Starting phenix.real_space_refine (version: 1.21rc1) on Mon May 15 15:11:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vq9_21345/05_2023/6vq9_21345_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vq9_21345/05_2023/6vq9_21345.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/6vq9_21345/05_2023/6vq9_21345.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vq9_21345/05_2023/6vq9_21345.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vq9_21345/05_2023/6vq9_21345_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vq9_21345/05_2023/6vq9_21345_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.097 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 2 5.49 5 Mg 1 5.21 5 S 203 5.16 5 C 22864 2.51 5 N 6223 2.21 5 O 6821 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 178": "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 ARG 323": "NH1" <-> "NH2" 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 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 388": "NH1" <-> "NH2" Residue "A ARG 400": "NH1" <-> "NH2" Residue "A ASP 436": "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 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 104": "NH1" <-> "NH2" Residue "B TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 388": "NH1" <-> "NH2" Residue "B ARG 400": "NH1" <-> "NH2" Residue "B PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 445": "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 ASP 529": "OD1" <-> "OD2" Residue "B PHE 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 68": "OE1" <-> "OE2" Residue "C TYR 117": "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 GLU 279": "OE1" <-> "OE2" 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 ARG 388": "NH1" <-> "NH2" Residue "C ASP 419": "OD1" <-> "OD2" Residue "C PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 270": "OE1" <-> "OE2" Residue "D TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F 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 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 216": "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 PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 214": "OE1" <-> "OE2" 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 PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 90": "OE1" <-> "OE2" Residue "S PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 36114 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 4651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4651 Classifications: {'peptide': 600} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 569} Chain: "B" Number of atoms: 4651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4651 Classifications: {'peptide': 600} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 569} Chain: "C" Number of atoms: 4651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4651 Classifications: {'peptide': 600} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 569} Chain: "D" Number of atoms: 3595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3595 Classifications: {'peptide': 459} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 431} Chain breaks: 1 Chain: "E" Number of atoms: 3595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3595 Classifications: {'peptide': 459} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 431} Chain breaks: 1 Chain: "F" Number of atoms: 3595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3595 Classifications: {'peptide': 459} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 431} Chain breaks: 1 Chain: "H" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 914 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 2, 'TRANS': 106} Chain breaks: 1 Chain: "I" Number of atoms: 1288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1288 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 5, 'TRANS': 155} Chain: "J" Number of atoms: 1288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1288 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 5, 'TRANS': 155} Chain: "K" Number of atoms: 1288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1288 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 5, 'TRANS': 155} Chain: "M" Number of atoms: 382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 382 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "N" Number of atoms: 382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 382 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "O" Number of atoms: 382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 382 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "Q" Number of atoms: 1824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1824 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 9, 'TRANS': 214} Chain: "R" 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: "S" 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: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 18.13, per 1000 atoms: 0.50 Number of scatterers: 36114 At special positions: 0 Unit cell: (174.9, 171.72, 143.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 203 16.00 P 2 15.00 Mg 1 11.99 O 6821 8.00 N 6223 7.00 C 22864 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.92 Conformation dependent library (CDL) restraints added in 5.3 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: 3.55 Creating SS restraints... Processing helix chain 'A' and resid 106 through 113 Processing helix chain 'A' and resid 232 through 235 No H-bonds generated for 'chain 'A' and resid 232 through 235' Processing helix chain 'A' and resid 256 through 266 Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 305 through 308 Processing helix chain 'A' and resid 320 through 340 removed outlier: 4.692A pdb=" N ILE A 327 " --> pdb=" O ARG A 323 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N TYR A 328 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N MET A 340 " --> pdb=" O TYR A 336 " (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 378 through 386 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: 4.321A pdb=" N GLU A 463 " --> pdb=" O ARG A 459 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N TYR A 464 " --> pdb=" O ALA A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 496 removed outlier: 3.571A pdb=" N ILE A 492 " --> pdb=" O ASP A 488 " (cutoff:3.500A) removed outlier: 3.869A 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 557 Processing helix chain 'A' and resid 567 through 573 Processing helix chain 'A' and resid 575 through 587 removed outlier: 5.087A pdb=" N LYS A 585 " --> pdb=" O LEU A 581 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N PHE A 586 " --> pdb=" O SER A 582 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LYS A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 615 Processing helix chain 'B' and resid 106 through 112 removed outlier: 3.661A pdb=" N SER B 111 " --> pdb=" O SER B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 254 No H-bonds generated for 'chain 'B' and resid 252 through 254' Processing helix chain 'B' and resid 257 through 266 Processing helix chain 'B' and resid 281 through 293 Proline residue: B 292 - end of helix Processing helix chain 'B' and resid 305 through 307 No H-bonds generated for 'chain 'B' and resid 305 through 307' Processing helix chain 'B' and resid 320 through 340 removed outlier: 4.568A pdb=" N ILE B 327 " --> pdb=" O ARG B 323 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N TYR B 328 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N MET B 340 " --> pdb=" O TYR B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 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 388 removed outlier: 3.746A pdb=" N ARG B 388 " --> pdb=" O SER B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 415 No H-bonds generated for 'chain 'B' and resid 413 through 415' Processing helix chain 'B' and resid 420 through 426 Processing helix chain 'B' and resid 438 through 441 No H-bonds generated for 'chain 'B' and resid 438 through 441' Processing helix chain 'B' and resid 462 through 468 Processing helix chain 'B' and resid 472 through 496 removed outlier: 4.560A pdb=" N GLU B 491 " --> pdb=" O GLU B 487 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ILE B 492 " --> pdb=" O ASP B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 518 Processing helix chain 'B' and resid 534 through 558 removed outlier: 3.894A pdb=" N THR B 558 " --> pdb=" O ALA B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 573 Processing helix chain 'B' and resid 575 through 586 removed outlier: 4.913A pdb=" N LYS B 585 " --> pdb=" O LEU B 581 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N PHE B 586 " --> pdb=" O SER B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 615 removed outlier: 4.043A pdb=" N LEU B 615 " --> pdb=" O ALA B 611 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 113 Processing helix chain 'C' and resid 256 through 265 Processing helix chain 'C' and resid 281 through 293 Proline residue: C 292 - end of helix Processing helix chain 'C' and resid 306 through 308 No H-bonds generated for 'chain 'C' and resid 306 through 308' Processing helix chain 'C' and resid 321 through 340 removed outlier: 3.636A pdb=" N SER C 326 " --> pdb=" O ARG C 323 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE C 331 " --> pdb=" O TYR C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 364 Processing helix chain 'C' and resid 371 through 373 No H-bonds generated for 'chain 'C' and resid 371 through 373' Processing helix chain 'C' and resid 376 through 388 removed outlier: 4.362A pdb=" N GLY C 379 " --> pdb=" O ALA C 376 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA C 383 " --> pdb=" O ALA C 380 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER C 384 " --> pdb=" O ARG C 381 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU C 387 " --> 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 437 through 441 Processing helix chain 'C' and resid 458 through 468 removed outlier: 4.472A pdb=" N GLU C 463 " --> pdb=" O ARG C 459 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N TYR C 464 " --> pdb=" O ALA C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 496 removed outlier: 4.192A pdb=" N ILE C 492 " --> pdb=" O ASP C 488 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LEU C 495 " --> pdb=" O GLU C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 518 Processing helix chain 'C' and resid 534 through 556 Processing helix chain 'C' and resid 567 through 573 Processing helix chain 'C' and resid 575 through 585 removed outlier: 5.083A pdb=" N LYS C 585 " --> pdb=" O LEU C 581 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 615 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 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 287 removed outlier: 3.636A pdb=" N THR D 274 " --> pdb=" O ARG D 271 " (cutoff:3.500A) Proline residue: D 275 - end of helix removed outlier: 3.580A pdb=" N ALA D 278 " --> pdb=" O PRO D 275 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU D 279 " --> pdb=" O ARG D 276 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR D 280 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA D 286 " --> pdb=" O GLU D 283 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR D 287 " --> pdb=" O PHE D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 313 Processing helix chain 'D' and resid 320 through 322 No H-bonds generated for 'chain 'D' and resid 320 through 322' Processing helix chain 'D' and resid 327 through 335 removed outlier: 3.971A pdb=" N ILE D 334 " --> pdb=" O ASP D 330 " (cutoff:3.500A) 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 382 through 385 No H-bonds generated for 'chain 'D' and resid 382 through 385' Processing helix chain 'D' and resid 400 through 403 removed outlier: 4.148A pdb=" N LYS D 403 " --> pdb=" O ARG D 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 400 through 403' Processing helix chain 'D' and resid 415 through 439 removed outlier: 4.081A 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 Processing helix chain 'D' and resid 473 through 486 removed outlier: 3.861A pdb=" N ILE D 486 " --> pdb=" O GLN D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 491 No H-bonds generated for 'chain 'D' and resid 489 through 491' Processing helix chain 'D' and resid 497 through 503 Processing helix chain 'E' and resid 160 through 162 No H-bonds generated for 'chain 'E' and resid 160 through 162' Processing helix chain 'E' and resid 175 through 177 No H-bonds generated for 'chain 'E' and resid 175 through 177' Processing helix chain 'E' and resid 199 through 209 Processing helix chain 'E' and resid 238 through 250 Processing helix chain 'E' and resid 253 through 256 Processing helix chain 'E' and resid 270 through 288 Proline residue: E 275 - end of helix 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 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 removed outlier: 3.839A pdb=" N ILE E 372 " --> pdb=" O LEU E 368 " (cutoff:3.500A) 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 402 through 405 No H-bonds generated for 'chain 'E' and resid 402 through 405' Processing helix chain 'E' and resid 415 through 439 removed outlier: 3.683A pdb=" N VAL E 438 " --> pdb=" O ALA E 434 " (cutoff:3.500A) Processing helix chain 'E' and resid 446 through 461 Processing helix chain 'E' and resid 473 through 486 removed outlier: 4.088A 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 125 through 127 No H-bonds generated for 'chain 'F' and resid 125 through 127' Processing helix chain 'F' and resid 175 through 178 No H-bonds generated for 'chain 'F' and resid 175 through 178' Processing helix chain 'F' and resid 199 through 209 removed outlier: 3.669A pdb=" N ARG F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 250 Processing helix chain 'F' and resid 254 through 256 No H-bonds generated for 'chain 'F' and resid 254 through 256' Processing helix chain 'F' and resid 270 through 272 No H-bonds generated for 'chain 'F' and resid 270 through 272' Processing helix chain 'F' and resid 274 through 287 Processing helix chain 'F' and resid 300 through 313 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 Processing helix chain 'F' and resid 381 through 386 removed outlier: 3.997A pdb=" N ARG F 386 " --> pdb=" O GLN F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 405 removed outlier: 4.235A pdb=" N LYS F 403 " --> pdb=" O ARG F 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 439 removed outlier: 4.293A pdb=" N VAL F 438 " --> pdb=" O ALA F 434 " (cutoff:3.500A) Processing helix chain 'F' and resid 441 through 443 No H-bonds generated for 'chain 'F' and resid 441 through 443' Processing helix chain 'F' and resid 446 through 461 removed outlier: 4.300A pdb=" N TYR F 451 " --> pdb=" O ASP F 447 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS F 460 " --> pdb=" O GLN F 456 " (cutoff:3.500A) Processing helix chain 'F' and resid 473 through 486 removed outlier: 4.162A 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 removed outlier: 5.038A pdb=" N GLU F 502 " --> pdb=" O SER F 498 " (cutoff:3.500A) Processing helix chain 'H' and resid 13 through 47 Processing helix chain 'H' and resid 156 through 174 Processing helix chain 'H' and resid 176 through 215 Processing helix chain 'I' and resid 67 through 106 Processing helix chain 'I' and resid 110 through 127 Processing helix chain 'I' and resid 138 through 159 Proline residue: I 142 - end of helix removed outlier: 3.706A pdb=" N LYS I 145 " --> pdb=" O PRO I 142 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ILE I 152 " --> pdb=" O GLN I 149 " (cutoff:3.500A) Proline residue: I 153 - end of helix removed outlier: 3.696A pdb=" N LYS I 156 " --> pdb=" O PRO I 153 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE I 157 " --> pdb=" O MET I 154 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR I 159 " --> pdb=" O LYS I 156 " (cutoff:3.500A) Processing helix chain 'I' and resid 196 through 204 Processing helix chain 'I' and resid 208 through 216 removed outlier: 3.565A pdb=" N GLY I 213 " --> pdb=" O PRO I 209 " (cutoff:3.500A) 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: 3.684A pdb=" N LYS J 145 " --> pdb=" O PRO J 142 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS J 150 " --> pdb=" O ALA J 147 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ILE J 152 " --> pdb=" O GLN J 149 " (cutoff:3.500A) Proline residue: J 153 - end of helix removed outlier: 3.655A pdb=" N LYS J 156 " --> pdb=" O PRO J 153 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR J 159 " --> pdb=" O LYS J 156 " (cutoff:3.500A) Processing helix chain 'J' and resid 196 through 206 Processing helix chain 'J' and resid 208 through 216 Processing helix chain 'K' and resid 67 through 106 Processing helix chain 'K' and resid 109 through 127 removed outlier: 4.593A pdb=" N VAL K 114 " --> pdb=" O THR K 110 " (cutoff:3.500A) Processing helix chain 'K' and resid 138 through 158 Proline residue: K 142 - end of helix removed outlier: 3.752A pdb=" N LYS K 145 " --> pdb=" O PRO K 142 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS K 150 " --> pdb=" O ALA K 147 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ILE K 152 " --> pdb=" O GLN K 149 " (cutoff:3.500A) Proline residue: K 153 - end of helix removed outlier: 3.605A pdb=" N LYS K 156 " --> pdb=" O PRO K 153 " (cutoff:3.500A) Processing helix chain 'K' and resid 196 through 216 removed outlier: 3.888A pdb=" N GLN K 206 " --> pdb=" O LEU K 202 " (cutoff:3.500A) Proline residue: K 209 - end of helix Processing helix chain 'M' and resid 71 through 103 removed outlier: 3.669A pdb=" N ASN M 91 " --> pdb=" O SER M 87 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N GLU M 93 " --> pdb=" O GLN M 89 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ARG M 94 " --> pdb=" O ARG M 90 " (cutoff:3.500A) Processing helix chain 'N' and resid 71 through 90 removed outlier: 3.551A pdb=" N ARG N 90 " --> pdb=" O SER N 86 " (cutoff:3.500A) Processing helix chain 'N' and resid 92 through 104 Processing helix chain 'O' and resid 71 through 90 removed outlier: 3.892A pdb=" N ARG O 90 " --> pdb=" O SER O 86 " (cutoff:3.500A) 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 55 removed outlier: 3.527A pdb=" N TYR Q 49 " --> pdb=" O ILE Q 45 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ASP Q 51 " --> pdb=" O GLU Q 47 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL Q 52 " --> pdb=" O ASP Q 48 " (cutoff:3.500A) removed outlier: 5.070A 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 96 Processing helix chain 'Q' and resid 105 through 117 Processing helix chain 'Q' and resid 121 through 123 No H-bonds generated for 'chain 'Q' and resid 121 through 123' Processing helix chain 'Q' and resid 125 through 142 removed outlier: 3.841A pdb=" N ASN Q 142 " --> pdb=" O ASP Q 138 " (cutoff:3.500A) Processing helix chain 'Q' and resid 147 through 166 Processing helix chain 'Q' and resid 173 through 186 Processing helix chain 'Q' and resid 193 through 205 Processing helix chain 'Q' and resid 219 through 234 Processing helix chain 'R' and resid 15 through 36 removed outlier: 3.530A pdb=" N HIS R 19 " --> pdb=" O SER R 15 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 53 removed outlier: 3.666A pdb=" N TYR R 49 " --> pdb=" O ILE R 45 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N ASP R 51 " --> pdb=" O GLU R 47 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL R 52 " --> pdb=" O ASP R 48 " (cutoff:3.500A) Processing helix chain 'R' and resid 63 through 71 Processing helix chain 'R' and resid 78 through 98 removed outlier: 3.982A pdb=" N ILE R 98 " --> pdb=" O LEU R 94 " (cutoff:3.500A) Processing helix chain 'R' and resid 105 through 116 Processing helix chain 'R' and resid 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: 3.814A pdb=" N LEU R 140 " --> pdb=" O LEU R 136 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS R 141 " --> pdb=" O THR R 137 " (cutoff:3.500A) removed outlier: 4.492A 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 194 through 206 Processing helix chain 'S' and resid 15 through 36 Processing helix chain 'S' and resid 43 through 48 Processing helix chain 'S' and resid 50 through 55 removed outlier: 5.034A pdb=" N TRP S 55 " --> pdb=" O ASP S 51 " (cutoff:3.500A) Processing helix chain 'S' and resid 62 through 70 Processing helix chain 'S' and resid 78 through 98 removed outlier: 3.930A pdb=" N LEU S 88 " --> pdb=" O ARG S 84 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU S 91 " --> pdb=" O ILE S 87 " (cutoff:3.500A) removed outlier: 3.980A 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 125 through 141 removed outlier: 3.526A pdb=" N LYS S 141 " --> pdb=" O THR S 137 " (cutoff:3.500A) Processing helix chain 'S' and resid 147 through 166 Processing helix chain 'S' and resid 173 through 187 Processing helix chain 'S' and resid 193 through 204 Processing helix chain 'S' and resid 219 through 232 removed outlier: 3.528A pdb=" N MET S 229 " --> pdb=" O LEU S 225 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 18 through 20 removed outlier: 6.898A pdb=" N THR A 63 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N LEU A 57 " --> pdb=" O MET A 61 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N MET A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N CYS A 32 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N VAL A 21 " --> pdb=" O CYS A 32 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 87 through 90 Processing sheet with id= C, first strand: chain 'A' and resid 183 through 185 removed outlier: 6.819A pdb=" N ILE A 166 " --> pdb=" O TYR A 153 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ILE A 155 " --> pdb=" O HIS A 164 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N HIS A 164 " --> pdb=" O ILE A 155 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 199 through 203 removed outlier: 6.200A pdb=" N GLU A 195 " --> pdb=" O VAL A 176 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N VAL A 176 " --> pdb=" O GLU A 195 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 219 through 221 removed outlier: 4.077A pdb=" N ARG A 391 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 245 through 247 removed outlier: 8.341A pdb=" N THR A 246 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ILE A 406 " --> pdb=" O THR A 246 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL A 271 " --> pdb=" O SER A 345 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N MET A 347 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE A 273 " --> pdb=" O MET A 347 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 295 through 297 Processing sheet with id= H, first strand: chain 'B' and resid 18 through 20 removed outlier: 3.569A pdb=" N LEU B 42 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N CYS B 32 " --> pdb=" O VAL B 21 " (cutoff:3.500A) removed outlier: 5.366A 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: 4.718A pdb=" N GLU B 134 " --> pdb=" O ASN B 157 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ILE B 166 " --> pdb=" O TYR B 153 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ILE B 155 " --> pdb=" O HIS B 164 " (cutoff:3.500A) removed outlier: 6.539A 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: 6.249A pdb=" N GLU B 195 " --> pdb=" O VAL B 176 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N VAL B 176 " --> pdb=" O GLU B 195 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 309 through 312 removed outlier: 6.298A pdb=" N ILE B 272 " --> pdb=" O ALA B 310 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N VAL B 312 " --> pdb=" O ILE B 272 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N TYR B 274 " --> pdb=" O VAL B 312 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N VAL B 344 " --> pdb=" O GLU B 401 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N SER B 403 " --> pdb=" O VAL B 344 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N MET B 346 " --> pdb=" O SER B 403 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N SER B 405 " --> pdb=" O MET B 346 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N ALA B 348 " --> pdb=" O SER B 405 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 295 through 297 Processing sheet with id= N, first strand: chain 'C' and resid 78 through 80 removed outlier: 6.510A pdb=" N THR C 30 " --> pdb=" O HIS C 22 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N VAL C 24 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N VAL C 28 " --> pdb=" O VAL C 24 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG C 56 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLN C 65 " --> pdb=" O ILE C 54 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ILE C 54 " --> pdb=" O GLN C 65 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N GLU C 41 " --> pdb=" O ILE C 54 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N LYS C 84 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ARG C 44 " --> pdb=" O THR C 82 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N THR C 82 " --> pdb=" O ARG C 44 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 87 through 90 Processing sheet with id= P, first strand: chain 'C' and resid 183 through 185 Processing sheet with id= Q, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.339A pdb=" N GLU C 195 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N VAL C 176 " --> pdb=" O GLU C 195 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 245 through 248 removed outlier: 8.619A pdb=" N THR C 246 " --> pdb=" O VAL C 404 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE C 406 " --> pdb=" O THR C 246 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ILE C 248 " --> pdb=" O ILE C 406 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N GLY C 408 " --> pdb=" O ILE C 248 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 272 through 277 Processing sheet with id= T, first strand: chain 'C' and resid 390 through 393 Processing sheet with id= U, first strand: chain 'D' and resid 50 through 54 removed outlier: 6.777A pdb=" N ILE D 59 " --> pdb=" O SER D 51 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N VAL D 53 " --> pdb=" O LEU D 57 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LEU D 57 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU D 88 " --> pdb=" O VAL D 95 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N GLN D 97 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 5.455A 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 130 through 133 removed outlier: 6.442A pdb=" N ILE D 229 " --> pdb=" O CYS D 258 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N PHE D 260 " --> pdb=" O ILE D 229 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N PHE D 231 " --> pdb=" O PHE D 260 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ASN D 262 " --> pdb=" O PHE D 231 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N ALA D 233 " --> pdb=" O ASN D 262 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N SER D 347 " --> pdb=" O VAL D 293 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N VAL D 295 " --> pdb=" O SER D 347 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N THR D 349 " --> pdb=" O VAL D 295 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N LEU D 297 " --> pdb=" O THR D 349 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 191 through 193 Processing sheet with id= Y, first strand: chain 'E' and resid 50 through 54 removed outlier: 6.675A pdb=" N ILE E 59 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N VAL E 53 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU E 57 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA E 94 " --> pdb=" O LEU E 60 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLN E 97 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N VAL E 86 " --> pdb=" O GLN E 97 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 120 through 123 Processing sheet with id= AA, first strand: chain 'E' and resid 131 through 133 removed outlier: 8.122A pdb=" N PHE E 132 " --> pdb=" O VAL E 257 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU E 259 " --> pdb=" O PHE E 132 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N CYS E 258 " --> pdb=" O PHE E 227 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE E 229 " --> pdb=" O CYS E 258 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N PHE E 260 " --> pdb=" O ILE E 229 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N PHE E 231 " --> pdb=" O PHE E 260 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N ASN E 262 " --> pdb=" O PHE E 231 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ALA E 233 " --> pdb=" O ASN E 262 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N HIS E 292 " --> pdb=" O ALA E 228 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N VAL E 230 " --> pdb=" O HIS E 292 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N LEU E 294 " --> pdb=" O VAL E 230 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ALA E 232 " --> pdb=" O LEU E 294 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE E 296 " --> pdb=" O ALA E 232 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N MET E 234 " --> pdb=" O ILE E 296 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N THR E 298 " --> pdb=" O MET E 234 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL E 236 " --> pdb=" O THR E 298 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N SER E 347 " --> pdb=" O VAL E 293 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N VAL E 295 " --> pdb=" O SER E 347 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N THR E 349 " --> pdb=" O VAL E 295 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N LEU E 297 " --> pdb=" O THR E 349 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'E' and resid 191 through 194 Processing sheet with id= AC, first strand: chain 'F' and resid 50 through 54 removed outlier: 6.801A pdb=" N ILE F 59 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL F 53 " --> pdb=" O LEU F 57 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU F 57 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU F 88 " --> pdb=" O VAL F 95 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLN F 97 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N VAL F 86 " --> pdb=" O GLN F 97 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 120 through 123 Processing sheet with id= AE, first strand: chain 'F' and resid 131 through 133 removed outlier: 8.035A pdb=" N PHE F 132 " --> pdb=" O VAL F 257 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LEU F 259 " --> pdb=" O PHE F 132 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE F 229 " --> pdb=" O CYS F 258 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N PHE F 260 " --> pdb=" O ILE F 229 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N PHE F 231 " --> pdb=" O PHE F 260 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N ASN F 262 " --> pdb=" O PHE F 231 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ALA F 233 " --> pdb=" O ASN F 262 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N SER F 347 " --> pdb=" O VAL F 293 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N VAL F 295 " --> pdb=" O SER F 347 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N THR F 349 " --> pdb=" O VAL F 295 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N LEU F 297 " --> pdb=" O THR F 349 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE F 351 " --> pdb=" O LEU F 297 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'I' and resid 164 through 167 Processing sheet with id= AG, first strand: chain 'J' and resid 164 through 167 Processing sheet with id= AH, first strand: chain 'K' and resid 164 through 167 removed outlier: 3.993A pdb=" N VAL K 181 " --> pdb=" O ASN K 194 " (cutoff:3.500A) 1588 hydrogen bonds defined for protein. 4491 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.39 Time building geometry restraints manager: 15.89 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: 6986 1.32 - 1.44: 8216 1.44 - 1.57: 21202 1.57 - 1.69: 3 1.69 - 1.81: 358 Bond restraints: 36765 Sorted by residual: bond pdb=" N PRO E 391 " pdb=" CA PRO E 391 " ideal model delta sigma weight residual 1.469 1.531 -0.063 7.40e-03 1.83e+04 7.13e+01 bond pdb=" C TYR D 504 " pdb=" N PRO D 505 " ideal model delta sigma weight residual 1.337 1.406 -0.070 1.06e-02 8.90e+03 4.33e+01 bond pdb=" N PRO D 352 " pdb=" CA PRO D 352 " ideal model delta sigma weight residual 1.466 1.538 -0.072 1.24e-02 6.50e+03 3.38e+01 bond pdb=" C ASP A 290 " pdb=" N PHE A 291 " ideal model delta sigma weight residual 1.331 1.215 0.116 2.07e-02 2.33e+03 3.13e+01 bond pdb=" N PRO E 396 " pdb=" CA PRO E 396 " ideal model delta sigma weight residual 1.469 1.539 -0.070 1.25e-02 6.40e+03 3.13e+01 ... (remaining 36760 not shown) Histogram of bond angle deviations from ideal: 100.10 - 106.94: 1208 106.94 - 113.77: 20117 113.77 - 120.61: 16395 120.61 - 127.45: 11677 127.45 - 134.28: 279 Bond angle restraints: 49676 Sorted by residual: angle pdb=" C ILE E 189 " pdb=" N PRO E 190 " pdb=" CA PRO E 190 " ideal model delta sigma weight residual 119.85 129.33 -9.48 1.01e+00 9.80e-01 8.80e+01 angle pdb=" C ARG C 215 " pdb=" N PRO C 216 " pdb=" CA PRO C 216 " ideal model delta sigma weight residual 119.76 129.28 -9.52 1.03e+00 9.43e-01 8.54e+01 angle pdb=" C SER A 411 " pdb=" N PRO A 412 " pdb=" CA PRO A 412 " ideal model delta sigma weight residual 120.38 129.08 -8.70 1.03e+00 9.43e-01 7.13e+01 angle pdb=" C LEU E 395 " pdb=" N PRO E 396 " pdb=" CA PRO E 396 " ideal model delta sigma weight residual 120.04 128.52 -8.48 1.08e+00 8.57e-01 6.16e+01 angle pdb=" C ASN C 397 " pdb=" N PRO C 398 " pdb=" CA PRO C 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: 22002 23.68 - 47.36: 426 47.36 - 71.03: 119 71.03 - 94.71: 31 94.71 - 118.39: 2 Dihedral angle restraints: 22580 sinusoidal: 9309 harmonic: 13271 Sorted by residual: dihedral pdb=" C5' ADP C 701 " pdb=" O5' ADP C 701 " pdb=" PA ADP C 701 " pdb=" O2A ADP C 701 " ideal model delta sinusoidal sigma weight residual -60.00 -178.38 118.39 1 2.00e+01 2.50e-03 3.54e+01 dihedral pdb=" O2A ADP C 701 " pdb=" O3A ADP C 701 " pdb=" PA ADP C 701 " pdb=" PB ADP C 701 " ideal model delta sinusoidal sigma weight residual -60.00 38.44 -98.43 1 2.00e+01 2.50e-03 2.75e+01 dihedral pdb=" CA ILE F 406 " pdb=" C ILE F 406 " pdb=" N GLY F 407 " pdb=" CA GLY F 407 " ideal model delta harmonic sigma weight residual 180.00 154.88 25.12 0 5.00e+00 4.00e-02 2.52e+01 ... (remaining 22577 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 3825 0.053 - 0.106: 1182 0.106 - 0.159: 462 0.159 - 0.211: 77 0.211 - 0.264: 29 Chirality restraints: 5575 Sorted by residual: chirality pdb=" CA VAL E 379 " pdb=" N VAL E 379 " pdb=" C VAL E 379 " pdb=" CB VAL E 379 " both_signs ideal model delta sigma weight residual False 2.44 2.71 -0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CA VAL A 404 " pdb=" N VAL A 404 " pdb=" C VAL A 404 " pdb=" CB VAL A 404 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA ASP A 529 " pdb=" N ASP A 529 " pdb=" C ASP A 529 " pdb=" CB ASP A 529 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 5572 not shown) Planarity restraints: 6440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO E 390 " 0.019 2.00e-02 2.50e+03 3.77e-02 1.42e+01 pdb=" C PRO E 390 " -0.065 2.00e-02 2.50e+03 pdb=" O PRO E 390 " 0.025 2.00e-02 2.50e+03 pdb=" N PRO E 391 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET C 584 " -0.016 2.00e-02 2.50e+03 3.40e-02 1.15e+01 pdb=" C MET C 584 " 0.059 2.00e-02 2.50e+03 pdb=" O MET C 584 " -0.022 2.00e-02 2.50e+03 pdb=" N LYS C 585 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 189 " -0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C ILE E 189 " 0.056 2.00e-02 2.50e+03 pdb=" O ILE E 189 " -0.021 2.00e-02 2.50e+03 pdb=" N PRO E 190 " -0.018 2.00e-02 2.50e+03 ... (remaining 6437 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 8 2.43 - 3.05: 23603 3.05 - 3.66: 54168 3.66 - 4.28: 85210 4.28 - 4.90: 139247 Nonbonded interactions: 302236 Sorted by model distance: nonbonded pdb=" OG1 THR C 257 " pdb="MG MG C 702 " model vdw 1.809 2.170 nonbonded pdb=" OG SER C 269 " pdb=" OG SER C 345 " model vdw 2.377 2.440 nonbonded pdb=" OG SER B 128 " pdb=" OD1 ASP B 130 " model vdw 2.378 2.440 nonbonded pdb=" NE ARG I 135 " pdb=" O ALA I 171 " model vdw 2.389 2.520 nonbonded pdb=" O ILE F 377 " pdb=" OG SER F 397 " model vdw 2.404 2.440 ... (remaining 302231 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = (chain 'C' and resid 17 through 616) } 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: 3.180 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: 11.900 Check model and map are aligned: 0.510 Set scattering table: 0.280 Process input model: 87.600 Find NCS groups from input model: 2.120 Set up NCS constraints: 0.260 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:3.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 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 0.116 36765 Z= 0.655 Angle : 0.896 10.657 49676 Z= 0.632 Chirality : 0.062 0.264 5575 Planarity : 0.004 0.038 6440 Dihedral : 11.231 118.388 14048 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 1.10 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.73 % Favored : 97.09 % Rotamer Outliers : 0.10 % 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: 0.65 (0.10), residues: 2072 sheet: -0.29 (0.19), residues: 679 loop : -0.03 (0.15), residues: 1787 *********************** 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 1504 residues out of total 3955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1500 time to evaluate : 4.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 1501 average time/residue: 0.5524 time to fit residues: 1279.2314 Evaluate side-chains 766 residues out of total 3955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 765 time to evaluate : 4.454 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 1.0772 time to fit residues: 7.4501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 380 optimal weight: 3.9990 chunk 341 optimal weight: 2.9990 chunk 189 optimal weight: 0.0270 chunk 116 optimal weight: 0.9980 chunk 230 optimal weight: 0.4980 chunk 182 optimal weight: 4.9990 chunk 353 optimal weight: 0.8980 chunk 136 optimal weight: 3.9990 chunk 214 optimal weight: 1.9990 chunk 263 optimal weight: 1.9990 chunk 409 optimal weight: 4.9990 overall best weight: 0.8840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN A 123 ASN A 317 ASN B 261 GLN B 603 GLN D 187 GLN D 456 GLN E 181 ASN E 345 ASN ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 126 GLN K 139 GLN O 80 GLN O 85 GLN ** R 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 207 GLN S 21 GLN ** S 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 134 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 36765 Z= 0.214 Angle : 0.621 8.845 49676 Z= 0.317 Chirality : 0.044 0.193 5575 Planarity : 0.004 0.045 6440 Dihedral : 4.873 110.015 5018 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.12 % Favored : 97.86 % Rotamer Outliers : 2.71 % 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: 0.99 (0.12), residues: 4538 helix: 1.62 (0.11), residues: 2087 sheet: -0.19 (0.20), residues: 637 loop : -0.06 (0.15), residues: 1814 *********************** 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 942 residues out of total 3955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 835 time to evaluate : 4.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 107 outliers final: 60 residues processed: 900 average time/residue: 0.4118 time to fit residues: 600.0801 Evaluate side-chains 736 residues out of total 3955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 676 time to evaluate : 3.224 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 0 residues processed: 60 average time/residue: 0.2554 time to fit residues: 32.9227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 227 optimal weight: 0.0020 chunk 127 optimal weight: 4.9990 chunk 340 optimal weight: 6.9990 chunk 278 optimal weight: 1.9990 chunk 112 optimal weight: 9.9990 chunk 410 optimal weight: 3.9990 chunk 443 optimal weight: 5.9990 chunk 365 optimal weight: 5.9990 chunk 406 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 329 optimal weight: 8.9990 overall best weight: 2.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 484 GLN C 523 ASN D 62 HIS D 156 GLN D 171 GLN ** D 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 497 GLN ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 ASN F 187 GLN ** F 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 19 HIS ** R 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 134 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.068 36765 Z= 0.337 Angle : 0.636 13.574 49676 Z= 0.321 Chirality : 0.045 0.207 5575 Planarity : 0.004 0.050 6440 Dihedral : 4.843 114.508 5018 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer Outliers : 2.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.13), residues: 4538 helix: 1.65 (0.11), residues: 2094 sheet: -0.42 (0.19), residues: 657 loop : -0.13 (0.15), residues: 1787 *********************** 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 822 residues out of total 3955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 718 time to evaluate : 4.696 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 outliers start: 104 outliers final: 51 residues processed: 778 average time/residue: 0.4782 time to fit residues: 613.7959 Evaluate side-chains 678 residues out of total 3955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 627 time to evaluate : 3.435 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 0 residues processed: 51 average time/residue: 0.2817 time to fit residues: 31.8635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 405 optimal weight: 0.0770 chunk 308 optimal weight: 8.9990 chunk 212 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 195 optimal weight: 0.8980 chunk 275 optimal weight: 0.9990 chunk 411 optimal weight: 8.9990 chunk 435 optimal weight: 0.2980 chunk 215 optimal weight: 2.9990 chunk 390 optimal weight: 4.9990 chunk 117 optimal weight: 8.9990 overall best weight: 1.0542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: