Starting phenix.real_space_refine on Fri Feb 16 11:44:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkj_11251/02_2024/6zkj_11251_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkj_11251/02_2024/6zkj_11251.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkj_11251/02_2024/6zkj_11251_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkj_11251/02_2024/6zkj_11251_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkj_11251/02_2024/6zkj_11251_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkj_11251/02_2024/6zkj_11251.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkj_11251/02_2024/6zkj_11251.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkj_11251/02_2024/6zkj_11251_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkj_11251/02_2024/6zkj_11251_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians K 1 8.98 5 Fe 28 7.16 5 Zn 1 6.06 5 P 46 5.49 5 S 465 5.16 5 C 43676 2.51 5 N 11156 2.21 5 O 12106 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1 ARG 68": "NH1" <-> "NH2" Residue "1 ARG 237": "NH1" <-> "NH2" Residue "1 ARG 249": "NH1" <-> "NH2" Residue "1 ARG 339": "NH1" <-> "NH2" Residue "1 ARG 423": "NH1" <-> "NH2" Residue "2 ARG 187": "NH1" <-> "NH2" Residue "3 ARG 53": "NH1" <-> "NH2" Residue "3 TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 418": "NH1" <-> "NH2" Residue "3 TYR 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 460": "NH1" <-> "NH2" Residue "3 TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 2": "NH1" <-> "NH2" Residue "4 PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 188": "NH1" <-> "NH2" Residue "4 PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 8": "NH1" <-> "NH2" Residue "5 ARG 12": "NH1" <-> "NH2" Residue "5 ARG 14": "NH1" <-> "NH2" Residue "5 PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 25": "NH1" <-> "NH2" Residue "6 ARG 81": "NH1" <-> "NH2" Residue "6 ARG 138": "NH1" <-> "NH2" Residue "6 TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 174": "NH1" <-> "NH2" Residue "6 ARG 178": "NH1" <-> "NH2" Residue "A ARG 48": "NH1" <-> "NH2" Residue "H ARG 62": "NH1" <-> "NH2" Residue "H ARG 134": "NH1" <-> "NH2" Residue "H TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 281": "NH1" <-> "NH2" Residue "J PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 161": "NH1" <-> "NH2" Residue "L PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 278": "NH1" <-> "NH2" Residue "M TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 19": "NH1" <-> "NH2" Residue "V ARG 103": "NH1" <-> "NH2" Residue "W ARG 26": "NH1" <-> "NH2" Residue "W ARG 77": "NH1" <-> "NH2" Residue "W ARG 115": "NH1" <-> "NH2" Residue "Y ARG 54": "NH1" <-> "NH2" Residue "Y ARG 165": "NH1" <-> "NH2" Residue "Y PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 14": "NH1" <-> "NH2" Residue "Z TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 64": "NH1" <-> "NH2" Residue "d ARG 82": "NH1" <-> "NH2" Residue "d ARG 97": "NH1" <-> "NH2" Residue "d TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 157": "NH1" <-> "NH2" Residue "d PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 186": "NH1" <-> "NH2" Residue "d ARG 251": "NH1" <-> "NH2" Residue "d ARG 292": "NH1" <-> "NH2" Residue "d ARG 320": "NH1" <-> "NH2" Residue "d ARG 322": "NH1" <-> "NH2" Residue "e ARG 33": "NH1" <-> "NH2" Residue "g ARG 22": "NH1" <-> "NH2" Residue "g ARG 32": "NH1" <-> "NH2" Residue "h ARG 17": "NH1" <-> "NH2" Residue "i ARG 9": "NH1" <-> "NH2" Residue "i PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 106": "NH1" <-> "NH2" Residue "i PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 95": "NH1" <-> "NH2" Residue "k ARG 305": "NH1" <-> "NH2" Residue "l ARG 68": "NH1" <-> "NH2" Residue "l ARG 82": "NH1" <-> "NH2" Residue "l ARG 104": "NH1" <-> "NH2" Residue "n ARG 38": "NH1" <-> "NH2" Residue "o ARG 5": "NH1" <-> "NH2" Residue "o ARG 49": "NH1" <-> "NH2" Residue "o ARG 50": "NH1" <-> "NH2" Residue "o ARG 120": "NH1" <-> "NH2" Residue "p ARG 9": "NH1" <-> "NH2" Residue "p ARG 41": "NH1" <-> "NH2" Residue "p ARG 56": "NH1" <-> "NH2" Residue "p ARG 108": "NH1" <-> "NH2" Residue "q ARG 26": "NH1" <-> "NH2" Residue "q ARG 27": "NH1" <-> "NH2" Residue "q ARG 51": "NH1" <-> "NH2" Residue "q ARG 87": "NH1" <-> "NH2" Residue "r ARG 19": "NH1" <-> "NH2" Residue "r ARG 30": "NH1" <-> "NH2" Residue "r ARG 37": "NH1" <-> "NH2" Residue "r ARG 65": "NH1" <-> "NH2" Residue "s PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 103": "NH1" <-> "NH2" Residue "s ARG 110": "NH1" <-> "NH2" Residue "s ARG 114": "NH1" <-> "NH2" Residue "s ARG 117": "NH1" <-> "NH2" Residue "t TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ARG 29": "NH1" <-> "NH2" Residue "t ARG 37": "NH1" <-> "NH2" Residue "t ARG 44": "NH1" <-> "NH2" Residue "t ARG 64": "NH1" <-> "NH2" Residue "t ARG 92": "NH1" <-> "NH2" Residue "t ARG 121": "NH1" <-> "NH2" Residue "t ARG 128": "NH1" <-> "NH2" Residue "t ARG 134": "NH1" <-> "NH2" Residue "t ARG 176": "NH1" <-> "NH2" Residue "u ARG 19": "NH1" <-> "NH2" Residue "v ARG 70": "NH1" <-> "NH2" Residue "w ARG 25": "NH1" <-> "NH2" Residue "w ARG 84": "NH1" <-> "NH2" Residue "z PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ARG 37": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 67479 Number of models: 1 Model: "" Number of chains: 71 Chain: "1" Number of atoms: 3312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3312 Classifications: {'peptide': 430} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 408} Chain: "2" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1655 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 191} Chain: "3" Number of atoms: 5275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5275 Classifications: {'peptide': 688} Link IDs: {'PTRANS': 32, 'TRANS': 655} Chain: "4" Number of atoms: 3427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3427 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 397} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'2MR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "5" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1726 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 15, 'TRANS': 192} Chain: "6" Number of atoms: 1247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1247 Classifications: {'peptide': 156} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 145} Chain: "9" Number of atoms: 1414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1414 Classifications: {'peptide': 176} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 165} Chain: "A" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 842 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain breaks: 1 Chain: "H" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2528 Classifications: {'peptide': 318} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 295} Chain: "J" Number of atoms: 1294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1294 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 2, 'TRANS': 166} Chain breaks: 1 Chain: "K" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 749 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 1, 'TRANS': 96} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 4806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4806 Classifications: {'peptide': 606} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 579} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 3647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3647 Classifications: {'peptide': 459} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 437} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 2723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2723 Classifications: {'peptide': 347} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 326} Chain: "V" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1028 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "W" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1155 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 10, 'TRANS': 128} Chain: "X" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 701 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 5, 'TRANS': 81} Chain: "Y" Number of atoms: 1403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1403 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 12, 'TRANS': 158} Chain: "Z" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1441 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "a" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 371 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 3, 'TRANS': 40} Chain: "b" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 737 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "c" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1024 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "d" Number of atoms: 2372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2372 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 15, 'TRANS': 281} Chain breaks: 3 Chain: "e" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 691 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain: "f" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 917 Classifications: {'peptide': 113} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 104} Chain: "g" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 969 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "h" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 769 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 11, 'TRANS': 84} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "i" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1209 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 11, 'TRANS': 133} Chain: "j" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 660 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "k" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2596 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 14, 'TRANS': 305} Chain: "l" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 874 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "m" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 626 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 11, 'TRANS': 68} Chain: "n" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 634 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "o" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1004 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 10, 'TRANS': 109} Chain: "p" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1059 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 118} Chain: "q" Number of atoms: 1142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1142 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 7, 'TRANS': 131} Chain: "r" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 846 Classifications: {'peptide': 99} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 86} Chain breaks: 1 Chain: "s" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1047 Classifications: {'peptide': 122} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 114} Chain: "t" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1520 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 16, 'TRANS': 160} Chain: "u" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 563 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 7, 'TRANS': 57} Chain: "v" Number of atoms: 1307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1307 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 20, 'TRANS': 134} Chain: "w" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 846 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 8, 'TRANS': 92} Chain: "x" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 412 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "y" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 436 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "z" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 576 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "1" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'FMN': 1, 'NAI': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "2" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 21 Unusual residues: {' K': 1, 'FES': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "4" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "6" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 128 Unusual residues: {'3PE': 1, 'DCQ': 1, 'PC1': 1, 'SF4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "9" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 70 Unusual residues: {'PC1': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'3PE': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "J" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "L" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 236 Unusual residues: {'3PE': 2, 'CDL': 1, 'PC1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "M" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 98 Unusual residues: {'3PE': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "N" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 251 Unusual residues: {'3PE': 2, 'CDL': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 51 Chain: "W" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Chain: "Y" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Chain: "i" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "k" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "o" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 196 Unusual residues: {'3PE': 1, 'CDL': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 55 Chain: "p" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 26 Chain: "s" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MYR:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "w" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Chain: "z" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 58 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 42 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2715 SG CYS 1 365 103.607 54.206 241.389 1.00 18.96 S ATOM 2676 SG CYS 1 359 110.599 54.666 242.095 1.00 35.06 S ATOM 3039 SG CYS 1 405 107.242 48.509 240.587 1.00 29.54 S ATOM 4116 SG CYS 2 103 101.150 49.837 260.353 1.00 43.88 S ATOM 4150 SG CYS 2 108 99.018 47.469 262.479 1.00 51.13 S ATOM 4430 SG CYS 2 144 102.751 46.087 256.871 1.00 58.29 S ATOM 4453 SG CYS 2 148 100.865 43.330 258.422 1.00 40.64 S ATOM 5793 SG CYS 3 114 106.137 72.216 226.470 1.00 35.27 S ATOM 5732 SG CYS 3 105 100.902 75.665 228.302 1.00 28.42 S ATOM 5753 SG CYS 3 108 107.024 77.361 230.102 1.00 21.96 S ATOM 6125 SG CYS 3 156 113.369 64.790 231.233 1.00 41.69 S ATOM 6102 SG CYS 3 153 111.170 67.935 236.668 1.00 20.70 S ATOM 6149 SG CYS 3 159 117.300 68.691 235.042 1.00 54.72 S ATOM 6479 SG CYS 3 203 113.177 71.123 231.209 1.00 40.55 S ATOM 5238 SG CYS 3 41 112.328 58.264 229.330 1.00 15.16 S ATOM 5324 SG CYS 3 52 108.633 59.360 228.710 1.00 24.35 S ATOM 5349 SG CYS 3 55 109.115 54.228 225.139 1.00 19.81 S ATOM 5450 SG CYS 3 69 112.644 54.322 226.709 1.00 23.39 S ATOM 16378 SG CYS 6 149 88.082 95.343 208.289 1.00 42.13 S ATOM 15644 SG CYS 6 54 84.748 95.299 202.469 1.00 74.42 S ATOM 17570 SG CYS 9 116 92.223 96.337 214.752 1.00 36.71 S ATOM 17617 SG CYS 9 122 92.879 92.059 219.584 1.00 19.61 S ATOM 17344 SG CYS 9 87 96.776 91.659 214.303 1.00 14.23 S ATOM 17646 SG CYS 9 126 94.980 88.813 226.931 1.00 9.15 S ATOM 17317 SG CYS 9 83 98.626 90.364 221.787 1.00 21.57 S ATOM 17275 SG CYS 9 77 100.737 92.065 227.554 1.00 27.82 S ATOM 17294 SG CYS 9 80 100.009 85.519 225.888 1.00 18.69 S ATOM 41210 SG CYS b 59 96.417 84.744 242.342 1.00 30.91 S ATOM 41388 SG CYS b 84 99.508 84.669 239.907 1.00 21.95 S ATOM 41410 SG CYS b 87 97.836 87.449 240.878 1.00 27.28 S Time building chain proxies: 26.48, per 1000 atoms: 0.39 Number of scatterers: 67479 At special positions: 0 Unit cell: (177.187, 199.468, 292.836, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 K 1 19.00 S 465 16.00 P 46 15.00 O 12106 8.00 N 11156 7.00 C 43676 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS V 94 " - pdb=" SG CYS V 114 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 112 " - pdb=" SG CYS Z 124 " distance=2.04 Simple disulfide: pdb=" SG CYS l 32 " - pdb=" SG CYS l 65 " distance=2.04 Simple disulfide: pdb=" SG CYS l 42 " - pdb=" SG CYS l 55 " distance=2.03 Simple disulfide: pdb=" SG CYS s 68 " - pdb=" SG CYS s 79 " 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: 21.50 Conformation dependent library (CDL) restraints added in 8.8 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES 2 300 " pdb="FE2 FES 2 300 " - pdb=" SG CYS 2 148 " pdb="FE1 FES 2 300 " - pdb=" SG CYS 2 108 " pdb="FE1 FES 2 300 " - pdb=" SG CYS 2 103 " pdb="FE2 FES 2 300 " - pdb=" SG CYS 2 144 " pdb=" FES 3 803 " pdb="FE2 FES 3 803 " - pdb=" SG CYS 3 55 " pdb="FE1 FES 3 803 " - pdb=" SG CYS 3 52 " pdb="FE1 FES 3 803 " - pdb=" SG CYS 3 41 " pdb="FE2 FES 3 803 " - pdb=" SG CYS 3 69 " pdb=" SF4 1 501 " pdb="FE1 SF4 1 501 " - pdb=" SG CYS 1 365 " pdb="FE3 SF4 1 501 " - pdb=" SG CYS 1 359 " pdb="FE4 SF4 1 501 " - pdb=" SG CYS 1 405 " pdb="FE2 SF4 1 501 " - pdb=" SG CYS 1 362 " pdb=" SF4 3 801 " pdb="FE3 SF4 3 801 " - pdb=" NE2 HIS 3 101 " pdb="FE2 SF4 3 801 " - pdb=" SG CYS 3 105 " pdb="FE4 SF4 3 801 " - pdb=" SG CYS 3 108 " pdb="FE1 SF4 3 801 " - pdb=" SG CYS 3 114 " pdb=" SF4 3 802 " pdb="FE3 SF4 3 802 " - pdb=" SG CYS 3 159 " pdb="FE1 SF4 3 802 " - pdb=" SG CYS 3 156 " pdb="FE2 SF4 3 802 " - pdb=" SG CYS 3 153 " pdb="FE4 SF4 3 802 " - pdb=" SG CYS 3 203 " pdb=" SF4 6 201 " pdb="FE4 SF4 6 201 " - pdb=" SG CYS 6 54 " pdb="FE3 SF4 6 201 " - pdb=" SG CYS 6 149 " pdb="FE2 SF4 6 201 " - pdb=" SG CYS 6 119 " pdb="FE1 SF4 6 201 " - pdb=" SG CYS 6 55 " pdb=" SF4 9 402 " pdb="FE3 SF4 9 402 " - pdb=" SG CYS 9 122 " pdb="FE2 SF4 9 402 " - pdb=" SG CYS 9 116 " pdb="FE4 SF4 9 402 " - pdb=" SG CYS 9 87 " pdb="FE1 SF4 9 402 " - pdb=" SG CYS 9 119 " pdb="FE2 SF4 9 402 " - pdb=" NE2 HIS 9 65 " pdb=" SF4 9 403 " pdb="FE2 SF4 9 403 " - pdb=" SG CYS 9 83 " pdb="FE4 SF4 9 403 " - pdb=" SG CYS 9 80 " pdb="FE3 SF4 9 403 " - pdb=" SG CYS 9 77 " pdb="FE1 SF4 9 403 " - pdb=" SG CYS 9 126 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN b 300 " pdb="ZN ZN b 300 " - pdb=" NE2 HIS b 68 " pdb="ZN ZN b 300 " - pdb=" SG CYS b 84 " pdb="ZN ZN b 300 " - pdb=" SG CYS b 87 " pdb="ZN ZN b 300 " - pdb=" SG CYS b 59 " Number of angles added : 3 16092 Ramachandran restraints generated. 8046 Oldfield, 0 Emsley, 8046 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15344 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 331 helices and 28 sheets defined 51.3% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.58 Creating SS restraints... Processing helix chain '1' and resid 17 through 19 No H-bonds generated for 'chain '1' and resid 17 through 19' Processing helix chain '1' and resid 33 through 37 Processing helix chain '1' and resid 45 through 63 removed outlier: 3.854A pdb=" N LYS 1 51 " --> pdb=" O GLU 1 47 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLY 1 52 " --> pdb=" O ILE 1 48 " (cutoff:3.500A) Proline residue: 1 53 - end of helix removed outlier: 3.812A pdb=" N ILE 1 56 " --> pdb=" O GLY 1 52 " (cutoff:3.500A) Processing helix chain '1' and resid 75 through 81 removed outlier: 3.782A pdb=" N PHE 1 81 " --> pdb=" O LEU 1 77 " (cutoff:3.500A) Processing helix chain '1' and resid 106 through 113 Processing helix chain '1' and resid 115 through 129 Processing helix chain '1' and resid 143 through 158 Processing helix chain '1' and resid 166 through 168 No H-bonds generated for 'chain '1' and resid 166 through 168' Processing helix chain '1' and resid 184 through 187 Processing helix chain '1' and resid 189 through 196 Processing helix chain '1' and resid 215 through 217 No H-bonds generated for 'chain '1' and resid 215 through 217' Processing helix chain '1' and resid 225 through 229 Processing helix chain '1' and resid 231 through 237 Processing helix chain '1' and resid 239 through 244 Processing helix chain '1' and resid 276 through 283 Processing helix chain '1' and resid 291 through 293 No H-bonds generated for 'chain '1' and resid 291 through 293' Processing helix chain '1' and resid 319 through 323 Processing helix chain '1' and resid 343 through 356 Processing helix chain '1' and resid 363 through 381 removed outlier: 4.392A pdb=" N ASP 1 370 " --> pdb=" O ARG 1 366 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG 1 381 " --> pdb=" O ALA 1 377 " (cutoff:3.500A) Processing helix chain '1' and resid 386 through 399 removed outlier: 3.776A pdb=" N ILE 1 389 " --> pdb=" O PRO 1 386 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ASP 1 390 " --> pdb=" O ALA 1 387 " (cutoff:3.500A) Processing helix chain '1' and resid 407 through 437 Proline residue: 1 414 - end of helix Proline residue: 1 424 - end of helix Processing helix chain '2' and resid 25 through 37 removed outlier: 3.928A pdb=" N ASN 2 37 " --> pdb=" O ALA 2 33 " (cutoff:3.500A) Processing helix chain '2' and resid 43 through 58 removed outlier: 3.756A pdb=" N VAL 2 47 " --> pdb=" O ALA 2 44 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N LEU 2 48 " --> pdb=" O ALA 2 45 " (cutoff:3.500A) Proline residue: 2 49 - end of helix removed outlier: 3.517A pdb=" N ASN 2 58 " --> pdb=" O GLN 2 55 " (cutoff:3.500A) Processing helix chain '2' and resid 65 through 72 Processing helix chain '2' and resid 77 through 86 removed outlier: 3.724A pdb=" N VAL 2 83 " --> pdb=" O ARG 2 79 " (cutoff:3.500A) Processing helix chain '2' and resid 106 through 109 No H-bonds generated for 'chain '2' and resid 106 through 109' Processing helix chain '2' and resid 113 through 124 Processing helix chain '2' and resid 148 through 150 No H-bonds generated for 'chain '2' and resid 148 through 150' Processing helix chain '2' and resid 166 through 177 Processing helix chain '3' and resid 26 through 33 removed outlier: 3.803A pdb=" N VAL 3 33 " --> pdb=" O ALA 3 29 " (cutoff:3.500A) Processing helix chain '3' and resid 84 through 97 Processing helix chain '3' and resid 115 through 123 Processing helix chain '3' and resid 150 through 152 No H-bonds generated for 'chain '3' and resid 150 through 152' Processing helix chain '3' and resid 158 through 165 Processing helix chain '3' and resid 178 through 180 No H-bonds generated for 'chain '3' and resid 178 through 180' Processing helix chain '3' and resid 198 through 201 No H-bonds generated for 'chain '3' and resid 198 through 201' Processing helix chain '3' and resid 219 through 221 No H-bonds generated for 'chain '3' and resid 219 through 221' Processing helix chain '3' and resid 265 through 275 removed outlier: 5.189A pdb=" N TYR 3 271 " --> pdb=" O THR 3 267 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ASP 3 272 " --> pdb=" O ARG 3 268 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N GLY 3 273 " --> pdb=" O PHE 3 269 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU 3 274 " --> pdb=" O ALA 3 270 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LYS 3 275 " --> pdb=" O TYR 3 271 " (cutoff:3.500A) Processing helix chain '3' and resid 296 through 307 removed outlier: 3.759A pdb=" N MET 3 306 " --> pdb=" O ARG 3 302 " (cutoff:3.500A) Processing helix chain '3' and resid 312 through 314 No H-bonds generated for 'chain '3' and resid 312 through 314' Processing helix chain '3' and resid 325 through 337 Processing helix chain '3' and resid 359 through 361 No H-bonds generated for 'chain '3' and resid 359 through 361' Processing helix chain '3' and resid 371 through 373 No H-bonds generated for 'chain '3' and resid 371 through 373' Processing helix chain '3' and resid 384 through 387 No H-bonds generated for 'chain '3' and resid 384 through 387' Processing helix chain '3' and resid 389 through 401 Processing helix chain '3' and resid 426 through 434 removed outlier: 4.037A pdb=" N ILE 3 432 " --> pdb=" O LEU 3 429 " (cutoff:3.500A) Processing helix chain '3' and resid 438 through 444 removed outlier: 3.863A pdb=" N VAL 3 442 " --> pdb=" O PRO 3 438 " (cutoff:3.500A) Processing helix chain '3' and resid 457 through 459 No H-bonds generated for 'chain '3' and resid 457 through 459' Processing helix chain '3' and resid 463 through 478 Processing helix chain '3' and resid 497 through 505 removed outlier: 4.617A pdb=" N ALA 3 501 " --> pdb=" O ALA 3 497 " (cutoff:3.500A) Processing helix chain '3' and resid 511 through 516 removed outlier: 4.114A pdb=" N LYS 3 516 " --> pdb=" O ALA 3 513 " (cutoff:3.500A) Processing helix chain '3' and resid 596 through 606 Processing helix chain '3' and resid 616 through 626 Processing helix chain '3' and resid 642 through 649 Processing helix chain '3' and resid 668 through 670 No H-bonds generated for 'chain '3' and resid 668 through 670' Processing helix chain '3' and resid 676 through 679 No H-bonds generated for 'chain '3' and resid 676 through 679' Processing helix chain '3' and resid 682 through 692 Processing helix chain '4' and resid 8 through 14 removed outlier: 3.960A pdb=" N GLN 4 13 " --> pdb=" O GLU 4 9 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N TYR 4 14 " --> pdb=" O TRP 4 10 " (cutoff:3.500A) Processing helix chain '4' and resid 87 through 93 removed outlier: 4.698A pdb=" N GLU 4 92 " --> pdb=" O GLU 4 88 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR 4 93 " --> pdb=" O LYS 4 89 " (cutoff:3.500A) Processing helix chain '4' and resid 96 through 102 Proline residue: 4 101 - end of helix Processing helix chain '4' and resid 111 through 126 Processing helix chain '4' and resid 132 through 161 removed outlier: 3.601A pdb=" N ILE 4 161 " --> pdb=" O HIS 4 157 " (cutoff:3.500A) Processing helix chain '4' and resid 165 through 184 removed outlier: 4.040A pdb=" N GLU 4 172 " --> pdb=" O PHE 4 168 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLU 4 173 " --> pdb=" O TRP 4 169 " (cutoff:3.500A) Processing helix chain '4' and resid 207 through 229 removed outlier: 3.906A pdb=" N ASN 4 217 " --> pdb=" O GLU 4 213 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N SER 4 219 " --> pdb=" O SER 4 215 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N LEU 4 220 " --> pdb=" O LYS 4 216 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG 4 221 " --> pdb=" O ASN 4 217 " (cutoff:3.500A) Processing helix chain '4' and resid 233 through 237 Processing helix chain '4' and resid 247 through 252 Processing helix chain '4' and resid 257 through 261 Processing helix chain '4' and resid 269 through 272 No H-bonds generated for 'chain '4' and resid 269 through 272' Processing helix chain '4' and resid 293 through 316 Processing helix chain '4' and resid 335 through 338 No H-bonds generated for 'chain '4' and resid 335 through 338' Processing helix chain '4' and resid 342 through 353 Processing helix chain '4' and resid 394 through 405 removed outlier: 4.661A pdb=" N ASP 4 403 " --> pdb=" O LEU 4 399 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N LYS 4 404 " --> pdb=" O ALA 4 400 " (cutoff:3.500A) Processing helix chain '4' and resid 411 through 420 removed outlier: 3.851A pdb=" N VAL 4 415 " --> pdb=" O LEU 4 411 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ALA 4 416 " --> pdb=" O ALA 4 412 " (cutoff:3.500A) Processing helix chain '4' and resid 425 through 429 Processing helix chain '5' and resid 16 through 32 Processing helix chain '5' and resid 54 through 66 removed outlier: 4.050A pdb=" N VAL 5 57 " --> pdb=" O PRO 5 54 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ILE 5 58 " --> pdb=" O ASP 5 55 " (cutoff:3.500A) Proline residue: 5 59 - end of helix removed outlier: 3.504A pdb=" N THR 5 62 " --> pdb=" O PRO 5 59 " (cutoff:3.500A) Processing helix chain '5' and resid 125 through 138 removed outlier: 3.738A pdb=" N TRP 5 129 " --> pdb=" O ALA 5 126 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N GLU 5 131 " --> pdb=" O ASN 5 128 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET 5 137 " --> pdb=" O ILE 5 134 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE 5 138 " --> pdb=" O TRP 5 135 " (cutoff:3.500A) Processing helix chain '5' and resid 207 through 209 No H-bonds generated for 'chain '5' and resid 207 through 209' Processing helix chain '6' and resid 26 through 44 Processing helix chain '6' and resid 54 through 62 Processing helix chain '6' and resid 69 through 72 Processing helix chain '6' and resid 97 through 105 Processing helix chain '6' and resid 117 through 122 Processing helix chain '6' and resid 124 through 126 No H-bonds generated for 'chain '6' and resid 124 through 126' Processing helix chain '6' and resid 136 through 138 No H-bonds generated for 'chain '6' and resid 136 through 138' Processing helix chain '6' and resid 153 through 168 Processing helix chain '6' and resid 172 through 178 Processing helix chain '9' and resid 14 through 26 Processing helix chain '9' and resid 28 through 41 Processing helix chain '9' and resid 82 through 86 Processing helix chain '9' and resid 121 through 125 Processing helix chain '9' and resid 145 through 147 No H-bonds generated for 'chain '9' and resid 145 through 147' Processing helix chain '9' and resid 151 through 175 removed outlier: 5.758A pdb=" N ALA 9 163 " --> pdb=" O ASP 9 159 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N GLU 9 164 " --> pdb=" O LYS 9 160 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ALA 9 167 " --> pdb=" O ALA 9 163 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N LEU 9 174 " --> pdb=" O GLN 9 170 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N TYR 9 175 " --> pdb=" O ALA 9 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 26 Proline residue: A 25 - end of helix Processing helix chain 'A' and resid 53 through 80 Proline residue: A 74 - end of helix removed outlier: 5.742A pdb=" N TRP A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N GLN A 80 " --> pdb=" O PRO A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 107 Processing helix chain 'H' and resid 2 through 32 Proline residue: H 12 - end of helix removed outlier: 3.559A pdb=" N THR H 21 " --> pdb=" O VAL H 17 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 44 No H-bonds generated for 'chain 'H' and resid 42 through 44' Processing helix chain 'H' and resid 47 through 57 Processing helix chain 'H' and resid 68 through 84 Proline residue: H 75 - end of helix Processing helix chain 'H' and resid 101 through 122 removed outlier: 3.572A pdb=" N ALA H 112 " --> pdb=" O MET H 108 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ILE H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 156 removed outlier: 3.810A pdb=" N VAL H 144 " --> pdb=" O ILE H 140 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N MET H 156 " --> pdb=" O SER H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 170 removed outlier: 3.719A pdb=" N GLN H 169 " --> pdb=" O LEU H 165 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU H 170 " --> pdb=" O ILE H 166 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 177 No H-bonds generated for 'chain 'H' and resid 174 through 177' Processing helix chain 'H' and resid 179 through 192 Processing helix chain 'H' and resid 220 through 242 Processing helix chain 'H' and resid 252 through 274 Processing helix chain 'H' and resid 282 through 290 Processing helix chain 'H' and resid 293 through 310 Proline residue: H 308 - end of helix Processing helix chain 'J' and resid 5 through 21 Processing helix chain 'J' and resid 26 through 47 removed outlier: 3.741A pdb=" N PHE J 47 " --> pdb=" O ILE J 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 58 Processing helix chain 'J' and resid 60 through 74 removed outlier: 4.453A pdb=" N MET J 65 " --> pdb=" O LEU J 61 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N VAL J 66 " --> pdb=" O GLY J 62 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET J 74 " --> pdb=" O TYR J 70 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 110 Processing helix chain 'J' and resid 138 through 148 removed outlier: 4.127A pdb=" N LEU J 146 " --> pdb=" O GLY J 142 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N TYR J 147 " --> pdb=" O ILE J 143 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N SER J 148 " --> pdb=" O ALA J 144 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 171 Processing helix chain 'K' and resid 3 through 19 removed outlier: 3.618A pdb=" N ASN K 7 " --> pdb=" O LEU K 3 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 51 Processing helix chain 'K' and resid 55 through 85 removed outlier: 3.799A pdb=" N MET K 58 " --> pdb=" O LEU K 55 " (cutoff:3.500A) Proline residue: K 60 - end of helix removed outlier: 3.621A pdb=" N PHE K 66 " --> pdb=" O LEU K 63 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA K 67 " --> pdb=" O LEU K 64 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR K 85 " --> pdb=" O SER K 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 92 No H-bonds generated for 'chain 'K' and resid 90 through 92' Processing helix chain 'K' and resid 95 through 97 No H-bonds generated for 'chain 'K' and resid 95 through 97' Processing helix chain 'L' and resid 4 through 23 removed outlier: 3.764A pdb=" N LEU L 12 " --> pdb=" O THR L 8 " (cutoff:3.500A) Proline residue: L 18 - end of helix Processing helix chain 'L' and resid 32 through 57 removed outlier: 4.113A pdb=" N ILE L 49 " --> pdb=" O ILE L 45 " (cutoff:3.500A) Proline residue: L 50 - end of helix removed outlier: 3.957A pdb=" N THR L 57 " --> pdb=" O MET L 53 " (cutoff:3.500A) Processing helix chain 'L' and resid 84 through 107 Proline residue: L 91 - end of helix removed outlier: 4.086A pdb=" N TRP L 106 " --> pdb=" O GLU L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 132 Processing helix chain 'L' and resid 137 through 155 Processing helix chain 'L' and resid 162 through 193 removed outlier: 3.934A pdb=" N GLY L 181 " --> pdb=" O ILE L 177 " (cutoff:3.500A) Processing helix chain 'L' and resid 198 through 204 Processing helix chain 'L' and resid 210 through 223 Processing helix chain 'L' and resid 231 through 238 removed outlier: 3.656A pdb=" N SER L 235 " --> pdb=" O PRO L 231 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N MET L 237 " --> pdb=" O LEU L 233 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N GLU L 238 " --> pdb=" O PRO L 234 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 250 removed outlier: 4.522A pdb=" N SER L 249 " --> pdb=" O ALA L 245 " (cutoff:3.500A) Processing helix chain 'L' and resid 255 through 262 Processing helix chain 'L' and resid 264 through 269 removed outlier: 4.237A pdb=" N ASN L 269 " --> pdb=" O PRO L 265 " (cutoff:3.500A) Processing helix chain 'L' and resid 271 through 293 removed outlier: 3.698A pdb=" N ALA L 289 " --> pdb=" O THR L 285 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU L 293 " --> pdb=" O ALA L 289 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 318 Processing helix chain 'L' and resid 322 through 349 removed outlier: 4.583A pdb=" N PHE L 334 " --> pdb=" O CYS L 330 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N PHE L 335 " --> pdb=" O THR L 331 " (cutoff:3.500A) Processing helix chain 'L' and resid 356 through 358 No H-bonds generated for 'chain 'L' and resid 356 through 358' Processing helix chain 'L' and resid 362 through 365 No H-bonds generated for 'chain 'L' and resid 362 through 365' Processing helix chain 'L' and resid 367 through 380 Processing helix chain 'L' and resid 389 through 400 removed outlier: 4.955A pdb=" N LEU L 394 " --> pdb=" O TYR L 390 " (cutoff:3.500A) Processing helix chain 'L' and resid 406 through 430 removed outlier: 3.591A pdb=" N ALA L 420 " --> pdb=" O THR L 416 " (cutoff:3.500A) Processing helix chain 'L' and resid 448 through 469 removed outlier: 3.838A pdb=" N LEU L 457 " --> pdb=" O SER L 453 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N GLY L 465 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N PHE L 466 " --> pdb=" O LEU L 462 " (cutoff:3.500A) Processing helix chain 'L' and resid 484 through 487 No H-bonds generated for 'chain 'L' and resid 484 through 487' Processing helix chain 'L' and resid 489 through 507 Processing helix chain 'L' and resid 518 through 524 Processing helix chain 'L' and resid 526 through 547 removed outlier: 3.838A pdb=" N TYR L 529 " --> pdb=" O LEU L 526 " (cutoff:3.500A) Proline residue: L 530 - end of helix removed outlier: 4.725A pdb=" N MET L 533 " --> pdb=" O PRO L 530 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N HIS L 534 " --> pdb=" O THR L 531 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N THR L 537 " --> pdb=" O HIS L 534 " (cutoff:3.500A) Proline residue: L 538 - end of helix removed outlier: 4.824A pdb=" N THR L 543 " --> pdb=" O MET L 540 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET L 544 " --> pdb=" O ASN L 541 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN L 546 " --> pdb=" O THR L 543 " (cutoff:3.500A) Processing helix chain 'L' and resid 557 through 561 Processing helix chain 'L' and resid 563 through 577 Processing helix chain 'L' and resid 584 through 600 Processing helix chain 'M' and resid 5 through 16 removed outlier: 4.037A pdb=" N MET M 12 " --> pdb=" O THR M 8 " (cutoff:3.500A) Proline residue: M 13 - end of helix Processing helix chain 'M' and resid 23 through 42 removed outlier: 4.005A pdb=" N THR M 27 " --> pdb=" O ILE M 23 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LEU M 39 " --> pdb=" O SER M 35 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N LEU M 40 " --> pdb=" O LEU M 36 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N LEU M 41 " --> pdb=" O THR M 37 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N LEU M 42 " --> pdb=" O SER M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 79 removed outlier: 3.612A pdb=" N LEU M 73 " --> pdb=" O THR M 69 " (cutoff:3.500A) Proline residue: M 74 - end of helix Processing helix chain 'M' and resid 89 through 107 Processing helix chain 'M' and resid 115 through 136 removed outlier: 4.484A pdb=" N LEU M 126 " --> pdb=" O PHE M 122 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N VAL M 127 " --> pdb=" O GLU M 123 " (cutoff:3.500A) Proline residue: M 128 - end of helix Processing helix chain 'M' and resid 140 through 171 removed outlier: 3.845A pdb=" N LEU M 143 " --> pdb=" O THR M 140 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN M 144 " --> pdb=" O GLU M 141 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA M 145 " --> pdb=" O ARG M 142 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N TYR M 152 " --> pdb=" O PHE M 149 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N LEU M 154 " --> pdb=" O PHE M 151 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LEU M 158 " --> pdb=" O ALA M 155 " (cutoff:3.500A) Proline residue: M 159 - end of helix removed outlier: 4.250A pdb=" N MET M 171 " --> pdb=" O GLN M 168 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 179 No H-bonds generated for 'chain 'M' and resid 176 through 179' Processing helix chain 'M' and resid 190 through 206 removed outlier: 4.832A pdb=" N ALA M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N PHE M 203 " --> pdb=" O CYS M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 213 through 219 Proline residue: M 217 - end of helix Processing helix chain 'M' and resid 225 through 233 Processing helix chain 'M' and resid 237 through 248 removed outlier: 4.679A pdb=" N LEU M 248 " --> pdb=" O MET M 244 " (cutoff:3.500A) Processing helix chain 'M' and resid 253 through 257 Processing helix chain 'M' and resid 259 through 277 removed outlier: 3.956A pdb=" N ILE M 270 " --> pdb=" O LEU M 266 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER M 273 " --> pdb=" O MET M 269 " (cutoff:3.500A) Processing helix chain 'M' and resid 282 through 303 removed outlier: 3.935A pdb=" N LEU M 296 " --> pdb=" O SER M 292 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL M 297 " --> pdb=" O HIS M 293 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 337 removed outlier: 4.170A pdb=" N ARG M 336 " --> pdb=" O SER M 332 " (cutoff:3.500A) Processing helix chain 'M' and resid 353 through 366 Processing helix chain 'M' and resid 373 through 388 Processing helix chain 'M' and resid 390 through 415 removed outlier: 3.623A pdb=" N ILE M 393 " --> pdb=" O ASN M 390 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET M 396 " --> pdb=" O ILE M 393 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY M 397 " --> pdb=" O ILE M 394 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU M 398 " --> pdb=" O LEU M 395 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER M 407 " --> pdb=" O ALA M 404 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU M 408 " --> pdb=" O LEU M 405 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR M 413 " --> pdb=" O MET M 410 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR M 414 " --> pdb=" O LEU M 411 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN M 415 " --> pdb=" O ILE M 412 " (cutoff:3.500A) Processing helix chain 'M' and resid 431 through 448 Proline residue: M 443 - end of helix removed outlier: 4.317A pdb=" N SER M 448 " --> pdb=" O LEU M 444 " (cutoff:3.500A) Processing helix chain 'M' and resid 451 through 454 Processing helix chain 'N' and resid 3 through 22 Processing helix chain 'N' and resid 26 through 44 Proline residue: N 42 - end of helix Processing helix chain 'N' and resid 50 through 81 Processing helix chain 'N' and resid 92 through 106 Processing helix chain 'N' and resid 112 through 121 Proline residue: N 116 - end of helix removed outlier: 3.528A pdb=" N THR N 119 " --> pdb=" O PRO N 116 " (cutoff:3.500A) Processing helix chain 'N' and resid 124 through 144 removed outlier: 4.159A pdb=" N GLN N 134 " --> pdb=" O LEU N 130 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N LYS N 135 " --> pdb=" O LEU N 131 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LEU N 136 " --> pdb=" O THR N 132 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ALA N 137 " --> pdb=" O TRP N 133 " (cutoff:3.500A) Proline residue: N 138 - end of helix Processing helix chain 'N' and resid 151 through 171 removed outlier: 4.103A pdb=" N GLY N 169 " --> pdb=" O GLY N 165 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU N 170 " --> pdb=" O GLY N 166 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ASN N 171 " --> pdb=" O TRP N 167 " (cutoff:3.500A) Processing helix chain 'N' and resid 175 through 192 Processing helix chain 'N' and resid 198 through 222 Processing helix chain 'N' and resid 227 through 233 removed outlier: 3.999A pdb=" N HIS N 232 " --> pdb=" O LEU N 228 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N THR N 233 " --> pdb=" O SER N 229 " (cutoff:3.500A) Processing helix chain 'N' and resid 238 through 251 removed outlier: 3.591A pdb=" N ILE N 242 " --> pdb=" O PRO N 238 " (cutoff:3.500A) Processing helix chain 'N' and resid 258 through 270 Proline residue: N 262 - end of helix Processing helix chain 'N' and resid 277 through 300 removed outlier: 3.863A pdb=" N LEU N 287 " --> pdb=" O ALA N 283 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N LEU N 288 " --> pdb=" O ILE N 284 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ASN N 289 " --> pdb=" O THR N 285 " (cutoff:3.500A) Processing helix chain 'N' and resid 309 through 316 removed outlier: 3.525A pdb=" N TRP N 315 " --> pdb=" O LYS N 312 " (cutoff:3.500A) Processing helix chain 'N' and resid 326 through 332 Processing helix chain 'N' and resid 337 through 346 Proline residue: N 341 - end of helix removed outlier: 3.642A pdb=" N SER N 344 " --> pdb=" O PRO N 341 " (cutoff:3.500A) Processing helix chain 'V' and resid 3 through 9 Processing helix chain 'V' and resid 17 through 42 Processing helix chain 'V' and resid 48 through 80 Processing helix chain 'V' and resid 86 through 104 Processing helix chain 'V' and resid 108 through 130 Processing helix chain 'W' and resid 16 through 46 removed outlier: 4.920A pdb=" N THR W 32 " --> pdb=" O TYR W 28 " (cutoff:3.500A) Proline residue: W 35 - end of helix Processing helix chain 'W' and resid 63 through 66 removed outlier: 3.924A pdb=" N TYR W 66 " --> pdb=" O HIS W 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 63 through 66' Processing helix chain 'W' and resid 70 through 78 Processing helix chain 'W' and resid 83 through 117 Processing helix chain 'W' and resid 130 through 132 No H-bonds generated for 'chain 'W' and resid 130 through 132' Processing helix chain 'X' and resid 8 through 21 Processing helix chain 'X' and resid 44 through 58 Processing helix chain 'X' and resid 64 through 69 removed outlier: 4.759A pdb=" N LYS X 69 " --> pdb=" O ILE X 65 " (cutoff:3.500A) Processing helix chain 'X' and resid 73 through 84 Processing helix chain 'Y' and resid 10 through 12 No H-bonds generated for 'chain 'Y' and resid 10 through 12' Processing helix chain 'Y' and resid 21 through 26 Processing helix chain 'Y' and resid 28 through 34 Processing helix chain 'Y' and resid 36 through 49 Processing helix chain 'Y' and resid 52 through 74 removed outlier: 4.279A pdb=" N LEU Y 56 " --> pdb=" O ARG Y 53 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N GLU Y 57 " --> pdb=" O ARG Y 54 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ALA Y 66 " --> pdb=" O ASN Y 63 " (cutoff:3.500A) Processing helix chain 'Y' and resid 78 through 90 removed outlier: 3.520A pdb=" N CYS Y 87 " --> pdb=" O GLU Y 83 " (cutoff:3.500A) Processing helix chain 'Y' and resid 100 through 113 Processing helix chain 'Z' and resid 28 through 39 Processing helix chain 'Z' and resid 41 through 57 Processing helix chain 'Z' and resid 73 through 75 No H-bonds generated for 'chain 'Z' and resid 73 through 75' Processing helix chain 'Z' and resid 81 through 116 removed outlier: 4.013A pdb=" N GLU Z 86 " --> pdb=" O LEU Z 82 " (cutoff:3.500A) Processing helix chain 'Z' and resid 125 through 142 Processing helix chain 'Z' and resid 151 through 171 Processing helix chain 'a' and resid 42 through 45 Processing helix chain 'a' and resid 50 through 60 removed outlier: 4.818A pdb=" N LYS a 60 " --> pdb=" O LEU a 56 " (cutoff:3.500A) Processing helix chain 'b' and resid 23 through 28 removed outlier: 3.785A pdb=" N ARG b 27 " --> pdb=" O ARG b 24 " (cutoff:3.500A) Processing helix chain 'b' and resid 40 through 44 Processing helix chain 'b' and resid 64 through 66 No H-bonds generated for 'chain 'b' and resid 64 through 66' Processing helix chain 'c' and resid 28 through 31 No H-bonds generated for 'chain 'c' and resid 28 through 31' Processing helix chain 'c' and resid 50 through 52 No H-bonds generated for 'chain 'c' and resid 50 through 52' Processing helix chain 'c' and resid 78 through 80 No H-bonds generated for 'chain 'c' and resid 78 through 80' Processing helix chain 'c' and resid 89 through 98 Processing helix chain 'c' and resid 119 through 122 Processing helix chain 'd' and resid 3 through 5 No H-bonds generated for 'chain 'd' and resid 3 through 5' Processing helix chain 'd' and resid 29 through 41 removed outlier: 3.735A pdb=" N TYR d 33 " --> pdb=" O PHE d 29 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N MET d 41 " --> pdb=" O HIS d 37 " (cutoff:3.500A) Processing helix chain 'd' and resid 53 through 62 removed outlier: 5.115A pdb=" N HIS d 58 " --> pdb=" O ASP d 55 " (cutoff:3.500A) Proline residue: d 61 - end of helix Processing helix chain 'd' and resid 78 through 85 Processing helix chain 'd' and resid 106 through 123 removed outlier: 4.781A pdb=" N ILE d 113 " --> pdb=" O VAL d 109 " (cutoff:3.500A) Proline residue: d 114 - end of helix Processing helix chain 'd' and resid 144 through 159 Processing helix chain 'd' and resid 179 through 183 Processing helix chain 'd' and resid 207 through 219 Processing helix chain 'd' and resid 221 through 223 No H-bonds generated for 'chain 'd' and resid 221 through 223' Processing helix chain 'd' and resid 238 through 248 Processing helix chain 'd' and resid 281 through 287 Processing helix chain 'd' and resid 301 through 303 No H-bonds generated for 'chain 'd' and resid 301 through 303' Processing helix chain 'd' and resid 310 through 318 removed outlier: 5.256A pdb=" N ILE d 315 " --> pdb=" O GLU d 311 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N GLU d 316 " --> pdb=" O LEU d 312 " (cutoff:3.500A) Processing helix chain 'e' and resid 27 through 38 removed outlier: 4.764A pdb=" N GLY e 31 " --> pdb=" O GLY e 28 " (cutoff:3.500A) Processing helix chain 'e' and resid 40 through 46 Processing helix chain 'e' and resid 69 through 71 No H-bonds generated for 'chain 'e' and resid 69 through 71' Processing helix chain 'e' and resid 83 through 96 Processing helix chain 'f' and resid 19 through 36 removed outlier: 4.444A pdb=" N HIS f 36 " --> pdb=" O ASP f 32 " (cutoff:3.500A) Processing helix chain 'f' and resid 42 through 59 Processing helix chain 'f' and resid 65 through 71 Processing helix chain 'f' and resid 76 through 96 removed outlier: 3.965A pdb=" N GLN f 95 " --> pdb=" O ARG f 91 " (cutoff:3.500A) Processing helix chain 'g' and resid 24 through 48 Proline residue: g 43 - end of helix Processing helix chain 'g' and resid 55 through 69 removed outlier: 4.125A pdb=" N ASN g 69 " --> pdb=" O MET g 65 " (cutoff:3.500A) Processing helix chain 'g' and resid 75 through 93 Processing helix chain 'g' and resid 99 through 105 removed outlier: 4.595A pdb=" N PHE g 105 " --> pdb=" O HIS g 101 " (cutoff:3.500A) Processing helix chain 'g' and resid 117 through 123 Processing helix chain 'h' and resid 5 through 15 Processing helix chain 'h' and resid 53 through 56 Processing helix chain 'i' and resid 3 through 16 Processing helix chain 'i' and resid 19 through 30 Processing helix chain 'i' and resid 79 through 81 No H-bonds generated for 'chain 'i' and resid 79 through 81' Processing helix chain 'i' and resid 84 through 90 removed outlier: 4.027A pdb=" N ARG i 88 " --> pdb=" O PRO i 84 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N TRP i 89 " --> pdb=" O GLU i 85 " (cutoff:3.500A) Processing helix chain 'j' and resid 8 through 21 Processing helix chain 'j' and resid 44 through 58 Processing helix chain 'j' and resid 73 through 82 Processing helix chain 'k' and resid 5 through 9 Processing helix chain 'k' and resid 35 through 45 removed outlier: 4.203A pdb=" N ALA k 39 " --> pdb=" O SEP k 36 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS k 45 " --> pdb=" O VAL k 42 " (cutoff:3.500A) Processing helix chain 'k' and resid 58 through 62 Processing helix chain 'k' and resid 79 through 84 Processing helix chain 'k' and resid 92 through 118 Processing helix chain 'k' and resid 128 through 130 No H-bonds generated for 'chain 'k' and resid 128 through 130' Processing helix chain 'k' and resid 132 through 140 Processing helix chain 'k' and resid 146 through 162 removed outlier: 4.550A pdb=" N CYS k 161 " --> pdb=" O LYS k 157 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N GLU k 162 " --> pdb=" O VAL k 158 " (cutoff:3.500A) Processing helix chain 'k' and resid 176 through 184 Processing helix chain 'k' and resid 191 through 193 No H-bonds generated for 'chain 'k' and resid 191 through 193' Processing helix chain 'k' and resid 196 through 217 removed outlier: 5.441A pdb=" N LEU k 211 " --> pdb=" O LYS k 207 " (cutoff:3.500A) Proline residue: k 212 - end of helix removed outlier: 5.180A pdb=" N GLU k 216 " --> pdb=" O PRO k 212 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LYS k 217 " --> pdb=" O GLU k 213 " (cutoff:3.500A) Processing helix chain 'k' and resid 231 through 239 Processing helix chain 'k' and resid 253 through 263 Processing helix chain 'k' and resid 266 through 269 No H-bonds generated for 'chain 'k' and resid 266 through 269' Processing helix chain 'k' and resid 271 through 273 No H-bonds generated for 'chain 'k' and resid 271 through 273' Processing helix chain 'k' and resid 286 through 297 Processing helix chain 'k' and resid 310 through 312 No H-bonds generated for 'chain 'k' and resid 310 through 312' Processing helix chain 'k' and resid 317 through 319 No H-bonds generated for 'chain 'k' and resid 317 through 319' Processing helix chain 'l' and resid 5 through 9 Processing helix chain 'l' and resid 25 through 27 No H-bonds generated for 'chain 'l' and resid 25 through 27' Processing helix chain 'l' and resid 33 through 43 Processing helix chain 'l' and resid 47 through 54 removed outlier: 4.056A pdb=" N LYS l 53 " --> pdb=" O ILE l 49 " (cutoff:3.500A) Processing helix chain 'l' and resid 56 through 67 Processing helix chain 'l' and resid 69 through 87 Processing helix chain 'l' and resid 95 through 97 No H-bonds generated for 'chain 'l' and resid 95 through 97' Processing helix chain 'm' and resid 6 through 14 Processing helix chain 'm' and resid 16 through 30 Processing helix chain 'm' and resid 38 through 46 removed outlier: 3.647A pdb=" N LEU m 42 " --> pdb=" O THR m 38 " (cutoff:3.500A) Processing helix chain 'm' and resid 78 through 82 Processing helix chain 'n' and resid 27 through 36 Processing helix chain 'n' and resid 45 through 52 removed outlier: 4.651A pdb=" N TRP n 50 " --> pdb=" O ARG n 46 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ARG n 51 " --> pdb=" O ASN n 47 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N TYR n 52 " --> pdb=" O GLU n 48 " (cutoff:3.500A) Processing helix chain 'n' and resid 62 through 66 Processing helix chain 'n' and resid 70 through 88 Processing helix chain 'o' and resid 5 through 7 No H-bonds generated for 'chain 'o' and resid 5 through 7' Processing helix chain 'o' and resid 16 through 20 Processing helix chain 'o' and resid 29 through 48 Processing helix chain 'o' and resid 58 through 96 removed outlier: 4.003A pdb=" N TYR o 74 " --> pdb=" O PHE o 70 " (cutoff:3.500A) Processing helix chain 'p' and resid 19 through 22 Processing helix chain 'p' and resid 26 through 50 removed outlier: 4.002A pdb=" N GLN p 49 " --> pdb=" O GLU p 45 " (cutoff:3.500A) Processing helix chain 'p' and resid 62 through 72 Processing helix chain 'p' and resid 83 through 91 Processing helix chain 'p' and resid 95 through 116 Processing helix chain 'q' and resid 31 through 96 removed outlier: 3.669A pdb=" N PHE q 35 " --> pdb=" O GLY q 31 " (cutoff:3.500A) Proline residue: q 72 - end of helix Processing helix chain 'q' and resid 120 through 123 No H-bonds generated for 'chain 'q' and resid 120 through 123' Processing helix chain 'q' and resid 129 through 136 Processing helix chain 'r' and resid 5 through 24 Processing helix chain 'r' and resid 68 through 72 Processing helix chain 'r' and resid 75 through 87 removed outlier: 3.566A pdb=" N TRP r 79 " --> pdb=" O LEU r 75 " (cutoff:3.500A) Processing helix chain 's' and resid 2 through 8 Processing helix chain 's' and resid 42 through 47 Processing helix chain 's' and resid 60 through 71 Processing helix chain 's' and resid 80 through 121 Processing helix chain 't' and resid 11 through 29 Processing helix chain 't' and resid 33 through 49 Processing helix chain 't' and resid 56 through 73 Processing helix chain 't' and resid 93 through 95 No H-bonds generated for 'chain 't' and resid 93 through 95' Processing helix chain 't' and resid 100 through 105 Processing helix chain 't' and resid 108 through 111 No H-bonds generated for 'chain 't' and resid 108 through 111' Processing helix chain 't' and resid 115 through 142 removed outlier: 4.392A pdb=" N GLN t 123 " --> pdb=" O ALA t 119 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TRP t 124 " --> pdb=" O LYS t 120 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N GLU t 133 " --> pdb=" O ARG t 129 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ARG t 134 " --> pdb=" O GLU t 130 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU t 141 " --> pdb=" O LYS t 137 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU t 142 " --> pdb=" O GLN t 138 " (cutoff:3.500A) Processing helix chain 't' and resid 167 through 170 No H-bonds generated for 'chain 't' and resid 167 through 170' Processing helix chain 'u' and resid 19 through 42 Processing helix chain 'u' and resid 61 through 64 No H-bonds generated for 'chain 'u' and resid 61 through 64' Processing helix chain 'v' and resid 17 through 26 Processing helix chain 'v' and resid 98 through 121 Processing helix chain 'v' and resid 134 through 138 Processing helix chain 'w' and resid 51 through 66 Processing helix chain 'w' and resid 69 through 78 Processing helix chain 'w' and resid 83 through 102 removed outlier: 4.138A pdb=" N GLN w 86 " --> pdb=" O TYR w 83 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N GLU w 87 " --> pdb=" O ARG w 84 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU w 92 " --> pdb=" O ALA w 89 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL w 97 " --> pdb=" O GLU w 94 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLU w 101 " --> pdb=" O LYS w 98 " (cutoff:3.500A) Processing helix chain 'w' and resid 115 through 117 No H-bonds generated for 'chain 'w' and resid 115 through 117' Processing helix chain 'x' and resid 14 through 46 Processing helix chain 'y' and resid 11 through 14 removed outlier: 3.736A pdb=" N VAL y 14 " --> pdb=" O TRP y 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 11 through 14' Processing helix chain 'y' and resid 16 through 33 removed outlier: 3.675A pdb=" N GLU y 32 " --> pdb=" O ARG y 28 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS y 33 " --> pdb=" O LYS y 29 " (cutoff:3.500A) Processing helix chain 'z' and resid 2 through 29 removed outlier: 3.674A pdb=" N VAL z 5 " --> pdb=" O TRP z 2 " (cutoff:3.500A) Proline residue: z 7 - end of helix removed outlier: 3.984A pdb=" N ILE z 18 " --> pdb=" O CYS z 15 " (cutoff:3.500A) Proline residue: z 19 - end of helix removed outlier: 3.556A pdb=" N ILE z 26 " --> pdb=" O THR z 23 " (cutoff:3.500A) Processing helix chain 'z' and resid 42 through 55 Processing sheet with id= A, first strand: chain '1' and resid 219 through 224 removed outlier: 6.076A pdb=" N ALA 1 133 " --> pdb=" O LEU 1 93 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N VAL 1 95 " --> pdb=" O ALA 1 133 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N TYR 1 135 " --> pdb=" O VAL 1 95 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ALA 1 97 " --> pdb=" O TYR 1 135 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N TYR 1 137 " --> pdb=" O ALA 1 97 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ASP 1 174 " --> pdb=" O ALA 1 134 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ILE 1 136 " --> pdb=" O ASP 1 174 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N PHE 1 176 " --> pdb=" O ILE 1 136 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ILE 1 138 " --> pdb=" O PHE 1 176 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N VAL 1 178 " --> pdb=" O ILE 1 138 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '1' and resid 266 through 271 Processing sheet with id= C, first strand: chain '2' and resid 137 through 142 removed outlier: 6.611A pdb=" N TYR 2 98 " --> pdb=" O THR 2 138 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N ILE 2 140 " --> pdb=" O TYR 2 98 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ILE 2 100 " --> pdb=" O ILE 2 140 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL 2 142 " --> pdb=" O ILE 2 100 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N VAL 2 102 " --> pdb=" O VAL 2 142 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '3' and resid 9 through 13 Processing sheet with id= E, first strand: chain '3' and resid 146 through 148 Processing sheet with id= F, first strand: chain '3' and resid 173 through 175 Processing sheet with id= G, first strand: chain '3' and resid 223 through 228 removed outlier: 3.603A pdb=" N ARG 3 249 " --> pdb=" O SER 3 241 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain '3' and resid 283 through 285 Processing sheet with id= I, first strand: chain '3' and resid 343 through 345 removed outlier: 8.521A pdb=" N CYS 3 344 " --> pdb=" O VAL 3 315 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ALA 3 317 " --> pdb=" O CYS 3 344 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N MET 3 521 " --> pdb=" O ALA 3 316 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N ILE 3 318 " --> pdb=" O MET 3 521 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N PHE 3 523 " --> pdb=" O ILE 3 318 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N PHE 3 542 " --> pdb=" O LEU 3 522 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N LEU 3 524 " --> pdb=" O PHE 3 542 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N VAL 3 544 " --> pdb=" O LEU 3 524 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL 3 559 " --> pdb=" O TYR 3 545 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N GLY 3 547 " --> pdb=" O VAL 3 559 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N LEU 3 561 " --> pdb=" O GLY 3 547 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain '3' and resid 490 through 493 removed outlier: 8.195A pdb=" N ASN 3 491 " --> pdb=" O PRO 3 449 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL 3 451 " --> pdb=" O ASN 3 491 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N LEU 3 493 " --> pdb=" O VAL 3 451 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU 3 453 " --> pdb=" O LEU 3 493 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N VAL 3 376 " --> pdb=" O MET 3 450 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N VAL 3 452 " --> pdb=" O VAL 3 376 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LEU 3 378 " --> pdb=" O VAL 3 452 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N GLY 3 454 " --> pdb=" O LEU 3 378 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N VAL 3 380 " --> pdb=" O GLY 3 454 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LYS 3 405 " --> pdb=" O VAL 3 377 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N LEU 3 379 " --> pdb=" O LYS 3 405 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ALA 3 407 " --> pdb=" O LEU 3 379 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ASP 3 420 " --> pdb=" O LEU 3 408 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain '3' and resid 572 through 574 Processing sheet with id= L, first strand: chain '4' and resid 50 through 52 removed outlier: 3.934A pdb=" N ARG 4 63 " --> pdb=" O HIS 4 79 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N SER 4 69 " --> pdb=" O VAL 4 73 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL 4 73 " --> pdb=" O SER 4 69 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain '4' and resid 361 through 369 removed outlier: 3.508A pdb=" N SER 4 380 " --> pdb=" O GLY 4 361 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain '5' and resid 74 through 82 removed outlier: 6.843A pdb=" N ASN 5 95 " --> pdb=" O ALA 5 76 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LEU 5 78 " --> pdb=" O VAL 5 93 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL 5 93 " --> pdb=" O LEU 5 78 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ALA 5 80 " --> pdb=" O GLU 5 91 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N GLU 5 91 " --> pdb=" O ALA 5 80 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU 5 48 " --> pdb=" O ARG 5 106 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N LYS 5 108 " --> pdb=" O LEU 5 48 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE 5 50 " --> pdb=" O LYS 5 108 " (cutoff:3.500A) removed outlier: 8.627A pdb=" N TYR 5 110 " --> pdb=" O ILE 5 50 " (cutoff:3.500A) removed outlier: 8.799A pdb=" N ILE 5 52 " --> pdb=" O TYR 5 110 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain '5' and resid 172 through 177 Processing sheet with id= P, first strand: chain '6' and resid 47 through 51 removed outlier: 6.353A pdb=" N VAL 6 85 " --> pdb=" O MET 6 48 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N PHE 6 50 " --> pdb=" O VAL 6 85 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE 6 87 " --> pdb=" O PHE 6 50 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N TYR 6 112 " --> pdb=" O MET 6 86 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N VAL 6 88 " --> pdb=" O TYR 6 112 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL 6 114 " --> pdb=" O VAL 6 88 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE 6 144 " --> pdb=" O SER 6 115 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain '9' and resid 65 through 67 Processing sheet with id= R, first strand: chain '9' and resid 92 through 98 removed outlier: 5.924A pdb=" N GLU 9 97 " --> pdb=" O THR 9 106 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N THR 9 106 " --> pdb=" O GLU 9 97 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'J' and resid 112 through 114 Processing sheet with id= T, first strand: chain 'L' and resid 61 through 67 removed outlier: 6.684A pdb=" N LEU L 78 " --> pdb=" O ASN L 65 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'b' and resid 50 through 52 Processing sheet with id= V, first strand: chain 'b' and resid 56 through 59 Processing sheet with id= W, first strand: chain 'c' and resid 102 through 105 Processing sheet with id= X, first strand: chain 'c' and resid 64 through 66 Processing sheet with id= Y, first strand: chain 'd' and resid 227 through 230 removed outlier: 6.484A pdb=" N ILE d 165 " --> pdb=" O PHE d 228 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N PHE d 230 " --> pdb=" O ILE d 165 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LYS d 167 " --> pdb=" O PHE d 230 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE d 132 " --> pdb=" O ASN d 93 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLN d 44 " --> pdb=" O ALA d 21 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N VAL d 23 " --> pdb=" O GLN d 44 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE d 46 " --> pdb=" O VAL d 23 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'e' and resid 51 through 57 removed outlier: 3.713A pdb=" N LEU e 22 " --> pdb=" O ARG e 55 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ARG e 67 " --> pdb=" O ARG e 16 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ILE e 18 " --> pdb=" O TRP e 65 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TRP e 65 " --> pdb=" O ILE e 18 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ILE e 20 " --> pdb=" O LYS e 63 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LYS e 63 " --> pdb=" O ILE e 20 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'i' and resid 60 through 63 removed outlier: 3.589A pdb=" N GLY i 40 " --> pdb=" O TYR i 48 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLU i 50 " --> pdb=" O LEU i 38 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N LEU i 38 " --> pdb=" O GLU i 50 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'k' and resid 122 through 125 removed outlier: 6.402A pdb=" N VAL k 168 " --> pdb=" O THR k 26 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N ASP k 28 " --> pdb=" O VAL k 168 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ILE k 170 " --> pdb=" O ASP k 28 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N GLU k 219 " --> pdb=" O VAL k 169 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N TYR k 171 " --> pdb=" O GLU k 219 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU k 221 " --> pdb=" O TYR k 171 " (cutoff:3.500A) 2785 hydrogen bonds defined for protein. 7716 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: 22.61 Time building geometry restraints manager: 23.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.43: 28316 1.43 - 1.66: 39978 1.66 - 1.89: 757 1.89 - 2.13: 0 2.13 - 2.36: 80 Bond restraints: 69131 Sorted by residual: bond pdb=" O2B NDP d 401 " pdb=" P2B NDP d 401 " ideal model delta sigma weight residual 1.833 1.596 0.237 3.80e-02 6.93e+02 3.89e+01 bond pdb=" C16 ZMP g 201 " pdb=" N2 ZMP g 201 " ideal model delta sigma weight residual 1.452 1.328 0.124 2.00e-02 2.50e+03 3.83e+01 bond pdb=" OB3 CDL W 201 " pdb=" PB2 CDL W 201 " ideal model delta sigma weight residual 1.529 1.470 0.059 1.00e-02 1.00e+04 3.44e+01 bond pdb=" C13 ZMP g 201 " pdb=" N1 ZMP g 201 " ideal model delta sigma weight residual 1.451 1.336 0.115 2.00e-02 2.50e+03 3.32e+01 bond pdb=" OA3 CDL z 101 " pdb=" PA1 CDL z 101 " ideal model delta sigma weight residual 1.529 1.472 0.057 1.00e-02 1.00e+04 3.21e+01 ... (remaining 69126 not shown) Histogram of bond angle deviations from ideal: 62.35 - 77.43: 74 77.43 - 92.50: 8 92.50 - 107.58: 3794 107.58 - 122.66: 82877 122.66 - 137.73: 6673 Bond angle restraints: 93426 Sorted by residual: angle pdb=" O1A NAI 1 503 " pdb=" PA NAI 1 503 " pdb=" O2A NAI 1 503 " ideal model delta sigma weight residual 120.60 73.16 47.44 3.00e+00 1.11e-01 2.50e+02 angle pdb=" O1A NAI 1 503 " pdb=" PA NAI 1 503 " pdb=" O5B NAI 1 503 " ideal model delta sigma weight residual 109.30 71.01 38.29 3.00e+00 1.11e-01 1.63e+02 angle pdb=" S1 FES 3 803 " pdb="FE2 FES 3 803 " pdb=" S2 FES 3 803 " ideal model delta sigma weight residual 104.33 90.08 14.25 1.14e+00 7.69e-01 1.56e+02 angle pdb=" S1 FES 3 803 " pdb="FE1 FES 3 803 " pdb=" S2 FES 3 803 " ideal model delta sigma weight residual 104.33 90.10 14.23 1.20e+00 6.94e-01 1.41e+02 angle pdb=" PA NDP d 401 " pdb=" O3 NDP d 401 " pdb=" PN NDP d 401 " ideal model delta sigma weight residual 107.74 130.55 -22.81 1.95e+00 2.62e-01 1.36e+02 ... (remaining 93421 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.85: 41339 35.85 - 71.71: 687 71.71 - 107.56: 39 107.56 - 143.42: 4 143.42 - 179.27: 4 Dihedral angle restraints: 42073 sinusoidal: 18290 harmonic: 23783 Sorted by residual: dihedral pdb=" CA TYR 4 275 " pdb=" C TYR 4 275 " pdb=" N ASP 4 276 " pdb=" CA ASP 4 276 " ideal model delta harmonic sigma weight residual 180.00 -127.58 -52.42 0 5.00e+00 4.00e-02 1.10e+02 dihedral pdb=" CA PRO H 60 " pdb=" C PRO H 60 " pdb=" N LEU H 61 " pdb=" CA LEU H 61 " ideal model delta harmonic sigma weight residual -180.00 -130.91 -49.09 0 5.00e+00 4.00e-02 9.64e+01 dihedral pdb=" CA ASN 3 259 " pdb=" C ASN 3 259 " pdb=" N GLU 3 260 " pdb=" CA GLU 3 260 " ideal model delta harmonic sigma weight residual -180.00 -138.59 -41.41 0 5.00e+00 4.00e-02 6.86e+01 ... (remaining 42070 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.232: 10089 4.232 - 8.464: 5 8.464 - 12.696: 0 12.696 - 16.928: 0 16.928 - 21.160: 24 Chirality restraints: 10118 Sorted by residual: chirality pdb="FE4 SF4 3 802 " pdb=" S1 SF4 3 802 " pdb=" S2 SF4 3 802 " pdb=" S3 SF4 3 802 " both_signs ideal model delta sigma weight residual False 10.55 -10.60 21.16 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE4 SF4 9 402 " pdb=" S1 SF4 9 402 " pdb=" S2 SF4 9 402 " pdb=" S3 SF4 9 402 " both_signs ideal model delta sigma weight residual False 10.55 -10.58 21.13 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE1 SF4 9 403 " pdb=" S2 SF4 9 403 " pdb=" S3 SF4 9 403 " pdb=" S4 SF4 9 403 " both_signs ideal model delta sigma weight residual False -10.55 10.57 -21.12 2.00e-01 2.50e+01 1.12e+04 ... (remaining 10115 not shown) Planarity restraints: 11647 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 DCQ 6 203 " 0.011 2.00e-02 2.50e+03 3.80e-02 4.33e+01 pdb=" C1M DCQ 6 203 " 0.019 2.00e-02 2.50e+03 pdb=" C2 DCQ 6 203 " -0.006 2.00e-02 2.50e+03 pdb=" C3 DCQ 6 203 " -0.009 2.00e-02 2.50e+03 pdb=" C4 DCQ 6 203 " 0.005 2.00e-02 2.50e+03 pdb=" C5 DCQ 6 203 " -0.011 2.00e-02 2.50e+03 pdb=" C6 DCQ 6 203 " 0.011 2.00e-02 2.50e+03 pdb=" C7 DCQ 6 203 " 0.013 2.00e-02 2.50e+03 pdb=" O2 DCQ 6 203 " -0.005 2.00e-02 2.50e+03 pdb=" O3 DCQ 6 203 " -0.044 2.00e-02 2.50e+03 pdb=" O4 DCQ 6 203 " 0.092 2.00e-02 2.50e+03 pdb=" O5 DCQ 6 203 " -0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR 9 40 " 0.018 2.00e-02 2.50e+03 3.10e-02 1.92e+01 pdb=" CG TYR 9 40 " -0.071 2.00e-02 2.50e+03 pdb=" CD1 TYR 9 40 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 TYR 9 40 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR 9 40 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR 9 40 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR 9 40 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR 9 40 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR 6 125 " 0.035 2.00e-02 2.50e+03 2.83e-02 1.61e+01 pdb=" CG TYR 6 125 " -0.068 2.00e-02 2.50e+03 pdb=" CD1 TYR 6 125 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR 6 125 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR 6 125 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR 6 125 " 0.015 2.00e-02 2.50e+03 pdb=" CZ TYR 6 125 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR 6 125 " 0.003 2.00e-02 2.50e+03 ... (remaining 11644 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.84: 21129 2.84 - 3.41: 73375 3.41 - 3.99: 139666 3.99 - 4.56: 196899 4.56 - 5.14: 282897 Nonbonded interactions: 713966 Sorted by model distance: nonbonded pdb=" O GLY k 29 " pdb=" OH TYR k 206 " model vdw 2.263 2.440 nonbonded pdb=" OH TYR H 114 " pdb=" O LEU J 61 " model vdw 2.264 2.440 nonbonded pdb=" O ILE L 556 " pdb=" OG1 THR L 560 " model vdw 2.270 2.440 nonbonded pdb=" OE2 GLU 4 224 " pdb=" OH TYR 9 40 " model vdw 2.272 2.440 nonbonded pdb=" O PHE u 40 " pdb=" OG SER u 44 " model vdw 2.274 2.440 ... (remaining 713961 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'X' and resid 5 through 86) selection = chain 'j' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 4.890 Check model and map are aligned: 0.750 Set scattering table: 0.480 Process input model: 160.720 Find NCS groups from input model: 2.310 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:12.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 182.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 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 : 0.007 0.237 69131 Z= 0.463 Angle : 0.993 47.444 93426 Z= 0.522 Chirality : 1.026 21.160 10118 Planarity : 0.008 0.078 11647 Dihedral : 12.646 179.273 26714 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.69 % Favored : 96.27 % Rotamer: Outliers : 0.07 % Allowed : 2.29 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.21 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.95 (0.08), residues: 8046 helix: -1.93 (0.06), residues: 4282 sheet: -1.54 (0.24), residues: 375 loop : -1.85 (0.09), residues: 3389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.003 TRP A 106 HIS 0.018 0.002 HIS 4 200 PHE 0.057 0.003 PHE 4 171 TYR 0.071 0.003 TYR 9 40 ARG 0.023 0.001 ARG Y 165 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16092 Ramachandran restraints generated. 8046 Oldfield, 0 Emsley, 8046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16092 Ramachandran restraints generated. 8046 Oldfield, 0 Emsley, 8046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1905 residues out of total 7132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1900 time to evaluate : 5.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 122 LYS cc_start: 0.8130 (pptt) cc_final: 0.7804 (tmtt) REVERT: 3 447 LYS cc_start: 0.8967 (mttm) cc_final: 0.8650 (mmpt) REVERT: 5 14 ARG cc_start: 0.8255 (ttt90) cc_final: 0.7786 (ttm110) REVERT: 6 25 ARG cc_start: 0.5286 (ttt180) cc_final: 0.4671 (mmp-170) REVERT: 6 62 MET cc_start: 0.8992 (tmm) cc_final: 0.8770 (ttp) REVERT: 6 67 TYR cc_start: 0.8873 (m-80) cc_final: 0.8627 (m-80) REVERT: 6 102 LYS cc_start: 0.9105 (tttt) cc_final: 0.8796 (ttmt) REVERT: 9 172 ASP cc_start: 0.9111 (t70) cc_final: 0.8877 (t0) REVERT: A 23 TRP cc_start: 0.6937 (m100) cc_final: 0.6244 (t60) REVERT: H 65 THR cc_start: 0.9062 (p) cc_final: 0.8837 (t) REVERT: H 103 LEU cc_start: 0.8844 (tp) cc_final: 0.8637 (tp) REVERT: L 238 GLU cc_start: 0.8082 (tp30) cc_final: 0.7796 (mm-30) REVERT: L 480 MET cc_start: 0.8449 (mtp) cc_final: 0.8189 (mtp) REVERT: L 503 GLU cc_start: 0.7787 (mt-10) cc_final: 0.6962 (tm-30) REVERT: M 70 MET cc_start: 0.8614 (mtm) cc_final: 0.8409 (mtp) REVERT: M 166 TYR cc_start: 0.8591 (t80) cc_final: 0.7919 (t80) REVERT: V 73 SER cc_start: 0.5801 (m) cc_final: 0.5523 (p) REVERT: V 91 ILE cc_start: 0.6886 (mt) cc_final: 0.6457 (tp) REVERT: V 117 MET cc_start: 0.6473 (mtp) cc_final: 0.5974 (tpt) REVERT: Y 120 ASP cc_start: 0.8547 (m-30) cc_final: 0.8252 (m-30) REVERT: Z 61 TYR cc_start: 0.7916 (m-80) cc_final: 0.7528 (m-80) REVERT: c 18 ASP cc_start: 0.8843 (t70) cc_final: 0.8609 (t70) REVERT: d 54 TYR cc_start: 0.9279 (t80) cc_final: 0.9050 (t80) REVERT: d 154 LYS cc_start: 0.8291 (tttm) cc_final: 0.7971 (mtpp) REVERT: d 222 ASP cc_start: 0.8582 (m-30) cc_final: 0.8138 (m-30) REVERT: d 224 ARG cc_start: 0.8245 (mtp85) cc_final: 0.7920 (mmp-170) REVERT: d 281 ARG cc_start: 0.8056 (ptp90) cc_final: 0.7540 (mpt180) REVERT: d 308 THR cc_start: 0.8765 (m) cc_final: 0.8425 (p) REVERT: e 58 SER cc_start: 0.8320 (t) cc_final: 0.7943 (m) REVERT: e 63 LYS cc_start: 0.9046 (tppp) cc_final: 0.8799 (tppt) REVERT: g 98 GLN cc_start: 0.9023 (mp10) cc_final: 0.8793 (mp10) REVERT: h 17 ARG cc_start: 0.8133 (mmm-85) cc_final: 0.7864 (tpp-160) REVERT: i 68 MET cc_start: 0.9168 (ttt) cc_final: 0.8945 (ttt) REVERT: j 12 LYS cc_start: 0.8451 (tmmt) cc_final: 0.8185 (tptp) REVERT: j 21 LEU cc_start: 0.8753 (mt) cc_final: 0.8456 (mt) REVERT: j 24 LYS cc_start: 0.7553 (ttmp) cc_final: 0.6990 (mmtp) REVERT: j 71 MET cc_start: 0.7512 (mmp) cc_final: 0.7187 (mmp) REVERT: j 74 GLN cc_start: 0.7680 (tp40) cc_final: 0.7263 (tp-100) REVERT: k 136 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7882 (tp30) REVERT: l 79 LYS cc_start: 0.7995 (tttm) cc_final: 0.7460 (pttm) REVERT: m 43 MET cc_start: 0.8718 (mtp) cc_final: 0.8514 (mtm) REVERT: n 72 TRP cc_start: 0.7376 (m100) cc_final: 0.7028 (m-90) REVERT: n 78 VAL cc_start: 0.8282 (t) cc_final: 0.8039 (p) REVERT: o 117 HIS cc_start: 0.8193 (m-70) cc_final: 0.7993 (m90) REVERT: q 128 THR cc_start: 0.8034 (p) cc_final: 0.7634 (t) REVERT: s 44 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7228 (mm-30) REVERT: t 19 TYR cc_start: 0.7880 (t80) cc_final: 0.7538 (t80) REVERT: t 161 ASP cc_start: 0.6653 (m-30) cc_final: 0.5907 (m-30) REVERT: u 60 THR cc_start: 0.7134 (p) cc_final: 0.6910 (t) REVERT: v 7 ASP cc_start: 0.7416 (p0) cc_final: 0.6816 (t0) REVERT: v 84 TYR cc_start: 0.8268 (m-80) cc_final: 0.8000 (m-80) REVERT: v 103 LYS cc_start: 0.7250 (mttt) cc_final: 0.6898 (mmtm) REVERT: v 105 LEU cc_start: 0.7531 (tp) cc_final: 0.7241 (tp) REVERT: x 38 ASP cc_start: 0.8020 (m-30) cc_final: 0.7613 (m-30) REVERT: y 8 ARG cc_start: 0.6861 (tpm170) cc_final: 0.5709 (mmm160) outliers start: 5 outliers final: 6 residues processed: 1904 average time/residue: 1.5857 time to fit residues: 3874.7217 Evaluate side-chains 1146 residues out of total 7132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1140 time to evaluate : 5.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 54 CYS Chi-restraints excluded: chain 6 residue 85 VAL Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain j residue 11 ILE Chi-restraints excluded: chain n residue 58 ASN Chi-restraints excluded: chain r residue 76 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 794 random chunks: chunk 670 optimal weight: 8.9990 chunk 601 optimal weight: 3.9990 chunk 333 optimal weight: 20.0000 chunk 205 optimal weight: 10.0000 chunk 405 optimal weight: 10.0000 chunk 321 optimal weight: 9.9990 chunk 622 optimal weight: 20.0000 chunk 240 optimal weight: 0.0980 chunk 378 optimal weight: 4.9990 chunk 463 optimal weight: 9.9990 chunk 721 optimal weight: 10.0000 overall best weight: 5.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 148 ASN ** 1 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 373 ASN 1 435 GLN 1 436 GLN 1 437 HIS 2 74 GLN 3 179 ASN ** 3 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 308 GLN 3 336 ASN ** 3 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 150 HIS 4 252 ASN ** 9 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 2 ASN A 28 ASN H 230 ASN ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 52 HIS K 83 ASN L 136 ASN L 170 GLN L 210 ASN L 248 HIS L 270 ASN L 296 ASN L 348 HIS L 442 ASN ** L 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 81 GLN M 138 ASN M 139 GLN M 169 ASN N 120 GLN N 174 GLN N 235 ASN V 7 GLN W 124 GLN Y 15 GLN Y 142 HIS ** Z 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 106 GLN Z 114 GLN Z 133 GLN c 44 ASN c 46 GLN d 36 ASN d 37 HIS d 87 HIS d 115 GLN d 203 GLN e 92 ASN ** f 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 49 GLN g 50 GLN g 69 ASN g 125 HIS i 31 ASN i 91 HIS ** i 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 153 ASN k 180 GLN k 184 GLN l 81 GLN n 20 GLN n 59 ASN p 32 GLN p 49 GLN p 125 ASN ** r 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 25 HIS t 77 GLN v 55 GLN ** w 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 46 ASN ** y 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 68 ASN Total number of N/Q/H flips: 66 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.280 69131 Z= 0.574 Angle : 1.593 51.130 93426 Z= 1.024 Chirality : 0.310 6.532 10118 Planarity : 0.006 0.060 11647 Dihedral : 13.296 171.847 10586 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.07 % Favored : 96.91 % Rotamer: Outliers : 2.93 % Allowed : 12.32 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.09), residues: 8046 helix: -0.26 (0.07), residues: 4290 sheet: -1.03 (0.25), residues: 366 loop : -1.25 (0.10), residues: 3390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP 1 371 HIS 0.017 0.001 HIS 9 65 PHE 0.031 0.002 PHE N 292 TYR 0.032 0.002 TYR H 215 ARG 0.012 0.001 ARG e 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16092 Ramachandran restraints generated. 8046 Oldfield, 0 Emsley, 8046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16092 Ramachandran restraints generated. 8046 Oldfield, 0 Emsley, 8046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1409 residues out of total 7132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 1200 time to evaluate : 6.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 14 LYS cc_start: 0.9154 (mppt) cc_final: 0.8829 (mmmm) REVERT: 2 122 LYS cc_start: 0.8168 (pptt) cc_final: 0.7959 (pptt) REVERT: 3 121 MET cc_start: 0.9272 (mmm) cc_final: 0.9026 (mmm) REVERT: 3 447 LYS cc_start: 0.9004 (mttm) cc_final: 0.8688 (mmpt) REVERT: 4 19 MET cc_start: 0.7622 (mmm) cc_final: 0.7386 (tpt) REVERT: 5 14 ARG cc_start: 0.8313 (ttt90) cc_final: 0.7860 (ttm110) REVERT: 6 25 ARG cc_start: 0.5589 (ttt180) cc_final: 0.4833 (mmp-170) REVERT: 6 62 MET cc_start: 0.9077 (tmm) cc_final: 0.8848 (ttp) REVERT: 9 78 ILE cc_start: 0.9310 (OUTLIER) cc_final: 0.8995 (pp) REVERT: A 23 TRP cc_start: 0.7027 (m100) cc_final: 0.6273 (t60) REVERT: H 65 THR cc_start: 0.9140 (p) cc_final: 0.8930 (t) REVERT: H 72 ILE cc_start: 0.9197 (OUTLIER) cc_final: 0.8968 (mp) REVERT: L 393 ASP cc_start: 0.8350 (t0) cc_final: 0.8077 (t0) REVERT: L 440 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.7105 (tt) REVERT: L 559 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7026 (tp30) REVERT: M 166 TYR cc_start: 0.8660 (t80) cc_final: 0.7924 (t80) REVERT: M 201 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.8525 (mmm) REVERT: M 454 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8499 (pp) REVERT: N 8 ILE cc_start: 0.9318 (OUTLIER) cc_final: 0.9109 (mp) REVERT: V 73 SER cc_start: 0.5807 (m) cc_final: 0.5560 (p) REVERT: V 117 MET cc_start: 0.6475 (mtp) cc_final: 0.6099 (tpt) REVERT: V 133 LYS cc_start: 0.7809 (mttp) cc_final: 0.7063 (mmtm) REVERT: W 62 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7357 (mm-30) REVERT: X 30 LEU cc_start: 0.5421 (pp) cc_final: 0.5065 (mm) REVERT: X 69 LYS cc_start: 0.7913 (OUTLIER) cc_final: 0.7700 (mttp) REVERT: Y 120 ASP cc_start: 0.8520 (m-30) cc_final: 0.8211 (m-30) REVERT: c 18 ASP cc_start: 0.8815 (t70) cc_final: 0.8606 (t70) REVERT: c 28 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8164 (tm-30) REVERT: c 31 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8610 (mtpp) REVERT: d 281 ARG cc_start: 0.8092 (ptp90) cc_final: 0.7453 (mpt180) REVERT: d 308 THR cc_start: 0.8780 (m) cc_final: 0.8448 (p) REVERT: e 58 SER cc_start: 0.8288 (t) cc_final: 0.7911 (m) REVERT: e 85 GLN cc_start: 0.8457 (mt0) cc_final: 0.8244 (mt0) REVERT: f 17 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8013 (mm-30) REVERT: g 98 GLN cc_start: 0.9029 (mp10) cc_final: 0.8772 (mp10) REVERT: h 17 ARG cc_start: 0.8104 (mmm-85) cc_final: 0.7755 (tpp-160) REVERT: h 60 ARG cc_start: 0.9319 (OUTLIER) cc_final: 0.7747 (mpp80) REVERT: i 9 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.7254 (mtp85) REVERT: i 68 MET cc_start: 0.9187 (ttt) cc_final: 0.8877 (ttt) REVERT: j 8 LEU cc_start: 0.8396 (tt) cc_final: 0.7697 (mt) REVERT: k 96 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8616 (tt) REVERT: l 82 ARG cc_start: 0.8550 (tmm-80) cc_final: 0.8111 (ttp-170) REVERT: m 43 MET cc_start: 0.8905 (mtp) cc_final: 0.8693 (mtm) REVERT: n 21 TRP cc_start: 0.7501 (m100) cc_final: 0.7023 (m100) REVERT: n 72 TRP cc_start: 0.7457 (m100) cc_final: 0.7096 (m-90) REVERT: n 85 TYR cc_start: 0.7331 (OUTLIER) cc_final: 0.6818 (t80) REVERT: v 7 ASP cc_start: 0.7521 (p0) cc_final: 0.6780 (t0) REVERT: v 50 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7933 (mp) REVERT: v 103 LYS cc_start: 0.7384 (mttt) cc_final: 0.6892 (mmtm) REVERT: v 105 LEU cc_start: 0.7612 (tp) cc_final: 0.7324 (tp) REVERT: y 8 ARG cc_start: 0.6883 (tpm170) cc_final: 0.5659 (mmm160) outliers start: 209 outliers final: 66 residues processed: 1306 average time/residue: 1.4968 time to fit residues: 2552.8789 Evaluate side-chains 1133 residues out of total 7132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 1050 time to evaluate : 5.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 314 THR Chi-restraints excluded: chain 2 residue 114 ASP Chi-restraints excluded: chain 3 residue 367 THR Chi-restraints excluded: chain 3 residue 537 LEU Chi-restraints excluded: chain 4 residue 66 MET Chi-restraints excluded: chain 6 residue 85 VAL Chi-restraints excluded: chain 6 residue 137 ASP Chi-restraints excluded: chain 9 residue 78 ILE Chi-restraints excluded: chain 9 residue 140 SER Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain H residue 72 ILE Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain J residue 133 SER Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 24 SER Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain L residue 424 THR Chi-restraints excluded: chain L residue 440 LEU Chi-restraints excluded: chain L residue 559 GLU Chi-restraints excluded: chain M residue 58 SER Chi-restraints excluded: chain M residue 201 MET Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain M residue 296 LEU Chi-restraints excluded: chain M residue 410 MET Chi-restraints excluded: chain M residue 454 ILE Chi-restraints excluded: chain N residue 8 ILE Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain V residue 39 SER Chi-restraints excluded: chain V residue 88 ASN Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain W residue 62 GLU Chi-restraints excluded: chain W residue 81 ASP Chi-restraints excluded: chain W residue 115 ARG Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain X residue 69 LYS Chi-restraints excluded: chain a residue 48 THR Chi-restraints excluded: chain b residue 4 THR Chi-restraints excluded: chain b residue 19 ASP Chi-restraints excluded: chain b residue 52 VAL Chi-restraints excluded: chain c residue 28 GLU Chi-restraints excluded: chain c residue 31 LYS Chi-restraints excluded: chain c residue 110 VAL Chi-restraints excluded: chain e residue 18 ILE Chi-restraints excluded: chain e residue 95 SER Chi-restraints excluded: chain f residue 17 GLU Chi-restraints excluded: chain f residue 18 THR Chi-restraints excluded: chain g residue 15 SER Chi-restraints excluded: chain g residue 28 LYS Chi-restraints excluded: chain h residue 60 ARG Chi-restraints excluded: chain i residue 9 ARG Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain k residue 96 LEU Chi-restraints excluded: chain k residue 218 CYS Chi-restraints excluded: chain m residue 42 LEU Chi-restraints excluded: chain n residue 60 VAL Chi-restraints excluded: chain n residue 85 TYR Chi-restraints excluded: chain o residue 3 THR Chi-restraints excluded: chain o residue 67 SER Chi-restraints excluded: chain p residue 87 LEU Chi-restraints excluded: chain q residue 133 LEU Chi-restraints excluded: chain r residue 11 LEU Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain r residue 76 ILE Chi-restraints excluded: chain r residue 90 THR Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain r residue 110 LEU Chi-restraints excluded: chain s residue 41 THR Chi-restraints excluded: chain t residue 15 VAL Chi-restraints excluded: chain t residue 27 GLU Chi-restraints excluded: chain t residue 84 SER Chi-restraints excluded: chain v residue 6 LYS Chi-restraints excluded: chain v residue 18 GLU Chi-restraints excluded: chain v residue 31 VAL Chi-restraints excluded: chain v residue 50 LEU Chi-restraints excluded: chain w residue 59 ARG Chi-restraints excluded: chain w residue 74 SER Chi-restraints excluded: chain x residue 40 LEU Chi-restraints excluded: chain x residue 45 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 794 random chunks: chunk 400 optimal weight: 5.9990 chunk 223 optimal weight: 10.0000 chunk 600 optimal weight: 9.9990 chunk 490 optimal weight: 9.9990 chunk 198 optimal weight: 9.9990 chunk 722 optimal weight: 20.0000 chunk 780 optimal weight: 20.0000 chunk 643 optimal weight: 30.0000 chunk 716 optimal weight: 9.9990 chunk 246 optimal weight: 6.9990 chunk 579 optimal weight: 3.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 326 GLN ** 1 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 74 GLN 2 99 HIS 2 101 GLN ** 3 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 277 GLN 3 402 ASN 3 459 GLN ** 3 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 54 GLN ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 28 ASN H 235 ASN H 317 GLN K 7 ASN K 83 ASN L 136 ASN L 175 ASN L 446 ASN M 139 GLN ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 235 ASN ** Z 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 129 GLN ** Z 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 61 GLN f 95 GLN g 50 GLN g 69 ASN h 50 ASN ** k 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 59 ASN o 61 GLN p 49 GLN ** s 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 24 GLN w 57 ASN x 5 GLN ** y 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 68 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.305 69131 Z= 0.597 Angle : 1.594 51.114 93426 Z= 1.023 Chirality : 0.312 6.621 10118 Planarity : 0.005 0.057 11647 Dihedral : 12.937 173.142 10579 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.36 % Favored : 96.62 % Rotamer: Outliers : 3.74 % Allowed : 13.28 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.09), residues: 8046 helix: 0.28 (0.08), residues: 4289 sheet: -0.75 (0.26), residues: 395 loop : -0.93 (0.11), residues: 3362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP 1 371 HIS 0.023 0.002 HIS 9 65 PHE 0.030 0.002 PHE N 292 TYR 0.030 0.002 TYR H 215 ARG 0.008 0.001 ARG m 46 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16092 Ramachandran restraints generated. 8046 Oldfield, 0 Emsley, 8046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16092 Ramachandran restraints generated. 8046 Oldfield, 0 Emsley, 8046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1369 residues out of total 7132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 267 poor density : 1102 time to evaluate : 5.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 14 LYS cc_start: 0.9189 (mppt) cc_final: 0.8805 (mmmm) REVERT: 2 118 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.8003 (tm-30) REVERT: 3 283 MET cc_start: 0.9254 (OUTLIER) cc_final: 0.9019 (mtt) REVERT: 3 447 LYS cc_start: 0.9058 (mttm) cc_final: 0.8690 (mmpt) REVERT: 3 654 GLN cc_start: 0.7640 (OUTLIER) cc_final: 0.7038 (tm-30) REVERT: 3 673 MET cc_start: 0.9040 (OUTLIER) cc_final: 0.8613 (mtm) REVERT: 5 14 ARG cc_start: 0.8278 (ttt90) cc_final: 0.7874 (ttm110) REVERT: 6 25 ARG cc_start: 0.5561 (ttt180) cc_final: 0.4763 (mmp-170) REVERT: 6 62 MET cc_start: 0.9161 (tmm) cc_final: 0.8955 (ttp) REVERT: 6 79 SER cc_start: 0.8671 (OUTLIER) cc_final: 0.8356 (p) REVERT: 6 107 MET cc_start: 0.9098 (OUTLIER) cc_final: 0.8882 (mtp) REVERT: 9 78 ILE cc_start: 0.9307 (OUTLIER) cc_final: 0.8934 (pp) REVERT: A 23 TRP cc_start: 0.6992 (m100) cc_final: 0.6435 (t60) REVERT: J 74 MET cc_start: 0.8721 (mtm) cc_final: 0.8424 (mtm) REVERT: K 9 MET cc_start: 0.8910 (OUTLIER) cc_final: 0.8515 (mpp) REVERT: K 85 TYR cc_start: 0.8588 (m-80) cc_final: 0.8292 (m-80) REVERT: L 440 LEU cc_start: 0.7439 (OUTLIER) cc_final: 0.7139 (tt) REVERT: L 559 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7132 (tp30) REVERT: L 573 MET cc_start: 0.7072 (mmt) cc_final: 0.6849 (mmm) REVERT: L 592 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8002 (pp) REVERT: M 166 TYR cc_start: 0.8659 (t80) cc_final: 0.7890 (t80) REVERT: M 454 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8495 (pp) REVERT: N 200 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.8526 (mpm) REVERT: N 282 MET cc_start: 0.8664 (mtm) cc_final: 0.8406 (mtp) REVERT: V 73 SER cc_start: 0.5975 (m) cc_final: 0.5711 (p) REVERT: V 117 MET cc_start: 0.6442 (mtp) cc_final: 0.5942 (tpt) REVERT: V 133 LYS cc_start: 0.7788 (OUTLIER) cc_final: 0.7010 (mmtm) REVERT: W 62 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7429 (mm-30) REVERT: Y 120 ASP cc_start: 0.8477 (m-30) cc_final: 0.8148 (m-30) REVERT: c 18 ASP cc_start: 0.8802 (t70) cc_final: 0.8580 (t70) REVERT: c 28 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8473 (tm-30) REVERT: c 31 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8501 (mtpp) REVERT: d 32 ARG cc_start: 0.9015 (OUTLIER) cc_final: 0.8046 (ttm170) REVERT: d 281 ARG cc_start: 0.8118 (ptp90) cc_final: 0.7635 (mpt180) REVERT: e 39 ARG cc_start: 0.7962 (mtt180) cc_final: 0.7637 (ttm110) REVERT: e 58 SER cc_start: 0.8428 (t) cc_final: 0.7988 (m) REVERT: e 85 GLN cc_start: 0.8475 (mt0) cc_final: 0.8271 (mt0) REVERT: e 90 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8530 (tt) REVERT: e 93 VAL cc_start: 0.8870 (t) cc_final: 0.8650 (t) REVERT: f 17 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7977 (mm-30) REVERT: h 17 ARG cc_start: 0.8226 (mmm-85) cc_final: 0.7789 (tpp-160) REVERT: i 9 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.7161 (mtp85) REVERT: j 8 LEU cc_start: 0.8306 (tt) cc_final: 0.7646 (mp) REVERT: j 20 LYS cc_start: 0.8398 (pttm) cc_final: 0.8085 (mppt) REVERT: k 18 MET cc_start: 0.7860 (tpp) cc_final: 0.7571 (tpt) REVERT: k 96 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8624 (tt) REVERT: n 18 TYR cc_start: 0.6554 (p90) cc_final: 0.6193 (p90) REVERT: n 72 TRP cc_start: 0.7476 (m100) cc_final: 0.7090 (m-90) REVERT: n 85 TYR cc_start: 0.7265 (OUTLIER) cc_final: 0.6830 (t80) REVERT: p 74 ASN cc_start: 0.8457 (t0) cc_final: 0.8064 (t160) REVERT: r 116 ILE cc_start: 0.8256 (mp) cc_final: 0.8031 (mp) REVERT: t 130 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7440 (mp0) REVERT: v 50 LEU cc_start: 0.8335 (mt) cc_final: 0.8049 (mp) REVERT: v 101 MET cc_start: 0.7719 (mtm) cc_final: 0.7487 (mtm) REVERT: v 103 LYS cc_start: 0.7348 (mttt) cc_final: 0.6875 (mmtt) REVERT: v 105 LEU cc_start: 0.7604 (tp) cc_final: 0.7330 (tp) REVERT: v 157 GLU cc_start: 0.7470 (mt-10) cc_final: 0.6884 (tt0) REVERT: w 82 ASP cc_start: 0.8786 (t70) cc_final: 0.8496 (t0) REVERT: y 8 ARG cc_start: 0.6871 (tpm170) cc_final: 0.5770 (mmm160) outliers start: 267 outliers final: 103 residues processed: 1250 average time/residue: 1.4801 time to fit residues: 2438.9467 Evaluate side-chains 1144 residues out of total 7132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 1017 time to evaluate : 5.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 314 THR Chi-restraints excluded: chain 2 residue 114 ASP Chi-restraints excluded: chain 2 residue 118 GLU Chi-restraints excluded: chain 3 residue 283 MET Chi-restraints excluded: chain 3 residue 367 THR Chi-restraints excluded: chain 3 residue 537 LEU Chi-restraints excluded: chain 3 residue 654 GLN Chi-restraints excluded: chain 3 residue 673 MET Chi-restraints excluded: chain 4 residue 49 LEU Chi-restraints excluded: chain 4 residue 66 MET Chi-restraints excluded: chain 6 residue 50 PHE Chi-restraints excluded: chain 6 residue 79 SER Chi-restraints excluded: chain 6 residue 84 ASP Chi-restraints excluded: chain 6 residue 85 VAL Chi-restraints excluded: chain 6 residue 107 MET Chi-restraints excluded: chain 6 residue 137 ASP Chi-restraints excluded: chain 9 residue 11 SER Chi-restraints excluded: chain 9 residue 78 ILE Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain 9 residue 140 SER Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain H residue 66 SER Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain H residue 215 TYR Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain J residue 133 SER Chi-restraints excluded: chain K residue 9 MET Chi-restraints excluded: chain K residue 24 SER Chi-restraints excluded: chain K residue 39 SER Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain L residue 53 MET Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 105 MET Chi-restraints excluded: chain L residue 250 SER Chi-restraints excluded: chain L residue 424 THR Chi-restraints excluded: chain L residue 440 LEU Chi-restraints excluded: chain L residue 543 THR Chi-restraints excluded: chain L residue 544 MET Chi-restraints excluded: chain L residue 559 GLU Chi-restraints excluded: chain L residue 592 LEU Chi-restraints excluded: chain L residue 594 THR Chi-restraints excluded: chain M residue 36 LEU Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 58 SER Chi-restraints excluded: chain M residue 204 MET Chi-restraints excluded: chain M residue 207 MET Chi-restraints excluded: chain M residue 308 SER Chi-restraints excluded: chain M residue 365 THR Chi-restraints excluded: chain M residue 454 ILE Chi-restraints excluded: chain N residue 45 MET Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 200 MET Chi-restraints excluded: chain N residue 281 LEU Chi-restraints excluded: chain N residue 284 ILE Chi-restraints excluded: chain N residue 329 MET Chi-restraints excluded: chain V residue 39 SER Chi-restraints excluded: chain V residue 49 LEU Chi-restraints excluded: chain V residue 88 ASN Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain V residue 126 MET Chi-restraints excluded: chain V residue 133 LYS Chi-restraints excluded: chain W residue 62 GLU Chi-restraints excluded: chain W residue 81 ASP Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain Z residue 8 VAL Chi-restraints excluded: chain a residue 48 THR Chi-restraints excluded: chain b residue 4 THR Chi-restraints excluded: chain b residue 19 ASP Chi-restraints excluded: chain b residue 52 VAL Chi-restraints excluded: chain c residue 28 GLU Chi-restraints excluded: chain c residue 31 LYS Chi-restraints excluded: chain c residue 44 ASN Chi-restraints excluded: chain c residue 110 VAL Chi-restraints excluded: chain d residue 32 ARG Chi-restraints excluded: chain e residue 56 GLU Chi-restraints excluded: chain e residue 86 VAL Chi-restraints excluded: chain e residue 90 LEU Chi-restraints excluded: chain e residue 95 SER Chi-restraints excluded: chain f residue 17 GLU Chi-restraints excluded: chain f residue 18 THR Chi-restraints excluded: chain g residue 15 SER Chi-restraints excluded: chain g residue 28 LYS Chi-restraints excluded: chain g residue 118 LEU Chi-restraints excluded: chain h residue 15 SER Chi-restraints excluded: chain h residue 60 ARG Chi-restraints excluded: chain i residue 9 ARG Chi-restraints excluded: chain j residue 86 VAL Chi-restraints excluded: chain k residue 24 LEU Chi-restraints excluded: chain k residue 96 LEU Chi-restraints excluded: chain k residue 118 THR Chi-restraints excluded: chain k residue 218 CYS Chi-restraints excluded: chain m residue 42 LEU Chi-restraints excluded: chain n residue 60 VAL Chi-restraints excluded: chain n residue 81 VAL Chi-restraints excluded: chain n residue 85 TYR Chi-restraints excluded: chain o residue 3 THR Chi-restraints excluded: chain o residue 67 SER Chi-restraints excluded: chain p residue 40 SER Chi-restraints excluded: chain p residue 87 LEU Chi-restraints excluded: chain q residue 133 LEU Chi-restraints excluded: chain r residue 11 LEU Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain r residue 76 ILE Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain r residue 110 LEU Chi-restraints excluded: chain s residue 23 THR Chi-restraints excluded: chain s residue 41 THR Chi-restraints excluded: chain t residue 15 VAL Chi-restraints excluded: chain t residue 27 GLU Chi-restraints excluded: chain t residue 84 SER Chi-restraints excluded: chain t residue 130 GLU Chi-restraints excluded: chain v residue 6 LYS Chi-restraints excluded: chain v residue 18 GLU Chi-restraints excluded: chain v residue 31 VAL Chi-restraints excluded: chain w residue 59 ARG Chi-restraints excluded: chain w residue 74 SER Chi-restraints excluded: chain x residue 5 GLN Chi-restraints excluded: chain x residue 15 LEU Chi-restraints excluded: chain x residue 40 LEU Chi-restraints excluded: chain x residue 45 ARG Chi-restraints excluded: chain y residue 9 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 794 random chunks: chunk 713 optimal weight: 20.0000 chunk 543 optimal weight: 10.0000 chunk 374 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 344 optimal weight: 10.0000 chunk 485 optimal weight: 4.9990 chunk 724 optimal weight: 0.9980 chunk 767 optimal weight: 9.9990 chunk 378 optimal weight: 5.9990 chunk 687 optimal weight: 10.0000 chunk 206 optimal weight: 9.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 402 ASN 3 517 ASN ** 3 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 144 HIS A 85 ASN H 212 ASN H 317 GLN K 83 ASN K 97 GLN ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 235 ASN Z 90 GLN ** Z 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 50 GLN i 123 GLN ** k 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 44 HIS ** n 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 30 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.284 69131 Z= 0.541 Angle : 1.570 51.007 93426 Z= 1.014 Chirality : 0.311 6.523 10118 Planarity : 0.004 0.051 11647 Dihedral : 12.567 174.153 10579 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.04 % Favored : 96.93 % Rotamer: Outliers : 3.44 % Allowed : 14.85 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.09), residues: 8046 helix: 0.61 (0.08), residues: 4281 sheet: -0.63 (0.26), residues: 395 loop : -0.73 (0.11), residues: 3370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP L 144 HIS 0.021 0.001 HIS 9 65 PHE 0.030 0.002 PHE N 292 TYR 0.029 0.002 TYR H 215 ARG 0.011 0.000 ARG n 51 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16092 Ramachandran restraints generated. 8046 Oldfield, 0 Emsley, 8046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16092 Ramachandran restraints generated. 8046 Oldfield, 0 Emsley, 8046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1349 residues out of total 7132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 245 poor density : 1104 time to evaluate : 5.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 127 ARG cc_start: 0.8449 (tpt90) cc_final: 0.8221 (tpt90) REVERT: 1 390 ASP cc_start: 0.8635 (m-30) cc_final: 0.8394 (m-30) REVERT: 2 14 LYS cc_start: 0.9199 (mppt) cc_final: 0.8810 (mmmm) REVERT: 2 127 LYS cc_start: 0.8574 (ptpt) cc_final: 0.8276 (ptmt) REVERT: 3 31 GLU cc_start: 0.8589 (tt0) cc_final: 0.8198 (tp30) REVERT: 3 447 LYS cc_start: 0.9060 (mttm) cc_final: 0.8690 (mmpt) REVERT: 3 654 GLN cc_start: 0.7598 (OUTLIER) cc_final: 0.6994 (tm-30) REVERT: 4 66 MET cc_start: 0.9100 (OUTLIER) cc_final: 0.8863 (mmt) REVERT: 5 14 ARG cc_start: 0.8262 (ttt90) cc_final: 0.7851 (ttm110) REVERT: 6 25 ARG cc_start: 0.5575 (ttt180) cc_final: 0.4896 (mmp-170) REVERT: 6 174 ARG cc_start: 0.9040 (mtm180) cc_final: 0.8813 (mtm180) REVERT: 9 78 ILE cc_start: 0.9299 (OUTLIER) cc_final: 0.8893 (pp) REVERT: A 23 TRP cc_start: 0.6969 (m100) cc_final: 0.6361 (t60) REVERT: J 74 MET cc_start: 0.8673 (mtm) cc_final: 0.8368 (mtm) REVERT: J 99 MET cc_start: 0.6914 (tmm) cc_final: 0.6705 (tmm) REVERT: K 9 MET cc_start: 0.8881 (OUTLIER) cc_final: 0.8506 (mpp) REVERT: K 85 TYR cc_start: 0.8568 (m-80) cc_final: 0.8356 (m-80) REVERT: L 592 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.7746 (pp) REVERT: L 597 ILE cc_start: 0.6716 (OUTLIER) cc_final: 0.6254 (tp) REVERT: M 166 TYR cc_start: 0.8600 (t80) cc_final: 0.7817 (t80) REVERT: M 454 ILE cc_start: 0.8784 (OUTLIER) cc_final: 0.8450 (pp) REVERT: N 200 MET cc_start: 0.8714 (OUTLIER) cc_final: 0.8465 (mpm) REVERT: N 282 MET cc_start: 0.8665 (mtm) cc_final: 0.8440 (mtp) REVERT: V 73 SER cc_start: 0.5950 (m) cc_final: 0.5719 (p) REVERT: V 117 MET cc_start: 0.6394 (mtp) cc_final: 0.6050 (tpt) REVERT: V 133 LYS cc_start: 0.7731 (OUTLIER) cc_final: 0.6947 (mmtm) REVERT: W 62 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7428 (mm-30) REVERT: Y 120 ASP cc_start: 0.8391 (m-30) cc_final: 0.8039 (m-30) REVERT: Z 162 MET cc_start: 0.8805 (mtt) cc_final: 0.8538 (mtt) REVERT: c 18 ASP cc_start: 0.8801 (t70) cc_final: 0.8579 (t70) REVERT: c 28 GLU cc_start: 0.8710 (tm-30) cc_final: 0.8490 (tm-30) REVERT: c 31 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8419 (mtpp) REVERT: d 224 ARG cc_start: 0.8612 (mtm-85) cc_final: 0.8146 (mmp80) REVERT: d 281 ARG cc_start: 0.8048 (ptp90) cc_final: 0.7633 (mpt180) REVERT: e 39 ARG cc_start: 0.7939 (mtt180) cc_final: 0.7648 (ttm110) REVERT: e 58 SER cc_start: 0.8427 (t) cc_final: 0.7970 (m) REVERT: e 93 VAL cc_start: 0.8793 (t) cc_final: 0.8567 (t) REVERT: f 17 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7986 (mm-30) REVERT: f 32 ASP cc_start: 0.8230 (OUTLIER) cc_final: 0.7878 (m-30) REVERT: h 17 ARG cc_start: 0.8235 (mmm-85) cc_final: 0.7951 (tpp-160) REVERT: h 60 ARG cc_start: 0.9296 (OUTLIER) cc_final: 0.7756 (mpp80) REVERT: i 9 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.7131 (mtp85) REVERT: k 18 MET cc_start: 0.7870 (tpp) cc_final: 0.7594 (tpt) REVERT: k 96 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8627 (tt) REVERT: k 214 MET cc_start: 0.8315 (tpp) cc_final: 0.7881 (tpp) REVERT: l 82 ARG cc_start: 0.8526 (tmm-80) cc_final: 0.8077 (ttp-170) REVERT: n 18 TYR cc_start: 0.6554 (p90) cc_final: 0.5982 (p90) REVERT: n 72 TRP cc_start: 0.7494 (m100) cc_final: 0.7065 (m-90) REVERT: n 85 TYR cc_start: 0.7294 (OUTLIER) cc_final: 0.6838 (t80) REVERT: o 50 ARG cc_start: 0.7652 (mtp-110) cc_final: 0.7252 (mtt180) REVERT: p 74 ASN cc_start: 0.8431 (t0) cc_final: 0.8085 (t160) REVERT: r 116 ILE cc_start: 0.8213 (mp) cc_final: 0.8004 (mp) REVERT: u 62 GLU cc_start: 0.7199 (pm20) cc_final: 0.6987 (pm20) REVERT: v 50 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7938 (mp) REVERT: v 103 LYS cc_start: 0.7326 (mttt) cc_final: 0.6843 (mmtt) REVERT: v 105 LEU cc_start: 0.7589 (tp) cc_final: 0.7332 (tp) REVERT: w 40 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8565 (mtpp) REVERT: w 82 ASP cc_start: 0.8765 (t70) cc_final: 0.8449 (t0) REVERT: y 8 ARG cc_start: 0.6793 (tpm170) cc_final: 0.5700 (mmm160) outliers start: 245 outliers final: 103 residues processed: 1249 average time/residue: 1.4446 time to fit residues: 2377.4569 Evaluate side-chains 1148 residues out of total 7132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 1026 time to evaluate : 5.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 314 THR Chi-restraints excluded: chain 2 residue 114 ASP Chi-restraints excluded: chain 3 residue 115 ASP Chi-restraints excluded: chain 3 residue 367 THR Chi-restraints excluded: chain 3 residue 517 ASN Chi-restraints excluded: chain 3 residue 537 LEU Chi-restraints excluded: chain 3 residue 654 GLN Chi-restraints excluded: chain 4 residue 49 LEU Chi-restraints excluded: chain 4 residue 66 MET Chi-restraints excluded: chain 4 residue 114 ASN Chi-restraints excluded: chain 6 residue 50 PHE Chi-restraints excluded: chain 6 residue 85 VAL Chi-restraints excluded: chain 6 residue 137 ASP Chi-restraints excluded: chain 9 residue 1 THR Chi-restraints excluded: chain 9 residue 78 ILE Chi-restraints excluded: chain 9 residue 84 GLU Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain 9 residue 140 SER Chi-restraints excluded: chain 9 residue 143 THR Chi-restraints excluded: chain H residue 66 SER Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain J residue 133 SER Chi-restraints excluded: chain K residue 9 MET Chi-restraints excluded: chain K residue 24 SER Chi-restraints excluded: chain K residue 39 SER Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain L residue 53 MET Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 151 SER Chi-restraints excluded: chain L residue 250 SER Chi-restraints excluded: chain L residue 424 THR Chi-restraints excluded: chain L residue 543 THR Chi-restraints excluded: chain L residue 544 MET Chi-restraints excluded: chain L residue 592 LEU Chi-restraints excluded: chain L residue 597 ILE Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 58 SER Chi-restraints excluded: chain M residue 296 LEU Chi-restraints excluded: chain M residue 365 THR Chi-restraints excluded: chain M residue 414 THR Chi-restraints excluded: chain M residue 454 ILE Chi-restraints excluded: chain N residue 14 MET Chi-restraints excluded: chain N residue 45 MET Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 200 MET Chi-restraints excluded: chain N residue 201 THR Chi-restraints excluded: chain N residue 284 ILE Chi-restraints excluded: chain N residue 320 THR Chi-restraints excluded: chain N residue 329 MET Chi-restraints excluded: chain V residue 39 SER Chi-restraints excluded: chain V residue 49 LEU Chi-restraints excluded: chain V residue 88 ASN Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain V residue 126 MET Chi-restraints excluded: chain V residue 133 LYS Chi-restraints excluded: chain W residue 62 GLU Chi-restraints excluded: chain W residue 81 ASP Chi-restraints excluded: chain W residue 115 ARG Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain Y residue 171 MET Chi-restraints excluded: chain Z residue 8 VAL Chi-restraints excluded: chain b residue 4 THR Chi-restraints excluded: chain b residue 19 ASP Chi-restraints excluded: chain b residue 52 VAL Chi-restraints excluded: chain c residue 31 LYS Chi-restraints excluded: chain c residue 110 VAL Chi-restraints excluded: chain d residue 170 ASP Chi-restraints excluded: chain e residue 95 SER Chi-restraints excluded: chain f residue 17 GLU Chi-restraints excluded: chain f residue 18 THR Chi-restraints excluded: chain f residue 32 ASP Chi-restraints excluded: chain g residue 15 SER Chi-restraints excluded: chain g residue 28 LYS Chi-restraints excluded: chain g residue 44 ASN Chi-restraints excluded: chain g residue 118 LEU Chi-restraints excluded: chain h residue 15 SER Chi-restraints excluded: chain h residue 60 ARG Chi-restraints excluded: chain i residue 9 ARG Chi-restraints excluded: chain j residue 7 THR Chi-restraints excluded: chain j residue 11 ILE Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain k residue 24 LEU Chi-restraints excluded: chain k residue 96 LEU Chi-restraints excluded: chain k residue 218 CYS Chi-restraints excluded: chain k residue 222 GLN Chi-restraints excluded: chain m residue 42 LEU Chi-restraints excluded: chain n residue 60 VAL Chi-restraints excluded: chain n residue 85 TYR Chi-restraints excluded: chain o residue 3 THR Chi-restraints excluded: chain o residue 67 SER Chi-restraints excluded: chain p residue 87 LEU Chi-restraints excluded: chain q residue 133 LEU Chi-restraints excluded: chain r residue 11 LEU Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain r residue 76 ILE Chi-restraints excluded: chain r residue 90 THR Chi-restraints excluded: chain r residue 102 ARG Chi-restraints excluded: chain r residue 110 LEU Chi-restraints excluded: chain s residue 14 VAL Chi-restraints excluded: chain s residue 23 THR Chi-restraints excluded: chain s residue 41 THR Chi-restraints excluded: chain t residue 27 GLU Chi-restraints excluded: chain t residue 84 SER Chi-restraints excluded: chain v residue 18 GLU Chi-restraints excluded: chain v residue 31 VAL Chi-restraints excluded: chain v residue 50 LEU Chi-restraints excluded: chain v residue 120 GLU Chi-restraints excluded: chain v residue 145 ASP Chi-restraints excluded: chain w residue 40 LYS Chi-restraints excluded: chain w residue 59 ARG Chi-restraints excluded: chain x residue 40 LEU Chi-restraints excluded: chain y residue 9 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 794 random chunks: chunk 639 optimal weight: 20.0000 chunk 435 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 571 optimal weight: 0.2980 chunk 316 optimal weight: 2.9990 chunk 654 optimal weight: 5.9990 chunk 530 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 391 optimal weight: 7.9990 chunk 688 optimal weight: 6.9990 chunk 193 optimal weight: 0.0770 overall best weight: 3.2744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 ASN H 317 GLN K 97 GLN ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 235 ASN Z 22 GLN ** Z 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 92 ASN g 50 GLN ** k 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 68 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.283 69131 Z= 0.527 Angle : 1.563 51.031 93426 Z= 1.011 Chirality : 0.310 6.517 10118 Planarity : 0.004 0.049 11647 Dihedral : 12.248 179.595 10579 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.18 % Favored : 96.79 % Rotamer: Outliers : 3.25 % Allowed : 15.73 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.09), residues: 8046 helix: 0.82 (0.08), residues: 4270 sheet: -0.47 (0.26), residues: 388 loop : -0.59 (0.11), residues: 3388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP Y 85 HIS 0.021 0.001 HIS 9 65 PHE 0.030 0.001 PHE N 292 TYR 0.026 0.001 TYR H 215 ARG 0.010 0.000 ARG n 51 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16092 Ramachandran restraints generated. 8046 Oldfield, 0 Emsley, 8046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16092 Ramachandran restraints generated. 8046 Oldfield, 0 Emsley, 8046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1325 residues out of total 7132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 1093 time to evaluate : 6.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 390 ASP cc_start: 0.8602 (m-30) cc_final: 0.8349 (m-30) REVERT: 1 428 GLU cc_start: 0.8608 (pp20) cc_final: 0.8365 (tm-30) REVERT: 2 14 LYS cc_start: 0.9213 (mppt) cc_final: 0.8826 (mmmm) REVERT: 2 127 LYS cc_start: 0.8530 (ptpt) cc_final: 0.8247 (ptmt) REVERT: 3 31 GLU cc_start: 0.8564 (tt0) cc_final: 0.8169 (tp30) REVERT: 3 447 LYS cc_start: 0.9061 (mttm) cc_final: 0.8691 (mmpt) REVERT: 3 654 GLN cc_start: 0.7590 (OUTLIER) cc_final: 0.6995 (tm-30) REVERT: 3 673 MET cc_start: 0.9008 (OUTLIER) cc_final: 0.8634 (mtm) REVERT: 4 66 MET cc_start: 0.9105 (OUTLIER) cc_final: 0.8868 (mmt) REVERT: 4 282 GLU cc_start: 0.8697 (tt0) cc_final: 0.8450 (tp30) REVERT: 5 14 ARG cc_start: 0.8285 (ttt90) cc_final: 0.7855 (ttm110) REVERT: 6 25 ARG cc_start: 0.5621 (ttt180) cc_final: 0.4939 (mmp-170) REVERT: 6 70 ASP cc_start: 0.8891 (OUTLIER) cc_final: 0.8681 (t70) REVERT: 9 78 ILE cc_start: 0.9284 (OUTLIER) cc_final: 0.8872 (pp) REVERT: A 23 TRP cc_start: 0.7001 (m100) cc_final: 0.6369 (t60) REVERT: J 74 MET cc_start: 0.8622 (mtm) cc_final: 0.8358 (mtm) REVERT: K 58 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.8256 (ptt) REVERT: L 559 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7127 (tm-30) REVERT: L 573 MET cc_start: 0.7205 (mmt) cc_final: 0.6901 (mmm) REVERT: L 592 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.7758 (pp) REVERT: M 166 TYR cc_start: 0.8557 (t80) cc_final: 0.7809 (t80) REVERT: M 454 ILE cc_start: 0.8751 (OUTLIER) cc_final: 0.8497 (pp) REVERT: N 200 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.8450 (mpm) REVERT: N 282 MET cc_start: 0.8635 (mtm) cc_final: 0.8428 (mtp) REVERT: V 117 MET cc_start: 0.6443 (mtp) cc_final: 0.6069 (tpt) REVERT: W 62 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7440 (mm-30) REVERT: X 30 LEU cc_start: 0.5169 (pp) cc_final: 0.4872 (mm) REVERT: X 57 GLU cc_start: 0.7615 (tp30) cc_final: 0.7106 (tm-30) REVERT: Y 120 ASP cc_start: 0.8432 (m-30) cc_final: 0.8074 (m-30) REVERT: a 63 MET cc_start: 0.8370 (mmp) cc_final: 0.8041 (mmm) REVERT: c 18 ASP cc_start: 0.8804 (t70) cc_final: 0.8586 (t70) REVERT: c 28 GLU cc_start: 0.8674 (tm-30) cc_final: 0.8466 (tm-30) REVERT: c 31 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8360 (mtpp) REVERT: d 224 ARG cc_start: 0.8608 (mtm-85) cc_final: 0.8144 (mmp80) REVERT: d 281 ARG cc_start: 0.8097 (ptp90) cc_final: 0.7674 (mpt180) REVERT: e 39 ARG cc_start: 0.7925 (mtt180) cc_final: 0.7629 (ttm110) REVERT: e 58 SER cc_start: 0.8398 (t) cc_final: 0.7960 (m) REVERT: e 93 VAL cc_start: 0.8754 (t) cc_final: 0.8520 (t) REVERT: f 17 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7967 (mm-30) REVERT: f 32 ASP cc_start: 0.8256 (OUTLIER) cc_final: 0.7955 (m-30) REVERT: h 17 ARG cc_start: 0.8217 (mmm-85) cc_final: 0.7894 (tpp-160) REVERT: h 60 ARG cc_start: 0.9313 (OUTLIER) cc_final: 0.7829 (mpp80) REVERT: i 9 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.7128 (mtp85) REVERT: k 96 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8633 (tt) REVERT: k 214 MET cc_start: 0.8354 (tpp) cc_final: 0.8030 (tpp) REVERT: l 82 ARG cc_start: 0.8507 (tmm-80) cc_final: 0.8045 (ttp-170) REVERT: l 101 GLU cc_start: 0.6874 (OUTLIER) cc_final: 0.6596 (tp30) REVERT: n 67 LEU cc_start: 0.8619 (mm) cc_final: 0.8084 (tm) REVERT: n 72 TRP cc_start: 0.7478 (m100) cc_final: 0.7033 (m-90) REVERT: n 85 TYR cc_start: 0.7327 (OUTLIER) cc_final: 0.6822 (t80) REVERT: o 50 ARG cc_start: 0.7668 (mtp-110) cc_final: 0.7249 (mtt180) REVERT: p 74 ASN cc_start: 0.8411 (t0) cc_final: 0.8187 (t160) REVERT: r 116 ILE cc_start: 0.8257 (mp) cc_final: 0.8027 (mp) REVERT: u 16 GLN cc_start: 0.7366 (tp40) cc_final: 0.7013 (tt0) REVERT: u 61 ASP cc_start: 0.7773 (m-30) cc_final: 0.7462 (t70) REVERT: v 42 MET cc_start: 0.8414 (mmm) cc_final: 0.8190 (tpp) REVERT: v 50 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7769 (mp) REVERT: v 103 LYS cc_start: 0.7315 (mttt) cc_final: 0.6831 (mmtm) REVERT: v 105 LEU cc_start: 0.7585 (tp) cc_final: 0.7339 (tp) REVERT: w 82 ASP cc_start: 0.8679 (t0) cc_final: 0.8338 (t0) REVERT: x 33 LYS cc_start: 0.8083 (tttt) cc_final: 0.7497 (tttt) REVERT: y 8 ARG cc_start: 0.6770 (tpm170) cc_final: 0.5676 (mmm160) outliers start: 232 outliers final: 116 residues processed: 1233 average time/residue: 1.4151 time to fit residues: 2305.6290 Evaluate side-chains 1164 residues out of total 7132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 1028 time to evaluate : 5.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 314 THR Chi-restraints excluded: chain 1 residue 343 ILE Chi-restraints excluded: chain 1 residue 409 ASP Chi-restraints excluded: chain 2 residue 114 ASP Chi-restraints excluded: chain 3 residue 115 ASP Chi-restraints excluded: chain 3 residue 148 THR Chi-restraints excluded: chain 3 residue 367 THR Chi-restraints excluded: chain 3 residue 537 LEU Chi-restraints excluded: chain 3 residue 654 GLN Chi-restraints excluded: chain 3 residue 673 MET Chi-restraints excluded: chain 4 residue 49 LEU Chi-restraints excluded: chain 4 residue 66 MET Chi-restraints excluded: chain 5 residue 109 THR Chi-restraints excluded: chain 6 residue 50 PHE Chi-restraints excluded: chain 6 residue 70 ASP Chi-restraints excluded: chain 6 residue 85 VAL Chi-restraints excluded: chain 6 residue 137 ASP Chi-restraints excluded: chain 6 residue 175 ILE Chi-restraints excluded: chain 9 residue 1 THR Chi-restraints excluded: chain 9 residue 78 ILE Chi-restraints excluded: chain 9 residue 84 GLU Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain 9 residue 126 CYS Chi-restraints excluded: chain 9 residue 140 SER Chi-restraints excluded: chain 9 residue 143 THR Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain H residue 66 SER Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 118 LYS Chi-restraints excluded: chain J residue 133 SER Chi-restraints excluded: chain K residue 24 SER Chi-restraints excluded: chain K residue 57 SER Chi-restraints excluded: chain K residue 58 MET Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain L residue 53 MET Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 151 SER Chi-restraints excluded: chain L residue 250 SER Chi-restraints excluded: chain L residue 424 THR Chi-restraints excluded: chain L residue 543 THR Chi-restraints excluded: chain L residue 544 MET Chi-restraints excluded: chain L residue 559 GLU Chi-restraints excluded: chain L residue 592 LEU Chi-restraints excluded: chain L residue 594 THR Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 58 SER Chi-restraints excluded: chain M residue 86 LYS Chi-restraints excluded: chain M residue 296 LEU Chi-restraints excluded: chain M residue 308 SER Chi-restraints excluded: chain M residue 365 THR Chi-restraints excluded: chain M residue 410 MET Chi-restraints excluded: chain M residue 414 THR Chi-restraints excluded: chain M residue 454 ILE Chi-restraints excluded: chain M residue 458 LEU Chi-restraints excluded: chain N residue 14 MET Chi-restraints excluded: chain N residue 45 MET Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 200 MET Chi-restraints excluded: chain N residue 201 THR Chi-restraints excluded: chain N residue 284 ILE Chi-restraints excluded: chain N residue 320 THR Chi-restraints excluded: chain N residue 329 MET Chi-restraints excluded: chain V residue 49 LEU Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain V residue 126 MET Chi-restraints excluded: chain W residue 62 GLU Chi-restraints excluded: chain W residue 81 ASP Chi-restraints excluded: chain W residue 136 SER Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain Z residue 8 VAL Chi-restraints excluded: chain Z residue 39 LEU Chi-restraints excluded: chain b residue 4 THR Chi-restraints excluded: chain b residue 52 VAL Chi-restraints excluded: chain c residue 31 LYS Chi-restraints excluded: chain c residue 110 VAL Chi-restraints excluded: chain d residue 154 LYS Chi-restraints excluded: chain f residue 17 GLU Chi-restraints excluded: chain f residue 18 THR Chi-restraints excluded: chain f residue 32 ASP Chi-restraints excluded: chain g residue 15 SER Chi-restraints excluded: chain g residue 28 LYS Chi-restraints excluded: chain g residue 118 LEU Chi-restraints excluded: chain h residue 15 SER Chi-restraints excluded: chain h residue 60 ARG Chi-restraints excluded: chain i residue 9 ARG Chi-restraints excluded: chain i residue 96 ASP Chi-restraints excluded: chain j residue 7 THR Chi-restraints excluded: chain j residue 11 ILE Chi-restraints excluded: chain j residue 49 GLU Chi-restraints excluded: chain k residue 24 LEU Chi-restraints excluded: chain k residue 96 LEU Chi-restraints excluded: chain k residue 218 CYS Chi-restraints excluded: chain k residue 222 GLN Chi-restraints excluded: chain l residue 101 GLU Chi-restraints excluded: chain m residue 27 LEU Chi-restraints excluded: chain m residue 42 LEU Chi-restraints excluded: chain n residue 60 VAL Chi-restraints excluded: chain n residue 81 VAL Chi-restraints excluded: chain n residue 85 TYR Chi-restraints excluded: chain o residue 3 THR Chi-restraints excluded: chain o residue 55 SER Chi-restraints excluded: chain o residue 67 SER Chi-restraints excluded: chain p residue 87 LEU Chi-restraints excluded: chain q residue 133 LEU Chi-restraints excluded: chain r residue 11 LEU Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain r residue 76 ILE Chi-restraints excluded: chain r residue 90 THR Chi-restraints excluded: chain r residue 102 ARG Chi-restraints excluded: chain r residue 103 ILE Chi-restraints excluded: chain r residue 110 LEU Chi-restraints excluded: chain s residue 14 VAL Chi-restraints excluded: chain s residue 41 THR Chi-restraints excluded: chain t residue 27 GLU Chi-restraints excluded: chain t residue 84 SER Chi-restraints excluded: chain u residue 32 MET Chi-restraints excluded: chain u residue 60 THR Chi-restraints excluded: chain v residue 18 GLU Chi-restraints excluded: chain v residue 31 VAL Chi-restraints excluded: chain v residue 50 LEU Chi-restraints excluded: chain v residue 145 ASP Chi-restraints excluded: chain w residue 59 ARG Chi-restraints excluded: chain x residue 40 LEU Chi-restraints excluded: chain y residue 9 ASP Chi-restraints excluded: chain z residue 1 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 794 random chunks: chunk 258 optimal weight: 5.9990 chunk 691 optimal weight: 2.9990 chunk 151 optimal weight: 8.9990 chunk 450 optimal weight: 20.0000 chunk 189 optimal weight: 10.0000 chunk 768 optimal weight: 10.0000 chunk 637 optimal weight: 9.9990 chunk 355 optimal weight: 7.9990 chunk 63 optimal weight: 30.0000 chunk 254 optimal weight: 0.7980 chunk 403 optimal weight: 10.0000 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 402 ASN ** 3 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 ASN H 317 GLN K 97 GLN ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 138 ASN M 188 ASN ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 235 ASN Z 22 GLN ** Z 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 50 GLN ** k 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 96 HIS ** s 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 77 GLN y 30 ASN z 68 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.289 69131 Z= 0.556 Angle : 1.574 51.066 93426 Z= 1.015 Chirality : 0.311 6.566 10118 Planarity : 0.004 0.051 11647 Dihedral : 12.118 175.397 10579 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.31 % Favored : 96.67 % Rotamer: Outliers : 3.32 % Allowed : 15.94 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.09), residues: 8046 helix: 0.85 (0.08), residues: 4267 sheet: -0.37 (0.26), residues: 391 loop : -0.52 (0.11), residues: 3388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP Y 85 HIS 0.022 0.001 HIS 9 65 PHE 0.032 0.002 PHE M 256 TYR 0.026 0.002 TYR o 81 ARG 0.012 0.000 ARG m 46 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16092 Ramachandran restraints generated. 8046 Oldfield, 0 Emsley, 8046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16092 Ramachandran restraints generated. 8046 Oldfield, 0 Emsley, 8046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1271 residues out of total 7132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 237 poor density : 1034 time to evaluate : 5.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 390 ASP cc_start: 0.8585 (m-30) cc_final: 0.8364 (m-30) REVERT: 1 428 GLU cc_start: 0.8609 (pp20) cc_final: 0.8384 (tm-30) REVERT: 2 14 LYS cc_start: 0.9216 (mppt) cc_final: 0.8816 (mmmm) REVERT: 2 127 LYS cc_start: 0.8595 (ptpt) cc_final: 0.8278 (ptmt) REVERT: 3 31 GLU cc_start: 0.8568 (tt0) cc_final: 0.8170 (tp30) REVERT: 3 447 LYS cc_start: 0.9075 (mttm) cc_final: 0.8691 (mmpt) REVERT: 3 613 TYR cc_start: 0.8423 (OUTLIER) cc_final: 0.7919 (p90) REVERT: 3 654 GLN cc_start: 0.7608 (OUTLIER) cc_final: 0.7047 (tm-30) REVERT: 3 673 MET cc_start: 0.8988 (OUTLIER) cc_final: 0.8685 (mtm) REVERT: 4 66 MET cc_start: 0.9131 (OUTLIER) cc_final: 0.8921 (mmt) REVERT: 5 14 ARG cc_start: 0.8302 (ttt90) cc_final: 0.7891 (ttm110) REVERT: 6 25 ARG cc_start: 0.5594 (ttt180) cc_final: 0.4910 (mmp-170) REVERT: 6 102 LYS cc_start: 0.9243 (ttmt) cc_final: 0.8742 (tttt) REVERT: 6 125 TYR cc_start: 0.9231 (OUTLIER) cc_final: 0.7469 (t80) REVERT: 9 78 ILE cc_start: 0.9284 (OUTLIER) cc_final: 0.8851 (pp) REVERT: A 23 TRP cc_start: 0.6860 (m100) cc_final: 0.6263 (t60) REVERT: J 74 MET cc_start: 0.8673 (mtm) cc_final: 0.8398 (mtm) REVERT: J 105 TYR cc_start: 0.6963 (t80) cc_final: 0.5612 (m-80) REVERT: K 9 MET cc_start: 0.8858 (OUTLIER) cc_final: 0.8473 (mpp) REVERT: K 58 MET cc_start: 0.8900 (OUTLIER) cc_final: 0.8469 (ptt) REVERT: L 559 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7103 (tm-30) REVERT: L 592 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.7804 (pp) REVERT: L 597 ILE cc_start: 0.6785 (OUTLIER) cc_final: 0.6343 (tp) REVERT: M 166 TYR cc_start: 0.8573 (t80) cc_final: 0.7820 (t80) REVERT: M 201 MET cc_start: 0.8848 (OUTLIER) cc_final: 0.8593 (mmm) REVERT: M 210 TYR cc_start: 0.8434 (t80) cc_final: 0.8219 (t80) REVERT: M 437 MET cc_start: 0.8678 (mmt) cc_final: 0.8302 (mmt) REVERT: M 454 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8462 (pp) REVERT: N 200 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.8468 (mpm) REVERT: N 282 MET cc_start: 0.8633 (mtm) cc_final: 0.8408 (mtp) REVERT: V 117 MET cc_start: 0.6457 (mtp) cc_final: 0.6067 (tpt) REVERT: V 126 MET cc_start: 0.8109 (OUTLIER) cc_final: 0.7476 (mtt) REVERT: W 62 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7445 (mm-30) REVERT: X 57 GLU cc_start: 0.7675 (tp30) cc_final: 0.7173 (tm-30) REVERT: Y 120 ASP cc_start: 0.8404 (m-30) cc_final: 0.8040 (m-30) REVERT: c 18 ASP cc_start: 0.8817 (t70) cc_final: 0.8609 (t70) REVERT: c 31 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8340 (mtpp) REVERT: d 32 ARG cc_start: 0.9160 (OUTLIER) cc_final: 0.8294 (ttm170) REVERT: d 224 ARG cc_start: 0.8657 (mtm-85) cc_final: 0.8187 (mmp80) REVERT: d 281 ARG cc_start: 0.8116 (ptp90) cc_final: 0.7678 (mpt180) REVERT: e 58 SER cc_start: 0.8460 (t) cc_final: 0.8017 (m) REVERT: e 93 VAL cc_start: 0.8773 (t) cc_final: 0.8535 (t) REVERT: f 17 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7994 (mm-30) REVERT: f 32 ASP cc_start: 0.8250 (OUTLIER) cc_final: 0.7946 (m-30) REVERT: h 60 ARG cc_start: 0.9380 (OUTLIER) cc_final: 0.7796 (mpp80) REVERT: i 9 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.7128 (mtp85) REVERT: k 96 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8630 (tt) REVERT: k 214 MET cc_start: 0.8342 (tpp) cc_final: 0.7962 (tpp) REVERT: l 82 ARG cc_start: 0.8522 (tmm-80) cc_final: 0.8056 (ttp-170) REVERT: l 101 GLU cc_start: 0.6892 (OUTLIER) cc_final: 0.6609 (tp30) REVERT: n 72 TRP cc_start: 0.7429 (m100) cc_final: 0.6941 (m-90) REVERT: n 85 TYR cc_start: 0.7356 (OUTLIER) cc_final: 0.6928 (t80) REVERT: o 50 ARG cc_start: 0.7669 (mtp-110) cc_final: 0.7277 (mtt180) REVERT: p 74 ASN cc_start: 0.8433 (t0) cc_final: 0.8197 (t160) REVERT: r 116 ILE cc_start: 0.8257 (mp) cc_final: 0.8000 (mp) REVERT: u 16 GLN cc_start: 0.7397 (tp40) cc_final: 0.7042 (tt0) REVERT: v 50 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7911 (mp) REVERT: v 55 GLN cc_start: 0.8720 (mm-40) cc_final: 0.8302 (mm-40) REVERT: v 103 LYS cc_start: 0.7367 (mttt) cc_final: 0.6877 (mmtm) REVERT: v 105 LEU cc_start: 0.7624 (tp) cc_final: 0.7373 (tp) REVERT: w 70 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8345 (mp) REVERT: w 82 ASP cc_start: 0.8711 (t0) cc_final: 0.8341 (t0) REVERT: y 8 ARG cc_start: 0.6810 (tpm170) cc_final: 0.5715 (mmm160) outliers start: 237 outliers final: 131 residues processed: 1178 average time/residue: 1.4318 time to fit residues: 2224.2204 Evaluate side-chains 1166 residues out of total 7132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 1008 time to evaluate : 5.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 314 THR Chi-restraints excluded: chain 1 residue 409 ASP Chi-restraints excluded: chain 2 residue 105 THR Chi-restraints excluded: chain 2 residue 114 ASP Chi-restraints excluded: chain 3 residue 115 ASP Chi-restraints excluded: chain 3 residue 148 THR Chi-restraints excluded: chain 3 residue 367 THR Chi-restraints excluded: chain 3 residue 537 LEU Chi-restraints excluded: chain 3 residue 561 LEU Chi-restraints excluded: chain 3 residue 613 TYR Chi-restraints excluded: chain 3 residue 654 GLN Chi-restraints excluded: chain 3 residue 673 MET Chi-restraints excluded: chain 4 residue 49 LEU Chi-restraints excluded: chain 4 residue 66 MET Chi-restraints excluded: chain 4 residue 225 LEU Chi-restraints excluded: chain 5 residue 109 THR Chi-restraints excluded: chain 6 residue 50 PHE Chi-restraints excluded: chain 6 residue 84 ASP Chi-restraints excluded: chain 6 residue 85 VAL Chi-restraints excluded: chain 6 residue 125 TYR Chi-restraints excluded: chain 6 residue 137 ASP Chi-restraints excluded: chain 6 residue 175 ILE Chi-restraints excluded: chain 9 residue 1 THR Chi-restraints excluded: chain 9 residue 78 ILE Chi-restraints excluded: chain 9 residue 83 CYS Chi-restraints excluded: chain 9 residue 84 GLU Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain 9 residue 126 CYS Chi-restraints excluded: chain 9 residue 140 SER Chi-restraints excluded: chain 9 residue 143 THR Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain H residue 66 SER Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain J residue 118 LYS Chi-restraints excluded: chain J residue 133 SER Chi-restraints excluded: chain K residue 9 MET Chi-restraints excluded: chain K residue 24 SER Chi-restraints excluded: chain K residue 39 SER Chi-restraints excluded: chain K residue 57 SER Chi-restraints excluded: chain K residue 58 MET Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain L residue 53 MET Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 105 MET Chi-restraints excluded: chain L residue 151 SER Chi-restraints excluded: chain L residue 250 SER Chi-restraints excluded: chain L residue 314 MET Chi-restraints excluded: chain L residue 424 THR Chi-restraints excluded: chain L residue 544 MET Chi-restraints excluded: chain L residue 559 GLU Chi-restraints excluded: chain L residue 560 THR Chi-restraints excluded: chain L residue 589 LEU Chi-restraints excluded: chain L residue 592 LEU Chi-restraints excluded: chain L residue 594 THR Chi-restraints excluded: chain L residue 597 ILE Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 58 SER Chi-restraints excluded: chain M residue 86 LYS Chi-restraints excluded: chain M residue 201 MET Chi-restraints excluded: chain M residue 207 MET Chi-restraints excluded: chain M residue 308 SER Chi-restraints excluded: chain M residue 365 THR Chi-restraints excluded: chain M residue 454 ILE Chi-restraints excluded: chain M residue 458 LEU Chi-restraints excluded: chain N residue 14 MET Chi-restraints excluded: chain N residue 45 MET Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 200 MET Chi-restraints excluded: chain N residue 201 THR Chi-restraints excluded: chain N residue 284 ILE Chi-restraints excluded: chain N residue 320 THR Chi-restraints excluded: chain N residue 329 MET Chi-restraints excluded: chain V residue 39 SER Chi-restraints excluded: chain V residue 49 LEU Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain V residue 126 MET Chi-restraints excluded: chain W residue 62 GLU Chi-restraints excluded: chain W residue 81 ASP Chi-restraints excluded: chain W residue 136 SER Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain Z residue 8 VAL Chi-restraints excluded: chain Z residue 39 LEU Chi-restraints excluded: chain Z residue 76 CYS Chi-restraints excluded: chain a residue 48 THR Chi-restraints excluded: chain b residue 4 THR Chi-restraints excluded: chain b residue 19 ASP Chi-restraints excluded: chain b residue 52 VAL Chi-restraints excluded: chain c residue 31 LYS Chi-restraints excluded: chain c residue 110 VAL Chi-restraints excluded: chain d residue 32 ARG Chi-restraints excluded: chain d residue 154 LYS Chi-restraints excluded: chain e residue 56 GLU Chi-restraints excluded: chain f residue 17 GLU Chi-restraints excluded: chain f residue 18 THR Chi-restraints excluded: chain f residue 32 ASP Chi-restraints excluded: chain g residue 15 SER Chi-restraints excluded: chain g residue 28 LYS Chi-restraints excluded: chain g residue 118 LEU Chi-restraints excluded: chain h residue 15 SER Chi-restraints excluded: chain h residue 60 ARG Chi-restraints excluded: chain i residue 9 ARG Chi-restraints excluded: chain i residue 96 ASP Chi-restraints excluded: chain j residue 7 THR Chi-restraints excluded: chain j residue 49 GLU Chi-restraints excluded: chain j residue 66 ASP Chi-restraints excluded: chain k residue 24 LEU Chi-restraints excluded: chain k residue 96 LEU Chi-restraints excluded: chain k residue 157 LYS Chi-restraints excluded: chain k residue 218 CYS Chi-restraints excluded: chain k residue 222 GLN Chi-restraints excluded: chain l residue 101 GLU Chi-restraints excluded: chain m residue 27 LEU Chi-restraints excluded: chain m residue 42 LEU Chi-restraints excluded: chain n residue 81 VAL Chi-restraints excluded: chain n residue 85 TYR Chi-restraints excluded: chain o residue 3 THR Chi-restraints excluded: chain o residue 55 SER Chi-restraints excluded: chain o residue 67 SER Chi-restraints excluded: chain p residue 87 LEU Chi-restraints excluded: chain q residue 133 LEU Chi-restraints excluded: chain r residue 11 LEU Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain r residue 76 ILE Chi-restraints excluded: chain r residue 102 ARG Chi-restraints excluded: chain r residue 103 ILE Chi-restraints excluded: chain r residue 110 LEU Chi-restraints excluded: chain s residue 14 VAL Chi-restraints excluded: chain s residue 23 THR Chi-restraints excluded: chain s residue 41 THR Chi-restraints excluded: chain s residue 77 LEU Chi-restraints excluded: chain t residue 15 VAL Chi-restraints excluded: chain t residue 27 GLU Chi-restraints excluded: chain t residue 84 SER Chi-restraints excluded: chain u residue 32 MET Chi-restraints excluded: chain u residue 60 THR Chi-restraints excluded: chain v residue 7 ASP Chi-restraints excluded: chain v residue 18 GLU Chi-restraints excluded: chain v residue 31 VAL Chi-restraints excluded: chain v residue 50 LEU Chi-restraints excluded: chain v residue 81 LEU Chi-restraints excluded: chain v residue 89 VAL Chi-restraints excluded: chain v residue 145 ASP Chi-restraints excluded: chain w residue 59 ARG Chi-restraints excluded: chain w residue 70 LEU Chi-restraints excluded: chain x residue 40 LEU Chi-restraints excluded: chain y residue 9 ASP Chi-restraints excluded: chain y residue 42 LEU Chi-restraints excluded: chain z residue 1 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 794 random chunks: chunk 740 optimal weight: 10.0000 chunk 86 optimal weight: 8.9990 chunk 437 optimal weight: 40.0000 chunk 561 optimal weight: 20.0000 chunk 434 optimal weight: 9.9990 chunk 646 optimal weight: 20.0000 chunk 428 optimal weight: 20.0000 chunk 765 optimal weight: 9.9990 chunk 478 optimal weight: 7.9990 chunk 466 optimal weight: 20.0000 chunk 353 optimal weight: 7.9990 overall best weight: 8.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 402 ASN 3 517 ASN 4 149 ASN ** 6 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 28 ASN A 85 ASN H 317 GLN K 97 GLN L 23 ASN ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 138 ASN M 188 ASN M 333 ASN ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 235 ASN Y 15 GLN ** Z 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 50 GLN ** k 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 36 ASN z 68 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.301 69131 Z= 0.631 Angle : 1.606 51.053 93426 Z= 1.027 Chirality : 0.312 6.577 10118 Planarity : 0.005 0.056 11647 Dihedral : 12.393 174.841 10579 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.68 % Favored : 96.28 % Rotamer: Outliers : 3.67 % Allowed : 16.03 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.09), residues: 8046 helix: 0.71 (0.08), residues: 4282 sheet: -0.41 (0.26), residues: 398 loop : -0.57 (0.11), residues: 3366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP Y 85 HIS 0.024 0.002 HIS 9 65 PHE 0.036 0.002 PHE M 256 TYR 0.029 0.002 TYR o 81 ARG 0.014 0.001 ARG m 46 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16092 Ramachandran restraints generated. 8046 Oldfield, 0 Emsley, 8046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16092 Ramachandran restraints generated. 8046 Oldfield, 0 Emsley, 8046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1278 residues out of total 7132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 262 poor density : 1016 time to evaluate : 5.866 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: 1 337 MET cc_start: 0.9345 (OUTLIER) cc_final: 0.8982 (mpp) REVERT: 1 376 MET cc_start: 0.9109 (mmm) cc_final: 0.8895 (mtp) REVERT: 1 390 ASP cc_start: 0.8697 (m-30) cc_final: 0.8443 (m-30) REVERT: 1 428 GLU cc_start: 0.8654 (pp20) cc_final: 0.8412 (tm-30) REVERT: 2 14 LYS cc_start: 0.9224 (mppt) cc_final: 0.8810 (mmmm) REVERT: 2 118 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8040 (tm-30) REVERT: 2 127 LYS cc_start: 0.8618 (ptpt) cc_final: 0.8323 (ptmt) REVERT: 3 447 LYS cc_start: 0.9105 (mttm) cc_final: 0.8668 (mmpt) REVERT: 3 654 GLN cc_start: 0.7663 (OUTLIER) cc_final: 0.7128 (tm-30) REVERT: 3 673 MET cc_start: 0.9046 (OUTLIER) cc_final: 0.8717 (mtm) REVERT: 4 66 MET cc_start: 0.9176 (OUTLIER) cc_final: 0.8857 (mmt) REVERT: 4 71 GLU cc_start: 0.8350 (mm-30) cc_final: 0.8096 (mm-30) REVERT: 5 14 ARG cc_start: 0.8272 (ttt90) cc_final: 0.7880 (ttm110) REVERT: 6 25 ARG cc_start: 0.5637 (ttt180) cc_final: 0.4877 (mmp-170) REVERT: 6 102 LYS cc_start: 0.9238 (ttmt) cc_final: 0.8752 (tttt) REVERT: 6 106 GLN cc_start: 0.9137 (mm110) cc_final: 0.8927 (mm-40) REVERT: 6 107 MET cc_start: 0.9099 (OUTLIER) cc_final: 0.8861 (mtp) REVERT: 6 125 TYR cc_start: 0.9274 (OUTLIER) cc_final: 0.7494 (t80) REVERT: 9 78 ILE cc_start: 0.9318 (OUTLIER) cc_final: 0.8934 (pp) REVERT: A 23 TRP cc_start: 0.6814 (m100) cc_final: 0.6207 (t60) REVERT: J 74 MET cc_start: 0.8698 (mtm) cc_final: 0.8424 (mtm) REVERT: K 9 MET cc_start: 0.8871 (OUTLIER) cc_final: 0.8552 (mpp) REVERT: K 58 MET cc_start: 0.8986 (OUTLIER) cc_final: 0.8576 (ptt) REVERT: L 559 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7278 (tm-30) REVERT: L 592 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.7780 (pp) REVERT: M 166 TYR cc_start: 0.8629 (t80) cc_final: 0.7834 (t80) REVERT: M 201 MET cc_start: 0.8863 (OUTLIER) cc_final: 0.8599 (mmm) REVERT: M 454 ILE cc_start: 0.8874 (OUTLIER) cc_final: 0.8537 (pp) REVERT: N 200 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8501 (mpm) REVERT: N 282 MET cc_start: 0.8654 (mtm) cc_final: 0.8424 (mtp) REVERT: V 117 MET cc_start: 0.6474 (mtp) cc_final: 0.6068 (tpt) REVERT: V 133 LYS cc_start: 0.7714 (mttp) cc_final: 0.6924 (mmtm) REVERT: W 62 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7486 (mm-30) REVERT: X 57 GLU cc_start: 0.7696 (tp30) cc_final: 0.7202 (tm-30) REVERT: Y 120 ASP cc_start: 0.8405 (m-30) cc_final: 0.8035 (m-30) REVERT: Z 82 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8649 (mm) REVERT: Z 162 MET cc_start: 0.8798 (mtt) cc_final: 0.8545 (mtt) REVERT: b 60 ASP cc_start: 0.8941 (p0) cc_final: 0.8663 (p0) REVERT: c 18 ASP cc_start: 0.8815 (t70) cc_final: 0.8594 (t70) REVERT: c 31 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8387 (mtpp) REVERT: d 32 ARG cc_start: 0.9214 (OUTLIER) cc_final: 0.8279 (ttm170) REVERT: d 224 ARG cc_start: 0.8677 (mtm-85) cc_final: 0.8163 (mmp80) REVERT: d 281 ARG cc_start: 0.8194 (ptp90) cc_final: 0.7687 (mpt180) REVERT: e 58 SER cc_start: 0.8518 (t) cc_final: 0.8024 (m) REVERT: e 85 GLN cc_start: 0.8500 (mt0) cc_final: 0.8246 (mt0) REVERT: e 93 VAL cc_start: 0.8820 (t) cc_final: 0.8583 (t) REVERT: f 17 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7929 (mm-30) REVERT: f 32 ASP cc_start: 0.8201 (OUTLIER) cc_final: 0.7934 (m-30) REVERT: g 73 THR cc_start: 0.8624 (p) cc_final: 0.8201 (t) REVERT: i 9 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.7078 (mtp85) REVERT: k 96 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8602 (tt) REVERT: k 214 MET cc_start: 0.8353 (tpp) cc_final: 0.7962 (tpp) REVERT: l 82 ARG cc_start: 0.8543 (tmm-80) cc_final: 0.8083 (ttp-170) REVERT: l 101 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.6937 (tp30) REVERT: n 72 TRP cc_start: 0.7496 (m100) cc_final: 0.6914 (m-90) REVERT: p 74 ASN cc_start: 0.8469 (t0) cc_final: 0.8173 (t160) REVERT: r 116 ILE cc_start: 0.8312 (mp) cc_final: 0.8039 (mp) REVERT: s 108 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7504 (tp) REVERT: v 42 MET cc_start: 0.8471 (mmm) cc_final: 0.8166 (tpp) REVERT: v 50 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8322 (OUTLIER) REVERT: v 103 LYS cc_start: 0.7433 (mttt) cc_final: 0.6922 (mmtm) REVERT: v 105 LEU cc_start: 0.7602 (tp) cc_final: 0.7371 (tp) REVERT: w 70 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8401 (mp) REVERT: y 8 ARG cc_start: 0.6829 (tpm170) cc_final: 0.5775 (mmm160) outliers start: 262 outliers final: 143 residues processed: 1173 average time/residue: 1.4916 time to fit residues: 2330.3261 Evaluate side-chains 1154 residues out of total 7132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 985 time to evaluate : 5.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 314 THR Chi-restraints excluded: chain 1 residue 337 MET Chi-restraints excluded: chain 1 residue 343 ILE Chi-restraints excluded: chain 2 residue 114 ASP Chi-restraints excluded: chain 2 residue 118 GLU Chi-restraints excluded: chain 3 residue 115 ASP Chi-restraints excluded: chain 3 residue 119 GLN Chi-restraints excluded: chain 3 residue 159 CYS Chi-restraints excluded: chain 3 residue 367 THR Chi-restraints excluded: chain 3 residue 486 ASP Chi-restraints excluded: chain 3 residue 517 ASN Chi-restraints excluded: chain 3 residue 537 LEU Chi-restraints excluded: chain 3 residue 561 LEU Chi-restraints excluded: chain 3 residue 654 GLN Chi-restraints excluded: chain 3 residue 673 MET Chi-restraints excluded: chain 4 residue 49 LEU Chi-restraints excluded: chain 4 residue 66 MET Chi-restraints excluded: chain 4 residue 225 LEU Chi-restraints excluded: chain 4 residue 245 VAL Chi-restraints excluded: chain 5 residue 109 THR Chi-restraints excluded: chain 6 residue 50 PHE Chi-restraints excluded: chain 6 residue 79 SER Chi-restraints excluded: chain 6 residue 84 ASP Chi-restraints excluded: chain 6 residue 85 VAL Chi-restraints excluded: chain 6 residue 107 MET Chi-restraints excluded: chain 6 residue 125 TYR Chi-restraints excluded: chain 6 residue 137 ASP Chi-restraints excluded: chain 6 residue 175 ILE Chi-restraints excluded: chain 9 residue 1 THR Chi-restraints excluded: chain 9 residue 78 ILE Chi-restraints excluded: chain 9 residue 83 CYS Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain 9 residue 126 CYS Chi-restraints excluded: chain 9 residue 140 SER Chi-restraints excluded: chain 9 residue 143 THR Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain H residue 66 SER Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain J residue 133 SER Chi-restraints excluded: chain K residue 9 MET Chi-restraints excluded: chain K residue 39 SER Chi-restraints excluded: chain K residue 58 MET Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain L residue 53 MET Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 105 MET Chi-restraints excluded: chain L residue 151 SER Chi-restraints excluded: chain L residue 250 SER Chi-restraints excluded: chain L residue 314 MET Chi-restraints excluded: chain L residue 424 THR Chi-restraints excluded: chain L residue 475 MET Chi-restraints excluded: chain L residue 544 MET Chi-restraints excluded: chain L residue 559 GLU Chi-restraints excluded: chain L residue 560 THR Chi-restraints excluded: chain L residue 592 LEU Chi-restraints excluded: chain L residue 594 THR Chi-restraints excluded: chain M residue 36 LEU Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 58 SER Chi-restraints excluded: chain M residue 86 LYS Chi-restraints excluded: chain M residue 201 MET Chi-restraints excluded: chain M residue 207 MET Chi-restraints excluded: chain M residue 231 LEU Chi-restraints excluded: chain M residue 296 LEU Chi-restraints excluded: chain M residue 308 SER Chi-restraints excluded: chain M residue 365 THR Chi-restraints excluded: chain M residue 454 ILE Chi-restraints excluded: chain M residue 458 LEU Chi-restraints excluded: chain N residue 45 MET Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 200 MET Chi-restraints excluded: chain N residue 201 THR Chi-restraints excluded: chain N residue 284 ILE Chi-restraints excluded: chain N residue 320 THR Chi-restraints excluded: chain N residue 329 MET Chi-restraints excluded: chain V residue 39 SER Chi-restraints excluded: chain V residue 49 LEU Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain V residue 126 MET Chi-restraints excluded: chain W residue 49 GLU Chi-restraints excluded: chain W residue 62 GLU Chi-restraints excluded: chain W residue 81 ASP Chi-restraints excluded: chain W residue 136 SER Chi-restraints excluded: chain W residue 143 ASN Chi-restraints excluded: chain Y residue 88 ILE Chi-restraints excluded: chain Y residue 171 MET Chi-restraints excluded: chain Z residue 8 VAL Chi-restraints excluded: chain Z residue 76 CYS Chi-restraints excluded: chain Z residue 82 LEU Chi-restraints excluded: chain a residue 48 THR Chi-restraints excluded: chain b residue 4 THR Chi-restraints excluded: chain b residue 19 ASP Chi-restraints excluded: chain b residue 52 VAL Chi-restraints excluded: chain c residue 31 LYS Chi-restraints excluded: chain c residue 110 VAL Chi-restraints excluded: chain c residue 130 VAL Chi-restraints excluded: chain d residue 5 VAL Chi-restraints excluded: chain d residue 32 ARG Chi-restraints excluded: chain d residue 154 LYS Chi-restraints excluded: chain e residue 56 GLU Chi-restraints excluded: chain e residue 95 SER Chi-restraints excluded: chain f residue 17 GLU Chi-restraints excluded: chain f residue 18 THR Chi-restraints excluded: chain f residue 32 ASP Chi-restraints excluded: chain g residue 15 SER Chi-restraints excluded: chain g residue 28 LYS Chi-restraints excluded: chain g residue 118 LEU Chi-restraints excluded: chain h residue 15 SER Chi-restraints excluded: chain h residue 60 ARG Chi-restraints excluded: chain i residue 9 ARG Chi-restraints excluded: chain i residue 62 VAL Chi-restraints excluded: chain j residue 7 THR Chi-restraints excluded: chain j residue 49 GLU Chi-restraints excluded: chain j residue 66 ASP Chi-restraints excluded: chain k residue 24 LEU Chi-restraints excluded: chain k residue 96 LEU Chi-restraints excluded: chain k residue 157 LYS Chi-restraints excluded: chain k residue 218 CYS Chi-restraints excluded: chain k residue 222 GLN Chi-restraints excluded: chain l residue 101 GLU Chi-restraints excluded: chain m residue 42 LEU Chi-restraints excluded: chain n residue 81 VAL Chi-restraints excluded: chain o residue 3 THR Chi-restraints excluded: chain o residue 55 SER Chi-restraints excluded: chain o residue 67 SER Chi-restraints excluded: chain p residue 49 GLN Chi-restraints excluded: chain p residue 87 LEU Chi-restraints excluded: chain q residue 133 LEU Chi-restraints excluded: chain r residue 11 LEU Chi-restraints excluded: chain r residue 19 ARG Chi-restraints excluded: chain r residue 33 VAL Chi-restraints excluded: chain r residue 68 ILE Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain r residue 76 ILE Chi-restraints excluded: chain r residue 81 ILE Chi-restraints excluded: chain r residue 102 ARG Chi-restraints excluded: chain r residue 110 LEU Chi-restraints excluded: chain s residue 14 VAL Chi-restraints excluded: chain s residue 23 THR Chi-restraints excluded: chain s residue 41 THR Chi-restraints excluded: chain s residue 77 LEU Chi-restraints excluded: chain s residue 108 LEU Chi-restraints excluded: chain t residue 27 GLU Chi-restraints excluded: chain t residue 84 SER Chi-restraints excluded: chain u residue 32 MET Chi-restraints excluded: chain u residue 60 THR Chi-restraints excluded: chain v residue 7 ASP Chi-restraints excluded: chain v residue 18 GLU Chi-restraints excluded: chain v residue 31 VAL Chi-restraints excluded: chain v residue 50 LEU Chi-restraints excluded: chain v residue 81 LEU Chi-restraints excluded: chain v residue 89 VAL Chi-restraints excluded: chain v residue 124 THR Chi-restraints excluded: chain v residue 145 ASP Chi-restraints excluded: chain w residue 59 ARG Chi-restraints excluded: chain w residue 70 LEU Chi-restraints excluded: chain x residue 21 LEU Chi-restraints excluded: chain y residue 9 ASP Chi-restraints excluded: chain y residue 42 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 794 random chunks: chunk 473 optimal weight: 10.0000 chunk 305 optimal weight: 5.9990 chunk 457 optimal weight: 7.9990 chunk 230 optimal weight: 6.9990 chunk 150 optimal weight: 5.9990 chunk 148 optimal weight: 0.9990 chunk 486 optimal weight: 30.0000 chunk 521 optimal weight: 7.9990 chunk 378 optimal weight: 0.9990 chunk 71 optimal weight: 9.9990 chunk 601 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 160 HIS ** 6 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 317 GLN K 97 GLN ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 235 ASN Y 15 GLN Z 114 GLN ** b 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 50 GLN ** k 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 68 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.279 69131 Z= 0.525 Angle : 1.570 51.119 93426 Z= 1.014 Chirality : 0.310 6.535 10118 Planarity : 0.004 0.048 11647 Dihedral : 11.993 174.684 10579 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.97 % Favored : 97.00 % Rotamer: Outliers : 2.86 % Allowed : 17.11 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.09), residues: 8046 helix: 0.92 (0.08), residues: 4270 sheet: -0.33 (0.26), residues: 396 loop : -0.45 (0.11), residues: 3380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP Y 85 HIS 0.019 0.001 HIS 9 65 PHE 0.041 0.001 PHE n 62 TYR 0.030 0.001 TYR H 215 ARG 0.015 0.000 ARG 3 515 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16092 Ramachandran restraints generated. 8046 Oldfield, 0 Emsley, 8046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16092 Ramachandran restraints generated. 8046 Oldfield, 0 Emsley, 8046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1261 residues out of total 7132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 1057 time to evaluate : 5.753 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: 1 390 ASP cc_start: 0.8538 (m-30) cc_final: 0.8295 (m-30) REVERT: 1 428 GLU cc_start: 0.8619 (pp20) cc_final: 0.8368 (tm-30) REVERT: 2 14 LYS cc_start: 0.9228 (mppt) cc_final: 0.8793 (mmmm) REVERT: 2 127 LYS cc_start: 0.8602 (ptpt) cc_final: 0.8306 (ptmt) REVERT: 3 31 GLU cc_start: 0.8522 (tt0) cc_final: 0.8110 (tp30) REVERT: 3 119 GLN cc_start: 0.9057 (OUTLIER) cc_final: 0.8782 (mt0) REVERT: 3 654 GLN cc_start: 0.7565 (OUTLIER) cc_final: 0.7077 (tm-30) REVERT: 3 673 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.8683 (mtm) REVERT: 4 66 MET cc_start: 0.9141 (OUTLIER) cc_final: 0.8905 (mmt) REVERT: 4 71 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7949 (mm-30) REVERT: 4 282 GLU cc_start: 0.8690 (tt0) cc_final: 0.8439 (tp30) REVERT: 5 14 ARG cc_start: 0.8250 (ttt90) cc_final: 0.7856 (ttm110) REVERT: 6 25 ARG cc_start: 0.5529 (ttt180) cc_final: 0.4898 (mmp-170) REVERT: 6 102 LYS cc_start: 0.9236 (ttmt) cc_final: 0.8737 (ttpp) REVERT: 6 125 TYR cc_start: 0.9217 (OUTLIER) cc_final: 0.7465 (t80) REVERT: 9 78 ILE cc_start: 0.9265 (OUTLIER) cc_final: 0.8851 (pp) REVERT: A 23 TRP cc_start: 0.6864 (m100) cc_final: 0.6221 (t60) REVERT: J 74 MET cc_start: 0.8687 (mtm) cc_final: 0.8434 (mtm) REVERT: K 9 MET cc_start: 0.8876 (OUTLIER) cc_final: 0.8477 (mpp) REVERT: K 58 MET cc_start: 0.8885 (OUTLIER) cc_final: 0.8376 (ptt) REVERT: L 592 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.7738 (pp) REVERT: M 166 TYR cc_start: 0.8528 (t80) cc_final: 0.7778 (t80) REVERT: M 201 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.8562 (mmm) REVERT: M 454 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8500 (pp) REVERT: N 282 MET cc_start: 0.8646 (mtm) cc_final: 0.8418 (mtp) REVERT: V 117 MET cc_start: 0.6408 (mtp) cc_final: 0.5986 (tpt) REVERT: W 62 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7495 (mm-30) REVERT: X 25 ILE cc_start: 0.8055 (mm) cc_final: 0.7777 (mm) REVERT: X 30 LEU cc_start: 0.5046 (pp) cc_final: 0.4803 (mm) REVERT: X 57 GLU cc_start: 0.7669 (tp30) cc_final: 0.7235 (tm-30) REVERT: Y 120 ASP cc_start: 0.8393 (m-30) cc_final: 0.7990 (m-30) REVERT: a 63 MET cc_start: 0.8240 (mmp) cc_final: 0.7978 (mmm) REVERT: c 18 ASP cc_start: 0.8800 (t70) cc_final: 0.8600 (t70) REVERT: c 31 LYS cc_start: 0.8837 (OUTLIER) cc_final: 0.8314 (mtpp) REVERT: d 32 ARG cc_start: 0.9104 (OUTLIER) cc_final: 0.8176 (ttm170) REVERT: d 224 ARG cc_start: 0.8648 (mtm-85) cc_final: 0.8148 (mmp80) REVERT: d 281 ARG cc_start: 0.8146 (ptp90) cc_final: 0.7688 (mpt180) REVERT: e 58 SER cc_start: 0.8415 (t) cc_final: 0.7955 (m) REVERT: e 93 VAL cc_start: 0.8846 (t) cc_final: 0.8616 (t) REVERT: f 17 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7993 (mm-30) REVERT: f 32 ASP cc_start: 0.8250 (OUTLIER) cc_final: 0.7939 (m-30) REVERT: g 73 THR cc_start: 0.8512 (p) cc_final: 0.8102 (t) REVERT: h 60 ARG cc_start: 0.9320 (OUTLIER) cc_final: 0.7762 (mpp80) REVERT: i 9 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.7130 (mtp85) REVERT: k 96 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8641 (tt) REVERT: k 214 MET cc_start: 0.8304 (tpp) cc_final: 0.7890 (tpp) REVERT: l 82 ARG cc_start: 0.8533 (tmm-80) cc_final: 0.8060 (ttp-170) REVERT: l 101 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6827 (tp30) REVERT: n 72 TRP cc_start: 0.7463 (m100) cc_final: 0.6889 (m-90) REVERT: n 88 GLU cc_start: 0.7201 (pm20) cc_final: 0.6977 (pm20) REVERT: o 50 ARG cc_start: 0.7575 (mtp-110) cc_final: 0.7240 (mtt180) REVERT: r 116 ILE cc_start: 0.8271 (mp) cc_final: 0.8023 (mp) REVERT: u 11 TYR cc_start: 0.7196 (t80) cc_final: 0.6227 (t80) REVERT: v 42 MET cc_start: 0.8437 (mmm) cc_final: 0.8173 (tpp) REVERT: v 50 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7976 (mp) REVERT: v 103 LYS cc_start: 0.7377 (mttt) cc_final: 0.6848 (mmtm) REVERT: w 70 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8415 (mp) REVERT: w 82 ASP cc_start: 0.8615 (t70) cc_final: 0.8315 (t0) REVERT: y 8 ARG cc_start: 0.7047 (tpm170) cc_final: 0.5858 (mmm160) outliers start: 204 outliers final: 105 residues processed: 1180 average time/residue: 1.4545 time to fit residues: 2264.9953 Evaluate side-chains 1135 residues out of total 7132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 1008 time to evaluate : 5.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 314 THR Chi-restraints excluded: chain 1 residue 409 ASP Chi-restraints excluded: chain 2 residue 105 THR Chi-restraints excluded: chain 2 residue 114 ASP Chi-restraints excluded: chain 3 residue 114 CYS Chi-restraints excluded: chain 3 residue 115 ASP Chi-restraints excluded: chain 3 residue 119 GLN Chi-restraints excluded: chain 3 residue 159 CYS Chi-restraints excluded: chain 3 residue 367 THR Chi-restraints excluded: chain 3 residue 517 ASN Chi-restraints excluded: chain 3 residue 654 GLN Chi-restraints excluded: chain 3 residue 673 MET Chi-restraints excluded: chain 4 residue 66 MET Chi-restraints excluded: chain 4 residue 245 VAL Chi-restraints excluded: chain 5 residue 109 THR Chi-restraints excluded: chain 6 residue 50 PHE Chi-restraints excluded: chain 6 residue 85 VAL Chi-restraints excluded: chain 6 residue 125 TYR Chi-restraints excluded: chain 6 residue 137 ASP Chi-restraints excluded: chain 6 residue 175 ILE Chi-restraints excluded: chain 9 residue 1 THR Chi-restraints excluded: chain 9 residue 78 ILE Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain 9 residue 126 CYS Chi-restraints excluded: chain 9 residue 140 SER Chi-restraints excluded: chain 9 residue 143 THR Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain H residue 66 SER Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 220 PHE Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain K residue 9 MET Chi-restraints excluded: chain K residue 24 SER Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 58 MET Chi-restraints excluded: chain L residue 53 MET Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 151 SER Chi-restraints excluded: chain L residue 250 SER Chi-restraints excluded: chain L residue 314 MET Chi-restraints excluded: chain L residue 424 THR Chi-restraints excluded: chain L residue 543 THR Chi-restraints excluded: chain L residue 544 MET Chi-restraints excluded: chain L residue 560 THR Chi-restraints excluded: chain L residue 592 LEU Chi-restraints excluded: chain L residue 594 THR Chi-restraints excluded: chain M residue 58 SER Chi-restraints excluded: chain M residue 201 MET Chi-restraints excluded: chain M residue 207 MET Chi-restraints excluded: chain M residue 365 THR Chi-restraints excluded: chain M residue 454 ILE Chi-restraints excluded: chain M residue 458 LEU Chi-restraints excluded: chain N residue 72 MET Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 201 THR Chi-restraints excluded: chain N residue 284 ILE Chi-restraints excluded: chain N residue 320 THR Chi-restraints excluded: chain N residue 329 MET Chi-restraints excluded: chain V residue 49 LEU Chi-restraints excluded: chain V residue 87 LEU Chi-restraints excluded: chain V residue 88 ASN Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain V residue 126 MET Chi-restraints excluded: chain W residue 49 GLU Chi-restraints excluded: chain W residue 62 GLU Chi-restraints excluded: chain W residue 81 ASP Chi-restraints excluded: chain W residue 136 SER Chi-restraints excluded: chain Z residue 39 LEU Chi-restraints excluded: chain Z residue 76 CYS Chi-restraints excluded: chain b residue 4 THR Chi-restraints excluded: chain b residue 52 VAL Chi-restraints excluded: chain c residue 31 LYS Chi-restraints excluded: chain c residue 110 VAL Chi-restraints excluded: chain c residue 130 VAL Chi-restraints excluded: chain d residue 5 VAL Chi-restraints excluded: chain d residue 32 ARG Chi-restraints excluded: chain d residue 154 LYS Chi-restraints excluded: chain e residue 56 GLU Chi-restraints excluded: chain e residue 86 VAL Chi-restraints excluded: chain f residue 17 GLU Chi-restraints excluded: chain f residue 32 ASP Chi-restraints excluded: chain g residue 15 SER Chi-restraints excluded: chain g residue 118 LEU Chi-restraints excluded: chain h residue 60 ARG Chi-restraints excluded: chain i residue 9 ARG Chi-restraints excluded: chain i residue 62 VAL Chi-restraints excluded: chain j residue 7 THR Chi-restraints excluded: chain j residue 49 GLU Chi-restraints excluded: chain j residue 66 ASP Chi-restraints excluded: chain k residue 24 LEU Chi-restraints excluded: chain k residue 96 LEU Chi-restraints excluded: chain k residue 183 ILE Chi-restraints excluded: chain k residue 218 CYS Chi-restraints excluded: chain l residue 101 GLU Chi-restraints excluded: chain m residue 34 LEU Chi-restraints excluded: chain m residue 42 LEU Chi-restraints excluded: chain n residue 81 VAL Chi-restraints excluded: chain o residue 3 THR Chi-restraints excluded: chain o residue 55 SER Chi-restraints excluded: chain o residue 67 SER Chi-restraints excluded: chain p residue 87 LEU Chi-restraints excluded: chain q residue 133 LEU Chi-restraints excluded: chain r residue 11 LEU Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain r residue 76 ILE Chi-restraints excluded: chain r residue 110 LEU Chi-restraints excluded: chain s residue 14 VAL Chi-restraints excluded: chain s residue 77 LEU Chi-restraints excluded: chain t residue 27 GLU Chi-restraints excluded: chain t residue 84 SER Chi-restraints excluded: chain u residue 32 MET Chi-restraints excluded: chain u residue 60 THR Chi-restraints excluded: chain v residue 18 GLU Chi-restraints excluded: chain v residue 31 VAL Chi-restraints excluded: chain v residue 50 LEU Chi-restraints excluded: chain v residue 145 ASP Chi-restraints excluded: chain w residue 70 LEU Chi-restraints excluded: chain x residue 15 LEU Chi-restraints excluded: chain x residue 21 LEU Chi-restraints excluded: chain y residue 9 ASP Chi-restraints excluded: chain y residue 42 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 794 random chunks: chunk 696 optimal weight: 0.0970 chunk 733 optimal weight: 20.0000 chunk 668 optimal weight: 20.0000 chunk 713 optimal weight: 3.9990 chunk 732 optimal weight: 20.0000 chunk 429 optimal weight: 10.0000 chunk 310 optimal weight: 6.9990 chunk 559 optimal weight: 5.9990 chunk 218 optimal weight: 5.9990 chunk 644 optimal weight: 0.9980 chunk 674 optimal weight: 0.0670 overall best weight: 2.2320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 517 ASN ** 3 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 317 GLN K 97 GLN ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 138 ASN M 188 ASN N 120 GLN N 174 GLN N 235 ASN ** b 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 50 GLN ** k 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 30 ASN z 68 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.281 69131 Z= 0.522 Angle : 1.567 51.095 93426 Z= 1.013 Chirality : 0.310 6.517 10118 Planarity : 0.004 0.053 11647 Dihedral : 11.688 171.126 10579 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.14 % Favored : 96.83 % Rotamer: Outliers : 2.34 % Allowed : 17.99 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.10), residues: 8046 helix: 1.02 (0.08), residues: 4266 sheet: -0.22 (0.26), residues: 397 loop : -0.36 (0.11), residues: 3383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP w 26 HIS 0.022 0.001 HIS 9 65 PHE 0.040 0.001 PHE n 62 TYR 0.029 0.001 TYR o 81 ARG 0.014 0.000 ARG m 46 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16092 Ramachandran restraints generated. 8046 Oldfield, 0 Emsley, 8046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16092 Ramachandran restraints generated. 8046 Oldfield, 0 Emsley, 8046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1238 residues out of total 7132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 1071 time to evaluate : 5.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 390 ASP cc_start: 0.8527 (m-30) cc_final: 0.8286 (m-30) REVERT: 2 14 LYS cc_start: 0.9214 (mppt) cc_final: 0.8769 (mmmm) REVERT: 2 127 LYS cc_start: 0.8603 (ptpt) cc_final: 0.8284 (ptmt) REVERT: 3 31 GLU cc_start: 0.8525 (tt0) cc_final: 0.8107 (tp30) REVERT: 3 119 GLN cc_start: 0.9032 (OUTLIER) cc_final: 0.8764 (mt0) REVERT: 3 654 GLN cc_start: 0.7542 (OUTLIER) cc_final: 0.7153 (tm-30) REVERT: 3 673 MET cc_start: 0.8948 (OUTLIER) cc_final: 0.8672 (mtm) REVERT: 4 66 MET cc_start: 0.9155 (OUTLIER) cc_final: 0.8923 (mmt) REVERT: 4 71 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7966 (mm-30) REVERT: 4 282 GLU cc_start: 0.8723 (tt0) cc_final: 0.8466 (tp30) REVERT: 5 14 ARG cc_start: 0.8247 (ttt90) cc_final: 0.7827 (ttm110) REVERT: 6 25 ARG cc_start: 0.5526 (ttt180) cc_final: 0.4883 (mmp-170) REVERT: 6 102 LYS cc_start: 0.9145 (ttmt) cc_final: 0.8688 (ttpp) REVERT: 6 125 TYR cc_start: 0.9207 (OUTLIER) cc_final: 0.7446 (t80) REVERT: 9 78 ILE cc_start: 0.9238 (OUTLIER) cc_final: 0.8785 (pp) REVERT: A 23 TRP cc_start: 0.6871 (m100) cc_final: 0.6226 (t60) REVERT: H 1 MET cc_start: 0.7968 (tpt) cc_final: 0.7706 (tpp) REVERT: J 74 MET cc_start: 0.8696 (mtm) cc_final: 0.8360 (mtm) REVERT: K 9 MET cc_start: 0.8840 (OUTLIER) cc_final: 0.8387 (mpp) REVERT: K 58 MET cc_start: 0.8840 (OUTLIER) cc_final: 0.8352 (ptt) REVERT: L 559 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7155 (tm-30) REVERT: L 592 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.7766 (pp) REVERT: M 166 TYR cc_start: 0.8490 (t80) cc_final: 0.7767 (t80) REVERT: M 201 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.8570 (mmm) REVERT: M 303 ILE cc_start: 0.8713 (pt) cc_final: 0.8509 (mt) REVERT: M 454 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8462 (pp) REVERT: N 282 MET cc_start: 0.8643 (mtm) cc_final: 0.8398 (mtp) REVERT: V 117 MET cc_start: 0.6380 (mtp) cc_final: 0.6015 (tpt) REVERT: W 62 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7476 (mm-30) REVERT: X 25 ILE cc_start: 0.8064 (mm) cc_final: 0.7792 (mm) REVERT: X 30 LEU cc_start: 0.5153 (pp) cc_final: 0.4898 (mm) REVERT: X 57 GLU cc_start: 0.7677 (tp30) cc_final: 0.7176 (tm-30) REVERT: Y 89 ASP cc_start: 0.8556 (t0) cc_final: 0.8297 (t0) REVERT: Y 120 ASP cc_start: 0.8311 (m-30) cc_final: 0.7893 (m-30) REVERT: a 63 MET cc_start: 0.8166 (mmp) cc_final: 0.7954 (mmm) REVERT: b 60 ASP cc_start: 0.8919 (p0) cc_final: 0.8684 (p0) REVERT: c 31 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8250 (mtpp) REVERT: d 32 ARG cc_start: 0.9120 (OUTLIER) cc_final: 0.8214 (ttm170) REVERT: d 224 ARG cc_start: 0.8646 (mtm-85) cc_final: 0.8140 (mmp80) REVERT: d 281 ARG cc_start: 0.8128 (ptp90) cc_final: 0.7690 (mpt180) REVERT: e 58 SER cc_start: 0.8332 (t) cc_final: 0.7888 (m) REVERT: e 93 VAL cc_start: 0.8743 (t) cc_final: 0.8508 (t) REVERT: f 32 ASP cc_start: 0.8219 (OUTLIER) cc_final: 0.7916 (m-30) REVERT: g 73 THR cc_start: 0.8579 (p) cc_final: 0.8153 (t) REVERT: h 17 ARG cc_start: 0.8162 (mmm-85) cc_final: 0.7873 (tpp-160) REVERT: h 60 ARG cc_start: 0.9310 (OUTLIER) cc_final: 0.7862 (mpp80) REVERT: i 9 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.7112 (mtp85) REVERT: k 18 MET cc_start: 0.7854 (tpp) cc_final: 0.7500 (tpt) REVERT: k 96 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8640 (tt) REVERT: k 214 MET cc_start: 0.8287 (tpp) cc_final: 0.7878 (tpp) REVERT: k 237 ASP cc_start: 0.7900 (m-30) cc_final: 0.7693 (m-30) REVERT: l 82 ARG cc_start: 0.8535 (tmm-80) cc_final: 0.8101 (ttp-170) REVERT: l 83 ASP cc_start: 0.8570 (OUTLIER) cc_final: 0.8302 (p0) REVERT: l 101 GLU cc_start: 0.7107 (OUTLIER) cc_final: 0.6800 (tp30) REVERT: n 72 TRP cc_start: 0.7497 (m100) cc_final: 0.6951 (m-90) REVERT: n 85 TYR cc_start: 0.7418 (OUTLIER) cc_final: 0.7003 (t80) REVERT: o 50 ARG cc_start: 0.7561 (mtp-110) cc_final: 0.7238 (mtt180) REVERT: r 116 ILE cc_start: 0.8209 (mp) cc_final: 0.7964 (mp) REVERT: v 42 MET cc_start: 0.8396 (mmm) cc_final: 0.8138 (tpp) REVERT: v 50 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7738 (mp) REVERT: v 103 LYS cc_start: 0.7438 (mttt) cc_final: 0.6952 (mmtm) REVERT: w 70 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8329 (mp) REVERT: x 33 LYS cc_start: 0.7766 (tttt) cc_final: 0.7540 (ttmm) REVERT: y 8 ARG cc_start: 0.7026 (tpm170) cc_final: 0.5845 (mmm160) outliers start: 167 outliers final: 93 residues processed: 1179 average time/residue: 1.4496 time to fit residues: 2251.6564 Evaluate side-chains 1137 residues out of total 7132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 1020 time to evaluate : 5.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 228 VAL Chi-restraints excluded: chain 1 residue 314 THR Chi-restraints excluded: chain 2 residue 105 THR Chi-restraints excluded: chain 2 residue 114 ASP Chi-restraints excluded: chain 3 residue 114 CYS Chi-restraints excluded: chain 3 residue 115 ASP Chi-restraints excluded: chain 3 residue 119 GLN Chi-restraints excluded: chain 3 residue 148 THR Chi-restraints excluded: chain 3 residue 159 CYS Chi-restraints excluded: chain 3 residue 367 THR Chi-restraints excluded: chain 3 residue 517 ASN Chi-restraints excluded: chain 3 residue 537 LEU Chi-restraints excluded: chain 3 residue 654 GLN Chi-restraints excluded: chain 3 residue 673 MET Chi-restraints excluded: chain 4 residue 66 MET Chi-restraints excluded: chain 5 residue 109 THR Chi-restraints excluded: chain 6 residue 85 VAL Chi-restraints excluded: chain 6 residue 125 TYR Chi-restraints excluded: chain 6 residue 137 ASP Chi-restraints excluded: chain 9 residue 1 THR Chi-restraints excluded: chain 9 residue 78 ILE Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain 9 residue 126 CYS Chi-restraints excluded: chain 9 residue 140 SER Chi-restraints excluded: chain 9 residue 143 THR Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain H residue 66 SER Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain K residue 9 MET Chi-restraints excluded: chain K residue 24 SER Chi-restraints excluded: chain K residue 58 MET Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 53 MET Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 151 SER Chi-restraints excluded: chain L residue 250 SER Chi-restraints excluded: chain L residue 404 THR Chi-restraints excluded: chain L residue 424 THR Chi-restraints excluded: chain L residue 543 THR Chi-restraints excluded: chain L residue 544 MET Chi-restraints excluded: chain L residue 559 GLU Chi-restraints excluded: chain L residue 560 THR Chi-restraints excluded: chain L residue 592 LEU Chi-restraints excluded: chain L residue 594 THR Chi-restraints excluded: chain M residue 201 MET Chi-restraints excluded: chain M residue 207 MET Chi-restraints excluded: chain M residue 365 THR Chi-restraints excluded: chain M residue 410 MET Chi-restraints excluded: chain M residue 454 ILE Chi-restraints excluded: chain N residue 201 THR Chi-restraints excluded: chain N residue 284 ILE Chi-restraints excluded: chain N residue 320 THR Chi-restraints excluded: chain V residue 49 LEU Chi-restraints excluded: chain V residue 87 LEU Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain V residue 126 MET Chi-restraints excluded: chain W residue 49 GLU Chi-restraints excluded: chain W residue 62 GLU Chi-restraints excluded: chain W residue 81 ASP Chi-restraints excluded: chain W residue 136 SER Chi-restraints excluded: chain Z residue 39 LEU Chi-restraints excluded: chain Z residue 76 CYS Chi-restraints excluded: chain b residue 4 THR Chi-restraints excluded: chain b residue 52 VAL Chi-restraints excluded: chain c residue 31 LYS Chi-restraints excluded: chain c residue 110 VAL Chi-restraints excluded: chain c residue 130 VAL Chi-restraints excluded: chain d residue 5 VAL Chi-restraints excluded: chain d residue 32 ARG Chi-restraints excluded: chain d residue 154 LYS Chi-restraints excluded: chain e residue 56 GLU Chi-restraints excluded: chain e residue 86 VAL Chi-restraints excluded: chain f residue 32 ASP Chi-restraints excluded: chain g residue 15 SER Chi-restraints excluded: chain g residue 118 LEU Chi-restraints excluded: chain h residue 60 ARG Chi-restraints excluded: chain i residue 9 ARG Chi-restraints excluded: chain j residue 7 THR Chi-restraints excluded: chain j residue 66 ASP Chi-restraints excluded: chain k residue 24 LEU Chi-restraints excluded: chain k residue 96 LEU Chi-restraints excluded: chain k residue 183 ILE Chi-restraints excluded: chain k residue 218 CYS Chi-restraints excluded: chain l residue 83 ASP Chi-restraints excluded: chain l residue 101 GLU Chi-restraints excluded: chain m residue 34 LEU Chi-restraints excluded: chain m residue 42 LEU Chi-restraints excluded: chain n residue 81 VAL Chi-restraints excluded: chain n residue 85 TYR Chi-restraints excluded: chain o residue 3 THR Chi-restraints excluded: chain o residue 55 SER Chi-restraints excluded: chain o residue 67 SER Chi-restraints excluded: chain p residue 87 LEU Chi-restraints excluded: chain q residue 133 LEU Chi-restraints excluded: chain r residue 19 ARG Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain r residue 76 ILE Chi-restraints excluded: chain r residue 110 LEU Chi-restraints excluded: chain s residue 14 VAL Chi-restraints excluded: chain s residue 77 LEU Chi-restraints excluded: chain t residue 27 GLU Chi-restraints excluded: chain u residue 32 MET Chi-restraints excluded: chain u residue 60 THR Chi-restraints excluded: chain v residue 31 VAL Chi-restraints excluded: chain v residue 50 LEU Chi-restraints excluded: chain v residue 89 VAL Chi-restraints excluded: chain v residue 145 ASP Chi-restraints excluded: chain w residue 59 ARG Chi-restraints excluded: chain w residue 70 LEU Chi-restraints excluded: chain x residue 40 LEU Chi-restraints excluded: chain y residue 9 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 794 random chunks: chunk 710 optimal weight: 30.0000 chunk 468 optimal weight: 30.0000 chunk 754 optimal weight: 9.9990 chunk 460 optimal weight: 0.0040 chunk 357 optimal weight: 10.0000 chunk 524 optimal weight: 9.9990 chunk 791 optimal weight: 8.9990 chunk 728 optimal weight: 20.0000 chunk 629 optimal weight: 20.0000 chunk 65 optimal weight: 2.9990 chunk 486 optimal weight: 30.0000 overall best weight: 6.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 79 HIS ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 317 GLN ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 138 ASN ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 171 ASN N 172 GLN ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 235 ASN ** b 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 49 GLN ** r 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 68 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.292 69131 Z= 0.577 Angle : 1.593 51.120 93426 Z= 1.022 Chirality : 0.311 6.586 10118 Planarity : 0.004 0.056 11647 Dihedral : 11.788 169.645 10579 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.34 % Favored : 96.63 % Rotamer: Outliers : 2.08 % Allowed : 18.65 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.09), residues: 8046 helix: 0.91 (0.08), residues: 4278 sheet: -0.23 (0.26), residues: 395 loop : -0.37 (0.11), residues: 3373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP n 50 HIS 0.022 0.001 HIS 9 65 PHE 0.041 0.002 PHE M 256 TYR 0.036 0.002 TYR o 81 ARG 0.017 0.001 ARG m 46 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16092 Ramachandran restraints generated. 8046 Oldfield, 0 Emsley, 8046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16092 Ramachandran restraints generated. 8046 Oldfield, 0 Emsley, 8046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1147 residues out of total 7132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 999 time to evaluate : 5.942 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: 1 390 ASP cc_start: 0.8630 (m-30) cc_final: 0.8381 (m-30) REVERT: 2 127 LYS cc_start: 0.8617 (ptpt) cc_final: 0.8320 (ptmt) REVERT: 3 31 GLU cc_start: 0.8575 (tt0) cc_final: 0.8159 (tp30) REVERT: 3 654 GLN cc_start: 0.7592 (OUTLIER) cc_final: 0.7166 (tm-30) REVERT: 3 673 MET cc_start: 0.9039 (OUTLIER) cc_final: 0.8687 (mtm) REVERT: 4 66 MET cc_start: 0.9224 (OUTLIER) cc_final: 0.8919 (mmt) REVERT: 4 282 GLU cc_start: 0.8767 (tt0) cc_final: 0.8479 (tp30) REVERT: 5 14 ARG cc_start: 0.8255 (ttt90) cc_final: 0.7841 (ttm110) REVERT: 6 25 ARG cc_start: 0.5578 (ttt180) cc_final: 0.4930 (mmp-170) REVERT: 6 125 TYR cc_start: 0.9262 (OUTLIER) cc_final: 0.7491 (t80) REVERT: 9 78 ILE cc_start: 0.9291 (OUTLIER) cc_final: 0.8855 (pp) REVERT: A 23 TRP cc_start: 0.6891 (m100) cc_final: 0.6226 (t60) REVERT: H 1 MET cc_start: 0.7985 (tpt) cc_final: 0.7656 (tpp) REVERT: J 74 MET cc_start: 0.8776 (mtm) cc_final: 0.8439 (mtm) REVERT: K 9 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.8414 (mpp) REVERT: L 592 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.7795 (pp) REVERT: M 166 TYR cc_start: 0.8538 (t80) cc_final: 0.7777 (t80) REVERT: M 210 TYR cc_start: 0.8399 (t80) cc_final: 0.8122 (t80) REVERT: M 454 ILE cc_start: 0.8788 (OUTLIER) cc_final: 0.8442 (pp) REVERT: N 282 MET cc_start: 0.8651 (mtm) cc_final: 0.8385 (mtp) REVERT: V 117 MET cc_start: 0.6265 (mtp) cc_final: 0.5895 (tpt) REVERT: W 62 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7512 (mm-30) REVERT: X 57 GLU cc_start: 0.7679 (tp30) cc_final: 0.7237 (tm-30) REVERT: Y 89 ASP cc_start: 0.8613 (t0) cc_final: 0.8339 (t0) REVERT: Y 120 ASP cc_start: 0.8349 (m-30) cc_final: 0.7931 (m-30) REVERT: a 63 MET cc_start: 0.8223 (mmp) cc_final: 0.8010 (mmm) REVERT: b 60 ASP cc_start: 0.8941 (p0) cc_final: 0.8701 (p0) REVERT: c 31 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8279 (mtpp) REVERT: d 32 ARG cc_start: 0.9192 (OUTLIER) cc_final: 0.8254 (ttm170) REVERT: d 224 ARG cc_start: 0.8656 (mtm-85) cc_final: 0.8145 (mmp80) REVERT: d 281 ARG cc_start: 0.8160 (ptp90) cc_final: 0.7687 (mpt180) REVERT: e 58 SER cc_start: 0.8457 (t) cc_final: 0.8002 (m) REVERT: e 85 GLN cc_start: 0.8507 (mt0) cc_final: 0.8239 (mt0) REVERT: e 93 VAL cc_start: 0.8763 (t) cc_final: 0.8526 (t) REVERT: f 32 ASP cc_start: 0.8213 (OUTLIER) cc_final: 0.7936 (m-30) REVERT: g 73 THR cc_start: 0.8602 (p) cc_final: 0.8200 (t) REVERT: g 79 ASP cc_start: 0.8775 (m-30) cc_final: 0.8548 (m-30) REVERT: h 60 ARG cc_start: 0.9386 (OUTLIER) cc_final: 0.7744 (mpp80) REVERT: i 9 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.7108 (mtp85) REVERT: k 18 MET cc_start: 0.7944 (tpp) cc_final: 0.7576 (tpt) REVERT: k 96 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8639 (tt) REVERT: k 214 MET cc_start: 0.8294 (tpp) cc_final: 0.7916 (tpp) REVERT: l 83 ASP cc_start: 0.8543 (OUTLIER) cc_final: 0.8227 (p0) REVERT: l 101 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6966 (tp30) REVERT: n 67 LEU cc_start: 0.8643 (mm) cc_final: 0.8143 (tm) REVERT: n 72 TRP cc_start: 0.7539 (m100) cc_final: 0.6944 (m-90) REVERT: n 88 GLU cc_start: 0.7233 (pm20) cc_final: 0.6745 (mp0) REVERT: r 116 ILE cc_start: 0.8219 (mp) cc_final: 0.7984 (mp) REVERT: t 130 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7366 (mp0) REVERT: v 50 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7870 (mp) REVERT: v 55 GLN cc_start: 0.8810 (mm-40) cc_final: 0.8349 (mm-40) REVERT: v 103 LYS cc_start: 0.7461 (mttt) cc_final: 0.6957 (mmtm) REVERT: w 70 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8347 (mp) REVERT: x 33 LYS cc_start: 0.7836 (tttt) cc_final: 0.7470 (ttmm) REVERT: y 8 ARG cc_start: 0.7019 (tpm170) cc_final: 0.5791 (mmm160) outliers start: 148 outliers final: 96 residues processed: 1098 average time/residue: 1.4616 time to fit residues: 2113.5168 Evaluate side-chains 1108 residues out of total 7132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 992 time to evaluate : 5.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 228 VAL Chi-restraints excluded: chain 1 residue 314 THR Chi-restraints excluded: chain 2 residue 105 THR Chi-restraints excluded: chain 2 residue 114 ASP Chi-restraints excluded: chain 3 residue 114 CYS Chi-restraints excluded: chain 3 residue 115 ASP Chi-restraints excluded: chain 3 residue 148 THR Chi-restraints excluded: chain 3 residue 159 CYS Chi-restraints excluded: chain 3 residue 367 THR Chi-restraints excluded: chain 3 residue 537 LEU Chi-restraints excluded: chain 3 residue 654 GLN Chi-restraints excluded: chain 3 residue 673 MET Chi-restraints excluded: chain 4 residue 49 LEU Chi-restraints excluded: chain 4 residue 66 MET Chi-restraints excluded: chain 5 residue 109 THR Chi-restraints excluded: chain 6 residue 79 SER Chi-restraints excluded: chain 6 residue 85 VAL Chi-restraints excluded: chain 6 residue 125 TYR Chi-restraints excluded: chain 6 residue 137 ASP Chi-restraints excluded: chain 9 residue 1 THR Chi-restraints excluded: chain 9 residue 78 ILE Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain 9 residue 126 CYS Chi-restraints excluded: chain 9 residue 140 SER Chi-restraints excluded: chain 9 residue 143 THR Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain H residue 66 SER Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain K residue 2 SER Chi-restraints excluded: chain K residue 9 MET Chi-restraints excluded: chain K residue 24 SER Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 53 MET Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 151 SER Chi-restraints excluded: chain L residue 250 SER Chi-restraints excluded: chain L residue 404 THR Chi-restraints excluded: chain L residue 424 THR Chi-restraints excluded: chain L residue 543 THR Chi-restraints excluded: chain L residue 544 MET Chi-restraints excluded: chain L residue 560 THR Chi-restraints excluded: chain L residue 592 LEU Chi-restraints excluded: chain L residue 594 THR Chi-restraints excluded: chain M residue 78 MET Chi-restraints excluded: chain M residue 86 LYS Chi-restraints excluded: chain M residue 207 MET Chi-restraints excluded: chain M residue 365 THR Chi-restraints excluded: chain M residue 410 MET Chi-restraints excluded: chain M residue 454 ILE Chi-restraints excluded: chain M residue 458 LEU Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 201 THR Chi-restraints excluded: chain N residue 284 ILE Chi-restraints excluded: chain N residue 320 THR Chi-restraints excluded: chain V residue 49 LEU Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain V residue 126 MET Chi-restraints excluded: chain W residue 49 GLU Chi-restraints excluded: chain W residue 62 GLU Chi-restraints excluded: chain W residue 81 ASP Chi-restraints excluded: chain W residue 136 SER Chi-restraints excluded: chain Z residue 39 LEU Chi-restraints excluded: chain Z residue 76 CYS Chi-restraints excluded: chain b residue 4 THR Chi-restraints excluded: chain b residue 52 VAL Chi-restraints excluded: chain c residue 31 LYS Chi-restraints excluded: chain c residue 110 VAL Chi-restraints excluded: chain c residue 130 VAL Chi-restraints excluded: chain d residue 5 VAL Chi-restraints excluded: chain d residue 32 ARG Chi-restraints excluded: chain d residue 154 LYS Chi-restraints excluded: chain e residue 56 GLU Chi-restraints excluded: chain f residue 32 ASP Chi-restraints excluded: chain g residue 15 SER Chi-restraints excluded: chain g residue 118 LEU Chi-restraints excluded: chain h residue 60 ARG Chi-restraints excluded: chain i residue 9 ARG Chi-restraints excluded: chain j residue 7 THR Chi-restraints excluded: chain j residue 66 ASP Chi-restraints excluded: chain k residue 24 LEU Chi-restraints excluded: chain k residue 96 LEU Chi-restraints excluded: chain k residue 218 CYS Chi-restraints excluded: chain l residue 83 ASP Chi-restraints excluded: chain l residue 101 GLU Chi-restraints excluded: chain m residue 42 LEU Chi-restraints excluded: chain n residue 81 VAL Chi-restraints excluded: chain o residue 3 THR Chi-restraints excluded: chain o residue 55 SER Chi-restraints excluded: chain o residue 67 SER Chi-restraints excluded: chain p residue 87 LEU Chi-restraints excluded: chain q residue 133 LEU Chi-restraints excluded: chain r residue 19 ARG Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain r residue 76 ILE Chi-restraints excluded: chain r residue 110 LEU Chi-restraints excluded: chain s residue 14 VAL Chi-restraints excluded: chain s residue 77 LEU Chi-restraints excluded: chain t residue 27 GLU Chi-restraints excluded: chain t residue 130 GLU Chi-restraints excluded: chain u residue 32 MET Chi-restraints excluded: chain u residue 60 THR Chi-restraints excluded: chain v residue 18 GLU Chi-restraints excluded: chain v residue 31 VAL Chi-restraints excluded: chain v residue 50 LEU Chi-restraints excluded: chain v residue 89 VAL Chi-restraints excluded: chain v residue 145 ASP Chi-restraints excluded: chain w residue 59 ARG Chi-restraints excluded: chain w residue 70 LEU Chi-restraints excluded: chain x residue 40 LEU Chi-restraints excluded: chain y residue 9 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 794 random chunks: chunk 386 optimal weight: 3.9990 chunk 500 optimal weight: 10.0000 chunk 670 optimal weight: 6.9990 chunk 192 optimal weight: 9.9990 chunk 580 optimal weight: 10.0000 chunk 93 optimal weight: 5.9990 chunk 175 optimal weight: 9.9990 chunk 630 optimal weight: 6.9990 chunk 264 optimal weight: 0.7980 chunk 647 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 517 ASN ** 3 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 317 GLN K 97 GLN ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 235 ASN ** b 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 49 GLN ** r 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 46 ASN z 68 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.108841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.086791 restraints weight = 113817.444| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 1.52 r_work: 0.3020 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.285 69131 Z= 0.546 Angle : 1.582 51.130 93426 Z= 1.018 Chirality : 0.311 6.561 10118 Planarity : 0.004 0.058 11647 Dihedral : 11.638 169.693 10579 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.27 % Favored : 96.71 % Rotamer: Outliers : 2.02 % Allowed : 18.89 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.09), residues: 8046 helix: 0.94 (0.08), residues: 4270 sheet: -0.19 (0.26), residues: 394 loop : -0.34 (0.11), residues: 3382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP Y 85 HIS 0.023 0.001 HIS 9 65 PHE 0.045 0.002 PHE M 256 TYR 0.035 0.002 TYR o 81 ARG 0.017 0.000 ARG m 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 31561.84 seconds wall clock time: 546 minutes 39.64 seconds (32799.64 seconds total)