Starting phenix.real_space_refine (version: dev) on Wed Feb 22 07:25:55 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gcs_4384/02_2023/6gcs_4384_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gcs_4384/02_2023/6gcs_4384.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gcs_4384/02_2023/6gcs_4384_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gcs_4384/02_2023/6gcs_4384_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gcs_4384/02_2023/6gcs_4384_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gcs_4384/02_2023/6gcs_4384.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gcs_4384/02_2023/6gcs_4384.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gcs_4384/02_2023/6gcs_4384_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gcs_4384/02_2023/6gcs_4384_updated.pdb" } resolution = 4.32 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A ARG 67": "NH1" <-> "NH2" Residue "A ARG 89": "NH1" <-> "NH2" Residue "A ARG 108": "NH1" <-> "NH2" Residue "A ARG 150": "NH1" <-> "NH2" Residue "A ARG 153": "NH1" <-> "NH2" Residue "A ARG 155": "NH1" <-> "NH2" Residue "A ARG 246": "NH1" <-> "NH2" Residue "A ARG 269": "NH1" <-> "NH2" Residue "A PHE 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 528": "NH1" <-> "NH2" Residue "A ARG 610": "NH1" <-> "NH2" Residue "A ARG 646": "NH1" <-> "NH2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B ARG 113": "NH1" <-> "NH2" Residue "B TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 130": "NH1" <-> "NH2" Residue "B ARG 149": "NH1" <-> "NH2" Residue "B ARG 161": "NH1" <-> "NH2" Residue "B ARG 201": "NH1" <-> "NH2" Residue "B ARG 226": "NH1" <-> "NH2" Residue "B ARG 240": "NH1" <-> "NH2" Residue "B ARG 258": "NH1" <-> "NH2" Residue "B ARG 259": "NH1" <-> "NH2" Residue "B ARG 269": "NH1" <-> "NH2" Residue "B ARG 271": "NH1" <-> "NH2" Residue "B ARG 299": "NH1" <-> "NH2" Residue "B ARG 367": "NH1" <-> "NH2" Residue "B ARG 388": "NH1" <-> "NH2" Residue "B ARG 402": "NH1" <-> "NH2" Residue "B ARG 409": "NH1" <-> "NH2" Residue "C ARG 121": "NH1" <-> "NH2" Residue "C TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 169": "NH1" <-> "NH2" Residue "C ARG 219": "NH1" <-> "NH2" Residue "C ARG 224": "NH1" <-> "NH2" Residue "C ARG 231": "NH1" <-> "NH2" Residue "C ARG 257": "NH1" <-> "NH2" Residue "C ARG 274": "NH1" <-> "NH2" Residue "C ARG 306": "NH1" <-> "NH2" Residue "C TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 421": "NH1" <-> "NH2" Residue "D ARG 32": "NH1" <-> "NH2" Residue "D ARG 37": "NH1" <-> "NH2" Residue "E ARG 91": "NH1" <-> "NH2" Residue "E ARG 110": "NH1" <-> "NH2" Residue "E ARG 120": "NH1" <-> "NH2" Residue "E ARG 131": "NH1" <-> "NH2" Residue "E ARG 149": "NH1" <-> "NH2" Residue "E ARG 150": "NH1" <-> "NH2" Residue "E ARG 201": "NH1" <-> "NH2" Residue "E ARG 208": "NH1" <-> "NH2" Residue "E PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 349": "NH1" <-> "NH2" Residue "G ARG 113": "NH1" <-> "NH2" Residue "G TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 116": "NH1" <-> "NH2" Residue "H ARG 215": "NH1" <-> "NH2" Residue "I ARG 197": "NH1" <-> "NH2" Residue "J ARG 47": "NH1" <-> "NH2" Residue "J ARG 55": "NH1" <-> "NH2" Residue "J ARG 91": "NH1" <-> "NH2" Residue "K PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 108": "NH1" <-> "NH2" Residue "K ARG 199": "NH1" <-> "NH2" Residue "L ARG 19": "NH1" <-> "NH2" Residue "L ARG 81": "NH1" <-> "NH2" Residue "M ARG 88": "NH1" <-> "NH2" Residue "M ARG 131": "NH1" <-> "NH2" Residue "O ARG 29": "NH1" <-> "NH2" Residue "P PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 57": "NH1" <-> "NH2" Residue "P ARG 62": "NH1" <-> "NH2" Residue "P ARG 109": "NH1" <-> "NH2" Residue "R ARG 20": "NH1" <-> "NH2" Residue "R ARG 27": "NH1" <-> "NH2" Residue "R ARG 57": "NH1" <-> "NH2" Residue "R ARG 67": "NH1" <-> "NH2" Residue "U ARG 74": "NH1" <-> "NH2" Residue "U ARG 95": "NH1" <-> "NH2" Residue "U ARG 112": "NH1" <-> "NH2" Residue "W ARG 20": "NH1" <-> "NH2" Residue "W ARG 21": "NH1" <-> "NH2" Residue "W ARG 29": "NH1" <-> "NH2" Residue "W ARG 47": "NH1" <-> "NH2" Residue "W ARG 60": "NH1" <-> "NH2" Residue "W ARG 66": "NH1" <-> "NH2" Residue "W ARG 83": "NH1" <-> "NH2" Residue "W ARG 84": "NH1" <-> "NH2" Residue "W ARG 91": "NH1" <-> "NH2" Residue "Y ARG 54": "NH1" <-> "NH2" Residue "Y ARG 79": "NH1" <-> "NH2" Residue "Y ARG 90": "NH1" <-> "NH2" Residue "Y TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 137": "NH1" <-> "NH2" Residue "Y ARG 140": "NH1" <-> "NH2" Residue "d ARG 6": "NH1" <-> "NH2" Residue "d ARG 24": "NH1" <-> "NH2" Residue "d ARG 37": "NH1" <-> "NH2" Residue "d ARG 45": "NH1" <-> "NH2" Residue "d ARG 87": "NH1" <-> "NH2" Residue "f ARG 6": "NH1" <-> "NH2" Residue "f ARG 9": "NH1" <-> "NH2" Residue "f ARG 23": "NH1" <-> "NH2" Residue "f ARG 45": "NH1" <-> "NH2" Residue "f ARG 57": "NH1" <-> "NH2" Residue "f ARG 79": "NH1" <-> "NH2" Residue "g ARG 17": "NH1" <-> "NH2" Residue "h ARG 10": "NH1" <-> "NH2" Residue "h ARG 18": "NH1" <-> "NH2" Residue "h ARG 34": "NH1" <-> "NH2" Residue "j ARG 34": "NH1" <-> "NH2" Residue "1 TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 162": "NH1" <-> "NH2" Residue "4 TYR 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 405": "NH1" <-> "NH2" Residue "5 ARG 33": "NH1" <-> "NH2" Residue "5 TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 115": "NH1" <-> "NH2" Residue "5 ARG 303": "NH1" <-> "NH2" Residue "5 TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ARG 25": "NH1" <-> "NH2" Residue "8 ARG 37": "NH1" <-> "NH2" Residue "8 TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ARG 51": "NH1" <-> "NH2" Residue "8 ARG 65": "NH1" <-> "NH2" Residue "9 ARG 34": "NH1" <-> "NH2" Residue "9 ARG 58": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 55137 Number of models: 1 Model: "" Number of chains: 53 Chain: "A" Number of atoms: 5236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 5236 Classifications: {'peptide': 689} Link IDs: {'PTRANS': 34, 'TRANS': 654} Chain: "B" Number of atoms: 3380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3380 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 20, 'TRANS': 422} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2, 'TRP:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "C" Number of atoms: 3190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3190 Classifications: {'peptide': 416} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 22, 'TRANS': 393} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 5, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 75 Chain: "D" Number of atoms: 559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 559 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 3, 'TRANS': 76} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 52 Chain: "E" Number of atoms: 2546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2546 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 15, 'TRANS': 302} Chain: "F" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 915 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 111} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "G" Number of atoms: 1680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1680 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 16, 'TRANS': 215} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 255 Unresolved non-hydrogen angles: 332 Unresolved non-hydrogen dihedrals: 217 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 3, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 164 Chain: "H" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1385 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 16, 'TRANS': 168} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "I" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1441 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 167} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "J" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 961 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 4, 'TRANS': 135} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 47 Chain: "K" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1339 Classifications: {'peptide': 169} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 155} Chain: "L" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 668 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'TRANS': 85} Chain: "M" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 726 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 9, 'TRANS': 95} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 60 Chain: "O" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 591 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 4, 'TRANS': 72} Chain: "P" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 982 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "Q" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 648 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 2, 'TRANS': 82} Chain: "R" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 820 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 93} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "S" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 796 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 158} Link IDs: {'TRANS': 158} Unresolved non-hydrogen bonds: 317 Unresolved non-hydrogen angles: 475 Unresolved non-hydrogen dihedrals: 159 Planarities with less than four sites: {'UNK:plan-1': 158} Unresolved non-hydrogen planarities: 158 Chain: "U" Number of atoms: 1141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1141 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 9, 'TRANS': 148} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 56 Chain: "W" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 929 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 8, 'TRANS': 109} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "X" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 638 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 73} Link IDs: {'PTRANS': 7, 'TRANS': 109} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 287 Unresolved non-hydrogen angles: 367 Unresolved non-hydrogen dihedrals: 251 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 6, 'TYR:plan': 6, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 5, 'GLU:plan': 4, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 160 Chain: "Y" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 957 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "Z" Number of atoms: 686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 686 Classifications: {'peptide': 137} Incomplete info: {'truncation_to_alanine': 136} Link IDs: {'TRANS': 136} Unresolved non-hydrogen bonds: 273 Unresolved non-hydrogen angles: 409 Unresolved non-hydrogen dihedrals: 137 Planarities with less than four sites: {'UNK:plan-1': 136} Unresolved non-hydrogen planarities: 136 Chain: "a" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 501 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'TRANS': 99} Unresolved non-hydrogen bonds: 199 Unresolved non-hydrogen angles: 298 Unresolved non-hydrogen dihedrals: 100 Planarities with less than four sites: {'UNK:plan-1': 99} Unresolved non-hydrogen planarities: 99 Chain: "b" Number of atoms: 321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 321 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'TRANS': 63} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 190 Unresolved non-hydrogen dihedrals: 64 Planarities with less than four sites: {'UNK:plan-1': 63} Unresolved non-hydrogen planarities: 63 Chain: "c" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 251 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 1, 'TRANS': 40} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 76 Chain: "d" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 752 Classifications: {'peptide': 89} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 84} Chain: "e" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 226 Classifications: {'peptide': 45} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'TRANS': 44} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'UNK:plan-1': 44} Unresolved non-hydrogen planarities: 44 Chain: "f" Number of atoms: 629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 629 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 3, 'TRANS': 76} Chain: "g" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 492 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 50} Chain: "h" Number of atoms: 1081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1081 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 10, 'TRANS': 119} Chain: "i" Number of atoms: 266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 266 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'TRANS': 52} Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 157 Unresolved non-hydrogen dihedrals: 53 Planarities with less than four sites: {'UNK:plan-1': 52} Unresolved non-hydrogen planarities: 52 Chain: "j" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 436 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 4, 'TRANS': 68} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 205 Unresolved non-hydrogen dihedrals: 140 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 3, 'ASN:plan1': 1, 'TRP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 86 Chain: "n" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 466 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'TRANS': 92} Unresolved non-hydrogen bonds: 185 Unresolved non-hydrogen angles: 277 Unresolved non-hydrogen dihedrals: 93 Planarities with less than four sites: {'UNK:plan-1': 92} Unresolved non-hydrogen planarities: 92 Chain: "1" Number of atoms: 2608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2608 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 14, 'TRANS': 325} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'TYR:plan': 4, 'GLU:plan': 3, 'ASN:plan1': 3, 'PHE:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 76 Chain: "2" Number of atoms: 3376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3376 Classifications: {'peptide': 452} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 7, 'TRANS': 444} Chain breaks: 1 Unresolved non-hydrogen bonds: 254 Unresolved non-hydrogen angles: 335 Unresolved non-hydrogen dihedrals: 198 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 5, 'ASN:plan1': 10, 'ASP:plan': 3, 'PHE:plan': 5, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 121 Chain: "3" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 871 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "4" Number of atoms: 3312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3312 Classifications: {'peptide': 475} Incomplete info: {'truncation_to_alanine': 128} Link IDs: {'PTRANS': 14, 'TRANS': 460} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 477 Unresolved non-hydrogen angles: 625 Unresolved non-hydrogen dihedrals: 399 Unresolved non-hydrogen chiralities: 51 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 3, 'TYR:plan': 6, 'ASN:plan1': 20, 'TRP:plan': 2, 'HIS:plan': 3, 'PHE:plan': 15, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 269 Chain: "5" Number of atoms: 4599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 639, 4599 Classifications: {'peptide': 639} Incomplete info: {'truncation_to_alanine': 141} Link IDs: {'PTRANS': 15, 'TRANS': 623} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 512 Unresolved non-hydrogen angles: 668 Unresolved non-hydrogen dihedrals: 426 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 3, 'TYR:plan': 8, 'ASN:plan1': 20, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 14, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 276 Chain: "6" Number of atoms: 1211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1211 Classifications: {'peptide': 183} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 3, 'TRANS': 179} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 239 Unresolved non-hydrogen angles: 316 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 11, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 104 Chain: "8" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 672 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 4, 'TRANS': 77} Chain: "9" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 468 Classifications: {'peptide': 59} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 57} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" 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: "B" 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: "E" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} 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: "K" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 126 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 25 Chain: "1" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 809 SG CYS A 142 61.709 151.145 157.126 1.00121.68 S ATOM 749 SG CYS A 133 59.181 153.188 151.957 1.00111.39 S ATOM 769 SG CYS A 136 63.702 156.538 155.841 1.00117.07 S ATOM 1163 SG CYS A 186 62.005 152.365 167.919 1.00120.46 S ATOM 1139 SG CYS A 183 59.207 157.197 166.711 1.00113.84 S ATOM 1187 SG CYS A 189 63.557 156.809 170.909 1.00115.56 S ATOM 1511 SG CYS A 233 64.133 155.183 164.395 1.00120.91 S ATOM 255 SG CYS A 69 58.513 146.645 171.189 1.00122.94 S ATOM 338 SG CYS A 80 57.646 144.811 168.508 1.00125.58 S ATOM 363 SG CYS A 83 57.526 139.739 170.567 1.00123.05 S ATOM 465 SG CYS A 97 57.788 141.722 173.569 1.00132.35 S ATOM 7941 SG CYS B 384 48.882 148.178 173.509 1.00133.27 S ATOM 7961 SG CYS B 387 44.714 151.769 172.110 1.00134.02 S ATOM 7922 SG CYS B 381 49.473 153.577 176.482 1.00131.90 S ATOM 8292 SG CYS B 427 45.387 149.036 178.072 1.00132.78 S ATOM 18235 SG CYS H 127 30.557 164.582 179.228 1.00169.19 S ATOM 18269 SG CYS H 132 27.426 164.260 179.607 1.00168.13 S ATOM 18538 SG CYS H 168 30.854 160.362 181.531 1.00175.31 S ATOM 18561 SG CYS H 172 27.998 159.111 182.968 1.00187.55 S ATOM 19870 SG CYS I 172 65.957 148.730 131.122 1.00 89.06 S ATOM 19844 SG CYS I 169 69.665 153.471 128.278 1.00 94.88 S ATOM 19892 SG CYS I 175 65.179 154.461 132.203 1.00 90.59 S ATOM 19617 SG CYS I 140 71.193 150.989 133.285 1.00 92.07 S ATOM 19922 SG CYS I 179 62.346 159.103 138.690 1.00 92.96 S ATOM 19589 SG CYS I 136 67.600 156.595 138.285 1.00 97.89 S ATOM 19547 SG CYS I 130 66.879 162.328 139.913 1.00104.37 S ATOM 19566 SG CYS I 133 64.351 156.893 143.231 1.00105.47 S ATOM 22143 SG CYS K 150 75.304 145.445 123.199 1.00110.57 S ATOM 21639 SG CYS K 86 72.145 146.561 117.397 1.00113.00 S ATOM 21633 SG CYS K 85 70.853 142.245 118.985 1.00112.64 S ATOM 22371 SG CYS K 180 71.347 147.359 123.433 1.00113.39 S ATOM 23743 SG CYS M 97 53.564 168.647 147.455 1.00130.95 S ATOM 23938 SG CYS M 125 56.110 167.980 149.185 1.00138.96 S ATOM 23965 SG CYS M 128 56.402 170.190 146.933 1.00125.59 S Time building chain proxies: 22.77, per 1000 atoms: 0.41 Number of scatterers: 55137 At special positions: 0 Unit cell: (211.46, 198.38, 228.9, 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 1 29.99 Fe 28 26.01 S 282 16.00 P 10 15.00 O 10146 8.00 N 9391 7.00 C 35279 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS U 46 " - pdb=" SG CYS U 78 " distance=2.04 Simple disulfide: pdb=" SG CYS U 90 " - pdb=" SG CYS U 121 " distance=2.03 Simple disulfide: pdb=" SG CYS U 100 " - pdb=" SG CYS U 111 " distance=2.05 Simple disulfide: pdb=" SG CYS d 51 " - pdb=" SG CYS d 63 " distance=2.05 Simple disulfide: pdb=" SG CYS 8 26 " - pdb=" SG CYS 8 57 " distance=2.03 Simple disulfide: pdb=" SG CYS 8 36 " - pdb=" SG CYS 8 47 " distance=2.04 Simple disulfide: pdb=" SG CYS 9 15 " - pdb=" SG CYS 9 47 " distance=2.05 Simple disulfide: pdb=" SG CYS 9 25 " - pdb=" SG CYS 9 37 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 17.47 Conformation dependent library (CDL) restraints added in 6.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES A 803 " pdb="FE1 FES A 803 " - pdb=" SG CYS A 69 " pdb="FE1 FES A 803 " - pdb=" SG CYS A 80 " pdb="FE2 FES A 803 " - pdb=" SG CYS A 83 " pdb="FE2 FES A 803 " - pdb=" SG CYS A 97 " pdb=" FES H 301 " pdb="FE1 FES H 301 " - pdb=" SG CYS H 127 " pdb="FE1 FES H 301 " - pdb=" SG CYS H 132 " pdb="FE2 FES H 301 " - pdb=" SG CYS H 168 " pdb="FE2 FES H 301 " - pdb=" SG CYS H 172 " pdb=" SF4 A 801 " pdb="FE3 SF4 A 801 " - pdb=" NE2 HIS A 129 " pdb="FE1 SF4 A 801 " - pdb=" SG CYS A 142 " pdb="FE2 SF4 A 801 " - pdb=" SG CYS A 133 " pdb="FE4 SF4 A 801 " - pdb=" SG CYS A 136 " pdb=" SF4 A 802 " pdb="FE2 SF4 A 802 " - pdb=" SG CYS A 183 " pdb="FE4 SF4 A 802 " - pdb=" SG CYS A 233 " pdb="FE3 SF4 A 802 " - pdb=" SG CYS A 189 " pdb="FE1 SF4 A 802 " - pdb=" SG CYS A 186 " pdb=" SF4 B 501 " pdb="FE4 SF4 B 501 " - pdb=" SG CYS B 427 " pdb="FE3 SF4 B 501 " - pdb=" SG CYS B 381 " pdb="FE2 SF4 B 501 " - pdb=" SG CYS B 387 " pdb="FE1 SF4 B 501 " - pdb=" SG CYS B 384 " pdb=" SF4 I 301 " pdb="FE4 SF4 I 301 " - pdb=" SG CYS I 140 " pdb="FE3 SF4 I 301 " - pdb=" SG CYS I 175 " pdb="FE2 SF4 I 301 " - pdb=" SG CYS I 169 " pdb="FE1 SF4 I 301 " - pdb=" SG CYS I 172 " pdb="FE2 SF4 I 301 " - pdb=" NE2 HIS I 118 " pdb=" SF4 I 302 " pdb="FE1 SF4 I 302 " - pdb=" SG CYS I 179 " pdb="FE3 SF4 I 302 " - pdb=" SG CYS I 130 " pdb="FE2 SF4 I 302 " - pdb=" SG CYS I 136 " pdb="FE4 SF4 I 302 " - pdb=" SG CYS I 133 " pdb=" SF4 K 301 " pdb="FE1 SF4 K 301 " - pdb=" SG CYS K 150 " pdb="FE2 SF4 K 301 " - pdb=" SG CYS K 86 " pdb="FE4 SF4 K 301 " - pdb=" SG CYS K 180 " pdb="FE3 SF4 K 301 " - pdb=" SG CYS K 85 " Number of angles added : 83 Zn2+ tetrahedral coordination pdb=" ZN M 201 " pdb="ZN ZN M 201 " - pdb=" NE2 HIS M 110 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 128 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 125 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 97 " Number of angles added : 3 13576 Ramachandran restraints generated. 6788 Oldfield, 0 Emsley, 6788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14160 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 293 helices and 24 sheets defined 49.8% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.56 Creating SS restraints... Processing helix chain 'A' and resid 54 through 60 Processing helix chain 'A' and resid 112 through 126 removed outlier: 4.610A pdb=" N ASN A 120 " --> pdb=" O GLN A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 134 No H-bonds generated for 'chain 'A' and resid 132 through 134' Processing helix chain 'A' and resid 143 through 146 No H-bonds generated for 'chain 'A' and resid 143 through 146' Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 188 through 195 Processing helix chain 'A' and resid 226 through 231 removed outlier: 3.764A pdb=" N ILE A 230 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 299 No H-bonds generated for 'chain 'A' and resid 297 through 299' Processing helix chain 'A' and resid 325 through 339 Processing helix chain 'A' and resid 356 through 369 Processing helix chain 'A' and resid 392 through 394 No H-bonds generated for 'chain 'A' and resid 392 through 394' Processing helix chain 'A' and resid 402 through 406 Processing helix chain 'A' and resid 422 through 434 Processing helix chain 'A' and resid 459 through 468 Processing helix chain 'A' and resid 470 through 476 removed outlier: 3.952A pdb=" N LYS A 475 " --> pdb=" O GLY A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 490 No H-bonds generated for 'chain 'A' and resid 487 through 490' Processing helix chain 'A' and resid 496 through 507 removed outlier: 3.844A pdb=" N ILE A 501 " --> pdb=" O PHE A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 534 Processing helix chain 'A' and resid 540 through 543 No H-bonds generated for 'chain 'A' and resid 540 through 543' Processing helix chain 'A' and resid 558 through 560 No H-bonds generated for 'chain 'A' and resid 558 through 560' Processing helix chain 'A' and resid 592 through 594 No H-bonds generated for 'chain 'A' and resid 592 through 594' Processing helix chain 'A' and resid 622 through 632 Processing helix chain 'A' and resid 642 through 652 removed outlier: 3.720A pdb=" N ARG A 646 " --> pdb=" O ALA A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 667 No H-bonds generated for 'chain 'A' and resid 665 through 667' Processing helix chain 'A' and resid 670 through 676 Processing helix chain 'A' and resid 704 through 706 No H-bonds generated for 'chain 'A' and resid 704 through 706' Processing helix chain 'A' and resid 708 through 714 removed outlier: 3.682A pdb=" N LYS A 712 " --> pdb=" O PRO A 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 58 Processing helix chain 'B' and resid 64 through 69 Processing helix chain 'B' and resid 72 through 82 Processing helix chain 'B' and resid 94 through 100 Processing helix chain 'B' and resid 104 through 107 removed outlier: 3.773A pdb=" N GLU B 107 " --> pdb=" O PRO B 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 104 through 107' Processing helix chain 'B' and resid 137 through 151 removed outlier: 4.080A pdb=" N GLU B 142 " --> pdb=" O HIS B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 180 removed outlier: 3.800A pdb=" N ALA B 169 " --> pdb=" O TYR B 165 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL B 170 " --> pdb=" O ASN B 166 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA B 178 " --> pdb=" O ALA B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 209 Processing helix chain 'B' and resid 211 through 218 Processing helix chain 'B' and resid 237 through 239 No H-bonds generated for 'chain 'B' and resid 237 through 239' Processing helix chain 'B' and resid 247 through 251 Processing helix chain 'B' and resid 253 through 258 Processing helix chain 'B' and resid 261 through 265 Processing helix chain 'B' and resid 298 through 305 removed outlier: 3.720A pdb=" N HIS B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 315 No H-bonds generated for 'chain 'B' and resid 313 through 315' Processing helix chain 'B' and resid 342 through 345 No H-bonds generated for 'chain 'B' and resid 342 through 345' Processing helix chain 'B' and resid 365 through 379 Processing helix chain 'B' and resid 385 through 403 removed outlier: 3.855A pdb=" N GLU B 389 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG B 400 " --> pdb=" O LYS B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 421 removed outlier: 4.408A pdb=" N ASP B 412 " --> pdb=" O GLU B 408 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE B 421 " --> pdb=" O LEU B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 441 Proline residue: B 436 - end of helix Processing helix chain 'B' and resid 447 through 454 removed outlier: 3.744A pdb=" N LYS B 454 " --> pdb=" O THR B 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 128 removed outlier: 4.628A pdb=" N GLU C 128 " --> pdb=" O GLU C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 139 removed outlier: 3.704A pdb=" N LEU C 136 " --> pdb=" O TYR C 132 " (cutoff:3.500A) Proline residue: C 137 - end of helix No H-bonds generated for 'chain 'C' and resid 132 through 139' Processing helix chain 'C' and resid 147 through 160 Processing helix chain 'C' and resid 168 through 197 Processing helix chain 'C' and resid 201 through 218 removed outlier: 3.815A pdb=" N GLU C 209 " --> pdb=" O TRP C 205 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS C 212 " --> pdb=" O GLU C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 262 removed outlier: 4.060A pdb=" N TYR C 248 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N MET C 249 " --> pdb=" O ASP C 245 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN C 253 " --> pdb=" O MET C 249 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLY C 255 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ASP C 256 " --> pdb=" O THR C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 288 removed outlier: 3.630A pdb=" N ASN C 288 " --> pdb=" O GLN C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 299 Processing helix chain 'C' and resid 329 through 352 removed outlier: 3.866A pdb=" N ARG C 336 " --> pdb=" O ARG C 332 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ARG C 341 " --> pdb=" O MET C 337 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ARG C 345 " --> pdb=" O ARG C 341 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE C 346 " --> pdb=" O GLN C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 375 No H-bonds generated for 'chain 'C' and resid 373 through 375' Processing helix chain 'C' and resid 378 through 389 Processing helix chain 'C' and resid 430 through 433 No H-bonds generated for 'chain 'C' and resid 430 through 433' Processing helix chain 'C' and resid 438 through 442 Processing helix chain 'C' and resid 447 through 457 removed outlier: 3.971A pdb=" N ALA C 452 " --> pdb=" O PRO C 448 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY C 455 " --> pdb=" O VAL C 451 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N MET C 457 " --> pdb=" O ILE C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 463 No H-bonds generated for 'chain 'C' and resid 461 through 463' Processing helix chain 'D' and resid 7 through 33 removed outlier: 4.004A pdb=" N TYR D 11 " --> pdb=" O ALA D 7 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU D 18 " --> pdb=" O ILE D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 56 removed outlier: 4.610A pdb=" N GLU D 51 " --> pdb=" O SER D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 72 No H-bonds generated for 'chain 'D' and resid 69 through 72' Processing helix chain 'E' and resid 64 through 74 removed outlier: 4.515A pdb=" N TYR E 68 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU E 69 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR E 70 " --> pdb=" O GLY E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 89 No H-bonds generated for 'chain 'E' and resid 87 through 89' Processing helix chain 'E' and resid 91 through 93 No H-bonds generated for 'chain 'E' and resid 91 through 93' Processing helix chain 'E' and resid 112 through 118 Processing helix chain 'E' and resid 146 through 158 removed outlier: 3.616A pdb=" N ILE E 151 " --> pdb=" O GLY E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 192 Processing helix chain 'E' and resid 215 through 218 No H-bonds generated for 'chain 'E' and resid 215 through 218' Processing helix chain 'E' and resid 238 through 249 Processing helix chain 'E' and resid 270 through 278 Processing helix chain 'E' and resid 295 through 303 removed outlier: 3.721A pdb=" N GLN E 302 " --> pdb=" O THR E 298 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ALA E 303 " --> pdb=" O LYS E 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 318 removed outlier: 3.765A pdb=" N PHE E 318 " --> pdb=" O VAL E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 341 through 347 removed outlier: 3.729A pdb=" N LYS E 346 " --> pdb=" O ASP E 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 58 removed outlier: 3.570A pdb=" N GLN F 58 " --> pdb=" O LEU F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 84 removed outlier: 3.975A pdb=" N ASN F 73 " --> pdb=" O GLN F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 95 Processing helix chain 'F' and resid 100 through 118 removed outlier: 3.893A pdb=" N GLU F 109 " --> pdb=" O ILE F 105 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLU F 110 " --> pdb=" O GLN F 106 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LEU F 111 " --> pdb=" O ALA F 107 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU F 112 " --> pdb=" O HIS F 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 81 removed outlier: 3.676A pdb=" N GLN G 73 " --> pdb=" O SER G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 110 Processing helix chain 'G' and resid 178 through 186 Processing helix chain 'H' and resid 49 through 61 removed outlier: 3.881A pdb=" N LYS H 53 " --> pdb=" O PRO H 49 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS H 61 " --> pdb=" O GLU H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 81 Processing helix chain 'H' and resid 87 through 96 Processing helix chain 'H' and resid 101 through 108 Processing helix chain 'H' and resid 130 through 135 Processing helix chain 'H' and resid 137 through 147 Processing helix chain 'H' and resid 190 through 202 removed outlier: 3.767A pdb=" N LYS H 201 " --> pdb=" O LEU H 197 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ALA H 202 " --> pdb=" O GLU H 198 " (cutoff:3.500A) Processing helix chain 'I' and resid 72 through 78 Processing helix chain 'I' and resid 81 through 94 removed outlier: 3.846A pdb=" N GLY I 86 " --> pdb=" O GLU I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 197 through 199 No H-bonds generated for 'chain 'I' and resid 197 through 199' Processing helix chain 'I' and resid 204 through 213 Processing helix chain 'I' and resid 216 through 224 Processing helix chain 'J' and resid 25 through 42 removed outlier: 4.084A pdb=" N GLN J 31 " --> pdb=" O GLY J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 60 through 64 Processing helix chain 'J' and resid 72 through 88 removed outlier: 3.611A pdb=" N ILE J 76 " --> pdb=" O THR J 72 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N PHE J 80 " --> pdb=" O ILE J 76 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR J 81 " --> pdb=" O ALA J 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 111 removed outlier: 3.969A pdb=" N MET J 98 " --> pdb=" O TRP J 95 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLY J 101 " --> pdb=" O MET J 98 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ALA J 102 " --> pdb=" O TRP J 99 " (cutoff:3.500A) Processing helix chain 'J' and resid 116 through 130 Processing helix chain 'K' and resid 61 through 74 Processing helix chain 'K' and resid 85 through 93 Processing helix chain 'K' and resid 128 through 136 Processing helix chain 'K' and resid 149 through 151 No H-bonds generated for 'chain 'K' and resid 149 through 151' Processing helix chain 'K' and resid 167 through 169 No H-bonds generated for 'chain 'K' and resid 167 through 169' Processing helix chain 'K' and resid 184 through 200 removed outlier: 3.804A pdb=" N ASN K 200 " --> pdb=" O ARG K 196 " (cutoff:3.500A) Processing helix chain 'K' and resid 203 through 207 Processing helix chain 'L' and resid 2 through 16 removed outlier: 4.248A pdb=" N ILE L 7 " --> pdb=" O ILE L 3 " (cutoff:3.500A) Processing helix chain 'L' and resid 22 through 47 removed outlier: 4.000A pdb=" N LEU L 33 " --> pdb=" O LEU L 29 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU L 34 " --> pdb=" O GLU L 30 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ASN L 37 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU L 38 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE L 39 " --> pdb=" O GLY L 35 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG L 42 " --> pdb=" O LEU L 38 " (cutoff:3.500A) Processing helix chain 'L' and resid 53 through 74 removed outlier: 3.755A pdb=" N VAL L 65 " --> pdb=" O ILE L 61 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 84 removed outlier: 3.975A pdb=" N ALA M 83 " --> pdb=" O ILE M 79 " (cutoff:3.500A) Processing helix chain 'O' and resid 32 through 42 removed outlier: 3.766A pdb=" N GLU O 41 " --> pdb=" O ALA O 37 " (cutoff:3.500A) Processing helix chain 'O' and resid 66 through 79 removed outlier: 3.642A pdb=" N VAL O 70 " --> pdb=" O SER O 66 " (cutoff:3.500A) Processing helix chain 'O' and resid 86 through 91 Processing helix chain 'O' and resid 95 through 104 removed outlier: 4.152A pdb=" N ALA O 104 " --> pdb=" O GLU O 100 " (cutoff:3.500A) Processing helix chain 'P' and resid 18 through 43 removed outlier: 4.396A pdb=" N ALA P 36 " --> pdb=" O PHE P 32 " (cutoff:3.500A) Proline residue: P 37 - end of helix Processing helix chain 'P' and resid 49 through 63 removed outlier: 4.072A pdb=" N HIS P 63 " --> pdb=" O GLU P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 69 through 87 removed outlier: 5.232A pdb=" N VAL P 74 " --> pdb=" O SER P 70 " (cutoff:3.500A) Processing helix chain 'P' and resid 93 through 99 removed outlier: 4.465A pdb=" N LYS P 98 " --> pdb=" O ALA P 94 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N TYR P 99 " --> pdb=" O GLN P 95 " (cutoff:3.500A) Processing helix chain 'Q' and resid 52 through 65 Processing helix chain 'Q' and resid 89 through 102 Processing helix chain 'Q' and resid 111 through 114 Processing helix chain 'Q' and resid 118 through 127 Processing helix chain 'R' and resid 12 through 29 removed outlier: 3.573A pdb=" N MET R 18 " --> pdb=" O LEU R 14 " (cutoff:3.500A) Processing helix chain 'R' and resid 33 through 48 Processing helix chain 'R' and resid 56 through 73 removed outlier: 3.617A pdb=" N PHE R 73 " --> pdb=" O HIS R 69 " (cutoff:3.500A) Processing helix chain 'S' and resid 76 through 89 removed outlier: 4.011A pdb=" N UNK S 81 " --> pdb=" O UNK S 77 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N UNK S 82 " --> pdb=" O UNK S 78 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N UNK S 83 " --> pdb=" O UNK S 79 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N UNK S 89 " --> pdb=" O UNK S 85 " (cutoff:3.500A) Processing helix chain 'S' and resid 101 through 114 removed outlier: 3.732A pdb=" N UNK S 108 " --> pdb=" O UNK S 104 " (cutoff:3.500A) Processing helix chain 'S' and resid 126 through 149 removed outlier: 3.791A pdb=" N UNK S 131 " --> pdb=" O UNK S 127 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N UNK S 141 " --> pdb=" O UNK S 137 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N UNK S 142 " --> pdb=" O UNK S 138 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N UNK S 143 " --> pdb=" O UNK S 139 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N UNK S 147 " --> pdb=" O UNK S 143 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N UNK S 148 " --> pdb=" O UNK S 144 " (cutoff:3.500A) Processing helix chain 'S' and resid 169 through 189 removed outlier: 4.400A pdb=" N UNK S 175 " --> pdb=" O UNK S 171 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N UNK S 176 " --> pdb=" O UNK S 172 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N UNK S 177 " --> pdb=" O UNK S 173 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N UNK S 178 " --> pdb=" O UNK S 174 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N UNK S 179 " --> pdb=" O UNK S 175 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N UNK S 187 " --> pdb=" O UNK S 183 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N UNK S 188 " --> pdb=" O UNK S 184 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N UNK S 189 " --> pdb=" O UNK S 185 " (cutoff:3.500A) Processing helix chain 'S' and resid 191 through 207 removed outlier: 4.837A pdb=" N UNK S 196 " --> pdb=" O UNK S 192 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N UNK S 199 " --> pdb=" O UNK S 195 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N UNK S 201 " --> pdb=" O UNK S 197 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N UNK S 207 " --> pdb=" O UNK S 203 " (cutoff:3.500A) Processing helix chain 'S' and resid 217 through 221 Processing helix chain 'U' and resid 33 through 36 Processing helix chain 'U' and resid 43 through 59 Proline residue: U 48 - end of helix Processing helix chain 'U' and resid 71 through 89 removed outlier: 4.242A pdb=" N THR U 76 " --> pdb=" O GLY U 72 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA U 79 " --> pdb=" O VAL U 75 " (cutoff:3.500A) Processing helix chain 'U' and resid 91 through 102 removed outlier: 3.510A pdb=" N HIS U 97 " --> pdb=" O GLU U 93 " (cutoff:3.500A) Processing helix chain 'U' and resid 104 through 106 No H-bonds generated for 'chain 'U' and resid 104 through 106' Processing helix chain 'U' and resid 108 through 111 removed outlier: 3.885A pdb=" N CYS U 111 " --> pdb=" O LEU U 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 108 through 111' Processing helix chain 'U' and resid 114 through 125 Processing helix chain 'U' and resid 158 through 166 Processing helix chain 'W' and resid 31 through 96 removed outlier: 5.179A pdb=" N ALA W 36 " --> pdb=" O TYR W 33 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N CYS W 41 " --> pdb=" O CYS W 38 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N PHE W 45 " --> pdb=" O GLY W 42 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N LEU W 49 " --> pdb=" O TYR W 46 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS W 59 " --> pdb=" O ARG W 56 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ARG W 60 " --> pdb=" O GLU W 57 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU W 63 " --> pdb=" O ARG W 60 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N TRP W 64 " --> pdb=" O GLU W 61 " (cutoff:3.500A) Proline residue: W 71 - end of helix removed outlier: 4.404A pdb=" N ARG W 79 " --> pdb=" O GLU W 76 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ARG W 84 " --> pdb=" O THR W 81 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ILE W 86 " --> pdb=" O ARG W 83 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA W 87 " --> pdb=" O ARG W 84 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET W 96 " --> pdb=" O LYS W 93 " (cutoff:3.500A) Processing helix chain 'X' and resid 34 through 37 No H-bonds generated for 'chain 'X' and resid 34 through 37' Processing helix chain 'X' and resid 42 through 60 removed outlier: 4.046A pdb=" N LEU X 45 " --> pdb=" O VAL X 42 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N THR X 47 " --> pdb=" O GLY X 44 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU X 50 " --> pdb=" O THR X 47 " (cutoff:3.500A) Proline residue: X 51 - end of helix removed outlier: 5.207A pdb=" N ILE X 54 " --> pdb=" O PRO X 51 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA X 57 " --> pdb=" O ILE X 54 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLU X 58 " --> pdb=" O CYS X 55 " (cutoff:3.500A) Processing helix chain 'X' and resid 74 through 91 removed outlier: 4.921A pdb=" N VAL X 85 " --> pdb=" O GLY X 82 " (cutoff:3.500A) Processing helix chain 'X' and resid 106 through 109 No H-bonds generated for 'chain 'X' and resid 106 through 109' Processing helix chain 'X' and resid 111 through 116 Processing helix chain 'Y' and resid 52 through 54 No H-bonds generated for 'chain 'Y' and resid 52 through 54' Processing helix chain 'Y' and resid 73 through 76 Processing helix chain 'Y' and resid 115 through 125 Processing helix chain 'Z' and resid 31 through 34 No H-bonds generated for 'chain 'Z' and resid 31 through 34' Processing helix chain 'Z' and resid 92 through 96 Processing helix chain 'Z' and resid 110 through 121 removed outlier: 4.062A pdb=" N UNK Z 114 " --> pdb=" O UNK Z 110 " (cutoff:3.500A) Processing helix chain 'a' and resid 92 through 94 No H-bonds generated for 'chain 'a' and resid 92 through 94' Processing helix chain 'a' and resid 96 through 107 removed outlier: 3.838A pdb=" N UNK a 104 " --> pdb=" O UNK a 100 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N UNK a 107 " --> pdb=" O UNK a 103 " (cutoff:3.500A) Processing helix chain 'a' and resid 121 through 123 No H-bonds generated for 'chain 'a' and resid 121 through 123' Processing helix chain 'b' and resid 2 through 22 removed outlier: 3.985A pdb=" N UNK b 21 " --> pdb=" O UNK b 17 " (cutoff:3.500A) Processing helix chain 'b' and resid 39 through 62 removed outlier: 3.780A pdb=" N UNK b 43 " --> pdb=" O UNK b 39 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N UNK b 44 " --> pdb=" O UNK b 40 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N UNK b 49 " --> pdb=" O UNK b 45 " (cutoff:3.500A) Processing helix chain 'c' and resid 17 through 19 No H-bonds generated for 'chain 'c' and resid 17 through 19' Processing helix chain 'c' and resid 23 through 27 removed outlier: 3.728A pdb=" N PHE c 27 " --> pdb=" O ARG c 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 23 through 27' Processing helix chain 'c' and resid 37 through 49 Processing helix chain 'd' and resid 12 through 14 No H-bonds generated for 'chain 'd' and resid 12 through 14' Processing helix chain 'd' and resid 20 through 55 removed outlier: 3.643A pdb=" N LYS d 50 " --> pdb=" O LYS d 46 " (cutoff:3.500A) Processing helix chain 'd' and resid 64 through 73 removed outlier: 4.035A pdb=" N GLN d 69 " --> pdb=" O ASN d 65 " (cutoff:3.500A) Processing helix chain 'e' and resid 19 through 35 removed outlier: 3.977A pdb=" N UNK e 26 " --> pdb=" O UNK e 22 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N UNK e 27 " --> pdb=" O UNK e 23 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N UNK e 28 " --> pdb=" O UNK e 24 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N UNK e 31 " --> pdb=" O UNK e 27 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N UNK e 32 " --> pdb=" O UNK e 28 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N UNK e 33 " --> pdb=" O UNK e 29 " (cutoff:3.500A) Processing helix chain 'e' and resid 38 through 42 Processing helix chain 'f' and resid 20 through 26 Processing helix chain 'f' and resid 30 through 36 removed outlier: 3.648A pdb=" N LYS f 35 " --> pdb=" O GLY f 31 " (cutoff:3.500A) Processing helix chain 'f' and resid 76 through 84 Processing helix chain 'g' and resid 12 through 17 removed outlier: 3.588A pdb=" N ARG g 17 " --> pdb=" O PHE g 13 " (cutoff:3.500A) Processing helix chain 'g' and resid 24 through 41 removed outlier: 4.073A pdb=" N ALA g 29 " --> pdb=" O HIS g 25 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE g 32 " --> pdb=" O PHE g 28 " (cutoff:3.500A) Proline residue: g 37 - end of helix Processing helix chain 'h' and resid 13 through 15 No H-bonds generated for 'chain 'h' and resid 13 through 15' Processing helix chain 'h' and resid 17 through 26 removed outlier: 3.798A pdb=" N LYS h 22 " --> pdb=" O ARG h 18 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN h 25 " --> pdb=" O TRP h 21 " (cutoff:3.500A) Processing helix chain 'h' and resid 78 through 82 Processing helix chain 'h' and resid 93 through 96 No H-bonds generated for 'chain 'h' and resid 93 through 96' Processing helix chain 'i' and resid 6 through 21 removed outlier: 4.891A pdb=" N UNK i 14 " --> pdb=" O UNK i 10 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N UNK i 15 " --> pdb=" O UNK i 11 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N UNK i 16 " --> pdb=" O UNK i 12 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N UNK i 17 " --> pdb=" O UNK i 13 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N UNK i 21 " --> pdb=" O UNK i 17 " (cutoff:3.500A) Processing helix chain 'i' and resid 34 through 53 removed outlier: 3.610A pdb=" N UNK i 41 " --> pdb=" O UNK i 37 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N UNK i 44 " --> pdb=" O UNK i 40 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N UNK i 46 " --> pdb=" O UNK i 42 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N UNK i 47 " --> pdb=" O UNK i 43 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N UNK i 48 " --> pdb=" O UNK i 44 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N UNK i 49 " --> pdb=" O UNK i 45 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N UNK i 52 " --> pdb=" O UNK i 48 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N UNK i 53 " --> pdb=" O UNK i 49 " (cutoff:3.500A) Processing helix chain 'j' and resid 30 through 39 Processing helix chain 'j' and resid 49 through 69 removed outlier: 3.818A pdb=" N GLY j 53 " --> pdb=" O THR j 49 " (cutoff:3.500A) Proline residue: j 64 - end of helix Processing helix chain 'n' and resid 54 through 71 removed outlier: 3.665A pdb=" N UNK n 59 " --> pdb=" O UNK n 55 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N UNK n 60 " --> pdb=" O UNK n 56 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N UNK n 64 " --> pdb=" O UNK n 60 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N UNK n 70 " --> pdb=" O UNK n 66 " (cutoff:3.500A) Processing helix chain 'n' and resid 88 through 108 removed outlier: 3.605A pdb=" N UNK n 95 " --> pdb=" O UNK n 91 " (cutoff:3.500A) Processing helix chain '1' and resid 3 through 33 removed outlier: 3.955A pdb=" N THR 1 23 " --> pdb=" O VAL 1 19 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL 1 24 " --> pdb=" O ALA 1 20 " (cutoff:3.500A) Processing helix chain '1' and resid 49 through 57 removed outlier: 4.422A pdb=" N VAL 1 55 " --> pdb=" O PHE 1 51 " (cutoff:3.500A) Processing helix chain '1' and resid 69 through 81 removed outlier: 4.238A pdb=" N VAL 1 74 " --> pdb=" O TYR 1 70 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N SER 1 76 " --> pdb=" O ILE 1 72 " (cutoff:3.500A) Proline residue: 1 77 - end of helix Processing helix chain '1' and resid 88 through 90 No H-bonds generated for 'chain '1' and resid 88 through 90' Processing helix chain '1' and resid 106 through 124 removed outlier: 4.587A pdb=" N VAL 1 117 " --> pdb=" O GLY 1 113 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N PHE 1 118 " --> pdb=" O SER 1 114 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLY 1 119 " --> pdb=" O LEU 1 115 " (cutoff:3.500A) Processing helix chain '1' and resid 126 through 128 No H-bonds generated for 'chain '1' and resid 126 through 128' Processing helix chain '1' and resid 133 through 154 removed outlier: 4.106A pdb=" N ILE 1 149 " --> pdb=" O SER 1 145 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ILE 1 153 " --> pdb=" O ILE 1 149 " (cutoff:3.500A) Processing helix chain '1' and resid 157 through 160 Processing helix chain '1' and resid 166 through 173 removed outlier: 4.203A pdb=" N ILE 1 170 " --> pdb=" O ILE 1 166 " (cutoff:3.500A) Processing helix chain '1' and resid 178 through 181 No H-bonds generated for 'chain '1' and resid 178 through 181' Processing helix chain '1' and resid 184 through 196 removed outlier: 4.025A pdb=" N VAL 1 194 " --> pdb=" O ILE 1 191 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLU 1 196 " --> pdb=" O SER 1 193 " (cutoff:3.500A) Processing helix chain '1' and resid 222 through 244 Processing helix chain '1' and resid 252 through 259 removed outlier: 4.147A pdb=" N LEU 1 258 " --> pdb=" O ASN 1 254 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N PHE 1 259 " --> pdb=" O TYR 1 255 " (cutoff:3.500A) Processing helix chain '1' and resid 261 through 263 No H-bonds generated for 'chain '1' and resid 261 through 263' Processing helix chain '1' and resid 274 through 298 removed outlier: 3.580A pdb=" N PHE 1 288 " --> pdb=" O ILE 1 284 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU 1 289 " --> pdb=" O LYS 1 285 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER 1 292 " --> pdb=" O PHE 1 288 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE 1 293 " --> pdb=" O LEU 1 289 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA 1 298 " --> pdb=" O ILE 1 294 " (cutoff:3.500A) Processing helix chain '1' and resid 305 through 313 Processing helix chain '1' and resid 316 through 334 Proline residue: 1 328 - end of helix removed outlier: 4.169A pdb=" N LEU 1 331 " --> pdb=" O ILE 1 327 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR 1 332 " --> pdb=" O PRO 1 328 " (cutoff:3.500A) Processing helix chain '2' and resid 2 through 13 removed outlier: 3.582A pdb=" N THR 2 11 " --> pdb=" O ILE 2 7 " (cutoff:3.500A) Processing helix chain '2' and resid 23 through 42 removed outlier: 5.445A pdb=" N SER 2 40 " --> pdb=" O LEU 2 36 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N PHE 2 41 " --> pdb=" O VAL 2 37 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N LEU 2 42 " --> pdb=" O LEU 2 38 " (cutoff:3.500A) Processing helix chain '2' and resid 65 through 83 removed outlier: 3.931A pdb=" N MET 2 70 " --> pdb=" O PHE 2 66 " (cutoff:3.500A) Processing helix chain '2' and resid 104 through 119 Processing helix chain '2' and resid 123 through 142 removed outlier: 3.957A pdb=" N ALA 2 142 " --> pdb=" O TYR 2 138 " (cutoff:3.500A) Processing helix chain '2' and resid 149 through 178 removed outlier: 3.680A pdb=" N MET 2 155 " --> pdb=" O SER 2 151 " (cutoff:3.500A) Processing helix chain '2' and resid 184 through 186 No H-bonds generated for 'chain '2' and resid 184 through 186' Processing helix chain '2' and resid 195 through 210 removed outlier: 3.895A pdb=" N PHE 2 210 " --> pdb=" O LEU 2 206 " (cutoff:3.500A) Processing helix chain '2' and resid 215 through 217 No H-bonds generated for 'chain '2' and resid 215 through 217' Processing helix chain '2' and resid 219 through 226 removed outlier: 3.839A pdb=" N SER 2 223 " --> pdb=" O TRP 2 220 " (cutoff:3.500A) Processing helix chain '2' and resid 230 through 236 removed outlier: 4.868A pdb=" N TYR 2 235 " --> pdb=" O LEU 2 231 " (cutoff:3.500A) Processing helix chain '2' and resid 239 through 250 removed outlier: 4.156A pdb=" N LEU 2 245 " --> pdb=" O LYS 2 241 " (cutoff:3.500A) Processing helix chain '2' and resid 261 through 271 Processing helix chain '2' and resid 281 through 296 removed outlier: 3.775A pdb=" N MET 2 296 " --> pdb=" O ASN 2 292 " (cutoff:3.500A) Processing helix chain '2' and resid 307 through 333 removed outlier: 3.923A pdb=" N THR 2 314 " --> pdb=" O LEU 2 310 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N SER 2 319 " --> pdb=" O GLN 2 315 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE 2 331 " --> pdb=" O ILE 2 327 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N TYR 2 332 " --> pdb=" O ILE 2 328 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N TYR 2 333 " --> pdb=" O PHE 2 329 " (cutoff:3.500A) Processing helix chain '2' and resid 347 through 349 No H-bonds generated for 'chain '2' and resid 347 through 349' Processing helix chain '2' and resid 353 through 355 No H-bonds generated for 'chain '2' and resid 353 through 355' Processing helix chain '2' and resid 358 through 372 removed outlier: 3.645A pdb=" N PHE 2 371 " --> pdb=" O VAL 2 367 " (cutoff:3.500A) Processing helix chain '2' and resid 379 through 393 removed outlier: 4.451A pdb=" N LEU 2 384 " --> pdb=" O PHE 2 380 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ASN 2 385 " --> pdb=" O PHE 2 381 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN 2 393 " --> pdb=" O SER 2 389 " (cutoff:3.500A) Processing helix chain '2' and resid 396 through 420 removed outlier: 3.741A pdb=" N ILE 2 400 " --> pdb=" O TYR 2 396 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR 2 412 " --> pdb=" O ILE 2 408 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU 2 416 " --> pdb=" O TYR 2 412 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU 2 417 " --> pdb=" O TYR 2 413 " (cutoff:3.500A) Processing helix chain '2' and resid 438 through 448 Processing helix chain '2' and resid 457 through 461 Processing helix chain '3' and resid 5 through 20 Proline residue: 3 12 - end of helix Processing helix chain '3' and resid 22 through 25 No H-bonds generated for 'chain '3' and resid 22 through 25' Processing helix chain '3' and resid 54 through 78 removed outlier: 4.272A pdb=" N VAL 3 59 " --> pdb=" O ALA 3 55 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ALA 3 60 " --> pdb=" O PHE 3 56 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU 3 64 " --> pdb=" O ALA 3 60 " (cutoff:3.500A) Proline residue: 3 65 - end of helix removed outlier: 3.991A pdb=" N ILE 3 70 " --> pdb=" O PHE 3 66 " (cutoff:3.500A) Proline residue: 3 75 - end of helix Processing helix chain '3' and resid 87 through 107 removed outlier: 3.892A pdb=" N GLY 3 101 " --> pdb=" O ILE 3 97 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ASN 3 107 " --> pdb=" O VAL 3 103 " (cutoff:3.500A) Processing helix chain '4' and resid 12 through 22 removed outlier: 3.688A pdb=" N GLY 4 22 " --> pdb=" O LEU 4 18 " (cutoff:3.500A) Processing helix chain '4' and resid 29 through 43 removed outlier: 3.977A pdb=" N LEU 4 35 " --> pdb=" O ALA 4 31 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL 4 40 " --> pdb=" O LEU 4 36 " (cutoff:3.500A) Processing helix chain '4' and resid 45 through 47 No H-bonds generated for 'chain '4' and resid 45 through 47' Processing helix chain '4' and resid 84 through 103 removed outlier: 4.309A pdb=" N THR 4 87 " --> pdb=" O LEU 4 84 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N VAL 4 93 " --> pdb=" O LEU 4 90 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LEU 4 94 " --> pdb=" O LEU 4 91 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ILE 4 96 " --> pdb=" O VAL 4 93 " (cutoff:3.500A) Proline residue: 4 97 - end of helix removed outlier: 4.258A pdb=" N LEU 4 101 " --> pdb=" O LEU 4 98 " (cutoff:3.500A) Processing helix chain '4' and resid 113 through 129 removed outlier: 3.551A pdb=" N LEU 4 126 " --> pdb=" O GLY 4 122 " (cutoff:3.500A) Processing helix chain '4' and resid 134 through 141 removed outlier: 3.620A pdb=" N LEU 4 140 " --> pdb=" O SER 4 136 " (cutoff:3.500A) Processing helix chain '4' and resid 144 through 153 Processing helix chain '4' and resid 160 through 188 removed outlier: 4.345A pdb=" N PHE 4 165 " --> pdb=" O GLU 4 161 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N TYR 4 166 " --> pdb=" O ARG 4 162 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL 4 167 " --> pdb=" O ALA 4 163 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU 4 168 " --> pdb=" O SER 4 164 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N LEU 4 172 " --> pdb=" O LEU 4 168 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER 4 175 " --> pdb=" O THR 4 171 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU 4 180 " --> pdb=" O LEU 4 176 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER 4 181 " --> pdb=" O PHE 4 177 " (cutoff:3.500A) Processing helix chain '4' and resid 208 through 221 removed outlier: 4.061A pdb=" N ALA 4 217 " --> pdb=" O GLY 4 213 " (cutoff:3.500A) Processing helix chain '4' and resid 229 through 234 removed outlier: 4.098A pdb=" N VAL 4 233 " --> pdb=" O VAL 4 229 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL 4 234 " --> pdb=" O TRP 4 230 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 229 through 234' Processing helix chain '4' and resid 246 through 250 Processing helix chain '4' and resid 255 through 260 Processing helix chain '4' and resid 277 through 290 removed outlier: 3.887A pdb=" N THR 4 284 " --> pdb=" O ILE 4 280 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N SER 4 289 " --> pdb=" O ILE 4 285 " (cutoff:3.500A) Processing helix chain '4' and resid 300 through 319 removed outlier: 3.688A pdb=" N SER 4 305 " --> pdb=" O ILE 4 301 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU 4 315 " --> pdb=" O GLY 4 311 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER 4 319 " --> pdb=" O LEU 4 315 " (cutoff:3.500A) Processing helix chain '4' and resid 322 through 348 removed outlier: 3.982A pdb=" N GLY 4 336 " --> pdb=" O GLY 4 332 " (cutoff:3.500A) Proline residue: 4 340 - end of helix Processing helix chain '4' and resid 370 through 382 removed outlier: 3.762A pdb=" N THR 4 374 " --> pdb=" O PRO 4 370 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE 4 378 " --> pdb=" O THR 4 374 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU 4 379 " --> pdb=" O TYR 4 375 " (cutoff:3.500A) Processing helix chain '4' and resid 393 through 405 Processing helix chain '4' and resid 407 through 427 removed outlier: 5.394A pdb=" N ILE 4 415 " --> pdb=" O GLY 4 411 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N SER 4 416 " --> pdb=" O ILE 4 412 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N VAL 4 417 " --> pdb=" O SER 4 413 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LEU 4 418 " --> pdb=" O CYS 4 414 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR 4 423 " --> pdb=" O LEU 4 419 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN 4 424 " --> pdb=" O ALA 4 420 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS 4 426 " --> pdb=" O ILE 4 422 " (cutoff:3.500A) Processing helix chain '4' and resid 450 through 464 removed outlier: 3.713A pdb=" N LEU 4 457 " --> pdb=" O ILE 4 453 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ILE 4 464 " --> pdb=" O SER 4 460 " (cutoff:3.500A) Processing helix chain '4' and resid 474 through 476 No H-bonds generated for 'chain '4' and resid 474 through 476' Processing helix chain '5' and resid 8 through 11 Processing helix chain '5' and resid 13 through 23 Proline residue: 5 19 - end of helix removed outlier: 3.652A pdb=" N PHE 5 22 " --> pdb=" O PHE 5 18 " (cutoff:3.500A) Processing helix chain '5' and resid 31 through 54 removed outlier: 4.807A pdb=" N THR 5 37 " --> pdb=" O ARG 5 33 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR 5 42 " --> pdb=" O LEU 5 38 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE 5 45 " --> pdb=" O ILE 5 41 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LEU 5 54 " --> pdb=" O PHE 5 50 " (cutoff:3.500A) Processing helix chain '5' and resid 83 through 102 removed outlier: 3.834A pdb=" N THR 5 87 " --> pdb=" O ALA 5 83 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N MET 5 88 " --> pdb=" O LEU 5 84 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR 5 94 " --> pdb=" O LEU 5 90 " (cutoff:3.500A) Processing helix chain '5' and resid 114 through 132 Processing helix chain '5' and resid 137 through 154 removed outlier: 4.401A pdb=" N GLY 5 147 " --> pdb=" O TRP 5 143 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU 5 152 " --> pdb=" O VAL 5 148 " (cutoff:3.500A) Processing helix chain '5' and resid 164 through 191 removed outlier: 3.982A pdb=" N LEU 5 168 " --> pdb=" O MET 5 164 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER 5 169 " --> pdb=" O LYS 5 165 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N MET 5 173 " --> pdb=" O SER 5 169 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLY 5 177 " --> pdb=" O MET 5 173 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHE 5 180 " --> pdb=" O PHE 5 176 " (cutoff:3.500A) Processing helix chain '5' and resid 198 through 203 removed outlier: 3.635A pdb=" N ALA 5 202 " --> pdb=" O SER 5 198 " (cutoff:3.500A) Processing helix chain '5' and resid 213 through 225 removed outlier: 4.381A pdb=" N ALA 5 218 " --> pdb=" O LEU 5 214 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU 5 219 " --> pdb=" O ILE 5 215 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA 5 222 " --> pdb=" O ALA 5 218 " (cutoff:3.500A) Processing helix chain '5' and resid 234 through 239 Processing helix chain '5' and resid 244 through 251 Processing helix chain '5' and resid 258 through 264 removed outlier: 4.176A pdb=" N LEU 5 263 " --> pdb=" O GLY 5 259 " (cutoff:3.500A) Processing helix chain '5' and resid 267 through 272 removed outlier: 3.693A pdb=" N GLU 5 271 " --> pdb=" O ALA 5 267 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N TYR 5 272 " --> pdb=" O ASN 5 268 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 267 through 272' Processing helix chain '5' and resid 274 through 297 removed outlier: 4.129A pdb=" N ILE 5 279 " --> pdb=" O THR 5 275 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY 5 284 " --> pdb=" O ILE 5 280 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU 5 289 " --> pdb=" O ALA 5 285 " (cutoff:3.500A) Processing helix chain '5' and resid 301 through 321 removed outlier: 3.756A pdb=" N MET 5 310 " --> pdb=" O ALA 5 306 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N MET 5 315 " --> pdb=" O SER 5 311 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N MET 5 316 " --> pdb=" O GLN 5 312 " (cutoff:3.500A) Processing helix chain '5' and resid 325 through 352 removed outlier: 3.683A pdb=" N LEU 5 341 " --> pdb=" O PHE 5 337 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE 5 343 " --> pdb=" O LYS 5 339 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N MET 5 344 " --> pdb=" O ALA 5 340 " (cutoff:3.500A) Processing helix chain '5' and resid 368 through 370 No H-bonds generated for 'chain '5' and resid 368 through 370' Processing helix chain '5' and resid 372 through 384 Processing helix chain '5' and resid 392 through 395 No H-bonds generated for 'chain '5' and resid 392 through 395' Processing helix chain '5' and resid 399 through 404 removed outlier: 3.600A pdb=" N TYR 5 404 " --> pdb=" O ILE 5 400 " (cutoff:3.500A) Processing helix chain '5' and resid 412 through 437 removed outlier: 3.876A pdb=" N TRP 5 416 " --> pdb=" O TYR 5 412 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER 5 429 " --> pdb=" O THR 5 425 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU 5 435 " --> pdb=" O LYS 5 431 " (cutoff:3.500A) Processing helix chain '5' and resid 458 through 470 removed outlier: 4.040A pdb=" N ILE 5 464 " --> pdb=" O LEU 5 460 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU 5 465 " --> pdb=" O PRO 5 461 " (cutoff:3.500A) Processing helix chain '5' and resid 503 through 506 No H-bonds generated for 'chain '5' and resid 503 through 506' Processing helix chain '5' and resid 511 through 514 No H-bonds generated for 'chain '5' and resid 511 through 514' Processing helix chain '5' and resid 516 through 531 removed outlier: 3.844A pdb=" N VAL 5 521 " --> pdb=" O SER 5 517 " (cutoff:3.500A) Processing helix chain '5' and resid 546 through 554 Processing helix chain '5' and resid 559 through 564 Processing helix chain '5' and resid 570 through 586 removed outlier: 3.814A pdb=" N HIS 5 577 " --> pdb=" O GLY 5 573 " (cutoff:3.500A) Processing helix chain '5' and resid 589 through 591 No H-bonds generated for 'chain '5' and resid 589 through 591' Processing helix chain '5' and resid 593 through 603 removed outlier: 4.487A pdb=" N ALA 5 599 " --> pdb=" O LEU 5 595 " (cutoff:3.500A) Processing helix chain '5' and resid 613 through 635 removed outlier: 3.561A pdb=" N ASN 5 617 " --> pdb=" O SER 5 613 " (cutoff:3.500A) Processing helix chain '5' and resid 643 through 649 removed outlier: 3.810A pdb=" N SER 5 648 " --> pdb=" O PRO 5 644 " (cutoff:3.500A) Processing helix chain '6' and resid 4 through 7 No H-bonds generated for 'chain '6' and resid 4 through 7' Processing helix chain '6' and resid 13 through 23 removed outlier: 3.607A pdb=" N PHE 6 22 " --> pdb=" O LEU 6 18 " (cutoff:3.500A) Processing helix chain '6' and resid 29 through 50 removed outlier: 4.403A pdb=" N ILE 6 33 " --> pdb=" O PRO 6 29 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE 6 37 " --> pdb=" O ILE 6 33 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA 6 38 " --> pdb=" O LEU 6 34 " (cutoff:3.500A) Processing helix chain '6' and resid 53 through 62 Processing helix chain '6' and resid 67 through 76 removed outlier: 3.598A pdb=" N THR 6 76 " --> pdb=" O LEU 6 72 " (cutoff:3.500A) Processing helix chain '6' and resid 95 through 111 removed outlier: 5.484A pdb=" N SER 6 100 " --> pdb=" O LEU 6 96 " (cutoff:3.500A) Processing helix chain '6' and resid 120 through 124 Processing helix chain '6' and resid 149 through 157 Processing helix chain '6' and resid 159 through 180 removed outlier: 3.731A pdb=" N ILE 6 167 " --> pdb=" O LEU 6 163 " (cutoff:3.500A) Proline residue: 6 176 - end of helix removed outlier: 3.561A pdb=" N THR 6 180 " --> pdb=" O PRO 6 176 " (cutoff:3.500A) Processing helix chain '8' and resid 11 through 15 Processing helix chain '8' and resid 27 through 39 Proline residue: 8 32 - end of helix removed outlier: 4.020A pdb=" N GLU 8 35 " --> pdb=" O PRO 8 32 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS 8 38 " --> pdb=" O GLU 8 35 " (cutoff:3.500A) Processing helix chain '8' and resid 48 through 84 removed outlier: 3.513A pdb=" N HIS 8 52 " --> pdb=" O GLY 8 48 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR 8 54 " --> pdb=" O GLU 8 50 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ALA 8 84 " --> pdb=" O ALA 8 80 " (cutoff:3.500A) Processing helix chain '9' and resid 16 through 18 No H-bonds generated for 'chain '9' and resid 16 through 18' Processing helix chain '9' and resid 20 through 23 No H-bonds generated for 'chain '9' and resid 20 through 23' Processing helix chain '9' and resid 38 through 49 Processing helix chain '9' and resid 51 through 65 Processing sheet with id= A, first strand: chain 'A' and resid 37 through 41 Processing sheet with id= B, first strand: chain 'A' and resid 176 through 178 Processing sheet with id= C, first strand: chain 'A' and resid 203 through 205 Processing sheet with id= D, first strand: chain 'A' and resid 313 through 315 Processing sheet with id= E, first strand: chain 'A' and resid 440 through 442 removed outlier: 3.769A pdb=" N ALA A 440 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU A 481 " --> pdb=" O LEU A 411 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N VAL A 413 " --> pdb=" O LEU A 481 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE A 483 " --> pdb=" O VAL A 413 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 550 through 552 removed outlier: 6.342A pdb=" N VAL A 585 " --> pdb=" O TYR A 571 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N GLY A 573 " --> pdb=" O VAL A 585 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N LEU A 587 " --> pdb=" O GLY A 573 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 268 through 272 removed outlier: 3.567A pdb=" N ARG A 279 " --> pdb=" O ASP A 271 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 114 through 118 removed outlier: 3.912A pdb=" N THR B 243 " --> pdb=" O TYR B 114 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 155 through 161 removed outlier: 5.979A pdb=" N ASP B 196 " --> pdb=" O ALA B 156 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ILE B 158 " --> pdb=" O ASP B 196 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TYR B 198 " --> pdb=" O ILE B 158 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ILE B 160 " --> pdb=" O TYR B 198 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N HIS B 200 " --> pdb=" O ILE B 160 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'B' and resid 288 through 293 Processing sheet with id= K, first strand: chain 'C' and resid 83 through 86 removed outlier: 3.843A pdb=" N ILE C 101 " --> pdb=" O ASP C 113 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASP C 113 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU C 103 " --> pdb=" O ARG C 111 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ARG C 111 " --> pdb=" O GLU C 103 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 397 through 405 Processing sheet with id= M, first strand: chain 'E' and resid 258 through 261 removed outlier: 7.323A pdb=" N PHE E 259 " --> pdb=" O ALA E 197 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE E 199 " --> pdb=" O PHE E 259 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N LEU E 261 " --> pdb=" O ILE E 199 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ARG E 201 " --> pdb=" O LEU E 261 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N TYR E 163 " --> pdb=" O THR E 198 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N VAL E 200 " --> pdb=" O TYR E 163 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N HIS E 165 " --> pdb=" O VAL E 200 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N SER E 167 " --> pdb=" O PRO E 202 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL E 125 " --> pdb=" O ILE E 164 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N VAL E 166 " --> pdb=" O VAL E 125 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ASN E 127 " --> pdb=" O VAL E 166 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N THR E 79 " --> pdb=" O ALA E 56 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N VAL E 58 " --> pdb=" O THR E 79 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL E 81 " --> pdb=" O VAL E 58 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N ASN E 103 " --> pdb=" O VAL E 82 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 204 through 206 Processing sheet with id= O, first strand: chain 'G' and resid 89 through 92 removed outlier: 7.559A pdb=" N ARG G 152 " --> pdb=" O LEU G 96 " (cutoff:3.500A) removed outlier: 8.800A pdb=" N LEU G 98 " --> pdb=" O ARG G 152 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ARG G 154 " --> pdb=" O LEU G 98 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N LEU G 145 " --> pdb=" O ILE G 123 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ILE G 123 " --> pdb=" O LEU G 145 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 161 through 166 removed outlier: 6.922A pdb=" N TYR H 122 " --> pdb=" O THR H 162 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N SER H 164 " --> pdb=" O TYR H 122 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LEU H 124 " --> pdb=" O SER H 164 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL H 166 " --> pdb=" O LEU H 124 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N ILE H 126 " --> pdb=" O VAL H 166 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP H 183 " --> pdb=" O ILE H 180 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'I' and resid 145 through 151 removed outlier: 6.014A pdb=" N GLU I 150 " --> pdb=" O THR I 159 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N THR I 159 " --> pdb=" O GLU I 150 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'K' and resid 78 through 80 removed outlier: 6.959A pdb=" N ILE K 116 " --> pdb=" O VAL K 79 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N TRP K 143 " --> pdb=" O MET K 117 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N VAL K 119 " --> pdb=" O TRP K 143 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE K 145 " --> pdb=" O VAL K 119 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N VAL K 175 " --> pdb=" O SER K 146 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'M' and resid 88 through 90 Processing sheet with id= T, first strand: chain 'M' and resid 94 through 97 removed outlier: 3.553A pdb=" N ILE M 113 " --> pdb=" O CYS M 97 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'Y' and resid 128 through 132 removed outlier: 3.529A pdb=" N TRP Y 78 " --> pdb=" O PHE Y 112 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU Y 80 " --> pdb=" O MET Y 110 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N MET Y 110 " --> pdb=" O LEU Y 80 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'f' and resid 41 through 43 removed outlier: 3.776A pdb=" N HIS f 11 " --> pdb=" O ILE f 53 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE f 53 " --> pdb=" O HIS f 11 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N HIS f 62 " --> pdb=" O PHE f 58 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'h' and resid 44 through 46 Processing sheet with id= X, first strand: chain '2' and resid 52 through 54 2051 hydrogen bonds defined for protein. 5721 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: 15.81 Time building geometry restraints manager: 18.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.40: 22884 1.40 - 1.63: 32828 1.63 - 1.85: 431 1.85 - 2.08: 0 2.08 - 2.31: 80 Bond restraints: 56223 Sorted by residual: bond pdb=" C5N NDP E 401 " pdb=" C6N NDP E 401 " ideal model delta sigma weight residual 1.337 1.546 -0.209 2.40e-02 1.74e+03 7.59e+01 bond pdb=" C1B NDP E 401 " pdb=" C2B NDP E 401 " ideal model delta sigma weight residual 1.575 1.297 0.278 3.70e-02 7.30e+02 5.66e+01 bond pdb=" C1D NDP E 401 " pdb=" C2D NDP E 401 " ideal model delta sigma weight residual 1.560 1.295 0.265 3.70e-02 7.30e+02 5.15e+01 bond pdb=" C1D NDP E 401 " pdb=" O4D NDP E 401 " ideal model delta sigma weight residual 1.402 1.606 -0.204 3.40e-02 8.65e+02 3.58e+01 bond pdb=" C1B NDP E 401 " pdb=" O4B NDP E 401 " ideal model delta sigma weight residual 1.412 1.613 -0.201 3.40e-02 8.65e+02 3.49e+01 ... (remaining 56218 not shown) Histogram of bond angle deviations from ideal: 69.08 - 82.71: 72 82.71 - 96.34: 10 96.34 - 109.98: 11131 109.98 - 123.61: 63339 123.61 - 137.24: 2045 Bond angle restraints: 76597 Sorted by residual: angle pdb=" S1 FES H 301 " pdb="FE2 FES H 301 " pdb=" S2 FES H 301 " ideal model delta sigma weight residual 104.33 89.62 14.71 1.14e+00 7.69e-01 1.67e+02 angle pdb=" S1 FES H 301 " pdb="FE1 FES H 301 " pdb=" S2 FES H 301 " ideal model delta sigma weight residual 104.33 89.83 14.50 1.20e+00 6.94e-01 1.46e+02 angle pdb=" N HIS C 115 " pdb=" CA HIS C 115 " pdb=" C HIS C 115 " ideal model delta sigma weight residual 112.41 128.07 -15.66 1.30e+00 5.92e-01 1.45e+02 angle pdb="FE1 FES A 803 " pdb=" S2 FES A 803 " pdb="FE2 FES A 803 " ideal model delta sigma weight residual 75.66 89.05 -13.39 1.14e+00 7.69e-01 1.38e+02 angle pdb=" S1 FES A 803 " pdb="FE2 FES A 803 " pdb=" S2 FES A 803 " ideal model delta sigma weight residual 104.33 91.20 13.13 1.14e+00 7.69e-01 1.33e+02 ... (remaining 76592 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.75: 33022 34.75 - 69.49: 391 69.49 - 104.24: 13 104.24 - 138.99: 1 138.99 - 173.74: 1 Dihedral angle restraints: 33428 sinusoidal: 11512 harmonic: 21916 Sorted by residual: dihedral pdb=" CA CYS K 180 " pdb=" C CYS K 180 " pdb=" N PRO K 181 " pdb=" CA PRO K 181 " ideal model delta harmonic sigma weight residual -180.00 -108.31 -71.69 0 5.00e+00 4.00e-02 2.06e+02 dihedral pdb=" CA PRO 4 226 " pdb=" C PRO 4 226 " pdb=" N ILE 4 227 " pdb=" CA ILE 4 227 " ideal model delta harmonic sigma weight residual -180.00 -119.53 -60.47 0 5.00e+00 4.00e-02 1.46e+02 dihedral pdb=" CA LEU 2 258 " pdb=" C LEU 2 258 " pdb=" N VAL 2 259 " pdb=" CA VAL 2 259 " ideal model delta harmonic sigma weight residual 180.00 -122.88 -57.12 0 5.00e+00 4.00e-02 1.31e+02 ... (remaining 33425 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.171: 8939 4.171 - 8.342: 0 8.342 - 12.514: 0 12.514 - 16.685: 0 16.685 - 20.856: 20 Chirality restraints: 8959 Sorted by residual: chirality pdb="FE1 SF4 A 802 " pdb=" S2 SF4 A 802 " pdb=" S3 SF4 A 802 " pdb=" S4 SF4 A 802 " both_signs ideal model delta sigma weight residual False -10.55 10.30 -20.86 2.00e-01 2.50e+01 1.09e+04 chirality pdb="FE4 SF4 K 301 " pdb=" S1 SF4 K 301 " pdb=" S2 SF4 K 301 " pdb=" S3 SF4 K 301 " both_signs ideal model delta sigma weight residual False 10.55 -10.26 20.82 2.00e-01 2.50e+01 1.08e+04 chirality pdb="FE3 SF4 A 801 " pdb=" S1 SF4 A 801 " pdb=" S2 SF4 A 801 " pdb=" S4 SF4 A 801 " both_signs ideal model delta sigma weight residual False -10.55 10.24 -20.79 2.00e-01 2.50e+01 1.08e+04 ... (remaining 8956 not shown) Planarity restraints: 9823 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2N NDP E 401 " -0.298 2.00e-02 2.50e+03 1.85e-01 4.26e+02 pdb=" C3N NDP E 401 " -0.061 2.00e-02 2.50e+03 pdb=" C4N NDP E 401 " -0.026 2.00e-02 2.50e+03 pdb=" C7N NDP E 401 " 0.152 2.00e-02 2.50e+03 pdb=" N1N NDP E 401 " 0.233 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C4N NDP E 401 " 0.034 2.00e-02 2.50e+03 5.53e-02 3.06e+01 pdb=" C5N NDP E 401 " -0.068 2.00e-02 2.50e+03 pdb=" C6N NDP E 401 " 0.071 2.00e-02 2.50e+03 pdb=" N1N NDP E 401 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE 1 321 " -0.034 2.00e-02 2.50e+03 3.55e-02 2.21e+01 pdb=" CG PHE 1 321 " 0.077 2.00e-02 2.50e+03 pdb=" CD1 PHE 1 321 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 PHE 1 321 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE 1 321 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE 1 321 " -0.026 2.00e-02 2.50e+03 pdb=" CZ PHE 1 321 " 0.003 2.00e-02 2.50e+03 ... (remaining 9820 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 11358 2.76 - 3.30: 55202 3.30 - 3.83: 93091 3.83 - 4.37: 105151 4.37 - 4.90: 169489 Nonbonded interactions: 434291 Sorted by model distance: nonbonded pdb=" O HIS C 115 " pdb=" ND1 HIS C 115 " model vdw 2.231 2.520 nonbonded pdb=" O TYR 5 374 " pdb=" OG1 THR 5 378 " model vdw 2.245 2.440 nonbonded pdb=" O HIS C 120 " pdb=" OG SER K 162 " model vdw 2.251 2.440 nonbonded pdb=" O GLU E 178 " pdb=" OG1 THR E 182 " model vdw 2.267 2.440 nonbonded pdb=" O PRO I 104 " pdb=" OH TYR h 63 " model vdw 2.269 2.440 ... (remaining 434286 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'S' and resid 96 through 232) selection = chain 'Z' } ncs_group { reference = (chain 'a' and resid 42 through 134) selection = chain 'n' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 28 7.16 5 Zn 1 6.06 5 P 10 5.49 5 S 282 5.16 5 C 35279 2.51 5 N 9391 2.21 5 O 10146 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.70 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: 4.500 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: 22.430 Check model and map are aligned: 0.700 Process input model: 117.280 Find NCS groups from input model: 1.730 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Set scattering table: 0.380 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 149.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.278 56223 Z= 0.638 Angle : 1.350 20.937 76597 Z= 0.729 Chirality : 0.974 20.856 8959 Planarity : 0.009 0.185 9823 Dihedral : 12.017 173.735 19244 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.75 % Allowed : 13.39 % Favored : 85.86 % Rotamer Outliers : 0.73 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.91 % Twisted General : 0.49 % 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: -4.79 (0.08), residues: 6788 helix: -2.76 (0.07), residues: 3280 sheet: -2.19 (0.28), residues: 295 loop : -3.78 (0.09), residues: 3213 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13576 Ramachandran restraints generated. 6788 Oldfield, 0 Emsley, 6788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13576 Ramachandran restraints generated. 6788 Oldfield, 0 Emsley, 6788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1409 residues out of total 5896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 1372 time to evaluate : 4.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 3 residues processed: 1396 average time/residue: 0.5505 time to fit residues: 1281.5122 Evaluate side-chains 765 residues out of total 5896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 762 time to evaluate : 4.771 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.3810 time to fit residues: 8.3212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 733 random chunks: chunk 618 optimal weight: 4.9990 chunk 555 optimal weight: 0.9980 chunk 308 optimal weight: 2.9990 chunk 189 optimal weight: 0.7980 chunk 374 optimal weight: 0.7980 chunk 296 optimal weight: 0.8980 chunk 574 optimal weight: 0.8980 chunk 222 optimal weight: 8.9990 chunk 349 optimal weight: 10.0000 chunk 427 optimal weight: 10.0000 chunk 665 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 HIS ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 HIS A 194 ASN A 459 HIS A 575 ASN B 42 GLN B 176 ASN B 424 HIS C 120 HIS ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 268 ASN C 288 ASN E 76 HIS ** E 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 181 HIS ** F 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 67 HIS ** G 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 193 GLN L 43 ASN M 103 ASN M 126 GLN ** U 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 106 GLN Y 109 GLN ** Y 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 28 ASN ** f 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 60 GLN 1 40 ASN 1 173 GLN 2 315 GLN ** 3 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 207 GLN 4 270 GLN ** 4 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 424 GLN 5 299 ASN ** 5 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.297 56223 Z= 0.580 Angle : 1.662 51.103 76597 Z= 1.055 Chirality : 0.301 6.443 8959 Planarity : 0.005 0.090 9823 Dihedral : 8.797 172.475 8256 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.48 % Favored : 88.26 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.61 (0.09), residues: 6788 helix: -1.46 (0.08), residues: 3290 sheet: -2.00 (0.29), residues: 287 loop : -3.54 (0.10), residues: 3211 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13576 Ramachandran restraints generated. 6788 Oldfield, 0 Emsley, 6788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13576 Ramachandran restraints generated. 6788 Oldfield, 0 Emsley, 6788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1166 residues out of total 5896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1160 time to evaluate : 4.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 1165 average time/residue: 0.5236 time to fit residues: 1039.7505 Evaluate side-chains 784 residues out of total 5896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 783 time to evaluate : 4.796 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3865 time to fit residues: 6.8354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 733 random chunks: chunk 369 optimal weight: 0.9980 chunk 206 optimal weight: 6.9990 chunk 554 optimal weight: 1.9990 chunk 453 optimal weight: 20.0000 chunk 183 optimal weight: 8.9990 chunk 666 optimal weight: 2.9990 chunk 720 optimal weight: 9.9990 chunk 593 optimal weight: 9.9990 chunk 661 optimal weight: 9.9990 chunk 227 optimal weight: 8.9990 chunk 534 optimal weight: 0.9980 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 HIS A 79 ASN ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 ASN A 220 ASN A 575 ASN B 42 GLN C 115 HIS ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 434 HIS ** E 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 180 ASN G 115 ASN G 136 ASN ** H 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 210 ASN K 73 GLN K 113 GLN L 21 ASN L 43 ASN P 63 HIS U 50 ASN U 99 GLN ** U 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 105 ASN ** U 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 58 ASN f 11 HIS ** f 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 21 HIS g 60 GLN ** 1 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 40 ASN 1 173 GLN ** 2 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 292 ASN 2 315 GLN ** 4 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 270 GLN ** 4 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.270 56223 Z= 0.592 Angle : 1.664 51.096 76597 Z= 1.058 Chirality : 0.301 6.443 8959 Planarity : 0.005 0.084 9823 Dihedral : 8.321 171.273 8256 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 18.32 Ramachandran Plot: Outliers : 0.25 % Allowed : 12.98 % Favored : 86.77 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.94 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.08 (0.10), residues: 6788 helix: -0.88 (0.09), residues: 3293 sheet: -1.91 (0.29), residues: 287 loop : -3.42 (0.10), residues: 3208 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13576 Ramachandran restraints generated. 6788 Oldfield, 0 Emsley, 6788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13576 Ramachandran restraints generated. 6788 Oldfield, 0 Emsley, 6788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1051 residues out of total 5896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1049 time to evaluate : 4.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 1051 average time/residue: 0.5157 time to fit residues: 926.8196 Evaluate side-chains 765 residues out of total 5896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 765 time to evaluate : 4.731 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.0484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 733 random chunks: chunk 658 optimal weight: 0.7980 chunk 501 optimal weight: 10.0000 chunk 346 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 318 optimal weight: 5.9990 chunk 447 optimal weight: 5.9990 chunk 669 optimal weight: 0.9980 chunk 708 optimal weight: 0.8980 chunk 349 optimal weight: 10.0000 chunk 634 optimal weight: 6.9990 chunk 190 optimal weight: 0.1980 overall best weight: 1.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN A 220 ASN ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 575 ASN A 696 ASN ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 57 ASN ** E 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 GLN G 136 ASN ** H 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 210 ASN I 219 GLN J 19 HIS ** K 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 100 GLN K 113 GLN L 21 ASN ** M 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 126 GLN ** U 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 119 ASN ** Y 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 60 GLN 1 40 ASN ** 1 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 315 GLN 4 207 GLN 4 270 GLN ** 4 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.266 56223 Z= 0.567 Angle : 1.643 50.994 76597 Z= 1.048 Chirality : 0.300 6.452 8959 Planarity : 0.005 0.081 9823 Dihedral : 7.965 170.279 8256 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.18 % Favored : 87.58 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.10), residues: 6788 helix: -0.50 (0.09), residues: 3279 sheet: -1.95 (0.28), residues: 299 loop : -3.29 (0.10), residues: 3210 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13576 Ramachandran restraints generated. 6788 Oldfield, 0 Emsley, 6788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13576 Ramachandran restraints generated. 6788 Oldfield, 0 Emsley, 6788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1072 residues out of total 5896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1067 time to evaluate : 5.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 1072 average time/residue: 0.5388 time to fit residues: 994.9455 Evaluate side-chains 770 residues out of total 5896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 769 time to evaluate : 4.742 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4003 time to fit residues: 6.9517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 733 random chunks: chunk 590 optimal weight: 4.9990 chunk 402 optimal weight: 0.2980 chunk 10 optimal weight: 5.9990 chunk 527 optimal weight: 5.9990 chunk 292 optimal weight: 0.6980 chunk 604 optimal weight: 7.9990 chunk 489 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 361 optimal weight: 0.0170 chunk 635 optimal weight: 30.0000 chunk 178 optimal weight: 10.0000 overall best weight: 2.4022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 ASN A 220 ASN ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 696 ASN B 378 HIS ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 GLN G 136 ASN ** H 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 100 GLN ** K 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 103 ASN ** M 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 105 ASN W 114 HIS ** Y 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 150 HIS f 28 ASN ** f 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 60 GLN 1 40 ASN 2 218 HIS 2 278 GLN 2 339 ASN 2 355 HIS ** 3 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 53 ASN 4 207 GLN 4 270 GLN 4 295 GLN ** 4 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 577 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.276 56223 Z= 0.578 Angle : 1.645 51.071 76597 Z= 1.049 Chirality : 0.300 6.472 8959 Planarity : 0.005 0.083 9823 Dihedral : 7.735 169.583 8256 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 18.38 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.83 % Favored : 86.93 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.10), residues: 6788 helix: -0.32 (0.09), residues: 3275 sheet: -1.81 (0.28), residues: 311 loop : -3.22 (0.10), residues: 3202 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13576 Ramachandran restraints generated. 6788 Oldfield, 0 Emsley, 6788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13576 Ramachandran restraints generated. 6788 Oldfield, 0 Emsley, 6788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1007 residues out of total 5896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1006 time to evaluate : 4.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 1007 average time/residue: 0.5367 time to fit residues: 927.3956 Evaluate side-chains 752 residues out of total 5896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 752 time to evaluate : 4.807 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.0651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 733 random chunks: chunk 238 optimal weight: 6.9990 chunk 638 optimal weight: 4.9990 chunk 140 optimal weight: 0.9990 chunk 415 optimal weight: 10.0000 chunk 174 optimal weight: 9.9990 chunk 709 optimal weight: 0.8980 chunk 588 optimal weight: 0.9980 chunk 328 optimal weight: 8.9990 chunk 58 optimal weight: 4.9990 chunk 234 optimal weight: 9.9990 chunk 372 optimal weight: 8.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN A 220 ASN A 289 ASN A 575 ASN A 696 ASN ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 GLN G 136 ASN G 193 HIS ** H 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 113 GLN K 137 GLN ** K 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 85 ASN ** M 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 105 ASN ** Y 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 69 GLN ** Y 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 60 GLN 1 40 ASN ** 1 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 270 GLN ** 4 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 577 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.260 56223 Z= 0.583 Angle : 1.649 51.115 76597 Z= 1.051 Chirality : 0.300 6.503 8959 Planarity : 0.005 0.131 9823 Dihedral : 7.638 168.863 8256 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 18.88 Ramachandran Plot: Outliers : 0.27 % Allowed : 12.93 % Favored : 86.80 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.10), residues: 6788 helix: -0.24 (0.09), residues: 3280 sheet: -1.68 (0.28), residues: 308 loop : -3.22 (0.10), residues: 3200 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13576 Ramachandran restraints generated. 6788 Oldfield, 0 Emsley, 6788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13576 Ramachandran restraints generated. 6788 Oldfield, 0 Emsley, 6788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 999 residues out of total 5896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 995 time to evaluate : 4.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 999 average time/residue: 0.5404 time to fit residues: 924.3743 Evaluate side-chains 759 residues out of total 5896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 758 time to evaluate : 4.774 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4757 time to fit residues: 6.9640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 733 random chunks: chunk 683 optimal weight: 8.9990 chunk 79 optimal weight: 4.9990 chunk 404 optimal weight: 9.9990 chunk 517 optimal weight: 0.9990 chunk 401 optimal weight: 2.9990 chunk 597 optimal weight: 20.0000 chunk 396 optimal weight: 0.0060 chunk 706 optimal weight: 0.7980 chunk 442 optimal weight: 10.0000 chunk 430 optimal weight: 30.0000 chunk 326 optimal weight: 4.9990 overall best weight: 1.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 GLN A 194 ASN A 220 ASN A 289 ASN A 575 ASN A 696 ASN ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 136 ASN G 208 HIS ** H 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 210 ASN ** K 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 50 ASN ** Y 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 69 GLN ** Y 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 28 ASN ** f 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 60 GLN h 50 HIS ** h 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 173 GLN ** 1 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 218 HIS ** 2 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 339 ASN ** 2 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.261 56223 Z= 0.571 Angle : 1.647 50.938 76597 Z= 1.049 Chirality : 0.300 6.485 8959 Planarity : 0.005 0.089 9823 Dihedral : 7.500 168.151 8256 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 17.87 Ramachandran Plot: Outliers : 0.25 % Allowed : 12.58 % Favored : 87.17 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.10), residues: 6788 helix: -0.18 (0.09), residues: 3283 sheet: -1.60 (0.29), residues: 308 loop : -3.14 (0.10), residues: 3197 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13576 Ramachandran restraints generated. 6788 Oldfield, 0 Emsley, 6788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13576 Ramachandran restraints generated. 6788 Oldfield, 0 Emsley, 6788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1000 residues out of total 5896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 996 time to evaluate : 4.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 999 average time/residue: 0.5288 time to fit residues: 906.8409 Evaluate side-chains 766 residues out of total 5896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 766 time to evaluate : 4.766 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.1129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 733 random chunks: chunk 437 optimal weight: 10.0000 chunk 282 optimal weight: 6.9990 chunk 421 optimal weight: 9.9990 chunk 212 optimal weight: 8.9990 chunk 138 optimal weight: 0.9980 chunk 136 optimal weight: 4.9990 chunk 449 optimal weight: 6.9990 chunk 481 optimal weight: 10.0000 chunk 349 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 chunk 555 optimal weight: 2.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 194 ASN A 220 ASN ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 696 ASN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 210 ASN ** K 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 50 ASN ** Y 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 69 GLN ** Y 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 60 GLN h 78 HIS 1 34 GLN ** 2 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.259 56223 Z= 0.646 Angle : 1.697 51.123 76597 Z= 1.073 Chirality : 0.300 6.373 8959 Planarity : 0.006 0.115 9823 Dihedral : 7.710 167.662 8256 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 21.92 Ramachandran Plot: Outliers : 0.27 % Allowed : 14.41 % Favored : 85.33 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.10), residues: 6788 helix: -0.24 (0.09), residues: 3293 sheet: -1.51 (0.29), residues: 308 loop : -3.24 (0.10), residues: 3187 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13576 Ramachandran restraints generated. 6788 Oldfield, 0 Emsley, 6788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13576 Ramachandran restraints generated. 6788 Oldfield, 0 Emsley, 6788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 931 residues out of total 5896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 928 time to evaluate : 5.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 931 average time/residue: 0.5589 time to fit residues: 893.6931 Evaluate side-chains 716 residues out of total 5896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 715 time to evaluate : 4.833 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4123 time to fit residues: 6.9118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 733 random chunks: chunk 642 optimal weight: 9.9990 chunk 676 optimal weight: 2.9990 chunk 617 optimal weight: 0.7980 chunk 658 optimal weight: 2.9990 chunk 396 optimal weight: 0.4980 chunk 286 optimal weight: 5.9990 chunk 516 optimal weight: 3.9990 chunk 202 optimal weight: 0.0020 chunk 594 optimal weight: 0.5980 chunk 622 optimal weight: 0.9990 chunk 656 optimal weight: 0.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 194 ASN ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 575 ASN A 696 ASN B 176 ASN ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 268 ASN F 106 GLN G 136 ASN ** H 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 189 ASN I 210 ASN ** K 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 85 ASN ** M 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 70 ASN ** U 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 50 ASN ** Y 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 69 GLN ** Y 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 60 GLN ** 1 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 218 HIS ** 2 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 162 GLN ** 5 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.264 56223 Z= 0.567 Angle : 1.650 50.948 76597 Z= 1.048 Chirality : 0.300 6.479 8959 Planarity : 0.005 0.104 9823 Dihedral : 7.422 167.035 8256 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.28 % Favored : 88.45 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.10), residues: 6788 helix: -0.08 (0.09), residues: 3264 sheet: -1.52 (0.29), residues: 309 loop : -3.06 (0.10), residues: 3215 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13576 Ramachandran restraints generated. 6788 Oldfield, 0 Emsley, 6788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13576 Ramachandran restraints generated. 6788 Oldfield, 0 Emsley, 6788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1009 residues out of total 5896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1006 time to evaluate : 4.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 1009 average time/residue: 0.5352 time to fit residues: 925.8237 Evaluate side-chains 756 residues out of total 5896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 756 time to evaluate : 4.785 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.1390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 733 random chunks: chunk 432 optimal weight: 10.0000 chunk 696 optimal weight: 8.9990 chunk 424 optimal weight: 10.0000 chunk 330 optimal weight: 0.0370 chunk 483 optimal weight: 20.0000 chunk 730 optimal weight: 2.9990 chunk 672 optimal weight: 0.9980 chunk 581 optimal weight: 4.9990 chunk 60 optimal weight: 0.0870 chunk 449 optimal weight: 7.9990 chunk 356 optimal weight: 10.0000 overall best weight: 1.8240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 ASN ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 696 ASN C 86 ASN ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 GLN ** C 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 GLN G 136 ASN ** H 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 189 ASN ** I 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 85 ASN ** M 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 50 ASN ** Y 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 59 HIS ** f 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 60 GLN ** 1 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.4331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.263 56223 Z= 0.573 Angle : 1.658 50.866 76597 Z= 1.052 Chirality : 0.301 6.443 8959 Planarity : 0.005 0.099 9823 Dihedral : 7.336 166.749 8256 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 19.24 Ramachandran Plot: Outliers : 0.27 % Allowed : 12.58 % Favored : 87.15 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.10), residues: 6788 helix: -0.06 (0.09), residues: 3275 sheet: -1.43 (0.29), residues: 313 loop : -3.07 (0.10), residues: 3200 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13576 Ramachandran restraints generated. 6788 Oldfield, 0 Emsley, 6788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13576 Ramachandran restraints generated. 6788 Oldfield, 0 Emsley, 6788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 958 residues out of total 5896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 958 time to evaluate : 4.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 958 average time/residue: 0.5395 time to fit residues: 890.3784 Evaluate side-chains 735 residues out of total 5896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 735 time to evaluate : 4.905 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.1983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 733 random chunks: chunk 461 optimal weight: 8.9990 chunk 619 optimal weight: 1.9990 chunk 178 optimal weight: 7.9990 chunk 536 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 161 optimal weight: 9.9990 chunk 582 optimal weight: 0.5980 chunk 243 optimal weight: 10.0000 chunk 598 optimal weight: 20.0000 chunk 73 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 ASN ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 696 ASN ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 GLN C 268 ASN ** E 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 189 ASN ** I 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 85 ASN ** M 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 60 GLN 1 34 GLN ** 1 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 335 HIS ** 4 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.062895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.054853 restraints weight = 319737.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.056081 restraints weight = 188389.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.056955 restraints weight = 126902.770| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3214 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3214 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.4386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.260 56223 Z= 0.588 Angle : 1.665 50.861 76597 Z= 1.056 Chirality : 0.301 6.442 8959 Planarity : 0.005 0.086 9823 Dihedral : 7.341 166.488 8256 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 20.00 Ramachandran Plot: Outliers : 0.27 % Allowed : 13.20 % Favored : 86.54 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.10), residues: 6788 helix: -0.06 (0.09), residues: 3291 sheet: -1.40 (0.29), residues: 318 loop : -3.11 (0.10), residues: 3179 =============================================================================== Job complete usr+sys time: 13506.14 seconds wall clock time: 237 minutes 36.81 seconds (14256.81 seconds total)