASP cc_start: 0.8258 (m-30) cc_final: 0.8055 (m-30) REVERT: C 248 ILE cc_start: 0.8265 (mt) cc_final: 0.7692 (pt) REVERT: C 268 ASN cc_start: 0.8080 (t0) cc_final: 0.7334 (t0) REVERT: C 303 GLU cc_start: 0.8334 (mm-30) cc_final: 0.8007 (tp30) REVERT: C 308 ARG cc_start: 0.6875 (ptp-110) cc_final: 0.6568 (ptt180) REVERT: C 347 MET cc_start: 0.7448 (tpp) cc_final: 0.7218 (tpt) REVERT: C 349 ASP cc_start: 0.7263 (p0) cc_final: 0.6748 (p0) REVERT: C 531 PHE cc_start: 0.6210 (p90) cc_final: 0.5259 (p90) REVERT: C 532 CYS cc_start: 0.7862 (t) cc_final: 0.6845 (t) REVERT: C 540 MET cc_start: 0.6097 (mtp) cc_final: 0.5824 (mtp) REVERT: C 573 HIS cc_start: 0.7750 (t70) cc_final: 0.7500 (t70) REVERT: C 612 PHE cc_start: 0.7559 (m-80) cc_final: 0.7288 (m-10) REVERT: D 88 GLU cc_start: 0.6981 (tt0) cc_final: 0.6525 (mt-10) REVERT: D 106 ASP cc_start: 0.8470 (p0) cc_final: 0.8091 (p0) REVERT: D 117 ASP cc_start: 0.7341 (t0) cc_final: 0.6969 (p0) REVERT: D 118 ILE cc_start: 0.8243 (pt) cc_final: 0.7820 (pt) REVERT: D 125 GLU cc_start: 0.8505 (tt0) cc_final: 0.8223 (tm-30) REVERT: D 152 ASP cc_start: 0.8354 (t0) cc_final: 0.8116 (t0) REVERT: D 153 ILE cc_start: 0.8639 (pt) cc_final: 0.8411 (pt) REVERT: D 247 ASP cc_start: 0.8031 (t70) cc_final: 0.7628 (t0) REVERT: D 299 ASP cc_start: 0.8340 (m-30) cc_final: 0.7879 (m-30) REVERT: D 368 LEU cc_start: 0.8225 (mt) cc_final: 0.8005 (tt) REVERT: D 380 ASP cc_start: 0.8401 (t0) cc_final: 0.7800 (p0) REVERT: D 388 ILE cc_start: 0.7909 (mt) cc_final: 0.7678 (mm) REVERT: D 393 ASN cc_start: 0.8095 (t0) cc_final: 0.7638 (t0) REVERT: D 431 ASP cc_start: 0.8745 (t70) cc_final: 0.8463 (m-30) REVERT: D 455 LEU cc_start: 0.7592 (tp) cc_final: 0.7332 (tp) REVERT: D 478 ASP cc_start: 0.8314 (m-30) cc_final: 0.8064 (m-30) REVERT: E 47 TYR cc_start: 0.7686 (m-80) cc_final: 0.6894 (m-80) REVERT: E 49 THR cc_start: 0.8178 (p) cc_final: 0.7843 (p) REVERT: E 88 GLU cc_start: 0.7469 (tt0) cc_final: 0.6744 (mt-10) REVERT: E 89 VAL cc_start: 0.8829 (m) cc_final: 0.8564 (p) REVERT: E 118 ILE cc_start: 0.8589 (tt) cc_final: 0.8133 (tt) REVERT: E 201 GLU cc_start: 0.7698 (mp0) cc_final: 0.7010 (tp30) REVERT: E 231 PHE cc_start: 0.8695 (t80) cc_final: 0.8475 (t80) REVERT: E 234 MET cc_start: 0.7021 (ptt) cc_final: 0.6515 (ptt) REVERT: E 262 ASN cc_start: 0.8588 (t0) cc_final: 0.8224 (t0) REVERT: E 268 THR cc_start: 0.8620 (p) cc_final: 0.8059 (t) REVERT: E 270 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7857 (mt-10) REVERT: E 283 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7084 (mt-10) REVERT: E 290 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8078 (mm-30) REVERT: E 309 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7615 (mt-10) REVERT: E 330 ASP cc_start: 0.8274 (t70) cc_final: 0.7592 (t0) REVERT: E 355 THR cc_start: 0.8409 (m) cc_final: 0.7915 (p) REVERT: E 360 ASP cc_start: 0.7517 (t0) cc_final: 0.7302 (t0) REVERT: E 361 ILE cc_start: 0.8174 (tt) cc_final: 0.7866 (mp) REVERT: E 380 ASP cc_start: 0.7842 (p0) cc_final: 0.7619 (p0) REVERT: E 408 GLU cc_start: 0.8294 (tp30) cc_final: 0.8034 (tp30) REVERT: E 442 GLU cc_start: 0.8515 (mp0) cc_final: 0.8221 (mp0) REVERT: E 448 ASP cc_start: 0.8374 (m-30) cc_final: 0.8174 (m-30) REVERT: E 490 GLU cc_start: 0.8848 (mp0) cc_final: 0.8438 (mp0) REVERT: F 49 THR cc_start: 0.8091 (p) cc_final: 0.7802 (p) REVERT: F 53 VAL cc_start: 0.8851 (t) cc_final: 0.8547 (p) REVERT: F 61 ASP cc_start: 0.7477 (t0) cc_final: 0.7251 (m-30) REVERT: F 117 ASP cc_start: 0.7477 (t0) cc_final: 0.7248 (t0) REVERT: F 167 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7639 (mt-10) REVERT: F 178 ASP cc_start: 0.7732 (m-30) cc_final: 0.7093 (m-30) REVERT: F 180 MET cc_start: 0.6732 (mtt) cc_final: 0.5889 (mtp) REVERT: F 201 GLU cc_start: 0.7846 (mp0) cc_final: 0.7065 (mp0) REVERT: F 238 MET cc_start: 0.8309 (tpp) cc_final: 0.7772 (tpt) REVERT: F 249 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8255 (mm-30) REVERT: F 262 ASN cc_start: 0.8876 (t0) cc_final: 0.8191 (t0) REVERT: F 268 THR cc_start: 0.8710 (p) cc_final: 0.8376 (t) REVERT: F 315 GLU cc_start: 0.9278 (mt-10) cc_final: 0.8757 (mt-10) REVERT: F 316 GLU cc_start: 0.8769 (tp30) cc_final: 0.8400 (tp30) REVERT: F 342 GLU cc_start: 0.7441 (tt0) cc_final: 0.6967 (mt-10) REVERT: F 354 LEU cc_start: 0.8690 (mp) cc_final: 0.8447 (mt) REVERT: F 355 THR cc_start: 0.8233 (m) cc_final: 0.7895 (p) REVERT: F 367 ASP cc_start: 0.8249 (t70) cc_final: 0.8010 (t0) REVERT: F 400 ARG cc_start: 0.7039 (tpt90) cc_final: 0.6739 (tpt170) REVERT: F 403 LYS cc_start: 0.8217 (tptt) cc_final: 0.7797 (tptp) REVERT: F 410 MET cc_start: 0.8380 (mtt) cc_final: 0.8039 (mtp) REVERT: F 447 ASP cc_start: 0.8791 (m-30) cc_final: 0.8560 (m-30) REVERT: F 460 LYS cc_start: 0.8658 (tttt) cc_final: 0.8378 (ttpp) REVERT: I 72 MET cc_start: 0.9017 (mmm) cc_final: 0.8296 (mmt) REVERT: I 76 MET cc_start: 0.8781 (mtm) cc_final: 0.8157 (mpp) REVERT: I 89 ASP cc_start: 0.8665 (m-30) cc_final: 0.8088 (t70) REVERT: I 132 MET cc_start: 0.8838 (mtt) cc_final: 0.8493 (mtt) REVERT: I 168 ASP cc_start: 0.8577 (t0) cc_final: 0.7988 (t0) REVERT: I 177 ILE cc_start: 0.8722 (mt) cc_final: 0.8469 (mp) REVERT: I 194 ASN cc_start: 0.8125 (t0) cc_final: 0.7638 (t0) REVERT: I 198 SER cc_start: 0.9061 (m) cc_final: 0.8818 (p) REVERT: I 210 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7525 (tm-30) REVERT: J 68 LYS cc_start: 0.7414 (mttt) cc_final: 0.6318 (tptt) REVERT: J 76 MET cc_start: 0.8983 (mmm) cc_final: 0.8687 (mtm) REVERT: J 89 ASP cc_start: 0.8686 (m-30) cc_final: 0.8147 (t0) REVERT: J 90 LEU cc_start: 0.9452 (mt) cc_final: 0.9233 (mt) REVERT: J 92 THR cc_start: 0.9350 (m) cc_final: 0.9127 (p) REVERT: J 93 ASP cc_start: 0.9105 (m-30) cc_final: 0.8649 (m-30) REVERT: J 96 ASN cc_start: 0.9402 (m-40) cc_final: 0.9195 (m110) REVERT: J 97 GLU cc_start: 0.9132 (tp30) cc_final: 0.8834 (tt0) REVERT: J 129 GLU cc_start: 0.9064 (mm-30) cc_final: 0.8658 (mm-30) REVERT: J 132 MET cc_start: 0.8933 (mmt) cc_final: 0.8478 (mmm) REVERT: J 140 ASP cc_start: 0.8835 (m-30) cc_final: 0.8618 (m-30) REVERT: J 159 THR cc_start: 0.8837 (p) cc_final: 0.8579 (p) REVERT: J 164 ASP cc_start: 0.8392 (t0) cc_final: 0.8020 (t0) REVERT: J 190 ILE cc_start: 0.8417 (mt) cc_final: 0.8202 (mt) REVERT: J 208 MET cc_start: 0.8292 (tpp) cc_final: 0.7927 (tpp) REVERT: K 72 MET cc_start: 0.8410 (mmm) cc_final: 0.7808 (tmm) REVERT: K 76 MET cc_start: 0.8290 (mtm) cc_final: 0.6970 (ptt) REVERT: K 90 LEU cc_start: 0.9572 (mt) cc_final: 0.9324 (mp) REVERT: K 93 ASP cc_start: 0.8959 (m-30) cc_final: 0.8739 (m-30) REVERT: K 97 GLU cc_start: 0.8975 (mt-10) cc_final: 0.8535 (mt-10) REVERT: K 113 GLN cc_start: 0.8506 (tp40) cc_final: 0.7987 (tm-30) REVERT: K 117 ASP cc_start: 0.8051 (m-30) cc_final: 0.7554 (m-30) REVERT: K 168 ASP cc_start: 0.7967 (t0) cc_final: 0.7527 (t0) REVERT: K 172 TYR cc_start: 0.7764 (m-80) cc_final: 0.7491 (m-10) REVERT: K 173 LEU cc_start: 0.8453 (mt) cc_final: 0.8174 (mt) REVERT: K 197 GLU cc_start: 0.8738 (mp0) cc_final: 0.7962 (tm-30) REVERT: K 198 SER cc_start: 0.8625 (m) cc_final: 0.8304 (p) REVERT: K 206 GLN cc_start: 0.8818 (mt0) cc_final: 0.8439 (mt0) REVERT: K 210 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7691 (tm-30) REVERT: K 219 ASN cc_start: 0.7472 (t0) cc_final: 0.7028 (t0) REVERT: K 221 ASN cc_start: 0.7473 (m-40) cc_final: 0.6693 (t0) REVERT: M 73 VAL cc_start: 0.8374 (t) cc_final: 0.8149 (p) REVERT: M 77 THR cc_start: 0.9303 (m) cc_final: 0.9098 (p) REVERT: M 78 ARG cc_start: 0.8892 (mtm-85) cc_final: 0.8603 (ptp-170) REVERT: M 84 MET cc_start: 0.8159 (mtt) cc_final: 0.7931 (mtm) REVERT: M 113 ASN cc_start: 0.8463 (m-40) cc_final: 0.8111 (m-40) REVERT: N 84 MET cc_start: 0.8891 (mtm) cc_final: 0.8337 (mtm) REVERT: N 98 GLN cc_start: 0.8436 (tp40) cc_final: 0.8204 (tp40) REVERT: O 75 GLN cc_start: 0.9070 (mt0) cc_final: 0.8764 (tp40) REVERT: O 78 ARG cc_start: 0.8517 (mtm-85) cc_final: 0.8189 (mtm110) REVERT: O 85 GLN cc_start: 0.8839 (mt0) cc_final: 0.8629 (tm-30) REVERT: O 102 MET cc_start: 0.8159 (mtp) cc_final: 0.7558 (mtp) REVERT: O 105 ASP cc_start: 0.7985 (t0) cc_final: 0.7743 (p0) REVERT: Q 43 LYS cc_start: 0.9176 (mmtm) cc_final: 0.8969 (mmtt) REVERT: Q 76 ASN cc_start: 0.7838 (p0) cc_final: 0.7430 (p0) REVERT: Q 104 LYS cc_start: 0.8784 (mttt) cc_final: 0.8577 (mtmm) REVERT: Q 106 ASP cc_start: 0.9167 (m-30) cc_final: 0.8661 (p0) REVERT: Q 109 GLU cc_start: 0.8606 (tt0) cc_final: 0.8059 (tm-30) REVERT: Q 139 TYR cc_start: 0.8590 (t80) cc_final: 0.8229 (t80) REVERT: Q 198 HIS cc_start: 0.8315 (m-70) cc_final: 0.7882 (m170) REVERT: R 42 LEU cc_start: 0.8664 (mt) cc_final: 0.8207 (mp) REVERT: R 79 ASP cc_start: 0.8760 (m-30) cc_final: 0.8261 (t0) REVERT: R 105 LEU cc_start: 0.7853 (mt) cc_final: 0.7598 (mp) REVERT: R 107 LEU cc_start: 0.7836 (tp) cc_final: 0.7327 (tp) REVERT: R 112 TYR cc_start: 0.8422 (t80) cc_final: 0.7981 (t80) REVERT: R 125 ASP cc_start: 0.8802 (m-30) cc_final: 0.8507 (t70) REVERT: R 127 HIS cc_start: 0.8263 (t70) cc_final: 0.7978 (t70) REVERT: R 139 TYR cc_start: 0.8965 (t80) cc_final: 0.8643 (t80) REVERT: R 150 ASN cc_start: 0.7865 (m-40) cc_final: 0.7484 (m-40) REVERT: R 171 ASP cc_start: 0.8470 (m-30) cc_final: 0.8269 (p0) REVERT: R 194 ASP cc_start: 0.8945 (m-30) cc_final: 0.8598 (p0) REVERT: R 195 GLU cc_start: 0.8947 (mp0) cc_final: 0.8715 (mp0) REVERT: R 221 ASP cc_start: 0.8556 (m-30) cc_final: 0.8304 (m-30) REVERT: R 229 MET cc_start: 0.5379 (tpp) cc_final: 0.4998 (tpt) REVERT: S 79 ASP cc_start: 0.8732 (m-30) cc_final: 0.7999 (t0) REVERT: S 113 GLU cc_start: 0.9154 (tp30) cc_final: 0.8853 (tp30) REVERT: S 114 LYS cc_start: 0.8610 (mttt) cc_final: 0.8351 (mmtp) REVERT: S 117 GLN cc_start: 0.8846 (mt0) cc_final: 0.8642 (pp30) REVERT: S 128 VAL cc_start: 0.9288 (t) cc_final: 0.9023 (p) REVERT: S 132 GLN cc_start: 0.8278 (mt0) cc_final: 0.7835 (mp10) REVERT: S 151 PHE cc_start: 0.7764 (m-10) cc_final: 0.7319 (m-10) REVERT: S 153 ARG cc_start: 0.8156 (ttm-80) cc_final: 0.7800 (ttm170) REVERT: S 159 LEU cc_start: 0.9130 (tp) cc_final: 0.8922 (tp) REVERT: S 160 GLN cc_start: 0.8205 (mt0) cc_final: 0.7985 (mt0) REVERT: S 172 ASN cc_start: 0.7964 (t0) cc_final: 0.7424 (m-40) REVERT: S 179 PHE cc_start: 0.6811 (m-80) cc_final: 0.6457 (m-80) REVERT: S 196 GLN cc_start: 0.8425 (mt0) cc_final: 0.8115 (mt0) REVERT: S 197 TYR cc_start: 0.7530 (t80) cc_final: 0.6945 (t80) REVERT: S 201 LYS cc_start: 0.7805 (tttt) cc_final: 0.7393 (pttm) REVERT: S 222 GLN cc_start: 0.8533 (mt0) cc_final: 0.7337 (tm-30) outliers start: 2 outliers final: 0 residues processed: 1618 average time/residue: 0.5326 time to fit residues: 1348.4562 Evaluate side-chains 937 residues out of total 3955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 937 time to evaluate : 4.168 ------------------------------------------------------------------------------- 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: 4.9990 chunk 341 optimal weight: 8.9990 chunk 189 optimal weight: 5.9990 chunk 116 optimal weight: 0.9980 chunk 230 optimal weight: 0.0970 chunk 182 optimal weight: 1.9990 chunk 353 optimal weight: 6.9990 chunk 136 optimal weight: 9.9990 chunk 214 optimal weight: 0.7980 chunk 263 optimal weight: 1.9990 chunk 409 optimal weight: 0.8980 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 36765 Z= 0.221 Angle : 0.625 7.647 49676 Z= 0.318 Chirality : 0.045 0.170 5575 Planarity : 0.005 0.045 6440 Dihedral : 4.828 113.710 5018 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.94 % Favored : 98.04 % Rotamer: Outliers : 2.60 % Allowed : 11.41 % Favored : 85.99 % 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: 1.03 (0.12), residues: 4538 helix: 1.60 (0.11), residues: 2097 sheet: -0.27 (0.21), residues: 613 loop : 0.08 (0.15), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 450 HIS 0.005 0.001 HIS S 118 PHE 0.022 0.002 PHE R 200 TYR 0.032 0.002 TYR R 197 ARG 0.008 0.001 ARG H 45 *********************** 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 1120 residues out of total 3955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 1017 time to evaluate : 4.329 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: A 30 THR cc_start: 0.8088 (m) cc_final: 0.7767 (p) REVERT: A 155 ILE cc_start: 0.8247 (mt) cc_final: 0.7795 (tt) REVERT: A 171 ARG cc_start: 0.8365 (mtt180) cc_final: 0.7804 (mtm180) REVERT: A 203 LEU cc_start: 0.8782 (mt) cc_final: 0.8566 (mt) REVERT: A 224 ASN cc_start: 0.8914 (p0) cc_final: 0.8614 (p0) REVERT: A 356 GLU cc_start: 0.8603 (tp30) cc_final: 0.7856 (tm-30) REVERT: A 371 ASP cc_start: 0.7066 (m-30) cc_final: 0.6702 (p0) REVERT: A 436 ASP cc_start: 0.8356 (t0) cc_final: 0.7805 (t70) REVERT: A 443 LYS cc_start: 0.8924 (mttt) cc_final: 0.8143 (tptp) REVERT: A 447 SER cc_start: 0.7235 (m) cc_final: 0.6409 (t) REVERT: A 472 PHE cc_start: 0.7399 (t80) cc_final: 0.7120 (t80) REVERT: A 476 ARG cc_start: 0.8388 (ttm170) cc_final: 0.8118 (ptp-170) REVERT: A 505 ASP cc_start: 0.7785 (t0) cc_final: 0.7540 (t0) REVERT: A 544 MET cc_start: 0.8080 (mtt) cc_final: 0.7851 (mtp) REVERT: B 18 PHE cc_start: 0.7047 (OUTLIER) cc_final: 0.6839 (m-80) REVERT: B 30 THR cc_start: 0.8387 (m) cc_final: 0.7957 (p) REVERT: B 34 MET cc_start: 0.8784 (mtm) cc_final: 0.8582 (mtm) REVERT: B 53 GLU cc_start: 0.7683 (tt0) cc_final: 0.7211 (tt0) REVERT: B 74 SER cc_start: 0.7475 (m) cc_final: 0.6815 (p) REVERT: B 77 ASP cc_start: 0.7593 (m-30) cc_final: 0.6856 (m-30) REVERT: B 84 LYS cc_start: 0.7673 (mmtt) cc_final: 0.7161 (mmtm) REVERT: B 130 ASP cc_start: 0.8320 (m-30) cc_final: 0.8035 (p0) REVERT: B 142 ARG cc_start: 0.7898 (mmt-90) cc_final: 0.7580 (mmt180) REVERT: B 231 GLN cc_start: 0.7559 (mm-40) cc_final: 0.7124 (mm-40) REVERT: B 254 CYS cc_start: 0.8685 (m) cc_final: 0.8477 (m) REVERT: B 274 TYR cc_start: 0.8613 (t80) cc_final: 0.8388 (t80) REVERT: B 285 SER cc_start: 0.8480 (t) cc_final: 0.8013 (p) REVERT: B 296 MET cc_start: 0.8148 (ttm) cc_final: 0.7423 (ppp) REVERT: B 297 GLU cc_start: 0.8658 (mp0) cc_final: 0.7816 (mm-30) REVERT: B 367 GLU cc_start: 0.8531 (tt0) cc_final: 0.8328 (tt0) REVERT: B 368 MET cc_start: 0.8907 (tpp) cc_final: 0.8365 (tpp) REVERT: B 436 ASP cc_start: 0.6393 (t0) cc_final: 0.6115 (t0) REVERT: B 447 SER cc_start: 0.8315 (p) cc_final: 0.7781 (p) REVERT: B 488 ASP cc_start: 0.7404 (m-30) cc_final: 0.7029 (m-30) REVERT: B 530 ARG cc_start: 0.7489 (ptm160) cc_final: 0.7126 (ttp80) REVERT: B 572 GLU cc_start: 0.9026 (mm-30) cc_final: 0.8679 (pp20) REVERT: C 74 SER cc_start: 0.7637 (m) cc_final: 0.6809 (p) REVERT: C 77 ASP cc_start: 0.7645 (m-30) cc_final: 0.7325 (m-30) REVERT: C 167 MET cc_start: 0.8394 (mtp) cc_final: 0.7942 (mtp) REVERT: C 168 LEU cc_start: 0.8301 (tp) cc_final: 0.8092 (tp) REVERT: C 205 MET cc_start: 0.9225 (mtm) cc_final: 0.9006 (mtm) REVERT: C 213 GLN cc_start: 0.7099 (mm-40) cc_final: 0.6597 (mt0) REVERT: C 248 ILE cc_start: 0.8280 (mt) cc_final: 0.7845 (pt) REVERT: C 268 ASN cc_start: 0.8004 (t0) cc_final: 0.7511 (t0) REVERT: C 296 MET cc_start: 0.6346 (ptp) cc_final: 0.6092 (ptp) REVERT: C 308 ARG cc_start: 0.6765 (ptp-110) cc_final: 0.6384 (ptt180) REVERT: C 340 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.8447 (mtm) REVERT: C 485 GLU cc_start: 0.8504 (tt0) cc_final: 0.8174 (tt0) REVERT: C 531 PHE cc_start: 0.6218 (p90) cc_final: 0.5506 (p90) REVERT: C 603 GLN cc_start: 0.8209 (tp40) cc_final: 0.7632 (tp-100) REVERT: D 118 ILE cc_start: 0.8225 (pt) cc_final: 0.7908 (pt) REVERT: D 125 GLU cc_start: 0.8403 (tt0) cc_final: 0.8202 (tm-30) REVERT: D 152 ASP cc_start: 0.8349 (t0) cc_final: 0.8134 (t0) REVERT: D 167 GLU cc_start: 0.7343 (mt-10) cc_final: 0.6901 (mt-10) REVERT: D 281 THR cc_start: 0.9130 (m) cc_final: 0.8835 (t) REVERT: D 299 ASP cc_start: 0.8235 (m-30) cc_final: 0.7793 (m-30) REVERT: D 360 ASP cc_start: 0.7148 (OUTLIER) cc_final: 0.6943 (p0) REVERT: D 380 ASP cc_start: 0.8361 (t0) cc_final: 0.7652 (p0) REVERT: D 393 ASN cc_start: 0.8448 (t0) cc_final: 0.7952 (t0) REVERT: D 431 ASP cc_start: 0.8814 (t70) cc_final: 0.8464 (m-30) REVERT: E 47 TYR cc_start: 0.7714 (m-80) cc_final: 0.6905 (m-80) REVERT: E 49 THR cc_start: 0.8147 (p) cc_final: 0.7855 (p) REVERT: E 88 GLU cc_start: 0.7512 (tt0) cc_final: 0.6860 (mt-10) REVERT: E 201 GLU cc_start: 0.7937 (mp0) cc_final: 0.7069 (tp30) REVERT: E 262 ASN cc_start: 0.8686 (t0) cc_final: 0.8181 (t0) REVERT: E 268 THR cc_start: 0.8727 (p) cc_final: 0.8192 (t) REVERT: E 270 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7944 (mt-10) REVERT: E 283 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7359 (tm-30) REVERT: E 290 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8197 (mm-30) REVERT: E 315 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7864 (tt0) REVERT: E 327 MET cc_start: 0.8107 (tpp) cc_final: 0.7624 (tpp) REVERT: E 330 ASP cc_start: 0.8018 (t70) cc_final: 0.7645 (t70) REVERT: E 358 ASN cc_start: 0.8672 (t0) cc_final: 0.8388 (t0) REVERT: E 360 ASP cc_start: 0.7649 (t0) cc_final: 0.7369 (t0) REVERT: E 380 ASP cc_start: 0.8289 (p0) cc_final: 0.8073 (p0) REVERT: E 402 MET cc_start: 0.7775 (ttm) cc_final: 0.7198 (ttm) REVERT: E 448 ASP cc_start: 0.8444 (m-30) cc_final: 0.8198 (m-30) REVERT: E 490 GLU cc_start: 0.8750 (mp0) cc_final: 0.8411 (mp0) REVERT: F 61 ASP cc_start: 0.7500 (t0) cc_final: 0.7230 (m-30) REVERT: F 167 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7052 (mp0) REVERT: F 174 ILE cc_start: 0.8083 (mt) cc_final: 0.7798 (mt) REVERT: F 178 ASP cc_start: 0.7631 (m-30) cc_final: 0.7098 (m-30) REVERT: F 201 GLU cc_start: 0.7977 (mp0) cc_final: 0.7368 (mp0) REVERT: F 238 MET cc_start: 0.8147 (tpp) cc_final: 0.7574 (tpt) REVERT: F 262 ASN cc_start: 0.9110 (t0) cc_final: 0.8567 (t0) REVERT: F 268 THR cc_start: 0.8859 (p) cc_final: 0.8525 (t) REVERT: F 300 MET cc_start: 0.8981 (mmm) cc_final: 0.8737 (mmm) REVERT: F 315 GLU cc_start: 0.9276 (mt-10) cc_final: 0.8733 (mt-10) REVERT: F 316 GLU cc_start: 0.8683 (tp30) cc_final: 0.8247 (tp30) REVERT: F 359 ASP cc_start: 0.8970 (OUTLIER) cc_final: 0.8676 (m-30) REVERT: F 367 ASP cc_start: 0.8096 (t70) cc_final: 0.7888 (t0) REVERT: F 400 ARG cc_start: 0.7032 (tpt90) cc_final: 0.6723 (tpt170) REVERT: F 402 MET cc_start: 0.7837 (tpt) cc_final: 0.7483 (tpt) REVERT: F 403 LYS cc_start: 0.8685 (tptt) cc_final: 0.7948 (tptp) REVERT: F 447 ASP cc_start: 0.8784 (m-30) cc_final: 0.8522 (m-30) REVERT: F 460 LYS cc_start: 0.8335 (tttt) cc_final: 0.8100 (ttpp) REVERT: H 12 SER cc_start: 0.6021 (p) cc_final: 0.5577 (p) REVERT: H 197 GLU cc_start: 0.7630 (pt0) cc_final: 0.7342 (pt0) REVERT: I 89 ASP cc_start: 0.8698 (m-30) cc_final: 0.8445 (t70) REVERT: I 132 MET cc_start: 0.8723 (mtt) cc_final: 0.8116 (mtt) REVERT: I 135 ARG cc_start: 0.7256 (ttm170) cc_final: 0.7044 (mtm-85) REVERT: I 164 ASP cc_start: 0.8159 (t0) cc_final: 0.7759 (t0) REVERT: I 168 ASP cc_start: 0.8247 (t0) cc_final: 0.7551 (t0) REVERT: I 177 ILE cc_start: 0.8589 (mt) cc_final: 0.8217 (mm) REVERT: I 194 ASN cc_start: 0.8432 (t0) cc_final: 0.8005 (t0) REVERT: I 198 SER cc_start: 0.9233 (m) cc_final: 0.8990 (p) REVERT: I 221 ASN cc_start: 0.7467 (m-40) cc_final: 0.6927 (t0) REVERT: J 68 LYS cc_start: 0.7336 (mttt) cc_final: 0.6535 (tttt) REVERT: J 76 MET cc_start: 0.8993 (mmm) cc_final: 0.8715 (mmp) REVERT: J 89 ASP cc_start: 0.8579 (m-30) cc_final: 0.8179 (t0) REVERT: J 90 LEU cc_start: 0.9535 (mt) cc_final: 0.9325 (mt) REVERT: J 92 THR cc_start: 0.9334 (m) cc_final: 0.8999 (p) REVERT: J 96 ASN cc_start: 0.9469 (m-40) cc_final: 0.9223 (m110) REVERT: J 129 GLU cc_start: 0.9036 (mm-30) cc_final: 0.8707 (mm-30) REVERT: J 154 MET cc_start: 0.9146 (OUTLIER) cc_final: 0.8942 (mtp) REVERT: J 190 ILE cc_start: 0.8467 (mt) cc_final: 0.8206 (mt) REVERT: J 207 MET cc_start: 0.7266 (ttt) cc_final: 0.6974 (ttt) REVERT: J 208 MET cc_start: 0.8377 (tpp) cc_final: 0.8042 (tpp) REVERT: J 210 GLU cc_start: 0.7691 (tm-30) cc_final: 0.7420 (tm-30) REVERT: K 72 MET cc_start: 0.8477 (mmm) cc_final: 0.7856 (tmm) REVERT: K 76 MET cc_start: 0.8272 (mtm) cc_final: 0.7178 (ptp) REVERT: K 88 ASP cc_start: 0.8345 (t70) cc_final: 0.8103 (t0) REVERT: K 90 LEU cc_start: 0.9509 (mt) cc_final: 0.9143 (mp) REVERT: K 92 THR cc_start: 0.9104 (m) cc_final: 0.8858 (p) REVERT: K 97 GLU cc_start: 0.8977 (mt-10) cc_final: 0.8567 (mt-10) REVERT: K 129 GLU cc_start: 0.8420 (mm-30) cc_final: 0.7690 (mm-30) REVERT: K 172 TYR cc_start: 0.8161 (m-80) cc_final: 0.7800 (m-10) REVERT: K 173 LEU cc_start: 0.8464 (mt) cc_final: 0.8209 (mt) REVERT: K 184 TYR cc_start: 0.7965 (m-80) cc_final: 0.7359 (m-80) REVERT: K 197 GLU cc_start: 0.8671 (mp0) cc_final: 0.7868 (tm-30) REVERT: K 198 SER cc_start: 0.8584 (m) cc_final: 0.8205 (p) REVERT: K 210 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7555 (tm-30) REVERT: K 221 ASN cc_start: 0.7268 (m-40) cc_final: 0.6689 (t0) REVERT: M 88 GLN cc_start: 0.8003 (pp30) cc_final: 0.7726 (pp30) REVERT: N 78 ARG cc_start: 0.8906 (mtm110) cc_final: 0.8544 (mtm-85) REVERT: N 109 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.8085 (pt0) REVERT: O 75 GLN cc_start: 0.9091 (mt0) cc_final: 0.8806 (tp40) REVERT: O 85 GLN cc_start: 0.9117 (mt0) cc_final: 0.8649 (tm-30) REVERT: O 88 GLN cc_start: 0.8775 (tt0) cc_final: 0.8139 (tm-30) REVERT: O 100 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8455 (mp) REVERT: O 102 MET cc_start: 0.8420 (mtp) cc_final: 0.7953 (mtp) REVERT: O 105 ASP cc_start: 0.8239 (t0) cc_final: 0.7880 (p0) REVERT: Q 76 ASN cc_start: 0.7914 (p0) cc_final: 0.7690 (p0) REVERT: Q 88 LEU cc_start: 0.7820 (tp) cc_final: 0.7589 (tp) REVERT: Q 106 ASP cc_start: 0.9176 (m-30) cc_final: 0.8725 (p0) REVERT: Q 109 GLU cc_start: 0.8553 (tt0) cc_final: 0.8156 (tm-30) REVERT: Q 139 TYR cc_start: 0.8688 (t80) cc_final: 0.8314 (t80) REVERT: Q 161 MET cc_start: 0.8512 (tmm) cc_final: 0.8028 (tpp) REVERT: Q 198 HIS cc_start: 0.8566 (m-70) cc_final: 0.7860 (m-70) REVERT: R 79 ASP cc_start: 0.8638 (m-30) cc_final: 0.7904 (t0) REVERT: R 90 GLU cc_start: 0.8989 (mm-30) cc_final: 0.8752 (mm-30) REVERT: R 107 LEU cc_start: 0.8357 (tp) cc_final: 0.7721 (tp) REVERT: R 112 TYR cc_start: 0.8357 (t80) cc_final: 0.7777 (t80) REVERT: R 125 ASP cc_start: 0.8735 (m-30) cc_final: 0.8485 (t70) REVERT: R 127 HIS cc_start: 0.8181 (t70) cc_final: 0.7805 (t70) REVERT: R 168 ILE cc_start: 0.8072 (OUTLIER) cc_final: 0.7835 (tp) REVERT: R 171 ASP cc_start: 0.8648 (m-30) cc_final: 0.8143 (p0) REVERT: R 196 GLN cc_start: 0.8391 (mt0) cc_final: 0.8159 (mt0) REVERT: R 197 TYR cc_start: 0.7965 (m-80) cc_final: 0.7594 (m-80) REVERT: R 216 ILE cc_start: 0.7872 (mm) cc_final: 0.7426 (tp) REVERT: R 228 THR cc_start: 0.8005 (m) cc_final: 0.7413 (p) REVERT: S 33 MET cc_start: 0.8454 (tpp) cc_final: 0.7885 (mtp) REVERT: S 61 ARG cc_start: 0.8484 (mtp-110) cc_final: 0.7853 (mtm110) REVERT: S 113 GLU cc_start: 0.9162 (tp30) cc_final: 0.8946 (tp30) REVERT: S 114 LYS cc_start: 0.8703 (mttt) cc_final: 0.8476 (mmtp) REVERT: S 117 GLN cc_start: 0.8845 (mt0) cc_final: 0.8585 (pp30) REVERT: S 160 GLN cc_start: 0.8212 (mt0) cc_final: 0.7934 (mt0) REVERT: S 201 LYS cc_start: 0.7771 (tttt) cc_final: 0.7532 (pttm) REVERT: S 222 GLN cc_start: 0.8360 (mt0) cc_final: 0.7272 (tm-30) outliers start: 103 outliers final: 56 residues processed: 1068 average time/residue: 0.4816 time to fit residues: 845.7503 Evaluate side-chains 912 residues out of total 3955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 848 time to evaluate : 4.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 32 CYS Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 306 MET Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 340 MET Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 545 ILE Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 187 GLN Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain D residue 360 ASP Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 207 CYS Chi-restraints excluded: chain E residue 423 TYR Chi-restraints excluded: chain E residue 432 VAL Chi-restraints excluded: chain E residue 464 THR Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 162 CYS Chi-restraints excluded: chain F residue 207 CYS Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 359 ASP Chi-restraints excluded: chain H residue 158 LEU Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 204 LYS Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 154 MET Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain M residue 105 ASP Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain N residue 109 GLN Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain Q residue 74 CYS Chi-restraints excluded: chain Q residue 142 ASN Chi-restraints excluded: chain Q residue 152 LEU Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain S residue 65 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 227 optimal weight: 0.6980 chunk 127 optimal weight: 3.9990 chunk 340 optimal weight: 8.9990 chunk 278 optimal weight: 0.2980 chunk 112 optimal weight: 0.9980 chunk 410 optimal weight: 4.9990 chunk 443 optimal weight: 0.9980 chunk 365 optimal weight: 9.9990 chunk 406 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 329 optimal weight: 9.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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** ** D 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 GLN E 465 GLN F 181 ASN Q 111 GLN ** R 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 150 ASN R 198 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 36765 Z= 0.201 Angle : 0.577 10.158 49676 Z= 0.288 Chirality : 0.043 0.178 5575 Planarity : 0.004 0.047 6440 Dihedral : 4.632 119.077 5018 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.63 % Allowed : 13.40 % Favored : 83.97 % 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: 1.11 (0.13), residues: 4538 helix: 1.72 (0.11), residues: 2105 sheet: -0.21 (0.21), residues: 613 loop : 0.01 (0.15), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 567 HIS 0.008 0.001 HIS R 198 PHE 0.027 0.002 PHE R 200 TYR 0.032 0.001 TYR Q 112 ARG 0.009 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 1007 residues out of total 3955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 903 time to evaluate : 4.534 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: A 30 THR cc_start: 0.8157 (m) cc_final: 0.7890 (p) REVERT: A 34 MET cc_start: 0.8175 (ttm) cc_final: 0.7691 (mmm) REVERT: A 155 ILE cc_start: 0.8346 (mt) cc_final: 0.7972 (tt) REVERT: A 171 ARG cc_start: 0.8390 (mtt180) cc_final: 0.7840 (mtm180) REVERT: A 224 ASN cc_start: 0.8917 (p0) cc_final: 0.8608 (p0) REVERT: A 306 MET cc_start: 0.8499 (tpp) cc_final: 0.8257 (mpp) REVERT: A 324 GLU cc_start: 0.8957 (tm-30) cc_final: 0.8531 (tm-30) REVERT: A 345 SER cc_start: 0.8529 (t) cc_final: 0.8201 (m) REVERT: A 356 GLU cc_start: 0.8525 (tp30) cc_final: 0.7813 (tm-30) REVERT: A 371 ASP cc_start: 0.7175 (m-30) cc_final: 0.6824 (p0) REVERT: A 436 ASP cc_start: 0.8481 (t0) cc_final: 0.8074 (t70) REVERT: A 443 LYS cc_start: 0.8940 (mttt) cc_final: 0.8111 (tptp) REVERT: A 447 SER cc_start: 0.7326 (m) cc_final: 0.6575 (t) REVERT: A 472 PHE cc_start: 0.7539 (t80) cc_final: 0.7098 (t80) REVERT: A 476 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7832 (ptp90) REVERT: A 505 ASP cc_start: 0.7820 (t0) cc_final: 0.7457 (t0) REVERT: A 547 PHE cc_start: 0.7423 (t80) cc_final: 0.7182 (t80) REVERT: B 20 TYR cc_start: 0.7652 (m-10) cc_final: 0.7421 (m-10) REVERT: B 30 THR cc_start: 0.8462 (m) cc_final: 0.8041 (p) REVERT: B 53 GLU cc_start: 0.7745 (tt0) cc_final: 0.7174 (tt0) REVERT: B 77 ASP cc_start: 0.7665 (m-30) cc_final: 0.7105 (m-30) REVERT: B 84 LYS cc_start: 0.7591 (mmtt) cc_final: 0.7058 (mmtm) REVERT: B 130 ASP cc_start: 0.8346 (m-30) cc_final: 0.8017 (p0) REVERT: B 224 ASN cc_start: 0.9060 (p0) cc_final: 0.8819 (p0) REVERT: B 231 GLN cc_start: 0.7366 (mm-40) cc_final: 0.7022 (mm-40) REVERT: B 254 CYS cc_start: 0.8707 (m) cc_final: 0.8487 (m) REVERT: B 274 TYR cc_start: 0.8533 (t80) cc_final: 0.8285 (t80) REVERT: B 296 MET cc_start: 0.8153 (ttm) cc_final: 0.7924 (ttm) REVERT: B 297 GLU cc_start: 0.8654 (mp0) cc_final: 0.7830 (mm-30) REVERT: B 436 ASP cc_start: 0.6558 (t0) cc_final: 0.6113 (m-30) REVERT: B 447 SER cc_start: 0.8468 (p) cc_final: 0.7952 (p) REVERT: B 530 ARG cc_start: 0.7503 (ptm160) cc_final: 0.6976 (ptm-80) REVERT: B 572 GLU cc_start: 0.8991 (mm-30) cc_final: 0.8678 (pp20) REVERT: B 600 ASP cc_start: 0.7856 (t0) cc_final: 0.7629 (t0) REVERT: B 603 GLN cc_start: 0.7751 (tm-30) cc_final: 0.7446 (tm-30) REVERT: B 612 PHE cc_start: 0.7251 (m-80) cc_final: 0.7045 (m-10) REVERT: C 74 SER cc_start: 0.7642 (m) cc_final: 0.6816 (p) REVERT: C 77 ASP cc_start: 0.7721 (m-30) cc_final: 0.7412 (m-30) REVERT: C 99 PHE cc_start: 0.8678 (m-10) cc_final: 0.8465 (m-10) REVERT: C 167 MET cc_start: 0.8361 (mtp) cc_final: 0.8106 (mtp) REVERT: C 168 LEU cc_start: 0.8336 (tp) cc_final: 0.8133 (tp) REVERT: C 218 THR cc_start: 0.8238 (m) cc_final: 0.7978 (m) REVERT: C 248 ILE cc_start: 0.8351 (mt) cc_final: 0.7933 (pt) REVERT: C 268 ASN cc_start: 0.7895 (t0) cc_final: 0.7451 (t0) REVERT: C 284 MET cc_start: 0.8145 (mmm) cc_final: 0.7799 (mmm) REVERT: C 295 THR cc_start: 0.8609 (p) cc_final: 0.8054 (t) REVERT: C 296 MET cc_start: 0.6508 (ptp) cc_final: 0.6306 (ptp) REVERT: C 308 ARG cc_start: 0.6756 (ptp-110) cc_final: 0.6351 (ptt180) REVERT: C 458 MET cc_start: 0.7558 (mmt) cc_final: 0.7030 (mmt) REVERT: C 485 GLU cc_start: 0.8522 (tt0) cc_final: 0.8186 (tt0) REVERT: C 531 PHE cc_start: 0.6218 (p90) cc_final: 0.5489 (p90) REVERT: D 118 ILE cc_start: 0.8268 (pt) cc_final: 0.8046 (pt) REVERT: D 180 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.8218 (mmm) REVERT: D 299 ASP cc_start: 0.8272 (m-30) cc_final: 0.7825 (m-30) REVERT: D 380 ASP cc_start: 0.8221 (t0) cc_final: 0.7911 (t70) REVERT: D 393 ASN cc_start: 0.8474 (t0) cc_final: 0.7944 (t0) REVERT: D 403 LYS cc_start: 0.9105 (tttt) cc_final: 0.8624 (mtmt) REVERT: D 431 ASP cc_start: 0.8801 (t70) cc_final: 0.8461 (m-30) REVERT: D 446 SER cc_start: 0.7757 (m) cc_final: 0.7514 (p) REVERT: E 47 TYR cc_start: 0.7834 (m-80) cc_final: 0.7148 (m-80) REVERT: E 49 THR cc_start: 0.8239 (p) cc_final: 0.7949 (p) REVERT: E 88 GLU cc_start: 0.7156 (tt0) cc_final: 0.6653 (mt-10) REVERT: E 100 GLU cc_start: 0.8511 (mp0) cc_final: 0.8093 (mp0) REVERT: E 106 ASP cc_start: 0.7876 (t70) cc_final: 0.7277 (t0) REVERT: E 201 GLU cc_start: 0.7967 (mp0) cc_final: 0.7524 (mt-10) REVERT: E 254 MET cc_start: 0.7650 (tpt) cc_final: 0.7419 (tpt) REVERT: E 262 ASN cc_start: 0.8689 (t0) cc_final: 0.8049 (t0) REVERT: E 268 THR cc_start: 0.8658 (p) cc_final: 0.8144 (t) REVERT: E 270 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7979 (mt-10) REVERT: E 283 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7349 (tm-30) REVERT: E 290 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8204 (mm-30) REVERT: E 315 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7804 (tt0) REVERT: E 327 MET cc_start: 0.8412 (tpp) cc_final: 0.7658 (tpp) REVERT: E 330 ASP cc_start: 0.8133 (t70) cc_final: 0.7372 (t0) REVERT: E 358 ASN cc_start: 0.8764 (t0) cc_final: 0.8440 (t0) REVERT: E 360 ASP cc_start: 0.7634 (t0) cc_final: 0.7286 (t0) REVERT: E 402 MET cc_start: 0.7578 (ttm) cc_final: 0.6754 (tpp) REVERT: E 408 GLU cc_start: 0.8408 (tp30) cc_final: 0.7939 (mm-30) REVERT: E 490 GLU cc_start: 0.8713 (mp0) cc_final: 0.8371 (mp0) REVERT: F 61 ASP cc_start: 0.7796 (t0) cc_final: 0.7476 (m-30) REVERT: F 167 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7110 (mp0) REVERT: F 174 ILE cc_start: 0.7981 (mt) cc_final: 0.7701 (mt) REVERT: F 178 ASP cc_start: 0.7542 (m-30) cc_final: 0.7044 (m-30) REVERT: F 180 MET cc_start: 0.7268 (OUTLIER) cc_final: 0.6640 (mtp) REVERT: F 201 GLU cc_start: 0.7944 (mp0) cc_final: 0.7397 (mp0) REVERT: F 238 MET cc_start: 0.8137 (tpp) cc_final: 0.7632 (tpt) REVERT: F 262 ASN cc_start: 0.9207 (t0) cc_final: 0.8743 (t0) REVERT: F 268 THR cc_start: 0.8895 (p) cc_final: 0.8551 (t) REVERT: F 300 MET cc_start: 0.9012 (mmm) cc_final: 0.8779 (mmp) REVERT: F 315 GLU cc_start: 0.9222 (mt-10) cc_final: 0.8660 (mt-10) REVERT: F 316 GLU cc_start: 0.8690 (tp30) cc_final: 0.8202 (tp30) REVERT: F 400 ARG cc_start: 0.7044 (tpt90) cc_final: 0.6661 (tpt170) REVERT: F 403 LYS cc_start: 0.8811 (tptt) cc_final: 0.8043 (tptp) REVERT: F 460 LYS cc_start: 0.8323 (tttt) cc_final: 0.8073 (ttpp) REVERT: H 14 MET cc_start: 0.8835 (ttt) cc_final: 0.8591 (ttt) REVERT: H 168 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7864 (ttp-170) REVERT: H 173 GLU cc_start: 0.7703 (tt0) cc_final: 0.7390 (tt0) REVERT: H 197 GLU cc_start: 0.7685 (pt0) cc_final: 0.7473 (pt0) REVERT: I 132 MET cc_start: 0.8741 (mtt) cc_final: 0.8237 (mtt) REVERT: I 190 ILE cc_start: 0.8612 (mt) cc_final: 0.8383 (tt) REVERT: I 194 ASN cc_start: 0.8522 (t0) cc_final: 0.8031 (t0) REVERT: I 198 SER cc_start: 0.9191 (m) cc_final: 0.8885 (p) REVERT: I 210 GLU cc_start: 0.7951 (mp0) cc_final: 0.7338 (tm-30) REVERT: I 221 ASN cc_start: 0.7341 (m-40) cc_final: 0.6885 (t0) REVERT: J 68 LYS cc_start: 0.7216 (mttt) cc_final: 0.6389 (tttt) REVERT: J 76 MET cc_start: 0.9060 (mmm) cc_final: 0.8842 (mmp) REVERT: J 89 ASP cc_start: 0.8530 (m-30) cc_final: 0.8142 (t0) REVERT: J 90 LEU cc_start: 0.9519 (mt) cc_final: 0.9148 (mt) REVERT: J 92 THR cc_start: 0.9259 (m) cc_final: 0.8891 (p) REVERT: J 96 ASN cc_start: 0.9441 (m-40) cc_final: 0.9111 (m110) REVERT: J 97 GLU cc_start: 0.9100 (tt0) cc_final: 0.8783 (tt0) REVERT: J 129 GLU cc_start: 0.9047 (mm-30) cc_final: 0.8760 (mm-30) REVERT: J 132 MET cc_start: 0.9117 (mmt) cc_final: 0.8851 (mmm) REVERT: J 190 ILE cc_start: 0.8527 (mt) cc_final: 0.8236 (mt) REVERT: J 207 MET cc_start: 0.7251 (ttt) cc_final: 0.6878 (ttt) REVERT: J 208 MET cc_start: 0.8405 (tpp) cc_final: 0.8076 (tpp) REVERT: J 210 GLU cc_start: 0.7691 (tm-30) cc_final: 0.7290 (tm-30) REVERT: K 72 MET cc_start: 0.8531 (mmm) cc_final: 0.7859 (tmm) REVERT: K 76 MET cc_start: 0.8246 (mtm) cc_final: 0.7133 (ptp) REVERT: K 88 ASP cc_start: 0.8287 (t70) cc_final: 0.8028 (t0) REVERT: K 90 LEU cc_start: 0.9488 (mt) cc_final: 0.9145 (mt) REVERT: K 92 THR cc_start: 0.9082 (m) cc_final: 0.8833 (p) REVERT: K 97 GLU cc_start: 0.8996 (mt-10) cc_final: 0.8676 (mt-10) REVERT: K 132 MET cc_start: 0.9158 (mmm) cc_final: 0.8849 (mmm) REVERT: K 172 TYR cc_start: 0.8257 (m-80) cc_final: 0.7926 (m-10) REVERT: K 173 LEU cc_start: 0.8548 (mt) cc_final: 0.8262 (mt) REVERT: K 184 TYR cc_start: 0.7982 (m-80) cc_final: 0.7573 (m-80) REVERT: K 197 GLU cc_start: 0.8671 (mp0) cc_final: 0.7848 (tm-30) REVERT: K 210 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7519 (tm-30) REVERT: M 88 GLN cc_start: 0.8172 (pp30) cc_final: 0.7895 (pp30) REVERT: M 107 ARG cc_start: 0.8159 (ttm-80) cc_final: 0.7856 (tpp80) REVERT: N 84 MET cc_start: 0.8685 (mtp) cc_final: 0.8371 (mtm) REVERT: N 94 ARG cc_start: 0.9015 (tmt170) cc_final: 0.8751 (tmt170) REVERT: N 109 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.8059 (pt0) REVERT: O 75 GLN cc_start: 0.9034 (mt0) cc_final: 0.8778 (tp40) REVERT: O 78 ARG cc_start: 0.8481 (mtm110) cc_final: 0.8235 (mtm110) REVERT: O 85 GLN cc_start: 0.9091 (mt0) cc_final: 0.8645 (tm-30) REVERT: O 88 GLN cc_start: 0.8797 (tt0) cc_final: 0.8128 (tm-30) REVERT: O 89 GLN cc_start: 0.8447 (tp40) cc_final: 0.8157 (tp40) REVERT: O 102 MET cc_start: 0.8381 (mtp) cc_final: 0.8067 (ttm) REVERT: O 105 ASP cc_start: 0.8258 (t0) cc_final: 0.7944 (p0) REVERT: Q 106 ASP cc_start: 0.9173 (m-30) cc_final: 0.8771 (p0) REVERT: Q 109 GLU cc_start: 0.8534 (tt0) cc_final: 0.8140 (tm-30) REVERT: Q 115 MET cc_start: 0.8992 (mmt) cc_final: 0.8767 (mmt) REVERT: Q 139 TYR cc_start: 0.8695 (t80) cc_final: 0.8211 (t80) REVERT: Q 161 MET cc_start: 0.8589 (tmm) cc_final: 0.8055 (tpp) REVERT: Q 192 LYS cc_start: 0.8373 (mttt) cc_final: 0.8144 (mtpp) REVERT: Q 198 HIS cc_start: 0.8621 (m-70) cc_final: 0.7852 (m-70) REVERT: R 103 MET cc_start: 0.7262 (ttm) cc_final: 0.6992 (ttm) REVERT: R 107 LEU cc_start: 0.8323 (tp) cc_final: 0.7877 (tp) REVERT: R 112 TYR cc_start: 0.8338 (t80) cc_final: 0.7708 (t80) REVERT: R 125 ASP cc_start: 0.8732 (m-30) cc_final: 0.8516 (t70) REVERT: R 127 HIS cc_start: 0.8125 (t70) cc_final: 0.7900 (t70) REVERT: R 171 ASP cc_start: 0.8640 (m-30) cc_final: 0.8106 (p0) REVERT: R 197 TYR cc_start: 0.8085 (m-80) cc_final: 0.7716 (m-80) REVERT: R 216 ILE cc_start: 0.7623 (mm) cc_final: 0.7194 (tp) REVERT: R 228 THR cc_start: 0.8239 (m) cc_final: 0.7679 (p) REVERT: S 33 MET cc_start: 0.8501 (tpp) cc_final: 0.7861 (mtp) REVERT: S 61 ARG cc_start: 0.8355 (mtp-110) cc_final: 0.8101 (ttm110) REVERT: S 64 GLU cc_start: 0.8833 (tp30) cc_final: 0.8603 (tm-30) REVERT: S 87 ILE cc_start: 0.9220 (mp) cc_final: 0.8969 (tp) REVERT: S 113 GLU cc_start: 0.9155 (tp30) cc_final: 0.8937 (tp30) REVERT: S 114 LYS cc_start: 0.8702 (mttt) cc_final: 0.8465 (mmtp) REVERT: S 117 GLN cc_start: 0.8854 (mt0) cc_final: 0.8557 (pp30) REVERT: S 159 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8601 (tp) REVERT: S 160 GLN cc_start: 0.8204 (mt0) cc_final: 0.7939 (mt0) REVERT: S 197 TYR cc_start: 0.7907 (m-80) cc_final: 0.7533 (m-80) REVERT: S 200 PHE cc_start: 0.8514 (t80) cc_final: 0.8167 (t80) REVERT: S 201 LYS cc_start: 0.8088 (tttt) cc_final: 0.7689 (pttm) REVERT: S 222 GLN cc_start: 0.8417 (mt0) cc_final: 0.7333 (tm-30) REVERT: S 232 TYR cc_start: 0.8152 (t80) cc_final: 0.7931 (t80) outliers start: 104 outliers final: 71 residues processed: 949 average time/residue: 0.4740 time to fit residues: 738.9671 Evaluate side-chains 885 residues out of total 3955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 808 time to evaluate : 4.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 476 ARG Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 494 GLN Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 65 GLN Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 306 MET Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 450 TRP Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 526 THR Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 187 GLN Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain D residue 410 MET Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 207 CYS Chi-restraints excluded: chain E residue 311 SER Chi-restraints excluded: chain E residue 423 TYR Chi-restraints excluded: chain E residue 432 VAL Chi-restraints excluded: chain E residue 464 THR Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 162 CYS Chi-restraints excluded: chain F residue 180 MET Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain H residue 168 ARG Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain K residue 152 ILE Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain M residue 105 ASP Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain N residue 109 GLN Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain O residue 116 ILE Chi-restraints excluded: chain Q residue 13 LEU Chi-restraints excluded: chain Q residue 74 CYS Chi-restraints excluded: chain Q residue 142 ASN Chi-restraints excluded: chain Q residue 152 LEU Chi-restraints excluded: chain Q residue 156 THR Chi-restraints excluded: chain Q residue 197 TYR Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 74 CYS Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain S residue 34 GLN Chi-restraints excluded: chain S residue 158 VAL Chi-restraints excluded: chain S residue 159 LEU Chi-restraints excluded: chain S residue 216 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 405 optimal weight: 3.9990 chunk 308 optimal weight: 0.6980 chunk 212 optimal weight: 1.9990 chunk 45 optimal weight: 0.0570 chunk 195 optimal weight: 0.8980 chunk 275 optimal weight: 3.9990 chunk 411 optimal weight: 5.9990 chunk 435 optimal weight: 8.9990 chunk 215 optimal weight: 4.9990 chunk 390 optimal weight: 4.9990 chunk 117 optimal weight: 9.9990 overall best weight: 1.5302 ------------------------------------------------------------------------------- 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 ** C 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 HIS ** D 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 251 ASN ** E 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 GLN ** M 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 134 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.4164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 36765 Z= 0.231 Angle : 0.567 10.343 49676 Z= 0.282 Chirality : 0.043 0.165 5575 Planarity : 0.004 0.047 6440 Dihedral : 4.589 127.640 5018 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.49 % Allowed : 14.11 % Favored : 82.40 % 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: 1.19 (0.13), residues: 4538 helix: 1.84 (0.11), residues: 2110 sheet: -0.06 (0.21), residues: 588 loop : -0.08 (0.15), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 567 HIS 0.006 0.001 HIS S 127 PHE 0.023 0.002 PHE R 200 TYR 0.029 0.001 TYR C 535 ARG 0.009 0.000 ARG M 78 *********************** 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 992 residues out of total 3955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 854 time to evaluate : 4.662 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: A 30 THR cc_start: 0.8258 (m) cc_final: 0.7999 (p) REVERT: A 34 MET cc_start: 0.8140 (ttm) cc_final: 0.7671 (mmm) REVERT: A 82 THR cc_start: 0.8350 (m) cc_final: 0.8140 (p) REVERT: A 155 ILE cc_start: 0.8382 (mt) cc_final: 0.7918 (tt) REVERT: A 171 ARG cc_start: 0.8331 (mtt180) cc_final: 0.7817 (mtm180) REVERT: A 203 LEU cc_start: 0.8799 (mt) cc_final: 0.8518 (mt) REVERT: A 324 GLU cc_start: 0.8967 (tm-30) cc_final: 0.8570 (tm-30) REVERT: A 345 SER cc_start: 0.8688 (t) cc_final: 0.8138 (p) REVERT: A 349 ASP cc_start: 0.7698 (t0) cc_final: 0.7426 (p0) REVERT: A 356 GLU cc_start: 0.8490 (tp30) cc_final: 0.7825 (tm-30) REVERT: A 436 ASP cc_start: 0.8618 (t0) cc_final: 0.8178 (t70) REVERT: A 443 LYS cc_start: 0.8971 (mttt) cc_final: 0.8172 (tptp) REVERT: A 447 SER cc_start: 0.7465 (m) cc_final: 0.6732 (t) REVERT: A 467 LYS cc_start: 0.8909 (tttt) cc_final: 0.8535 (tttm) REVERT: A 472 PHE cc_start: 0.7515 (t80) cc_final: 0.7120 (t80) REVERT: A 476 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.7948 (ptp90) REVERT: A 505 ASP cc_start: 0.7934 (t0) cc_final: 0.7518 (t0) REVERT: A 550 MET cc_start: 0.8939 (mmm) cc_final: 0.8315 (mtt) REVERT: B 18 PHE cc_start: 0.7207 (OUTLIER) cc_final: 0.6729 (m-80) REVERT: B 30 THR cc_start: 0.8495 (m) cc_final: 0.8090 (p) REVERT: B 53 GLU cc_start: 0.7828 (tt0) cc_final: 0.7141 (tt0) REVERT: B 77 ASP cc_start: 0.7774 (m-30) cc_final: 0.7404 (m-30) REVERT: B 84 LYS cc_start: 0.7594 (mmtt) cc_final: 0.7104 (mmtm) REVERT: B 130 ASP cc_start: 0.8375 (m-30) cc_final: 0.8029 (p0) REVERT: B 224 ASN cc_start: 0.9167 (p0) cc_final: 0.8869 (p0) REVERT: B 231 GLN cc_start: 0.7521 (mm-40) cc_final: 0.7104 (mm-40) REVERT: B 274 TYR cc_start: 0.8469 (t80) cc_final: 0.8201 (t80) REVERT: B 279 GLU cc_start: 0.6739 (tp30) cc_final: 0.6526 (tp30) REVERT: B 297 GLU cc_start: 0.8692 (mp0) cc_final: 0.7721 (mm-30) REVERT: B 324 GLU cc_start: 0.8473 (tt0) cc_final: 0.8195 (tm-30) REVERT: B 436 ASP cc_start: 0.6872 (t0) cc_final: 0.6075 (m-30) REVERT: B 447 SER cc_start: 0.8573 (p) cc_final: 0.7736 (t) REVERT: B 530 ARG cc_start: 0.7542 (ptm160) cc_final: 0.7012 (ptm-80) REVERT: B 572 GLU cc_start: 0.9062 (mm-30) cc_final: 0.8735 (pp20) REVERT: B 613 ARG cc_start: 0.8455 (mtp85) cc_final: 0.8251 (mmt-90) REVERT: C 74 SER cc_start: 0.7658 (m) cc_final: 0.6826 (p) REVERT: C 77 ASP cc_start: 0.7795 (m-30) cc_final: 0.7436 (m-30) REVERT: C 99 PHE cc_start: 0.8740 (m-10) cc_final: 0.8473 (m-10) REVERT: C 167 MET cc_start: 0.8401 (mtp) cc_final: 0.8165 (mtp) REVERT: C 168 LEU cc_start: 0.8353 (tp) cc_final: 0.8149 (tp) REVERT: C 205 MET cc_start: 0.9295 (mtm) cc_final: 0.8544 (ttp) REVERT: C 218 THR cc_start: 0.8223 (m) cc_final: 0.7961 (m) REVERT: C 248 ILE cc_start: 0.8457 (mt) cc_final: 0.8054 (pt) REVERT: C 268 ASN cc_start: 0.7952 (t0) cc_final: 0.7512 (t0) REVERT: C 284 MET cc_start: 0.8125 (mmm) cc_final: 0.7845 (mmm) REVERT: C 296 MET cc_start: 0.6539 (ptp) cc_final: 0.6295 (ptp) REVERT: C 308 ARG cc_start: 0.6918 (ptp-110) cc_final: 0.6443 (ptt180) REVERT: C 456 LYS cc_start: 0.8108 (mttt) cc_final: 0.7710 (mmmt) REVERT: C 458 MET cc_start: 0.7492 (mmt) cc_final: 0.6968 (mmt) REVERT: C 485 GLU cc_start: 0.8608 (tt0) cc_final: 0.8280 (tt0) REVERT: C 531 PHE cc_start: 0.6215 (p90) cc_final: 0.5523 (p90) REVERT: D 169 MET cc_start: 0.8473 (OUTLIER) cc_final: 0.8222 (tmm) REVERT: D 234 MET cc_start: 0.9330 (mtm) cc_final: 0.9043 (mtm) REVERT: D 299 ASP cc_start: 0.8002 (m-30) cc_final: 0.7625 (m-30) REVERT: D 380 ASP cc_start: 0.8284 (t0) cc_final: 0.7867 (t70) REVERT: D 393 ASN cc_start: 0.8510 (t0) cc_final: 0.7902 (t0) REVERT: D 403 LYS cc_start: 0.9143 (tttt) cc_final: 0.8735 (mtmt) REVERT: D 431 ASP cc_start: 0.8781 (t70) cc_final: 0.8451 (m-30) REVERT: D 446 SER cc_start: 0.7832 (m) cc_final: 0.7592 (p) REVERT: E 47 TYR cc_start: 0.7885 (m-80) cc_final: 0.7180 (m-80) REVERT: E 49 THR cc_start: 0.8297 (p) cc_final: 0.8013 (p) REVERT: E 88 GLU cc_start: 0.7352 (tt0) cc_final: 0.6767 (mt-10) REVERT: E 102 THR cc_start: 0.7895 (OUTLIER) cc_final: 0.7689 (m) REVERT: E 106 ASP cc_start: 0.7800 (t70) cc_final: 0.7353 (t0) REVERT: E 127 MET cc_start: 0.8228 (mmm) cc_final: 0.7920 (tpp) REVERT: E 169 MET cc_start: 0.7366 (OUTLIER) cc_final: 0.7149 (tmm) REVERT: E 201 GLU cc_start: 0.8009 (mp0) cc_final: 0.7595 (mt-10) REVERT: E 262 ASN cc_start: 0.8753 (t0) cc_final: 0.8120 (t0) REVERT: E 268 THR cc_start: 0.8712 (p) cc_final: 0.8241 (t) REVERT: E 270 GLU cc_start: 0.8304 (mt-10) cc_final: 0.8047 (mt-10) REVERT: E 283 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7427 (tm-30) REVERT: E 290 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8265 (mm-30) REVERT: E 315 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7885 (tt0) REVERT: E 327 MET cc_start: 0.8525 (tpp) cc_final: 0.7726 (tpp) REVERT: E 330 ASP cc_start: 0.8213 (t70) cc_final: 0.7811 (t70) REVERT: E 358 ASN cc_start: 0.8797 (t0) cc_final: 0.8425 (t0) REVERT: E 402 MET cc_start: 0.7633 (ttm) cc_final: 0.7088 (ttm) REVERT: E 490 GLU cc_start: 0.8691 (mp0) cc_final: 0.8315 (mp0) REVERT: F 61 ASP cc_start: 0.8075 (t0) cc_final: 0.7719 (m-30) REVERT: F 167 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7178 (mp0) REVERT: F 174 ILE cc_start: 0.8035 (mt) cc_final: 0.7803 (mt) REVERT: F 178 ASP cc_start: 0.7452 (m-30) cc_final: 0.7105 (m-30) REVERT: F 189 ILE cc_start: 0.9006 (tt) cc_final: 0.8663 (tp) REVERT: F 201 GLU cc_start: 0.7851 (mp0) cc_final: 0.7243 (mp0) REVERT: F 238 MET cc_start: 0.8175 (tpp) cc_final: 0.7728 (tpt) REVERT: F 249 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8111 (mm-30) REVERT: F 262 ASN cc_start: 0.9272 (t0) cc_final: 0.8875 (t0) REVERT: F 268 THR cc_start: 0.8885 (p) cc_final: 0.8561 (t) REVERT: F 315 GLU cc_start: 0.9225 (mt-10) cc_final: 0.8648 (mt-10) REVERT: F 316 GLU cc_start: 0.8697 (tp30) cc_final: 0.8142 (tp30) REVERT: F 356 MET cc_start: 0.7894 (OUTLIER) cc_final: 0.7682 (ttm) REVERT: F 400 ARG cc_start: 0.7066 (tpt90) cc_final: 0.6752 (tpt170) REVERT: F 403 LYS cc_start: 0.8871 (tptt) cc_final: 0.8089 (tptp) REVERT: F 460 LYS cc_start: 0.8304 (tttt) cc_final: 0.8039 (ttpp) REVERT: H 168 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7832 (ttp-170) REVERT: H 173 GLU cc_start: 0.7709 (tt0) cc_final: 0.7492 (tt0) REVERT: I 132 MET cc_start: 0.8694 (mtt) cc_final: 0.8331 (mtt) REVERT: I 194 ASN cc_start: 0.8619 (t0) cc_final: 0.8051 (t0) REVERT: I 198 SER cc_start: 0.9145 (m) cc_final: 0.8851 (p) REVERT: I 210 GLU cc_start: 0.7926 (mp0) cc_final: 0.7363 (tm-30) REVERT: I 221 ASN cc_start: 0.7408 (m-40) cc_final: 0.7154 (t0) REVERT: J 68 LYS cc_start: 0.7319 (mttt) cc_final: 0.6488 (tttt) REVERT: J 76 MET cc_start: 0.9070 (mmm) cc_final: 0.8804 (mmp) REVERT: J 89 ASP cc_start: 0.8537 (m-30) cc_final: 0.8155 (t0) REVERT: J 90 LEU cc_start: 0.9522 (mt) cc_final: 0.9260 (mt) REVERT: J 92 THR cc_start: 0.9225 (m) cc_final: 0.8846 (p) REVERT: J 96 ASN cc_start: 0.9371 (m-40) cc_final: 0.9036 (m110) REVERT: J 120 VAL cc_start: 0.9307 (m) cc_final: 0.9053 (p) REVERT: J 129 GLU cc_start: 0.9034 (mm-30) cc_final: 0.8747 (mm-30) REVERT: J 132 MET cc_start: 0.9129 (mmt) cc_final: 0.8530 (mmm) REVERT: J 190 ILE cc_start: 0.8547 (mt) cc_final: 0.8269 (mt) REVERT: J 207 MET cc_start: 0.7272 (ttt) cc_final: 0.6891 (ttt) REVERT: J 208 MET cc_start: 0.8456 (tpp) cc_final: 0.8101 (tpp) REVERT: J 210 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7187 (tm-30) REVERT: K 72 MET cc_start: 0.8528 (mmm) cc_final: 0.7764 (tmm) REVERT: K 76 MET cc_start: 0.8209 (mtm) cc_final: 0.6973 (ptt) REVERT: K 88 ASP cc_start: 0.8253 (t70) cc_final: 0.8000 (t0) REVERT: K 92 THR cc_start: 0.9053 (m) cc_final: 0.8805 (p) REVERT: K 97 GLU cc_start: 0.8977 (mt-10) cc_final: 0.8652 (mt-10) REVERT: K 132 MET cc_start: 0.9170 (mmm) cc_final: 0.8768 (mmm) REVERT: K 172 TYR cc_start: 0.8360 (m-80) cc_final: 0.7937 (m-10) REVERT: K 173 LEU cc_start: 0.8561 (mt) cc_final: 0.8277 (mt) REVERT: K 184 TYR cc_start: 0.7985 (m-80) cc_final: 0.7584 (m-80) REVERT: K 197 GLU cc_start: 0.8651 (mp0) cc_final: 0.7880 (tm-30) REVERT: K 210 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7480 (tm-30) REVERT: M 75 GLN cc_start: 0.9395 (OUTLIER) cc_final: 0.9136 (mp10) REVERT: M 78 ARG cc_start: 0.8653 (mtm-85) cc_final: 0.8370 (mtt180) REVERT: N 84 MET cc_start: 0.8760 (mtp) cc_final: 0.8517 (mtp) REVERT: N 94 ARG cc_start: 0.8979 (tmt170) cc_final: 0.8719 (tmt170) REVERT: N 109 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.8005 (pt0) REVERT: N 113 ASN cc_start: 0.8718 (m-40) cc_final: 0.8394 (m-40) REVERT: O 75 GLN cc_start: 0.9067 (mt0) cc_final: 0.8734 (tp40) REVERT: O 78 ARG cc_start: 0.8465 (mtm110) cc_final: 0.8241 (mtm110) REVERT: O 85 GLN cc_start: 0.9089 (mt0) cc_final: 0.8827 (tm-30) REVERT: O 89 GLN cc_start: 0.8493 (tp40) cc_final: 0.8252 (tp40) REVERT: O 102 MET cc_start: 0.8425 (mtp) cc_final: 0.8055 (ttm) REVERT: O 105 ASP cc_start: 0.8326 (t0) cc_final: 0.8095 (p0) REVERT: Q 106 ASP cc_start: 0.9157 (m-30) cc_final: 0.8843 (p0) REVERT: Q 109 GLU cc_start: 0.8566 (tt0) cc_final: 0.8129 (tm-30) REVERT: Q 139 TYR cc_start: 0.8671 (t80) cc_final: 0.8275 (t80) REVERT: Q 161 MET cc_start: 0.8529 (tmm) cc_final: 0.8036 (tpp) REVERT: Q 192 LYS cc_start: 0.8294 (mttt) cc_final: 0.7986 (mtpp) REVERT: Q 198 HIS cc_start: 0.8570 (m-70) cc_final: 0.8065 (m170) REVERT: R 103 MET cc_start: 0.7180 (ttm) cc_final: 0.6923 (ttm) REVERT: R 105 LEU cc_start: 0.7475 (mm) cc_final: 0.7197 (mp) REVERT: R 107 LEU cc_start: 0.8315 (tp) cc_final: 0.8008 (tp) REVERT: R 112 TYR cc_start: 0.8462 (t80) cc_final: 0.7697 (t80) REVERT: R 125 ASP cc_start: 0.8676 (m-30) cc_final: 0.8384 (t70) REVERT: R 127 HIS cc_start: 0.8068 (t70) cc_final: 0.7865 (t70) REVERT: R 171 ASP cc_start: 0.8739 (m-30) cc_final: 0.8127 (p0) REVERT: R 196 GLN cc_start: 0.8270 (mt0) cc_final: 0.7646 (mt0) REVERT: R 197 TYR cc_start: 0.8122 (m-80) cc_final: 0.7843 (m-80) REVERT: R 228 THR cc_start: 0.8368 (m) cc_final: 0.7840 (p) REVERT: S 33 MET cc_start: 0.8589 (tpp) cc_final: 0.7881 (mtp) REVERT: S 60 TYR cc_start: 0.8028 (m-80) cc_final: 0.7739 (m-10) REVERT: S 61 ARG cc_start: 0.8505 (mtp-110) cc_final: 0.8271 (ttm110) REVERT: S 113 GLU cc_start: 0.9162 (tp30) cc_final: 0.8937 (tp30) REVERT: S 114 LYS cc_start: 0.8754 (mttt) cc_final: 0.8495 (mmtp) REVERT: S 117 GLN cc_start: 0.8856 (mt0) cc_final: 0.8525 (pp30) REVERT: S 160 GLN cc_start: 0.8260 (mt0) cc_final: 0.7968 (mt0) REVERT: S 197 TYR cc_start: 0.8004 (m-80) cc_final: 0.7714 (m-80) REVERT: S 200 PHE cc_start: 0.8342 (t80) cc_final: 0.8022 (t80) REVERT: S 201 LYS cc_start: 0.8075 (tttt) cc_final: 0.7700 (pttm) REVERT: S 222 GLN cc_start: 0.8423 (mt0) cc_final: 0.7220 (tm-30) outliers start: 138 outliers final: 92 residues processed: 914 average time/residue: 0.4831 time to fit residues: 734.0131 Evaluate side-chains 900 residues out of total 3955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 799 time to evaluate : 4.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 32 CYS Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 476 ARG Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 306 MET Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 450 TRP Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 526 THR Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 187 GLN Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain D residue 408 GLU Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 169 MET Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 311 SER Chi-restraints excluded: chain E residue 423 TYR Chi-restraints excluded: chain E residue 432 VAL Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 464 THR Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 162 CYS Chi-restraints excluded: chain F residue 207 CYS Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 226 ASN Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 356 MET Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain H residue 5 ASP Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 167 ARG Chi-restraints excluded: chain H residue 168 ARG Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 103 SER Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 137 ARG Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 152 ILE Chi-restraints excluded: chain M residue 74 GLU Chi-restraints excluded: chain M residue 75 GLN Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain N residue 109 GLN Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain O residue 116 ILE Chi-restraints excluded: chain Q residue 13 LEU Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 74 CYS Chi-restraints excluded: chain Q residue 81 LEU Chi-restraints excluded: chain Q residue 142 ASN Chi-restraints excluded: chain Q residue 156 THR Chi-restraints excluded: chain Q residue 197 TYR Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 74 CYS Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 137 THR Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain S residue 158 VAL Chi-restraints excluded: chain S residue 216 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 363 optimal weight: 4.9990 chunk 247 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 324 optimal weight: 0.7980 chunk 179 optimal weight: 10.0000 chunk 372 optimal weight: 8.9990 chunk 301 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 222 optimal weight: 5.9990 chunk 391 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 HIS B 164 HIS B 610 ASN C 65 GLN C 103 GLN ** C 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 HIS ** D 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 GLN R 21 GLN ** R 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 134 ASN S 160 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.4540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 36765 Z= 0.318 Angle : 0.600 8.791 49676 Z= 0.303 Chirality : 0.044 0.170 5575 Planarity : 0.004 0.046 6440 Dihedral : 4.669 133.179 5018 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 4.10 % Allowed : 14.92 % Favored : 80.98 % 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: 1.11 (0.13), residues: 4538 helix: 1.83 (0.11), residues: 2107 sheet: -0.16 (0.21), residues: 587 loop : -0.16 (0.15), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 567 HIS 0.005 0.001 HIS E 73 PHE 0.031 0.002 PHE R 200 TYR 0.029 0.002 TYR C 535 ARG 0.009 0.001 ARG N 79 *********************** 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 972 residues out of total 3955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 810 time to evaluate : 4.271 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: A 30 THR cc_start: 0.8346 (m) cc_final: 0.8125 (p) REVERT: A 82 THR cc_start: 0.8308 (m) cc_final: 0.8074 (p) REVERT: A 155 ILE cc_start: 0.8442 (mt) cc_final: 0.7979 (tt) REVERT: A 171 ARG cc_start: 0.8330 (mtt180) cc_final: 0.8044 (ptp90) REVERT: A 203 LEU cc_start: 0.8846 (mt) cc_final: 0.8575 (mt) REVERT: A 306 MET cc_start: 0.8640 (tpp) cc_final: 0.8354 (tpp) REVERT: A 324 GLU cc_start: 0.8997 (tm-30) cc_final: 0.8620 (tm-30) REVERT: A 356 GLU cc_start: 0.8482 (tp30) cc_final: 0.7793 (tm-30) REVERT: A 436 ASP cc_start: 0.8731 (t0) cc_final: 0.8290 (t70) REVERT: A 443 LYS cc_start: 0.8972 (mttt) cc_final: 0.8169 (tptp) REVERT: A 447 SER cc_start: 0.7905 (m) cc_final: 0.7115 (t) REVERT: A 472 PHE cc_start: 0.7667 (t80) cc_final: 0.7321 (t80) REVERT: A 476 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.7876 (ptp90) REVERT: A 505 ASP cc_start: 0.8026 (t0) cc_final: 0.7684 (t70) REVERT: A 550 MET cc_start: 0.8840 (mmm) cc_final: 0.8344 (mtt) REVERT: B 18 PHE cc_start: 0.7565 (OUTLIER) cc_final: 0.6983 (m-80) REVERT: B 30 THR cc_start: 0.8549 (m) cc_final: 0.8157 (p) REVERT: B 53 GLU cc_start: 0.7991 (tt0) cc_final: 0.7253 (tt0) REVERT: B 77 ASP cc_start: 0.7883 (m-30) cc_final: 0.7227 (m-30) REVERT: B 84 LYS cc_start: 0.7691 (mmtt) cc_final: 0.7204 (mmtm) REVERT: B 89 GLU cc_start: 0.7530 (mt-10) cc_final: 0.7097 (tt0) REVERT: B 130 ASP cc_start: 0.8506 (m-30) cc_final: 0.8131 (p0) REVERT: B 142 ARG cc_start: 0.7911 (mmt-90) cc_final: 0.7494 (mmt180) REVERT: B 205 MET cc_start: 0.9515 (mtm) cc_final: 0.9255 (mtm) REVERT: B 224 ASN cc_start: 0.9252 (p0) cc_final: 0.8978 (p0) REVERT: B 231 GLN cc_start: 0.7751 (mm-40) cc_final: 0.7292 (mm-40) REVERT: B 295 THR cc_start: 0.9024 (m) cc_final: 0.8650 (t) REVERT: B 297 GLU cc_start: 0.8692 (mp0) cc_final: 0.7764 (mm-30) REVERT: B 324 GLU cc_start: 0.8635 (tt0) cc_final: 0.8257 (tm-30) REVERT: B 367 GLU cc_start: 0.8632 (tt0) cc_final: 0.8024 (tt0) REVERT: B 436 ASP cc_start: 0.6956 (t0) cc_final: 0.6696 (m-30) REVERT: B 530 ARG cc_start: 0.7548 (ptm160) cc_final: 0.6971 (ptm-80) REVERT: B 558 THR cc_start: 0.7331 (p) cc_final: 0.7024 (p) REVERT: B 565 ILE cc_start: 0.8078 (OUTLIER) cc_final: 0.7821 (mm) REVERT: B 572 GLU cc_start: 0.9047 (mm-30) cc_final: 0.8755 (pp20) REVERT: C 74 SER cc_start: 0.7625 (m) cc_final: 0.6827 (p) REVERT: C 77 ASP cc_start: 0.7818 (m-30) cc_final: 0.7349 (m-30) REVERT: C 99 PHE cc_start: 0.8977 (m-10) cc_final: 0.8761 (m-10) REVERT: C 168 LEU cc_start: 0.8407 (tp) cc_final: 0.8179 (tp) REVERT: C 205 MET cc_start: 0.9334 (mtm) cc_final: 0.8751 (ttp) REVERT: C 218 THR cc_start: 0.8251 (m) cc_final: 0.7984 (m) REVERT: C 268 ASN cc_start: 0.7951 (t0) cc_final: 0.7446 (t0) REVERT: C 284 MET cc_start: 0.8137 (mmm) cc_final: 0.7746 (mmm) REVERT: C 296 MET cc_start: 0.6656 (ptp) cc_final: 0.5844 (ptp) REVERT: C 308 ARG cc_start: 0.6984 (ptp-110) cc_final: 0.6603 (ptt180) REVERT: C 456 LYS cc_start: 0.8151 (mttt) cc_final: 0.7711 (mmmt) REVERT: C 485 GLU cc_start: 0.8581 (tt0) cc_final: 0.8282 (tt0) REVERT: C 517 ASP cc_start: 0.7289 (m-30) cc_final: 0.6492 (t0) REVERT: C 531 PHE cc_start: 0.6230 (p90) cc_final: 0.5560 (p90) REVERT: C 565 ILE cc_start: 0.6503 (mt) cc_final: 0.5913 (tp) REVERT: C 603 GLN cc_start: 0.8080 (tp40) cc_final: 0.7545 (tp-100) REVERT: D 169 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.8182 (tmm) REVERT: D 234 MET cc_start: 0.9457 (mtm) cc_final: 0.9208 (mtm) REVERT: D 270 GLU cc_start: 0.8724 (tp30) cc_final: 0.8501 (tp30) REVERT: D 299 ASP cc_start: 0.7942 (m-30) cc_final: 0.7527 (m-30) REVERT: D 380 ASP cc_start: 0.8278 (t0) cc_final: 0.7793 (t70) REVERT: D 403 LYS cc_start: 0.9139 (tttt) cc_final: 0.8688 (pttt) REVERT: D 431 ASP cc_start: 0.8719 (t70) cc_final: 0.8314 (m-30) REVERT: D 446 SER cc_start: 0.8002 (m) cc_final: 0.7797 (p) REVERT: D 452 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8349 (mp) REVERT: E 47 TYR cc_start: 0.8019 (m-80) cc_final: 0.7571 (m-80) REVERT: E 49 THR cc_start: 0.8545 (p) cc_final: 0.8262 (p) REVERT: E 106 ASP cc_start: 0.7824 (t70) cc_final: 0.7344 (t0) REVERT: E 169 MET cc_start: 0.7458 (OUTLIER) cc_final: 0.7193 (tmm) REVERT: E 201 GLU cc_start: 0.7963 (mp0) cc_final: 0.7618 (mt-10) REVERT: E 238 MET cc_start: 0.6882 (tmm) cc_final: 0.6460 (tmm) REVERT: E 262 ASN cc_start: 0.8757 (t0) cc_final: 0.8110 (t0) REVERT: E 268 THR cc_start: 0.8880 (p) cc_final: 0.8469 (t) REVERT: E 283 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7608 (tm-30) REVERT: E 290 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8205 (mm-30) REVERT: E 315 GLU cc_start: 0.8298 (mt-10) cc_final: 0.7880 (tt0) REVERT: E 327 MET cc_start: 0.8698 (tpp) cc_final: 0.7922 (tpp) REVERT: E 330 ASP cc_start: 0.8271 (t70) cc_final: 0.7702 (t70) REVERT: E 354 LEU cc_start: 0.8369 (pp) cc_final: 0.8102 (pp) REVERT: E 358 ASN cc_start: 0.8793 (t0) cc_final: 0.8407 (t0) REVERT: E 360 ASP cc_start: 0.7604 (t70) cc_final: 0.7317 (t0) REVERT: E 402 MET cc_start: 0.7818 (ttm) cc_final: 0.6964 (tpp) REVERT: E 490 GLU cc_start: 0.8821 (mp0) cc_final: 0.8555 (mp0) REVERT: F 61 ASP cc_start: 0.8382 (t0) cc_final: 0.7855 (m-30) REVERT: F 167 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7197 (mp0) REVERT: F 178 ASP cc_start: 0.7416 (m-30) cc_final: 0.7135 (m-30) REVERT: F 189 ILE cc_start: 0.8963 (tt) cc_final: 0.8619 (tp) REVERT: F 201 GLU cc_start: 0.7878 (mp0) cc_final: 0.7242 (mp0) REVERT: F 238 MET cc_start: 0.8208 (tpp) cc_final: 0.7763 (tpt) REVERT: F 249 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8168 (mm-30) REVERT: F 268 THR cc_start: 0.8882 (p) cc_final: 0.8559 (t) REVERT: F 316 GLU cc_start: 0.8656 (tp30) cc_final: 0.8051 (tp30) REVERT: F 336 GLU cc_start: 0.8785 (mm-30) cc_final: 0.7434 (tp30) REVERT: F 400 ARG cc_start: 0.7036 (tpt90) cc_final: 0.6648 (tpt170) REVERT: F 403 LYS cc_start: 0.8814 (tptt) cc_final: 0.7997 (tptp) REVERT: F 460 LYS cc_start: 0.8297 (tttt) cc_final: 0.8051 (ttpp) REVERT: H 163 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8374 (mmmm) REVERT: H 168 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7830 (ttp-170) REVERT: H 173 GLU cc_start: 0.7656 (tt0) cc_final: 0.7408 (tt0) REVERT: I 132 MET cc_start: 0.8709 (mtt) cc_final: 0.8308 (mtt) REVERT: I 198 SER cc_start: 0.9129 (m) cc_final: 0.8822 (p) REVERT: I 210 GLU cc_start: 0.8106 (mp0) cc_final: 0.7534 (tm-30) REVERT: I 221 ASN cc_start: 0.7889 (m-40) cc_final: 0.7502 (t0) REVERT: J 68 LYS cc_start: 0.7418 (mttt) cc_final: 0.6544 (tptt) REVERT: J 76 MET cc_start: 0.9078 (mmm) cc_final: 0.8810 (mmp) REVERT: J 89 ASP cc_start: 0.8606 (m-30) cc_final: 0.8222 (t0) REVERT: J 90 LEU cc_start: 0.9527 (mt) cc_final: 0.9282 (mt) REVERT: J 92 THR cc_start: 0.9237 (m) cc_final: 0.8855 (p) REVERT: J 96 ASN cc_start: 0.9312 (m-40) cc_final: 0.8950 (m110) REVERT: J 97 GLU cc_start: 0.9048 (tt0) cc_final: 0.8832 (tt0) REVERT: J 116 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8686 (mp) REVERT: J 129 GLU cc_start: 0.9074 (mm-30) cc_final: 0.8715 (mm-30) REVERT: J 190 ILE cc_start: 0.8557 (mt) cc_final: 0.8316 (mt) REVERT: J 207 MET cc_start: 0.7318 (ttt) cc_final: 0.7093 (ttt) REVERT: J 208 MET cc_start: 0.8579 (tpp) cc_final: 0.8183 (tpp) REVERT: J 210 GLU cc_start: 0.7746 (tm-30) cc_final: 0.7405 (tm-30) REVERT: K 72 MET cc_start: 0.8545 (mmm) cc_final: 0.8086 (tmm) REVERT: K 76 MET cc_start: 0.8218 (mtm) cc_final: 0.7847 (tpp) REVERT: K 88 ASP cc_start: 0.8200 (t70) cc_final: 0.7943 (t0) REVERT: K 92 THR cc_start: 0.9067 (m) cc_final: 0.8808 (p) REVERT: K 97 GLU cc_start: 0.8995 (mt-10) cc_final: 0.8544 (mt-10) REVERT: K 132 MET cc_start: 0.9154 (mmm) cc_final: 0.8621 (mmm) REVERT: K 172 TYR cc_start: 0.8454 (m-80) cc_final: 0.8008 (m-10) REVERT: K 173 LEU cc_start: 0.8622 (mt) cc_final: 0.8363 (mt) REVERT: K 175 GLU cc_start: 0.8755 (pm20) cc_final: 0.7868 (tp30) REVERT: K 184 TYR cc_start: 0.7958 (m-80) cc_final: 0.7563 (m-80) REVERT: K 197 GLU cc_start: 0.8617 (mp0) cc_final: 0.7911 (tm-30) REVERT: K 210 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7605 (tm-30) REVERT: M 107 ARG cc_start: 0.8099 (ttm-80) cc_final: 0.7865 (tpp80) REVERT: M 109 GLN cc_start: 0.8288 (tt0) cc_final: 0.8036 (tt0) REVERT: M 115 ARG cc_start: 0.8381 (ptt180) cc_final: 0.8111 (ptt180) REVERT: N 78 ARG cc_start: 0.8776 (mtm110) cc_final: 0.8351 (mtm110) REVERT: N 84 MET cc_start: 0.8821 (mtp) cc_final: 0.8541 (mtp) REVERT: N 94 ARG cc_start: 0.8983 (tmt170) cc_final: 0.8704 (tmt170) REVERT: N 109 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.7852 (pt0) REVERT: O 75 GLN cc_start: 0.9107 (mt0) cc_final: 0.8695 (tp40) REVERT: O 78 ARG cc_start: 0.8439 (mtm110) cc_final: 0.8233 (mtm110) REVERT: O 85 GLN cc_start: 0.9119 (mt0) cc_final: 0.8813 (tm-30) REVERT: Q 106 ASP cc_start: 0.9136 (m-30) cc_final: 0.8852 (p0) REVERT: Q 109 GLU cc_start: 0.8394 (tt0) cc_final: 0.8047 (tm-30) REVERT: Q 123 LYS cc_start: 0.8857 (mmmt) cc_final: 0.8366 (mttp) REVERT: Q 139 TYR cc_start: 0.8703 (t80) cc_final: 0.8249 (t80) REVERT: Q 161 MET cc_start: 0.8594 (tmm) cc_final: 0.8191 (tpp) REVERT: Q 192 LYS cc_start: 0.8276 (mttt) cc_final: 0.7721 (mtpp) REVERT: Q 198 HIS cc_start: 0.8591 (m-70) cc_final: 0.8119 (m-70) REVERT: R 83 ARG cc_start: 0.7806 (ttp-170) cc_final: 0.7594 (ttp-170) REVERT: R 90 GLU cc_start: 0.9039 (mm-30) cc_final: 0.8642 (mm-30) REVERT: R 103 MET cc_start: 0.7234 (ttm) cc_final: 0.6915 (ttm) REVERT: R 105 LEU cc_start: 0.7595 (mm) cc_final: 0.7335 (mp) REVERT: R 107 LEU cc_start: 0.8384 (tp) cc_final: 0.7944 (tp) REVERT: R 112 TYR cc_start: 0.8596 (t80) cc_final: 0.7888 (t80) REVERT: R 125 ASP cc_start: 0.8719 (m-30) cc_final: 0.8413 (t70) REVERT: R 127 HIS cc_start: 0.8161 (t70) cc_final: 0.7888 (t70) REVERT: R 153 ARG cc_start: 0.8698 (tpp80) cc_final: 0.8425 (tpp80) REVERT: R 171 ASP cc_start: 0.8740 (m-30) cc_final: 0.8183 (p0) REVERT: R 188 MET cc_start: 0.7109 (tmm) cc_final: 0.6865 (ppp) REVERT: R 196 GLN cc_start: 0.8045 (mt0) cc_final: 0.7657 (mt0) REVERT: R 197 TYR cc_start: 0.8301 (m-80) cc_final: 0.8052 (m-80) REVERT: R 228 THR cc_start: 0.8412 (OUTLIER) cc_final: 0.7914 (p) REVERT: S 33 MET cc_start: 0.8637 (tpp) cc_final: 0.7924 (mtp) REVERT: S 57 GLU cc_start: 0.7239 (mt-10) cc_final: 0.6665 (tp30) REVERT: S 113 GLU cc_start: 0.9190 (tp30) cc_final: 0.8878 (tp30) REVERT: S 117 GLN cc_start: 0.8822 (mt0) cc_final: 0.8560 (pp30) REVERT: S 156 THR cc_start: 0.9237 (p) cc_final: 0.9024 (p) REVERT: S 160 GLN cc_start: 0.8121 (mt0) cc_final: 0.7808 (mt0) REVERT: S 197 TYR cc_start: 0.8033 (m-80) cc_final: 0.7733 (m-10) REVERT: S 200 PHE cc_start: 0.8347 (t80) cc_final: 0.8117 (t80) REVERT: S 201 LYS cc_start: 0.8081 (tttt) cc_final: 0.7702 (pttm) REVERT: S 222 GLN cc_start: 0.8480 (mt0) cc_final: 0.7221 (tm-30) outliers start: 162 outliers final: 115 residues processed: 882 average time/residue: 0.4783 time to fit residues: 692.5213 Evaluate side-chains 886 residues out of total 3955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 760 time to evaluate : 4.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 32 CYS Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 476 ARG Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 544 MET Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 306 MET Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 450 TRP Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 526 THR Chi-restraints excluded: chain C residue 532 CYS Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 187 GLN Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 408 GLU Chi-restraints excluded: chain D residue 410 MET Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 169 MET Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 311 SER Chi-restraints excluded: chain E residue 423 TYR Chi-restraints excluded: chain E residue 432 VAL Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 464 THR Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 144 VAL Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 207 CYS Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 226 ASN Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 498 SER Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 19 MET Chi-restraints excluded: chain H residue 163 LYS Chi-restraints excluded: chain H residue 167 ARG Chi-restraints excluded: chain H residue 168 ARG Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 103 SER Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain I residue 211 VAL Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain J residue 137 ARG Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain K residue 152 ILE Chi-restraints excluded: chain M residue 75 GLN Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 95 VAL Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain M residue 105 ASP Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain N residue 109 GLN Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain Q residue 13 LEU Chi-restraints excluded: chain Q residue 42 LEU Chi-restraints excluded: chain Q residue 45 ILE Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 74 CYS Chi-restraints excluded: chain Q residue 81 LEU Chi-restraints excluded: chain Q residue 142 ASN Chi-restraints excluded: chain Q residue 156 THR Chi-restraints excluded: chain Q residue 197 TYR Chi-restraints excluded: chain R residue 10 MET Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 74 CYS Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 137 THR Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 228 THR Chi-restraints excluded: chain S residue 107 LEU Chi-restraints excluded: chain S residue 146 THR Chi-restraints excluded: chain S residue 158 VAL Chi-restraints excluded: chain S residue 216 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 146 optimal weight: 7.9990 chunk 392 optimal weight: 9.9990 chunk 86 optimal weight: 7.9990 chunk 255 optimal weight: 0.7980 chunk 107 optimal weight: 6.9990 chunk 436 optimal weight: 7.9990 chunk 362 optimal weight: 6.9990 chunk 202 optimal weight: 0.0870 chunk 36 optimal weight: 0.7980 chunk 144 optimal weight: 6.9990 chunk 229 optimal weight: 0.5980 overall best weight: 1.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 573 HIS B 610 ASN C 103 GLN ** C 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 603 GLN ** D 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 421 GLN H 27 GLN I 74 ASN N 98 GLN Q 196 GLN ** R 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 207 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.4782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 36765 Z= 0.250 Angle : 0.574 10.400 49676 Z= 0.287 Chirality : 0.043 0.188 5575 Planarity : 0.004 0.045 6440 Dihedral : 4.618 133.139 5018 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.84 % Allowed : 16.01 % Favored : 80.15 % 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: 1.08 (0.13), residues: 4538 helix: 1.90 (0.11), residues: 2094 sheet: -0.33 (0.21), residues: 585 loop : -0.23 (0.15), residues: 1859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 567 HIS 0.004 0.001 HIS E 73 PHE 0.033 0.002 PHE R 200 TYR 0.033 0.001 TYR C 535 ARG 0.016 0.001 ARG M 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 946 residues out of total 3955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 794 time to evaluate : 4.403 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: A 30 THR cc_start: 0.8372 (m) cc_final: 0.8149 (p) REVERT: A 82 THR cc_start: 0.8419 (m) cc_final: 0.8209 (p) REVERT: A 130 ASP cc_start: 0.8381 (t0) cc_final: 0.8172 (t0) REVERT: A 155 ILE cc_start: 0.8450 (mt) cc_final: 0.7978 (tt) REVERT: A 171 ARG cc_start: 0.8323 (mtt180) cc_final: 0.8016 (ptp90) REVERT: A 203 LEU cc_start: 0.8896 (mt) cc_final: 0.8598 (mt) REVERT: A 306 MET cc_start: 0.8624 (tpp) cc_final: 0.8278 (tpp) REVERT: A 356 GLU cc_start: 0.8461 (tp30) cc_final: 0.7791 (tm-30) REVERT: A 436 ASP cc_start: 0.8808 (t0) cc_final: 0.8363 (t70) REVERT: A 443 LYS cc_start: 0.8965 (mttt) cc_final: 0.8137 (tptp) REVERT: A 447 SER cc_start: 0.7869 (m) cc_final: 0.7189 (t) REVERT: A 472 PHE cc_start: 0.7618 (t80) cc_final: 0.7201 (t80) REVERT: A 476 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.7966 (ptp90) REVERT: A 505 ASP cc_start: 0.8092 (t0) cc_final: 0.7722 (t70) REVERT: B 18 PHE cc_start: 0.7534 (OUTLIER) cc_final: 0.7002 (m-80) REVERT: B 30 THR cc_start: 0.8544 (m) cc_final: 0.8172 (p) REVERT: B 53 GLU cc_start: 0.7982 (tt0) cc_final: 0.7388 (tt0) REVERT: B 61 MET cc_start: 0.7282 (mtt) cc_final: 0.6464 (ttm) REVERT: B 77 ASP cc_start: 0.7944 (m-30) cc_final: 0.7328 (m-30) REVERT: B 84 LYS cc_start: 0.7611 (mmtt) cc_final: 0.7372 (mmtm) REVERT: B 89 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7344 (mt-10) REVERT: B 130 ASP cc_start: 0.8578 (m-30) cc_final: 0.8142 (p0) REVERT: B 142 ARG cc_start: 0.7913 (mmt-90) cc_final: 0.7482 (mmt180) REVERT: B 205 MET cc_start: 0.9515 (mtm) cc_final: 0.9313 (mtm) REVERT: B 295 THR cc_start: 0.8973 (m) cc_final: 0.8703 (t) REVERT: B 297 GLU cc_start: 0.8727 (mp0) cc_final: 0.7867 (mm-30) REVERT: B 324 GLU cc_start: 0.8677 (tt0) cc_final: 0.8267 (tm-30) REVERT: B 367 GLU cc_start: 0.8651 (tt0) cc_final: 0.8037 (tt0) REVERT: B 436 ASP cc_start: 0.7082 (t0) cc_final: 0.6867 (m-30) REVERT: B 486 GLU cc_start: 0.7966 (tm-30) cc_final: 0.7727 (tm-30) REVERT: B 527 PRO cc_start: 0.9115 (Cg_exo) cc_final: 0.8861 (Cg_endo) REVERT: B 530 ARG cc_start: 0.7641 (ptm160) cc_final: 0.7103 (ptm-80) REVERT: B 565 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7871 (mm) REVERT: B 572 GLU cc_start: 0.9062 (mm-30) cc_final: 0.8753 (pp20) REVERT: C 74 SER cc_start: 0.7730 (m) cc_final: 0.6901 (p) REVERT: C 77 ASP cc_start: 0.7809 (m-30) cc_final: 0.7377 (m-30) REVERT: C 168 LEU cc_start: 0.8367 (tp) cc_final: 0.8145 (tp) REVERT: C 205 MET cc_start: 0.9324 (mtm) cc_final: 0.8790 (ttp) REVERT: C 218 THR cc_start: 0.8183 (m) cc_final: 0.7926 (m) REVERT: C 284 MET cc_start: 0.8104 (mmm) cc_final: 0.7799 (mmm) REVERT: C 296 MET cc_start: 0.6636 (ptp) cc_final: 0.5724 (ptp) REVERT: C 308 ARG cc_start: 0.7069 (ptp-110) cc_final: 0.6626 (ptt180) REVERT: C 456 LYS cc_start: 0.8094 (mttt) cc_final: 0.7672 (mmmt) REVERT: C 517 ASP cc_start: 0.7336 (m-30) cc_final: 0.6516 (t0) REVERT: C 531 PHE cc_start: 0.6067 (p90) cc_final: 0.5363 (p90) REVERT: C 565 ILE cc_start: 0.6626 (mt) cc_final: 0.6043 (tp) REVERT: D 169 MET cc_start: 0.8505 (OUTLIER) cc_final: 0.8209 (tmm) REVERT: D 171 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7572 (tt0) REVERT: D 234 MET cc_start: 0.9413 (mtm) cc_final: 0.9071 (mtm) REVERT: D 270 GLU cc_start: 0.8694 (tp30) cc_final: 0.8429 (tp30) REVERT: D 299 ASP cc_start: 0.7944 (m-30) cc_final: 0.7527 (m-30) REVERT: D 380 ASP cc_start: 0.8372 (t0) cc_final: 0.7881 (t70) REVERT: D 403 LYS cc_start: 0.9108 (tttt) cc_final: 0.8666 (pttt) REVERT: D 431 ASP cc_start: 0.8726 (t70) cc_final: 0.8365 (m-30) REVERT: D 446 SER cc_start: 0.8052 (m) cc_final: 0.7808 (p) REVERT: D 452 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8235 (mp) REVERT: E 47 TYR cc_start: 0.7988 (m-80) cc_final: 0.7594 (m-80) REVERT: E 49 THR cc_start: 0.8594 (p) cc_final: 0.8312 (p) REVERT: E 106 ASP cc_start: 0.7800 (t70) cc_final: 0.7391 (t0) REVERT: E 169 MET cc_start: 0.7531 (OUTLIER) cc_final: 0.7262 (tmm) REVERT: E 201 GLU cc_start: 0.8011 (mp0) cc_final: 0.7651 (mt-10) REVERT: E 238 MET cc_start: 0.6932 (tmm) cc_final: 0.6572 (tmm) REVERT: E 262 ASN cc_start: 0.8755 (t0) cc_final: 0.8140 (t0) REVERT: E 268 THR cc_start: 0.8956 (p) cc_final: 0.8547 (t) REVERT: E 283 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7600 (tm-30) REVERT: E 290 GLU cc_start: 0.8455 (mt-10) cc_final: 0.8217 (mm-30) REVERT: E 315 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7842 (tt0) REVERT: E 327 MET cc_start: 0.8683 (tpp) cc_final: 0.7632 (tpp) REVERT: E 330 ASP cc_start: 0.8322 (t70) cc_final: 0.7803 (t70) REVERT: E 358 ASN cc_start: 0.8899 (t0) cc_final: 0.8483 (t0) REVERT: E 360 ASP cc_start: 0.7549 (t70) cc_final: 0.7239 (t0) REVERT: E 402 MET cc_start: 0.7988 (ttm) cc_final: 0.7120 (tpp) REVERT: E 490 GLU cc_start: 0.8818 (mp0) cc_final: 0.8529 (mp0) REVERT: F 167 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7237 (mp0) REVERT: F 189 ILE cc_start: 0.8943 (tt) cc_final: 0.8592 (tp) REVERT: F 201 GLU cc_start: 0.7928 (mp0) cc_final: 0.7293 (mp0) REVERT: F 238 MET cc_start: 0.8192 (tpp) cc_final: 0.7770 (tpt) REVERT: F 249 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8204 (mm-30) REVERT: F 268 THR cc_start: 0.8889 (p) cc_final: 0.8562 (t) REVERT: F 316 GLU cc_start: 0.8686 (tp30) cc_final: 0.8044 (tp30) REVERT: F 336 GLU cc_start: 0.8767 (mm-30) cc_final: 0.7605 (tp30) REVERT: F 398 LEU cc_start: 0.7662 (mt) cc_final: 0.7408 (mm) REVERT: F 400 ARG cc_start: 0.7158 (tpt90) cc_final: 0.6707 (tpt170) REVERT: F 403 LYS cc_start: 0.8838 (tptt) cc_final: 0.8047 (tptp) REVERT: F 460 LYS cc_start: 0.8268 (tttt) cc_final: 0.7993 (ttpp) REVERT: H 163 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8451 (mmmm) REVERT: H 168 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7801 (ttp-170) REVERT: H 173 GLU cc_start: 0.7654 (tt0) cc_final: 0.7415 (tt0) REVERT: I 74 ASN cc_start: 0.7741 (OUTLIER) cc_final: 0.7440 (m110) REVERT: I 132 MET cc_start: 0.8727 (mtt) cc_final: 0.8385 (mtt) REVERT: I 190 ILE cc_start: 0.8630 (mt) cc_final: 0.8359 (tt) REVERT: I 198 SER cc_start: 0.9145 (m) cc_final: 0.8826 (p) REVERT: I 210 GLU cc_start: 0.8074 (mp0) cc_final: 0.7551 (tm-30) REVERT: I 221 ASN cc_start: 0.7900 (m-40) cc_final: 0.7438 (t0) REVERT: J 68 LYS cc_start: 0.7425 (mttt) cc_final: 0.6546 (tptt) REVERT: J 76 MET cc_start: 0.9077 (mmm) cc_final: 0.8809 (mmp) REVERT: J 89 ASP cc_start: 0.8489 (m-30) cc_final: 0.8068 (t0) REVERT: J 90 LEU cc_start: 0.9488 (mt) cc_final: 0.9251 (mt) REVERT: J 92 THR cc_start: 0.9228 (m) cc_final: 0.8823 (p) REVERT: J 96 ASN cc_start: 0.9289 (m-40) cc_final: 0.8919 (m110) REVERT: J 97 GLU cc_start: 0.9063 (tt0) cc_final: 0.8818 (tt0) REVERT: J 116 LEU cc_start: 0.8928 (tp) cc_final: 0.8624 (mp) REVERT: J 190 ILE cc_start: 0.8527 (mt) cc_final: 0.8287 (mt) REVERT: J 208 MET cc_start: 0.8590 (tpp) cc_final: 0.8104 (tpp) REVERT: J 210 GLU cc_start: 0.7710 (tm-30) cc_final: 0.7298 (tm-30) REVERT: K 76 MET cc_start: 0.8189 (mtm) cc_final: 0.7784 (ptp) REVERT: K 88 ASP cc_start: 0.8140 (t70) cc_final: 0.7881 (t0) REVERT: K 92 THR cc_start: 0.9052 (m) cc_final: 0.8791 (p) REVERT: K 97 GLU cc_start: 0.8997 (mt-10) cc_final: 0.8532 (mt-10) REVERT: K 132 MET cc_start: 0.9135 (mmm) cc_final: 0.8593 (mmm) REVERT: K 172 TYR cc_start: 0.8474 (m-80) cc_final: 0.8053 (m-10) REVERT: K 173 LEU cc_start: 0.8616 (mt) cc_final: 0.8307 (mt) REVERT: K 175 GLU cc_start: 0.8779 (pm20) cc_final: 0.7947 (tp30) REVERT: K 184 TYR cc_start: 0.7985 (m-80) cc_final: 0.7518 (m-80) REVERT: K 197 GLU cc_start: 0.8577 (mp0) cc_final: 0.7914 (tm-30) REVERT: K 210 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7605 (tm-30) REVERT: M 78 ARG cc_start: 0.8569 (mtt180) cc_final: 0.8305 (ptt-90) REVERT: M 107 ARG cc_start: 0.8127 (ttm-80) cc_final: 0.7885 (tpp80) REVERT: N 78 ARG cc_start: 0.8777 (mtm110) cc_final: 0.8360 (mtm110) REVERT: N 79 ARG cc_start: 0.8949 (ttp-110) cc_final: 0.8729 (ttm110) REVERT: N 84 MET cc_start: 0.8825 (mtp) cc_final: 0.8550 (mtp) REVERT: N 94 ARG cc_start: 0.9024 (tmt170) cc_final: 0.8763 (tmt170) REVERT: N 109 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.7861 (pt0) REVERT: O 75 GLN cc_start: 0.9043 (mt0) cc_final: 0.8663 (tp40) REVERT: O 85 GLN cc_start: 0.9146 (mt0) cc_final: 0.8849 (tm-30) REVERT: O 102 MET cc_start: 0.8385 (mtp) cc_final: 0.7829 (ttm) REVERT: O 105 ASP cc_start: 0.8644 (t0) cc_final: 0.7862 (p0) REVERT: Q 106 ASP cc_start: 0.9134 (m-30) cc_final: 0.8842 (p0) REVERT: Q 109 GLU cc_start: 0.8394 (tt0) cc_final: 0.8047 (tm-30) REVERT: Q 115 MET cc_start: 0.9189 (mmt) cc_final: 0.8930 (mmm) REVERT: Q 123 LYS cc_start: 0.8816 (mmmt) cc_final: 0.8275 (mttp) REVERT: Q 139 TYR cc_start: 0.8672 (t80) cc_final: 0.8168 (t80) REVERT: Q 161 MET cc_start: 0.8558 (tmm) cc_final: 0.8159 (tpp) REVERT: Q 198 HIS cc_start: 0.8583 (m-70) cc_final: 0.8076 (m-70) REVERT: R 83 ARG cc_start: 0.7837 (ttp-170) cc_final: 0.7598 (ttp-170) REVERT: R 90 GLU cc_start: 0.9057 (mm-30) cc_final: 0.8707 (mm-30) REVERT: R 103 MET cc_start: 0.7224 (ttm) cc_final: 0.6904 (ttm) REVERT: R 105 LEU cc_start: 0.7613 (mm) cc_final: 0.7381 (mp) REVERT: R 107 LEU cc_start: 0.8366 (tp) cc_final: 0.7989 (tp) REVERT: R 112 TYR cc_start: 0.8568 (t80) cc_final: 0.7758 (t80) REVERT: R 125 ASP cc_start: 0.8707 (m-30) cc_final: 0.8365 (t70) REVERT: R 127 HIS cc_start: 0.8183 (t70) cc_final: 0.7905 (t70) REVERT: R 171 ASP cc_start: 0.8728 (m-30) cc_final: 0.8174 (p0) REVERT: R 188 MET cc_start: 0.7178 (tmm) cc_final: 0.6893 (ppp) REVERT: R 197 TYR cc_start: 0.8343 (m-80) cc_final: 0.8076 (m-80) REVERT: R 228 THR cc_start: 0.8508 (OUTLIER) cc_final: 0.8081 (p) REVERT: S 33 MET cc_start: 0.8645 (tpp) cc_final: 0.7926 (mtp) REVERT: S 113 GLU cc_start: 0.9197 (tp30) cc_final: 0.8884 (tp30) REVERT: S 117 GLN cc_start: 0.8822 (mt0) cc_final: 0.8513 (pp30) REVERT: S 160 GLN cc_start: 0.8032 (mt0) cc_final: 0.7723 (mt0) REVERT: S 172 ASN cc_start: 0.8758 (t0) cc_final: 0.7561 (m110) REVERT: S 197 TYR cc_start: 0.8030 (m-80) cc_final: 0.7779 (m-10) REVERT: S 201 LYS cc_start: 0.8040 (tttt) cc_final: 0.7661 (pttm) REVERT: S 222 GLN cc_start: 0.8458 (mt0) cc_final: 0.7153 (tm-30) outliers start: 152 outliers final: 112 residues processed: 872 average time/residue: 0.4846 time to fit residues: 695.4074 Evaluate side-chains 876 residues out of total 3955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 752 time to evaluate : 4.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 32 CYS Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 476 ARG Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 544 MET Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 306 MET Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 450 TRP Chi-restraints excluded: chain C residue 488 ASP Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 526 THR Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 187 GLN Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 408 GLU Chi-restraints excluded: chain D residue 410 MET Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 169 MET Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 311 SER Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 423 TYR Chi-restraints excluded: chain E residue 432 VAL Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 447 ASP Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 226 ASN Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 498 SER Chi-restraints excluded: chain H residue 5 ASP Chi-restraints excluded: chain H residue 19 MET Chi-restraints excluded: chain H residue 163 LYS Chi-restraints excluded: chain H residue 167 ARG Chi-restraints excluded: chain H residue 168 ARG Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain I residue 74 ASN Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 103 SER Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain I residue 211 VAL Chi-restraints excluded: chain J residue 91 ILE Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain K residue 91 ILE Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain K residue 152 ILE Chi-restraints excluded: chain M residue 75 GLN Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 95 VAL Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain M residue 105 ASP Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain N residue 109 GLN Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain O residue 116 ILE Chi-restraints excluded: chain Q residue 13 LEU Chi-restraints excluded: chain Q residue 42 LEU Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 74 CYS Chi-restraints excluded: chain Q residue 81 LEU Chi-restraints excluded: chain Q residue 107 LEU Chi-restraints excluded: chain Q residue 142 ASN Chi-restraints excluded: chain Q residue 146 THR Chi-restraints excluded: chain Q residue 156 THR Chi-restraints excluded: chain Q residue 169 THR Chi-restraints excluded: chain Q residue 197 TYR Chi-restraints excluded: chain R residue 10 MET Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 74 CYS Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 228 THR Chi-restraints excluded: chain S residue 138 ASP Chi-restraints excluded: chain S residue 146 THR Chi-restraints excluded: chain S residue 158 VAL Chi-restraints excluded: chain S residue 159 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 420 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 chunk 248 optimal weight: 0.8980 chunk 318 optimal weight: 3.9990 chunk 246 optimal weight: 0.9990 chunk 367 optimal weight: 10.0000 chunk 243 optimal weight: 1.9990 chunk 434 optimal weight: 6.9990 chunk 272 optimal weight: 5.9990 chunk 265 optimal weight: 5.9990 chunk 200 optimal weight: 6.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 573 HIS B 610 ASN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 HIS ** D 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 421 GLN H 27 GLN O 82 GLN Q 160 GLN Q 165 GLN ** R 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.4989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 36765 Z= 0.286 Angle : 0.595 11.546 49676 Z= 0.297 Chirality : 0.044 0.231 5575 Planarity : 0.004 0.045 6440 Dihedral : 4.632 132.200 5018 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.12 % Allowed : 16.24 % Favored : 79.64 % 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: 1.04 (0.13), residues: 4538 helix: 1.93 (0.11), residues: 2095 sheet: -0.43 (0.22), residues: 555 loop : -0.31 (0.14), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 567 HIS 0.005 0.001 HIS S 127 PHE 0.036 0.002 PHE R 200 TYR 0.032 0.001 TYR C 535 ARG 0.010 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 943 residues out of total 3955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 780 time to evaluate : 4.314 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: A 82 THR cc_start: 0.8458 (m) cc_final: 0.8235 (p) REVERT: A 130 ASP cc_start: 0.8383 (t0) cc_final: 0.8145 (t0) REVERT: A 155 ILE cc_start: 0.8458 (mt) cc_final: 0.7982 (tt) REVERT: A 171 ARG cc_start: 0.8301 (mtt180) cc_final: 0.7990 (ptp90) REVERT: A 203 LEU cc_start: 0.8937 (mt) cc_final: 0.8640 (mt) REVERT: A 306 MET cc_start: 0.8642 (tpp) cc_final: 0.8226 (tpp) REVERT: A 324 GLU cc_start: 0.8980 (tm-30) cc_final: 0.8626 (tm-30) REVERT: A 356 GLU cc_start: 0.8444 (tp30) cc_final: 0.7768 (tm-30) REVERT: A 360 GLU cc_start: 0.7247 (tm-30) cc_final: 0.7025 (tm-30) REVERT: A 436 ASP cc_start: 0.8867 (t0) cc_final: 0.8449 (t70) REVERT: A 443 LYS cc_start: 0.8931 (mttt) cc_final: 0.8127 (tptp) REVERT: A 447 SER cc_start: 0.8131 (m) cc_final: 0.7465 (t) REVERT: A 476 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.8055 (ptp90) REVERT: A 481 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7904 (mm-30) REVERT: A 505 ASP cc_start: 0.8220 (t0) cc_final: 0.7824 (t70) REVERT: B 18 PHE cc_start: 0.7582 (OUTLIER) cc_final: 0.6852 (m-80) REVERT: B 30 THR cc_start: 0.8539 (m) cc_final: 0.8144 (p) REVERT: B 53 GLU cc_start: 0.8018 (tt0) cc_final: 0.7408 (tt0) REVERT: B 77 ASP cc_start: 0.8079 (m-30) cc_final: 0.7503 (m-30) REVERT: B 84 LYS cc_start: 0.7551 (mmtt) cc_final: 0.7305 (mmtm) REVERT: B 89 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7408 (mt-10) REVERT: B 130 ASP cc_start: 0.8590 (m-30) cc_final: 0.8255 (p0) REVERT: B 205 MET cc_start: 0.9513 (mtm) cc_final: 0.9305 (mtm) REVERT: B 324 GLU cc_start: 0.8722 (tt0) cc_final: 0.8324 (tm-30) REVERT: B 367 GLU cc_start: 0.8690 (tt0) cc_final: 0.8090 (tt0) REVERT: B 436 ASP cc_start: 0.7094 (t0) cc_final: 0.6878 (m-30) REVERT: B 527 PRO cc_start: 0.9133 (Cg_exo) cc_final: 0.8849 (Cg_endo) REVERT: B 530 ARG cc_start: 0.7612 (ptm160) cc_final: 0.7133 (ptm-80) REVERT: B 565 ILE cc_start: 0.8121 (OUTLIER) cc_final: 0.7858 (mm) REVERT: B 572 GLU cc_start: 0.8978 (mm-30) cc_final: 0.8761 (pp20) REVERT: C 69 GLU cc_start: 0.8096 (mm-30) cc_final: 0.6979 (pt0) REVERT: C 74 SER cc_start: 0.7740 (m) cc_final: 0.6901 (p) REVERT: C 77 ASP cc_start: 0.7717 (m-30) cc_final: 0.7275 (m-30) REVERT: C 168 LEU cc_start: 0.8431 (tp) cc_final: 0.8195 (tp) REVERT: C 205 MET cc_start: 0.9263 (mtm) cc_final: 0.8757 (ttp) REVERT: C 218 THR cc_start: 0.8151 (m) cc_final: 0.7884 (m) REVERT: C 284 MET cc_start: 0.8135 (mmm) cc_final: 0.7914 (mmm) REVERT: C 296 MET cc_start: 0.6707 (ptp) cc_final: 0.5820 (ptp) REVERT: C 308 ARG cc_start: 0.7069 (ptp-110) cc_final: 0.6622 (ptt180) REVERT: C 456 LYS cc_start: 0.8092 (mttt) cc_final: 0.7668 (mtpt) REVERT: C 517 ASP cc_start: 0.7347 (m-30) cc_final: 0.6524 (t0) REVERT: C 531 PHE cc_start: 0.6097 (p90) cc_final: 0.5463 (p90) REVERT: C 565 ILE cc_start: 0.6665 (mt) cc_final: 0.6136 (tp) REVERT: D 40 LEU cc_start: 0.8679 (mm) cc_final: 0.8442 (mt) REVERT: D 169 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.8134 (tmm) REVERT: D 171 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7602 (tt0) REVERT: D 234 MET cc_start: 0.9426 (mtm) cc_final: 0.9187 (mtm) REVERT: D 380 ASP cc_start: 0.8543 (t0) cc_final: 0.8119 (t70) REVERT: D 403 LYS cc_start: 0.9095 (tttt) cc_final: 0.8676 (pttt) REVERT: D 431 ASP cc_start: 0.8696 (t70) cc_final: 0.8321 (m-30) REVERT: D 452 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8265 (mp) REVERT: E 47 TYR cc_start: 0.8026 (m-80) cc_final: 0.7691 (m-80) REVERT: E 106 ASP cc_start: 0.7826 (t70) cc_final: 0.7578 (t70) REVERT: E 169 MET cc_start: 0.7596 (OUTLIER) cc_final: 0.7308 (tmm) REVERT: E 201 GLU cc_start: 0.8008 (mp0) cc_final: 0.7641 (mt-10) REVERT: E 238 MET cc_start: 0.6944 (tmm) cc_final: 0.6692 (tmm) REVERT: E 262 ASN cc_start: 0.8733 (t0) cc_final: 0.8184 (t0) REVERT: E 268 THR cc_start: 0.8917 (p) cc_final: 0.8533 (t) REVERT: E 283 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7615 (tm-30) REVERT: E 290 GLU cc_start: 0.8438 (mt-10) cc_final: 0.7968 (mm-30) REVERT: E 315 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7884 (tt0) REVERT: E 327 MET cc_start: 0.8706 (tpp) cc_final: 0.7645 (tpp) REVERT: E 330 ASP cc_start: 0.8304 (t70) cc_final: 0.7804 (t70) REVERT: E 358 ASN cc_start: 0.8950 (t0) cc_final: 0.8531 (t0) REVERT: E 360 ASP cc_start: 0.7543 (t70) cc_final: 0.7260 (t0) REVERT: E 402 MET cc_start: 0.8082 (ttm) cc_final: 0.7196 (tpp) REVERT: E 490 GLU cc_start: 0.8811 (mp0) cc_final: 0.8532 (mp0) REVERT: F 167 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7262 (mp0) REVERT: F 189 ILE cc_start: 0.8909 (tt) cc_final: 0.8639 (tp) REVERT: F 201 GLU cc_start: 0.7963 (mp0) cc_final: 0.7302 (mp0) REVERT: F 238 MET cc_start: 0.8159 (tpp) cc_final: 0.7750 (tpt) REVERT: F 249 GLU cc_start: 0.8719 (mt-10) cc_final: 0.8122 (mm-30) REVERT: F 268 THR cc_start: 0.8910 (p) cc_final: 0.8602 (t) REVERT: F 316 GLU cc_start: 0.8723 (tp30) cc_final: 0.8052 (tp30) REVERT: F 336 GLU cc_start: 0.8786 (mm-30) cc_final: 0.7601 (tp30) REVERT: F 400 ARG cc_start: 0.7214 (tpt90) cc_final: 0.6756 (tpt170) REVERT: F 403 LYS cc_start: 0.8853 (tptt) cc_final: 0.8052 (tptp) REVERT: F 460 LYS cc_start: 0.8229 (tttt) cc_final: 0.7981 (ttpp) REVERT: H 163 LYS cc_start: 0.8753 (OUTLIER) cc_final: 0.8435 (mmmm) REVERT: H 173 GLU cc_start: 0.7631 (tt0) cc_final: 0.7276 (tt0) REVERT: H 190 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8080 (mm-30) REVERT: I 76 MET cc_start: 0.8717 (mpp) cc_final: 0.8219 (mpp) REVERT: I 132 MET cc_start: 0.8754 (mtt) cc_final: 0.8405 (mtt) REVERT: I 198 SER cc_start: 0.9165 (m) cc_final: 0.8842 (p) REVERT: I 210 GLU cc_start: 0.8068 (mp0) cc_final: 0.7573 (tm-30) REVERT: I 221 ASN cc_start: 0.7722 (m-40) cc_final: 0.7236 (t0) REVERT: J 68 LYS cc_start: 0.7438 (mttt) cc_final: 0.6525 (tptt) REVERT: J 76 MET cc_start: 0.9081 (mmm) cc_final: 0.8810 (mmp) REVERT: J 89 ASP cc_start: 0.8405 (m-30) cc_final: 0.8009 (t0) REVERT: J 90 LEU cc_start: 0.9486 (mt) cc_final: 0.9285 (mt) REVERT: J 92 THR cc_start: 0.9188 (m) cc_final: 0.8771 (p) REVERT: J 96 ASN cc_start: 0.9264 (m-40) cc_final: 0.8882 (m110) REVERT: J 97 GLU cc_start: 0.9026 (tt0) cc_final: 0.8795 (tt0) REVERT: J 185 ASN cc_start: 0.7427 (p0) cc_final: 0.7174 (p0) REVERT: J 208 MET cc_start: 0.8687 (tpp) cc_final: 0.8256 (tpp) REVERT: J 210 GLU cc_start: 0.7649 (tm-30) cc_final: 0.7270 (tm-30) REVERT: J 223 LYS cc_start: 0.9056 (mttt) cc_final: 0.8769 (mtpt) REVERT: K 76 MET cc_start: 0.8181 (mtm) cc_final: 0.7811 (tpp) REVERT: K 88 ASP cc_start: 0.8120 (t70) cc_final: 0.7861 (t0) REVERT: K 92 THR cc_start: 0.9040 (m) cc_final: 0.8773 (p) REVERT: K 97 GLU cc_start: 0.8926 (mt-10) cc_final: 0.8464 (mt-10) REVERT: K 172 TYR cc_start: 0.8498 (m-80) cc_final: 0.8052 (m-10) REVERT: K 173 LEU cc_start: 0.8612 (mt) cc_final: 0.8288 (mt) REVERT: K 175 GLU cc_start: 0.8805 (pm20) cc_final: 0.7907 (tp30) REVERT: K 197 GLU cc_start: 0.8572 (mp0) cc_final: 0.7952 (tm-30) REVERT: K 210 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7626 (tm-30) REVERT: M 107 ARG cc_start: 0.8138 (ttm-80) cc_final: 0.7892 (tpp80) REVERT: M 115 ARG cc_start: 0.8229 (ptt180) cc_final: 0.7802 (mtm110) REVERT: N 78 ARG cc_start: 0.8767 (mtm110) cc_final: 0.8334 (mtm110) REVERT: N 79 ARG cc_start: 0.8951 (ttp-110) cc_final: 0.8727 (ttm110) REVERT: N 84 MET cc_start: 0.8853 (mtp) cc_final: 0.8566 (mtp) REVERT: N 109 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.7841 (pt0) REVERT: N 115 ARG cc_start: 0.7225 (mmt-90) cc_final: 0.6966 (mmt180) REVERT: O 75 GLN cc_start: 0.9073 (mt0) cc_final: 0.8681 (tp40) REVERT: O 85 GLN cc_start: 0.9147 (mt0) cc_final: 0.8859 (tm-30) REVERT: O 102 MET cc_start: 0.8326 (mtp) cc_final: 0.7748 (mtp) REVERT: O 105 ASP cc_start: 0.8678 (t0) cc_final: 0.7892 (p0) REVERT: Q 106 ASP cc_start: 0.9153 (m-30) cc_final: 0.8935 (p0) REVERT: Q 109 GLU cc_start: 0.8362 (tt0) cc_final: 0.7801 (tm-30) REVERT: Q 123 LYS cc_start: 0.8778 (mmmt) cc_final: 0.8221 (mttp) REVERT: Q 161 MET cc_start: 0.8562 (tmm) cc_final: 0.8160 (tpp) REVERT: Q 198 HIS cc_start: 0.8580 (m-70) cc_final: 0.8066 (m-70) REVERT: R 79 ASP cc_start: 0.8676 (m-30) cc_final: 0.7735 (t0) REVERT: R 83 ARG cc_start: 0.7874 (ttp-170) cc_final: 0.7615 (ttp-170) REVERT: R 90 GLU cc_start: 0.9079 (mm-30) cc_final: 0.8728 (mm-30) REVERT: R 103 MET cc_start: 0.7300 (ttm) cc_final: 0.6945 (ttm) REVERT: R 107 LEU cc_start: 0.8384 (tp) cc_final: 0.8008 (tp) REVERT: R 112 TYR cc_start: 0.8629 (t80) cc_final: 0.7794 (t80) REVERT: R 125 ASP cc_start: 0.8716 (m-30) cc_final: 0.8358 (t70) REVERT: R 127 HIS cc_start: 0.8218 (t70) cc_final: 0.7871 (t70) REVERT: R 151 PHE cc_start: 0.8026 (m-10) cc_final: 0.7776 (m-80) REVERT: R 153 ARG cc_start: 0.8637 (tpp80) cc_final: 0.8409 (tpp80) REVERT: R 171 ASP cc_start: 0.8744 (m-30) cc_final: 0.8203 (p0) REVERT: R 188 MET cc_start: 0.7242 (tmm) cc_final: 0.6913 (ppp) REVERT: R 197 TYR cc_start: 0.8360 (m-80) cc_final: 0.7987 (m-80) REVERT: R 228 THR cc_start: 0.8605 (OUTLIER) cc_final: 0.8173 (p) REVERT: S 33 MET cc_start: 0.8632 (tpp) cc_final: 0.7921 (mtp) REVERT: S 113 GLU cc_start: 0.9225 (tp30) cc_final: 0.8893 (tp30) REVERT: S 117 GLN cc_start: 0.8810 (mt0) cc_final: 0.8515 (pp30) REVERT: S 160 GLN cc_start: 0.8065 (mt0) cc_final: 0.7762 (mt0) REVERT: S 201 LYS cc_start: 0.8049 (tttt) cc_final: 0.7665 (pttm) REVERT: S 222 GLN cc_start: 0.8415 (mt0) cc_final: 0.7101 (tm-30) outliers start: 163 outliers final: 126 residues processed: 865 average time/residue: 0.4806 time to fit residues: 687.7460 Evaluate side-chains 869 residues out of total 3955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 733 time to evaluate : 4.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 32 CYS Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 476 ARG Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 544 MET Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 306 MET Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 450 TRP Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 526 THR Chi-restraints excluded: chain C residue 532 CYS Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 187 GLN Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 408 GLU Chi-restraints excluded: chain D residue 410 MET Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 169 MET Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 311 SER Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 423 TYR Chi-restraints excluded: chain E residue 432 VAL Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 447 ASP Chi-restraints excluded: chain E residue 464 THR Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 88 GLU Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 207 CYS Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 226 ASN Chi-restraints excluded: chain F residue 290 GLU Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 498 SER Chi-restraints excluded: chain H residue 5 ASP Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 19 MET Chi-restraints excluded: chain H residue 163 LYS Chi-restraints excluded: chain H residue 167 ARG Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain H residue 202 LEU Chi-restraints excluded: chain H residue 206 GLN Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 103 SER Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain I residue 211 VAL Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain K residue 91 ILE Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain K residue 104 LYS Chi-restraints excluded: chain K residue 152 ILE Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 95 VAL Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain M residue 105 ASP Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain N residue 95 VAL Chi-restraints excluded: chain N residue 109 GLN Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain Q residue 13 LEU Chi-restraints excluded: chain Q residue 42 LEU Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 74 CYS Chi-restraints excluded: chain Q residue 81 LEU Chi-restraints excluded: chain Q residue 142 ASN Chi-restraints excluded: chain Q residue 146 THR Chi-restraints excluded: chain Q residue 156 THR Chi-restraints excluded: chain Q residue 197 TYR Chi-restraints excluded: chain R residue 10 MET Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 74 CYS Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 228 THR Chi-restraints excluded: chain S residue 138 ASP Chi-restraints excluded: chain S residue 146 THR Chi-restraints excluded: chain S residue 158 VAL Chi-restraints excluded: chain S residue 159 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 268 optimal weight: 5.9990 chunk 173 optimal weight: 5.9990 chunk 259 optimal weight: 0.1980 chunk 130 optimal weight: 0.0170 chunk 85 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 276 optimal weight: 0.9990 chunk 296 optimal weight: 7.9990 chunk 214 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 341 optimal weight: 0.9990 overall best weight: 0.6220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 610 ASN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 350 GLN E 181 ASN ** E 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 421 GLN H 27 GLN O 82 GLN R 21 GLN ** R 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.5091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 36765 Z= 0.180 Angle : 0.564 14.227 49676 Z= 0.278 Chirality : 0.043 0.257 5575 Planarity : 0.004 0.047 6440 Dihedral : 4.490 131.287 5018 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.06 % Allowed : 17.80 % 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: 1.09 (0.13), residues: 4538 helix: 1.96 (0.12), residues: 2099 sheet: -0.50 (0.22), residues: 562 loop : -0.25 (0.14), residues: 1877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 567 HIS 0.003 0.001 HIS N 111 PHE 0.037 0.001 PHE R 200 TYR 0.033 0.001 TYR C 535 ARG 0.012 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 918 residues out of total 3955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 797 time to evaluate : 4.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ASP cc_start: 0.8454 (t0) cc_final: 0.8215 (t0) REVERT: A 136 ILE cc_start: 0.8346 (OUTLIER) cc_final: 0.8051 (pt) REVERT: A 155 ILE cc_start: 0.8462 (mt) cc_final: 0.8029 (tt) REVERT: A 171 ARG cc_start: 0.8231 (mtt180) cc_final: 0.7943 (ptp90) REVERT: A 203 LEU cc_start: 0.8877 (mt) cc_final: 0.8614 (mt) REVERT: A 306 MET cc_start: 0.8418 (tpp) cc_final: 0.8116 (tpp) REVERT: A 356 GLU cc_start: 0.8443 (tp30) cc_final: 0.7785 (tm-30) REVERT: A 436 ASP cc_start: 0.8873 (t0) cc_final: 0.8450 (t70) REVERT: A 443 LYS cc_start: 0.8920 (mttt) cc_final: 0.8106 (tptp) REVERT: A 447 SER cc_start: 0.8026 (m) cc_final: 0.7414 (t) REVERT: A 462 ASP cc_start: 0.8181 (m-30) cc_final: 0.7845 (m-30) REVERT: A 476 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.8075 (ptp90) REVERT: A 481 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7890 (mm-30) REVERT: A 484 GLN cc_start: 0.8033 (tp40) cc_final: 0.7601 (tp-100) REVERT: A 505 ASP cc_start: 0.8171 (t0) cc_final: 0.7744 (t70) REVERT: B 18 PHE cc_start: 0.7782 (OUTLIER) cc_final: 0.7257 (m-80) REVERT: B 30 THR cc_start: 0.8528 (m) cc_final: 0.8124 (p) REVERT: B 53 GLU cc_start: 0.7865 (tt0) cc_final: 0.7255 (tt0) REVERT: B 61 MET cc_start: 0.7203 (mtt) cc_final: 0.6459 (ttm) REVERT: B 77 ASP cc_start: 0.8098 (m-30) cc_final: 0.7617 (m-30) REVERT: B 84 LYS cc_start: 0.7486 (mmtt) cc_final: 0.7249 (mmtm) REVERT: B 89 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7379 (mt-10) REVERT: B 130 ASP cc_start: 0.8569 (m-30) cc_final: 0.8213 (p0) REVERT: B 284 MET cc_start: 0.9278 (mmm) cc_final: 0.9073 (tpp) REVERT: B 324 GLU cc_start: 0.8668 (tt0) cc_final: 0.8232 (tm-30) REVERT: B 367 GLU cc_start: 0.8698 (tt0) cc_final: 0.8102 (tt0) REVERT: B 436 ASP cc_start: 0.7088 (t0) cc_final: 0.6879 (m-30) REVERT: B 486 GLU cc_start: 0.7995 (tm-30) cc_final: 0.7758 (tm-30) REVERT: B 523 ASN cc_start: 0.8275 (t0) cc_final: 0.7839 (t0) REVERT: B 527 PRO cc_start: 0.9120 (Cg_exo) cc_final: 0.8836 (Cg_endo) REVERT: B 530 ARG cc_start: 0.7531 (ptm160) cc_final: 0.7067 (ptm-80) REVERT: B 565 ILE cc_start: 0.8125 (OUTLIER) cc_final: 0.7880 (mm) REVERT: C 74 SER cc_start: 0.7803 (m) cc_final: 0.6953 (p) REVERT: C 77 ASP cc_start: 0.7816 (m-30) cc_final: 0.7413 (m-30) REVERT: C 168 LEU cc_start: 0.8428 (tp) cc_final: 0.8159 (tp) REVERT: C 190 VAL cc_start: 0.9034 (t) cc_final: 0.8821 (p) REVERT: C 205 MET cc_start: 0.9257 (mtm) cc_final: 0.8797 (ttp) REVERT: C 218 THR cc_start: 0.8074 (m) cc_final: 0.7816 (m) REVERT: C 284 MET cc_start: 0.8057 (mmm) cc_final: 0.7771 (mmm) REVERT: C 296 MET cc_start: 0.6574 (ptp) cc_final: 0.4982 (ptp) REVERT: C 308 ARG cc_start: 0.7057 (ptp-110) cc_final: 0.6533 (ptt180) REVERT: C 456 LYS cc_start: 0.8042 (mttt) cc_final: 0.7629 (mtpt) REVERT: C 458 MET cc_start: 0.7322 (mmt) cc_final: 0.6810 (mmt) REVERT: C 505 ASP cc_start: 0.8396 (m-30) cc_final: 0.7968 (t70) REVERT: C 517 ASP cc_start: 0.7321 (m-30) cc_final: 0.6503 (t0) REVERT: C 531 PHE cc_start: 0.5963 (p90) cc_final: 0.5328 (p90) REVERT: C 565 ILE cc_start: 0.6604 (mt) cc_final: 0.6093 (tp) REVERT: D 40 LEU cc_start: 0.8703 (mm) cc_final: 0.8457 (mt) REVERT: D 109 LYS cc_start: 0.8831 (mttt) cc_final: 0.8535 (mtmt) REVERT: D 171 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.7603 (tt0) REVERT: D 234 MET cc_start: 0.9330 (mtm) cc_final: 0.9106 (mtm) REVERT: D 270 GLU cc_start: 0.8698 (tp30) cc_final: 0.8127 (tp30) REVERT: D 305 GLU cc_start: 0.8721 (tm-30) cc_final: 0.8409 (tm-30) REVERT: D 350 GLN cc_start: 0.7453 (OUTLIER) cc_final: 0.7071 (mt0) REVERT: D 380 ASP cc_start: 0.8555 (t0) cc_final: 0.8073 (t70) REVERT: D 403 LYS cc_start: 0.9105 (tttt) cc_final: 0.8662 (pttt) REVERT: D 431 ASP cc_start: 0.8676 (t70) cc_final: 0.8307 (m-30) REVERT: D 452 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8238 (mp) REVERT: E 47 TYR cc_start: 0.8066 (m-80) cc_final: 0.7751 (m-80) REVERT: E 154 MET cc_start: 0.8221 (mmt) cc_final: 0.7987 (mmm) REVERT: E 169 MET cc_start: 0.7630 (OUTLIER) cc_final: 0.7323 (tmm) REVERT: E 201 GLU cc_start: 0.8014 (mp0) cc_final: 0.7616 (mt-10) REVERT: E 238 MET cc_start: 0.6858 (tmm) cc_final: 0.6641 (tmm) REVERT: E 262 ASN cc_start: 0.8648 (t0) cc_final: 0.8092 (t0) REVERT: E 268 THR cc_start: 0.8919 (p) cc_final: 0.8537 (t) REVERT: E 283 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7571 (tm-30) REVERT: E 290 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8027 (mm-30) REVERT: E 315 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7813 (tt0) REVERT: E 327 MET cc_start: 0.8658 (tpp) cc_final: 0.7663 (tpp) REVERT: E 330 ASP cc_start: 0.8248 (t70) cc_final: 0.7803 (t70) REVERT: E 358 ASN cc_start: 0.8956 (t0) cc_final: 0.8523 (t0) REVERT: E 360 ASP cc_start: 0.7564 (t70) cc_final: 0.7241 (t0) REVERT: E 402 MET cc_start: 0.7973 (ttm) cc_final: 0.7120 (tpp) REVERT: E 490 GLU cc_start: 0.8749 (mp0) cc_final: 0.8474 (mp0) REVERT: F 90 SER cc_start: 0.8494 (t) cc_final: 0.8181 (m) REVERT: F 167 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7194 (mp0) REVERT: F 189 ILE cc_start: 0.8922 (tt) cc_final: 0.8568 (tp) REVERT: F 201 GLU cc_start: 0.7912 (mp0) cc_final: 0.7282 (mp0) REVERT: F 238 MET cc_start: 0.8169 (tpp) cc_final: 0.7752 (tpt) REVERT: F 249 GLU cc_start: 0.8702 (mt-10) cc_final: 0.8151 (mm-30) REVERT: F 268 THR cc_start: 0.8906 (p) cc_final: 0.8627 (t) REVERT: F 316 GLU cc_start: 0.8706 (tp30) cc_final: 0.8038 (tp30) REVERT: F 374 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.7938 (mt-10) REVERT: F 400 ARG cc_start: 0.7197 (tpt90) cc_final: 0.6658 (tpt170) REVERT: F 403 LYS cc_start: 0.8849 (tptt) cc_final: 0.8003 (tptp) REVERT: F 460 LYS cc_start: 0.8247 (tttt) cc_final: 0.7976 (ttpp) REVERT: H 24 LYS cc_start: 0.8509 (tppt) cc_final: 0.8185 (tppt) REVERT: H 163 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8451 (mmmm) REVERT: I 76 MET cc_start: 0.8730 (mpp) cc_final: 0.8260 (mpp) REVERT: I 198 SER cc_start: 0.9159 (m) cc_final: 0.8824 (p) REVERT: I 210 GLU cc_start: 0.8066 (mp0) cc_final: 0.7606 (tm-30) REVERT: I 221 ASN cc_start: 0.7713 (m-40) cc_final: 0.7223 (t0) REVERT: J 68 LYS cc_start: 0.7388 (mttt) cc_final: 0.6520 (tptt) REVERT: J 76 MET cc_start: 0.9081 (mmm) cc_final: 0.8834 (mmp) REVERT: J 89 ASP cc_start: 0.8376 (m-30) cc_final: 0.7980 (t0) REVERT: J 90 LEU cc_start: 0.9422 (mt) cc_final: 0.9089 (mt) REVERT: J 92 THR cc_start: 0.9128 (m) cc_final: 0.8615 (p) REVERT: J 96 ASN cc_start: 0.9234 (m-40) cc_final: 0.8838 (m110) REVERT: J 97 GLU cc_start: 0.9106 (tt0) cc_final: 0.8864 (tt0) REVERT: J 162 ASP cc_start: 0.7898 (t70) cc_final: 0.7323 (m-30) REVERT: J 208 MET cc_start: 0.8605 (tpp) cc_final: 0.8190 (tpp) REVERT: J 210 GLU cc_start: 0.7657 (tm-30) cc_final: 0.7226 (tm-30) REVERT: J 223 LYS cc_start: 0.9037 (mttt) cc_final: 0.8744 (mtpt) REVERT: K 76 MET cc_start: 0.8157 (mtm) cc_final: 0.7793 (tpp) REVERT: K 97 GLU cc_start: 0.8931 (mt-10) cc_final: 0.8521 (mt-10) REVERT: K 132 MET cc_start: 0.9098 (mmm) cc_final: 0.8731 (mmm) REVERT: K 172 TYR cc_start: 0.8496 (m-80) cc_final: 0.8014 (m-10) REVERT: K 173 LEU cc_start: 0.8606 (mt) cc_final: 0.8283 (mt) REVERT: K 175 GLU cc_start: 0.8830 (pm20) cc_final: 0.7928 (tp30) REVERT: K 184 TYR cc_start: 0.8152 (m-80) cc_final: 0.7266 (m-80) REVERT: K 194 ASN cc_start: 0.8543 (t0) cc_final: 0.8229 (t0) REVERT: K 197 GLU cc_start: 0.8543 (mp0) cc_final: 0.7896 (tm-30) REVERT: K 210 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7688 (tm-30) REVERT: M 107 ARG cc_start: 0.8109 (ttm-80) cc_final: 0.7872 (tpp80) REVERT: M 115 ARG cc_start: 0.8179 (ptt180) cc_final: 0.7783 (mtm110) REVERT: N 78 ARG cc_start: 0.8747 (mtm110) cc_final: 0.8301 (mtm110) REVERT: N 109 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.7866 (pt0) REVERT: N 113 ASN cc_start: 0.8773 (m-40) cc_final: 0.8297 (m110) REVERT: O 75 GLN cc_start: 0.9024 (mt0) cc_final: 0.8704 (tp40) REVERT: O 82 GLN cc_start: 0.8724 (pt0) cc_final: 0.8417 (tp40) REVERT: O 85 GLN cc_start: 0.9174 (mt0) cc_final: 0.8776 (tm-30) REVERT: O 102 MET cc_start: 0.8254 (mtp) cc_final: 0.7718 (ttm) REVERT: O 105 ASP cc_start: 0.8720 (t0) cc_final: 0.7994 (p0) REVERT: Q 106 ASP cc_start: 0.9130 (m-30) cc_final: 0.8910 (p0) REVERT: Q 109 GLU cc_start: 0.8376 (tt0) cc_final: 0.7787 (tm-30) REVERT: Q 123 LYS cc_start: 0.8748 (mmmt) cc_final: 0.8176 (mttp) REVERT: Q 161 MET cc_start: 0.8541 (tmm) cc_final: 0.8134 (tpp) REVERT: Q 197 TYR cc_start: 0.7937 (OUTLIER) cc_final: 0.7493 (m-80) REVERT: Q 198 HIS cc_start: 0.8548 (m-70) cc_final: 0.8014 (m-70) REVERT: R 79 ASP cc_start: 0.8644 (m-30) cc_final: 0.7640 (t0) REVERT: R 83 ARG cc_start: 0.7846 (ttp-170) cc_final: 0.7565 (ttp-170) REVERT: R 90 GLU cc_start: 0.9054 (mm-30) cc_final: 0.8738 (mm-30) REVERT: R 107 LEU cc_start: 0.8392 (tp) cc_final: 0.8041 (tp) REVERT: R 112 TYR cc_start: 0.8584 (t80) cc_final: 0.7792 (t80) REVERT: R 125 ASP cc_start: 0.8678 (m-30) cc_final: 0.8322 (t70) REVERT: R 127 HIS cc_start: 0.8192 (t70) cc_final: 0.7878 (t70) REVERT: R 151 PHE cc_start: 0.8010 (m-10) cc_final: 0.7783 (m-80) REVERT: R 153 ARG cc_start: 0.8670 (tpp80) cc_final: 0.8406 (tpp80) REVERT: R 171 ASP cc_start: 0.8745 (m-30) cc_final: 0.8212 (p0) REVERT: R 188 MET cc_start: 0.7355 (OUTLIER) cc_final: 0.7063 (ppp) REVERT: R 197 TYR cc_start: 0.8335 (m-80) cc_final: 0.7999 (m-80) REVERT: R 228 THR cc_start: 0.8643 (OUTLIER) cc_final: 0.8229 (p) REVERT: S 33 MET cc_start: 0.8644 (tpp) cc_final: 0.7919 (mtp) REVERT: S 74 CYS cc_start: 0.8369 (m) cc_final: 0.7110 (m) REVERT: S 113 GLU cc_start: 0.9191 (tp30) cc_final: 0.8876 (tp30) REVERT: S 117 GLN cc_start: 0.8811 (mt0) cc_final: 0.8470 (pp30) REVERT: S 160 GLN cc_start: 0.7993 (mt0) cc_final: 0.7750 (mt0) REVERT: S 201 LYS cc_start: 0.8035 (tttt) cc_final: 0.7651 (pttm) REVERT: S 222 GLN cc_start: 0.8404 (mt0) cc_final: 0.7070 (tm-30) REVERT: S 232 TYR cc_start: 0.8188 (t80) cc_final: 0.7837 (t80) outliers start: 121 outliers final: 87 residues processed: 858 average time/residue: 0.3869 time to fit residues: 548.7036 Evaluate side-chains 862 residues out of total 3955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 761 time to evaluate : 2.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 476 ARG Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 450 TRP Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 526 THR Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 187 GLN Chi-restraints excluded: chain D residue 350 GLN Chi-restraints excluded: chain D residue 410 MET Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 169 MET Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 311 SER Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 423 TYR Chi-restraints excluded: chain E residue 432 VAL Chi-restraints excluded: chain E residue 447 ASP Chi-restraints excluded: chain E residue 464 THR Chi-restraints excluded: chain F residue 88 GLU Chi-restraints excluded: chain F residue 207 CYS Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 290 GLU Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 374 GLU Chi-restraints excluded: chain F residue 498 SER Chi-restraints excluded: chain H residue 5 ASP Chi-restraints excluded: chain H residue 19 MET Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 163 LYS Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain H residue 202 LEU Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 159 THR Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain J residue 91 ILE Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain K residue 91 ILE Chi-restraints excluded: chain K residue 104 LYS Chi-restraints excluded: chain K residue 152 ILE Chi-restraints excluded: chain M residue 105 ASP Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain N residue 109 GLN Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain Q residue 13 LEU Chi-restraints excluded: chain Q residue 45 ILE Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 74 CYS Chi-restraints excluded: chain Q residue 81 LEU Chi-restraints excluded: chain Q residue 142 ASN Chi-restraints excluded: chain Q residue 146 THR Chi-restraints excluded: chain Q residue 197 TYR Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 74 CYS Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 188 MET Chi-restraints excluded: chain R residue 228 THR Chi-restraints excluded: chain S residue 138 ASP Chi-restraints excluded: chain S residue 146 THR Chi-restraints excluded: chain S residue 158 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 395 optimal weight: 6.9990 chunk 416 optimal weight: 5.9990 chunk 379 optimal weight: 10.0000 chunk 405 optimal weight: 0.9980 chunk 243 optimal weight: 5.9990 chunk 176 optimal weight: 5.9990 chunk 318 optimal weight: 7.9990 chunk 124 optimal weight: 2.9990 chunk 366 optimal weight: 6.9990 chunk 383 optimal weight: 10.0000 chunk 403 optimal weight: 5.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN ** B 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 610 ASN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 HIS ** D 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 421 GLN I 78 GLN K 66 GLN ** K 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 21 GLN ** R 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 50 GLN ** S 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.5390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.097 36765 Z= 0.515 Angle : 0.756 13.479 49676 Z= 0.382 Chirality : 0.050 0.400 5575 Planarity : 0.005 0.062 6440 Dihedral : 5.022 137.495 5018 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.25 % Favored : 95.72 % Rotamer: Outliers : 3.46 % Allowed : 17.68 % Favored : 78.86 % 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: 0.61 (0.13), residues: 4538 helix: 1.61 (0.11), residues: 2112 sheet: -0.66 (0.22), residues: 575 loop : -0.59 (0.14), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP B 433 HIS 0.008 0.002 HIS D 384 PHE 0.042 0.003 PHE R 200 TYR 0.035 0.002 TYR C 535 ARG 0.014 0.001 ARG N 79 *********************** 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 862 residues out of total 3955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 725 time to evaluate : 4.412 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: A 130 ASP cc_start: 0.8446 (t0) cc_final: 0.8206 (t0) REVERT: A 155 ILE cc_start: 0.8471 (mt) cc_final: 0.7985 (tt) REVERT: A 171 ARG cc_start: 0.8331 (mtt180) cc_final: 0.8044 (ptp90) REVERT: A 203 LEU cc_start: 0.8767 (mt) cc_final: 0.8435 (mt) REVERT: A 291 PHE cc_start: 0.8080 (OUTLIER) cc_final: 0.7840 (m-80) REVERT: A 306 MET cc_start: 0.8748 (tpp) cc_final: 0.8337 (tpp) REVERT: A 324 GLU cc_start: 0.8932 (tm-30) cc_final: 0.8592 (tm-30) REVERT: A 356 GLU cc_start: 0.8533 (tp30) cc_final: 0.8171 (tp30) REVERT: A 436 ASP cc_start: 0.8967 (t0) cc_final: 0.8513 (t70) REVERT: A 437 LYS cc_start: 0.9128 (mtmt) cc_final: 0.8867 (mtpp) REVERT: A 443 LYS cc_start: 0.8934 (mttt) cc_final: 0.8206 (tptp) REVERT: A 447 SER cc_start: 0.8409 (m) cc_final: 0.7654 (t) REVERT: A 476 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.8031 (ptp-170) REVERT: A 481 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7917 (mm-30) REVERT: A 505 ASP cc_start: 0.8240 (t0) cc_final: 0.7872 (t70) REVERT: A 609 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.7942 (mp10) REVERT: B 18 PHE cc_start: 0.8108 (OUTLIER) cc_final: 0.7723 (m-80) REVERT: B 30 THR cc_start: 0.8605 (m) cc_final: 0.8263 (p) REVERT: B 53 GLU cc_start: 0.8094 (tt0) cc_final: 0.7448 (tt0) REVERT: B 77 ASP cc_start: 0.8116 (m-30) cc_final: 0.7626 (m-30) REVERT: B 84 LYS cc_start: 0.7643 (mmtt) cc_final: 0.7396 (mmtm) REVERT: B 89 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7236 (tt0) REVERT: B 130 ASP cc_start: 0.8615 (m-30) cc_final: 0.8298 (p0) REVERT: B 324 GLU cc_start: 0.8717 (tt0) cc_final: 0.8360 (tm-30) REVERT: B 523 ASN cc_start: 0.8576 (t0) cc_final: 0.8120 (t0) REVERT: B 527 PRO cc_start: 0.9175 (Cg_exo) cc_final: 0.8939 (Cg_endo) REVERT: B 530 ARG cc_start: 0.7769 (ptm160) cc_final: 0.7270 (ptm-80) REVERT: C 69 GLU cc_start: 0.8108 (mm-30) cc_final: 0.6935 (pt0) REVERT: C 74 SER cc_start: 0.7651 (m) cc_final: 0.6863 (p) REVERT: C 77 ASP cc_start: 0.7723 (m-30) cc_final: 0.7144 (m-30) REVERT: C 168 LEU cc_start: 0.8509 (tp) cc_final: 0.8164 (tp) REVERT: C 190 VAL cc_start: 0.9028 (t) cc_final: 0.8811 (p) REVERT: C 218 THR cc_start: 0.8264 (m) cc_final: 0.8005 (m) REVERT: C 284 MET cc_start: 0.8149 (mmm) cc_final: 0.7899 (mmm) REVERT: C 308 ARG cc_start: 0.6737 (ptp-110) cc_final: 0.6492 (ptt180) REVERT: C 456 LYS cc_start: 0.8126 (mttt) cc_final: 0.7692 (mtpt) REVERT: C 517 ASP cc_start: 0.7297 (m-30) cc_final: 0.6413 (t0) REVERT: C 531 PHE cc_start: 0.6021 (p90) cc_final: 0.5420 (p90) REVERT: D 40 LEU cc_start: 0.8920 (mm) cc_final: 0.8639 (mt) REVERT: D 127 MET cc_start: 0.8315 (ptp) cc_final: 0.7539 (ptp) REVERT: D 180 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.8270 (tpp) REVERT: D 234 MET cc_start: 0.9486 (mtm) cc_final: 0.9118 (mtm) REVERT: D 270 GLU cc_start: 0.8804 (tp30) cc_final: 0.8600 (tp30) REVERT: D 281 THR cc_start: 0.9228 (m) cc_final: 0.8980 (t) REVERT: D 302 SER cc_start: 0.8350 (m) cc_final: 0.7848 (t) REVERT: D 309 GLU cc_start: 0.8586 (tm-30) cc_final: 0.8216 (tm-30) REVERT: D 380 ASP cc_start: 0.8533 (t0) cc_final: 0.8056 (t70) REVERT: D 403 LYS cc_start: 0.9129 (tttt) cc_final: 0.8661 (pttt) REVERT: D 431 ASP cc_start: 0.8725 (t70) cc_final: 0.8307 (m-30) REVERT: D 447 ASP cc_start: 0.7809 (t0) cc_final: 0.7447 (t0) REVERT: E 154 MET cc_start: 0.8116 (mmt) cc_final: 0.7865 (mmm) REVERT: E 180 MET cc_start: 0.8542 (mmm) cc_final: 0.8100 (mtp) REVERT: E 201 GLU cc_start: 0.7971 (mp0) cc_final: 0.7691 (mt-10) REVERT: E 262 ASN cc_start: 0.8800 (t0) cc_final: 0.8299 (t0) REVERT: E 268 THR cc_start: 0.8991 (p) cc_final: 0.8676 (t) REVERT: E 283 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7611 (tm-30) REVERT: E 290 GLU cc_start: 0.8413 (mt-10) cc_final: 0.7849 (mm-30) REVERT: E 315 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7904 (tt0) REVERT: E 327 MET cc_start: 0.8815 (tpp) cc_final: 0.7800 (tpp) REVERT: E 330 ASP cc_start: 0.8409 (t70) cc_final: 0.7884 (t0) REVERT: E 358 ASN cc_start: 0.9022 (t0) cc_final: 0.8508 (t0) REVERT: E 359 ASP cc_start: 0.8647 (t0) cc_final: 0.8382 (t0) REVERT: E 402 MET cc_start: 0.8240 (ttm) cc_final: 0.7402 (tpp) REVERT: E 490 GLU cc_start: 0.8852 (mp0) cc_final: 0.8311 (mp0) REVERT: F 189 ILE cc_start: 0.8802 (tt) cc_final: 0.8514 (tp) REVERT: F 201 GLU cc_start: 0.7768 (mp0) cc_final: 0.7332 (mp0) REVERT: F 238 MET cc_start: 0.8113 (tpp) cc_final: 0.7769 (tpp) REVERT: F 249 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8193 (mm-30) REVERT: F 268 THR cc_start: 0.8880 (p) cc_final: 0.8558 (t) REVERT: F 316 GLU cc_start: 0.8726 (tp30) cc_final: 0.8093 (tp30) REVERT: F 400 ARG cc_start: 0.7368 (tpt90) cc_final: 0.6887 (tpt170) REVERT: F 403 LYS cc_start: 0.8834 (tptt) cc_final: 0.8057 (tptp) REVERT: F 410 MET cc_start: 0.7132 (mtm) cc_final: 0.6891 (ptp) REVERT: F 460 LYS cc_start: 0.8233 (tttt) cc_final: 0.7962 (ttpp) REVERT: H 163 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8466 (mmmm) REVERT: I 193 SER cc_start: 0.8658 (m) cc_final: 0.7969 (p) REVERT: I 194 ASN cc_start: 0.8649 (t0) cc_final: 0.8303 (t0) REVERT: I 198 SER cc_start: 0.9180 (m) cc_final: 0.8797 (p) REVERT: I 210 GLU cc_start: 0.8136 (mp0) cc_final: 0.7764 (tm-30) REVERT: I 221 ASN cc_start: 0.8010 (m-40) cc_final: 0.7482 (t0) REVERT: J 68 LYS cc_start: 0.7500 (mttt) cc_final: 0.6661 (tptt) REVERT: J 76 MET cc_start: 0.9166 (mmm) cc_final: 0.8923 (mmm) REVERT: J 89 ASP cc_start: 0.8497 (m-30) cc_final: 0.8117 (t0) REVERT: J 92 THR cc_start: 0.9203 (m) cc_final: 0.8781 (p) REVERT: J 96 ASN cc_start: 0.9205 (m-40) cc_final: 0.8838 (m110) REVERT: J 97 GLU cc_start: 0.9100 (tt0) cc_final: 0.8832 (tt0) REVERT: J 116 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8839 (mp) REVERT: J 208 MET cc_start: 0.8697 (tpp) cc_final: 0.8321 (tpp) REVERT: J 210 GLU cc_start: 0.7686 (tm-30) cc_final: 0.7255 (tm-30) REVERT: J 223 LYS cc_start: 0.9077 (mttt) cc_final: 0.8766 (mtpt) REVERT: K 76 MET cc_start: 0.8158 (mtm) cc_final: 0.7788 (mmt) REVERT: K 97 GLU cc_start: 0.8925 (mt-10) cc_final: 0.8437 (mt-10) REVERT: K 132 MET cc_start: 0.9096 (mmm) cc_final: 0.8753 (mmm) REVERT: K 172 TYR cc_start: 0.8608 (m-80) cc_final: 0.8213 (m-10) REVERT: K 173 LEU cc_start: 0.8601 (mt) cc_final: 0.8279 (mt) REVERT: K 175 GLU cc_start: 0.8854 (pm20) cc_final: 0.8018 (tp30) REVERT: K 197 GLU cc_start: 0.8514 (mp0) cc_final: 0.7988 (tm-30) REVERT: K 210 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7767 (tm-30) REVERT: N 78 ARG cc_start: 0.8715 (mtm110) cc_final: 0.8279 (mtm110) REVERT: N 79 ARG cc_start: 0.9014 (ttm110) cc_final: 0.8748 (ttp80) REVERT: N 107 ARG cc_start: 0.7853 (mmp-170) cc_final: 0.7603 (mmp-170) REVERT: N 109 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.8096 (pt0) REVERT: O 75 GLN cc_start: 0.9066 (mt0) cc_final: 0.8745 (tp40) REVERT: O 85 GLN cc_start: 0.9176 (mt0) cc_final: 0.8863 (tm-30) REVERT: Q 39 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8456 (mp0) REVERT: Q 106 ASP cc_start: 0.9191 (m-30) cc_final: 0.8962 (p0) REVERT: Q 109 GLU cc_start: 0.8413 (tt0) cc_final: 0.7840 (tm-30) REVERT: Q 123 LYS cc_start: 0.8854 (mmmt) cc_final: 0.8284 (mttp) REVERT: Q 139 TYR cc_start: 0.8471 (t80) cc_final: 0.8053 (t80) REVERT: Q 161 MET cc_start: 0.8596 (tmm) cc_final: 0.8253 (tmm) REVERT: Q 198 HIS cc_start: 0.8662 (m-70) cc_final: 0.8397 (m-70) REVERT: R 79 ASP cc_start: 0.8631 (m-30) cc_final: 0.7673 (t0) REVERT: R 83 ARG cc_start: 0.7915 (ttp-170) cc_final: 0.7662 (ttp-170) REVERT: R 103 MET cc_start: 0.7435 (ttm) cc_final: 0.7010 (ttm) REVERT: R 107 LEU cc_start: 0.8457 (tp) cc_final: 0.8031 (tp) REVERT: R 125 ASP cc_start: 0.8691 (m-30) cc_final: 0.8250 (t70) REVERT: R 127 HIS cc_start: 0.8241 (t70) cc_final: 0.7695 (t70) REVERT: R 153 ARG cc_start: 0.8682 (tpp80) cc_final: 0.8480 (tpp80) REVERT: R 171 ASP cc_start: 0.8770 (m-30) cc_final: 0.8215 (p0) REVERT: R 188 MET cc_start: 0.7259 (OUTLIER) cc_final: 0.7014 (ppp) REVERT: R 197 TYR cc_start: 0.8349 (m-80) cc_final: 0.8062 (m-80) REVERT: R 228 THR cc_start: 0.8759 (OUTLIER) cc_final: 0.8403 (p) REVERT: S 74 CYS cc_start: 0.8064 (m) cc_final: 0.7742 (m) REVERT: S 113 GLU cc_start: 0.9277 (tp30) cc_final: 0.8878 (tp30) REVERT: S 117 GLN cc_start: 0.8797 (mt0) cc_final: 0.8562 (pp30) REVERT: S 160 GLN cc_start: 0.8065 (mt0) cc_final: 0.7788 (mt0) REVERT: S 198 HIS cc_start: 0.7717 (t-90) cc_final: 0.7367 (t-90) REVERT: S 201 LYS cc_start: 0.8054 (tttt) cc_final: 0.7625 (pttm) outliers start: 137 outliers final: 108 residues processed: 803 average time/residue: 0.4443 time to fit residues: 590.0273 Evaluate side-chains 822 residues out of total 3955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 703 time to evaluate : 3.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 476 ARG Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain A residue 609 GLN Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 306 MET Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 450 TRP Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 526 THR Chi-restraints excluded: chain C residue 532 CYS Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 187 GLN Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 311 SER Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 423 TYR Chi-restraints excluded: chain E residue 432 VAL Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 447 ASP Chi-restraints excluded: chain E residue 464 THR Chi-restraints excluded: chain F residue 88 GLU Chi-restraints excluded: chain F residue 144 VAL Chi-restraints excluded: chain F residue 207 CYS Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 226 ASN Chi-restraints excluded: chain F residue 290 GLU Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 498 SER Chi-restraints excluded: chain H residue 5 ASP Chi-restraints excluded: chain H residue 19 MET Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 163 LYS Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain H residue 202 LEU Chi-restraints excluded: chain H residue 206 GLN Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain J residue 91 ILE Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain K residue 91 ILE Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain K residue 104 LYS Chi-restraints excluded: chain K residue 152 ILE Chi-restraints excluded: chain M residue 105 ASP Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain N residue 109 GLN Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain Q residue 13 LEU Chi-restraints excluded: chain Q residue 39 GLU Chi-restraints excluded: chain Q residue 42 LEU Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 74 CYS Chi-restraints excluded: chain Q residue 81 LEU Chi-restraints excluded: chain Q residue 126 TYR Chi-restraints excluded: chain Q residue 142 ASN Chi-restraints excluded: chain Q residue 146 THR Chi-restraints excluded: chain Q residue 169 THR Chi-restraints excluded: chain Q residue 197 TYR Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 74 CYS Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 188 MET Chi-restraints excluded: chain R residue 228 THR Chi-restraints excluded: chain S residue 146 THR Chi-restraints excluded: chain S residue 158 VAL Chi-restraints excluded: chain S residue 159 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 266 optimal weight: 0.7980 chunk 428 optimal weight: 10.0000 chunk 261 optimal weight: 0.9980 chunk 203 optimal weight: 2.9990 chunk 297 optimal weight: 3.9990 chunk 449 optimal weight: 9.9990 chunk 413 optimal weight: 5.9990 chunk 357 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 276 optimal weight: 1.9990 chunk 219 optimal weight: 6.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: