Starting phenix.real_space_refine on Tue Mar 12 04:36:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ar8_11876/03_2024/7ar8_11876_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ar8_11876/03_2024/7ar8_11876.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ar8_11876/03_2024/7ar8_11876_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ar8_11876/03_2024/7ar8_11876_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ar8_11876/03_2024/7ar8_11876_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ar8_11876/03_2024/7ar8_11876.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ar8_11876/03_2024/7ar8_11876.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ar8_11876/03_2024/7ar8_11876_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ar8_11876/03_2024/7ar8_11876_updated.pdb" } resolution = 3.53 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 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 420 5.16 5 C 39719 2.51 5 N 10271 2.21 5 O 11006 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 74": "OD1" <-> "OD2" Residue "B ASP 211": "OD1" <-> "OD2" Residue "C ASP 36": "OD1" <-> "OD2" Residue "C ASP 58": "OD1" <-> "OD2" Residue "C GLU 112": "OE1" <-> "OE2" Residue "C TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 158": "OD1" <-> "OD2" Residue "C ASP 159": "OD1" <-> "OD2" Residue "C GLU 174": "OE1" <-> "OE2" Residue "C ASP 179": "OD1" <-> "OD2" Residue "C GLU 185": "OE1" <-> "OE2" Residue "D ASP 205": "OD1" <-> "OD2" Residue "D ASP 240": "OD1" <-> "OD2" Residue "D ASP 367": "OD1" <-> "OD2" Residue "E ASP 161": "OD1" <-> "OD2" Residue "E PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 185": "OD1" <-> "OD2" Residue "E TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 102": "OE1" <-> "OE2" Residue "F GLU 144": "OE1" <-> "OE2" Residue "F ASP 150": "OD1" <-> "OD2" Residue "F TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 123": "OE1" <-> "OE2" Residue "G ASP 169": "OD1" <-> "OD2" Residue "G ASP 204": "OD1" <-> "OD2" Residue "G GLU 326": "OE1" <-> "OE2" Residue "G ASP 389": "OD1" <-> "OD2" Residue "G GLU 435": "OE1" <-> "OE2" Residue "G TYR 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 599": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 649": "OD1" <-> "OD2" Residue "G TYR 670": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 169": "OE1" <-> "OE2" Residue "H TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 219": "OE1" <-> "OE2" Residue "H PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 89": "OD1" <-> "OD2" Residue "I GLU 143": "OE1" <-> "OE2" Residue "I TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 156": "OD1" <-> "OD2" Residue "I GLU 218": "OE1" <-> "OE2" Residue "K TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 55": "OD1" <-> "OD2" Residue "K PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 71": "OD1" <-> "OD2" Residue "L TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 70": "OE1" <-> "OE2" Residue "M PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 210": "OE1" <-> "OE2" Residue "M GLU 243": "OE1" <-> "OE2" Residue "M PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 22": "OE1" <-> "OE2" Residue "N ASP 90": "OD1" <-> "OD2" Residue "N GLU 170": "OE1" <-> "OE2" Residue "N PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 376": "OD1" <-> "OD2" Residue "N GLU 459": "OE1" <-> "OE2" Residue "O ASP 79": "OD1" <-> "OD2" Residue "O GLU 101": "OE1" <-> "OE2" Residue "O GLU 152": "OE1" <-> "OE2" Residue "P GLU 148": "OE1" <-> "OE2" Residue "P GLU 226": "OE1" <-> "OE2" Residue "P TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 112": "OE1" <-> "OE2" Residue "Q GLU 119": "OE1" <-> "OE2" Residue "T GLU 96": "OE1" <-> "OE2" Residue "T GLU 113": "OE1" <-> "OE2" Residue "U ASP 46": "OD1" <-> "OD2" Residue "U PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 94": "OE1" <-> "OE2" Residue "U PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 100": "OE1" <-> "OE2" Residue "V PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 116": "OE1" <-> "OE2" Residue "W PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 47": "OE1" <-> "OE2" Residue "X GLU 74": "OE1" <-> "OE2" Residue "X TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 90": "OD1" <-> "OD2" Residue "Z GLU 93": "OE1" <-> "OE2" Residue "Z ASP 94": "OD1" <-> "OD2" Residue "Z GLU 95": "OE1" <-> "OE2" Residue "Z GLU 100": "OE1" <-> "OE2" Residue "Z TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 106": "OE1" <-> "OE2" Residue "a GLU 7": "OE1" <-> "OE2" Residue "a TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 43": "OD1" <-> "OD2" Residue "c GLU 85": "OE1" <-> "OE2" Residue "d ASP 59": "OD1" <-> "OD2" Residue "d ASP 61": "OD1" <-> "OD2" Residue "d GLU 72": "OE1" <-> "OE2" Residue "g GLU 38": "OE1" <-> "OE2" Residue "g GLU 60": "OE1" <-> "OE2" Residue "i GLU 17": "OE1" <-> "OE2" Residue "i GLU 20": "OE1" <-> "OE2" Residue "j TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 15": "OE1" <-> "OE2" Residue "o TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 11": "OE1" <-> "OE2" Residue "p PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ASP 19": "OD1" <-> "OD2" Residue "p ASP 26": "OD1" <-> "OD2" Residue "p GLU 53": "OE1" <-> "OE2" Residue "p TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ASP 79": "OD1" <-> "OD2" Residue "x PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y GLU 226": "OE1" <-> "OE2" Residue "y GLU 251": "OE1" <-> "OE2" Residue "z TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 61461 Number of models: 1 Model: "" Number of chains: 64 Chain: "A" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 785 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 3, 'TRANS': 88} Chain breaks: 1 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: 2536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2536 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 18, 'TRANS': 305} Chain: "I" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1381 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 8, 'TRANS': 160} Chain: "J" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1093 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 3, 'TRANS': 134} 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: "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: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 616 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} 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: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 893 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} 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: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 990 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 10, 'TRANS': 113} 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: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 288 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 3, 'TRANS': 35} Chain: "c" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 595 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 7, 'TRANS': 65} Chain: "d" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 574 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "e" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 546 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 1, 'TRANS': 62} Chain: "f" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 734 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} 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: 721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 721 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 5, 'TRANS': 77} 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: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 384 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 4, 'TRANS': 45} Chain: "m" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} 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: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 631 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} 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: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 88 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: 1637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1637 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 14, 'TRANS': 196} Chain: "y" Number of atoms: 2001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2001 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 9, 'TRANS': 253} Chain: "z" Number of atoms: 1763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1763 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 225} 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: "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: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 85 Unusual residues: {'PTY': 1, 'UQ9': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'PC7': 1, 'PTY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'PGT': 1, 'PTY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 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: "d" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'LMN': 1} Classifications: {'undetermined': 1} 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: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'PSF': 1, 'T7X': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1538 SG CYS B 158 71.669 91.878 100.906 1.00 34.25 S ATOM 1038 SG CYS B 94 73.127 90.421 94.358 1.00 29.73 S ATOM 1768 SG CYS B 188 70.975 86.321 98.702 1.00 39.14 S ATOM 1032 SG CYS B 93 76.333 88.301 97.592 1.00 15.62 S ATOM 7523 SG CYS E 135 36.568 26.070 124.140 1.00 99.60 S ATOM 7796 SG CYS E 171 36.554 27.579 129.763 1.00106.96 S ATOM 10912 SG CYS F 405 50.973 49.459 133.719 1.00 47.51 S ATOM 10932 SG CYS F 408 49.161 45.440 130.763 1.00 34.27 S ATOM 10893 SG CYS F 402 44.306 47.591 134.501 1.00 31.97 S ATOM 11257 SG CYS F 448 48.785 44.238 137.001 1.00 24.66 S ATOM 11933 SG CYS G 106 51.693 59.849 136.600 1.00 47.51 S ATOM 12017 SG CYS G 117 52.923 59.007 133.627 1.00 47.51 S ATOM 12042 SG CYS G 120 57.308 58.718 138.495 1.00 47.51 S ATOM 12144 SG CYS G 134 54.175 59.158 140.144 1.00 28.85 S ATOM 12478 SG CYS G 179 53.339 67.253 123.223 1.00 30.26 S ATOM 12417 SG CYS G 170 54.172 66.215 116.632 1.00 47.51 S ATOM 12438 SG CYS G 173 48.824 68.943 119.239 1.00 47.51 S ATOM 12830 SG CYS G 224 41.064 64.293 131.399 1.00 37.89 S ATOM 12783 SG CYS G 218 43.687 61.468 126.411 1.00 38.93 S ATOM 12806 SG CYS G 221 47.512 62.767 131.480 1.00 47.51 S ATOM 13151 SG CYS G 268 45.603 67.161 127.530 1.00 32.51 S ATOM 20279 SG CYS I 168 60.717 78.626 101.523 1.00 47.51 S ATOM 20232 SG CYS I 162 62.768 84.107 99.579 1.00 47.51 S ATOM 20258 SG CYS I 165 66.756 80.225 102.925 1.00 39.24 S ATOM 20000 SG CYS I 133 62.476 83.531 105.882 1.00 45.18 S ATOM 20308 SG CYS I 172 55.972 73.912 103.553 1.00 40.93 S ATOM 19931 SG CYS I 123 49.993 76.996 104.667 1.00 47.51 S ATOM 19973 SG CYS I 129 56.034 78.766 106.175 1.00 47.51 S ATOM 19950 SG CYS I 126 53.951 73.727 109.111 1.00 47.51 S ATOM 35451 SG CYS O 91 125.544 147.077 112.188 1.00 69.90 S ATOM 35477 SG CYS O 95 121.982 145.169 113.836 1.00 77.18 S ATOM 39683 SG CYS R 72 43.635 60.822 103.331 1.00 39.81 S ATOM 39869 SG CYS R 97 43.361 63.576 106.074 1.00 32.48 S ATOM 39896 SG CYS R 100 44.889 64.387 102.568 1.00 35.75 S Time building chain proxies: 24.10, per 1000 atoms: 0.39 Number of scatterers: 61461 At special positions: 0 Unit cell: (216.783, 261.144, 192.51, 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 420 16.00 P 14 15.00 O 11006 8.00 N 10271 7.00 C 39719 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS E 174 " - pdb=" SG CYS F 148 " distance=2.03 Simple disulfide: pdb=" SG CYS N 336 " - pdb=" SG CYS N 420 " distance=2.03 Simple disulfide: pdb=" SG CYS X 29 " - pdb=" SG CYS X 59 " distance=2.04 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=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 19.15 Conformation dependent library (CDL) restraints added in 7.7 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 500 " pdb="FE1 FES E 500 " - pdb=" SG CYS E 135 " pdb="FE2 FES E 500 " - pdb=" SG CYS E 171 " pdb=" FES G 801 " pdb="FE2 FES G 801 " - pdb=" SG CYS G 120 " pdb="FE1 FES G 801 " - pdb=" SG CYS G 106 " pdb="FE2 FES G 801 " - pdb=" SG CYS G 134 " pdb="FE1 FES G 801 " - pdb=" SG CYS G 117 " 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="FE4 SF4 F 501 " - pdb=" SG CYS F 448 " pdb="FE1 SF4 F 501 " - pdb=" SG CYS F 405 " pdb="FE3 SF4 F 501 " - pdb=" SG CYS F 402 " pdb="FE2 SF4 F 501 " - pdb=" SG CYS F 408 " 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="FE4 SF4 G 802 " - pdb=" SG CYS G 173 " pdb="FE3 SF4 G 802 " - pdb=" SG CYS G 170 " pdb=" SF4 G 803 " pdb="FE2 SF4 G 803 " - pdb=" SG CYS G 218 " pdb="FE4 SF4 G 803 " - pdb=" SG CYS G 268 " pdb="FE3 SF4 G 803 " - pdb=" SG CYS G 221 " pdb="FE1 SF4 G 803 " - pdb=" SG CYS G 224 " 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="FE1 SF4 I 500 " - pdb=" SG CYS I 168 " pdb="FE3 SF4 I 500 " - pdb=" SG CYS I 165 " pdb=" SF4 I 501 " pdb="FE1 SF4 I 501 " - pdb=" SG CYS I 172 " pdb="FE4 SF4 I 501 " - pdb=" SG CYS I 126 " pdb="FE2 SF4 I 501 " - pdb=" SG CYS I 123 " pdb="FE3 SF4 I 501 " - pdb=" SG CYS I 129 " Number of angles added : 77 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 72 " pdb="ZN ZN R 200 " - pdb=" SG CYS R 100 " pdb="ZN ZN R 200 " - pdb=" SG CYS R 97 " 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=" ND1 HIS y 107 " Number of angles added : 3 15156 Ramachandran restraints generated. 7578 Oldfield, 0 Emsley, 7578 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14274 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 298 helices and 37 sheets defined 48.5% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.94 Creating SS restraints... Processing helix chain 'A' and resid 2 through 4 No H-bonds generated for 'chain 'A' and resid 2 through 4' Processing helix chain 'A' and resid 6 through 28 removed outlier: 3.542A pdb=" N LEU A 23 " --> pdb=" O SER A 19 " (cutoff:3.500A) Proline residue: A 26 - end of helix Processing helix chain 'A' and resid 60 through 83 Proline residue: A 80 - end of helix Processing helix chain 'A' and resid 92 through 112 removed outlier: 3.557A pdb=" N PHE A 99 " --> pdb=" O SER A 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 82 Processing helix chain 'B' and resid 93 through 101 removed outlier: 3.599A pdb=" N GLU B 97 " --> pdb=" O CYS B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 111 Processing helix chain 'B' and resid 136 through 145 Processing helix chain 'B' and resid 192 through 208 removed outlier: 3.724A pdb=" N ARG B 208 " --> pdb=" O LYS B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 217 Processing helix chain 'C' and resid 3 through 12 Processing helix chain 'C' and resid 38 through 47 Processing helix chain 'C' and resid 106 through 118 removed outlier: 3.737A pdb=" N TRP C 110 " --> pdb=" O SER C 107 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLU C 112 " --> pdb=" O GLY C 109 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET C 118 " --> pdb=" O VAL C 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 22 No H-bonds generated for 'chain 'D' and resid 20 through 22' Processing helix chain 'D' and resid 51 through 57 removed outlier: 4.222A pdb=" N GLU D 56 " --> pdb=" O GLU D 52 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N TYR D 57 " --> pdb=" O LYS D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 69 removed outlier: 3.820A pdb=" N ASP D 68 " --> pdb=" O LEU D 64 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG D 69 " --> pdb=" O PRO D 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 64 through 69' Processing helix chain 'D' and resid 75 through 90 removed outlier: 3.535A pdb=" N HIS D 80 " --> pdb=" O MET D 76 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ALA D 81 " --> pdb=" O ALA D 77 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR D 82 " --> pdb=" O GLN D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 125 Processing helix chain 'D' and resid 129 through 148 removed outlier: 3.606A pdb=" N TRP D 133 " --> pdb=" O THR D 129 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LYS D 140 " --> pdb=" O GLU D 136 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU D 141 " --> pdb=" O GLU D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 191 removed outlier: 3.917A pdb=" N GLN D 181 " --> pdb=" O SER D 177 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ALA D 183 " --> pdb=" O THR D 179 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N SER D 184 " --> pdb=" O GLN D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 203 Processing helix chain 'D' and resid 211 through 217 Processing helix chain 'D' and resid 222 through 227 removed outlier: 3.724A 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 257 through 280 Processing helix chain 'D' and resid 306 through 316 Processing helix chain 'D' and resid 358 through 369 removed outlier: 3.511A pdb=" N HIS D 362 " --> pdb=" O PRO D 358 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU D 366 " --> pdb=" O HIS D 362 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ASP D 367 " --> pdb=" O SER D 363 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N PHE D 368 " --> pdb=" O GLN D 364 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET D 369 " --> pdb=" O GLY D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 385 removed outlier: 4.146A pdb=" N THR D 380 " --> pdb=" O ALA D 376 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE D 381 " --> pdb=" O ASP D 377 " (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 61 Processing helix chain 'E' and resid 66 through 84 removed outlier: 3.569A pdb=" N LYS E 69 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N GLN E 70 " --> pdb=" O ASN E 67 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA E 72 " --> pdb=" O LYS E 69 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ILE E 74 " --> pdb=" O SER E 71 " (cutoff:3.500A) Proline residue: E 75 - end of helix Processing helix chain 'E' and resid 90 through 100 Processing helix chain 'E' and resid 104 through 113 removed outlier: 3.857A pdb=" N VAL E 110 " --> pdb=" O ARG E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 138 No H-bonds generated for 'chain 'E' and resid 136 through 138' Processing helix chain 'E' and resid 140 through 149 removed outlier: 3.705A pdb=" N GLU E 144 " --> pdb=" O ARG E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 215 removed outlier: 3.591A pdb=" N VAL E 207 " --> pdb=" O PRO E 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 82 Processing helix chain 'F' and resid 88 through 93 Processing helix chain 'F' and resid 97 through 106 Processing helix chain 'F' and resid 118 through 124 removed outlier: 3.540A pdb=" N PHE F 124 " --> pdb=" O LEU F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 151 through 156 Processing helix chain 'F' and resid 158 through 171 removed outlier: 3.548A pdb=" N LEU F 166 " --> pdb=" O LEU F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 202 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 227 through 230 Processing helix chain 'F' and resid 234 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 275 through 278 No H-bonds generated for 'chain 'F' and resid 275 through 278' Processing helix chain 'F' and resid 283 through 286 No H-bonds generated for 'chain 'F' and resid 283 through 286' 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 Processing helix chain 'F' and resid 386 through 399 Processing helix chain 'F' and resid 406 through 423 removed outlier: 4.462A pdb=" N GLY F 413 " --> pdb=" O ARG F 409 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TRP F 416 " --> pdb=" O THR F 412 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 442 Processing helix chain 'F' and resid 450 through 464 Proline residue: F 457 - end of helix Processing helix chain 'F' and resid 466 through 482 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 98 Processing helix chain 'G' and resid 149 through 164 Processing helix chain 'G' and resid 180 through 187 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 261 through 267 removed outlier: 3.748A pdb=" N VAL G 264 " --> pdb=" O SER G 261 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE G 267 " --> pdb=" O VAL G 264 " (cutoff:3.500A) 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 361 through 371 Processing helix chain 'G' and resid 390 through 403 removed outlier: 3.836A pdb=" N MET G 403 " --> pdb=" O PHE G 399 " (cutoff:3.500A) Processing helix chain 'G' and resid 432 through 436 removed outlier: 3.573A pdb=" N GLU G 435 " --> pdb=" O SER G 432 " (cutoff:3.500A) Processing helix chain 'G' and resid 452 through 465 removed outlier: 3.529A pdb=" N ARG G 457 " --> pdb=" O MET G 453 " (cutoff:3.500A) Processing helix chain 'G' and resid 489 through 496 Processing helix chain 'G' and resid 501 through 507 Processing helix chain 'G' and resid 518 through 522 removed outlier: 3.887A pdb=" N ASN G 522 " --> pdb=" O GLY G 519 " (cutoff:3.500A) Processing helix chain 'G' and resid 526 through 540 Processing helix chain 'G' and resid 557 through 565 removed outlier: 4.742A pdb=" N ALA G 561 " --> pdb=" O ALA G 557 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA G 562 " --> pdb=" O ALA G 558 " (cutoff:3.500A) Processing helix chain 'G' and resid 653 through 664 Processing helix chain 'G' and resid 673 through 682 removed outlier: 3.785A pdb=" N SER G 682 " --> pdb=" O SER G 678 " (cutoff:3.500A) Processing helix chain 'G' and resid 685 through 688 removed outlier: 3.644A pdb=" N VAL G 688 " --> pdb=" O PRO G 685 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 685 through 688' 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 740 removed outlier: 4.262A pdb=" N ALA G 740 " --> pdb=" O ALA G 736 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 34 Proline residue: H 15 - end of helix removed outlier: 3.664A pdb=" N LEU H 25 " --> pdb=" O ALA H 21 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA H 32 " --> pdb=" O ARG H 28 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL H 34 " --> pdb=" O VAL H 30 " (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: 3.903A pdb=" N ALA H 88 " --> pdb=" O LEU H 84 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N TRP H 89 " --> pdb=" O SER H 85 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ALA H 90 " --> pdb=" O LEU H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 121 removed outlier: 4.869A pdb=" N VAL H 118 " --> pdb=" O SER H 114 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N TYR H 119 " --> pdb=" O SER H 115 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N GLY H 120 " --> pdb=" O LEU H 116 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE H 121 " --> pdb=" O GLY H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 123 through 127 Processing helix chain 'H' and resid 131 through 162 removed outlier: 4.031A pdb=" N VAL H 149 " --> pdb=" O VAL H 145 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N SER H 150 " --> pdb=" O SER H 146 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N CYS H 161 " --> pdb=" O THR H 157 " (cutoff:3.500A) Processing helix chain 'H' and resid 167 through 174 removed outlier: 3.746A pdb=" N VAL H 171 " --> pdb=" O LEU H 167 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET H 172 " --> pdb=" O SER H 168 " (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 205 through 207 No H-bonds generated for 'chain 'H' and resid 205 through 207' Processing helix chain 'H' and resid 222 through 246 Processing helix chain 'H' and resid 260 through 262 No H-bonds generated for 'chain 'H' and resid 260 through 262' Processing helix chain 'H' and resid 266 through 284 removed outlier: 3.637A pdb=" N SER H 270 " --> pdb=" O SER H 266 " (cutoff:3.500A) Processing helix chain 'H' and resid 292 through 301 Processing helix chain 'H' and resid 304 through 320 Processing helix chain 'I' and resid 62 through 72 Processing helix chain 'I' and resid 74 through 84 removed outlier: 3.884A pdb=" N GLY I 79 " --> pdb=" O GLU I 75 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU I 84 " --> pdb=" O LEU I 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 128 through 132 Processing helix chain 'I' and resid 167 through 171 Processing helix chain 'I' and resid 190 through 193 No H-bonds generated for 'chain 'I' and resid 190 through 193' Processing helix chain 'I' and resid 197 through 206 Processing helix chain 'I' and resid 208 through 219 removed outlier: 3.965A pdb=" N GLU I 213 " --> pdb=" O THR I 209 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 17 Processing helix chain 'J' and resid 23 through 44 removed outlier: 3.546A pdb=" N PHE J 34 " --> pdb=" O PHE J 30 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLY J 39 " --> pdb=" O CYS J 35 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU J 40 " --> pdb=" O ASP J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 48 through 56 removed outlier: 3.590A pdb=" N LEU J 54 " --> pdb=" O ALA J 50 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 70 Processing helix chain 'J' and resid 136 through 144 removed outlier: 4.680A pdb=" N LEU J 143 " --> pdb=" O THR J 139 " (cutoff:3.500A) Processing helix chain 'J' and resid 149 through 168 removed outlier: 3.809A pdb=" N ILE J 167 " --> pdb=" O MET J 163 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 22 removed outlier: 3.766A pdb=" N PHE K 9 " --> pdb=" O LYS K 5 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 53 removed outlier: 4.074A pdb=" N ILE K 35 " --> pdb=" O MET K 31 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU K 36 " --> pdb=" O LEU K 32 " (cutoff:3.500A) Processing helix chain 'K' and resid 58 through 84 removed outlier: 3.670A pdb=" N LEU K 66 " --> pdb=" O ALA K 62 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N THR K 67 " --> pdb=" O LEU K 63 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL K 68 " --> pdb=" O LEU K 64 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE K 84 " --> pdb=" O PHE K 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 18 removed outlier: 4.145A pdb=" N VAL L 6 " --> pdb=" O TYR L 2 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU L 8 " --> pdb=" O LEU L 4 " (cutoff:3.500A) Proline residue: L 9 - end of helix Processing helix chain 'L' and resid 27 through 50 removed outlier: 3.608A pdb=" N THR L 33 " --> pdb=" O ALA L 29 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR L 34 " --> pdb=" O ILE L 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 105 removed outlier: 3.671A pdb=" N VAL L 84 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET L 85 " --> pdb=" O LEU L 81 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE L 101 " --> pdb=" O HIS L 97 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N SER L 102 " --> pdb=" O LEU L 98 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR L 103 " --> pdb=" O TYR L 99 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 129 Processing helix chain 'L' and resid 133 through 153 removed outlier: 4.074A pdb=" N GLY L 139 " --> pdb=" O GLN L 135 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY L 144 " --> pdb=" O TRP L 140 " (cutoff:3.500A) Processing helix chain 'L' and resid 158 through 189 removed outlier: 4.458A pdb=" N GLY L 177 " --> pdb=" O VAL L 173 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LEU L 178 " --> pdb=" O GLY L 174 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU L 183 " --> pdb=" O ALA L 179 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU L 188 " --> pdb=" O GLY L 184 " (cutoff:3.500A) Processing helix chain 'L' and resid 218 through 231 removed outlier: 3.674A pdb=" N GLY L 231 " --> pdb=" O ILE L 227 " (cutoff:3.500A) Processing helix chain 'L' and resid 240 through 244 removed outlier: 4.232A pdb=" N ASP L 244 " --> pdb=" O THR L 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 240 through 244' Processing helix chain 'L' and resid 250 through 256 removed outlier: 3.929A pdb=" N LEU L 255 " --> pdb=" O PRO L 251 " (cutoff:3.500A) Processing helix chain 'L' and resid 261 through 271 removed outlier: 4.010A pdb=" N GLY L 265 " --> pdb=" O VAL L 262 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL L 266 " --> pdb=" O THR L 263 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG L 271 " --> pdb=" O MET L 268 " (cutoff:3.500A) Processing helix chain 'L' and resid 273 through 276 No H-bonds generated for 'chain 'L' and resid 273 through 276' Processing helix chain 'L' and resid 280 through 300 removed outlier: 3.507A pdb=" N VAL L 285 " --> pdb=" O THR L 281 " (cutoff:3.500A) Processing helix chain 'L' and resid 307 through 327 removed outlier: 3.679A pdb=" N ILE L 311 " --> pdb=" O LEU L 307 " (cutoff:3.500A) Processing helix chain 'L' and resid 331 through 344 removed outlier: 3.621A pdb=" N PHE L 343 " --> pdb=" O MET L 339 " (cutoff:3.500A) Processing helix chain 'L' and resid 346 through 357 Processing helix chain 'L' and resid 372 through 374 No H-bonds generated for 'chain 'L' and resid 372 through 374' Processing helix chain 'L' and resid 377 through 390 Processing helix chain 'L' and resid 398 through 410 removed outlier: 4.391A pdb=" N VAL L 403 " --> pdb=" O TYR L 399 " (cutoff:3.500A) Processing helix chain 'L' and resid 414 through 440 removed outlier: 3.889A pdb=" N PHE L 418 " --> pdb=" O ILE L 414 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU L 428 " --> pdb=" O SER L 424 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE L 429 " --> pdb=" O VAL L 425 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE L 435 " --> pdb=" O SER L 431 " (cutoff:3.500A) Processing helix chain 'L' and resid 450 through 454 removed outlier: 4.061A pdb=" N SER L 454 " --> pdb=" O GLY L 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 450 through 454' Processing helix chain 'L' and resid 461 through 485 Proline residue: L 466 - end of helix removed outlier: 3.701A pdb=" N LEU L 475 " --> pdb=" O ALA L 471 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE L 476 " --> pdb=" O LEU L 472 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLY L 478 " --> pdb=" O SER L 474 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N TYR L 479 " --> pdb=" O LEU L 475 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ASP L 483 " --> pdb=" O TYR L 479 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N MET L 484 " --> pdb=" O LEU L 480 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET L 485 " --> pdb=" O ALA L 481 " (cutoff:3.500A) Processing helix chain 'L' and resid 507 through 509 No H-bonds generated for 'chain 'L' and resid 507 through 509' Processing helix chain 'L' and resid 520 through 537 Processing helix chain 'L' and resid 553 through 560 removed outlier: 3.584A pdb=" N PHE L 559 " --> pdb=" O LEU L 555 " (cutoff:3.500A) Processing helix chain 'L' and resid 562 through 583 removed outlier: 5.739A pdb=" N ASP L 566 " --> pdb=" O TRP L 563 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL L 568 " --> pdb=" O PHE L 565 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N LEU L 569 " --> pdb=" O ASP L 566 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP L 571 " --> pdb=" O VAL L 568 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE L 572 " --> pdb=" O LEU L 569 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N VAL L 574 " --> pdb=" O ASP L 571 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ARG L 575 " --> pdb=" O PHE L 572 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER L 576 " --> pdb=" O LEU L 573 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY L 581 " --> pdb=" O LEU L 578 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLU L 583 " --> pdb=" O PHE L 580 " (cutoff:3.500A) Processing helix chain 'L' and resid 594 through 597 Processing helix chain 'L' and resid 605 through 607 No H-bonds generated for 'chain 'L' and resid 605 through 607' Processing helix chain 'L' and resid 611 through 613 No H-bonds generated for 'chain 'L' and resid 611 through 613' Processing helix chain 'M' and resid 12 through 28 Proline residue: M 19 - end of helix removed outlier: 3.843A pdb=" N PHE M 28 " --> pdb=" O ILE M 24 " (cutoff:3.500A) Processing helix chain 'M' and resid 34 through 57 removed outlier: 3.740A pdb=" N ARG M 38 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU M 39 " --> pdb=" O ARG M 35 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU M 55 " --> pdb=" O TYR M 51 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TRP M 56 " --> pdb=" O SER M 52 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE M 57 " --> pdb=" O LEU M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 90 through 107 removed outlier: 3.550A 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 112 through 115 No H-bonds generated for 'chain 'M' and resid 112 through 115' Processing helix chain 'M' and resid 117 through 134 removed outlier: 3.516A pdb=" N ILE M 121 " --> pdb=" O GLU M 118 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA M 122 " --> pdb=" O TYR M 119 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE M 134 " --> pdb=" O ILE M 131 " (cutoff:3.500A) Processing helix chain 'M' and resid 139 through 159 removed outlier: 3.996A pdb=" N VAL M 149 " --> pdb=" O PHE M 145 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N LEU M 150 " --> pdb=" O PHE M 146 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N ILE M 151 " --> pdb=" O GLU M 147 " (cutoff:3.500A) Proline residue: M 152 - end of helix Processing helix chain 'M' and resid 164 through 195 removed outlier: 3.885A pdb=" N ILE M 167 " --> pdb=" O GLN M 164 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA M 170 " --> pdb=" O ILE M 167 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR M 171 " --> pdb=" O LYS M 168 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN M 172 " --> pdb=" O ALA M 169 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N TYR M 176 " --> pdb=" O PHE M 173 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU M 179 " --> pdb=" O TYR M 176 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU M 186 " --> pdb=" O PHE M 183 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE M 193 " --> pdb=" O LEU M 190 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR M 195 " --> pdb=" O LEU M 192 " (cutoff:3.500A) Processing helix chain 'M' and resid 200 through 205 removed outlier: 3.987A pdb=" N THR M 205 " --> pdb=" O GLN M 201 " (cutoff:3.500A) Processing helix chain 'M' and resid 210 through 227 removed outlier: 3.713A pdb=" N PHE M 215 " --> pdb=" O ARG M 211 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N SER M 223 " --> pdb=" O ALA M 219 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N VAL M 226 " --> pdb=" O ALA M 222 " (cutoff:3.500A) Processing helix chain 'M' and resid 235 through 239 removed outlier: 3.666A pdb=" N GLU M 239 " --> pdb=" O ILE M 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 235 through 239' Processing helix chain 'M' and resid 246 through 252 removed outlier: 4.678A pdb=" N ILE M 251 " --> pdb=" O ALA M 247 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU M 252 " --> pdb=" O GLY M 248 " (cutoff:3.500A) Processing helix chain 'M' and resid 258 through 267 removed outlier: 3.704A pdb=" N LEU M 265 " --> pdb=" O THR M 261 " (cutoff:3.500A) Processing helix chain 'M' and resid 273 through 278 removed outlier: 3.977A pdb=" N LEU M 277 " --> pdb=" O PRO M 273 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N CYS M 278 " --> pdb=" O GLU M 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 273 through 278' Processing helix chain 'M' and resid 280 through 299 removed outlier: 3.945A pdb=" N ILE M 289 " --> pdb=" O THR M 285 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE M 292 " --> pdb=" O ALA M 288 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER M 295 " --> pdb=" O ILE M 291 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU M 299 " --> pdb=" O SER M 295 " (cutoff:3.500A) Processing helix chain 'M' and resid 304 through 324 removed outlier: 4.108A pdb=" N ILE M 308 " --> pdb=" O LEU M 304 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE M 321 " --> pdb=" O ASN M 317 " (cutoff:3.500A) Processing helix chain 'M' and resid 328 through 359 removed outlier: 3.908A pdb=" N GLY M 332 " --> pdb=" O ILE M 328 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER M 346 " --> pdb=" O GLY M 342 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU M 355 " --> pdb=" O CYS M 351 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR M 356 " --> pdb=" O VAL M 352 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG M 358 " --> pdb=" O VAL M 354 " (cutoff:3.500A) Processing helix chain 'M' and resid 375 through 388 Processing helix chain 'M' and resid 395 through 410 removed outlier: 3.830A pdb=" N LEU M 402 " --> pdb=" O ILE M 398 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE M 403 " --> pdb=" O GLY M 399 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG M 410 " --> pdb=" O GLY M 406 " (cutoff:3.500A) Processing helix chain 'M' and resid 412 through 436 removed outlier: 3.657A pdb=" N THR M 416 " --> pdb=" O SER M 412 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N MET M 422 " --> pdb=" O ALA M 418 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA M 426 " --> pdb=" O MET M 422 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ALA M 427 " --> pdb=" O ILE M 423 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TYR M 428 " --> pdb=" O LEU M 424 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER M 429 " --> pdb=" O GLY M 425 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LEU M 430 " --> pdb=" O ALA M 426 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N TRP M 431 " --> pdb=" O ALA M 427 " (cutoff:3.500A) Processing helix chain 'M' and resid 454 through 472 removed outlier: 3.518A pdb=" N PHE M 460 " --> pdb=" O GLU M 456 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE M 461 " --> pdb=" O VAL M 457 " (cutoff:3.500A) Proline residue: M 462 - end of helix Processing helix chain 'M' and resid 475 through 489 removed outlier: 3.854A pdb=" N MET M 481 " --> pdb=" O PHE M 477 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N THR M 483 " --> pdb=" O ASP M 479 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N SER M 484 " --> pdb=" O CYS M 480 " (cutoff:3.500A) Processing helix chain 'N' and resid 14 through 17 Processing helix chain 'N' and resid 20 through 38 Processing helix chain 'N' and resid 52 through 71 Processing helix chain 'N' and resid 91 through 115 removed outlier: 3.538A pdb=" N PHE N 99 " --> pdb=" O PHE N 95 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU N 102 " --> pdb=" O ILE N 98 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N PHE N 112 " --> pdb=" O ILE N 108 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ASP N 113 " --> pdb=" O SER N 109 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N PHE N 114 " --> pdb=" O MET N 110 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N PHE N 115 " --> pdb=" O CYS N 111 " (cutoff:3.500A) Processing helix chain 'N' and resid 123 through 140 removed outlier: 3.595A pdb=" N ILE N 140 " --> pdb=" O LEU N 137 " (cutoff:3.500A) Processing helix chain 'N' and resid 147 through 163 removed outlier: 3.672A pdb=" N CYS N 158 " --> pdb=" O LEU N 154 " (cutoff:3.500A) Processing helix chain 'N' and resid 171 through 201 removed outlier: 3.822A pdb=" N SER N 200 " --> pdb=" O MET N 196 " (cutoff:3.500A) Processing helix chain 'N' and resid 206 through 209 No H-bonds generated for 'chain 'N' and resid 206 through 209' 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 Processing helix chain 'N' and resid 268 through 281 Processing helix chain 'N' and resid 291 through 309 Processing helix chain 'N' and resid 316 through 336 removed outlier: 3.724A pdb=" N GLY N 333 " --> pdb=" O TYR N 329 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE N 334 " --> pdb=" O ILE N 330 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS N 336 " --> pdb=" O ILE N 332 " (cutoff:3.500A) Processing helix chain 'N' and resid 339 through 369 removed outlier: 4.156A pdb=" N GLN N 368 " --> pdb=" O LEU N 364 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N THR N 369 " --> pdb=" O ALA N 365 " (cutoff:3.500A) 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 385 through 399 Processing helix chain 'N' and resid 407 through 419 Processing helix chain 'N' and resid 423 through 448 removed outlier: 3.790A pdb=" N LEU N 443 " --> pdb=" O TYR N 439 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL N 444 " --> pdb=" O TYR N 440 " (cutoff:3.500A) Processing helix chain 'N' and resid 463 through 479 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: 3.577A pdb=" N HIS O 74 " --> pdb=" O ARG O 70 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N THR O 75 " --> pdb=" O ALA O 71 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 103 No H-bonds generated for 'chain 'O' and resid 101 through 103' Processing helix chain 'O' and resid 114 through 120 removed outlier: 3.761A pdb=" N LEU O 118 " --> pdb=" O GLU O 114 " (cutoff:3.500A) Processing helix chain 'P' and resid 81 through 91 removed outlier: 4.073A pdb=" N GLN P 86 " --> pdb=" O ARG P 82 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N MET P 91 " --> pdb=" O GLN P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 105 through 111 removed outlier: 4.613A pdb=" N HIS P 108 " --> pdb=" O SER P 105 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU P 109 " --> pdb=" O PRO P 106 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU P 111 " --> pdb=" O HIS P 108 " (cutoff:3.500A) Processing helix chain 'P' and resid 131 through 134 Processing helix chain 'P' and resid 157 through 160 No H-bonds generated for 'chain 'P' and resid 157 through 160' Processing helix chain 'P' and resid 162 through 174 Processing helix chain 'P' and resid 195 through 210 removed outlier: 3.646A pdb=" N ALA P 199 " --> pdb=" O ARG P 195 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU P 208 " --> pdb=" O GLU P 204 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ASN P 209 " --> pdb=" O GLU P 205 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA P 210 " --> pdb=" O ALA P 206 " (cutoff:3.500A) Processing helix chain 'P' and resid 231 through 239 Processing helix chain 'P' and resid 258 through 270 Processing helix chain 'P' and resid 290 through 301 removed outlier: 4.679A pdb=" N MET P 300 " --> pdb=" O ILE P 296 " (cutoff:3.500A) Processing helix chain 'P' and resid 312 through 323 Proline residue: P 321 - end of helix Processing helix chain 'P' and resid 341 through 348 removed outlier: 4.008A pdb=" N ASN P 345 " --> pdb=" O LEU P 341 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N THR P 348 " --> pdb=" O ILE P 344 " (cutoff:3.500A) Processing helix chain 'P' and resid 361 through 363 No H-bonds generated for 'chain 'P' and resid 361 through 363' Processing helix chain 'P' and resid 377 through 380 Processing helix chain 'Q' and resid 37 through 42 Processing helix chain 'Q' and resid 47 through 51 removed outlier: 3.697A pdb=" N SER Q 51 " --> pdb=" O GLU Q 48 " (cutoff:3.500A) 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 '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 7 through 10 No H-bonds generated for 'chain 'S' and resid 7 through 10' Processing helix chain 'S' and resid 23 through 34 Proline residue: S 27 - end of helix Processing helix chain 'S' and resid 37 through 40 No H-bonds generated for 'chain 'S' and resid 37 through 40' Processing helix chain 'S' and resid 79 through 92 Processing helix chain 'T' and resid 43 through 55 removed outlier: 4.728A pdb=" N ASP T 48 " --> pdb=" O GLU T 44 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ARG T 49 " --> pdb=" O ALA T 45 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU T 51 " --> pdb=" O VAL T 47 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL T 53 " --> pdb=" O ARG T 49 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N VAL T 54 " --> pdb=" O VAL T 50 " (cutoff:3.500A) Processing helix chain 'T' and resid 82 through 90 removed outlier: 3.964A pdb=" N VAL T 86 " --> pdb=" O THR T 82 " (cutoff:3.500A) 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: 3.545A pdb=" N ASP U 52 " --> pdb=" O SER U 48 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ARG U 53 " --> pdb=" O GLU U 49 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N SER U 56 " --> pdb=" O ASP U 52 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL U 57 " --> pdb=" O ARG U 53 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL U 58 " --> pdb=" O VAL U 54 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS U 59 " --> pdb=" O LEU U 55 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ASN U 60 " --> pdb=" O SER U 56 " (cutoff:3.500A) Processing helix chain 'U' and resid 66 through 68 No H-bonds generated for 'chain 'U' and resid 66 through 68' Processing helix chain 'U' and resid 83 through 96 Processing helix chain 'U' and resid 105 through 107 No H-bonds generated for 'chain 'U' and resid 105 through 107' Processing helix chain 'U' and resid 112 through 120 Processing helix chain 'V' and resid 29 through 46 removed outlier: 4.600A pdb=" N GLN V 45 " --> pdb=" O LEU V 41 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ALA V 46 " --> pdb=" O LYS V 42 " (cutoff:3.500A) Processing helix chain 'V' and resid 52 through 70 removed outlier: 3.908A pdb=" N SER V 59 " --> pdb=" O LYS V 55 " (cutoff:3.500A) Processing helix chain 'V' and resid 74 through 81 removed outlier: 3.922A pdb=" N LYS V 79 " --> pdb=" O GLU V 75 " (cutoff:3.500A) Processing helix chain 'V' and resid 88 through 106 Processing helix chain 'V' and resid 140 through 150 removed outlier: 4.222A pdb=" N LEU V 146 " --> pdb=" O PHE V 142 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU V 147 " --> pdb=" O TYR V 143 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY V 148 " --> pdb=" O LYS V 144 " (cutoff:3.500A) Processing helix chain 'W' and resid 19 through 43 removed outlier: 3.720A pdb=" N ARG W 24 " --> pdb=" O THR W 20 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG W 25 " --> pdb=" O GLU W 21 " (cutoff:3.500A) Proline residue: W 38 - end of helix removed outlier: 3.551A pdb=" N MET W 41 " --> pdb=" O ILE W 37 " (cutoff:3.500A) Processing helix chain 'W' and resid 52 through 65 removed outlier: 3.632A pdb=" N ARG W 56 " --> pdb=" O PRO W 52 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR W 57 " --> pdb=" O SER W 53 " (cutoff:3.500A) Processing helix chain 'W' and resid 72 through 90 Processing helix chain 'W' and resid 99 through 102 No H-bonds generated for 'chain 'W' and resid 99 through 102' Processing helix chain 'W' and resid 122 through 129 Processing helix chain 'X' and resid 15 through 20 Processing helix chain 'X' and resid 22 through 27 removed outlier: 4.161A 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 51 through 53 No H-bonds generated for 'chain 'X' and resid 51 through 53' Processing helix chain 'X' and resid 55 through 70 Processing helix chain 'X' and resid 76 through 84 Processing helix chain 'X' and resid 95 through 102 Processing helix chain 'Z' and resid 48 through 83 removed outlier: 3.942A pdb=" N ALA Z 56 " --> pdb=" O ALA Z 52 " (cutoff:3.500A) Processing helix chain 'Z' and resid 86 through 112 removed outlier: 3.608A pdb=" N SER Z 99 " --> pdb=" O GLU Z 95 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU Z 100 " --> pdb=" O ARG Z 96 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL Z 111 " --> pdb=" O TYR Z 107 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET Z 112 " --> pdb=" O GLU Z 108 " (cutoff:3.500A) Processing helix chain 'Z' and resid 140 through 142 No H-bonds generated for 'chain 'Z' and resid 140 through 142' Processing helix chain 'a' and resid 5 through 28 Proline residue: a 11 - end of helix removed outlier: 3.506A pdb=" N MET a 18 " --> pdb=" O ILE a 15 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER a 25 " --> pdb=" O MET a 22 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN a 26 " --> pdb=" O GLY a 23 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR a 28 " --> pdb=" O SER a 25 " (cutoff:3.500A) Processing helix chain 'a' and resid 30 through 34 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 39 Proline residue: b 31 - end of helix removed outlier: 4.486A 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 33 through 57 Proline residue: c 50 - end of helix removed outlier: 4.310A pdb=" N LYS c 57 " --> pdb=" O LYS c 53 " (cutoff:3.500A) Processing helix chain 'd' and resid 7 through 24 removed outlier: 3.700A pdb=" N ARG d 24 " --> pdb=" O SER d 20 " (cutoff:3.500A) Processing helix chain 'd' and resid 32 through 74 removed outlier: 3.595A pdb=" N VAL d 62 " --> pdb=" O GLU d 58 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N MET d 63 " --> pdb=" O ASP d 59 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS d 66 " --> pdb=" O VAL d 62 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ARG d 74 " --> pdb=" O ALA d 70 " (cutoff:3.500A) Processing helix chain 'e' and resid 15 through 27 removed outlier: 3.956A pdb=" N HIS e 27 " --> pdb=" O GLU e 23 " (cutoff:3.500A) Processing helix chain 'e' and resid 35 through 46 removed outlier: 3.619A pdb=" N ASP e 40 " --> pdb=" O LEU e 36 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N HIS e 46 " --> pdb=" O LEU e 42 " (cutoff:3.500A) Processing helix chain 'e' and resid 50 through 64 removed outlier: 4.243A pdb=" N LYS e 64 " --> pdb=" O GLU e 60 " (cutoff:3.500A) Processing helix chain 'f' and resid 22 through 27 Processing helix chain 'f' and resid 31 through 53 removed outlier: 3.655A pdb=" N ILE f 40 " --> pdb=" O ARG f 36 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR f 41 " --> pdb=" O PHE f 37 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ILE f 53 " --> pdb=" O TYR f 49 " (cutoff:3.500A) Processing helix chain 'f' and resid 60 through 86 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 61 through 79 Proline residue: g 65 - end of helix Processing helix chain 'g' and resid 91 through 101 Processing helix chain 'i' and resid 4 through 15 removed outlier: 4.324A pdb=" N ASN i 10 " --> pdb=" O GLU i 6 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LEU i 11 " --> pdb=" O PHE i 7 " (cutoff:3.500A) Processing helix chain 'i' and resid 19 through 44 removed outlier: 3.591A pdb=" N LYS i 38 " --> pdb=" O HIS i 34 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS i 39 " --> pdb=" O GLU i 35 " (cutoff:3.500A) Processing helix chain 'i' and resid 66 through 69 No H-bonds generated for 'chain 'i' and resid 66 through 69' Processing helix chain 'i' and resid 80 through 83 No H-bonds generated for 'chain 'i' and resid 80 through 83' Processing helix chain 'j' and resid 22 through 24 No H-bonds generated for 'chain 'j' and resid 22 through 24' Processing helix chain 'j' and resid 26 through 44 removed outlier: 4.066A pdb=" N VAL j 34 " --> pdb=" O GLY j 30 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET j 35 " --> pdb=" O LEU j 31 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU j 40 " --> pdb=" O TRP j 36 " (cutoff:3.500A) Processing helix chain 'j' and resid 49 through 51 No H-bonds generated for 'chain 'j' and resid 49 through 51' Processing helix chain 'k' and resid 9 through 15 Processing helix chain 'k' and resid 17 through 19 No H-bonds generated for 'chain 'k' and resid 17 through 19' Processing helix chain 'k' and resid 22 through 24 No H-bonds generated for 'chain 'k' and resid 22 through 24' Processing helix chain 'k' and resid 33 through 48 removed outlier: 4.174A pdb=" N GLY k 36 " --> pdb=" O PRO k 33 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE k 37 " --> pdb=" O GLY k 34 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N VAL k 39 " --> pdb=" O GLY k 36 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL k 47 " --> pdb=" O VAL k 44 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLY k 48 " --> pdb=" O TYR k 45 " (cutoff:3.500A) Processing helix chain 'l' and resid 77 through 98 removed outlier: 3.528A pdb=" N GLY l 84 " --> pdb=" O ALA l 80 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE l 89 " --> pdb=" O GLY l 85 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL l 97 " --> pdb=" O GLY l 93 " (cutoff:3.500A) Processing helix chain 'l' and resid 113 through 117 Processing helix chain 'm' and resid 11 through 20 removed outlier: 3.614A pdb=" N ASP m 15 " --> pdb=" O LYS m 11 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N TRP m 16 " --> pdb=" O PHE m 12 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG m 20 " --> pdb=" O TRP m 16 " (cutoff:3.500A) Processing helix chain 'm' and resid 31 through 40 Processing helix chain 'm' and resid 43 through 63 Processing helix chain 'n' and resid 10 through 34 removed outlier: 3.795A pdb=" N ARG n 21 " --> pdb=" O LYS n 17 " (cutoff:3.500A) Processing helix chain 'n' and resid 41 through 53 Processing helix chain 'n' and resid 65 through 77 Processing helix chain 'o' and resid 15 through 19 Processing helix chain 'o' and resid 32 through 43 removed outlier: 3.976A pdb=" N ILE o 35 " --> pdb=" O HIS o 32 " (cutoff:3.500A) Proline residue: o 36 - end of helix removed outlier: 3.550A pdb=" N CYS o 40 " --> pdb=" O LEU o 37 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG o 41 " --> pdb=" O ASN o 38 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLN o 42 " --> pdb=" O LYS o 39 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA o 43 " --> pdb=" O CYS o 40 " (cutoff:3.500A) Processing helix chain 'o' and resid 55 through 83 removed outlier: 3.752A pdb=" N LYS o 75 " --> pdb=" O LEU o 71 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE o 76 " --> pdb=" O ALA o 72 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ALA o 81 " --> pdb=" O ARG o 77 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N LEU o 82 " --> pdb=" O GLU o 78 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ALA o 83 " --> pdb=" O GLU o 79 " (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 59 removed outlier: 3.836A pdb=" N VAL p 31 " --> pdb=" O PRO p 27 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLU p 32 " --> pdb=" O VAL p 28 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL p 38 " --> pdb=" O ARG p 34 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE p 43 " --> pdb=" O ARG p 39 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN p 44 " --> pdb=" O GLU p 40 " (cutoff:3.500A) Processing helix chain 'p' and resid 71 through 81 removed outlier: 3.888A pdb=" N GLN p 76 " --> pdb=" O HIS p 72 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP p 79 " --> pdb=" O GLN p 75 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER p 80 " --> pdb=" O GLN p 76 " (cutoff:3.500A) Processing helix chain 'q' and resid 83 through 85 No H-bonds generated for 'chain 'q' and resid 83 through 85' Processing helix chain 'q' and resid 91 through 97 removed outlier: 4.202A pdb=" N GLY q 95 " --> pdb=" O ALA q 91 " (cutoff:3.500A) removed outlier: 4.434A 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: 3.671A pdb=" N UNK u 24 " --> pdb=" O UNK u 20 " (cutoff:3.500A) Processing helix chain 'v' and resid 82 through 102 Processing helix chain 'x' and resid 211 through 214 No H-bonds generated for 'chain 'x' and resid 211 through 214' Processing helix chain 'x' and resid 216 through 234 removed outlier: 4.188A pdb=" N GLU x 234 " --> pdb=" O ASP x 230 " (cutoff:3.500A) Processing helix chain 'x' and resid 240 through 251 Processing helix chain 'y' and resid 3 through 30 Processing helix chain 'y' and resid 194 through 219 removed outlier: 4.242A pdb=" N GLN y 212 " --> pdb=" O ILE y 208 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N ILE y 213 " --> pdb=" O ASN y 209 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N HIS y 214 " --> pdb=" O LEU y 210 " (cutoff:3.500A) Processing helix chain 'y' and resid 222 through 234 removed outlier: 4.054A pdb=" N VAL y 227 " --> pdb=" O GLU y 223 " (cutoff:3.500A) Processing helix chain 'y' and resid 240 through 245 Processing helix chain 'y' and resid 254 through 256 No H-bonds generated for 'chain 'y' and resid 254 through 256' 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: 3.859A pdb=" N SER z 201 " --> pdb=" O ILE z 197 " (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: 7.143A pdb=" N CYS B 124 " --> pdb=" O MET B 87 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N PHE B 89 " --> pdb=" O CYS B 124 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ILE B 126 " --> pdb=" O PHE B 89 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N TRP B 151 " --> pdb=" O MET B 125 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N VAL B 127 " --> pdb=" O TRP B 151 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ILE B 153 " --> pdb=" O VAL B 127 " (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 59 removed outlier: 6.896A pdb=" N ASN C 76 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ILE C 59 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N VAL C 74 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE C 86 " --> pdb=" O LEU C 77 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 153 through 158 removed outlier: 3.907A pdb=" N ASP C 158 " --> pdb=" O ARG C 163 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ARG C 163 " --> pdb=" O ASP C 158 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 12 through 14 removed outlier: 3.968A pdb=" N LEU D 13 " --> pdb=" O LEU D 30 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU D 30 " --> pdb=" O LEU D 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'D' and resid 326 through 328 removed outlier: 3.501A pdb=" N GLY D 339 " --> pdb=" O ARG D 356 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 125 through 128 removed outlier: 3.576A pdb=" N SER E 165 " --> pdb=" O TYR E 125 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 180 through 184 removed outlier: 3.578A pdb=" N VAL E 183 " --> pdb=" O ASN E 196 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN E 196 " --> pdb=" O VAL E 183 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 263 through 267 removed outlier: 7.153A pdb=" N TYR F 135 " --> pdb=" O THR F 264 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N THR F 266 " --> pdb=" O TYR F 135 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL F 137 " --> pdb=" O THR F 266 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ALA F 176 " --> pdb=" O LEU F 136 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N VAL F 138 " --> pdb=" O ALA F 176 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N TYR F 178 " --> pdb=" O VAL F 138 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 339 through 341 removed outlier: 3.586A pdb=" N ILE F 378 " --> pdb=" O ILE F 341 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'G' and resid 74 through 77 Processing sheet with id= K, first strand: chain 'G' and resid 211 through 213 Processing sheet with id= L, first strand: chain 'G' and resid 288 through 293 removed outlier: 6.241A pdb=" N ARG G 308 " --> pdb=" O VAL G 312 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N VAL G 312 " --> pdb=" O ARG G 308 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 348 through 350 Processing sheet with id= N, first strand: chain 'G' and resid 514 through 517 Processing sheet with id= O, first strand: chain 'G' and resid 601 through 604 removed outlier: 6.039A pdb=" N VAL G 616 " --> pdb=" O TYR G 602 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N GLY G 604 " --> pdb=" O VAL G 616 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N LEU G 618 " --> pdb=" O GLY G 604 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'I' and resid 111 through 113 Processing sheet with id= Q, first strand: chain 'I' and resid 138 through 144 removed outlier: 6.501A pdb=" N GLU I 143 " --> pdb=" O THR I 152 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N THR I 152 " --> pdb=" O GLU I 143 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'L' and resid 57 through 59 removed outlier: 3.633A pdb=" N LEU L 59 " --> pdb=" O PHE L 76 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'M' and resid 71 through 73 Processing sheet with id= T, first strand: chain 'O' and resid 45 through 48 Processing sheet with id= U, first strand: chain 'O' and resid 131 through 133 Processing sheet with id= V, first strand: chain 'P' and resid 72 through 74 removed outlier: 6.443A pdb=" N ARG P 179 " --> pdb=" O VAL P 141 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N ASN P 143 " --> pdb=" O ARG P 179 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE P 181 " --> pdb=" O ASN P 143 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N THR P 215 " --> pdb=" O GLN P 182 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N SER P 184 " --> pdb=" O THR P 215 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N MET P 217 " --> pdb=" O SER P 184 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'Q' and resid 124 through 128 removed outlier: 4.590A pdb=" N SER Q 58 " --> pdb=" O LYS Q 128 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'Q' and resid 83 through 85 Processing sheet with id= Y, first strand: chain 'R' and resid 63 through 65 Processing sheet with id= Z, first strand: chain 'R' and resid 69 through 72 Processing sheet with id= AA, first strand: chain 'S' and resid 48 through 51 removed outlier: 6.382A pdb=" N LEU S 14 " --> pdb=" O LEU S 49 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ARG S 51 " --> pdb=" O LEU S 14 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ILE S 16 " --> pdb=" O ARG S 51 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'q' and resid 50 through 52 removed outlier: 3.537A pdb=" N THR q 50 " --> pdb=" O GLN q 63 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN q 63 " --> pdb=" O THR q 50 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N TYR q 61 " --> pdb=" O VAL q 52 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TRP q 75 " --> pdb=" O TYR q 62 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'x' and resid 62 through 64 removed outlier: 6.609A pdb=" N LEU x 84 " --> pdb=" O ILE x 63 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'x' and resid 109 through 111 removed outlier: 6.799A pdb=" N THR x 137 " --> pdb=" O THR x 110 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain 'x' and resid 197 through 199 removed outlier: 5.931A pdb=" N GLY x 199 " --> pdb=" O PHE x 205 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N PHE x 205 " --> pdb=" O GLY x 199 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'y' and resid 66 through 69 Processing sheet with id= AG, first strand: chain 'y' and resid 71 through 73 removed outlier: 6.338A pdb=" N ILE y 92 " --> pdb=" O GLN y 72 " (cutoff:3.500A) No H-bonds generated for sheet with id= AG Processing sheet with id= AH, first strand: chain 'y' and resid 105 through 107 Processing sheet with id= AI, first strand: chain 'y' and resid 179 through 181 removed outlier: 4.034A pdb=" N ARG y 190 " --> pdb=" O VAL y 180 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'z' and resid 68 through 73 removed outlier: 8.173A pdb=" N VAL z 89 " --> pdb=" O ASP z 70 " (cutoff:3.500A) removed outlier: 11.496A pdb=" N HIS z 72 " --> pdb=" O VAL z 89 " (cutoff:3.500A) removed outlier: 9.368A pdb=" N THR z 91 " --> pdb=" O HIS z 72 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'z' and resid 179 through 182 removed outlier: 4.276A pdb=" N ARG z 190 " --> pdb=" O VAL z 180 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLY z 182 " --> pdb=" O PHE z 188 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N PHE z 188 " --> pdb=" O GLY z 182 " (cutoff:3.500A) 2327 hydrogen bonds defined for protein. 6498 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: 16.68 Time building geometry restraints manager: 20.98 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: 25428 1.40 - 1.62: 36764 1.62 - 1.84: 655 1.84 - 2.06: 0 2.06 - 2.28: 80 Bond restraints: 62927 Sorted by residual: bond pdb=" C PRO r 83 " pdb=" N ILE r 84 " ideal model delta sigma weight residual 1.330 1.512 -0.182 1.23e-02 6.61e+03 2.19e+02 bond pdb=" C1 UQ9 H 401 " pdb=" C6 UQ9 H 401 " ideal model delta sigma weight residual 1.345 1.540 -0.195 2.00e-02 2.50e+03 9.52e+01 bond pdb=" C3 UQ9 H 401 " pdb=" C4 UQ9 H 401 " ideal model delta sigma weight residual 1.340 1.533 -0.193 2.00e-02 2.50e+03 9.34e+01 bond pdb=" C1 LMN d 101 " pdb=" O5 LMN d 101 " ideal model delta sigma weight residual 1.403 1.535 -0.132 2.00e-02 2.50e+03 4.33e+01 bond pdb=" CBS LMN d 101 " pdb=" CCM LMN d 101 " ideal model delta sigma weight residual 1.529 1.633 -0.104 2.00e-02 2.50e+03 2.70e+01 ... (remaining 62922 not shown) Histogram of bond angle deviations from ideal: 73.56 - 86.49: 76 86.49 - 99.41: 17 99.41 - 112.34: 32901 112.34 - 125.26: 51110 125.26 - 138.18: 1105 Bond angle restraints: 85209 Sorted by residual: angle pdb=" C PRO r 83 " pdb=" N ILE r 84 " pdb=" CA ILE r 84 " ideal model delta sigma weight residual 123.10 90.96 32.14 1.33e+00 5.65e-01 5.84e+02 angle pdb=" O PRO r 83 " pdb=" C PRO r 83 " pdb=" N ILE r 84 " ideal model delta sigma weight residual 123.00 138.18 -15.18 1.60e+00 3.91e-01 9.01e+01 angle pdb=" CA PRO r 83 " pdb=" C PRO r 83 " pdb=" N ILE r 84 " ideal model delta sigma weight residual 116.20 98.25 17.95 2.00e+00 2.50e-01 8.06e+01 angle pdb=" CA PRO r 83 " pdb=" N PRO r 83 " pdb=" CD PRO r 83 " ideal model delta sigma weight residual 112.00 99.51 12.49 1.40e+00 5.10e-01 7.96e+01 angle pdb=" O11 PTY N 502 " pdb=" P1 PTY N 502 " pdb=" O14 PTY N 502 " ideal model delta sigma weight residual 92.90 109.76 -16.86 3.00e+00 1.11e-01 3.16e+01 ... (remaining 85204 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.51: 36541 34.51 - 69.02: 884 69.02 - 103.53: 119 103.53 - 138.04: 22 138.04 - 172.55: 4 Dihedral angle restraints: 37570 sinusoidal: 15366 harmonic: 22204 Sorted by residual: 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 85.04 172.55 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" CA VAL P 329 " pdb=" C VAL P 329 " pdb=" N PRO P 330 " pdb=" CA PRO P 330 " ideal model delta harmonic sigma weight residual -180.00 -153.90 -26.10 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA GLU i 17 " pdb=" C GLU i 17 " pdb=" N ASN i 18 " pdb=" CA ASN i 18 " ideal model delta harmonic sigma weight residual 180.00 154.66 25.34 0 5.00e+00 4.00e-02 2.57e+01 ... (remaining 37567 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.974: 9448 0.974 - 1.949: 0 1.949 - 2.923: 0 2.923 - 3.897: 0 3.897 - 4.871: 1 Chirality restraints: 9449 Sorted by residual: chirality pdb=" C1 T7X z 302 " pdb=" C2 T7X z 302 " pdb=" C6 T7X z 302 " pdb=" O1 T7X z 302 " both_signs ideal model delta sigma weight residual False -2.42 2.45 -4.87 2.00e-01 2.50e+01 5.93e+02 chirality pdb=" C5 PGT N 501 " pdb=" C4 PGT N 501 " pdb=" C6 PGT N 501 " pdb=" O5 PGT N 501 " both_signs ideal model delta sigma weight residual False -2.30 -2.51 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA THR E 133 " pdb=" N THR E 133 " pdb=" C THR E 133 " pdb=" CB THR E 133 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 9446 not shown) Planarity restraints: 10724 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU L 500 " 0.059 5.00e-02 4.00e+02 8.93e-02 1.28e+01 pdb=" N PRO L 501 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO L 501 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO L 501 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO x 237 " -0.016 2.00e-02 2.50e+03 3.19e-02 1.01e+01 pdb=" C PRO x 237 " 0.055 2.00e-02 2.50e+03 pdb=" O PRO x 237 " -0.021 2.00e-02 2.50e+03 pdb=" N TYR x 238 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE P 312 " 0.045 5.00e-02 4.00e+02 6.78e-02 7.35e+00 pdb=" N PRO P 313 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO P 313 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO P 313 " 0.038 5.00e-02 4.00e+02 ... (remaining 10721 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 577 2.58 - 3.16: 52779 3.16 - 3.74: 97534 3.74 - 4.32: 132882 4.32 - 4.90: 222554 Nonbonded interactions: 506326 Sorted by model distance: nonbonded pdb=" NE2 HIS O 83 " pdb="FE FE O 200 " model vdw 2.002 2.340 nonbonded pdb=" O PHE A 77 " pdb=" OH TYR J 145 " model vdw 2.023 2.440 nonbonded pdb=" OH TYR x 148 " pdb=" O ASN z 103 " model vdw 2.098 2.440 nonbonded pdb=" OD1 ASP G 294 " pdb=" OG1 THR G 332 " model vdw 2.138 2.440 nonbonded pdb=" OG1 THR S 30 " pdb=" NZ LYS S 34 " model vdw 2.138 2.520 ... (remaining 506321 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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 40.850 Check model and map are aligned: 0.680 Set scattering table: 0.420 Process input model: 135.010 Find NCS groups from input model: 1.710 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 192.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 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 0.195 62927 Z= 0.287 Angle : 0.727 32.135 85209 Z= 0.353 Chirality : 0.066 4.871 9449 Planarity : 0.004 0.089 10724 Dihedral : 15.821 172.551 23287 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.26 % Favored : 92.72 % Rotamer: Outliers : 0.03 % Allowed : 0.28 % Favored : 99.69 % 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: -0.59 (0.10), residues: 7578 helix: 0.86 (0.09), residues: 3704 sheet: -1.37 (0.26), residues: 412 loop : -1.69 (0.11), residues: 3462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP L 563 HIS 0.011 0.001 HIS y 160 PHE 0.034 0.001 PHE D 135 TYR 0.038 0.001 TYR B 164 ARG 0.011 0.000 ARG P 152 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15156 Ramachandran restraints generated. 7578 Oldfield, 0 Emsley, 7578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15156 Ramachandran restraints generated. 7578 Oldfield, 0 Emsley, 7578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1354 residues out of total 6530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1352 time to evaluate : 5.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 113 ILE cc_start: 0.9194 (mm) cc_final: 0.8804 (mm) REVERT: D 56 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7637 (mt-10) REVERT: D 76 MET cc_start: 0.8407 (mtt) cc_final: 0.8074 (mtt) REVERT: D 78 GLN cc_start: 0.8283 (mm110) cc_final: 0.8007 (mm-40) REVERT: F 436 GLN cc_start: 0.8274 (tp-100) cc_final: 0.7778 (tp-100) REVERT: G 294 ASP cc_start: 0.7598 (t70) cc_final: 0.7300 (t70) REVERT: H 197 GLU cc_start: 0.8294 (tp30) cc_final: 0.8015 (tp30) REVERT: L 1 MET cc_start: 0.5735 (ttt) cc_final: 0.4744 (ttm) REVERT: M 39 LEU cc_start: 0.8804 (mt) cc_final: 0.8067 (tt) REVERT: M 84 LEU cc_start: 0.8470 (mt) cc_final: 0.8261 (mt) REVERT: M 243 GLU cc_start: 0.7148 (mt-10) cc_final: 0.6748 (mt-10) REVERT: M 349 PHE cc_start: 0.8324 (m-80) cc_final: 0.8074 (m-80) REVERT: N 121 ASP cc_start: 0.7141 (p0) cc_final: 0.6641 (p0) REVERT: O 120 ARG cc_start: 0.7798 (ttp-170) cc_final: 0.7372 (tpt-90) REVERT: O 135 CYS cc_start: 0.8426 (t) cc_final: 0.8225 (t) REVERT: T 43 ARG cc_start: 0.6838 (mpt-90) cc_final: 0.6277 (tpp80) REVERT: T 89 ILE cc_start: 0.6150 (tt) cc_final: 0.5945 (tt) REVERT: Z 45 SER cc_start: 0.7823 (p) cc_final: 0.7458 (p) REVERT: Z 93 GLU cc_start: 0.8046 (tp30) cc_final: 0.7793 (tp30) REVERT: Z 95 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7534 (mm-30) REVERT: a 14 ILE cc_start: 0.8332 (mm) cc_final: 0.7919 (mm) REVERT: d 14 LEU cc_start: 0.9307 (tp) cc_final: 0.8980 (tt) REVERT: i 20 GLU cc_start: 0.7371 (tm-30) cc_final: 0.7155 (tm-30) REVERT: i 27 ARG cc_start: 0.8089 (mtm110) cc_final: 0.7669 (mtm110) REVERT: l 108 THR cc_start: 0.5741 (p) cc_final: 0.5452 (p) outliers start: 2 outliers final: 0 residues processed: 1353 average time/residue: 0.5770 time to fit residues: 1321.2084 Evaluate side-chains 1112 residues out of total 6530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1112 time to evaluate : 5.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 750 random chunks: chunk 633 optimal weight: 4.9990 chunk 568 optimal weight: 0.9990 chunk 315 optimal weight: 0.6980 chunk 194 optimal weight: 0.8980 chunk 383 optimal weight: 3.9990 chunk 303 optimal weight: 0.9980 chunk 587 optimal weight: 0.9980 chunk 227 optimal weight: 0.6980 chunk 357 optimal weight: 3.9990 chunk 437 optimal weight: 4.9990 chunk 681 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 HIS D 10 ASN ** E 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 221 HIS ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 446 GLN G 716 GLN L 457 HIS ** M 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 464 ASN Q 65 GLN S 43 ASN ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 131 ASN ** X 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 126 ASN a 30 HIS e 52 GLN g 47 ASN ** g 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 8 ASN q 88 GLN y 101 GLN ** z 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.0911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 62927 Z= 0.219 Angle : 0.597 10.730 85209 Z= 0.295 Chirality : 0.043 0.223 9449 Planarity : 0.004 0.068 10724 Dihedral : 10.651 172.664 8941 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.46 % Favored : 92.52 % Rotamer: Outliers : 1.85 % Allowed : 10.09 % Favored : 88.06 % 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: -0.55 (0.10), residues: 7578 helix: 0.88 (0.09), residues: 3734 sheet: -1.32 (0.25), residues: 426 loop : -1.67 (0.11), residues: 3418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 563 HIS 0.010 0.001 HIS M 241 PHE 0.032 0.001 PHE V 60 TYR 0.027 0.001 TYR L 433 ARG 0.007 0.000 ARG d 74 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15156 Ramachandran restraints generated. 7578 Oldfield, 0 Emsley, 7578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15156 Ramachandran restraints generated. 7578 Oldfield, 0 Emsley, 7578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1338 residues out of total 6530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 1217 time to evaluate : 5.143 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 212 PHE cc_start: 0.7985 (t80) cc_final: 0.7705 (t80) REVERT: D 78 GLN cc_start: 0.8281 (mm110) cc_final: 0.7813 (mm-40) REVERT: D 377 ASP cc_start: 0.8357 (t0) cc_final: 0.8139 (t0) REVERT: F 436 GLN cc_start: 0.8330 (tp-100) cc_final: 0.8006 (tp-100) REVERT: G 178 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8311 (pm20) REVERT: G 294 ASP cc_start: 0.7695 (t70) cc_final: 0.7375 (t70) REVERT: G 600 VAL cc_start: 0.8829 (OUTLIER) cc_final: 0.8596 (p) REVERT: L 1 MET cc_start: 0.6179 (ttt) cc_final: 0.5505 (ttm) REVERT: L 506 LEU cc_start: 0.7782 (tp) cc_final: 0.7507 (mm) REVERT: M 39 LEU cc_start: 0.8691 (mt) cc_final: 0.8482 (tt) REVERT: M 241 HIS cc_start: 0.7377 (t-170) cc_final: 0.7080 (t70) REVERT: O 120 ARG cc_start: 0.7836 (ttp-170) cc_final: 0.7408 (tpt-90) REVERT: P 86 GLN cc_start: 0.8369 (tm-30) cc_final: 0.7862 (tm-30) REVERT: T 43 ARG cc_start: 0.6669 (mpt-90) cc_final: 0.6280 (tpp-160) REVERT: T 113 GLU cc_start: 0.6220 (OUTLIER) cc_final: 0.5563 (mp0) REVERT: U 72 LYS cc_start: 0.7187 (mmtt) cc_final: 0.6909 (mtpt) REVERT: U 91 MET cc_start: 0.7031 (mmt) cc_final: 0.6580 (mmp) REVERT: U 109 ILE cc_start: 0.7907 (pt) cc_final: 0.7522 (mt) REVERT: Z 45 SER cc_start: 0.8179 (p) cc_final: 0.7868 (m) REVERT: Z 93 GLU cc_start: 0.8155 (tp30) cc_final: 0.7812 (tp30) REVERT: Z 106 GLU cc_start: 0.8318 (mp0) cc_final: 0.7795 (mp0) REVERT: a 14 ILE cc_start: 0.8261 (mm) cc_final: 0.7816 (mm) REVERT: d 59 ASP cc_start: 0.7801 (m-30) cc_final: 0.7577 (m-30) REVERT: i 3 PHE cc_start: 0.6878 (t80) cc_final: 0.6251 (t80) REVERT: i 5 MET cc_start: 0.7887 (mmt) cc_final: 0.7667 (mmp) REVERT: i 7 PHE cc_start: 0.7415 (OUTLIER) cc_final: 0.7096 (m-80) REVERT: i 27 ARG cc_start: 0.8108 (mtm110) cc_final: 0.7769 (mtm110) REVERT: l 118 ARG cc_start: 0.7040 (tmm-80) cc_final: 0.6605 (ptt90) REVERT: n 94 LYS cc_start: 0.8639 (pttm) cc_final: 0.8373 (ptpp) REVERT: y 189 MET cc_start: 0.7631 (mpp) cc_final: 0.7388 (mtm) REVERT: y 224 GLN cc_start: 0.8558 (tm-30) cc_final: 0.8118 (tm-30) outliers start: 121 outliers final: 88 residues processed: 1267 average time/residue: 0.5726 time to fit residues: 1225.6653 Evaluate side-chains 1196 residues out of total 6530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 1104 time to evaluate : 5.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain D residue 10 ASN Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 434 MET Chi-restraints excluded: chain F residue 443 GLU Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 178 GLU Chi-restraints excluded: chain G residue 284 ASN Chi-restraints excluded: chain G residue 392 SER Chi-restraints excluded: chain G residue 446 GLN Chi-restraints excluded: chain G residue 583 LEU Chi-restraints excluded: chain G residue 600 VAL Chi-restraints excluded: chain H residue 70 ASN Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 217 ASN Chi-restraints excluded: chain H residue 232 GLU Chi-restraints excluded: chain I residue 81 SER Chi-restraints excluded: chain I residue 104 SER Chi-restraints excluded: chain I residue 196 ASP Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 125 THR Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain L residue 119 ILE Chi-restraints excluded: chain L residue 138 LEU Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain L residue 260 THR Chi-restraints excluded: chain L residue 361 ASP Chi-restraints excluded: chain L residue 452 ASP Chi-restraints excluded: chain L residue 485 MET Chi-restraints excluded: chain M residue 68 PHE Chi-restraints excluded: chain M residue 178 LEU Chi-restraints excluded: chain M residue 274 GLU Chi-restraints excluded: chain M residue 339 LEU Chi-restraints excluded: chain M residue 432 LEU Chi-restraints excluded: chain M residue 452 LEU Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain N residue 252 ASP Chi-restraints excluded: chain N residue 332 ILE Chi-restraints excluded: chain O residue 67 THR Chi-restraints excluded: chain O residue 113 ASP Chi-restraints excluded: chain O residue 140 THR Chi-restraints excluded: chain O residue 148 VAL Chi-restraints excluded: chain Q residue 143 ASN Chi-restraints excluded: chain R residue 87 ILE Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain S residue 57 GLN Chi-restraints excluded: chain T residue 42 SER Chi-restraints excluded: chain T residue 108 CYS Chi-restraints excluded: chain T residue 113 GLU Chi-restraints excluded: chain U residue 50 VAL Chi-restraints excluded: chain U residue 52 ASP Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain V residue 35 ASP Chi-restraints excluded: chain W residue 18 ASN Chi-restraints excluded: chain W residue 131 ASN Chi-restraints excluded: chain X residue 67 LEU Chi-restraints excluded: chain Z residue 54 SER Chi-restraints excluded: chain a residue 21 ILE Chi-restraints excluded: chain a residue 29 ILE Chi-restraints excluded: chain b residue 7 LEU Chi-restraints excluded: chain c residue 49 ILE Chi-restraints excluded: chain e residue 46 HIS Chi-restraints excluded: chain f residue 5 ILE Chi-restraints excluded: chain g residue 61 ASP Chi-restraints excluded: chain g residue 64 LEU Chi-restraints excluded: chain i residue 7 PHE Chi-restraints excluded: chain i residue 48 ILE Chi-restraints excluded: chain k residue 23 MET Chi-restraints excluded: chain m residue 42 ILE Chi-restraints excluded: chain n residue 48 LEU Chi-restraints excluded: chain p residue 65 ASN Chi-restraints excluded: chain x residue 88 VAL Chi-restraints excluded: chain x residue 89 THR Chi-restraints excluded: chain x residue 128 SER Chi-restraints excluded: chain x residue 138 LEU Chi-restraints excluded: chain y residue 124 ASP Chi-restraints excluded: chain y residue 240 GLU Chi-restraints excluded: chain z residue 124 ASP Chi-restraints excluded: chain z residue 153 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 750 random chunks: chunk 378 optimal weight: 0.6980 chunk 211 optimal weight: 0.6980 chunk 566 optimal weight: 6.9990 chunk 463 optimal weight: 5.9990 chunk 187 optimal weight: 2.9990 chunk 682 optimal weight: 1.9990 chunk 737 optimal weight: 3.9990 chunk 607 optimal weight: 2.9990 chunk 676 optimal weight: 9.9990 chunk 232 optimal weight: 0.6980 chunk 547 optimal weight: 0.5980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 446 GLN ** H 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 73 HIS L 457 HIS ** M 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 329 GLN M 409 GLN ** M 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 98 GLN ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 52 GLN ** g 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 88 GLN ** v 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 101 GLN ** z 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 62927 Z= 0.225 Angle : 0.581 10.844 85209 Z= 0.288 Chirality : 0.042 0.288 9449 Planarity : 0.004 0.067 10724 Dihedral : 9.810 172.808 8941 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.53 % Favored : 92.44 % Rotamer: Outliers : 2.43 % Allowed : 13.26 % Favored : 84.30 % 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: -0.52 (0.10), residues: 7578 helix: 0.87 (0.09), residues: 3752 sheet: -1.30 (0.25), residues: 447 loop : -1.64 (0.11), residues: 3379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP Q 146 HIS 0.006 0.001 HIS E 221 PHE 0.031 0.001 PHE D 11 TYR 0.025 0.001 TYR L 433 ARG 0.008 0.000 ARG d 74 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15156 Ramachandran restraints generated. 7578 Oldfield, 0 Emsley, 7578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15156 Ramachandran restraints generated. 7578 Oldfield, 0 Emsley, 7578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1324 residues out of total 6530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 1165 time to evaluate : 5.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 212 PHE cc_start: 0.8034 (t80) cc_final: 0.7806 (t80) REVERT: D 78 GLN cc_start: 0.8331 (mm110) cc_final: 0.8011 (mm-40) REVERT: D 377 ASP cc_start: 0.8350 (t0) cc_final: 0.8090 (t0) REVERT: F 360 MET cc_start: 0.8602 (mmm) cc_final: 0.8388 (mmp) REVERT: F 436 GLN cc_start: 0.8388 (tp-100) cc_final: 0.8027 (tp-100) REVERT: G 117 CYS cc_start: 0.9246 (OUTLIER) cc_final: 0.8870 (p) REVERT: G 294 ASP cc_start: 0.7748 (t70) cc_final: 0.7413 (t70) REVERT: G 600 VAL cc_start: 0.8889 (OUTLIER) cc_final: 0.8615 (p) REVERT: L 1 MET cc_start: 0.5978 (ttt) cc_final: 0.5456 (ttm) REVERT: L 261 MET cc_start: 0.6886 (tmm) cc_final: 0.5422 (ttm) REVERT: L 506 LEU cc_start: 0.7829 (tp) cc_final: 0.7553 (mm) REVERT: M 349 PHE cc_start: 0.8554 (m-80) cc_final: 0.7994 (m-80) REVERT: M 400 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.7266 (pm20) REVERT: O 120 ARG cc_start: 0.7876 (ttp-170) cc_final: 0.7440 (tpt-90) REVERT: P 86 GLN cc_start: 0.8377 (tm-30) cc_final: 0.7803 (tm-30) REVERT: Q 96 ASP cc_start: 0.8456 (t0) cc_final: 0.8251 (t70) REVERT: T 43 ARG cc_start: 0.6502 (mpt-90) cc_final: 0.6272 (tpp-160) REVERT: T 113 GLU cc_start: 0.6204 (OUTLIER) cc_final: 0.5493 (mp0) REVERT: U 72 LYS cc_start: 0.7256 (mmtt) cc_final: 0.6921 (mtpt) REVERT: U 91 MET cc_start: 0.6947 (mmt) cc_final: 0.6593 (mmp) REVERT: U 110 GLN cc_start: 0.6734 (mp10) cc_final: 0.6325 (mp10) REVERT: Z 45 SER cc_start: 0.8167 (p) cc_final: 0.7825 (m) REVERT: Z 93 GLU cc_start: 0.8154 (tp30) cc_final: 0.7856 (tp30) REVERT: Z 106 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7755 (mp0) REVERT: a 14 ILE cc_start: 0.8353 (mm) cc_final: 0.7892 (mm) REVERT: d 23 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8879 (tt) REVERT: d 59 ASP cc_start: 0.7834 (m-30) cc_final: 0.7578 (m-30) REVERT: g 89 ILE cc_start: 0.8465 (tp) cc_final: 0.8175 (tp) REVERT: i 3 PHE cc_start: 0.6755 (t80) cc_final: 0.6435 (t80) REVERT: i 5 MET cc_start: 0.7947 (mmt) cc_final: 0.7713 (mmp) REVERT: i 7 PHE cc_start: 0.7453 (OUTLIER) cc_final: 0.7136 (m-80) REVERT: i 27 ARG cc_start: 0.8090 (mtm110) cc_final: 0.7751 (mtm110) REVERT: l 118 ARG cc_start: 0.7047 (tmm-80) cc_final: 0.6606 (ptt90) REVERT: p 79 ASP cc_start: 0.7426 (p0) cc_final: 0.6238 (m-30) outliers start: 159 outliers final: 116 residues processed: 1239 average time/residue: 0.5750 time to fit residues: 1208.3229 Evaluate side-chains 1215 residues out of total 6530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 1092 time to evaluate : 5.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 196 ASN Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 434 MET Chi-restraints excluded: chain F residue 443 GLU Chi-restraints excluded: chain G residue 117 CYS Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 284 ASN Chi-restraints excluded: chain G residue 297 ASP Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain G residue 392 SER Chi-restraints excluded: chain G residue 583 LEU Chi-restraints excluded: chain G residue 600 VAL Chi-restraints excluded: chain H residue 70 ASN Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 217 ASN Chi-restraints excluded: chain H residue 232 GLU Chi-restraints excluded: chain I residue 81 SER Chi-restraints excluded: chain I residue 104 SER Chi-restraints excluded: chain I residue 196 ASP Chi-restraints excluded: chain J residue 4 SER Chi-restraints excluded: chain J residue 13 SER Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 125 THR Chi-restraints excluded: chain K residue 10 SER Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 119 ILE Chi-restraints excluded: chain L residue 138 LEU Chi-restraints excluded: chain L residue 260 THR Chi-restraints excluded: chain L residue 361 ASP Chi-restraints excluded: chain L residue 452 ASP Chi-restraints excluded: chain L residue 461 ILE Chi-restraints excluded: chain L residue 485 MET Chi-restraints excluded: chain L residue 550 THR Chi-restraints excluded: chain L residue 555 LEU Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain M residue 68 PHE Chi-restraints excluded: chain M residue 77 TYR Chi-restraints excluded: chain M residue 178 LEU Chi-restraints excluded: chain M residue 250 VAL Chi-restraints excluded: chain M residue 274 GLU Chi-restraints excluded: chain M residue 302 ILE Chi-restraints excluded: chain M residue 339 LEU Chi-restraints excluded: chain M residue 400 GLU Chi-restraints excluded: chain M residue 432 LEU Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain N residue 110 MET Chi-restraints excluded: chain N residue 252 ASP Chi-restraints excluded: chain N residue 281 PHE Chi-restraints excluded: chain N residue 332 ILE Chi-restraints excluded: chain N residue 464 ASN Chi-restraints excluded: chain O residue 67 THR Chi-restraints excluded: chain O residue 94 GLU Chi-restraints excluded: chain O residue 113 ASP Chi-restraints excluded: chain O residue 135 CYS Chi-restraints excluded: chain O residue 140 THR Chi-restraints excluded: chain Q residue 143 ASN Chi-restraints excluded: chain R residue 87 ILE Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 90 ASP Chi-restraints excluded: chain S residue 57 GLN Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain T residue 113 GLU Chi-restraints excluded: chain U residue 50 VAL Chi-restraints excluded: chain U residue 52 ASP Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain V residue 35 ASP Chi-restraints excluded: chain W residue 18 ASN Chi-restraints excluded: chain W residue 19 LEU Chi-restraints excluded: chain W residue 66 ASN Chi-restraints excluded: chain W residue 104 VAL Chi-restraints excluded: chain X residue 67 LEU Chi-restraints excluded: chain Z residue 54 SER Chi-restraints excluded: chain Z residue 106 GLU Chi-restraints excluded: chain a residue 21 ILE Chi-restraints excluded: chain a residue 29 ILE Chi-restraints excluded: chain b residue 7 LEU Chi-restraints excluded: chain c residue 49 ILE Chi-restraints excluded: chain d residue 23 LEU Chi-restraints excluded: chain e residue 46 HIS Chi-restraints excluded: chain f residue 2 ASN Chi-restraints excluded: chain f residue 5 ILE Chi-restraints excluded: chain f residue 38 SER Chi-restraints excluded: chain f residue 46 THR Chi-restraints excluded: chain g residue 61 ASP Chi-restraints excluded: chain g residue 64 LEU Chi-restraints excluded: chain i residue 7 PHE Chi-restraints excluded: chain i residue 13 LEU Chi-restraints excluded: chain i residue 48 ILE Chi-restraints excluded: chain k residue 23 MET Chi-restraints excluded: chain k residue 35 ILE Chi-restraints excluded: chain p residue 10 PHE Chi-restraints excluded: chain p residue 65 ASN Chi-restraints excluded: chain p residue 81 THR Chi-restraints excluded: chain x residue 88 VAL Chi-restraints excluded: chain x residue 89 THR Chi-restraints excluded: chain x residue 138 LEU Chi-restraints excluded: chain x residue 149 SER Chi-restraints excluded: chain x residue 215 LEU Chi-restraints excluded: chain y residue 124 ASP Chi-restraints excluded: chain y residue 240 GLU Chi-restraints excluded: chain z residue 13 PHE Chi-restraints excluded: chain z residue 124 ASP Chi-restraints excluded: chain z residue 153 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 750 random chunks: chunk 674 optimal weight: 9.9990 chunk 512 optimal weight: 10.0000 chunk 354 optimal weight: 0.0570 chunk 75 optimal weight: 1.9990 chunk 325 optimal weight: 9.9990 chunk 458 optimal weight: 0.9990 chunk 684 optimal weight: 3.9990 chunk 724 optimal weight: 0.4980 chunk 357 optimal weight: 2.9990 chunk 648 optimal weight: 2.9990 chunk 195 optimal weight: 10.0000 overall best weight: 1.3104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 4 GLN D 10 ASN D 62 GLN D 78 GLN ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 446 GLN ** H 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 132 ASN L 457 HIS ** M 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 329 GLN M 490 GLN O 98 GLN ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 45 ASN e 52 GLN ** g 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 88 GLN ** v 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 101 GLN ** z 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 62927 Z= 0.274 Angle : 0.591 10.819 85209 Z= 0.293 Chirality : 0.043 0.325 9449 Planarity : 0.004 0.066 10724 Dihedral : 9.354 173.436 8941 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.65 % Favored : 92.31 % Rotamer: Outliers : 3.20 % Allowed : 15.21 % Favored : 81.59 % 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: -0.57 (0.10), residues: 7578 helix: 0.82 (0.09), residues: 3775 sheet: -1.36 (0.25), residues: 446 loop : -1.66 (0.11), residues: 3357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 216 HIS 0.007 0.001 HIS M 241 PHE 0.025 0.001 PHE V 60 TYR 0.026 0.001 TYR a 33 ARG 0.008 0.000 ARG C 81 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15156 Ramachandran restraints generated. 7578 Oldfield, 0 Emsley, 7578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15156 Ramachandran restraints generated. 7578 Oldfield, 0 Emsley, 7578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1370 residues out of total 6530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 1161 time to evaluate : 5.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 MET cc_start: 0.8626 (mmp) cc_final: 0.8267 (mmp) REVERT: B 212 PHE cc_start: 0.8069 (t80) cc_final: 0.7787 (t80) REVERT: D 18 GLN cc_start: 0.3219 (OUTLIER) cc_final: 0.2633 (pm20) REVERT: D 78 GLN cc_start: 0.8336 (mm-40) cc_final: 0.8109 (mm-40) REVERT: D 377 ASP cc_start: 0.8417 (t0) cc_final: 0.8123 (t0) REVERT: F 360 MET cc_start: 0.8603 (mmm) cc_final: 0.8340 (mmp) REVERT: F 436 GLN cc_start: 0.8428 (tp-100) cc_final: 0.8054 (tp-100) REVERT: G 117 CYS cc_start: 0.9256 (OUTLIER) cc_final: 0.8911 (p) REVERT: G 178 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8333 (pm20) REVERT: G 294 ASP cc_start: 0.7859 (t70) cc_final: 0.7482 (t70) REVERT: G 600 VAL cc_start: 0.8953 (OUTLIER) cc_final: 0.8677 (p) REVERT: G 710 MET cc_start: 0.5744 (tpt) cc_final: 0.4965 (mmm) REVERT: L 1 MET cc_start: 0.5931 (ttt) cc_final: 0.5385 (ttm) REVERT: L 256 ILE cc_start: 0.8346 (OUTLIER) cc_final: 0.7935 (tt) REVERT: L 506 LEU cc_start: 0.7634 (tp) cc_final: 0.7404 (mm) REVERT: M 271 MET cc_start: 0.8887 (OUTLIER) cc_final: 0.8378 (mtm) REVERT: M 349 PHE cc_start: 0.8436 (m-80) cc_final: 0.7980 (m-80) REVERT: M 400 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.7239 (pm20) REVERT: N 117 GLN cc_start: 0.7027 (tp-100) cc_final: 0.6513 (tm-30) REVERT: N 292 GLN cc_start: 0.7755 (mp10) cc_final: 0.7523 (mt0) REVERT: N 497 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8784 (tp) REVERT: O 120 ARG cc_start: 0.7926 (ttp-170) cc_final: 0.7494 (tpt-90) REVERT: P 86 GLN cc_start: 0.8405 (tm-30) cc_final: 0.8099 (tm-30) REVERT: Q 96 ASP cc_start: 0.8440 (t0) cc_final: 0.7727 (t70) REVERT: T 113 GLU cc_start: 0.6311 (OUTLIER) cc_final: 0.5616 (mp0) REVERT: U 72 LYS cc_start: 0.7300 (mmtt) cc_final: 0.6934 (mtpt) REVERT: U 91 MET cc_start: 0.6883 (mmt) cc_final: 0.6637 (mmp) REVERT: U 107 ASP cc_start: 0.7401 (t0) cc_final: 0.7156 (t0) REVERT: U 109 ILE cc_start: 0.7853 (pt) cc_final: 0.7398 (mt) REVERT: Z 93 GLU cc_start: 0.8240 (tp30) cc_final: 0.7985 (tp30) REVERT: Z 106 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7774 (mp0) REVERT: a 14 ILE cc_start: 0.8381 (mm) cc_final: 0.7984 (mm) REVERT: d 59 ASP cc_start: 0.7877 (m-30) cc_final: 0.7634 (m-30) REVERT: g 89 ILE cc_start: 0.8489 (tp) cc_final: 0.8205 (tp) REVERT: i 3 PHE cc_start: 0.6607 (t80) cc_final: 0.6370 (t80) REVERT: i 7 PHE cc_start: 0.7467 (OUTLIER) cc_final: 0.7140 (m-80) REVERT: i 27 ARG cc_start: 0.8060 (mtm110) cc_final: 0.7681 (mtm110) REVERT: j 35 MET cc_start: 0.8643 (tmm) cc_final: 0.8097 (tmm) REVERT: l 107 PHE cc_start: 0.5455 (p90) cc_final: 0.5143 (p90) REVERT: l 118 ARG cc_start: 0.7086 (tmm-80) cc_final: 0.6763 (ptt90) REVERT: m 60 ASP cc_start: 0.7097 (m-30) cc_final: 0.6714 (t0) REVERT: p 75 GLN cc_start: 0.8759 (mt0) cc_final: 0.8434 (mt0) REVERT: p 79 ASP cc_start: 0.7483 (p0) cc_final: 0.6319 (m-30) REVERT: z 107 HIS cc_start: 0.7073 (m-70) cc_final: 0.6828 (m-70) outliers start: 209 outliers final: 156 residues processed: 1271 average time/residue: 0.5762 time to fit residues: 1245.3598 Evaluate side-chains 1255 residues out of total 6530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 1088 time to evaluate : 5.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain B residue 100 HIS Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain D residue 10 ASN Chi-restraints excluded: chain D residue 18 GLN Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 196 ASN Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 434 MET Chi-restraints excluded: chain F residue 443 GLU Chi-restraints excluded: chain G residue 117 CYS Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 178 GLU Chi-restraints excluded: chain G residue 257 THR Chi-restraints excluded: chain G residue 284 ASN Chi-restraints excluded: chain G residue 297 ASP Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain G residue 392 SER Chi-restraints excluded: chain G residue 446 GLN Chi-restraints excluded: chain G residue 583 LEU Chi-restraints excluded: chain G residue 600 VAL Chi-restraints excluded: chain H residue 70 ASN Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 217 ASN Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain I residue 81 SER Chi-restraints excluded: chain I residue 104 SER Chi-restraints excluded: chain I residue 196 ASP Chi-restraints excluded: chain I residue 217 SER Chi-restraints excluded: chain J residue 4 SER Chi-restraints excluded: chain J residue 13 SER Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 125 THR Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain K residue 10 SER Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 119 ILE Chi-restraints excluded: chain L residue 138 LEU Chi-restraints excluded: chain L residue 256 ILE Chi-restraints excluded: chain L residue 260 THR Chi-restraints excluded: chain L residue 281 THR Chi-restraints excluded: chain L residue 339 MET Chi-restraints excluded: chain L residue 361 ASP Chi-restraints excluded: chain L residue 399 TYR Chi-restraints excluded: chain L residue 452 ASP Chi-restraints excluded: chain L residue 461 ILE Chi-restraints excluded: chain L residue 550 THR Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain M residue 43 CYS Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain M residue 68 PHE Chi-restraints excluded: chain M residue 178 LEU Chi-restraints excluded: chain M residue 250 VAL Chi-restraints excluded: chain M residue 271 MET Chi-restraints excluded: chain M residue 302 ILE Chi-restraints excluded: chain M residue 339 LEU Chi-restraints excluded: chain M residue 346 SER Chi-restraints excluded: chain M residue 391 LEU Chi-restraints excluded: chain M residue 400 GLU Chi-restraints excluded: chain M residue 413 LEU Chi-restraints excluded: chain M residue 432 LEU Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain N residue 110 MET Chi-restraints excluded: chain N residue 252 ASP Chi-restraints excluded: chain N residue 281 PHE Chi-restraints excluded: chain N residue 332 ILE Chi-restraints excluded: chain N residue 464 ASN Chi-restraints excluded: chain N residue 497 LEU Chi-restraints excluded: chain O residue 59 ASP Chi-restraints excluded: chain O residue 67 THR Chi-restraints excluded: chain O residue 94 GLU Chi-restraints excluded: chain O residue 111 THR Chi-restraints excluded: chain O residue 113 ASP Chi-restraints excluded: chain O residue 135 CYS Chi-restraints excluded: chain O residue 140 THR Chi-restraints excluded: chain O residue 147 VAL Chi-restraints excluded: chain O residue 148 VAL Chi-restraints excluded: chain P residue 95 VAL Chi-restraints excluded: chain P residue 272 ASP Chi-restraints excluded: chain P residue 366 VAL Chi-restraints excluded: chain Q residue 88 LEU Chi-restraints excluded: chain Q residue 143 ASN Chi-restraints excluded: chain R residue 87 ILE Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 90 ASP Chi-restraints excluded: chain S residue 57 GLN Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain T residue 42 SER Chi-restraints excluded: chain T residue 113 GLU Chi-restraints excluded: chain U residue 50 VAL Chi-restraints excluded: chain U residue 52 ASP Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 87 VAL Chi-restraints excluded: chain V residue 35 ASP Chi-restraints excluded: chain W residue 18 ASN Chi-restraints excluded: chain W residue 19 LEU Chi-restraints excluded: chain W residue 66 ASN Chi-restraints excluded: chain W residue 104 VAL Chi-restraints excluded: chain X residue 67 LEU Chi-restraints excluded: chain Z residue 54 SER Chi-restraints excluded: chain Z residue 106 GLU Chi-restraints excluded: chain a residue 21 ILE Chi-restraints excluded: chain a residue 29 ILE Chi-restraints excluded: chain b residue 7 LEU Chi-restraints excluded: chain b residue 22 LEU Chi-restraints excluded: chain c residue 69 ILE Chi-restraints excluded: chain c residue 84 TYR Chi-restraints excluded: chain d residue 12 LEU Chi-restraints excluded: chain d residue 37 VAL Chi-restraints excluded: chain e residue 46 HIS Chi-restraints excluded: chain f residue 2 ASN Chi-restraints excluded: chain f residue 5 ILE Chi-restraints excluded: chain f residue 46 THR Chi-restraints excluded: chain g residue 64 LEU Chi-restraints excluded: chain i residue 7 PHE Chi-restraints excluded: chain i residue 13 LEU Chi-restraints excluded: chain j residue 12 TYR Chi-restraints excluded: chain k residue 23 MET Chi-restraints excluded: chain k residue 35 ILE Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain n residue 48 LEU Chi-restraints excluded: chain p residue 10 PHE Chi-restraints excluded: chain p residue 65 ASN Chi-restraints excluded: chain p residue 67 TYR Chi-restraints excluded: chain p residue 81 THR Chi-restraints excluded: chain x residue 88 VAL Chi-restraints excluded: chain x residue 89 THR Chi-restraints excluded: chain x residue 128 SER Chi-restraints excluded: chain x residue 138 LEU Chi-restraints excluded: chain x residue 149 SER Chi-restraints excluded: chain x residue 194 SER Chi-restraints excluded: chain x residue 215 LEU Chi-restraints excluded: chain y residue 85 LEU Chi-restraints excluded: chain y residue 124 ASP Chi-restraints excluded: chain y residue 240 GLU Chi-restraints excluded: chain z residue 13 PHE Chi-restraints excluded: chain z residue 124 ASP Chi-restraints excluded: chain z residue 138 THR Chi-restraints excluded: chain z residue 153 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 750 random chunks: chunk 603 optimal weight: 0.5980 chunk 411 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 539 optimal weight: 3.9990 chunk 299 optimal weight: 2.9990 chunk 618 optimal weight: 2.9990 chunk 501 optimal weight: 0.0970 chunk 0 optimal weight: 3.9990 chunk 370 optimal weight: 0.8980 chunk 650 optimal weight: 2.9990 chunk 182 optimal weight: 0.8980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 221 HIS ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 446 GLN G 686 ASN G 716 GLN ** H 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 457 HIS ** N 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 368 GLN O 98 GLN ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 52 GLN ** f 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 95 GLN m 8 ASN q 88 GLN ** v 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 101 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 62927 Z= 0.186 Angle : 0.567 14.582 85209 Z= 0.279 Chirality : 0.042 0.352 9449 Planarity : 0.004 0.065 10724 Dihedral : 8.930 177.049 8941 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.23 % Favored : 92.74 % Rotamer: Outliers : 3.22 % Allowed : 16.71 % Favored : 80.08 % 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: -0.48 (0.10), residues: 7578 helix: 0.91 (0.09), residues: 3763 sheet: -1.16 (0.25), residues: 436 loop : -1.64 (0.11), residues: 3379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 216 HIS 0.008 0.001 HIS M 241 PHE 0.042 0.001 PHE L 324 TYR 0.025 0.001 TYR P 257 ARG 0.009 0.000 ARG C 81 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15156 Ramachandran restraints generated. 7578 Oldfield, 0 Emsley, 7578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15156 Ramachandran restraints generated. 7578 Oldfield, 0 Emsley, 7578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1369 residues out of total 6530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 1159 time to evaluate : 5.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 212 PHE cc_start: 0.8056 (t80) cc_final: 0.7762 (t80) REVERT: D 78 GLN cc_start: 0.8283 (mm-40) cc_final: 0.8060 (mm110) REVERT: D 377 ASP cc_start: 0.8373 (t0) cc_final: 0.8063 (t0) REVERT: F 317 ILE cc_start: 0.7264 (OUTLIER) cc_final: 0.6894 (mm) REVERT: F 436 GLN cc_start: 0.8392 (tp-100) cc_final: 0.7998 (tp-100) REVERT: G 117 CYS cc_start: 0.9235 (OUTLIER) cc_final: 0.8859 (p) REVERT: G 178 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8295 (pm20) REVERT: G 294 ASP cc_start: 0.7777 (t70) cc_final: 0.7408 (t70) REVERT: G 600 VAL cc_start: 0.8896 (OUTLIER) cc_final: 0.8639 (p) REVERT: G 710 MET cc_start: 0.5731 (tpt) cc_final: 0.5331 (mmm) REVERT: I 69 ASN cc_start: 0.8484 (m-40) cc_final: 0.8095 (m-40) REVERT: J 51 MET cc_start: 0.7829 (mmp) cc_final: 0.7585 (mmt) REVERT: L 1 MET cc_start: 0.5770 (ttt) cc_final: 0.5327 (ttm) REVERT: L 381 MET cc_start: 0.6734 (mmt) cc_final: 0.6459 (mmp) REVERT: L 443 LEU cc_start: 0.6029 (OUTLIER) cc_final: 0.5726 (mt) REVERT: M 241 HIS cc_start: 0.7349 (t70) cc_final: 0.7066 (t70) REVERT: M 400 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.7201 (pm20) REVERT: N 77 THR cc_start: 0.8917 (OUTLIER) cc_final: 0.8582 (m) REVERT: N 159 PHE cc_start: 0.8724 (m-10) cc_final: 0.8445 (m-10) REVERT: N 292 GLN cc_start: 0.7709 (mp10) cc_final: 0.7422 (mt0) REVERT: N 497 LEU cc_start: 0.9032 (tp) cc_final: 0.8741 (tt) REVERT: O 120 ARG cc_start: 0.7910 (ttp-170) cc_final: 0.7483 (tpt-90) REVERT: P 86 GLN cc_start: 0.8338 (tm-30) cc_final: 0.8013 (tm-30) REVERT: Q 96 ASP cc_start: 0.8412 (t0) cc_final: 0.7802 (t70) REVERT: S 82 ILE cc_start: 0.7735 (mt) cc_final: 0.7505 (mp) REVERT: T 43 ARG cc_start: 0.6941 (tpp-160) cc_final: 0.6566 (tpp80) REVERT: T 113 GLU cc_start: 0.6331 (OUTLIER) cc_final: 0.5675 (mp0) REVERT: U 72 LYS cc_start: 0.7292 (mmtt) cc_final: 0.6921 (mtpt) REVERT: U 100 GLU cc_start: 0.7819 (tt0) cc_final: 0.7354 (mm-30) REVERT: U 108 LYS cc_start: 0.6754 (mmtm) cc_final: 0.6375 (mptt) REVERT: U 109 ILE cc_start: 0.7811 (pt) cc_final: 0.7181 (mt) REVERT: U 110 GLN cc_start: 0.6933 (mp10) cc_final: 0.6647 (mp10) REVERT: Z 49 MET cc_start: 0.7790 (mpp) cc_final: 0.7278 (mtm) REVERT: Z 93 GLU cc_start: 0.8179 (tp30) cc_final: 0.7920 (tp30) REVERT: Z 106 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7722 (mp0) REVERT: a 14 ILE cc_start: 0.8355 (mm) cc_final: 0.7962 (mm) REVERT: b 5 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6774 (pm20) REVERT: d 55 LYS cc_start: 0.8491 (tmtt) cc_final: 0.8205 (tmmt) REVERT: d 59 ASP cc_start: 0.7849 (m-30) cc_final: 0.7564 (m-30) REVERT: g 58 LYS cc_start: 0.7844 (tppt) cc_final: 0.6954 (tmmt) REVERT: g 89 ILE cc_start: 0.8467 (tp) cc_final: 0.8176 (tp) REVERT: i 3 PHE cc_start: 0.6558 (t80) cc_final: 0.6239 (t80) REVERT: i 5 MET cc_start: 0.7827 (mmp) cc_final: 0.7611 (mtt) REVERT: i 7 PHE cc_start: 0.7505 (OUTLIER) cc_final: 0.7235 (m-80) REVERT: i 27 ARG cc_start: 0.8063 (mtm110) cc_final: 0.7651 (mtm110) REVERT: j 35 MET cc_start: 0.8647 (tmm) cc_final: 0.8083 (tmm) REVERT: l 107 PHE cc_start: 0.5547 (p90) cc_final: 0.5205 (p90) REVERT: l 118 ARG cc_start: 0.7075 (tmm-80) cc_final: 0.6663 (ptt90) REVERT: p 79 ASP cc_start: 0.7376 (p0) cc_final: 0.6341 (m-30) REVERT: x 56 TYR cc_start: 0.8497 (OUTLIER) cc_final: 0.7549 (t80) outliers start: 210 outliers final: 142 residues processed: 1279 average time/residue: 0.5725 time to fit residues: 1247.4576 Evaluate side-chains 1250 residues out of total 6530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 1096 time to evaluate : 5.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain B residue 100 HIS Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain E residue 34 TYR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain G residue 117 CYS Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 178 GLU Chi-restraints excluded: chain G residue 257 THR Chi-restraints excluded: chain G residue 274 THR Chi-restraints excluded: chain G residue 284 ASN Chi-restraints excluded: chain G residue 297 ASP Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain G residue 392 SER Chi-restraints excluded: chain G residue 543 VAL Chi-restraints excluded: chain G residue 583 LEU Chi-restraints excluded: chain G residue 600 VAL Chi-restraints excluded: chain H residue 70 ASN Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 217 ASN Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain I residue 81 SER Chi-restraints excluded: chain I residue 104 SER Chi-restraints excluded: chain I residue 121 GLU Chi-restraints excluded: chain I residue 196 ASP Chi-restraints excluded: chain I residue 217 SER Chi-restraints excluded: chain J residue 4 SER Chi-restraints excluded: chain J residue 13 SER Chi-restraints excluded: chain K residue 10 SER Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 119 ILE Chi-restraints excluded: chain L residue 138 LEU Chi-restraints excluded: chain L residue 208 TRP Chi-restraints excluded: chain L residue 260 THR Chi-restraints excluded: chain L residue 338 LEU Chi-restraints excluded: chain L residue 378 THR Chi-restraints excluded: chain L residue 399 TYR Chi-restraints excluded: chain L residue 443 LEU Chi-restraints excluded: chain L residue 452 ASP Chi-restraints excluded: chain L residue 461 ILE Chi-restraints excluded: chain L residue 490 THR Chi-restraints excluded: chain L residue 550 THR Chi-restraints excluded: chain L residue 555 LEU Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain M residue 43 CYS Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain M residue 68 PHE Chi-restraints excluded: chain M residue 77 TYR Chi-restraints excluded: chain M residue 147 GLU Chi-restraints excluded: chain M residue 178 LEU Chi-restraints excluded: chain M residue 250 VAL Chi-restraints excluded: chain M residue 302 ILE Chi-restraints excluded: chain M residue 339 LEU Chi-restraints excluded: chain M residue 346 SER Chi-restraints excluded: chain M residue 391 LEU Chi-restraints excluded: chain M residue 400 GLU Chi-restraints excluded: chain M residue 413 LEU Chi-restraints excluded: chain M residue 432 LEU Chi-restraints excluded: chain N residue 77 THR Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain N residue 110 MET Chi-restraints excluded: chain N residue 252 ASP Chi-restraints excluded: chain N residue 281 PHE Chi-restraints excluded: chain N residue 332 ILE Chi-restraints excluded: chain N residue 464 ASN Chi-restraints excluded: chain O residue 59 ASP Chi-restraints excluded: chain O residue 67 THR Chi-restraints excluded: chain O residue 94 GLU Chi-restraints excluded: chain O residue 111 THR Chi-restraints excluded: chain O residue 113 ASP Chi-restraints excluded: chain O residue 135 CYS Chi-restraints excluded: chain O residue 148 VAL Chi-restraints excluded: chain P residue 95 VAL Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain Q residue 88 LEU Chi-restraints excluded: chain Q residue 143 ASN Chi-restraints excluded: chain R residue 87 ILE Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain S residue 34 LYS Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 57 GLN Chi-restraints excluded: chain S residue 60 MET Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain T residue 42 SER Chi-restraints excluded: chain T residue 113 GLU Chi-restraints excluded: chain U residue 50 VAL Chi-restraints excluded: chain U residue 52 ASP Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 87 VAL Chi-restraints excluded: chain V residue 35 ASP Chi-restraints excluded: chain W residue 18 ASN Chi-restraints excluded: chain W residue 19 LEU Chi-restraints excluded: chain W residue 104 VAL Chi-restraints excluded: chain X residue 67 LEU Chi-restraints excluded: chain Z residue 54 SER Chi-restraints excluded: chain Z residue 106 GLU Chi-restraints excluded: chain a residue 21 ILE Chi-restraints excluded: chain a residue 29 ILE Chi-restraints excluded: chain b residue 5 GLU Chi-restraints excluded: chain b residue 7 LEU Chi-restraints excluded: chain d residue 37 VAL Chi-restraints excluded: chain e residue 37 LEU Chi-restraints excluded: chain e residue 46 HIS Chi-restraints excluded: chain f residue 5 ILE Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain f residue 38 SER Chi-restraints excluded: chain f residue 80 ASN Chi-restraints excluded: chain i residue 7 PHE Chi-restraints excluded: chain i residue 13 LEU Chi-restraints excluded: chain i residue 48 ILE Chi-restraints excluded: chain j residue 12 TYR Chi-restraints excluded: chain k residue 23 MET Chi-restraints excluded: chain k residue 35 ILE Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain n residue 48 LEU Chi-restraints excluded: chain p residue 10 PHE Chi-restraints excluded: chain p residue 65 ASN Chi-restraints excluded: chain p residue 67 TYR Chi-restraints excluded: chain p residue 81 THR Chi-restraints excluded: chain x residue 56 TYR Chi-restraints excluded: chain x residue 74 VAL Chi-restraints excluded: chain x residue 88 VAL Chi-restraints excluded: chain x residue 89 THR Chi-restraints excluded: chain x residue 138 LEU Chi-restraints excluded: chain x residue 149 SER Chi-restraints excluded: chain y residue 124 ASP Chi-restraints excluded: chain y residue 240 GLU Chi-restraints excluded: chain z residue 13 PHE Chi-restraints excluded: chain z residue 48 VAL Chi-restraints excluded: chain z residue 124 ASP Chi-restraints excluded: chain z residue 153 ASP Chi-restraints excluded: chain z residue 169 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 750 random chunks: chunk 243 optimal weight: 0.6980 chunk 652 optimal weight: 5.9990 chunk 143 optimal weight: 7.9990 chunk 425 optimal weight: 2.9990 chunk 178 optimal weight: 3.9990 chunk 725 optimal weight: 3.9990 chunk 602 optimal weight: 0.9980 chunk 335 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 240 optimal weight: 0.6980 chunk 380 optimal weight: 0.7980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 10 ASN ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 457 HIS M 490 GLN ** N 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 368 GLN O 98 GLN ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 66 GLN Z 126 ASN e 52 GLN ** f 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 88 GLN v 83 ASN ** x 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 101 GLN ** z 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 62927 Z= 0.269 Angle : 0.600 14.739 85209 Z= 0.296 Chirality : 0.043 0.350 9449 Planarity : 0.004 0.069 10724 Dihedral : 8.690 173.450 8941 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.08 % Favored : 91.88 % Rotamer: Outliers : 3.77 % Allowed : 17.47 % Favored : 78.76 % 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: -0.54 (0.10), residues: 7578 helix: 0.86 (0.09), residues: 3775 sheet: -1.28 (0.25), residues: 452 loop : -1.67 (0.11), residues: 3351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 216 HIS 0.010 0.001 HIS M 241 PHE 0.033 0.002 PHE L 324 TYR 0.024 0.001 TYR P 257 ARG 0.008 0.000 ARG C 81 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15156 Ramachandran restraints generated. 7578 Oldfield, 0 Emsley, 7578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15156 Ramachandran restraints generated. 7578 Oldfield, 0 Emsley, 7578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1381 residues out of total 6530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 246 poor density : 1135 time to evaluate : 5.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 212 PHE cc_start: 0.8075 (t80) cc_final: 0.7800 (t80) REVERT: D 377 ASP cc_start: 0.8439 (t0) cc_final: 0.8083 (t0) REVERT: F 436 GLN cc_start: 0.8412 (tp-100) cc_final: 0.8039 (tp-100) REVERT: G 117 CYS cc_start: 0.9284 (OUTLIER) cc_final: 0.8926 (p) REVERT: G 178 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8287 (pm20) REVERT: G 294 ASP cc_start: 0.7937 (t70) cc_final: 0.7603 (t70) REVERT: G 600 VAL cc_start: 0.8934 (OUTLIER) cc_final: 0.8659 (p) REVERT: G 710 MET cc_start: 0.5853 (tpt) cc_final: 0.5474 (mmm) REVERT: H 211 GLU cc_start: 0.5059 (OUTLIER) cc_final: 0.4749 (mp0) REVERT: I 69 ASN cc_start: 0.8492 (m-40) cc_final: 0.8125 (m-40) REVERT: L 1 MET cc_start: 0.5897 (ttt) cc_final: 0.5440 (ttm) REVERT: L 288 PHE cc_start: 0.8031 (m-10) cc_final: 0.7778 (m-80) REVERT: L 306 ASP cc_start: 0.7681 (t70) cc_final: 0.7470 (t0) REVERT: L 368 MET cc_start: 0.5291 (tmm) cc_final: 0.5028 (tpt) REVERT: L 381 MET cc_start: 0.6712 (mmt) cc_final: 0.6374 (mmp) REVERT: L 506 LEU cc_start: 0.7822 (tp) cc_final: 0.7506 (mm) REVERT: M 259 PHE cc_start: 0.8737 (OUTLIER) cc_final: 0.7822 (m-10) REVERT: M 400 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7143 (pm20) REVERT: N 20 PHE cc_start: 0.8647 (OUTLIER) cc_final: 0.7235 (t80) REVERT: N 77 THR cc_start: 0.8957 (OUTLIER) cc_final: 0.8649 (m) REVERT: N 117 GLN cc_start: 0.7021 (tm-30) cc_final: 0.6766 (tm-30) REVERT: N 159 PHE cc_start: 0.8767 (m-10) cc_final: 0.8477 (m-10) REVERT: N 292 GLN cc_start: 0.7745 (mp10) cc_final: 0.7425 (mt0) REVERT: O 120 ARG cc_start: 0.7949 (ttp-170) cc_final: 0.7519 (tpt-90) REVERT: P 86 GLN cc_start: 0.8372 (tm-30) cc_final: 0.8056 (tm-30) REVERT: Q 96 ASP cc_start: 0.8380 (t0) cc_final: 0.7830 (t70) REVERT: S 53 CYS cc_start: 0.7353 (m) cc_final: 0.6892 (m) REVERT: T 43 ARG cc_start: 0.7095 (tpp-160) cc_final: 0.6682 (tpp-160) REVERT: T 59 LYS cc_start: 0.4544 (mmmm) cc_final: 0.4057 (mttt) REVERT: T 113 GLU cc_start: 0.6416 (OUTLIER) cc_final: 0.5715 (mp0) REVERT: U 100 GLU cc_start: 0.7819 (tt0) cc_final: 0.7403 (mm-30) REVERT: U 105 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7550 (mm-30) REVERT: U 108 LYS cc_start: 0.6734 (mmtm) cc_final: 0.6353 (mptt) REVERT: U 110 GLN cc_start: 0.6812 (mp10) cc_final: 0.6589 (mp10) REVERT: Z 93 GLU cc_start: 0.8234 (tp30) cc_final: 0.8000 (tp30) REVERT: Z 106 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7749 (mp0) REVERT: a 43 ASP cc_start: 0.7221 (p0) cc_final: 0.7015 (p0) REVERT: c 72 GLN cc_start: 0.7304 (OUTLIER) cc_final: 0.6922 (mp10) REVERT: d 55 LYS cc_start: 0.8533 (tmtt) cc_final: 0.8231 (tmmt) REVERT: d 59 ASP cc_start: 0.7891 (m-30) cc_final: 0.7621 (m-30) REVERT: g 89 ILE cc_start: 0.8520 (tp) cc_final: 0.8237 (tp) REVERT: i 3 PHE cc_start: 0.6517 (t80) cc_final: 0.6144 (t80) REVERT: i 7 PHE cc_start: 0.7518 (OUTLIER) cc_final: 0.7236 (m-80) REVERT: i 27 ARG cc_start: 0.8100 (mtm110) cc_final: 0.7725 (mtm110) REVERT: j 35 MET cc_start: 0.8672 (tmm) cc_final: 0.8156 (tmm) REVERT: l 107 PHE cc_start: 0.5673 (p90) cc_final: 0.5282 (p90) REVERT: l 118 ARG cc_start: 0.7108 (tmm-80) cc_final: 0.6846 (ptt90) REVERT: m 60 ASP cc_start: 0.7111 (m-30) cc_final: 0.6727 (t0) REVERT: p 75 GLN cc_start: 0.8725 (mt0) cc_final: 0.8392 (mt0) REVERT: p 79 ASP cc_start: 0.7477 (p0) cc_final: 0.6445 (m-30) REVERT: x 56 TYR cc_start: 0.8711 (OUTLIER) cc_final: 0.7852 (t80) REVERT: y 245 MET cc_start: 0.8754 (tmm) cc_final: 0.8440 (ttt) REVERT: z 100 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8587 (mm) outliers start: 246 outliers final: 177 residues processed: 1277 average time/residue: 0.5687 time to fit residues: 1234.2737 Evaluate side-chains 1280 residues out of total 6530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 1089 time to evaluate : 5.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain B residue 100 HIS Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain E residue 34 TYR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 196 ASN Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 434 MET Chi-restraints excluded: chain F residue 443 GLU Chi-restraints excluded: chain G residue 117 CYS Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 178 GLU Chi-restraints excluded: chain G residue 257 THR Chi-restraints excluded: chain G residue 274 THR Chi-restraints excluded: chain G residue 284 ASN Chi-restraints excluded: chain G residue 297 ASP Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain G residue 392 SER Chi-restraints excluded: chain G residue 543 VAL Chi-restraints excluded: chain G residue 583 LEU Chi-restraints excluded: chain G residue 600 VAL Chi-restraints excluded: chain H residue 70 ASN Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 211 GLU Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 217 ASN Chi-restraints excluded: chain I residue 81 SER Chi-restraints excluded: chain I residue 104 SER Chi-restraints excluded: chain I residue 121 GLU Chi-restraints excluded: chain I residue 196 ASP Chi-restraints excluded: chain I residue 217 SER Chi-restraints excluded: chain J residue 4 SER Chi-restraints excluded: chain J residue 13 SER Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 125 THR Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain K residue 10 SER Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 138 LEU Chi-restraints excluded: chain L residue 208 TRP Chi-restraints excluded: chain L residue 260 THR Chi-restraints excluded: chain L residue 378 THR Chi-restraints excluded: chain L residue 399 TYR Chi-restraints excluded: chain L residue 452 ASP Chi-restraints excluded: chain L residue 463 MET Chi-restraints excluded: chain L residue 490 THR Chi-restraints excluded: chain L residue 550 THR Chi-restraints excluded: chain L residue 555 LEU Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain M residue 43 CYS Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 68 PHE Chi-restraints excluded: chain M residue 178 LEU Chi-restraints excluded: chain M residue 190 LEU Chi-restraints excluded: chain M residue 250 VAL Chi-restraints excluded: chain M residue 259 PHE Chi-restraints excluded: chain M residue 271 MET Chi-restraints excluded: chain M residue 302 ILE Chi-restraints excluded: chain M residue 339 LEU Chi-restraints excluded: chain M residue 346 SER Chi-restraints excluded: chain M residue 391 LEU Chi-restraints excluded: chain M residue 400 GLU Chi-restraints excluded: chain M residue 413 LEU Chi-restraints excluded: chain M residue 432 LEU Chi-restraints excluded: chain N residue 20 PHE Chi-restraints excluded: chain N residue 77 THR Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain N residue 110 MET Chi-restraints excluded: chain N residue 112 PHE Chi-restraints excluded: chain N residue 252 ASP Chi-restraints excluded: chain N residue 281 PHE Chi-restraints excluded: chain N residue 282 ILE Chi-restraints excluded: chain N residue 332 ILE Chi-restraints excluded: chain N residue 356 THR Chi-restraints excluded: chain N residue 464 ASN Chi-restraints excluded: chain O residue 59 ASP Chi-restraints excluded: chain O residue 67 THR Chi-restraints excluded: chain O residue 94 GLU Chi-restraints excluded: chain O residue 111 THR Chi-restraints excluded: chain O residue 113 ASP Chi-restraints excluded: chain O residue 135 CYS Chi-restraints excluded: chain O residue 140 THR Chi-restraints excluded: chain O residue 147 VAL Chi-restraints excluded: chain O residue 148 VAL Chi-restraints excluded: chain P residue 95 VAL Chi-restraints excluded: chain P residue 160 ASN Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain P residue 272 ASP Chi-restraints excluded: chain P residue 366 VAL Chi-restraints excluded: chain Q residue 88 LEU Chi-restraints excluded: chain Q residue 143 ASN Chi-restraints excluded: chain R residue 87 ILE Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 90 ASP Chi-restraints excluded: chain S residue 34 LYS Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 57 GLN Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain T residue 42 SER Chi-restraints excluded: chain T residue 113 GLU Chi-restraints excluded: chain U residue 50 VAL Chi-restraints excluded: chain U residue 52 ASP Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain V residue 35 ASP Chi-restraints excluded: chain W residue 18 ASN Chi-restraints excluded: chain W residue 66 ASN Chi-restraints excluded: chain W residue 104 VAL Chi-restraints excluded: chain X residue 67 LEU Chi-restraints excluded: chain Z residue 54 SER Chi-restraints excluded: chain Z residue 106 GLU Chi-restraints excluded: chain a residue 7 GLU Chi-restraints excluded: chain a residue 21 ILE Chi-restraints excluded: chain a residue 29 ILE Chi-restraints excluded: chain b residue 7 LEU Chi-restraints excluded: chain b residue 22 LEU Chi-restraints excluded: chain c residue 69 ILE Chi-restraints excluded: chain c residue 72 GLN Chi-restraints excluded: chain d residue 37 VAL Chi-restraints excluded: chain e residue 37 LEU Chi-restraints excluded: chain e residue 46 HIS Chi-restraints excluded: chain f residue 2 ASN Chi-restraints excluded: chain f residue 5 ILE Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain f residue 38 SER Chi-restraints excluded: chain f residue 46 THR Chi-restraints excluded: chain i residue 7 PHE Chi-restraints excluded: chain i residue 13 LEU Chi-restraints excluded: chain j residue 12 TYR Chi-restraints excluded: chain k residue 23 MET Chi-restraints excluded: chain k residue 35 ILE Chi-restraints excluded: chain l residue 105 VAL Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain m residue 30 THR Chi-restraints excluded: chain n residue 48 LEU Chi-restraints excluded: chain p residue 10 PHE Chi-restraints excluded: chain p residue 65 ASN Chi-restraints excluded: chain p residue 67 TYR Chi-restraints excluded: chain p residue 81 THR Chi-restraints excluded: chain x residue 56 TYR Chi-restraints excluded: chain x residue 72 VAL Chi-restraints excluded: chain x residue 74 VAL Chi-restraints excluded: chain x residue 88 VAL Chi-restraints excluded: chain x residue 89 THR Chi-restraints excluded: chain x residue 128 SER Chi-restraints excluded: chain x residue 137 THR Chi-restraints excluded: chain x residue 138 LEU Chi-restraints excluded: chain x residue 149 SER Chi-restraints excluded: chain x residue 194 SER Chi-restraints excluded: chain y residue 85 LEU Chi-restraints excluded: chain y residue 124 ASP Chi-restraints excluded: chain y residue 152 LEU Chi-restraints excluded: chain y residue 240 GLU Chi-restraints excluded: chain z residue 13 PHE Chi-restraints excluded: chain z residue 48 VAL Chi-restraints excluded: chain z residue 100 ILE Chi-restraints excluded: chain z residue 124 ASP Chi-restraints excluded: chain z residue 138 THR Chi-restraints excluded: chain z residue 153 ASP Chi-restraints excluded: chain z residue 169 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 750 random chunks: chunk 699 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 413 optimal weight: 0.8980 chunk 529 optimal weight: 0.9980 chunk 410 optimal weight: 6.9990 chunk 610 optimal weight: 3.9990 chunk 405 optimal weight: 0.8980 chunk 722 optimal weight: 1.9990 chunk 452 optimal weight: 1.9990 chunk 440 optimal weight: 2.9990 chunk 333 optimal weight: 5.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 10 ASN F 191 ASN G 446 GLN G 686 ASN G 716 GLN L 457 HIS ** N 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 368 GLN O 98 GLN R 109 HIS ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 66 GLN Z 126 ASN e 52 GLN ** f 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 26 ASN ** x 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 165 HIS y 101 GLN z 107 HIS ** z 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 62927 Z= 0.219 Angle : 0.586 15.633 85209 Z= 0.289 Chirality : 0.042 0.295 9449 Planarity : 0.004 0.067 10724 Dihedral : 8.464 172.959 8941 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.44 % Favored : 92.53 % Rotamer: Outliers : 3.69 % Allowed : 18.44 % Favored : 77.87 % 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: -0.49 (0.10), residues: 7578 helix: 0.90 (0.09), residues: 3775 sheet: -1.28 (0.25), residues: 440 loop : -1.64 (0.11), residues: 3363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP k 18 HIS 0.012 0.001 HIS M 241 PHE 0.037 0.001 PHE L 324 TYR 0.024 0.001 TYR L 433 ARG 0.012 0.000 ARG k 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15156 Ramachandran restraints generated. 7578 Oldfield, 0 Emsley, 7578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15156 Ramachandran restraints generated. 7578 Oldfield, 0 Emsley, 7578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1377 residues out of total 6530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 1136 time to evaluate : 5.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 212 PHE cc_start: 0.8106 (t80) cc_final: 0.7887 (t80) REVERT: C 170 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7616 (tt0) REVERT: D 377 ASP cc_start: 0.8472 (t0) cc_final: 0.8088 (t0) REVERT: F 436 GLN cc_start: 0.8385 (tp-100) cc_final: 0.7988 (tp-100) REVERT: G 117 CYS cc_start: 0.9262 (OUTLIER) cc_final: 0.8908 (p) REVERT: G 178 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8292 (pm20) REVERT: G 294 ASP cc_start: 0.7902 (t70) cc_final: 0.7568 (t70) REVERT: G 600 VAL cc_start: 0.8911 (OUTLIER) cc_final: 0.8652 (p) REVERT: I 66 ARG cc_start: 0.8018 (ttm110) cc_final: 0.7670 (ttp-110) REVERT: I 69 ASN cc_start: 0.8448 (m-40) cc_final: 0.8107 (m-40) REVERT: J 51 MET cc_start: 0.7856 (mmp) cc_final: 0.7561 (mmt) REVERT: L 1 MET cc_start: 0.5892 (ttt) cc_final: 0.5410 (ttm) REVERT: L 288 PHE cc_start: 0.8031 (m-10) cc_final: 0.7806 (m-80) REVERT: L 381 MET cc_start: 0.6689 (mmt) cc_final: 0.6360 (mmp) REVERT: L 506 LEU cc_start: 0.7813 (tp) cc_final: 0.7494 (mm) REVERT: M 400 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.7111 (pm20) REVERT: N 20 PHE cc_start: 0.8638 (OUTLIER) cc_final: 0.7019 (t80) REVERT: N 77 THR cc_start: 0.8915 (OUTLIER) cc_final: 0.8584 (m) REVERT: N 159 PHE cc_start: 0.8752 (m-10) cc_final: 0.8458 (m-10) REVERT: O 120 ARG cc_start: 0.7981 (ttp-170) cc_final: 0.7519 (tpt-90) REVERT: P 86 GLN cc_start: 0.8336 (tm-30) cc_final: 0.7988 (tm-30) REVERT: Q 38 GLU cc_start: 0.8206 (pm20) cc_final: 0.7775 (pm20) REVERT: Q 96 ASP cc_start: 0.8376 (t0) cc_final: 0.7863 (t70) REVERT: S 53 CYS cc_start: 0.7337 (m) cc_final: 0.6868 (m) REVERT: S 82 ILE cc_start: 0.7712 (mt) cc_final: 0.7416 (mp) REVERT: T 43 ARG cc_start: 0.7179 (tpp-160) cc_final: 0.6910 (tpp-160) REVERT: T 59 LYS cc_start: 0.4421 (mmmm) cc_final: 0.4219 (mmmm) REVERT: T 113 GLU cc_start: 0.6385 (OUTLIER) cc_final: 0.5731 (mp0) REVERT: U 72 LYS cc_start: 0.7210 (mmtt) cc_final: 0.6847 (mtpt) REVERT: U 100 GLU cc_start: 0.7805 (tt0) cc_final: 0.7397 (mm-30) REVERT: W 79 ILE cc_start: 0.8990 (OUTLIER) cc_final: 0.8640 (mm) REVERT: Z 93 GLU cc_start: 0.8191 (tp30) cc_final: 0.7958 (tp30) REVERT: Z 106 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7735 (mp0) REVERT: a 14 ILE cc_start: 0.8450 (mm) cc_final: 0.8217 (mm) REVERT: c 72 GLN cc_start: 0.7207 (OUTLIER) cc_final: 0.6917 (mp10) REVERT: d 55 LYS cc_start: 0.8508 (tmtt) cc_final: 0.8275 (tmmt) REVERT: d 59 ASP cc_start: 0.7838 (m-30) cc_final: 0.7580 (m-30) REVERT: g 89 ILE cc_start: 0.8474 (tp) cc_final: 0.8179 (tp) REVERT: i 7 PHE cc_start: 0.7550 (OUTLIER) cc_final: 0.7304 (m-80) REVERT: i 27 ARG cc_start: 0.8138 (mtm110) cc_final: 0.7780 (mtm110) REVERT: j 35 MET cc_start: 0.8669 (tmm) cc_final: 0.8182 (tmm) REVERT: j 41 TYR cc_start: 0.5917 (t80) cc_final: 0.5599 (t80) REVERT: l 107 PHE cc_start: 0.5779 (p90) cc_final: 0.5473 (p90) REVERT: l 118 ARG cc_start: 0.7089 (tmm-80) cc_final: 0.6714 (ptt90) REVERT: m 60 ASP cc_start: 0.7111 (m-30) cc_final: 0.6733 (t0) REVERT: n 94 LYS cc_start: 0.8700 (ptpp) cc_final: 0.8463 (ptpp) REVERT: p 75 GLN cc_start: 0.8767 (mt0) cc_final: 0.8442 (mt0) REVERT: p 79 ASP cc_start: 0.7442 (p0) cc_final: 0.6515 (m-30) REVERT: x 56 TYR cc_start: 0.8702 (OUTLIER) cc_final: 0.7826 (t80) REVERT: y 245 MET cc_start: 0.8746 (tmm) cc_final: 0.8402 (ttt) REVERT: z 100 ILE cc_start: 0.8885 (OUTLIER) cc_final: 0.8568 (mm) outliers start: 241 outliers final: 187 residues processed: 1272 average time/residue: 0.6443 time to fit residues: 1406.8060 Evaluate side-chains 1282 residues out of total 6530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 1081 time to evaluate : 5.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 100 HIS Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain E residue 34 TYR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 196 ASN Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 293 ASN Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 434 MET Chi-restraints excluded: chain G residue 117 CYS Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 178 GLU Chi-restraints excluded: chain G residue 257 THR Chi-restraints excluded: chain G residue 274 THR Chi-restraints excluded: chain G residue 284 ASN Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain G residue 392 SER Chi-restraints excluded: chain G residue 543 VAL Chi-restraints excluded: chain G residue 583 LEU Chi-restraints excluded: chain G residue 591 VAL Chi-restraints excluded: chain G residue 600 VAL Chi-restraints excluded: chain G residue 680 ILE Chi-restraints excluded: chain G residue 712 THR Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 70 ASN Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 217 ASN Chi-restraints excluded: chain I residue 81 SER Chi-restraints excluded: chain I residue 104 SER Chi-restraints excluded: chain I residue 121 GLU Chi-restraints excluded: chain I residue 196 ASP Chi-restraints excluded: chain I residue 217 SER Chi-restraints excluded: chain I residue 218 GLU Chi-restraints excluded: chain J residue 4 SER Chi-restraints excluded: chain J residue 13 SER Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain K residue 10 SER Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 138 LEU Chi-restraints excluded: chain L residue 208 TRP Chi-restraints excluded: chain L residue 260 THR Chi-restraints excluded: chain L residue 281 THR Chi-restraints excluded: chain L residue 292 MET Chi-restraints excluded: chain L residue 378 THR Chi-restraints excluded: chain L residue 399 TYR Chi-restraints excluded: chain L residue 452 ASP Chi-restraints excluded: chain L residue 461 ILE Chi-restraints excluded: chain L residue 490 THR Chi-restraints excluded: chain L residue 550 THR Chi-restraints excluded: chain L residue 555 LEU Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain M residue 43 CYS Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 68 PHE Chi-restraints excluded: chain M residue 77 TYR Chi-restraints excluded: chain M residue 147 GLU Chi-restraints excluded: chain M residue 178 LEU Chi-restraints excluded: chain M residue 190 LEU Chi-restraints excluded: chain M residue 250 VAL Chi-restraints excluded: chain M residue 302 ILE Chi-restraints excluded: chain M residue 328 ILE Chi-restraints excluded: chain M residue 339 LEU Chi-restraints excluded: chain M residue 346 SER Chi-restraints excluded: chain M residue 391 LEU Chi-restraints excluded: chain M residue 400 GLU Chi-restraints excluded: chain M residue 413 LEU Chi-restraints excluded: chain M residue 432 LEU Chi-restraints excluded: chain N residue 20 PHE Chi-restraints excluded: chain N residue 77 THR Chi-restraints excluded: chain N residue 110 MET Chi-restraints excluded: chain N residue 112 PHE Chi-restraints excluded: chain N residue 252 ASP Chi-restraints excluded: chain N residue 281 PHE Chi-restraints excluded: chain N residue 282 ILE Chi-restraints excluded: chain N residue 310 MET Chi-restraints excluded: chain N residue 332 ILE Chi-restraints excluded: chain N residue 464 ASN Chi-restraints excluded: chain O residue 59 ASP Chi-restraints excluded: chain O residue 67 THR Chi-restraints excluded: chain O residue 94 GLU Chi-restraints excluded: chain O residue 111 THR Chi-restraints excluded: chain O residue 113 ASP Chi-restraints excluded: chain O residue 135 CYS Chi-restraints excluded: chain O residue 140 THR Chi-restraints excluded: chain O residue 147 VAL Chi-restraints excluded: chain O residue 148 VAL Chi-restraints excluded: chain P residue 95 VAL Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain P residue 276 MET Chi-restraints excluded: chain P residue 366 VAL Chi-restraints excluded: chain Q residue 88 LEU Chi-restraints excluded: chain Q residue 103 ASP Chi-restraints excluded: chain Q residue 143 ASN Chi-restraints excluded: chain R residue 87 ILE Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 90 ASP Chi-restraints excluded: chain S residue 34 LYS Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain T residue 42 SER Chi-restraints excluded: chain T residue 113 GLU Chi-restraints excluded: chain T residue 118 HIS Chi-restraints excluded: chain U residue 50 VAL Chi-restraints excluded: chain U residue 52 ASP Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain V residue 35 ASP Chi-restraints excluded: chain W residue 18 ASN Chi-restraints excluded: chain W residue 19 LEU Chi-restraints excluded: chain W residue 66 ASN Chi-restraints excluded: chain W residue 79 ILE Chi-restraints excluded: chain W residue 104 VAL Chi-restraints excluded: chain X residue 67 LEU Chi-restraints excluded: chain X residue 96 GLN Chi-restraints excluded: chain Z residue 45 SER Chi-restraints excluded: chain Z residue 54 SER Chi-restraints excluded: chain Z residue 106 GLU Chi-restraints excluded: chain a residue 6 LEU Chi-restraints excluded: chain a residue 21 ILE Chi-restraints excluded: chain a residue 29 ILE Chi-restraints excluded: chain b residue 7 LEU Chi-restraints excluded: chain c residue 72 GLN Chi-restraints excluded: chain d residue 37 VAL Chi-restraints excluded: chain e residue 37 LEU Chi-restraints excluded: chain e residue 46 HIS Chi-restraints excluded: chain f residue 2 ASN Chi-restraints excluded: chain f residue 5 ILE Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain f residue 38 SER Chi-restraints excluded: chain f residue 46 THR Chi-restraints excluded: chain f residue 88 PHE Chi-restraints excluded: chain i residue 7 PHE Chi-restraints excluded: chain i residue 13 LEU Chi-restraints excluded: chain j residue 12 TYR Chi-restraints excluded: chain k residue 35 ILE Chi-restraints excluded: chain l residue 105 VAL Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain m residue 30 THR Chi-restraints excluded: chain n residue 48 LEU Chi-restraints excluded: chain p residue 10 PHE Chi-restraints excluded: chain p residue 65 ASN Chi-restraints excluded: chain p residue 67 TYR Chi-restraints excluded: chain p residue 81 THR Chi-restraints excluded: chain p residue 86 TRP Chi-restraints excluded: chain p residue 93 ILE Chi-restraints excluded: chain x residue 56 TYR Chi-restraints excluded: chain x residue 72 VAL Chi-restraints excluded: chain x residue 74 VAL Chi-restraints excluded: chain x residue 88 VAL Chi-restraints excluded: chain x residue 89 THR Chi-restraints excluded: chain x residue 128 SER Chi-restraints excluded: chain x residue 138 LEU Chi-restraints excluded: chain x residue 149 SER Chi-restraints excluded: chain x residue 194 SER Chi-restraints excluded: chain y residue 85 LEU Chi-restraints excluded: chain y residue 124 ASP Chi-restraints excluded: chain y residue 152 LEU Chi-restraints excluded: chain y residue 206 ASN Chi-restraints excluded: chain y residue 240 GLU Chi-restraints excluded: chain z residue 13 PHE Chi-restraints excluded: chain z residue 48 VAL Chi-restraints excluded: chain z residue 100 ILE Chi-restraints excluded: chain z residue 124 ASP Chi-restraints excluded: chain z residue 138 THR Chi-restraints excluded: chain z residue 153 ASP Chi-restraints excluded: chain z residue 169 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 750 random chunks: chunk 447 optimal weight: 0.0470 chunk 288 optimal weight: 0.7980 chunk 431 optimal weight: 0.6980 chunk 217 optimal weight: 0.8980 chunk 142 optimal weight: 0.0970 chunk 140 optimal weight: 0.0970 chunk 459 optimal weight: 0.3980 chunk 492 optimal weight: 0.9980 chunk 357 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 568 optimal weight: 2.9990 overall best weight: 0.2674 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 385 GLN ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 457 HIS N 368 GLN O 98 GLN R 109 HIS ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 126 ASN q 88 GLN ** y 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 62927 Z= 0.158 Angle : 0.580 15.933 85209 Z= 0.284 Chirality : 0.041 0.253 9449 Planarity : 0.004 0.068 10724 Dihedral : 8.123 171.927 8941 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.13 % Favored : 92.85 % Rotamer: Outliers : 2.89 % Allowed : 19.77 % Favored : 77.34 % 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: -0.38 (0.10), residues: 7578 helix: 0.99 (0.09), residues: 3767 sheet: -1.05 (0.25), residues: 439 loop : -1.61 (0.11), residues: 3372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.001 TRP k 18 HIS 0.013 0.001 HIS M 241 PHE 0.038 0.001 PHE L 324 TYR 0.036 0.001 TYR L 379 ARG 0.008 0.000 ARG d 68 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15156 Ramachandran restraints generated. 7578 Oldfield, 0 Emsley, 7578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15156 Ramachandran restraints generated. 7578 Oldfield, 0 Emsley, 7578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1363 residues out of total 6530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 1174 time to evaluate : 5.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 212 PHE cc_start: 0.8083 (t80) cc_final: 0.7850 (t80) REVERT: D 377 ASP cc_start: 0.8266 (t0) cc_final: 0.7927 (t0) REVERT: F 436 GLN cc_start: 0.8344 (tp-100) cc_final: 0.7937 (tp-100) REVERT: G 117 CYS cc_start: 0.9205 (OUTLIER) cc_final: 0.8821 (p) REVERT: G 178 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8283 (pm20) REVERT: G 540 ASN cc_start: 0.7800 (m-40) cc_final: 0.7404 (m-40) REVERT: G 666 VAL cc_start: 0.8411 (OUTLIER) cc_final: 0.8129 (p) REVERT: I 66 ARG cc_start: 0.8003 (ttm110) cc_final: 0.7659 (ttp-110) REVERT: I 69 ASN cc_start: 0.8405 (m-40) cc_final: 0.8075 (m-40) REVERT: J 145 TYR cc_start: 0.8883 (m-80) cc_final: 0.8465 (m-80) REVERT: L 1 MET cc_start: 0.5829 (ttt) cc_final: 0.5385 (ttm) REVERT: L 288 PHE cc_start: 0.8027 (m-10) cc_final: 0.7821 (m-80) REVERT: L 306 ASP cc_start: 0.7807 (t0) cc_final: 0.7497 (t70) REVERT: L 506 LEU cc_start: 0.7781 (tp) cc_final: 0.7491 (mm) REVERT: M 400 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.7068 (pm20) REVERT: N 20 PHE cc_start: 0.8601 (OUTLIER) cc_final: 0.6947 (t80) REVERT: N 77 THR cc_start: 0.8888 (OUTLIER) cc_final: 0.8607 (m) REVERT: N 159 PHE cc_start: 0.8673 (m-10) cc_final: 0.8372 (m-10) REVERT: N 391 PHE cc_start: 0.8433 (OUTLIER) cc_final: 0.8152 (t80) REVERT: O 120 ARG cc_start: 0.7945 (ttp-170) cc_final: 0.7492 (tpt-90) REVERT: P 86 GLN cc_start: 0.8282 (tm-30) cc_final: 0.7702 (tm-30) REVERT: Q 38 GLU cc_start: 0.8183 (pm20) cc_final: 0.7775 (pm20) REVERT: Q 96 ASP cc_start: 0.8374 (t0) cc_final: 0.7867 (t70) REVERT: S 53 CYS cc_start: 0.7197 (m) cc_final: 0.6776 (m) REVERT: T 113 GLU cc_start: 0.6378 (OUTLIER) cc_final: 0.5736 (mp0) REVERT: U 72 LYS cc_start: 0.7344 (mmtt) cc_final: 0.6854 (mtpp) REVERT: W 79 ILE cc_start: 0.8914 (OUTLIER) cc_final: 0.8689 (mm) REVERT: X 72 GLN cc_start: 0.8197 (tp40) cc_final: 0.7975 (tp40) REVERT: Z 93 GLU cc_start: 0.8119 (tp30) cc_final: 0.7881 (tp30) REVERT: Z 106 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7736 (mp0) REVERT: a 14 ILE cc_start: 0.8437 (mm) cc_final: 0.8202 (mm) REVERT: a 49 MET cc_start: 0.8438 (mmp) cc_final: 0.8235 (mmp) REVERT: d 55 LYS cc_start: 0.8523 (tmtt) cc_final: 0.8278 (tmtt) REVERT: d 59 ASP cc_start: 0.7821 (m-30) cc_final: 0.7613 (m-30) REVERT: f 86 MET cc_start: 0.8708 (mpp) cc_final: 0.7650 (mpp) REVERT: g 89 ILE cc_start: 0.8460 (tp) cc_final: 0.8148 (tp) REVERT: i 7 PHE cc_start: 0.7469 (OUTLIER) cc_final: 0.7240 (m-80) REVERT: i 27 ARG cc_start: 0.8116 (mtm110) cc_final: 0.7781 (mtm110) REVERT: j 35 MET cc_start: 0.8660 (tmm) cc_final: 0.8176 (tmm) REVERT: j 41 TYR cc_start: 0.6000 (t80) cc_final: 0.5750 (t80) REVERT: l 79 LEU cc_start: 0.8235 (tt) cc_final: 0.7709 (pp) REVERT: l 107 PHE cc_start: 0.5728 (p90) cc_final: 0.5375 (p90) REVERT: l 118 ARG cc_start: 0.7017 (tmm-80) cc_final: 0.6725 (ptt90) REVERT: p 75 GLN cc_start: 0.8755 (mt0) cc_final: 0.8165 (mt0) REVERT: p 77 TYR cc_start: 0.6727 (t80) cc_final: 0.6328 (t80) REVERT: p 79 ASP cc_start: 0.7336 (p0) cc_final: 0.6064 (t0) REVERT: x 56 TYR cc_start: 0.8593 (OUTLIER) cc_final: 0.7614 (t80) REVERT: y 224 GLN cc_start: 0.8588 (tm-30) cc_final: 0.8330 (tm-30) REVERT: z 100 ILE cc_start: 0.8815 (OUTLIER) cc_final: 0.8521 (mm) outliers start: 189 outliers final: 139 residues processed: 1281 average time/residue: 0.5721 time to fit residues: 1249.9064 Evaluate side-chains 1266 residues out of total 6530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 1114 time to evaluate : 5.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 HIS Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain E residue 34 TYR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 434 MET Chi-restraints excluded: chain G residue 117 CYS Chi-restraints excluded: chain G residue 178 GLU Chi-restraints excluded: chain G residue 257 THR Chi-restraints excluded: chain G residue 274 THR Chi-restraints excluded: chain G residue 284 ASN Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain G residue 392 SER Chi-restraints excluded: chain G residue 543 VAL Chi-restraints excluded: chain G residue 583 LEU Chi-restraints excluded: chain G residue 591 VAL Chi-restraints excluded: chain G residue 666 VAL Chi-restraints excluded: chain G residue 680 ILE Chi-restraints excluded: chain G residue 712 THR Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 217 ASN Chi-restraints excluded: chain I residue 81 SER Chi-restraints excluded: chain I residue 121 GLU Chi-restraints excluded: chain I residue 196 ASP Chi-restraints excluded: chain I residue 218 GLU Chi-restraints excluded: chain J residue 13 SER Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain L residue 208 TRP Chi-restraints excluded: chain L residue 260 THR Chi-restraints excluded: chain L residue 292 MET Chi-restraints excluded: chain L residue 338 LEU Chi-restraints excluded: chain L residue 378 THR Chi-restraints excluded: chain L residue 399 TYR Chi-restraints excluded: chain L residue 452 ASP Chi-restraints excluded: chain L residue 461 ILE Chi-restraints excluded: chain L residue 550 THR Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain M residue 43 CYS Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain M residue 68 PHE Chi-restraints excluded: chain M residue 77 TYR Chi-restraints excluded: chain M residue 147 GLU Chi-restraints excluded: chain M residue 178 LEU Chi-restraints excluded: chain M residue 190 LEU Chi-restraints excluded: chain M residue 302 ILE Chi-restraints excluded: chain M residue 328 ILE Chi-restraints excluded: chain M residue 391 LEU Chi-restraints excluded: chain M residue 400 GLU Chi-restraints excluded: chain M residue 413 LEU Chi-restraints excluded: chain M residue 432 LEU Chi-restraints excluded: chain N residue 20 PHE Chi-restraints excluded: chain N residue 77 THR Chi-restraints excluded: chain N residue 110 MET Chi-restraints excluded: chain N residue 112 PHE Chi-restraints excluded: chain N residue 310 MET Chi-restraints excluded: chain N residue 332 ILE Chi-restraints excluded: chain N residue 391 PHE Chi-restraints excluded: chain N residue 464 ASN Chi-restraints excluded: chain O residue 59 ASP Chi-restraints excluded: chain O residue 111 THR Chi-restraints excluded: chain O residue 135 CYS Chi-restraints excluded: chain O residue 140 THR Chi-restraints excluded: chain O residue 147 VAL Chi-restraints excluded: chain O residue 148 VAL Chi-restraints excluded: chain P residue 160 ASN Chi-restraints excluded: chain P residue 366 VAL Chi-restraints excluded: chain Q residue 88 LEU Chi-restraints excluded: chain Q residue 143 ASN Chi-restraints excluded: chain R residue 87 ILE Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 90 ASP Chi-restraints excluded: chain S residue 34 LYS Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 60 MET Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain T residue 113 GLU Chi-restraints excluded: chain U residue 50 VAL Chi-restraints excluded: chain U residue 52 ASP Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain V residue 35 ASP Chi-restraints excluded: chain V residue 36 LEU Chi-restraints excluded: chain W residue 18 ASN Chi-restraints excluded: chain W residue 19 LEU Chi-restraints excluded: chain W residue 66 ASN Chi-restraints excluded: chain W residue 79 ILE Chi-restraints excluded: chain W residue 104 VAL Chi-restraints excluded: chain X residue 67 LEU Chi-restraints excluded: chain X residue 96 GLN Chi-restraints excluded: chain Z residue 106 GLU Chi-restraints excluded: chain a residue 6 LEU Chi-restraints excluded: chain a residue 7 GLU Chi-restraints excluded: chain a residue 21 ILE Chi-restraints excluded: chain a residue 29 ILE Chi-restraints excluded: chain a residue 43 ASP Chi-restraints excluded: chain d residue 37 VAL Chi-restraints excluded: chain e residue 37 LEU Chi-restraints excluded: chain e residue 46 HIS Chi-restraints excluded: chain f residue 5 ILE Chi-restraints excluded: chain f residue 38 SER Chi-restraints excluded: chain f residue 80 ASN Chi-restraints excluded: chain f residue 88 PHE Chi-restraints excluded: chain i residue 7 PHE Chi-restraints excluded: chain i residue 13 LEU Chi-restraints excluded: chain j residue 12 TYR Chi-restraints excluded: chain k residue 23 MET Chi-restraints excluded: chain l residue 105 VAL Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain n residue 85 ILE Chi-restraints excluded: chain p residue 10 PHE Chi-restraints excluded: chain p residue 50 ILE Chi-restraints excluded: chain p residue 65 ASN Chi-restraints excluded: chain p residue 67 TYR Chi-restraints excluded: chain p residue 81 THR Chi-restraints excluded: chain p residue 86 TRP Chi-restraints excluded: chain p residue 93 ILE Chi-restraints excluded: chain x residue 56 TYR Chi-restraints excluded: chain x residue 72 VAL Chi-restraints excluded: chain x residue 74 VAL Chi-restraints excluded: chain x residue 88 VAL Chi-restraints excluded: chain x residue 89 THR Chi-restraints excluded: chain x residue 137 THR Chi-restraints excluded: chain x residue 138 LEU Chi-restraints excluded: chain x residue 149 SER Chi-restraints excluded: chain x residue 194 SER Chi-restraints excluded: chain y residue 152 LEU Chi-restraints excluded: chain y residue 206 ASN Chi-restraints excluded: chain y residue 240 GLU Chi-restraints excluded: chain z residue 13 PHE Chi-restraints excluded: chain z residue 48 VAL Chi-restraints excluded: chain z residue 100 ILE Chi-restraints excluded: chain z residue 153 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 750 random chunks: chunk 657 optimal weight: 7.9990 chunk 692 optimal weight: 7.9990 chunk 631 optimal weight: 0.9990 chunk 673 optimal weight: 7.9990 chunk 405 optimal weight: 2.9990 chunk 293 optimal weight: 4.9990 chunk 528 optimal weight: 0.8980 chunk 206 optimal weight: 0.4980 chunk 608 optimal weight: 0.9990 chunk 637 optimal weight: 3.9990 chunk 671 optimal weight: 2.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 221 HIS ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 446 GLN L 457 HIS N 368 GLN O 98 GLN O 141 GLN ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 126 ASN c 72 GLN e 52 GLN ** g 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 88 GLN ** x 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 62927 Z= 0.279 Angle : 0.626 15.337 85209 Z= 0.308 Chirality : 0.043 0.254 9449 Planarity : 0.004 0.067 10724 Dihedral : 8.168 173.514 8941 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.86 % Favored : 92.10 % Rotamer: Outliers : 3.06 % Allowed : 20.12 % Favored : 76.81 % 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: -0.48 (0.10), residues: 7578 helix: 0.91 (0.09), residues: 3772 sheet: -1.24 (0.25), residues: 429 loop : -1.63 (0.11), residues: 3377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.001 TRP k 18 HIS 0.008 0.001 HIS L 457 PHE 0.036 0.002 PHE L 324 TYR 0.029 0.001 TYR L 379 ARG 0.010 0.000 ARG C 81 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15156 Ramachandran restraints generated. 7578 Oldfield, 0 Emsley, 7578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15156 Ramachandran restraints generated. 7578 Oldfield, 0 Emsley, 7578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1323 residues out of total 6530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 1123 time to evaluate : 5.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 170 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7661 (tt0) REVERT: D 377 ASP cc_start: 0.8347 (t0) cc_final: 0.7942 (t0) REVERT: F 436 GLN cc_start: 0.8392 (tp-100) cc_final: 0.8002 (tp-100) REVERT: G 117 CYS cc_start: 0.9258 (OUTLIER) cc_final: 0.8910 (p) REVERT: G 178 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8301 (pm20) REVERT: G 294 ASP cc_start: 0.7901 (t70) cc_final: 0.7589 (t70) REVERT: G 540 ASN cc_start: 0.7867 (m-40) cc_final: 0.7493 (m-40) REVERT: G 666 VAL cc_start: 0.8516 (OUTLIER) cc_final: 0.8219 (p) REVERT: G 710 MET cc_start: 0.5879 (tpt) cc_final: 0.5035 (mmm) REVERT: I 61 ASN cc_start: 0.8527 (t0) cc_final: 0.8315 (t0) REVERT: L 1 MET cc_start: 0.5760 (ttt) cc_final: 0.5256 (ttm) REVERT: L 288 PHE cc_start: 0.8026 (m-10) cc_final: 0.7799 (m-80) REVERT: L 506 LEU cc_start: 0.7851 (tp) cc_final: 0.7547 (mm) REVERT: M 259 PHE cc_start: 0.8778 (OUTLIER) cc_final: 0.8119 (m-10) REVERT: M 400 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7156 (pm20) REVERT: N 20 PHE cc_start: 0.8647 (OUTLIER) cc_final: 0.7053 (t80) REVERT: N 77 THR cc_start: 0.8985 (OUTLIER) cc_final: 0.8672 (m) REVERT: N 159 PHE cc_start: 0.8764 (m-10) cc_final: 0.8452 (m-10) REVERT: O 120 ARG cc_start: 0.7996 (ttp-170) cc_final: 0.7591 (tpt170) REVERT: P 86 GLN cc_start: 0.8377 (tm-30) cc_final: 0.8024 (tm-30) REVERT: Q 38 GLU cc_start: 0.8214 (pm20) cc_final: 0.7765 (pm20) REVERT: Q 96 ASP cc_start: 0.8401 (t0) cc_final: 0.7923 (t70) REVERT: S 53 CYS cc_start: 0.7336 (m) cc_final: 0.6900 (m) REVERT: T 103 ASP cc_start: 0.1414 (OUTLIER) cc_final: 0.0191 (t0) REVERT: T 113 GLU cc_start: 0.6261 (OUTLIER) cc_final: 0.5739 (mp0) REVERT: U 100 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7575 (mm-30) REVERT: U 109 ILE cc_start: 0.7911 (pt) cc_final: 0.7565 (mt) REVERT: X 72 GLN cc_start: 0.8243 (tp40) cc_final: 0.8033 (tp40) REVERT: Z 93 GLU cc_start: 0.8196 (tp30) cc_final: 0.7961 (tp30) REVERT: Z 106 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7723 (mp0) REVERT: a 14 ILE cc_start: 0.8465 (mm) cc_final: 0.8216 (mm) REVERT: a 50 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8333 (mt-10) REVERT: c 57 LYS cc_start: 0.7068 (mmtt) cc_final: 0.6827 (ptmm) REVERT: d 55 LYS cc_start: 0.8518 (tmtt) cc_final: 0.8261 (tmtt) REVERT: d 59 ASP cc_start: 0.7834 (m-30) cc_final: 0.7618 (m-30) REVERT: g 89 ILE cc_start: 0.8529 (tp) cc_final: 0.8232 (tp) REVERT: i 7 PHE cc_start: 0.7492 (OUTLIER) cc_final: 0.7233 (m-80) REVERT: i 27 ARG cc_start: 0.8110 (mtm110) cc_final: 0.7757 (mtm110) REVERT: j 35 MET cc_start: 0.8668 (tmm) cc_final: 0.8180 (tmm) REVERT: l 79 LEU cc_start: 0.8232 (tt) cc_final: 0.7725 (pp) REVERT: l 107 PHE cc_start: 0.5762 (p90) cc_final: 0.5440 (p90) REVERT: l 118 ARG cc_start: 0.7149 (tmm-80) cc_final: 0.6904 (ptt90) REVERT: m 60 ASP cc_start: 0.7154 (m-30) cc_final: 0.6758 (t0) REVERT: p 75 GLN cc_start: 0.8768 (mt0) cc_final: 0.8468 (mt0) REVERT: p 79 ASP cc_start: 0.7505 (p0) cc_final: 0.6703 (m-30) REVERT: x 56 TYR cc_start: 0.8664 (OUTLIER) cc_final: 0.7766 (t80) REVERT: y 224 GLN cc_start: 0.8670 (tm-30) cc_final: 0.8363 (tm-30) REVERT: z 100 ILE cc_start: 0.8946 (OUTLIER) cc_final: 0.8617 (mm) outliers start: 200 outliers final: 164 residues processed: 1238 average time/residue: 0.6506 time to fit residues: 1377.3899 Evaluate side-chains 1271 residues out of total 6530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 1093 time to evaluate : 5.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain B residue 100 HIS Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain E residue 34 TYR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 434 MET Chi-restraints excluded: chain G residue 117 CYS Chi-restraints excluded: chain G residue 178 GLU Chi-restraints excluded: chain G residue 248 ILE Chi-restraints excluded: chain G residue 257 THR Chi-restraints excluded: chain G residue 274 THR Chi-restraints excluded: chain G residue 284 ASN Chi-restraints excluded: chain G residue 297 ASP Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain G residue 392 SER Chi-restraints excluded: chain G residue 446 GLN Chi-restraints excluded: chain G residue 543 VAL Chi-restraints excluded: chain G residue 583 LEU Chi-restraints excluded: chain G residue 591 VAL Chi-restraints excluded: chain G residue 666 VAL Chi-restraints excluded: chain G residue 680 ILE Chi-restraints excluded: chain G residue 712 THR Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 217 ASN Chi-restraints excluded: chain I residue 121 GLU Chi-restraints excluded: chain I residue 196 ASP Chi-restraints excluded: chain J residue 13 SER Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 208 TRP Chi-restraints excluded: chain L residue 260 THR Chi-restraints excluded: chain L residue 292 MET Chi-restraints excluded: chain L residue 361 ASP Chi-restraints excluded: chain L residue 378 THR Chi-restraints excluded: chain L residue 399 TYR Chi-restraints excluded: chain L residue 452 ASP Chi-restraints excluded: chain L residue 461 ILE Chi-restraints excluded: chain L residue 490 THR Chi-restraints excluded: chain L residue 550 THR Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain M residue 43 CYS Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain M residue 68 PHE Chi-restraints excluded: chain M residue 147 GLU Chi-restraints excluded: chain M residue 178 LEU Chi-restraints excluded: chain M residue 190 LEU Chi-restraints excluded: chain M residue 243 GLU Chi-restraints excluded: chain M residue 259 PHE Chi-restraints excluded: chain M residue 302 ILE Chi-restraints excluded: chain M residue 328 ILE Chi-restraints excluded: chain M residue 346 SER Chi-restraints excluded: chain M residue 400 GLU Chi-restraints excluded: chain M residue 413 LEU Chi-restraints excluded: chain M residue 432 LEU Chi-restraints excluded: chain N residue 20 PHE Chi-restraints excluded: chain N residue 77 THR Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain N residue 110 MET Chi-restraints excluded: chain N residue 112 PHE Chi-restraints excluded: chain N residue 252 ASP Chi-restraints excluded: chain N residue 281 PHE Chi-restraints excluded: chain N residue 282 ILE Chi-restraints excluded: chain N residue 332 ILE Chi-restraints excluded: chain N residue 464 ASN Chi-restraints excluded: chain O residue 94 GLU Chi-restraints excluded: chain O residue 111 THR Chi-restraints excluded: chain O residue 113 ASP Chi-restraints excluded: chain O residue 135 CYS Chi-restraints excluded: chain O residue 140 THR Chi-restraints excluded: chain O residue 147 VAL Chi-restraints excluded: chain O residue 148 VAL Chi-restraints excluded: chain P residue 95 VAL Chi-restraints excluded: chain P residue 160 ASN Chi-restraints excluded: chain P residue 366 VAL Chi-restraints excluded: chain Q residue 88 LEU Chi-restraints excluded: chain Q residue 103 ASP Chi-restraints excluded: chain Q residue 143 ASN Chi-restraints excluded: chain R residue 87 ILE Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 90 ASP Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 60 MET Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain T residue 103 ASP Chi-restraints excluded: chain T residue 113 GLU Chi-restraints excluded: chain U residue 50 VAL Chi-restraints excluded: chain U residue 52 ASP Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain V residue 35 ASP Chi-restraints excluded: chain V residue 36 LEU Chi-restraints excluded: chain W residue 18 ASN Chi-restraints excluded: chain W residue 104 VAL Chi-restraints excluded: chain X residue 67 LEU Chi-restraints excluded: chain X residue 96 GLN Chi-restraints excluded: chain Z residue 45 SER Chi-restraints excluded: chain Z residue 54 SER Chi-restraints excluded: chain Z residue 85 ILE Chi-restraints excluded: chain Z residue 106 GLU Chi-restraints excluded: chain a residue 6 LEU Chi-restraints excluded: chain a residue 7 GLU Chi-restraints excluded: chain a residue 21 ILE Chi-restraints excluded: chain a residue 29 ILE Chi-restraints excluded: chain a residue 43 ASP Chi-restraints excluded: chain d residue 23 LEU Chi-restraints excluded: chain d residue 37 VAL Chi-restraints excluded: chain e residue 37 LEU Chi-restraints excluded: chain e residue 46 HIS Chi-restraints excluded: chain f residue 2 ASN Chi-restraints excluded: chain f residue 5 ILE Chi-restraints excluded: chain f residue 6 THR Chi-restraints excluded: chain f residue 38 SER Chi-restraints excluded: chain f residue 80 ASN Chi-restraints excluded: chain f residue 88 PHE Chi-restraints excluded: chain i residue 4 ILE Chi-restraints excluded: chain i residue 7 PHE Chi-restraints excluded: chain i residue 13 LEU Chi-restraints excluded: chain j residue 12 TYR Chi-restraints excluded: chain l residue 105 VAL Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain m residue 30 THR Chi-restraints excluded: chain o residue 10 MET Chi-restraints excluded: chain p residue 10 PHE Chi-restraints excluded: chain p residue 50 ILE Chi-restraints excluded: chain p residue 65 ASN Chi-restraints excluded: chain p residue 67 TYR Chi-restraints excluded: chain p residue 81 THR Chi-restraints excluded: chain p residue 93 ILE Chi-restraints excluded: chain x residue 56 TYR Chi-restraints excluded: chain x residue 72 VAL Chi-restraints excluded: chain x residue 74 VAL Chi-restraints excluded: chain x residue 88 VAL Chi-restraints excluded: chain x residue 89 THR Chi-restraints excluded: chain x residue 137 THR Chi-restraints excluded: chain x residue 138 LEU Chi-restraints excluded: chain x residue 149 SER Chi-restraints excluded: chain x residue 194 SER Chi-restraints excluded: chain y residue 46 MET Chi-restraints excluded: chain y residue 124 ASP Chi-restraints excluded: chain y residue 152 LEU Chi-restraints excluded: chain y residue 206 ASN Chi-restraints excluded: chain y residue 240 GLU Chi-restraints excluded: chain z residue 13 PHE Chi-restraints excluded: chain z residue 100 ILE Chi-restraints excluded: chain z residue 124 ASP Chi-restraints excluded: chain z residue 138 THR Chi-restraints excluded: chain z residue 153 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 750 random chunks: chunk 442 optimal weight: 7.9990 chunk 712 optimal weight: 0.9980 chunk 434 optimal weight: 2.9990 chunk 337 optimal weight: 4.9990 chunk 495 optimal weight: 0.9980 chunk 747 optimal weight: 4.9990 chunk 687 optimal weight: 0.0980 chunk 594 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 459 optimal weight: 0.0050 chunk 364 optimal weight: 1.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 716 GLN L 457 HIS N 368 GLN O 98 GLN ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 34 HIS q 88 GLN ** x 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 62927 Z= 0.191 Angle : 0.607 16.573 85209 Z= 0.297 Chirality : 0.042 0.221 9449 Planarity : 0.004 0.068 10724 Dihedral : 8.046 172.494 8941 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.22 % Favored : 92.76 % Rotamer: Outliers : 2.66 % Allowed : 20.77 % Favored : 76.57 % 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: -0.42 (0.10), residues: 7578 helix: 0.96 (0.09), residues: 3749 sheet: -1.08 (0.25), residues: 440 loop : -1.62 (0.11), residues: 3389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP k 18 HIS 0.009 0.001 HIS L 457 PHE 0.041 0.001 PHE L 324 TYR 0.027 0.001 TYR a 33 ARG 0.011 0.000 ARG B 116 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15156 Ramachandran restraints generated. 7578 Oldfield, 0 Emsley, 7578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15156 Ramachandran restraints generated. 7578 Oldfield, 0 Emsley, 7578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1300 residues out of total 6530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 1126 time to evaluate : 5.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 170 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7588 (tt0) REVERT: D 39 ARG cc_start: 0.8023 (ttp-110) cc_final: 0.7781 (ttp-110) REVERT: D 377 ASP cc_start: 0.8331 (t0) cc_final: 0.7948 (t0) REVERT: F 436 GLN cc_start: 0.8378 (tp-100) cc_final: 0.7975 (tp-100) REVERT: G 117 CYS cc_start: 0.9206 (OUTLIER) cc_final: 0.8883 (p) REVERT: G 178 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8286 (pm20) REVERT: G 294 ASP cc_start: 0.7829 (t70) cc_final: 0.7523 (t70) REVERT: G 540 ASN cc_start: 0.7816 (m-40) cc_final: 0.7459 (m-40) REVERT: G 666 VAL cc_start: 0.8455 (OUTLIER) cc_final: 0.8157 (p) REVERT: G 710 MET cc_start: 0.5827 (tpt) cc_final: 0.4940 (mmm) REVERT: I 61 ASN cc_start: 0.8477 (t0) cc_final: 0.8254 (t0) REVERT: I 66 ARG cc_start: 0.8006 (ttm110) cc_final: 0.7653 (ttp-110) REVERT: K 57 MET cc_start: 0.8679 (mmm) cc_final: 0.8470 (mmm) REVERT: L 1 MET cc_start: 0.5775 (ttt) cc_final: 0.5270 (ttm) REVERT: L 288 PHE cc_start: 0.7999 (m-10) cc_final: 0.7798 (m-80) REVERT: L 331 TYR cc_start: 0.7307 (m-80) cc_final: 0.7052 (m-80) REVERT: L 506 LEU cc_start: 0.7841 (tp) cc_final: 0.7561 (mm) REVERT: M 259 PHE cc_start: 0.8691 (OUTLIER) cc_final: 0.7942 (m-10) REVERT: M 400 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7080 (pm20) REVERT: N 20 PHE cc_start: 0.8609 (OUTLIER) cc_final: 0.6987 (t80) REVERT: N 77 THR cc_start: 0.8913 (OUTLIER) cc_final: 0.8567 (m) REVERT: N 159 PHE cc_start: 0.8710 (m-10) cc_final: 0.8423 (m-10) REVERT: O 120 ARG cc_start: 0.7988 (ttp-170) cc_final: 0.7423 (ttp-170) REVERT: P 86 GLN cc_start: 0.8311 (tm-30) cc_final: 0.7970 (tm-30) REVERT: Q 38 GLU cc_start: 0.8186 (pm20) cc_final: 0.7757 (pm20) REVERT: Q 96 ASP cc_start: 0.8398 (t0) cc_final: 0.7920 (t70) REVERT: S 53 CYS cc_start: 0.7278 (m) cc_final: 0.6877 (m) REVERT: T 59 LYS cc_start: 0.4783 (mmmm) cc_final: 0.4239 (mtmt) REVERT: T 113 GLU cc_start: 0.6346 (OUTLIER) cc_final: 0.5788 (mp0) REVERT: U 100 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7536 (mm-30) REVERT: U 109 ILE cc_start: 0.7754 (pt) cc_final: 0.7337 (mt) REVERT: Z 93 GLU cc_start: 0.8152 (tp30) cc_final: 0.7924 (tp30) REVERT: Z 106 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7754 (mp0) REVERT: a 14 ILE cc_start: 0.8444 (mm) cc_final: 0.8206 (mm) REVERT: c 57 LYS cc_start: 0.7023 (mmtt) cc_final: 0.6791 (ptmm) REVERT: d 55 LYS cc_start: 0.8494 (tmtt) cc_final: 0.8239 (tmtt) REVERT: d 59 ASP cc_start: 0.7843 (m-30) cc_final: 0.7630 (m-30) REVERT: f 86 MET cc_start: 0.8689 (mpp) cc_final: 0.7586 (mpp) REVERT: g 89 ILE cc_start: 0.8460 (tp) cc_final: 0.8153 (tp) REVERT: i 7 PHE cc_start: 0.7451 (OUTLIER) cc_final: 0.7221 (m-80) REVERT: i 27 ARG cc_start: 0.8099 (mtm110) cc_final: 0.7766 (mtm110) REVERT: j 35 MET cc_start: 0.8664 (tmm) cc_final: 0.8174 (tmm) REVERT: j 41 TYR cc_start: 0.5924 (t80) cc_final: 0.5663 (t80) REVERT: l 79 LEU cc_start: 0.8232 (tt) cc_final: 0.7711 (pp) REVERT: l 107 PHE cc_start: 0.5693 (p90) cc_final: 0.5405 (p90) REVERT: l 118 ARG cc_start: 0.7098 (tmm-80) cc_final: 0.6769 (ptt90) REVERT: m 60 ASP cc_start: 0.7120 (m-30) cc_final: 0.6758 (t0) REVERT: p 77 TYR cc_start: 0.6926 (t80) cc_final: 0.6516 (t80) REVERT: p 79 ASP cc_start: 0.7306 (p0) cc_final: 0.6546 (m-30) REVERT: x 56 TYR cc_start: 0.8628 (OUTLIER) cc_final: 0.7737 (t80) REVERT: y 224 GLN cc_start: 0.8626 (tm-30) cc_final: 0.8322 (tm-30) REVERT: z 100 ILE cc_start: 0.8909 (OUTLIER) cc_final: 0.8596 (mm) outliers start: 174 outliers final: 148 residues processed: 1226 average time/residue: 0.5781 time to fit residues: 1206.2550 Evaluate side-chains 1270 residues out of total 6530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 1109 time to evaluate : 5.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 100 HIS Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain E residue 34 TYR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain G residue 117 CYS Chi-restraints excluded: chain G residue 178 GLU Chi-restraints excluded: chain G residue 257 THR Chi-restraints excluded: chain G residue 274 THR Chi-restraints excluded: chain G residue 284 ASN Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain G residue 543 VAL Chi-restraints excluded: chain G residue 591 VAL Chi-restraints excluded: chain G residue 666 VAL Chi-restraints excluded: chain G residue 680 ILE Chi-restraints excluded: chain G residue 712 THR Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 217 ASN Chi-restraints excluded: chain I residue 121 GLU Chi-restraints excluded: chain I residue 196 ASP Chi-restraints excluded: chain I residue 217 SER Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain L residue 208 TRP Chi-restraints excluded: chain L residue 260 THR Chi-restraints excluded: chain L residue 292 MET Chi-restraints excluded: chain L residue 378 THR Chi-restraints excluded: chain L residue 399 TYR Chi-restraints excluded: chain L residue 452 ASP Chi-restraints excluded: chain L residue 461 ILE Chi-restraints excluded: chain L residue 550 THR Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain M residue 43 CYS Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain M residue 68 PHE Chi-restraints excluded: chain M residue 77 TYR Chi-restraints excluded: chain M residue 147 GLU Chi-restraints excluded: chain M residue 178 LEU Chi-restraints excluded: chain M residue 190 LEU Chi-restraints excluded: chain M residue 243 GLU Chi-restraints excluded: chain M residue 259 PHE Chi-restraints excluded: chain M residue 302 ILE Chi-restraints excluded: chain M residue 328 ILE Chi-restraints excluded: chain M residue 338 MET Chi-restraints excluded: chain M residue 346 SER Chi-restraints excluded: chain M residue 391 LEU Chi-restraints excluded: chain M residue 400 GLU Chi-restraints excluded: chain M residue 413 LEU Chi-restraints excluded: chain M residue 432 LEU Chi-restraints excluded: chain N residue 20 PHE Chi-restraints excluded: chain N residue 77 THR Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain N residue 110 MET Chi-restraints excluded: chain N residue 112 PHE Chi-restraints excluded: chain N residue 252 ASP Chi-restraints excluded: chain N residue 281 PHE Chi-restraints excluded: chain N residue 332 ILE Chi-restraints excluded: chain N residue 464 ASN Chi-restraints excluded: chain O residue 94 GLU Chi-restraints excluded: chain O residue 111 THR Chi-restraints excluded: chain O residue 135 CYS Chi-restraints excluded: chain O residue 140 THR Chi-restraints excluded: chain O residue 147 VAL Chi-restraints excluded: chain O residue 148 VAL Chi-restraints excluded: chain P residue 95 VAL Chi-restraints excluded: chain P residue 160 ASN Chi-restraints excluded: chain P residue 366 VAL Chi-restraints excluded: chain Q residue 88 LEU Chi-restraints excluded: chain Q residue 103 ASP Chi-restraints excluded: chain Q residue 143 ASN Chi-restraints excluded: chain R residue 87 ILE Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 90 ASP Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 60 MET Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain T residue 113 GLU Chi-restraints excluded: chain U residue 50 VAL Chi-restraints excluded: chain U residue 52 ASP Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain V residue 35 ASP Chi-restraints excluded: chain V residue 36 LEU Chi-restraints excluded: chain W residue 18 ASN Chi-restraints excluded: chain W residue 19 LEU Chi-restraints excluded: chain W residue 104 VAL Chi-restraints excluded: chain X residue 67 LEU Chi-restraints excluded: chain X residue 96 GLN Chi-restraints excluded: chain Z residue 45 SER Chi-restraints excluded: chain Z residue 106 GLU Chi-restraints excluded: chain a residue 6 LEU Chi-restraints excluded: chain a residue 7 GLU Chi-restraints excluded: chain a residue 21 ILE Chi-restraints excluded: chain a residue 29 ILE Chi-restraints excluded: chain a residue 43 ASP Chi-restraints excluded: chain d residue 23 LEU Chi-restraints excluded: chain d residue 37 VAL Chi-restraints excluded: chain e residue 37 LEU Chi-restraints excluded: chain e residue 46 HIS Chi-restraints excluded: chain f residue 5 ILE Chi-restraints excluded: chain f residue 6 THR Chi-restraints excluded: chain f residue 38 SER Chi-restraints excluded: chain f residue 80 ASN Chi-restraints excluded: chain i residue 7 PHE Chi-restraints excluded: chain i residue 13 LEU Chi-restraints excluded: chain j residue 12 TYR Chi-restraints excluded: chain l residue 105 VAL Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain m residue 30 THR Chi-restraints excluded: chain o residue 10 MET Chi-restraints excluded: chain p residue 10 PHE Chi-restraints excluded: chain p residue 50 ILE Chi-restraints excluded: chain p residue 65 ASN Chi-restraints excluded: chain p residue 67 TYR Chi-restraints excluded: chain p residue 81 THR Chi-restraints excluded: chain p residue 86 TRP Chi-restraints excluded: chain p residue 93 ILE Chi-restraints excluded: chain x residue 56 TYR Chi-restraints excluded: chain x residue 72 VAL Chi-restraints excluded: chain x residue 88 VAL Chi-restraints excluded: chain x residue 89 THR Chi-restraints excluded: chain x residue 137 THR Chi-restraints excluded: chain x residue 138 LEU Chi-restraints excluded: chain x residue 149 SER Chi-restraints excluded: chain x residue 194 SER Chi-restraints excluded: chain y residue 152 LEU Chi-restraints excluded: chain y residue 206 ASN Chi-restraints excluded: chain y residue 240 GLU Chi-restraints excluded: chain z residue 13 PHE Chi-restraints excluded: chain z residue 48 VAL Chi-restraints excluded: chain z residue 100 ILE Chi-restraints excluded: chain z residue 138 THR Chi-restraints excluded: chain z residue 153 ASP Chi-restraints excluded: chain z residue 169 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 750 random chunks: chunk 472 optimal weight: 3.9990 chunk 633 optimal weight: 0.8980 chunk 182 optimal weight: 0.9990 chunk 548 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 chunk 165 optimal weight: 0.7980 chunk 595 optimal weight: 1.9990 chunk 249 optimal weight: 0.9990 chunk 611 optimal weight: 0.1980 chunk 75 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 446 GLN L 457 HIS N 368 GLN O 98 GLN ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 126 ASN ** e 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 75 GLN q 88 GLN ** y 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.125015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.100035 restraints weight = 117598.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.099784 restraints weight = 72082.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.100339 restraints weight = 67612.109| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 62927 Z= 0.194 Angle : 0.606 16.492 85209 Z= 0.296 Chirality : 0.042 0.203 9449 Planarity : 0.004 0.067 10724 Dihedral : 7.933 172.583 8941 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.36 % Favored : 92.61 % Rotamer: Outliers : 2.85 % Allowed : 20.78 % Favored : 76.37 % 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: -0.40 (0.10), residues: 7578 helix: 0.97 (0.09), residues: 3753 sheet: -1.17 (0.25), residues: 440 loop : -1.59 (0.11), residues: 3385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP k 18 HIS 0.008 0.001 HIS L 457 PHE 0.037 0.001 PHE L 324 TYR 0.027 0.001 TYR a 33 ARG 0.010 0.000 ARG B 116 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17620.16 seconds wall clock time: 308 minutes 40.19 seconds (18520.19 seconds total)