Starting phenix.real_space_refine on Fri Feb 23 05:27:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqb_21347/02_2024/6vqb_21347_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqb_21347/02_2024/6vqb_21347.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqb_21347/02_2024/6vqb_21347.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqb_21347/02_2024/6vqb_21347.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqb_21347/02_2024/6vqb_21347_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqb_21347/02_2024/6vqb_21347_updated.pdb" } resolution = 3.6 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= 0.093 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 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 TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 68": "OE1" <-> "OE2" Residue "A TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 279": "OE1" <-> "OE2" 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 ARG 388": "NH1" <-> "NH2" Residue "A ASP 419": "OD1" <-> "OD2" 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 PHE 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 323": "NH1" <-> "NH2" 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 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 388": "NH1" <-> "NH2" Residue "B ARG 400": "NH1" <-> "NH2" Residue "B ASP 436": "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 531": "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 PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 104": "NH1" <-> "NH2" Residue "C TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 388": "NH1" <-> "NH2" Residue "C ARG 400": "NH1" <-> "NH2" Residue "C PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 454": "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 ASP 529": "OD1" <-> "OD2" Residue "C PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 260": "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 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 458": "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 "D TYR 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 270": "OE1" <-> "OE2" Residue "E TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 423": "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 PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 323": "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 "F TYR 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 155": "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 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 90": "OE1" <-> "OE2" 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 TYR 197": "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 PHE 101": "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 "R GLU 214": "OE1" <-> "OE2" 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 ASP 77": "OD1" <-> "OD2" 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" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 36113 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: 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: "R" 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: "S" 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: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 18.57, per 1000 atoms: 0.51 Number of scatterers: 36113 At special positions: 0 Unit cell: (173.84, 171.72, 145.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 203 16.00 P 2 15.00 O 6821 8.00 N 6223 7.00 C 22864 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.78 Conformation dependent library (CDL) restraints added in 7.0 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 34 sheets defined 45.6% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.64 Creating SS restraints... Processing helix chain 'A' and resid 106 through 113 Processing helix chain 'A' and resid 256 through 265 Processing helix chain 'A' and resid 281 through 293 Proline residue: A 292 - end of helix Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 321 through 340 removed outlier: 3.641A pdb=" N SER A 326 " --> pdb=" O ARG A 323 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY A 330 " --> pdb=" O ILE A 327 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE A 331 " --> pdb=" O TYR A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 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 376 through 388 removed outlier: 4.358A pdb=" N GLY A 379 " --> pdb=" O ALA A 376 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA A 383 " --> pdb=" O ALA A 380 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER A 384 " --> pdb=" O ARG A 381 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLU A 387 " --> 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 437 through 441 Processing helix chain 'A' and resid 458 through 468 removed outlier: 4.455A pdb=" N GLU A 463 " --> pdb=" O ARG A 459 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N TYR A 464 " --> pdb=" O ALA A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 496 removed outlier: 4.140A pdb=" N ILE A 492 " --> pdb=" O ASP A 488 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 518 Processing helix chain 'A' and resid 534 through 556 Processing helix chain 'A' and resid 567 through 573 Processing helix chain 'A' and resid 575 through 585 removed outlier: 4.967A pdb=" N LYS A 585 " --> pdb=" O LEU A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 615 Processing helix chain 'B' and resid 106 through 113 Processing helix chain 'B' and resid 232 through 235 No H-bonds generated for 'chain 'B' and resid 232 through 235' Processing helix chain 'B' and resid 256 through 266 Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 305 through 308 Processing helix chain 'B' and resid 320 through 340 removed outlier: 4.617A pdb=" N ILE B 327 " --> pdb=" O ARG B 323 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N TYR B 328 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N MET B 340 " --> pdb=" O TYR B 336 " (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 378 through 386 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: 4.281A pdb=" N GLU B 463 " --> pdb=" O ARG B 459 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N TYR B 464 " --> pdb=" O ALA B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 496 removed outlier: 3.867A 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 557 Processing helix chain 'B' and resid 567 through 573 Processing helix chain 'B' and resid 575 through 586 removed outlier: 5.130A pdb=" N LYS B 585 " --> pdb=" O LEU B 581 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N PHE B 586 " --> pdb=" O SER B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 615 Processing helix chain 'C' and resid 106 through 112 removed outlier: 3.652A pdb=" N SER C 111 " --> pdb=" O SER C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 254 No H-bonds generated for 'chain 'C' and resid 252 through 254' Processing helix chain 'C' and resid 257 through 266 Processing helix chain 'C' and resid 281 through 293 Proline residue: C 292 - end of helix Processing helix chain 'C' and resid 305 through 307 No H-bonds generated for 'chain 'C' and resid 305 through 307' Processing helix chain 'C' and resid 320 through 340 removed outlier: 4.594A pdb=" N ILE C 327 " --> pdb=" O ARG C 323 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N TYR C 328 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N MET C 340 " --> pdb=" O TYR C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 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 388 removed outlier: 3.725A pdb=" N ARG C 388 " --> pdb=" O SER C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 415 No H-bonds generated for 'chain 'C' and resid 413 through 415' Processing helix chain 'C' and resid 420 through 426 Processing helix chain 'C' and resid 438 through 441 No H-bonds generated for 'chain 'C' and resid 438 through 441' Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 472 through 496 removed outlier: 4.597A pdb=" N GLU C 491 " --> pdb=" O GLU C 487 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ILE C 492 " --> pdb=" O ASP C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 518 Processing helix chain 'C' and resid 534 through 558 removed outlier: 3.809A pdb=" N THR C 558 " --> pdb=" O ALA C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 573 Processing helix chain 'C' and resid 575 through 586 removed outlier: 4.851A pdb=" N LYS C 585 " --> pdb=" O LEU C 581 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N PHE C 586 " --> pdb=" O SER C 582 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 615 removed outlier: 3.972A pdb=" N LEU C 615 " --> pdb=" O ALA C 611 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 127 No H-bonds generated for 'chain 'D' and resid 125 through 127' Processing helix chain 'D' and resid 175 through 178 No H-bonds generated for 'chain 'D' and resid 175 through 178' Processing helix chain 'D' and resid 199 through 209 removed outlier: 3.601A pdb=" N ARG D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 250 Processing helix chain 'D' and resid 254 through 256 No H-bonds generated for 'chain 'D' and resid 254 through 256' Processing helix chain 'D' and resid 270 through 272 No H-bonds generated for 'chain 'D' and resid 270 through 272' Processing helix chain 'D' and resid 274 through 287 Processing helix chain 'D' and resid 300 through 313 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 Processing helix chain 'D' and resid 381 through 386 removed outlier: 4.048A pdb=" N ARG D 386 " --> pdb=" O GLN D 382 " (cutoff:3.500A) 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: 4.343A pdb=" N VAL D 438 " --> pdb=" O ALA D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 443 No H-bonds generated for 'chain 'D' and resid 441 through 443' Processing helix chain 'D' and resid 446 through 461 removed outlier: 4.348A pdb=" N TYR D 451 " --> pdb=" O ASP D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 486 removed outlier: 4.005A 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 removed outlier: 5.012A pdb=" N GLU D 502 " --> pdb=" O SER D 498 " (cutoff:3.500A) 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 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 287 removed outlier: 3.580A pdb=" N THR E 274 " --> pdb=" O ARG E 271 " (cutoff:3.500A) Proline residue: E 275 - end of helix removed outlier: 3.591A pdb=" N ALA E 278 " --> pdb=" O PRO E 275 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU E 279 " --> pdb=" O ARG E 276 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR E 280 " --> pdb=" O LEU E 277 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA E 286 " --> pdb=" O GLU E 283 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR E 287 " --> pdb=" O PHE E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 313 Processing helix chain 'E' and resid 320 through 322 No H-bonds generated for 'chain 'E' and resid 320 through 322' Processing helix chain 'E' and resid 327 through 335 removed outlier: 3.853A pdb=" N ILE E 334 " --> pdb=" O ASP E 330 " (cutoff:3.500A) 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 382 through 385 No H-bonds generated for 'chain 'E' and resid 382 through 385' Processing helix chain 'E' and resid 400 through 403 removed outlier: 4.189A pdb=" N LYS E 403 " --> pdb=" O ARG E 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 400 through 403' Processing helix chain 'E' and resid 415 through 439 removed outlier: 4.031A 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 Processing helix chain 'E' and resid 473 through 486 removed outlier: 3.830A 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 Processing helix chain 'F' and resid 160 through 162 No H-bonds generated for 'chain 'F' and resid 160 through 162' Processing helix chain 'F' and resid 175 through 177 No H-bonds generated for 'chain 'F' and resid 175 through 177' Processing helix chain 'F' and resid 199 through 209 Processing helix chain 'F' and resid 238 through 250 Processing helix chain 'F' and resid 253 through 256 Processing helix chain 'F' and resid 268 through 288 removed outlier: 3.580A pdb=" N ILE F 272 " --> pdb=" O THR F 268 " (cutoff:3.500A) Proline residue: F 275 - end of helix 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 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 removed outlier: 3.844A pdb=" N ILE F 372 " --> pdb=" O LEU F 368 " (cutoff:3.500A) 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 402 through 405 No H-bonds generated for 'chain 'F' and resid 402 through 405' Processing helix chain 'F' and resid 415 through 439 removed outlier: 3.691A pdb=" N VAL F 438 " --> pdb=" O ALA F 434 " (cutoff:3.500A) Processing helix chain 'F' and resid 446 through 461 Processing helix chain 'F' and resid 473 through 486 removed outlier: 4.109A 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 109 through 127 removed outlier: 4.628A pdb=" N VAL I 114 " --> pdb=" O THR I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 138 through 158 Proline residue: I 142 - end of helix removed outlier: 3.833A pdb=" N LYS I 145 " --> pdb=" O PRO I 142 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS I 150 " --> pdb=" O ALA I 147 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE I 152 " --> pdb=" O GLN I 149 " (cutoff:3.500A) Proline residue: I 153 - end of helix removed outlier: 3.691A pdb=" N LYS I 156 " --> pdb=" O PRO I 153 " (cutoff:3.500A) Processing helix chain 'I' and resid 196 through 216 removed outlier: 3.950A pdb=" N GLN I 206 " --> pdb=" O LEU I 202 " (cutoff:3.500A) Proline residue: I 209 - end of helix Processing helix chain 'J' and resid 67 through 106 Processing helix chain 'J' and resid 110 through 127 Processing helix chain 'J' and resid 138 through 159 Proline residue: J 142 - end of helix removed outlier: 3.751A pdb=" N LYS J 145 " --> pdb=" O PRO J 142 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ILE J 152 " --> pdb=" O GLN J 149 " (cutoff:3.500A) Proline residue: J 153 - end of helix removed outlier: 3.722A pdb=" N LYS J 156 " --> pdb=" O PRO J 153 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE J 157 " --> pdb=" O MET J 154 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR J 159 " --> pdb=" O LYS J 156 " (cutoff:3.500A) Processing helix chain 'J' and resid 196 through 204 Processing helix chain 'J' and resid 208 through 216 removed outlier: 3.613A pdb=" N GLY J 213 " --> pdb=" O PRO J 209 " (cutoff:3.500A) 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: 3.713A pdb=" N LYS K 145 " --> pdb=" O PRO K 142 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS K 150 " --> pdb=" O ALA K 147 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ILE K 152 " --> pdb=" O GLN K 149 " (cutoff:3.500A) Proline residue: K 153 - end of helix removed outlier: 3.695A pdb=" N LYS K 156 " --> pdb=" O PRO K 153 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR K 159 " --> pdb=" O LYS K 156 " (cutoff:3.500A) Processing helix chain 'K' and resid 196 through 206 Processing helix chain 'K' and resid 208 through 216 removed outlier: 3.507A pdb=" N GLY K 213 " --> pdb=" O PRO K 209 " (cutoff:3.500A) Processing helix chain 'M' and resid 71 through 90 removed outlier: 3.919A pdb=" N ARG M 90 " --> pdb=" O SER M 86 " (cutoff:3.500A) Processing helix chain 'M' and resid 92 through 104 Processing helix chain 'N' and resid 71 through 103 removed outlier: 3.648A pdb=" N ASN N 91 " --> pdb=" O SER N 87 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N GLU N 93 " --> pdb=" O GLN N 89 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N ARG N 94 " --> pdb=" O ARG N 90 " (cutoff:3.500A) Processing helix chain 'O' and resid 71 through 90 Processing helix chain 'O' and resid 92 through 104 Processing helix chain 'Q' and resid 15 through 36 Processing helix chain 'Q' and resid 43 through 48 Processing helix chain 'Q' and resid 50 through 55 removed outlier: 5.007A pdb=" N TRP Q 55 " --> pdb=" O ASP Q 51 " (cutoff:3.500A) Processing helix chain 'Q' and resid 62 through 70 Processing helix chain 'Q' and resid 78 through 98 removed outlier: 3.907A pdb=" N LEU Q 88 " --> pdb=" O ARG Q 84 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU Q 91 " --> pdb=" O ILE Q 87 " (cutoff:3.500A) removed outlier: 3.983A 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 125 through 141 removed outlier: 3.524A pdb=" N LEU Q 140 " --> pdb=" O LEU Q 136 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS Q 141 " --> pdb=" O THR Q 137 " (cutoff:3.500A) Processing helix chain 'Q' and resid 147 through 166 Processing helix chain 'Q' and resid 173 through 187 Processing helix chain 'Q' and resid 193 through 204 Processing helix chain 'Q' and resid 219 through 232 removed outlier: 3.561A pdb=" N MET Q 229 " --> pdb=" O LEU Q 225 " (cutoff:3.500A) Processing helix chain 'R' and resid 15 through 36 Processing helix chain 'R' and resid 43 through 55 removed outlier: 3.673A pdb=" N TYR R 49 " --> pdb=" O ILE R 45 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ASP R 51 " --> pdb=" O GLU R 47 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL R 52 " --> pdb=" O ASP R 48 " (cutoff:3.500A) removed outlier: 5.149A 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 96 Processing helix chain 'R' and resid 105 through 117 Processing helix chain 'R' and resid 121 through 123 No H-bonds generated for 'chain 'R' and resid 121 through 123' Processing helix chain 'R' and resid 125 through 142 removed outlier: 3.949A pdb=" N ASN R 142 " --> pdb=" O ASP R 138 " (cutoff:3.500A) Processing helix chain 'R' and resid 147 through 166 Processing helix chain 'R' and resid 173 through 186 Processing helix chain 'R' and resid 193 through 206 Processing helix chain 'R' and resid 219 through 234 Processing helix chain 'S' and resid 15 through 36 removed outlier: 3.506A pdb=" N HIS S 19 " --> pdb=" O SER S 15 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 53 removed outlier: 3.679A pdb=" N TYR S 49 " --> pdb=" O ILE S 45 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N ASP S 51 " --> pdb=" O GLU S 47 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL S 52 " --> pdb=" O ASP S 48 " (cutoff:3.500A) Processing helix chain 'S' and resid 63 through 71 Processing helix chain 'S' and resid 78 through 98 removed outlier: 4.015A pdb=" N ILE S 98 " --> pdb=" O LEU S 94 " (cutoff:3.500A) Processing helix chain 'S' and resid 105 through 116 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: 3.694A pdb=" N LEU S 140 " --> pdb=" O LEU S 136 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS S 141 " --> pdb=" O THR S 137 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ASN S 142 " --> pdb=" O ASP S 138 " (cutoff:3.500A) Processing helix chain 'S' and resid 147 through 166 removed outlier: 3.541A pdb=" N GLN S 165 " --> pdb=" O MET S 161 " (cutoff:3.500A) Processing helix chain 'S' and resid 173 through 186 Processing helix chain 'S' and resid 194 through 206 Processing sheet with id= A, first strand: chain 'A' and resid 78 through 80 removed outlier: 6.478A pdb=" N THR A 30 " --> pdb=" O HIS A 22 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N VAL A 24 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL A 28 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG A 56 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N GLN A 65 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ILE A 54 " --> pdb=" O GLN A 65 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N GLU A 41 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N LYS A 84 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ARG A 44 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N THR A 82 " --> pdb=" O ARG A 44 " (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 Processing sheet with id= D, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.320A pdb=" N GLU A 195 " --> pdb=" O VAL A 176 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N VAL A 176 " --> pdb=" O GLU A 195 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 245 through 248 removed outlier: 8.572A pdb=" N THR A 246 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE A 406 " --> pdb=" O THR A 246 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ILE A 248 " --> pdb=" O ILE A 406 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N GLY A 408 " --> pdb=" O ILE A 248 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 272 through 277 Processing sheet with id= G, first strand: chain 'A' and resid 390 through 393 Processing sheet with id= H, first strand: chain 'B' and resid 18 through 20 removed outlier: 6.881A pdb=" N THR B 63 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LEU B 57 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N MET B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N CYS B 32 " --> pdb=" O VAL B 21 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N VAL B 21 " --> pdb=" O CYS B 32 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 87 through 90 Processing sheet with id= J, first strand: chain 'B' and resid 183 through 185 removed outlier: 6.908A pdb=" N ILE B 166 " --> pdb=" O TYR B 153 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ILE B 155 " --> pdb=" O HIS B 164 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N HIS B 164 " --> pdb=" O ILE B 155 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 199 through 203 removed outlier: 6.175A pdb=" N GLU B 195 " --> pdb=" O VAL B 176 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N VAL B 176 " --> pdb=" O GLU B 195 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 219 through 221 removed outlier: 4.066A pdb=" N ARG B 391 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 245 through 247 removed outlier: 8.414A pdb=" N THR B 246 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ILE B 406 " --> pdb=" O THR B 246 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL B 271 " --> pdb=" O SER B 345 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N MET B 347 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE B 273 " --> pdb=" O MET B 347 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 295 through 297 Processing sheet with id= O, first strand: chain 'C' and resid 18 through 20 removed outlier: 3.557A pdb=" N LEU C 42 " --> pdb=" O THR C 82 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N CYS C 32 " --> pdb=" O VAL C 21 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N VAL C 21 " --> pdb=" O CYS C 32 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 87 through 90 Processing sheet with id= Q, first strand: chain 'C' and resid 183 through 185 removed outlier: 4.722A pdb=" N GLU C 134 " --> pdb=" O ASN C 157 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ILE C 166 " --> pdb=" O TYR C 153 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ILE C 155 " --> pdb=" O HIS C 164 " (cutoff:3.500A) removed outlier: 6.565A 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: 6.263A pdb=" N GLU C 195 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N VAL C 176 " --> pdb=" O GLU C 195 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 309 through 312 removed outlier: 6.306A pdb=" N ILE C 272 " --> pdb=" O ALA C 310 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N VAL C 312 " --> pdb=" O ILE C 272 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N TYR C 274 " --> pdb=" O VAL C 312 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N VAL C 344 " --> pdb=" O GLU C 401 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N SER C 403 " --> pdb=" O VAL C 344 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N MET C 346 " --> pdb=" O SER C 403 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N SER C 405 " --> pdb=" O MET C 346 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N ALA C 348 " --> pdb=" O SER C 405 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 295 through 297 Processing sheet with id= U, first strand: chain 'D' and resid 50 through 54 removed outlier: 6.807A pdb=" N ILE D 59 " --> pdb=" O SER D 51 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N VAL D 53 " --> pdb=" O LEU D 57 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LEU D 57 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU D 88 " --> pdb=" O VAL D 95 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLN D 97 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N VAL D 86 " --> pdb=" O GLN D 97 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 120 through 123 Processing sheet with id= W, first strand: chain 'D' and resid 131 through 133 removed outlier: 7.955A pdb=" N PHE D 132 " --> pdb=" O VAL D 257 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N LEU D 259 " --> pdb=" O PHE D 132 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE D 229 " --> pdb=" O CYS D 258 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N PHE D 260 " --> pdb=" O ILE D 229 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N PHE D 231 " --> pdb=" O PHE D 260 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ASN D 262 " --> pdb=" O PHE D 231 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALA D 233 " --> pdb=" O ASN D 262 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N SER D 347 " --> pdb=" O VAL D 293 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N VAL D 295 " --> pdb=" O SER D 347 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N THR D 349 " --> pdb=" O VAL D 295 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N LEU D 297 " --> pdb=" O THR D 349 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE D 351 " --> pdb=" O LEU D 297 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 50 through 54 removed outlier: 6.724A pdb=" N ILE E 59 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N VAL E 53 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU E 57 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU E 88 " --> pdb=" O VAL E 95 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N GLN E 97 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N VAL E 86 " --> pdb=" O GLN E 97 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 120 through 123 Processing sheet with id= Z, first strand: chain 'E' and resid 130 through 133 removed outlier: 3.642A pdb=" N ARG E 130 " --> pdb=" O VAL E 257 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE E 229 " --> pdb=" O CYS E 258 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N PHE E 260 " --> pdb=" O ILE E 229 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N PHE E 231 " --> pdb=" O PHE E 260 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ASN E 262 " --> pdb=" O PHE E 231 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ALA E 233 " --> pdb=" O ASN E 262 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N SER E 347 " --> pdb=" O VAL E 293 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N VAL E 295 " --> pdb=" O SER E 347 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N THR E 349 " --> pdb=" O VAL E 295 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N LEU E 297 " --> pdb=" O THR E 349 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 191 through 193 Processing sheet with id= AB, first strand: chain 'F' and resid 50 through 54 removed outlier: 6.651A pdb=" N ILE F 59 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N VAL F 53 " --> pdb=" O LEU F 57 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU F 57 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA F 94 " --> pdb=" O LEU F 60 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLN F 97 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL F 86 " --> pdb=" O GLN F 97 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 120 through 123 Processing sheet with id= AD, first strand: chain 'F' and resid 131 through 133 removed outlier: 8.181A pdb=" N PHE F 132 " --> pdb=" O VAL F 257 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU F 259 " --> pdb=" O PHE F 132 " (cutoff:3.500A) removed outlier: 8.751A pdb=" N CYS F 258 " --> pdb=" O PHE F 227 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE F 229 " --> pdb=" O CYS F 258 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N PHE F 260 " --> pdb=" O ILE F 229 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N PHE F 231 " --> pdb=" O PHE F 260 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ASN F 262 " --> pdb=" O PHE F 231 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ALA F 233 " --> pdb=" O ASN F 262 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N HIS F 292 " --> pdb=" O ALA F 228 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL F 230 " --> pdb=" O HIS F 292 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LEU F 294 " --> pdb=" O VAL F 230 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N ALA F 232 " --> pdb=" O LEU F 294 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE F 296 " --> pdb=" O ALA F 232 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N MET F 234 " --> pdb=" O ILE F 296 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N THR F 298 " --> pdb=" O MET F 234 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL F 236 " --> pdb=" O THR F 298 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N SER F 347 " --> pdb=" O VAL F 293 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N VAL F 295 " --> pdb=" O SER F 347 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N THR F 349 " --> pdb=" O VAL F 295 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N LEU F 297 " --> pdb=" O THR F 349 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain 'F' and resid 191 through 194 Processing sheet with id= AF, first strand: chain 'I' and resid 164 through 167 removed outlier: 4.057A pdb=" N VAL I 181 " --> pdb=" O ASN I 194 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'J' and resid 164 through 167 removed outlier: 3.506A pdb=" N VAL J 181 " --> pdb=" O ASN J 194 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'K' and resid 164 through 167 1585 hydrogen bonds defined for protein. 4494 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: 13.76 Time building geometry restraints manager: 14.90 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: 7012 1.32 - 1.44: 8198 1.44 - 1.57: 21194 1.57 - 1.69: 3 1.69 - 1.81: 358 Bond restraints: 36765 Sorted by residual: bond pdb=" C ASP B 290 " pdb=" N PHE B 291 " ideal model delta sigma weight residual 1.334 1.217 0.118 1.26e-02 6.30e+03 8.73e+01 bond pdb=" N PRO F 391 " pdb=" CA PRO F 391 " ideal model delta sigma weight residual 1.469 1.531 -0.063 7.40e-03 1.83e+04 7.20e+01 bond pdb=" C TYR E 504 " pdb=" N PRO E 505 " ideal model delta sigma weight residual 1.337 1.406 -0.070 1.06e-02 8.90e+03 4.34e+01 bond pdb=" N PRO E 352 " pdb=" CA PRO E 352 " ideal model delta sigma weight residual 1.466 1.538 -0.071 1.24e-02 6.50e+03 3.32e+01 bond pdb=" N PRO F 396 " pdb=" CA PRO F 396 " ideal model delta sigma weight residual 1.469 1.540 -0.071 1.25e-02 6.40e+03 3.19e+01 ... (remaining 36760 not shown) Histogram of bond angle deviations from ideal: 100.82 - 107.49: 1381 107.49 - 114.17: 20680 114.17 - 120.85: 17489 120.85 - 127.52: 9858 127.52 - 134.20: 268 Bond angle restraints: 49676 Sorted by residual: angle pdb=" C ILE F 189 " pdb=" N PRO F 190 " pdb=" CA PRO F 190 " ideal model delta sigma weight residual 119.85 129.34 -9.49 1.01e+00 9.80e-01 8.83e+01 angle pdb=" C ARG A 215 " pdb=" N PRO A 216 " pdb=" CA PRO A 216 " ideal model delta sigma weight residual 119.76 129.31 -9.55 1.03e+00 9.43e-01 8.61e+01 angle pdb=" C SER B 411 " pdb=" N PRO B 412 " pdb=" CA PRO B 412 " ideal model delta sigma weight residual 120.38 129.06 -8.68 1.03e+00 9.43e-01 7.11e+01 angle pdb=" C LEU F 395 " pdb=" N PRO F 396 " pdb=" CA PRO F 396 " ideal model delta sigma weight residual 120.04 128.53 -8.49 1.08e+00 8.57e-01 6.18e+01 angle pdb=" C ASN A 397 " pdb=" N PRO A 398 " pdb=" CA PRO A 398 " ideal model delta sigma weight residual 119.82 127.35 -7.53 9.80e-01 1.04e+00 5.90e+01 ... (remaining 49671 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.68: 22034 23.68 - 47.35: 399 47.35 - 71.03: 111 71.03 - 94.71: 34 94.71 - 118.38: 2 Dihedral angle restraints: 22580 sinusoidal: 9309 harmonic: 13271 Sorted by residual: dihedral pdb=" C5' ADP A 701 " pdb=" O5' ADP A 701 " pdb=" PA ADP A 701 " pdb=" O2A ADP A 701 " ideal model delta sinusoidal sigma weight residual -60.00 -178.38 118.38 1 2.00e+01 2.50e-03 3.54e+01 dihedral pdb=" O2A ADP A 701 " pdb=" O3A ADP A 701 " pdb=" PA ADP A 701 " pdb=" PB ADP A 701 " ideal model delta sinusoidal sigma weight residual -60.00 38.49 -98.49 1 2.00e+01 2.50e-03 2.75e+01 dihedral pdb=" CA VAL A 392 " pdb=" C VAL A 392 " pdb=" N LYS A 393 " pdb=" CA LYS A 393 " ideal model delta harmonic sigma weight residual 180.00 158.57 21.43 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 22577 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 3842 0.053 - 0.107: 1180 0.107 - 0.160: 459 0.160 - 0.214: 71 0.214 - 0.267: 23 Chirality restraints: 5575 Sorted by residual: chirality pdb=" CA VAL F 379 " pdb=" N VAL F 379 " pdb=" C VAL F 379 " pdb=" CB VAL F 379 " both_signs ideal model delta sigma weight residual False 2.44 2.71 -0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CA VAL B 404 " pdb=" N VAL B 404 " pdb=" C VAL B 404 " pdb=" CB VAL B 404 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CA VAL B 448 " pdb=" N VAL B 448 " pdb=" C VAL B 448 " pdb=" CB VAL B 448 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 5572 not shown) Planarity restraints: 6440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO F 390 " -0.019 2.00e-02 2.50e+03 3.77e-02 1.42e+01 pdb=" C PRO F 390 " 0.065 2.00e-02 2.50e+03 pdb=" O PRO F 390 " -0.025 2.00e-02 2.50e+03 pdb=" N PRO F 391 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 584 " 0.016 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C MET A 584 " -0.058 2.00e-02 2.50e+03 pdb=" O MET A 584 " 0.022 2.00e-02 2.50e+03 pdb=" N LYS A 585 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE F 189 " -0.016 2.00e-02 2.50e+03 3.23e-02 1.04e+01 pdb=" C ILE F 189 " 0.056 2.00e-02 2.50e+03 pdb=" O ILE F 189 " -0.021 2.00e-02 2.50e+03 pdb=" N PRO F 190 " -0.018 2.00e-02 2.50e+03 ... (remaining 6437 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 5126 2.76 - 3.29: 36923 3.29 - 3.83: 60317 3.83 - 4.36: 74451 4.36 - 4.90: 124416 Nonbonded interactions: 301233 Sorted by model distance: nonbonded pdb=" OH TYR Q 126 " pdb=" OG1 THR Q 169 " model vdw 2.221 2.440 nonbonded pdb=" OD1 ASP D 266 " pdb=" NZ LYS S 9 " model vdw 2.304 2.520 nonbonded pdb=" OD2 ASP F 360 " pdb=" NZ LYS H 20 " model vdw 2.362 2.520 nonbonded pdb=" NE ARG J 135 " pdb=" O ALA J 171 " model vdw 2.364 2.520 nonbonded pdb=" OG SER C 128 " pdb=" OD1 ASP C 130 " model vdw 2.370 2.440 ... (remaining 301228 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 17 through 616) selection = chain 'B' 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: 1.900 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: 0.020 Extract box with map and model: 10.330 Check model and map are aligned: 0.480 Set scattering table: 0.280 Process input model: 94.050 Find NCS groups from input model: 2.220 Set up NCS constraints: 0.320 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 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 0.118 36765 Z= 0.649 Angle : 0.894 10.658 49676 Z= 0.631 Chirality : 0.062 0.267 5575 Planarity : 0.004 0.038 6440 Dihedral : 10.798 118.383 14048 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.62 % Favored : 97.18 % Rotamer: Outliers : 0.05 % Allowed : 0.56 % Favored : 99.39 % 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: 0.25 (0.12), residues: 4538 helix: 0.59 (0.10), residues: 2089 sheet: -0.21 (0.20), residues: 616 loop : -0.01 (0.15), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Q 55 HIS 0.002 0.000 HIS F 199 PHE 0.011 0.000 PHE A 252 TYR 0.016 0.000 TYR D 389 ARG 0.004 0.000 ARG D 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 1506 residues out of total 3955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1504 time to evaluate : 4.114 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 60 ASP cc_start: 0.7728 (p0) cc_final: 0.7298 (p0) REVERT: A 73 VAL cc_start: 0.9189 (t) cc_final: 0.8888 (m) REVERT: A 84 LYS cc_start: 0.8491 (mttt) cc_final: 0.8180 (mtmt) REVERT: A 95 MET cc_start: 0.8765 (mmm) cc_final: 0.8099 (mmm) REVERT: A 173 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.8235 (ptp90) REVERT: A 254 CYS cc_start: 0.8512 (m) cc_final: 0.7913 (m) REVERT: A 284 MET cc_start: 0.8484 (mmm) cc_final: 0.8210 (mpp) REVERT: A 290 ASP cc_start: 0.8252 (t70) cc_final: 0.7683 (t0) REVERT: A 302 VAL cc_start: 0.9046 (t) cc_final: 0.8582 (p) REVERT: A 360 GLU cc_start: 0.8052 (tt0) cc_final: 0.7750 (mt-10) REVERT: A 399 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7399 (mp0) REVERT: A 436 ASP cc_start: 0.7120 (t0) cc_final: 0.6874 (t0) REVERT: A 510 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7439 (mm-30) REVERT: B 51 VAL cc_start: 0.8019 (t) cc_final: 0.7245 (t) REVERT: B 57 LEU cc_start: 0.8188 (mt) cc_final: 0.7938 (mt) REVERT: B 61 MET cc_start: 0.8012 (mtp) cc_final: 0.7782 (mtp) REVERT: B 65 GLN cc_start: 0.8260 (tp40) cc_final: 0.8050 (tt0) REVERT: B 74 SER cc_start: 0.8371 (m) cc_final: 0.7222 (p) REVERT: B 77 ASP cc_start: 0.7661 (m-30) cc_final: 0.6989 (m-30) REVERT: B 84 LYS cc_start: 0.7701 (mmtt) cc_final: 0.7344 (mmtt) REVERT: B 115 SER cc_start: 0.8512 (t) cc_final: 0.8298 (p) REVERT: B 116 ILE cc_start: 0.8641 (pt) cc_final: 0.8359 (pt) REVERT: B 147 ILE cc_start: 0.8792 (pt) cc_final: 0.8580 (tt) REVERT: B 148 THR cc_start: 0.8204 (t) cc_final: 0.7618 (t) REVERT: B 151 ASP cc_start: 0.6340 (m-30) cc_final: 0.6108 (m-30) REVERT: B 257 THR cc_start: 0.8639 (p) cc_final: 0.8143 (t) REVERT: B 266 TYR cc_start: 0.7617 (m-80) cc_final: 0.7171 (m-80) REVERT: B 284 MET cc_start: 0.8965 (tpt) cc_final: 0.8709 (mmm) REVERT: B 296 MET cc_start: 0.7245 (ptm) cc_final: 0.6741 (ptm) REVERT: B 306 MET cc_start: 0.8253 (ptm) cc_final: 0.8012 (ptp) REVERT: B 308 ARG cc_start: 0.7138 (ptp-110) cc_final: 0.6660 (ptt180) REVERT: B 454 TYR cc_start: 0.8680 (p90) cc_final: 0.8437 (p90) REVERT: B 485 GLU cc_start: 0.8154 (tp30) cc_final: 0.7530 (tp30) REVERT: B 486 GLU cc_start: 0.8668 (tm-30) cc_final: 0.8312 (tm-30) REVERT: B 488 ASP cc_start: 0.8707 (m-30) cc_final: 0.8051 (t0) REVERT: C 55 ILE cc_start: 0.7823 (mt) cc_final: 0.7439 (pt) REVERT: C 82 THR cc_start: 0.7994 (m) cc_final: 0.7580 (p) REVERT: C 84 LYS cc_start: 0.7871 (mmtt) cc_final: 0.7301 (pttm) REVERT: C 140 ASN cc_start: 0.8633 (m-40) cc_final: 0.8062 (m110) REVERT: C 248 ILE cc_start: 0.8512 (mp) cc_final: 0.8084 (pt) REVERT: C 262 SER cc_start: 0.8810 (m) cc_final: 0.8598 (p) REVERT: C 299 ASP cc_start: 0.7376 (m-30) cc_final: 0.6631 (p0) REVERT: C 327 ILE cc_start: 0.8871 (tp) cc_final: 0.8531 (tp) REVERT: C 345 SER cc_start: 0.9012 (t) cc_final: 0.8729 (m) REVERT: C 371 ASP cc_start: 0.8324 (m-30) cc_final: 0.7995 (m-30) REVERT: C 447 SER cc_start: 0.7927 (m) cc_final: 0.7533 (p) REVERT: C 449 ASN cc_start: 0.8687 (t0) cc_final: 0.8394 (t0) REVERT: C 466 ASP cc_start: 0.8964 (t70) cc_final: 0.8746 (t0) REVERT: C 484 GLN cc_start: 0.8464 (tp40) cc_final: 0.7358 (tp-100) REVERT: C 487 GLU cc_start: 0.9135 (tp30) cc_final: 0.8666 (tm-30) REVERT: C 522 GLN cc_start: 0.8273 (tt0) cc_final: 0.6864 (tt0) REVERT: C 574 MET cc_start: 0.7603 (ptp) cc_final: 0.7193 (mtm) REVERT: D 40 LEU cc_start: 0.8185 (mt) cc_final: 0.7978 (mt) REVERT: D 87 LEU cc_start: 0.8489 (mt) cc_final: 0.8232 (mt) REVERT: D 97 GLN cc_start: 0.7753 (tt0) cc_final: 0.7546 (pt0) REVERT: D 123 VAL cc_start: 0.9129 (m) cc_final: 0.8801 (p) REVERT: D 268 THR cc_start: 0.8132 (p) cc_final: 0.7831 (t) REVERT: D 328 TYR cc_start: 0.8810 (t80) cc_final: 0.8367 (t80) REVERT: D 360 ASP cc_start: 0.8298 (t0) cc_final: 0.8022 (t0) REVERT: D 406 ILE cc_start: 0.8758 (pt) cc_final: 0.8303 (pt) REVERT: D 410 MET cc_start: 0.8277 (mmm) cc_final: 0.7984 (mpp) REVERT: D 445 THR cc_start: 0.8416 (t) cc_final: 0.8198 (p) REVERT: E 49 THR cc_start: 0.8902 (p) cc_final: 0.8688 (p) REVERT: E 158 ILE cc_start: 0.8623 (mt) cc_final: 0.8158 (tp) REVERT: E 159 ASN cc_start: 0.6785 (t0) cc_final: 0.6241 (t0) REVERT: E 161 GLN cc_start: 0.8354 (tp40) cc_final: 0.7994 (tm-30) REVERT: E 187 GLN cc_start: 0.8618 (tt0) cc_final: 0.8366 (tt0) REVERT: E 355 THR cc_start: 0.8654 (m) cc_final: 0.8273 (p) REVERT: E 356 MET cc_start: 0.8424 (mtm) cc_final: 0.8128 (mtm) REVERT: E 382 GLN cc_start: 0.8473 (mm-40) cc_final: 0.7914 (mm-40) REVERT: E 491 MET cc_start: 0.8663 (mtp) cc_final: 0.8309 (mtp) REVERT: F 63 VAL cc_start: 0.9474 (t) cc_final: 0.9211 (p) REVERT: F 164 ILE cc_start: 0.7865 (mm) cc_final: 0.7462 (mm) REVERT: F 180 MET cc_start: 0.8797 (mmm) cc_final: 0.8063 (mpp) REVERT: F 238 MET cc_start: 0.7977 (tpt) cc_final: 0.7739 (tpp) REVERT: F 298 THR cc_start: 0.8233 (m) cc_final: 0.7615 (p) REVERT: F 299 ASP cc_start: 0.8236 (m-30) cc_final: 0.7723 (m-30) REVERT: F 309 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7842 (tt0) REVERT: F 315 GLU cc_start: 0.8518 (mt-10) cc_final: 0.7836 (mt-10) REVERT: F 317 VAL cc_start: 0.9099 (t) cc_final: 0.8824 (p) REVERT: F 342 GLU cc_start: 0.8508 (tt0) cc_final: 0.7936 (tp30) REVERT: F 351 ILE cc_start: 0.8878 (mt) cc_final: 0.8637 (mm) REVERT: F 355 THR cc_start: 0.8565 (m) cc_final: 0.8348 (p) REVERT: F 441 GLU cc_start: 0.8731 (tt0) cc_final: 0.8472 (tm-30) REVERT: H 16 GLN cc_start: 0.7761 (tt0) cc_final: 0.7537 (tt0) REVERT: H 46 GLN cc_start: 0.7684 (mt0) cc_final: 0.7465 (mt0) REVERT: H 154 SER cc_start: 0.6618 (m) cc_final: 0.6253 (t) REVERT: H 173 GLU cc_start: 0.8383 (tt0) cc_final: 0.8054 (tt0) REVERT: H 192 ASP cc_start: 0.8751 (m-30) cc_final: 0.8509 (t70) REVERT: H 198 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7697 (mm-30) REVERT: H 210 LYS cc_start: 0.9243 (tttm) cc_final: 0.8663 (ttmm) REVERT: I 78 GLN cc_start: 0.9036 (mm-40) cc_final: 0.8736 (mm110) REVERT: I 88 ASP cc_start: 0.8735 (t70) cc_final: 0.8355 (t0) REVERT: I 104 LYS cc_start: 0.8775 (mttt) cc_final: 0.8468 (tppt) REVERT: I 121 LEU cc_start: 0.8888 (tp) cc_final: 0.8590 (mt) REVERT: I 129 GLU cc_start: 0.8323 (mm-30) cc_final: 0.8031 (mm-30) REVERT: I 132 MET cc_start: 0.9278 (mmt) cc_final: 0.8742 (mmt) REVERT: I 167 ILE cc_start: 0.7979 (mt) cc_final: 0.7778 (mt) REVERT: I 183 ILE cc_start: 0.8888 (mt) cc_final: 0.8661 (mm) REVERT: I 221 ASN cc_start: 0.8847 (m-40) cc_final: 0.8325 (t0) REVERT: J 97 GLU cc_start: 0.8558 (tp30) cc_final: 0.8214 (tm-30) REVERT: J 100 GLN cc_start: 0.9184 (mm-40) cc_final: 0.8807 (mp10) REVERT: J 108 ASP cc_start: 0.8350 (t0) cc_final: 0.7693 (m-30) REVERT: J 109 THR cc_start: 0.9176 (m) cc_final: 0.8785 (p) REVERT: J 110 THR cc_start: 0.9181 (m) cc_final: 0.8927 (p) REVERT: J 120 VAL cc_start: 0.8915 (t) cc_final: 0.8714 (p) REVERT: J 121 LEU cc_start: 0.8350 (tp) cc_final: 0.8089 (tp) REVERT: J 149 GLN cc_start: 0.8679 (mt0) cc_final: 0.8399 (tm-30) REVERT: J 154 MET cc_start: 0.8276 (mtp) cc_final: 0.7906 (ttm) REVERT: J 168 ASP cc_start: 0.8346 (t0) cc_final: 0.8028 (t0) REVERT: J 172 TYR cc_start: 0.8163 (m-80) cc_final: 0.7910 (m-80) REVERT: J 182 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7853 (mt-10) REVERT: J 184 TYR cc_start: 0.7916 (m-80) cc_final: 0.7682 (m-80) REVERT: J 191 LYS cc_start: 0.7675 (pttt) cc_final: 0.7390 (ptmt) REVERT: J 198 SER cc_start: 0.9126 (m) cc_final: 0.8907 (p) REVERT: J 208 MET cc_start: 0.8487 (mmt) cc_final: 0.8127 (mmp) REVERT: J 223 LYS cc_start: 0.8595 (mmtt) cc_final: 0.8277 (mptt) REVERT: K 93 ASP cc_start: 0.8997 (m-30) cc_final: 0.8794 (t0) REVERT: K 96 ASN cc_start: 0.9331 (m-40) cc_final: 0.9036 (m-40) REVERT: K 103 SER cc_start: 0.9491 (t) cc_final: 0.9256 (p) REVERT: K 104 LYS cc_start: 0.9472 (mttt) cc_final: 0.9213 (tppt) REVERT: K 129 GLU cc_start: 0.8294 (mm-30) cc_final: 0.7733 (mm-30) REVERT: K 190 ILE cc_start: 0.8646 (mt) cc_final: 0.8388 (mt) REVERT: K 210 GLU cc_start: 0.8482 (mt-10) cc_final: 0.8160 (tt0) REVERT: K 226 ASP cc_start: 0.6299 (t70) cc_final: 0.6020 (m-30) REVERT: M 78 ARG cc_start: 0.8415 (mtt180) cc_final: 0.8206 (ttp-110) REVERT: M 85 GLN cc_start: 0.8624 (tt0) cc_final: 0.8279 (tm-30) REVERT: M 91 ASN cc_start: 0.8413 (m-40) cc_final: 0.8036 (m-40) REVERT: M 97 THR cc_start: 0.8542 (m) cc_final: 0.8187 (t) REVERT: M 98 GLN cc_start: 0.7764 (tt0) cc_final: 0.7242 (tt0) REVERT: M 105 ASP cc_start: 0.7821 (t0) cc_final: 0.7617 (p0) REVERT: N 78 ARG cc_start: 0.8015 (mtm-85) cc_final: 0.7662 (ptp-110) REVERT: N 91 ASN cc_start: 0.7713 (m-40) cc_final: 0.7365 (m-40) REVERT: N 96 LEU cc_start: 0.8029 (tp) cc_final: 0.7634 (tt) REVERT: O 86 SER cc_start: 0.8648 (t) cc_final: 0.8319 (m) REVERT: O 97 THR cc_start: 0.8940 (m) cc_final: 0.8716 (p) REVERT: Q 33 MET cc_start: 0.7617 (mmm) cc_final: 0.7133 (tpp) REVERT: Q 48 ASP cc_start: 0.8307 (t70) cc_final: 0.7908 (t0) REVERT: Q 74 CYS cc_start: 0.8572 (p) cc_final: 0.8158 (p) REVERT: Q 113 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8367 (tp30) REVERT: Q 166 TYR cc_start: 0.8265 (m-80) cc_final: 0.8046 (m-80) REVERT: Q 170 GLU cc_start: 0.7416 (tt0) cc_final: 0.6974 (mp0) REVERT: Q 171 ASP cc_start: 0.8462 (m-30) cc_final: 0.7934 (t0) REVERT: Q 180 LYS cc_start: 0.8415 (tttt) cc_final: 0.8212 (tppt) REVERT: Q 199 LEU cc_start: 0.8588 (tp) cc_final: 0.8382 (tp) REVERT: Q 203 TYR cc_start: 0.7116 (t80) cc_final: 0.6812 (t80) REVERT: Q 221 ASP cc_start: 0.7727 (m-30) cc_final: 0.7354 (m-30) REVERT: R 60 TYR cc_start: 0.6556 (m-80) cc_final: 0.6115 (m-80) REVERT: R 77 ASP cc_start: 0.8249 (t0) cc_final: 0.8034 (t70) REVERT: R 79 ASP cc_start: 0.8498 (m-30) cc_final: 0.7826 (t0) REVERT: R 103 MET cc_start: 0.5664 (ttm) cc_final: 0.5161 (mtt) REVERT: R 125 ASP cc_start: 0.8618 (m-30) cc_final: 0.8390 (m-30) REVERT: R 139 TYR cc_start: 0.8500 (t80) cc_final: 0.8006 (t80) REVERT: R 165 GLN cc_start: 0.8113 (mm-40) cc_final: 0.7822 (mt0) REVERT: R 172 ASN cc_start: 0.8235 (t0) cc_final: 0.7902 (t0) REVERT: R 200 PHE cc_start: 0.7717 (t80) cc_final: 0.7346 (t80) REVERT: S 37 ASP cc_start: 0.6952 (t0) cc_final: 0.5454 (t70) REVERT: S 55 TRP cc_start: 0.8332 (m100) cc_final: 0.8053 (m100) REVERT: S 61 ARG cc_start: 0.7932 (mtm-85) cc_final: 0.7653 (mtm-85) REVERT: S 106 ASP cc_start: 0.9289 (m-30) cc_final: 0.8955 (t70) REVERT: S 115 MET cc_start: 0.8968 (mtm) cc_final: 0.8641 (mtm) outliers start: 2 outliers final: 0 residues processed: 1505 average time/residue: 0.5284 time to fit residues: 1253.8815 Evaluate side-chains 842 residues out of total 3955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 841 time to evaluate : 4.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 380 optimal weight: 7.9990 chunk 341 optimal weight: 1.9990 chunk 189 optimal weight: 10.0000 chunk 116 optimal weight: 0.9990 chunk 230 optimal weight: 2.9990 chunk 182 optimal weight: 0.9990 chunk 353 optimal weight: 0.9980 chunk 136 optimal weight: 0.9990 chunk 214 optimal weight: 0.9990 chunk 263 optimal weight: 0.9990 chunk 409 optimal weight: 0.6980 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 468 HIS B 573 HIS C 609 GLN ** E 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 181 ASN ** F 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 66 GLN ** J 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 80 GLN Q 34 GLN Q 134 ASN R 50 GLN R 118 HIS ** S 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 36765 Z= 0.219 Angle : 0.618 11.143 49676 Z= 0.313 Chirality : 0.044 0.212 5575 Planarity : 0.004 0.047 6440 Dihedral : 4.818 110.278 5022 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.92 % Favored : 98.06 % Rotamer: Outliers : 2.43 % Allowed : 11.13 % Favored : 86.44 % 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 (0.12), residues: 4538 helix: 1.67 (0.11), residues: 2071 sheet: -0.17 (0.20), residues: 638 loop : 0.06 (0.15), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 450 HIS 0.009 0.001 HIS F 363 PHE 0.033 0.002 PHE C 612 TYR 0.024 0.002 TYR H 186 ARG 0.005 0.001 ARG M 79 *********************** 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 1017 residues out of total 3955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 921 time to evaluate : 4.320 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 60 ASP cc_start: 0.7885 (p0) cc_final: 0.7362 (p0) REVERT: A 73 VAL cc_start: 0.9183 (t) cc_final: 0.8886 (m) REVERT: A 84 LYS cc_start: 0.8403 (mttt) cc_final: 0.8146 (mmmt) REVERT: A 95 MET cc_start: 0.8842 (mmm) cc_final: 0.8385 (mmm) REVERT: A 131 ILE cc_start: 0.8722 (mt) cc_final: 0.8322 (pt) REVERT: A 173 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.8166 (ptp90) REVERT: A 235 ASP cc_start: 0.8539 (t70) cc_final: 0.8286 (t0) REVERT: A 254 CYS cc_start: 0.8531 (m) cc_final: 0.8069 (m) REVERT: A 284 MET cc_start: 0.8261 (mmm) cc_final: 0.8017 (mmm) REVERT: A 290 ASP cc_start: 0.8412 (t70) cc_final: 0.7823 (t0) REVERT: A 296 MET cc_start: 0.7665 (ttm) cc_final: 0.7210 (ttp) REVERT: A 360 GLU cc_start: 0.8021 (tt0) cc_final: 0.7777 (mt-10) REVERT: A 487 GLU cc_start: 0.8217 (tm-30) cc_final: 0.7884 (tm-30) REVERT: A 523 ASN cc_start: 0.8121 (t0) cc_final: 0.7809 (t0) REVERT: B 50 LEU cc_start: 0.8575 (mt) cc_final: 0.8333 (tp) REVERT: B 74 SER cc_start: 0.8380 (m) cc_final: 0.7420 (p) REVERT: B 77 ASP cc_start: 0.7647 (m-30) cc_final: 0.6980 (m-30) REVERT: B 84 LYS cc_start: 0.7867 (mmtt) cc_final: 0.7426 (mmtt) REVERT: B 115 SER cc_start: 0.8632 (t) cc_final: 0.8327 (p) REVERT: B 116 ILE cc_start: 0.8768 (pt) cc_final: 0.8302 (pt) REVERT: B 142 ARG cc_start: 0.8756 (mmm160) cc_final: 0.8179 (tpp80) REVERT: B 148 THR cc_start: 0.8381 (t) cc_final: 0.7738 (t) REVERT: B 151 ASP cc_start: 0.6290 (m-30) cc_final: 0.6049 (m-30) REVERT: B 270 ASP cc_start: 0.7428 (OUTLIER) cc_final: 0.7064 (m-30) REVERT: B 272 ILE cc_start: 0.8630 (mm) cc_final: 0.8333 (mt) REVERT: B 284 MET cc_start: 0.8955 (tpt) cc_final: 0.8621 (tpt) REVERT: B 299 ASP cc_start: 0.7091 (m-30) cc_final: 0.6853 (m-30) REVERT: B 308 ARG cc_start: 0.6659 (ptp-110) cc_final: 0.6182 (ptt180) REVERT: B 349 ASP cc_start: 0.7099 (p0) cc_final: 0.6681 (p0) REVERT: B 423 SER cc_start: 0.8849 (t) cc_final: 0.8614 (p) REVERT: B 485 GLU cc_start: 0.8199 (tp30) cc_final: 0.7423 (tp30) REVERT: B 488 ASP cc_start: 0.8524 (m-30) cc_final: 0.7734 (t0) REVERT: C 55 ILE cc_start: 0.8230 (mt) cc_final: 0.7905 (pt) REVERT: C 82 THR cc_start: 0.8457 (m) cc_final: 0.8104 (p) REVERT: C 84 LYS cc_start: 0.8405 (mmtt) cc_final: 0.7472 (pttm) REVERT: C 140 ASN cc_start: 0.8403 (m-40) cc_final: 0.8017 (m110) REVERT: C 155 ILE cc_start: 0.8211 (mm) cc_final: 0.7722 (mm) REVERT: C 299 ASP cc_start: 0.7669 (m-30) cc_final: 0.6924 (p0) REVERT: C 447 SER cc_start: 0.7958 (m) cc_final: 0.7541 (p) REVERT: C 466 ASP cc_start: 0.8846 (t70) cc_final: 0.8606 (t0) REVERT: C 484 GLN cc_start: 0.8493 (tp40) cc_final: 0.7165 (tp-100) REVERT: C 487 GLU cc_start: 0.9050 (tp30) cc_final: 0.8690 (tm-30) REVERT: C 520 LEU cc_start: 0.8477 (mp) cc_final: 0.8207 (tt) REVERT: C 577 ILE cc_start: 0.7774 (OUTLIER) cc_final: 0.7570 (tp) REVERT: C 584 MET cc_start: 0.6312 (mtm) cc_final: 0.6034 (mtm) REVERT: C 604 LEU cc_start: 0.8702 (mp) cc_final: 0.8421 (tt) REVERT: C 606 GLU cc_start: 0.8733 (tt0) cc_final: 0.8026 (tp30) REVERT: D 97 GLN cc_start: 0.8010 (tt0) cc_final: 0.7689 (pt0) REVERT: D 328 TYR cc_start: 0.8820 (t80) cc_final: 0.7830 (t80) REVERT: D 358 ASN cc_start: 0.8928 (t0) cc_final: 0.8709 (t0) REVERT: D 360 ASP cc_start: 0.8253 (t0) cc_final: 0.8040 (t0) REVERT: D 406 ILE cc_start: 0.8760 (pt) cc_final: 0.8307 (pt) REVERT: D 410 MET cc_start: 0.8307 (mmm) cc_final: 0.7844 (mtm) REVERT: D 471 ARG cc_start: 0.7985 (mtt180) cc_final: 0.7748 (mtt180) REVERT: D 497 GLN cc_start: 0.8520 (pm20) cc_final: 0.8212 (pp30) REVERT: E 158 ILE cc_start: 0.8731 (mt) cc_final: 0.8307 (tp) REVERT: E 161 GLN cc_start: 0.8366 (tp40) cc_final: 0.8017 (tm-30) REVERT: E 261 LEU cc_start: 0.8803 (mt) cc_final: 0.8559 (mt) REVERT: E 270 GLU cc_start: 0.8195 (tt0) cc_final: 0.7293 (tm-30) REVERT: E 355 THR cc_start: 0.8697 (m) cc_final: 0.8186 (p) REVERT: E 382 GLN cc_start: 0.8619 (mm-40) cc_final: 0.8013 (tp40) REVERT: E 410 MET cc_start: 0.8016 (mpp) cc_final: 0.6801 (mtp) REVERT: E 491 MET cc_start: 0.8461 (mtp) cc_final: 0.8251 (mtp) REVERT: F 164 ILE cc_start: 0.7848 (mm) cc_final: 0.7435 (mm) REVERT: F 214 LYS cc_start: 0.9152 (pttt) cc_final: 0.8667 (tppt) REVERT: F 238 MET cc_start: 0.7936 (tpt) cc_final: 0.7243 (ptp) REVERT: F 298 THR cc_start: 0.8301 (m) cc_final: 0.7824 (p) REVERT: F 299 ASP cc_start: 0.8299 (m-30) cc_final: 0.7991 (m-30) REVERT: F 309 GLU cc_start: 0.8241 (tm-30) cc_final: 0.7794 (tt0) REVERT: F 317 VAL cc_start: 0.9121 (t) cc_final: 0.8916 (p) REVERT: F 341 VAL cc_start: 0.9506 (m) cc_final: 0.9283 (t) REVERT: F 342 GLU cc_start: 0.8774 (tt0) cc_final: 0.8133 (tp30) REVERT: F 351 ILE cc_start: 0.8861 (mt) cc_final: 0.8612 (mm) REVERT: F 355 THR cc_start: 0.8838 (m) cc_final: 0.8614 (p) REVERT: F 368 LEU cc_start: 0.8844 (mm) cc_final: 0.8572 (mt) REVERT: F 441 GLU cc_start: 0.8765 (tt0) cc_final: 0.8530 (tm-30) REVERT: H 154 SER cc_start: 0.6575 (m) cc_final: 0.6200 (t) REVERT: H 210 LYS cc_start: 0.9000 (tttm) cc_final: 0.8746 (ttmm) REVERT: I 78 GLN cc_start: 0.9025 (mm-40) cc_final: 0.8685 (mm110) REVERT: I 121 LEU cc_start: 0.8777 (tp) cc_final: 0.8563 (mt) REVERT: I 129 GLU cc_start: 0.8375 (mm-30) cc_final: 0.8061 (mm-30) REVERT: I 132 MET cc_start: 0.9288 (mmt) cc_final: 0.8672 (mmm) REVERT: I 183 ILE cc_start: 0.9071 (mt) cc_final: 0.8835 (mm) REVERT: I 221 ASN cc_start: 0.8854 (m-40) cc_final: 0.8396 (t0) REVERT: J 78 GLN cc_start: 0.7445 (tp40) cc_final: 0.7049 (tm-30) REVERT: J 154 MET cc_start: 0.8235 (mtp) cc_final: 0.7803 (ttm) REVERT: J 172 TYR cc_start: 0.8153 (m-80) cc_final: 0.7872 (m-80) REVERT: J 173 LEU cc_start: 0.8625 (mt) cc_final: 0.8226 (mt) REVERT: J 184 TYR cc_start: 0.8003 (m-80) cc_final: 0.7660 (m-80) REVERT: J 198 SER cc_start: 0.9065 (m) cc_final: 0.8824 (p) REVERT: J 208 MET cc_start: 0.8575 (mmt) cc_final: 0.8118 (mmp) REVERT: J 223 LYS cc_start: 0.8608 (mmtt) cc_final: 0.8252 (mptt) REVERT: K 93 ASP cc_start: 0.8995 (m-30) cc_final: 0.8751 (t0) REVERT: K 96 ASN cc_start: 0.9337 (m-40) cc_final: 0.9040 (m-40) REVERT: K 103 SER cc_start: 0.9371 (t) cc_final: 0.9110 (p) REVERT: K 114 VAL cc_start: 0.9180 (t) cc_final: 0.8540 (p) REVERT: K 129 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8060 (mm-30) REVERT: K 132 MET cc_start: 0.9091 (mtt) cc_final: 0.8658 (mpp) REVERT: K 141 PHE cc_start: 0.7912 (t80) cc_final: 0.7528 (t80) REVERT: K 226 ASP cc_start: 0.6380 (t70) cc_final: 0.6112 (m-30) REVERT: M 78 ARG cc_start: 0.8539 (mtt180) cc_final: 0.8260 (ttp-110) REVERT: M 85 GLN cc_start: 0.8631 (tt0) cc_final: 0.8191 (tm-30) REVERT: M 90 ARG cc_start: 0.7888 (mtm-85) cc_final: 0.7657 (mtm110) REVERT: M 91 ASN cc_start: 0.8470 (m-40) cc_final: 0.7976 (m-40) REVERT: M 93 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8388 (tm-30) REVERT: M 97 THR cc_start: 0.8331 (m) cc_final: 0.7976 (m) REVERT: M 105 ASP cc_start: 0.7632 (t0) cc_final: 0.7419 (p0) REVERT: M 107 ARG cc_start: 0.8003 (mmp80) cc_final: 0.7621 (mmm-85) REVERT: N 78 ARG cc_start: 0.7853 (mtm-85) cc_final: 0.7517 (mtm-85) REVERT: O 78 ARG cc_start: 0.8815 (mmm-85) cc_final: 0.8541 (tpt90) REVERT: O 97 THR cc_start: 0.9039 (m) cc_final: 0.8769 (p) REVERT: O 114 TYR cc_start: 0.8052 (t80) cc_final: 0.7820 (t80) REVERT: Q 48 ASP cc_start: 0.8537 (t70) cc_final: 0.8156 (t0) REVERT: Q 61 ARG cc_start: 0.8023 (mtm110) cc_final: 0.7086 (mtp85) REVERT: Q 65 ILE cc_start: 0.8557 (mt) cc_final: 0.8297 (mp) REVERT: Q 74 CYS cc_start: 0.8357 (p) cc_final: 0.8090 (p) REVERT: Q 101 PHE cc_start: 0.7030 (m-80) cc_final: 0.6730 (m-80) REVERT: Q 170 GLU cc_start: 0.7355 (tt0) cc_final: 0.6946 (mp0) REVERT: Q 171 ASP cc_start: 0.8373 (m-30) cc_final: 0.7949 (t0) REVERT: Q 201 LYS cc_start: 0.7847 (tttt) cc_final: 0.7551 (ptmt) REVERT: Q 203 TYR cc_start: 0.7128 (t80) cc_final: 0.6926 (t80) REVERT: Q 213 PHE cc_start: 0.8622 (m-10) cc_final: 0.8395 (m-80) REVERT: Q 221 ASP cc_start: 0.7479 (m-30) cc_final: 0.7216 (m-30) REVERT: R 33 MET cc_start: 0.7950 (mmm) cc_final: 0.7586 (mmm) REVERT: R 63 GLU cc_start: 0.8267 (mp0) cc_final: 0.7704 (mp0) REVERT: R 79 ASP cc_start: 0.8370 (m-30) cc_final: 0.7586 (t0) REVERT: R 125 ASP cc_start: 0.8686 (m-30) cc_final: 0.8438 (m-30) REVERT: R 200 PHE cc_start: 0.7589 (t80) cc_final: 0.7329 (t80) REVERT: S 37 ASP cc_start: 0.6920 (t0) cc_final: 0.6129 (t0) REVERT: S 48 ASP cc_start: 0.8013 (OUTLIER) cc_final: 0.7726 (t0) REVERT: S 51 ASP cc_start: 0.7955 (p0) cc_final: 0.7714 (p0) REVERT: S 106 ASP cc_start: 0.9395 (m-30) cc_final: 0.9075 (t70) REVERT: S 139 TYR cc_start: 0.8650 (t80) cc_final: 0.8427 (t80) outliers start: 96 outliers final: 59 residues processed: 979 average time/residue: 0.4610 time to fit residues: 747.5151 Evaluate side-chains 800 residues out of total 3955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 737 time to evaluate : 4.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 594 GLU Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 32 CYS Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 515 ILE Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 464 THR Chi-restraints excluded: chain D residue 498 SER Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain K residue 195 THR Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain N residue 97 THR Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain Q residue 15 SER Chi-restraints excluded: chain Q residue 142 ASN Chi-restraints excluded: chain Q residue 163 ILE Chi-restraints excluded: chain Q residue 198 HIS Chi-restraints excluded: chain Q residue 209 GLU Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 64 GLU Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain S residue 48 ASP Chi-restraints excluded: chain S residue 99 SER Chi-restraints excluded: chain S residue 130 LEU Chi-restraints excluded: chain S residue 156 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 227 optimal weight: 5.9990 chunk 127 optimal weight: 0.9990 chunk 340 optimal weight: 0.3980 chunk 278 optimal weight: 0.9980 chunk 112 optimal weight: 6.9990 chunk 410 optimal weight: 0.9990 chunk 443 optimal weight: 5.9990 chunk 365 optimal weight: 0.7980 chunk 406 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 329 optimal weight: 10.0000 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 GLN ** C 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 433 GLN ** E 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 66 GLN J 67 GLN J 149 GLN K 194 ASN ** N 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 135 GLN R 118 HIS ** S 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 198 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 36765 Z= 0.185 Angle : 0.564 9.117 49676 Z= 0.280 Chirality : 0.043 0.179 5575 Planarity : 0.004 0.054 6440 Dihedral : 4.629 112.767 5022 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.14 % Favored : 97.84 % Rotamer: Outliers : 2.73 % Allowed : 13.63 % Favored : 83.64 % 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: 1.23 (0.13), residues: 4538 helix: 1.85 (0.11), residues: 2069 sheet: -0.01 (0.21), residues: 618 loop : 0.01 (0.15), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Q 55 HIS 0.013 0.001 HIS F 363 PHE 0.020 0.001 PHE C 337 TYR 0.026 0.001 TYR S 112 ARG 0.019 0.000 ARG Q 61 *********************** 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 899 residues out of total 3955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 791 time to evaluate : 5.032 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 60 ASP cc_start: 0.8012 (p0) cc_final: 0.7608 (p0) REVERT: A 73 VAL cc_start: 0.9116 (t) cc_final: 0.8805 (m) REVERT: A 95 MET cc_start: 0.8903 (mmm) cc_final: 0.8580 (mmm) REVERT: A 131 ILE cc_start: 0.8776 (OUTLIER) cc_final: 0.8436 (pt) REVERT: A 235 ASP cc_start: 0.8497 (t70) cc_final: 0.8271 (t0) REVERT: A 254 CYS cc_start: 0.8537 (m) cc_final: 0.8094 (m) REVERT: A 279 GLU cc_start: 0.6242 (tp30) cc_final: 0.6027 (tp30) REVERT: A 290 ASP cc_start: 0.8455 (t70) cc_final: 0.7943 (t0) REVERT: A 296 MET cc_start: 0.7421 (ttm) cc_final: 0.7198 (ttp) REVERT: A 360 GLU cc_start: 0.8028 (tt0) cc_final: 0.7808 (mt-10) REVERT: A 485 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7803 (mp0) REVERT: A 487 GLU cc_start: 0.8247 (tm-30) cc_final: 0.7881 (tm-30) REVERT: A 523 ASN cc_start: 0.8127 (t0) cc_final: 0.7780 (t0) REVERT: B 70 THR cc_start: 0.8745 (p) cc_final: 0.8370 (p) REVERT: B 74 SER cc_start: 0.8207 (m) cc_final: 0.7544 (p) REVERT: B 77 ASP cc_start: 0.7909 (m-30) cc_final: 0.7162 (m-30) REVERT: B 84 LYS cc_start: 0.7822 (mmtt) cc_final: 0.7393 (mmtt) REVERT: B 115 SER cc_start: 0.8716 (t) cc_final: 0.8431 (p) REVERT: B 116 ILE cc_start: 0.8807 (pt) cc_final: 0.8602 (pt) REVERT: B 142 ARG cc_start: 0.8751 (mmm160) cc_final: 0.8220 (tpp80) REVERT: B 148 THR cc_start: 0.8315 (t) cc_final: 0.7825 (t) REVERT: B 284 MET cc_start: 0.8866 (tpt) cc_final: 0.8627 (tpt) REVERT: B 296 MET cc_start: 0.6944 (ptm) cc_final: 0.6708 (ptm) REVERT: B 308 ARG cc_start: 0.6667 (ptp-110) cc_final: 0.6169 (ptt180) REVERT: B 349 ASP cc_start: 0.7048 (p0) cc_final: 0.6421 (p0) REVERT: B 423 SER cc_start: 0.8909 (t) cc_final: 0.8662 (p) REVERT: B 485 GLU cc_start: 0.8134 (tp30) cc_final: 0.7315 (tp30) REVERT: B 486 GLU cc_start: 0.8815 (tm-30) cc_final: 0.8502 (tm-30) REVERT: B 488 ASP cc_start: 0.8450 (m-30) cc_final: 0.7667 (t0) REVERT: B 540 MET cc_start: 0.6969 (mtp) cc_final: 0.6719 (mtp) REVERT: B 579 TYR cc_start: 0.7422 (t80) cc_final: 0.7196 (t80) REVERT: C 39 MET cc_start: 0.7918 (ttp) cc_final: 0.7703 (ttm) REVERT: C 55 ILE cc_start: 0.8296 (mt) cc_final: 0.7533 (pt) REVERT: C 82 THR cc_start: 0.8632 (m) cc_final: 0.8323 (p) REVERT: C 84 LYS cc_start: 0.8369 (mmtt) cc_final: 0.7445 (pttm) REVERT: C 140 ASN cc_start: 0.8317 (m-40) cc_final: 0.7905 (m110) REVERT: C 155 ILE cc_start: 0.8301 (mm) cc_final: 0.7905 (mm) REVERT: C 299 ASP cc_start: 0.7582 (m-30) cc_final: 0.6904 (p0) REVERT: C 387 GLU cc_start: 0.7872 (tp30) cc_final: 0.7609 (tp30) REVERT: C 447 SER cc_start: 0.7838 (m) cc_final: 0.7567 (p) REVERT: C 466 ASP cc_start: 0.8809 (t70) cc_final: 0.8595 (t0) REVERT: C 520 LEU cc_start: 0.8512 (mp) cc_final: 0.8257 (tt) REVERT: C 577 ILE cc_start: 0.7859 (OUTLIER) cc_final: 0.7653 (tp) REVERT: C 584 MET cc_start: 0.6774 (mtm) cc_final: 0.6534 (mtm) REVERT: C 604 LEU cc_start: 0.8760 (mp) cc_final: 0.8559 (tt) REVERT: C 606 GLU cc_start: 0.8690 (tt0) cc_final: 0.7916 (tp30) REVERT: D 97 GLN cc_start: 0.8117 (tt0) cc_final: 0.7710 (pt0) REVERT: D 141 ARG cc_start: 0.7763 (ttm-80) cc_final: 0.6968 (ttm-80) REVERT: D 351 ILE cc_start: 0.8870 (mt) cc_final: 0.8651 (mm) REVERT: D 358 ASN cc_start: 0.8972 (t0) cc_final: 0.8650 (t0) REVERT: D 360 ASP cc_start: 0.8176 (t0) cc_final: 0.7885 (t0) REVERT: D 406 ILE cc_start: 0.8863 (pt) cc_final: 0.8423 (pt) REVERT: D 410 MET cc_start: 0.8235 (mmm) cc_final: 0.7950 (mtm) REVERT: D 497 GLN cc_start: 0.8568 (pm20) cc_final: 0.8295 (pp30) REVERT: E 70 GLU cc_start: 0.7520 (tt0) cc_final: 0.6896 (tt0) REVERT: E 161 GLN cc_start: 0.8357 (tp40) cc_final: 0.8032 (tm-30) REVERT: E 249 GLU cc_start: 0.8384 (mt-10) cc_final: 0.8161 (mt-10) REVERT: E 270 GLU cc_start: 0.8314 (tt0) cc_final: 0.7319 (tm-30) REVERT: E 355 THR cc_start: 0.8668 (m) cc_final: 0.7968 (p) REVERT: E 382 GLN cc_start: 0.8657 (mm-40) cc_final: 0.8117 (tp40) REVERT: F 164 ILE cc_start: 0.7839 (mm) cc_final: 0.7407 (mm) REVERT: F 214 LYS cc_start: 0.9146 (pttt) cc_final: 0.8676 (tppt) REVERT: F 234 MET cc_start: 0.8470 (mtm) cc_final: 0.8198 (mtm) REVERT: F 238 MET cc_start: 0.8012 (tpt) cc_final: 0.7709 (tpp) REVERT: F 309 GLU cc_start: 0.8238 (tm-30) cc_final: 0.7766 (tt0) REVERT: F 315 GLU cc_start: 0.8643 (mt-10) cc_final: 0.7891 (mm-30) REVERT: F 317 VAL cc_start: 0.9103 (t) cc_final: 0.8886 (p) REVERT: F 342 GLU cc_start: 0.8847 (tt0) cc_final: 0.8270 (tp30) REVERT: F 355 THR cc_start: 0.8841 (m) cc_final: 0.8633 (p) REVERT: F 368 LEU cc_start: 0.8848 (mm) cc_final: 0.8633 (mt) REVERT: F 441 GLU cc_start: 0.8731 (tt0) cc_final: 0.8511 (tm-30) REVERT: H 154 SER cc_start: 0.6664 (m) cc_final: 0.6248 (t) REVERT: H 206 GLN cc_start: 0.8437 (tm-30) cc_final: 0.8236 (tm-30) REVERT: H 210 LYS cc_start: 0.9059 (tttm) cc_final: 0.8682 (ttmm) REVERT: I 78 GLN cc_start: 0.9013 (mm-40) cc_final: 0.8699 (mm110) REVERT: I 97 GLU cc_start: 0.8776 (tp30) cc_final: 0.8556 (tt0) REVERT: I 129 GLU cc_start: 0.8423 (mm-30) cc_final: 0.8180 (mm-30) REVERT: I 132 MET cc_start: 0.9342 (mmt) cc_final: 0.9006 (mmt) REVERT: I 183 ILE cc_start: 0.9042 (mt) cc_final: 0.8763 (mm) REVERT: I 208 MET cc_start: 0.7960 (tpp) cc_final: 0.7753 (tpp) REVERT: I 221 ASN cc_start: 0.8844 (m-40) cc_final: 0.8340 (t0) REVERT: J 78 GLN cc_start: 0.7619 (tp40) cc_final: 0.7166 (tm-30) REVERT: J 97 GLU cc_start: 0.8539 (tt0) cc_final: 0.8233 (tm-30) REVERT: J 127 LEU cc_start: 0.7892 (mt) cc_final: 0.7667 (mt) REVERT: J 154 MET cc_start: 0.8438 (mtp) cc_final: 0.7814 (ttm) REVERT: J 173 LEU cc_start: 0.8690 (mt) cc_final: 0.8284 (mt) REVERT: J 184 TYR cc_start: 0.8046 (m-80) cc_final: 0.7844 (m-80) REVERT: J 198 SER cc_start: 0.9038 (m) cc_final: 0.8748 (p) REVERT: J 201 ASP cc_start: 0.8772 (t70) cc_final: 0.8192 (m-30) REVERT: J 206 GLN cc_start: 0.8710 (mt0) cc_final: 0.8383 (mt0) REVERT: J 208 MET cc_start: 0.8562 (mmt) cc_final: 0.8107 (mmp) REVERT: J 223 LYS cc_start: 0.8635 (mmtt) cc_final: 0.8290 (mptt) REVERT: K 93 ASP cc_start: 0.8989 (m-30) cc_final: 0.8754 (t0) REVERT: K 96 ASN cc_start: 0.9310 (m-40) cc_final: 0.9004 (m-40) REVERT: K 103 SER cc_start: 0.9411 (t) cc_final: 0.9150 (p) REVERT: K 128 LEU cc_start: 0.8372 (mt) cc_final: 0.7626 (mt) REVERT: K 129 GLU cc_start: 0.8304 (mm-30) cc_final: 0.7236 (mm-30) REVERT: K 132 MET cc_start: 0.9120 (mtt) cc_final: 0.8677 (mpp) REVERT: K 141 PHE cc_start: 0.8042 (t80) cc_final: 0.7806 (t80) REVERT: K 192 VAL cc_start: 0.8948 (t) cc_final: 0.8721 (p) REVERT: K 226 ASP cc_start: 0.6391 (t70) cc_final: 0.6136 (m-30) REVERT: M 78 ARG cc_start: 0.8497 (mtt180) cc_final: 0.8163 (ttp-110) REVERT: M 85 GLN cc_start: 0.8638 (tt0) cc_final: 0.8215 (tm-30) REVERT: M 90 ARG cc_start: 0.7899 (mtm-85) cc_final: 0.7490 (mtm110) REVERT: M 91 ASN cc_start: 0.8472 (m-40) cc_final: 0.8004 (m-40) REVERT: M 93 GLU cc_start: 0.8656 (tm-30) cc_final: 0.8403 (tm-30) REVERT: M 97 THR cc_start: 0.8380 (m) cc_final: 0.7983 (m) REVERT: N 78 ARG cc_start: 0.7856 (mtm-85) cc_final: 0.7561 (mtm-85) REVERT: N 96 LEU cc_start: 0.7522 (tt) cc_final: 0.6949 (tt) REVERT: O 78 ARG cc_start: 0.8835 (mmm-85) cc_final: 0.8567 (tpt90) REVERT: O 97 THR cc_start: 0.9180 (m) cc_final: 0.8928 (p) REVERT: O 107 ARG cc_start: 0.7985 (ptt180) cc_final: 0.7428 (tmm-80) REVERT: Q 37 ASP cc_start: 0.7648 (t0) cc_final: 0.6642 (t0) REVERT: Q 48 ASP cc_start: 0.8670 (t70) cc_final: 0.8268 (t0) REVERT: Q 65 ILE cc_start: 0.8585 (mt) cc_final: 0.8366 (mp) REVERT: Q 74 CYS cc_start: 0.8310 (p) cc_final: 0.8075 (p) REVERT: Q 101 PHE cc_start: 0.7080 (m-80) cc_final: 0.6757 (m-80) REVERT: Q 170 GLU cc_start: 0.7428 (tt0) cc_final: 0.7131 (mp0) REVERT: Q 201 LYS cc_start: 0.7788 (tttt) cc_final: 0.7503 (ptmt) REVERT: Q 221 ASP cc_start: 0.7584 (m-30) cc_final: 0.7307 (m-30) REVERT: R 33 MET cc_start: 0.8040 (mmm) cc_final: 0.7680 (mmm) REVERT: R 64 GLU cc_start: 0.9084 (OUTLIER) cc_final: 0.8867 (tp30) REVERT: R 77 ASP cc_start: 0.8724 (t0) cc_final: 0.8406 (t70) REVERT: R 79 ASP cc_start: 0.8387 (m-30) cc_final: 0.7580 (t0) REVERT: R 125 ASP cc_start: 0.8746 (m-30) cc_final: 0.8525 (m-30) REVERT: R 200 PHE cc_start: 0.7577 (t80) cc_final: 0.7290 (t80) REVERT: S 37 ASP cc_start: 0.6897 (t0) cc_final: 0.6195 (t0) REVERT: S 48 ASP cc_start: 0.8196 (OUTLIER) cc_final: 0.7673 (t0) REVERT: S 106 ASP cc_start: 0.9400 (m-30) cc_final: 0.9032 (t70) REVERT: S 112 TYR cc_start: 0.8485 (t80) cc_final: 0.7955 (t80) outliers start: 108 outliers final: 74 residues processed: 862 average time/residue: 0.4750 time to fit residues: 687.5514 Evaluate side-chains 779 residues out of total 3955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 701 time to evaluate : 4.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 553 ARG Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain B residue 553 ARG Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 32 CYS Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 371 ASP Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 498 SER Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 253 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain I residue 91 ILE Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 133 ILE Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain J residue 66 GLN Chi-restraints excluded: chain J residue 73 SER Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 185 ASN Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain K residue 117 ASP Chi-restraints excluded: chain K residue 195 THR Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain N residue 97 THR Chi-restraints excluded: chain Q residue 15 SER Chi-restraints excluded: chain Q residue 88 LEU Chi-restraints excluded: chain Q residue 142 ASN Chi-restraints excluded: chain Q residue 163 ILE Chi-restraints excluded: chain R residue 64 GLU Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 171 ASP Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 194 ASP Chi-restraints excluded: chain S residue 48 ASP Chi-restraints excluded: chain S residue 142 ASN Chi-restraints excluded: chain S residue 156 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 405 optimal weight: 5.9990 chunk 308 optimal weight: 7.9990 chunk 212 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 195 optimal weight: 0.6980 chunk 275 optimal weight: 5.9990 chunk 411 optimal weight: 10.0000 chunk 435 optimal weight: 8.9990 chunk 215 optimal weight: 10.0000 chunk 390 optimal weight: 6.9990 chunk 117 optimal weight: 8.9990 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 164 HIS A 314 ASN ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 GLN ** D 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 67 GLN K 149 GLN ** N 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 89 GLN Q 111 GLN ** Q 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 19 HIS R 21 GLN ** S 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 142 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.4692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.098 36765 Z= 0.615 Angle : 0.814 10.538 49676 Z= 0.415 Chirality : 0.052 0.347 5575 Planarity : 0.006 0.067 6440 Dihedral : 5.328 111.977 5022 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.79 % Favored : 96.19 % Rotamer: Outliers : 4.93 % Allowed : 13.83 % Favored : 81.23 % 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: 0.64 (0.12), residues: 4538 helix: 1.48 (0.11), residues: 2058 sheet: -0.54 (0.20), residues: 647 loop : -0.34 (0.15), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP S 122 HIS 0.009 0.002 HIS E 62 PHE 0.028 0.003 PHE F 244 TYR 0.029 0.002 TYR S 139 ARG 0.008 0.001 ARG A 353 *********************** 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 899 residues out of total 3955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 704 time to evaluate : 4.272 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: A 131 ILE cc_start: 0.8874 (OUTLIER) cc_final: 0.8355 (tp) REVERT: A 235 ASP cc_start: 0.8622 (t70) cc_final: 0.8370 (t0) REVERT: A 254 CYS cc_start: 0.8518 (m) cc_final: 0.8096 (m) REVERT: A 290 ASP cc_start: 0.8685 (t70) cc_final: 0.8351 (t0) REVERT: A 346 MET cc_start: 0.7949 (ttt) cc_final: 0.7529 (ttt) REVERT: A 347 MET cc_start: 0.8369 (mtm) cc_final: 0.7985 (mtp) REVERT: A 360 GLU cc_start: 0.8085 (tt0) cc_final: 0.7855 (mt-10) REVERT: A 485 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7735 (mp0) REVERT: A 523 ASN cc_start: 0.8345 (t0) cc_final: 0.8073 (t0) REVERT: B 30 THR cc_start: 0.8567 (m) cc_final: 0.8085 (p) REVERT: B 73 VAL cc_start: 0.9255 (t) cc_final: 0.8987 (m) REVERT: B 74 SER cc_start: 0.7895 (m) cc_final: 0.6861 (p) REVERT: B 77 ASP cc_start: 0.8112 (m-30) cc_final: 0.7077 (m-30) REVERT: B 84 LYS cc_start: 0.8101 (mmtt) cc_final: 0.7503 (mmtt) REVERT: B 98 ILE cc_start: 0.8642 (mp) cc_final: 0.8052 (tt) REVERT: B 115 SER cc_start: 0.9006 (t) cc_final: 0.8615 (p) REVERT: B 116 ILE cc_start: 0.9032 (pt) cc_final: 0.8685 (pt) REVERT: B 419 ASP cc_start: 0.7337 (t0) cc_final: 0.7117 (t0) REVERT: B 463 GLU cc_start: 0.8608 (tt0) cc_final: 0.8320 (tp30) REVERT: B 485 GLU cc_start: 0.8227 (tp30) cc_final: 0.7755 (tp30) REVERT: B 486 GLU cc_start: 0.8826 (tm-30) cc_final: 0.8514 (tm-30) REVERT: B 488 ASP cc_start: 0.8392 (m-30) cc_final: 0.7737 (t0) REVERT: C 100 ASP cc_start: 0.8394 (t0) cc_final: 0.8168 (t0) REVERT: C 140 ASN cc_start: 0.8231 (m-40) cc_final: 0.7898 (m-40) REVERT: C 155 ILE cc_start: 0.8693 (mm) cc_final: 0.8237 (mm) REVERT: C 299 ASP cc_start: 0.8071 (m-30) cc_final: 0.7375 (p0) REVERT: C 447 SER cc_start: 0.8623 (m) cc_final: 0.7953 (p) REVERT: C 484 GLN cc_start: 0.8363 (tp-100) cc_final: 0.7368 (tp40) REVERT: C 487 GLU cc_start: 0.9062 (tp30) cc_final: 0.8619 (tm-30) REVERT: C 604 LEU cc_start: 0.8736 (mp) cc_final: 0.8535 (tt) REVERT: D 358 ASN cc_start: 0.9170 (t0) cc_final: 0.8887 (t0) REVERT: D 360 ASP cc_start: 0.8531 (t0) cc_final: 0.8231 (t0) REVERT: D 410 MET cc_start: 0.8663 (mmm) cc_final: 0.8023 (mtm) REVERT: E 70 GLU cc_start: 0.7788 (tt0) cc_final: 0.7347 (tt0) REVERT: E 256 ASN cc_start: 0.7780 (m-40) cc_final: 0.7030 (p0) REVERT: E 268 THR cc_start: 0.8879 (p) cc_final: 0.8403 (t) REVERT: E 341 VAL cc_start: 0.8845 (m) cc_final: 0.8565 (t) REVERT: E 380 ASP cc_start: 0.8406 (t0) cc_final: 0.8070 (t0) REVERT: E 382 GLN cc_start: 0.8958 (mm-40) cc_final: 0.8623 (tp40) REVERT: E 410 MET cc_start: 0.8433 (mpp) cc_final: 0.7535 (mtp) REVERT: E 491 MET cc_start: 0.8791 (mtp) cc_final: 0.8564 (mtm) REVERT: F 106 ASP cc_start: 0.8340 (p0) cc_final: 0.8104 (p0) REVERT: F 164 ILE cc_start: 0.7717 (mm) cc_final: 0.7466 (mm) REVERT: F 214 LYS cc_start: 0.9178 (pttt) cc_final: 0.8755 (tppt) REVERT: F 315 GLU cc_start: 0.8784 (mt-10) cc_final: 0.8096 (mm-30) REVERT: F 317 VAL cc_start: 0.9251 (t) cc_final: 0.8964 (p) REVERT: F 371 TYR cc_start: 0.8124 (t80) cc_final: 0.7897 (t80) REVERT: H 181 GLU cc_start: 0.8367 (mt-10) cc_final: 0.7803 (pt0) REVERT: H 206 GLN cc_start: 0.8587 (tm-30) cc_final: 0.8384 (tm-30) REVERT: H 210 LYS cc_start: 0.9167 (tttm) cc_final: 0.8790 (ttmm) REVERT: I 74 ASN cc_start: 0.8952 (t0) cc_final: 0.8549 (t0) REVERT: I 78 GLN cc_start: 0.9085 (mm-40) cc_final: 0.8735 (mm110) REVERT: I 129 GLU cc_start: 0.8871 (mm-30) cc_final: 0.8667 (mm-30) REVERT: I 132 MET cc_start: 0.9382 (mmt) cc_final: 0.8996 (mmt) REVERT: I 183 ILE cc_start: 0.9019 (mt) cc_final: 0.8737 (mm) REVERT: I 208 MET cc_start: 0.8098 (tpp) cc_final: 0.7791 (tpp) REVERT: I 221 ASN cc_start: 0.8681 (m-40) cc_final: 0.8145 (t0) REVERT: J 78 GLN cc_start: 0.7728 (tp40) cc_final: 0.7253 (tm-30) REVERT: J 97 GLU cc_start: 0.8615 (tt0) cc_final: 0.8263 (tm-30) REVERT: J 117 ASP cc_start: 0.7924 (m-30) cc_final: 0.7626 (m-30) REVERT: J 124 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8722 (mm) REVERT: J 138 LYS cc_start: 0.7530 (tttt) cc_final: 0.7160 (tptp) REVERT: J 154 MET cc_start: 0.8589 (mtp) cc_final: 0.8342 (ttm) REVERT: J 195 THR cc_start: 0.8245 (p) cc_final: 0.8027 (t) REVERT: J 196 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7802 (mm) REVERT: J 198 SER cc_start: 0.9061 (m) cc_final: 0.8811 (p) REVERT: J 206 GLN cc_start: 0.8864 (mt0) cc_final: 0.8607 (mt0) REVERT: J 208 MET cc_start: 0.8629 (mmt) cc_final: 0.8356 (mmp) REVERT: K 92 THR cc_start: 0.8766 (m) cc_final: 0.8442 (p) REVERT: K 96 ASN cc_start: 0.9381 (m-40) cc_final: 0.9110 (m-40) REVERT: K 103 SER cc_start: 0.9457 (t) cc_final: 0.9237 (p) REVERT: K 143 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8399 (tp) REVERT: K 192 VAL cc_start: 0.9052 (OUTLIER) cc_final: 0.8798 (p) REVERT: M 78 ARG cc_start: 0.8574 (mtt180) cc_final: 0.8268 (ttp-110) REVERT: M 85 GLN cc_start: 0.8693 (tt0) cc_final: 0.8218 (tm-30) REVERT: M 91 ASN cc_start: 0.8637 (m-40) cc_final: 0.8236 (m-40) REVERT: M 102 MET cc_start: 0.7960 (mtm) cc_final: 0.7662 (mtm) REVERT: O 78 ARG cc_start: 0.8962 (mmm-85) cc_final: 0.8606 (tpt90) REVERT: O 94 ARG cc_start: 0.8220 (ttt-90) cc_final: 0.7898 (ttp-170) REVERT: O 114 TYR cc_start: 0.8337 (t80) cc_final: 0.7980 (t80) REVERT: Q 33 MET cc_start: 0.8579 (tpp) cc_final: 0.8168 (tpp) REVERT: Q 48 ASP cc_start: 0.8815 (t70) cc_final: 0.8379 (t0) REVERT: Q 74 CYS cc_start: 0.8409 (p) cc_final: 0.8087 (p) REVERT: Q 153 ARG cc_start: 0.7759 (tpp80) cc_final: 0.7342 (ttm110) REVERT: Q 166 TYR cc_start: 0.8595 (m-10) cc_final: 0.8059 (m-10) REVERT: Q 170 GLU cc_start: 0.7551 (tt0) cc_final: 0.7035 (mp0) REVERT: Q 171 ASP cc_start: 0.8733 (OUTLIER) cc_final: 0.8510 (p0) REVERT: Q 201 LYS cc_start: 0.8043 (tttt) cc_final: 0.7723 (ptmt) REVERT: Q 221 ASP cc_start: 0.7668 (m-30) cc_final: 0.7217 (m-30) REVERT: R 79 ASP cc_start: 0.8518 (m-30) cc_final: 0.7652 (t0) REVERT: R 107 LEU cc_start: 0.9098 (pp) cc_final: 0.8837 (tt) REVERT: R 109 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8166 (mp0) REVERT: S 37 ASP cc_start: 0.7022 (t0) cc_final: 0.6416 (t70) REVERT: S 48 ASP cc_start: 0.8382 (OUTLIER) cc_final: 0.7990 (t0) REVERT: S 64 GLU cc_start: 0.8927 (mt-10) cc_final: 0.8527 (mt-10) REVERT: S 103 MET cc_start: 0.8340 (ptm) cc_final: 0.8084 (ptm) REVERT: S 106 ASP cc_start: 0.9420 (m-30) cc_final: 0.9067 (t70) REVERT: S 112 TYR cc_start: 0.8544 (t80) cc_final: 0.8274 (t80) outliers start: 195 outliers final: 148 residues processed: 844 average time/residue: 0.4602 time to fit residues: 644.2499 Evaluate side-chains 773 residues out of total 3955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 618 time to evaluate : 4.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 553 ARG Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 553 ARG Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 32 CYS Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 371 ASP Chi-restraints excluded: chain C residue 395 LEU Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 532 CYS Chi-restraints excluded: chain C residue 545 ILE Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 498 SER Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 181 ASN Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 356 MET Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 253 SER Chi-restraints excluded: chain F residue 281 THR Chi-restraints excluded: chain F residue 316 GLU Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 369 THR Chi-restraints excluded: chain F residue 383 LEU Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain H residue 213 LYS Chi-restraints excluded: chain I residue 91 ILE Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain J residue 67 GLN Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 117 ASP Chi-restraints excluded: chain K residue 143 LEU Chi-restraints excluded: chain K residue 148 VAL Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 192 VAL Chi-restraints excluded: chain K residue 195 THR Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain N residue 86 SER Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain O residue 116 ILE Chi-restraints excluded: chain Q residue 15 SER Chi-restraints excluded: chain Q residue 45 ILE Chi-restraints excluded: chain Q residue 54 ILE Chi-restraints excluded: chain Q residue 87 ILE Chi-restraints excluded: chain Q residue 88 LEU Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 142 ASN Chi-restraints excluded: chain Q residue 163 ILE Chi-restraints excluded: chain Q residue 171 ASP Chi-restraints excluded: chain Q residue 206 ASP Chi-restraints excluded: chain Q residue 230 ILE Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 64 GLU Chi-restraints excluded: chain R residue 85 SER Chi-restraints excluded: chain R residue 140 LEU Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 171 ASP Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 194 ASP Chi-restraints excluded: chain R residue 227 LYS Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain S residue 48 ASP Chi-restraints excluded: chain S residue 142 ASN Chi-restraints excluded: chain S residue 146 THR Chi-restraints excluded: chain S residue 158 VAL Chi-restraints excluded: chain S residue 183 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 363 optimal weight: 1.9990 chunk 247 optimal weight: 0.3980 chunk 6 optimal weight: 0.9980 chunk 324 optimal weight: 4.9990 chunk 179 optimal weight: 9.9990 chunk 372 optimal weight: 3.9990 chunk 301 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 222 optimal weight: 3.9990 chunk 391 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 181 ASN E 262 ASN ** E 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 GLN Q 207 GLN ** S 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.4802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 36765 Z= 0.207 Angle : 0.580 10.163 49676 Z= 0.287 Chirality : 0.043 0.201 5575 Planarity : 0.004 0.051 6440 Dihedral : 4.841 112.648 5022 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.93 % Favored : 97.05 % Rotamer: Outliers : 3.34 % Allowed : 16.72 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.13), residues: 4538 helix: 1.81 (0.12), residues: 2069 sheet: -0.54 (0.20), residues: 674 loop : -0.25 (0.15), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Q 55 HIS 0.014 0.001 HIS F 363 PHE 0.024 0.002 PHE R 200 TYR 0.020 0.001 TYR S 139 ARG 0.006 0.000 ARG R 153 *********************** 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 824 residues out of total 3955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 692 time to evaluate : 4.481 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 108 ASP cc_start: 0.8288 (m-30) cc_final: 0.8023 (t0) REVERT: A 131 ILE cc_start: 0.8890 (mt) cc_final: 0.8571 (pt) REVERT: A 219 GLU cc_start: 0.8140 (tt0) cc_final: 0.7586 (pt0) REVERT: A 235 ASP cc_start: 0.8603 (t70) cc_final: 0.8325 (t0) REVERT: A 254 CYS cc_start: 0.8573 (m) cc_final: 0.8033 (m) REVERT: A 290 ASP cc_start: 0.8743 (t70) cc_final: 0.8356 (t0) REVERT: A 346 MET cc_start: 0.7849 (ttt) cc_final: 0.7385 (ttt) REVERT: A 481 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7485 (mm-30) REVERT: A 485 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7699 (mp0) REVERT: A 487 GLU cc_start: 0.8305 (tm-30) cc_final: 0.7992 (tm-30) REVERT: A 523 ASN cc_start: 0.8250 (t0) cc_final: 0.7961 (t0) REVERT: A 606 GLU cc_start: 0.7198 (tt0) cc_final: 0.6892 (mm-30) REVERT: B 30 THR cc_start: 0.8570 (m) cc_final: 0.8246 (p) REVERT: B 61 MET cc_start: 0.7367 (mtp) cc_final: 0.7154 (ttm) REVERT: B 74 SER cc_start: 0.7916 (m) cc_final: 0.7048 (p) REVERT: B 77 ASP cc_start: 0.8174 (m-30) cc_final: 0.7210 (m-30) REVERT: B 84 LYS cc_start: 0.8145 (mmtt) cc_final: 0.7543 (mmtt) REVERT: B 98 ILE cc_start: 0.8598 (mp) cc_final: 0.8024 (tt) REVERT: B 115 SER cc_start: 0.9082 (t) cc_final: 0.8636 (p) REVERT: B 116 ILE cc_start: 0.9008 (pt) cc_final: 0.8762 (pt) REVERT: B 161 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8396 (tp) REVERT: B 201 GLU cc_start: 0.7207 (tm-30) cc_final: 0.6517 (tm-30) REVERT: B 308 ARG cc_start: 0.6728 (ptp-110) cc_final: 0.6231 (ptt180) REVERT: B 346 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7906 (ttt) REVERT: B 349 ASP cc_start: 0.7338 (p0) cc_final: 0.6962 (p0) REVERT: B 399 GLU cc_start: 0.8758 (tp30) cc_final: 0.8421 (mm-30) REVERT: B 419 ASP cc_start: 0.7177 (t0) cc_final: 0.6926 (t0) REVERT: B 485 GLU cc_start: 0.8167 (tp30) cc_final: 0.7372 (tp30) REVERT: B 486 GLU cc_start: 0.8803 (tm-30) cc_final: 0.8501 (tm-30) REVERT: B 488 ASP cc_start: 0.8315 (m-30) cc_final: 0.7613 (t0) REVERT: C 30 THR cc_start: 0.8354 (m) cc_final: 0.7941 (p) REVERT: C 100 ASP cc_start: 0.8334 (t0) cc_final: 0.8067 (t0) REVERT: C 140 ASN cc_start: 0.8418 (m-40) cc_final: 0.7996 (m110) REVERT: C 155 ILE cc_start: 0.8676 (mm) cc_final: 0.8359 (mm) REVERT: C 254 CYS cc_start: 0.8035 (p) cc_final: 0.7771 (m) REVERT: C 299 ASP cc_start: 0.7994 (m-30) cc_final: 0.7441 (p0) REVERT: C 387 GLU cc_start: 0.7844 (tp30) cc_final: 0.7478 (tp30) REVERT: C 447 SER cc_start: 0.8617 (m) cc_final: 0.8138 (p) REVERT: C 484 GLN cc_start: 0.8431 (tp-100) cc_final: 0.8227 (tp40) REVERT: C 520 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.7982 (tt) REVERT: D 358 ASN cc_start: 0.9103 (t0) cc_final: 0.8823 (t0) REVERT: D 360 ASP cc_start: 0.8519 (t0) cc_final: 0.8201 (t0) REVERT: D 410 MET cc_start: 0.8586 (mmm) cc_final: 0.7981 (mtm) REVERT: D 497 GLN cc_start: 0.8654 (pm20) cc_final: 0.8405 (pp30) REVERT: E 70 GLU cc_start: 0.7849 (tt0) cc_final: 0.7449 (tt0) REVERT: E 201 GLU cc_start: 0.8638 (mp0) cc_final: 0.8007 (mp0) REVERT: E 256 ASN cc_start: 0.7674 (m-40) cc_final: 0.6921 (p0) REVERT: E 330 ASP cc_start: 0.8945 (m-30) cc_final: 0.8421 (t0) REVERT: E 382 GLN cc_start: 0.8917 (mm-40) cc_final: 0.8379 (tp40) REVERT: E 410 MET cc_start: 0.8351 (mpp) cc_final: 0.7637 (mtp) REVERT: F 164 ILE cc_start: 0.7618 (mm) cc_final: 0.7296 (mm) REVERT: F 214 LYS cc_start: 0.9169 (pttt) cc_final: 0.8757 (tppt) REVERT: F 234 MET cc_start: 0.8872 (mtm) cc_final: 0.8593 (mtm) REVERT: F 309 GLU cc_start: 0.8427 (tm-30) cc_final: 0.7909 (tt0) REVERT: F 315 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8087 (mm-30) REVERT: F 317 VAL cc_start: 0.9199 (t) cc_final: 0.8979 (p) REVERT: F 342 GLU cc_start: 0.8998 (tt0) cc_final: 0.8447 (tp30) REVERT: F 351 ILE cc_start: 0.8742 (mt) cc_final: 0.8409 (mm) REVERT: F 371 TYR cc_start: 0.8023 (t80) cc_final: 0.7789 (t80) REVERT: F 464 THR cc_start: 0.8691 (m) cc_final: 0.7973 (p) REVERT: F 482 GLN cc_start: 0.7903 (mt0) cc_final: 0.7644 (tt0) REVERT: H 206 GLN cc_start: 0.8516 (tm-30) cc_final: 0.8150 (tm-30) REVERT: H 210 LYS cc_start: 0.9141 (tttm) cc_final: 0.8868 (ttmm) REVERT: I 74 ASN cc_start: 0.8911 (t0) cc_final: 0.8487 (t0) REVERT: I 78 GLN cc_start: 0.9104 (mm-40) cc_final: 0.8743 (mm110) REVERT: I 121 LEU cc_start: 0.8737 (mt) cc_final: 0.8465 (mt) REVERT: I 129 GLU cc_start: 0.8782 (mm-30) cc_final: 0.8458 (mm-30) REVERT: I 132 MET cc_start: 0.9371 (mmt) cc_final: 0.9096 (mmt) REVERT: I 183 ILE cc_start: 0.9017 (mt) cc_final: 0.8714 (mm) REVERT: I 197 GLU cc_start: 0.8311 (mp0) cc_final: 0.8039 (mp0) REVERT: I 221 ASN cc_start: 0.8577 (m-40) cc_final: 0.8093 (t0) REVERT: J 78 GLN cc_start: 0.7679 (tp40) cc_final: 0.7178 (tm-30) REVERT: J 97 GLU cc_start: 0.8622 (tt0) cc_final: 0.8223 (tm-30) REVERT: J 154 MET cc_start: 0.8345 (mtp) cc_final: 0.8118 (ttm) REVERT: J 172 TYR cc_start: 0.8110 (m-80) cc_final: 0.7552 (m-10) REVERT: J 184 TYR cc_start: 0.8205 (m-80) cc_final: 0.7978 (m-80) REVERT: J 185 ASN cc_start: 0.7601 (p0) cc_final: 0.7151 (p0) REVERT: J 195 THR cc_start: 0.8113 (p) cc_final: 0.7894 (t) REVERT: J 196 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7823 (mm) REVERT: J 198 SER cc_start: 0.9068 (m) cc_final: 0.8790 (p) REVERT: J 208 MET cc_start: 0.8593 (mmt) cc_final: 0.8349 (mmp) REVERT: J 223 LYS cc_start: 0.8824 (mmtt) cc_final: 0.8358 (mptt) REVERT: K 92 THR cc_start: 0.8663 (m) cc_final: 0.8445 (p) REVERT: K 96 ASN cc_start: 0.9311 (m-40) cc_final: 0.9044 (m-40) REVERT: K 103 SER cc_start: 0.9403 (t) cc_final: 0.9180 (p) REVERT: K 129 GLU cc_start: 0.8495 (mm-30) cc_final: 0.7737 (mm-30) REVERT: K 132 MET cc_start: 0.9157 (mtt) cc_final: 0.8358 (mmm) REVERT: M 78 ARG cc_start: 0.8557 (mtt180) cc_final: 0.8239 (ttp-110) REVERT: M 85 GLN cc_start: 0.8657 (tt0) cc_final: 0.8225 (tm-30) REVERT: M 90 ARG cc_start: 0.8104 (mtp-110) cc_final: 0.7892 (mtm110) REVERT: M 91 ASN cc_start: 0.8547 (m-40) cc_final: 0.8064 (m-40) REVERT: N 78 ARG cc_start: 0.7920 (mtm-85) cc_final: 0.7629 (mtm110) REVERT: O 78 ARG cc_start: 0.8984 (mmm-85) cc_final: 0.8613 (tpt90) REVERT: O 94 ARG cc_start: 0.8136 (ttt-90) cc_final: 0.7820 (ttp-170) REVERT: Q 33 MET cc_start: 0.8452 (tpp) cc_final: 0.8187 (tpp) REVERT: Q 48 ASP cc_start: 0.8735 (t70) cc_final: 0.8217 (t0) REVERT: Q 74 CYS cc_start: 0.8253 (p) cc_final: 0.7986 (p) REVERT: Q 112 TYR cc_start: 0.8308 (t80) cc_final: 0.8040 (t80) REVERT: Q 153 ARG cc_start: 0.7710 (tpp80) cc_final: 0.7151 (ttm110) REVERT: Q 166 TYR cc_start: 0.8541 (m-10) cc_final: 0.7885 (m-10) REVERT: Q 170 GLU cc_start: 0.7598 (tt0) cc_final: 0.7117 (mp0) REVERT: Q 171 ASP cc_start: 0.8644 (OUTLIER) cc_final: 0.8246 (p0) REVERT: Q 201 LYS cc_start: 0.7946 (tttt) cc_final: 0.7553 (ptmt) REVERT: Q 221 ASP cc_start: 0.7723 (m-30) cc_final: 0.7392 (m-30) REVERT: R 79 ASP cc_start: 0.8448 (m-30) cc_final: 0.7531 (t0) REVERT: R 107 LEU cc_start: 0.9061 (pp) cc_final: 0.8768 (tt) REVERT: S 37 ASP cc_start: 0.6796 (t0) cc_final: 0.6126 (t70) REVERT: S 48 ASP cc_start: 0.8342 (OUTLIER) cc_final: 0.7804 (t0) REVERT: S 64 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8467 (mt-10) REVERT: S 103 MET cc_start: 0.8512 (ptm) cc_final: 0.8206 (ptm) REVERT: S 106 ASP cc_start: 0.9404 (m-30) cc_final: 0.9048 (t70) REVERT: S 112 TYR cc_start: 0.8575 (t80) cc_final: 0.8007 (t80) outliers start: 132 outliers final: 91 residues processed: 786 average time/residue: 0.4696 time to fit residues: 614.8970 Evaluate side-chains 742 residues out of total 3955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 645 time to evaluate : 4.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 553 ARG Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 553 ARG Chi-restraints excluded: chain C residue 18 PHE Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 371 ASP Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 515 ILE Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 545 ILE Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 181 ASN Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 262 ASN Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 253 SER Chi-restraints excluded: chain F residue 316 GLU Chi-restraints excluded: chain F residue 365 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 214 GLU Chi-restraints excluded: chain I residue 91 ILE Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain K residue 70 ILE Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain K residue 117 ASP Chi-restraints excluded: chain K residue 195 THR Chi-restraints excluded: chain K residue 226 ASP Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain N residue 106 VAL Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain O residue 116 ILE Chi-restraints excluded: chain Q residue 15 SER Chi-restraints excluded: chain Q residue 107 LEU Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 142 ASN Chi-restraints excluded: chain Q residue 171 ASP Chi-restraints excluded: chain Q residue 206 ASP Chi-restraints excluded: chain Q residue 230 ILE Chi-restraints excluded: chain R residue 64 GLU Chi-restraints excluded: chain R residue 156 THR Chi-restraints excluded: chain R residue 171 ASP Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 194 ASP Chi-restraints excluded: chain R residue 227 LYS Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain S residue 48 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 146 optimal weight: 8.9990 chunk 392 optimal weight: 0.5980 chunk 86 optimal weight: 7.9990 chunk 255 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 436 optimal weight: 0.0170 chunk 362 optimal weight: 4.9990 chunk 202 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 144 optimal weight: 0.9980 chunk 229 optimal weight: 5.9990 overall best weight: 1.2820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 ASN ** A 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 GLN ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 181 ASN ** E 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 GLN ** S 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.4922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 36765 Z= 0.213 Angle : 0.580 10.529 49676 Z= 0.283 Chirality : 0.043 0.244 5575 Planarity : 0.004 0.049 6440 Dihedral : 4.686 112.880 5022 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.22 % Favored : 96.76 % Rotamer: Outliers : 3.44 % Allowed : 17.15 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.13), residues: 4538 helix: 1.90 (0.12), residues: 2076 sheet: -0.56 (0.20), residues: 669 loop : -0.28 (0.15), residues: 1793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Q 55 HIS 0.010 0.001 HIS F 363 PHE 0.035 0.001 PHE R 200 TYR 0.020 0.001 TYR H 200 ARG 0.005 0.000 ARG D 337 *********************** 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 821 residues out of total 3955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 685 time to evaluate : 4.236 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: A 108 ASP cc_start: 0.8300 (m-30) cc_final: 0.8012 (t0) REVERT: A 131 ILE cc_start: 0.8888 (mt) cc_final: 0.8489 (pt) REVERT: A 219 GLU cc_start: 0.8078 (tt0) cc_final: 0.7584 (pt0) REVERT: A 235 ASP cc_start: 0.8552 (t70) cc_final: 0.8300 (t0) REVERT: A 254 CYS cc_start: 0.8548 (m) cc_final: 0.8001 (m) REVERT: A 290 ASP cc_start: 0.8747 (t70) cc_final: 0.8354 (t0) REVERT: A 318 MET cc_start: 0.8976 (mtt) cc_final: 0.8607 (mmm) REVERT: A 346 MET cc_start: 0.7887 (ttt) cc_final: 0.7442 (ttt) REVERT: A 485 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7944 (mm-30) REVERT: A 487 GLU cc_start: 0.8263 (tm-30) cc_final: 0.7892 (tm-30) REVERT: A 523 ASN cc_start: 0.8218 (t0) cc_final: 0.7981 (t0) REVERT: B 30 THR cc_start: 0.8557 (m) cc_final: 0.8242 (p) REVERT: B 61 MET cc_start: 0.7357 (mtp) cc_final: 0.7151 (ttm) REVERT: B 74 SER cc_start: 0.7999 (m) cc_final: 0.7148 (p) REVERT: B 77 ASP cc_start: 0.8267 (m-30) cc_final: 0.7312 (m-30) REVERT: B 84 LYS cc_start: 0.8047 (mmtt) cc_final: 0.7457 (mmtt) REVERT: B 98 ILE cc_start: 0.8586 (mp) cc_final: 0.8014 (tt) REVERT: B 115 SER cc_start: 0.9074 (t) cc_final: 0.8621 (p) REVERT: B 116 ILE cc_start: 0.9017 (pt) cc_final: 0.8765 (pt) REVERT: B 142 ARG cc_start: 0.8779 (mmm160) cc_final: 0.8167 (tpp80) REVERT: B 161 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8413 (tp) REVERT: B 201 GLU cc_start: 0.7255 (tm-30) cc_final: 0.6532 (tm-30) REVERT: B 308 ARG cc_start: 0.6679 (ptp-110) cc_final: 0.6182 (ptt180) REVERT: B 349 ASP cc_start: 0.7285 (p0) cc_final: 0.6595 (p0) REVERT: B 419 ASP cc_start: 0.7170 (t0) cc_final: 0.6885 (t0) REVERT: B 485 GLU cc_start: 0.8113 (tp30) cc_final: 0.7317 (tp30) REVERT: B 486 GLU cc_start: 0.8854 (tm-30) cc_final: 0.8543 (tm-30) REVERT: B 488 ASP cc_start: 0.8295 (m-30) cc_final: 0.7597 (t0) REVERT: C 30 THR cc_start: 0.8335 (m) cc_final: 0.7931 (p) REVERT: C 84 LYS cc_start: 0.8374 (mmtt) cc_final: 0.7470 (pttm) REVERT: C 100 ASP cc_start: 0.8305 (t0) cc_final: 0.8027 (t0) REVERT: C 140 ASN cc_start: 0.8251 (m-40) cc_final: 0.7843 (m110) REVERT: C 155 ILE cc_start: 0.8661 (mm) cc_final: 0.8259 (mm) REVERT: C 299 ASP cc_start: 0.7878 (m-30) cc_final: 0.7208 (p0) REVERT: C 387 GLU cc_start: 0.7860 (tp30) cc_final: 0.7515 (tp30) REVERT: C 447 SER cc_start: 0.8627 (m) cc_final: 0.8157 (p) REVERT: C 484 GLN cc_start: 0.8429 (tp-100) cc_final: 0.8204 (tp40) REVERT: C 520 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.7961 (tt) REVERT: C 606 GLU cc_start: 0.8694 (tt0) cc_final: 0.7762 (tp30) REVERT: D 315 GLU cc_start: 0.8772 (tt0) cc_final: 0.8239 (tm-30) REVERT: D 356 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.8417 (mtp) REVERT: D 357 PRO cc_start: 0.9102 (Cg_exo) cc_final: 0.8768 (Cg_endo) REVERT: D 358 ASN cc_start: 0.9112 (t0) cc_final: 0.8826 (t0) REVERT: D 360 ASP cc_start: 0.8539 (t0) cc_final: 0.8157 (t70) REVERT: D 410 MET cc_start: 0.8551 (mmm) cc_final: 0.7955 (mtm) REVERT: E 70 GLU cc_start: 0.7830 (tt0) cc_final: 0.7275 (tt0) REVERT: E 201 GLU cc_start: 0.8634 (mp0) cc_final: 0.7971 (mp0) REVERT: E 256 ASN cc_start: 0.7661 (m-40) cc_final: 0.6917 (p0) REVERT: E 330 ASP cc_start: 0.8847 (m-30) cc_final: 0.8349 (t0) REVERT: E 382 GLN cc_start: 0.8905 (mm-40) cc_final: 0.8416 (tp40) REVERT: E 410 MET cc_start: 0.8391 (mpp) cc_final: 0.7690 (mtp) REVERT: F 121 THR cc_start: 0.8638 (m) cc_final: 0.8438 (t) REVERT: F 164 ILE cc_start: 0.7676 (mm) cc_final: 0.7347 (mm) REVERT: F 180 MET cc_start: 0.8775 (mmm) cc_final: 0.8428 (tpp) REVERT: F 214 LYS cc_start: 0.9173 (pttt) cc_final: 0.8717 (tppt) REVERT: F 234 MET cc_start: 0.8841 (mtm) cc_final: 0.8543 (mtm) REVERT: F 309 GLU cc_start: 0.8430 (tm-30) cc_final: 0.7917 (tt0) REVERT: F 315 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8117 (mm-30) REVERT: F 317 VAL cc_start: 0.9198 (t) cc_final: 0.8989 (p) REVERT: F 342 GLU cc_start: 0.8958 (tt0) cc_final: 0.8401 (tp30) REVERT: F 351 ILE cc_start: 0.8736 (mt) cc_final: 0.8413 (mm) REVERT: F 464 THR cc_start: 0.8706 (m) cc_final: 0.7998 (p) REVERT: F 482 GLN cc_start: 0.7893 (mt0) cc_final: 0.7649 (tt0) REVERT: H 206 GLN cc_start: 0.8566 (tm-30) cc_final: 0.8207 (tm-30) REVERT: H 210 LYS cc_start: 0.9268 (tttm) cc_final: 0.8896 (ttmm) REVERT: I 74 ASN cc_start: 0.8904 (t0) cc_final: 0.8477 (t0) REVERT: I 78 GLN cc_start: 0.9082 (mm-40) cc_final: 0.8715 (mm110) REVERT: I 129 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8399 (mm-30) REVERT: I 132 MET cc_start: 0.9381 (mmt) cc_final: 0.9066 (mmt) REVERT: I 167 ILE cc_start: 0.8024 (mm) cc_final: 0.7817 (mm) REVERT: I 173 LEU cc_start: 0.8999 (mt) cc_final: 0.8751 (mt) REVERT: I 183 ILE cc_start: 0.9023 (mt) cc_final: 0.8770 (mm) REVERT: J 78 GLN cc_start: 0.7692 (tp40) cc_final: 0.7195 (tm-30) REVERT: J 97 GLU cc_start: 0.8650 (tt0) cc_final: 0.8251 (tm-30) REVERT: J 172 TYR cc_start: 0.8114 (m-80) cc_final: 0.7583 (m-10) REVERT: J 184 TYR cc_start: 0.8200 (m-80) cc_final: 0.7987 (m-80) REVERT: J 196 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7916 (mm) REVERT: J 198 SER cc_start: 0.9054 (m) cc_final: 0.8766 (p) REVERT: J 208 MET cc_start: 0.8592 (mmt) cc_final: 0.8355 (mmp) REVERT: K 96 ASN cc_start: 0.9299 (m-40) cc_final: 0.9057 (m-40) REVERT: K 103 SER cc_start: 0.9389 (t) cc_final: 0.9166 (p) REVERT: K 129 GLU cc_start: 0.8458 (mm-30) cc_final: 0.7737 (mm-30) REVERT: K 132 MET cc_start: 0.9144 (mtt) cc_final: 0.8367 (mmm) REVERT: K 143 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8240 (tp) REVERT: M 78 ARG cc_start: 0.8550 (mtt180) cc_final: 0.8213 (ttp-110) REVERT: M 85 GLN cc_start: 0.8657 (tt0) cc_final: 0.8240 (tm-30) REVERT: M 90 ARG cc_start: 0.8103 (mtp-110) cc_final: 0.7868 (mtm110) REVERT: M 91 ASN cc_start: 0.8524 (m-40) cc_final: 0.8033 (m-40) REVERT: M 102 MET cc_start: 0.7745 (OUTLIER) cc_final: 0.7458 (ttm) REVERT: O 78 ARG cc_start: 0.8994 (mmm-85) cc_final: 0.8288 (tpt90) REVERT: O 94 ARG cc_start: 0.8148 (ttt-90) cc_final: 0.7787 (ttp-170) REVERT: Q 33 MET cc_start: 0.8477 (tpp) cc_final: 0.8263 (tpp) REVERT: Q 48 ASP cc_start: 0.8733 (t70) cc_final: 0.8241 (t0) REVERT: Q 112 TYR cc_start: 0.8341 (t80) cc_final: 0.8047 (t80) REVERT: Q 153 ARG cc_start: 0.7627 (tpp80) cc_final: 0.7072 (ttm110) REVERT: Q 166 TYR cc_start: 0.8528 (m-10) cc_final: 0.7843 (m-10) REVERT: Q 170 GLU cc_start: 0.7589 (tt0) cc_final: 0.7115 (mp0) REVERT: Q 171 ASP cc_start: 0.8629 (OUTLIER) cc_final: 0.8280 (p0) REVERT: Q 201 LYS cc_start: 0.8015 (tttt) cc_final: 0.7602 (ptmt) REVERT: Q 221 ASP cc_start: 0.7729 (m-30) cc_final: 0.7351 (m-30) REVERT: R 78 LEU cc_start: 0.8585 (tp) cc_final: 0.8238 (tp) REVERT: R 79 ASP cc_start: 0.8434 (m-30) cc_final: 0.7577 (t0) REVERT: S 37 ASP cc_start: 0.6724 (t0) cc_final: 0.6047 (t70) REVERT: S 48 ASP cc_start: 0.8279 (OUTLIER) cc_final: 0.7777 (t0) REVERT: S 57 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.5908 (mp0) REVERT: S 64 GLU cc_start: 0.8817 (mt-10) cc_final: 0.8477 (mt-10) REVERT: S 106 ASP cc_start: 0.9404 (m-30) cc_final: 0.9037 (t70) REVERT: S 112 TYR cc_start: 0.8551 (t80) cc_final: 0.8058 (t80) outliers start: 136 outliers final: 104 residues processed: 770 average time/residue: 0.4615 time to fit residues: 593.2312 Evaluate side-chains 761 residues out of total 3955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 648 time to evaluate : 4.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 553 ARG Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 553 ARG Chi-restraints excluded: chain C residue 18 PHE Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 371 ASP Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 515 ILE Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 498 SER Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 356 MET Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 253 SER Chi-restraints excluded: chain F residue 316 GLU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 214 GLU Chi-restraints excluded: chain I residue 91 ILE Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 192 VAL Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 73 SER Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain K residue 117 ASP Chi-restraints excluded: chain K residue 143 LEU Chi-restraints excluded: chain K residue 195 THR Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 102 MET Chi-restraints excluded: chain N residue 86 SER Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain N residue 106 VAL Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain O residue 116 ILE Chi-restraints excluded: chain Q residue 15 SER Chi-restraints excluded: chain Q residue 88 LEU Chi-restraints excluded: chain Q residue 107 LEU Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 142 ASN Chi-restraints excluded: chain Q residue 171 ASP Chi-restraints excluded: chain Q residue 230 ILE Chi-restraints excluded: chain R residue 64 GLU Chi-restraints excluded: chain R residue 156 THR Chi-restraints excluded: chain R residue 171 ASP Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 188 MET Chi-restraints excluded: chain R residue 194 ASP Chi-restraints excluded: chain R residue 227 LYS Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain S residue 48 ASP Chi-restraints excluded: chain S residue 57 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 420 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 248 optimal weight: 1.9990 chunk 318 optimal weight: 8.9990 chunk 246 optimal weight: 3.9990 chunk 367 optimal weight: 0.8980 chunk 243 optimal weight: 0.7980 chunk 434 optimal weight: 8.9990 chunk 272 optimal weight: 2.9990 chunk 265 optimal weight: 5.9990 chunk 200 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 ASN A 444 HIS B 65 GLN ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 497 GLN ** E 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 GLN ** I 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 50 GLN ** S 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 177 GLN ** S 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.5085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 36765 Z= 0.289 Angle : 0.599 10.823 49676 Z= 0.294 Chirality : 0.044 0.203 5575 Planarity : 0.004 0.049 6440 Dihedral : 4.690 110.707 5022 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.48 % Favored : 96.50 % Rotamer: Outliers : 3.79 % Allowed : 17.17 % Favored : 79.03 % 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: 0.96 (0.13), residues: 4538 helix: 1.94 (0.12), residues: 2074 sheet: -0.69 (0.20), residues: 639 loop : -0.31 (0.15), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP Q 55 HIS 0.010 0.001 HIS F 363 PHE 0.027 0.002 PHE R 200 TYR 0.017 0.001 TYR S 112 ARG 0.005 0.000 ARG E 400 *********************** 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 818 residues out of total 3955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 668 time to evaluate : 4.261 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 108 ASP cc_start: 0.8312 (m-30) cc_final: 0.8025 (t0) REVERT: A 131 ILE cc_start: 0.8908 (mt) cc_final: 0.8507 (pt) REVERT: A 219 GLU cc_start: 0.8040 (tt0) cc_final: 0.7602 (pt0) REVERT: A 235 ASP cc_start: 0.8441 (t70) cc_final: 0.8169 (t0) REVERT: A 254 CYS cc_start: 0.8493 (m) cc_final: 0.8009 (m) REVERT: A 318 MET cc_start: 0.8978 (mtt) cc_final: 0.8614 (mmm) REVERT: A 346 MET cc_start: 0.7937 (ttt) cc_final: 0.7481 (ttt) REVERT: A 349 ASP cc_start: 0.9001 (t0) cc_final: 0.8741 (t0) REVERT: A 487 GLU cc_start: 0.8303 (tm-30) cc_final: 0.7922 (tm-30) REVERT: A 523 ASN cc_start: 0.8229 (t0) cc_final: 0.8007 (t0) REVERT: B 30 THR cc_start: 0.8552 (m) cc_final: 0.8201 (p) REVERT: B 61 MET cc_start: 0.7381 (mtp) cc_final: 0.7072 (ttm) REVERT: B 74 SER cc_start: 0.7971 (m) cc_final: 0.7087 (p) REVERT: B 77 ASP cc_start: 0.8265 (m-30) cc_final: 0.7299 (m-30) REVERT: B 84 LYS cc_start: 0.8064 (mmtt) cc_final: 0.7461 (mmtt) REVERT: B 98 ILE cc_start: 0.8586 (mp) cc_final: 0.8007 (tt) REVERT: B 115 SER cc_start: 0.9056 (t) cc_final: 0.8610 (p) REVERT: B 116 ILE cc_start: 0.9070 (pt) cc_final: 0.8797 (pt) REVERT: B 161 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8584 (tp) REVERT: B 201 GLU cc_start: 0.7321 (tm-30) cc_final: 0.6575 (tm-30) REVERT: B 308 ARG cc_start: 0.6744 (ptp-110) cc_final: 0.6323 (ptt180) REVERT: B 399 GLU cc_start: 0.8783 (tp30) cc_final: 0.8350 (mm-30) REVERT: B 419 ASP cc_start: 0.7126 (t0) cc_final: 0.6832 (t0) REVERT: B 485 GLU cc_start: 0.8122 (tp30) cc_final: 0.7336 (tp30) REVERT: B 486 GLU cc_start: 0.8810 (tm-30) cc_final: 0.8506 (tm-30) REVERT: B 488 ASP cc_start: 0.8313 (m-30) cc_final: 0.7590 (t0) REVERT: C 100 ASP cc_start: 0.8331 (t0) cc_final: 0.8054 (t0) REVERT: C 140 ASN cc_start: 0.8201 (m-40) cc_final: 0.7808 (m110) REVERT: C 155 ILE cc_start: 0.8696 (mm) cc_final: 0.8379 (mm) REVERT: C 299 ASP cc_start: 0.7997 (m-30) cc_final: 0.7315 (p0) REVERT: C 436 ASP cc_start: 0.8358 (t0) cc_final: 0.7962 (t70) REVERT: C 447 SER cc_start: 0.8746 (m) cc_final: 0.8199 (p) REVERT: C 484 GLN cc_start: 0.8443 (tp-100) cc_final: 0.8175 (tp40) REVERT: C 606 GLU cc_start: 0.8645 (tt0) cc_final: 0.7729 (tp30) REVERT: D 117 ASP cc_start: 0.8320 (t0) cc_final: 0.8105 (t0) REVERT: D 315 GLU cc_start: 0.8754 (tt0) cc_final: 0.8284 (tm-30) REVERT: D 357 PRO cc_start: 0.9101 (Cg_exo) cc_final: 0.8767 (Cg_endo) REVERT: D 358 ASN cc_start: 0.9154 (t0) cc_final: 0.8860 (t0) REVERT: D 360 ASP cc_start: 0.8550 (t0) cc_final: 0.8175 (t70) REVERT: D 402 MET cc_start: 0.8497 (tmm) cc_final: 0.7713 (tmm) REVERT: D 410 MET cc_start: 0.8635 (mmm) cc_final: 0.8003 (mtm) REVERT: E 70 GLU cc_start: 0.7807 (tt0) cc_final: 0.7338 (tt0) REVERT: E 201 GLU cc_start: 0.8678 (mp0) cc_final: 0.7987 (mp0) REVERT: E 256 ASN cc_start: 0.7693 (m-40) cc_final: 0.6971 (p0) REVERT: E 330 ASP cc_start: 0.8931 (m-30) cc_final: 0.8416 (t0) REVERT: E 382 GLN cc_start: 0.8920 (mm-40) cc_final: 0.8430 (tp40) REVERT: E 410 MET cc_start: 0.8393 (mpp) cc_final: 0.7699 (mtp) REVERT: F 164 ILE cc_start: 0.7827 (mm) cc_final: 0.7518 (mm) REVERT: F 180 MET cc_start: 0.8772 (mmm) cc_final: 0.8433 (tpp) REVERT: F 214 LYS cc_start: 0.9164 (pttt) cc_final: 0.8776 (tppt) REVERT: F 234 MET cc_start: 0.8826 (mtm) cc_final: 0.8479 (mtm) REVERT: F 254 MET cc_start: 0.8015 (tpp) cc_final: 0.7682 (tpp) REVERT: F 309 GLU cc_start: 0.8417 (tm-30) cc_final: 0.7907 (tt0) REVERT: F 315 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8133 (mm-30) REVERT: F 317 VAL cc_start: 0.9201 (t) cc_final: 0.8993 (p) REVERT: F 342 GLU cc_start: 0.8969 (tt0) cc_final: 0.8404 (tp30) REVERT: F 351 ILE cc_start: 0.8791 (mt) cc_final: 0.8465 (mm) REVERT: F 464 THR cc_start: 0.8740 (m) cc_final: 0.8054 (p) REVERT: F 482 GLN cc_start: 0.7911 (mt0) cc_final: 0.7650 (tt0) REVERT: H 206 GLN cc_start: 0.8602 (tm-30) cc_final: 0.8282 (tm-30) REVERT: H 210 LYS cc_start: 0.9265 (tttm) cc_final: 0.8914 (ttmm) REVERT: I 74 ASN cc_start: 0.8910 (t0) cc_final: 0.8479 (t0) REVERT: I 78 GLN cc_start: 0.9084 (mm-40) cc_final: 0.8719 (mm110) REVERT: I 129 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8379 (mm-30) REVERT: I 132 MET cc_start: 0.9377 (mmt) cc_final: 0.8990 (mmt) REVERT: I 167 ILE cc_start: 0.7998 (mm) cc_final: 0.7771 (mm) REVERT: I 173 LEU cc_start: 0.9001 (mt) cc_final: 0.8761 (mt) REVERT: I 183 ILE cc_start: 0.9001 (mt) cc_final: 0.8735 (mm) REVERT: J 78 GLN cc_start: 0.7695 (tp40) cc_final: 0.7202 (tm-30) REVERT: J 97 GLU cc_start: 0.8650 (tt0) cc_final: 0.8295 (tm-30) REVERT: J 172 TYR cc_start: 0.8162 (m-80) cc_final: 0.7584 (m-10) REVERT: J 184 TYR cc_start: 0.8159 (m-80) cc_final: 0.7934 (m-80) REVERT: J 194 ASN cc_start: 0.9007 (t0) cc_final: 0.8691 (t0) REVERT: J 195 THR cc_start: 0.8091 (p) cc_final: 0.7890 (t) REVERT: J 196 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7835 (mm) REVERT: J 198 SER cc_start: 0.9067 (m) cc_final: 0.8798 (p) REVERT: J 206 GLN cc_start: 0.8926 (mt0) cc_final: 0.8541 (mt0) REVERT: J 208 MET cc_start: 0.8597 (mmt) cc_final: 0.8362 (mmp) REVERT: K 96 ASN cc_start: 0.9333 (m-40) cc_final: 0.9054 (m-40) REVERT: K 103 SER cc_start: 0.9389 (t) cc_final: 0.9185 (p) REVERT: K 129 GLU cc_start: 0.8426 (mm-30) cc_final: 0.7794 (mm-30) REVERT: K 132 MET cc_start: 0.9199 (mtt) cc_final: 0.8560 (mmm) REVERT: K 143 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8257 (tp) REVERT: M 78 ARG cc_start: 0.8558 (mtt180) cc_final: 0.8235 (ttp-110) REVERT: M 85 GLN cc_start: 0.8658 (tt0) cc_final: 0.8250 (tm-30) REVERT: M 91 ASN cc_start: 0.8528 (m-40) cc_final: 0.8095 (m-40) REVERT: M 102 MET cc_start: 0.7780 (OUTLIER) cc_final: 0.7520 (ttm) REVERT: O 78 ARG cc_start: 0.9001 (mmm-85) cc_final: 0.8616 (tpt90) REVERT: O 94 ARG cc_start: 0.8208 (ttt-90) cc_final: 0.7844 (ttp-170) REVERT: O 114 TYR cc_start: 0.8330 (t80) cc_final: 0.7949 (t80) REVERT: Q 33 MET cc_start: 0.8478 (tpp) cc_final: 0.8217 (tpp) REVERT: Q 48 ASP cc_start: 0.8753 (t70) cc_final: 0.8210 (t0) REVERT: Q 112 TYR cc_start: 0.8409 (t80) cc_final: 0.7655 (t80) REVERT: Q 153 ARG cc_start: 0.7647 (tpp80) cc_final: 0.7102 (ttm110) REVERT: Q 166 TYR cc_start: 0.8556 (m-10) cc_final: 0.7938 (m-10) REVERT: Q 170 GLU cc_start: 0.7506 (tt0) cc_final: 0.7022 (mp0) REVERT: Q 171 ASP cc_start: 0.8615 (OUTLIER) cc_final: 0.8300 (p0) REVERT: Q 201 LYS cc_start: 0.8046 (tttt) cc_final: 0.7563 (ptmt) REVERT: Q 205 LYS cc_start: 0.5999 (mmtt) cc_final: 0.5735 (pttm) REVERT: Q 221 ASP cc_start: 0.7817 (m-30) cc_final: 0.7450 (m-30) REVERT: R 79 ASP cc_start: 0.8449 (m-30) cc_final: 0.7619 (t0) REVERT: S 37 ASP cc_start: 0.6671 (t0) cc_final: 0.6022 (t70) REVERT: S 48 ASP cc_start: 0.8255 (OUTLIER) cc_final: 0.7790 (t0) REVERT: S 57 GLU cc_start: 0.7070 (OUTLIER) cc_final: 0.5920 (mp0) REVERT: S 64 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8511 (mt-10) REVERT: S 106 ASP cc_start: 0.9419 (m-30) cc_final: 0.9045 (t70) REVERT: S 112 TYR cc_start: 0.8541 (t80) cc_final: 0.8138 (t80) outliers start: 150 outliers final: 118 residues processed: 763 average time/residue: 0.4700 time to fit residues: 594.8605 Evaluate side-chains 775 residues out of total 3955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 650 time to evaluate : 4.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 553 ARG Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 553 ARG Chi-restraints excluded: chain C residue 18 PHE Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 32 CYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 371 ASP Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 545 ILE Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 497 GLN Chi-restraints excluded: chain D residue 498 SER Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 356 MET Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 253 SER Chi-restraints excluded: chain F residue 281 THR Chi-restraints excluded: chain F residue 316 GLU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain I residue 91 ILE Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 133 ILE Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 192 VAL Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain K residue 117 ASP Chi-restraints excluded: chain K residue 143 LEU Chi-restraints excluded: chain K residue 159 THR Chi-restraints excluded: chain K residue 195 THR Chi-restraints excluded: chain K residue 226 ASP Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 102 MET Chi-restraints excluded: chain N residue 86 SER Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain N residue 106 VAL Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain O residue 116 ILE Chi-restraints excluded: chain Q residue 15 SER Chi-restraints excluded: chain Q residue 88 LEU Chi-restraints excluded: chain Q residue 91 LEU Chi-restraints excluded: chain Q residue 107 LEU Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 142 ASN Chi-restraints excluded: chain Q residue 171 ASP Chi-restraints excluded: chain Q residue 230 ILE Chi-restraints excluded: chain R residue 64 GLU Chi-restraints excluded: chain R residue 85 SER Chi-restraints excluded: chain R residue 156 THR Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 171 ASP Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 188 MET Chi-restraints excluded: chain R residue 227 LYS Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain S residue 48 ASP Chi-restraints excluded: chain S residue 57 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 268 optimal weight: 0.9990 chunk 173 optimal weight: 9.9990 chunk 259 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 chunk 84 optimal weight: 0.7980 chunk 276 optimal weight: 1.9990 chunk 296 optimal weight: 2.9990 chunk 214 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 341 optimal weight: 0.1980 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 ASN C 114 GLN C 123 ASN D 465 GLN E 262 ASN ** E 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.5162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 36765 Z= 0.193 Angle : 0.570 10.611 49676 Z= 0.278 Chirality : 0.043 0.331 5575 Planarity : 0.004 0.048 6440 Dihedral : 4.564 110.435 5022 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.20 % Favored : 96.78 % Rotamer: Outliers : 3.11 % Allowed : 18.18 % Favored : 78.71 % 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: 1.01 (0.13), residues: 4538 helix: 2.00 (0.12), residues: 2069 sheet: -0.67 (0.20), residues: 639 loop : -0.32 (0.15), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP Q 55 HIS 0.010 0.001 HIS F 363 PHE 0.035 0.001 PHE R 200 TYR 0.025 0.001 TYR H 200 ARG 0.006 0.000 ARG H 13 *********************** 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 810 residues out of total 3955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 687 time to evaluate : 4.398 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 56 ARG cc_start: 0.7483 (mtm180) cc_final: 0.6993 (mtm180) REVERT: A 108 ASP cc_start: 0.8287 (m-30) cc_final: 0.8010 (t0) REVERT: A 131 ILE cc_start: 0.8902 (mt) cc_final: 0.8437 (tp) REVERT: A 173 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.7513 (pmt100) REVERT: A 219 GLU cc_start: 0.8058 (tt0) cc_final: 0.7594 (pt0) REVERT: A 235 ASP cc_start: 0.8410 (t70) cc_final: 0.8171 (t0) REVERT: A 254 CYS cc_start: 0.8491 (m) cc_final: 0.7989 (m) REVERT: A 318 MET cc_start: 0.8943 (mtt) cc_final: 0.8661 (mmm) REVERT: A 346 MET cc_start: 0.7880 (ttt) cc_final: 0.7405 (ttt) REVERT: A 349 ASP cc_start: 0.8996 (t0) cc_final: 0.8679 (t0) REVERT: A 485 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7764 (mp0) REVERT: A 487 GLU cc_start: 0.8278 (tm-30) cc_final: 0.7893 (tm-30) REVERT: A 523 ASN cc_start: 0.8217 (t0) cc_final: 0.7997 (t0) REVERT: A 544 MET cc_start: 0.8200 (ttm) cc_final: 0.7742 (mtt) REVERT: B 30 THR cc_start: 0.8544 (m) cc_final: 0.8243 (p) REVERT: B 39 MET cc_start: 0.8252 (mtp) cc_final: 0.7994 (ttt) REVERT: B 74 SER cc_start: 0.8001 (m) cc_final: 0.7052 (p) REVERT: B 77 ASP cc_start: 0.8285 (m-30) cc_final: 0.7278 (m-30) REVERT: B 84 LYS cc_start: 0.8062 (mmtt) cc_final: 0.7458 (mmtt) REVERT: B 115 SER cc_start: 0.9058 (t) cc_final: 0.8610 (p) REVERT: B 116 ILE cc_start: 0.9070 (pt) cc_final: 0.8802 (pt) REVERT: B 142 ARG cc_start: 0.8799 (mmm160) cc_final: 0.8343 (tpp80) REVERT: B 161 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8529 (tp) REVERT: B 201 GLU cc_start: 0.7388 (tm-30) cc_final: 0.6591 (tm-30) REVERT: B 308 ARG cc_start: 0.6605 (ptp-110) cc_final: 0.6232 (ptt180) REVERT: B 349 ASP cc_start: 0.7081 (p0) cc_final: 0.6712 (p0) REVERT: B 399 GLU cc_start: 0.8683 (tp30) cc_final: 0.8193 (mm-30) REVERT: B 419 ASP cc_start: 0.7113 (t0) cc_final: 0.6799 (t0) REVERT: B 485 GLU cc_start: 0.8116 (tp30) cc_final: 0.7321 (tp30) REVERT: B 486 GLU cc_start: 0.8852 (tm-30) cc_final: 0.8535 (tm-30) REVERT: B 488 ASP cc_start: 0.8278 (m-30) cc_final: 0.7570 (t0) REVERT: C 30 THR cc_start: 0.8341 (m) cc_final: 0.7934 (p) REVERT: C 84 LYS cc_start: 0.8341 (mmtt) cc_final: 0.7489 (pttm) REVERT: C 100 ASP cc_start: 0.8264 (t0) cc_final: 0.8003 (t0) REVERT: C 140 ASN cc_start: 0.8221 (m-40) cc_final: 0.7801 (m110) REVERT: C 155 ILE cc_start: 0.8685 (mm) cc_final: 0.8378 (mm) REVERT: C 299 ASP cc_start: 0.7948 (m-30) cc_final: 0.7356 (p0) REVERT: C 306 MET cc_start: 0.8826 (mmt) cc_final: 0.8554 (tpp) REVERT: C 387 GLU cc_start: 0.7895 (tp30) cc_final: 0.7654 (tp30) REVERT: C 436 ASP cc_start: 0.8326 (t0) cc_final: 0.7979 (t70) REVERT: C 447 SER cc_start: 0.8731 (m) cc_final: 0.8171 (p) REVERT: C 484 GLN cc_start: 0.8477 (tp-100) cc_final: 0.8249 (tp40) REVERT: C 606 GLU cc_start: 0.8636 (tt0) cc_final: 0.7741 (tp30) REVERT: D 238 MET cc_start: 0.8018 (tmm) cc_final: 0.7426 (tmm) REVERT: D 315 GLU cc_start: 0.8728 (tt0) cc_final: 0.8236 (tm-30) REVERT: D 336 GLU cc_start: 0.8956 (mm-30) cc_final: 0.8645 (mm-30) REVERT: D 356 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.8439 (mtp) REVERT: D 357 PRO cc_start: 0.9119 (Cg_exo) cc_final: 0.8783 (Cg_endo) REVERT: D 358 ASN cc_start: 0.9122 (t0) cc_final: 0.8824 (t0) REVERT: D 360 ASP cc_start: 0.8563 (t0) cc_final: 0.8167 (t70) REVERT: D 402 MET cc_start: 0.8486 (tmm) cc_final: 0.7691 (tmm) REVERT: D 410 MET cc_start: 0.8578 (mmm) cc_final: 0.7995 (mtm) REVERT: E 70 GLU cc_start: 0.7718 (tt0) cc_final: 0.7243 (tt0) REVERT: E 201 GLU cc_start: 0.8626 (mp0) cc_final: 0.7959 (mp0) REVERT: E 256 ASN cc_start: 0.7677 (m-40) cc_final: 0.6938 (p0) REVERT: E 270 GLU cc_start: 0.8324 (tt0) cc_final: 0.7618 (tm-30) REVERT: E 330 ASP cc_start: 0.8812 (m-30) cc_final: 0.8271 (t0) REVERT: E 382 GLN cc_start: 0.8889 (mm-40) cc_final: 0.8408 (tp40) REVERT: E 410 MET cc_start: 0.8519 (mpp) cc_final: 0.7979 (mtp) REVERT: F 164 ILE cc_start: 0.7876 (mm) cc_final: 0.7565 (mm) REVERT: F 180 MET cc_start: 0.8733 (mmm) cc_final: 0.8404 (tpp) REVERT: F 214 LYS cc_start: 0.9135 (pttt) cc_final: 0.8700 (tppt) REVERT: F 234 MET cc_start: 0.8741 (mtm) cc_final: 0.8472 (mtm) REVERT: F 254 MET cc_start: 0.7995 (tpp) cc_final: 0.7674 (tpp) REVERT: F 309 GLU cc_start: 0.8410 (tm-30) cc_final: 0.7879 (tt0) REVERT: F 315 GLU cc_start: 0.8781 (mt-10) cc_final: 0.8144 (mm-30) REVERT: F 317 VAL cc_start: 0.9195 (t) cc_final: 0.8992 (p) REVERT: F 342 GLU cc_start: 0.8920 (tt0) cc_final: 0.8399 (tp30) REVERT: F 351 ILE cc_start: 0.8771 (mt) cc_final: 0.8451 (mm) REVERT: F 464 THR cc_start: 0.8711 (m) cc_final: 0.8010 (p) REVERT: F 482 GLN cc_start: 0.7898 (mt0) cc_final: 0.7662 (tt0) REVERT: H 206 GLN cc_start: 0.8624 (tm-30) cc_final: 0.8083 (tm-30) REVERT: H 210 LYS cc_start: 0.9256 (tttm) cc_final: 0.8883 (ttmm) REVERT: I 74 ASN cc_start: 0.8891 (t0) cc_final: 0.8288 (t0) REVERT: I 78 GLN cc_start: 0.9095 (mm-40) cc_final: 0.8685 (mm110) REVERT: I 129 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8443 (mm-30) REVERT: I 132 MET cc_start: 0.9379 (mmt) cc_final: 0.9047 (mmt) REVERT: I 167 ILE cc_start: 0.7949 (mm) cc_final: 0.7684 (mm) REVERT: I 173 LEU cc_start: 0.9003 (mt) cc_final: 0.8750 (mt) REVERT: I 183 ILE cc_start: 0.8985 (mt) cc_final: 0.8740 (mm) REVERT: J 78 GLN cc_start: 0.7719 (tp40) cc_final: 0.7198 (tm-30) REVERT: J 97 GLU cc_start: 0.8660 (tt0) cc_final: 0.8247 (tp30) REVERT: J 172 TYR cc_start: 0.8168 (m-80) cc_final: 0.7617 (m-10) REVERT: J 185 ASN cc_start: 0.7702 (p0) cc_final: 0.7354 (p0) REVERT: J 194 ASN cc_start: 0.9070 (t0) cc_final: 0.8738 (t0) REVERT: J 196 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7904 (mm) REVERT: J 198 SER cc_start: 0.8977 (m) cc_final: 0.8691 (p) REVERT: J 206 GLN cc_start: 0.8932 (mt0) cc_final: 0.8575 (mt0) REVERT: J 208 MET cc_start: 0.8593 (mmt) cc_final: 0.8360 (mmp) REVERT: J 223 LYS cc_start: 0.8853 (mmtt) cc_final: 0.8363 (mptt) REVERT: K 96 ASN cc_start: 0.9297 (m-40) cc_final: 0.9026 (m-40) REVERT: K 103 SER cc_start: 0.9378 (t) cc_final: 0.9149 (p) REVERT: K 129 GLU cc_start: 0.8389 (mm-30) cc_final: 0.7690 (mm-30) REVERT: K 132 MET cc_start: 0.9133 (mtt) cc_final: 0.8436 (mmm) REVERT: K 187 ASP cc_start: 0.8397 (p0) cc_final: 0.7792 (p0) REVERT: K 189 LYS cc_start: 0.8467 (mttt) cc_final: 0.8095 (mttm) REVERT: M 78 ARG cc_start: 0.8545 (mtt180) cc_final: 0.8277 (ttp-110) REVERT: M 85 GLN cc_start: 0.8709 (tt0) cc_final: 0.8296 (tm-30) REVERT: M 91 ASN cc_start: 0.8482 (m-40) cc_final: 0.8025 (m-40) REVERT: M 102 MET cc_start: 0.7754 (OUTLIER) cc_final: 0.7446 (ttm) REVERT: N 100 LEU cc_start: 0.8249 (tt) cc_final: 0.8022 (mt) REVERT: O 78 ARG cc_start: 0.9001 (mmm-85) cc_final: 0.8537 (tpt90) REVERT: O 94 ARG cc_start: 0.8191 (ttt-90) cc_final: 0.7828 (ttp-170) REVERT: O 114 TYR cc_start: 0.8307 (t80) cc_final: 0.7914 (t80) REVERT: Q 33 MET cc_start: 0.8436 (tpp) cc_final: 0.8233 (tpp) REVERT: Q 48 ASP cc_start: 0.8726 (t70) cc_final: 0.8211 (t0) REVERT: Q 112 TYR cc_start: 0.8361 (t80) cc_final: 0.8049 (t80) REVERT: Q 166 TYR cc_start: 0.8540 (m-10) cc_final: 0.7808 (m-10) REVERT: Q 171 ASP cc_start: 0.8574 (OUTLIER) cc_final: 0.8313 (p0) REVERT: Q 188 MET cc_start: 0.7159 (ttm) cc_final: 0.6677 (ttt) REVERT: Q 201 LYS cc_start: 0.8004 (tttt) cc_final: 0.7514 (ptmt) REVERT: Q 205 LYS cc_start: 0.5953 (mmtt) cc_final: 0.5706 (pttm) REVERT: Q 221 ASP cc_start: 0.7826 (m-30) cc_final: 0.7535 (m-30) REVERT: R 33 MET cc_start: 0.8023 (mmm) cc_final: 0.7532 (mmm) REVERT: R 78 LEU cc_start: 0.8540 (tp) cc_final: 0.8207 (tp) REVERT: R 79 ASP cc_start: 0.8376 (m-30) cc_final: 0.7544 (t0) REVERT: S 37 ASP cc_start: 0.6652 (t0) cc_final: 0.5945 (t70) REVERT: S 48 ASP cc_start: 0.8231 (OUTLIER) cc_final: 0.7438 (t0) REVERT: S 57 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.5739 (mp0) REVERT: S 64 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8560 (mt-10) REVERT: S 106 ASP cc_start: 0.9408 (m-30) cc_final: 0.9009 (t70) REVERT: S 112 TYR cc_start: 0.8523 (t80) cc_final: 0.8063 (t80) outliers start: 123 outliers final: 99 residues processed: 763 average time/residue: 0.4794 time to fit residues: 605.1151 Evaluate side-chains 771 residues out of total 3955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 664 time to evaluate : 4.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 553 ARG Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 553 ARG Chi-restraints excluded: chain C residue 18 PHE Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 32 CYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 117 TYR Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 371 ASP Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 498 SER Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 262 ASN Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 356 MET Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 316 GLU Chi-restraints excluded: chain F residue 365 ILE Chi-restraints excluded: chain F residue 383 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain I residue 91 ILE Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 192 VAL Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain J residue 73 SER Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain K residue 117 ASP Chi-restraints excluded: chain K residue 159 THR Chi-restraints excluded: chain K residue 195 THR Chi-restraints excluded: chain K residue 226 ASP Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 102 MET Chi-restraints excluded: chain N residue 106 VAL Chi-restraints excluded: chain O residue 116 ILE Chi-restraints excluded: chain Q residue 15 SER Chi-restraints excluded: chain Q residue 88 LEU Chi-restraints excluded: chain Q residue 91 LEU Chi-restraints excluded: chain Q residue 107 LEU Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 142 ASN Chi-restraints excluded: chain Q residue 171 ASP Chi-restraints excluded: chain Q residue 230 ILE Chi-restraints excluded: chain R residue 64 GLU Chi-restraints excluded: chain R residue 85 SER Chi-restraints excluded: chain R residue 156 THR Chi-restraints excluded: chain R residue 171 ASP Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 188 MET Chi-restraints excluded: chain R residue 200 PHE Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain S residue 48 ASP Chi-restraints excluded: chain S residue 57 GLU Chi-restraints excluded: chain S residue 142 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 395 optimal weight: 0.9990 chunk 416 optimal weight: 6.9990 chunk 379 optimal weight: 7.9990 chunk 405 optimal weight: 0.0570 chunk 243 optimal weight: 0.9990 chunk 176 optimal weight: 7.9990 chunk 318 optimal weight: 8.9990 chunk 124 optimal weight: 0.7980 chunk 366 optimal weight: 3.9990 chunk 383 optimal weight: 1.9990 chunk 403 optimal weight: 4.9990 overall best weight: 0.9704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 262 ASN ** E 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 198 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.5236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 36765 Z= 0.185 Angle : 0.573 10.873 49676 Z= 0.277 Chirality : 0.043 0.212 5575 Planarity : 0.004 0.048 6440 Dihedral : 4.484 109.393 5022 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.24 % Favored : 96.74 % Rotamer: Outliers : 3.01 % Allowed : 18.61 % Favored : 78.38 % 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: 1.01 (0.13), residues: 4538 helix: 1.98 (0.12), residues: 2079 sheet: -0.69 (0.20), residues: 632 loop : -0.29 (0.15), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP Q 55 HIS 0.010 0.001 HIS F 363 PHE 0.023 0.001 PHE R 200 TYR 0.022 0.001 TYR H 200 ARG 0.013 0.000 ARG E 271 *********************** 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 806 residues out of total 3955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 687 time to evaluate : 4.639 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: A 56 ARG cc_start: 0.7467 (mtm180) cc_final: 0.6999 (mtm180) REVERT: A 108 ASP cc_start: 0.8317 (m-30) cc_final: 0.8046 (t0) REVERT: A 131 ILE cc_start: 0.8910 (mt) cc_final: 0.8458 (tp) REVERT: A 219 GLU cc_start: 0.8053 (tt0) cc_final: 0.7585 (pt0) REVERT: A 254 CYS cc_start: 0.8463 (m) cc_final: 0.7971 (m) REVERT: A 296 MET cc_start: 0.7600 (ttm) cc_final: 0.7356 (ttp) REVERT: A 346 MET cc_start: 0.7859 (ttt) cc_final: 0.7376 (ttt) REVERT: A 349 ASP cc_start: 0.8993 (t0) cc_final: 0.8670 (t0) REVERT: A 485 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7485 (mp0) REVERT: A 523 ASN cc_start: 0.8209 (t0) cc_final: 0.7988 (t0) REVERT: B 30 THR cc_start: 0.8636 (m) cc_final: 0.8242 (p) REVERT: B 74 SER cc_start: 0.7987 (m) cc_final: 0.7206 (p) REVERT: B 77 ASP cc_start: 0.8279 (m-30) cc_final: 0.7346 (m-30) REVERT: B 84 LYS cc_start: 0.7991 (mmtt) cc_final: 0.7401 (mmtt) REVERT: B 115 SER cc_start: 0.9072 (t) cc_final: 0.8625 (p) REVERT: B 116 ILE cc_start: 0.9117 (pt) cc_final: 0.8862 (pt) REVERT: B 142 ARG cc_start: 0.8805 (mmm160) cc_final: 0.8359 (tpp80) REVERT: B 161 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8519 (tp) REVERT: B 201 GLU cc_start: 0.7461 (tm-30) cc_final: 0.6650 (tm-30) REVERT: B 308 ARG cc_start: 0.6658 (ptp-110) cc_final: 0.6127 (ptt180) REVERT: B 349 ASP cc_start: 0.7112 (p0) cc_final: 0.6799 (p0) REVERT: B 399 GLU cc_start: 0.8651 (tp30) cc_final: 0.8182 (mm-30) REVERT: B 419 ASP cc_start: 0.7087 (t0) cc_final: 0.6804 (t0) REVERT: B 485 GLU cc_start: 0.8042 (tp30) cc_final: 0.7232 (tp30) REVERT: B 486 GLU cc_start: 0.8852 (tm-30) cc_final: 0.8537 (tm-30) REVERT: B 488 ASP cc_start: 0.8242 (m-30) cc_final: 0.7528 (t0) REVERT: C 30 THR cc_start: 0.8350 (m) cc_final: 0.7914 (p) REVERT: C 84 LYS cc_start: 0.8329 (mmtt) cc_final: 0.7461 (pttm) REVERT: C 100 ASP cc_start: 0.8284 (t0) cc_final: 0.8025 (t0) REVERT: C 140 ASN cc_start: 0.8161 (m-40) cc_final: 0.7772 (m110) REVERT: C 155 ILE cc_start: 0.8699 (mm) cc_final: 0.8399 (mm) REVERT: C 299 ASP cc_start: 0.7997 (m-30) cc_final: 0.7456 (p0) REVERT: C 306 MET cc_start: 0.8819 (mmt) cc_final: 0.8544 (tpp) REVERT: C 387 GLU cc_start: 0.7916 (tp30) cc_final: 0.7698 (tp30) REVERT: C 447 SER cc_start: 0.8734 (m) cc_final: 0.8226 (p) REVERT: C 448 VAL cc_start: 0.7558 (t) cc_final: 0.7233 (m) REVERT: C 449 ASN cc_start: 0.7970 (t0) cc_final: 0.7493 (t0) REVERT: C 484 GLN cc_start: 0.8476 (tp-100) cc_final: 0.8239 (tp40) REVERT: C 520 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.7946 (tt) REVERT: D 238 MET cc_start: 0.8210 (tmm) cc_final: 0.7831 (tmm) REVERT: D 247 ASP cc_start: 0.8163 (t0) cc_final: 0.7927 (t0) REVERT: D 315 GLU cc_start: 0.8733 (tt0) cc_final: 0.8298 (tm-30) REVERT: D 336 GLU cc_start: 0.8954 (mm-30) cc_final: 0.8647 (mm-30) REVERT: D 356 MET cc_start: 0.8708 (mtp) cc_final: 0.8445 (mtp) REVERT: D 357 PRO cc_start: 0.9133 (Cg_exo) cc_final: 0.8813 (Cg_endo) REVERT: D 358 ASN cc_start: 0.9154 (t0) cc_final: 0.8867 (t0) REVERT: D 360 ASP cc_start: 0.8557 (t0) cc_final: 0.8162 (t70) REVERT: D 402 MET cc_start: 0.8497 (tmm) cc_final: 0.7738 (tmm) REVERT: D 410 MET cc_start: 0.8603 (mmm) cc_final: 0.8077 (mtm) REVERT: E 70 GLU cc_start: 0.7709 (tt0) cc_final: 0.7265 (tt0) REVERT: E 201 GLU cc_start: 0.8621 (mp0) cc_final: 0.8096 (mp0) REVERT: E 256 ASN cc_start: 0.7713 (m-40) cc_final: 0.6983 (p0) REVERT: E 330 ASP cc_start: 0.8812 (m-30) cc_final: 0.8273 (t0) REVERT: E 371 TYR cc_start: 0.7723 (m-10) cc_final: 0.7505 (m-10) REVERT: E 382 GLN cc_start: 0.8886 (mm-40) cc_final: 0.8422 (tp40) REVERT: E 410 MET cc_start: 0.8512 (mpp) cc_final: 0.8020 (mtp) REVERT: F 164 ILE cc_start: 0.7919 (mm) cc_final: 0.7638 (mm) REVERT: F 180 MET cc_start: 0.8754 (mmm) cc_final: 0.8465 (tpp) REVERT: F 214 LYS cc_start: 0.9136 (pttt) cc_final: 0.8711 (tppt) REVERT: F 234 MET cc_start: 0.8747 (mtm) cc_final: 0.8430 (mtm) REVERT: F 254 MET cc_start: 0.7864 (tpp) cc_final: 0.7614 (tpp) REVERT: F 309 GLU cc_start: 0.8396 (tm-30) cc_final: 0.7881 (tt0) REVERT: F 315 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8161 (mm-30) REVERT: F 336 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8356 (mm-30) REVERT: F 351 ILE cc_start: 0.8747 (mt) cc_final: 0.8461 (mm) REVERT: F 464 THR cc_start: 0.8704 (m) cc_final: 0.7996 (p) REVERT: F 482 GLN cc_start: 0.8009 (mt0) cc_final: 0.7789 (tt0) REVERT: H 193 GLU cc_start: 0.8437 (tm-30) cc_final: 0.8203 (tm-30) REVERT: H 206 GLN cc_start: 0.8678 (tm-30) cc_final: 0.8126 (tm-30) REVERT: H 210 LYS cc_start: 0.9208 (tttm) cc_final: 0.8851 (ttmm) REVERT: I 74 ASN cc_start: 0.8884 (t0) cc_final: 0.8289 (t0) REVERT: I 78 GLN cc_start: 0.9092 (mm-40) cc_final: 0.8681 (mm110) REVERT: I 129 GLU cc_start: 0.8726 (mm-30) cc_final: 0.8450 (mm-30) REVERT: I 132 MET cc_start: 0.9374 (mmt) cc_final: 0.9041 (mmt) REVERT: I 167 ILE cc_start: 0.7948 (mm) cc_final: 0.7665 (mm) REVERT: I 183 ILE cc_start: 0.8943 (mt) cc_final: 0.8616 (mm) REVERT: J 78 GLN cc_start: 0.7721 (tp40) cc_final: 0.7206 (tm-30) REVERT: J 97 GLU cc_start: 0.8634 (tt0) cc_final: 0.8228 (tp30) REVERT: J 172 TYR cc_start: 0.8180 (m-80) cc_final: 0.7654 (m-10) REVERT: J 185 ASN cc_start: 0.7429 (p0) cc_final: 0.7105 (p0) REVERT: J 194 ASN cc_start: 0.9011 (t0) cc_final: 0.8627 (t0) REVERT: J 196 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7893 (mm) REVERT: J 198 SER cc_start: 0.8984 (m) cc_final: 0.8701 (p) REVERT: J 206 GLN cc_start: 0.8857 (mt0) cc_final: 0.8548 (mt0) REVERT: J 208 MET cc_start: 0.8594 (mmt) cc_final: 0.8362 (mmp) REVERT: J 223 LYS cc_start: 0.8854 (mmtt) cc_final: 0.8358 (mptt) REVERT: K 96 ASN cc_start: 0.9260 (m-40) cc_final: 0.8990 (m-40) REVERT: K 103 SER cc_start: 0.9361 (t) cc_final: 0.9118 (p) REVERT: K 129 GLU cc_start: 0.8372 (mm-30) cc_final: 0.7524 (mm-30) REVERT: K 132 MET cc_start: 0.9120 (mtt) cc_final: 0.8585 (mmm) REVERT: M 78 ARG cc_start: 0.8543 (mtt180) cc_final: 0.8281 (ttp-110) REVERT: M 85 GLN cc_start: 0.8710 (tt0) cc_final: 0.8314 (tm-30) REVERT: M 90 ARG cc_start: 0.7954 (mtm110) cc_final: 0.7578 (mtm110) REVERT: M 91 ASN cc_start: 0.8495 (m-40) cc_final: 0.8026 (m-40) REVERT: M 102 MET cc_start: 0.7714 (OUTLIER) cc_final: 0.7393 (ttm) REVERT: N 100 LEU cc_start: 0.8250 (tt) cc_final: 0.8048 (mt) REVERT: O 78 ARG cc_start: 0.9083 (mmm-85) cc_final: 0.8623 (tpt90) REVERT: O 94 ARG cc_start: 0.8169 (ttt-90) cc_final: 0.7811 (ttp-170) REVERT: O 114 TYR cc_start: 0.8316 (t80) cc_final: 0.7877 (t80) REVERT: Q 33 MET cc_start: 0.8472 (tpp) cc_final: 0.8261 (tpp) REVERT: Q 48 ASP cc_start: 0.8733 (t70) cc_final: 0.8239 (t0) REVERT: Q 112 TYR cc_start: 0.8340 (t80) cc_final: 0.8054 (t80) REVERT: Q 166 TYR cc_start: 0.8542 (m-10) cc_final: 0.7817 (m-10) REVERT: Q 171 ASP cc_start: 0.8567 (OUTLIER) cc_final: 0.7999 (t0) REVERT: Q 188 MET cc_start: 0.7097 (ttm) cc_final: 0.6499 (ttt) REVERT: Q 201 LYS cc_start: 0.7978 (tttt) cc_final: 0.7520 (ptmt) REVERT: Q 221 ASP cc_start: 0.7779 (m-30) cc_final: 0.7456 (m-30) REVERT: R 78 LEU cc_start: 0.8542 (tp) cc_final: 0.8214 (tp) REVERT: R 79 ASP cc_start: 0.8390 (m-30) cc_final: 0.7592 (t0) REVERT: S 37 ASP cc_start: 0.6588 (t0) cc_final: 0.5886 (t70) REVERT: S 48 ASP cc_start: 0.8188 (OUTLIER) cc_final: 0.7378 (t0) REVERT: S 57 GLU cc_start: 0.6980 (OUTLIER) cc_final: 0.5731 (mp0) REVERT: S 64 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8523 (mt-10) REVERT: S 103 MET cc_start: 0.8430 (ptm) cc_final: 0.7540 (ptm) REVERT: S 106 ASP cc_start: 0.9414 (m-30) cc_final: 0.9024 (t70) REVERT: S 112 TYR cc_start: 0.8507 (t80) cc_final: 0.8048 (t80) outliers start: 119 outliers final: 102 residues processed: 761 average time/residue: 0.5026 time to fit residues: 639.1881 Evaluate side-chains 768 residues out of total 3955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 659 time to evaluate : 4.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 553 ARG Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 553 ARG Chi-restraints excluded: chain C residue 18 PHE Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 32 CYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 117 TYR Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 371 ASP Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 356 MET Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 365 ILE Chi-restraints excluded: chain F residue 383 LEU Chi-restraints excluded: chain F residue 444 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain I residue 91 ILE Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 192 VAL Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain K residue 117 ASP Chi-restraints excluded: chain K residue 159 THR Chi-restraints excluded: chain K residue 195 THR Chi-restraints excluded: chain K residue 226 ASP Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 102 MET Chi-restraints excluded: chain N residue 106 VAL Chi-restraints excluded: chain O residue 116 ILE Chi-restraints excluded: chain Q residue 15 SER Chi-restraints excluded: chain Q residue 88 LEU Chi-restraints excluded: chain Q residue 91 LEU Chi-restraints excluded: chain Q residue 107 LEU Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 142 ASN Chi-restraints excluded: chain Q residue 171 ASP Chi-restraints excluded: chain Q residue 230 ILE Chi-restraints excluded: chain R residue 64 GLU Chi-restraints excluded: chain R residue 85 SER Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 188 MET Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain S residue 48 ASP Chi-restraints excluded: chain S residue 57 GLU Chi-restraints excluded: chain S residue 142 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 266 optimal weight: 3.9990 chunk 428 optimal weight: 9.9990 chunk 261 optimal weight: 6.9990 chunk 203 optimal weight: 7.9990 chunk 297 optimal weight: 1.9990 chunk 449 optimal weight: 2.9990 chunk 413 optimal weight: 5.9990 chunk 357 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 276 optimal weight: 0.7980 chunk 219 optimal weight: 9.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 ASN C 603 GLN D 181 ASN D 497 GLN ** E 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.5396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 36765 Z= 0.396 Angle : 0.664 11.889 49676 Z= 0.327 Chirality : 0.046 0.221 5575 Planarity : 0.004 0.078 6440 Dihedral : 4.752 106.378 5022 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.12 % Favored : 95.86 % Rotamer: Outliers : 3.34 % Allowed : 18.49 % Favored : 78.17 % 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: 0.78 (0.13), residues: 4538 helix: 1.83 (0.12), residues: 2087 sheet: -0.87 (0.20), residues: 623 loop : -0.45 (0.15), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP Q 55 HIS 0.013 0.001 HIS F 363 PHE 0.039 0.002 PHE R 200 TYR 0.031 0.002 TYR H 186 ARG 0.030 0.001 ARG O 115 ********************** REFINEMENT MACRO_CYCLE 10 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 794 residues out of total 3955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 662 time to evaluate : 4.395 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 108 ASP cc_start: 0.8361 (m-30) cc_final: 0.8033 (t0) REVERT: A 131 ILE cc_start: 0.8942 (OUTLIER) cc_final: 0.8475 (tp) REVERT: A 219 GLU cc_start: 0.8088 (tt0) cc_final: 0.7592 (pt0) REVERT: A 254 CYS cc_start: 0.8297 (m) cc_final: 0.7928 (m) REVERT: A 346 MET cc_start: 0.7896 (ttt) cc_final: 0.7406 (ttt) REVERT: A 399 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7611 (mp0) REVERT: A 485 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7521 (mp0) REVERT: A 523 ASN cc_start: 0.8324 (t0) cc_final: 0.8115 (t0) REVERT: B 30 THR cc_start: 0.8593 (m) cc_final: 0.8197 (p) REVERT: B 74 SER cc_start: 0.7893 (m) cc_final: 0.6970 (p) REVERT: B 77 ASP cc_start: 0.8265 (m-30) cc_final: 0.7255 (m-30) REVERT: B 142 ARG cc_start: 0.8824 (mmm160) cc_final: 0.8371 (tpp80) REVERT: B 161 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8660 (tp) REVERT: B 201 GLU cc_start: 0.7473 (tm-30) cc_final: 0.6619 (tm-30) REVERT: B 308 ARG cc_start: 0.6958 (ptp-110) cc_final: 0.6409 (ptt180) REVERT: B 349 ASP cc_start: 0.7080 (p0) cc_final: 0.6793 (p0) REVERT: B 392 VAL cc_start: 0.9102 (OUTLIER) cc_final: 0.8893 (p) REVERT: B 419 ASP cc_start: 0.7167 (t0) cc_final: 0.6886 (t0) REVERT: B 485 GLU cc_start: 0.8137 (tp30) cc_final: 0.7322 (tp30) REVERT: B 486 GLU cc_start: 0.8800 (tm-30) cc_final: 0.8484 (tm-30) REVERT: B 488 ASP cc_start: 0.8309 (m-30) cc_final: 0.7570 (t0) REVERT: C 100 ASP cc_start: 0.8402 (t0) cc_final: 0.8143 (t0) REVERT: C 140 ASN cc_start: 0.8198 (m-40) cc_final: 0.7785 (m110) REVERT: C 155 ILE cc_start: 0.8870 (mm) cc_final: 0.8400 (mm) REVERT: C 284 MET cc_start: 0.8475 (tpp) cc_final: 0.7576 (mpp) REVERT: C 299 ASP cc_start: 0.8165 (m-30) cc_final: 0.7680 (p0) REVERT: C 387 GLU cc_start: 0.7912 (tp30) cc_final: 0.7671 (tp30) REVERT: C 447 SER cc_start: 0.8832 (m) cc_final: 0.8142 (p) REVERT: D 238 MET cc_start: 0.8228 (tmm) cc_final: 0.7888 (tmm) REVERT: D 247 ASP cc_start: 0.8254 (t0) cc_final: 0.8022 (t0) REVERT: D 315 GLU cc_start: 0.8756 (tt0) cc_final: 0.8311 (tm-30) REVERT: D 357 PRO cc_start: 0.9126 (Cg_exo) cc_final: 0.8816 (Cg_endo) REVERT: D 358 ASN cc_start: 0.9205 (t0) cc_final: 0.8925 (t0) REVERT: D 360 ASP cc_start: 0.8627 (t0) cc_final: 0.8291 (t0) REVERT: D 402 MET cc_start: 0.8569 (tmm) cc_final: 0.7689 (tmm) REVERT: D 410 MET cc_start: 0.8631 (mmm) cc_final: 0.8089 (mtm) REVERT: E 256 ASN cc_start: 0.7691 (m-40) cc_final: 0.6956 (p0) REVERT: E 330 ASP cc_start: 0.8927 (m-30) cc_final: 0.8439 (t0) REVERT: E 382 GLN cc_start: 0.8927 (mm-40) cc_final: 0.8491 (tp40) REVERT: E 410 MET cc_start: 0.8503 (mpp) cc_final: 0.8009 (mtp) REVERT: F 164 ILE cc_start: 0.8004 (mm) cc_final: 0.7727 (mm) REVERT: F 180 MET cc_start: 0.8793 (mmm) cc_final: 0.8381 (tpp) REVERT: F 214 LYS cc_start: 0.9163 (pttt) cc_final: 0.8777 (tppt) REVERT: F 234 MET cc_start: 0.8842 (mtm) cc_final: 0.8525 (mtm) REVERT: F 254 MET cc_start: 0.8201 (tpp) cc_final: 0.7849 (tpp) REVERT: F 309 GLU cc_start: 0.8445 (tm-30) cc_final: 0.7949 (tt0) REVERT: F 315 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8215 (mm-30) REVERT: F 464 THR cc_start: 0.8752 (m) cc_final: 0.8081 (p) REVERT: F 482 GLN cc_start: 0.7921 (mt0) cc_final: 0.7649 (tt0) REVERT: H 193 GLU cc_start: 0.8446 (tm-30) cc_final: 0.8180 (tm-30) REVERT: H 206 GLN cc_start: 0.8667 (tm-30) cc_final: 0.8127 (tm-30) REVERT: H 210 LYS cc_start: 0.9269 (tttm) cc_final: 0.8901 (ttmm) REVERT: I 74 ASN cc_start: 0.8910 (t0) cc_final: 0.8318 (t0) REVERT: I 78 GLN cc_start: 0.9083 (mm-40) cc_final: 0.8667 (mm110) REVERT: I 129 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8592 (mm-30) REVERT: I 132 MET cc_start: 0.9356 (mmt) cc_final: 0.8979 (mmt) REVERT: I 167 ILE cc_start: 0.7974 (mm) cc_final: 0.7700 (mm) REVERT: I 183 ILE cc_start: 0.8909 (mt) cc_final: 0.8628 (mm) REVERT: J 97 GLU cc_start: 0.8619 (tt0) cc_final: 0.8230 (tp30) REVERT: J 172 TYR cc_start: 0.8070 (m-80) cc_final: 0.7435 (m-10) REVERT: J 194 ASN cc_start: 0.9052 (t0) cc_final: 0.8727 (t0) REVERT: J 196 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7840 (mm) REVERT: J 198 SER cc_start: 0.9056 (m) cc_final: 0.8792 (p) REVERT: J 206 GLN cc_start: 0.8903 (mt0) cc_final: 0.8542 (mt0) REVERT: J 208 MET cc_start: 0.8596 (mmt) cc_final: 0.8378 (mmp) REVERT: K 96 ASN cc_start: 0.9263 (m-40) cc_final: 0.8968 (m-40) REVERT: K 103 SER cc_start: 0.9361 (t) cc_final: 0.9151 (p) REVERT: K 129 GLU cc_start: 0.8338 (mm-30) cc_final: 0.7645 (mm-30) REVERT: K 132 MET cc_start: 0.9230 (mtt) cc_final: 0.8560 (mmm) REVERT: K 143 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8377 (tp) REVERT: K 189 LYS cc_start: 0.8324 (mttm) cc_final: 0.8080 (mttm) REVERT: M 78 ARG cc_start: 0.8571 (mtt180) cc_final: 0.8333 (ttp-110) REVERT: M 85 GLN cc_start: 0.8712 (tt0) cc_final: 0.8340 (tm-30) REVERT: M 91 ASN cc_start: 0.8463 (m-40) cc_final: 0.7943 (m-40) REVERT: N 74 GLU cc_start: 0.7962 (tp30) cc_final: 0.7698 (tp30) REVERT: N 79 ARG cc_start: 0.8700 (mtm110) cc_final: 0.8290 (mtm-85) REVERT: N 96 LEU cc_start: 0.7749 (tt) cc_final: 0.7082 (tp) REVERT: N 100 LEU cc_start: 0.8232 (tt) cc_final: 0.8012 (mt) REVERT: O 78 ARG cc_start: 0.9050 (mmm-85) cc_final: 0.8669 (tpt90) REVERT: O 94 ARG cc_start: 0.8229 (ttt-90) cc_final: 0.7811 (ttp-170) REVERT: Q 33 MET cc_start: 0.8446 (tpp) cc_final: 0.8079 (tpp) REVERT: Q 48 ASP cc_start: 0.8813 (t70) cc_final: 0.8396 (t0) REVERT: Q 166 TYR cc_start: 0.8583 (m-10) cc_final: 0.7860 (m-10) REVERT: Q 171 ASP cc_start: 0.8586 (OUTLIER) cc_final: 0.8035 (t0) REVERT: Q 201 LYS cc_start: 0.8005 (tttt) cc_final: 0.7580 (ptmt) REVERT: Q 221 ASP cc_start: 0.7906 (m-30) cc_final: 0.7609 (m-30) REVERT: R 79 ASP cc_start: 0.8375 (m-30) cc_final: 0.7560 (t0) REVERT: S 37 ASP cc_start: 0.6511 (t0) cc_final: 0.5807 (t70) REVERT: S 48 ASP cc_start: 0.8241 (OUTLIER) cc_final: 0.7529 (t0) REVERT: S 57 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.5794 (mp0) REVERT: S 64 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8508 (mt-10) REVERT: S 76 ASN cc_start: 0.8398 (t160) cc_final: 0.8173 (t0) REVERT: S 103 MET cc_start: 0.8506 (ptm) cc_final: 0.7603 (ptm) REVERT: S 106 ASP cc_start: 0.9426 (m-30) cc_final: 0.9072 (t70) REVERT: S 112 TYR cc_start: 0.8508 (t80) cc_final: 0.8096 (t80) outliers start: 132 outliers final: 110 residues processed: 749 average time/residue: 0.4621 time to fit residues: 577.4495 Evaluate side-chains 763 residues out of total 3955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 645 time to evaluate : 4.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 553 ARG Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 553 ARG Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 32 CYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 117 TYR Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 340 MET Chi-restraints excluded: chain C residue 371 ASP Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 497 GLN Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 356 MET Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 316 GLU Chi-restraints excluded: chain F residue 365 ILE Chi-restraints excluded: chain F residue 383 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain I residue 91 ILE Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 133 ILE Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 192 VAL Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 117 ASP Chi-restraints excluded: chain K residue 143 LEU Chi-restraints excluded: chain K residue 159 THR Chi-restraints excluded: chain K residue 195 THR Chi-restraints excluded: chain K residue 226 ASP Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain N residue 86 SER Chi-restraints excluded: chain N residue 106 VAL Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain O residue 116 ILE Chi-restraints excluded: chain Q residue 15 SER Chi-restraints excluded: chain Q residue 88 LEU Chi-restraints excluded: chain Q residue 91 LEU Chi-restraints excluded: chain Q residue 107 LEU Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 142 ASN Chi-restraints excluded: chain Q residue 171 ASP Chi-restraints excluded: chain Q residue 230 ILE Chi-restraints excluded: chain R residue 85 SER Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 171 ASP Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 188 MET Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain S residue 48 ASP Chi-restraints excluded: chain S residue 57 GLU Chi-restraints excluded: chain S residue 142 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 284 optimal weight: 0.9990 chunk 381 optimal weight: 0.9990 chunk 109 optimal weight: 5.9990 chunk 329 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 358 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 chunk 367 optimal weight: 8.9990 chunk 45 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 ASN D 262 ASN ** E 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 GLN ** I 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 221 ASN ** S 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 198 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.095344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.078058 restraints weight = 73580.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.080952 restraints weight = 33806.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.082865 restraints weight = 19786.726| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.5410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.231 36765 Z= 0.365 Angle : 0.753 59.162 49676 Z= 0.389 Chirality : 0.045 0.627 5575 Planarity : 0.004 0.066 6440 Dihedral : 4.735 106.311 5018 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.10 % Favored : 95.88 % Rotamer: Outliers : 3.31 % Allowed : 18.77 % Favored : 77.92 % Cbeta Deviations : 0.02 % 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: 0.78 (0.13), residues: 4538 helix: 1.84 (0.12), residues: 2087 sheet: -0.90 (0.20), residues: 623 loop : -0.47 (0.15), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 450 HIS 0.011 0.001 HIS F 363 PHE 0.032 0.002 PHE R 200 TYR 0.024 0.002 TYR H 186 ARG 0.015 0.000 ARG O 115 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10572.77 seconds wall clock time: 191 minutes 28.35 seconds (11488.35 seconds total)