Starting phenix.real_space_refine (version: dev) on Sat Feb 25 08:47:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rfr_4873/02_2023/6rfr_4873_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rfr_4873/02_2023/6rfr_4873.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rfr_4873/02_2023/6rfr_4873_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rfr_4873/02_2023/6rfr_4873_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rfr_4873/02_2023/6rfr_4873_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rfr_4873/02_2023/6rfr_4873.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rfr_4873/02_2023/6rfr_4873.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rfr_4873/02_2023/6rfr_4873_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rfr_4873/02_2023/6rfr_4873_updated.pdb" } resolution = 3.2 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= 0.004 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 ARG 427": "NH1" <-> "NH2" Residue "A ARG 524": "NH1" <-> "NH2" Residue "A ARG 528": "NH1" <-> "NH2" Residue "A ARG 610": "NH1" <-> "NH2" Residue "A ARG 646": "NH1" <-> "NH2" Residue "B ARG 113": "NH1" <-> "NH2" Residue "B ARG 130": "NH1" <-> "NH2" Residue "B ARG 134": "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 54": "NH1" <-> "NH2" Residue "C ARG 121": "NH1" <-> "NH2" 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 ARG 466": "NH1" <-> "NH2" Residue "D ARG 32": "NH1" <-> "NH2" Residue "D ARG 37": "NH1" <-> "NH2" Residue "D ARG 62": "NH1" <-> "NH2" Residue "E ARG 48": "NH1" <-> "NH2" Residue "E ARG 51": "NH1" <-> "NH2" Residue "E ARG 85": "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 ARG 216": "NH1" <-> "NH2" Residue "E ARG 349": "NH1" <-> "NH2" Residue "G ARG 43": "NH1" <-> "NH2" Residue "G PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 113": "NH1" <-> "NH2" Residue "G ARG 223": "NH1" <-> "NH2" Residue "G ARG 230": "NH1" <-> "NH2" Residue "G ARG 259": "NH1" <-> "NH2" Residue "G ARG 262": "NH1" <-> "NH2" Residue "H ARG 116": "NH1" <-> "NH2" Residue "H ARG 216": "NH1" <-> "NH2" Residue "I ARG 59": "NH1" <-> "NH2" Residue "I ARG 115": "NH1" <-> "NH2" Residue "I ARG 129": "NH1" <-> "NH2" Residue "J ARG 55": "NH1" <-> "NH2" Residue "J ARG 91": "NH1" <-> "NH2" Residue "J ARG 143": "NH1" <-> "NH2" Residue "J ARG 183": "NH1" <-> "NH2" Residue "K ARG 196": "NH1" <-> "NH2" Residue "K ARG 199": "NH1" <-> "NH2" Residue "L ARG 19": "NH1" <-> "NH2" Residue "L ARG 20": "NH1" <-> "NH2" Residue "L ARG 79": "NH1" <-> "NH2" Residue "L TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 42": "NH1" <-> "NH2" Residue "M ARG 88": "NH1" <-> "NH2" Residue "M ARG 131": "NH1" <-> "NH2" Residue "O ARG 29": "NH1" <-> "NH2" Residue "O ARG 35": "NH1" <-> "NH2" Residue "P ARG 30": "NH1" <-> "NH2" Residue "P ARG 57": "NH1" <-> "NH2" Residue "P ARG 62": "NH1" <-> "NH2" Residue "P ARG 109": "NH1" <-> "NH2" Residue "R ARG 44": "NH1" <-> "NH2" Residue "R ARG 57": "NH1" <-> "NH2" Residue "R ARG 67": "NH1" <-> "NH2" Residue "S ARG 49": "NH1" <-> "NH2" Residue "S ARG 62": "NH1" <-> "NH2" Residue "S ARG 120": "NH1" <-> "NH2" Residue "S ARG 135": "NH1" <-> "NH2" Residue "S ARG 188": "NH1" <-> "NH2" Residue "U ARG 74": "NH1" <-> "NH2" Residue "U ARG 95": "NH1" <-> "NH2" Residue "U ARG 112": "NH1" <-> "NH2" Residue "U ARG 161": "NH1" <-> "NH2" Residue "W ARG 20": "NH1" <-> "NH2" Residue "W ARG 21": "NH1" <-> "NH2" Residue "W ARG 26": "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 "X ARG 76": "NH1" <-> "NH2" Residue "X ARG 118": "NH1" <-> "NH2" Residue "X ARG 166": "NH1" <-> "NH2" Residue "Y ARG 79": "NH1" <-> "NH2" Residue "Y ARG 140": "NH1" <-> "NH2" Residue "Y ARG 159": "NH1" <-> "NH2" Residue "Z PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 77": "NH1" <-> "NH2" Residue "Z ARG 80": "NH1" <-> "NH2" Residue "Z ARG 179": "NH1" <-> "NH2" Residue "a ARG 84": "NH1" <-> "NH2" Residue "a ARG 123": "NH1" <-> "NH2" Residue "b ARG 25": "NH1" <-> "NH2" Residue "c ARG 11": "NH1" <-> "NH2" Residue "c ARG 16": "NH1" <-> "NH2" Residue "c ARG 23": "NH1" <-> "NH2" Residue "c ARG 26": "NH1" <-> "NH2" Residue "d ARG 6": "NH1" <-> "NH2" Residue "d ARG 32": "NH1" <-> "NH2" Residue "d ARG 37": "NH1" <-> "NH2" Residue "d ARG 45": "NH1" <-> "NH2" Residue "d TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 41": "NH1" <-> "NH2" Residue "f ARG 6": "NH1" <-> "NH2" Residue "f ARG 9": "NH1" <-> "NH2" Residue "f PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "g ARG 47": "NH1" <-> "NH2" Residue "g ARG 69": "NH1" <-> "NH2" Residue "h ARG 18": "NH1" <-> "NH2" Residue "h ARG 57": "NH1" <-> "NH2" Residue "h TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 137": "NH1" <-> "NH2" Residue "i PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 53": "NH1" <-> "NH2" Residue "i ARG 55": "NH1" <-> "NH2" Residue "i ARG 75": "NH1" <-> "NH2" Residue "i ARG 77": "NH1" <-> "NH2" Residue "j ARG 34": "NH1" <-> "NH2" Residue "j ARG 39": "NH1" <-> "NH2" Residue "j ARG 50": "NH1" <-> "NH2" Residue "n TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 162": "NH1" <-> "NH2" Residue "4 ARG 353": "NH1" <-> "NH2" Residue "4 ARG 405": "NH1" <-> "NH2" Residue "4 ARG 449": "NH1" <-> "NH2" Residue "4 TYR 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 115": "NH1" <-> "NH2" Residue "5 ARG 175": "NH1" <-> "NH2" Residue "5 ARG 303": "NH1" <-> "NH2" Residue "5 ARG 611": "NH1" <-> "NH2" Residue "6 ARG 92": "NH1" <-> "NH2" Residue "8 ARG 37": "NH1" <-> "NH2" Residue "8 ARG 51": "NH1" <-> "NH2" Residue "8 ARG 65": "NH1" <-> "NH2" Residue "9 ARG 14": "NH1" <-> "NH2" Residue "9 ARG 58": "NH1" <-> "NH2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 65934 Number of models: 1 Model: "" Number of chains: 65 Chain: "A" Number of atoms: 5258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 692, 5258 Classifications: {'peptide': 692} Link IDs: {'PTRANS': 34, 'TRANS': 657} Chain: "B" Number of atoms: 3528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3528 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 22, 'TRANS': 433} Chain: "C" Number of atoms: 3472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3472 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 25, 'TRANS': 412} Chain: "D" Number of atoms: 681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 681 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain: "E" Number of atoms: 2798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2798 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 15, 'TRANS': 333} Chain breaks: 1 Chain: "F" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 990 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 7, 'TRANS': 113} Chain: "G" Number of atoms: 1978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1978 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 18, 'TRANS': 220} Chain: "H" Number of atoms: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1688 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 18, 'TRANS': 197} Chain: "I" Number of atoms: 1519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1519 Classifications: {'peptide': 190} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 177} Chain: "J" Number of atoms: 1329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1329 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 7, 'TRANS': 171} Chain: "K" Number of atoms: 1395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1395 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 14, 'TRANS': 162} Chain: "L" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 691 Classifications: {'peptide': 89} Link IDs: {'TRANS': 88} Chain: "M" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 912 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 9, 'TRANS': 107} 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: 1036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1036 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} 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: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 884 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 10, 'TRANS': 95} Chain: "S" Number of atoms: 1430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1430 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 6, 'TRANS': 167} Chain breaks: 2 Chain: "U" Number of atoms: 1345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1345 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "W" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 974 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 9, 'TRANS': 111} Chain: "X" Number of atoms: 1296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1296 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 11, 'TRANS': 155} Chain: "Y" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1021 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain: "Z" Number of atoms: 1389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1389 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 160} Chain: "a" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1030 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 10, 'TRANS': 113} Chain: "b" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 490 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "c" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 353 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 2, 'TRANS': 41} Chain: "d" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 760 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 4, 'TRANS': 85} Chain: "e" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 436 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 6, 'TRANS': 45} 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: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 617 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 10, 'TRANS': 65} Chain: "h" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1130 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 10, 'TRANS': 125} Chain: "i" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 646 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain: "j" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 724 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 4, 'TRANS': 85} Chain: "n" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 914 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 9, 'TRANS': 104} Chain: "1" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2714 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 14, 'TRANS': 325} Chain: "2" Number of atoms: 3774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3774 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 7, 'TRANS': 461} Chain: "3" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1017 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "4" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3855 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 14, 'TRANS': 471} Chain: "5" Number of atoms: 5197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 654, 5197 Classifications: {'peptide': 654} Link IDs: {'PTRANS': 15, 'TRANS': 638} Chain: "6" Number of atoms: 1443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1443 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 3, 'TRANS': 179} 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: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 672 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} 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: "C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 156 Unusual residues: {'3PE': 1, 'CDL': 1, 'NDP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 43 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: "J" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 154 Unusual residues: {'3PE': 2, 'LMN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "K" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 47 Unusual residues: {'PLC': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 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: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Chain: "Q" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Chain: "W" Number of atoms: 159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 159 Unusual residues: {'3PE': 1, 'PLC': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Chain: "X" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 86 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "Z" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 76 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 24 Chain: "b" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 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: "j" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 143 Unusual residues: {'CDL': 1, 'LMN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 26 Chain: "n" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'PLC': 1} Classifications: {'undetermined': 1} Chain: "1" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 142 Unusual residues: {'3PE': 2, 'PLC': 1, 'UQ9': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'UQ9:plan-8': 1, 'UQ9:plan-9': 1, 'UQ9:plan-10': 1, 'UQ9:plan-7': 1, 'UQ9:plan-2': 1} Unresolved non-hydrogen planarities: 23 Chain: "2" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 152 Unusual residues: {'CPL': 1, 'T7X': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "3" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'T7X': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'T7X:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "4" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 270 Unusual residues: {'3PE': 4, 'CDL': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 34 Chain: "5" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 167 Unusual residues: {'3PE': 2, 'PLC': 1, 'T7X': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'T7X:plan-5': 1, 'T7X:plan-4': 1, 'T7X:plan-6': 1} Unresolved non-hydrogen planarities: 9 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 809 SG CYS A 142 63.128 149.390 160.207 1.00 9.73 S ATOM 749 SG CYS A 133 60.150 151.725 154.851 1.00 21.16 S ATOM 769 SG CYS A 136 64.678 154.692 158.530 1.00 16.96 S ATOM 1163 SG CYS A 186 62.439 150.663 171.163 1.00 10.04 S ATOM 1139 SG CYS A 183 59.875 156.065 169.223 1.00 13.25 S ATOM 1187 SG CYS A 189 64.966 155.869 173.703 1.00 9.38 S ATOM 1511 SG CYS A 233 64.993 153.803 167.579 1.00 25.48 S ATOM 255 SG CYS A 69 59.485 145.180 174.491 1.00 7.43 S ATOM 338 SG CYS A 80 57.990 143.885 171.413 1.00 6.34 S ATOM 363 SG CYS A 83 58.034 138.617 173.572 1.00 8.91 S ATOM 465 SG CYS A 97 59.233 140.457 176.891 1.00 8.64 S ATOM 7999 SG CYS B 384 49.380 147.613 175.820 1.00 8.24 S ATOM 8019 SG CYS B 387 44.886 150.050 175.413 1.00 10.06 S ATOM 7980 SG CYS B 381 49.471 152.442 179.949 1.00 10.80 S ATOM 8350 SG CYS B 427 45.931 147.886 181.067 1.00 10.96 S ATOM 19522 SG CYS H 127 31.274 163.391 182.611 1.00 28.82 S ATOM 19556 SG CYS H 132 27.771 163.887 183.000 1.00 28.59 S ATOM 19825 SG CYS H 168 32.232 159.160 185.407 1.00 31.19 S ATOM 19848 SG CYS H 172 29.268 158.215 186.137 1.00 41.16 S ATOM 21450 SG CYS I 172 66.880 146.817 133.676 1.00 14.37 S ATOM 21424 SG CYS I 169 70.716 151.175 130.785 1.00 25.48 S ATOM 21472 SG CYS I 175 66.402 152.956 135.160 1.00 16.71 S ATOM 21197 SG CYS I 140 71.818 148.930 136.370 1.00 22.33 S ATOM 21502 SG CYS I 179 62.607 157.289 141.904 1.00 18.08 S ATOM 21169 SG CYS I 136 68.850 154.886 141.174 1.00 25.48 S ATOM 21127 SG CYS I 130 68.058 160.616 142.849 1.00 11.49 S ATOM 21146 SG CYS I 133 65.259 155.492 146.278 1.00 15.53 S ATOM 24148 SG CYS K 150 75.920 142.740 125.303 1.00 8.32 S ATOM 23644 SG CYS K 86 73.141 144.498 119.717 1.00 11.54 S ATOM 23638 SG CYS K 85 71.146 139.132 122.399 1.00 12.38 S ATOM 24376 SG CYS K 180 71.257 144.686 125.618 1.00 11.96 S ATOM 25956 SG CYS M 97 53.685 167.063 150.351 1.00 12.99 S ATOM 26151 SG CYS M 125 57.270 166.431 151.708 1.00 10.89 S ATOM 26178 SG CYS M 128 56.914 168.433 149.067 1.00 9.80 S Time building chain proxies: 28.09, per 1000 atoms: 0.43 Number of scatterers: 65934 At special positions: 0 Unit cell: (215.4, 197.091, 230.478, 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 311 16.00 P 45 15.00 O 12027 8.00 N 10720 7.00 C 42802 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS U 46 " - pdb=" SG CYS U 78 " distance=2.04 Simple disulfide: pdb=" SG CYS U 56 " - pdb=" SG CYS U 68 " distance=2.05 Simple disulfide: pdb=" SG CYS U 90 " - pdb=" SG CYS U 121 " distance=2.05 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=2.06 Simple disulfide: pdb=" SG CYS 8 36 " - pdb=" SG CYS 8 47 " distance=2.05 Simple disulfide: pdb=" SG CYS 9 15 " - pdb=" SG CYS 9 47 " distance=2.04 Simple disulfide: pdb=" SG CYS 9 25 " - pdb=" SG CYS 9 37 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 22.24 Conformation dependent library (CDL) restraints added in 7.1 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="FE2 FES H 301 " - pdb=" SG CYS H 172 " pdb="FE1 FES H 301 " - pdb=" SG CYS H 127 " pdb="FE2 FES H 301 " - pdb=" SG CYS H 168 " pdb="FE1 FES H 301 " - pdb=" SG CYS H 132 " pdb=" SF4 A 801 " pdb="FE3 SF4 A 801 " - pdb=" NE2 HIS A 129 " pdb="FE4 SF4 A 801 " - pdb=" SG CYS A 136 " pdb="FE2 SF4 A 801 " - pdb=" SG CYS A 133 " pdb="FE1 SF4 A 801 " - pdb=" SG CYS A 142 " pdb=" SF4 A 802 " pdb="FE3 SF4 A 802 " - pdb=" SG CYS A 189 " pdb="FE2 SF4 A 802 " - pdb=" SG CYS A 183 " pdb="FE1 SF4 A 802 " - pdb=" SG CYS A 186 " pdb="FE4 SF4 A 802 " - pdb=" SG CYS A 233 " pdb=" SF4 B 501 " pdb="FE3 SF4 B 501 " - pdb=" SG CYS B 381 " pdb="FE4 SF4 B 501 " - pdb=" SG CYS B 427 " 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="FE3 SF4 I 301 " - pdb=" SG CYS I 175 " pdb="FE2 SF4 I 301 " - pdb=" SG CYS I 169 " pdb="FE4 SF4 I 301 " - pdb=" SG CYS I 140 " pdb="FE1 SF4 I 301 " - pdb=" SG CYS I 172 " pdb=" SF4 I 302 " pdb="FE4 SF4 I 302 " - pdb=" SG CYS I 133 " 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=" SF4 K 301 " pdb="FE2 SF4 K 301 " - pdb=" SG CYS K 86 " pdb="FE1 SF4 K 301 " - pdb=" SG CYS K 150 " pdb="FE4 SF4 K 301 " - pdb=" SG CYS K 180 " pdb="FE3 SF4 K 301 " - pdb=" SG CYS K 85 " Number of angles added : 81 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 97 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 128 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 125 " Number of angles added : 3 15934 Ramachandran restraints generated. 7967 Oldfield, 0 Emsley, 7967 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15064 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 320 helices and 34 sheets defined 49.1% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.97 Creating SS restraints... Processing helix chain 'A' and resid 54 through 60 Processing helix chain 'A' and resid 112 through 127 removed outlier: 3.634A pdb=" N GLN A 127 " --> pdb=" O GLU A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 150 removed outlier: 3.593A pdb=" N MET A 149 " --> pdb=" O GLN A 145 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG A 150 " --> pdb=" O ASP A 146 " (cutoff:3.500A) 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 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 226 through 228 No H-bonds generated for 'chain 'A' and resid 226 through 228' Processing helix chain 'A' and resid 295 through 301 removed outlier: 3.611A pdb=" N ALA A 300 " --> pdb=" O LYS A 296 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N CYS A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) 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 removed outlier: 3.600A pdb=" N GLU A 405 " --> pdb=" O ALA A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 434 removed outlier: 3.502A pdb=" N ALA A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 468 Processing helix chain 'A' and resid 470 through 476 Processing helix chain 'A' and resid 494 through 507 Processing helix chain 'A' and resid 527 through 534 Processing helix chain 'A' and resid 578 through 581 No H-bonds generated for 'chain 'A' and resid 578 through 581' Processing helix chain 'A' and resid 622 through 632 removed outlier: 3.728A pdb=" N LEU A 626 " --> pdb=" O ASP A 622 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU A 631 " --> pdb=" O ARG A 627 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR A 632 " --> pdb=" O ALA A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 652 Processing helix chain 'A' and resid 668 through 677 removed outlier: 3.708A pdb=" N VAL A 672 " --> pdb=" O GLY A 668 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN A 673 " --> pdb=" O ASP A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 716 removed outlier: 3.945A pdb=" N ILE A 715 " --> pdb=" O ALA A 711 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA A 716 " --> pdb=" O LYS A 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 38 No H-bonds generated for 'chain 'B' and resid 36 through 38' Processing helix chain 'B' and resid 52 through 58 Processing helix chain 'B' and resid 64 through 69 Processing helix chain 'B' and resid 72 through 82 removed outlier: 3.552A pdb=" N LYS B 81 " --> pdb=" O ASP B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 99 Processing helix chain 'B' and resid 107 through 109 No H-bonds generated for 'chain 'B' and resid 107 through 109' Processing helix chain 'B' and resid 128 through 135 removed outlier: 3.644A pdb=" N LYS B 135 " --> pdb=" O GLU B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 150 Processing helix chain 'B' and resid 165 through 180 Processing helix chain 'B' and resid 188 through 190 No H-bonds generated for 'chain 'B' and resid 188 through 190' Processing helix chain 'B' and resid 207 through 209 No H-bonds generated for 'chain 'B' and resid 207 through 209' Processing helix chain 'B' and resid 211 through 219 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 259 Processing helix chain 'B' and resid 261 through 266 removed outlier: 3.601A pdb=" N SER B 266 " --> pdb=" O ASP B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 305 removed outlier: 3.541A pdb=" N LYS B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) removed outlier: 3.983A 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 333 through 335 No H-bonds generated for 'chain 'B' and resid 333 through 335' 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: 3.936A pdb=" N THR B 392 " --> pdb=" O ARG B 388 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TRP B 393 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG B 400 " --> pdb=" O LYS B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 419 Processing helix chain 'B' and resid 429 through 443 removed outlier: 3.595A pdb=" N TRP B 435 " --> pdb=" O ASP B 431 " (cutoff:3.500A) Proline residue: B 436 - end of helix Processing helix chain 'B' and resid 445 through 458 removed outlier: 3.685A pdb=" N ARG B 451 " --> pdb=" O GLU B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 466 No H-bonds generated for 'chain 'B' and resid 464 through 466' Processing helix chain 'C' and resid 46 through 48 No H-bonds generated for 'chain 'C' and resid 46 through 48' Processing helix chain 'C' and resid 92 through 94 No H-bonds generated for 'chain 'C' and resid 92 through 94' Processing helix chain 'C' and resid 123 through 129 removed outlier: 3.881A pdb=" N GLU C 128 " --> pdb=" O GLU C 124 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N TYR C 129 " --> pdb=" O LYS C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 141 Proline residue: C 137 - end of helix removed outlier: 4.189A pdb=" N ASP C 140 " --> pdb=" O LEU C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 162 removed outlier: 3.631A pdb=" N PHE C 154 " --> pdb=" O ASN C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 176 removed outlier: 3.537A pdb=" N ARG C 174 " --> pdb=" O GLY C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 197 Processing helix chain 'C' and resid 201 through 220 removed outlier: 4.110A pdb=" N PHE C 216 " --> pdb=" O LYS C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 261 removed outlier: 3.794A pdb=" N TYR C 248 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N MET C 249 " --> pdb=" O ASP C 245 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLN C 253 " --> pdb=" O MET C 249 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ASP C 256 " --> pdb=" O THR C 252 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP C 259 " --> pdb=" O GLY C 255 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE C 261 " --> pdb=" O ARG C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 266 No H-bonds generated for 'chain 'C' and resid 263 through 266' Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 285 through 288 No H-bonds generated for 'chain 'C' and resid 285 through 288' Processing helix chain 'C' and resid 305 through 308 No H-bonds generated for 'chain 'C' and resid 305 through 308' Processing helix chain 'C' and resid 329 through 352 removed outlier: 3.681A pdb=" N ARG C 336 " --> pdb=" O ARG C 332 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ARG C 341 " --> pdb=" O MET C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 374 No H-bonds generated for 'chain 'C' and resid 371 through 374' Processing helix chain 'C' and resid 378 through 389 removed outlier: 3.813A pdb=" N TYR C 388 " --> pdb=" O HIS C 384 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 436 removed outlier: 3.549A pdb=" N HIS C 434 " --> pdb=" O PRO C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 441 No H-bonds generated for 'chain 'C' and resid 438 through 441' Processing helix chain 'C' and resid 448 through 450 No H-bonds generated for 'chain 'C' and resid 448 through 450' Processing helix chain 'C' and resid 454 through 457 No H-bonds generated for 'chain 'C' and resid 454 through 457' Processing helix chain 'D' and resid 5 through 33 Proline residue: D 10 - end of helix Processing helix chain 'D' and resid 44 through 57 Processing helix chain 'E' and resid 64 through 73 removed outlier: 4.097A pdb=" N TYR E 68 " --> pdb=" O PHE E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 96 removed outlier: 4.515A pdb=" N VAL E 95 " --> pdb=" O HIS E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 118 Processing helix chain 'E' and resid 140 through 144 Processing helix chain 'E' and resid 146 through 158 Processing helix chain 'E' and resid 178 through 193 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 227 through 229 No H-bonds generated for 'chain 'E' and resid 227 through 229' Processing helix chain 'E' and resid 238 through 250 removed outlier: 3.654A pdb=" N PHE E 250 " --> pdb=" O GLU E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 254 No H-bonds generated for 'chain 'E' and resid 252 through 254' Processing helix chain 'E' and resid 269 through 280 removed outlier: 3.514A pdb=" N THR E 279 " --> pdb=" O MET E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 303 removed outlier: 4.660A pdb=" N ALA E 303 " --> pdb=" O LYS E 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 317 No H-bonds generated for 'chain 'E' and resid 315 through 317' Processing helix chain 'E' and resid 340 through 347 removed outlier: 4.819A pdb=" N PHE E 345 " --> pdb=" O PRO E 341 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N LYS E 346 " --> pdb=" O ASP E 342 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU E 347 " --> pdb=" O LEU E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 351 No H-bonds generated for 'chain 'E' and resid 349 through 351' Processing helix chain 'E' and resid 362 through 366 Processing helix chain 'F' and resid 42 through 60 Processing helix chain 'F' and resid 66 through 84 Processing helix chain 'F' and resid 88 through 95 removed outlier: 3.693A pdb=" N ASN F 93 " --> pdb=" O GLU F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 120 removed outlier: 4.028A pdb=" N SER F 118 " --> pdb=" O ALA F 114 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLU F 119 " --> pdb=" O LYS F 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 81 removed outlier: 3.568A pdb=" N LEU G 65 " --> pdb=" O ASP G 62 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N GLN G 66 " --> pdb=" O ARG G 63 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR G 74 " --> pdb=" O LEU G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 114 removed outlier: 5.165A pdb=" N ILE G 106 " --> pdb=" O SER G 103 " (cutoff:3.500A) Proline residue: G 107 - end of helix removed outlier: 4.190A pdb=" N THR G 110 " --> pdb=" O PRO G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 175 through 186 removed outlier: 3.513A pdb=" N TYR G 186 " --> pdb=" O ALA G 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 264 through 266 No H-bonds generated for 'chain 'G' and resid 264 through 266' Processing helix chain 'H' and resid 49 through 61 removed outlier: 3.602A pdb=" N ALA H 60 " --> pdb=" O GLU H 56 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS H 61 " --> pdb=" O GLU H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 81 removed outlier: 4.283A pdb=" N MET H 72 " --> pdb=" O ALA H 69 " (cutoff:3.500A) Proline residue: H 73 - end of helix Processing helix chain 'H' and resid 87 through 96 Processing helix chain 'H' and resid 101 through 110 removed outlier: 3.775A pdb=" N VAL H 107 " --> pdb=" O ARG H 103 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 133 No H-bonds generated for 'chain 'H' and resid 130 through 133' Processing helix chain 'H' and resid 137 through 147 removed outlier: 3.867A pdb=" N THR H 147 " --> pdb=" O ALA H 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 190 through 202 removed outlier: 3.865A pdb=" N VAL H 194 " --> pdb=" O PRO H 190 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS H 195 " --> pdb=" O GLU H 191 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA H 202 " --> pdb=" O GLU H 198 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 78 removed outlier: 3.512A pdb=" N LYS I 76 " --> pdb=" O SER I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 95 removed outlier: 3.694A pdb=" N VAL I 90 " --> pdb=" O GLY I 86 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N PHE I 95 " --> pdb=" O LEU I 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 135 through 139 Processing helix chain 'I' and resid 174 through 178 Processing helix chain 'I' and resid 198 through 200 No H-bonds generated for 'chain 'I' and resid 198 through 200' Processing helix chain 'I' and resid 204 through 213 Processing helix chain 'I' and resid 215 through 225 removed outlier: 3.688A pdb=" N TYR I 220 " --> pdb=" O LEU I 216 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA I 224 " --> pdb=" O TYR I 220 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 49 Processing helix chain 'J' and resid 58 through 60 No H-bonds generated for 'chain 'J' and resid 58 through 60' Processing helix chain 'J' and resid 67 through 89 Processing helix chain 'J' and resid 95 through 109 Processing helix chain 'J' and resid 115 through 134 Processing helix chain 'J' and resid 172 through 178 Processing helix chain 'K' and resid 56 through 74 Processing helix chain 'K' and resid 85 through 93 removed outlier: 3.930A pdb=" N GLU K 89 " --> pdb=" O CYS K 85 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL K 93 " --> pdb=" O GLU K 89 " (cutoff:3.500A) Processing helix chain 'K' and resid 101 through 103 No H-bonds generated for 'chain 'K' and resid 101 through 103' Processing helix chain 'K' and resid 128 through 137 removed outlier: 3.694A pdb=" N GLN K 137 " --> pdb=" O GLN K 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 155 through 157 No H-bonds generated for 'chain 'K' and resid 155 through 157' Processing helix chain 'K' and resid 184 through 199 Processing helix chain 'L' and resid 2 through 16 Processing helix chain 'L' and resid 23 through 47 Processing helix chain 'L' and resid 51 through 79 removed outlier: 3.800A pdb=" N ILE L 61 " --> pdb=" O ILE L 57 " (cutoff:3.500A) Processing helix chain 'M' and resid 53 through 59 Processing helix chain 'M' and resid 61 through 63 No H-bonds generated for 'chain 'M' and resid 61 through 63' Processing helix chain 'M' and resid 78 through 83 removed outlier: 3.745A pdb=" N ALA M 83 " --> pdb=" O ILE M 79 " (cutoff:3.500A) Processing helix chain 'O' and resid 30 through 41 Processing helix chain 'O' and resid 49 through 51 No H-bonds generated for 'chain 'O' and resid 49 through 51' Processing helix chain 'O' and resid 66 through 80 removed outlier: 4.643A pdb=" N VAL O 70 " --> pdb=" O SER O 66 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL O 74 " --> pdb=" O VAL O 70 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU O 79 " --> pdb=" O ALA O 75 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE O 80 " --> pdb=" O ILE O 76 " (cutoff:3.500A) Processing helix chain 'O' and resid 95 through 104 removed outlier: 5.183A pdb=" N LEU O 103 " --> pdb=" O VAL O 99 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ALA O 104 " --> pdb=" O GLU O 100 " (cutoff:3.500A) Processing helix chain 'P' and resid 18 through 34 Processing helix chain 'P' and resid 36 through 42 Processing helix chain 'P' and resid 49 through 63 removed outlier: 4.403A pdb=" N HIS P 63 " --> pdb=" O GLU P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 69 through 87 Processing helix chain 'P' and resid 93 through 96 No H-bonds generated for 'chain 'P' and resid 93 through 96' Processing helix chain 'P' and resid 115 through 120 Processing helix chain 'Q' and resid 52 through 65 removed outlier: 3.516A pdb=" N ALA Q 61 " --> pdb=" O GLU Q 57 " (cutoff:3.500A) Processing helix chain 'Q' and resid 91 through 102 Processing helix chain 'Q' and resid 109 through 112 No H-bonds generated for 'chain 'Q' and resid 109 through 112' Processing helix chain 'Q' and resid 118 through 127 Processing helix chain 'R' and resid 9 through 29 removed outlier: 3.746A pdb=" N ASN R 28 " --> pdb=" O LYS R 24 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TRP R 29 " --> pdb=" O LEU R 25 " (cutoff:3.500A) Processing helix chain 'R' and resid 33 through 49 Processing helix chain 'R' and resid 57 through 72 Processing helix chain 'S' and resid 53 through 65 removed outlier: 4.221A pdb=" N GLN S 65 " --> pdb=" O GLN S 61 " (cutoff:3.500A) Processing helix chain 'S' and resid 89 through 99 removed outlier: 4.158A pdb=" N GLU S 93 " --> pdb=" O ALA S 89 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE S 94 " --> pdb=" O GLU S 90 " (cutoff:3.500A) Processing helix chain 'S' and resid 105 through 110 removed outlier: 3.740A pdb=" N LEU S 109 " --> pdb=" O ILE S 105 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU S 110 " --> pdb=" O LEU S 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 105 through 110' Processing helix chain 'S' and resid 113 through 136 removed outlier: 3.721A pdb=" N GLY S 133 " --> pdb=" O TYR S 129 " (cutoff:3.500A) Processing helix chain 'S' and resid 165 through 169 removed outlier: 3.611A pdb=" N TYR S 169 " --> pdb=" O VAL S 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 165 through 169' Processing helix chain 'S' and resid 172 through 188 removed outlier: 4.150A pdb=" N ARG S 188 " --> pdb=" O VAL S 184 " (cutoff:3.500A) Processing helix chain 'S' and resid 191 through 206 Processing helix chain 'S' and resid 208 through 212 Processing helix chain 'S' and resid 215 through 226 removed outlier: 4.240A pdb=" N ASP S 219 " --> pdb=" O GLU S 215 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ALA S 220 " --> pdb=" O ASN S 216 " (cutoff:3.500A) Processing helix chain 'S' and resid 234 through 237 No H-bonds generated for 'chain 'S' and resid 234 through 237' Processing helix chain 'U' and resid 32 through 37 Processing helix chain 'U' and resid 39 through 45 Processing helix chain 'U' and resid 47 through 59 Processing helix chain 'U' and resid 66 through 102 removed outlier: 3.906A pdb=" N LEU U 69 " --> pdb=" O ILE U 66 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N LYS U 70 " --> pdb=" O ASP U 67 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU U 71 " --> pdb=" O CYS U 68 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ARG U 73 " --> pdb=" O LYS U 70 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL U 75 " --> pdb=" O GLY U 72 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU U 84 " --> pdb=" O SER U 81 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS U 88 " --> pdb=" O ASP U 85 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N CYS U 90 " --> pdb=" O ASN U 87 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N LEU U 91 " --> pdb=" O LYS U 88 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ASP U 92 " --> pdb=" O SER U 89 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU U 93 " --> pdb=" O CYS U 90 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE U 94 " --> pdb=" O LEU U 91 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TRP U 98 " --> pdb=" O ARG U 95 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN U 99 " --> pdb=" O LEU U 96 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU U 102 " --> pdb=" O GLN U 99 " (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 110 No H-bonds generated for 'chain 'U' and resid 108 through 110' Processing helix chain 'U' and resid 112 through 125 removed outlier: 3.873A pdb=" N LEU U 117 " --> pdb=" O LYS U 113 " (cutoff:3.500A) Processing helix chain 'U' and resid 142 through 144 No H-bonds generated for 'chain 'U' and resid 142 through 144' Processing helix chain 'U' and resid 157 through 169 Processing helix chain 'W' and resid 30 through 95 Proline residue: W 71 - end of helix removed outlier: 3.775A pdb=" N GLU W 76 " --> pdb=" O LEU W 72 " (cutoff:3.500A) Processing helix chain 'X' and resid 28 through 33 Processing helix chain 'X' and resid 37 through 60 removed outlier: 3.752A pdb=" N LEU X 50 " --> pdb=" O ALA X 46 " (cutoff:3.500A) Proline residue: X 51 - end of helix Processing helix chain 'X' and resid 72 through 99 removed outlier: 3.702A pdb=" N VAL X 77 " --> pdb=" O LYS X 73 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG X 97 " --> pdb=" O ARG X 93 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE X 98 " --> pdb=" O SER X 94 " (cutoff:3.500A) Processing helix chain 'X' and resid 105 through 121 removed outlier: 3.921A pdb=" N LYS X 109 " --> pdb=" O ALA X 105 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LYS X 110 " --> pdb=" O ARG X 106 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS X 119 " --> pdb=" O MET X 115 " (cutoff:3.500A) Processing helix chain 'X' and resid 133 through 142 Processing helix chain 'Y' and resid 50 through 55 Processing helix chain 'Y' and resid 115 through 124 Processing helix chain 'Y' and resid 145 through 148 removed outlier: 3.830A pdb=" N PHE Y 148 " --> pdb=" O ALA Y 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 145 through 148' Processing helix chain 'Z' and resid 19 through 27 removed outlier: 3.709A pdb=" N LEU Z 24 " --> pdb=" O TRP Z 21 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL Z 26 " --> pdb=" O LYS Z 23 " (cutoff:3.500A) Processing helix chain 'Z' and resid 64 through 67 No H-bonds generated for 'chain 'Z' and resid 64 through 67' Processing helix chain 'Z' and resid 74 through 77 No H-bonds generated for 'chain 'Z' and resid 74 through 77' Processing helix chain 'Z' and resid 91 through 99 Processing helix chain 'Z' and resid 111 through 123 removed outlier: 4.187A pdb=" N LYS Z 116 " --> pdb=" O GLU Z 112 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASN Z 120 " --> pdb=" O LYS Z 116 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ILE Z 121 " --> pdb=" O ALA Z 117 " (cutoff:3.500A) Processing helix chain 'Z' and resid 128 through 134 Processing helix chain 'Z' and resid 137 through 142 Processing helix chain 'a' and resid 28 through 32 Processing helix chain 'a' and resid 74 through 76 No H-bonds generated for 'chain 'a' and resid 74 through 76' Processing helix chain 'a' and resid 90 through 111 Processing helix chain 'a' and resid 126 through 130 Processing helix chain 'a' and resid 138 through 140 No H-bonds generated for 'chain 'a' and resid 138 through 140' Processing helix chain 'b' and resid 3 through 24 Processing helix chain 'b' and resid 33 through 64 removed outlier: 3.601A pdb=" N SER b 39 " --> pdb=" O TYR b 36 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TRP b 43 " --> pdb=" O GLY b 40 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU b 50 " --> pdb=" O GLY b 47 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS b 64 " --> pdb=" O LEU b 61 " (cutoff:3.500A) Processing helix chain 'c' and resid 23 through 26 No H-bonds generated for 'chain 'c' and resid 23 through 26' Processing helix chain 'c' and resid 34 through 48 removed outlier: 3.804A pdb=" N VAL c 39 " --> pdb=" O GLY c 35 " (cutoff:3.500A) Processing helix chain 'd' and resid 20 through 55 removed outlier: 3.503A pdb=" N GLU d 25 " --> pdb=" O LYS d 21 " (cutoff:3.500A) Processing helix chain 'd' and resid 58 through 62 removed outlier: 3.905A pdb=" N ASP d 62 " --> pdb=" O HIS d 59 " (cutoff:3.500A) Processing helix chain 'd' and resid 64 through 73 Processing helix chain 'd' and resid 82 through 87 Processing helix chain 'e' and resid 21 through 44 removed outlier: 3.572A pdb=" N ALA e 26 " --> pdb=" O GLY e 22 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS e 28 " --> pdb=" O ARG e 24 " (cutoff:3.500A) Processing helix chain 'e' and resid 46 through 50 removed outlier: 3.532A pdb=" N LEU e 50 " --> pdb=" O TYR e 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 46 through 50' Processing helix chain 'f' and resid 20 through 36 removed outlier: 6.547A pdb=" N GLY f 31 " --> pdb=" O LYS f 27 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ALA f 32 " --> pdb=" O ASN f 28 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS f 35 " --> pdb=" O GLY f 31 " (cutoff:3.500A) Processing helix chain 'f' and resid 59 through 61 No H-bonds generated for 'chain 'f' and resid 59 through 61' Processing helix chain 'f' and resid 73 through 84 Processing helix chain 'g' and resid 12 through 22 Processing helix chain 'g' and resid 24 through 42 removed outlier: 3.882A pdb=" N GLY g 36 " --> pdb=" O ILE g 32 " (cutoff:3.500A) Proline residue: g 37 - end of helix Processing helix chain 'g' and resid 44 through 50 Processing helix chain 'h' and resid 5 through 15 Processing helix chain 'h' and resid 17 through 26 Processing helix chain 'h' and resid 75 through 81 removed outlier: 3.640A pdb=" N PHE h 79 " --> pdb=" O PRO h 75 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TRP h 80 " --> pdb=" O GLY h 76 " (cutoff:3.500A) Processing helix chain 'i' and resid 26 through 47 removed outlier: 3.662A pdb=" N PHE i 32 " --> pdb=" O LEU i 28 " (cutoff:3.500A) Processing helix chain 'i' and resid 61 through 77 Processing helix chain 'j' and resid 30 through 40 Processing helix chain 'j' and resid 42 through 44 No H-bonds generated for 'chain 'j' and resid 42 through 44' Processing helix chain 'j' and resid 50 through 60 Processing helix chain 'j' and resid 62 through 73 Processing helix chain 'n' and resid 19 through 45 removed outlier: 3.875A pdb=" N ALA n 43 " --> pdb=" O SER n 39 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS n 44 " --> pdb=" O SER n 40 " (cutoff:3.500A) Processing helix chain 'n' and resid 50 through 53 Processing helix chain 'n' and resid 59 through 61 No H-bonds generated for 'chain 'n' and resid 59 through 61' Processing helix chain 'n' and resid 63 through 88 removed outlier: 3.650A pdb=" N ILE n 69 " --> pdb=" O GLU n 65 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN n 76 " --> pdb=" O ALA n 72 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS n 87 " --> pdb=" O MET n 83 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ARG n 88 " --> pdb=" O HIS n 84 " (cutoff:3.500A) Processing helix chain 'n' and resid 93 through 96 No H-bonds generated for 'chain 'n' and resid 93 through 96' Processing helix chain '1' and resid 2 through 33 removed outlier: 3.532A pdb=" N PHE 1 17 " --> pdb=" O VAL 1 13 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA 1 20 " --> pdb=" O LEU 1 16 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU 1 22 " --> pdb=" O SER 1 18 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N THR 1 23 " --> pdb=" O VAL 1 19 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL 1 24 " --> pdb=" O ALA 1 20 " (cutoff:3.500A) Processing helix chain '1' and resid 49 through 57 Processing helix chain '1' and resid 70 through 88 Proline residue: 1 77 - end of helix removed outlier: 3.942A pdb=" N GLY 1 87 " --> pdb=" O THR 1 83 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N TRP 1 88 " --> pdb=" O ALA 1 84 " (cutoff:3.500A) Processing helix chain '1' and resid 105 through 112 Processing helix chain '1' and resid 115 through 125 removed outlier: 3.749A pdb=" N PHE 1 118 " --> pdb=" O LEU 1 115 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLY 1 119 " --> pdb=" O GLY 1 116 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N LEU 1 122 " --> pdb=" O GLY 1 119 " (cutoff:3.500A) Processing helix chain '1' and resid 130 through 161 removed outlier: 3.884A pdb=" N LEU 1 134 " --> pdb=" O LYS 1 130 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLY 1 135 " --> pdb=" O TYR 1 131 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ILE 1 149 " --> pdb=" O SER 1 145 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N PHE 1 160 " --> pdb=" O ILE 1 156 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL 1 161 " --> pdb=" O ILE 1 157 " (cutoff:3.500A) Processing helix chain '1' and resid 167 through 174 removed outlier: 3.605A pdb=" N ARG 1 174 " --> pdb=" O ILE 1 170 " (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 183 through 196 removed outlier: 3.542A pdb=" N LEU 1 187 " --> pdb=" O LEU 1 183 " (cutoff:3.500A) Processing helix chain '1' and resid 214 through 216 No H-bonds generated for 'chain '1' and resid 214 through 216' Processing helix chain '1' and resid 221 through 245 removed outlier: 4.305A pdb=" N PHE 1 226 " --> pdb=" O PRO 1 223 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE 1 228 " --> pdb=" O VAL 1 225 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU 1 231 " --> pdb=" O PHE 1 228 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER 1 233 " --> pdb=" O ALA 1 230 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE 1 238 " --> pdb=" O ILE 1 235 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU 1 245 " --> pdb=" O ASN 1 242 " (cutoff:3.500A) Processing helix chain '1' and resid 257 through 262 Processing helix chain '1' and resid 268 through 298 Processing helix chain '1' and resid 305 through 314 Processing helix chain '1' and resid 316 through 333 Proline residue: 1 328 - end of helix Processing helix chain '2' and resid 2 through 15 removed outlier: 3.825A pdb=" N THR 2 11 " --> pdb=" O ILE 2 7 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET 2 15 " --> pdb=" O THR 2 11 " (cutoff:3.500A) Processing helix chain '2' and resid 21 through 36 Processing helix chain '2' and resid 40 through 45 Processing helix chain '2' and resid 63 through 84 Processing helix chain '2' and resid 93 through 96 No H-bonds generated for 'chain '2' and resid 93 through 96' Processing helix chain '2' and resid 103 through 118 removed outlier: 3.967A pdb=" N ILE 2 117 " --> pdb=" O GLY 2 113 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL 2 118 " --> pdb=" O ALA 2 114 " (cutoff:3.500A) Processing helix chain '2' and resid 123 through 142 Processing helix chain '2' and resid 148 through 178 removed outlier: 3.692A pdb=" N LEU 2 164 " --> pdb=" O MET 2 160 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE 2 168 " --> pdb=" O LEU 2 164 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL 2 178 " --> pdb=" O THR 2 174 " (cutoff:3.500A) Processing helix chain '2' and resid 191 through 194 No H-bonds generated for 'chain '2' and resid 191 through 194' Processing helix chain '2' and resid 198 through 209 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 227 Processing helix chain '2' and resid 238 through 248 Processing helix chain '2' and resid 258 through 272 removed outlier: 3.559A pdb=" N SER 2 272 " --> pdb=" O LEU 2 268 " (cutoff:3.500A) Processing helix chain '2' and resid 281 through 300 removed outlier: 3.589A pdb=" N SER 2 288 " --> pdb=" O LEU 2 284 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY 2 289 " --> pdb=" O LEU 2 285 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N MET 2 296 " --> pdb=" O ASN 2 292 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N MET 2 297 " --> pdb=" O ALA 2 293 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU 2 299 " --> pdb=" O TYR 2 295 " (cutoff:3.500A) Processing helix chain '2' and resid 306 through 332 removed outlier: 3.811A pdb=" N LEU 2 310 " --> pdb=" O GLU 2 306 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE 2 327 " --> pdb=" O ILE 2 323 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE 2 328 " --> pdb=" O PHE 2 324 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE 2 329 " --> pdb=" O MET 2 325 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ILE 2 331 " --> pdb=" O ILE 2 327 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N TYR 2 332 " --> pdb=" O ILE 2 328 " (cutoff:3.500A) Processing helix chain '2' and resid 347 through 350 removed outlier: 3.713A pdb=" N LEU 2 350 " --> pdb=" O VAL 2 347 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 347 through 350' Processing helix chain '2' and resid 358 through 372 Processing helix chain '2' and resid 378 through 392 removed outlier: 3.599A pdb=" N GLY 2 382 " --> pdb=" O LEU 2 378 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER 2 389 " --> pdb=" O ASN 2 385 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN 2 392 " --> pdb=" O MET 2 388 " (cutoff:3.500A) Processing helix chain '2' and resid 396 through 420 removed outlier: 3.613A pdb=" N ILE 2 400 " --> pdb=" O TYR 2 396 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU 2 411 " --> pdb=" O LEU 2 407 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N TYR 2 412 " --> pdb=" O ILE 2 408 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR 2 413 " --> pdb=" O SER 2 409 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU 2 416 " --> pdb=" O TYR 2 412 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU 2 417 " --> pdb=" O TYR 2 413 " (cutoff:3.500A) Processing helix chain '2' and resid 437 through 453 removed outlier: 3.798A pdb=" N ILE 2 442 " --> pdb=" O VAL 2 438 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU 2 443 " --> pdb=" O LEU 2 439 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE 2 450 " --> pdb=" O LEU 2 446 " (cutoff:3.500A) Processing helix chain '2' and resid 457 through 467 Processing helix chain '3' and resid 5 through 25 Proline residue: 3 12 - end of helix Processing helix chain '3' and resid 54 through 70 removed outlier: 4.227A pdb=" N ALA 3 60 " --> pdb=" O PHE 3 56 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU 3 64 " --> pdb=" O ALA 3 60 " (cutoff:3.500A) Proline residue: 3 65 - end of helix removed outlier: 3.693A pdb=" N GLU 3 69 " --> pdb=" O PRO 3 65 " (cutoff:3.500A) Processing helix chain '3' and resid 74 through 78 removed outlier: 4.034A pdb=" N MET 3 78 " --> pdb=" O LEU 3 74 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 74 through 78' Processing helix chain '3' and resid 87 through 108 removed outlier: 3.711A pdb=" N GLY 3 101 " --> pdb=" O ILE 3 97 " (cutoff:3.500A) Processing helix chain '4' and resid 2 through 20 removed outlier: 3.660A pdb=" N LEU 4 7 " --> pdb=" O LEU 4 3 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR 4 12 " --> pdb=" O LEU 4 8 " (cutoff:3.500A) Processing helix chain '4' and resid 25 through 44 Processing helix chain '4' and resid 83 through 102 removed outlier: 4.117A pdb=" N PHE 4 88 " --> pdb=" O LEU 4 84 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU 4 95 " --> pdb=" O LEU 4 91 " (cutoff:3.500A) Proline residue: 4 97 - end of helix Processing helix chain '4' and resid 111 through 127 Processing helix chain '4' and resid 134 through 142 removed outlier: 3.976A pdb=" N LEU 4 140 " --> pdb=" O SER 4 136 " (cutoff:3.500A) Processing helix chain '4' and resid 144 through 154 Processing helix chain '4' and resid 160 through 188 removed outlier: 4.371A pdb=" N THR 4 171 " --> pdb=" O VAL 4 167 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N PHE 4 177 " --> pdb=" O SER 4 173 " (cutoff:3.500A) Processing helix chain '4' and resid 204 through 221 removed outlier: 3.885A pdb=" N ILE 4 209 " --> pdb=" O ASP 4 205 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LEU 4 212 " --> pdb=" O THR 4 208 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLY 4 213 " --> pdb=" O ILE 4 209 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU 4 214 " --> pdb=" O ILE 4 210 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA 4 217 " --> pdb=" O GLY 4 213 " (cutoff:3.500A) Processing helix chain '4' and resid 231 through 236 Processing helix chain '4' and resid 240 through 261 removed outlier: 5.438A pdb=" N LEU 4 251 " --> pdb=" O ALA 4 247 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N LYS 4 252 " --> pdb=" O GLY 4 248 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU 4 259 " --> pdb=" O LEU 4 255 " (cutoff:3.500A) Processing helix chain '4' and resid 267 through 291 removed outlier: 4.223A pdb=" N LEU 4 272 " --> pdb=" O GLU 4 268 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR 4 273 " --> pdb=" O ALA 4 269 " (cutoff:3.500A) Proline residue: 4 275 - end of helix removed outlier: 3.548A pdb=" N LEU 4 287 " --> pdb=" O LEU 4 283 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR 4 288 " --> pdb=" O THR 4 284 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA 4 291 " --> pdb=" O LEU 4 287 " (cutoff:3.500A) Processing helix chain '4' and resid 299 through 319 removed outlier: 4.063A pdb=" N LEU 4 315 " --> pdb=" O GLY 4 311 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLY 4 316 " --> pdb=" O ILE 4 312 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL 4 317 " --> pdb=" O ALA 4 313 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N SER 4 319 " --> pdb=" O LEU 4 315 " (cutoff:3.500A) Processing helix chain '4' and resid 322 through 347 Proline residue: 4 340 - end of helix Processing helix chain '4' and resid 359 through 361 No H-bonds generated for 'chain '4' and resid 359 through 361' Processing helix chain '4' and resid 370 through 384 Processing helix chain '4' and resid 391 through 405 removed outlier: 3.521A pdb=" N ARG 4 405 " --> pdb=" O GLY 4 401 " (cutoff:3.500A) Processing helix chain '4' and resid 407 through 432 removed outlier: 3.516A pdb=" N ILE 4 412 " --> pdb=" O ILE 4 408 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ILE 4 415 " --> pdb=" O GLY 4 411 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N SER 4 416 " --> pdb=" O ILE 4 412 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N VAL 4 417 " --> pdb=" O SER 4 413 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N LEU 4 418 " --> pdb=" O CYS 4 414 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA 4 421 " --> pdb=" O VAL 4 417 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N TYR 4 423 " --> pdb=" O LEU 4 419 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLN 4 424 " --> pdb=" O ALA 4 420 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS 4 430 " --> pdb=" O LYS 4 426 " (cutoff:3.500A) Processing helix chain '4' and resid 448 through 466 removed outlier: 3.946A pdb=" N THR 4 461 " --> pdb=" O LEU 4 457 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE 4 464 " --> pdb=" O SER 4 460 " (cutoff:3.500A) Processing helix chain '4' and resid 468 through 480 removed outlier: 3.948A pdb=" N MET 4 471 " --> pdb=" O PRO 4 468 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ASN 4 473 " --> pdb=" O ILE 4 470 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU 4 474 " --> pdb=" O MET 4 471 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N TYR 4 476 " --> pdb=" O ASN 4 473 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N TRP 4 477 " --> pdb=" O LEU 4 474 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL 4 479 " --> pdb=" O TYR 4 476 " (cutoff:3.500A) Processing helix chain '5' and resid 4 through 21 removed outlier: 3.546A pdb=" N ILE 5 8 " --> pdb=" O ALA 5 4 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ILE 5 9 " --> pdb=" O ILE 5 5 " (cutoff:3.500A) Proline residue: 5 12 - end of helix removed outlier: 3.542A pdb=" N TRP 5 16 " --> pdb=" O PRO 5 12 " (cutoff:3.500A) Proline residue: 5 19 - end of helix Processing helix chain '5' and resid 23 through 26 No H-bonds generated for 'chain '5' and resid 23 through 26' Processing helix chain '5' and resid 28 through 55 removed outlier: 4.119A pdb=" N ARG 5 33 " --> pdb=" O VAL 5 29 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY 5 55 " --> pdb=" O TYR 5 51 " (cutoff:3.500A) Processing helix chain '5' and resid 83 through 106 removed outlier: 3.635A pdb=" N ALA 5 91 " --> pdb=" O THR 5 87 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLY 5 105 " --> pdb=" O ILE 5 101 " (cutoff:3.500A) Processing helix chain '5' and resid 113 through 132 Processing helix chain '5' and resid 136 through 154 removed outlier: 3.827A pdb=" N GLY 5 147 " --> pdb=" O TRP 5 143 " (cutoff:3.500A) Processing helix chain '5' and resid 161 through 191 Processing helix chain '5' and resid 197 through 202 Processing helix chain '5' and resid 209 through 226 Processing helix chain '5' and resid 230 through 239 removed outlier: 3.770A pdb=" N HIS 5 233 " --> pdb=" O PHE 5 230 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASN 5 234 " --> pdb=" O GLY 5 231 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TRP 5 235 " --> pdb=" O LEU 5 232 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU 5 236 " --> pdb=" O HIS 5 233 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU 5 238 " --> pdb=" O TRP 5 235 " (cutoff:3.500A) Processing helix chain '5' and resid 244 through 252 removed outlier: 3.634A pdb=" N ALA 5 252 " --> pdb=" O SER 5 248 " (cutoff:3.500A) Processing helix chain '5' and resid 254 through 270 removed outlier: 4.242A pdb=" N GLY 5 259 " --> pdb=" O LEU 5 255 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE 5 260 " --> pdb=" O VAL 5 256 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU 5 263 " --> pdb=" O GLY 5 259 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ASN 5 268 " --> pdb=" O LEU 5 264 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ILE 5 269 " --> pdb=" O ARG 5 265 " (cutoff:3.500A) Processing helix chain '5' and resid 274 through 297 removed outlier: 3.982A pdb=" N LEU 5 289 " --> pdb=" O ALA 5 285 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N CYS 5 297 " --> pdb=" O LEU 5 293 " (cutoff:3.500A) Processing helix chain '5' and resid 301 through 321 removed outlier: 3.923A pdb=" N GLN 5 312 " --> pdb=" O SER 5 308 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLY 5 314 " --> pdb=" O MET 5 310 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N MET 5 315 " --> pdb=" O SER 5 311 " (cutoff:3.500A) Processing helix chain '5' and resid 325 through 352 removed outlier: 3.783A pdb=" N ALA 5 336 " --> pdb=" O LEU 5 332 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N PHE 5 337 " --> pdb=" O LEU 5 333 " (cutoff:3.500A) Processing helix chain '5' and resid 360 through 362 No H-bonds generated for 'chain '5' and resid 360 through 362' Processing helix chain '5' and resid 371 through 384 Processing helix chain '5' and resid 391 through 405 removed outlier: 4.703A pdb=" N ILE 5 398 " --> pdb=" O TYR 5 394 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ILE 5 399 " --> pdb=" O THR 5 395 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE 5 400 " --> pdb=" O LYS 5 396 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR 5 404 " --> pdb=" O ILE 5 400 " (cutoff:3.500A) Processing helix chain '5' and resid 410 through 434 removed outlier: 4.814A pdb=" N TYR 5 428 " --> pdb=" O THR 5 425 " (cutoff:3.500A) Processing helix chain '5' and resid 445 through 449 Processing helix chain '5' and resid 456 through 480 Proline residue: 5 461 - end of helix removed outlier: 6.241A pdb=" N GLY 5 473 " --> pdb=" O ALA 5 469 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N TRP 5 474 " --> pdb=" O MET 5 470 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ASP 5 478 " --> pdb=" O TRP 5 474 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ILE 5 479 " --> pdb=" O ILE 5 475 " (cutoff:3.500A) Processing helix chain '5' and resid 499 through 504 removed outlier: 3.525A pdb=" N GLU 5 503 " --> pdb=" O TYR 5 499 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE 5 504 " --> pdb=" O PHE 5 500 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 499 through 504' Processing helix chain '5' and resid 508 through 530 Proline residue: 5 514 - end of helix removed outlier: 3.725A pdb=" N SER 5 522 " --> pdb=" O ALA 5 518 " (cutoff:3.500A) Processing helix chain '5' and resid 541 through 551 Processing helix chain '5' and resid 556 through 561 Processing helix chain '5' and resid 565 through 578 removed outlier: 3.505A pdb=" N HIS 5 577 " --> pdb=" O GLY 5 573 " (cutoff:3.500A) Processing helix chain '5' and resid 583 through 586 No H-bonds generated for 'chain '5' and resid 583 through 586' Processing helix chain '5' and resid 589 through 607 removed outlier: 3.792A pdb=" N ASN 5 593 " --> pdb=" O PRO 5 589 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG 5 594 " --> pdb=" O VAL 5 590 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N SER 5 607 " --> pdb=" O VAL 5 603 " (cutoff:3.500A) Processing helix chain '5' and resid 613 through 637 removed outlier: 3.922A pdb=" N LEU 5 622 " --> pdb=" O SER 5 618 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR 5 624 " --> pdb=" O LEU 5 620 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE 5 625 " --> pdb=" O ILE 5 621 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU 5 629 " --> pdb=" O ILE 5 625 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N VAL 5 637 " --> pdb=" O LEU 5 633 " (cutoff:3.500A) Processing helix chain '5' and resid 640 through 654 Proline residue: 5 644 - end of helix Processing helix chain '6' and resid 3 through 5 No H-bonds generated for 'chain '6' and resid 3 through 5' Processing helix chain '6' and resid 8 through 24 Processing helix chain '6' and resid 29 through 50 Processing helix chain '6' and resid 53 through 62 removed outlier: 3.917A pdb=" N LEU 6 57 " --> pdb=" O GLY 6 53 " (cutoff:3.500A) Processing helix chain '6' and resid 67 through 76 Processing helix chain '6' and resid 87 through 90 No H-bonds generated for 'chain '6' and resid 87 through 90' Processing helix chain '6' and resid 94 through 110 Processing helix chain '6' and resid 118 through 125 removed outlier: 3.677A pdb=" N LEU 6 122 " --> pdb=" O LEU 6 118 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU 6 124 " --> pdb=" O ASN 6 120 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA 6 125 " --> pdb=" O LYS 6 121 " (cutoff:3.500A) Processing helix chain '6' and resid 146 through 153 Processing helix chain '6' and resid 159 through 179 Proline residue: 6 176 - end of helix Processing helix chain '8' and resid 10 through 16 Processing helix chain '8' and resid 20 through 22 No H-bonds generated for 'chain '8' and resid 20 through 22' Processing helix chain '8' and resid 27 through 39 removed outlier: 4.152A pdb=" N VAL 8 31 " --> pdb=" O ALA 8 28 " (cutoff:3.500A) Proline residue: 8 32 - end of helix Processing helix chain '8' and resid 49 through 84 removed outlier: 3.553A pdb=" N ALA 8 74 " --> pdb=" O ASP 8 70 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU 8 75 " --> pdb=" O LYS 8 71 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS 8 76 " --> pdb=" O LEU 8 72 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE 8 77 " --> pdb=" O LYS 8 73 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA 8 84 " --> pdb=" O ALA 8 80 " (cutoff:3.500A) Processing helix chain '9' and resid 16 through 27 Processing helix chain '9' and resid 34 through 49 removed outlier: 3.624A pdb=" N LEU 9 38 " --> pdb=" O ALA 9 35 " (cutoff:3.500A) Proline residue: 9 39 - end of helix removed outlier: 3.597A pdb=" N GLU 9 46 " --> pdb=" O ASP 9 43 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N HIS 9 49 " --> pdb=" O GLU 9 46 " (cutoff:3.500A) Processing helix chain '9' and resid 51 through 66 removed outlier: 3.865A pdb=" N VAL 9 63 " --> pdb=" O GLU 9 59 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLN 9 66 " --> pdb=" O SER 9 62 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 36 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 253 through 255 removed outlier: 3.606A pdb=" N ARG A 279 " --> pdb=" O ASP A 271 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 312 through 315 Processing sheet with id= E, first strand: chain 'A' and resid 346 through 350 removed outlier: 6.266A pdb=" N MET A 549 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N VAL A 349 " --> pdb=" O MET A 549 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N TRP A 551 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N PHE A 568 " --> pdb=" O VAL A 550 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N LEU A 552 " --> pdb=" O PHE A 568 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL A 570 " --> pdb=" O LEU A 552 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL A 585 " --> pdb=" O TYR A 571 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N GLY A 573 " --> pdb=" O VAL A 585 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N LEU A 587 " --> pdb=" O GLY A 573 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 519 through 521 removed outlier: 5.796A pdb=" N ILE A 482 " --> pdb=" O ASN A 520 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU A 481 " --> pdb=" O ALA A 409 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N GLU A 438 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N LEU A 412 " --> pdb=" O GLU A 438 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA A 440 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ALA A 453 " --> pdb=" O SER A 441 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 597 through 600 Processing sheet with id= H, first strand: chain 'B' and resid 242 through 246 removed outlier: 7.443A pdb=" N TYR B 114 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N THR B 245 " --> pdb=" O TYR B 114 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL B 116 " --> pdb=" O THR B 245 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ALA B 155 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N VAL B 117 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N TYR B 157 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ALA B 119 " --> pdb=" O TYR B 157 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N TYR B 159 " --> pdb=" O ALA B 119 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ASP B 196 " --> pdb=" O ALA B 156 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ILE B 158 " --> pdb=" O ASP B 196 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N TYR B 198 " --> pdb=" O ILE B 158 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ILE B 160 " --> pdb=" O TYR B 198 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N HIS B 200 " --> pdb=" O ILE B 160 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 288 through 293 removed outlier: 3.721A pdb=" N VAL B 358 " --> pdb=" O SER B 281 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY B 318 " --> pdb=" O ILE B 359 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 83 through 87 removed outlier: 3.595A pdb=" N ARG C 99 " --> pdb=" O HIS C 115 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG C 111 " --> pdb=" O GLU C 103 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N SER C 105 " --> pdb=" O ILE C 109 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE C 109 " --> pdb=" O SER C 105 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 397 through 405 Processing sheet with id= L, first strand: chain 'E' and resid 31 through 33 Processing sheet with id= M, first strand: chain 'E' and resid 258 through 261 removed outlier: 7.038A pdb=" N ILE E 199 " --> pdb=" O PHE E 259 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N LEU E 261 " --> pdb=" O ILE E 199 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ARG E 201 " --> pdb=" O LEU E 261 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL E 125 " --> pdb=" O ILE E 164 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N VAL E 166 " --> pdb=" O VAL E 125 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ASN E 127 " --> pdb=" O VAL E 166 " (cutoff:3.500A) removed outlier: 9.223A pdb=" N ALA E 168 " --> pdb=" O ASN E 127 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N THR E 79 " --> pdb=" O ALA E 56 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N VAL E 58 " --> pdb=" O THR E 79 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL E 81 " --> pdb=" O VAL E 58 " (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 122 through 130 removed outlier: 6.755A pdb=" N ASN G 143 " --> pdb=" O ILE G 124 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE G 126 " --> pdb=" O VAL G 141 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL G 141 " --> pdb=" O ILE G 126 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ALA G 128 " --> pdb=" O GLU G 139 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLU G 139 " --> pdb=" O ALA G 128 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N LEU G 96 " --> pdb=" O ARG G 152 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N TYR G 158 " --> pdb=" O VAL G 100 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 164 through 166 removed outlier: 5.686A pdb=" N PHE G 189 " --> pdb=" O VAL G 165 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'G' and resid 220 through 225 removed outlier: 3.724A pdb=" N ARG G 230 " --> pdb=" O ASP G 225 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'H' and resid 122 through 127 Processing sheet with id= S, first strand: chain 'H' and resid 177 through 179 Processing sheet with id= T, first strand: chain 'I' and resid 118 through 120 Processing sheet with id= U, first strand: chain 'I' and resid 145 through 151 removed outlier: 5.861A pdb=" N GLU I 150 " --> pdb=" O THR I 159 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N THR I 159 " --> pdb=" O GLU I 150 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'K' and resid 76 through 78 removed outlier: 3.606A pdb=" N ILE K 106 " --> pdb=" O PHE K 76 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'K' and resid 116 through 120 removed outlier: 6.850A pdb=" N TRP K 143 " --> pdb=" O MET K 117 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N VAL K 119 " --> pdb=" O TRP K 143 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ILE K 145 " --> pdb=" O VAL K 119 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL K 175 " --> pdb=" O SER K 146 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'M' and resid 20 through 22 Processing sheet with id= Y, first strand: chain 'M' and resid 88 through 90 Processing sheet with id= Z, first strand: chain 'M' and resid 94 through 97 Processing sheet with id= AA, first strand: chain 'Y' and resid 128 through 132 removed outlier: 4.617A pdb=" N GLN Y 62 " --> pdb=" O GLN Y 132 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'Y' and resid 90 through 92 Processing sheet with id= AC, first strand: chain 'f' and resid 41 through 46 Processing sheet with id= AD, first strand: chain 'h' and resid 44 through 47 Processing sheet with id= AE, first strand: chain '2' and resid 52 through 54 Processing sheet with id= AF, first strand: chain '4' and resid 57 through 59 Processing sheet with id= AG, first strand: chain '5' and resid 61 through 63 Processing sheet with id= AH, first strand: chain '5' and resid 66 through 69 removed outlier: 6.644A pdb=" N ILE 5 75 " --> pdb=" O TYR 5 67 " (cutoff:3.500A) 2512 hydrogen bonds defined for protein. 7029 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 20.43 Time building geometry restraints manager: 24.20 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: 27088 1.40 - 1.62: 39751 1.62 - 1.85: 548 1.85 - 2.08: 3 2.08 - 2.31: 80 Bond restraints: 67470 Sorted by residual: bond pdb=" C3 UQ9 1 501 " pdb=" C4 UQ9 1 501 " ideal model delta sigma weight residual 1.340 1.522 -0.182 2.00e-02 2.50e+03 8.26e+01 bond pdb=" C5N NDP E 401 " pdb=" C6N NDP E 401 " ideal model delta sigma weight residual 1.337 1.547 -0.210 2.40e-02 1.74e+03 7.64e+01 bond pdb=" C1 UQ9 1 501 " pdb=" C6 UQ9 1 501 " ideal model delta sigma weight residual 1.345 1.519 -0.174 2.00e-02 2.50e+03 7.58e+01 bond pdb=" CA PRO C 395 " pdb=" C PRO C 395 " ideal model delta sigma weight residual 1.514 1.473 0.041 5.50e-03 3.31e+04 5.62e+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 ... (remaining 67465 not shown) Histogram of bond angle deviations from ideal: 68.83 - 83.07: 72 83.07 - 97.31: 36 97.31 - 111.55: 29605 111.55 - 125.80: 60397 125.80 - 140.04: 1213 Bond angle restraints: 91323 Sorted by residual: angle pdb=" S1 FES A 803 " pdb="FE2 FES A 803 " pdb=" S2 FES A 803 " ideal model delta sigma weight residual 104.33 89.47 14.86 1.14e+00 7.69e-01 1.70e+02 angle pdb=" S1 FES A 803 " pdb="FE1 FES A 803 " pdb=" S2 FES A 803 " ideal model delta sigma weight residual 104.33 89.32 15.01 1.20e+00 6.94e-01 1.56e+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 88.89 -13.23 1.14e+00 7.69e-01 1.35e+02 angle pdb=" S1 FES H 301 " pdb="FE2 FES H 301 " pdb=" S2 FES H 301 " ideal model delta sigma weight residual 104.33 91.11 13.22 1.14e+00 7.69e-01 1.34e+02 angle pdb="FE1 FES H 301 " pdb=" S2 FES H 301 " pdb="FE2 FES H 301 " ideal model delta sigma weight residual 75.66 88.67 -13.01 1.14e+00 7.69e-01 1.30e+02 ... (remaining 91318 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.00: 39533 35.00 - 69.99: 556 69.99 - 104.99: 42 104.99 - 139.99: 5 139.99 - 174.98: 2 Dihedral angle restraints: 40138 sinusoidal: 16677 harmonic: 23461 Sorted by residual: dihedral pdb=" CA LEU 5 554 " pdb=" C LEU 5 554 " pdb=" N VAL 5 555 " pdb=" CA VAL 5 555 " ideal model delta harmonic sigma weight residual 180.00 -121.20 -58.80 0 5.00e+00 4.00e-02 1.38e+02 dihedral pdb=" CB CYS 9 25 " pdb=" SG CYS 9 25 " pdb=" SG CYS 9 37 " pdb=" CB CYS 9 37 " ideal model delta sinusoidal sigma weight residual -86.00 -175.66 89.66 1 1.00e+01 1.00e-02 9.54e+01 dihedral pdb=" CA ALA 5 253 " pdb=" C ALA 5 253 " pdb=" N THR 5 254 " pdb=" CA THR 5 254 " ideal model delta harmonic sigma weight residual 180.00 -131.20 -48.80 0 5.00e+00 4.00e-02 9.52e+01 ... (remaining 40135 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.167: 10081 4.167 - 8.334: 4 8.334 - 12.502: 0 12.502 - 16.669: 0 16.669 - 20.836: 20 Chirality restraints: 10105 Sorted by residual: chirality pdb="FE1 SF4 A 801 " pdb=" S2 SF4 A 801 " pdb=" S3 SF4 A 801 " pdb=" S4 SF4 A 801 " both_signs ideal model delta sigma weight residual False -10.55 10.28 -20.84 2.00e-01 2.50e+01 1.09e+04 chirality pdb="FE3 SF4 A 802 " pdb=" S1 SF4 A 802 " pdb=" S2 SF4 A 802 " pdb=" S4 SF4 A 802 " both_signs ideal model delta sigma weight residual False -10.55 10.26 -20.81 2.00e-01 2.50e+01 1.08e+04 chirality pdb="FE3 SF4 K 301 " pdb=" S1 SF4 K 301 " pdb=" S2 SF4 K 301 " pdb=" S4 SF4 K 301 " both_signs ideal model delta sigma weight residual False -10.55 10.18 -20.74 2.00e-01 2.50e+01 1.07e+04 ... (remaining 10102 not shown) Planarity restraints: 11400 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2N NDP E 401 " -0.149 2.00e-02 2.50e+03 1.01e-01 1.27e+02 pdb=" C3N NDP E 401 " -0.057 2.00e-02 2.50e+03 pdb=" C4N NDP E 401 " -0.016 2.00e-02 2.50e+03 pdb=" C7N NDP E 401 " 0.097 2.00e-02 2.50e+03 pdb=" N1N NDP E 401 " 0.125 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C4N NDP E 401 " -0.056 2.00e-02 2.50e+03 9.33e-02 8.70e+01 pdb=" C5N NDP E 401 " 0.115 2.00e-02 2.50e+03 pdb=" C6N NDP E 401 " -0.121 2.00e-02 2.50e+03 pdb=" N1N NDP E 401 " 0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG K 112 " -0.826 9.50e-02 1.11e+02 3.70e-01 8.33e+01 pdb=" NE ARG K 112 " 0.049 2.00e-02 2.50e+03 pdb=" CZ ARG K 112 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG K 112 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG K 112 " -0.023 2.00e-02 2.50e+03 ... (remaining 11397 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 852 2.64 - 3.21: 59277 3.21 - 3.77: 103425 3.77 - 4.34: 145102 4.34 - 4.90: 235679 Nonbonded interactions: 544335 Sorted by model distance: nonbonded pdb=" N GLU X 167 " pdb=" OE1 GLU X 167 " model vdw 2.078 2.520 nonbonded pdb=" O ASN 4 480 " pdb=" OD1 ASN 4 480 " model vdw 2.154 3.040 nonbonded pdb=" OE2 GLU 1 171 " pdb=" OH TYR 1 250 " model vdw 2.197 2.440 nonbonded pdb=" O ASN 4 103 " pdb=" OH TYR 4 115 " model vdw 2.213 2.440 nonbonded pdb=" OH TYR h 20 " pdb=" OH TYR 1 45 " model vdw 2.220 2.440 ... (remaining 544330 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 28 7.16 5 Zn 1 6.06 5 P 45 5.49 5 S 311 5.16 5 C 42802 2.51 5 N 10720 2.21 5 O 12027 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.280 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: 0.070 Extract box with map and model: 23.210 Check model and map are aligned: 0.730 Process input model: 147.180 Find NCS groups from input model: 2.060 Set up NCS constraints: 0.220 Set refine NCS operators: 0.010 Set scattering table: 0.460 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 181.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 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 : 0.012 0.265 67470 Z= 0.792 Angle : 1.516 21.064 91323 Z= 0.748 Chirality : 0.923 20.836 10105 Planarity : 0.011 0.370 11400 Dihedral : 12.032 174.985 25047 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.00 % Favored : 93.89 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.25 % Cis-general : 0.00 % Twisted Proline : 0.25 % 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: -3.68 (0.07), residues: 7967 helix: -2.38 (0.06), residues: 4037 sheet: -1.71 (0.24), residues: 391 loop : -2.51 (0.09), residues: 3539 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15934 Ramachandran restraints generated. 7967 Oldfield, 0 Emsley, 7967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15934 Ramachandran restraints generated. 7967 Oldfield, 0 Emsley, 7967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2161 residues out of total 6895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 2150 time to evaluate : 5.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 2 residues processed: 2158 average time/residue: 0.7369 time to fit residues: 2617.9098 Evaluate side-chains 1131 residues out of total 6895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1129 time to evaluate : 5.849 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.4850 time to fit residues: 9.8135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 787 random chunks: chunk 664 optimal weight: 5.9990 chunk 596 optimal weight: 1.9990 chunk 330 optimal weight: 5.9990 chunk 203 optimal weight: 0.7980 chunk 402 optimal weight: 0.9980 chunk 318 optimal weight: 0.9990 chunk 616 optimal weight: 1.9990 chunk 238 optimal weight: 0.8980 chunk 375 optimal weight: 1.9990 chunk 459 optimal weight: 1.9990 chunk 714 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 GLN A 367 ASN A 398 ASN A 479 ASN A 673 GLN B 42 GLN B 47 ASN B 283 ASN ** B 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 424 HIS B 443 ASN C 43 HIS C 49 GLN C 77 ASN C 95 HIS C 134 GLN C 284 GLN C 440 HIS E 180 ASN ** E 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 GLN ** F 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 GLN ** F 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 136 ASN H 224 GLN ** I 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 54 ASN K 73 GLN K 100 GLN K 137 GLN K 158 HIS M 41 ASN M 116 ASN ** M 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 97 GLN Q 110 HIS Q 128 GLN R 21 GLN R 50 ASN R 69 HIS R 105 ASN S 132 ASN U 99 GLN W 74 GLN ** X 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 161 HIS Y 55 ASN Z 161 GLN a 60 GLN ** a 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 59 HIS e 54 ASN g 22 ASN h 55 HIS h 78 HIS h 136 GLN i 78 HIS n 95 HIS 1 49 GLN 2 90 ASN 2 110 ASN ** 2 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 173 ASN 2 393 ASN 3 22 ASN 3 109 ASN 4 371 GLN 4 424 GLN ** 4 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 233 HIS 5 251 HIS Total number of N/Q/H flips: 63 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.266 67470 Z= 0.509 Angle : 1.513 51.419 91323 Z= 0.961 Chirality : 0.284 6.495 10105 Planarity : 0.005 0.093 11400 Dihedral : 12.104 177.373 9944 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.88 % Favored : 96.08 % Rotamer Outliers : 2.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.08), residues: 7967 helix: -0.64 (0.07), residues: 4073 sheet: -1.21 (0.24), residues: 396 loop : -2.04 (0.09), residues: 3498 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15934 Ramachandran restraints generated. 7967 Oldfield, 0 Emsley, 7967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15934 Ramachandran restraints generated. 7967 Oldfield, 0 Emsley, 7967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1418 residues out of total 6895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 1238 time to evaluate : 5.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 180 outliers final: 90 residues processed: 1351 average time/residue: 0.6674 time to fit residues: 1520.1618 Evaluate side-chains 1095 residues out of total 6895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 1005 time to evaluate : 5.807 Switching outliers to nearest non-outliers outliers start: 90 outliers final: 0 residues processed: 90 average time/residue: 0.4871 time to fit residues: 91.7676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 787 random chunks: chunk 397 optimal weight: 6.9990 chunk 221 optimal weight: 2.9990 chunk 594 optimal weight: 2.9990 chunk 486 optimal weight: 3.9990 chunk 197 optimal weight: 5.9990 chunk 715 optimal weight: 0.8980 chunk 773 optimal weight: 4.9990 chunk 637 optimal weight: 1.9990 chunk 710 optimal weight: 0.9990 chunk 244 optimal weight: 6.9990 chunk 574 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 228 ASN A 337 GLN B 42 GLN ** B 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 HIS ** C 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 ASN ** E 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 286 HIS F 39 HIS F 58 GLN ** F 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 54 ASN ** L 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 27 ASN M 41 ASN ** M 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 73 ASN R 49 GLN R 105 ASN S 52 ASN U 106 HIS ** X 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 55 ASN Y 157 HIS Z 56 ASN ** a 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 4 HIS d 69 GLN ** e 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 136 GLN n 38 ASN ** 2 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 227 ASN ** 4 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 371 GLN ** 4 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 251 HIS 8 40 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.248 67470 Z= 0.536 Angle : 1.498 50.814 91323 Z= 0.955 Chirality : 0.285 6.422 10105 Planarity : 0.005 0.088 11400 Dihedral : 11.237 177.073 9944 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.42 % Favored : 95.56 % Rotamer Outliers : 2.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.09), residues: 7967 helix: 0.10 (0.08), residues: 4094 sheet: -0.94 (0.25), residues: 408 loop : -1.79 (0.10), residues: 3465 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15934 Ramachandran restraints generated. 7967 Oldfield, 0 Emsley, 7967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15934 Ramachandran restraints generated. 7967 Oldfield, 0 Emsley, 7967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1234 residues out of total 6895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 1070 time to evaluate : 5.914 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 outliers start: 164 outliers final: 80 residues processed: 1181 average time/residue: 0.6810 time to fit residues: 1364.4245 Evaluate side-chains 1037 residues out of total 6895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 957 time to evaluate : 5.865 Switching outliers to nearest non-outliers outliers start: 80 outliers final: 0 residues processed: 80 average time/residue: 0.5013 time to fit residues: 84.5404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 787 random chunks: chunk 707 optimal weight: 3.9990 chunk 538 optimal weight: 5.9990 chunk 371 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 341 optimal weight: 3.9990 chunk 480 optimal weight: 4.9990 chunk 718 optimal weight: 1.9990 chunk 760 optimal weight: 3.9990 chunk 375 optimal weight: 1.9990 chunk 680 optimal weight: 4.9990 chunk 205 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN B 42 GLN ** B 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 HIS ** C 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 ASN ** C 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 26 GLN D 78 HIS E 127 ASN ** E 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 GLN ** F 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 174 ASN K 54 ASN M 41 ASN ** M 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 110 HIS Q 128 GLN R 105 ASN X 114 GLN ** X 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 56 ASN ** a 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 73 ASN b 22 ASN c 20 ASN e 11 ASN e 23 HIS h 136 GLN j 73 GLN ** 2 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 251 HIS 5 331 HIS ** 5 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 617 ASN 6 152 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.4164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.247 67470 Z= 0.599 Angle : 1.521 50.775 91323 Z= 0.965 Chirality : 0.286 6.456 10105 Planarity : 0.005 0.087 11400 Dihedral : 11.125 174.753 9944 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.57 % Favored : 95.41 % Rotamer Outliers : 2.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.09), residues: 7967 helix: 0.30 (0.08), residues: 4097 sheet: -0.85 (0.25), residues: 425 loop : -1.73 (0.10), residues: 3445 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15934 Ramachandran restraints generated. 7967 Oldfield, 0 Emsley, 7967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15934 Ramachandran restraints generated. 7967 Oldfield, 0 Emsley, 7967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1160 residues out of total 6895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 1004 time to evaluate : 5.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 156 outliers final: 84 residues processed: 1113 average time/residue: 0.6864 time to fit residues: 1287.4877 Evaluate side-chains 996 residues out of total 6895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 912 time to evaluate : 5.951 Switching outliers to nearest non-outliers outliers start: 84 outliers final: 0 residues processed: 84 average time/residue: 0.5151 time to fit residues: 90.4620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 787 random chunks: chunk 633 optimal weight: 0.7980 chunk 431 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 566 optimal weight: 0.6980 chunk 313 optimal weight: 0.8980 chunk 649 optimal weight: 0.7980 chunk 525 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 388 optimal weight: 3.9990 chunk 682 optimal weight: 0.7980 chunk 191 optimal weight: 7.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 ASN ** B 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 363 GLN ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 HIS E 127 ASN ** E 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 GLN H 40 ASN K 54 ASN M 41 ASN ** M 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 96 ASN Q 110 HIS R 49 GLN ** X 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 56 ASN a 60 GLN ** a 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 69 GLN e 11 ASN ** e 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 136 GLN j 27 HIS j 73 GLN ** 2 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 153 HIS ** 4 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 36 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.4306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.245 67470 Z= 0.490 Angle : 1.466 50.832 91323 Z= 0.943 Chirality : 0.283 6.378 10105 Planarity : 0.004 0.083 11400 Dihedral : 10.539 172.445 9944 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.12 % Favored : 95.86 % Rotamer Outliers : 1.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.09), residues: 7967 helix: 0.71 (0.08), residues: 4096 sheet: -0.69 (0.26), residues: 424 loop : -1.53 (0.10), residues: 3447 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15934 Ramachandran restraints generated. 7967 Oldfield, 0 Emsley, 7967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15934 Ramachandran restraints generated. 7967 Oldfield, 0 Emsley, 7967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1082 residues out of total 6895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 975 time to evaluate : 6.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 107 outliers final: 50 residues processed: 1043 average time/residue: 0.6808 time to fit residues: 1204.8621 Evaluate side-chains 962 residues out of total 6895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 912 time to evaluate : 5.928 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 0 residues processed: 50 average time/residue: 0.5082 time to fit residues: 56.3144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 787 random chunks: chunk 255 optimal weight: 5.9990 chunk 685 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 446 optimal weight: 1.9990 chunk 187 optimal weight: 5.9990 chunk 761 optimal weight: 0.7980 chunk 632 optimal weight: 4.9990 chunk 352 optimal weight: 2.9990 chunk 63 optimal weight: 8.9990 chunk 251 optimal weight: 8.9990 chunk 399 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 HIS ** C 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 ASN ** E 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 54 ASN K 100 GLN ** L 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 41 ASN ** M 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 69 HIS ** X 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 42 HIS Z 56 ASN Z 123 ASN a 60 GLN ** a 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 20 ASN d 86 GLN ** e 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 54 ASN ** f 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 136 GLN j 73 GLN ** 2 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 103 ASN ** 4 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 251 HIS ** 5 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 136 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.4500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.249 67470 Z= 0.577 Angle : 1.503 50.859 91323 Z= 0.957 Chirality : 0.285 6.416 10105 Planarity : 0.005 0.077 11400 Dihedral : 10.538 171.092 9944 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.88 % Favored : 95.09 % Rotamer Outliers : 1.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.09), residues: 7967 helix: 0.64 (0.08), residues: 4108 sheet: -0.72 (0.25), residues: 424 loop : -1.55 (0.10), residues: 3435 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15934 Ramachandran restraints generated. 7967 Oldfield, 0 Emsley, 7967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15934 Ramachandran restraints generated. 7967 Oldfield, 0 Emsley, 7967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1055 residues out of total 6895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 921 time to evaluate : 5.870 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 134 outliers final: 67 residues processed: 998 average time/residue: 0.6822 time to fit residues: 1152.5683 Evaluate side-chains 954 residues out of total 6895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 887 time to evaluate : 6.072 Switching outliers to nearest non-outliers outliers start: 67 outliers final: 0 residues processed: 67 average time/residue: 0.5016 time to fit residues: 71.8710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 787 random chunks: chunk 734 optimal weight: 0.8980 chunk 85 optimal weight: 7.9990 chunk 433 optimal weight: 0.0980 chunk 556 optimal weight: 3.9990 chunk 430 optimal weight: 1.9990 chunk 640 optimal weight: 0.8980 chunk 425 optimal weight: 2.9990 chunk 758 optimal weight: 0.0040 chunk 474 optimal weight: 0.0870 chunk 462 optimal weight: 5.9990 chunk 350 optimal weight: 6.9990 overall best weight: 0.3970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 54 ASN K 100 GLN L 43 ASN M 41 ASN M 126 GLN O 96 ASN R 49 GLN R 69 HIS ** S 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 56 ASN ** a 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 18 ASN d 69 GLN ** e 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 136 GLN ** 2 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 185 HIS ** 4 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 537 ASN 5 539 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.4595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.246 67470 Z= 0.476 Angle : 1.458 50.733 91323 Z= 0.939 Chirality : 0.283 6.385 10105 Planarity : 0.004 0.070 11400 Dihedral : 10.006 168.915 9944 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.88 % Favored : 96.11 % Rotamer Outliers : 0.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.09), residues: 7967 helix: 1.02 (0.08), residues: 4077 sheet: -0.63 (0.26), residues: 426 loop : -1.37 (0.10), residues: 3464 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15934 Ramachandran restraints generated. 7967 Oldfield, 0 Emsley, 7967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15934 Ramachandran restraints generated. 7967 Oldfield, 0 Emsley, 7967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1043 residues out of total 6895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 978 time to evaluate : 6.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 30 residues processed: 1019 average time/residue: 0.6921 time to fit residues: 1195.2824 Evaluate side-chains 940 residues out of total 6895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 910 time to evaluate : 7.193 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.5496 time to fit residues: 38.9522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 787 random chunks: chunk 469 optimal weight: 4.9990 chunk 302 optimal weight: 2.9990 chunk 453 optimal weight: 0.0040 chunk 228 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 chunk 146 optimal weight: 0.5980 chunk 482 optimal weight: 2.9990 chunk 516 optimal weight: 4.9990 chunk 375 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 596 optimal weight: 4.9990 overall best weight: 0.8794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 HIS ** C 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 ASN ** E 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 GLN G 119 GLN K 54 ASN K 100 GLN M 126 GLN R 49 GLN R 69 HIS ** S 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 60 GLN ** a 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 20 ASN d 69 GLN ** e 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 136 GLN j 73 GLN ** 2 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.4664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.247 67470 Z= 0.490 Angle : 1.462 50.719 91323 Z= 0.940 Chirality : 0.284 6.387 10105 Planarity : 0.004 0.050 11400 Dihedral : 9.761 168.458 9944 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.32 % Favored : 95.66 % Rotamer Outliers : 0.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.09), residues: 7967 helix: 1.10 (0.08), residues: 4090 sheet: -0.56 (0.26), residues: 427 loop : -1.32 (0.10), residues: 3450 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15934 Ramachandran restraints generated. 7967 Oldfield, 0 Emsley, 7967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15934 Ramachandran restraints generated. 7967 Oldfield, 0 Emsley, 7967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 972 residues out of total 6895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 922 time to evaluate : 7.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 30 residues processed: 948 average time/residue: 0.6965 time to fit residues: 1114.9884 Evaluate side-chains 922 residues out of total 6895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 892 time to evaluate : 5.968 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.5524 time to fit residues: 39.2112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 787 random chunks: chunk 690 optimal weight: 1.9990 chunk 726 optimal weight: 6.9990 chunk 663 optimal weight: 0.8980 chunk 706 optimal weight: 5.9990 chunk 425 optimal weight: 3.9990 chunk 307 optimal weight: 1.9990 chunk 555 optimal weight: 0.9990 chunk 216 optimal weight: 1.9990 chunk 638 optimal weight: 0.6980 chunk 668 optimal weight: 1.9990 chunk 704 optimal weight: 6.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 479 ASN ** B 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 HIS ** C 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 GLN K 54 ASN K 100 GLN O 96 ASN O 105 GLN R 49 GLN R 69 HIS ** S 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 20 ASN ** e 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 136 GLN ** 2 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.4735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.247 67470 Z= 0.507 Angle : 1.471 50.737 91323 Z= 0.944 Chirality : 0.284 6.382 10105 Planarity : 0.004 0.051 11400 Dihedral : 9.702 169.275 9944 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.37 % Favored : 95.61 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.09), residues: 7967 helix: 1.09 (0.08), residues: 4090 sheet: -0.51 (0.26), residues: 418 loop : -1.28 (0.10), residues: 3459 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15934 Ramachandran restraints generated. 7967 Oldfield, 0 Emsley, 7967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15934 Ramachandran restraints generated. 7967 Oldfield, 0 Emsley, 7967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 930 residues out of total 6895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 905 time to evaluate : 5.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 15 residues processed: 916 average time/residue: 0.7141 time to fit residues: 1102.9607 Evaluate side-chains 887 residues out of total 6895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 872 time to evaluate : 5.872 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.5052 time to fit residues: 22.4359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 787 random chunks: chunk 464 optimal weight: 10.0000 chunk 747 optimal weight: 5.9990 chunk 456 optimal weight: 5.9990 chunk 354 optimal weight: 9.9990 chunk 519 optimal weight: 4.9990 chunk 784 optimal weight: 3.9990 chunk 721 optimal weight: 3.9990 chunk 624 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 482 optimal weight: 1.9990 chunk 382 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 459 HIS ** B 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 HIS ** C 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 ASN E 237 HIS ** H 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 40 ASN K 54 ASN K 100 GLN K 200 ASN Q 110 HIS R 49 GLN R 69 HIS ** X 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 136 GLN j 73 GLN ** 2 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 251 HIS 5 561 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.4850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.242 67470 Z= 0.657 Angle : 1.534 50.859 91323 Z= 0.968 Chirality : 0.286 6.434 10105 Planarity : 0.005 0.067 11400 Dihedral : 10.188 174.870 9944 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.27 % Favored : 94.69 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.09), residues: 7967 helix: 0.69 (0.08), residues: 4112 sheet: -0.59 (0.26), residues: 425 loop : -1.42 (0.10), residues: 3430 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15934 Ramachandran restraints generated. 7967 Oldfield, 0 Emsley, 7967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15934 Ramachandran restraints generated. 7967 Oldfield, 0 Emsley, 7967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 931 residues out of total 6895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 902 time to evaluate : 5.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 18 residues processed: 920 average time/residue: 0.7098 time to fit residues: 1098.1454 Evaluate side-chains 895 residues out of total 6895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 877 time to evaluate : 5.952 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.5040 time to fit residues: 25.5250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 787 random chunks: chunk 495 optimal weight: 4.9990 chunk 665 optimal weight: 3.9990 chunk 191 optimal weight: 7.9990 chunk 575 optimal weight: 0.8980 chunk 92 optimal weight: 0.1980 chunk 173 optimal weight: 1.9990 chunk 625 optimal weight: 1.9990 chunk 261 optimal weight: 1.9990 chunk 642 optimal weight: 0.9980 chunk 79 optimal weight: 0.6980 chunk 115 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 HIS ** C 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 GLN ** F 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 54 ASN K 100 GLN M 41 ASN O 96 ASN Q 110 HIS R 49 GLN R 69 HIS ** S 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 20 ASN ** e 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 136 GLN j 27 HIS j 73 GLN ** 2 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 561 ASN ** 8 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.123945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.098802 restraints weight = 85998.854| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.56 r_work: 0.2976 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3450 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3450 r_free = 0.3450 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3449 r_free = 0.3449 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3449 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.4912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.247 67470 Z= 0.488 Angle : 1.469 50.653 91323 Z= 0.943 Chirality : 0.283 6.377 10105 Planarity : 0.004 0.053 11400 Dihedral : 9.685 174.714 9944 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.02 % Favored : 95.96 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.09), residues: 7967 helix: 1.02 (0.08), residues: 4099 sheet: -0.58 (0.26), residues: 418 loop : -1.29 (0.10), residues: 3450 =============================================================================== Job complete usr+sys time: 20157.52 seconds wall clock time: 352 minutes 13.53 seconds (21133.53 seconds total)