Starting phenix.real_space_refine on Sat Mar 23 23:53:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6voh_21264/03_2024/6voh_21264_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6voh_21264/03_2024/6voh_21264.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6voh_21264/03_2024/6voh_21264.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6voh_21264/03_2024/6voh_21264.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6voh_21264/03_2024/6voh_21264_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6voh_21264/03_2024/6voh_21264_updated.pdb" } resolution = 4.16 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= 0.003 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 14 5.49 5 S 131 5.16 5 C 24854 2.51 5 N 6674 2.21 5 O 7486 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 14": "NH1" <-> "NH2" Residue "A ASP 79": "OD1" <-> "OD2" Residue "A GLU 126": "OE1" <-> "OE2" Residue "A ARG 140": "NH1" <-> "NH2" Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 155": "OD1" <-> "OD2" Residue "A ARG 165": "NH1" <-> "NH2" Residue "A TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 216": "NH1" <-> "NH2" Residue "A TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 255": "NH1" <-> "NH2" Residue "A ASP 348": "OD1" <-> "OD2" Residue "A PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 366": "NH1" <-> "NH2" Residue "A ASP 402": "OD1" <-> "OD2" Residue "A ARG 413": "NH1" <-> "NH2" Residue "C ARG 16": "NH1" <-> "NH2" Residue "C TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 58": "OE1" <-> "OE2" Residue "C GLU 68": "OE1" <-> "OE2" Residue "C ARG 94": "NH1" <-> "NH2" Residue "C ARG 141": "NH1" <-> "NH2" Residue "C ARG 172": "NH1" <-> "NH2" Residue "C TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 248": "OE1" <-> "OE2" Residue "C ARG 279": "NH1" <-> "NH2" Residue "C TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 301": "NH1" <-> "NH2" Residue "C ASP 348": "OD1" <-> "OD2" Residue "C PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 402": "OD1" <-> "OD2" Residue "C ARG 416": "NH1" <-> "NH2" Residue "C ASP 447": "OD1" <-> "OD2" Residue "C ASP 452": "OD1" <-> "OD2" Residue "C ARG 462": "NH1" <-> "NH2" Residue "C TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 474": "OE1" <-> "OE2" Residue "C GLU 496": "OE1" <-> "OE2" Residue "C GLU 499": "OE1" <-> "OE2" Residue "B ARG 5": "NH1" <-> "NH2" Residue "B GLU 18": "OE1" <-> "OE2" Residue "B ARG 22": "NH1" <-> "NH2" Residue "B ARG 107": "NH1" <-> "NH2" Residue "B GLU 126": "OE1" <-> "OE2" Residue "B ARG 172": "NH1" <-> "NH2" Residue "B ARG 216": "NH1" <-> "NH2" Residue "B TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 300": "OE1" <-> "OE2" Residue "B ASP 340": "OD1" <-> "OD2" Residue "B PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 366": "NH1" <-> "NH2" Residue "B GLU 386": "OE1" <-> "OE2" Residue "B PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 419": "OE1" <-> "OE2" Residue "B TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 455": "NH1" <-> "NH2" Residue "B TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 482": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 485": "OE1" <-> "OE2" Residue "D ARG 52": "NH1" <-> "NH2" Residue "D ASP 83": "OD1" <-> "OD2" Residue "D ARG 87": "NH1" <-> "NH2" Residue "D GLU 116": "OE1" <-> "OE2" Residue "D PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 163": "NH1" <-> "NH2" Residue "D GLU 184": "OE1" <-> "OE2" Residue "D PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 207": "NH1" <-> "NH2" Residue "D TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 267": "OD1" <-> "OD2" Residue "D PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 305": "OE1" <-> "OE2" Residue "D TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 397": "NH1" <-> "NH2" Residue "D GLU 412": "OE1" <-> "OE2" Residue "D GLU 416": "OE1" <-> "OE2" Residue "E ASP 32": "OD1" <-> "OD2" Residue "E PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 52": "NH1" <-> "NH2" Residue "E GLU 229": "OE1" <-> "OE2" Residue "E ARG 246": "NH1" <-> "NH2" Residue "E TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 277": "NH1" <-> "NH2" Residue "E PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 311": "OE1" <-> "OE2" Residue "E ASP 333": "OD1" <-> "OD2" Residue "E ASP 369": "OD1" <-> "OD2" Residue "E GLU 415": "OE1" <-> "OE2" Residue "E ARG 423": "NH1" <-> "NH2" Residue "E PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 481": "OD1" <-> "OD2" Residue "F ARG 52": "NH1" <-> "NH2" Residue "F ARG 87": "NH1" <-> "NH2" Residue "F ASP 119": "OD1" <-> "OD2" Residue "F PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 164": "NH1" <-> "NH2" Residue "F PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 224": "OE1" <-> "OE2" Residue "F GLU 241": "OE1" <-> "OE2" Residue "F PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 305": "OE1" <-> "OE2" Residue "F TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 333": "OD1" <-> "OD2" Residue "F ASP 369": "OD1" <-> "OD2" Residue "F ARG 425": "NH1" <-> "NH2" Residue "F PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 77": "NH1" <-> "NH2" Residue "d TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 108": "OE1" <-> "OE2" Residue "d TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 130": "OD1" <-> "OD2" Residue "d PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 208": "NH1" <-> "NH2" Residue "d ASP 214": "OD1" <-> "OD2" Residue "d PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 234": "OD1" <-> "OD2" Residue "g ARG 48": "NH1" <-> "NH2" Residue "g GLU 62": "OE1" <-> "OE2" Residue "g ARG 73": "NH1" <-> "NH2" Residue "g ARG 83": "NH1" <-> "NH2" Residue "g GLU 98": "OE1" <-> "OE2" Residue "g ASP 106": "OD1" <-> "OD2" Residue "g ARG 127": "NH1" <-> "NH2" Residue "g ARG 144": "NH1" <-> "NH2" Residue "g PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 170": "NH1" <-> "NH2" Residue "g ARG 171": "NH1" <-> "NH2" Residue "g TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 197": "OD1" <-> "OD2" Residue "g TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 287": "OD1" <-> "OD2" Residue "g TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 306": "NH1" <-> "NH2" Residue "e ARG 12": "NH1" <-> "NH2" Residue "e ARG 50": "NH1" <-> "NH2" Residue "e ARG 68": "NH1" <-> "NH2" Residue "e GLU 100": "OE1" <-> "OE2" Residue "e ARG 104": "NH1" <-> "NH2" Residue "e ARG 110": "NH1" <-> "NH2" Residue "e ARG 120": "NH1" <-> "NH2" Residue "J PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 120": "OD1" <-> "OD2" Residue "J GLU 141": "OE1" <-> "OE2" Residue "J GLU 154": "OE1" <-> "OE2" Residue "J ASP 212": "OD1" <-> "OD2" Residue "I ARG 59": "NH1" <-> "NH2" Residue "I ARG 71": "NH1" <-> "NH2" Residue "I GLU 79": "OE1" <-> "OE2" Residue "I ARG 82": "NH1" <-> "NH2" Residue "I PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 102": "OE1" <-> "OE2" Residue "I TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 59": "NH1" <-> "NH2" Residue "a PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 179": "OD1" <-> "OD2" Residue "a PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 241": "OE1" <-> "OE2" Residue "T GLU 37": "OE1" <-> "OE2" Residue "Y ARG 41": "NH1" <-> "NH2" Residue "Y GLU 44": "OE1" <-> "OE2" Residue "X ARG 41": "NH1" <-> "NH2" Residue "W GLU 37": "OE1" <-> "OE2" Residue "V GLU 37": "OE1" <-> "OE2" Residue "V GLU 61": "OE1" <-> "OE2" Residue "U TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 37": "OE1" <-> "OE2" Residue "Z ARG 41": "NH1" <-> "NH2" Residue "M GLU 44": "OE1" <-> "OE2" Residue "M GLU 46": "OE1" <-> "OE2" Residue "N ARG 41": "NH1" <-> "NH2" Residue "N GLU 44": "OE1" <-> "OE2" Residue "N PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 41": "NH1" <-> "NH2" Residue "P ARG 41": "NH1" <-> "NH2" Residue "P GLU 44": "OE1" <-> "OE2" Residue "P GLU 61": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 39159 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 3850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3850 Classifications: {'peptide': 501} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 483} Chain: "C" Number of atoms: 3843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3843 Classifications: {'peptide': 500} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 482} Chain: "B" Number of atoms: 3854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 3854 Classifications: {'peptide': 502} Link IDs: {'PTRANS': 17, 'TRANS': 484} Chain: "D" Number of atoms: 3619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3619 Classifications: {'peptide': 478} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 452} Chain: "E" Number of atoms: 3645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3645 Classifications: {'peptide': 481} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 455} Chain: "F" Number of atoms: 3636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3636 Classifications: {'peptide': 480} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 454} Chain: "d" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1384 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 4, 'TRANS': 174} Chain: "g" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2508 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 12, 'TRANS': 310} Chain: "e" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1007 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 126} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1068 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 3, 'TRANS': 132} Chain: "I" Number of atoms: 1237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1237 Classifications: {'peptide': 153} Link IDs: {'TRANS': 152} Chain: "a" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1741 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 14, 'TRANS': 208} Chain: "T" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "Y" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "X" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "W" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "V" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "U" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "Z" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "S" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "R" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "Q" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "M" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "N" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "O" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "P" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" 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: 19.20, per 1000 atoms: 0.49 Number of scatterers: 39159 At special positions: 0 Unit cell: (163.28, 204.88, 168.48, 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 131 16.00 P 14 15.00 O 7486 8.00 N 6674 7.00 C 24854 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS g 240 " - pdb=" SG CYS g 246 " distance=2.05 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: 14.39 Conformation dependent library (CDL) restraints added in 6.5 seconds 10282 Ramachandran restraints generated. 5141 Oldfield, 0 Emsley, 5141 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9436 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 170 helices and 21 sheets defined 53.5% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.42 Creating SS restraints... Processing helix chain 'A' and resid 9 through 24 removed outlier: 4.154A pdb=" N ILE A 12 " --> pdb=" O ILE A 9 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU A 18 " --> pdb=" O GLU A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 155 No H-bonds generated for 'chain 'A' and resid 152 through 155' Processing helix chain 'A' and resid 176 through 186 Processing helix chain 'A' and resid 203 through 215 Processing helix chain 'A' and resid 233 through 252 Proline residue: A 240 - end of helix removed outlier: 3.902A pdb=" N PHE A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 277 Processing helix chain 'A' and resid 284 through 286 No H-bonds generated for 'chain 'A' and resid 284 through 286' Processing helix chain 'A' and resid 289 through 299 removed outlier: 4.523A pdb=" N PHE A 292 " --> pdb=" O GLY A 289 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR A 293 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU A 294 " --> pdb=" O VAL A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 330 through 336 Processing helix chain 'A' and resid 347 through 350 No H-bonds generated for 'chain 'A' and resid 347 through 350' Processing helix chain 'A' and resid 368 through 371 Processing helix chain 'A' and resid 374 through 379 Processing helix chain 'A' and resid 383 through 396 removed outlier: 4.137A pdb=" N GLU A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 418 removed outlier: 3.699A pdb=" N ALA A 412 " --> pdb=" O GLN A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 442 removed outlier: 4.536A pdb=" N THR A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 446 No H-bonds generated for 'chain 'A' and resid 444 through 446' Processing helix chain 'A' and resid 454 through 467 Processing helix chain 'A' and resid 470 through 477 Processing helix chain 'A' and resid 484 through 503 removed outlier: 4.093A pdb=" N ALA A 488 " --> pdb=" O GLU A 484 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A 489 " --> pdb=" O GLU A 485 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 19 removed outlier: 3.698A pdb=" N ILE C 13 " --> pdb=" O ILE C 9 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU C 15 " --> pdb=" O LYS C 11 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG C 16 " --> pdb=" O ILE C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 104 No H-bonds generated for 'chain 'C' and resid 102 through 104' Processing helix chain 'C' and resid 153 through 156 No H-bonds generated for 'chain 'C' and resid 153 through 156' Processing helix chain 'C' and resid 176 through 186 Processing helix chain 'C' and resid 203 through 216 Processing helix chain 'C' and resid 218 through 221 Processing helix chain 'C' and resid 233 through 252 Proline residue: C 240 - end of helix removed outlier: 3.535A pdb=" N TYR C 249 " --> pdb=" O ALA C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 277 Processing helix chain 'C' and resid 284 through 286 No H-bonds generated for 'chain 'C' and resid 284 through 286' Processing helix chain 'C' and resid 291 through 299 Processing helix chain 'C' and resid 330 through 338 Processing helix chain 'C' and resid 347 through 351 Processing helix chain 'C' and resid 374 through 399 removed outlier: 4.481A pdb=" N GLY C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LYS C 382 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N ALA C 395 " --> pdb=" O ALA C 391 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N PHE C 396 " --> pdb=" O GLU C 392 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA C 397 " --> pdb=" O LEU C 393 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLN C 398 " --> pdb=" O GLU C 394 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N PHE C 399 " --> pdb=" O ALA C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 421 removed outlier: 3.908A pdb=" N GLU C 419 " --> pdb=" O GLN C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 442 Processing helix chain 'C' and resid 452 through 468 removed outlier: 3.618A pdb=" N ARG C 455 " --> pdb=" O ASP C 452 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR C 457 " --> pdb=" O VAL C 454 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU C 460 " --> pdb=" O TYR C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 478 Processing helix chain 'C' and resid 484 through 502 Processing helix chain 'B' and resid 10 through 18 removed outlier: 3.535A pdb=" N GLU B 15 " --> pdb=" O LYS B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 157 Processing helix chain 'B' and resid 177 through 188 removed outlier: 3.585A pdb=" N GLN B 187 " --> pdb=" O THR B 183 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLN B 188 " --> pdb=" O ILE B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 218 through 220 No H-bonds generated for 'chain 'B' and resid 218 through 220' Processing helix chain 'B' and resid 233 through 252 Proline residue: B 240 - end of helix removed outlier: 4.299A pdb=" N PHE B 250 " --> pdb=" O LEU B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 276 Processing helix chain 'B' and resid 284 through 286 No H-bonds generated for 'chain 'B' and resid 284 through 286' Processing helix chain 'B' and resid 291 through 299 Processing helix chain 'B' and resid 331 through 338 Processing helix chain 'B' and resid 347 through 352 Processing helix chain 'B' and resid 368 through 370 No H-bonds generated for 'chain 'B' and resid 368 through 370' Processing helix chain 'B' and resid 376 through 395 Processing helix chain 'B' and resid 411 through 420 Processing helix chain 'B' and resid 431 through 442 removed outlier: 3.903A pdb=" N GLY B 441 " --> pdb=" O THR B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 468 removed outlier: 4.463A pdb=" N GLU B 460 " --> pdb=" O LYS B 456 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS B 466 " --> pdb=" O ARG B 462 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N THR B 467 " --> pdb=" O THR B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 478 Processing helix chain 'B' and resid 484 through 502 Processing helix chain 'D' and resid 104 through 106 No H-bonds generated for 'chain 'D' and resid 104 through 106' Processing helix chain 'D' and resid 154 through 158 Processing helix chain 'D' and resid 178 through 188 removed outlier: 3.837A pdb=" N ILE D 182 " --> pdb=" O LYS D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 219 Processing helix chain 'D' and resid 228 through 230 No H-bonds generated for 'chain 'D' and resid 228 through 230' Processing helix chain 'D' and resid 249 through 262 removed outlier: 3.641A pdb=" N PHE D 260 " --> pdb=" O MET D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 288 removed outlier: 3.560A pdb=" N VAL D 279 " --> pdb=" O ILE D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 311 Processing helix chain 'D' and resid 330 through 332 No H-bonds generated for 'chain 'D' and resid 330 through 332' Processing helix chain 'D' and resid 337 through 345 removed outlier: 3.887A pdb=" N THR D 342 " --> pdb=" O ALA D 338 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA D 344 " --> pdb=" O ALA D 340 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N HIS D 345 " --> pdb=" O THR D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 359 Processing helix chain 'D' and resid 377 through 380 No H-bonds generated for 'chain 'D' and resid 377 through 380' Processing helix chain 'D' and resid 382 through 405 removed outlier: 4.703A pdb=" N ASP D 403 " --> pdb=" O LYS D 399 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ILE D 404 " --> pdb=" O GLU D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 412 No H-bonds generated for 'chain 'D' and resid 410 through 412' Processing helix chain 'D' and resid 415 through 430 Processing helix chain 'D' and resid 451 through 462 removed outlier: 4.054A pdb=" N ARG D 456 " --> pdb=" O ALA D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 471 through 473 No H-bonds generated for 'chain 'D' and resid 471 through 473' Processing helix chain 'D' and resid 480 through 493 Processing helix chain 'E' and resid 154 through 159 Processing helix chain 'E' and resid 178 through 191 Processing helix chain 'E' and resid 206 through 219 Processing helix chain 'E' and resid 245 through 264 removed outlier: 5.486A pdb=" N GLY E 250 " --> pdb=" O ARG E 246 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU E 251 " --> pdb=" O MET E 247 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE E 260 " --> pdb=" O MET E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 289 Processing helix chain 'E' and resid 300 through 310 removed outlier: 4.641A pdb=" N SER E 303 " --> pdb=" O PRO E 300 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR E 304 " --> pdb=" O THR E 301 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET E 306 " --> pdb=" O SER E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 343 Processing helix chain 'E' and resid 354 through 359 Processing helix chain 'E' and resid 377 through 380 No H-bonds generated for 'chain 'E' and resid 377 through 380' Processing helix chain 'E' and resid 382 through 401 Processing helix chain 'E' and resid 415 through 431 removed outlier: 3.661A pdb=" N LEU E 419 " --> pdb=" O GLU E 415 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N THR E 420 " --> pdb=" O GLU E 416 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 442 Processing helix chain 'E' and resid 451 through 463 Processing helix chain 'E' and resid 471 through 473 No H-bonds generated for 'chain 'E' and resid 471 through 473' Processing helix chain 'E' and resid 480 through 495 removed outlier: 4.082A pdb=" N LYS E 495 " --> pdb=" O GLU E 491 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 158 Processing helix chain 'F' and resid 180 through 192 removed outlier: 5.166A pdb=" N LYS F 191 " --> pdb=" O ASN F 187 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA F 192 " --> pdb=" O ASN F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 218 Processing helix chain 'F' and resid 227 through 229 No H-bonds generated for 'chain 'F' and resid 227 through 229' Processing helix chain 'F' and resid 245 through 247 No H-bonds generated for 'chain 'F' and resid 245 through 247' Processing helix chain 'F' and resid 249 through 262 Processing helix chain 'F' and resid 275 through 288 removed outlier: 4.778A pdb=" N ALA F 281 " --> pdb=" O PHE F 278 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ALA F 287 " --> pdb=" O GLU F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 310 Processing helix chain 'F' and resid 330 through 332 No H-bonds generated for 'chain 'F' and resid 330 through 332' Processing helix chain 'F' and resid 337 through 340 No H-bonds generated for 'chain 'F' and resid 337 through 340' Processing helix chain 'F' and resid 342 through 345 No H-bonds generated for 'chain 'F' and resid 342 through 345' Processing helix chain 'F' and resid 354 through 358 Processing helix chain 'F' and resid 377 through 380 No H-bonds generated for 'chain 'F' and resid 377 through 380' Processing helix chain 'F' and resid 382 through 407 removed outlier: 4.659A pdb=" N ASP F 403 " --> pdb=" O LYS F 399 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ILE F 404 " --> pdb=" O GLU F 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 410 through 412 No H-bonds generated for 'chain 'F' and resid 410 through 412' Processing helix chain 'F' and resid 415 through 430 Processing helix chain 'F' and resid 439 through 442 No H-bonds generated for 'chain 'F' and resid 439 through 442' Processing helix chain 'F' and resid 451 through 462 Processing helix chain 'F' and resid 471 through 473 No H-bonds generated for 'chain 'F' and resid 471 through 473' Processing helix chain 'F' and resid 480 through 495 removed outlier: 3.650A pdb=" N LYS F 495 " --> pdb=" O GLU F 491 " (cutoff:3.500A) Processing helix chain 'd' and resid 74 through 88 Processing helix chain 'd' and resid 92 through 106 Processing helix chain 'd' and resid 109 through 115 Processing helix chain 'd' and resid 122 through 136 Processing helix chain 'd' and resid 140 through 151 Processing helix chain 'd' and resid 154 through 173 removed outlier: 5.107A pdb=" N LYS d 159 " --> pdb=" O ASN d 156 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE d 165 " --> pdb=" O LEU d 162 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU d 166 " --> pdb=" O ASN d 163 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR d 173 " --> pdb=" O ASN d 170 " (cutoff:3.500A) Processing helix chain 'd' and resid 188 through 202 Processing helix chain 'd' and resid 237 through 248 Processing helix chain 'g' and resid 44 through 99 Proline residue: g 84 - end of helix removed outlier: 3.741A pdb=" N TYR g 94 " --> pdb=" O VAL g 90 " (cutoff:3.500A) Processing helix chain 'g' and resid 108 through 110 No H-bonds generated for 'chain 'g' and resid 108 through 110' Processing helix chain 'g' and resid 133 through 151 removed outlier: 3.798A pdb=" N LEU g 151 " --> pdb=" O GLU g 147 " (cutoff:3.500A) Processing helix chain 'g' and resid 162 through 170 removed outlier: 3.880A pdb=" N ARG g 170 " --> pdb=" O THR g 166 " (cutoff:3.500A) Processing helix chain 'g' and resid 188 through 203 Processing helix chain 'g' and resid 288 through 361 removed outlier: 3.963A pdb=" N LEU g 292 " --> pdb=" O PRO g 288 " (cutoff:3.500A) Proline residue: g 297 - end of helix removed outlier: 3.702A pdb=" N SER g 311 " --> pdb=" O ALA g 307 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN g 361 " --> pdb=" O VAL g 357 " (cutoff:3.500A) Processing helix chain 'e' and resid 89 through 103 Processing helix chain 'e' and resid 112 through 130 removed outlier: 4.468A pdb=" N GLU e 127 " --> pdb=" O ARG e 123 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ALA e 128 " --> pdb=" O THR e 124 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N SER e 129 " --> pdb=" O ARG e 125 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 218 removed outlier: 4.030A pdb=" N GLU J 96 " --> pdb=" O ILE J 92 " (cutoff:3.500A) Proline residue: J 111 - end of helix removed outlier: 4.042A pdb=" N ASN J 145 " --> pdb=" O GLU J 141 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N MET J 148 " --> pdb=" O ALA J 144 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA J 158 " --> pdb=" O GLU J 154 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU J 197 " --> pdb=" O GLU J 193 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N SER J 205 " --> pdb=" O LYS J 201 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N GLN J 206 " --> pdb=" O SER J 202 " (cutoff:3.500A) Processing helix chain 'I' and resid 31 through 69 removed outlier: 3.538A pdb=" N ASN I 55 " --> pdb=" O ASP I 51 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N GLN I 58 " --> pdb=" O ASP I 54 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG I 59 " --> pdb=" O ASN I 55 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLU I 68 " --> pdb=" O ILE I 64 " (cutoff:3.500A) Processing helix chain 'I' and resid 72 through 103 removed outlier: 3.806A pdb=" N VAL I 97 " --> pdb=" O ASP I 93 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY I 99 " --> pdb=" O PHE I 95 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N SER I 101 " --> pdb=" O VAL I 97 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N GLU I 102 " --> pdb=" O ASN I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 158 removed outlier: 4.040A pdb=" N THR I 114 " --> pdb=" O LEU I 110 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS I 116 " --> pdb=" O ASN I 112 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR I 117 " --> pdb=" O SER I 113 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE I 129 " --> pdb=" O LYS I 125 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY I 154 " --> pdb=" O GLN I 150 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER I 158 " --> pdb=" O GLY I 154 " (cutoff:3.500A) Processing helix chain 'I' and resid 165 through 181 Processing helix chain 'a' and resid 37 through 55 removed outlier: 3.847A pdb=" N THR a 42 " --> pdb=" O GLN a 38 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ALA a 54 " --> pdb=" O LEU a 50 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ALA a 55 " --> pdb=" O LEU a 51 " (cutoff:3.500A) Processing helix chain 'a' and resid 67 through 84 removed outlier: 4.050A pdb=" N PHE a 71 " --> pdb=" O GLY a 67 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N TYR a 74 " --> pdb=" O ASN a 70 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL a 75 " --> pdb=" O PHE a 71 " (cutoff:3.500A) Processing helix chain 'a' and resid 92 through 113 Proline residue: a 96 - end of helix removed outlier: 4.183A pdb=" N THR a 100 " --> pdb=" O PHE a 97 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N MET a 101 " --> pdb=" O ILE a 98 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU a 103 " --> pdb=" O THR a 100 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE a 104 " --> pdb=" O MET a 101 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL a 107 " --> pdb=" O PHE a 104 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA a 113 " --> pdb=" O TRP a 110 " (cutoff:3.500A) Processing helix chain 'a' and resid 134 through 155 removed outlier: 3.607A pdb=" N THR a 154 " --> pdb=" O TYR a 150 " (cutoff:3.500A) Processing helix chain 'a' and resid 177 through 207 removed outlier: 3.826A pdb=" N THR a 181 " --> pdb=" O LEU a 177 " (cutoff:3.500A) Proline residue: a 183 - end of helix removed outlier: 3.547A pdb=" N ASN a 193 " --> pdb=" O ARG a 189 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU a 204 " --> pdb=" O VAL a 200 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL a 205 " --> pdb=" O VAL a 201 " (cutoff:3.500A) Processing helix chain 'a' and resid 213 through 243 removed outlier: 4.399A pdb=" N PHE a 218 " --> pdb=" O PRO a 215 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N THR a 223 " --> pdb=" O GLY a 220 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLN a 227 " --> pdb=" O SER a 224 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA a 228 " --> pdb=" O GLY a 225 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE a 230 " --> pdb=" O GLN a 227 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA a 235 " --> pdb=" O ALA a 232 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA a 236 " --> pdb=" O THR a 233 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU a 243 " --> pdb=" O GLY a 240 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 41 removed outlier: 4.377A pdb=" N VAL T 10 " --> pdb=" O ALA T 6 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE T 11 " --> pdb=" O ALA T 7 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N GLY T 23 " --> pdb=" O LEU T 19 " (cutoff:3.500A) Proline residue: T 24 - end of helix Processing helix chain 'T' and resid 47 through 68 removed outlier: 4.008A pdb=" N PHE T 59 " --> pdb=" O LEU T 55 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR T 64 " --> pdb=" O MET T 60 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU T 68 " --> pdb=" O THR T 64 " (cutoff:3.500A) Processing helix chain 'T' and resid 72 through 75 No H-bonds generated for 'chain 'T' and resid 72 through 75' Processing helix chain 'Y' and resid 5 through 41 removed outlier: 4.732A pdb=" N ALA Y 13 " --> pdb=" O SER Y 9 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLY Y 14 " --> pdb=" O VAL Y 10 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU Y 15 " --> pdb=" O ILE Y 11 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA Y 20 " --> pdb=" O ALA Y 16 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLY Y 23 " --> pdb=" O LEU Y 19 " (cutoff:3.500A) Proline residue: Y 24 - end of helix removed outlier: 4.925A pdb=" N GLY Y 29 " --> pdb=" O GLY Y 25 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLN Y 34 " --> pdb=" O THR Y 30 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU Y 37 " --> pdb=" O GLY Y 33 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE Y 39 " --> pdb=" O ALA Y 35 " (cutoff:3.500A) Processing helix chain 'Y' and resid 45 through 75 removed outlier: 4.714A pdb=" N ARG Y 50 " --> pdb=" O GLY Y 47 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU Y 53 " --> pdb=" O ARG Y 50 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU Y 54 " --> pdb=" O GLY Y 51 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE Y 65 " --> pdb=" O ALA Y 62 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA Y 73 " --> pdb=" O VAL Y 70 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU Y 74 " --> pdb=" O ALA Y 71 " (cutoff:3.500A) Processing helix chain 'X' and resid 4 through 22 removed outlier: 4.198A pdb=" N ILE X 11 " --> pdb=" O ALA X 7 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA X 12 " --> pdb=" O ALA X 8 " (cutoff:3.500A) Processing helix chain 'X' and resid 24 through 41 removed outlier: 3.723A pdb=" N ALA X 35 " --> pdb=" O ALA X 31 " (cutoff:3.500A) Processing helix chain 'X' and resid 45 through 75 removed outlier: 5.307A pdb=" N ARG X 50 " --> pdb=" O GLY X 47 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLY X 51 " --> pdb=" O LYS X 48 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N LEU X 54 " --> pdb=" O GLY X 51 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LEU X 55 " --> pdb=" O THR X 52 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU X 61 " --> pdb=" O ALA X 58 " (cutoff:3.500A) Processing helix chain 'W' and resid 7 through 41 removed outlier: 3.690A pdb=" N GLY W 18 " --> pdb=" O GLY W 14 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N GLY W 23 " --> pdb=" O LEU W 19 " (cutoff:3.500A) Proline residue: W 24 - end of helix Processing helix chain 'W' and resid 46 through 76 removed outlier: 4.056A pdb=" N GLY W 67 " --> pdb=" O LEU W 63 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N VAL W 70 " --> pdb=" O TYR W 66 " (cutoff:3.500A) Processing helix chain 'V' and resid 7 through 20 Processing helix chain 'V' and resid 23 through 41 removed outlier: 3.514A pdb=" N ILE V 39 " --> pdb=" O ALA V 35 " (cutoff:3.500A) Processing helix chain 'V' and resid 46 through 53 removed outlier: 3.518A pdb=" N ARG V 50 " --> pdb=" O GLU V 46 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLY V 51 " --> pdb=" O GLY V 47 " (cutoff:3.500A) Processing helix chain 'V' and resid 57 through 77 removed outlier: 3.856A pdb=" N TYR V 66 " --> pdb=" O ALA V 62 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLY V 67 " --> pdb=" O LEU V 63 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LEU V 74 " --> pdb=" O VAL V 70 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU V 75 " --> pdb=" O ALA V 71 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA V 77 " --> pdb=" O ALA V 73 " (cutoff:3.500A) Processing helix chain 'U' and resid 4 through 41 removed outlier: 4.250A pdb=" N SER U 21 " --> pdb=" O VAL U 17 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ILE U 22 " --> pdb=" O GLY U 18 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N GLY U 23 " --> pdb=" O LEU U 19 " (cutoff:3.500A) Proline residue: U 24 - end of helix removed outlier: 3.611A pdb=" N GLY U 27 " --> pdb=" O GLY U 23 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLY U 29 " --> pdb=" O GLY U 25 " (cutoff:3.500A) Processing helix chain 'U' and resid 46 through 75 removed outlier: 4.253A pdb=" N GLY U 67 " --> pdb=" O LEU U 63 " (cutoff:3.500A) Processing helix chain 'Z' and resid 4 through 41 removed outlier: 4.287A pdb=" N SER Z 21 " --> pdb=" O VAL Z 17 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ILE Z 22 " --> pdb=" O GLY Z 18 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N GLY Z 23 " --> pdb=" O LEU Z 19 " (cutoff:3.500A) Proline residue: Z 24 - end of helix removed outlier: 3.600A pdb=" N ARG Z 41 " --> pdb=" O GLU Z 37 " (cutoff:3.500A) Processing helix chain 'Z' and resid 43 through 75 removed outlier: 3.536A pdb=" N GLU Z 46 " --> pdb=" O PRO Z 43 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N GLY Z 47 " --> pdb=" O GLU Z 44 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LEU Z 54 " --> pdb=" O GLY Z 51 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ALA Z 58 " --> pdb=" O LEU Z 55 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU Z 61 " --> pdb=" O ALA Z 58 " (cutoff:3.500A) Processing helix chain 'S' and resid 4 through 20 removed outlier: 3.996A pdb=" N ILE S 11 " --> pdb=" O ALA S 7 " (cutoff:3.500A) Processing helix chain 'S' and resid 22 through 41 removed outlier: 3.803A pdb=" N ARG S 41 " --> pdb=" O GLU S 37 " (cutoff:3.500A) Processing helix chain 'S' and resid 46 through 75 removed outlier: 4.417A pdb=" N THR S 52 " --> pdb=" O LYS S 48 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU S 53 " --> pdb=" O ILE S 49 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU S 55 " --> pdb=" O GLY S 51 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY S 67 " --> pdb=" O LEU S 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 41 removed outlier: 3.766A pdb=" N ALA R 8 " --> pdb=" O LEU R 4 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY R 18 " --> pdb=" O GLY R 14 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N GLY R 23 " --> pdb=" O LEU R 19 " (cutoff:3.500A) Proline residue: R 24 - end of helix removed outlier: 3.754A pdb=" N THR R 30 " --> pdb=" O VAL R 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 75 removed outlier: 3.637A pdb=" N GLY R 67 " --> pdb=" O LEU R 63 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL R 70 " --> pdb=" O TYR R 66 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 41 removed outlier: 3.842A pdb=" N ILE Q 11 " --> pdb=" O ALA Q 7 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N SER Q 21 " --> pdb=" O VAL Q 17 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE Q 22 " --> pdb=" O GLY Q 18 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLY Q 23 " --> pdb=" O LEU Q 19 " (cutoff:3.500A) Proline residue: Q 24 - end of helix Processing helix chain 'Q' and resid 46 through 75 removed outlier: 4.093A pdb=" N GLY Q 67 " --> pdb=" O LEU Q 63 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU Q 75 " --> pdb=" O ALA Q 71 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 41 removed outlier: 3.919A pdb=" N ILE M 11 " --> pdb=" O ALA M 7 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N SER M 21 " --> pdb=" O VAL M 17 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ILE M 22 " --> pdb=" O GLY M 18 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLY M 23 " --> pdb=" O LEU M 19 " (cutoff:3.500A) Proline residue: M 24 - end of helix Processing helix chain 'M' and resid 46 through 75 removed outlier: 4.083A pdb=" N THR M 52 " --> pdb=" O LYS M 48 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE M 59 " --> pdb=" O LEU M 55 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE M 65 " --> pdb=" O GLU M 61 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR M 66 " --> pdb=" O ALA M 62 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY M 67 " --> pdb=" O LEU M 63 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 36 removed outlier: 4.207A pdb=" N GLY N 23 " --> pdb=" O LEU N 19 " (cutoff:3.500A) Proline residue: N 24 - end of helix Processing helix chain 'N' and resid 42 through 44 No H-bonds generated for 'chain 'N' and resid 42 through 44' Processing helix chain 'N' and resid 48 through 75 removed outlier: 3.538A pdb=" N LEU N 55 " --> pdb=" O GLY N 51 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLY N 67 " --> pdb=" O LEU N 63 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 41 removed outlier: 3.612A pdb=" N ILE O 11 " --> pdb=" O ALA O 7 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N GLY O 23 " --> pdb=" O LEU O 19 " (cutoff:3.500A) Proline residue: O 24 - end of helix removed outlier: 3.594A pdb=" N GLN O 34 " --> pdb=" O THR O 30 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL O 36 " --> pdb=" O ALA O 32 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N GLU O 37 " --> pdb=" O GLY O 33 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 71 removed outlier: 4.730A pdb=" N ARG O 50 " --> pdb=" O GLY O 47 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N LEU O 53 " --> pdb=" O ARG O 50 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LEU O 54 " --> pdb=" O GLY O 51 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N SER O 56 " --> pdb=" O LEU O 53 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU O 57 " --> pdb=" O LEU O 54 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET O 60 " --> pdb=" O LEU O 57 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR O 64 " --> pdb=" O GLU O 61 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR O 66 " --> pdb=" O LEU O 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 41 removed outlier: 3.905A pdb=" N GLY P 18 " --> pdb=" O GLY P 14 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLY P 23 " --> pdb=" O LEU P 19 " (cutoff:3.500A) Proline residue: P 24 - end of helix removed outlier: 3.981A pdb=" N GLY P 27 " --> pdb=" O GLY P 23 " (cutoff:3.500A) Processing helix chain 'P' and resid 47 through 75 removed outlier: 3.511A pdb=" N LEU P 55 " --> pdb=" O GLY P 51 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY P 67 " --> pdb=" O LEU P 63 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL P 70 " --> pdb=" O TYR P 66 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 88 through 90 removed outlier: 6.444A pdb=" N ARG A 41 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL A 75 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N ALA A 64 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLU A 52 " --> pdb=" O ALA A 64 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 258 through 262 Processing sheet with id= C, first strand: chain 'C' and resid 72 through 75 removed outlier: 3.541A pdb=" N GLN C 34 " --> pdb=" O ARG C 41 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N HIS C 43 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N VAL C 32 " --> pdb=" O HIS C 43 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 97 through 99 Processing sheet with id= E, first strand: chain 'C' and resid 318 through 321 removed outlier: 3.541A pdb=" N GLY C 170 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ILE C 343 " --> pdb=" O ILE C 169 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 53 through 55 Processing sheet with id= G, first strand: chain 'B' and resid 193 through 198 removed outlier: 3.884A pdb=" N LEU B 258 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N SER B 313 " --> pdb=" O THR B 257 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE B 259 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N THR B 315 " --> pdb=" O ILE B 259 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N TYR B 261 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 22 through 27 removed outlier: 6.696A pdb=" N ASP D 32 " --> pdb=" O ALA D 24 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ILE D 26 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL D 30 " --> pdb=" O ILE D 26 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL D 77 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N VAL D 65 " --> pdb=" O VAL D 77 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 99 through 101 removed outlier: 3.538A pdb=" N SER D 130 " --> pdb=" O VAL D 100 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 167 through 169 removed outlier: 6.436A pdb=" N SER D 323 " --> pdb=" O ILE D 168 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'D' and resid 170 through 172 removed outlier: 6.012A pdb=" N THR D 350 " --> pdb=" O PHE D 171 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'E' and resid 23 through 27 removed outlier: 6.386A pdb=" N ASP E 32 " --> pdb=" O ALA E 24 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ILE E 26 " --> pdb=" O VAL E 30 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL E 30 " --> pdb=" O ILE E 26 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL E 33 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL E 77 " --> pdb=" O VAL E 65 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N VAL E 65 " --> pdb=" O VAL E 77 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 196 through 199 Processing sheet with id= N, first strand: chain 'F' and resid 23 through 27 removed outlier: 6.947A pdb=" N ASP F 32 " --> pdb=" O ALA F 24 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ILE F 26 " --> pdb=" O VAL F 30 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL F 30 " --> pdb=" O ILE F 26 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N VAL F 77 " --> pdb=" O VAL F 65 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N VAL F 65 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL F 61 " --> pdb=" O VAL F 49 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'F' and resid 99 through 101 Processing sheet with id= P, first strand: chain 'F' and resid 167 through 169 removed outlier: 6.445A pdb=" N SER F 323 " --> pdb=" O ILE F 168 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL F 202 " --> pdb=" O ASP F 273 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE F 199 " --> pdb=" O ALA F 233 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'd' and resid 180 through 182 Processing sheet with id= R, first strand: chain 'g' and resid 254 through 259 removed outlier: 3.679A pdb=" N THR g 265 " --> pdb=" O THR g 258 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'e' and resid 73 through 77 removed outlier: 6.359A pdb=" N ASN e 4 " --> pdb=" O ILE e 74 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ILE e 76 " --> pdb=" O ASN e 4 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N CYS e 6 " --> pdb=" O ILE e 76 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU e 3 " --> pdb=" O VAL e 19 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL e 19 " --> pdb=" O LEU e 3 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL e 7 " --> pdb=" O TRP e 15 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TRP e 15 " --> pdb=" O VAL e 7 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N THR e 9 " --> pdb=" O SER e 13 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N SER e 13 " --> pdb=" O THR e 9 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'e' and resid 40 through 42 Processing sheet with id= U, first strand: chain 'e' and resid 47 through 50 removed outlier: 3.538A pdb=" N GLY e 47 " --> pdb=" O LEU e 62 " (cutoff:3.500A) 1968 hydrogen bonds defined for protein. 5325 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: 12.46 Time building geometry restraints manager: 15.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13121 1.34 - 1.47: 8096 1.47 - 1.59: 18220 1.59 - 1.71: 23 1.71 - 1.84: 249 Bond restraints: 39709 Sorted by residual: bond pdb=" C4 ATP D 601 " pdb=" C5 ATP D 601 " ideal model delta sigma weight residual 1.388 1.473 -0.085 1.00e-02 1.00e+04 7.20e+01 bond pdb=" C4 ATP A 601 " pdb=" C5 ATP A 601 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.47e+01 bond pdb=" C4 ATP B 601 " pdb=" C5 ATP B 601 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.34e+01 bond pdb=" C4 ATP C 601 " pdb=" C5 ATP C 601 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.06e+01 bond pdb=" C5 ATP D 601 " pdb=" C6 ATP D 601 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.37e+01 ... (remaining 39704 not shown) Histogram of bond angle deviations from ideal: 95.57 - 103.67: 590 103.67 - 111.77: 18802 111.77 - 119.87: 16118 119.87 - 127.97: 18189 127.97 - 136.07: 149 Bond angle restraints: 53848 Sorted by residual: angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 117.60 22.27 1.00e+00 1.00e+00 4.96e+02 angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 117.70 22.17 1.00e+00 1.00e+00 4.92e+02 angle pdb=" PB ATP D 601 " pdb=" O3B ATP D 601 " pdb=" PG ATP D 601 " ideal model delta sigma weight residual 139.87 119.31 20.56 1.00e+00 1.00e+00 4.23e+02 angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 119.73 20.14 1.00e+00 1.00e+00 4.06e+02 angle pdb=" PA ATP D 601 " pdb=" O3A ATP D 601 " pdb=" PB ATP D 601 " ideal model delta sigma weight residual 136.83 116.72 20.11 1.00e+00 1.00e+00 4.04e+02 ... (remaining 53843 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.82: 22519 23.82 - 47.65: 1479 47.65 - 71.47: 148 71.47 - 95.30: 54 95.30 - 119.12: 3 Dihedral angle restraints: 24203 sinusoidal: 9472 harmonic: 14731 Sorted by residual: dihedral pdb=" CA PRO R 79 " pdb=" C PRO R 79 " pdb=" N PHE R 80 " pdb=" CA PHE R 80 " ideal model delta harmonic sigma weight residual -180.00 -123.70 -56.30 0 5.00e+00 4.00e-02 1.27e+02 dihedral pdb=" CA ALA D 295 " pdb=" C ALA D 295 " pdb=" N VAL D 296 " pdb=" CA VAL D 296 " ideal model delta harmonic sigma weight residual -180.00 -129.56 -50.44 0 5.00e+00 4.00e-02 1.02e+02 dihedral pdb=" CA ALA E 295 " pdb=" C ALA E 295 " pdb=" N VAL E 296 " pdb=" CA VAL E 296 " ideal model delta harmonic sigma weight residual -180.00 -131.69 -48.31 0 5.00e+00 4.00e-02 9.33e+01 ... (remaining 24200 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 5541 0.070 - 0.141: 822 0.141 - 0.211: 66 0.211 - 0.281: 8 0.281 - 0.351: 3 Chirality restraints: 6440 Sorted by residual: chirality pdb=" CB ILE N 65 " pdb=" CA ILE N 65 " pdb=" CG1 ILE N 65 " pdb=" CG2 ILE N 65 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" CB ILE e 69 " pdb=" CA ILE e 69 " pdb=" CG1 ILE e 69 " pdb=" CG2 ILE e 69 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" CG LEU J 100 " pdb=" CB LEU J 100 " pdb=" CD1 LEU J 100 " pdb=" CD2 LEU J 100 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 6437 not shown) Planarity restraints: 6950 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU O 54 " -0.020 2.00e-02 2.50e+03 4.06e-02 1.65e+01 pdb=" C LEU O 54 " 0.070 2.00e-02 2.50e+03 pdb=" O LEU O 54 " -0.026 2.00e-02 2.50e+03 pdb=" N LEU O 55 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER V 56 " -0.019 2.00e-02 2.50e+03 3.72e-02 1.38e+01 pdb=" C SER V 56 " 0.064 2.00e-02 2.50e+03 pdb=" O SER V 56 " -0.024 2.00e-02 2.50e+03 pdb=" N LEU V 57 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU T 46 " -0.018 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C GLU T 46 " 0.064 2.00e-02 2.50e+03 pdb=" O GLU T 46 " -0.024 2.00e-02 2.50e+03 pdb=" N GLY T 47 " -0.022 2.00e-02 2.50e+03 ... (remaining 6947 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 2121 2.72 - 3.26: 43007 3.26 - 3.81: 66919 3.81 - 4.35: 82115 4.35 - 4.90: 135715 Nonbonded interactions: 329877 Sorted by model distance: nonbonded pdb=" O ALA F 295 " pdb=" N GLY F 297 " model vdw 2.172 2.520 nonbonded pdb=" OG1 THR d 181 " pdb=" OG1 THR d 222 " model vdw 2.176 2.440 nonbonded pdb=" OH TYR N 66 " pdb=" OE2 GLU O 61 " model vdw 2.179 2.440 nonbonded pdb=" O ALA X 20 " pdb=" OG1 THR X 64 " model vdw 2.179 2.440 nonbonded pdb=" OH TYR C 20 " pdb=" OE2 GLU d 249 " model vdw 2.213 2.440 ... (remaining 329872 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 6 through 503 or resid 601)) selection = (chain 'B' and (resid 6 through 503 or resid 601)) selection = (chain 'C' and (resid 6 through 503 or resid 601)) } ncs_group { reference = (chain 'D' and resid 17 through 494) selection = (chain 'E' and resid 17 through 494) selection = (chain 'F' and resid 17 through 494) } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 12.520 Check model and map are aligned: 0.560 Set scattering table: 0.350 Process input model: 96.560 Find NCS groups from input model: 2.580 Set up NCS constraints: 0.430 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 118.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 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 : 0.005 0.085 39709 Z= 0.348 Angle : 0.988 22.267 53848 Z= 0.609 Chirality : 0.050 0.351 6440 Planarity : 0.006 0.079 6950 Dihedral : 15.675 119.121 14764 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.68 % Favored : 92.02 % Rotamer: Outliers : 0.49 % Allowed : 10.06 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.16 % 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: -3.96 (0.10), residues: 5141 helix: -2.04 (0.08), residues: 2735 sheet: -3.77 (0.19), residues: 431 loop : -3.04 (0.12), residues: 1975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP e 15 HIS 0.007 0.001 HIS F 345 PHE 0.043 0.002 PHE I 145 TYR 0.022 0.002 TYR B 144 ARG 0.008 0.001 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10282 Ramachandran restraints generated. 5141 Oldfield, 0 Emsley, 5141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10282 Ramachandran restraints generated. 5141 Oldfield, 0 Emsley, 5141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1034 residues out of total 4097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 1014 time to evaluate : 3.791 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: A 241 TYR cc_start: 0.9330 (m-10) cc_final: 0.9120 (m-10) REVERT: A 251 MET cc_start: 0.8149 (ttp) cc_final: 0.7887 (ttp) REVERT: A 262 ASP cc_start: 0.6930 (t0) cc_final: 0.6382 (t0) REVERT: A 396 PHE cc_start: 0.8243 (t80) cc_final: 0.8003 (t80) REVERT: A 408 GLN cc_start: 0.5557 (tt0) cc_final: 0.4945 (tt0) REVERT: A 413 ARG cc_start: 0.6780 (tpp80) cc_final: 0.6362 (mtt-85) REVERT: C 39 ILE cc_start: 0.8464 (pt) cc_final: 0.8126 (mt) REVERT: C 82 MET cc_start: 0.7829 (mmm) cc_final: 0.7421 (mmm) REVERT: C 128 ARG cc_start: 0.9091 (tpp80) cc_final: 0.7989 (tpp80) REVERT: C 148 GLN cc_start: 0.8491 (mp10) cc_final: 0.8245 (mp10) REVERT: C 185 LEU cc_start: 0.9057 (mt) cc_final: 0.8828 (mp) REVERT: C 202 LYS cc_start: 0.7827 (pttp) cc_final: 0.7563 (ptmt) REVERT: C 251 MET cc_start: 0.8594 (ttp) cc_final: 0.7776 (ttp) REVERT: C 261 TYR cc_start: 0.8916 (m-80) cc_final: 0.8496 (m-80) REVERT: C 274 MET cc_start: 0.8492 (ptm) cc_final: 0.8088 (tmm) REVERT: C 343 ILE cc_start: 0.8919 (pt) cc_final: 0.8638 (pt) REVERT: C 399 PHE cc_start: 0.7831 (m-80) cc_final: 0.7122 (m-80) REVERT: C 405 LYS cc_start: 0.7669 (ttmt) cc_final: 0.7082 (tptp) REVERT: C 436 MET cc_start: 0.7821 (ptp) cc_final: 0.7362 (ptp) REVERT: B 8 GLU cc_start: 0.7195 (mt-10) cc_final: 0.6920 (mt-10) REVERT: B 20 TYR cc_start: 0.5812 (t80) cc_final: 0.5599 (t80) REVERT: B 76 LEU cc_start: 0.8960 (pp) cc_final: 0.8737 (pp) REVERT: B 151 LEU cc_start: 0.9051 (mt) cc_final: 0.8823 (mt) REVERT: B 155 ASP cc_start: 0.8140 (t0) cc_final: 0.7788 (t0) REVERT: B 251 MET cc_start: 0.8730 (ttp) cc_final: 0.8278 (ttp) REVERT: B 292 PHE cc_start: 0.8387 (t80) cc_final: 0.8079 (t80) REVERT: B 298 LEU cc_start: 0.9439 (tp) cc_final: 0.9045 (tp) REVERT: B 321 GLU cc_start: 0.8160 (pt0) cc_final: 0.7344 (pt0) REVERT: B 323 GLN cc_start: 0.7638 (mt0) cc_final: 0.7197 (mm110) REVERT: D 22 ARG cc_start: 0.7504 (ptm-80) cc_final: 0.7219 (ttp-110) REVERT: D 184 GLU cc_start: 0.7712 (tm-30) cc_final: 0.7480 (tm-30) REVERT: D 256 MET cc_start: 0.8649 (ttm) cc_final: 0.8408 (mtt) REVERT: D 292 MET cc_start: 0.9060 (ttt) cc_final: 0.8734 (ttm) REVERT: D 469 LEU cc_start: 0.7247 (mp) cc_final: 0.7023 (mt) REVERT: D 488 MET cc_start: 0.7817 (ttp) cc_final: 0.7420 (ttt) REVERT: E 18 LYS cc_start: 0.6995 (ttpp) cc_final: 0.6320 (pptt) REVERT: E 69 LEU cc_start: 0.8666 (tp) cc_final: 0.8268 (tp) REVERT: E 79 MET cc_start: 0.7931 (mmt) cc_final: 0.7639 (mmt) REVERT: E 158 LEU cc_start: 0.8945 (tp) cc_final: 0.8688 (tp) REVERT: E 247 MET cc_start: 0.8586 (ttp) cc_final: 0.8331 (ttp) REVERT: E 437 VAL cc_start: 0.8043 (t) cc_final: 0.7812 (p) REVERT: E 480 ILE cc_start: 0.8472 (tp) cc_final: 0.8170 (tt) REVERT: E 488 MET cc_start: 0.5892 (ptp) cc_final: 0.5136 (ptm) REVERT: F 79 MET cc_start: 0.8546 (mmt) cc_final: 0.8330 (mmt) REVERT: F 83 ASP cc_start: 0.7799 (m-30) cc_final: 0.7591 (p0) REVERT: F 92 ILE cc_start: 0.8963 (pt) cc_final: 0.8640 (mp) REVERT: F 119 ASP cc_start: 0.7713 (p0) cc_final: 0.7302 (p0) REVERT: F 265 GLU cc_start: 0.8363 (mt-10) cc_final: 0.7977 (pt0) REVERT: F 362 TYR cc_start: 0.7767 (m-80) cc_final: 0.7543 (m-80) REVERT: F 366 ASP cc_start: 0.7998 (t0) cc_final: 0.7564 (t0) REVERT: F 412 GLU cc_start: 0.7110 (tt0) cc_final: 0.6744 (tt0) REVERT: F 456 ARG cc_start: 0.7879 (tpt-90) cc_final: 0.7285 (ttp80) REVERT: d 210 LYS cc_start: 0.7454 (ptpt) cc_final: 0.7116 (ptmm) REVERT: g 185 LEU cc_start: 0.8676 (mt) cc_final: 0.7965 (pp) REVERT: g 209 LYS cc_start: 0.7176 (tptp) cc_final: 0.6961 (tptp) REVERT: g 222 LYS cc_start: 0.7838 (tmmt) cc_final: 0.7553 (mttp) REVERT: g 281 ILE cc_start: 0.7376 (mm) cc_final: 0.6702 (mm) REVERT: e 1 MET cc_start: 0.6889 (ptt) cc_final: 0.6391 (ptm) REVERT: e 18 GLU cc_start: 0.6469 (mp0) cc_final: 0.6211 (mp0) REVERT: e 34 LEU cc_start: 0.7542 (pp) cc_final: 0.7043 (pp) REVERT: e 36 ASN cc_start: 0.7877 (t0) cc_final: 0.7555 (t0) REVERT: e 50 ARG cc_start: 0.7338 (mtm-85) cc_final: 0.6995 (tpp80) REVERT: e 97 GLU cc_start: 0.7656 (tt0) cc_final: 0.7178 (pt0) REVERT: e 125 ARG cc_start: 0.7682 (mmt180) cc_final: 0.7147 (mmt-90) REVERT: J 139 GLN cc_start: 0.5895 (mt0) cc_final: 0.5266 (tm-30) REVERT: J 162 MET cc_start: 0.5131 (mmm) cc_final: 0.4799 (mmt) REVERT: I 90 MET cc_start: 0.7552 (tmm) cc_final: 0.7295 (tmm) REVERT: a 77 GLU cc_start: 0.7695 (mt-10) cc_final: 0.7466 (mt-10) REVERT: a 197 ASP cc_start: 0.6411 (p0) cc_final: 0.6072 (p0) REVERT: a 198 GLU cc_start: 0.5948 (mm-30) cc_final: 0.5315 (tp30) REVERT: T 50 ARG cc_start: 0.3223 (mtp85) cc_final: 0.2553 (ttt-90) REVERT: T 60 MET cc_start: 0.6697 (mtp) cc_final: 0.5644 (mtp) REVERT: Y 41 ARG cc_start: 0.7178 (mtt180) cc_final: 0.6958 (mmp80) REVERT: Y 54 LEU cc_start: 0.6876 (mm) cc_final: 0.6540 (mm) REVERT: Y 76 PHE cc_start: 0.5977 (m-80) cc_final: 0.5302 (m-80) REVERT: X 28 GLN cc_start: 0.5546 (mt0) cc_final: 0.5288 (mp10) REVERT: X 55 LEU cc_start: 0.5483 (tt) cc_final: 0.5029 (mt) REVERT: X 60 MET cc_start: 0.7557 (ttt) cc_final: 0.5854 (ttt) REVERT: W 49 ILE cc_start: 0.6256 (mt) cc_final: 0.5913 (mm) REVERT: Z 48 LYS cc_start: 0.4143 (mttt) cc_final: 0.3674 (mmtp) REVERT: S 22 ILE cc_start: 0.7923 (tp) cc_final: 0.7662 (mt) REVERT: R 66 TYR cc_start: 0.7068 (m-10) cc_final: 0.6833 (m-80) REVERT: M 50 ARG cc_start: 0.6988 (ttm170) cc_final: 0.6089 (ptm160) REVERT: N 50 ARG cc_start: 0.5685 (mtp180) cc_final: 0.5463 (ttp-170) outliers start: 20 outliers final: 4 residues processed: 1027 average time/residue: 0.5109 time to fit residues: 842.5445 Evaluate side-chains 691 residues out of total 4097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 687 time to evaluate : 4.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 424 optimal weight: 0.3980 chunk 381 optimal weight: 0.6980 chunk 211 optimal weight: 0.1980 chunk 130 optimal weight: 0.0980 chunk 257 optimal weight: 0.0870 chunk 203 optimal weight: 6.9990 chunk 394 optimal weight: 5.9990 chunk 152 optimal weight: 8.9990 chunk 239 optimal weight: 0.9990 chunk 293 optimal weight: 1.9990 chunk 456 optimal weight: 2.9990 overall best weight: 0.2958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 GLN A 423 GLN ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 HIS C 186 ASN C 188 GLN C 256 HIS ** C 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 GLN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 ASN ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 479 ASN ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 193 HIS F 66 GLN ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 299 GLN d 139 GLN d 190 HIS d 199 GLN d 247 GLN g 301 ASN e 27 ASN I 147 GLN I 180 ASN ** a 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 175 ASN Y 78 ASN X 34 GLN ** W 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 GLN ** P 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 39709 Z= 0.210 Angle : 0.715 12.053 53848 Z= 0.362 Chirality : 0.045 0.276 6440 Planarity : 0.006 0.078 6950 Dihedral : 8.016 119.939 5697 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.98 % Favored : 92.76 % Rotamer: Outliers : 0.22 % Allowed : 6.20 % Favored : 93.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.22 % 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: -2.69 (0.11), residues: 5141 helix: -0.93 (0.09), residues: 2751 sheet: -3.20 (0.21), residues: 414 loop : -2.59 (0.13), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP e 15 HIS 0.011 0.001 HIS g 228 PHE 0.045 0.002 PHE I 145 TYR 0.034 0.001 TYR N 66 ARG 0.018 0.001 ARG e 83 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10282 Ramachandran restraints generated. 5141 Oldfield, 0 Emsley, 5141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10282 Ramachandran restraints generated. 5141 Oldfield, 0 Emsley, 5141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 951 residues out of total 4097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 942 time to evaluate : 4.348 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: A 251 MET cc_start: 0.8334 (ttp) cc_final: 0.7805 (ttp) REVERT: A 408 GLN cc_start: 0.5018 (tt0) cc_final: 0.4781 (tt0) REVERT: A 485 GLU cc_start: 0.7485 (pt0) cc_final: 0.7012 (tp30) REVERT: C 148 GLN cc_start: 0.8321 (mp10) cc_final: 0.8103 (mp10) REVERT: C 219 MET cc_start: 0.8598 (tpp) cc_final: 0.8229 (tpp) REVERT: C 241 TYR cc_start: 0.8532 (m-80) cc_final: 0.8287 (m-10) REVERT: C 251 MET cc_start: 0.8527 (ttp) cc_final: 0.7617 (ttp) REVERT: C 261 TYR cc_start: 0.8894 (m-80) cc_final: 0.8528 (m-80) REVERT: C 274 MET cc_start: 0.8327 (ptm) cc_final: 0.8074 (tmm) REVERT: C 405 LYS cc_start: 0.7735 (ttmt) cc_final: 0.7183 (tmtt) REVERT: C 436 MET cc_start: 0.7764 (ptp) cc_final: 0.7317 (ptp) REVERT: B 5 ARG cc_start: 0.7494 (ttm170) cc_final: 0.7284 (ttp80) REVERT: B 20 TYR cc_start: 0.5953 (t80) cc_final: 0.5738 (t80) REVERT: B 251 MET cc_start: 0.8753 (ttp) cc_final: 0.8258 (ttp) REVERT: B 298 LEU cc_start: 0.9339 (tp) cc_final: 0.9003 (tp) REVERT: B 366 ARG cc_start: 0.6992 (ttt-90) cc_final: 0.6703 (ttt-90) REVERT: B 416 ARG cc_start: 0.7622 (mpt180) cc_final: 0.7421 (mpt-90) REVERT: D 22 ARG cc_start: 0.7444 (ptm-80) cc_final: 0.7119 (tmm160) REVERT: D 184 GLU cc_start: 0.7068 (tm-30) cc_final: 0.6781 (tm-30) REVERT: D 256 MET cc_start: 0.8574 (ttm) cc_final: 0.8314 (mtt) REVERT: D 274 ASN cc_start: 0.8636 (t0) cc_final: 0.8231 (t0) REVERT: D 284 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7643 (mm-30) REVERT: D 292 MET cc_start: 0.9010 (ttt) cc_final: 0.8694 (ttm) REVERT: E 18 LYS cc_start: 0.6895 (ttpp) cc_final: 0.6280 (pptt) REVERT: E 69 LEU cc_start: 0.8525 (tp) cc_final: 0.8128 (tp) REVERT: E 79 MET cc_start: 0.7997 (mmt) cc_final: 0.7671 (mmt) REVERT: E 222 ILE cc_start: 0.8379 (pt) cc_final: 0.8064 (mp) REVERT: E 417 ASP cc_start: 0.7818 (p0) cc_final: 0.7613 (p0) REVERT: E 437 VAL cc_start: 0.8134 (t) cc_final: 0.7811 (p) REVERT: E 480 ILE cc_start: 0.8452 (tp) cc_final: 0.8136 (tt) REVERT: E 488 MET cc_start: 0.5584 (ptp) cc_final: 0.5223 (ptm) REVERT: F 30 VAL cc_start: 0.9098 (t) cc_final: 0.8771 (p) REVERT: F 92 ILE cc_start: 0.8786 (pt) cc_final: 0.8542 (mp) REVERT: F 274 ASN cc_start: 0.7556 (m-40) cc_final: 0.7215 (m-40) REVERT: F 362 TYR cc_start: 0.7762 (m-80) cc_final: 0.7394 (m-80) REVERT: F 366 ASP cc_start: 0.7916 (t0) cc_final: 0.7667 (t0) REVERT: F 412 GLU cc_start: 0.6641 (tt0) cc_final: 0.6177 (tt0) REVERT: F 456 ARG cc_start: 0.7888 (tpt-90) cc_final: 0.7283 (ttp-170) REVERT: d 92 LEU cc_start: 0.6787 (tp) cc_final: 0.6166 (pt) REVERT: g 129 LEU cc_start: 0.7472 (tp) cc_final: 0.6992 (tp) REVERT: g 185 LEU cc_start: 0.8616 (mt) cc_final: 0.7959 (pt) REVERT: g 222 LYS cc_start: 0.7911 (tmmt) cc_final: 0.7537 (mttp) REVERT: g 323 MET cc_start: 0.7225 (mmt) cc_final: 0.6947 (mmt) REVERT: e 1 MET cc_start: 0.6609 (ptt) cc_final: 0.6135 (ptm) REVERT: e 34 LEU cc_start: 0.7401 (pp) cc_final: 0.7084 (pp) REVERT: e 50 ARG cc_start: 0.7070 (mtm-85) cc_final: 0.6839 (tpp80) REVERT: e 91 GLU cc_start: 0.7902 (tp30) cc_final: 0.7660 (tp30) REVERT: e 97 GLU cc_start: 0.7633 (tt0) cc_final: 0.7089 (pt0) REVERT: e 112 LYS cc_start: 0.6180 (mmmt) cc_final: 0.5969 (mmmt) REVERT: e 125 ARG cc_start: 0.7725 (mmt180) cc_final: 0.7356 (mmt-90) REVERT: J 139 GLN cc_start: 0.5497 (mt0) cc_final: 0.5111 (tm-30) REVERT: J 162 MET cc_start: 0.4702 (mmm) cc_final: 0.4392 (mmt) REVERT: I 90 MET cc_start: 0.7595 (tmm) cc_final: 0.6787 (tmm) REVERT: I 116 LYS cc_start: 0.6798 (mtmm) cc_final: 0.6070 (mmtm) REVERT: I 179 MET cc_start: 0.5000 (tmm) cc_final: 0.4462 (tmm) REVERT: a 73 GLU cc_start: 0.7345 (tt0) cc_final: 0.7050 (tt0) REVERT: a 161 PHE cc_start: 0.4176 (p90) cc_final: 0.3790 (p90) REVERT: a 175 ASN cc_start: 0.3756 (OUTLIER) cc_final: 0.3530 (t0) REVERT: a 197 ASP cc_start: 0.6283 (p0) cc_final: 0.6001 (p0) REVERT: T 50 ARG cc_start: 0.3215 (mtp85) cc_final: 0.2862 (ttt-90) REVERT: Y 76 PHE cc_start: 0.5961 (m-80) cc_final: 0.5426 (m-80) REVERT: X 19 LEU cc_start: 0.8712 (mt) cc_final: 0.8456 (mt) REVERT: X 59 PHE cc_start: 0.4960 (m-10) cc_final: 0.4537 (m-10) REVERT: X 60 MET cc_start: 0.6525 (ttt) cc_final: 0.5532 (ttt) REVERT: W 49 ILE cc_start: 0.6054 (mt) cc_final: 0.5824 (mm) REVERT: R 66 TYR cc_start: 0.7186 (m-10) cc_final: 0.6974 (m-80) REVERT: M 74 LEU cc_start: 0.7092 (OUTLIER) cc_final: 0.6755 (mm) REVERT: N 50 ARG cc_start: 0.5737 (mtp180) cc_final: 0.5499 (ttp-170) outliers start: 9 outliers final: 3 residues processed: 947 average time/residue: 0.4922 time to fit residues: 764.1383 Evaluate side-chains 694 residues out of total 4097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 689 time to evaluate : 4.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 253 optimal weight: 2.9990 chunk 141 optimal weight: 0.9990 chunk 380 optimal weight: 9.9990 chunk 311 optimal weight: 0.9990 chunk 126 optimal weight: 0.9990 chunk 457 optimal weight: 9.9990 chunk 494 optimal weight: 0.9980 chunk 407 optimal weight: 0.7980 chunk 453 optimal weight: 1.9990 chunk 156 optimal weight: 6.9990 chunk 367 optimal weight: 6.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 GLN A 389 GLN A 423 GLN ** C 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 GLN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 HIS ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 266 GLN ** E 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 299 GLN ** F 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 199 GLN ** d 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 301 ASN e 79 ASN I 147 GLN ** a 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 39709 Z= 0.227 Angle : 0.694 13.051 53848 Z= 0.349 Chirality : 0.044 0.254 6440 Planarity : 0.005 0.072 6950 Dihedral : 7.799 120.065 5697 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 18.62 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.80 % Favored : 91.99 % Rotamer: Outliers : 0.02 % Allowed : 5.08 % Favored : 94.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.18 % 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: -2.22 (0.11), residues: 5141 helix: -0.52 (0.09), residues: 2732 sheet: -3.07 (0.21), residues: 439 loop : -2.37 (0.13), residues: 1970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP e 15 HIS 0.008 0.001 HIS D 133 PHE 0.042 0.002 PHE a 218 TYR 0.018 0.001 TYR X 66 ARG 0.008 0.001 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10282 Ramachandran restraints generated. 5141 Oldfield, 0 Emsley, 5141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10282 Ramachandran restraints generated. 5141 Oldfield, 0 Emsley, 5141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 884 residues out of total 4097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 883 time to evaluate : 4.023 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 155 ASP cc_start: 0.7909 (m-30) cc_final: 0.7671 (m-30) REVERT: A 251 MET cc_start: 0.8323 (ttp) cc_final: 0.7910 (ttp) REVERT: A 396 PHE cc_start: 0.7934 (t80) cc_final: 0.7393 (t80) REVERT: A 463 THR cc_start: 0.8494 (p) cc_final: 0.8183 (t) REVERT: A 485 GLU cc_start: 0.7494 (pt0) cc_final: 0.7142 (tp30) REVERT: C 241 TYR cc_start: 0.8549 (m-80) cc_final: 0.8315 (m-80) REVERT: C 251 MET cc_start: 0.8467 (ttp) cc_final: 0.7930 (ttp) REVERT: C 261 TYR cc_start: 0.8922 (m-80) cc_final: 0.8579 (m-80) REVERT: C 274 MET cc_start: 0.8485 (ptm) cc_final: 0.8159 (tmm) REVERT: C 405 LYS cc_start: 0.7813 (ttmt) cc_final: 0.7219 (tmtt) REVERT: C 430 THR cc_start: 0.8496 (t) cc_final: 0.8250 (p) REVERT: C 433 GLU cc_start: 0.7793 (pm20) cc_final: 0.7250 (mp0) REVERT: C 436 MET cc_start: 0.7840 (ptp) cc_final: 0.7469 (ptp) REVERT: B 20 TYR cc_start: 0.6048 (t80) cc_final: 0.5626 (t80) REVERT: B 251 MET cc_start: 0.8884 (ttp) cc_final: 0.8299 (ttp) REVERT: B 298 LEU cc_start: 0.9367 (tp) cc_final: 0.8944 (tp) REVERT: B 366 ARG cc_start: 0.7236 (ttt-90) cc_final: 0.6949 (ttt-90) REVERT: B 416 ARG cc_start: 0.7732 (mpt180) cc_final: 0.7443 (mpt-90) REVERT: B 423 GLN cc_start: 0.8136 (tp-100) cc_final: 0.7900 (tp40) REVERT: D 256 MET cc_start: 0.8643 (ttm) cc_final: 0.8361 (mtt) REVERT: D 284 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7605 (mm-30) REVERT: D 292 MET cc_start: 0.8968 (ttt) cc_final: 0.8711 (ttm) REVERT: D 343 PHE cc_start: 0.8275 (m-80) cc_final: 0.8031 (m-10) REVERT: D 366 ASP cc_start: 0.8379 (t0) cc_final: 0.7758 (t70) REVERT: E 18 LYS cc_start: 0.6902 (ttpp) cc_final: 0.6308 (pptt) REVERT: E 69 LEU cc_start: 0.8631 (tp) cc_final: 0.8148 (tp) REVERT: E 79 MET cc_start: 0.8053 (mmt) cc_final: 0.7747 (mmt) REVERT: E 146 LEU cc_start: 0.8021 (pt) cc_final: 0.7755 (pt) REVERT: E 208 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7703 (tm-30) REVERT: E 212 LEU cc_start: 0.8805 (tp) cc_final: 0.8585 (tp) REVERT: E 222 ILE cc_start: 0.8430 (pt) cc_final: 0.8158 (mp) REVERT: E 480 ILE cc_start: 0.8470 (tp) cc_final: 0.8178 (tt) REVERT: E 488 MET cc_start: 0.5430 (ptp) cc_final: 0.5184 (ptm) REVERT: F 30 VAL cc_start: 0.9126 (t) cc_final: 0.8852 (p) REVERT: F 32 ASP cc_start: 0.8384 (p0) cc_final: 0.8037 (p0) REVERT: F 92 ILE cc_start: 0.8729 (pt) cc_final: 0.8503 (mp) REVERT: F 119 ASP cc_start: 0.7771 (p0) cc_final: 0.7472 (p0) REVERT: F 247 MET cc_start: 0.8330 (mtp) cc_final: 0.8029 (mtp) REVERT: F 274 ASN cc_start: 0.7624 (m-40) cc_final: 0.7264 (m-40) REVERT: F 332 ASP cc_start: 0.8087 (m-30) cc_final: 0.7736 (m-30) REVERT: F 362 TYR cc_start: 0.7853 (m-80) cc_final: 0.7497 (m-80) REVERT: F 366 ASP cc_start: 0.7917 (t0) cc_final: 0.7678 (t0) REVERT: F 456 ARG cc_start: 0.7913 (tpt-90) cc_final: 0.7359 (ttp-110) REVERT: d 92 LEU cc_start: 0.6822 (tp) cc_final: 0.6311 (pt) REVERT: d 99 VAL cc_start: 0.9268 (p) cc_final: 0.8893 (p) REVERT: d 144 ASN cc_start: 0.7011 (t0) cc_final: 0.6523 (t0) REVERT: g 64 MET cc_start: 0.8125 (ttm) cc_final: 0.7803 (ttm) REVERT: g 129 LEU cc_start: 0.7436 (tp) cc_final: 0.7235 (tp) REVERT: g 185 LEU cc_start: 0.8660 (mt) cc_final: 0.8007 (pt) REVERT: g 222 LYS cc_start: 0.7997 (tmmt) cc_final: 0.7633 (mttp) REVERT: e 1 MET cc_start: 0.6600 (ptt) cc_final: 0.6163 (ptm) REVERT: e 34 LEU cc_start: 0.7333 (pp) cc_final: 0.7108 (pp) REVERT: e 50 ARG cc_start: 0.6963 (mtm-85) cc_final: 0.6648 (tpt-90) REVERT: e 97 GLU cc_start: 0.7603 (tt0) cc_final: 0.7063 (pt0) REVERT: e 112 LYS cc_start: 0.6000 (mmmt) cc_final: 0.5704 (mmmt) REVERT: e 125 ARG cc_start: 0.7700 (mmt180) cc_final: 0.7154 (mmt-90) REVERT: J 88 LEU cc_start: 0.5053 (pt) cc_final: 0.4200 (tp) REVERT: J 139 GLN cc_start: 0.5480 (mt0) cc_final: 0.5107 (tm-30) REVERT: J 162 MET cc_start: 0.4782 (mmm) cc_final: 0.4451 (mmt) REVERT: I 90 MET cc_start: 0.7621 (tmm) cc_final: 0.6810 (tmm) REVERT: I 113 SER cc_start: 0.7650 (m) cc_final: 0.7426 (m) REVERT: I 116 LYS cc_start: 0.6881 (mtmm) cc_final: 0.6198 (mmtm) REVERT: I 179 MET cc_start: 0.4884 (tmm) cc_final: 0.4193 (tmm) REVERT: a 73 GLU cc_start: 0.7262 (tt0) cc_final: 0.6859 (tt0) REVERT: a 161 PHE cc_start: 0.4255 (p90) cc_final: 0.3798 (p90) REVERT: T 39 ILE cc_start: 0.7635 (mt) cc_final: 0.7430 (mt) REVERT: Y 34 GLN cc_start: 0.7221 (mt0) cc_final: 0.7012 (mm110) REVERT: Y 76 PHE cc_start: 0.5991 (m-80) cc_final: 0.5544 (m-80) REVERT: X 19 LEU cc_start: 0.8599 (mt) cc_final: 0.8343 (mt) REVERT: W 49 ILE cc_start: 0.6346 (mt) cc_final: 0.6071 (mm) REVERT: W 50 ARG cc_start: 0.6803 (mmm160) cc_final: 0.5247 (ttp-170) REVERT: W 60 MET cc_start: 0.6977 (mmt) cc_final: 0.6265 (tpt) REVERT: S 64 THR cc_start: 0.6144 (p) cc_final: 0.5942 (p) REVERT: R 66 TYR cc_start: 0.7242 (m-10) cc_final: 0.6990 (m-80) REVERT: M 74 LEU cc_start: 0.7078 (OUTLIER) cc_final: 0.6773 (mm) REVERT: O 19 LEU cc_start: 0.7733 (mp) cc_final: 0.7246 (tt) REVERT: P 28 GLN cc_start: 0.8740 (mm110) cc_final: 0.8432 (mm110) outliers start: 1 outliers final: 0 residues processed: 883 average time/residue: 0.4878 time to fit residues: 715.2147 Evaluate side-chains 659 residues out of total 4097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 658 time to evaluate : 4.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 452 optimal weight: 0.9990 chunk 344 optimal weight: 0.7980 chunk 237 optimal weight: 0.9990 chunk 50 optimal weight: 10.0000 chunk 218 optimal weight: 1.9990 chunk 307 optimal weight: 0.3980 chunk 459 optimal weight: 7.9990 chunk 486 optimal weight: 7.9990 chunk 239 optimal weight: 2.9990 chunk 435 optimal weight: 5.9990 chunk 131 optimal weight: 5.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 GLN C 410 GLN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN B 410 GLN ** B 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 GLN D 133 HIS ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 266 GLN ** E 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 299 GLN ** F 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 193 GLN ** d 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 228 HIS ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 147 GLN ** a 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 86 GLN ** a 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 34 GLN ** X 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 78 ASN ** R 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 39709 Z= 0.223 Angle : 0.687 11.981 53848 Z= 0.344 Chirality : 0.044 0.387 6440 Planarity : 0.005 0.068 6950 Dihedral : 7.689 116.880 5697 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 18.06 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.74 % Favored : 92.10 % Rotamer: Outliers : 0.05 % Allowed : 5.37 % Favored : 94.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.20 % 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: -1.96 (0.11), residues: 5141 helix: -0.30 (0.10), residues: 2731 sheet: -2.89 (0.20), residues: 471 loop : -2.25 (0.13), residues: 1939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP e 15 HIS 0.009 0.001 HIS D 133 PHE 0.042 0.002 PHE I 145 TYR 0.037 0.001 TYR N 66 ARG 0.006 0.000 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10282 Ramachandran restraints generated. 5141 Oldfield, 0 Emsley, 5141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10282 Ramachandran restraints generated. 5141 Oldfield, 0 Emsley, 5141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 874 residues out of total 4097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 872 time to evaluate : 4.297 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: A 251 MET cc_start: 0.8182 (ttp) cc_final: 0.7971 (ttp) REVERT: A 485 GLU cc_start: 0.7450 (pt0) cc_final: 0.7072 (tp30) REVERT: C 28 ASN cc_start: 0.8945 (m110) cc_final: 0.8730 (m-40) REVERT: C 241 TYR cc_start: 0.8535 (m-80) cc_final: 0.8290 (m-80) REVERT: C 251 MET cc_start: 0.8477 (ttp) cc_final: 0.7865 (ttp) REVERT: C 261 TYR cc_start: 0.8859 (m-80) cc_final: 0.8465 (m-80) REVERT: C 274 MET cc_start: 0.8588 (ptm) cc_final: 0.8185 (tmm) REVERT: C 405 LYS cc_start: 0.7865 (ttmt) cc_final: 0.7237 (tmtt) REVERT: C 436 MET cc_start: 0.7927 (ptp) cc_final: 0.7662 (ptm) REVERT: C 451 LEU cc_start: 0.8119 (mt) cc_final: 0.7899 (mt) REVERT: B 8 GLU cc_start: 0.7122 (mt-10) cc_final: 0.5774 (mt-10) REVERT: B 20 TYR cc_start: 0.6078 (t80) cc_final: 0.5865 (t80) REVERT: B 251 MET cc_start: 0.8920 (ttp) cc_final: 0.8277 (ttp) REVERT: B 298 LEU cc_start: 0.9344 (tp) cc_final: 0.8935 (tp) REVERT: B 410 GLN cc_start: 0.5906 (OUTLIER) cc_final: 0.5620 (tp-100) REVERT: B 416 ARG cc_start: 0.7668 (mpt180) cc_final: 0.6415 (ttp80) REVERT: D 184 GLU cc_start: 0.7306 (tm-30) cc_final: 0.7098 (tm-30) REVERT: D 247 MET cc_start: 0.8166 (ttp) cc_final: 0.7925 (ttm) REVERT: D 292 MET cc_start: 0.8994 (ttt) cc_final: 0.8658 (ttm) REVERT: D 343 PHE cc_start: 0.8250 (m-80) cc_final: 0.8002 (m-10) REVERT: E 18 LYS cc_start: 0.6910 (ttpp) cc_final: 0.6327 (pptt) REVERT: E 69 LEU cc_start: 0.8578 (tp) cc_final: 0.8077 (tp) REVERT: E 79 MET cc_start: 0.8026 (mmt) cc_final: 0.7760 (mmt) REVERT: E 143 ASP cc_start: 0.8057 (t70) cc_final: 0.7773 (m-30) REVERT: E 146 LEU cc_start: 0.8443 (pt) cc_final: 0.8240 (pt) REVERT: E 347 ASP cc_start: 0.8091 (m-30) cc_final: 0.7873 (m-30) REVERT: E 455 ILE cc_start: 0.8343 (tp) cc_final: 0.8097 (pt) REVERT: E 480 ILE cc_start: 0.8499 (tp) cc_final: 0.8190 (tt) REVERT: E 488 MET cc_start: 0.5439 (ptp) cc_final: 0.5213 (ptm) REVERT: F 30 VAL cc_start: 0.9143 (t) cc_final: 0.8909 (p) REVERT: F 79 MET cc_start: 0.8678 (mmm) cc_final: 0.8340 (mmt) REVERT: F 92 ILE cc_start: 0.8760 (pt) cc_final: 0.8521 (mp) REVERT: F 119 ASP cc_start: 0.7810 (p0) cc_final: 0.7535 (p0) REVERT: F 362 TYR cc_start: 0.7809 (m-80) cc_final: 0.7556 (m-80) REVERT: F 366 ASP cc_start: 0.7923 (t0) cc_final: 0.7635 (t0) REVERT: F 456 ARG cc_start: 0.8014 (tpt-90) cc_final: 0.7441 (tmm160) REVERT: F 476 LEU cc_start: 0.8827 (tp) cc_final: 0.8556 (tp) REVERT: d 154 ARG cc_start: 0.6878 (tpp80) cc_final: 0.6414 (tpp80) REVERT: g 136 MET cc_start: 0.7486 (mmp) cc_final: 0.7282 (mmp) REVERT: g 139 LYS cc_start: 0.7823 (ttpt) cc_final: 0.7026 (mmtp) REVERT: g 185 LEU cc_start: 0.8635 (mt) cc_final: 0.7984 (pt) REVERT: g 222 LYS cc_start: 0.7935 (tmmt) cc_final: 0.7586 (mttp) REVERT: e 34 LEU cc_start: 0.7354 (pp) cc_final: 0.7036 (pp) REVERT: e 91 GLU cc_start: 0.8021 (tp30) cc_final: 0.7659 (tp30) REVERT: e 95 THR cc_start: 0.8663 (m) cc_final: 0.7736 (m) REVERT: e 97 GLU cc_start: 0.7571 (tt0) cc_final: 0.6997 (pt0) REVERT: e 112 LYS cc_start: 0.5995 (mmmt) cc_final: 0.5731 (mmmt) REVERT: e 114 GLU cc_start: 0.6993 (mt-10) cc_final: 0.5814 (mt-10) REVERT: J 88 LEU cc_start: 0.5377 (pt) cc_final: 0.4467 (tp) REVERT: J 162 MET cc_start: 0.4766 (mmm) cc_final: 0.4456 (mmt) REVERT: I 90 MET cc_start: 0.7654 (tmm) cc_final: 0.6822 (tmm) REVERT: I 116 LYS cc_start: 0.7028 (mtmm) cc_final: 0.6193 (mmtm) REVERT: I 179 MET cc_start: 0.4770 (tmm) cc_final: 0.4104 (tmm) REVERT: a 161 PHE cc_start: 0.4200 (p90) cc_final: 0.3636 (p90) REVERT: a 203 VAL cc_start: 0.7945 (m) cc_final: 0.7719 (p) REVERT: a 231 PHE cc_start: 0.6522 (t80) cc_final: 0.6248 (t80) REVERT: T 39 ILE cc_start: 0.7630 (mt) cc_final: 0.7410 (mt) REVERT: Y 76 PHE cc_start: 0.6149 (m-80) cc_final: 0.5743 (m-80) REVERT: X 19 LEU cc_start: 0.8586 (mt) cc_final: 0.8347 (mt) REVERT: X 34 GLN cc_start: 0.6270 (mm110) cc_final: 0.5777 (mm-40) REVERT: W 49 ILE cc_start: 0.6266 (mt) cc_final: 0.5977 (mm) REVERT: W 50 ARG cc_start: 0.6820 (mmm160) cc_final: 0.5157 (ttp-170) REVERT: W 54 LEU cc_start: 0.6439 (mm) cc_final: 0.6054 (mm) REVERT: W 60 MET cc_start: 0.6952 (mmt) cc_final: 0.6250 (tpt) REVERT: V 50 ARG cc_start: 0.7143 (mtt90) cc_final: 0.5265 (ttt180) REVERT: Z 59 PHE cc_start: 0.7145 (m-80) cc_final: 0.6824 (m-80) REVERT: Z 68 LEU cc_start: 0.6491 (tp) cc_final: 0.6181 (tp) REVERT: S 64 THR cc_start: 0.6152 (p) cc_final: 0.5832 (p) REVERT: R 66 TYR cc_start: 0.7241 (m-10) cc_final: 0.6947 (m-80) REVERT: M 42 GLN cc_start: 0.6977 (mt0) cc_final: 0.6746 (mt0) REVERT: M 50 ARG cc_start: 0.6507 (mtp85) cc_final: 0.6154 (ttt180) outliers start: 2 outliers final: 0 residues processed: 873 average time/residue: 0.4891 time to fit residues: 704.3000 Evaluate side-chains 652 residues out of total 4097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 651 time to evaluate : 4.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.0715 > 50: distance: 45 - 59: 8.018 distance: 49 - 64: 14.233 distance: 53 - 68: 15.770 distance: 56 - 59: 6.621 distance: 57 - 77: 8.741 distance: 59 - 60: 13.429 distance: 60 - 61: 4.648 distance: 60 - 63: 16.724 distance: 61 - 62: 11.549 distance: 61 - 64: 10.133 distance: 62 - 82: 24.934 distance: 64 - 65: 4.183 distance: 65 - 66: 3.662 distance: 66 - 67: 6.886 distance: 66 - 68: 8.702 distance: 67 - 89: 33.593 distance: 68 - 69: 8.907 distance: 69 - 70: 5.848 distance: 69 - 72: 9.388 distance: 70 - 71: 16.860 distance: 70 - 77: 3.135 distance: 71 - 98: 21.654 distance: 72 - 73: 22.991 distance: 73 - 74: 14.733 distance: 74 - 75: 5.847 distance: 74 - 76: 15.006 distance: 77 - 78: 6.632 distance: 78 - 79: 13.133 distance: 78 - 81: 9.521 distance: 79 - 80: 12.664 distance: 79 - 82: 5.948 distance: 82 - 83: 7.738 distance: 83 - 86: 15.603 distance: 84 - 85: 10.916 distance: 84 - 89: 8.167 distance: 85 - 110: 32.940 distance: 86 - 87: 11.270 distance: 86 - 88: 22.591 distance: 89 - 90: 16.313 distance: 90 - 91: 17.569 distance: 90 - 93: 13.129 distance: 91 - 98: 5.259 distance: 92 - 115: 10.309 distance: 93 - 94: 17.999 distance: 94 - 95: 18.437 distance: 95 - 96: 12.815 distance: 95 - 97: 24.906 distance: 98 - 99: 24.042 distance: 99 - 100: 14.516 distance: 100 - 101: 4.193 distance: 100 - 102: 31.800 distance: 102 - 103: 18.419 distance: 103 - 104: 39.919 distance: 103 - 106: 27.192 distance: 104 - 105: 14.160 distance: 104 - 110: 3.652 distance: 106 - 107: 26.380 distance: 106 - 108: 18.658 distance: 107 - 109: 9.817 distance: 110 - 111: 9.756 distance: 111 - 112: 21.572 distance: 111 - 114: 13.976 distance: 112 - 113: 15.831 distance: 112 - 115: 10.609 distance: 115 - 116: 10.888 distance: 116 - 117: 3.539 distance: 116 - 119: 8.306 distance: 117 - 118: 13.113 distance: 117 - 126: 4.879 distance: 119 - 120: 14.145 distance: 120 - 121: 8.642 distance: 121 - 122: 10.340 distance: 122 - 123: 21.388 distance: 123 - 124: 16.516 distance: 123 - 125: 25.135