Starting phenix.real_space_refine (version: dev) on Thu Feb 23 20:57:32 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7arb_11878/02_2023/7arb_11878_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7arb_11878/02_2023/7arb_11878.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7arb_11878/02_2023/7arb_11878_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7arb_11878/02_2023/7arb_11878_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7arb_11878/02_2023/7arb_11878_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7arb_11878/02_2023/7arb_11878.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7arb_11878/02_2023/7arb_11878.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7arb_11878/02_2023/7arb_11878_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7arb_11878/02_2023/7arb_11878_updated.pdb" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 Process input model Symmetric amino acids flipped Residue "A ASP 58": "OD1" <-> "OD2" Residue "A PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 117": "OD1" <-> "OD2" Residue "B PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 107": "OD1" <-> "OD2" Residue "B ASP 109": "OD1" <-> "OD2" Residue "B ASP 123": "OD1" <-> "OD2" Residue "B ASP 144": "OD1" <-> "OD2" Residue "C PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 58": "OD1" <-> "OD2" Residue "D GLU 79": "OE1" <-> "OE2" Residue "D GLU 87": "OE1" <-> "OE2" Residue "D ASP 377": "OD1" <-> "OD2" Residue "E GLU 48": "OE1" <-> "OE2" Residue "E GLU 59": "OE1" <-> "OE2" Residue "E GLU 157": "OE1" <-> "OE2" Residue "E TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 144": "OE1" <-> "OE2" Residue "F PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 388": "OD1" <-> "OD2" Residue "F GLU 410": "OE1" <-> "OE2" Residue "G TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 438": "OD1" <-> "OD2" Residue "G GLU 634": "OE1" <-> "OE2" Residue "G GLU 674": "OE1" <-> "OE2" Residue "H GLU 27": "OE1" <-> "OE2" Residue "H ASP 95": "OD1" <-> "OD2" Residue "H TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 204": "OD1" <-> "OD2" Residue "H PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 120": "OE1" <-> "OE2" Residue "K GLU 36": "OE1" <-> "OE2" Residue "K ASP 54": "OD1" <-> "OD2" Residue "L TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 175": "OD1" <-> "OD2" Residue "L PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 361": "OD1" <-> "OD2" Residue "L TYR 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 542": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 479": "OD1" <-> "OD2" Residue "N ASP 113": "OD1" <-> "OD2" Residue "N GLU 170": "OE1" <-> "OE2" Residue "N TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 358": "OD1" <-> "OD2" Residue "N ASP 376": "OD1" <-> "OD2" Residue "N TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 462": "OD1" <-> "OD2" Residue "O GLU 115": "OE1" <-> "OE2" Residue "O TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 364": "OD1" <-> "OD2" Residue "Q PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 85": "OE1" <-> "OE2" Residue "R ASP 107": "OD1" <-> "OD2" Residue "S GLU 13": "OE1" <-> "OE2" Residue "S ASP 38": "OD1" <-> "OD2" Residue "T ASP 81": "OD1" <-> "OD2" Residue "T ASP 99": "OD1" <-> "OD2" Residue "T TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 114": "OD1" <-> "OD2" Residue "W TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 32": "OE1" <-> "OE2" Residue "X ASP 66": "OD1" <-> "OD2" Residue "X ASP 76": "OD1" <-> "OD2" Residue "X ASP 77": "OD1" <-> "OD2" Residue "X TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 88": "OE1" <-> "OE2" Residue "X GLU 97": "OE1" <-> "OE2" Residue "Z GLU 92": "OE1" <-> "OE2" Residue "Z TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 44": "OE1" <-> "OE2" Residue "a ASP 53": "OD1" <-> "OD2" Residue "b GLU 14": "OE1" <-> "OE2" Residue "c GLU 59": "OE1" <-> "OE2" Residue "c ASP 82": "OD1" <-> "OD2" Residue "c ASP 83": "OD1" <-> "OD2" Residue "c GLU 85": "OE1" <-> "OE2" Residue "c GLU 87": "OE1" <-> "OE2" Residue "d ASP 53": "OD1" <-> "OD2" Residue "e ASP 20": "OD1" <-> "OD2" Residue "e GLU 50": "OE1" <-> "OE2" Residue "e GLU 61": "OE1" <-> "OE2" Residue "f ASP 17": "OD1" <-> "OD2" Residue "f PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 90": "OE1" <-> "OE2" Residue "g GLU 99": "OE1" <-> "OE2" Residue "i GLU 57": "OE1" <-> "OE2" Residue "l ASP 115": "OD1" <-> "OD2" Residue "m ASP 60": "OD1" <-> "OD2" Residue "n GLU 18": "OE1" <-> "OE2" Residue "n TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ASP 115": "OD1" <-> "OD2" Residue "p GLU 9": "OE1" <-> "OE2" Residue "p GLU 32": "OE1" <-> "OE2" Residue "x ASP 92": "OD1" <-> "OD2" Residue "y ASP 23": "OD1" <-> "OD2" Residue "z ASP 23": "OD1" <-> "OD2" Residue "z ASP 50": "OD1" <-> "OD2" Residue "z ASP 141": "OD1" <-> "OD2" Residue "z GLU 158": "OE1" <-> "OE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 61765 Number of models: 1 Model: "" Number of chains: 66 Chain: "A" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 779 Classifications: {'peptide': 92} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 88} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 1244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1244 Classifications: {'peptide': 157} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 146} Chain: "C" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1581 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 9, 'TRANS': 175} Chain: "D" Number of atoms: 3077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3077 Classifications: {'peptide': 385} Link IDs: {'PTRANS': 17, 'TRANS': 367} Chain: "E" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1500 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 12, 'TRANS': 179} Chain: "F" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3368 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 21, 'TRANS': 412} Chain: "G" Number of atoms: 5252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5252 Classifications: {'peptide': 688} Link IDs: {'PTRANS': 35, 'TRANS': 652} Chain: "H" Number of atoms: 2439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2439 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 18, 'TRANS': 292} Chain breaks: 1 Chain: "I" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1349 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 8, 'TRANS': 156} Chain: "J" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1162 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 3, 'TRANS': 143} Chain breaks: 1 Chain: "K" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 707 Classifications: {'peptide': 90} Link IDs: {'TRANS': 89} Chain: "L" Number of atoms: 4807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4807 Classifications: {'peptide': 615} Link IDs: {'PTRANS': 20, 'TRANS': 594} Chain: "M" Number of atoms: 3887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3887 Classifications: {'peptide': 487} Link IDs: {'PTRANS': 17, 'TRANS': 469} Chain breaks: 1 Chain: "N" Number of atoms: 3820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3820 Classifications: {'peptide': 488} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 471} Chain: "O" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 956 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 6, 'TRANS': 115} Chain: "P" Number of atoms: 2560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2560 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 21, 'TRANS': 310} Chain: "Q" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 939 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 8, 'TRANS': 110} Chain: "R" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 482 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 6, 'TRANS': 55} Chain: "S" Number of atoms: 727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 727 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain: "T" Number of atoms: 667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 667 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 5, 'TRANS': 78} Chain: "U" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 650 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain: "V" Number of atoms: 1123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1123 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 10, 'TRANS': 129} Chain: "W" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 904 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain breaks: 1 Chain: "X" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 767 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 6, 'TRANS': 90} Chain: "Z" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 997 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 10, 'TRANS': 114} Chain: "a" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 469 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "b" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 295 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 3, 'TRANS': 36} Chain: "c" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 617 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 7, 'TRANS': 68} Chain: "d" Number of atoms: 592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 592 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "e" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 557 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "f" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 763 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain: "g" Number of atoms: 615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 615 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 7, 'TRANS': 67} Chain: "i" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 737 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 5, 'TRANS': 79} Chain: "j" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 415 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "k" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 374 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "l" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 502 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 5, 'TRANS': 60} Chain breaks: 1 Chain: "m" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 577 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "n" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 911 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 7, 'TRANS': 101} Chain: "o" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 657 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "p" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 778 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain: "q" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 536 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "r" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 89 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "u" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 150 Classifications: {'peptide': 30} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'TRANS': 29} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'UNK:plan-1': 30} Unresolved non-hydrogen planarities: 30 Chain: "v" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 226 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "x" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1659 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 14, 'TRANS': 199} Chain: "y" Number of atoms: 2032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2032 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 10, 'TRANS': 257} Chain: "z" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1772 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 226} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Unusual residues: {'FES': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'UQ9': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'UQ9:plan-8': 1, 'UQ9:plan-9': 1, 'UQ9:plan-10': 1, 'UQ9:plan-7': 1, 'UQ9:plan-2': 1} Unresolved non-hydrogen planarities: 23 Chain: "I" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 119 Unusual residues: {'LMN': 1, 'PTY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Chain: "c" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PC7': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'PGT': 1, 'T7X': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "n" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Chain: "v" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PC7': 1} Classifications: {'undetermined': 1} Chain: "y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "z" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'PSF': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1532 SG CYS B 158 69.953 96.751 102.634 1.00 25.27 S ATOM 1032 SG CYS B 94 71.302 95.537 96.040 1.00 32.60 S ATOM 1762 SG CYS B 188 68.980 91.233 100.530 1.00 29.69 S ATOM 1026 SG CYS B 93 74.391 92.952 99.119 1.00 34.05 S ATOM 7790 SG CYS E 171 36.201 32.618 126.293 1.00 73.97 S ATOM 7814 SG CYS E 175 37.536 28.812 128.565 1.00 82.36 S ATOM 10906 SG CYS F 405 50.290 52.552 134.055 1.00 33.96 S ATOM 10926 SG CYS F 408 48.813 48.367 131.077 1.00 38.84 S ATOM 10887 SG CYS F 402 43.825 50.814 134.849 1.00 33.15 S ATOM 11251 SG CYS F 448 48.279 47.207 137.321 1.00 33.83 S ATOM 11927 SG CYS G 106 50.393 62.563 136.730 1.00 28.48 S ATOM 12011 SG CYS G 117 52.930 62.289 134.396 1.00 30.04 S ATOM 12036 SG CYS G 120 56.331 61.895 139.210 1.00 33.08 S ATOM 12138 SG CYS G 134 53.212 61.880 141.044 1.00 32.90 S ATOM 12472 SG CYS G 179 51.926 70.865 124.224 1.00 33.23 S ATOM 12411 SG CYS G 170 53.181 70.027 117.787 1.00 26.82 S ATOM 12432 SG CYS G 173 47.460 72.286 120.234 1.00 26.74 S ATOM 12824 SG CYS G 224 39.982 66.809 132.145 1.00 31.10 S ATOM 12777 SG CYS G 218 42.696 63.722 127.337 1.00 28.92 S ATOM 12800 SG CYS G 221 46.342 65.990 132.246 1.00 29.26 S ATOM 13145 SG CYS G 268 44.362 70.003 128.339 1.00 30.60 S ATOM 20144 SG CYS I 168 59.291 82.887 103.115 1.00 26.64 S ATOM 20097 SG CYS I 162 61.348 88.497 101.041 1.00 30.44 S ATOM 20123 SG CYS I 165 65.206 84.537 104.549 1.00 34.86 S ATOM 19865 SG CYS I 133 60.608 87.693 107.423 1.00 23.90 S ATOM 20173 SG CYS I 172 53.576 76.671 104.694 1.00 24.01 S ATOM 19796 SG CYS I 123 48.593 80.757 105.833 1.00 28.36 S ATOM 19838 SG CYS I 129 54.530 82.489 107.453 1.00 24.25 S ATOM 19815 SG CYS I 126 52.240 77.556 110.465 1.00 25.55 S ATOM 35385 SG CYS O 91 121.514 153.643 111.447 1.00 82.69 S ATOM 35411 SG CYS O 95 120.107 152.060 114.895 1.00 82.32 S ATOM 35750 SG CYS O 135 122.511 154.748 115.158 1.00 80.80 S ATOM 39617 SG CYS R 72 42.938 64.367 104.317 1.00 36.73 S ATOM 39803 SG CYS R 97 42.676 67.150 106.993 1.00 32.48 S ATOM 39830 SG CYS R 100 44.064 67.981 103.463 1.00 34.37 S Time building chain proxies: 26.02, per 1000 atoms: 0.42 Number of scatterers: 61765 At special positions: 0 Unit cell: (216.783, 270.351, 191.673, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 Fe 29 26.01 S 421 16.00 P 14 15.00 O 11060 8.00 N 10330 7.00 C 39909 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS E 174 " - pdb=" SG CYS F 300 " distance=2.03 Simple disulfide: pdb=" SG CYS F 148 " - pdb=" SG CYS F 300 " distance=2.03 Simple disulfide: pdb=" SG CYS N 336 " - pdb=" SG CYS N 420 " distance=2.03 Simple disulfide: pdb=" SG CYS e 24 " - pdb=" SG CYS e 34 " distance=2.03 Simple disulfide: pdb=" SG CYS o 30 " - pdb=" SG CYS o 61 " distance=2.03 Simple disulfide: pdb=" SG CYS p 58 " - pdb=" SG CYS p 70 " distance=2.03 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: 20.68 Conformation dependent library (CDL) restraints added in 7.2 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 500 " pdb="FE1 FES E 500 " - pdb=" SD MET E 169 " pdb="FE1 FES E 500 " - pdb=" SG CYS E 171 " pdb="FE2 FES E 500 " - pdb=" SG CYS E 175 " pdb="FE2 FES E 500 " - pdb=" SG CYS E 135 " pdb=" FES G 801 " pdb="FE2 FES G 801 " - pdb=" SG CYS G 120 " pdb="FE1 FES G 801 " - pdb=" SG CYS G 117 " pdb="FE1 FES G 801 " - pdb=" SG CYS G 106 " pdb="FE2 FES G 801 " - pdb=" SG CYS G 134 " pdb=" SF4 B 500 " pdb="FE4 SF4 B 500 " - pdb=" SG CYS B 93 " pdb="FE1 SF4 B 500 " - pdb=" SG CYS B 158 " pdb="FE3 SF4 B 500 " - pdb=" SG CYS B 188 " pdb="FE2 SF4 B 500 " - pdb=" SG CYS B 94 " pdb=" SF4 F 501 " pdb="FE3 SF4 F 501 " - pdb=" SG CYS F 402 " pdb="FE4 SF4 F 501 " - pdb=" SG CYS F 448 " pdb="FE2 SF4 F 501 " - pdb=" SG CYS F 408 " pdb="FE1 SF4 F 501 " - pdb=" SG CYS F 405 " pdb=" SF4 G 802 " pdb="FE2 SF4 G 802 " - pdb=" NE2 HIS G 166 " pdb="FE1 SF4 G 802 " - pdb=" SG CYS G 179 " pdb="FE3 SF4 G 802 " - pdb=" SG CYS G 170 " pdb="FE4 SF4 G 802 " - pdb=" SG CYS G 173 " pdb=" SF4 G 803 " pdb="FE3 SF4 G 803 " - pdb=" SG CYS G 221 " pdb="FE2 SF4 G 803 " - pdb=" SG CYS G 218 " pdb="FE1 SF4 G 803 " - pdb=" SG CYS G 224 " pdb="FE4 SF4 G 803 " - pdb=" SG CYS G 268 " pdb=" SF4 I 500 " pdb="FE2 SF4 I 500 " - pdb=" SG CYS I 162 " pdb="FE4 SF4 I 500 " - pdb=" SG CYS I 133 " pdb="FE3 SF4 I 500 " - pdb=" SG CYS I 165 " pdb="FE1 SF4 I 500 " - pdb=" SG CYS I 168 " pdb=" SF4 I 501 " pdb="FE4 SF4 I 501 " - pdb=" SG CYS I 126 " pdb="FE1 SF4 I 501 " - pdb=" SG CYS I 172 " pdb="FE2 SF4 I 501 " - pdb=" SG CYS I 123 " pdb="FE3 SF4 I 501 " - pdb=" SG CYS I 129 " Number of angles added : 83 Zn2+ tetrahedral coordination pdb=" ZN R 200 " pdb="ZN ZN R 200 " - pdb=" NE2 HIS R 82 " pdb="ZN ZN R 200 " - pdb=" SG CYS R 100 " pdb="ZN ZN R 200 " - pdb=" SG CYS R 97 " pdb="ZN ZN R 200 " - pdb=" SG CYS R 72 " pdb=" ZN y 300 " pdb="ZN ZN y 300 " - pdb=" NE2 HIS y 135 " pdb="ZN ZN y 300 " - pdb=" NE2 HIS z 130 " pdb="ZN ZN y 300 " - pdb=" NE2 HIS y 107 " Number of angles added : 3 15224 Ramachandran restraints generated. 7612 Oldfield, 0 Emsley, 7612 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14346 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 316 helices and 41 sheets defined 51.5% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.93 Creating SS restraints... Processing helix chain 'A' and resid 6 through 28 Proline residue: A 26 - end of helix Processing helix chain 'A' and resid 59 through 85 removed outlier: 4.269A pdb=" N VAL A 64 " --> pdb=" O PHE A 61 " (cutoff:3.500A) Proline residue: A 80 - end of helix removed outlier: 3.593A pdb=" N VAL A 83 " --> pdb=" O PRO A 80 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER A 84 " --> pdb=" O TRP A 81 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU A 85 " --> pdb=" O ALA A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 112 Processing helix chain 'B' and resid 65 through 82 removed outlier: 4.121A pdb=" N SER B 70 " --> pdb=" O GLU B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 101 Processing helix chain 'B' and resid 108 through 111 Processing helix chain 'B' and resid 119 through 121 No H-bonds generated for 'chain 'B' and resid 119 through 121' Processing helix chain 'B' and resid 133 through 145 Proline residue: B 137 - end of helix Processing helix chain 'B' and resid 156 through 161 Processing helix chain 'B' and resid 163 through 165 No H-bonds generated for 'chain 'B' and resid 163 through 165' Processing helix chain 'B' and resid 175 through 177 No H-bonds generated for 'chain 'B' and resid 175 through 177' Processing helix chain 'B' and resid 192 through 208 Processing helix chain 'B' and resid 211 through 216 Processing helix chain 'C' and resid 3 through 13 removed outlier: 3.795A pdb=" N LYS C 8 " --> pdb=" O GLN C 4 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 47 Processing helix chain 'C' and resid 106 through 119 removed outlier: 3.689A pdb=" N GLY C 109 " --> pdb=" O PRO C 106 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TRP C 110 " --> pdb=" O SER C 107 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TRP C 111 " --> pdb=" O ALA C 108 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE C 119 " --> pdb=" O TRP C 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 57 removed outlier: 3.901A pdb=" N GLU D 56 " --> pdb=" O GLU D 52 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TYR D 57 " --> pdb=" O LYS D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 68 No H-bonds generated for 'chain 'D' and resid 65 through 68' Processing helix chain 'D' and resid 75 through 90 removed outlier: 3.533A pdb=" N GLU D 79 " --> pdb=" O MET D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 125 Processing helix chain 'D' and resid 129 through 148 removed outlier: 3.517A pdb=" N TRP D 133 " --> pdb=" O THR D 129 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU D 137 " --> pdb=" O TRP D 133 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE D 144 " --> pdb=" O LYS D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 193 removed outlier: 3.862A pdb=" N GLN D 181 " --> pdb=" O SER D 177 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ALA D 183 " --> pdb=" O THR D 179 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N SER D 184 " --> pdb=" O GLN D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 201 Processing helix chain 'D' and resid 211 through 216 Processing helix chain 'D' and resid 222 through 227 removed outlier: 4.291A pdb=" N SER D 227 " --> pdb=" O MET D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 236 No H-bonds generated for 'chain 'D' and resid 233 through 236' Processing helix chain 'D' and resid 242 through 244 No H-bonds generated for 'chain 'D' and resid 242 through 244' Processing helix chain 'D' and resid 257 through 281 removed outlier: 3.515A pdb=" N MET D 268 " --> pdb=" O ARG D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 302 No H-bonds generated for 'chain 'D' and resid 299 through 302' Processing helix chain 'D' and resid 306 through 317 Processing helix chain 'D' and resid 358 through 369 removed outlier: 3.530A pdb=" N GLY D 365 " --> pdb=" O ALA D 361 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU D 366 " --> pdb=" O HIS D 362 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ASP D 367 " --> pdb=" O SER D 363 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N PHE D 368 " --> pdb=" O GLN D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 385 removed outlier: 4.268A pdb=" N VAL D 379 " --> pdb=" O LEU D 375 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N THR D 380 " --> pdb=" O ALA D 376 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN D 385 " --> pdb=" O ILE D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 392 No H-bonds generated for 'chain 'D' and resid 389 through 392' Processing helix chain 'E' and resid 53 through 63 removed outlier: 3.756A pdb=" N TYR E 63 " --> pdb=" O GLU E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 72 removed outlier: 3.978A pdb=" N LYS E 69 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N GLN E 70 " --> pdb=" O ASN E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 84 removed outlier: 3.829A pdb=" N LEU E 79 " --> pdb=" O PRO E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 100 Processing helix chain 'E' and resid 104 through 113 Processing helix chain 'E' and resid 133 through 136 No H-bonds generated for 'chain 'E' and resid 133 through 136' Processing helix chain 'E' and resid 144 through 151 Processing helix chain 'E' and resid 189 through 191 No H-bonds generated for 'chain 'E' and resid 189 through 191' Processing helix chain 'E' and resid 205 through 215 Processing helix chain 'F' and resid 76 through 82 Processing helix chain 'F' and resid 88 through 94 Processing helix chain 'F' and resid 96 through 106 Processing helix chain 'F' and resid 118 through 124 removed outlier: 3.538A pdb=" N PHE F 124 " --> pdb=" O LEU F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 149 through 156 Processing helix chain 'F' and resid 158 through 171 Processing helix chain 'F' and resid 186 through 201 Processing helix chain 'F' and resid 209 through 211 No H-bonds generated for 'chain 'F' and resid 209 through 211' Processing helix chain 'F' and resid 228 through 230 No H-bonds generated for 'chain 'F' and resid 228 through 230' Processing helix chain 'F' and resid 232 through 239 Processing helix chain 'F' and resid 258 through 260 No H-bonds generated for 'chain 'F' and resid 258 through 260' Processing helix chain 'F' and resid 268 through 272 Processing helix chain 'F' and resid 274 through 280 removed outlier: 3.518A pdb=" N ARG F 279 " --> pdb=" O PRO F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 287 Processing helix chain 'F' and resid 319 through 325 Processing helix chain 'F' and resid 352 through 355 No H-bonds generated for 'chain 'F' and resid 352 through 355' Processing helix chain 'F' and resid 362 through 368 removed outlier: 3.510A pdb=" N LYS F 366 " --> pdb=" O PHE F 362 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 400 Processing helix chain 'F' and resid 406 through 424 removed outlier: 4.460A pdb=" N GLY F 413 " --> pdb=" O ARG F 409 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N VAL F 424 " --> pdb=" O GLU F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 442 removed outlier: 3.987A pdb=" N ILE F 432 " --> pdb=" O LEU F 429 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP F 433 " --> pdb=" O GLU F 430 " (cutoff:3.500A) Processing helix chain 'F' and resid 450 through 481 Proline residue: F 457 - end of helix removed outlier: 3.541A pdb=" N ARG F 466 " --> pdb=" O ILE F 462 " (cutoff:3.500A) Proline residue: F 467 - end of helix Processing helix chain 'G' and resid 60 through 62 No H-bonds generated for 'chain 'G' and resid 60 through 62' Processing helix chain 'G' and resid 91 through 97 Processing helix chain 'G' and resid 149 through 162 Processing helix chain 'G' and resid 176 through 178 No H-bonds generated for 'chain 'G' and resid 176 through 178' Processing helix chain 'G' and resid 180 through 188 Processing helix chain 'G' and resid 215 through 217 No H-bonds generated for 'chain 'G' and resid 215 through 217' Processing helix chain 'G' and resid 223 through 230 Processing helix chain 'G' and resid 243 through 245 No H-bonds generated for 'chain 'G' and resid 243 through 245' Processing helix chain 'G' and resid 261 through 267 removed outlier: 3.809A pdb=" N ILE G 267 " --> pdb=" O VAL G 264 " (cutoff:3.500A) Processing helix chain 'G' and resid 284 through 286 No H-bonds generated for 'chain 'G' and resid 284 through 286' Processing helix chain 'G' and resid 330 through 333 No H-bonds generated for 'chain 'G' and resid 330 through 333' Processing helix chain 'G' and resid 336 through 340 removed outlier: 3.523A pdb=" N LYS G 340 " --> pdb=" O ASP G 337 " (cutoff:3.500A) Processing helix chain 'G' and resid 361 through 374 removed outlier: 3.812A pdb=" N HIS G 373 " --> pdb=" O GLY G 369 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLN G 374 " --> pdb=" O ASP G 370 " (cutoff:3.500A) Processing helix chain 'G' and resid 377 through 379 No H-bonds generated for 'chain 'G' and resid 377 through 379' Processing helix chain 'G' and resid 390 through 402 Processing helix chain 'G' and resid 432 through 436 removed outlier: 3.582A pdb=" N GLU G 435 " --> pdb=" O SER G 432 " (cutoff:3.500A) Processing helix chain 'G' and resid 452 through 465 Processing helix chain 'G' and resid 489 through 497 Processing helix chain 'G' and resid 501 through 507 removed outlier: 3.890A pdb=" N ALA G 505 " --> pdb=" O PRO G 501 " (cutoff:3.500A) Processing helix chain 'G' and resid 518 through 521 Processing helix chain 'G' and resid 526 through 539 Processing helix chain 'G' and resid 559 through 564 Processing helix chain 'G' and resid 591 through 593 No H-bonds generated for 'chain 'G' and resid 591 through 593' Processing helix chain 'G' and resid 623 through 625 No H-bonds generated for 'chain 'G' and resid 623 through 625' Processing helix chain 'G' and resid 653 through 663 Processing helix chain 'G' and resid 673 through 682 removed outlier: 3.717A pdb=" N SER G 682 " --> pdb=" O SER G 678 " (cutoff:3.500A) Processing helix chain 'G' and resid 700 through 702 No H-bonds generated for 'chain 'G' and resid 700 through 702' Processing helix chain 'G' and resid 727 through 730 No H-bonds generated for 'chain 'G' and resid 727 through 730' Processing helix chain 'G' and resid 733 through 741 removed outlier: 3.608A pdb=" N GLN G 737 " --> pdb=" O LYS G 733 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 34 Proline residue: H 15 - end of helix removed outlier: 3.640A pdb=" N ALA H 32 " --> pdb=" O ARG H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 59 Processing helix chain 'H' and resid 73 through 90 Proline residue: H 78 - end of helix removed outlier: 3.809A pdb=" N ALA H 88 " --> pdb=" O LEU H 84 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N TRP H 89 " --> pdb=" O SER H 85 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ALA H 90 " --> pdb=" O LEU H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 127 removed outlier: 4.762A pdb=" N VAL H 118 " --> pdb=" O SER H 114 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N TYR H 119 " --> pdb=" O SER H 115 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N GLY H 120 " --> pdb=" O LEU H 116 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ILE H 121 " --> pdb=" O GLY H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 162 removed outlier: 4.132A pdb=" N SER H 150 " --> pdb=" O SER H 146 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N CYS H 161 " --> pdb=" O THR H 157 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL H 162 " --> pdb=" O VAL H 158 " (cutoff:3.500A) Processing helix chain 'H' and resid 167 through 174 removed outlier: 3.621A pdb=" N MET H 172 " --> pdb=" O SER H 168 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN H 174 " --> pdb=" O ILE H 170 " (cutoff:3.500A) Processing helix chain 'H' and resid 179 through 182 No H-bonds generated for 'chain 'H' and resid 179 through 182' Processing helix chain 'H' and resid 184 through 197 Processing helix chain 'H' and resid 201 through 203 No H-bonds generated for 'chain 'H' and resid 201 through 203' Processing helix chain 'H' and resid 223 through 246 Processing helix chain 'H' and resid 265 through 286 Processing helix chain 'H' and resid 292 through 301 removed outlier: 3.778A pdb=" N GLY H 297 " --> pdb=" O ASP H 293 " (cutoff:3.500A) Processing helix chain 'H' and resid 304 through 320 Processing helix chain 'I' and resid 60 through 72 Processing helix chain 'I' and resid 74 through 87 removed outlier: 3.818A pdb=" N ARG I 78 " --> pdb=" O THR I 74 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLY I 79 " --> pdb=" O GLU I 75 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU I 82 " --> pdb=" O ARG I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 128 through 132 removed outlier: 3.518A pdb=" N VAL I 132 " --> pdb=" O LEU I 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 128 through 132' Processing helix chain 'I' and resid 167 through 171 Processing helix chain 'I' and resid 191 through 193 No H-bonds generated for 'chain 'I' and resid 191 through 193' Processing helix chain 'I' and resid 197 through 206 Processing helix chain 'I' and resid 208 through 220 removed outlier: 4.625A pdb=" N LEU I 220 " --> pdb=" O ARG I 216 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 18 removed outlier: 3.865A pdb=" N ALA J 10 " --> pdb=" O LEU J 6 " (cutoff:3.500A) Processing helix chain 'J' and resid 23 through 44 removed outlier: 3.584A pdb=" N PHE J 34 " --> pdb=" O PHE J 30 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY J 39 " --> pdb=" O CYS J 35 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU J 44 " --> pdb=" O LEU J 40 " (cutoff:3.500A) Processing helix chain 'J' and resid 47 through 56 Processing helix chain 'J' and resid 61 through 72 removed outlier: 3.698A pdb=" N PHE J 72 " --> pdb=" O VAL J 68 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 through 129 No H-bonds generated for 'chain 'J' and resid 127 through 129' Processing helix chain 'J' and resid 136 through 144 removed outlier: 4.150A pdb=" N LEU J 143 " --> pdb=" O THR J 139 " (cutoff:3.500A) Processing helix chain 'J' and resid 149 through 169 removed outlier: 3.686A pdb=" N ILE J 167 " --> pdb=" O MET J 163 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 23 Processing helix chain 'K' and resid 29 through 53 removed outlier: 3.952A pdb=" N ILE K 35 " --> pdb=" O MET K 31 " (cutoff:3.500A) Processing helix chain 'K' and resid 59 through 87 removed outlier: 3.825A pdb=" N THR K 67 " --> pdb=" O LEU K 63 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL K 68 " --> pdb=" O LEU K 64 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL K 86 " --> pdb=" O ILE K 82 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG K 87 " --> pdb=" O THR K 83 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 18 removed outlier: 3.744A pdb=" N VAL L 6 " --> pdb=" O TYR L 2 " (cutoff:3.500A) Proline residue: L 9 - end of helix Processing helix chain 'L' and resid 20 through 49 removed outlier: 7.386A pdb=" N SER L 25 " --> pdb=" O ARG L 21 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N GLU L 26 " --> pdb=" O PHE L 22 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA L 29 " --> pdb=" O SER L 25 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 103 removed outlier: 3.773A pdb=" N PHE L 91 " --> pdb=" O ILE L 87 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N SER L 102 " --> pdb=" O LEU L 98 " (cutoff:3.500A) Processing helix chain 'L' and resid 110 through 128 Processing helix chain 'L' and resid 133 through 151 removed outlier: 3.921A pdb=" N GLY L 144 " --> pdb=" O TRP L 140 " (cutoff:3.500A) Processing helix chain 'L' and resid 158 through 189 Processing helix chain 'L' and resid 194 through 199 Processing helix chain 'L' and resid 217 through 233 Processing helix chain 'L' and resid 240 through 247 removed outlier: 3.751A pdb=" N ASP L 244 " --> pdb=" O THR L 240 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N MET L 246 " --> pdb=" O LEU L 242 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N GLU L 247 " --> pdb=" O PRO L 243 " (cutoff:3.500A) Processing helix chain 'L' and resid 250 through 256 Processing helix chain 'L' and resid 264 through 278 Proline residue: L 274 - end of helix removed outlier: 5.207A pdb=" N TYR L 278 " --> pdb=" O PRO L 274 " (cutoff:3.500A) Processing helix chain 'L' and resid 280 through 302 removed outlier: 3.578A pdb=" N ILE L 284 " --> pdb=" O PRO L 280 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL L 285 " --> pdb=" O THR L 281 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE L 302 " --> pdb=" O ALA L 298 " (cutoff:3.500A) Processing helix chain 'L' and resid 307 through 327 removed outlier: 3.865A pdb=" N ILE L 311 " --> pdb=" O LEU L 307 " (cutoff:3.500A) Processing helix chain 'L' and resid 331 through 344 removed outlier: 3.785A pdb=" N PHE L 343 " --> pdb=" O MET L 339 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE L 344 " --> pdb=" O ASN L 340 " (cutoff:3.500A) Processing helix chain 'L' and resid 346 through 358 Processing helix chain 'L' and resid 365 through 367 No H-bonds generated for 'chain 'L' and resid 365 through 367' Processing helix chain 'L' and resid 376 through 390 Processing helix chain 'L' and resid 398 through 410 removed outlier: 3.739A pdb=" N ASP L 402 " --> pdb=" O PHE L 398 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N VAL L 403 " --> pdb=" O TYR L 399 " (cutoff:3.500A) Processing helix chain 'L' and resid 414 through 442 removed outlier: 3.593A pdb=" N PHE L 418 " --> pdb=" O ILE L 414 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU L 428 " --> pdb=" O SER L 424 " (cutoff:3.500A) Processing helix chain 'L' and resid 450 through 454 Processing helix chain 'L' and resid 462 through 486 Proline residue: L 466 - end of helix removed outlier: 5.909A pdb=" N GLY L 478 " --> pdb=" O SER L 474 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N TYR L 479 " --> pdb=" O LEU L 475 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ASP L 483 " --> pdb=" O TYR L 479 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N MET L 484 " --> pdb=" O LEU L 480 " (cutoff:3.500A) Processing helix chain 'L' and resid 506 through 510 removed outlier: 3.774A pdb=" N GLU L 510 " --> pdb=" O LEU L 506 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 506 through 510' Processing helix chain 'L' and resid 517 through 536 Proline residue: L 521 - end of helix Processing helix chain 'L' and resid 542 through 548 Processing helix chain 'L' and resid 550 through 560 Processing helix chain 'L' and resid 562 through 582 removed outlier: 6.234A pdb=" N ASP L 566 " --> pdb=" O TRP L 563 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLN L 567 " --> pdb=" O PHE L 564 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU L 569 " --> pdb=" O ASP L 566 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN L 570 " --> pdb=" O GLN L 567 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N VAL L 574 " --> pdb=" O ASP L 571 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ARG L 575 " --> pdb=" O PHE L 572 " (cutoff:3.500A) Processing helix chain 'L' and resid 593 through 596 No H-bonds generated for 'chain 'L' and resid 593 through 596' Processing helix chain 'L' and resid 603 through 614 removed outlier: 3.720A pdb=" N PHE L 606 " --> pdb=" O SER L 603 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ALA L 610 " --> pdb=" O ARG L 607 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N GLU L 611 " --> pdb=" O ARG L 608 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N SER L 614 " --> pdb=" O GLU L 611 " (cutoff:3.500A) Processing helix chain 'M' and resid 12 through 28 Proline residue: M 19 - end of helix removed outlier: 3.677A pdb=" N PHE M 28 " --> pdb=" O ILE M 24 " (cutoff:3.500A) Processing helix chain 'M' and resid 34 through 57 Processing helix chain 'M' and resid 91 through 107 removed outlier: 4.146A pdb=" N ILE M 101 " --> pdb=" O THR M 97 " (cutoff:3.500A) Proline residue: M 102 - end of helix Processing helix chain 'M' and resid 110 through 115 removed outlier: 4.471A pdb=" N ARG M 113 " --> pdb=" O SER M 110 " (cutoff:3.500A) Processing helix chain 'M' and resid 117 through 135 removed outlier: 3.523A pdb=" N PHE M 134 " --> pdb=" O MET M 130 " (cutoff:3.500A) Processing helix chain 'M' and resid 139 through 146 Processing helix chain 'M' and resid 149 through 159 Processing helix chain 'M' and resid 164 through 195 removed outlier: 3.629A pdb=" N ILE M 167 " --> pdb=" O GLN M 164 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA M 169 " --> pdb=" O LYS M 166 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA M 170 " --> pdb=" O ILE M 167 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LEU M 182 " --> pdb=" O LEU M 179 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU M 186 " --> pdb=" O PHE M 183 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR M 195 " --> pdb=" O LEU M 192 " (cutoff:3.500A) Processing helix chain 'M' and resid 200 through 203 No H-bonds generated for 'chain 'M' and resid 200 through 203' Processing helix chain 'M' and resid 210 through 227 removed outlier: 3.995A pdb=" N ILE M 214 " --> pdb=" O GLU M 210 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE M 215 " --> pdb=" O ARG M 211 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER M 223 " --> pdb=" O ALA M 219 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL M 226 " --> pdb=" O ALA M 222 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS M 227 " --> pdb=" O SER M 223 " (cutoff:3.500A) Processing helix chain 'M' and resid 235 through 242 removed outlier: 4.222A pdb=" N GLU M 239 " --> pdb=" O ILE M 235 " (cutoff:3.500A) Processing helix chain 'M' and resid 246 through 254 removed outlier: 3.616A pdb=" N VAL M 250 " --> pdb=" O THR M 246 " (cutoff:3.500A) Processing helix chain 'M' and resid 256 through 267 removed outlier: 3.794A pdb=" N PHE M 259 " --> pdb=" O LEU M 256 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLY M 260 " --> pdb=" O LEU M 257 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR M 261 " --> pdb=" O LYS M 258 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG M 266 " --> pdb=" O GLY M 263 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE M 267 " --> pdb=" O PHE M 264 " (cutoff:3.500A) Processing helix chain 'M' and resid 273 through 278 Processing helix chain 'M' and resid 280 through 300 removed outlier: 4.422A pdb=" N LEU M 299 " --> pdb=" O SER M 295 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ARG M 300 " --> pdb=" O LEU M 296 " (cutoff:3.500A) Processing helix chain 'M' and resid 304 through 325 removed outlier: 3.624A pdb=" N ILE M 308 " --> pdb=" O LEU M 304 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR M 310 " --> pdb=" O LYS M 306 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL M 313 " --> pdb=" O ALA M 309 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA M 314 " --> pdb=" O TYR M 310 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS M 315 " --> pdb=" O SER M 311 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE M 321 " --> pdb=" O ASN M 317 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY M 322 " --> pdb=" O LEU M 318 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE M 324 " --> pdb=" O THR M 320 " (cutoff:3.500A) Processing helix chain 'M' and resid 328 through 358 removed outlier: 3.783A pdb=" N LEU M 336 " --> pdb=" O GLY M 332 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N SER M 346 " --> pdb=" O GLY M 342 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG M 358 " --> pdb=" O VAL M 354 " (cutoff:3.500A) Processing helix chain 'M' and resid 364 through 366 No H-bonds generated for 'chain 'M' and resid 364 through 366' Processing helix chain 'M' and resid 370 through 372 No H-bonds generated for 'chain 'M' and resid 370 through 372' Processing helix chain 'M' and resid 375 through 388 Processing helix chain 'M' and resid 395 through 408 removed outlier: 3.584A pdb=" N GLY M 399 " --> pdb=" O SER M 395 " (cutoff:3.500A) Processing helix chain 'M' and resid 412 through 436 removed outlier: 3.921A pdb=" N GLY M 421 " --> pdb=" O LEU M 417 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N MET M 422 " --> pdb=" O ALA M 418 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE M 423 " --> pdb=" O ALA M 419 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA M 427 " --> pdb=" O ILE M 423 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU M 430 " --> pdb=" O ALA M 426 " (cutoff:3.500A) Processing helix chain 'M' and resid 454 through 472 Proline residue: M 462 - end of helix removed outlier: 3.510A pdb=" N VAL M 468 " --> pdb=" O LEU M 464 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N MET M 470 " --> pdb=" O GLY M 466 " (cutoff:3.500A) Processing helix chain 'M' and resid 475 through 480 removed outlier: 3.967A pdb=" N CYS M 480 " --> pdb=" O VAL M 476 " (cutoff:3.500A) Processing helix chain 'M' and resid 482 through 489 removed outlier: 3.726A pdb=" N ASN M 487 " --> pdb=" O THR M 483 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 18 removed outlier: 4.089A pdb=" N ALA N 18 " --> pdb=" O LEU N 15 " (cutoff:3.500A) Processing helix chain 'N' and resid 20 through 40 Processing helix chain 'N' and resid 51 through 71 Processing helix chain 'N' and resid 74 through 77 removed outlier: 4.166A pdb=" N THR N 77 " --> pdb=" O PRO N 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 74 through 77' Processing helix chain 'N' and resid 91 through 117 removed outlier: 3.635A pdb=" N PHE N 112 " --> pdb=" O ILE N 108 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N ASP N 113 " --> pdb=" O SER N 109 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N PHE N 114 " --> pdb=" O MET N 110 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE N 115 " --> pdb=" O CYS N 111 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP N 116 " --> pdb=" O PHE N 112 " (cutoff:3.500A) Processing helix chain 'N' and resid 123 through 140 removed outlier: 3.587A pdb=" N ILE N 140 " --> pdb=" O LEU N 137 " (cutoff:3.500A) Processing helix chain 'N' and resid 145 through 163 removed outlier: 3.533A pdb=" N ILE N 162 " --> pdb=" O CYS N 158 " (cutoff:3.500A) Processing helix chain 'N' and resid 170 through 201 Processing helix chain 'N' and resid 206 through 211 Processing helix chain 'N' and resid 224 through 241 Processing helix chain 'N' and resid 250 through 256 Processing helix chain 'N' and resid 259 through 265 removed outlier: 3.524A pdb=" N PHE N 264 " --> pdb=" O PRO N 260 " (cutoff:3.500A) Processing helix chain 'N' and resid 268 through 284 removed outlier: 3.598A pdb=" N SER N 272 " --> pdb=" O ALA N 268 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N TYR N 283 " --> pdb=" O ARG N 279 " (cutoff:3.500A) Processing helix chain 'N' and resid 289 through 311 removed outlier: 3.983A pdb=" N MET N 310 " --> pdb=" O ALA N 306 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ALA N 311 " --> pdb=" O LEU N 307 " (cutoff:3.500A) Processing helix chain 'N' and resid 315 through 335 removed outlier: 4.078A pdb=" N GLY N 333 " --> pdb=" O TYR N 329 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE N 334 " --> pdb=" O ILE N 330 " (cutoff:3.500A) Processing helix chain 'N' and resid 339 through 369 removed outlier: 3.688A pdb=" N GLN N 368 " --> pdb=" O LEU N 364 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N THR N 369 " --> pdb=" O ALA N 365 " (cutoff:3.500A) Processing helix chain 'N' and resid 374 through 377 Processing helix chain 'N' and resid 380 through 383 No H-bonds generated for 'chain 'N' and resid 380 through 383' Processing helix chain 'N' and resid 387 through 399 Processing helix chain 'N' and resid 405 through 419 removed outlier: 3.891A pdb=" N SER N 409 " --> pdb=" O GLY N 406 " (cutoff:3.500A) Processing helix chain 'N' and resid 423 through 448 removed outlier: 3.918A pdb=" N LEU N 443 " --> pdb=" O TYR N 439 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL N 444 " --> pdb=" O TYR N 440 " (cutoff:3.500A) Processing helix chain 'N' and resid 463 through 477 Processing helix chain 'N' and resid 484 through 497 Processing helix chain 'O' and resid 41 through 44 Processing helix chain 'O' and resid 68 through 75 removed outlier: 4.275A pdb=" N THR O 75 " --> pdb=" O ALA O 71 " (cutoff:3.500A) Processing helix chain 'O' and resid 80 through 82 No H-bonds generated for 'chain 'O' and resid 80 through 82' Processing helix chain 'O' and resid 112 through 122 removed outlier: 3.575A pdb=" N SER O 121 " --> pdb=" O VAL O 117 " (cutoff:3.500A) Processing helix chain 'O' and resid 134 through 136 No H-bonds generated for 'chain 'O' and resid 134 through 136' Processing helix chain 'O' and resid 141 through 143 No H-bonds generated for 'chain 'O' and resid 141 through 143' Processing helix chain 'P' and resid 79 through 90 removed outlier: 4.131A pdb=" N TYR P 83 " --> pdb=" O PHE P 79 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN P 86 " --> pdb=" O ARG P 82 " (cutoff:3.500A) Processing helix chain 'P' and resid 107 through 109 No H-bonds generated for 'chain 'P' and resid 107 through 109' Processing helix chain 'P' and resid 128 through 135 Processing helix chain 'P' and resid 156 through 160 Processing helix chain 'P' and resid 162 through 173 Processing helix chain 'P' and resid 195 through 210 Processing helix chain 'P' and resid 230 through 240 Processing helix chain 'P' and resid 258 through 269 Processing helix chain 'P' and resid 290 through 301 Processing helix chain 'P' and resid 312 through 324 Proline residue: P 321 - end of helix removed outlier: 3.500A pdb=" N PHE P 324 " --> pdb=" O ALA P 320 " (cutoff:3.500A) Processing helix chain 'P' and resid 341 through 346 Processing helix chain 'P' and resid 360 through 362 No H-bonds generated for 'chain 'P' and resid 360 through 362' Processing helix chain 'P' and resid 373 through 381 removed outlier: 4.761A pdb=" N PHE P 377 " --> pdb=" O PRO P 374 " (cutoff:3.500A) Processing helix chain 'Q' and resid 38 through 41 No H-bonds generated for 'chain 'Q' and resid 38 through 41' Processing helix chain 'Q' and resid 49 through 51 No H-bonds generated for 'chain 'Q' and resid 49 through 51' Processing helix chain 'Q' and resid 97 through 99 No H-bonds generated for 'chain 'Q' and resid 97 through 99' Processing helix chain 'Q' and resid 101 through 104 No H-bonds generated for 'chain 'Q' and resid 101 through 104' Processing helix chain 'Q' and resid 111 through 121 Processing helix chain 'Q' and resid 140 through 143 Processing helix chain 'R' and resid 53 through 57 Processing helix chain 'R' and resid 78 through 80 No H-bonds generated for 'chain 'R' and resid 78 through 80' Processing helix chain 'S' and resid 3 through 5 No H-bonds generated for 'chain 'S' and resid 3 through 5' Processing helix chain 'S' and resid 7 through 10 No H-bonds generated for 'chain 'S' and resid 7 through 10' Processing helix chain 'S' and resid 26 through 42 removed outlier: 5.223A pdb=" N LYS S 37 " --> pdb=" O GLU S 33 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N ASP S 38 " --> pdb=" O LYS S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 79 through 93 Processing helix chain 'T' and resid 43 through 55 Processing helix chain 'T' and resid 81 through 93 Processing helix chain 'T' and resid 99 through 102 No H-bonds generated for 'chain 'T' and resid 99 through 102' Processing helix chain 'T' and resid 108 through 117 Processing helix chain 'U' and resid 47 through 60 removed outlier: 3.793A pdb=" N VAL U 57 " --> pdb=" O ARG U 53 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL U 58 " --> pdb=" O VAL U 54 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N LYS U 59 " --> pdb=" O LEU U 55 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ASN U 60 " --> pdb=" O SER U 56 " (cutoff:3.500A) Processing helix chain 'U' and resid 83 through 93 removed outlier: 4.007A pdb=" N VAL U 90 " --> pdb=" O SER U 86 " (cutoff:3.500A) Processing helix chain 'U' and resid 103 through 105 No H-bonds generated for 'chain 'U' and resid 103 through 105' Processing helix chain 'U' and resid 112 through 120 Processing helix chain 'V' and resid 30 through 46 removed outlier: 3.747A pdb=" N ILE V 34 " --> pdb=" O ARG V 30 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP V 35 " --> pdb=" O ALA V 31 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLN V 45 " --> pdb=" O LEU V 41 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N ALA V 46 " --> pdb=" O LYS V 42 " (cutoff:3.500A) Processing helix chain 'V' and resid 52 through 70 removed outlier: 3.683A pdb=" N ARG V 62 " --> pdb=" O GLU V 58 " (cutoff:3.500A) Processing helix chain 'V' and resid 74 through 81 Processing helix chain 'V' and resid 86 through 106 removed outlier: 3.904A pdb=" N GLU V 91 " --> pdb=" O GLU V 87 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU V 92 " --> pdb=" O GLU V 88 " (cutoff:3.500A) Processing helix chain 'V' and resid 140 through 150 removed outlier: 3.811A pdb=" N LEU V 146 " --> pdb=" O PHE V 142 " (cutoff:3.500A) Processing helix chain 'W' and resid 19 through 35 Processing helix chain 'W' and resid 37 through 43 Processing helix chain 'W' and resid 54 through 65 Processing helix chain 'W' and resid 72 through 90 Processing helix chain 'W' and resid 96 through 102 removed outlier: 3.638A pdb=" N ILE W 100 " --> pdb=" O ARG W 96 " (cutoff:3.500A) Processing helix chain 'W' and resid 122 through 129 Processing helix chain 'X' and resid 15 through 28 removed outlier: 4.888A pdb=" N LYS X 23 " --> pdb=" O THR X 19 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N HIS X 24 " --> pdb=" O ALA X 20 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N MET X 27 " --> pdb=" O LYS X 23 " (cutoff:3.500A) Processing helix chain 'X' and resid 30 through 42 Processing helix chain 'X' and resid 46 through 48 No H-bonds generated for 'chain 'X' and resid 46 through 48' Processing helix chain 'X' and resid 50 through 70 Processing helix chain 'X' and resid 72 through 84 removed outlier: 3.621A pdb=" N ASP X 77 " --> pdb=" O LYS X 73 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N TYR X 78 " --> pdb=" O GLU X 74 " (cutoff:3.500A) Processing helix chain 'X' and resid 94 through 102 removed outlier: 3.718A pdb=" N VAL X 102 " --> pdb=" O ALA X 98 " (cutoff:3.500A) Processing helix chain 'Z' and resid 46 through 111 removed outlier: 3.697A pdb=" N PHE Z 50 " --> pdb=" O ALA Z 46 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR Z 84 " --> pdb=" O ALA Z 80 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE Z 85 " --> pdb=" O ALA Z 81 " (cutoff:3.500A) Proline residue: Z 87 - end of helix Processing helix chain 'a' and resid 5 through 34 removed outlier: 3.864A pdb=" N LEU a 10 " --> pdb=" O GLU a 7 " (cutoff:3.500A) Proline residue: a 11 - end of helix removed outlier: 3.686A pdb=" N SER a 25 " --> pdb=" O MET a 22 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN a 26 " --> pdb=" O GLY a 23 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ILE a 29 " --> pdb=" O GLN a 26 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N HIS a 30 " --> pdb=" O TYR a 27 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LYS a 31 " --> pdb=" O TYR a 28 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR a 33 " --> pdb=" O HIS a 30 " (cutoff:3.500A) Processing helix chain 'a' and resid 44 through 59 Processing helix chain 'b' and resid 6 through 13 Processing helix chain 'b' and resid 15 through 40 Proline residue: b 31 - end of helix removed outlier: 4.677A pdb=" N ARG b 35 " --> pdb=" O PRO b 31 " (cutoff:3.500A) Proline residue: b 36 - end of helix Processing helix chain 'c' and resid 16 through 18 No H-bonds generated for 'chain 'c' and resid 16 through 18' Processing helix chain 'c' and resid 33 through 58 Proline residue: c 50 - end of helix removed outlier: 3.553A pdb=" N LYS c 57 " --> pdb=" O LYS c 53 " (cutoff:3.500A) Processing helix chain 'c' and resid 70 through 72 No H-bonds generated for 'chain 'c' and resid 70 through 72' Processing helix chain 'c' and resid 84 through 86 No H-bonds generated for 'chain 'c' and resid 84 through 86' Processing helix chain 'd' and resid 5 through 24 Processing helix chain 'd' and resid 32 through 75 removed outlier: 4.306A pdb=" N ARG d 74 " --> pdb=" O ALA d 70 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N TYR d 75 " --> pdb=" O ASN d 71 " (cutoff:3.500A) Processing helix chain 'e' and resid 15 through 27 removed outlier: 3.870A pdb=" N HIS e 27 " --> pdb=" O GLU e 23 " (cutoff:3.500A) Processing helix chain 'e' and resid 35 through 46 removed outlier: 3.510A pdb=" N HIS e 46 " --> pdb=" O LEU e 42 " (cutoff:3.500A) Processing helix chain 'e' and resid 48 through 65 Processing helix chain 'f' and resid 22 through 28 Processing helix chain 'f' and resid 31 through 51 Processing helix chain 'f' and resid 59 through 86 Processing helix chain 'f' and resid 92 through 100 removed outlier: 3.777A pdb=" N ALA f 96 " --> pdb=" O ASP f 92 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LYS f 100 " --> pdb=" O ALA f 96 " (cutoff:3.500A) Processing helix chain 'g' and resid 45 through 47 No H-bonds generated for 'chain 'g' and resid 45 through 47' Processing helix chain 'g' and resid 63 through 81 Processing helix chain 'g' and resid 92 through 103 removed outlier: 3.612A pdb=" N GLU g 99 " --> pdb=" O GLN g 95 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU g 102 " --> pdb=" O LEU g 98 " (cutoff:3.500A) Processing helix chain 'i' and resid 4 through 15 Processing helix chain 'i' and resid 19 through 44 Processing helix chain 'i' and resid 53 through 55 No H-bonds generated for 'chain 'i' and resid 53 through 55' Processing helix chain 'i' and resid 62 through 65 No H-bonds generated for 'chain 'i' and resid 62 through 65' Processing helix chain 'j' and resid 22 through 51 Proline residue: j 48 - end of helix Processing helix chain 'k' and resid 6 through 20 removed outlier: 3.811A pdb=" N GLU k 17 " --> pdb=" O ARG k 13 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N TRP k 18 " --> pdb=" O ARG k 14 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ARG k 19 " --> pdb=" O ARG k 15 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LYS k 20 " --> pdb=" O ASP k 16 " (cutoff:3.500A) Processing helix chain 'k' and resid 22 through 25 No H-bonds generated for 'chain 'k' and resid 22 through 25' Processing helix chain 'k' and resid 28 through 30 No H-bonds generated for 'chain 'k' and resid 28 through 30' Processing helix chain 'k' and resid 35 through 49 Processing helix chain 'l' and resid 75 through 99 removed outlier: 3.632A pdb=" N PHE l 89 " --> pdb=" O GLY l 85 " (cutoff:3.500A) Processing helix chain 'l' and resid 101 through 104 Processing helix chain 'l' and resid 113 through 117 Processing helix chain 'm' and resid 11 through 21 Processing helix chain 'm' and resid 23 through 25 No H-bonds generated for 'chain 'm' and resid 23 through 25' Processing helix chain 'm' and resid 31 through 39 Processing helix chain 'm' and resid 44 through 62 Processing helix chain 'n' and resid 14 through 34 removed outlier: 3.891A pdb=" N ARG n 21 " --> pdb=" O LYS n 17 " (cutoff:3.500A) Processing helix chain 'n' and resid 38 through 57 removed outlier: 3.899A pdb=" N TYR n 42 " --> pdb=" O ARG n 38 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N ARG n 43 " --> pdb=" O HIS n 39 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP n 44 " --> pdb=" O ILE n 40 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE n 52 " --> pdb=" O LEU n 48 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASN n 55 " --> pdb=" O LYS n 51 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN n 56 " --> pdb=" O PHE n 52 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N ASP n 57 " --> pdb=" O ASN n 53 " (cutoff:3.500A) Processing helix chain 'n' and resid 61 through 78 removed outlier: 3.714A pdb=" N ASP n 65 " --> pdb=" O VAL n 61 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N LYS n 66 " --> pdb=" O ASP n 62 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU n 67 " --> pdb=" O ARG n 63 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS n 77 " --> pdb=" O ALA n 73 " (cutoff:3.500A) Processing helix chain 'o' and resid 14 through 20 Processing helix chain 'o' and resid 31 through 43 removed outlier: 3.513A pdb=" N ILE o 35 " --> pdb=" O ALA o 31 " (cutoff:3.500A) Proline residue: o 36 - end of helix Processing helix chain 'o' and resid 53 through 85 removed outlier: 3.502A pdb=" N ALA o 72 " --> pdb=" O GLU o 68 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN o 85 " --> pdb=" O ALA o 81 " (cutoff:3.500A) Processing helix chain 'p' and resid 20 through 22 No H-bonds generated for 'chain 'p' and resid 20 through 22' Processing helix chain 'p' and resid 27 through 69 removed outlier: 6.929A pdb=" N VAL p 64 " --> pdb=" O ARG p 60 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ASN p 65 " --> pdb=" O VAL p 61 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N HIS p 66 " --> pdb=" O GLU p 62 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N TYR p 67 " --> pdb=" O GLY p 63 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N GLN p 68 " --> pdb=" O VAL p 64 " (cutoff:3.500A) Processing helix chain 'p' and resid 71 through 80 Processing helix chain 'q' and resid 91 through 97 removed outlier: 3.916A pdb=" N GLY q 95 " --> pdb=" O ALA q 91 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N TRP q 96 " --> pdb=" O GLU q 92 " (cutoff:3.500A) Processing helix chain 'q' and resid 106 through 109 No H-bonds generated for 'chain 'q' and resid 106 through 109' Processing helix chain 'u' and resid 2 through 25 removed outlier: 3.606A pdb=" N UNK u 24 " --> pdb=" O UNK u 20 " (cutoff:3.500A) Processing helix chain 'v' and resid 80 through 102 Processing helix chain 'x' and resid 211 through 234 Proline residue: x 218 - end of helix removed outlier: 3.674A pdb=" N ALA x 221 " --> pdb=" O ILE x 217 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER x 233 " --> pdb=" O GLY x 229 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLU x 234 " --> pdb=" O ASP x 230 " (cutoff:3.500A) Processing helix chain 'x' and resid 241 through 252 Processing helix chain 'y' and resid 3 through 29 Processing helix chain 'y' and resid 194 through 218 removed outlier: 4.170A pdb=" N GLN y 212 " --> pdb=" O ILE y 208 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ILE y 213 " --> pdb=" O ASN y 209 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N HIS y 214 " --> pdb=" O LEU y 210 " (cutoff:3.500A) Processing helix chain 'y' and resid 222 through 234 Processing helix chain 'y' and resid 240 through 246 Processing helix chain 'y' and resid 254 through 256 No H-bonds generated for 'chain 'y' and resid 254 through 256' Processing helix chain 'y' and resid 260 through 262 No H-bonds generated for 'chain 'y' and resid 260 through 262' Processing helix chain 'z' and resid 3 through 29 Processing helix chain 'z' and resid 34 through 36 No H-bonds generated for 'chain 'z' and resid 34 through 36' Processing helix chain 'z' and resid 194 through 218 removed outlier: 3.587A pdb=" N ALA z 204 " --> pdb=" O ILE z 200 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR z 205 " --> pdb=" O SER z 201 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA z 213 " --> pdb=" O ASN z 209 " (cutoff:3.500A) Processing helix chain 'z' and resid 224 through 231 Processing sheet with id= A, first strand: chain 'B' and resid 86 through 90 removed outlier: 6.852A pdb=" N CYS B 124 " --> pdb=" O MET B 87 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N PHE B 89 " --> pdb=" O CYS B 124 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE B 126 " --> pdb=" O PHE B 89 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N TRP B 151 " --> pdb=" O MET B 125 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N VAL B 127 " --> pdb=" O TRP B 151 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE B 153 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ILE B 183 " --> pdb=" O SER B 154 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'C' and resid 55 through 63 removed outlier: 6.959A pdb=" N ASN C 76 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE C 59 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL C 74 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLY C 61 " --> pdb=" O GLU C 72 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N GLU C 72 " --> pdb=" O GLY C 61 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N SER C 91 " --> pdb=" O THR C 33 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 97 through 99 removed outlier: 6.385A pdb=" N SER C 122 " --> pdb=" O ILE C 98 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'C' and resid 153 through 158 Processing sheet with id= E, first strand: chain 'D' and resid 11 through 17 removed outlier: 4.232A pdb=" N LEU D 26 " --> pdb=" O PRO D 17 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG D 39 " --> pdb=" O GLU D 31 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 325 through 332 Processing sheet with id= G, first strand: chain 'E' and resid 194 through 198 removed outlier: 3.585A pdb=" N THR E 194 " --> pdb=" O ASP E 185 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 263 through 267 removed outlier: 6.913A pdb=" N TYR F 135 " --> pdb=" O THR F 264 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N THR F 266 " --> pdb=" O TYR F 135 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL F 137 " --> pdb=" O THR F 266 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ALA F 176 " --> pdb=" O LEU F 136 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N VAL F 138 " --> pdb=" O ALA F 176 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N TYR F 178 " --> pdb=" O VAL F 138 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ALA F 140 " --> pdb=" O TYR F 178 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N TYR F 180 " --> pdb=" O ALA F 140 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N GLU F 217 " --> pdb=" O ALA F 177 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N ILE F 179 " --> pdb=" O GLU F 217 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N TYR F 219 " --> pdb=" O ILE F 179 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ILE F 181 " --> pdb=" O TYR F 219 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N HIS F 221 " --> pdb=" O ILE F 181 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'F' and resid 296 through 301 Processing sheet with id= J, first strand: chain 'F' and resid 349 through 351 removed outlier: 7.162A pdb=" N MET F 380 " --> pdb=" O LEU F 338 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ILE F 340 " --> pdb=" O ILE F 378 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ILE F 378 " --> pdb=" O ILE F 340 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 74 through 77 Processing sheet with id= L, first strand: chain 'G' and resid 211 through 213 Processing sheet with id= M, first strand: chain 'G' and resid 238 through 240 Processing sheet with id= N, first strand: chain 'G' and resid 288 through 293 Processing sheet with id= O, first strand: chain 'G' and resid 348 through 350 Processing sheet with id= P, first strand: chain 'G' and resid 407 through 409 removed outlier: 4.642A pdb=" N ASN G 407 " --> pdb=" O ILE G 380 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N PHE G 580 " --> pdb=" O VAL G 381 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N VAL G 383 " --> pdb=" O PHE G 580 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N TYR G 582 " --> pdb=" O VAL G 383 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N PHE G 599 " --> pdb=" O VAL G 581 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N LEU G 583 " --> pdb=" O PHE G 599 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N VAL G 601 " --> pdb=" O LEU G 583 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N VAL G 616 " --> pdb=" O TYR G 602 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N GLY G 604 " --> pdb=" O VAL G 616 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N LEU G 618 " --> pdb=" O GLY G 604 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'G' and resid 550 through 553 removed outlier: 7.814A pdb=" N ASN G 551 " --> pdb=" O PRO G 512 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ILE G 514 " --> pdb=" O ASN G 551 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LEU G 553 " --> pdb=" O ILE G 514 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL G 516 " --> pdb=" O LEU G 553 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N LEU G 439 " --> pdb=" O ALA G 513 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ILE G 515 " --> pdb=" O LEU G 439 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU G 441 " --> pdb=" O ILE G 515 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N GLY G 517 " --> pdb=" O LEU G 441 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ILE G 443 " --> pdb=" O GLY G 517 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LYS G 468 " --> pdb=" O PHE G 440 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N LEU G 442 " --> pdb=" O LYS G 468 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLY G 470 " --> pdb=" O LEU G 442 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N LYS G 483 " --> pdb=" O TYR G 471 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'G' and resid 629 through 631 Processing sheet with id= S, first strand: chain 'I' and resid 111 through 113 Processing sheet with id= T, first strand: chain 'I' and resid 138 through 144 removed outlier: 6.329A pdb=" N GLU I 143 " --> pdb=" O THR I 152 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N THR I 152 " --> pdb=" O GLU I 143 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'L' and resid 57 through 60 Processing sheet with id= V, first strand: chain 'L' and resid 207 through 210 Processing sheet with id= W, first strand: chain 'M' and resid 70 through 73 Processing sheet with id= X, first strand: chain 'O' and resid 57 through 63 removed outlier: 6.444A pdb=" N MET O 146 " --> pdb=" O SER O 49 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N ILE O 51 " --> pdb=" O MET O 146 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL O 148 " --> pdb=" O ILE O 51 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'P' and resid 279 through 282 removed outlier: 6.505A pdb=" N ILE P 216 " --> pdb=" O TYR P 280 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N LEU P 282 " --> pdb=" O ILE P 216 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ARG P 218 " --> pdb=" O LEU P 282 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLN P 94 " --> pdb=" O ALA P 71 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N VAL P 73 " --> pdb=" O GLN P 94 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU P 96 " --> pdb=" O VAL P 73 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'P' and resid 243 through 245 removed outlier: 3.755A pdb=" N VAL P 308 " --> pdb=" O LEU P 243 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'Q' and resid 124 through 128 Processing sheet with id= AB, first strand: chain 'Q' and resid 83 through 85 Processing sheet with id= AC, first strand: chain 'R' and resid 63 through 65 Processing sheet with id= AD, first strand: chain 'R' and resid 69 through 72 Processing sheet with id= AE, first strand: chain 'S' and resid 47 through 53 removed outlier: 4.032A pdb=" N GLU S 13 " --> pdb=" O ARG S 63 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'q' and resid 74 through 77 removed outlier: 3.550A pdb=" N GLY q 53 " --> pdb=" O TYR q 61 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLN q 63 " --> pdb=" O LEU q 51 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N LEU q 51 " --> pdb=" O GLN q 63 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'x' and resid 83 through 86 Processing sheet with id= AH, first strand: chain 'x' and resid 88 through 90 removed outlier: 6.670A pdb=" N ILE x 109 " --> pdb=" O THR x 89 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR x 137 " --> pdb=" O THR x 110 " (cutoff:3.500A) No H-bonds generated for sheet with id= AH Processing sheet with id= AI, first strand: chain 'x' and resid 160 through 162 removed outlier: 6.825A pdb=" N SER x 178 " --> pdb=" O ILE x 161 " (cutoff:3.500A) No H-bonds generated for sheet with id= AI Processing sheet with id= AJ, first strand: chain 'x' and resid 196 through 199 removed outlier: 3.592A pdb=" N ARG x 207 " --> pdb=" O LEU x 197 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLY x 199 " --> pdb=" O PHE x 205 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N PHE x 205 " --> pdb=" O GLY x 199 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'y' and resid 66 through 69 Processing sheet with id= AL, first strand: chain 'y' and resid 71 through 73 removed outlier: 6.642A pdb=" N ILE y 92 " --> pdb=" O GLN y 72 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N THR y 120 " --> pdb=" O SER y 93 " (cutoff:3.500A) No H-bonds generated for sheet with id= AL Processing sheet with id= AM, first strand: chain 'z' and resid 66 through 69 Processing sheet with id= AN, first strand: chain 'z' and resid 71 through 73 removed outlier: 6.830A pdb=" N VAL z 92 " --> pdb=" O HIS z 72 " (cutoff:3.500A) No H-bonds generated for sheet with id= AN Processing sheet with id= AO, first strand: chain 'z' and resid 179 through 182 removed outlier: 3.706A pdb=" N ARG z 190 " --> pdb=" O VAL z 180 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLY z 182 " --> pdb=" O PHE z 188 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N PHE z 188 " --> pdb=" O GLY z 182 " (cutoff:3.500A) 2636 hydrogen bonds defined for protein. 7362 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: 20.52 Time building geometry restraints manager: 22.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 25641 1.40 - 1.62: 36857 1.62 - 1.84: 657 1.84 - 2.06: 0 2.06 - 2.28: 80 Bond restraints: 63235 Sorted by residual: bond pdb=" C3 UQ9 H 500 " pdb=" C4 UQ9 H 500 " ideal model delta sigma weight residual 1.340 1.534 -0.194 2.00e-02 2.50e+03 9.42e+01 bond pdb=" C1 UQ9 H 500 " pdb=" C6 UQ9 H 500 " ideal model delta sigma weight residual 1.345 1.526 -0.181 2.00e-02 2.50e+03 8.21e+01 bond pdb=" C1 LMN M 502 " pdb=" O5 LMN M 502 " ideal model delta sigma weight residual 1.403 1.534 -0.131 2.00e-02 2.50e+03 4.29e+01 bond pdb=" CBS LMN M 502 " pdb=" CCM LMN M 502 " ideal model delta sigma weight residual 1.529 1.627 -0.098 2.00e-02 2.50e+03 2.42e+01 bond pdb=" C4 LMN M 502 " pdb=" O4 LMN M 502 " ideal model delta sigma weight residual 1.409 1.506 -0.097 2.00e-02 2.50e+03 2.37e+01 ... (remaining 63230 not shown) Histogram of bond angle deviations from ideal: 73.53 - 85.88: 76 85.88 - 98.24: 4 98.24 - 110.60: 19254 110.60 - 122.96: 62453 122.96 - 135.32: 3829 Bond angle restraints: 85616 Sorted by residual: angle pdb=" N VAL F 368 " pdb=" CA VAL F 368 " pdb=" C VAL F 368 " ideal model delta sigma weight residual 111.91 106.22 5.69 8.90e-01 1.26e+00 4.09e+01 angle pdb=" O11 PTY M 501 " pdb=" P1 PTY M 501 " pdb=" O14 PTY M 501 " ideal model delta sigma weight residual 92.90 110.16 -17.26 3.00e+00 1.11e-01 3.31e+01 angle pdb=" O3P PGT f 201 " pdb=" P PGT f 201 " pdb=" O4P PGT f 201 " ideal model delta sigma weight residual 92.82 109.61 -16.79 3.00e+00 1.11e-01 3.13e+01 angle pdb=" N ILE P 338 " pdb=" CA ILE P 338 " pdb=" C ILE P 338 " ideal model delta sigma weight residual 113.71 108.40 5.31 9.50e-01 1.11e+00 3.13e+01 angle pdb=" O11 PTY N 501 " pdb=" P1 PTY N 501 " pdb=" O14 PTY N 501 " ideal model delta sigma weight residual 92.90 109.49 -16.59 3.00e+00 1.11e-01 3.06e+01 ... (remaining 85611 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.15: 36871 35.15 - 70.29: 619 70.29 - 105.44: 64 105.44 - 140.58: 2 140.58 - 175.73: 4 Dihedral angle restraints: 37560 sinusoidal: 15248 harmonic: 22312 Sorted by residual: dihedral pdb=" CB CYS E 174 " pdb=" SG CYS E 174 " pdb=" SG CYS F 300 " pdb=" CB CYS F 300 " ideal model delta sinusoidal sigma weight residual 93.00 154.64 -61.64 1 1.00e+01 1.00e-02 5.04e+01 dihedral pdb=" C10 FMN F 500 " pdb=" C1' FMN F 500 " pdb=" N10 FMN F 500 " pdb=" C2' FMN F 500 " ideal model delta sinusoidal sigma weight residual 257.59 81.86 175.73 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" CA PHE D 15 " pdb=" C PHE D 15 " pdb=" N GLY D 16 " pdb=" CA GLY D 16 " ideal model delta harmonic sigma weight residual 180.00 156.16 23.84 0 5.00e+00 4.00e-02 2.27e+01 ... (remaining 37557 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.973: 9492 0.973 - 1.946: 0 1.946 - 2.919: 0 2.919 - 3.892: 0 3.892 - 4.865: 1 Chirality restraints: 9493 Sorted by residual: chirality pdb=" C1 T7X f 202 " pdb=" C2 T7X f 202 " pdb=" C6 T7X f 202 " pdb=" O1 T7X f 202 " both_signs ideal model delta sigma weight residual False -2.42 2.45 -4.87 2.00e-01 2.50e+01 5.92e+02 chirality pdb=" CA SER Z 45 " pdb=" N SER Z 45 " pdb=" C SER Z 45 " pdb=" CB SER Z 45 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.17e+00 chirality pdb=" CA TYR G 251 " pdb=" N TYR G 251 " pdb=" C TYR G 251 " pdb=" CB TYR G 251 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 2.99e+00 ... (remaining 9490 not shown) Planarity restraints: 10776 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU N 459 " 0.070 5.00e-02 4.00e+02 1.05e-01 1.75e+01 pdb=" N PRO N 460 " -0.181 5.00e-02 4.00e+02 pdb=" CA PRO N 460 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO N 460 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR Z 42 " 0.020 2.00e-02 2.50e+03 3.91e-02 1.53e+01 pdb=" C THR Z 42 " -0.068 2.00e-02 2.50e+03 pdb=" O THR Z 42 " 0.025 2.00e-02 2.50e+03 pdb=" N GLY Z 43 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR U 70 " -0.039 5.00e-02 4.00e+02 5.94e-02 5.64e+00 pdb=" N PRO U 71 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO U 71 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO U 71 " -0.033 5.00e-02 4.00e+02 ... (remaining 10773 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 416 2.57 - 3.15: 49797 3.15 - 3.73: 98004 3.73 - 4.32: 139159 4.32 - 4.90: 233681 Nonbonded interactions: 521057 Sorted by model distance: nonbonded pdb=" OE2 GLU K 36 " pdb=" OG SER K 73 " model vdw 1.982 2.440 nonbonded pdb=" OH TYR x 148 " pdb=" O ASN z 103 " model vdw 2.101 2.440 nonbonded pdb=" O GLY G 176 " pdb=" NE2 GLN G 182 " model vdw 2.110 2.520 nonbonded pdb=" NE2 HIS O 83 " pdb="FE FE O 200 " model vdw 2.111 2.340 nonbonded pdb=" OE1 GLN V 63 " pdb=" NE2 GLN V 141 " model vdw 2.122 2.520 ... (remaining 521052 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 29 7.16 5 Zn 2 6.06 5 P 14 5.49 5 S 421 5.16 5 C 39909 2.51 5 N 10330 2.21 5 O 11060 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 individual isotropic 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: 7.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 42.430 Check model and map are aligned: 0.710 Process input model: 139.800 Find NCS groups from input model: 1.740 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Set scattering table: 0.430 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 195.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 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 : 0.004 0.194 63235 Z= 0.287 Angle : 0.649 17.263 85616 Z= 0.312 Chirality : 0.066 4.865 9493 Planarity : 0.004 0.105 10776 Dihedral : 13.951 175.730 23196 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.81 % Favored : 96.14 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.10), residues: 7612 helix: 1.14 (0.08), residues: 3941 sheet: -0.41 (0.24), residues: 523 loop : -0.50 (0.11), residues: 3148 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15224 Ramachandran restraints generated. 7612 Oldfield, 0 Emsley, 7612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15224 Ramachandran restraints generated. 7612 Oldfield, 0 Emsley, 7612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1175 residues out of total 6566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1174 time to evaluate : 5.347 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 1175 average time/residue: 0.6490 time to fit residues: 1241.4803 Evaluate side-chains 965 residues out of total 6566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 965 time to evaluate : 5.276 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.1301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 638 optimal weight: 10.0000 chunk 573 optimal weight: 0.9980 chunk 317 optimal weight: 0.9990 chunk 195 optimal weight: 5.9990 chunk 386 optimal weight: 1.9990 chunk 306 optimal weight: 1.9990 chunk 592 optimal weight: 1.9990 chunk 229 optimal weight: 0.8980 chunk 360 optimal weight: 2.9990 chunk 441 optimal weight: 5.9990 chunk 686 optimal weight: 10.0000 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 GLN D 364 GLN E 70 GLN E 84 ASN F 243 GLN F 336 ASN ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 ASN L 132 ASN L 152 HIS M 31 ASN M 58 GLN N 53 ASN N 368 GLN O 130 HIS P 291 HIS P 343 GLN T 70 HIS W 97 HIS c 88 HIS d 17 GLN e 62 GLN i 10 ASN x 116 ASN x 164 GLN x 165 HIS ** y 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 107 HIS z 212 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.053 63235 Z= 0.306 Angle : 0.556 10.028 85616 Z= 0.284 Chirality : 0.044 0.238 9493 Planarity : 0.005 0.075 10776 Dihedral : 8.554 178.302 8763 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.64 % Favored : 96.32 % Rotamer Outliers : 1.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.10), residues: 7612 helix: 1.16 (0.08), residues: 3972 sheet: -0.51 (0.23), residues: 532 loop : -0.58 (0.11), residues: 3108 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15224 Ramachandran restraints generated. 7612 Oldfield, 0 Emsley, 7612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15224 Ramachandran restraints generated. 7612 Oldfield, 0 Emsley, 7612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1073 residues out of total 6566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 996 time to evaluate : 5.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 77 outliers final: 50 residues processed: 1040 average time/residue: 0.6365 time to fit residues: 1088.9858 Evaluate side-chains 1008 residues out of total 6566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 958 time to evaluate : 5.363 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 0 residues processed: 50 average time/residue: 0.4584 time to fit residues: 50.4801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 381 optimal weight: 0.9980 chunk 213 optimal weight: 0.7980 chunk 571 optimal weight: 0.6980 chunk 467 optimal weight: 0.7980 chunk 189 optimal weight: 0.9990 chunk 687 optimal weight: 0.3980 chunk 742 optimal weight: 0.4980 chunk 612 optimal weight: 0.9990 chunk 682 optimal weight: 9.9990 chunk 234 optimal weight: 4.9990 chunk 551 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 70 GLN F 336 ASN ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 ASN L 132 ASN L 212 ASN N 368 GLN ** O 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 70 HIS V 122 ASN ** W 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 42 HIS ** d 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 116 ASN x 164 GLN ** z 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 212 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 63235 Z= 0.182 Angle : 0.487 9.843 85616 Z= 0.248 Chirality : 0.041 0.214 9493 Planarity : 0.004 0.063 10776 Dihedral : 8.142 177.356 8763 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.52 % Favored : 96.44 % Rotamer Outliers : 0.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.10), residues: 7612 helix: 1.30 (0.08), residues: 3975 sheet: -0.40 (0.23), residues: 528 loop : -0.53 (0.11), residues: 3109 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15224 Ramachandran restraints generated. 7612 Oldfield, 0 Emsley, 7612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15224 Ramachandran restraints generated. 7612 Oldfield, 0 Emsley, 7612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1058 residues out of total 6566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 1003 time to evaluate : 6.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 22 residues processed: 1033 average time/residue: 0.6644 time to fit residues: 1130.7143 Evaluate side-chains 972 residues out of total 6566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 950 time to evaluate : 5.443 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.4758 time to fit residues: 26.8870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 679 optimal weight: 0.0670 chunk 517 optimal weight: 2.9990 chunk 356 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 328 optimal weight: 0.3980 chunk 461 optimal weight: 0.0970 chunk 690 optimal weight: 2.9990 chunk 730 optimal weight: 3.9990 chunk 360 optimal weight: 2.9990 chunk 654 optimal weight: 0.8980 chunk 196 optimal weight: 2.9990 overall best weight: 0.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 GLN E 70 GLN E 126 HIS ** F 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 ASN N 368 GLN ** O 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 291 HIS T 70 HIS V 122 ASN d 17 GLN ** k 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 25 HIS ** y 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 212 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 63235 Z= 0.164 Angle : 0.483 10.117 85616 Z= 0.244 Chirality : 0.040 0.186 9493 Planarity : 0.004 0.067 10776 Dihedral : 7.886 176.919 8763 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.43 % Favored : 96.53 % Rotamer Outliers : 0.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.10), residues: 7612 helix: 1.40 (0.08), residues: 3978 sheet: -0.40 (0.23), residues: 531 loop : -0.48 (0.11), residues: 3103 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15224 Ramachandran restraints generated. 7612 Oldfield, 0 Emsley, 7612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15224 Ramachandran restraints generated. 7612 Oldfield, 0 Emsley, 7612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1056 residues out of total 6566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 993 time to evaluate : 5.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 28 residues processed: 1033 average time/residue: 0.6525 time to fit residues: 1112.4510 Evaluate side-chains 976 residues out of total 6566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 948 time to evaluate : 5.977 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.4960 time to fit residues: 35.5490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 608 optimal weight: 1.9990 chunk 414 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 544 optimal weight: 3.9990 chunk 301 optimal weight: 8.9990 chunk 623 optimal weight: 2.9990 chunk 505 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 373 optimal weight: 0.9980 chunk 655 optimal weight: 0.6980 chunk 184 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 70 GLN F 336 ASN ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 ASN L 132 ASN M 31 ASN N 368 GLN ** O 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 70 HIS V 122 ASN ** k 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 14 GLN ** y 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 212 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 63235 Z= 0.210 Angle : 0.491 9.902 85616 Z= 0.249 Chirality : 0.041 0.194 9493 Planarity : 0.004 0.067 10776 Dihedral : 7.771 179.805 8763 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.52 % Favored : 96.44 % Rotamer Outliers : 0.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.10), residues: 7612 helix: 1.39 (0.08), residues: 3992 sheet: -0.39 (0.23), residues: 533 loop : -0.49 (0.11), residues: 3087 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15224 Ramachandran restraints generated. 7612 Oldfield, 0 Emsley, 7612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15224 Ramachandran restraints generated. 7612 Oldfield, 0 Emsley, 7612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1037 residues out of total 6566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 979 time to evaluate : 5.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 29 residues processed: 1008 average time/residue: 0.6798 time to fit residues: 1128.6214 Evaluate side-chains 971 residues out of total 6566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 942 time to evaluate : 5.411 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.5005 time to fit residues: 34.6864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 245 optimal weight: 3.9990 chunk 658 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 429 optimal weight: 0.6980 chunk 180 optimal weight: 3.9990 chunk 731 optimal weight: 6.9990 chunk 607 optimal weight: 1.9990 chunk 338 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 chunk 241 optimal weight: 1.9990 chunk 384 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 70 GLN F 441 GLN ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 ASN L 257 HIS M 31 ASN N 368 GLN ** O 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 291 HIS T 70 HIS V 122 ASN k 21 HIS l 99 ASN ** y 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 212 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 63235 Z= 0.287 Angle : 0.525 10.019 85616 Z= 0.267 Chirality : 0.043 0.211 9493 Planarity : 0.004 0.066 10776 Dihedral : 7.742 177.980 8763 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.81 % Favored : 96.15 % Rotamer Outliers : 1.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.10), residues: 7612 helix: 1.32 (0.08), residues: 3989 sheet: -0.39 (0.23), residues: 533 loop : -0.55 (0.11), residues: 3090 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15224 Ramachandran restraints generated. 7612 Oldfield, 0 Emsley, 7612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15224 Ramachandran restraints generated. 7612 Oldfield, 0 Emsley, 7612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1039 residues out of total 6566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 972 time to evaluate : 5.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 36 residues processed: 1012 average time/residue: 0.6560 time to fit residues: 1093.5634 Evaluate side-chains 973 residues out of total 6566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 937 time to evaluate : 5.390 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.4671 time to fit residues: 39.1905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 705 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 416 optimal weight: 4.9990 chunk 534 optimal weight: 0.7980 chunk 413 optimal weight: 0.7980 chunk 615 optimal weight: 0.9990 chunk 408 optimal weight: 0.8980 chunk 728 optimal weight: 0.7980 chunk 456 optimal weight: 0.9990 chunk 444 optimal weight: 3.9990 chunk 336 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 70 GLN F 304 HIS ** F 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 ASN L 132 ASN L 212 ASN N 368 GLN ** O 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 70 HIS V 122 ASN W 102 GLN a 42 HIS i 10 ASN ** k 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 98 ASN ** y 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 212 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 63235 Z= 0.198 Angle : 0.497 9.833 85616 Z= 0.252 Chirality : 0.041 0.227 9493 Planarity : 0.004 0.067 10776 Dihedral : 7.584 177.190 8763 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.36 % Favored : 96.60 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.10), residues: 7612 helix: 1.40 (0.08), residues: 3981 sheet: -0.38 (0.23), residues: 534 loop : -0.49 (0.11), residues: 3097 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15224 Ramachandran restraints generated. 7612 Oldfield, 0 Emsley, 7612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15224 Ramachandran restraints generated. 7612 Oldfield, 0 Emsley, 7612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1017 residues out of total 6566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 975 time to evaluate : 5.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 23 residues processed: 1001 average time/residue: 0.7154 time to fit residues: 1183.2824 Evaluate side-chains 971 residues out of total 6566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 948 time to evaluate : 5.427 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.5718 time to fit residues: 32.9710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 450 optimal weight: 10.0000 chunk 290 optimal weight: 5.9990 chunk 435 optimal weight: 0.0050 chunk 219 optimal weight: 2.9990 chunk 143 optimal weight: 0.0470 chunk 141 optimal weight: 0.8980 chunk 463 optimal weight: 0.9980 chunk 496 optimal weight: 1.9990 chunk 360 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 572 optimal weight: 0.7980 overall best weight: 0.5492 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 GLN E 70 GLN ** F 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 129 ASN K 43 ASN L 132 ASN L 417 ASN N 368 GLN ** O 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 291 HIS ** P 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 380 GLN T 70 HIS V 122 ASN ** W 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 21 HIS l 99 ASN ** y 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 212 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 63235 Z= 0.171 Angle : 0.491 9.584 85616 Z= 0.249 Chirality : 0.041 0.257 9493 Planarity : 0.004 0.068 10776 Dihedral : 7.412 176.636 8763 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.44 % Favored : 96.52 % Rotamer Outliers : 0.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.10), residues: 7612 helix: 1.47 (0.08), residues: 3972 sheet: -0.36 (0.23), residues: 540 loop : -0.46 (0.11), residues: 3100 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15224 Ramachandran restraints generated. 7612 Oldfield, 0 Emsley, 7612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15224 Ramachandran restraints generated. 7612 Oldfield, 0 Emsley, 7612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1003 residues out of total 6566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 974 time to evaluate : 5.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 20 residues processed: 989 average time/residue: 0.6699 time to fit residues: 1092.8470 Evaluate side-chains 960 residues out of total 6566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 940 time to evaluate : 5.501 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.4933 time to fit residues: 26.1691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 662 optimal weight: 0.6980 chunk 698 optimal weight: 0.3980 chunk 636 optimal weight: 4.9990 chunk 679 optimal weight: 0.8980 chunk 697 optimal weight: 0.8980 chunk 408 optimal weight: 0.6980 chunk 295 optimal weight: 0.8980 chunk 533 optimal weight: 0.9980 chunk 208 optimal weight: 0.7980 chunk 613 optimal weight: 0.9980 chunk 642 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 70 GLN ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 ASN L 132 ASN L 212 ASN N 368 GLN ** O 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 70 HIS V 122 ASN k 21 HIS ** y 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 212 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 63235 Z= 0.194 Angle : 0.502 10.444 85616 Z= 0.254 Chirality : 0.041 0.286 9493 Planarity : 0.004 0.067 10776 Dihedral : 7.339 176.836 8763 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.48 % Favored : 96.48 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.10), residues: 7612 helix: 1.45 (0.08), residues: 3970 sheet: -0.27 (0.23), residues: 532 loop : -0.48 (0.11), residues: 3110 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15224 Ramachandran restraints generated. 7612 Oldfield, 0 Emsley, 7612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15224 Ramachandran restraints generated. 7612 Oldfield, 0 Emsley, 7612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 979 residues out of total 6566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 958 time to evaluate : 5.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 13 residues processed: 973 average time/residue: 0.6786 time to fit residues: 1089.2915 Evaluate side-chains 956 residues out of total 6566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 943 time to evaluate : 5.513 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.4929 time to fit residues: 19.6221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 676 optimal weight: 0.0980 chunk 445 optimal weight: 0.2980 chunk 718 optimal weight: 0.1980 chunk 438 optimal weight: 0.9990 chunk 340 optimal weight: 8.9990 chunk 499 optimal weight: 2.9990 chunk 753 optimal weight: 0.8980 chunk 693 optimal weight: 3.9990 chunk 599 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 463 optimal weight: 0.8980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 70 GLN ** F 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 129 ASN K 43 ASN L 132 ASN M 31 ASN N 368 GLN ** O 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 291 HIS ** P 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 70 HIS V 122 ASN k 21 HIS ** y 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 212 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.057 63235 Z= 0.160 Angle : 0.492 10.984 85616 Z= 0.249 Chirality : 0.041 0.278 9493 Planarity : 0.004 0.067 10776 Dihedral : 7.200 176.280 8763 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.30 % Favored : 96.66 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.10), residues: 7612 helix: 1.51 (0.08), residues: 3969 sheet: -0.28 (0.23), residues: 541 loop : -0.43 (0.11), residues: 3102 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15224 Ramachandran restraints generated. 7612 Oldfield, 0 Emsley, 7612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15224 Ramachandran restraints generated. 7612 Oldfield, 0 Emsley, 7612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 991 residues out of total 6566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 984 time to evaluate : 5.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 988 average time/residue: 0.6719 time to fit residues: 1102.0290 Evaluate side-chains 950 residues out of total 6566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 946 time to evaluate : 5.441 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.4965 time to fit residues: 10.9187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 367 optimal weight: 5.9990 chunk 476 optimal weight: 0.0270 chunk 638 optimal weight: 9.9990 chunk 183 optimal weight: 0.5980 chunk 553 optimal weight: 4.9990 chunk 88 optimal weight: 0.0670 chunk 166 optimal weight: 3.9990 chunk 600 optimal weight: 0.0370 chunk 251 optimal weight: 1.9990 chunk 616 optimal weight: 5.9990 chunk 76 optimal weight: 0.6980 overall best weight: 0.2854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 70 GLN ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 386 GLN ** G 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 ASN L 212 ASN M 31 ASN N 368 GLN ** O 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 70 HIS V 122 ASN k 21 HIS ** y 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 212 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.119017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.097358 restraints weight = 97155.911| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.69 r_work: 0.2958 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.047 63235 Z= 0.145 Angle : 0.487 10.632 85616 Z= 0.246 Chirality : 0.040 0.259 9493 Planarity : 0.004 0.067 10776 Dihedral : 7.048 175.888 8763 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.26 % Favored : 96.70 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.10), residues: 7612 helix: 1.56 (0.09), residues: 3967 sheet: -0.32 (0.23), residues: 553 loop : -0.37 (0.12), residues: 3092 =============================================================================== Job complete usr+sys time: 17711.97 seconds wall clock time: 310 minutes 13.72 seconds (18613.72 seconds total)