Starting phenix.real_space_refine on Fri Feb 16 13:11:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkh_11249/02_2024/6zkh_11249_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkh_11249/02_2024/6zkh_11249.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkh_11249/02_2024/6zkh_11249_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/6zkh_11249/02_2024/6zkh_11249_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkh_11249/02_2024/6zkh_11249_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkh_11249/02_2024/6zkh_11249.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkh_11249/02_2024/6zkh_11249.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkh_11249/02_2024/6zkh_11249_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkh_11249/02_2024/6zkh_11249_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= 0.027 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 "3 PHE 642": "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 "5 TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 25": "NH1" <-> "NH2" Residue "6 ARG 77": "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 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 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 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 "g PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "j PHE 58": "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 ARG 103": "NH1" <-> "NH2" Residue "s ARG 110": "NH1" <-> "NH2" Residue "s ARG 114": "NH1" <-> "NH2" Residue "s ARG 117": "NH1" <-> "NH2" 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" Residue "z TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.17s 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: 68 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: "6" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 77 Unusual residues: {'DCQ': 1, 'PC1': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: "H" 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: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 282 Unusual residues: {'3PE': 2, 'CDL': 1, 'PC1': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 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: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 278 Unusual residues: {'3PE': 3, 'CDL': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 77 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: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 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: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 45 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: "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 1 365 104.133 54.097 241.574 1.00 12.24 S ATOM 2676 SG CYS 1 359 111.283 54.251 242.184 1.00 28.28 S ATOM 3039 SG CYS 1 405 107.736 48.397 240.762 1.00 22.76 S ATOM 4116 SG CYS 2 103 102.078 49.376 260.495 1.00 52.98 S ATOM 4150 SG CYS 2 108 100.163 46.832 262.571 1.00 71.94 S ATOM 4430 SG CYS 2 144 103.779 45.664 256.856 1.00 49.11 S ATOM 4453 SG CYS 2 148 101.760 42.923 258.400 1.00 66.85 S ATOM 5793 SG CYS 3 114 106.322 72.263 226.726 1.00 42.39 S ATOM 5732 SG CYS 3 105 101.058 75.593 228.775 1.00 21.64 S ATOM 5753 SG CYS 3 108 107.202 77.412 230.316 1.00 28.24 S ATOM 6125 SG CYS 3 156 113.605 64.800 231.353 1.00 48.53 S ATOM 6102 SG CYS 3 153 111.611 67.813 236.870 1.00 13.92 S ATOM 6149 SG CYS 3 159 117.791 68.637 234.916 1.00 48.82 S ATOM 6479 SG CYS 3 203 113.491 71.087 231.425 1.00 39.79 S ATOM 5238 SG CYS 3 41 112.652 58.305 229.313 1.00 24.11 S ATOM 5324 SG CYS 3 52 109.008 59.367 228.431 1.00 38.91 S ATOM 5349 SG CYS 3 55 109.362 54.259 225.138 1.00 26.14 S ATOM 5450 SG CYS 3 69 113.075 54.420 226.607 1.00 22.25 S ATOM 16378 SG CYS 6 149 87.977 95.415 209.150 1.00 49.69 S ATOM 15644 SG CYS 6 54 84.508 95.369 203.461 1.00 67.64 S ATOM 17570 SG CYS 9 116 92.163 96.494 215.670 1.00 31.63 S ATOM 17617 SG CYS 9 122 92.764 92.127 220.427 1.00 21.52 S ATOM 17344 SG CYS 9 87 96.671 91.839 215.089 1.00 36.32 S ATOM 17646 SG CYS 9 126 95.061 88.750 227.622 1.00 22.42 S ATOM 17317 SG CYS 9 83 98.612 90.390 222.425 1.00 35.30 S ATOM 17275 SG CYS 9 77 100.805 92.060 228.145 1.00 49.29 S ATOM 17294 SG CYS 9 80 100.057 85.511 226.388 1.00 25.38 S ATOM 41210 SG CYS b 59 96.748 84.686 242.967 1.00 30.90 S ATOM 41388 SG CYS b 84 99.776 84.350 240.618 1.00 15.17 S ATOM 41410 SG CYS b 87 98.134 87.335 241.408 1.00 20.50 S Time building chain proxies: 27.31, per 1000 atoms: 0.40 Number of scatterers: 67479 At special positions: 0 Unit cell: (177.187, 199.468, 291.775, 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=2.04 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: 22.24 Conformation dependent library (CDL) restraints added in 9.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES 2 300 " 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 2 148 " pdb="FE2 FES 2 300 " - pdb=" SG CYS 2 144 " pdb=" FES 3 803 " pdb="FE1 FES 3 803 " - pdb=" SG CYS 3 52 " pdb="FE2 FES 3 803 " - pdb=" SG CYS 3 55 " pdb="FE2 FES 3 803 " - pdb=" SG CYS 3 69 " pdb="FE1 FES 3 803 " - pdb=" SG CYS 3 41 " 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="FE4 SF4 3 801 " - pdb=" SG CYS 3 108 " pdb="FE1 SF4 3 801 " - pdb=" SG CYS 3 114 " pdb="FE2 SF4 3 801 " - pdb=" SG CYS 3 105 " pdb=" SF4 3 802 " pdb="FE3 SF4 3 802 " - pdb=" SG CYS 3 159 " pdb="FE2 SF4 3 802 " - pdb=" SG CYS 3 153 " pdb="FE4 SF4 3 802 " - pdb=" SG CYS 3 203 " pdb="FE1 SF4 3 802 " - pdb=" SG CYS 3 156 " 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 87 " pdb="ZN ZN b 300 " - pdb=" SG CYS b 59 " pdb="ZN ZN b 300 " - pdb=" SG CYS b 84 " 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: 339 helices and 28 sheets defined 51.6% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.81 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 36 No H-bonds generated for 'chain '1' and resid 33 through 36' Processing helix chain '1' and resid 45 through 62 removed outlier: 3.822A pdb=" N LYS 1 51 " --> pdb=" O GLU 1 47 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLY 1 52 " --> pdb=" O ILE 1 48 " (cutoff:3.500A) Proline residue: 1 53 - end of helix removed outlier: 3.896A pdb=" N ILE 1 56 " --> pdb=" O GLY 1 52 " (cutoff:3.500A) Processing helix chain '1' and resid 75 through 82 removed outlier: 3.515A pdb=" N PHE 1 81 " --> pdb=" O LEU 1 77 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N MET 1 82 " --> pdb=" O LYS 1 78 " (cutoff:3.500A) Processing helix chain '1' and resid 106 through 113 Processing helix chain '1' and resid 115 through 128 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 243 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: 4.298A pdb=" N ASP 1 370 " --> pdb=" O ARG 1 366 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG 1 381 " --> pdb=" O ALA 1 377 " (cutoff:3.500A) Processing helix chain '1' and resid 387 through 399 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: 3.751A pdb=" N ASN 2 37 " --> pdb=" O ALA 2 33 " (cutoff:3.500A) Processing helix chain '2' and resid 43 through 58 removed outlier: 3.754A pdb=" N VAL 2 47 " --> pdb=" O ALA 2 44 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N LEU 2 48 " --> pdb=" O ALA 2 45 " (cutoff:3.500A) Proline residue: 2 49 - end of helix removed outlier: 3.528A pdb=" N ASN 2 58 " --> pdb=" O GLN 2 55 " (cutoff:3.500A) Processing helix chain '2' and resid 65 through 73 Processing helix chain '2' and resid 77 through 86 removed outlier: 3.940A 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 31 Processing helix chain '3' and resid 84 through 97 Processing helix chain '3' and resid 115 through 123 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 265 through 269 Processing helix chain '3' and resid 273 through 275 No H-bonds generated for 'chain '3' and resid 273 through 275' Processing helix chain '3' and resid 296 through 308 removed outlier: 3.867A 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 360 through 362 No H-bonds generated for 'chain '3' and resid 360 through 362' Processing helix chain '3' and resid 369 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: 3.746A pdb=" N ILE 3 432 " --> pdb=" O LEU 3 429 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER 3 434 " --> pdb=" O ASP 3 431 " (cutoff:3.500A) Processing helix chain '3' and resid 438 through 444 removed outlier: 3.997A 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 499 through 505 Processing helix chain '3' and resid 511 through 515 removed outlier: 3.535A pdb=" N ARG 3 515 " --> pdb=" O GLU 3 512 " (cutoff:3.500A) Processing helix chain '3' and resid 566 through 568 No H-bonds generated for 'chain '3' and resid 566 through 568' 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 669 through 671 No H-bonds generated for 'chain '3' and resid 669 through 671' 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: 4.111A pdb=" N GLN 4 13 " --> pdb=" O GLU 4 9 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N TYR 4 14 " --> pdb=" O TRP 4 10 " (cutoff:3.500A) Processing helix chain '4' and resid 24 through 26 No H-bonds generated for 'chain '4' and resid 24 through 26' Processing helix chain '4' and resid 87 through 93 removed outlier: 4.555A pdb=" N GLU 4 92 " --> pdb=" O GLU 4 88 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N TYR 4 93 " --> pdb=" O LYS 4 89 " (cutoff:3.500A) Processing helix chain '4' and resid 96 through 100 Processing helix chain '4' and resid 111 through 125 Processing helix chain '4' and resid 132 through 161 removed outlier: 3.623A pdb=" N ILE 4 161 " --> pdb=" O HIS 4 157 " (cutoff:3.500A) Processing helix chain '4' and resid 165 through 185 removed outlier: 4.043A pdb=" N GLU 4 172 " --> pdb=" O PHE 4 168 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLU 4 173 " --> pdb=" O TRP 4 169 " (cutoff:3.500A) Processing helix chain '4' and resid 207 through 229 removed outlier: 3.894A pdb=" N ASN 4 217 " --> pdb=" O GLU 4 213 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N SER 4 219 " --> pdb=" O SER 4 215 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N LEU 4 220 " --> pdb=" O LYS 4 216 " (cutoff:3.500A) removed outlier: 3.691A 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 263 removed outlier: 4.605A pdb=" N GLY 4 262 " --> pdb=" O MET 4 259 " (cutoff:3.500A) 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 352 Processing helix chain '4' and resid 394 through 405 removed outlier: 4.548A pdb=" N ASP 4 403 " --> pdb=" O LEU 4 399 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N LYS 4 404 " --> pdb=" O ALA 4 400 " (cutoff:3.500A) Processing helix chain '4' and resid 411 through 420 removed outlier: 4.018A pdb=" N VAL 4 415 " --> pdb=" O LEU 4 411 " (cutoff:3.500A) removed outlier: 3.837A 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: 4.073A pdb=" N VAL 5 57 " --> pdb=" O PRO 5 54 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ILE 5 58 " --> pdb=" O ASP 5 55 " (cutoff:3.500A) Proline residue: 5 59 - end of helix Processing helix chain '5' and resid 120 through 122 No H-bonds generated for 'chain '5' and resid 120 through 122' Processing helix chain '5' and resid 125 through 138 removed outlier: 3.557A pdb=" N ASN 5 128 " --> pdb=" O LYS 5 125 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N TRP 5 129 " --> pdb=" O ALA 5 126 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N GLU 5 131 " --> pdb=" O ASN 5 128 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG 5 132 " --> pdb=" O TRP 5 129 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET 5 137 " --> pdb=" O ILE 5 134 " (cutoff:3.500A) removed outlier: 4.016A 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 25 through 42 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: 5.918A pdb=" N ALA 9 163 " --> pdb=" O ASP 9 159 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N GLU 9 164 " --> pdb=" O LYS 9 160 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ALA 9 167 " --> pdb=" O ALA 9 163 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N LEU 9 174 " --> pdb=" O GLN 9 170 " (cutoff:3.500A) removed outlier: 6.017A 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: 5.507A pdb=" N TRP A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.720A 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: 3.637A pdb=" N THR H 21 " --> pdb=" O VAL H 17 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN H 32 " --> pdb=" O LEU H 28 " (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 56 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: 3.721A pdb=" N ALA H 112 " --> pdb=" O MET H 108 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ILE H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 156 removed outlier: 3.667A pdb=" N ILE H 130 " --> pdb=" O LYS H 126 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL H 144 " --> pdb=" O ILE H 140 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N MET H 156 " --> pdb=" O SER H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 170 removed outlier: 3.704A pdb=" N GLN H 169 " --> pdb=" O LEU H 165 " (cutoff:3.500A) removed outlier: 3.766A 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 2 through 21 removed outlier: 5.116A pdb=" N VAL J 6 " --> pdb=" O THR J 3 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE J 20 " --> pdb=" O PHE J 17 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER J 21 " --> pdb=" O VAL J 18 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 47 removed outlier: 3.565A pdb=" N PHE J 47 " --> pdb=" O ILE J 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 74 removed outlier: 4.297A pdb=" N LEU J 61 " --> pdb=" O PHE J 57 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY J 62 " --> pdb=" O LEU J 58 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N MET J 65 " --> pdb=" O LEU J 61 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N VAL J 66 " --> pdb=" O GLY J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 110 Processing helix chain 'J' and resid 138 through 148 removed outlier: 4.008A pdb=" N LEU J 146 " --> pdb=" O GLY J 142 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N TYR J 147 " --> pdb=" O ILE J 143 " (cutoff:3.500A) removed outlier: 4.198A 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: 3.657A pdb=" N ASN K 7 " --> pdb=" O LEU K 3 " (cutoff:3.500A) Processing helix chain 'K' and resid 27 through 51 Processing helix chain 'K' and resid 55 through 85 removed outlier: 3.577A pdb=" N MET K 58 " --> pdb=" O LEU K 55 " (cutoff:3.500A) Proline residue: K 60 - end of helix removed outlier: 3.616A pdb=" N PHE K 66 " --> pdb=" O LEU K 63 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA K 67 " --> pdb=" O LEU K 64 " (cutoff:3.500A) removed outlier: 3.948A 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: 3.687A 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: 4.076A pdb=" N ILE L 49 " --> pdb=" O ILE L 45 " (cutoff:3.500A) Proline residue: L 50 - end of helix removed outlier: 3.884A pdb=" N THR L 57 " --> pdb=" O MET L 53 " (cutoff:3.500A) Processing helix chain 'L' and resid 84 through 110 Proline residue: L 91 - end of helix removed outlier: 4.010A pdb=" N TRP L 106 " --> pdb=" O GLU L 102 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N HIS L 109 " --> pdb=" O MET L 105 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N SER L 110 " --> pdb=" O TRP L 106 " (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: 3.985A 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: 3.503A pdb=" N SER L 235 " --> pdb=" O PRO L 231 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N MET L 237 " --> pdb=" O LEU L 233 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N GLU L 238 " --> pdb=" O PRO L 234 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 247 Processing helix chain 'L' and resid 255 through 262 Processing helix chain 'L' and resid 264 through 267 No H-bonds generated for 'chain 'L' and resid 264 through 267' Processing helix chain 'L' and resid 271 through 293 removed outlier: 3.684A pdb=" N ALA L 289 " --> pdb=" O THR L 285 " (cutoff:3.500A) removed outlier: 3.759A 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: 4.422A pdb=" N PHE L 334 " --> pdb=" O CYS L 330 " (cutoff:3.500A) removed outlier: 4.052A 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 381 Processing helix chain 'L' and resid 389 through 400 removed outlier: 5.187A pdb=" N LEU L 394 " --> pdb=" O TYR L 390 " (cutoff:3.500A) Processing helix chain 'L' and resid 406 through 431 removed outlier: 3.703A pdb=" N ALA L 420 " --> pdb=" O THR L 416 " (cutoff:3.500A) Processing helix chain 'L' and resid 448 through 471 removed outlier: 3.757A pdb=" N LEU L 457 " --> pdb=" O SER L 453 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N GLY L 465 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 5.279A 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 506 Processing helix chain 'L' and resid 518 through 524 Processing helix chain 'L' and resid 526 through 546 removed outlier: 4.003A pdb=" N TYR L 529 " --> pdb=" O LEU L 526 " (cutoff:3.500A) Proline residue: L 530 - end of helix removed outlier: 4.679A pdb=" N MET L 533 " --> pdb=" O PRO L 530 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N HIS L 534 " --> pdb=" O THR L 531 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N THR L 537 " --> pdb=" O HIS L 534 " (cutoff:3.500A) Proline residue: L 538 - end of helix removed outlier: 3.530A pdb=" N ASN L 541 " --> pdb=" O PRO L 538 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N THR L 543 " --> pdb=" O MET L 540 " (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: 4.194A 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 25 through 42 removed outlier: 4.119A pdb=" N LEU M 39 " --> pdb=" O SER M 35 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU M 40 " --> pdb=" O LEU M 36 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N LEU M 41 " --> pdb=" O THR M 37 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N LEU M 42 " --> pdb=" O SER M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 81 removed outlier: 3.719A pdb=" N LEU M 73 " --> pdb=" O THR M 69 " (cutoff:3.500A) Proline residue: M 74 - end of helix removed outlier: 3.704A pdb=" N GLN M 81 " --> pdb=" O LEU M 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 89 through 107 Processing helix chain 'M' and resid 115 through 136 removed outlier: 4.587A pdb=" N LEU M 126 " --> pdb=" O PHE M 122 " (cutoff:3.500A) removed outlier: 4.669A 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: 3.767A pdb=" N LEU M 143 " --> pdb=" O THR M 140 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASN M 144 " --> pdb=" O GLU M 141 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA M 145 " --> pdb=" O ARG M 142 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE M 149 " --> pdb=" O GLY M 146 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE M 151 " --> pdb=" O TYR M 148 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N TYR M 152 " --> pdb=" O PHE M 149 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LEU M 154 " --> pdb=" O PHE M 151 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LEU M 158 " --> pdb=" O ALA M 155 " (cutoff:3.500A) Proline residue: M 159 - end of helix removed outlier: 4.342A 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: 4.834A pdb=" N ALA M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N PHE M 203 " --> pdb=" O CYS M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 216 through 222 removed outlier: 4.614A pdb=" N VAL M 221 " --> pdb=" O PRO M 217 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 233 Processing helix chain 'M' and resid 237 through 248 removed outlier: 4.632A 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 278 removed outlier: 4.075A pdb=" N ILE M 270 " --> pdb=" O LEU M 266 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER M 273 " --> pdb=" O MET M 269 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG M 278 " --> pdb=" O SER M 274 " (cutoff:3.500A) Processing helix chain 'M' and resid 282 through 303 removed outlier: 4.125A pdb=" N LEU M 296 " --> pdb=" O SER M 292 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL M 297 " --> pdb=" O HIS M 293 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 337 removed outlier: 4.193A pdb=" N ARG M 336 " --> pdb=" O SER M 332 " (cutoff:3.500A) Processing helix chain 'M' and resid 348 through 351 No H-bonds generated for 'chain 'M' and resid 348 through 351' 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: 3.642A pdb=" N ILE M 393 " --> pdb=" O ASN M 390 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET M 396 " --> pdb=" O ILE M 393 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY M 397 " --> pdb=" O ILE M 394 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER M 407 " --> pdb=" O ALA M 404 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU M 408 " --> pdb=" O LEU M 405 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE M 412 " --> pdb=" O TYR M 409 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR M 414 " --> pdb=" O LEU M 411 " (cutoff:3.500A) removed outlier: 3.891A 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: 3.846A pdb=" N SER M 448 " --> pdb=" O LEU M 444 " (cutoff:3.500A) Processing helix chain 'M' and resid 451 through 454 removed outlier: 3.529A pdb=" N ILE M 454 " --> pdb=" O PRO M 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 451 through 454' Processing helix chain 'M' and resid 456 through 458 No H-bonds generated for 'chain 'M' and resid 456 through 458' 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 Processing helix chain 'N' and resid 124 through 144 removed outlier: 4.275A pdb=" N GLN N 134 " --> pdb=" O LEU N 130 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N LYS N 135 " --> pdb=" O LEU N 131 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU N 136 " --> pdb=" O THR N 132 " (cutoff:3.500A) removed outlier: 4.593A 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: 4.150A pdb=" N GLY N 169 " --> pdb=" O GLY N 165 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU N 170 " --> pdb=" O GLY N 166 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ASN N 171 " --> pdb=" O TRP N 167 " (cutoff:3.500A) Processing helix chain 'N' and resid 175 through 193 removed outlier: 3.922A pdb=" N VAL N 193 " --> pdb=" O TRP N 189 " (cutoff:3.500A) Processing helix chain 'N' and resid 198 through 222 Processing helix chain 'N' and resid 227 through 235 removed outlier: 4.108A pdb=" N HIS N 232 " --> pdb=" O LEU N 228 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N THR N 233 " --> pdb=" O SER N 229 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N TRP N 234 " --> pdb=" O LEU N 230 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N ASN N 235 " --> pdb=" O SER N 231 " (cutoff:3.500A) Processing helix chain 'N' and resid 238 through 251 removed outlier: 3.599A pdb=" N ILE N 242 " --> pdb=" O PRO N 238 " (cutoff:3.500A) Processing helix chain 'N' and resid 259 through 270 removed outlier: 4.664A pdb=" N LYS N 263 " --> pdb=" O GLY N 259 " (cutoff:3.500A) Processing helix chain 'N' and resid 277 through 300 removed outlier: 3.945A pdb=" N LEU N 287 " --> pdb=" O ALA N 283 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LEU N 288 " --> pdb=" O ILE N 284 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASN N 289 " --> pdb=" O THR N 285 " (cutoff:3.500A) Processing helix chain 'N' and resid 309 through 316 removed outlier: 3.685A pdb=" N TRP N 315 " --> pdb=" O LYS N 312 " (cutoff:3.500A) Processing helix chain 'N' and resid 326 through 334 Processing helix chain 'N' and resid 337 through 346 Proline residue: N 341 - end of helix removed outlier: 3.629A 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 49 through 80 Processing helix chain 'V' and resid 86 through 103 Processing helix chain 'V' and resid 107 through 130 Processing helix chain 'W' and resid 15 through 46 removed outlier: 3.659A pdb=" N LYS W 19 " --> pdb=" O GLY W 15 " (cutoff:3.500A) removed outlier: 4.617A 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: 3.761A 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 116 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 20 Processing helix chain 'X' and resid 44 through 58 Processing helix chain 'X' and resid 64 through 69 removed outlier: 4.596A 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 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 54 No H-bonds generated for 'chain 'Y' and resid 52 through 54' Processing helix chain 'Y' and resid 56 through 76 removed outlier: 4.082A pdb=" N HIS Y 76 " --> pdb=" O GLN Y 72 " (cutoff:3.500A) Processing helix chain 'Y' and resid 78 through 90 removed outlier: 3.593A 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 56 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: 4.249A 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: 4.720A pdb=" N LYS a 60 " --> pdb=" O LEU a 56 " (cutoff:3.500A) Processing helix chain 'b' and resid 23 through 28 removed outlier: 3.799A pdb=" N ARG b 27 " --> pdb=" O ARG b 24 " (cutoff:3.500A) Processing helix chain 'b' and resid 40 through 45 removed outlier: 3.838A pdb=" N ALA b 45 " --> pdb=" O ILE b 41 " (cutoff:3.500A) 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 27 through 31 removed outlier: 4.321A pdb=" N LYS c 31 " --> pdb=" O GLU c 28 " (cutoff:3.500A) 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 81 removed outlier: 4.276A pdb=" N ASN c 81 " --> pdb=" O PRO c 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 78 through 81' 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 39 removed outlier: 3.893A pdb=" N TYR d 33 " --> pdb=" O PHE d 29 " (cutoff:3.500A) Processing helix chain 'd' and resid 53 through 62 removed outlier: 5.122A 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 87 removed outlier: 5.848A pdb=" N HIS d 87 " --> pdb=" O ARG d 83 " (cutoff:3.500A) Processing helix chain 'd' and resid 106 through 110 Processing helix chain 'd' and resid 112 through 123 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 310 through 312 No H-bonds generated for 'chain 'd' and resid 310 through 312' Processing helix chain 'd' and resid 314 through 321 removed outlier: 5.458A pdb=" N ARG d 320 " --> pdb=" O GLU d 316 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N HIS d 321 " --> pdb=" O VAL d 317 " (cutoff:3.500A) Processing helix chain 'e' and resid 27 through 38 removed outlier: 4.633A pdb=" N GLY e 31 " --> pdb=" O GLY e 28 " (cutoff:3.500A) Processing helix chain 'e' and resid 41 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: 4.324A 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: 3.715A 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: 3.920A 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: 4.779A 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 55 No H-bonds generated for 'chain 'h' and resid 53 through 55' Processing helix chain 'h' and resid 59 through 61 No H-bonds generated for 'chain 'h' and resid 59 through 61' Processing helix chain 'i' and resid 2 through 16 Processing helix chain 'i' and resid 20 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: 3.974A pdb=" N ARG i 88 " --> pdb=" O PRO i 84 " (cutoff:3.500A) removed outlier: 4.599A 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 64 through 67 No H-bonds generated for 'chain 'j' and resid 64 through 67' Processing helix chain 'j' and resid 73 through 83 Processing helix chain 'k' and resid 5 through 10 Processing helix chain 'k' and resid 35 through 45 removed outlier: 4.217A pdb=" N ALA k 39 " --> pdb=" O SEP k 36 " (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 131 through 140 Processing helix chain 'k' and resid 146 through 162 removed outlier: 4.331A pdb=" N CYS k 161 " --> pdb=" O LYS k 157 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU k 162 " --> pdb=" O VAL k 158 " (cutoff:3.500A) Processing helix chain 'k' and resid 176 through 186 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: 5.576A pdb=" N LEU k 211 " --> pdb=" O LYS k 207 " (cutoff:3.500A) Proline residue: k 212 - end of helix removed outlier: 4.631A pdb=" N GLU k 216 " --> pdb=" O PRO k 212 " (cutoff:3.500A) removed outlier: 4.293A 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 264 Processing helix chain 'k' and resid 266 through 271 Processing helix chain 'k' and resid 286 through 297 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 48 through 54 removed outlier: 3.847A 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 88 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 5 through 14 Processing helix chain 'm' and resid 16 through 34 Proline residue: m 32 - end of helix Processing helix chain 'm' and resid 38 through 46 removed outlier: 3.689A 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 48 through 50 No H-bonds generated for 'chain 'n' and resid 48 through 50' Processing helix chain 'n' and resid 54 through 56 No H-bonds generated for 'chain 'n' and resid 54 through 56' Processing helix chain 'n' and resid 62 through 66 Processing helix chain 'n' and resid 70 through 88 removed outlier: 3.753A pdb=" N GLU n 88 " --> pdb=" O GLU n 84 " (cutoff:3.500A) 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 removed outlier: 3.628A pdb=" N ARG o 19 " --> pdb=" O ASP o 16 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER o 20 " --> pdb=" O GLU o 17 " (cutoff:3.500A) No H-bonds generated for '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: 3.929A pdb=" N TYR o 74 " --> pdb=" O PHE o 70 " (cutoff:3.500A) Processing helix chain 'p' and resid 19 through 22 removed outlier: 3.716A pdb=" N TYR p 22 " --> pdb=" O PRO p 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 19 through 22' Processing helix chain 'p' and resid 26 through 50 removed outlier: 4.062A pdb=" N GLN p 49 " --> pdb=" O GLU p 45 " (cutoff:3.500A) Processing helix chain 'p' and resid 62 through 72 removed outlier: 3.589A pdb=" N SER p 72 " --> pdb=" O THR p 68 " (cutoff:3.500A) Processing helix chain 'p' and resid 76 through 78 No H-bonds generated for 'chain 'p' and resid 76 through 78' Processing helix chain 'p' and resid 83 through 92 Processing helix chain 'p' and resid 95 through 116 Processing helix chain 'q' and resid 31 through 96 Proline residue: q 72 - end of helix Processing helix chain 'q' and resid 120 through 124 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: 3.544A 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 59 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 72 Processing helix chain 't' and resid 92 through 95 removed outlier: 4.401A pdb=" N CYS t 95 " --> pdb=" O ARG t 92 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 92 through 95' Processing helix chain 't' and resid 100 through 103 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: 4.129A pdb=" N GLN t 123 " --> pdb=" O ALA t 119 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TRP t 124 " --> pdb=" O LYS t 120 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N GLU t 133 " --> pdb=" O ARG t 129 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ARG t 134 " --> pdb=" O GLU t 130 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU t 141 " --> pdb=" O LYS t 137 " (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 56 through 58 No H-bonds generated for 'chain 'u' and resid 56 through 58' 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 55 through 57 No H-bonds generated for 'chain 'v' and resid 55 through 57' Processing helix chain 'v' and resid 98 through 121 Processing helix chain 'v' and resid 134 through 138 Processing helix chain 'w' and resid 37 through 40 No H-bonds generated for 'chain 'w' and resid 37 through 40' 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: 4.087A pdb=" N GLN w 86 " --> pdb=" O TYR w 83 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N GLU w 87 " --> pdb=" O ARG w 84 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TRP w 88 " --> pdb=" O MET w 85 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU w 92 " --> pdb=" O ALA w 89 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL w 97 " --> pdb=" O GLU w 94 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLU w 101 " --> pdb=" O LYS w 98 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA w 102 " --> pdb=" O TYR w 99 " (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 45 Processing helix chain 'y' and resid 11 through 14 removed outlier: 3.733A 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: 3.630A pdb=" N GLU y 32 " --> pdb=" O ARG y 28 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS y 33 " --> pdb=" O LYS y 29 " (cutoff:3.500A) Processing helix chain 'z' and resid 2 through 29 Proline residue: z 7 - end of helix removed outlier: 4.141A pdb=" N ILE z 18 " --> pdb=" O CYS z 15 " (cutoff:3.500A) Proline residue: z 19 - end of helix Processing helix chain 'z' and resid 42 through 55 Processing helix chain 'z' and resid 66 through 68 No H-bonds generated for 'chain 'z' and resid 66 through 68' Processing sheet with id= A, first strand: chain '1' and resid 219 through 224 removed outlier: 6.086A pdb=" N ALA 1 133 " --> pdb=" O LEU 1 93 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL 1 95 " --> pdb=" O ALA 1 133 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N TYR 1 135 " --> pdb=" O VAL 1 95 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ALA 1 97 " --> pdb=" O TYR 1 135 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N TYR 1 137 " --> pdb=" O ALA 1 97 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ASP 1 174 " --> pdb=" O ALA 1 134 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ILE 1 136 " --> pdb=" O ASP 1 174 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE 1 176 " --> pdb=" O ILE 1 136 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ILE 1 138 " --> pdb=" O PHE 1 176 " (cutoff:3.500A) removed outlier: 6.029A 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: 6.442A pdb=" N TYR 2 98 " --> pdb=" O THR 2 138 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ILE 2 140 " --> pdb=" O TYR 2 98 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ILE 2 100 " --> pdb=" O ILE 2 140 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL 2 142 " --> pdb=" O ILE 2 100 " (cutoff:3.500A) removed outlier: 6.133A 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: 3.609A 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: 8.757A pdb=" N CYS 3 344 " --> pdb=" O VAL 3 315 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA 3 317 " --> pdb=" O CYS 3 344 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N MET 3 521 " --> pdb=" O ALA 3 316 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ILE 3 318 " --> pdb=" O MET 3 521 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N PHE 3 523 " --> pdb=" O ILE 3 318 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N PHE 3 542 " --> pdb=" O LEU 3 522 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N LEU 3 524 " --> pdb=" O PHE 3 542 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL 3 544 " --> pdb=" O LEU 3 524 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL 3 559 " --> pdb=" O TYR 3 545 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N GLY 3 547 " --> pdb=" O VAL 3 559 " (cutoff:3.500A) removed outlier: 6.153A 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: 8.301A pdb=" N ASN 3 491 " --> pdb=" O PRO 3 449 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N VAL 3 451 " --> pdb=" O ASN 3 491 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N LEU 3 493 " --> pdb=" O VAL 3 451 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU 3 453 " --> pdb=" O LEU 3 493 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL 3 376 " --> pdb=" O MET 3 450 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N VAL 3 452 " --> pdb=" O VAL 3 376 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU 3 378 " --> pdb=" O VAL 3 452 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N GLY 3 454 " --> pdb=" O LEU 3 378 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N VAL 3 380 " --> pdb=" O GLY 3 454 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LYS 3 405 " --> pdb=" O VAL 3 377 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N LEU 3 379 " --> pdb=" O LYS 3 405 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ALA 3 407 " --> pdb=" O LEU 3 379 " (cutoff:3.500A) removed outlier: 6.391A 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 47 through 51 removed outlier: 3.523A pdb=" N ARG 4 63 " --> pdb=" O HIS 4 79 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS 4 75 " --> pdb=" O GLU 4 67 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N SER 4 69 " --> pdb=" O VAL 4 73 " (cutoff:3.500A) removed outlier: 6.423A 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 Processing sheet with id= N, first strand: chain '5' and resid 74 through 79 removed outlier: 6.706A pdb=" N ASN 5 95 " --> pdb=" O ALA 5 76 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU 5 78 " --> pdb=" O VAL 5 93 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL 5 93 " --> pdb=" O LEU 5 78 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE 5 105 " --> pdb=" O LEU 5 96 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LEU 5 48 " --> pdb=" O ARG 5 106 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N LYS 5 108 " --> pdb=" O LEU 5 48 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE 5 50 " --> pdb=" O LYS 5 108 " (cutoff:3.500A) removed outlier: 8.618A pdb=" N TYR 5 110 " --> pdb=" O ILE 5 50 " (cutoff:3.500A) removed outlier: 8.677A 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: 6.480A pdb=" N VAL 6 85 " --> pdb=" O MET 6 48 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N PHE 6 50 " --> pdb=" O VAL 6 85 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE 6 87 " --> pdb=" O PHE 6 50 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TYR 6 112 " --> pdb=" O MET 6 86 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N VAL 6 88 " --> pdb=" O TYR 6 112 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL 6 114 " --> pdb=" O VAL 6 88 " (cutoff:3.500A) removed outlier: 6.222A 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: 5.880A pdb=" N GLU 9 97 " --> pdb=" O THR 9 106 " (cutoff:3.500A) removed outlier: 5.077A 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: 6.522A 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: 7.721A pdb=" N PHE d 228 " --> pdb=" O ALA d 163 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE d 165 " --> pdb=" O PHE d 228 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N PHE d 230 " --> pdb=" O ILE d 165 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N LYS d 167 " --> pdb=" O PHE d 230 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N PHE d 129 " --> pdb=" O THR d 164 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N ILE d 166 " --> pdb=" O PHE d 129 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N HIS d 131 " --> pdb=" O ILE d 166 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N SER d 133 " --> pdb=" O PRO d 168 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE d 132 " --> pdb=" O ASN d 93 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N GLN d 44 " --> pdb=" O ALA d 21 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N VAL d 23 " --> pdb=" O GLN d 44 " (cutoff:3.500A) removed outlier: 6.817A 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: 3.626A pdb=" N LEU e 22 " --> pdb=" O ARG e 55 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ARG e 67 " --> pdb=" O ARG e 16 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ILE e 18 " --> pdb=" O TRP e 65 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TRP e 65 " --> pdb=" O ILE e 18 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ILE e 20 " --> pdb=" O LYS e 63 " (cutoff:3.500A) removed outlier: 6.684A 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: 3.617A pdb=" N GLY i 40 " --> pdb=" O TYR i 48 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLU i 50 " --> pdb=" O LEU i 38 " (cutoff:3.500A) removed outlier: 5.560A 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: 6.374A pdb=" N VAL k 168 " --> pdb=" O THR k 26 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ASP k 28 " --> pdb=" O VAL k 168 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILE k 170 " --> pdb=" O ASP k 28 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N GLU k 219 " --> pdb=" O VAL k 169 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N TYR k 171 " --> pdb=" O GLU k 219 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N LEU k 221 " --> pdb=" O TYR k 171 " (cutoff:3.500A) 2784 hydrogen bonds defined for protein. 7746 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: 23.55 Time building geometry restraints manager: 24.38 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: 28401 1.43 - 1.66: 39894 1.66 - 1.90: 756 1.90 - 2.13: 0 2.13 - 2.36: 80 Bond restraints: 69131 Sorted by residual: bond pdb=" OA3 CDL z 101 " pdb=" PA1 CDL z 101 " ideal model delta sigma weight residual 1.529 1.466 0.063 1.00e-02 1.00e+04 3.91e+01 bond pdb=" C16 ZMP g 201 " pdb=" N2 ZMP g 201 " ideal model delta sigma weight residual 1.452 1.329 0.123 2.00e-02 2.50e+03 3.76e+01 bond pdb=" O2B NDP d 401 " pdb=" P2B NDP d 401 " ideal model delta sigma weight residual 1.833 1.600 0.233 3.80e-02 6.93e+02 3.75e+01 bond pdb=" OB3 CDL W 201 " pdb=" PB2 CDL W 201 " ideal model delta sigma weight residual 1.529 1.469 0.060 1.00e-02 1.00e+04 3.63e+01 bond pdb=" C13 ZMP g 201 " pdb=" N1 ZMP g 201 " ideal model delta sigma weight residual 1.451 1.338 0.113 2.00e-02 2.50e+03 3.16e+01 ... (remaining 69126 not shown) Histogram of bond angle deviations from ideal: 61.98 - 77.61: 74 77.61 - 93.24: 9 93.24 - 108.86: 5977 108.86 - 124.49: 85655 124.49 - 140.12: 1711 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 72.90 47.70 3.00e+00 1.11e-01 2.53e+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 71.32 37.98 3.00e+00 1.11e-01 1.60e+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 90.00 14.33 1.14e+00 7.69e-01 1.58e+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 89.94 14.39 1.20e+00 6.94e-01 1.44e+02 angle pdb=" PA NDP d 401 " pdb=" O3 NDP d 401 " pdb=" PN NDP d 401 " ideal model delta sigma weight residual 107.74 130.71 -22.97 1.95e+00 2.62e-01 1.38e+02 ... (remaining 93421 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.78: 41313 34.78 - 69.55: 701 69.55 - 104.33: 50 104.33 - 139.10: 4 139.10 - 173.88: 5 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 -131.04 -48.96 0 5.00e+00 4.00e-02 9.59e+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 -136.39 -43.61 0 5.00e+00 4.00e-02 7.61e+01 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 -138.45 -41.55 0 5.00e+00 4.00e-02 6.91e+01 ... (remaining 42070 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.224: 10089 4.224 - 8.448: 5 8.448 - 12.672: 0 12.672 - 16.896: 0 16.896 - 21.120: 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 -10.57 21.12 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 -10.55 21.11 2.00e-01 2.50e+01 1.11e+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 10.55 -21.10 2.00e-01 2.50e+01 1.11e+04 ... (remaining 10115 not shown) Planarity restraints: 11647 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 DCQ 6 203 " 0.002 2.00e-02 2.50e+03 6.01e-02 1.08e+02 pdb=" C1M DCQ 6 203 " 0.017 2.00e-02 2.50e+03 pdb=" C2 DCQ 6 203 " -0.017 2.00e-02 2.50e+03 pdb=" C3 DCQ 6 203 " -0.008 2.00e-02 2.50e+03 pdb=" C4 DCQ 6 203 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DCQ 6 203 " -0.029 2.00e-02 2.50e+03 pdb=" C6 DCQ 6 203 " 0.019 2.00e-02 2.50e+03 pdb=" C7 DCQ 6 203 " 0.070 2.00e-02 2.50e+03 pdb=" O2 DCQ 6 203 " -0.027 2.00e-02 2.50e+03 pdb=" O3 DCQ 6 203 " -0.022 2.00e-02 2.50e+03 pdb=" O4 DCQ 6 203 " 0.128 2.00e-02 2.50e+03 pdb=" O5 DCQ 6 203 " -0.137 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR 9 40 " 0.022 2.00e-02 2.50e+03 3.05e-02 1.86e+01 pdb=" CG TYR 9 40 " -0.070 2.00e-02 2.50e+03 pdb=" CD1 TYR 9 40 " 0.039 2.00e-02 2.50e+03 pdb=" CD2 TYR 9 40 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR 9 40 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR 9 40 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR 9 40 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR 9 40 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP 1 371 " 0.032 2.00e-02 2.50e+03 2.57e-02 1.65e+01 pdb=" CG TRP 1 371 " -0.068 2.00e-02 2.50e+03 pdb=" CD1 TRP 1 371 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP 1 371 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP 1 371 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP 1 371 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP 1 371 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP 1 371 " 0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP 1 371 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP 1 371 " 0.000 2.00e-02 2.50e+03 ... (remaining 11644 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.81: 18599 2.81 - 3.39: 72503 3.39 - 3.97: 139752 3.97 - 4.56: 197246 4.56 - 5.14: 286520 Nonbonded interactions: 714620 Sorted by model distance: nonbonded pdb=" O ILE L 556 " pdb=" OG1 THR L 560 " model vdw 2.224 2.440 nonbonded pdb=" OE2 GLU 4 224 " pdb=" OH TYR 9 40 " model vdw 2.237 2.440 nonbonded pdb=" O PHE M 105 " pdb=" OG1 THR M 109 " model vdw 2.250 2.440 nonbonded pdb=" OH TYR k 108 " pdb=" O LEU k 164 " model vdw 2.252 2.440 nonbonded pdb=" O GLU c 28 " pdb=" OG1 THR c 32 " model vdw 2.253 2.440 ... (remaining 714615 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 5.380 Check model and map are aligned: 0.760 Set scattering table: 0.510 Process input model: 166.880 Find NCS groups from input model: 2.230 Set up NCS constraints: 0.270 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:12.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 188.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 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 : 0.008 0.233 69131 Z= 0.505 Angle : 1.016 47.703 93426 Z= 0.532 Chirality : 1.026 21.120 10118 Planarity : 0.008 0.067 11647 Dihedral : 12.601 173.877 26714 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.01 % Favored : 95.95 % Rotamer: Outliers : 0.04 % Allowed : 2.26 % Favored : 97.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.97 (0.08), residues: 8046 helix: -1.91 (0.06), residues: 4235 sheet: -1.64 (0.25), residues: 320 loop : -1.93 (0.09), residues: 3491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.004 TRP 1 371 HIS 0.018 0.003 HIS t 25 PHE 0.057 0.004 PHE 4 171 TYR 0.070 0.003 TYR 9 40 ARG 0.021 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 1887 residues out of total 7132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1884 time to evaluate : 6.079 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 16 LYS cc_start: 0.8044 (mtmm) cc_final: 0.7808 (tptm) REVERT: 1 436 GLN cc_start: 0.7761 (pt0) cc_final: 0.7370 (tm-30) REVERT: 2 127 LYS cc_start: 0.8362 (ptpt) cc_final: 0.7603 (mmmm) REVERT: 3 16 GLN cc_start: 0.8660 (tt0) cc_final: 0.8395 (tm-30) REVERT: 3 95 GLU cc_start: 0.8866 (tt0) cc_final: 0.8515 (tp30) REVERT: 3 169 VAL cc_start: 0.8358 (t) cc_final: 0.7873 (t) REVERT: 3 347 GLU cc_start: 0.8581 (tt0) cc_final: 0.8243 (mm-30) REVERT: 3 444 GLN cc_start: 0.7250 (mm-40) cc_final: 0.7035 (tt0) REVERT: 3 450 MET cc_start: 0.8914 (ttt) cc_final: 0.8693 (ttt) REVERT: 3 640 ASN cc_start: 0.8013 (t0) cc_final: 0.7592 (m-40) REVERT: 4 170 MET cc_start: 0.9105 (mmm) cc_final: 0.8569 (mmm) REVERT: 5 43 SER cc_start: 0.9107 (p) cc_final: 0.8634 (m) REVERT: 6 25 ARG cc_start: 0.5950 (ttt180) cc_final: 0.5545 (tpp-160) REVERT: 6 102 LYS cc_start: 0.8872 (tttt) cc_final: 0.8634 (tppt) REVERT: 9 1 THR cc_start: 0.8438 (t) cc_final: 0.8180 (m) REVERT: 9 8 ARG cc_start: 0.7396 (mmt90) cc_final: 0.7069 (mpp-170) REVERT: A 16 LEU cc_start: 0.8510 (tp) cc_final: 0.8139 (mm) REVERT: A 23 TRP cc_start: 0.6935 (m100) cc_final: 0.5983 (t60) REVERT: H 31 MET cc_start: 0.9151 (mtt) cc_final: 0.8913 (mtm) REVERT: J 169 MET cc_start: 0.7990 (mtp) cc_final: 0.7780 (mtp) REVERT: L 214 MET cc_start: 0.8526 (mmp) cc_final: 0.8012 (ttt) REVERT: L 544 MET cc_start: 0.6395 (tmm) cc_final: 0.6140 (tpp) REVERT: L 566 ILE cc_start: 0.7614 (mt) cc_final: 0.7383 (tt) REVERT: M 114 GLU cc_start: 0.8755 (tm-30) cc_final: 0.8495 (tt0) REVERT: M 157 SER cc_start: 0.8315 (p) cc_final: 0.7991 (m) REVERT: M 355 MET cc_start: 0.9176 (tpp) cc_final: 0.8891 (tpp) REVERT: N 181 TYR cc_start: 0.9107 (m-80) cc_final: 0.8797 (m-80) REVERT: V 57 ARG cc_start: 0.7041 (ttp-110) cc_final: 0.6655 (tpp-160) REVERT: V 72 THR cc_start: 0.7542 (m) cc_final: 0.7207 (p) REVERT: V 119 LEU cc_start: 0.8283 (mt) cc_final: 0.7914 (tt) REVERT: W 18 ASP cc_start: 0.8344 (m-30) cc_final: 0.8128 (m-30) REVERT: X 48 VAL cc_start: 0.8148 (t) cc_final: 0.7820 (m) REVERT: b 54 SER cc_start: 0.8713 (t) cc_final: 0.8369 (m) REVERT: b 80 LYS cc_start: 0.7772 (ttpp) cc_final: 0.7535 (tttp) REVERT: c 91 ASP cc_start: 0.8780 (m-30) cc_final: 0.8502 (m-30) REVERT: d 301 GLU cc_start: 0.8558 (mp0) cc_final: 0.7973 (pm20) REVERT: e 34 ASP cc_start: 0.8551 (m-30) cc_final: 0.8312 (m-30) REVERT: g 56 LYS cc_start: 0.8967 (tmmt) cc_final: 0.8746 (tppt) REVERT: g 67 LYS cc_start: 0.8790 (mttt) cc_final: 0.8520 (mmtm) REVERT: g 84 LYS cc_start: 0.9061 (mtpt) cc_final: 0.8767 (mtmm) REVERT: h 6 LEU cc_start: 0.8605 (tt) cc_final: 0.8396 (mp) REVERT: h 18 ASP cc_start: 0.8444 (t0) cc_final: 0.8193 (t70) REVERT: h 39 LYS cc_start: 0.8760 (tptm) cc_final: 0.8309 (ttpt) REVERT: i 1 MET cc_start: 0.7617 (tpt) cc_final: 0.6699 (mtt) REVERT: i 25 ARG cc_start: 0.8968 (ttt90) cc_final: 0.8307 (ttm170) REVERT: i 145 LYS cc_start: 0.6782 (mmtt) cc_final: 0.6568 (mmpt) REVERT: j 37 MET cc_start: 0.7094 (mmt) cc_final: 0.6665 (mpp) REVERT: j 66 ASP cc_start: 0.7507 (p0) cc_final: 0.7204 (p0) REVERT: j 70 LEU cc_start: 0.8435 (mt) cc_final: 0.8121 (mt) REVERT: k 19 THR cc_start: 0.8257 (t) cc_final: 0.8018 (m) REVERT: m 11 VAL cc_start: 0.9187 (p) cc_final: 0.8876 (m) REVERT: m 14 LYS cc_start: 0.8700 (mtmt) cc_final: 0.8417 (mmtt) REVERT: m 37 TYR cc_start: 0.8106 (m-10) cc_final: 0.7749 (m-10) REVERT: o 25 LYS cc_start: 0.8017 (mttt) cc_final: 0.7530 (mttm) REVERT: p 5 TYR cc_start: 0.6832 (t80) cc_final: 0.6567 (t80) REVERT: q 95 THR cc_start: 0.8328 (t) cc_final: 0.7846 (p) REVERT: q 104 LYS cc_start: 0.8544 (mmmt) cc_final: 0.8199 (ttpt) REVERT: s 61 TYR cc_start: 0.7375 (m-80) cc_final: 0.7160 (m-80) REVERT: u 16 GLN cc_start: 0.8274 (tt0) cc_final: 0.7900 (tp40) REVERT: u 32 MET cc_start: 0.8119 (ttp) cc_final: 0.7787 (ttp) REVERT: u 53 TYR cc_start: 0.7788 (t80) cc_final: 0.7572 (t80) REVERT: v 18 GLU cc_start: 0.6493 (pm20) cc_final: 0.6241 (tp30) REVERT: v 30 ARG cc_start: 0.7201 (mtp-110) cc_final: 0.6483 (mtp180) REVERT: v 117 TRP cc_start: 0.6537 (t60) cc_final: 0.6295 (t60) REVERT: w 56 TRP cc_start: 0.7255 (t60) cc_final: 0.7003 (m-10) REVERT: x 16 LYS cc_start: 0.8065 (ttmt) cc_final: 0.7635 (tptm) REVERT: y 30 ASN cc_start: 0.8634 (t0) cc_final: 0.8370 (t0) REVERT: z 25 ARG cc_start: 0.8557 (mtp85) cc_final: 0.8036 (ttp-170) REVERT: z 53 ARG cc_start: 0.8441 (mtm-85) cc_final: 0.8160 (mtm-85) outliers start: 3 outliers final: 4 residues processed: 1887 average time/residue: 1.6255 time to fit residues: 3912.0547 Evaluate side-chains 1127 residues out of total 7132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1123 time to evaluate : 5.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 54 CYS Chi-restraints excluded: chain L residue 426 ILE Chi-restraints excluded: chain N residue 335 MET Chi-restraints excluded: chain p residue 60 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 794 random chunks: chunk 670 optimal weight: 7.9990 chunk 601 optimal weight: 0.9990 chunk 333 optimal weight: 30.0000 chunk 205 optimal weight: 6.9990 chunk 405 optimal weight: 0.9980 chunk 321 optimal weight: 10.0000 chunk 622 optimal weight: 20.0000 chunk 240 optimal weight: 8.9990 chunk 378 optimal weight: 9.9990 chunk 463 optimal weight: 4.9990 chunk 721 optimal weight: 7.9990 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 24 ASN 1 148 ASN 1 250 ASN 1 356 HIS ** 1 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 121 GLN 3 179 ASN 3 237 ASN ** 3 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 401 HIS 3 441 GLN 3 444 GLN 3 546 GLN ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 150 HIS 4 201 GLN 4 409 HIS 5 69 ASN 5 200 ASN 6 162 GLN A 10 ASN H 97 ASN H 194 ASN ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 317 GLN K 7 ASN K 25 HIS K 50 ASN K 52 HIS K 83 ASN ** L 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 175 ASN L 296 ASN L 446 ASN ** L 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 605 HIS M 81 GLN M 82 HIS M 138 ASN M 144 ASN M 169 ASN M 175 ASN M 192 ASN M 279 GLN M 333 ASN M 366 ASN V 128 GLN Y 29 HIS Y 72 GLN Y 142 HIS Z 55 HIS Z 106 GLN Z 123 ASN ** Z 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 40 ASN a 55 ASN b 74 ASN b 95 HIS c 44 ASN d 87 HIS d 203 GLN d 250 HIS e 80 ASN g 57 GLN g 125 HIS h 8 GLN h 72 GLN h 107 GLN i 69 ASN i 91 HIS k 180 GLN k 200 GLN k 204 ASN l 6 GLN l 20 GLN ** l 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 81 GLN o 61 GLN p 49 GLN ** p 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 125 ASN s 46 ASN t 25 HIS t 61 GLN ** t 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 13 GLN u 50 HIS v 66 HIS v 137 ASN w 57 ASN x 13 ASN x 34 GLN x 46 ASN z 58 ASN Total number of N/Q/H flips: 84 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.336 69131 Z= 0.558 Angle : 1.586 51.334 93426 Z= 1.023 Chirality : 0.305 6.448 10118 Planarity : 0.005 0.058 11647 Dihedral : 13.026 174.382 10585 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.90 % Favored : 97.07 % Rotamer: Outliers : 3.31 % Allowed : 11.95 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.09), residues: 8046 helix: -0.20 (0.07), residues: 4256 sheet: -1.38 (0.24), residues: 354 loop : -1.29 (0.10), residues: 3436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP 1 371 HIS 0.017 0.001 HIS 9 65 PHE 0.035 0.002 PHE N 292 TYR 0.035 0.002 TYR H 215 ARG 0.008 0.001 ARG p 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 1451 residues out of total 7132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 1215 time to evaluate : 6.265 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: 1 16 LYS cc_start: 0.8066 (mtmm) cc_final: 0.7833 (tptm) REVERT: 1 129 MET cc_start: 0.9117 (mtm) cc_final: 0.8893 (ptp) REVERT: 1 302 SER cc_start: 0.8739 (m) cc_final: 0.8326 (p) REVERT: 1 436 GLN cc_start: 0.7632 (pt0) cc_final: 0.7358 (tm-30) REVERT: 2 127 LYS cc_start: 0.8357 (ptpt) cc_final: 0.7631 (mmmm) REVERT: 2 153 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.8531 (ppp) REVERT: 2 183 LYS cc_start: 0.8819 (mmtp) cc_final: 0.8608 (mmtp) REVERT: 3 95 GLU cc_start: 0.8832 (tt0) cc_final: 0.8556 (tp30) REVERT: 3 192 MET cc_start: 0.8332 (mmp) cc_final: 0.8118 (mmp) REVERT: 3 347 GLU cc_start: 0.8632 (tt0) cc_final: 0.8273 (mm-30) REVERT: 3 444 GLN cc_start: 0.7515 (mm110) cc_final: 0.7206 (tt0) REVERT: 3 450 MET cc_start: 0.8936 (ttt) cc_final: 0.8636 (ttt) REVERT: 3 640 ASN cc_start: 0.8004 (t0) cc_final: 0.7637 (m-40) REVERT: 4 12 GLU cc_start: 0.8734 (mm-30) cc_final: 0.8219 (tm-30) REVERT: 5 43 SER cc_start: 0.9086 (p) cc_final: 0.8656 (m) REVERT: 6 102 LYS cc_start: 0.8982 (tttt) cc_final: 0.8767 (tppt) REVERT: 9 1 THR cc_start: 0.8346 (t) cc_final: 0.8095 (m) REVERT: 9 15 LYS cc_start: 0.8334 (tptp) cc_final: 0.8048 (tppp) REVERT: A 16 LEU cc_start: 0.8513 (tp) cc_final: 0.8164 (mm) REVERT: A 23 TRP cc_start: 0.6724 (m100) cc_final: 0.6042 (t60) REVERT: H 1 MET cc_start: 0.7446 (tpp) cc_final: 0.7164 (tpp) REVERT: H 31 MET cc_start: 0.9130 (mtt) cc_final: 0.8801 (mtm) REVERT: H 199 ASP cc_start: 0.8364 (p0) cc_final: 0.8135 (p0) REVERT: K 10 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.8014 (ttp) REVERT: K 27 MET cc_start: 0.8755 (tpp) cc_final: 0.8539 (mmm) REVERT: L 214 MET cc_start: 0.8598 (mmp) cc_final: 0.8009 (ttt) REVERT: L 535 ARG cc_start: 0.8010 (mtt90) cc_final: 0.7794 (ttm170) REVERT: L 589 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.7031 (tt) REVERT: M 114 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8414 (tt0) REVERT: M 294 MET cc_start: 0.8506 (mmp) cc_final: 0.8225 (mmp) REVERT: M 355 MET cc_start: 0.9185 (tpp) cc_final: 0.8959 (tpp) REVERT: M 405 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8478 (mp) REVERT: N 71 MET cc_start: 0.9029 (tpp) cc_final: 0.8728 (tpt) REVERT: N 98 MET cc_start: 0.9005 (ttm) cc_final: 0.8686 (ttm) REVERT: N 181 TYR cc_start: 0.9197 (m-80) cc_final: 0.8922 (m-80) REVERT: V 57 ARG cc_start: 0.7028 (ttp-110) cc_final: 0.6654 (tpp-160) REVERT: V 119 LEU cc_start: 0.8293 (mt) cc_final: 0.7948 (tt) REVERT: X 48 VAL cc_start: 0.8053 (t) cc_final: 0.7744 (m) REVERT: X 68 GLU cc_start: 0.7039 (OUTLIER) cc_final: 0.6172 (tm-30) REVERT: Y 15 GLN cc_start: 0.7776 (OUTLIER) cc_final: 0.7549 (tt0) REVERT: Y 87 CYS cc_start: 0.8737 (t) cc_final: 0.8468 (p) REVERT: Y 89 ASP cc_start: 0.8385 (t0) cc_final: 0.7977 (t0) REVERT: Z 3 SER cc_start: 0.7523 (OUTLIER) cc_final: 0.7310 (m) REVERT: Z 39 LEU cc_start: 0.8384 (mm) cc_final: 0.7754 (mt) REVERT: Z 89 MET cc_start: 0.8823 (mmp) cc_final: 0.8591 (mmp) REVERT: a 74 ARG cc_start: 0.8742 (mtm-85) cc_final: 0.8486 (mtm110) REVERT: b 21 GLU cc_start: 0.8764 (pm20) cc_final: 0.8476 (pm20) REVERT: b 54 SER cc_start: 0.8811 (t) cc_final: 0.8512 (m) REVERT: b 78 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.7936 (mp0) REVERT: b 80 LYS cc_start: 0.7682 (ttpp) cc_final: 0.7391 (tttp) REVERT: c 91 ASP cc_start: 0.8877 (m-30) cc_final: 0.8606 (m-30) REVERT: e 34 ASP cc_start: 0.8803 (m-30) cc_final: 0.8540 (m-30) REVERT: e 56 GLU cc_start: 0.8865 (mt-10) cc_final: 0.8410 (mt-10) REVERT: e 74 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7663 (mttt) REVERT: g 56 LYS cc_start: 0.9046 (tmmt) cc_final: 0.8814 (ttmt) REVERT: h 17 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.6877 (mpp80) REVERT: h 18 ASP cc_start: 0.8496 (t0) cc_final: 0.8130 (t70) REVERT: h 39 LYS cc_start: 0.8752 (tptm) cc_final: 0.8265 (ttpt) REVERT: h 63 MET cc_start: 0.8896 (mmm) cc_final: 0.8646 (mmp) REVERT: i 1 MET cc_start: 0.7710 (tpt) cc_final: 0.6709 (mtt) REVERT: j 52 MET cc_start: 0.8262 (mtp) cc_final: 0.7846 (ttm) REVERT: j 66 ASP cc_start: 0.7913 (p0) cc_final: 0.7485 (p0) REVERT: k 19 THR cc_start: 0.8283 (t) cc_final: 0.8030 (m) REVERT: k 203 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8146 (mp0) REVERT: k 236 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7559 (mt-10) REVERT: m 14 LYS cc_start: 0.8690 (mtmt) cc_final: 0.8369 (mmmt) REVERT: m 31 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.9001 (mt) REVERT: m 37 TYR cc_start: 0.8127 (m-10) cc_final: 0.7767 (m-10) REVERT: m 43 MET cc_start: 0.9055 (OUTLIER) cc_final: 0.8845 (mtm) REVERT: n 13 MET cc_start: 0.5976 (pmm) cc_final: 0.4503 (tmm) REVERT: o 25 LYS cc_start: 0.7834 (mttt) cc_final: 0.7453 (mttm) REVERT: p 9 ARG cc_start: 0.7551 (OUTLIER) cc_final: 0.7183 (ttm-80) REVERT: q 95 THR cc_start: 0.8415 (t) cc_final: 0.7939 (p) REVERT: q 104 LYS cc_start: 0.8563 (mmmt) cc_final: 0.8040 (ttmt) REVERT: s 56 ASP cc_start: 0.7050 (OUTLIER) cc_final: 0.6795 (p0) REVERT: s 75 ASN cc_start: 0.8022 (t0) cc_final: 0.7815 (t0) REVERT: s 100 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7898 (mp0) REVERT: t 83 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.8061 (mp0) REVERT: u 16 GLN cc_start: 0.8092 (tt0) cc_final: 0.7775 (tp40) REVERT: u 26 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7538 (tt0) REVERT: u 53 TYR cc_start: 0.7756 (t80) cc_final: 0.7518 (t80) REVERT: v 30 ARG cc_start: 0.7024 (mtp-110) cc_final: 0.6708 (mtp180) REVERT: v 117 TRP cc_start: 0.6537 (t60) cc_final: 0.6299 (t60) REVERT: v 157 GLU cc_start: 0.6552 (mm-30) cc_final: 0.6321 (mp0) REVERT: w 56 TRP cc_start: 0.7439 (t60) cc_final: 0.6958 (m-10) REVERT: w 109 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.7987 (mp0) REVERT: x 16 LYS cc_start: 0.8160 (ttmt) cc_final: 0.7776 (tptm) REVERT: y 26 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8827 (mp) outliers start: 236 outliers final: 72 residues processed: 1332 average time/residue: 1.5403 time to fit residues: 2663.2600 Evaluate side-chains 1149 residues out of total 7132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 1058 time to evaluate : 6.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 249 ARG Chi-restraints excluded: chain 1 residue 292 ASP Chi-restraints excluded: chain 1 residue 314 THR Chi-restraints excluded: chain 2 residue 128 VAL Chi-restraints excluded: chain 2 residue 153 MET Chi-restraints excluded: chain 3 residue 128 SER Chi-restraints excluded: chain 3 residue 418 ARG Chi-restraints excluded: chain 3 residue 424 ASP Chi-restraints excluded: chain 3 residue 471 SER Chi-restraints excluded: chain 3 residue 532 VAL Chi-restraints excluded: chain 3 residue 659 ASP Chi-restraints excluded: chain 4 residue 164 MET Chi-restraints excluded: chain 4 residue 407 LYS Chi-restraints excluded: chain 6 residue 49 THR Chi-restraints excluded: chain 6 residue 84 ASP Chi-restraints excluded: chain 6 residue 137 ASP Chi-restraints excluded: chain 9 residue 16 SER Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 24 GLU Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain K residue 3 LEU Chi-restraints excluded: chain K residue 10 MET Chi-restraints excluded: chain L residue 217 ILE Chi-restraints excluded: chain L residue 426 ILE Chi-restraints excluded: chain L residue 484 HIS Chi-restraints excluded: chain L residue 505 SER Chi-restraints excluded: chain L residue 583 LEU Chi-restraints excluded: chain L residue 589 LEU Chi-restraints excluded: chain M residue 405 LEU Chi-restraints excluded: chain N residue 183 SER Chi-restraints excluded: chain N residue 308 THR Chi-restraints excluded: chain V residue 100 LEU Chi-restraints excluded: chain V residue 134 VAL Chi-restraints excluded: chain W residue 140 THR Chi-restraints excluded: chain X residue 26 ASP Chi-restraints excluded: chain X residue 68 GLU Chi-restraints excluded: chain Y residue 15 GLN Chi-restraints excluded: chain Y residue 63 ASN Chi-restraints excluded: chain Y residue 154 GLU Chi-restraints excluded: chain Z residue 3 SER Chi-restraints excluded: chain Z residue 61 TYR Chi-restraints excluded: chain Z residue 169 THR Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 78 GLU Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain c residue 115 SER Chi-restraints excluded: chain d residue 284 VAL Chi-restraints excluded: chain e residue 63 LYS Chi-restraints excluded: chain e residue 74 LYS Chi-restraints excluded: chain e residue 90 LEU Chi-restraints excluded: chain f residue 15 VAL Chi-restraints excluded: chain f residue 21 GLU Chi-restraints excluded: chain f residue 32 ASP Chi-restraints excluded: chain h residue 17 ARG Chi-restraints excluded: chain h residue 100 ILE Chi-restraints excluded: chain k residue 28 ASP Chi-restraints excluded: chain k residue 203 GLU Chi-restraints excluded: chain m residue 30 ILE Chi-restraints excluded: chain m residue 31 LEU Chi-restraints excluded: chain m residue 43 MET Chi-restraints excluded: chain n residue 78 VAL Chi-restraints excluded: chain n residue 81 VAL Chi-restraints excluded: chain n residue 87 LEU Chi-restraints excluded: chain o residue 55 SER Chi-restraints excluded: chain p residue 8 SER Chi-restraints excluded: chain p residue 9 ARG Chi-restraints excluded: chain q residue 97 MET Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 86 LYS Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain s residue 56 ASP Chi-restraints excluded: chain s residue 69 LYS Chi-restraints excluded: chain s residue 100 GLU Chi-restraints excluded: chain s residue 121 MET Chi-restraints excluded: chain t residue 31 VAL Chi-restraints excluded: chain t residue 83 GLU Chi-restraints excluded: chain u residue 8 GLU Chi-restraints excluded: chain u residue 60 THR Chi-restraints excluded: chain v residue 31 VAL Chi-restraints excluded: chain v residue 124 THR Chi-restraints excluded: chain w residue 60 VAL Chi-restraints excluded: chain w residue 74 SER Chi-restraints excluded: chain w residue 109 GLU Chi-restraints excluded: chain y residue 9 ASP Chi-restraints excluded: chain y residue 26 LEU Chi-restraints excluded: chain z residue 42 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 794 random chunks: chunk 400 optimal weight: 9.9990 chunk 223 optimal weight: 4.9990 chunk 600 optimal weight: 10.0000 chunk 490 optimal weight: 8.9990 chunk 198 optimal weight: 0.0570 chunk 722 optimal weight: 9.9990 chunk 780 optimal weight: 5.9990 chunk 643 optimal weight: 8.9990 chunk 716 optimal weight: 0.6980 chunk 246 optimal weight: 4.9990 chunk 579 optimal weight: 7.9990 overall best weight: 3.3504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 373 ASN 3 277 GLN ** 3 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 437 HIS ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 162 GLN A 10 ASN ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 HIS ** L 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 268 GLN V 128 GLN ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 103 GLN Z 123 ASN ** Z 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 50 GLN h 72 GLN h 107 GLN i 123 GLN k 97 GLN ** k 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 239 GLN l 69 GLN l 76 ASN ** p 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 125 ASN ** t 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 25 HIS x 13 ASN x 46 ASN y 30 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.289 69131 Z= 0.526 Angle : 1.565 51.051 93426 Z= 1.012 Chirality : 0.311 6.548 10118 Planarity : 0.004 0.045 11647 Dihedral : 12.292 175.551 10578 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.24 % Favored : 96.73 % Rotamer: Outliers : 3.20 % Allowed : 13.73 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.09), residues: 8046 helix: 0.43 (0.08), residues: 4269 sheet: -1.17 (0.24), residues: 348 loop : -0.95 (0.10), residues: 3429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP q 47 HIS 0.022 0.001 HIS 9 65 PHE 0.033 0.002 PHE N 292 TYR 0.034 0.002 TYR H 215 ARG 0.008 0.000 ARG q 67 *********************** 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 1372 residues out of total 7132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 1144 time to evaluate : 7.304 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 16 LYS cc_start: 0.8065 (mtmm) cc_final: 0.7802 (tptm) REVERT: 1 82 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.8547 (mtm) REVERT: 1 129 MET cc_start: 0.9111 (mtm) cc_final: 0.8742 (ptp) REVERT: 1 302 SER cc_start: 0.8669 (m) cc_final: 0.8236 (p) REVERT: 2 127 LYS cc_start: 0.8381 (ptpt) cc_final: 0.7680 (mmmm) REVERT: 3 95 GLU cc_start: 0.8819 (tt0) cc_final: 0.8530 (tp30) REVERT: 3 347 GLU cc_start: 0.8518 (tt0) cc_final: 0.8295 (tp30) REVERT: 3 444 GLN cc_start: 0.7513 (mm110) cc_final: 0.7214 (tt0) REVERT: 3 450 MET cc_start: 0.8925 (ttt) cc_final: 0.8634 (ttt) REVERT: 3 477 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.8116 (tp) REVERT: 3 640 ASN cc_start: 0.8043 (t0) cc_final: 0.7655 (m-40) REVERT: 5 43 SER cc_start: 0.9047 (p) cc_final: 0.8595 (m) REVERT: 6 50 PHE cc_start: 0.8748 (OUTLIER) cc_final: 0.8320 (m-80) REVERT: 6 102 LYS cc_start: 0.9023 (tttt) cc_final: 0.8791 (tppt) REVERT: 9 1 THR cc_start: 0.8291 (t) cc_final: 0.8043 (m) REVERT: 9 15 LYS cc_start: 0.8441 (tptp) cc_final: 0.8111 (tppp) REVERT: A 16 LEU cc_start: 0.8473 (tp) cc_final: 0.8152 (mm) REVERT: A 23 TRP cc_start: 0.6783 (m100) cc_final: 0.6092 (t60) REVERT: H 1 MET cc_start: 0.7344 (tpp) cc_final: 0.7118 (tpp) REVERT: H 199 ASP cc_start: 0.8494 (p0) cc_final: 0.8162 (p0) REVERT: K 3 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.7369 (mt) REVERT: K 10 MET cc_start: 0.8321 (OUTLIER) cc_final: 0.8041 (ttp) REVERT: L 101 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8499 (mtp) REVERT: L 108 MET cc_start: 0.8910 (OUTLIER) cc_final: 0.7643 (mmm) REVERT: L 214 MET cc_start: 0.8683 (mmp) cc_final: 0.8033 (ttt) REVERT: L 352 ASP cc_start: 0.7790 (OUTLIER) cc_final: 0.7568 (m-30) REVERT: L 589 LEU cc_start: 0.7283 (OUTLIER) cc_final: 0.7068 (tt) REVERT: M 294 MET cc_start: 0.8470 (mmp) cc_final: 0.8195 (mmp) REVERT: M 355 MET cc_start: 0.9185 (tpp) cc_final: 0.8918 (tpp) REVERT: N 98 MET cc_start: 0.8962 (ttm) cc_final: 0.8724 (ttm) REVERT: N 181 TYR cc_start: 0.9183 (m-80) cc_final: 0.8957 (m-80) REVERT: N 295 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7277 (mtm-85) REVERT: V 57 ARG cc_start: 0.7050 (ttp-110) cc_final: 0.6692 (tpp-160) REVERT: V 119 LEU cc_start: 0.8216 (mt) cc_final: 0.7901 (tp) REVERT: X 8 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7523 (mm) REVERT: Y 15 GLN cc_start: 0.7755 (OUTLIER) cc_final: 0.7539 (tt0) REVERT: Y 89 ASP cc_start: 0.8419 (t0) cc_final: 0.8003 (t0) REVERT: Z 39 LEU cc_start: 0.8476 (mm) cc_final: 0.7855 (mt) REVERT: Z 89 MET cc_start: 0.8874 (mmp) cc_final: 0.8566 (mmp) REVERT: a 34 ASP cc_start: 0.6579 (t0) cc_final: 0.6272 (m-30) REVERT: b 54 SER cc_start: 0.8858 (t) cc_final: 0.8589 (m) REVERT: b 78 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7885 (mp0) REVERT: b 80 LYS cc_start: 0.7682 (ttpp) cc_final: 0.7390 (tttp) REVERT: e 34 ASP cc_start: 0.8784 (m-30) cc_final: 0.8539 (m-30) REVERT: e 56 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8365 (mt-10) REVERT: e 74 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7725 (mttt) REVERT: g 56 LYS cc_start: 0.9027 (tmmt) cc_final: 0.8805 (ttmt) REVERT: h 17 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.6900 (mpp80) REVERT: h 18 ASP cc_start: 0.8536 (t0) cc_final: 0.8159 (t70) REVERT: h 39 LYS cc_start: 0.8680 (tptm) cc_final: 0.8194 (ttpt) REVERT: h 63 MET cc_start: 0.8902 (mmm) cc_final: 0.8679 (mmp) REVERT: i 1 MET cc_start: 0.7693 (tpt) cc_final: 0.6891 (mtt) REVERT: i 2 GLU cc_start: 0.8133 (pt0) cc_final: 0.7443 (pm20) REVERT: i 68 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8524 (ttt) REVERT: j 52 MET cc_start: 0.8323 (mtp) cc_final: 0.8040 (mtm) REVERT: k 40 LYS cc_start: 0.7822 (OUTLIER) cc_final: 0.7594 (mtmp) REVERT: k 203 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8058 (mp0) REVERT: k 236 GLU cc_start: 0.8069 (tm-30) cc_final: 0.7564 (mt-10) REVERT: k 250 ASP cc_start: 0.7972 (p0) cc_final: 0.7730 (p0) REVERT: m 14 LYS cc_start: 0.8709 (mtmt) cc_final: 0.8400 (mmtt) REVERT: m 37 TYR cc_start: 0.8139 (m-10) cc_final: 0.7792 (m-10) REVERT: n 13 MET cc_start: 0.5755 (pmm) cc_final: 0.4310 (tmm) REVERT: o 25 LYS cc_start: 0.7774 (mttt) cc_final: 0.7370 (mmtt) REVERT: o 111 GLU cc_start: 0.7583 (mp0) cc_final: 0.7048 (mt-10) REVERT: o 114 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7569 (mt-10) REVERT: p 5 TYR cc_start: 0.6471 (t80) cc_final: 0.6215 (t80) REVERT: p 104 PHE cc_start: 0.8942 (m-80) cc_final: 0.8677 (m-80) REVERT: q 22 ARG cc_start: 0.8697 (mtp180) cc_final: 0.8426 (mtm180) REVERT: q 95 THR cc_start: 0.8323 (t) cc_final: 0.8042 (p) REVERT: q 104 LYS cc_start: 0.8578 (mmmt) cc_final: 0.8004 (ttmt) REVERT: s 100 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7911 (mp0) REVERT: t 83 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.8075 (mp0) REVERT: u 26 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7550 (tt0) REVERT: u 53 TYR cc_start: 0.7701 (t80) cc_final: 0.7438 (t80) REVERT: v 117 TRP cc_start: 0.6578 (t60) cc_final: 0.6360 (t60) REVERT: v 157 GLU cc_start: 0.6604 (mm-30) cc_final: 0.6392 (mp0) REVERT: w 56 TRP cc_start: 0.7318 (t60) cc_final: 0.7026 (m-10) REVERT: w 109 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7953 (mp0) REVERT: x 16 LYS cc_start: 0.8199 (ttmt) cc_final: 0.7806 (tptm) REVERT: y 26 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8748 (mp) REVERT: z 34 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7564 (mtp180) outliers start: 228 outliers final: 83 residues processed: 1268 average time/residue: 1.5176 time to fit residues: 2497.3299 Evaluate side-chains 1152 residues out of total 7132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 1046 time to evaluate : 6.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 82 MET Chi-restraints excluded: chain 1 residue 249 ARG Chi-restraints excluded: chain 1 residue 292 ASP Chi-restraints excluded: chain 1 residue 314 THR Chi-restraints excluded: chain 1 residue 337 MET Chi-restraints excluded: chain 2 residue 128 VAL Chi-restraints excluded: chain 3 residue 424 ASP Chi-restraints excluded: chain 3 residue 471 SER Chi-restraints excluded: chain 3 residue 477 ILE Chi-restraints excluded: chain 3 residue 532 VAL Chi-restraints excluded: chain 3 residue 535 GLN Chi-restraints excluded: chain 3 residue 613 TYR Chi-restraints excluded: chain 3 residue 659 ASP Chi-restraints excluded: chain 4 residue 164 MET Chi-restraints excluded: chain 6 residue 50 PHE Chi-restraints excluded: chain 6 residue 84 ASP Chi-restraints excluded: chain 6 residue 137 ASP Chi-restraints excluded: chain 9 residue 16 SER Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain H residue 24 GLU Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain H residue 274 ARG Chi-restraints excluded: chain J residue 55 MET Chi-restraints excluded: chain K residue 3 LEU Chi-restraints excluded: chain K residue 10 MET Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 101 MET Chi-restraints excluded: chain L residue 108 MET Chi-restraints excluded: chain L residue 217 ILE Chi-restraints excluded: chain L residue 352 ASP Chi-restraints excluded: chain L residue 393 ASP Chi-restraints excluded: chain L residue 484 HIS Chi-restraints excluded: chain L residue 505 SER Chi-restraints excluded: chain L residue 583 LEU Chi-restraints excluded: chain L residue 589 LEU Chi-restraints excluded: chain L residue 601 LEU Chi-restraints excluded: chain M residue 157 SER Chi-restraints excluded: chain M residue 454 ILE Chi-restraints excluded: chain N residue 37 MET Chi-restraints excluded: chain N residue 146 LEU Chi-restraints excluded: chain N residue 161 SER Chi-restraints excluded: chain N residue 258 SER Chi-restraints excluded: chain N residue 295 ARG Chi-restraints excluded: chain N residue 308 THR Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain V residue 134 VAL Chi-restraints excluded: chain W residue 43 ILE Chi-restraints excluded: chain W residue 98 SER Chi-restraints excluded: chain W residue 140 THR Chi-restraints excluded: chain X residue 8 LEU Chi-restraints excluded: chain X residue 26 ASP Chi-restraints excluded: chain X residue 40 LEU Chi-restraints excluded: chain Y residue 15 GLN Chi-restraints excluded: chain Y residue 63 ASN Chi-restraints excluded: chain Y residue 154 GLU Chi-restraints excluded: chain Z residue 61 TYR Chi-restraints excluded: chain Z residue 169 THR Chi-restraints excluded: chain a residue 45 ASP Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 78 GLU Chi-restraints excluded: chain c residue 115 SER Chi-restraints excluded: chain d residue 284 VAL Chi-restraints excluded: chain e residue 74 LYS Chi-restraints excluded: chain e residue 90 LEU Chi-restraints excluded: chain f residue 15 VAL Chi-restraints excluded: chain h residue 17 ARG Chi-restraints excluded: chain i residue 68 MET Chi-restraints excluded: chain j residue 26 ASP Chi-restraints excluded: chain k residue 28 ASP Chi-restraints excluded: chain k residue 40 LYS Chi-restraints excluded: chain k residue 160 VAL Chi-restraints excluded: chain k residue 203 GLU Chi-restraints excluded: chain m residue 8 LEU Chi-restraints excluded: chain m residue 58 ASP Chi-restraints excluded: chain n residue 78 VAL Chi-restraints excluded: chain n residue 81 VAL Chi-restraints excluded: chain o residue 20 SER Chi-restraints excluded: chain o residue 55 SER Chi-restraints excluded: chain o residue 96 SER Chi-restraints excluded: chain o residue 110 ARG Chi-restraints excluded: chain r residue 76 ILE Chi-restraints excluded: chain r residue 86 LYS Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain s residue 69 LYS Chi-restraints excluded: chain s residue 100 GLU Chi-restraints excluded: chain t residue 31 VAL Chi-restraints excluded: chain t residue 34 ASP Chi-restraints excluded: chain t residue 56 MET Chi-restraints excluded: chain t residue 83 GLU Chi-restraints excluded: chain u residue 8 GLU Chi-restraints excluded: chain u residue 60 THR Chi-restraints excluded: chain v residue 31 VAL Chi-restraints excluded: chain v residue 40 ASP Chi-restraints excluded: chain w residue 60 VAL Chi-restraints excluded: chain w residue 74 SER Chi-restraints excluded: chain w residue 109 GLU Chi-restraints excluded: chain y residue 9 ASP Chi-restraints excluded: chain y residue 26 LEU Chi-restraints excluded: chain z residue 16 LEU Chi-restraints excluded: chain z residue 34 ARG Chi-restraints excluded: chain z residue 42 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 794 random chunks: chunk 713 optimal weight: 6.9990 chunk 543 optimal weight: 0.9990 chunk 374 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 chunk 344 optimal weight: 20.0000 chunk 485 optimal weight: 5.9990 chunk 724 optimal weight: 6.9990 chunk 767 optimal weight: 10.0000 chunk 378 optimal weight: 0.9990 chunk 687 optimal weight: 9.9990 chunk 206 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 24 ASN 1 436 GLN 3 682 GLN 4 79 HIS ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 201 GLN ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 23 ASN ** L 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 580 GLN M 279 GLN N 63 GLN V 128 GLN ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 180 ASN g 50 GLN h 72 GLN h 107 GLN i 123 GLN ** k 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 239 GLN l 76 ASN p 78 ASN p 125 ASN x 13 ASN y 30 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.286 69131 Z= 0.535 Angle : 1.567 51.106 93426 Z= 1.013 Chirality : 0.311 6.574 10118 Planarity : 0.004 0.053 11647 Dihedral : 11.907 176.889 10576 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.29 % Favored : 96.68 % Rotamer: Outliers : 3.52 % Allowed : 14.95 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.09), residues: 8046 helix: 0.75 (0.08), residues: 4268 sheet: -0.98 (0.25), residues: 359 loop : -0.72 (0.11), residues: 3419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP q 47 HIS 0.021 0.001 HIS 9 65 PHE 0.031 0.002 PHE N 292 TYR 0.033 0.002 TYR H 215 ARG 0.006 0.000 ARG p 41 *********************** 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 1347 residues out of total 7132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 251 poor density : 1096 time to evaluate : 6.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 16 LYS cc_start: 0.8095 (mtmm) cc_final: 0.7781 (tptm) REVERT: 1 82 MET cc_start: 0.8906 (OUTLIER) cc_final: 0.8638 (mtm) REVERT: 1 129 MET cc_start: 0.9166 (mtm) cc_final: 0.8754 (ptp) REVERT: 1 302 SER cc_start: 0.8591 (m) cc_final: 0.8196 (p) REVERT: 2 127 LYS cc_start: 0.8330 (ptpt) cc_final: 0.7548 (mmmm) REVERT: 2 153 MET cc_start: 0.8986 (OUTLIER) cc_final: 0.8454 (ppp) REVERT: 3 16 GLN cc_start: 0.8511 (tt0) cc_final: 0.8201 (tm-30) REVERT: 3 95 GLU cc_start: 0.8820 (tt0) cc_final: 0.8558 (tp30) REVERT: 3 347 GLU cc_start: 0.8518 (tt0) cc_final: 0.8296 (tp30) REVERT: 3 444 GLN cc_start: 0.7518 (mm110) cc_final: 0.7217 (tt0) REVERT: 3 450 MET cc_start: 0.8915 (ttt) cc_final: 0.8660 (ttt) REVERT: 3 477 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.8116 (tp) REVERT: 3 640 ASN cc_start: 0.8010 (t0) cc_final: 0.7615 (m-40) REVERT: 4 66 MET cc_start: 0.9108 (OUTLIER) cc_final: 0.8512 (mmt) REVERT: 4 410 MET cc_start: 0.8746 (mtt) cc_final: 0.8466 (mtm) REVERT: 6 50 PHE cc_start: 0.8807 (OUTLIER) cc_final: 0.8167 (m-80) REVERT: 6 102 LYS cc_start: 0.9051 (tttt) cc_final: 0.8766 (tppt) REVERT: 9 1 THR cc_start: 0.8216 (t) cc_final: 0.7995 (m) REVERT: A 16 LEU cc_start: 0.8475 (tp) cc_final: 0.8153 (mm) REVERT: A 23 TRP cc_start: 0.6804 (m100) cc_final: 0.6128 (t60) REVERT: H 1 MET cc_start: 0.7368 (tpp) cc_final: 0.7007 (tpp) REVERT: H 199 ASP cc_start: 0.8593 (p0) cc_final: 0.8312 (p0) REVERT: K 10 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.8223 (ttp) REVERT: K 27 MET cc_start: 0.8834 (tpp) cc_final: 0.8594 (mmm) REVERT: L 214 MET cc_start: 0.8683 (mmp) cc_final: 0.7966 (ttt) REVERT: L 535 ARG cc_start: 0.8084 (mtt90) cc_final: 0.7791 (mtt90) REVERT: L 566 ILE cc_start: 0.7702 (mt) cc_final: 0.7468 (tt) REVERT: M 294 MET cc_start: 0.8510 (mmp) cc_final: 0.8200 (mmp) REVERT: N 98 MET cc_start: 0.8981 (ttm) cc_final: 0.8667 (ttm) REVERT: N 295 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.7285 (mtm-85) REVERT: N 311 MET cc_start: 0.8870 (OUTLIER) cc_final: 0.8595 (mtp) REVERT: V 57 ARG cc_start: 0.7049 (ttp-110) cc_final: 0.6697 (tpp-160) REVERT: V 119 LEU cc_start: 0.8153 (mt) cc_final: 0.7913 (tp) REVERT: X 8 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7527 (mm) REVERT: Y 5 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6880 (pp20) REVERT: Y 89 ASP cc_start: 0.8327 (t0) cc_final: 0.7883 (t0) REVERT: Z 38 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7933 (mm) REVERT: Z 39 LEU cc_start: 0.8513 (mm) cc_final: 0.8216 (mm) REVERT: a 34 ASP cc_start: 0.6618 (t0) cc_final: 0.6309 (m-30) REVERT: b 54 SER cc_start: 0.8663 (t) cc_final: 0.8423 (m) REVERT: b 78 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7880 (mp0) REVERT: b 80 LYS cc_start: 0.7850 (ttpp) cc_final: 0.7531 (tttp) REVERT: d 155 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8304 (tp30) REVERT: e 56 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8379 (mt-10) REVERT: g 56 LYS cc_start: 0.9053 (tmmt) cc_final: 0.8822 (ttmt) REVERT: h 17 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.7160 (mpp80) REVERT: h 18 ASP cc_start: 0.8589 (t0) cc_final: 0.8283 (t70) REVERT: h 39 LYS cc_start: 0.8714 (tptm) cc_final: 0.8218 (ttpt) REVERT: h 63 MET cc_start: 0.8920 (mmm) cc_final: 0.8710 (mmp) REVERT: i 1 MET cc_start: 0.7805 (tpt) cc_final: 0.7064 (mtt) REVERT: i 2 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7561 (pm20) REVERT: j 25 ILE cc_start: 0.6727 (pp) cc_final: 0.6510 (tt) REVERT: j 75 GLU cc_start: 0.7841 (pm20) cc_final: 0.7584 (pm20) REVERT: k 40 LYS cc_start: 0.7861 (OUTLIER) cc_final: 0.7634 (mtmp) REVERT: k 203 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8080 (mp0) REVERT: k 236 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7600 (mt-10) REVERT: k 250 ASP cc_start: 0.8040 (p0) cc_final: 0.7780 (p0) REVERT: m 14 LYS cc_start: 0.8762 (mtmt) cc_final: 0.8445 (mmtt) REVERT: m 31 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.9008 (mt) REVERT: m 37 TYR cc_start: 0.8151 (m-10) cc_final: 0.7786 (m-10) REVERT: m 81 LYS cc_start: 0.8831 (mtpp) cc_final: 0.8338 (mtmm) REVERT: o 25 LYS cc_start: 0.7768 (mttt) cc_final: 0.7350 (mmtt) REVERT: o 77 LYS cc_start: 0.9280 (OUTLIER) cc_final: 0.8938 (mtmm) REVERT: o 111 GLU cc_start: 0.7547 (mp0) cc_final: 0.6995 (mt-10) REVERT: o 114 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7559 (mt-10) REVERT: p 5 TYR cc_start: 0.6499 (t80) cc_final: 0.6189 (t80) REVERT: p 30 LYS cc_start: 0.6589 (OUTLIER) cc_final: 0.6320 (ptmm) REVERT: p 104 PHE cc_start: 0.8881 (m-80) cc_final: 0.8615 (m-80) REVERT: q 104 LYS cc_start: 0.8606 (mmmt) cc_final: 0.8035 (ttmt) REVERT: s 100 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7941 (mp0) REVERT: u 26 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7561 (tt0) REVERT: u 53 TYR cc_start: 0.7695 (t80) cc_final: 0.7401 (t80) REVERT: w 49 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.7595 (pttt) REVERT: w 56 TRP cc_start: 0.7405 (t60) cc_final: 0.7080 (m-10) REVERT: w 109 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7864 (mp0) REVERT: x 16 LYS cc_start: 0.8265 (ttmt) cc_final: 0.7833 (tptm) REVERT: y 26 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8871 (mp) REVERT: z 34 ARG cc_start: 0.8000 (mtm-85) cc_final: 0.7707 (mtm-85) outliers start: 251 outliers final: 101 residues processed: 1237 average time/residue: 1.5197 time to fit residues: 2463.5028 Evaluate side-chains 1149 residues out of total 7132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 1025 time to evaluate : 6.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 61 LYS Chi-restraints excluded: chain 1 residue 82 MET Chi-restraints excluded: chain 1 residue 86 SER Chi-restraints excluded: chain 1 residue 249 ARG Chi-restraints excluded: chain 1 residue 292 ASP Chi-restraints excluded: chain 1 residue 314 THR Chi-restraints excluded: chain 1 residue 337 MET Chi-restraints excluded: chain 2 residue 134 ASP Chi-restraints excluded: chain 2 residue 135 LYS Chi-restraints excluded: chain 2 residue 153 MET Chi-restraints excluded: chain 3 residue 424 ASP Chi-restraints excluded: chain 3 residue 471 SER Chi-restraints excluded: chain 3 residue 477 ILE Chi-restraints excluded: chain 3 residue 532 VAL Chi-restraints excluded: chain 3 residue 535 GLN Chi-restraints excluded: chain 3 residue 613 TYR Chi-restraints excluded: chain 3 residue 659 ASP Chi-restraints excluded: chain 4 residue 66 MET Chi-restraints excluded: chain 4 residue 164 MET Chi-restraints excluded: chain 6 residue 34 ASP Chi-restraints excluded: chain 6 residue 50 PHE Chi-restraints excluded: chain 6 residue 84 ASP Chi-restraints excluded: chain 9 residue 16 SER Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain H residue 24 GLU Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain J residue 55 MET Chi-restraints excluded: chain J residue 117 PHE Chi-restraints excluded: chain K residue 3 LEU Chi-restraints excluded: chain K residue 10 MET Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 217 ILE Chi-restraints excluded: chain L residue 445 GLU Chi-restraints excluded: chain L residue 484 HIS Chi-restraints excluded: chain L residue 505 SER Chi-restraints excluded: chain L residue 583 LEU Chi-restraints excluded: chain L residue 601 LEU Chi-restraints excluded: chain M residue 157 SER Chi-restraints excluded: chain M residue 454 ILE Chi-restraints excluded: chain N residue 37 MET Chi-restraints excluded: chain N residue 146 LEU Chi-restraints excluded: chain N residue 161 SER Chi-restraints excluded: chain N residue 258 SER Chi-restraints excluded: chain N residue 295 ARG Chi-restraints excluded: chain N residue 308 THR Chi-restraints excluded: chain N residue 311 MET Chi-restraints excluded: chain N residue 335 MET Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain V residue 134 VAL Chi-restraints excluded: chain W residue 36 VAL Chi-restraints excluded: chain W residue 98 SER Chi-restraints excluded: chain W residue 140 THR Chi-restraints excluded: chain X residue 8 LEU Chi-restraints excluded: chain X residue 26 ASP Chi-restraints excluded: chain X residue 40 LEU Chi-restraints excluded: chain Y residue 5 GLU Chi-restraints excluded: chain Y residue 63 ASN Chi-restraints excluded: chain Y residue 154 GLU Chi-restraints excluded: chain Z residue 38 LEU Chi-restraints excluded: chain Z residue 169 THR Chi-restraints excluded: chain a residue 45 ASP Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 19 ASP Chi-restraints excluded: chain b residue 78 GLU Chi-restraints excluded: chain c residue 44 ASN Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain c residue 115 SER Chi-restraints excluded: chain d residue 140 LYS Chi-restraints excluded: chain d residue 185 ILE Chi-restraints excluded: chain d residue 284 VAL Chi-restraints excluded: chain d residue 340 VAL Chi-restraints excluded: chain e residue 63 LYS Chi-restraints excluded: chain e residue 84 ASP Chi-restraints excluded: chain e residue 90 LEU Chi-restraints excluded: chain f residue 15 VAL Chi-restraints excluded: chain f residue 32 ASP Chi-restraints excluded: chain h residue 17 ARG Chi-restraints excluded: chain i residue 2 GLU Chi-restraints excluded: chain i residue 11 LEU Chi-restraints excluded: chain j residue 26 ASP Chi-restraints excluded: chain k residue 28 ASP Chi-restraints excluded: chain k residue 40 LYS Chi-restraints excluded: chain k residue 160 VAL Chi-restraints excluded: chain k residue 203 GLU Chi-restraints excluded: chain m residue 8 LEU Chi-restraints excluded: chain m residue 31 LEU Chi-restraints excluded: chain n residue 66 LEU Chi-restraints excluded: chain n residue 78 VAL Chi-restraints excluded: chain n residue 81 VAL Chi-restraints excluded: chain n residue 87 LEU Chi-restraints excluded: chain o residue 20 SER Chi-restraints excluded: chain o residue 55 SER Chi-restraints excluded: chain o residue 77 LYS Chi-restraints excluded: chain o residue 96 SER Chi-restraints excluded: chain o residue 110 ARG Chi-restraints excluded: chain p residue 8 SER Chi-restraints excluded: chain p residue 30 LYS Chi-restraints excluded: chain r residue 68 ILE Chi-restraints excluded: chain r residue 76 ILE Chi-restraints excluded: chain r residue 86 LYS Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain s residue 69 LYS Chi-restraints excluded: chain s residue 100 GLU Chi-restraints excluded: chain t residue 31 VAL Chi-restraints excluded: chain t residue 56 MET Chi-restraints excluded: chain u residue 8 GLU Chi-restraints excluded: chain u residue 60 THR Chi-restraints excluded: chain v residue 31 VAL Chi-restraints excluded: chain v residue 40 ASP Chi-restraints excluded: chain w residue 49 LYS Chi-restraints excluded: chain w residue 60 VAL Chi-restraints excluded: chain w residue 74 SER Chi-restraints excluded: chain w residue 100 ARG Chi-restraints excluded: chain w residue 109 GLU Chi-restraints excluded: chain y residue 26 LEU Chi-restraints excluded: chain z residue 16 LEU Chi-restraints excluded: chain z residue 42 SER 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: 10.0000 chunk 11 optimal weight: 20.0000 chunk 571 optimal weight: 9.9990 chunk 316 optimal weight: 10.0000 chunk 654 optimal weight: 20.0000 chunk 530 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 391 optimal weight: 6.9990 chunk 688 optimal weight: 5.9990 chunk 193 optimal weight: 9.9990 overall best weight: 8.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 436 GLN 3 475 GLN ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 284 GLN J 46 ASN ** L 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 175 ASN L 210 ASN ** L 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 366 ASN N 134 GLN V 128 GLN ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 288 HIS h 24 GLN h 72 GLN h 107 GLN i 123 GLN ** k 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 239 GLN l 26 HIS l 44 HIS l 76 ASN ** l 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 78 ASN p 125 ASN q 53 ASN ** t 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 136 ASN x 13 ASN y 30 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.300 69131 Z= 0.614 Angle : 1.599 51.132 93426 Z= 1.025 Chirality : 0.312 6.693 10118 Planarity : 0.005 0.057 11647 Dihedral : 12.128 179.040 10576 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.63 % Favored : 96.33 % Rotamer: Outliers : 3.83 % Allowed : 15.44 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.09), residues: 8046 helix: 0.71 (0.08), residues: 4264 sheet: -1.05 (0.25), residues: 372 loop : -0.61 (0.11), residues: 3410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP L 144 HIS 0.023 0.002 HIS 9 65 PHE 0.033 0.002 PHE Y 167 TYR 0.031 0.002 TYR H 215 ARG 0.009 0.001 ARG g 99 *********************** 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 1336 residues out of total 7132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 273 poor density : 1063 time to evaluate : 6.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 16 LYS cc_start: 0.8066 (mtmm) cc_final: 0.7747 (tptm) REVERT: 1 82 MET cc_start: 0.8995 (OUTLIER) cc_final: 0.8787 (mtm) REVERT: 1 129 MET cc_start: 0.9276 (mtm) cc_final: 0.8894 (ptp) REVERT: 2 127 LYS cc_start: 0.8412 (ptpt) cc_final: 0.7556 (mmmm) REVERT: 3 16 GLN cc_start: 0.8553 (tt0) cc_final: 0.8161 (tm-30) REVERT: 3 95 GLU cc_start: 0.8802 (tt0) cc_final: 0.8592 (tp30) REVERT: 3 477 ILE cc_start: 0.8376 (OUTLIER) cc_final: 0.8117 (tp) REVERT: 3 640 ASN cc_start: 0.8001 (t0) cc_final: 0.7601 (m-40) REVERT: 4 410 MET cc_start: 0.8829 (mtt) cc_final: 0.8541 (mtm) REVERT: 4 422 ASP cc_start: 0.7445 (t0) cc_final: 0.7216 (t70) REVERT: 4 430 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.6347 (mpp-170) REVERT: 6 50 PHE cc_start: 0.8917 (OUTLIER) cc_final: 0.8044 (m-80) REVERT: 6 102 LYS cc_start: 0.9132 (tttt) cc_final: 0.8894 (tppt) REVERT: 9 13 ASP cc_start: 0.8755 (OUTLIER) cc_final: 0.8242 (p0) REVERT: A 16 LEU cc_start: 0.8480 (tp) cc_final: 0.8144 (mm) REVERT: A 22 PHE cc_start: 0.8604 (m-80) cc_final: 0.8355 (m-80) REVERT: J 31 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8459 (mt) REVERT: K 10 MET cc_start: 0.8612 (OUTLIER) cc_final: 0.8389 (ttp) REVERT: L 214 MET cc_start: 0.8684 (mmp) cc_final: 0.7920 (ttm) REVERT: L 352 ASP cc_start: 0.7855 (OUTLIER) cc_final: 0.7651 (m-30) REVERT: L 425 ARG cc_start: 0.7681 (OUTLIER) cc_final: 0.6968 (ptm-80) REVERT: L 535 ARG cc_start: 0.8160 (mtt90) cc_final: 0.7873 (mtt90) REVERT: M 335 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7622 (mt-10) REVERT: M 378 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8341 (tm-30) REVERT: N 98 MET cc_start: 0.9025 (ttm) cc_final: 0.8784 (ttm) REVERT: N 295 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7429 (mtm-85) REVERT: V 57 ARG cc_start: 0.7025 (ttp-110) cc_final: 0.6682 (tpp-160) REVERT: V 119 LEU cc_start: 0.8205 (mt) cc_final: 0.7914 (tp) REVERT: Y 5 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7170 (pp20) REVERT: Y 43 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.8298 (mmm) REVERT: Y 89 ASP cc_start: 0.8346 (t0) cc_final: 0.7902 (t0) REVERT: Z 39 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8389 (mm) REVERT: a 34 ASP cc_start: 0.6473 (t0) cc_final: 0.6235 (m-30) REVERT: b 54 SER cc_start: 0.8769 (t) cc_final: 0.8400 (p) REVERT: b 78 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.7894 (mp0) REVERT: b 80 LYS cc_start: 0.7914 (ttpp) cc_final: 0.7675 (tttp) REVERT: e 56 GLU cc_start: 0.8904 (mt-10) cc_final: 0.8489 (mt-10) REVERT: g 56 LYS cc_start: 0.9086 (tmmt) cc_final: 0.8822 (tppt) REVERT: h 17 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.6999 (mpp80) REVERT: h 18 ASP cc_start: 0.8647 (t0) cc_final: 0.8357 (t70) REVERT: i 1 MET cc_start: 0.7814 (tpt) cc_final: 0.7102 (mtt) REVERT: i 2 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7527 (pm20) REVERT: i 68 MET cc_start: 0.8857 (OUTLIER) cc_final: 0.8484 (ttt) REVERT: j 25 ILE cc_start: 0.6746 (pp) cc_final: 0.6526 (tt) REVERT: j 74 GLN cc_start: 0.7754 (tm-30) cc_final: 0.7507 (tm-30) REVERT: j 75 GLU cc_start: 0.7795 (pm20) cc_final: 0.7452 (pm20) REVERT: k 203 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8060 (mp0) REVERT: k 236 GLU cc_start: 0.8231 (tm-30) cc_final: 0.7650 (mt-10) REVERT: m 10 ASN cc_start: 0.8784 (t0) cc_final: 0.8522 (t0) REVERT: m 14 LYS cc_start: 0.8784 (mtmt) cc_final: 0.8326 (tmtm) REVERT: m 31 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.9023 (mt) REVERT: m 37 TYR cc_start: 0.8227 (m-10) cc_final: 0.7877 (m-10) REVERT: m 81 LYS cc_start: 0.8925 (mtpp) cc_final: 0.8404 (mtmm) REVERT: n 13 MET cc_start: 0.5751 (pmm) cc_final: 0.3664 (tmm) REVERT: n 14 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.6820 (mp0) REVERT: o 25 LYS cc_start: 0.7978 (mttt) cc_final: 0.7515 (mmtt) REVERT: o 77 LYS cc_start: 0.9292 (OUTLIER) cc_final: 0.8908 (mtmm) REVERT: q 104 LYS cc_start: 0.8765 (mmmt) cc_final: 0.8271 (ttpp) REVERT: r 12 GLN cc_start: 0.7631 (pt0) cc_final: 0.6958 (tm-30) REVERT: r 30 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.6323 (ppp80) REVERT: r 119 MET cc_start: 0.7551 (mtm) cc_final: 0.7321 (mtp) REVERT: s 100 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7867 (mp0) REVERT: u 19 ARG cc_start: 0.7726 (OUTLIER) cc_final: 0.7190 (mtt-85) REVERT: u 26 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7611 (tt0) REVERT: u 53 TYR cc_start: 0.7676 (t80) cc_final: 0.7365 (t80) REVERT: v 112 MET cc_start: 0.7514 (mmp) cc_final: 0.7259 (mmp) REVERT: v 157 GLU cc_start: 0.6625 (OUTLIER) cc_final: 0.6328 (mp0) REVERT: w 49 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.7681 (ptpt) REVERT: w 56 TRP cc_start: 0.7539 (t60) cc_final: 0.7127 (m-10) REVERT: w 100 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7802 (ptm160) REVERT: w 109 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7824 (mp0) REVERT: x 16 LYS cc_start: 0.8277 (ttmt) cc_final: 0.7861 (tptm) REVERT: y 26 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8932 (mp) REVERT: z 34 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7797 (mtm-85) outliers start: 273 outliers final: 127 residues processed: 1219 average time/residue: 1.5020 time to fit residues: 2382.2462 Evaluate side-chains 1167 residues out of total 7132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 1009 time to evaluate : 6.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 61 LYS Chi-restraints excluded: chain 1 residue 82 MET Chi-restraints excluded: chain 1 residue 249 ARG Chi-restraints excluded: chain 1 residue 292 ASP Chi-restraints excluded: chain 1 residue 314 THR Chi-restraints excluded: chain 1 residue 337 MET Chi-restraints excluded: chain 2 residue 128 VAL Chi-restraints excluded: chain 2 residue 134 ASP Chi-restraints excluded: chain 2 residue 135 LYS Chi-restraints excluded: chain 3 residue 338 VAL Chi-restraints excluded: chain 3 residue 424 ASP Chi-restraints excluded: chain 3 residue 471 SER Chi-restraints excluded: chain 3 residue 477 ILE Chi-restraints excluded: chain 3 residue 532 VAL Chi-restraints excluded: chain 3 residue 535 GLN Chi-restraints excluded: chain 3 residue 613 TYR Chi-restraints excluded: chain 3 residue 659 ASP Chi-restraints excluded: chain 3 residue 667 THR Chi-restraints excluded: chain 4 residue 66 MET Chi-restraints excluded: chain 4 residue 75 LYS Chi-restraints excluded: chain 4 residue 164 MET Chi-restraints excluded: chain 4 residue 430 ARG Chi-restraints excluded: chain 5 residue 153 THR Chi-restraints excluded: chain 6 residue 34 ASP Chi-restraints excluded: chain 6 residue 49 THR Chi-restraints excluded: chain 6 residue 50 PHE Chi-restraints excluded: chain 6 residue 84 ASP Chi-restraints excluded: chain 9 residue 13 ASP Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain 9 residue 126 CYS Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain H residue 24 GLU Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 55 MET Chi-restraints excluded: chain J residue 169 MET Chi-restraints excluded: chain K residue 3 LEU Chi-restraints excluded: chain K residue 10 MET Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 217 ILE Chi-restraints excluded: chain L residue 352 ASP Chi-restraints excluded: chain L residue 425 ARG Chi-restraints excluded: chain L residue 445 GLU Chi-restraints excluded: chain L residue 505 SER Chi-restraints excluded: chain L residue 583 LEU Chi-restraints excluded: chain L residue 601 LEU Chi-restraints excluded: chain M residue 14 LEU Chi-restraints excluded: chain M residue 36 LEU Chi-restraints excluded: chain M residue 157 SER Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain M residue 378 GLU Chi-restraints excluded: chain M residue 394 ILE Chi-restraints excluded: chain N residue 146 LEU Chi-restraints excluded: chain N residue 161 SER Chi-restraints excluded: chain N residue 258 SER Chi-restraints excluded: chain N residue 274 ASP Chi-restraints excluded: chain N residue 295 ARG Chi-restraints excluded: chain N residue 308 THR Chi-restraints excluded: chain N residue 335 MET Chi-restraints excluded: chain V residue 100 LEU Chi-restraints excluded: chain V residue 109 ILE Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain V residue 134 VAL Chi-restraints excluded: chain W residue 23 LYS Chi-restraints excluded: chain W residue 36 VAL Chi-restraints excluded: chain W residue 98 SER Chi-restraints excluded: chain W residue 140 THR Chi-restraints excluded: chain X residue 26 ASP Chi-restraints excluded: chain X residue 40 LEU Chi-restraints excluded: chain X residue 65 ILE Chi-restraints excluded: chain Y residue 5 GLU Chi-restraints excluded: chain Y residue 43 MET Chi-restraints excluded: chain Y residue 63 ASN Chi-restraints excluded: chain Y residue 154 GLU Chi-restraints excluded: chain Z residue 39 LEU Chi-restraints excluded: chain Z residue 61 TYR Chi-restraints excluded: chain Z residue 169 THR Chi-restraints excluded: chain a residue 45 ASP Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 19 ASP Chi-restraints excluded: chain b residue 78 GLU Chi-restraints excluded: chain c residue 44 ASN Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain c residue 115 SER Chi-restraints excluded: chain d residue 140 LYS Chi-restraints excluded: chain d residue 185 ILE Chi-restraints excluded: chain d residue 284 VAL Chi-restraints excluded: chain d residue 340 VAL Chi-restraints excluded: chain e residue 90 LEU Chi-restraints excluded: chain f residue 15 VAL Chi-restraints excluded: chain g residue 67 LYS Chi-restraints excluded: chain h residue 17 ARG Chi-restraints excluded: chain h residue 101 LYS Chi-restraints excluded: chain i residue 2 GLU Chi-restraints excluded: chain i residue 11 LEU Chi-restraints excluded: chain i residue 68 MET Chi-restraints excluded: chain i residue 134 ILE Chi-restraints excluded: chain j residue 26 ASP Chi-restraints excluded: chain k residue 60 ASP Chi-restraints excluded: chain k residue 96 LEU Chi-restraints excluded: chain k residue 160 VAL Chi-restraints excluded: chain k residue 162 GLU Chi-restraints excluded: chain k residue 178 GLU Chi-restraints excluded: chain k residue 192 MET Chi-restraints excluded: chain k residue 203 GLU Chi-restraints excluded: chain m residue 8 LEU Chi-restraints excluded: chain m residue 30 ILE Chi-restraints excluded: chain m residue 31 LEU Chi-restraints excluded: chain m residue 42 LEU Chi-restraints excluded: chain n residue 14 GLU Chi-restraints excluded: chain n residue 78 VAL Chi-restraints excluded: chain n residue 81 VAL Chi-restraints excluded: chain n residue 87 LEU Chi-restraints excluded: chain o residue 20 SER Chi-restraints excluded: chain o residue 55 SER Chi-restraints excluded: chain o residue 77 LYS Chi-restraints excluded: chain o residue 96 SER Chi-restraints excluded: chain o residue 110 ARG Chi-restraints excluded: chain p residue 8 SER Chi-restraints excluded: chain p residue 30 LYS Chi-restraints excluded: chain p residue 36 LEU Chi-restraints excluded: chain p residue 98 ILE Chi-restraints excluded: chain p residue 103 VAL Chi-restraints excluded: chain r residue 30 ARG Chi-restraints excluded: chain r residue 68 ILE Chi-restraints excluded: chain r residue 76 ILE Chi-restraints excluded: chain r residue 78 VAL Chi-restraints excluded: chain r residue 86 LYS Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain s residue 69 LYS Chi-restraints excluded: chain s residue 100 GLU Chi-restraints excluded: chain t residue 31 VAL Chi-restraints excluded: chain t residue 34 ASP Chi-restraints excluded: chain t residue 54 LYS Chi-restraints excluded: chain t residue 98 VAL Chi-restraints excluded: chain u residue 8 GLU Chi-restraints excluded: chain u residue 19 ARG Chi-restraints excluded: chain u residue 60 THR Chi-restraints excluded: chain v residue 31 VAL Chi-restraints excluded: chain v residue 101 MET Chi-restraints excluded: chain v residue 124 THR Chi-restraints excluded: chain v residue 140 LEU Chi-restraints excluded: chain v residue 157 GLU Chi-restraints excluded: chain w residue 49 LYS Chi-restraints excluded: chain w residue 60 VAL Chi-restraints excluded: chain w residue 74 SER Chi-restraints excluded: chain w residue 100 ARG Chi-restraints excluded: chain w residue 109 GLU Chi-restraints excluded: chain y residue 26 LEU Chi-restraints excluded: chain z residue 16 LEU Chi-restraints excluded: chain z residue 34 ARG Chi-restraints excluded: chain z residue 42 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 794 random chunks: chunk 258 optimal weight: 6.9990 chunk 691 optimal weight: 20.0000 chunk 151 optimal weight: 2.9990 chunk 450 optimal weight: 10.0000 chunk 189 optimal weight: 0.9980 chunk 768 optimal weight: 5.9990 chunk 637 optimal weight: 4.9990 chunk 355 optimal weight: 5.9990 chunk 63 optimal weight: 20.0000 chunk 254 optimal weight: 0.8980 chunk 403 optimal weight: 6.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 373 ASN 1 436 GLN 3 459 GLN ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 248 HIS ** L 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 366 ASN V 128 GLN ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 123 ASN ** Z 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 180 ASN d 243 GLN h 24 GLN h 72 GLN h 107 GLN i 12 GLN i 123 GLN k 97 GLN ** k 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 239 GLN ** l 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 74 ASN ** t 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 13 ASN y 30 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 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 : 0.008 0.277 69131 Z= 0.521 Angle : 1.568 51.165 93426 Z= 1.012 Chirality : 0.310 6.571 10118 Planarity : 0.004 0.047 11647 Dihedral : 11.750 175.603 10576 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.09 % Favored : 96.88 % Rotamer: Outliers : 3.21 % Allowed : 16.76 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.09), residues: 8046 helix: 0.94 (0.08), residues: 4277 sheet: -1.08 (0.24), residues: 374 loop : -0.44 (0.11), residues: 3395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP L 144 HIS 0.021 0.001 HIS 9 65 PHE 0.035 0.001 PHE M 256 TYR 0.026 0.001 TYR o 81 ARG 0.007 0.000 ARG g 99 *********************** 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 1312 residues out of total 7132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 1083 time to evaluate : 6.179 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 16 LYS cc_start: 0.8072 (mtmm) cc_final: 0.7759 (tptm) REVERT: 1 129 MET cc_start: 0.9212 (mtm) cc_final: 0.8843 (ptp) REVERT: 1 302 SER cc_start: 0.8476 (m) cc_final: 0.8058 (p) REVERT: 2 127 LYS cc_start: 0.8351 (ptpt) cc_final: 0.7534 (mmmm) REVERT: 3 95 GLU cc_start: 0.8775 (tt0) cc_final: 0.8561 (tp30) REVERT: 3 477 ILE cc_start: 0.8279 (OUTLIER) cc_final: 0.8049 (tp) REVERT: 3 640 ASN cc_start: 0.7977 (t0) cc_final: 0.7573 (m-40) REVERT: 4 66 MET cc_start: 0.9067 (OUTLIER) cc_final: 0.8408 (mmt) REVERT: 4 410 MET cc_start: 0.8825 (mtt) cc_final: 0.8543 (mtm) REVERT: 4 422 ASP cc_start: 0.7309 (t0) cc_final: 0.7106 (t70) REVERT: 6 50 PHE cc_start: 0.8835 (OUTLIER) cc_final: 0.8042 (m-80) REVERT: 6 86 MET cc_start: 0.8662 (ttm) cc_final: 0.8457 (ttp) REVERT: 6 102 LYS cc_start: 0.9028 (tttt) cc_final: 0.8747 (tppp) REVERT: A 16 LEU cc_start: 0.8452 (tp) cc_final: 0.8132 (mm) REVERT: A 22 PHE cc_start: 0.8526 (m-80) cc_final: 0.8218 (m-80) REVERT: H 199 ASP cc_start: 0.8528 (p0) cc_final: 0.8285 (p0) REVERT: J 31 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8444 (mt) REVERT: K 10 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.8377 (ttp) REVERT: K 27 MET cc_start: 0.8809 (tpp) cc_final: 0.8561 (mmm) REVERT: L 214 MET cc_start: 0.8635 (mmp) cc_final: 0.7871 (ttt) REVERT: L 535 ARG cc_start: 0.8086 (mtt90) cc_final: 0.7853 (mtt90) REVERT: L 559 GLU cc_start: 0.7597 (tp30) cc_final: 0.7372 (tp30) REVERT: M 234 ILE cc_start: 0.8622 (mp) cc_final: 0.8353 (mt) REVERT: M 394 ILE cc_start: 0.8901 (mt) cc_final: 0.8682 (mp) REVERT: N 98 MET cc_start: 0.8970 (ttm) cc_final: 0.8721 (ttm) REVERT: N 295 ARG cc_start: 0.7910 (OUTLIER) cc_final: 0.7330 (mtm-85) REVERT: N 311 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8611 (mtp) REVERT: V 57 ARG cc_start: 0.6992 (ttp-110) cc_final: 0.6671 (tpp-160) REVERT: V 119 LEU cc_start: 0.8166 (mt) cc_final: 0.7892 (tp) REVERT: Y 43 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8211 (mmm) REVERT: Y 89 ASP cc_start: 0.8287 (t0) cc_final: 0.7681 (t0) REVERT: Z 39 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8323 (mm) REVERT: a 34 ASP cc_start: 0.6534 (t0) cc_final: 0.6298 (m-30) REVERT: b 54 SER cc_start: 0.8743 (t) cc_final: 0.8412 (p) REVERT: b 78 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.7890 (mp0) REVERT: b 80 LYS cc_start: 0.7881 (ttpp) cc_final: 0.7646 (tttp) REVERT: e 56 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8339 (mt-10) REVERT: g 56 LYS cc_start: 0.9075 (tmmt) cc_final: 0.8761 (ttmt) REVERT: g 60 ASP cc_start: 0.8338 (m-30) cc_final: 0.8093 (m-30) REVERT: h 17 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7145 (mpp80) REVERT: h 18 ASP cc_start: 0.8582 (t0) cc_final: 0.8286 (t70) REVERT: h 63 MET cc_start: 0.8876 (mmp) cc_final: 0.8650 (mmp) REVERT: i 1 MET cc_start: 0.7826 (tpt) cc_final: 0.7117 (mtt) REVERT: i 2 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7464 (pm20) REVERT: j 75 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7488 (pm20) REVERT: k 203 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8109 (mp0) REVERT: k 236 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7628 (mt-10) REVERT: m 14 LYS cc_start: 0.8756 (mtmt) cc_final: 0.8450 (mmtt) REVERT: m 37 TYR cc_start: 0.8203 (m-10) cc_final: 0.7835 (m-10) REVERT: n 13 MET cc_start: 0.5998 (pmm) cc_final: 0.4123 (tmm) REVERT: o 25 LYS cc_start: 0.7838 (mttt) cc_final: 0.7375 (mmtt) REVERT: o 77 LYS cc_start: 0.9263 (OUTLIER) cc_final: 0.8881 (mtmm) REVERT: o 114 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7568 (mt-10) REVERT: p 5 TYR cc_start: 0.6500 (t80) cc_final: 0.6203 (t80) REVERT: p 30 LYS cc_start: 0.6725 (OUTLIER) cc_final: 0.6168 (ptmm) REVERT: p 60 GLU cc_start: 0.8346 (pp20) cc_final: 0.8034 (pm20) REVERT: q 104 LYS cc_start: 0.8640 (mmmt) cc_final: 0.8092 (ttmt) REVERT: r 12 GLN cc_start: 0.7523 (pt0) cc_final: 0.7011 (tm-30) REVERT: r 30 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.6263 (ppp80) REVERT: r 66 HIS cc_start: 0.4982 (t70) cc_final: 0.4289 (m90) REVERT: s 100 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7939 (mp0) REVERT: u 26 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7587 (tt0) REVERT: u 53 TYR cc_start: 0.7648 (t80) cc_final: 0.7361 (t80) REVERT: v 157 GLU cc_start: 0.6571 (OUTLIER) cc_final: 0.6282 (mp0) REVERT: w 56 TRP cc_start: 0.7362 (t60) cc_final: 0.7069 (m-10) REVERT: w 109 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7902 (mp0) REVERT: x 16 LYS cc_start: 0.8273 (ttmt) cc_final: 0.7827 (tptm) REVERT: y 26 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8838 (mp) REVERT: z 53 ARG cc_start: 0.8210 (mtm-85) cc_final: 0.7923 (mtm-85) outliers start: 229 outliers final: 99 residues processed: 1216 average time/residue: 1.5119 time to fit residues: 2401.5206 Evaluate side-chains 1153 residues out of total 7132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 1033 time to evaluate : 6.153 ------------------------------------------------------------------------------- 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 355 LYS Chi-restraints excluded: chain 2 residue 128 VAL Chi-restraints excluded: chain 2 residue 134 ASP Chi-restraints excluded: chain 2 residue 135 LYS Chi-restraints excluded: chain 3 residue 159 CYS Chi-restraints excluded: chain 3 residue 424 ASP Chi-restraints excluded: chain 3 residue 471 SER Chi-restraints excluded: chain 3 residue 477 ILE Chi-restraints excluded: chain 3 residue 517 ASN Chi-restraints excluded: chain 3 residue 532 VAL Chi-restraints excluded: chain 3 residue 535 GLN Chi-restraints excluded: chain 3 residue 613 TYR Chi-restraints excluded: chain 3 residue 659 ASP Chi-restraints excluded: chain 3 residue 667 THR Chi-restraints excluded: chain 4 residue 66 MET Chi-restraints excluded: chain 4 residue 164 MET Chi-restraints excluded: chain 6 residue 34 ASP Chi-restraints excluded: chain 6 residue 50 PHE Chi-restraints excluded: chain 6 residue 84 ASP Chi-restraints excluded: chain 9 residue 1 THR Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 24 GLU Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain H residue 274 ARG Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 55 MET Chi-restraints excluded: chain K residue 3 LEU Chi-restraints excluded: chain K residue 10 MET Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain L residue 217 ILE Chi-restraints excluded: chain L residue 505 SER Chi-restraints excluded: chain L residue 583 LEU Chi-restraints excluded: chain L residue 601 LEU Chi-restraints excluded: chain N residue 146 LEU Chi-restraints excluded: chain N residue 161 SER Chi-restraints excluded: chain N residue 258 SER Chi-restraints excluded: chain N residue 280 THR Chi-restraints excluded: chain N residue 285 THR Chi-restraints excluded: chain N residue 295 ARG Chi-restraints excluded: chain N residue 308 THR Chi-restraints excluded: chain N residue 311 MET Chi-restraints excluded: chain N residue 335 MET Chi-restraints excluded: chain V residue 100 LEU Chi-restraints excluded: chain V residue 109 ILE Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain V residue 134 VAL Chi-restraints excluded: chain W residue 36 VAL Chi-restraints excluded: chain W residue 98 SER Chi-restraints excluded: chain W residue 140 THR Chi-restraints excluded: chain X residue 26 ASP Chi-restraints excluded: chain X residue 40 LEU Chi-restraints excluded: chain X residue 65 ILE Chi-restraints excluded: chain Y residue 43 MET Chi-restraints excluded: chain Y residue 63 ASN Chi-restraints excluded: chain Y residue 154 GLU Chi-restraints excluded: chain Z residue 39 LEU Chi-restraints excluded: chain a residue 45 ASP Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 78 GLU Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain c residue 115 SER Chi-restraints excluded: chain d residue 140 LYS Chi-restraints excluded: chain d residue 154 LYS Chi-restraints excluded: chain d residue 243 GLN Chi-restraints excluded: chain d residue 280 THR Chi-restraints excluded: chain f residue 15 VAL Chi-restraints excluded: chain g residue 67 LYS Chi-restraints excluded: chain h residue 17 ARG Chi-restraints excluded: chain h residue 101 LYS Chi-restraints excluded: chain i residue 2 GLU Chi-restraints excluded: chain i residue 11 LEU Chi-restraints excluded: chain j residue 26 ASP Chi-restraints excluded: chain j residue 75 GLU Chi-restraints excluded: chain k residue 65 ASP Chi-restraints excluded: chain k residue 192 MET Chi-restraints excluded: chain k residue 203 GLU Chi-restraints excluded: chain m residue 42 LEU Chi-restraints excluded: chain n residue 78 VAL Chi-restraints excluded: chain n residue 81 VAL Chi-restraints excluded: chain n residue 87 LEU Chi-restraints excluded: chain o residue 20 SER Chi-restraints excluded: chain o residue 55 SER Chi-restraints excluded: chain o residue 77 LYS Chi-restraints excluded: chain o residue 96 SER Chi-restraints excluded: chain o residue 110 ARG Chi-restraints excluded: chain p residue 30 LYS Chi-restraints excluded: chain p residue 36 LEU Chi-restraints excluded: chain p residue 98 ILE Chi-restraints excluded: chain r residue 30 ARG Chi-restraints excluded: chain r residue 68 ILE Chi-restraints excluded: chain r residue 76 ILE Chi-restraints excluded: chain r residue 78 VAL Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain s residue 79 CYS Chi-restraints excluded: chain s residue 100 GLU Chi-restraints excluded: chain t residue 31 VAL Chi-restraints excluded: chain t residue 56 MET Chi-restraints excluded: chain u residue 8 GLU Chi-restraints excluded: chain u residue 60 THR Chi-restraints excluded: chain v residue 29 MET Chi-restraints excluded: chain v residue 31 VAL Chi-restraints excluded: chain v residue 49 LYS Chi-restraints excluded: chain v residue 68 ASP Chi-restraints excluded: chain v residue 157 GLU Chi-restraints excluded: chain w residue 74 SER Chi-restraints excluded: chain w residue 100 ARG Chi-restraints excluded: chain w residue 109 GLU Chi-restraints excluded: chain y residue 9 ASP Chi-restraints excluded: chain y residue 26 LEU Chi-restraints excluded: chain z residue 16 LEU Chi-restraints excluded: chain z residue 42 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 794 random chunks: chunk 740 optimal weight: 7.9990 chunk 86 optimal weight: 20.0000 chunk 437 optimal weight: 30.0000 chunk 561 optimal weight: 30.0000 chunk 434 optimal weight: 20.0000 chunk 646 optimal weight: 2.9990 chunk 428 optimal weight: 10.0000 chunk 765 optimal weight: 0.0030 chunk 478 optimal weight: 9.9990 chunk 466 optimal weight: 2.9990 chunk 353 optimal weight: 6.9990 overall best weight: 4.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 248 HIS ** L 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 128 GLN ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 123 ASN ** Z 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 203 GLN h 24 GLN h 72 GLN h 107 GLN i 12 GLN ** k 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 239 GLN ** l 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 46 ASN ** t 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 136 ASN x 13 ASN y 30 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.3047 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= 0.536 Angle : 1.572 51.129 93426 Z= 1.014 Chirality : 0.310 6.566 10118 Planarity : 0.004 0.056 11647 Dihedral : 11.610 175.427 10576 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.33 % Favored : 96.64 % Rotamer: Outliers : 3.38 % Allowed : 17.05 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.09), residues: 8046 helix: 1.01 (0.08), residues: 4263 sheet: -0.82 (0.24), residues: 378 loop : -0.36 (0.11), residues: 3405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP L 144 HIS 0.019 0.001 HIS 9 65 PHE 0.036 0.002 PHE M 256 TYR 0.030 0.002 TYR H 215 ARG 0.007 0.000 ARG 1 385 *********************** 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 1307 residues out of total 7132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 1066 time to evaluate : 6.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 16 LYS cc_start: 0.8083 (mtmm) cc_final: 0.7758 (tptm) REVERT: 1 302 SER cc_start: 0.8475 (m) cc_final: 0.8066 (p) REVERT: 2 127 LYS cc_start: 0.8315 (ptpt) cc_final: 0.7517 (mmmm) REVERT: 3 95 GLU cc_start: 0.8768 (tt0) cc_final: 0.8562 (tp30) REVERT: 3 477 ILE cc_start: 0.8276 (OUTLIER) cc_final: 0.8061 (tp) REVERT: 3 640 ASN cc_start: 0.7978 (t0) cc_final: 0.7606 (m-40) REVERT: 4 66 MET cc_start: 0.9057 (OUTLIER) cc_final: 0.8399 (mmt) REVERT: 4 410 MET cc_start: 0.8820 (mtt) cc_final: 0.8541 (mtm) REVERT: 4 422 ASP cc_start: 0.7346 (t0) cc_final: 0.7121 (t70) REVERT: 4 430 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.6291 (mpp-170) REVERT: 5 182 ARG cc_start: 0.9262 (OUTLIER) cc_final: 0.7862 (ttp80) REVERT: 6 50 PHE cc_start: 0.8842 (OUTLIER) cc_final: 0.8048 (m-80) REVERT: 6 102 LYS cc_start: 0.9043 (tttt) cc_final: 0.8760 (tppp) REVERT: A 16 LEU cc_start: 0.8439 (tp) cc_final: 0.8110 (mm) REVERT: A 22 PHE cc_start: 0.8534 (m-80) cc_final: 0.8245 (m-80) REVERT: H 199 ASP cc_start: 0.8546 (p0) cc_final: 0.8266 (p0) REVERT: J 31 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8449 (mt) REVERT: L 214 MET cc_start: 0.8658 (mmp) cc_final: 0.7896 (ttt) REVERT: L 475 MET cc_start: 0.8015 (mmm) cc_final: 0.7547 (mtp) REVERT: L 535 ARG cc_start: 0.8085 (mtt90) cc_final: 0.7852 (mtt90) REVERT: L 559 GLU cc_start: 0.7611 (tp30) cc_final: 0.7352 (tp30) REVERT: M 394 ILE cc_start: 0.8885 (mt) cc_final: 0.8665 (mp) REVERT: N 79 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.8563 (mtt) REVERT: N 98 MET cc_start: 0.8984 (ttm) cc_final: 0.8738 (ttm) REVERT: N 295 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.7333 (mtm-85) REVERT: N 311 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8614 (mtp) REVERT: V 57 ARG cc_start: 0.7043 (ttp-110) cc_final: 0.6683 (tpp-160) REVERT: V 119 LEU cc_start: 0.8166 (mt) cc_final: 0.7891 (tp) REVERT: Y 43 MET cc_start: 0.8759 (OUTLIER) cc_final: 0.8225 (mmm) REVERT: Y 89 ASP cc_start: 0.8285 (t0) cc_final: 0.7677 (t0) REVERT: Z 39 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8361 (mm) REVERT: a 34 ASP cc_start: 0.6413 (t0) cc_final: 0.6208 (m-30) REVERT: b 54 SER cc_start: 0.8742 (t) cc_final: 0.8423 (p) REVERT: b 78 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7832 (mp0) REVERT: b 80 LYS cc_start: 0.7925 (ttpp) cc_final: 0.7684 (tttp) REVERT: e 56 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8343 (mt-10) REVERT: g 56 LYS cc_start: 0.9076 (tmmt) cc_final: 0.8751 (tppt) REVERT: g 60 ASP cc_start: 0.8339 (m-30) cc_final: 0.8095 (m-30) REVERT: h 18 ASP cc_start: 0.8578 (t0) cc_final: 0.8228 (t70) REVERT: i 1 MET cc_start: 0.7806 (tpt) cc_final: 0.7121 (mtt) REVERT: i 2 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7459 (pm20) REVERT: i 25 ARG cc_start: 0.8810 (ttt90) cc_final: 0.8144 (ttm170) REVERT: j 74 GLN cc_start: 0.7732 (OUTLIER) cc_final: 0.7131 (tp40) REVERT: j 75 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7389 (pm20) REVERT: k 40 LYS cc_start: 0.7886 (OUTLIER) cc_final: 0.7623 (mtmp) REVERT: k 203 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8103 (mp0) REVERT: k 236 GLU cc_start: 0.8240 (tm-30) cc_final: 0.7639 (mt-10) REVERT: m 14 LYS cc_start: 0.8759 (mtmt) cc_final: 0.8434 (mmtt) REVERT: m 37 TYR cc_start: 0.8220 (m-10) cc_final: 0.7874 (m-10) REVERT: m 81 LYS cc_start: 0.8999 (mtpp) cc_final: 0.8466 (mtmm) REVERT: o 25 LYS cc_start: 0.7887 (mttt) cc_final: 0.7425 (mmtt) REVERT: o 77 LYS cc_start: 0.9270 (OUTLIER) cc_final: 0.8884 (mtmm) REVERT: o 107 LYS cc_start: 0.7935 (mtpt) cc_final: 0.7552 (ttmm) REVERT: o 114 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7584 (mt-10) REVERT: p 5 TYR cc_start: 0.6460 (t80) cc_final: 0.6173 (t80) REVERT: p 30 LYS cc_start: 0.6697 (OUTLIER) cc_final: 0.6459 (ptmm) REVERT: q 95 THR cc_start: 0.8477 (t) cc_final: 0.8118 (m) REVERT: q 104 LYS cc_start: 0.8655 (mmmt) cc_final: 0.8098 (ttmt) REVERT: r 12 GLN cc_start: 0.7526 (pt0) cc_final: 0.7033 (tm-30) REVERT: r 30 ARG cc_start: 0.7715 (OUTLIER) cc_final: 0.6305 (ppp80) REVERT: r 66 HIS cc_start: 0.5161 (t70) cc_final: 0.4363 (m90) REVERT: s 46 ASN cc_start: 0.8092 (OUTLIER) cc_final: 0.7713 (t0) REVERT: s 100 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7937 (mp0) REVERT: u 19 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.7105 (mtt-85) REVERT: u 26 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7586 (tt0) REVERT: u 53 TYR cc_start: 0.7703 (t80) cc_final: 0.7395 (t80) REVERT: v 151 GLU cc_start: 0.5411 (tp30) cc_final: 0.4310 (tp30) REVERT: v 157 GLU cc_start: 0.6585 (mp0) cc_final: 0.6309 (mp0) REVERT: w 56 TRP cc_start: 0.7448 (t60) cc_final: 0.7122 (m-10) REVERT: w 109 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7897 (mp0) REVERT: x 16 LYS cc_start: 0.8284 (ttmt) cc_final: 0.7817 (tptm) REVERT: y 26 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8870 (mp) REVERT: z 53 ARG cc_start: 0.8171 (mtm-85) cc_final: 0.7900 (mtm-85) outliers start: 241 outliers final: 128 residues processed: 1196 average time/residue: 1.5019 time to fit residues: 2345.8575 Evaluate side-chains 1170 residues out of total 7132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 1017 time to evaluate : 6.087 ------------------------------------------------------------------------------- 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 355 LYS Chi-restraints excluded: chain 2 residue 128 VAL Chi-restraints excluded: chain 2 residue 134 ASP Chi-restraints excluded: chain 2 residue 135 LYS Chi-restraints excluded: chain 3 residue 159 CYS Chi-restraints excluded: chain 3 residue 190 MET Chi-restraints excluded: chain 3 residue 338 VAL Chi-restraints excluded: chain 3 residue 424 ASP Chi-restraints excluded: chain 3 residue 471 SER Chi-restraints excluded: chain 3 residue 477 ILE Chi-restraints excluded: chain 3 residue 517 ASN Chi-restraints excluded: chain 3 residue 532 VAL Chi-restraints excluded: chain 3 residue 535 GLN Chi-restraints excluded: chain 3 residue 654 GLN Chi-restraints excluded: chain 3 residue 659 ASP Chi-restraints excluded: chain 3 residue 667 THR Chi-restraints excluded: chain 4 residue 66 MET Chi-restraints excluded: chain 4 residue 164 MET Chi-restraints excluded: chain 4 residue 430 ARG Chi-restraints excluded: chain 5 residue 153 THR Chi-restraints excluded: chain 5 residue 182 ARG Chi-restraints excluded: chain 6 residue 34 ASP Chi-restraints excluded: chain 6 residue 50 PHE Chi-restraints excluded: chain 9 residue 1 THR Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain 9 residue 126 CYS Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 24 GLU Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 215 TYR Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain H residue 274 ARG Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 55 MET Chi-restraints excluded: chain K residue 3 LEU Chi-restraints excluded: chain K residue 50 ASN Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain L residue 217 ILE Chi-restraints excluded: chain L residue 445 GLU Chi-restraints excluded: chain L residue 505 SER Chi-restraints excluded: chain L residue 565 THR Chi-restraints excluded: chain L residue 583 LEU Chi-restraints excluded: chain L residue 601 LEU Chi-restraints excluded: chain M residue 14 LEU Chi-restraints excluded: chain M residue 98 MET Chi-restraints excluded: chain M residue 186 MET Chi-restraints excluded: chain M residue 247 THR Chi-restraints excluded: chain M residue 418 LYS Chi-restraints excluded: chain N residue 37 MET Chi-restraints excluded: chain N residue 79 MET Chi-restraints excluded: chain N residue 146 LEU Chi-restraints excluded: chain N residue 161 SER Chi-restraints excluded: chain N residue 258 SER Chi-restraints excluded: chain N residue 280 THR Chi-restraints excluded: chain N residue 285 THR Chi-restraints excluded: chain N residue 295 ARG Chi-restraints excluded: chain N residue 308 THR Chi-restraints excluded: chain N residue 311 MET Chi-restraints excluded: chain N residue 335 MET Chi-restraints excluded: chain V residue 100 LEU Chi-restraints excluded: chain V residue 109 ILE Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain V residue 134 VAL Chi-restraints excluded: chain W residue 36 VAL Chi-restraints excluded: chain W residue 98 SER Chi-restraints excluded: chain W residue 140 THR Chi-restraints excluded: chain X residue 26 ASP Chi-restraints excluded: chain X residue 40 LEU Chi-restraints excluded: chain Y residue 43 MET Chi-restraints excluded: chain Y residue 63 ASN Chi-restraints excluded: chain Y residue 154 GLU Chi-restraints excluded: chain Z residue 16 THR Chi-restraints excluded: chain Z residue 29 ILE Chi-restraints excluded: chain Z residue 39 LEU Chi-restraints excluded: chain Z residue 61 TYR Chi-restraints excluded: chain a residue 45 ASP Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 19 ASP Chi-restraints excluded: chain b residue 78 GLU Chi-restraints excluded: chain c residue 44 ASN Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain c residue 115 SER Chi-restraints excluded: chain c residue 131 SER Chi-restraints excluded: chain d residue 140 LYS Chi-restraints excluded: chain d residue 154 LYS Chi-restraints excluded: chain d residue 280 THR Chi-restraints excluded: chain d residue 284 VAL Chi-restraints excluded: chain d residue 340 VAL Chi-restraints excluded: chain f residue 15 VAL Chi-restraints excluded: chain g residue 67 LYS Chi-restraints excluded: chain g residue 95 VAL Chi-restraints excluded: chain h residue 101 LYS Chi-restraints excluded: chain i residue 2 GLU Chi-restraints excluded: chain i residue 11 LEU Chi-restraints excluded: chain j residue 26 ASP Chi-restraints excluded: chain j residue 33 ASN Chi-restraints excluded: chain j residue 74 GLN Chi-restraints excluded: chain j residue 75 GLU Chi-restraints excluded: chain k residue 40 LYS Chi-restraints excluded: chain k residue 65 ASP Chi-restraints excluded: chain k residue 96 LEU Chi-restraints excluded: chain k residue 162 GLU Chi-restraints excluded: chain k residue 192 MET Chi-restraints excluded: chain k residue 203 GLU Chi-restraints excluded: chain m residue 8 LEU Chi-restraints excluded: chain m residue 30 ILE Chi-restraints excluded: chain m residue 42 LEU Chi-restraints excluded: chain n residue 78 VAL Chi-restraints excluded: chain n residue 81 VAL Chi-restraints excluded: chain n residue 87 LEU Chi-restraints excluded: chain o residue 20 SER Chi-restraints excluded: chain o residue 55 SER Chi-restraints excluded: chain o residue 77 LYS Chi-restraints excluded: chain o residue 96 SER Chi-restraints excluded: chain o residue 105 ASP Chi-restraints excluded: chain o residue 111 GLU Chi-restraints excluded: chain p residue 30 LYS Chi-restraints excluded: chain p residue 36 LEU Chi-restraints excluded: chain p residue 94 ILE Chi-restraints excluded: chain p residue 98 ILE Chi-restraints excluded: chain r residue 30 ARG Chi-restraints excluded: chain r residue 68 ILE Chi-restraints excluded: chain r residue 76 ILE Chi-restraints excluded: chain r residue 78 VAL Chi-restraints excluded: chain r residue 86 LYS Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain s residue 46 ASN Chi-restraints excluded: chain s residue 79 CYS Chi-restraints excluded: chain s residue 95 VAL Chi-restraints excluded: chain s residue 100 GLU Chi-restraints excluded: chain t residue 31 VAL Chi-restraints excluded: chain t residue 54 LYS Chi-restraints excluded: chain t residue 56 MET Chi-restraints excluded: chain u residue 8 GLU Chi-restraints excluded: chain u residue 19 ARG Chi-restraints excluded: chain u residue 60 THR Chi-restraints excluded: chain v residue 29 MET Chi-restraints excluded: chain v residue 31 VAL Chi-restraints excluded: chain v residue 101 MET Chi-restraints excluded: chain w residue 74 SER Chi-restraints excluded: chain w residue 100 ARG Chi-restraints excluded: chain w residue 109 GLU Chi-restraints excluded: chain x residue 19 LEU Chi-restraints excluded: chain y residue 26 LEU Chi-restraints excluded: chain z residue 16 LEU Chi-restraints excluded: chain z residue 42 SER 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: 6.9990 chunk 457 optimal weight: 6.9990 chunk 230 optimal weight: 9.9990 chunk 150 optimal weight: 5.9990 chunk 148 optimal weight: 9.9990 chunk 486 optimal weight: 10.0000 chunk 521 optimal weight: 4.9990 chunk 378 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 601 optimal weight: 1.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 317 GLN L 248 HIS V 128 GLN ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 123 ASN ** Z 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 180 ASN d 243 GLN h 24 GLN h 72 GLN h 107 GLN i 12 GLN ** k 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 239 GLN ** l 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 136 ASN x 13 ASN y 30 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.282 69131 Z= 0.522 Angle : 1.569 51.256 93426 Z= 1.013 Chirality : 0.310 6.605 10118 Planarity : 0.004 0.046 11647 Dihedral : 11.387 173.762 10576 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.13 % Favored : 96.84 % Rotamer: Outliers : 3.00 % Allowed : 17.65 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.10), residues: 8046 helix: 1.08 (0.08), residues: 4259 sheet: -0.72 (0.25), residues: 367 loop : -0.28 (0.11), residues: 3420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP H 121 HIS 0.025 0.001 HIS 9 65 PHE 0.039 0.001 PHE M 256 TYR 0.029 0.001 TYR o 81 ARG 0.007 0.000 ARG q 51 *********************** 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 1267 residues out of total 7132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 1053 time to evaluate : 6.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 16 LYS cc_start: 0.8032 (mtmm) cc_final: 0.7668 (tptm) REVERT: 1 302 SER cc_start: 0.8299 (m) cc_final: 0.7891 (p) REVERT: 2 127 LYS cc_start: 0.8152 (ptpt) cc_final: 0.7439 (mmmm) REVERT: 3 477 ILE cc_start: 0.8246 (OUTLIER) cc_final: 0.8044 (tp) REVERT: 3 640 ASN cc_start: 0.8006 (t0) cc_final: 0.7625 (m-40) REVERT: 4 66 MET cc_start: 0.9033 (OUTLIER) cc_final: 0.8310 (mmt) REVERT: 4 410 MET cc_start: 0.8810 (mtt) cc_final: 0.8543 (mtm) REVERT: 4 422 ASP cc_start: 0.7259 (t0) cc_final: 0.7026 (t70) REVERT: 4 430 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.6312 (mpp-170) REVERT: 5 43 SER cc_start: 0.9027 (p) cc_final: 0.8572 (m) REVERT: 5 182 ARG cc_start: 0.9262 (OUTLIER) cc_final: 0.7878 (ttp80) REVERT: 6 50 PHE cc_start: 0.8905 (OUTLIER) cc_final: 0.8259 (m-80) REVERT: 6 86 MET cc_start: 0.8605 (ttm) cc_final: 0.8356 (ttp) REVERT: 6 102 LYS cc_start: 0.9025 (tttt) cc_final: 0.8752 (tppp) REVERT: 6 125 TYR cc_start: 0.9079 (OUTLIER) cc_final: 0.8614 (t80) REVERT: A 16 LEU cc_start: 0.8422 (tp) cc_final: 0.8105 (mm) REVERT: A 22 PHE cc_start: 0.8526 (m-80) cc_final: 0.8209 (m-80) REVERT: H 199 ASP cc_start: 0.8555 (p0) cc_final: 0.8292 (p0) REVERT: J 31 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8427 (mt) REVERT: K 27 MET cc_start: 0.8856 (tpp) cc_final: 0.8611 (mmm) REVERT: L 214 MET cc_start: 0.8640 (mmp) cc_final: 0.7928 (ttt) REVERT: L 352 ASP cc_start: 0.7783 (OUTLIER) cc_final: 0.7582 (m-30) REVERT: L 475 MET cc_start: 0.8008 (mmm) cc_final: 0.7584 (mtp) REVERT: L 559 GLU cc_start: 0.7610 (tp30) cc_final: 0.7283 (tp30) REVERT: N 295 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7347 (mtm-85) REVERT: V 57 ARG cc_start: 0.7046 (ttp-110) cc_final: 0.6681 (tpp-160) REVERT: V 119 LEU cc_start: 0.8151 (mt) cc_final: 0.7875 (tp) REVERT: Y 43 MET cc_start: 0.8759 (OUTLIER) cc_final: 0.8212 (mmm) REVERT: Y 89 ASP cc_start: 0.8277 (t0) cc_final: 0.7692 (t0) REVERT: Z 39 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8417 (mm) REVERT: a 34 ASP cc_start: 0.6420 (t0) cc_final: 0.6214 (m-30) REVERT: b 54 SER cc_start: 0.8707 (t) cc_final: 0.8408 (p) REVERT: b 78 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7809 (mp0) REVERT: b 80 LYS cc_start: 0.7911 (ttpp) cc_final: 0.7663 (tttp) REVERT: e 56 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8323 (mt-10) REVERT: g 56 LYS cc_start: 0.9069 (tmmt) cc_final: 0.8733 (ttmt) REVERT: g 60 ASP cc_start: 0.8319 (m-30) cc_final: 0.8069 (m-30) REVERT: h 18 ASP cc_start: 0.8568 (t0) cc_final: 0.8285 (t70) REVERT: i 1 MET cc_start: 0.7737 (tpt) cc_final: 0.7082 (mtt) REVERT: i 2 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7387 (pm20) REVERT: i 25 ARG cc_start: 0.8823 (ttt90) cc_final: 0.8166 (ttm170) REVERT: k 203 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8071 (mp0) REVERT: k 236 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7649 (mt-10) REVERT: m 14 LYS cc_start: 0.8762 (mtmt) cc_final: 0.8394 (mmtt) REVERT: m 37 TYR cc_start: 0.8181 (m-10) cc_final: 0.7864 (m-10) REVERT: m 81 LYS cc_start: 0.9009 (mtpp) cc_final: 0.8496 (mtmm) REVERT: n 13 MET cc_start: 0.5708 (pmm) cc_final: 0.3629 (ttt) REVERT: o 25 LYS cc_start: 0.7897 (mttt) cc_final: 0.7418 (mmtt) REVERT: o 77 LYS cc_start: 0.9263 (OUTLIER) cc_final: 0.8881 (mtmm) REVERT: o 107 LYS cc_start: 0.7964 (mtpt) cc_final: 0.7593 (ttmm) REVERT: o 114 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7590 (mt-10) REVERT: p 5 TYR cc_start: 0.6423 (t80) cc_final: 0.6184 (t80) REVERT: q 95 THR cc_start: 0.8459 (t) cc_final: 0.8120 (m) REVERT: q 104 LYS cc_start: 0.8673 (mmmt) cc_final: 0.8123 (ttmt) REVERT: r 12 GLN cc_start: 0.7498 (pt0) cc_final: 0.7033 (tm-30) REVERT: r 30 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.6416 (ppp80) REVERT: r 66 HIS cc_start: 0.5368 (t70) cc_final: 0.4571 (m90) REVERT: s 42 GLN cc_start: 0.7858 (mt0) cc_final: 0.7601 (mt0) REVERT: s 100 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7949 (mp0) REVERT: u 19 ARG cc_start: 0.7656 (OUTLIER) cc_final: 0.7102 (mtt-85) REVERT: u 26 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7572 (tt0) REVERT: u 53 TYR cc_start: 0.7672 (t80) cc_final: 0.7358 (t80) REVERT: u 55 ASP cc_start: 0.7030 (t0) cc_final: 0.6460 (p0) REVERT: v 148 LYS cc_start: 0.6504 (tmmt) cc_final: 0.6038 (mtpt) REVERT: v 157 GLU cc_start: 0.6524 (OUTLIER) cc_final: 0.6263 (mp0) REVERT: w 56 TRP cc_start: 0.7425 (t60) cc_final: 0.7080 (m-10) REVERT: w 109 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7946 (mp0) REVERT: x 16 LYS cc_start: 0.8292 (ttmt) cc_final: 0.7804 (tptm) REVERT: y 26 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8841 (mp) REVERT: z 53 ARG cc_start: 0.8146 (mtm-85) cc_final: 0.7907 (mtm-85) outliers start: 214 outliers final: 111 residues processed: 1172 average time/residue: 1.5548 time to fit residues: 2399.5798 Evaluate side-chains 1152 residues out of total 7132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 1020 time to evaluate : 6.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 86 SER Chi-restraints excluded: chain 1 residue 314 THR Chi-restraints excluded: chain 1 residue 337 MET Chi-restraints excluded: chain 1 residue 355 LYS Chi-restraints excluded: chain 2 residue 128 VAL Chi-restraints excluded: chain 2 residue 134 ASP Chi-restraints excluded: chain 2 residue 135 LYS Chi-restraints excluded: chain 3 residue 338 VAL Chi-restraints excluded: chain 3 residue 424 ASP Chi-restraints excluded: chain 3 residue 471 SER Chi-restraints excluded: chain 3 residue 477 ILE Chi-restraints excluded: chain 3 residue 517 ASN Chi-restraints excluded: chain 3 residue 532 VAL Chi-restraints excluded: chain 3 residue 535 GLN Chi-restraints excluded: chain 3 residue 659 ASP Chi-restraints excluded: chain 3 residue 667 THR Chi-restraints excluded: chain 4 residue 66 MET Chi-restraints excluded: chain 4 residue 164 MET Chi-restraints excluded: chain 4 residue 430 ARG Chi-restraints excluded: chain 5 residue 153 THR Chi-restraints excluded: chain 5 residue 182 ARG Chi-restraints excluded: chain 6 residue 34 ASP Chi-restraints excluded: chain 6 residue 50 PHE Chi-restraints excluded: chain 6 residue 125 TYR Chi-restraints excluded: chain 9 residue 1 THR Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain H residue 24 GLU Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 215 TYR Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 55 MET Chi-restraints excluded: chain K residue 3 LEU Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain L residue 217 ILE Chi-restraints excluded: chain L residue 352 ASP Chi-restraints excluded: chain L residue 445 GLU Chi-restraints excluded: chain L residue 505 SER Chi-restraints excluded: chain L residue 565 THR Chi-restraints excluded: chain L residue 583 LEU Chi-restraints excluded: chain L residue 601 LEU Chi-restraints excluded: chain M residue 14 LEU Chi-restraints excluded: chain M residue 36 LEU Chi-restraints excluded: chain M residue 98 MET Chi-restraints excluded: chain M residue 247 THR Chi-restraints excluded: chain M residue 418 LYS Chi-restraints excluded: chain M residue 454 ILE Chi-restraints excluded: chain N residue 146 LEU Chi-restraints excluded: chain N residue 161 SER Chi-restraints excluded: chain N residue 258 SER Chi-restraints excluded: chain N residue 285 THR Chi-restraints excluded: chain N residue 295 ARG Chi-restraints excluded: chain N residue 308 THR Chi-restraints excluded: chain N residue 335 MET Chi-restraints excluded: chain V residue 100 LEU Chi-restraints excluded: chain V residue 109 ILE Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain V residue 134 VAL Chi-restraints excluded: chain W residue 18 ASP Chi-restraints excluded: chain W residue 36 VAL Chi-restraints excluded: chain W residue 98 SER Chi-restraints excluded: chain W residue 140 THR Chi-restraints excluded: chain X residue 26 ASP Chi-restraints excluded: chain X residue 40 LEU Chi-restraints excluded: chain X residue 65 ILE Chi-restraints excluded: chain Y residue 43 MET Chi-restraints excluded: chain Y residue 63 ASN Chi-restraints excluded: chain Y residue 154 GLU Chi-restraints excluded: chain Z residue 16 THR Chi-restraints excluded: chain Z residue 39 LEU Chi-restraints excluded: chain a residue 45 ASP Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 78 GLU Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain c residue 115 SER Chi-restraints excluded: chain c residue 131 SER Chi-restraints excluded: chain d residue 140 LYS Chi-restraints excluded: chain d residue 340 VAL Chi-restraints excluded: chain f residue 15 VAL Chi-restraints excluded: chain g residue 67 LYS Chi-restraints excluded: chain i residue 2 GLU Chi-restraints excluded: chain i residue 11 LEU Chi-restraints excluded: chain j residue 26 ASP Chi-restraints excluded: chain j residue 33 ASN Chi-restraints excluded: chain k residue 65 ASP Chi-restraints excluded: chain k residue 162 GLU Chi-restraints excluded: chain k residue 192 MET Chi-restraints excluded: chain k residue 203 GLU Chi-restraints excluded: chain m residue 30 ILE Chi-restraints excluded: chain m residue 42 LEU Chi-restraints excluded: chain n residue 78 VAL Chi-restraints excluded: chain n residue 81 VAL Chi-restraints excluded: chain n residue 87 LEU Chi-restraints excluded: chain o residue 20 SER Chi-restraints excluded: chain o residue 55 SER Chi-restraints excluded: chain o residue 77 LYS Chi-restraints excluded: chain o residue 96 SER Chi-restraints excluded: chain o residue 105 ASP Chi-restraints excluded: chain o residue 111 GLU Chi-restraints excluded: chain p residue 36 LEU Chi-restraints excluded: chain p residue 94 ILE Chi-restraints excluded: chain p residue 98 ILE Chi-restraints excluded: chain r residue 30 ARG Chi-restraints excluded: chain r residue 68 ILE Chi-restraints excluded: chain r residue 76 ILE Chi-restraints excluded: chain r residue 78 VAL Chi-restraints excluded: chain r residue 86 LYS Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain s residue 45 MET Chi-restraints excluded: chain s residue 95 VAL Chi-restraints excluded: chain s residue 100 GLU Chi-restraints excluded: chain t residue 31 VAL Chi-restraints excluded: chain t residue 56 MET Chi-restraints excluded: chain u residue 8 GLU Chi-restraints excluded: chain u residue 19 ARG Chi-restraints excluded: chain u residue 60 THR Chi-restraints excluded: chain v residue 96 VAL Chi-restraints excluded: chain v residue 157 GLU Chi-restraints excluded: chain w residue 74 SER Chi-restraints excluded: chain w residue 100 ARG Chi-restraints excluded: chain w residue 109 GLU Chi-restraints excluded: chain x residue 19 LEU Chi-restraints excluded: chain y residue 9 ASP Chi-restraints excluded: chain y residue 26 LEU Chi-restraints excluded: chain z residue 16 LEU Chi-restraints excluded: chain z residue 42 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 794 random chunks: chunk 696 optimal weight: 0.9990 chunk 733 optimal weight: 20.0000 chunk 668 optimal weight: 7.9990 chunk 713 optimal weight: 5.9990 chunk 732 optimal weight: 7.9990 chunk 429 optimal weight: 20.0000 chunk 310 optimal weight: 10.0000 chunk 559 optimal weight: 0.9990 chunk 218 optimal weight: 5.9990 chunk 644 optimal weight: 10.0000 chunk 674 optimal weight: 0.0040 overall best weight: 2.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 444 GLN ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 95 ASN H 317 GLN V 128 GLN ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 123 ASN ** Z 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 180 ASN d 243 GLN g 50 GLN h 24 GLN h 72 GLN h 107 GLN i 12 GLN ** k 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 239 GLN ** l 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 46 ASN ** s 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 50 HIS x 13 ASN y 30 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3198 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= 0.521 Angle : 1.569 51.338 93426 Z= 1.013 Chirality : 0.310 6.630 10118 Planarity : 0.004 0.046 11647 Dihedral : 11.201 172.815 10576 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.13 % Favored : 96.84 % Rotamer: Outliers : 2.66 % Allowed : 18.17 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.10), residues: 8046 helix: 1.15 (0.08), residues: 4241 sheet: -0.68 (0.25), residues: 377 loop : -0.19 (0.11), residues: 3428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP H 121 HIS 0.028 0.001 HIS 9 65 PHE 0.031 0.001 PHE N 292 TYR 0.034 0.001 TYR o 81 ARG 0.007 0.000 ARG q 51 *********************** 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 1245 residues out of total 7132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 1055 time to evaluate : 6.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 16 LYS cc_start: 0.8032 (mtmm) cc_final: 0.7668 (tptm) REVERT: 1 302 SER cc_start: 0.8190 (m) cc_final: 0.7844 (p) REVERT: 1 385 ARG cc_start: 0.8398 (ptp-110) cc_final: 0.7965 (mmt180) REVERT: 2 187 ARG cc_start: 0.8188 (mmt90) cc_final: 0.7944 (mmm160) REVERT: 3 477 ILE cc_start: 0.8207 (OUTLIER) cc_final: 0.7999 (tp) REVERT: 3 640 ASN cc_start: 0.8001 (t0) cc_final: 0.7634 (m-40) REVERT: 4 12 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8302 (tm-30) REVERT: 4 66 MET cc_start: 0.9026 (OUTLIER) cc_final: 0.8279 (mmt) REVERT: 4 410 MET cc_start: 0.8804 (mtt) cc_final: 0.8536 (mtm) REVERT: 4 422 ASP cc_start: 0.7260 (t0) cc_final: 0.7011 (t70) REVERT: 4 425 PHE cc_start: 0.8993 (m-80) cc_final: 0.8712 (m-80) REVERT: 4 430 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.6325 (mpp-170) REVERT: 5 43 SER cc_start: 0.9027 (p) cc_final: 0.8632 (m) REVERT: 5 118 GLU cc_start: 0.8720 (tp30) cc_final: 0.8358 (tp30) REVERT: 5 182 ARG cc_start: 0.9264 (OUTLIER) cc_final: 0.7901 (ttp80) REVERT: 6 50 PHE cc_start: 0.8887 (OUTLIER) cc_final: 0.8141 (m-80) REVERT: 6 86 MET cc_start: 0.8590 (ttm) cc_final: 0.8375 (ttp) REVERT: 6 102 LYS cc_start: 0.9023 (tttt) cc_final: 0.8741 (tppp) REVERT: A 16 LEU cc_start: 0.8405 (tp) cc_final: 0.8095 (mm) REVERT: A 22 PHE cc_start: 0.8550 (m-80) cc_final: 0.8244 (m-80) REVERT: H 199 ASP cc_start: 0.8524 (p0) cc_final: 0.8267 (p0) REVERT: J 31 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8418 (mt) REVERT: K 27 MET cc_start: 0.8842 (tpp) cc_final: 0.8631 (mmm) REVERT: L 214 MET cc_start: 0.8647 (mmp) cc_final: 0.7944 (ttt) REVERT: L 475 MET cc_start: 0.8038 (mmm) cc_final: 0.7595 (mtp) REVERT: M 378 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8340 (tm-30) REVERT: V 57 ARG cc_start: 0.7053 (ttp-110) cc_final: 0.6677 (tpp-160) REVERT: V 119 LEU cc_start: 0.8143 (mt) cc_final: 0.7870 (tp) REVERT: Y 43 MET cc_start: 0.8773 (OUTLIER) cc_final: 0.8224 (mmm) REVERT: Y 89 ASP cc_start: 0.8240 (t0) cc_final: 0.7648 (t0) REVERT: Z 3 SER cc_start: 0.7804 (OUTLIER) cc_final: 0.7567 (m) REVERT: a 34 ASP cc_start: 0.6484 (t0) cc_final: 0.6250 (m-30) REVERT: b 54 SER cc_start: 0.8689 (t) cc_final: 0.8410 (p) REVERT: b 80 LYS cc_start: 0.7927 (ttpp) cc_final: 0.7675 (tttp) REVERT: b 95 HIS cc_start: 0.6444 (m90) cc_final: 0.6067 (t-90) REVERT: d 57 MET cc_start: 0.9070 (mmm) cc_final: 0.8732 (mmm) REVERT: d 62 MET cc_start: 0.9032 (OUTLIER) cc_final: 0.8796 (mmt) REVERT: e 56 GLU cc_start: 0.8741 (mt-10) cc_final: 0.8340 (mt-10) REVERT: g 56 LYS cc_start: 0.9071 (tmmt) cc_final: 0.8729 (ttmt) REVERT: g 60 ASP cc_start: 0.8301 (m-30) cc_final: 0.8061 (m-30) REVERT: h 18 ASP cc_start: 0.8545 (t0) cc_final: 0.8200 (t70) REVERT: i 1 MET cc_start: 0.7718 (tpt) cc_final: 0.7068 (mtt) REVERT: i 2 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7341 (pm20) REVERT: i 25 ARG cc_start: 0.8798 (ttt90) cc_final: 0.8160 (ttm170) REVERT: j 12 LYS cc_start: 0.7765 (ttpt) cc_final: 0.7356 (OUTLIER) REVERT: j 74 GLN cc_start: 0.7713 (OUTLIER) cc_final: 0.7327 (tm-30) REVERT: k 203 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8117 (mp0) REVERT: k 236 GLU cc_start: 0.8240 (tm-30) cc_final: 0.7643 (mt-10) REVERT: m 14 LYS cc_start: 0.8699 (mtmt) cc_final: 0.8348 (tmtm) REVERT: m 37 TYR cc_start: 0.8225 (m-10) cc_final: 0.7889 (m-10) REVERT: m 43 MET cc_start: 0.8979 (mtm) cc_final: 0.8745 (mtp) REVERT: m 81 LYS cc_start: 0.8956 (mtpp) cc_final: 0.8433 (mtmm) REVERT: n 13 MET cc_start: 0.5646 (pmm) cc_final: 0.3610 (ttt) REVERT: o 25 LYS cc_start: 0.7916 (mttt) cc_final: 0.7431 (mmtt) REVERT: o 107 LYS cc_start: 0.7967 (mtpt) cc_final: 0.7588 (ttmm) REVERT: o 114 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7579 (mt-10) REVERT: p 5 TYR cc_start: 0.6447 (t80) cc_final: 0.6152 (t80) REVERT: q 22 ARG cc_start: 0.8637 (mtp180) cc_final: 0.8403 (mtm180) REVERT: q 95 THR cc_start: 0.8484 (t) cc_final: 0.8166 (m) REVERT: q 104 LYS cc_start: 0.8668 (mmmt) cc_final: 0.8120 (ttmt) REVERT: r 12 GLN cc_start: 0.7435 (pt0) cc_final: 0.7042 (tm-30) REVERT: r 30 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.6172 (ppp80) REVERT: r 66 HIS cc_start: 0.5397 (t70) cc_final: 0.4593 (m90) REVERT: s 42 GLN cc_start: 0.7839 (mt0) cc_final: 0.7550 (mt0) REVERT: s 46 ASN cc_start: 0.7950 (OUTLIER) cc_final: 0.7514 (t0) REVERT: s 100 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7960 (mp0) REVERT: u 19 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.7070 (mtt-85) REVERT: u 26 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7565 (tt0) REVERT: u 53 TYR cc_start: 0.7633 (t80) cc_final: 0.7318 (t80) REVERT: u 55 ASP cc_start: 0.7226 (t0) cc_final: 0.6677 (p0) REVERT: v 131 LYS cc_start: 0.7872 (tptp) cc_final: 0.7650 (tmtt) REVERT: v 148 LYS cc_start: 0.6455 (tmmt) cc_final: 0.6015 (mtpt) REVERT: w 56 TRP cc_start: 0.7406 (t60) cc_final: 0.7042 (m-10) REVERT: w 109 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7910 (mp0) REVERT: x 13 ASN cc_start: 0.8486 (t0) cc_final: 0.8285 (t160) REVERT: x 16 LYS cc_start: 0.8293 (ttmt) cc_final: 0.7778 (tptm) REVERT: y 26 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8831 (mp) REVERT: z 53 ARG cc_start: 0.8118 (mtm-85) cc_final: 0.7898 (mtm-85) outliers start: 190 outliers final: 111 residues processed: 1156 average time/residue: 1.5381 time to fit residues: 2332.4348 Evaluate side-chains 1147 residues out of total 7132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 1018 time to evaluate : 6.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 314 THR Chi-restraints excluded: chain 1 residue 350 LEU Chi-restraints excluded: chain 1 residue 355 LYS Chi-restraints excluded: chain 2 residue 128 VAL Chi-restraints excluded: chain 2 residue 134 ASP Chi-restraints excluded: chain 2 residue 135 LYS Chi-restraints excluded: chain 3 residue 159 CYS Chi-restraints excluded: chain 3 residue 338 VAL Chi-restraints excluded: chain 3 residue 424 ASP Chi-restraints excluded: chain 3 residue 471 SER Chi-restraints excluded: chain 3 residue 477 ILE Chi-restraints excluded: chain 3 residue 532 VAL Chi-restraints excluded: chain 3 residue 535 GLN Chi-restraints excluded: chain 3 residue 659 ASP Chi-restraints excluded: chain 3 residue 667 THR Chi-restraints excluded: chain 4 residue 66 MET Chi-restraints excluded: chain 4 residue 164 MET Chi-restraints excluded: chain 4 residue 430 ARG Chi-restraints excluded: chain 5 residue 153 THR Chi-restraints excluded: chain 5 residue 182 ARG Chi-restraints excluded: chain 6 residue 34 ASP Chi-restraints excluded: chain 6 residue 50 PHE Chi-restraints excluded: chain 9 residue 1 THR Chi-restraints excluded: chain 9 residue 37 THR Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain H residue 24 GLU Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 215 TYR Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 55 MET Chi-restraints excluded: chain J residue 163 ILE Chi-restraints excluded: chain K residue 3 LEU Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain L residue 217 ILE Chi-restraints excluded: chain L residue 445 GLU Chi-restraints excluded: chain L residue 488 MET Chi-restraints excluded: chain L residue 505 SER Chi-restraints excluded: chain L residue 565 THR Chi-restraints excluded: chain L residue 583 LEU Chi-restraints excluded: chain L residue 601 LEU Chi-restraints excluded: chain M residue 98 MET Chi-restraints excluded: chain M residue 247 THR Chi-restraints excluded: chain M residue 378 GLU Chi-restraints excluded: chain M residue 394 ILE Chi-restraints excluded: chain M residue 454 ILE Chi-restraints excluded: chain N residue 161 SER Chi-restraints excluded: chain N residue 258 SER Chi-restraints excluded: chain N residue 285 THR Chi-restraints excluded: chain N residue 308 THR Chi-restraints excluded: chain N residue 335 MET Chi-restraints excluded: chain V residue 25 THR Chi-restraints excluded: chain V residue 100 LEU Chi-restraints excluded: chain V residue 109 ILE Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain V residue 134 VAL Chi-restraints excluded: chain W residue 18 ASP Chi-restraints excluded: chain W residue 36 VAL Chi-restraints excluded: chain W residue 98 SER Chi-restraints excluded: chain W residue 140 THR Chi-restraints excluded: chain X residue 26 ASP Chi-restraints excluded: chain X residue 40 LEU Chi-restraints excluded: chain X residue 65 ILE Chi-restraints excluded: chain Y residue 43 MET Chi-restraints excluded: chain Y residue 63 ASN Chi-restraints excluded: chain Y residue 154 GLU Chi-restraints excluded: chain Z residue 3 SER Chi-restraints excluded: chain Z residue 16 THR Chi-restraints excluded: chain Z residue 61 TYR Chi-restraints excluded: chain a residue 45 ASP Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain c residue 115 SER Chi-restraints excluded: chain c residue 131 SER Chi-restraints excluded: chain d residue 62 MET Chi-restraints excluded: chain d residue 140 LYS Chi-restraints excluded: chain d residue 316 GLU Chi-restraints excluded: chain d residue 340 VAL Chi-restraints excluded: chain f residue 15 VAL Chi-restraints excluded: chain g residue 67 LYS Chi-restraints excluded: chain i residue 2 GLU Chi-restraints excluded: chain i residue 11 LEU Chi-restraints excluded: chain j residue 26 ASP Chi-restraints excluded: chain j residue 74 GLN Chi-restraints excluded: chain k residue 65 ASP Chi-restraints excluded: chain k residue 162 GLU Chi-restraints excluded: chain k residue 192 MET Chi-restraints excluded: chain k residue 203 GLU Chi-restraints excluded: chain m residue 30 ILE Chi-restraints excluded: chain n residue 78 VAL Chi-restraints excluded: chain n residue 81 VAL Chi-restraints excluded: chain o residue 20 SER Chi-restraints excluded: chain o residue 55 SER Chi-restraints excluded: chain o residue 96 SER Chi-restraints excluded: chain o residue 105 ASP Chi-restraints excluded: chain o residue 111 GLU Chi-restraints excluded: chain p residue 8 SER Chi-restraints excluded: chain p residue 94 ILE Chi-restraints excluded: chain p residue 98 ILE Chi-restraints excluded: chain r residue 30 ARG Chi-restraints excluded: chain r residue 68 ILE Chi-restraints excluded: chain r residue 76 ILE Chi-restraints excluded: chain r residue 78 VAL Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain s residue 46 ASN Chi-restraints excluded: chain s residue 95 VAL Chi-restraints excluded: chain s residue 100 GLU Chi-restraints excluded: chain t residue 31 VAL Chi-restraints excluded: chain t residue 56 MET Chi-restraints excluded: chain u residue 8 GLU Chi-restraints excluded: chain u residue 19 ARG Chi-restraints excluded: chain u residue 60 THR Chi-restraints excluded: chain v residue 96 VAL Chi-restraints excluded: chain v residue 140 LEU Chi-restraints excluded: chain w residue 74 SER Chi-restraints excluded: chain w residue 100 ARG Chi-restraints excluded: chain w residue 109 GLU Chi-restraints excluded: chain x residue 19 LEU Chi-restraints excluded: chain y residue 9 ASP Chi-restraints excluded: chain y residue 26 LEU Chi-restraints excluded: chain z residue 16 LEU Chi-restraints excluded: chain z residue 42 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 794 random chunks: chunk 710 optimal weight: 6.9990 chunk 468 optimal weight: 20.0000 chunk 754 optimal weight: 5.9990 chunk 460 optimal weight: 20.0000 chunk 357 optimal weight: 7.9990 chunk 524 optimal weight: 20.0000 chunk 791 optimal weight: 5.9990 chunk 728 optimal weight: 20.0000 chunk 629 optimal weight: 20.0000 chunk 65 optimal weight: 0.9980 chunk 486 optimal weight: 7.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 95 ASN ** L 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 603 ASN V 128 GLN ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 123 ASN ** Z 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 50 GLN h 24 GLN h 72 GLN h 107 GLN i 12 GLN ** k 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 96 HIS s 54 GLN ** t 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 50 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.3236 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= 0.559 Angle : 1.590 51.370 93426 Z= 1.020 Chirality : 0.311 6.688 10118 Planarity : 0.004 0.047 11647 Dihedral : 11.311 173.464 10576 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.46 % Favored : 96.52 % Rotamer: Outliers : 2.36 % Allowed : 18.84 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.10), residues: 8046 helix: 1.06 (0.08), residues: 4245 sheet: -0.72 (0.25), residues: 379 loop : -0.20 (0.11), residues: 3422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP H 121 HIS 0.029 0.001 HIS 9 65 PHE 0.040 0.002 PHE M 256 TYR 0.036 0.002 TYR o 81 ARG 0.007 0.000 ARG q 51 ********************** 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 1189 residues out of total 7132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 1021 time to evaluate : 6.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 16 LYS cc_start: 0.8041 (mtmm) cc_final: 0.7669 (tptm) REVERT: 1 302 SER cc_start: 0.8315 (m) cc_final: 0.7911 (p) REVERT: 2 118 GLU cc_start: 0.8865 (tp30) cc_final: 0.8578 (tp30) REVERT: 2 187 ARG cc_start: 0.8212 (mmt90) cc_final: 0.7977 (mmm160) REVERT: 3 640 ASN cc_start: 0.7968 (t0) cc_final: 0.7604 (m-40) REVERT: 4 12 GLU cc_start: 0.8764 (mm-30) cc_final: 0.8322 (tm-30) REVERT: 4 66 MET cc_start: 0.9047 (OUTLIER) cc_final: 0.8379 (mmt) REVERT: 4 410 MET cc_start: 0.8865 (mtt) cc_final: 0.8594 (mtm) REVERT: 4 422 ASP cc_start: 0.7382 (t0) cc_final: 0.7141 (t70) REVERT: 4 425 PHE cc_start: 0.9020 (m-80) cc_final: 0.8699 (m-80) REVERT: 4 430 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.6398 (mpp-170) REVERT: 5 182 ARG cc_start: 0.9269 (OUTLIER) cc_final: 0.8138 (ttp80) REVERT: 6 50 PHE cc_start: 0.8857 (OUTLIER) cc_final: 0.8238 (m-80) REVERT: 6 86 MET cc_start: 0.8665 (ttm) cc_final: 0.8447 (ttp) REVERT: 6 102 LYS cc_start: 0.9051 (tttt) cc_final: 0.8780 (tppp) REVERT: A 16 LEU cc_start: 0.8428 (tp) cc_final: 0.8091 (mm) REVERT: A 22 PHE cc_start: 0.8569 (m-80) cc_final: 0.8288 (m-80) REVERT: H 124 ASN cc_start: 0.8343 (t0) cc_final: 0.8121 (t0) REVERT: J 31 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8411 (mt) REVERT: J 99 MET cc_start: 0.4208 (tpt) cc_final: 0.3899 (mtt) REVERT: L 214 MET cc_start: 0.8649 (mmp) cc_final: 0.7953 (ttt) REVERT: L 475 MET cc_start: 0.8138 (mmm) cc_final: 0.7611 (mtp) REVERT: M 378 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8282 (tm-30) REVERT: V 57 ARG cc_start: 0.7069 (ttp-110) cc_final: 0.6683 (tpp-160) REVERT: V 119 LEU cc_start: 0.8162 (mt) cc_final: 0.7883 (tp) REVERT: Y 43 MET cc_start: 0.8801 (OUTLIER) cc_final: 0.8256 (mmm) REVERT: Y 89 ASP cc_start: 0.8295 (t0) cc_final: 0.7713 (t0) REVERT: a 34 ASP cc_start: 0.6647 (t0) cc_final: 0.6407 (m-30) REVERT: b 54 SER cc_start: 0.8687 (t) cc_final: 0.8402 (p) REVERT: b 80 LYS cc_start: 0.7987 (ttpp) cc_final: 0.7730 (tttp) REVERT: d 57 MET cc_start: 0.9062 (mmm) cc_final: 0.8630 (mmm) REVERT: e 56 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8406 (mt-10) REVERT: g 56 LYS cc_start: 0.9076 (tmmt) cc_final: 0.8728 (ttmt) REVERT: g 60 ASP cc_start: 0.8318 (m-30) cc_final: 0.8077 (m-30) REVERT: h 18 ASP cc_start: 0.8581 (t0) cc_final: 0.8239 (t70) REVERT: i 1 MET cc_start: 0.7785 (tpt) cc_final: 0.7131 (mtt) REVERT: i 2 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7362 (pm20) REVERT: i 25 ARG cc_start: 0.8836 (ttt90) cc_final: 0.8167 (ttm170) REVERT: k 203 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8130 (mp0) REVERT: k 236 GLU cc_start: 0.8256 (tm-30) cc_final: 0.7643 (mt-10) REVERT: m 14 LYS cc_start: 0.8815 (mtmt) cc_final: 0.8387 (tmtm) REVERT: m 37 TYR cc_start: 0.8202 (m-10) cc_final: 0.7886 (m-10) REVERT: m 81 LYS cc_start: 0.8944 (mtpp) cc_final: 0.8430 (mtmm) REVERT: n 13 MET cc_start: 0.5673 (pmm) cc_final: 0.3621 (ttt) REVERT: o 25 LYS cc_start: 0.7973 (mttt) cc_final: 0.7471 (mmtt) REVERT: o 77 LYS cc_start: 0.9257 (OUTLIER) cc_final: 0.8878 (mtmm) REVERT: o 107 LYS cc_start: 0.7984 (mtpt) cc_final: 0.7598 (ttmm) REVERT: p 5 TYR cc_start: 0.6583 (t80) cc_final: 0.6338 (t80) REVERT: q 22 ARG cc_start: 0.8653 (mtp180) cc_final: 0.8411 (mtm180) REVERT: q 95 THR cc_start: 0.8443 (t) cc_final: 0.8158 (m) REVERT: q 104 LYS cc_start: 0.8753 (mmmt) cc_final: 0.8141 (ttmt) REVERT: r 30 ARG cc_start: 0.7733 (OUTLIER) cc_final: 0.6267 (ppp80) REVERT: r 66 HIS cc_start: 0.5531 (t70) cc_final: 0.4570 (m90) REVERT: s 42 GLN cc_start: 0.7896 (mt0) cc_final: 0.7610 (mt0) REVERT: s 100 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7995 (mp0) REVERT: u 19 ARG cc_start: 0.7657 (OUTLIER) cc_final: 0.7078 (mtt-85) REVERT: u 26 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7585 (tt0) REVERT: u 53 TYR cc_start: 0.7685 (t80) cc_final: 0.7343 (t80) REVERT: v 131 LYS cc_start: 0.7900 (tptp) cc_final: 0.7683 (tmtt) REVERT: w 56 TRP cc_start: 0.7507 (t60) cc_final: 0.7137 (m-10) REVERT: w 109 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7847 (mp0) REVERT: x 16 LYS cc_start: 0.8271 (ttmt) cc_final: 0.7762 (tptm) REVERT: y 26 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8869 (mp) REVERT: z 53 ARG cc_start: 0.8199 (mtm-85) cc_final: 0.7955 (mtm-85) outliers start: 168 outliers final: 118 residues processed: 1118 average time/residue: 1.5245 time to fit residues: 2222.8038 Evaluate side-chains 1138 residues out of total 7132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 1005 time to evaluate : 6.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 314 THR Chi-restraints excluded: chain 1 residue 350 LEU Chi-restraints excluded: chain 1 residue 355 LYS Chi-restraints excluded: chain 2 residue 128 VAL Chi-restraints excluded: chain 2 residue 134 ASP Chi-restraints excluded: chain 2 residue 135 LYS Chi-restraints excluded: chain 3 residue 159 CYS Chi-restraints excluded: chain 3 residue 338 VAL Chi-restraints excluded: chain 3 residue 424 ASP Chi-restraints excluded: chain 3 residue 471 SER Chi-restraints excluded: chain 3 residue 517 ASN Chi-restraints excluded: chain 3 residue 532 VAL Chi-restraints excluded: chain 3 residue 535 GLN Chi-restraints excluded: chain 3 residue 659 ASP Chi-restraints excluded: chain 3 residue 667 THR Chi-restraints excluded: chain 4 residue 66 MET Chi-restraints excluded: chain 4 residue 75 LYS Chi-restraints excluded: chain 4 residue 164 MET Chi-restraints excluded: chain 4 residue 430 ARG Chi-restraints excluded: chain 5 residue 153 THR Chi-restraints excluded: chain 5 residue 182 ARG Chi-restraints excluded: chain 6 residue 34 ASP Chi-restraints excluded: chain 6 residue 50 PHE Chi-restraints excluded: chain 9 residue 1 THR Chi-restraints excluded: chain 9 residue 37 THR Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain 9 residue 126 CYS Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain H residue 24 GLU Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 215 TYR Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 55 MET Chi-restraints excluded: chain K residue 3 LEU Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain L residue 217 ILE Chi-restraints excluded: chain L residue 445 GLU Chi-restraints excluded: chain L residue 488 MET Chi-restraints excluded: chain L residue 505 SER Chi-restraints excluded: chain L residue 565 THR Chi-restraints excluded: chain L residue 583 LEU Chi-restraints excluded: chain L residue 601 LEU Chi-restraints excluded: chain M residue 36 LEU Chi-restraints excluded: chain M residue 98 MET Chi-restraints excluded: chain M residue 247 THR Chi-restraints excluded: chain M residue 378 GLU Chi-restraints excluded: chain M residue 394 ILE Chi-restraints excluded: chain M residue 454 ILE Chi-restraints excluded: chain N residue 161 SER Chi-restraints excluded: chain N residue 258 SER Chi-restraints excluded: chain N residue 285 THR Chi-restraints excluded: chain N residue 308 THR Chi-restraints excluded: chain N residue 335 MET Chi-restraints excluded: chain V residue 25 THR Chi-restraints excluded: chain V residue 100 LEU Chi-restraints excluded: chain V residue 109 ILE Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain V residue 134 VAL Chi-restraints excluded: chain W residue 18 ASP Chi-restraints excluded: chain W residue 23 LYS Chi-restraints excluded: chain W residue 36 VAL Chi-restraints excluded: chain W residue 98 SER Chi-restraints excluded: chain W residue 140 THR Chi-restraints excluded: chain X residue 26 ASP Chi-restraints excluded: chain X residue 40 LEU Chi-restraints excluded: chain Y residue 43 MET Chi-restraints excluded: chain Y residue 63 ASN Chi-restraints excluded: chain Y residue 154 GLU Chi-restraints excluded: chain Z residue 16 THR Chi-restraints excluded: chain Z residue 61 TYR Chi-restraints excluded: chain a residue 45 ASP Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain c residue 44 ASN Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain c residue 115 SER Chi-restraints excluded: chain c residue 131 SER Chi-restraints excluded: chain d residue 140 LYS Chi-restraints excluded: chain d residue 185 ILE Chi-restraints excluded: chain d residue 280 THR Chi-restraints excluded: chain d residue 284 VAL Chi-restraints excluded: chain d residue 316 GLU Chi-restraints excluded: chain d residue 340 VAL Chi-restraints excluded: chain f residue 15 VAL Chi-restraints excluded: chain g residue 67 LYS Chi-restraints excluded: chain i residue 2 GLU Chi-restraints excluded: chain i residue 11 LEU Chi-restraints excluded: chain j residue 26 ASP Chi-restraints excluded: chain k residue 28 ASP Chi-restraints excluded: chain k residue 65 ASP Chi-restraints excluded: chain k residue 96 LEU Chi-restraints excluded: chain k residue 160 VAL Chi-restraints excluded: chain k residue 162 GLU Chi-restraints excluded: chain k residue 192 MET Chi-restraints excluded: chain k residue 203 GLU Chi-restraints excluded: chain m residue 30 ILE Chi-restraints excluded: chain n residue 53 MET Chi-restraints excluded: chain n residue 66 LEU Chi-restraints excluded: chain n residue 78 VAL Chi-restraints excluded: chain n residue 81 VAL Chi-restraints excluded: chain o residue 20 SER Chi-restraints excluded: chain o residue 55 SER Chi-restraints excluded: chain o residue 77 LYS Chi-restraints excluded: chain o residue 96 SER Chi-restraints excluded: chain o residue 105 ASP Chi-restraints excluded: chain o residue 111 GLU Chi-restraints excluded: chain p residue 94 ILE Chi-restraints excluded: chain p residue 98 ILE Chi-restraints excluded: chain r residue 30 ARG Chi-restraints excluded: chain r residue 68 ILE Chi-restraints excluded: chain r residue 76 ILE Chi-restraints excluded: chain r residue 78 VAL Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain s residue 95 VAL Chi-restraints excluded: chain s residue 100 GLU Chi-restraints excluded: chain t residue 31 VAL Chi-restraints excluded: chain t residue 56 MET Chi-restraints excluded: chain u residue 8 GLU Chi-restraints excluded: chain u residue 19 ARG Chi-restraints excluded: chain u residue 60 THR Chi-restraints excluded: chain v residue 96 VAL Chi-restraints excluded: chain w residue 60 VAL Chi-restraints excluded: chain w residue 74 SER Chi-restraints excluded: chain w residue 100 ARG Chi-restraints excluded: chain w residue 109 GLU Chi-restraints excluded: chain y residue 26 LEU Chi-restraints excluded: chain z residue 16 LEU Chi-restraints excluded: chain z residue 42 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 794 random chunks: chunk 386 optimal weight: 20.0000 chunk 500 optimal weight: 30.0000 chunk 670 optimal weight: 0.9980 chunk 192 optimal weight: 5.9990 chunk 580 optimal weight: 10.0000 chunk 93 optimal weight: 5.9990 chunk 175 optimal weight: 10.0000 chunk 630 optimal weight: 7.9990 chunk 264 optimal weight: 8.9990 chunk 647 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 317 GLN ** L 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 128 GLN ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 123 ASN ** Z 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 130 GLN ** Z 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 36 ASN d 180 ASN d 243 GLN g 50 GLN h 24 GLN h 72 GLN h 107 GLN ** k 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 46 ASN s 54 GLN ** t 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 50 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.115476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.095689 restraints weight = 107579.613| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.40 r_work: 0.3138 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.3281 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= 0.546 Angle : 1.585 51.416 93426 Z= 1.019 Chirality : 0.311 6.672 10118 Planarity : 0.004 0.048 11647 Dihedral : 11.290 173.724 10576 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.49 % Favored : 96.48 % Rotamer: Outliers : 2.30 % Allowed : 19.03 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.10), residues: 8046 helix: 1.05 (0.08), residues: 4250 sheet: -0.79 (0.24), residues: 384 loop : -0.19 (0.11), residues: 3412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP H 121 HIS 0.030 0.001 HIS 9 65 PHE 0.034 0.002 PHE v 111 TYR 0.031 0.002 TYR o 81 ARG 0.007 0.000 ARG q 51 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 32233.87 seconds wall clock time: 558 minutes 10.08 seconds (33490.08 seconds total)