Starting phenix.real_space_refine on Thu Mar 28 01:03:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7msz_23972/03_2024/7msz_23972_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7msz_23972/03_2024/7msz_23972.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7msz_23972/03_2024/7msz_23972_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7msz_23972/03_2024/7msz_23972_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7msz_23972/03_2024/7msz_23972_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7msz_23972/03_2024/7msz_23972.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7msz_23972/03_2024/7msz_23972.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7msz_23972/03_2024/7msz_23972_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7msz_23972/03_2024/7msz_23972_updated.pdb" } resolution = 3.1 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= 0.001 sd= 0.013 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 V 2 8.30 5 Zn 6 6.06 5 P 4840 5.49 5 Mg 417 5.21 5 S 102 5.16 5 C 76255 2.51 5 N 28449 2.21 5 O 42274 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "2 ARG 6": "NH1" <-> "NH2" Residue "6 ARG 25": "NH1" <-> "NH2" Residue "6 ARG 57": "NH1" <-> "NH2" Residue "8 ARG 9": "NH1" <-> "NH2" Residue "8 ARG 17": "NH1" <-> "NH2" Residue "8 ARG 53": "NH1" <-> "NH2" Residue "8 ARG 60": "NH1" <-> "NH2" Residue "8 ARG 74": "NH1" <-> "NH2" Residue "8 ARG 103": "NH1" <-> "NH2" Residue "8 ARG 126": "NH1" <-> "NH2" Residue "8 ARG 134": "NH1" <-> "NH2" Residue "8 ARG 164": "NH1" <-> "NH2" Residue "8 ARG 207": "NH1" <-> "NH2" Residue "C ARG 4": "NH1" <-> "NH2" Residue "E TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 126": "NH1" <-> "NH2" Residue "F ARG 10": "NH1" <-> "NH2" Residue "F ARG 16": "NH1" <-> "NH2" Residue "F ARG 76": "NH1" <-> "NH2" Residue "G ARG 55": "NH1" <-> "NH2" Residue "K ARG 94": "NH1" <-> "NH2" Residue "L PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 134": "NH1" <-> "NH2" Residue "P PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 102": "NH1" <-> "NH2" Residue "V TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 11": "NH1" <-> "NH2" Residue "W PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 73": "NH1" <-> "NH2" Residue "c PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 131": "NH1" <-> "NH2" Residue "c ARG 134": "NH1" <-> "NH2" Residue "d TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 69": "NH1" <-> "NH2" Residue "d ARG 141": "NH1" <-> "NH2" Residue "f ARG 46": "NH1" <-> "NH2" Residue "g ARG 41": "NH1" <-> "NH2" Residue "g TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 32": "NH1" <-> "NH2" Residue "i ARG 33": "NH1" <-> "NH2" Residue "i ARG 41": "NH1" <-> "NH2" Residue "i ARG 78": "NH1" <-> "NH2" Residue "i PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 151": "NH1" <-> "NH2" Residue "k ARG 103": "NH1" <-> "NH2" Residue "k ARG 136": "NH1" <-> "NH2" Residue "l ARG 9": "NH1" <-> "NH2" Residue "o ARG 77": "NH1" <-> "NH2" Residue "p ARG 92": "NH1" <-> "NH2" Residue "q ARG 49": "NH1" <-> "NH2" Residue "q ARG 60": "NH1" <-> "NH2" Residue "s PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ARG 12": "NH1" <-> "NH2" Residue "x ARG 233": "NH1" <-> "NH2" Residue "x ARG 265": "NH1" <-> "NH2" Residue "x ARG 274": "NH1" <-> "NH2" Residue "x ARG 280": "NH1" <-> "NH2" Residue "x ARG 302": "NH1" <-> "NH2" Residue "x ARG 334": "NH1" <-> "NH2" Residue "x ARG 346": "NH1" <-> "NH2" Residue "x ARG 539": "NH1" <-> "NH2" Residue "x ARG 553": "NH1" <-> "NH2" Residue "x ARG 557": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 152345 Number of models: 1 Model: "" Number of chains: 72 Chain: "0" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 429 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "1" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 400 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 3, 'TRANS': 44} Chain: "2" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 374 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "3" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 494 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 1, 'TRANS': 60} Chain: "4" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 299 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "6" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 446 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 3, 'TRANS': 53} Chain breaks: 1 Chain: "7" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 134 Classifications: {'peptide': 16} Link IDs: {'PTRANS': 1, 'TRANS': 14} Chain breaks: 1 Chain: "8" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1704 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 11, 'TRANS': 218} Chain: "A" Number of atoms: 66958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3118, 66958 Classifications: {'RNA': 3118} Modifications used: {'rna2p': 1, 'rna2p_pur': 299, 'rna2p_pyr': 161, 'rna3p': 1, 'rna3p_pur': 1483, 'rna3p_pyr': 1173} Link IDs: {'rna2p': 461, 'rna3p': 2656} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Chain: "B" Number of atoms: 2458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 2458 Classifications: {'RNA': 115} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 5, 'rna3p_pur': 54, 'rna3p_pyr': 48} Link IDs: {'rna2p': 12, 'rna3p': 102} Chain: "C" Number of atoms: 2088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2088 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 17, 'TRANS': 254} Chain: "D" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1590 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 203} Chain: "E" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1552 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 11, 'TRANS': 195} Chain: "F" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1408 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 7, 'TRANS': 170} Chain: "G" Number of atoms: 1330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1330 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 11, 'TRANS': 162} Chain: "H" Number of atoms: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 350 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "J" Number of atoms: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1143 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 10, 'TRANS': 135} Chain: "K" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 941 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 6, 'TRANS': 115} Chain: "L" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1075 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 5, 'TRANS': 138} Chain: "M" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1072 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 9, 'TRANS': 124} Chain: "N" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 908 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 6, 'TRANS': 109} Chain: "O" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 905 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "P" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 907 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "Q" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 993 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "R" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 757 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 2, 'TRANS': 97} Chain: "S" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 860 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 8, 'TRANS': 104} Chain: "T" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 741 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "U" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 699 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 3, 'TRANS': 86} Chain breaks: 1 Chain: "V" Number of atoms: 1319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1319 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 9, 'TRANS': 167} Chain: "W" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 543 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "X" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 468 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 3, 'TRANS': 58} Chain: "Y" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 560 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "Z" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 476 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 1, 'TRANS': 57} Chain: "a" Number of atoms: 32620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1519, 32620 Classifications: {'RNA': 1519} Modifications used: {'rna2p': 1, 'rna2p_pur': 122, 'rna2p_pyr': 93, 'rna3p': 6, 'rna3p_pur': 728, 'rna3p_pyr': 569} Link IDs: {'rna2p': 216, 'rna3p': 1302} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 4 Chain: "c" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1654 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 5, 'TRANS': 201} Chain: "d" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1650 Classifications: {'peptide': 200} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 188} Chain: "e" Number of atoms: 1222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1222 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 8, 'TRANS': 160} Chain: "f" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 757 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 4, 'TRANS': 90} Chain: "g" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1230 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain: "h" Number of atoms: 1006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1006 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "i" Number of atoms: 992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 992 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 9, 'TRANS': 117} Chain: "j" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 789 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 91} Chain: "k" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 873 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 108} Chain: "l" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 959 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "m" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 945 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "n" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 468 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "o" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 718 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "p" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 884 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 8, 'TRANS': 104} Chain: "q" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 770 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 88} Chain: "r" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 506 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 1, 'TRANS': 62} Chain: "s" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 672 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain: "t" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 652 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'TRANS': 84} Chain: "x" Number of atoms: 4307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4307 Classifications: {'peptide': 552} Link IDs: {'PTRANS': 23, 'TRANS': 528} Chain breaks: 1 Chain: "y" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1644 Classifications: {'RNA': 77} Modifications used: {'p5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 3, 'rna3p_pur': 31, 'rna3p_pyr': 35} Link IDs: {'rna2p': 10, 'rna3p': 66} Chain: "z" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 149 Classifications: {'RNA': 7} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 3, 'rna3p_pyr': 2} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "1" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 284 Unusual residues: {' MG': 284} Classifications: {'undetermined': 284} Link IDs: {None: 283} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 115 Unusual residues: {' MG': 115} Classifications: {'undetermined': 115} Link IDs: {None: 114} Chain: "n" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "r" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "t" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "x" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {' MG': 2, 'ADP': 2, 'VO4': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "y" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {' MG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} 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 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 497 SG CYS 1 15 114.702 178.352 186.846 1.00 53.38 S ATOM 519 SG CYS 1 18 114.461 181.874 185.815 1.00 54.69 S ATOM 734 SG CYS 1 42 118.005 180.480 185.976 1.00 49.11 S ATOM 755 SG CYS 1 45 116.226 182.649 189.076 1.00 52.32 S ATOM 1778 SG CYS 4 11 182.231 97.703 134.467 1.00104.82 S ATOM 1801 SG CYS 4 14 182.649 100.902 132.991 1.00104.50 S ATOM 2121 SG CYS 6 16 110.045 112.380 222.347 1.00132.66 S ATOM 2280 SG CYS 6 38 114.171 111.187 222.899 1.00132.37 S ATOM 94900 SG CYS X 5 89.753 200.874 122.444 1.00 49.61 S ATOM 94922 SG CYS X 8 91.438 202.910 124.928 1.00 49.82 S ATOM 95265 SG CYS X 52 89.193 199.908 126.178 1.00 49.77 S ATOM 95284 SG CYS X 55 87.548 203.073 125.680 1.00 53.79 S ATOM A0VTY SG CYS n 24 86.981 55.251 168.241 1.00 66.54 S ATOM A0VUJ SG CYS n 27 88.732 56.764 165.279 1.00 66.35 S ATOM A0VXH SG CYS n 40 85.844 58.764 166.445 1.00 64.68 S ATOM A0VY6 SG CYS n 43 84.900 55.904 164.492 1.00 65.98 S ATOM A0Y4M SG CYS r 57 35.697 119.022 103.031 1.00105.60 S Time building chain proxies: 53.73, per 1000 atoms: 0.35 Number of scatterers: 152345 At special positions: 0 Unit cell: (239.175, 271.065, 242.364, 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 6 29.99 V 2 22.97 S 102 16.00 P 4840 15.00 Mg 417 11.99 O 42274 8.00 N 28449 7.00 C 76255 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 59.35 Conformation dependent library (CDL) restraints added in 7.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 1 101 " pdb="ZN ZN 1 101 " - pdb=" SG CYS 1 18 " pdb="ZN ZN 1 101 " - pdb=" SG CYS 1 42 " pdb="ZN ZN 1 101 " - pdb=" SG CYS 1 15 " pdb="ZN ZN 1 101 " - pdb=" SG CYS 1 45 " pdb=" ZN 4 101 " pdb="ZN ZN 4 101 " - pdb=" ND1 HIS 4 32 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 14 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 11 " pdb=" ZN 6 101 " pdb="ZN ZN 6 101 " - pdb=" SG CYS 6 38 " pdb="ZN ZN 6 101 " - pdb=" SG CYS 6 16 " pdb=" ZN X 101 " pdb="ZN ZN X 101 " - pdb=" SG CYS X 8 " pdb="ZN ZN X 101 " - pdb=" SG CYS X 5 " pdb="ZN ZN X 101 " - pdb=" SG CYS X 55 " pdb="ZN ZN X 101 " - pdb=" SG CYS X 52 " pdb=" ZN n 101 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 43 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 27 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 40 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 24 " pdb=" ZN r 101 " pdb="ZN ZN r 101 " - pdb=" ND1 HIS r 60 " pdb="ZN ZN r 101 " - pdb=" SG CYS r 57 " Number of angles added : 18 12124 Ramachandran restraints generated. 6062 Oldfield, 0 Emsley, 6062 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11244 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 180 helices and 78 sheets defined 36.6% alpha, 18.1% beta 973 base pairs and 2589 stacking pairs defined. Time for finding SS restraints: 70.60 Creating SS restraints... Processing helix chain '0' and resid 9 through 21 removed outlier: 4.478A pdb=" N ARG 0 14 " --> pdb=" O ARG 0 10 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N SER 0 15 " --> pdb=" O SER 0 11 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG 0 16 " --> pdb=" O ASN 0 12 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ARG 0 17 " --> pdb=" O THR 0 13 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N GLN 0 19 " --> pdb=" O SER 0 15 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N TRP 0 20 " --> pdb=" O ARG 0 16 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N LYS 0 21 " --> pdb=" O ARG 0 17 " (cutoff:3.500A) Processing helix chain '0' and resid 40 through 50 removed outlier: 3.797A pdb=" N LEU 0 44 " --> pdb=" O PRO 0 40 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N LYS 0 45 " --> pdb=" O ARG 0 41 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ALA 0 46 " --> pdb=" O ARG 0 42 " (cutoff:3.500A) Processing helix chain '1' and resid 28 through 33 Proline residue: 1 33 - end of helix Processing helix chain '2' and resid 11 through 19 removed outlier: 3.690A pdb=" N ALA 2 16 " --> pdb=" O ASN 2 12 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL 2 18 " --> pdb=" O ARG 2 14 " (cutoff:3.500A) Processing helix chain '2' and resid 20 through 28 removed outlier: 4.682A pdb=" N ARG 2 26 " --> pdb=" O ARG 2 22 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N THR 2 27 " --> pdb=" O LEU 2 23 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N ARG 2 28 " --> pdb=" O ARG 2 24 " (cutoff:3.500A) Processing helix chain '2' and resid 29 through 41 removed outlier: 3.588A pdb=" N ILE 2 33 " --> pdb=" O ALA 2 29 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER 2 36 " --> pdb=" O SER 2 32 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS 2 40 " --> pdb=" O SER 2 36 " (cutoff:3.500A) Processing helix chain '3' and resid 7 through 14 removed outlier: 3.743A pdb=" N LYS 3 12 " --> pdb=" O SER 3 8 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG 3 13 " --> pdb=" O GLY 3 9 " (cutoff:3.500A) Processing helix chain '3' and resid 37 through 45 removed outlier: 4.334A pdb=" N ARG 3 42 " --> pdb=" O SER 3 38 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ARG 3 43 " --> pdb=" O THR 3 39 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU 3 44 " --> pdb=" O ARG 3 40 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ASP 3 45 " --> pdb=" O THR 3 41 " (cutoff:3.500A) Processing helix chain '3' and resid 51 through 63 removed outlier: 5.788A pdb=" N LYS 3 56 " --> pdb=" O ALA 3 52 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ARG 3 57 " --> pdb=" O ASN 3 53 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL 3 58 " --> pdb=" O ASP 3 54 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N THR 3 59 " --> pdb=" O THR 3 55 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN 3 63 " --> pdb=" O THR 3 59 " (cutoff:3.500A) Processing helix chain '6' and resid 38 through 43 removed outlier: 5.187A pdb=" N HIS 6 42 " --> pdb=" O CYS 6 38 " (cutoff:3.500A) Proline residue: 6 43 - end of helix No H-bonds generated for 'chain '6' and resid 38 through 43' Processing helix chain '6' and resid 57 through 64 removed outlier: 4.513A pdb=" N PHE 6 61 " --> pdb=" O VAL 6 58 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLU 6 62 " --> pdb=" O ALA 6 59 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS 6 63 " --> pdb=" O ARG 6 60 " (cutoff:3.500A) Processing helix chain '7' and resid 2 through 10 Processing helix chain '8' and resid 5 through 16 removed outlier: 3.840A pdb=" N ALA 8 10 " --> pdb=" O LYS 8 6 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL 8 15 " --> pdb=" O ALA 8 11 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ASP 8 16 " --> pdb=" O ALA 8 12 " (cutoff:3.500A) Processing helix chain '8' and resid 22 through 37 removed outlier: 4.031A pdb=" N LYS 8 28 " --> pdb=" O LEU 8 24 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR 8 36 " --> pdb=" O GLU 8 32 " (cutoff:3.500A) Processing helix chain '8' and resid 81 through 91 removed outlier: 3.762A pdb=" N ASP 8 85 " --> pdb=" O GLY 8 81 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA 8 89 " --> pdb=" O ASP 8 85 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA 8 90 " --> pdb=" O ALA 8 86 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY 8 91 " --> pdb=" O ALA 8 87 " (cutoff:3.500A) Processing helix chain '8' and resid 97 through 107 removed outlier: 3.881A pdb=" N ILE 8 101 " --> pdb=" O SER 8 97 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLU 8 102 " --> pdb=" O ASP 8 98 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG 8 103 " --> pdb=" O ASP 8 99 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLN 8 105 " --> pdb=" O ILE 8 101 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLY 8 106 " --> pdb=" O GLU 8 102 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N GLY 8 107 " --> pdb=" O ARG 8 103 " (cutoff:3.500A) Processing helix chain '8' and resid 125 through 132 removed outlier: 4.633A pdb=" N ARG 8 129 " --> pdb=" O GLY 8 125 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N VAL 8 130 " --> pdb=" O ARG 8 126 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU 8 131 " --> pdb=" O ILE 8 127 " (cutoff:3.500A) Processing helix chain '8' and resid 148 through 159 removed outlier: 4.227A pdb=" N ALA 8 152 " --> pdb=" O ASP 8 148 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL 8 153 " --> pdb=" O VAL 8 149 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ALA 8 154 " --> pdb=" O ALA 8 150 " (cutoff:3.500A) Processing helix chain '8' and resid 181 through 200 removed outlier: 3.814A pdb=" N ALA 8 186 " --> pdb=" O GLU 8 182 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN 8 188 " --> pdb=" O LEU 8 184 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA 8 191 " --> pdb=" O GLU 8 187 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA 8 192 " --> pdb=" O ASN 8 188 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE 8 193 " --> pdb=" O TYR 8 189 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG 8 198 " --> pdb=" O ASP 8 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 137 removed outlier: 3.668A pdb=" N ILE C 136 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Proline residue: C 137 - end of helix No H-bonds generated for 'chain 'C' and resid 132 through 137' Processing helix chain 'C' and resid 208 through 216 removed outlier: 3.985A pdb=" N MET C 212 " --> pdb=" O LYS C 208 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS C 215 " --> pdb=" O ARG C 211 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLY C 216 " --> pdb=" O MET C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 227 removed outlier: 4.773A pdb=" N MET C 226 " --> pdb=" O ARG C 222 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N ASN C 227 " --> pdb=" O GLY C 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 222 through 227' Processing helix chain 'C' and resid 264 through 269 removed outlier: 3.665A pdb=" N ILE C 268 " --> pdb=" O SER C 264 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N VAL C 269 " --> pdb=" O ASN C 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 264 through 269' Processing helix chain 'D' and resid 63 through 74 removed outlier: 3.832A pdb=" N GLN D 69 " --> pdb=" O PRO D 65 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR D 70 " --> pdb=" O LEU D 66 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA D 72 " --> pdb=" O GLY D 68 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ALA D 73 " --> pdb=" O GLN D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 130 removed outlier: 3.923A pdb=" N HIS D 130 " --> pdb=" O THR D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 107 removed outlier: 3.704A pdb=" N ILE D 105 " --> pdb=" O THR D 102 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE D 106 " --> pdb=" O ALA D 103 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ALA D 107 " --> pdb=" O GLU D 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 102 through 107' Processing helix chain 'D' and resid 41 through 46 removed outlier: 3.712A pdb=" N GLY D 46 " --> pdb=" O THR D 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 41 through 46' Processing helix chain 'E' and resid 36 through 52 removed outlier: 3.535A pdb=" N GLN E 42 " --> pdb=" O ALA E 38 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG E 52 " --> pdb=" O ARG E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 65 removed outlier: 7.022A pdb=" N SER E 65 " --> pdb=" O ARG E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 128 removed outlier: 3.929A pdb=" N ALA E 115 " --> pdb=" O LYS E 111 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA E 116 " --> pdb=" O MET E 112 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLY E 119 " --> pdb=" O ALA E 115 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER E 122 " --> pdb=" O ARG E 118 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN E 127 " --> pdb=" O ASP E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 155 removed outlier: 3.682A pdb=" N SER E 153 " --> pdb=" O ALA E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 177 removed outlier: 3.553A pdb=" N ALA E 172 " --> pdb=" O ASP E 168 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LYS E 173 " --> pdb=" O GLU E 169 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL E 175 " --> pdb=" O GLY E 171 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG E 176 " --> pdb=" O ALA E 172 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N ASN E 177 " --> pdb=" O LYS E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 198 removed outlier: 3.794A pdb=" N ALA E 197 " --> pdb=" O ASP E 193 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N ASP E 198 " --> pdb=" O VAL E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 215 removed outlier: 3.501A pdb=" N TYR E 210 " --> pdb=" O ALA E 206 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA E 212 " --> pdb=" O ASN E 208 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA E 213 " --> pdb=" O ALA E 209 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN E 214 " --> pdb=" O TYR E 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 28 removed outlier: 3.624A pdb=" N ARG F 16 " --> pdb=" O LYS F 12 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER F 17 " --> pdb=" O GLU F 13 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLU F 18 " --> pdb=" O ARG F 14 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N ARG F 20 " --> pdb=" O ARG F 16 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ASP F 21 " --> pdb=" O SER F 17 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ARG F 24 " --> pdb=" O ARG F 20 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LYS F 25 " --> pdb=" O ASP F 21 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN F 26 " --> pdb=" O ALA F 22 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N GLY F 28 " --> pdb=" O ARG F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 54 removed outlier: 5.229A pdb=" N ASP F 53 " --> pdb=" O GLU F 49 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ALA F 54 " --> pdb=" O ALA F 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 49 through 54' Processing helix chain 'F' and resid 59 through 69 removed outlier: 4.903A pdb=" N ASP F 63 " --> pdb=" O GLY F 59 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU F 64 " --> pdb=" O ALA F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 113 removed outlier: 3.566A pdb=" N TRP F 104 " --> pdb=" O GLY F 100 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLU F 105 " --> pdb=" O ASP F 101 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG F 109 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE F 113 " --> pdb=" O ARG F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 181 removed outlier: 4.007A pdb=" N ALA F 179 " --> pdb=" O ALA F 175 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU F 180 " --> pdb=" O LEU F 176 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLY F 181 " --> pdb=" O LEU F 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 82 removed outlier: 3.569A pdb=" N SER G 64 " --> pdb=" O ARG G 60 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLY G 67 " --> pdb=" O ARG G 63 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N THR G 71 " --> pdb=" O GLY G 67 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N VAL G 73 " --> pdb=" O SER G 69 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N LEU G 76 " --> pdb=" O LEU G 72 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N VAL G 80 " --> pdb=" O LEU G 76 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N THR G 81 " --> pdb=" O VAL G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 152 removed outlier: 3.573A pdb=" N ILE G 145 " --> pdb=" O LYS G 141 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG G 151 " --> pdb=" O ALA G 147 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LEU G 152 " --> pdb=" O ASN G 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 28 removed outlier: 6.292A pdb=" N GLY H 26 " --> pdb=" O LYS H 22 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ARG H 27 " --> pdb=" O ASP H 23 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ASN H 28 " --> pdb=" O GLY H 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 22 through 28' Processing helix chain 'H' and resid 29 through 34 removed outlier: 4.031A pdb=" N ARG H 33 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 39 through 46 removed outlier: 5.995A pdb=" N ALA H 43 " --> pdb=" O ALA H 39 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N GLN H 44 " --> pdb=" O SER H 40 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 removed outlier: 3.578A pdb=" N LEU J 28 " --> pdb=" O VAL J 24 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA J 33 " --> pdb=" O ALA J 29 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU J 35 " --> pdb=" O ALA J 31 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG J 37 " --> pdb=" O ALA J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 65 through 72 removed outlier: 3.970A pdb=" N GLN J 70 " --> pdb=" O GLY J 66 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N HIS J 71 " --> pdb=" O ASP J 67 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 96 removed outlier: 3.604A pdb=" N GLN J 94 " --> pdb=" O GLY J 90 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ARG J 95 " --> pdb=" O GLU J 91 " (cutoff:3.500A) Processing helix chain 'J' and resid 97 through 110 removed outlier: 4.125A pdb=" N VAL J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU J 102 " --> pdb=" O ASP J 98 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA J 104 " --> pdb=" O VAL J 100 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE J 105 " --> pdb=" O VAL J 101 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N MET J 108 " --> pdb=" O ALA J 104 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU J 109 " --> pdb=" O ILE J 105 " (cutoff:3.500A) Proline residue: J 110 - end of helix Processing helix chain 'J' and resid 112 through 122 removed outlier: 4.191A pdb=" N ARG J 116 " --> pdb=" O ASN J 112 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN J 117 " --> pdb=" O ARG J 113 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ARG J 120 " --> pdb=" O ARG J 116 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N LYS J 121 " --> pdb=" O GLN J 117 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU J 122 " --> pdb=" O ILE J 118 " (cutoff:3.500A) Processing helix chain 'K' and resid 104 through 110 removed outlier: 4.592A pdb=" N GLU K 108 " --> pdb=" O ARG K 104 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS K 109 " --> pdb=" O GLU K 105 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 118 Processing helix chain 'L' and resid 38 through 43 removed outlier: 4.221A pdb=" N ARG L 42 " --> pdb=" O GLY L 38 " (cutoff:3.500A) Processing helix chain 'L' and resid 55 through 61 removed outlier: 3.778A pdb=" N LEU L 60 " --> pdb=" O ILE L 56 " (cutoff:3.500A) Proline residue: L 61 - end of helix Processing helix chain 'L' and resid 78 through 86 removed outlier: 4.060A pdb=" N ARG L 84 " --> pdb=" O GLY L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 93 through 101 removed outlier: 4.012A pdb=" N VAL L 98 " --> pdb=" O VAL L 94 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ALA L 99 " --> pdb=" O ASP L 95 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS L 100 " --> pdb=" O ASP L 96 " (cutoff:3.500A) Processing helix chain 'L' and resid 129 through 140 removed outlier: 3.954A pdb=" N ALA L 134 " --> pdb=" O GLY L 130 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS L 135 " --> pdb=" O SER L 131 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ALA L 138 " --> pdb=" O ALA L 134 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA L 139 " --> pdb=" O LYS L 135 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY L 140 " --> pdb=" O ILE L 136 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 59 removed outlier: 3.553A pdb=" N ILE M 47 " --> pdb=" O THR M 43 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ALA M 50 " --> pdb=" O GLN M 46 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ILE M 52 " --> pdb=" O GLU M 48 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA M 53 " --> pdb=" O SER M 49 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N HIS M 57 " --> pdb=" O ALA M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 110 through 126 removed outlier: 3.611A pdb=" N ALA M 114 " --> pdb=" O ASN M 110 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR M 119 " --> pdb=" O ARG M 115 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ALA M 121 " --> pdb=" O ALA M 117 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE M 122 " --> pdb=" O LEU M 118 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N HIS M 123 " --> pdb=" O THR M 119 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LYS M 124 " --> pdb=" O ARG M 120 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU M 125 " --> pdb=" O ALA M 121 " (cutoff:3.500A) Proline residue: M 126 - end of helix Processing helix chain 'N' and resid 13 through 32 removed outlier: 3.847A pdb=" N GLN N 17 " --> pdb=" O SER N 13 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS N 18 " --> pdb=" O SER N 14 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ALA N 19 " --> pdb=" O SER N 15 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 58 removed outlier: 3.568A pdb=" N ALA N 43 " --> pdb=" O PRO N 39 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU N 44 " --> pdb=" O LYS N 40 " (cutoff:3.500A) Proline residue: N 46 - end of helix removed outlier: 3.539A pdb=" N GLU N 49 " --> pdb=" O ARG N 45 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LYS N 50 " --> pdb=" O PRO N 46 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU N 51 " --> pdb=" O TYR N 47 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR N 53 " --> pdb=" O GLU N 49 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N HIS N 54 " --> pdb=" O LYS N 50 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA N 55 " --> pdb=" O LEU N 51 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS N 57 " --> pdb=" O THR N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 70 removed outlier: 3.624A pdb=" N LYS N 68 " --> pdb=" O ARG N 64 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LYS N 69 " --> pdb=" O GLU N 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 89 removed outlier: 3.543A pdb=" N VAL N 76 " --> pdb=" O ASP N 72 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR N 78 " --> pdb=" O ASP N 74 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU N 82 " --> pdb=" O THR N 78 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ILE N 83 " --> pdb=" O LEU N 79 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N GLY N 84 " --> pdb=" O PHE N 80 " (cutoff:3.500A) Proline residue: N 85 - end of helix removed outlier: 3.911A pdb=" N ALA N 88 " --> pdb=" O GLY N 84 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ASP N 89 " --> pdb=" O PRO N 85 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 24 removed outlier: 3.874A pdb=" N ARG O 9 " --> pdb=" O VAL O 5 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ARG O 10 " --> pdb=" O SER O 6 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N ARG O 16 " --> pdb=" O SER O 12 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR O 18 " --> pdb=" O LEU O 14 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG O 19 " --> pdb=" O ARG O 15 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS O 22 " --> pdb=" O THR O 18 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N LYS O 23 " --> pdb=" O ARG O 19 " (cutoff:3.500A) Processing helix chain 'O' and resid 62 through 68 removed outlier: 5.027A pdb=" N VAL O 68 " --> pdb=" O ASP O 64 " (cutoff:3.500A) Processing helix chain 'O' and resid 71 through 91 removed outlier: 3.522A pdb=" N GLN O 81 " --> pdb=" O VAL O 77 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA O 84 " --> pdb=" O GLY O 80 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU O 85 " --> pdb=" O GLN O 81 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LYS O 88 " --> pdb=" O ALA O 84 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ALA O 89 " --> pdb=" O GLU O 85 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ALA O 90 " --> pdb=" O ARG O 86 " (cutoff:3.500A) Processing helix chain 'O' and resid 106 through 119 removed outlier: 3.507A pdb=" N LEU O 111 " --> pdb=" O ARG O 107 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA O 114 " --> pdb=" O ALA O 110 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLU O 117 " --> pdb=" O ASP O 113 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ASN O 118 " --> pdb=" O ALA O 114 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLY O 119 " --> pdb=" O ALA O 115 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 10 removed outlier: 3.699A pdb=" N ASP P 8 " --> pdb=" O LEU P 4 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS P 9 " --> pdb=" O ASP P 5 " (cutoff:3.500A) Proline residue: P 10 - end of helix No H-bonds generated for 'chain 'P' and resid 4 through 10' Processing helix chain 'P' and resid 96 through 103 removed outlier: 4.821A pdb=" N ARG P 100 " --> pdb=" O LEU P 96 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N GLU P 101 " --> pdb=" O TYR P 97 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LEU P 102 " --> pdb=" O TYR P 98 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ARG P 103 " --> pdb=" O LEU P 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 96 through 103' Processing helix chain 'Q' and resid 7 through 22 removed outlier: 3.546A pdb=" N HIS Q 11 " --> pdb=" O ALA Q 7 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N LYS Q 12 " --> pdb=" O VAL Q 8 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N LYS Q 13 " --> pdb=" O ASN Q 9 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ARG Q 14 " --> pdb=" O ALA Q 10 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N SER Q 16 " --> pdb=" O LYS Q 12 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE Q 17 " --> pdb=" O LYS Q 13 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU Q 18 " --> pdb=" O ARG Q 14 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA Q 20 " --> pdb=" O SER Q 16 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG Q 22 " --> pdb=" O LEU Q 18 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 31 removed outlier: 4.048A pdb=" N ARG Q 30 " --> pdb=" O GLY Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 39 through 73 removed outlier: 3.821A pdb=" N ARG Q 51 " --> pdb=" O TYR Q 47 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LYS Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLY Q 55 " --> pdb=" O ARG Q 51 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ARG Q 58 " --> pdb=" O LYS Q 54 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ALA Q 63 " --> pdb=" O LYS Q 59 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA Q 67 " --> pdb=" O ALA Q 63 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG Q 70 " --> pdb=" O ASN Q 66 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASN Q 72 " --> pdb=" O ALA Q 68 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 87 removed outlier: 3.506A pdb=" N ILE Q 80 " --> pdb=" O TYR Q 76 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLN Q 81 " --> pdb=" O ASN Q 77 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY Q 87 " --> pdb=" O LEU Q 83 " (cutoff:3.500A) Processing helix chain 'Q' and resid 91 through 102 removed outlier: 3.544A pdb=" N ALA Q 96 " --> pdb=" O ARG Q 92 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP Q 97 " --> pdb=" O LYS Q 93 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA Q 99 " --> pdb=" O LEU Q 95 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ILE Q 100 " --> pdb=" O ALA Q 96 " (cutoff:3.500A) Processing helix chain 'Q' and resid 103 through 118 removed outlier: 3.687A pdb=" N THR Q 107 " --> pdb=" O PRO Q 103 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA Q 108 " --> pdb=" O ALA Q 104 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA Q 115 " --> pdb=" O ASP Q 111 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA Q 116 " --> pdb=" O VAL Q 112 " (cutoff:3.500A) Proline residue: Q 118 - end of helix Processing helix chain 'R' and resid 52 through 60 removed outlier: 3.935A pdb=" N ALA R 57 " --> pdb=" O ALA R 53 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N LYS R 58 " --> pdb=" O LYS R 54 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N VAL R 59 " --> pdb=" O ALA R 55 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ALA R 60 " --> pdb=" O LEU R 56 " (cutoff:3.500A) Processing helix chain 'S' and resid 23 through 35 removed outlier: 3.569A pdb=" N ARG S 28 " --> pdb=" O PRO S 24 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG S 29 " --> pdb=" O ARG S 25 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N VAL S 30 " --> pdb=" O LYS S 26 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N LEU S 33 " --> pdb=" O ARG S 29 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL S 34 " --> pdb=" O VAL S 30 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ARG S 35 " --> pdb=" O ILE S 31 " (cutoff:3.500A) Processing helix chain 'S' and resid 38 through 49 removed outlier: 3.921A pdb=" N ASP S 44 " --> pdb=" O SER S 40 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ILE S 45 " --> pdb=" O ASP S 41 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU S 46 " --> pdb=" O ALA S 42 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG S 47 " --> pdb=" O LEU S 43 " (cutoff:3.500A) Processing helix chain 'S' and resid 51 through 71 removed outlier: 4.887A pdb=" N GLY S 55 " --> pdb=" O GLN S 51 " (cutoff:3.500A) Proline residue: S 56 - end of helix removed outlier: 4.218A pdb=" N VAL S 60 " --> pdb=" O PRO S 56 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER S 63 " --> pdb=" O LYS S 59 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN S 71 " --> pdb=" O ASN S 67 " (cutoff:3.500A) Processing helix chain 'T' and resid 6 through 12 removed outlier: 4.711A pdb=" N ILE T 10 " --> pdb=" O ASP T 6 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE T 11 " --> pdb=" O PRO T 7 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N LEU T 12 " --> pdb=" O ARG T 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 6 through 12' Processing helix chain 'T' and resid 17 through 27 removed outlier: 4.060A pdb=" N GLY T 22 " --> pdb=" O GLU T 18 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ASP T 25 " --> pdb=" O TYR T 21 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N ASP T 26 " --> pdb=" O GLY T 22 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASN T 27 " --> pdb=" O LEU T 23 " (cutoff:3.500A) Processing helix chain 'T' and resid 38 through 50 removed outlier: 3.622A pdb=" N LYS T 48 " --> pdb=" O ILE T 44 " (cutoff:3.500A) Processing helix chain 'U' and resid 67 through 72 removed outlier: 4.365A pdb=" N VAL U 71 " --> pdb=" O HIS U 67 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N MET U 72 " --> pdb=" O VAL U 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 67 through 72' Processing helix chain 'V' and resid 18 through 29 removed outlier: 3.587A pdb=" N ARG V 23 " --> pdb=" O LYS V 19 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA V 25 " --> pdb=" O ALA V 21 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG V 26 " --> pdb=" O SER V 22 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG V 27 " --> pdb=" O ARG V 23 " (cutoff:3.500A) Processing helix chain 'V' and resid 49 through 59 removed outlier: 4.463A pdb=" N ALA V 53 " --> pdb=" O GLY V 49 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA V 54 " --> pdb=" O HIS V 50 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL V 55 " --> pdb=" O ASP V 51 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU V 56 " --> pdb=" O TYR V 52 " (cutoff:3.500A) Processing helix chain 'X' and resid 52 through 59 removed outlier: 4.582A pdb=" N ALA X 58 " --> pdb=" O SER X 54 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLY X 59 " --> pdb=" O CYS X 55 " (cutoff:3.500A) Processing helix chain 'Y' and resid 6 through 14 removed outlier: 3.861A pdb=" N LEU Y 10 " --> pdb=" O SER Y 6 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ARG Y 11 " --> pdb=" O PRO Y 7 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLU Y 12 " --> pdb=" O GLY Y 8 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LEU Y 13 " --> pdb=" O GLU Y 9 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N THR Y 14 " --> pdb=" O LEU Y 10 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 6 through 14' Processing helix chain 'Y' and resid 15 through 39 removed outlier: 4.187A pdb=" N ALA Y 19 " --> pdb=" O ASP Y 15 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG Y 23 " --> pdb=" O ALA Y 19 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU Y 28 " --> pdb=" O GLU Y 24 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN Y 35 " --> pdb=" O ASN Y 31 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY Y 39 " --> pdb=" O GLN Y 35 " (cutoff:3.500A) Processing helix chain 'Y' and resid 43 through 67 removed outlier: 4.881A pdb=" N LEU Y 47 " --> pdb=" O ASN Y 43 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ARG Y 48 " --> pdb=" O ASN Y 44 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR Y 49 " --> pdb=" O ARG Y 45 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG Y 51 " --> pdb=" O LEU Y 47 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN Y 52 " --> pdb=" O ARG Y 48 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU Y 65 " --> pdb=" O LEU Y 61 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 removed outlier: 3.753A pdb=" N SER Z 22 " --> pdb=" O LYS Z 18 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU Z 23 " --> pdb=" O GLN Z 19 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG Z 24 " --> pdb=" O ARG Z 20 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR Z 25 " --> pdb=" O GLU Z 21 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU Z 26 " --> pdb=" O SER Z 22 " (cutoff:3.500A) Processing helix chain 'Z' and resid 40 through 51 removed outlier: 4.088A pdb=" N GLY Z 45 " --> pdb=" O ALA Z 41 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU Z 46 " --> pdb=" O ALA Z 42 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ALA Z 48 " --> pdb=" O ARG Z 44 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL Z 49 " --> pdb=" O GLY Z 45 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL Z 50 " --> pdb=" O LEU Z 46 " (cutoff:3.500A) Processing helix chain 'c' and resid 6 through 12 removed outlier: 3.778A pdb=" N ARG c 11 " --> pdb=" O PRO c 7 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU c 12 " --> pdb=" O HIS c 8 " (cutoff:3.500A) Processing helix chain 'c' and resid 27 through 46 removed outlier: 3.594A pdb=" N VAL c 32 " --> pdb=" O TYR c 28 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA c 37 " --> pdb=" O LYS c 33 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG c 39 " --> pdb=" O ASP c 35 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU c 41 " --> pdb=" O ALA c 37 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER c 43 " --> pdb=" O ARG c 39 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER c 44 " --> pdb=" O ARG c 40 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N GLY c 45 " --> pdb=" O LEU c 41 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N LEU c 46 " --> pdb=" O LEU c 42 " (cutoff:3.500A) Processing helix chain 'c' and resid 71 through 77 removed outlier: 3.882A pdb=" N VAL c 75 " --> pdb=" O ARG c 71 " (cutoff:3.500A) Processing helix chain 'c' and resid 80 through 95 removed outlier: 5.146A pdb=" N ASP c 84 " --> pdb=" O GLY c 80 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ARG c 85 " --> pdb=" O THR c 81 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE c 86 " --> pdb=" O GLU c 82 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG c 87 " --> pdb=" O ALA c 83 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP c 89 " --> pdb=" O ARG c 85 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS c 92 " --> pdb=" O ALA c 88 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU c 93 " --> pdb=" O ASP c 89 " (cutoff:3.500A) Processing helix chain 'c' and resid 107 through 112 removed outlier: 3.767A pdb=" N GLN c 111 " --> pdb=" O ASN c 107 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ALA c 112 " --> pdb=" O PRO c 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 107 through 112' Processing helix chain 'c' and resid 113 through 126 removed outlier: 4.025A pdb=" N GLN c 117 " --> pdb=" O GLN c 113 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ALA c 120 " --> pdb=" O ALA c 116 " (cutoff:3.500A) Processing helix chain 'c' and resid 128 through 143 removed outlier: 3.848A pdb=" N ALA c 136 " --> pdb=" O ALA c 132 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ARG c 142 " --> pdb=" O GLN c 138 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N GLN c 143 " --> pdb=" O SER c 139 " (cutoff:3.500A) Processing helix chain 'd' and resid 7 through 16 removed outlier: 4.229A pdb=" N LYS d 11 " --> pdb=" O PRO d 7 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU d 15 " --> pdb=" O LYS d 11 " (cutoff:3.500A) Processing helix chain 'd' and resid 23 through 30 removed outlier: 4.723A pdb=" N GLU d 27 " --> pdb=" O ASP d 23 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS d 28 " --> pdb=" O GLN d 24 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ARG d 29 " --> pdb=" O ALA d 25 " (cutoff:3.500A) Proline residue: d 30 - end of helix No H-bonds generated for 'chain 'd' and resid 23 through 30' Processing helix chain 'd' and resid 44 through 61 removed outlier: 4.038A pdb=" N LEU d 48 " --> pdb=" O SER d 44 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA d 56 " --> pdb=" O GLU d 52 " (cutoff:3.500A) Processing helix chain 'd' and resid 63 through 78 removed outlier: 3.707A pdb=" N ARG d 76 " --> pdb=" O GLU d 72 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLN d 77 " --> pdb=" O GLU d 73 " (cutoff:3.500A) Proline residue: d 78 - end of helix Processing helix chain 'd' and resid 80 through 92 removed outlier: 5.164A pdb=" N GLU d 84 " --> pdb=" O LYS d 80 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU d 85 " --> pdb=" O THR d 81 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU d 86 " --> pdb=" O GLY d 82 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ARG d 92 " --> pdb=" O ILE d 88 " (cutoff:3.500A) Processing helix chain 'd' and resid 93 through 101 removed outlier: 3.754A pdb=" N TYR d 98 " --> pdb=" O ASP d 94 " (cutoff:3.500A) Processing helix chain 'd' and resid 105 through 116 removed outlier: 3.641A pdb=" N GLN d 111 " --> pdb=" O ARG d 107 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N VAL d 113 " --> pdb=" O ALA d 109 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLY d 116 " --> pdb=" O LEU d 112 " (cutoff:3.500A) Processing helix chain 'd' and resid 147 through 157 removed outlier: 3.953A pdb=" N ALA d 153 " --> pdb=" O PRO d 149 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG d 154 " --> pdb=" O PHE d 150 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLU d 155 " --> pdb=" O GLN d 151 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N THR d 156 " --> pdb=" O ILE d 152 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N ALA d 157 " --> pdb=" O ALA d 153 " (cutoff:3.500A) Processing helix chain 'd' and resid 192 through 200 removed outlier: 3.941A pdb=" N VAL d 196 " --> pdb=" O GLU d 192 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU d 197 " --> pdb=" O GLN d 193 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR d 198 " --> pdb=" O LEU d 194 " (cutoff:3.500A) Processing helix chain 'e' and resid 86 through 102 removed outlier: 3.520A pdb=" N GLU e 97 " --> pdb=" O LYS e 93 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS e 100 " --> pdb=" O GLU e 96 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER e 101 " --> pdb=" O GLU e 97 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N PHE e 102 " --> pdb=" O ALA e 98 " (cutoff:3.500A) Processing helix chain 'e' and resid 140 through 150 removed outlier: 4.602A pdb=" N ALA e 144 " --> pdb=" O GLY e 140 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N VAL e 145 " --> pdb=" O ALA e 141 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N CYS e 148 " --> pdb=" O ALA e 144 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA e 149 " --> pdb=" O VAL e 145 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY e 150 " --> pdb=" O LEU e 146 " (cutoff:3.500A) Processing helix chain 'e' and resid 163 through 179 removed outlier: 3.531A pdb=" N HIS e 169 " --> pdb=" O ILE e 165 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU e 177 " --> pdb=" O ALA e 173 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU e 178 " --> pdb=" O ALA e 174 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N GLN e 179 " --> pdb=" O LEU e 175 " (cutoff:3.500A) Processing helix chain 'e' and resid 180 through 189 removed outlier: 3.706A pdb=" N ALA e 185 " --> pdb=" O PRO e 181 " (cutoff:3.500A) Processing helix chain 'e' and resid 191 through 196 removed outlier: 4.111A pdb=" N VAL e 195 " --> pdb=" O PRO e 191 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ALA e 196 " --> pdb=" O ILE e 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 191 through 196' Processing helix chain 'e' and resid 197 through 207 removed outlier: 3.818A pdb=" N LEU e 201 " --> pdb=" O PRO e 197 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYS e 202 " --> pdb=" O ALA e 198 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ALA e 203 " --> pdb=" O GLY e 199 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG e 204 " --> pdb=" O MET e 200 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ARG e 205 " --> pdb=" O LEU e 201 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS e 206 " --> pdb=" O LYS e 202 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N SER e 207 " --> pdb=" O ALA e 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 197 through 207' Processing helix chain 'f' and resid 15 through 28 removed outlier: 4.662A pdb=" N VAL f 19 " --> pdb=" O ASP f 15 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ALA f 20 " --> pdb=" O GLU f 16 " (cutoff:3.500A) Proline residue: f 21 - end of helix removed outlier: 6.313A pdb=" N GLU f 24 " --> pdb=" O ALA f 20 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N THR f 25 " --> pdb=" O PRO f 21 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N PHE f 26 " --> pdb=" O SER f 22 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU f 27 " --> pdb=" O LEU f 23 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ASN f 28 " --> pdb=" O GLU f 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 15 through 28' Processing helix chain 'f' and resid 29 through 34 removed outlier: 4.405A pdb=" N ASP f 33 " --> pdb=" O VAL f 29 " (cutoff:3.500A) Processing helix chain 'f' and resid 71 through 82 removed outlier: 4.592A pdb=" N ARG f 77 " --> pdb=" O SER f 73 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLN f 78 " --> pdb=" O GLU f 74 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER f 80 " --> pdb=" O ASP f 76 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N LEU f 81 " --> pdb=" O ARG f 77 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ASN f 82 " --> pdb=" O GLN f 78 " (cutoff:3.500A) Processing helix chain 'g' and resid 20 through 32 removed outlier: 4.095A pdb=" N THR g 24 " --> pdb=" O SER g 20 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS g 29 " --> pdb=" O GLN g 25 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N LEU g 32 " --> pdb=" O ASN g 28 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 55 removed outlier: 3.509A pdb=" N VAL g 43 " --> pdb=" O ALA g 39 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR g 44 " --> pdb=" O GLU g 40 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLY g 45 " --> pdb=" O ARG g 41 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN g 49 " --> pdb=" O GLY g 45 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA g 50 " --> pdb=" O ALA g 46 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG g 51 " --> pdb=" O LEU g 47 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASP g 52 " --> pdb=" O GLU g 48 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LYS g 53 " --> pdb=" O GLN g 49 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N THR g 54 " --> pdb=" O ALA g 50 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 70 removed outlier: 3.544A pdb=" N ARG g 64 " --> pdb=" O ILE g 60 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP g 67 " --> pdb=" O LYS g 63 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL g 69 " --> pdb=" O ALA g 65 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 111 removed outlier: 3.532A pdb=" N THR g 97 " --> pdb=" O PRO g 93 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N THR g 98 " --> pdb=" O ASP g 94 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR g 107 " --> pdb=" O TRP g 103 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N GLN g 110 " --> pdb=" O GLY g 106 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG g 111 " --> pdb=" O TYR g 107 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 130 removed outlier: 3.850A pdb=" N ALA g 121 " --> pdb=" O ILE g 117 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU g 123 " --> pdb=" O ARG g 119 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASP g 126 " --> pdb=" O ASN g 122 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN g 129 " --> pdb=" O LEU g 125 " (cutoff:3.500A) Processing helix chain 'g' and resid 132 through 149 removed outlier: 3.870A pdb=" N ARG g 138 " --> pdb=" O SER g 134 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU g 139 " --> pdb=" O VAL g 135 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASN g 148 " --> pdb=" O MET g 144 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ARG g 149 " --> pdb=" O ALA g 145 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 21 removed outlier: 3.638A pdb=" N ASP h 9 " --> pdb=" O ASP h 5 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU h 14 " --> pdb=" O PHE h 10 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA h 20 " --> pdb=" O ASN h 16 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N TYR h 21 " --> pdb=" O ALA h 17 " (cutoff:3.500A) Processing helix chain 'h' and resid 30 through 44 removed outlier: 3.813A pdb=" N ASN h 35 " --> pdb=" O LYS h 31 " (cutoff:3.500A) Processing helix chain 'h' and resid 114 through 122 removed outlier: 4.385A pdb=" N ARG h 120 " --> pdb=" O ARG h 116 " (cutoff:3.500A) Processing helix chain 'i' and resid 55 through 60 removed outlier: 3.975A pdb=" N TYR i 59 " --> pdb=" O SER i 55 " (cutoff:3.500A) Processing helix chain 'i' and resid 62 through 77 removed outlier: 3.629A pdb=" N LEU i 68 " --> pdb=" O VAL i 64 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS i 70 " --> pdb=" O GLN i 66 " (cutoff:3.500A) Proline residue: i 72 - end of helix removed outlier: 4.438A pdb=" N THR i 75 " --> pdb=" O ALA i 71 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL i 76 " --> pdb=" O PRO i 72 " (cutoff:3.500A) Processing helix chain 'i' and resid 92 through 112 removed outlier: 3.719A pdb=" N LEU i 102 " --> pdb=" O GLY i 98 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ILE i 109 " --> pdb=" O ALA i 105 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU i 110 " --> pdb=" O ARG i 106 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N SER i 112 " --> pdb=" O LEU i 108 " (cutoff:3.500A) Processing helix chain 'i' and resid 115 through 123 removed outlier: 3.753A pdb=" N LEU i 119 " --> pdb=" O ASP i 115 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS i 121 " --> pdb=" O PRO i 117 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA i 122 " --> pdb=" O ALA i 118 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY i 123 " --> pdb=" O LEU i 119 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 25 removed outlier: 4.048A pdb=" N ILE j 18 " --> pdb=" O ASP j 14 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ASP j 19 " --> pdb=" O HIS j 15 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N ALA j 20 " --> pdb=" O GLU j 16 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N SER j 21 " --> pdb=" O ALA j 17 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYS j 24 " --> pdb=" O ALA j 20 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ILE j 25 " --> pdb=" O SER j 21 " (cutoff:3.500A) Processing helix chain 'j' and resid 28 through 33 removed outlier: 5.347A pdb=" N THR j 32 " --> pdb=" O THR j 28 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY j 33 " --> pdb=" O VAL j 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 28 through 33' Processing helix chain 'j' and resid 80 through 88 removed outlier: 5.263A pdb=" N ASP j 85 " --> pdb=" O PRO j 81 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ALA j 86 " --> pdb=" O LYS j 82 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU j 87 " --> pdb=" O THR j 83 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N MET j 88 " --> pdb=" O VAL j 84 " (cutoff:3.500A) Processing helix chain 'k' and resid 56 through 61 removed outlier: 3.775A pdb=" N VAL k 60 " --> pdb=" O SER k 56 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLY k 61 " --> pdb=" O SER k 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 56 through 61' Processing helix chain 'k' and resid 69 through 88 removed outlier: 3.635A pdb=" N ALA k 73 " --> pdb=" O THR k 69 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN k 74 " --> pdb=" O PRO k 70 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA k 76 " --> pdb=" O ALA k 72 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN k 79 " --> pdb=" O LEU k 75 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA k 80 " --> pdb=" O ALA k 76 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LYS k 83 " --> pdb=" O ASN k 79 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP k 86 " --> pdb=" O ARG k 82 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N HIS k 87 " --> pdb=" O LYS k 83 " (cutoff:3.500A) Processing helix chain 'k' and resid 102 through 114 removed outlier: 4.410A pdb=" N ALA k 106 " --> pdb=" O GLY k 102 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ILE k 107 " --> pdb=" O ARG k 103 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER k 109 " --> pdb=" O THR k 105 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU k 110 " --> pdb=" O ALA k 106 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLN k 111 " --> pdb=" O ILE k 107 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ALA k 112 " --> pdb=" O ARG k 108 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ALA k 113 " --> pdb=" O SER k 109 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY k 114 " --> pdb=" O LEU k 110 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 11 removed outlier: 3.961A pdb=" N LEU l 7 " --> pdb=" O THR l 3 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY l 11 " --> pdb=" O LEU l 7 " (cutoff:3.500A) Processing helix chain 'l' and resid 113 through 118 removed outlier: 4.785A pdb=" N TYR l 117 " --> pdb=" O ALA l 113 " (cutoff:3.500A) Processing helix chain 'm' and resid 14 through 22 removed outlier: 3.678A pdb=" N LEU m 19 " --> pdb=" O MET m 15 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N THR m 20 " --> pdb=" O GLU m 16 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N TYR m 21 " --> pdb=" O VAL m 17 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ILE m 22 " --> pdb=" O ALA m 18 " (cutoff:3.500A) Processing helix chain 'm' and resid 26 through 38 removed outlier: 3.704A pdb=" N SER m 30 " --> pdb=" O GLY m 26 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASN m 31 " --> pdb=" O ARG m 27 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA m 35 " --> pdb=" O ASN m 31 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA m 36 " --> pdb=" O GLU m 32 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR m 37 " --> pdb=" O ILE m 33 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N GLY m 38 " --> pdb=" O LEU m 34 " (cutoff:3.500A) Processing helix chain 'm' and resid 49 through 63 removed outlier: 3.651A pdb=" N ILE m 54 " --> pdb=" O GLU m 50 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP m 58 " --> pdb=" O ILE m 54 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR m 59 " --> pdb=" O HIS m 55 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ILE m 60 " --> pdb=" O LEU m 56 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLU m 61 " --> pdb=" O ARG m 57 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN m 63 " --> pdb=" O TYR m 59 " (cutoff:3.500A) Processing helix chain 'm' and resid 67 through 85 removed outlier: 6.109A pdb=" N ARG m 71 " --> pdb=" O GLU m 67 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ARG m 72 " --> pdb=" O GLY m 68 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS m 81 " --> pdb=" O ASP m 77 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU m 83 " --> pdb=" O ARG m 79 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLY m 85 " --> pdb=" O LYS m 81 " (cutoff:3.500A) Processing helix chain 'm' and resid 86 through 95 removed outlier: 3.672A pdb=" N ARG m 93 " --> pdb=" O GLY m 89 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ARG m 94 " --> pdb=" O LEU m 90 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY m 95 " --> pdb=" O ARG m 91 " (cutoff:3.500A) Processing helix chain 'm' and resid 107 through 112 removed outlier: 3.897A pdb=" N LYS m 111 " --> pdb=" O ALA m 107 " (cutoff:3.500A) Processing helix chain 'n' and resid 3 through 13 removed outlier: 3.901A pdb=" N ALA n 11 " --> pdb=" O VAL n 7 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY n 12 " --> pdb=" O ASN n 8 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N LYS n 13 " --> pdb=" O LYS n 9 " (cutoff:3.500A) Processing helix chain 'n' and resid 40 through 51 removed outlier: 3.878A pdb=" N ARG n 45 " --> pdb=" O ARG n 41 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N HIS n 49 " --> pdb=" O ARG n 45 " (cutoff:3.500A) Processing helix chain 'o' and resid 4 through 16 removed outlier: 3.552A pdb=" N GLU o 10 " --> pdb=" O GLU o 6 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ILE o 11 " --> pdb=" O GLN o 7 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU o 12 " --> pdb=" O LYS o 8 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG o 13 " --> pdb=" O LYS o 9 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N SER o 14 " --> pdb=" O GLU o 10 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR o 15 " --> pdb=" O ILE o 11 " (cutoff:3.500A) Processing helix chain 'o' and resid 24 through 47 removed outlier: 5.322A pdb=" N GLU o 41 " --> pdb=" O ALA o 37 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS o 44 " --> pdb=" O THR o 40 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N VAL o 45 " --> pdb=" O GLU o 41 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N HIS o 46 " --> pdb=" O HIS o 42 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LYS o 47 " --> pdb=" O LEU o 43 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 74 removed outlier: 3.750A pdb=" N ARG o 54 " --> pdb=" O HIS o 50 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLY o 55 " --> pdb=" O HIS o 51 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU o 56 " --> pdb=" O SER o 52 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU o 59 " --> pdb=" O GLY o 55 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLN o 72 " --> pdb=" O LYS o 68 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE o 73 " --> pdb=" O TYR o 69 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP o 74 " --> pdb=" O ILE o 70 " (cutoff:3.500A) Processing helix chain 'o' and resid 75 through 86 removed outlier: 3.574A pdb=" N ARG o 79 " --> pdb=" O VAL o 75 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER o 80 " --> pdb=" O GLU o 76 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU o 81 " --> pdb=" O ARG o 77 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ARG o 84 " --> pdb=" O SER o 80 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU o 85 " --> pdb=" O LEU o 81 " (cutoff:3.500A) Processing helix chain 'p' and resid 52 through 63 removed outlier: 6.001A pdb=" N ALA p 56 " --> pdb=" O ASN p 52 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLN p 57 " --> pdb=" O SER p 53 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N TYR p 58 " --> pdb=" O GLU p 54 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU p 60 " --> pdb=" O ALA p 56 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N SER p 61 " --> pdb=" O GLN p 57 " (cutoff:3.500A) Processing helix chain 'p' and resid 67 through 78 removed outlier: 4.277A pdb=" N LYS p 72 " --> pdb=" O GLU p 68 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU p 73 " --> pdb=" O PRO p 69 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS p 75 " --> pdb=" O LEU p 71 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR p 77 " --> pdb=" O LEU p 73 " (cutoff:3.500A) Processing helix chain 'p' and resid 79 through 85 removed outlier: 4.004A pdb=" N PHE p 83 " --> pdb=" O ASP p 79 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS p 84 " --> pdb=" O TRP p 80 " (cutoff:3.500A) Processing helix chain 'p' and resid 101 through 114 removed outlier: 3.601A pdb=" N ASN p 107 " --> pdb=" O LEU p 103 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA p 108 " --> pdb=" O GLU p 104 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA p 109 " --> pdb=" O VAL p 105 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU p 110 " --> pdb=" O PHE p 106 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA p 112 " --> pdb=" O ALA p 108 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ALA p 113 " --> pdb=" O ALA p 109 " (cutoff:3.500A) Processing helix chain 'r' and resid 20 through 25 Processing helix chain 'r' and resid 34 through 43 removed outlier: 4.127A pdb=" N ARG r 39 " --> pdb=" O THR r 35 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N THR r 40 " --> pdb=" O ALA r 36 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N TYR r 41 " --> pdb=" O LEU r 37 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ILE r 42 " --> pdb=" O LEU r 38 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N SER r 43 " --> pdb=" O ARG r 39 " (cutoff:3.500A) Processing helix chain 'r' and resid 50 through 55 removed outlier: 3.626A pdb=" N THR r 54 " --> pdb=" O ALA r 50 " (cutoff:3.500A) Processing helix chain 'r' and resid 57 through 75 removed outlier: 3.696A pdb=" N ARG r 62 " --> pdb=" O VAL r 58 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS r 69 " --> pdb=" O ALA r 65 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLU r 73 " --> pdb=" O LYS r 69 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL r 74 " --> pdb=" O ASN r 70 " (cutoff:3.500A) Processing helix chain 's' and resid 12 through 26 removed outlier: 4.055A pdb=" N LYS s 18 " --> pdb=" O HIS s 14 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN s 22 " --> pdb=" O LYS s 18 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU s 24 " --> pdb=" O ASP s 20 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N LYS s 25 " --> pdb=" O VAL s 21 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN s 26 " --> pdb=" O GLN s 22 " (cutoff:3.500A) Processing helix chain 's' and resid 41 through 46 removed outlier: 4.717A pdb=" N ILE s 45 " --> pdb=" O ILE s 41 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N GLY s 46 " --> pdb=" O PRO s 42 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 41 through 46' Processing helix chain 's' and resid 70 through 76 removed outlier: 4.948A pdb=" N PHE s 74 " --> pdb=" O LYS s 70 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ALA s 75 " --> pdb=" O LEU s 71 " (cutoff:3.500A) Proline residue: s 76 - end of helix No H-bonds generated for 'chain 's' and resid 70 through 76' Processing helix chain 't' and resid 4 through 40 removed outlier: 3.677A pdb=" N LYS t 9 " --> pdb=" O LYS t 5 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG t 12 " --> pdb=" O GLN t 8 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ALA t 17 " --> pdb=" O THR t 13 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU t 19 " --> pdb=" O GLU t 15 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ARG t 20 " --> pdb=" O ARG t 16 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN t 21 " --> pdb=" O ALA t 17 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL t 24 " --> pdb=" O ARG t 20 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU t 28 " --> pdb=" O VAL t 24 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG t 29 " --> pdb=" O LYS t 25 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR t 30 " --> pdb=" O SER t 26 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA t 31 " --> pdb=" O SER t 27 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE t 35 " --> pdb=" O ALA t 31 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N HIS t 40 " --> pdb=" O ARG t 36 " (cutoff:3.500A) Processing helix chain 't' and resid 44 through 65 removed outlier: 4.549A pdb=" N ALA t 48 " --> pdb=" O LYS t 44 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLU t 49 " --> pdb=" O ALA t 45 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA t 52 " --> pdb=" O ALA t 48 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG t 56 " --> pdb=" O ALA t 52 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU t 58 " --> pdb=" O THR t 54 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS t 60 " --> pdb=" O ARG t 56 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS t 64 " --> pdb=" O LYS t 60 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY t 65 " --> pdb=" O ALA t 61 " (cutoff:3.500A) Processing helix chain 't' and resid 68 through 86 removed outlier: 3.533A pdb=" N ALA t 72 " --> pdb=" O HIS t 68 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER t 77 " --> pdb=" O ALA t 73 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ALA t 82 " --> pdb=" O ALA t 78 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASN t 84 " --> pdb=" O ALA t 80 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU t 86 " --> pdb=" O ALA t 82 " (cutoff:3.500A) Processing helix chain 'x' and resid 43 through 53 removed outlier: 3.578A pdb=" N VAL x 47 " --> pdb=" O GLY x 43 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE x 50 " --> pdb=" O SER x 46 " (cutoff:3.500A) Processing helix chain 'x' and resid 83 through 92 removed outlier: 3.679A pdb=" N ASN x 88 " --> pdb=" O THR x 84 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N VAL x 89 " --> pdb=" O VAL x 85 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLU x 91 " --> pdb=" O GLY x 87 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N GLY x 92 " --> pdb=" O ASN x 88 " (cutoff:3.500A) Processing helix chain 'x' and resid 94 through 107 removed outlier: 3.931A pdb=" N ILE x 98 " --> pdb=" O GLY x 94 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N LYS x 99 " --> pdb=" O ASP x 95 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP x 101 " --> pdb=" O LYS x 97 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ARG x 102 " --> pdb=" O ILE x 98 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE x 103 " --> pdb=" O LYS x 99 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASN x 104 " --> pdb=" O LEU x 100 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU x 105 " --> pdb=" O ASP x 101 " (cutoff:3.500A) Processing helix chain 'x' and resid 115 through 132 removed outlier: 4.489A pdb=" N MET x 119 " --> pdb=" O THR x 115 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU x 121 " --> pdb=" O GLU x 117 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N MET x 122 " --> pdb=" O LEU x 118 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG x 124 " --> pdb=" O GLU x 120 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LEU x 125 " --> pdb=" O GLU x 121 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASP x 130 " --> pdb=" O GLN x 126 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ALA x 132 " --> pdb=" O GLU x 128 " (cutoff:3.500A) Processing helix chain 'x' and resid 136 through 149 removed outlier: 6.897A pdb=" N GLN x 140 " --> pdb=" O ASP x 136 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LEU x 141 " --> pdb=" O LEU x 137 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N GLU x 142 " --> pdb=" O ASP x 138 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLN x 143 " --> pdb=" O ALA x 139 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA x 147 " --> pdb=" O GLN x 143 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU x 148 " --> pdb=" O ALA x 144 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG x 149 " --> pdb=" O MET x 145 " (cutoff:3.500A) Processing helix chain 'x' and resid 163 through 177 removed outlier: 4.835A pdb=" N ARG x 167 " --> pdb=" O GLY x 163 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL x 168 " --> pdb=" O GLU x 164 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS x 171 " --> pdb=" O ARG x 167 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU x 175 " --> pdb=" O CYS x 171 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS x 177 " --> pdb=" O LEU x 173 " (cutoff:3.500A) Processing helix chain 'x' and resid 191 through 205 removed outlier: 3.785A pdb=" N VAL x 195 " --> pdb=" O ASP x 191 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLN x 196 " --> pdb=" O ALA x 192 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N GLN x 200 " --> pdb=" O GLN x 196 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ALA x 203 " --> pdb=" O GLU x 199 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N TYR x 205 " --> pdb=" O HIS x 201 " (cutoff:3.500A) Processing helix chain 'x' and resid 215 through 223 removed outlier: 3.997A pdb=" N LEU x 219 " --> pdb=" O ASP x 215 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP x 220 " --> pdb=" O ARG x 216 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASN x 221 " --> pdb=" O TYR x 217 " (cutoff:3.500A) Processing helix chain 'x' and resid 240 through 276 removed outlier: 3.661A pdb=" N TYR x 244 " --> pdb=" O ASN x 240 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS x 258 " --> pdb=" O VAL x 254 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP x 259 " --> pdb=" O GLN x 255 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N LYS x 264 " --> pdb=" O ALA x 260 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU x 268 " --> pdb=" O LYS x 264 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU x 269 " --> pdb=" O ARG x 265 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU x 270 " --> pdb=" O LEU x 266 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL x 273 " --> pdb=" O GLU x 269 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N GLY x 276 " --> pdb=" O TRP x 272 " (cutoff:3.500A) Processing helix chain 'x' and resid 284 through 301 removed outlier: 3.603A pdb=" N LEU x 288 " --> pdb=" O SER x 284 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN x 289 " --> pdb=" O LYS x 285 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG x 290 " --> pdb=" O ALA x 286 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ALA x 296 " --> pdb=" O GLU x 292 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU x 297 " --> pdb=" O GLU x 293 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA x 298 " --> pdb=" O MET x 294 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLU x 299 " --> pdb=" O ALA x 295 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS x 300 " --> pdb=" O ALA x 296 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N THR x 301 " --> pdb=" O GLU x 297 " (cutoff:3.500A) Processing helix chain 'x' and resid 359 through 369 removed outlier: 3.821A pdb=" N PHE x 364 " --> pdb=" O LYS x 360 " (cutoff:3.500A) Processing helix chain 'x' and resid 401 through 407 removed outlier: 3.694A pdb=" N VAL x 406 " --> pdb=" O VAL x 402 " (cutoff:3.500A) Processing helix chain 'x' and resid 421 through 430 removed outlier: 3.803A pdb=" N ALA x 428 " --> pdb=" O ALA x 424 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N PHE x 429 " --> pdb=" O TYR x 425 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY x 430 " --> pdb=" O VAL x 426 " (cutoff:3.500A) Processing helix chain 'x' and resid 433 through 439 removed outlier: 4.698A pdb=" N GLN x 437 " --> pdb=" O GLY x 433 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LYS x 438 " --> pdb=" O PRO x 434 " (cutoff:3.500A) Proline residue: x 439 - end of helix No H-bonds generated for 'chain 'x' and resid 433 through 439' Processing helix chain 'x' and resid 444 through 459 removed outlier: 4.860A pdb=" N LEU x 453 " --> pdb=" O ASN x 449 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LYS x 458 " --> pdb=" O ALA x 454 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N GLN x 459 " --> pdb=" O LEU x 455 " (cutoff:3.500A) Processing helix chain 'x' and resid 474 through 488 removed outlier: 4.127A pdb=" N GLY x 479 " --> pdb=" O VAL x 475 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER x 480 " --> pdb=" O GLU x 476 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA x 484 " --> pdb=" O SER x 480 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU x 485 " --> pdb=" O LEU x 481 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU x 486 " --> pdb=" O GLU x 482 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ASN x 487 " --> pdb=" O ASN x 483 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N PHE x 488 " --> pdb=" O ALA x 484 " (cutoff:3.500A) Processing helix chain 'x' and resid 498 through 506 removed outlier: 3.757A pdb=" N ASP x 503 " --> pdb=" O ARG x 499 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ARG x 504 " --> pdb=" O TRP x 500 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N CYS x 506 " --> pdb=" O LEU x 502 " (cutoff:3.500A) Processing helix chain 'x' and resid 528 through 540 removed outlier: 3.603A pdb=" N GLU x 533 " --> pdb=" O PHE x 529 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLU x 534 " --> pdb=" O GLY x 530 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASN x 535 " --> pdb=" O ALA x 531 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLU x 538 " --> pdb=" O GLU x 534 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain '0' and resid 28 through 31 removed outlier: 3.785A pdb=" N VAL 0 30 " --> pdb=" O HIS 0 37 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain '1' and resid 10 through 14 removed outlier: 3.571A pdb=" N TYR 1 23 " --> pdb=" O LEU 1 13 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain '3' and resid 22 through 25 removed outlier: 6.191A pdb=" N ILE 3 22 " --> pdb=" O VAL 3 50 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain '6' and resid 12 through 15 No H-bonds generated for sheet with id= 4 Processing sheet with id= 5, first strand: chain '8' and resid 75 through 79 removed outlier: 4.018A pdb=" N PHE 8 78 " --> pdb=" O ILE 8 115 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain '8' and resid 170 through 176 removed outlier: 5.548A pdb=" N VAL 8 42 " --> pdb=" O ILE 8 175 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS 8 211 " --> pdb=" O ARG 8 47 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ILE 8 212 " --> pdb=" O VAL 8 224 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL 8 224 " --> pdb=" O ILE 8 212 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'C' and resid 2 through 5 removed outlier: 6.321A pdb=" N ALA C 2 " --> pdb=" O ASP C 20 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP C 20 " --> pdb=" O ALA C 2 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'C' and resid 33 through 36 No H-bonds generated for sheet with id= 8 Processing sheet with id= 9, first strand: chain 'C' and resid 81 through 84 removed outlier: 4.080A pdb=" N HIS C 81 " --> pdb=" O LEU C 94 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU C 94 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N VAL C 75 " --> pdb=" O SER C 119 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N SER C 119 " --> pdb=" O VAL C 75 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP C 115 " --> pdb=" O VAL C 79 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'C' and resid 139 through 143 removed outlier: 4.407A pdb=" N THR C 140 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU C 165 " --> pdb=" O THR C 140 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN C 164 " --> pdb=" O ARG C 176 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N SER C 174 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU C 181 " --> pdb=" O MET C 177 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'C' and resid 91 through 97 removed outlier: 5.232A pdb=" N ARG C 91 " --> pdb=" O ALA C 107 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N GLU C 101 " --> pdb=" O TYR C 97 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'D' and resid 4 through 8 removed outlier: 5.136A pdb=" N LYS D 4 " --> pdb=" O SER D 210 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL D 175 " --> pdb=" O GLY D 116 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ASP D 173 " --> pdb=" O SER D 118 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'D' and resid 12 through 18 removed outlier: 3.883A pdb=" N GLY D 12 " --> pdb=" O VAL D 28 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ARG D 22 " --> pdb=" O ASP D 18 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS D 184 " --> pdb=" O LEU D 193 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'D' and resid 48 through 55 removed outlier: 4.793A pdb=" N SER D 48 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'D' and resid 110 through 113 removed outlier: 4.881A pdb=" N SER D 110 " --> pdb=" O VAL D 182 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'E' and resid 9 through 13 removed outlier: 5.456A pdb=" N LEU E 9 " --> pdb=" O LEU E 26 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL E 13 " --> pdb=" O GLY E 22 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLY E 22 " --> pdb=" O VAL E 13 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'E' and resid 129 through 132 Processing sheet with id= 18, first strand: chain 'F' and resid 72 through 76 removed outlier: 3.689A pdb=" N GLY F 93 " --> pdb=" O ARG F 75 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N VAL F 92 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL F 94 " --> pdb=" O MET F 45 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N GLY F 46 " --> pdb=" O GLY F 158 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N GLY F 158 " --> pdb=" O GLY F 46 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET F 159 " --> pdb=" O LEU F 139 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'F' and resid 79 through 82 removed outlier: 6.450A pdb=" N LYS F 79 " --> pdb=" O GLU F 88 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLU F 88 " --> pdb=" O LYS F 79 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'G' and resid 24 through 27 removed outlier: 3.789A pdb=" N ILE G 24 " --> pdb=" O LEU G 35 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'G' and resid 41 through 46 removed outlier: 3.588A pdb=" N LYS G 42 " --> pdb=" O THR G 54 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ALA G 50 " --> pdb=" O ASN G 46 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'G' and resid 83 through 90 removed outlier: 5.753A pdb=" N THR G 130 " --> pdb=" O ILE G 90 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LYS G 131 " --> pdb=" O GLN G 127 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA G 125 " --> pdb=" O THR G 133 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'G' and resid 95 through 99 removed outlier: 4.179A pdb=" N ARG G 96 " --> pdb=" O ALA G 107 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE G 116 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL G 114 " --> pdb=" O PHE G 106 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'J' and resid 52 through 57 removed outlier: 4.943A pdb=" N ASP J 19 " --> pdb=" O TYR J 140 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'J' and resid 74 through 78 removed outlier: 3.599A pdb=" N SER J 78 " --> pdb=" O GLY J 83 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N GLY J 83 " --> pdb=" O SER J 78 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'K' and resid 6 through 9 removed outlier: 4.705A pdb=" N SER K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU K 8 " --> pdb=" O ILE K 19 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'K' and resid 63 through 66 removed outlier: 3.555A pdb=" N ARG K 64 " --> pdb=" O ALA K 83 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N VAL K 66 " --> pdb=" O GLU K 81 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N GLU K 81 " --> pdb=" O VAL K 66 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'K' and resid 68 through 71 removed outlier: 4.259A pdb=" N SER K 75 " --> pdb=" O ARG K 71 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'L' and resid 74 through 77 removed outlier: 3.700A pdb=" N VAL L 77 " --> pdb=" O LYS L 110 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'M' and resid 38 through 41 removed outlier: 6.876A pdb=" N GLU M 38 " --> pdb=" O PRO M 99 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA M 40 " --> pdb=" O VAL M 97 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER M 89 " --> pdb=" O LYS M 76 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU M 74 " --> pdb=" O GLU M 91 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N TRP M 93 " --> pdb=" O ARG M 72 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ARG M 72 " --> pdb=" O TRP M 93 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'M' and resid 62 through 66 removed outlier: 3.970A pdb=" N PHE M 104 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE M 34 " --> pdb=" O LEU M 103 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ARG M 101 " --> pdb=" O ALA M 36 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'M' and resid 32 through 37 removed outlier: 6.173A pdb=" N LYS M 128 " --> pdb=" O LEU M 37 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'N' and resid 33 through 37 Processing sheet with id= 34, first strand: chain 'O' and resid 31 through 37 removed outlier: 6.665A pdb=" N ARG O 32 " --> pdb=" O VAL O 47 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N LEU O 46 " --> pdb=" O VAL O 55 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASN O 48 " --> pdb=" O THR O 53 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR O 53 " --> pdb=" O ASN O 48 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'O' and resid 42 through 46 removed outlier: 5.368A pdb=" N ILE O 42 " --> pdb=" O SER O 60 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL O 44 " --> pdb=" O ALA O 58 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA O 56 " --> pdb=" O LEU O 46 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'P' and resid 37 through 44 removed outlier: 3.650A pdb=" N VAL P 31 " --> pdb=" O ARG P 38 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N THR P 24 " --> pdb=" O VAL P 86 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N HIS P 28 " --> pdb=" O HIS P 82 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N HIS P 82 " --> pdb=" O HIS P 28 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'P' and resid 48 through 52 removed outlier: 3.746A pdb=" N ARG P 48 " --> pdb=" O THR P 59 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N GLY P 52 " --> pdb=" O ARG P 55 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ARG P 55 " --> pdb=" O GLY P 52 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N GLU P 56 " --> pdb=" O VAL P 75 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'R' and resid 6 through 9 Processing sheet with id= 39, first strand: chain 'R' and resid 20 through 23 removed outlier: 4.317A pdb=" N ASP R 21 " --> pdb=" O VAL R 100 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LEU R 95 " --> pdb=" O HIS R 68 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N HIS R 68 " --> pdb=" O LEU R 95 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL R 97 " --> pdb=" O LEU R 66 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N THR R 62 " --> pdb=" O THR R 101 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL R 65 " --> pdb=" O GLU R 34 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N GLU R 34 " --> pdb=" O VAL R 65 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'R' and resid 73 through 80 removed outlier: 3.519A pdb=" N LYS R 80 " --> pdb=" O TYR R 85 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N TYR R 85 " --> pdb=" O LYS R 80 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'S' and resid 11 through 18 removed outlier: 6.801A pdb=" N VAL S 116 " --> pdb=" O ALA S 82 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N THR S 78 " --> pdb=" O ARG S 120 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'S' and resid 83 through 89 removed outlier: 4.956A pdb=" N THR S 110 " --> pdb=" O GLY S 89 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'S' and resid 91 through 98 removed outlier: 3.542A pdb=" N ARG S 98 " --> pdb=" O ARG S 102 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ARG S 102 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'T' and resid 28 through 33 removed outlier: 4.209A pdb=" N LYS T 80 " --> pdb=" O VAL T 33 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N LYS T 65 " --> pdb=" O ARG T 76 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N SER T 78 " --> pdb=" O GLN T 63 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N GLN T 63 " --> pdb=" O SER T 78 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LYS T 80 " --> pdb=" O ASN T 61 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ASN T 61 " --> pdb=" O LYS T 80 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ALA T 82 " --> pdb=" O THR T 59 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N THR T 59 " --> pdb=" O ALA T 82 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL T 84 " --> pdb=" O VAL T 57 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N VAL T 57 " --> pdb=" O VAL T 84 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'U' and resid 25 through 28 removed outlier: 3.827A pdb=" N GLN U 25 " --> pdb=" O LEU U 34 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'U' and resid 83 through 87 removed outlier: 3.510A pdb=" N ARG U 86 " --> pdb=" O VAL U 95 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'V' and resid 7 through 10 removed outlier: 5.400A pdb=" N ASN V 7 " --> pdb=" O VAL V 64 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU V 9 " --> pdb=" O THR V 66 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N LEU V 75 " --> pdb=" O VAL V 98 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU V 96 " --> pdb=" O LEU V 77 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'V' and resid 120 through 124 removed outlier: 3.846A pdb=" N LEU V 121 " --> pdb=" O VAL V 180 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL V 180 " --> pdb=" O LEU V 121 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'V' and resid 127 through 132 removed outlier: 5.597A pdb=" N ASN V 127 " --> pdb=" O VAL V 110 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL V 110 " --> pdb=" O ASN V 127 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL V 111 " --> pdb=" O LEU V 142 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL V 144 " --> pdb=" O VAL V 111 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'V' and resid 79 through 83 removed outlier: 4.206A pdb=" N ALA V 80 " --> pdb=" O ASP V 94 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N HIS V 92 " --> pdb=" O HIS V 82 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'W' and resid 37 through 40 removed outlier: 3.976A pdb=" N VAL W 38 " --> pdb=" O LEU W 59 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU W 59 " --> pdb=" O VAL W 38 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N ASP W 57 " --> pdb=" O GLN W 40 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'W' and resid 65 through 70 Processing sheet with id= 53, first strand: chain 'Z' and resid 32 through 38 removed outlier: 3.992A pdb=" N HIS Z 33 " --> pdb=" O GLN Z 8 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG Z 37 " --> pdb=" O LEU Z 4 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N LEU Z 53 " --> pdb=" O VAL Z 9 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'c' and resid 52 through 58 removed outlier: 4.078A pdb=" N ASP c 53 " --> pdb=" O HIS c 68 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N VAL c 63 " --> pdb=" O GLN c 97 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL c 65 " --> pdb=" O GLN c 99 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE c 67 " --> pdb=" O ASN c 101 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR c 69 " --> pdb=" O LEU c 103 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'c' and resid 164 through 170 removed outlier: 3.523A pdb=" N ARG c 164 " --> pdb=" O GLY c 155 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N CYS c 153 " --> pdb=" O GLU c 166 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY c 148 " --> pdb=" O TYR c 203 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'd' and resid 135 through 139 removed outlier: 4.362A pdb=" N ASP d 136 " --> pdb=" O ILE d 177 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'e' and resid 42 through 47 removed outlier: 6.777A pdb=" N LEU e 67 " --> pdb=" O VAL e 47 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'e' and resid 115 through 119 removed outlier: 3.814A pdb=" N VAL e 124 " --> pdb=" O LEU e 159 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA e 130 " --> pdb=" O ASP e 153 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ASP e 153 " --> pdb=" O ALA e 130 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'e' and resid 64 through 72 removed outlier: 3.921A pdb=" N ALA e 66 " --> pdb=" O GLY e 82 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N GLY e 82 " --> pdb=" O ALA e 66 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N MET e 76 " --> pdb=" O ASP e 72 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'f' and resid 2 through 11 removed outlier: 3.806A pdb=" N ALA f 67 " --> pdb=" O ARG f 2 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR f 4 " --> pdb=" O VAL f 65 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ILE f 6 " --> pdb=" O ILE f 63 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N TYR f 60 " --> pdb=" O TRP f 43 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'g' and resid 72 through 79 removed outlier: 6.377A pdb=" N ALA g 72 " --> pdb=" O VAL g 91 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL g 91 " --> pdb=" O ALA g 72 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG g 78 " --> pdb=" O TYR g 85 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'h' and resid 24 through 29 removed outlier: 3.515A pdb=" N ILE h 62 " --> pdb=" O VAL h 25 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N HIS h 29 " --> pdb=" O LYS h 58 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LYS h 58 " --> pdb=" O HIS h 29 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'h' and resid 76 through 79 removed outlier: 4.199A pdb=" N GLY h 76 " --> pdb=" O TRP h 132 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA h 129 " --> pdb=" O ILE h 105 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE h 105 " --> pdb=" O LEU h 128 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'i' and resid 27 through 32 removed outlier: 4.234A pdb=" N ILE i 27 " --> pdb=" O LEU i 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL i 43 " --> pdb=" O ASP i 83 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'j' and resid 69 through 76 removed outlier: 3.875A pdb=" N ALA j 12 " --> pdb=" O HIS j 70 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU j 10 " --> pdb=" O ARG j 72 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ILE j 74 " --> pdb=" O ILE j 8 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ILE j 8 " --> pdb=" O ILE j 74 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ILE j 76 " --> pdb=" O ILE j 6 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE j 6 " --> pdb=" O ILE j 76 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG j 9 " --> pdb=" O ASN j 99 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'k' and resid 39 through 46 removed outlier: 4.726A pdb=" N ASN k 39 " --> pdb=" O THR k 36 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLY k 118 " --> pdb=" O VAL k 92 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL k 94 " --> pdb=" O GLY k 118 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'k' and resid 94 through 97 No H-bonds generated for sheet with id= 67 Processing sheet with id= 68, first strand: chain 'l' and resid 29 through 32 removed outlier: 3.711A pdb=" N VAL l 80 " --> pdb=" O GLY l 32 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N LEU l 81 " --> pdb=" O ILE l 98 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'l' and resid 36 through 41 removed outlier: 4.832A pdb=" N ARG l 36 " --> pdb=" O ARG l 54 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N LYS l 51 " --> pdb=" O ILE l 67 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'p' and resid 5 through 11 removed outlier: 3.846A pdb=" N GLN p 17 " --> pdb=" O LEU p 10 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'q' and resid 58 through 63 removed outlier: 5.324A pdb=" N LYS q 58 " --> pdb=" O GLU q 115 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG q 60 " --> pdb=" O LEU q 113 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY q 62 " --> pdb=" O VAL q 111 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N SER q 112 " --> pdb=" O VAL q 128 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL q 128 " --> pdb=" O SER q 112 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'q' and resid 71 through 80 No H-bonds generated for sheet with id= 72 Processing sheet with id= 73, first strand: chain 's' and resid 30 through 33 removed outlier: 3.816A pdb=" N ILE s 31 " --> pdb=" O THR s 48 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N HIS s 52 " --> pdb=" O THR s 33 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'x' and resid 25 through 29 removed outlier: 3.929A pdb=" N LEU x 26 " --> pdb=" O MET x 8 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TYR x 6 " --> pdb=" O PHE x 28 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N ILE x 5 " --> pdb=" O ALA x 65 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ASP x 61 " --> pdb=" O LYS x 9 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'x' and resid 33 through 38 removed outlier: 3.826A pdb=" N LEU x 229 " --> pdb=" O VAL x 37 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ILE x 226 " --> pdb=" O TYR x 237 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N TYR x 235 " --> pdb=" O GLU x 228 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG x 233 " --> pdb=" O ASP x 230 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'x' and resid 69 through 74 Processing sheet with id= 77, first strand: chain 'x' and resid 341 through 344 removed outlier: 4.403A pdb=" N VAL x 322 " --> pdb=" O LEU x 344 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'x' and resid 385 through 390 removed outlier: 3.631A pdb=" N LEU x 463 " --> pdb=" O LYS x 385 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP x 467 " --> pdb=" O VAL x 389 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N CYS x 491 " --> pdb=" O ASN x 462 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE x 464 " --> pdb=" O CYS x 491 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N GLY x 348 " --> pdb=" O GLY x 490 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N THR x 507 " --> pdb=" O GLY x 527 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N LYS x 521 " --> pdb=" O GLU x 513 " (cutoff:3.500A) 1348 hydrogen bonds defined for protein. 3999 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2351 hydrogen bonds 3798 hydrogen bond angles 0 basepair planarities 973 basepair parallelities 2589 stacking parallelities Total time for adding SS restraints: 248.04 Time building geometry restraints manager: 64.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.30: 15076 1.30 - 1.45: 81652 1.45 - 1.61: 67417 1.61 - 1.76: 748 1.76 - 1.91: 172 Bond restraints: 165065 Sorted by residual: bond pdb=" C5 5MU A2177 " pdb=" C6 5MU A2177 " ideal model delta sigma weight residual 1.155 1.434 -0.279 2.00e-02 2.50e+03 1.94e+02 bond pdb=" C4 5MU A2177 " pdb=" C5 5MU A2177 " ideal model delta sigma weight residual 1.802 1.580 0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" C1' ADP x 601 " pdb=" C2' ADP x 601 " ideal model delta sigma weight residual 1.306 1.513 -0.207 2.00e-02 2.50e+03 1.07e+02 bond pdb=" C1' ADP x 603 " pdb=" C2' ADP x 603 " ideal model delta sigma weight residual 1.306 1.509 -0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" C1' ADP x 601 " pdb=" O4' ADP x 601 " ideal model delta sigma weight residual 1.615 1.417 0.198 2.00e-02 2.50e+03 9.82e+01 ... (remaining 165060 not shown) Histogram of bond angle deviations from ideal: 97.48 - 105.70: 27205 105.70 - 113.92: 102920 113.92 - 122.13: 80816 122.13 - 130.35: 34077 130.35 - 138.57: 2054 Bond angle restraints: 247072 Sorted by residual: angle pdb=" N VAL j 29 " pdb=" CA VAL j 29 " pdb=" C VAL j 29 " ideal model delta sigma weight residual 113.71 104.74 8.97 9.50e-01 1.11e+00 8.91e+01 angle pdb=" N GLN c 3 " pdb=" CA GLN c 3 " pdb=" C GLN c 3 " ideal model delta sigma weight residual 114.62 105.92 8.70 1.14e+00 7.69e-01 5.83e+01 angle pdb=" C1' OMG A2791 " pdb=" N9 OMG A2791 " pdb=" C4 OMG A2791 " ideal model delta sigma weight residual 108.29 130.88 -22.59 3.00e+00 1.11e-01 5.67e+01 angle pdb=" C1' OMG A2791 " pdb=" N9 OMG A2791 " pdb=" C8 OMG A2791 " ideal model delta sigma weight residual 142.82 120.33 22.49 3.00e+00 1.11e-01 5.62e+01 angle pdb=" C1' 2MG a 959 " pdb=" N9 2MG a 959 " pdb=" C8 2MG a 959 " ideal model delta sigma weight residual 110.07 127.82 -17.75 3.00e+00 1.11e-01 3.50e+01 ... (remaining 247067 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.86: 94208 35.86 - 71.71: 10612 71.71 - 107.57: 1332 107.57 - 143.42: 7 143.42 - 179.28: 28 Dihedral angle restraints: 106187 sinusoidal: 88683 harmonic: 17504 Sorted by residual: dihedral pdb=" CA PRO 6 43 " pdb=" C PRO 6 43 " pdb=" N PHE 6 44 " pdb=" CA PHE 6 44 " ideal model delta harmonic sigma weight residual -180.00 -129.06 -50.94 0 5.00e+00 4.00e-02 1.04e+02 dihedral pdb=" O4' C A3060 " pdb=" C1' C A3060 " pdb=" N1 C A3060 " pdb=" C2 C A3060 " ideal model delta sinusoidal sigma weight residual -160.00 19.28 -179.28 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C A 946 " pdb=" C1' C A 946 " pdb=" N1 C A 946 " pdb=" C2 C A 946 " ideal model delta sinusoidal sigma weight residual -160.00 18.36 -178.36 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 106184 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 28945 0.103 - 0.206: 2448 0.206 - 0.309: 103 0.309 - 0.412: 10 0.412 - 0.515: 2 Chirality restraints: 31508 Sorted by residual: chirality pdb=" CB VAL k 131 " pdb=" CA VAL k 131 " pdb=" CG1 VAL k 131 " pdb=" CG2 VAL k 131 " both_signs ideal model delta sigma weight residual False -2.63 -2.11 -0.52 2.00e-01 2.50e+01 6.63e+00 chirality pdb=" C3' U a1322 " pdb=" C4' U a1322 " pdb=" O3' U a1322 " pdb=" C2' U a1322 " both_signs ideal model delta sigma weight residual False -2.48 -2.04 -0.44 2.00e-01 2.50e+01 4.73e+00 chirality pdb=" CB VAL Z 50 " pdb=" CA VAL Z 50 " pdb=" CG1 VAL Z 50 " pdb=" CG2 VAL Z 50 " both_signs ideal model delta sigma weight residual False -2.63 -2.24 -0.39 2.00e-01 2.50e+01 3.73e+00 ... (remaining 31505 not shown) Planarity restraints: 13398 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG a 959 " 0.027 2.00e-02 2.50e+03 5.50e-01 6.80e+03 pdb=" C4' 2MG a 959 " 0.422 2.00e-02 2.50e+03 pdb=" O4' 2MG a 959 " 0.602 2.00e-02 2.50e+03 pdb=" C3' 2MG a 959 " -0.595 2.00e-02 2.50e+03 pdb=" O3' 2MG a 959 " -0.526 2.00e-02 2.50e+03 pdb=" C2' 2MG a 959 " -0.229 2.00e-02 2.50e+03 pdb=" O2' 2MG a 959 " 0.880 2.00e-02 2.50e+03 pdb=" C1' 2MG a 959 " 0.234 2.00e-02 2.50e+03 pdb=" N9 2MG a 959 " -0.816 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG A2791 " 0.007 2.00e-02 2.50e+03 5.29e-01 6.30e+03 pdb=" C4' OMG A2791 " 0.418 2.00e-02 2.50e+03 pdb=" O4' OMG A2791 " 0.573 2.00e-02 2.50e+03 pdb=" C3' OMG A2791 " -0.585 2.00e-02 2.50e+03 pdb=" O3' OMG A2791 " -0.482 2.00e-02 2.50e+03 pdb=" C2' OMG A2791 " -0.238 2.00e-02 2.50e+03 pdb=" O2' OMG A2791 " 0.843 2.00e-02 2.50e+03 pdb=" C1' OMG A2791 " 0.247 2.00e-02 2.50e+03 pdb=" N9 OMG A2791 " -0.782 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ADP x 601 " -0.411 2.00e-02 2.50e+03 4.79e-01 5.15e+03 pdb=" C2' ADP x 601 " 0.486 2.00e-02 2.50e+03 pdb=" C3' ADP x 601 " 0.446 2.00e-02 2.50e+03 pdb=" C4' ADP x 601 " -0.332 2.00e-02 2.50e+03 pdb=" C5' ADP x 601 " 0.558 2.00e-02 2.50e+03 pdb=" N9 ADP x 601 " 0.421 2.00e-02 2.50e+03 pdb=" O2' ADP x 601 " -0.021 2.00e-02 2.50e+03 pdb=" O3' ADP x 601 " -0.257 2.00e-02 2.50e+03 pdb=" O4' ADP x 601 " -0.890 2.00e-02 2.50e+03 ... (remaining 13395 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 1257 2.54 - 3.13: 101557 3.13 - 3.72: 276283 3.72 - 4.31: 404398 4.31 - 4.90: 560007 Nonbonded interactions: 1343502 Sorted by model distance: nonbonded pdb=" OP2 U A2920 " pdb="MG MG A3338 " model vdw 1.949 2.170 nonbonded pdb=" OP2 G A1318 " pdb="MG MG A3286 " model vdw 1.956 2.170 nonbonded pdb=" OP1 C A 807 " pdb="MG MG A3203 " model vdw 1.956 2.170 nonbonded pdb=" O6 G A 905 " pdb="MG MG A3203 " model vdw 1.960 2.170 nonbonded pdb=" OP1 U A 955 " pdb="MG MG A3279 " model vdw 1.962 2.170 ... (remaining 1343497 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 2.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.160 Extract box with map and model: 12.890 Check model and map are aligned: 1.630 Set scattering table: 1.040 Process input model: 558.870 Find NCS groups from input model: 3.040 Set up NCS constraints: 0.350 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: 0.030 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 582.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 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 : 0.013 0.279 165065 Z= 0.778 Angle : 1.137 22.591 247072 Z= 0.545 Chirality : 0.058 0.515 31508 Planarity : 0.012 0.550 13398 Dihedral : 22.784 179.276 94943 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.29 % Favored : 90.61 % Rotamer: Outliers : 0.54 % Allowed : 5.41 % Favored : 94.06 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.96 (0.08), residues: 6062 helix: -4.55 (0.06), residues: 1619 sheet: -2.47 (0.14), residues: 1123 loop : -2.95 (0.09), residues: 3320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.004 TRP J 15 HIS 0.030 0.004 HIS S 112 PHE 0.052 0.005 PHE E 90 TYR 0.046 0.004 TYR C 6 ARG 0.028 0.002 ARG L 59 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12124 Ramachandran restraints generated. 6062 Oldfield, 0 Emsley, 6062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12124 Ramachandran restraints generated. 6062 Oldfield, 0 Emsley, 6062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1488 residues out of total 5032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 1461 time to evaluate : 6.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 35 ARG cc_start: 0.7722 (mtm180) cc_final: 0.7114 (mtp180) REVERT: 6 1 MET cc_start: 0.6930 (mtp) cc_final: 0.6675 (mtt) REVERT: 8 71 LYS cc_start: 0.6424 (ttpp) cc_final: 0.6148 (ttpp) REVERT: 8 131 LEU cc_start: 0.8130 (mt) cc_final: 0.7504 (mt) REVERT: 8 155 ASP cc_start: 0.8359 (m-30) cc_final: 0.7665 (m-30) REVERT: 8 193 ILE cc_start: 0.8363 (mt) cc_final: 0.7996 (mt) REVERT: 8 198 ARG cc_start: 0.5905 (mtt-85) cc_final: 0.5560 (ttp80) REVERT: 8 212 ILE cc_start: 0.8424 (tt) cc_final: 0.7930 (pt) REVERT: C 99 ASP cc_start: 0.8449 (p0) cc_final: 0.8105 (p0) REVERT: C 205 ASN cc_start: 0.8528 (t0) cc_final: 0.8272 (t0) REVERT: D 26 VAL cc_start: 0.8792 (m) cc_final: 0.8586 (p) REVERT: E 24 ILE cc_start: 0.8268 (mm) cc_final: 0.7970 (mm) REVERT: E 81 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7791 (ptt90) REVERT: E 178 LEU cc_start: 0.8838 (mt) cc_final: 0.8611 (mt) REVERT: E 181 VAL cc_start: 0.8835 (t) cc_final: 0.8632 (m) REVERT: G 37 VAL cc_start: 0.8626 (t) cc_final: 0.8379 (p) REVERT: G 60 ARG cc_start: 0.7785 (tmm-80) cc_final: 0.7405 (ttt-90) REVERT: G 61 ARG cc_start: 0.7786 (ttt-90) cc_final: 0.7394 (tpp80) REVERT: G 84 TYR cc_start: 0.7671 (m-80) cc_final: 0.7361 (m-80) REVERT: G 90 ILE cc_start: 0.8385 (mm) cc_final: 0.8132 (mt) REVERT: G 152 LEU cc_start: 0.8709 (mt) cc_final: 0.8345 (mp) REVERT: G 159 LYS cc_start: 0.8936 (mmmt) cc_final: 0.8691 (mmtp) REVERT: G 170 ILE cc_start: 0.8674 (pt) cc_final: 0.8460 (pt) REVERT: J 54 VAL cc_start: 0.8873 (t) cc_final: 0.8597 (p) REVERT: K 105 GLU cc_start: 0.8016 (mp0) cc_final: 0.7615 (mp0) REVERT: L 95 ASP cc_start: 0.7568 (m-30) cc_final: 0.7296 (m-30) REVERT: M 26 THR cc_start: 0.8899 (p) cc_final: 0.8656 (t) REVERT: M 83 MET cc_start: 0.8189 (mmp) cc_final: 0.7949 (mmp) REVERT: M 120 ARG cc_start: 0.8114 (mtt-85) cc_final: 0.7579 (mtt90) REVERT: P 38 ARG cc_start: 0.7945 (ptm-80) cc_final: 0.7649 (ptt90) REVERT: P 93 ARG cc_start: 0.8845 (mmt-90) cc_final: 0.8604 (mpt180) REVERT: R 62 THR cc_start: 0.8793 (m) cc_final: 0.8394 (p) REVERT: R 99 LYS cc_start: 0.8631 (tptm) cc_final: 0.8273 (tptp) REVERT: S 30 VAL cc_start: 0.8854 (p) cc_final: 0.8621 (m) REVERT: S 31 ILE cc_start: 0.8640 (pt) cc_final: 0.8372 (mt) REVERT: S 106 ILE cc_start: 0.8303 (mm) cc_final: 0.8101 (mt) REVERT: T 58 ASN cc_start: 0.8461 (m-40) cc_final: 0.8216 (m110) REVERT: U 11 VAL cc_start: 0.8883 (t) cc_final: 0.8516 (m) REVERT: U 17 LYS cc_start: 0.8952 (tttm) cc_final: 0.8686 (ttmt) REVERT: V 140 GLU cc_start: 0.7633 (tp30) cc_final: 0.7042 (mm-30) REVERT: W 12 ASN cc_start: 0.7472 (m-40) cc_final: 0.7200 (m-40) REVERT: X 27 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.6955 (ppp80) REVERT: c 74 ILE cc_start: 0.8430 (mm) cc_final: 0.7238 (mm) REVERT: c 96 LYS cc_start: 0.8714 (mtmt) cc_final: 0.8393 (mtmm) REVERT: d 63 MET cc_start: 0.7328 (mmp) cc_final: 0.6897 (mmp) REVERT: d 167 GLN cc_start: 0.6505 (tm-30) cc_final: 0.6301 (tm-30) REVERT: e 104 ARG cc_start: 0.7811 (tpp-160) cc_final: 0.7541 (tpp-160) REVERT: e 107 LEU cc_start: 0.8776 (mp) cc_final: 0.8442 (mt) REVERT: e 128 ARG cc_start: 0.7694 (ppp80) cc_final: 0.7349 (ptp-110) REVERT: g 23 VAL cc_start: 0.8237 (t) cc_final: 0.8004 (p) REVERT: g 49 GLN cc_start: 0.8192 (tt0) cc_final: 0.7922 (mt0) REVERT: g 53 LYS cc_start: 0.7786 (ptpt) cc_final: 0.7577 (ttpt) REVERT: g 86 GLN cc_start: 0.7705 (mp10) cc_final: 0.7484 (mp10) REVERT: g 107 TYR cc_start: 0.7981 (m-80) cc_final: 0.7697 (m-80) REVERT: g 125 LEU cc_start: 0.8346 (mm) cc_final: 0.8146 (mp) REVERT: g 131 LEU cc_start: 0.8529 (mm) cc_final: 0.7986 (tt) REVERT: g 144 MET cc_start: 0.7762 (tpt) cc_final: 0.7512 (ttm) REVERT: h 41 LYS cc_start: 0.7929 (ttpt) cc_final: 0.7490 (ttmt) REVERT: h 42 ASN cc_start: 0.8372 (m-40) cc_final: 0.8129 (m110) REVERT: i 51 LEU cc_start: 0.7336 (mt) cc_final: 0.7120 (mt) REVERT: i 52 ASN cc_start: 0.7770 (m-40) cc_final: 0.7318 (m-40) REVERT: i 63 LYS cc_start: 0.8957 (mmpt) cc_final: 0.8412 (mmmt) REVERT: i 100 LEU cc_start: 0.9247 (tp) cc_final: 0.9021 (tt) REVERT: i 130 ARG cc_start: 0.8431 (mtp180) cc_final: 0.8221 (mtm110) REVERT: k 34 LYS cc_start: 0.7154 (tptm) cc_final: 0.6899 (tptp) REVERT: l 30 ARG cc_start: 0.8093 (tpp80) cc_final: 0.7867 (mmt90) REVERT: l 54 ARG cc_start: 0.7405 (mmm160) cc_final: 0.7200 (mmm160) REVERT: l 59 SER cc_start: 0.9080 (m) cc_final: 0.8773 (m) REVERT: m 41 ARG cc_start: 0.7516 (mtp-110) cc_final: 0.7235 (ttm110) REVERT: o 57 LEU cc_start: 0.8579 (mt) cc_final: 0.8347 (mp) REVERT: p 28 ARG cc_start: 0.7629 (ppt-90) cc_final: 0.7360 (ppt-90) REVERT: q 110 ARG cc_start: 0.8046 (mmm-85) cc_final: 0.7837 (mtp85) REVERT: q 115 GLU cc_start: 0.7456 (pp20) cc_final: 0.6873 (pp20) REVERT: q 131 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7901 (mm) REVERT: s 32 LYS cc_start: 0.8748 (ttmm) cc_final: 0.8382 (tttm) REVERT: t 57 LYS cc_start: 0.8259 (mptt) cc_final: 0.7856 (mptt) REVERT: t 60 LYS cc_start: 0.8737 (tptm) cc_final: 0.8448 (mtpp) REVERT: x 8 MET cc_start: 0.7923 (mtt) cc_final: 0.7647 (mtp) REVERT: x 10 LYS cc_start: 0.8532 (mptt) cc_final: 0.8253 (mmmt) REVERT: x 55 ASP cc_start: 0.7175 (t0) cc_final: 0.6706 (t0) REVERT: x 83 LYS cc_start: 0.7557 (tppt) cc_final: 0.7069 (tppt) REVERT: x 164 GLU cc_start: 0.5945 (pm20) cc_final: 0.5382 (pm20) REVERT: x 184 ASP cc_start: 0.7708 (m-30) cc_final: 0.7479 (t70) REVERT: x 185 GLU cc_start: 0.7195 (tp30) cc_final: 0.6911 (tp30) REVERT: x 196 GLN cc_start: 0.7961 (tm-30) cc_final: 0.6966 (tm-30) REVERT: x 200 GLN cc_start: 0.7892 (mp-120) cc_final: 0.7377 (mp10) REVERT: x 229 LEU cc_start: 0.8747 (mm) cc_final: 0.8364 (mp) REVERT: x 268 GLU cc_start: 0.7603 (mp0) cc_final: 0.7065 (mp0) REVERT: x 297 GLU cc_start: 0.6581 (mp0) cc_final: 0.6291 (mp0) REVERT: x 419 GLU cc_start: 0.7266 (mm-30) cc_final: 0.6965 (mm-30) REVERT: x 447 GLU cc_start: 0.7427 (mt-10) cc_final: 0.6831 (mt-10) REVERT: x 471 ASN cc_start: 0.7494 (m-40) cc_final: 0.6886 (p0) REVERT: x 540 LEU cc_start: 0.6598 (mt) cc_final: 0.6217 (mp) REVERT: x 554 LYS cc_start: 0.7929 (mmtm) cc_final: 0.7719 (mttt) outliers start: 27 outliers final: 6 residues processed: 1478 average time/residue: 1.4721 time to fit residues: 3599.5403 Evaluate side-chains 1111 residues out of total 5032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1102 time to evaluate : 6.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 123 VAL Chi-restraints excluded: chain X residue 27 ARG Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain g residue 73 LEU Chi-restraints excluded: chain l residue 61 VAL Chi-restraints excluded: chain q residue 131 LEU Chi-restraints excluded: chain x residue 356 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1074 random chunks: chunk 906 optimal weight: 6.9990 chunk 814 optimal weight: 9.9990 chunk 451 optimal weight: 1.9990 chunk 278 optimal weight: 0.7980 chunk 549 optimal weight: 5.9990 chunk 434 optimal weight: 20.0000 chunk 841 optimal weight: 9.9990 chunk 325 optimal weight: 0.9990 chunk 511 optimal weight: 4.9990 chunk 626 optimal weight: 50.0000 chunk 975 optimal weight: 6.9990 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 20 HIS ** 1 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 63 ASN 8 231 ASN C 70 ASN C 96 HIS C 122 ASN D 15 GLN D 34 ASN E 127 ASN E 159 GLN F 142 GLN G 22 GLN J 71 HIS J 147 GLN M 13 HIS M 14 HIS M 57 HIS N 54 HIS N 61 HIS N 62 ASN O 48 ASN P 82 HIS Q 44 ASN Q 122 ASN U 4 HIS ** V 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 43 ASN d 54 GLN d 66 GLN d 117 HIS d 126 ASN e 163 ASN f 78 GLN ** g 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 35 ASN i 65 HIS i 96 GLN k 32 HIS k 59 HIS ** k 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 7 GLN o 72 GLN p 15 ASN ** p 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 57 HIS t 71 GLN t 81 GLN x 40 ASN ** x 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 255 GLN ** x 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 414 GLN x 449 ASN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 165065 Z= 0.247 Angle : 0.679 19.516 247072 Z= 0.344 Chirality : 0.039 0.309 31508 Planarity : 0.006 0.125 13398 Dihedral : 23.416 179.912 82993 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.76 % Favored : 93.17 % Rotamer: Outliers : 3.22 % Allowed : 11.61 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.92 (0.09), residues: 6062 helix: -3.16 (0.09), residues: 1748 sheet: -1.90 (0.15), residues: 1080 loop : -2.52 (0.09), residues: 3234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP p 59 HIS 0.013 0.001 HIS M 13 PHE 0.020 0.002 PHE e 103 TYR 0.019 0.002 TYR C 6 ARG 0.008 0.001 ARG C 222 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12124 Ramachandran restraints generated. 6062 Oldfield, 0 Emsley, 6062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12124 Ramachandran restraints generated. 6062 Oldfield, 0 Emsley, 6062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1323 residues out of total 5032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 1161 time to evaluate : 6.373 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: 0 38 LYS cc_start: 0.8710 (mmmm) cc_final: 0.8388 (mmmt) REVERT: 0 39 VAL cc_start: 0.8933 (m) cc_final: 0.8682 (t) REVERT: 1 35 ARG cc_start: 0.7460 (mtm180) cc_final: 0.7072 (mtm180) REVERT: 8 37 LYS cc_start: 0.6583 (mppt) cc_final: 0.6038 (mmmt) REVERT: 8 160 LYS cc_start: 0.8057 (tmtt) cc_final: 0.7840 (tmtt) REVERT: 8 198 ARG cc_start: 0.5603 (mtt-85) cc_final: 0.5336 (ttp80) REVERT: C 23 GLU cc_start: 0.7632 (pm20) cc_final: 0.7365 (pm20) REVERT: C 26 ARG cc_start: 0.8298 (ttm170) cc_final: 0.7911 (ttt180) REVERT: C 99 ASP cc_start: 0.8353 (p0) cc_final: 0.7923 (p0) REVERT: C 205 ASN cc_start: 0.8291 (t0) cc_final: 0.8083 (t0) REVERT: D 144 VAL cc_start: 0.8362 (m) cc_final: 0.8157 (t) REVERT: E 24 ILE cc_start: 0.8149 (mm) cc_final: 0.7802 (mt) REVERT: E 81 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7531 (ptt90) REVERT: F 67 ILE cc_start: 0.7751 (mt) cc_final: 0.7521 (mt) REVERT: G 61 ARG cc_start: 0.7806 (ttt-90) cc_final: 0.7455 (tpp80) REVERT: G 66 HIS cc_start: 0.8235 (t70) cc_final: 0.7954 (t-170) REVERT: G 84 TYR cc_start: 0.7627 (m-80) cc_final: 0.7411 (m-80) REVERT: G 131 LYS cc_start: 0.7725 (mtmt) cc_final: 0.7473 (mtmt) REVERT: G 152 LEU cc_start: 0.8838 (mt) cc_final: 0.8473 (mp) REVERT: H 12 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8380 (tm) REVERT: J 54 VAL cc_start: 0.8680 (t) cc_final: 0.8426 (p) REVERT: K 105 GLU cc_start: 0.7916 (mp0) cc_final: 0.7669 (mp0) REVERT: M 83 MET cc_start: 0.8086 (mmp) cc_final: 0.7784 (mmp) REVERT: M 120 ARG cc_start: 0.7933 (mtt-85) cc_final: 0.7104 (mmt-90) REVERT: O 20 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8657 (pt) REVERT: O 59 SER cc_start: 0.8355 (p) cc_final: 0.8138 (m) REVERT: R 62 THR cc_start: 0.8597 (m) cc_final: 0.8014 (p) REVERT: S 120 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.8414 (ptt180) REVERT: U 11 VAL cc_start: 0.8792 (t) cc_final: 0.8478 (m) REVERT: V 140 GLU cc_start: 0.7316 (tp30) cc_final: 0.6814 (mm-30) REVERT: W 14 ARG cc_start: 0.8002 (ptt-90) cc_final: 0.7773 (ptt180) REVERT: X 27 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.7038 (ppp80) REVERT: Y 36 MET cc_start: 0.8557 (mmm) cc_final: 0.8324 (tpt) REVERT: Z 44 ARG cc_start: 0.7241 (ptp-110) cc_final: 0.7034 (ttp80) REVERT: c 109 GLU cc_start: 0.7584 (pm20) cc_final: 0.7211 (pm20) REVERT: c 110 SER cc_start: 0.8814 (t) cc_final: 0.8438 (t) REVERT: d 65 LYS cc_start: 0.8724 (tppp) cc_final: 0.8482 (mtpp) REVERT: d 89 LEU cc_start: 0.8688 (mt) cc_final: 0.8459 (mt) REVERT: d 108 MET cc_start: 0.7904 (ttt) cc_final: 0.7626 (ttt) REVERT: g 53 LYS cc_start: 0.7692 (ptpt) cc_final: 0.7490 (ttpt) REVERT: g 131 LEU cc_start: 0.8483 (mm) cc_final: 0.8190 (mp) REVERT: g 144 MET cc_start: 0.7831 (tpt) cc_final: 0.7565 (ttm) REVERT: h 41 LYS cc_start: 0.7613 (ttpt) cc_final: 0.7229 (ttmt) REVERT: h 42 ASN cc_start: 0.7776 (m-40) cc_final: 0.7435 (m110) REVERT: i 63 LYS cc_start: 0.8672 (mmpt) cc_final: 0.8197 (mmmt) REVERT: i 134 ARG cc_start: 0.7455 (ptm-80) cc_final: 0.7142 (ptm-80) REVERT: p 28 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.6613 (ppt-90) REVERT: q 115 GLU cc_start: 0.7357 (pp20) cc_final: 0.6961 (pp20) REVERT: s 32 LYS cc_start: 0.8524 (ttmm) cc_final: 0.8296 (tttp) REVERT: t 19 LEU cc_start: 0.6926 (OUTLIER) cc_final: 0.6629 (mp) REVERT: t 60 LYS cc_start: 0.8885 (tptm) cc_final: 0.8440 (mtpp) REVERT: t 84 ASN cc_start: 0.8311 (m-40) cc_final: 0.8004 (m-40) REVERT: x 10 LYS cc_start: 0.8524 (mptt) cc_final: 0.8198 (mmmt) REVERT: x 55 ASP cc_start: 0.7022 (t0) cc_final: 0.6663 (t0) REVERT: x 196 GLN cc_start: 0.7426 (tm-30) cc_final: 0.7044 (tm-30) REVERT: x 199 GLU cc_start: 0.7464 (mt-10) cc_final: 0.7230 (mt-10) REVERT: x 200 GLN cc_start: 0.7496 (mp-120) cc_final: 0.7290 (mp10) REVERT: x 268 GLU cc_start: 0.7629 (mp0) cc_final: 0.7089 (mp0) REVERT: x 404 GLU cc_start: 0.7816 (mp0) cc_final: 0.7402 (mp0) REVERT: x 410 LEU cc_start: 0.7657 (OUTLIER) cc_final: 0.7428 (pp) REVERT: x 412 TYR cc_start: 0.8410 (m-80) cc_final: 0.7743 (m-80) REVERT: x 419 GLU cc_start: 0.7233 (mm-30) cc_final: 0.6912 (tp30) REVERT: x 471 ASN cc_start: 0.7430 (m-40) cc_final: 0.6930 (p0) REVERT: x 472 ASP cc_start: 0.7115 (m-30) cc_final: 0.6826 (t70) outliers start: 162 outliers final: 96 residues processed: 1240 average time/residue: 1.3897 time to fit residues: 2938.5603 Evaluate side-chains 1198 residues out of total 5032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 1094 time to evaluate : 5.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 12 THR Chi-restraints excluded: chain 2 residue 32 SER Chi-restraints excluded: chain 2 residue 33 ILE Chi-restraints excluded: chain 2 residue 44 THR Chi-restraints excluded: chain 3 residue 3 LYS Chi-restraints excluded: chain 4 residue 8 LYS Chi-restraints excluded: chain 4 residue 24 MET Chi-restraints excluded: chain 8 residue 15 VAL Chi-restraints excluded: chain 8 residue 51 ASP Chi-restraints excluded: chain 8 residue 85 ASP Chi-restraints excluded: chain 8 residue 171 LEU Chi-restraints excluded: chain 8 residue 209 LEU Chi-restraints excluded: chain 8 residue 216 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 143 SER Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 44 ASN Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 63 ASP Chi-restraints excluded: chain F residue 155 ARG Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 116 SER Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain L residue 123 VAL Chi-restraints excluded: chain M residue 10 ARG Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 50 LEU Chi-restraints excluded: chain O residue 93 ASP Chi-restraints excluded: chain Q residue 112 VAL Chi-restraints excluded: chain R residue 23 VAL Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain S residue 80 VAL Chi-restraints excluded: chain S residue 120 ARG Chi-restraints excluded: chain T residue 79 THR Chi-restraints excluded: chain U residue 8 THR Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 73 VAL Chi-restraints excluded: chain U residue 87 VAL Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 111 VAL Chi-restraints excluded: chain X residue 27 ARG Chi-restraints excluded: chain X residue 53 THR Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 186 LEU Chi-restraints excluded: chain d residue 90 GLU Chi-restraints excluded: chain d residue 93 LEU Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 129 SER Chi-restraints excluded: chain d residue 132 VAL Chi-restraints excluded: chain d residue 175 VAL Chi-restraints excluded: chain d residue 180 LEU Chi-restraints excluded: chain d residue 188 VAL Chi-restraints excluded: chain e residue 68 VAL Chi-restraints excluded: chain e residue 154 ILE Chi-restraints excluded: chain f residue 9 ILE Chi-restraints excluded: chain g residue 87 VAL Chi-restraints excluded: chain g residue 135 VAL Chi-restraints excluded: chain i residue 75 THR Chi-restraints excluded: chain j residue 26 VAL Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain k residue 96 VAL Chi-restraints excluded: chain l residue 47 SER Chi-restraints excluded: chain l residue 61 VAL Chi-restraints excluded: chain m residue 5 VAL Chi-restraints excluded: chain m residue 14 ARG Chi-restraints excluded: chain o residue 7 GLN Chi-restraints excluded: chain p residue 28 ARG Chi-restraints excluded: chain p residue 30 ASP Chi-restraints excluded: chain p residue 34 ILE Chi-restraints excluded: chain p residue 67 THR Chi-restraints excluded: chain q residue 102 ASP Chi-restraints excluded: chain q residue 112 SER Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain s residue 62 VAL Chi-restraints excluded: chain t residue 19 LEU Chi-restraints excluded: chain x residue 25 THR Chi-restraints excluded: chain x residue 47 VAL Chi-restraints excluded: chain x residue 51 MET Chi-restraints excluded: chain x residue 148 LEU Chi-restraints excluded: chain x residue 157 VAL Chi-restraints excluded: chain x residue 173 LEU Chi-restraints excluded: chain x residue 321 VAL Chi-restraints excluded: chain x residue 349 ILE Chi-restraints excluded: chain x residue 356 ASN Chi-restraints excluded: chain x residue 378 VAL Chi-restraints excluded: chain x residue 380 VAL Chi-restraints excluded: chain x residue 410 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1074 random chunks: chunk 542 optimal weight: 4.9990 chunk 302 optimal weight: 10.0000 chunk 811 optimal weight: 9.9990 chunk 664 optimal weight: 50.0000 chunk 269 optimal weight: 7.9990 chunk 977 optimal weight: 5.9990 chunk 1055 optimal weight: 0.0010 chunk 870 optimal weight: 6.9990 chunk 968 optimal weight: 7.9990 chunk 333 optimal weight: 6.9990 chunk 783 optimal weight: 10.0000 overall best weight: 4.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 49 GLN 1 51 HIS ** 6 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 ASN C 122 ASN J 71 HIS J 147 GLN K 3 GLN P 2 ASN ** P 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 77 ASN U 4 HIS ** V 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 43 ASN Z 52 HIS c 143 GLN ** d 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 49 GLN h 93 ASN i 28 GLN i 52 ASN ** k 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 46 HIS ** p 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 255 GLN ** x 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 414 GLN x 449 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 165065 Z= 0.361 Angle : 0.701 18.627 247072 Z= 0.352 Chirality : 0.041 0.297 31508 Planarity : 0.006 0.124 13398 Dihedral : 23.274 178.516 82989 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.64 % Favored : 92.30 % Rotamer: Outliers : 4.35 % Allowed : 13.77 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.32 (0.10), residues: 6062 helix: -2.37 (0.11), residues: 1752 sheet: -1.66 (0.15), residues: 1087 loop : -2.30 (0.10), residues: 3223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP p 59 HIS 0.013 0.002 HIS U 4 PHE 0.023 0.002 PHE c 129 TYR 0.024 0.002 TYR g 85 ARG 0.012 0.001 ARG r 45 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12124 Ramachandran restraints generated. 6062 Oldfield, 0 Emsley, 6062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12124 Ramachandran restraints generated. 6062 Oldfield, 0 Emsley, 6062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1320 residues out of total 5032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 1101 time to evaluate : 6.368 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: 0 38 LYS cc_start: 0.8733 (mmmm) cc_final: 0.8459 (mmmt) REVERT: 8 115 ILE cc_start: 0.7541 (mt) cc_final: 0.7263 (tt) REVERT: 8 151 LYS cc_start: 0.8255 (tptp) cc_final: 0.7910 (tptt) REVERT: 8 198 ARG cc_start: 0.5741 (mtt-85) cc_final: 0.5403 (ttp80) REVERT: 8 199 LEU cc_start: 0.6260 (OUTLIER) cc_final: 0.6036 (mm) REVERT: 8 212 ILE cc_start: 0.8167 (tt) cc_final: 0.7631 (pt) REVERT: C 23 GLU cc_start: 0.7623 (pm20) cc_final: 0.7358 (pm20) REVERT: C 26 ARG cc_start: 0.8304 (ttm170) cc_final: 0.8073 (ttt180) REVERT: C 99 ASP cc_start: 0.8353 (p0) cc_final: 0.8081 (p0) REVERT: C 205 ASN cc_start: 0.8307 (t0) cc_final: 0.8069 (t0) REVERT: E 24 ILE cc_start: 0.8190 (mm) cc_final: 0.7839 (mt) REVERT: E 81 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7658 (ptt90) REVERT: F 34 GLN cc_start: 0.8155 (mt0) cc_final: 0.6942 (mp10) REVERT: G 32 THR cc_start: 0.8227 (t) cc_final: 0.7990 (m) REVERT: G 61 ARG cc_start: 0.7804 (ttt-90) cc_final: 0.7532 (tpp80) REVERT: G 66 HIS cc_start: 0.8216 (t70) cc_final: 0.7768 (t-170) REVERT: G 131 LYS cc_start: 0.7578 (mtmt) cc_final: 0.7284 (mtmt) REVERT: H 12 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8384 (tm) REVERT: J 49 ASP cc_start: 0.8141 (t70) cc_final: 0.7939 (t70) REVERT: K 105 GLU cc_start: 0.7919 (mp0) cc_final: 0.7704 (mp0) REVERT: M 67 ASN cc_start: 0.7846 (p0) cc_final: 0.7627 (p0) REVERT: M 83 MET cc_start: 0.8191 (mmp) cc_final: 0.7928 (mmp) REVERT: M 120 ARG cc_start: 0.7896 (mtt-85) cc_final: 0.6992 (mmt-90) REVERT: O 20 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8572 (pt) REVERT: O 59 SER cc_start: 0.8457 (p) cc_final: 0.8209 (m) REVERT: S 120 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.8405 (ptt180) REVERT: U 11 VAL cc_start: 0.8786 (t) cc_final: 0.8436 (m) REVERT: V 134 GLU cc_start: 0.6140 (OUTLIER) cc_final: 0.5863 (pp20) REVERT: X 27 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.7901 (ppp80) REVERT: Y 36 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.8194 (tpp) REVERT: c 109 GLU cc_start: 0.7620 (pm20) cc_final: 0.7168 (pm20) REVERT: c 110 SER cc_start: 0.8788 (t) cc_final: 0.8404 (t) REVERT: d 65 LYS cc_start: 0.8721 (tppp) cc_final: 0.8364 (mtpp) REVERT: d 89 LEU cc_start: 0.8767 (mt) cc_final: 0.8563 (mt) REVERT: d 108 MET cc_start: 0.7989 (ttt) cc_final: 0.7622 (ttt) REVERT: e 128 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.7460 (ptp-110) REVERT: g 53 LYS cc_start: 0.7776 (ptpt) cc_final: 0.7455 (ttpt) REVERT: g 131 LEU cc_start: 0.8523 (mm) cc_final: 0.8180 (mp) REVERT: g 144 MET cc_start: 0.7844 (tpt) cc_final: 0.7551 (ttm) REVERT: h 41 LYS cc_start: 0.7681 (ttpt) cc_final: 0.7238 (ttmt) REVERT: h 42 ASN cc_start: 0.7702 (m-40) cc_final: 0.7314 (m110) REVERT: i 63 LYS cc_start: 0.8743 (mmpt) cc_final: 0.8196 (mmmt) REVERT: i 130 ARG cc_start: 0.8349 (mtp180) cc_final: 0.7953 (mtp-110) REVERT: p 28 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.6690 (ppt-90) REVERT: q 115 GLU cc_start: 0.7362 (pp20) cc_final: 0.6883 (pp20) REVERT: t 19 LEU cc_start: 0.7032 (OUTLIER) cc_final: 0.6576 (mp) REVERT: t 60 LYS cc_start: 0.8838 (tptm) cc_final: 0.8360 (mtpp) REVERT: t 84 ASN cc_start: 0.8415 (m-40) cc_final: 0.8147 (m110) REVERT: x 10 LYS cc_start: 0.8489 (mptt) cc_final: 0.8203 (mmmt) REVERT: x 55 ASP cc_start: 0.7201 (t0) cc_final: 0.6799 (t0) REVERT: x 196 GLN cc_start: 0.7444 (tm-30) cc_final: 0.7148 (tm-30) REVERT: x 199 GLU cc_start: 0.7497 (mt-10) cc_final: 0.7173 (mt-10) REVERT: x 404 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7581 (mp0) REVERT: x 412 TYR cc_start: 0.8445 (m-80) cc_final: 0.7810 (m-80) REVERT: x 419 GLU cc_start: 0.7338 (mm-30) cc_final: 0.6204 (pm20) REVERT: x 471 ASN cc_start: 0.7208 (m-40) cc_final: 0.6850 (p0) REVERT: x 512 TRP cc_start: 0.8101 (t60) cc_final: 0.7674 (t60) outliers start: 219 outliers final: 163 residues processed: 1201 average time/residue: 1.3588 time to fit residues: 2784.5657 Evaluate side-chains 1225 residues out of total 5032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 1050 time to evaluate : 5.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 25 THR Chi-restraints excluded: chain 1 residue 12 THR Chi-restraints excluded: chain 2 residue 2 THR Chi-restraints excluded: chain 2 residue 23 LEU Chi-restraints excluded: chain 2 residue 32 SER Chi-restraints excluded: chain 2 residue 33 ILE Chi-restraints excluded: chain 3 residue 3 LYS Chi-restraints excluded: chain 3 residue 60 SER Chi-restraints excluded: chain 4 residue 8 LYS Chi-restraints excluded: chain 4 residue 24 MET Chi-restraints excluded: chain 8 residue 15 VAL Chi-restraints excluded: chain 8 residue 46 ILE Chi-restraints excluded: chain 8 residue 51 ASP Chi-restraints excluded: chain 8 residue 56 ASP Chi-restraints excluded: chain 8 residue 85 ASP Chi-restraints excluded: chain 8 residue 171 LEU Chi-restraints excluded: chain 8 residue 199 LEU Chi-restraints excluded: chain 8 residue 207 ARG Chi-restraints excluded: chain 8 residue 209 LEU Chi-restraints excluded: chain 8 residue 216 THR Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain D residue 21 ASN Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 143 SER Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 44 ASN Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 63 ASP Chi-restraints excluded: chain F residue 155 ARG Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 143 LYS Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain K residue 3 GLN Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain L residue 123 VAL Chi-restraints excluded: chain M residue 10 ARG Chi-restraints excluded: chain M residue 31 ASP Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 12 SER Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 50 LEU Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain P residue 16 ILE Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 95 LEU Chi-restraints excluded: chain Q residue 112 VAL Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 30 VAL Chi-restraints excluded: chain S residue 80 VAL Chi-restraints excluded: chain S residue 120 ARG Chi-restraints excluded: chain T residue 36 ASP Chi-restraints excluded: chain T residue 59 THR Chi-restraints excluded: chain T residue 79 THR Chi-restraints excluded: chain U residue 8 THR Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 73 VAL Chi-restraints excluded: chain U residue 87 VAL Chi-restraints excluded: chain V residue 9 LEU Chi-restraints excluded: chain V residue 41 GLU Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 78 THR Chi-restraints excluded: chain V residue 111 VAL Chi-restraints excluded: chain V residue 134 GLU Chi-restraints excluded: chain W residue 71 ILE Chi-restraints excluded: chain X residue 27 ARG Chi-restraints excluded: chain X residue 53 THR Chi-restraints excluded: chain Y residue 36 MET Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 123 LEU Chi-restraints excluded: chain c residue 186 LEU Chi-restraints excluded: chain d residue 73 GLU Chi-restraints excluded: chain d residue 90 GLU Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 129 SER Chi-restraints excluded: chain d residue 132 VAL Chi-restraints excluded: chain d residue 175 VAL Chi-restraints excluded: chain d residue 180 LEU Chi-restraints excluded: chain d residue 188 VAL Chi-restraints excluded: chain e residue 68 VAL Chi-restraints excluded: chain e residue 128 ARG Chi-restraints excluded: chain e residue 154 ILE Chi-restraints excluded: chain f residue 9 ILE Chi-restraints excluded: chain f residue 27 LEU Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 87 VAL Chi-restraints excluded: chain g residue 104 LEU Chi-restraints excluded: chain g residue 135 VAL Chi-restraints excluded: chain i residue 37 VAL Chi-restraints excluded: chain i residue 51 LEU Chi-restraints excluded: chain i residue 75 THR Chi-restraints excluded: chain i residue 85 PHE Chi-restraints excluded: chain j residue 26 VAL Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain k residue 36 THR Chi-restraints excluded: chain k residue 96 VAL Chi-restraints excluded: chain k residue 131 VAL Chi-restraints excluded: chain l residue 47 SER Chi-restraints excluded: chain l residue 49 LEU Chi-restraints excluded: chain l residue 61 VAL Chi-restraints excluded: chain l residue 102 LEU Chi-restraints excluded: chain m residue 4 LEU Chi-restraints excluded: chain m residue 5 VAL Chi-restraints excluded: chain m residue 7 VAL Chi-restraints excluded: chain m residue 14 ARG Chi-restraints excluded: chain m residue 87 TYR Chi-restraints excluded: chain n residue 18 VAL Chi-restraints excluded: chain p residue 28 ARG Chi-restraints excluded: chain p residue 30 ASP Chi-restraints excluded: chain p residue 34 ILE Chi-restraints excluded: chain p residue 35 GLU Chi-restraints excluded: chain q residue 78 GLU Chi-restraints excluded: chain q residue 102 ASP Chi-restraints excluded: chain q residue 112 SER Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain s residue 30 VAL Chi-restraints excluded: chain s residue 62 VAL Chi-restraints excluded: chain t residue 19 LEU Chi-restraints excluded: chain x residue 47 VAL Chi-restraints excluded: chain x residue 48 LEU Chi-restraints excluded: chain x residue 64 LEU Chi-restraints excluded: chain x residue 148 LEU Chi-restraints excluded: chain x residue 157 VAL Chi-restraints excluded: chain x residue 173 LEU Chi-restraints excluded: chain x residue 265 ARG Chi-restraints excluded: chain x residue 299 GLU Chi-restraints excluded: chain x residue 321 VAL Chi-restraints excluded: chain x residue 349 ILE Chi-restraints excluded: chain x residue 356 ASN Chi-restraints excluded: chain x residue 380 VAL Chi-restraints excluded: chain x residue 396 ILE Chi-restraints excluded: chain x residue 404 GLU Chi-restraints excluded: chain x residue 427 SER Chi-restraints excluded: chain x residue 505 THR Chi-restraints excluded: chain x residue 526 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1074 random chunks: chunk 965 optimal weight: 7.9990 chunk 734 optimal weight: 8.9990 chunk 507 optimal weight: 1.9990 chunk 108 optimal weight: 7.9990 chunk 466 optimal weight: 9.9990 chunk 656 optimal weight: 3.9990 chunk 980 optimal weight: 10.0000 chunk 1038 optimal weight: 5.9990 chunk 512 optimal weight: 3.9990 chunk 929 optimal weight: 9.9990 chunk 279 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 ASN C 122 ASN F 162 ASN J 147 GLN K 3 GLN ** P 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 88 GLN T 61 ASN ** V 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 42 ASN h 93 ASN ** k 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 106 ASN ** p 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 47 HIS ** x 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 165065 Z= 0.343 Angle : 0.675 18.100 247072 Z= 0.340 Chirality : 0.040 0.296 31508 Planarity : 0.006 0.124 13398 Dihedral : 23.205 177.775 82989 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.13 % Favored : 92.81 % Rotamer: Outliers : 4.75 % Allowed : 15.26 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.94 (0.10), residues: 6062 helix: -1.94 (0.11), residues: 1739 sheet: -1.51 (0.15), residues: 1080 loop : -2.11 (0.10), residues: 3243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP c 22 HIS 0.009 0.001 HIS C 231 PHE 0.022 0.002 PHE c 129 TYR 0.022 0.002 TYR g 85 ARG 0.011 0.001 ARG C 183 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12124 Ramachandran restraints generated. 6062 Oldfield, 0 Emsley, 6062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12124 Ramachandran restraints generated. 6062 Oldfield, 0 Emsley, 6062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1319 residues out of total 5032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 239 poor density : 1080 time to evaluate : 6.140 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: 0 38 LYS cc_start: 0.8703 (mmmm) cc_final: 0.8483 (mmmt) REVERT: 2 28 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.7645 (ttm110) REVERT: 6 1 MET cc_start: 0.7117 (mtm) cc_final: 0.6818 (mtm) REVERT: 8 115 ILE cc_start: 0.7641 (mt) cc_final: 0.7271 (tt) REVERT: 8 198 ARG cc_start: 0.5706 (mtt-85) cc_final: 0.5248 (ttp80) REVERT: 8 199 LEU cc_start: 0.6205 (OUTLIER) cc_final: 0.5993 (mm) REVERT: C 99 ASP cc_start: 0.8368 (p0) cc_final: 0.7972 (p0) REVERT: C 205 ASN cc_start: 0.8297 (t0) cc_final: 0.8054 (t0) REVERT: E 47 GLN cc_start: 0.9004 (mt0) cc_final: 0.8776 (mt0) REVERT: E 81 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7658 (ptt90) REVERT: E 123 ASP cc_start: 0.7512 (t0) cc_final: 0.7293 (t0) REVERT: G 32 THR cc_start: 0.8231 (t) cc_final: 0.7998 (m) REVERT: G 61 ARG cc_start: 0.7806 (ttt-90) cc_final: 0.7521 (tpp80) REVERT: G 66 HIS cc_start: 0.8181 (t70) cc_final: 0.7768 (t-170) REVERT: G 131 LYS cc_start: 0.7566 (mtmt) cc_final: 0.7246 (mtmt) REVERT: H 12 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8361 (tm) REVERT: J 143 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.8063 (ttpt) REVERT: K 105 GLU cc_start: 0.7919 (mp0) cc_final: 0.7710 (mp0) REVERT: M 83 MET cc_start: 0.8186 (mmp) cc_final: 0.7914 (mmp) REVERT: M 120 ARG cc_start: 0.7877 (mtt-85) cc_final: 0.6887 (mmt-90) REVERT: O 20 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8564 (pt) REVERT: S 120 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.8376 (ptt180) REVERT: U 11 VAL cc_start: 0.8790 (t) cc_final: 0.8442 (m) REVERT: U 17 LYS cc_start: 0.8903 (tttm) cc_final: 0.8604 (ttmt) REVERT: V 44 HIS cc_start: 0.7824 (m170) cc_final: 0.7563 (m90) REVERT: V 134 GLU cc_start: 0.6116 (OUTLIER) cc_final: 0.5707 (pp20) REVERT: X 27 ARG cc_start: 0.8833 (OUTLIER) cc_final: 0.7492 (ppp80) REVERT: c 109 GLU cc_start: 0.7673 (pm20) cc_final: 0.7294 (pm20) REVERT: c 110 SER cc_start: 0.8784 (t) cc_final: 0.8405 (t) REVERT: d 108 MET cc_start: 0.8064 (ttt) cc_final: 0.7693 (ttt) REVERT: e 76 MET cc_start: 0.6941 (tpp) cc_final: 0.6700 (mmt) REVERT: e 104 ARG cc_start: 0.7820 (tpp-160) cc_final: 0.7589 (ttm-80) REVERT: e 128 ARG cc_start: 0.7712 (OUTLIER) cc_final: 0.7486 (ptp-110) REVERT: e 182 GLU cc_start: 0.8064 (mp0) cc_final: 0.7830 (mp0) REVERT: g 53 LYS cc_start: 0.7783 (ptpt) cc_final: 0.7563 (ttpt) REVERT: g 74 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.7192 (tt0) REVERT: g 131 LEU cc_start: 0.8549 (mm) cc_final: 0.8210 (mp) REVERT: g 144 MET cc_start: 0.7916 (tpt) cc_final: 0.7629 (ttm) REVERT: h 42 ASN cc_start: 0.7586 (m110) cc_final: 0.7347 (m110) REVERT: i 63 LYS cc_start: 0.8758 (mmpt) cc_final: 0.8202 (mmmt) REVERT: i 130 ARG cc_start: 0.8294 (mtp180) cc_final: 0.7893 (mtp-110) REVERT: p 28 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.6651 (ppt-90) REVERT: q 115 GLU cc_start: 0.7352 (pp20) cc_final: 0.6862 (pp20) REVERT: t 60 LYS cc_start: 0.8777 (tptm) cc_final: 0.8324 (mtpp) REVERT: t 84 ASN cc_start: 0.8410 (m-40) cc_final: 0.8136 (m-40) REVERT: x 10 LYS cc_start: 0.8381 (mptt) cc_final: 0.8128 (mmmt) REVERT: x 196 GLN cc_start: 0.7792 (tm-30) cc_final: 0.7405 (tm-30) REVERT: x 199 GLU cc_start: 0.7334 (mt-10) cc_final: 0.6812 (mt-10) REVERT: x 404 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7510 (mp0) REVERT: x 410 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7434 (pp) REVERT: x 412 TYR cc_start: 0.8460 (m-80) cc_final: 0.7647 (m-80) REVERT: x 419 GLU cc_start: 0.7371 (mm-30) cc_final: 0.6264 (pm20) REVERT: x 512 TRP cc_start: 0.8151 (t60) cc_final: 0.7939 (t60) outliers start: 239 outliers final: 184 residues processed: 1187 average time/residue: 1.3129 time to fit residues: 2658.0443 Evaluate side-chains 1244 residues out of total 5032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 1046 time to evaluate : 5.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 25 THR Chi-restraints excluded: chain 0 residue 32 VAL Chi-restraints excluded: chain 1 residue 12 THR Chi-restraints excluded: chain 2 residue 2 THR Chi-restraints excluded: chain 2 residue 7 THR Chi-restraints excluded: chain 2 residue 23 LEU Chi-restraints excluded: chain 2 residue 28 ARG Chi-restraints excluded: chain 2 residue 32 SER Chi-restraints excluded: chain 2 residue 33 ILE Chi-restraints excluded: chain 3 residue 3 LYS Chi-restraints excluded: chain 3 residue 50 VAL Chi-restraints excluded: chain 3 residue 60 SER Chi-restraints excluded: chain 4 residue 8 LYS Chi-restraints excluded: chain 8 residue 44 VAL Chi-restraints excluded: chain 8 residue 46 ILE Chi-restraints excluded: chain 8 residue 51 ASP Chi-restraints excluded: chain 8 residue 85 ASP Chi-restraints excluded: chain 8 residue 171 LEU Chi-restraints excluded: chain 8 residue 199 LEU Chi-restraints excluded: chain 8 residue 207 ARG Chi-restraints excluded: chain 8 residue 209 LEU Chi-restraints excluded: chain 8 residue 216 THR Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain D residue 21 ASN Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 143 SER Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 44 ASN Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 63 ASP Chi-restraints excluded: chain F residue 155 ARG Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 143 LYS Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 123 VAL Chi-restraints excluded: chain M residue 10 ARG Chi-restraints excluded: chain M residue 31 ASP Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 74 ASP Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 12 SER Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 50 LEU Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain P residue 14 ASP Chi-restraints excluded: chain P residue 16 ILE Chi-restraints excluded: chain Q residue 16 SER Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 95 LEU Chi-restraints excluded: chain Q residue 112 VAL Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 30 VAL Chi-restraints excluded: chain S residue 80 VAL Chi-restraints excluded: chain S residue 120 ARG Chi-restraints excluded: chain T residue 36 ASP Chi-restraints excluded: chain T residue 59 THR Chi-restraints excluded: chain T residue 79 THR Chi-restraints excluded: chain U residue 8 THR Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 73 VAL Chi-restraints excluded: chain U residue 87 VAL Chi-restraints excluded: chain V residue 9 LEU Chi-restraints excluded: chain V residue 41 GLU Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 65 LEU Chi-restraints excluded: chain V residue 78 THR Chi-restraints excluded: chain V residue 111 VAL Chi-restraints excluded: chain V residue 134 GLU Chi-restraints excluded: chain W residue 12 ASN Chi-restraints excluded: chain W residue 71 ILE Chi-restraints excluded: chain X residue 27 ARG Chi-restraints excluded: chain X residue 53 THR Chi-restraints excluded: chain Y residue 9 GLU Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 123 LEU Chi-restraints excluded: chain c residue 186 LEU Chi-restraints excluded: chain d residue 73 GLU Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 129 SER Chi-restraints excluded: chain d residue 132 VAL Chi-restraints excluded: chain d residue 175 VAL Chi-restraints excluded: chain d residue 180 LEU Chi-restraints excluded: chain d residue 188 VAL Chi-restraints excluded: chain e residue 68 VAL Chi-restraints excluded: chain e residue 108 ILE Chi-restraints excluded: chain e residue 124 VAL Chi-restraints excluded: chain e residue 128 ARG Chi-restraints excluded: chain e residue 154 ILE Chi-restraints excluded: chain f residue 9 ILE Chi-restraints excluded: chain f residue 27 LEU Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 74 GLU Chi-restraints excluded: chain g residue 87 VAL Chi-restraints excluded: chain g residue 104 LEU Chi-restraints excluded: chain g residue 135 VAL Chi-restraints excluded: chain i residue 29 THR Chi-restraints excluded: chain i residue 37 VAL Chi-restraints excluded: chain i residue 51 LEU Chi-restraints excluded: chain i residue 54 ARG Chi-restraints excluded: chain i residue 75 THR Chi-restraints excluded: chain i residue 85 PHE Chi-restraints excluded: chain j residue 26 VAL Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain k residue 36 THR Chi-restraints excluded: chain k residue 96 VAL Chi-restraints excluded: chain k residue 131 VAL Chi-restraints excluded: chain l residue 33 VAL Chi-restraints excluded: chain l residue 47 SER Chi-restraints excluded: chain l residue 49 LEU Chi-restraints excluded: chain l residue 61 VAL Chi-restraints excluded: chain m residue 4 LEU Chi-restraints excluded: chain m residue 5 VAL Chi-restraints excluded: chain m residue 7 VAL Chi-restraints excluded: chain m residue 14 ARG Chi-restraints excluded: chain m residue 87 TYR Chi-restraints excluded: chain n residue 53 LEU Chi-restraints excluded: chain p residue 28 ARG Chi-restraints excluded: chain p residue 30 ASP Chi-restraints excluded: chain p residue 34 ILE Chi-restraints excluded: chain p residue 35 GLU Chi-restraints excluded: chain p residue 67 THR Chi-restraints excluded: chain q residue 78 GLU Chi-restraints excluded: chain q residue 102 ASP Chi-restraints excluded: chain q residue 112 SER Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain s residue 67 VAL Chi-restraints excluded: chain x residue 25 THR Chi-restraints excluded: chain x residue 47 VAL Chi-restraints excluded: chain x residue 48 LEU Chi-restraints excluded: chain x residue 51 MET Chi-restraints excluded: chain x residue 64 LEU Chi-restraints excluded: chain x residue 148 LEU Chi-restraints excluded: chain x residue 157 VAL Chi-restraints excluded: chain x residue 160 LEU Chi-restraints excluded: chain x residue 164 GLU Chi-restraints excluded: chain x residue 173 LEU Chi-restraints excluded: chain x residue 191 ASP Chi-restraints excluded: chain x residue 265 ARG Chi-restraints excluded: chain x residue 270 LEU Chi-restraints excluded: chain x residue 294 MET Chi-restraints excluded: chain x residue 321 VAL Chi-restraints excluded: chain x residue 336 LEU Chi-restraints excluded: chain x residue 349 ILE Chi-restraints excluded: chain x residue 356 ASN Chi-restraints excluded: chain x residue 378 VAL Chi-restraints excluded: chain x residue 380 VAL Chi-restraints excluded: chain x residue 404 GLU Chi-restraints excluded: chain x residue 410 LEU Chi-restraints excluded: chain x residue 420 VAL Chi-restraints excluded: chain x residue 427 SER Chi-restraints excluded: chain x residue 505 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1074 random chunks: chunk 864 optimal weight: 10.0000 chunk 589 optimal weight: 8.9990 chunk 15 optimal weight: 6.9990 chunk 772 optimal weight: 20.0000 chunk 428 optimal weight: 0.9980 chunk 885 optimal weight: 7.9990 chunk 717 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 530 optimal weight: 9.9990 chunk 931 optimal weight: 30.0000 chunk 261 optimal weight: 10.0000 overall best weight: 6.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 42 HIS 7 17 ASN 7 23 ASN C 70 ASN C 122 ASN D 15 GLN J 147 GLN L 106 ASN M 17 GLN Q 77 ASN T 61 ASN ** V 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 93 ASN ** k 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 106 ASN ** p 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 56 ASN r 59 GLN s 83 HIS ** x 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 165065 Z= 0.452 Angle : 0.750 18.448 247072 Z= 0.372 Chirality : 0.043 0.302 31508 Planarity : 0.006 0.125 13398 Dihedral : 23.220 178.048 82989 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.25 % Favored : 91.69 % Rotamer: Outliers : 5.58 % Allowed : 16.24 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.85 (0.10), residues: 6062 helix: -1.80 (0.11), residues: 1747 sheet: -1.46 (0.15), residues: 1073 loop : -2.09 (0.10), residues: 3242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP c 22 HIS 0.011 0.002 HIS U 4 PHE 0.025 0.002 PHE c 129 TYR 0.026 0.002 TYR g 85 ARG 0.011 0.001 ARG 1 8 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12124 Ramachandran restraints generated. 6062 Oldfield, 0 Emsley, 6062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12124 Ramachandran restraints generated. 6062 Oldfield, 0 Emsley, 6062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1365 residues out of total 5032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 281 poor density : 1084 time to evaluate : 5.926 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: 0 38 LYS cc_start: 0.8733 (mmmm) cc_final: 0.8528 (mmmt) REVERT: 2 28 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.7709 (ttm110) REVERT: 8 115 ILE cc_start: 0.7671 (mt) cc_final: 0.7315 (tt) REVERT: 8 151 LYS cc_start: 0.8095 (tppt) cc_final: 0.7877 (tptt) REVERT: 8 160 LYS cc_start: 0.8010 (tmtt) cc_final: 0.7555 (tmtt) REVERT: 8 198 ARG cc_start: 0.5633 (mtt-85) cc_final: 0.5149 (ttp80) REVERT: 8 199 LEU cc_start: 0.6234 (OUTLIER) cc_final: 0.6012 (mm) REVERT: C 70 ASN cc_start: 0.7685 (OUTLIER) cc_final: 0.7380 (p0) REVERT: C 99 ASP cc_start: 0.8385 (p0) cc_final: 0.8011 (p0) REVERT: C 205 ASN cc_start: 0.8347 (t0) cc_final: 0.8091 (t0) REVERT: E 24 ILE cc_start: 0.8164 (mm) cc_final: 0.7835 (mt) REVERT: E 47 GLN cc_start: 0.9042 (mt0) cc_final: 0.8631 (mt0) REVERT: E 81 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.7708 (ptt90) REVERT: E 123 ASP cc_start: 0.7619 (t0) cc_final: 0.7261 (t0) REVERT: F 157 ARG cc_start: 0.7506 (ptp90) cc_final: 0.7198 (ptp90) REVERT: F 170 ASP cc_start: 0.7526 (t0) cc_final: 0.7325 (t0) REVERT: G 32 THR cc_start: 0.8228 (t) cc_final: 0.7999 (m) REVERT: G 61 ARG cc_start: 0.7827 (ttt-90) cc_final: 0.7614 (tpp-160) REVERT: G 66 HIS cc_start: 0.8242 (t70) cc_final: 0.7780 (t-170) REVERT: G 131 LYS cc_start: 0.7606 (mtmt) cc_final: 0.7277 (mtmt) REVERT: H 12 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8390 (tm) REVERT: K 105 GLU cc_start: 0.7913 (mp0) cc_final: 0.7687 (mp0) REVERT: M 10 ARG cc_start: 0.7523 (OUTLIER) cc_final: 0.7240 (mtm-85) REVERT: M 67 ASN cc_start: 0.8071 (p0) cc_final: 0.7773 (p0) REVERT: M 83 MET cc_start: 0.8247 (mmp) cc_final: 0.8003 (mmp) REVERT: M 120 ARG cc_start: 0.7828 (mtt-85) cc_final: 0.7283 (mtt90) REVERT: O 20 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8566 (pt) REVERT: O 59 SER cc_start: 0.8609 (OUTLIER) cc_final: 0.8348 (m) REVERT: S 96 ARG cc_start: 0.7356 (ttm-80) cc_final: 0.7155 (ttm-80) REVERT: S 120 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.8415 (ptt180) REVERT: T 41 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7755 (tt0) REVERT: U 17 LYS cc_start: 0.8924 (tttm) cc_final: 0.8608 (ttmt) REVERT: V 44 HIS cc_start: 0.7794 (m170) cc_final: 0.7484 (m90) REVERT: V 134 GLU cc_start: 0.6270 (OUTLIER) cc_final: 0.5836 (pp20) REVERT: Y 36 MET cc_start: 0.8413 (tpp) cc_final: 0.8142 (tpp) REVERT: c 30 GLU cc_start: 0.7539 (tp30) cc_final: 0.7196 (tp30) REVERT: c 58 ARG cc_start: 0.7507 (OUTLIER) cc_final: 0.6726 (mtp-110) REVERT: e 76 MET cc_start: 0.6974 (tpp) cc_final: 0.6704 (mmt) REVERT: e 103 PHE cc_start: 0.8331 (p90) cc_final: 0.8043 (p90) REVERT: e 104 ARG cc_start: 0.7817 (tpp-160) cc_final: 0.7497 (ttm-80) REVERT: e 128 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.7589 (ptp-110) REVERT: e 182 GLU cc_start: 0.8070 (mp0) cc_final: 0.7830 (mp0) REVERT: g 66 LEU cc_start: 0.7017 (OUTLIER) cc_final: 0.6454 (tt) REVERT: g 86 GLN cc_start: 0.7983 (mp10) cc_final: 0.7716 (mp10) REVERT: g 131 LEU cc_start: 0.8568 (mm) cc_final: 0.8212 (mp) REVERT: g 144 MET cc_start: 0.7905 (tpt) cc_final: 0.7667 (ttm) REVERT: i 63 LYS cc_start: 0.8809 (mmpt) cc_final: 0.8239 (mmmt) REVERT: i 130 ARG cc_start: 0.8354 (mtp180) cc_final: 0.8099 (mtm180) REVERT: j 49 TYR cc_start: 0.8459 (m-80) cc_final: 0.7643 (m-80) REVERT: p 28 ARG cc_start: 0.7792 (OUTLIER) cc_final: 0.7083 (ppt-90) REVERT: p 74 LEU cc_start: 0.7113 (mt) cc_final: 0.6872 (mp) REVERT: q 115 GLU cc_start: 0.7354 (pp20) cc_final: 0.6877 (pp20) REVERT: t 60 LYS cc_start: 0.8805 (tptm) cc_final: 0.8297 (mtpp) REVERT: t 84 ASN cc_start: 0.8342 (m-40) cc_final: 0.8083 (m-40) REVERT: x 4 PHE cc_start: 0.8284 (m-10) cc_final: 0.7702 (m-10) REVERT: x 10 LYS cc_start: 0.8404 (mptt) cc_final: 0.8117 (mmmt) REVERT: x 145 MET cc_start: 0.7022 (mmm) cc_final: 0.6707 (mmp) REVERT: x 175 LEU cc_start: 0.8609 (mm) cc_final: 0.8315 (mm) REVERT: x 196 GLN cc_start: 0.7873 (tm-30) cc_final: 0.7409 (tm-30) REVERT: x 199 GLU cc_start: 0.7166 (mt-10) cc_final: 0.6827 (mt-10) REVERT: x 404 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7652 (mp0) REVERT: x 410 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7451 (pp) REVERT: x 412 TYR cc_start: 0.8456 (m-80) cc_final: 0.7712 (m-80) REVERT: x 419 GLU cc_start: 0.7418 (mm-30) cc_final: 0.6415 (pm20) outliers start: 281 outliers final: 207 residues processed: 1218 average time/residue: 1.2476 time to fit residues: 2606.6091 Evaluate side-chains 1293 residues out of total 5032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 1069 time to evaluate : 5.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 25 THR Chi-restraints excluded: chain 0 residue 32 VAL Chi-restraints excluded: chain 1 residue 12 THR Chi-restraints excluded: chain 1 residue 24 ILE Chi-restraints excluded: chain 2 residue 2 THR Chi-restraints excluded: chain 2 residue 7 THR Chi-restraints excluded: chain 2 residue 28 ARG Chi-restraints excluded: chain 2 residue 32 SER Chi-restraints excluded: chain 2 residue 33 ILE Chi-restraints excluded: chain 2 residue 44 THR Chi-restraints excluded: chain 3 residue 3 LYS Chi-restraints excluded: chain 3 residue 50 VAL Chi-restraints excluded: chain 3 residue 60 SER Chi-restraints excluded: chain 4 residue 24 MET Chi-restraints excluded: chain 8 residue 9 ARG Chi-restraints excluded: chain 8 residue 44 VAL Chi-restraints excluded: chain 8 residue 46 ILE Chi-restraints excluded: chain 8 residue 51 ASP Chi-restraints excluded: chain 8 residue 85 ASP Chi-restraints excluded: chain 8 residue 171 LEU Chi-restraints excluded: chain 8 residue 193 ILE Chi-restraints excluded: chain 8 residue 199 LEU Chi-restraints excluded: chain 8 residue 205 LYS Chi-restraints excluded: chain 8 residue 209 LEU Chi-restraints excluded: chain 8 residue 216 THR Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain D residue 21 ASN Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 143 SER Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 44 ASN Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 63 ASP Chi-restraints excluded: chain F residue 155 ARG Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 123 VAL Chi-restraints excluded: chain M residue 10 ARG Chi-restraints excluded: chain M residue 31 ASP Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 12 SER Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 50 LEU Chi-restraints excluded: chain O residue 59 SER Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain P residue 16 ILE Chi-restraints excluded: chain Q residue 16 SER Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 95 LEU Chi-restraints excluded: chain Q residue 112 VAL Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 30 VAL Chi-restraints excluded: chain S residue 80 VAL Chi-restraints excluded: chain S residue 120 ARG Chi-restraints excluded: chain T residue 36 ASP Chi-restraints excluded: chain T residue 41 GLN Chi-restraints excluded: chain T residue 59 THR Chi-restraints excluded: chain T residue 79 THR Chi-restraints excluded: chain U residue 8 THR Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 20 LYS Chi-restraints excluded: chain U residue 73 VAL Chi-restraints excluded: chain U residue 83 ILE Chi-restraints excluded: chain U residue 87 VAL Chi-restraints excluded: chain V residue 9 LEU Chi-restraints excluded: chain V residue 41 GLU Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 65 LEU Chi-restraints excluded: chain V residue 77 LEU Chi-restraints excluded: chain V residue 78 THR Chi-restraints excluded: chain V residue 111 VAL Chi-restraints excluded: chain V residue 134 GLU Chi-restraints excluded: chain W residue 12 ASN Chi-restraints excluded: chain W residue 71 ILE Chi-restraints excluded: chain X residue 21 SER Chi-restraints excluded: chain X residue 27 ARG Chi-restraints excluded: chain X residue 53 THR Chi-restraints excluded: chain Y residue 9 GLU Chi-restraints excluded: chain Y residue 38 THR Chi-restraints excluded: chain Z residue 9 VAL Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain Z residue 57 GLU Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 57 GLU Chi-restraints excluded: chain c residue 58 ARG Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 123 LEU Chi-restraints excluded: chain c residue 186 LEU Chi-restraints excluded: chain d residue 62 VAL Chi-restraints excluded: chain d residue 73 GLU Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 129 SER Chi-restraints excluded: chain d residue 132 VAL Chi-restraints excluded: chain d residue 140 VAL Chi-restraints excluded: chain d residue 175 VAL Chi-restraints excluded: chain d residue 180 LEU Chi-restraints excluded: chain d residue 188 VAL Chi-restraints excluded: chain e residue 68 VAL Chi-restraints excluded: chain e residue 108 ILE Chi-restraints excluded: chain e residue 128 ARG Chi-restraints excluded: chain e residue 154 ILE Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 8 VAL Chi-restraints excluded: chain f residue 9 ILE Chi-restraints excluded: chain f residue 27 LEU Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 66 LEU Chi-restraints excluded: chain g residue 87 VAL Chi-restraints excluded: chain g residue 94 ASP Chi-restraints excluded: chain g residue 108 SER Chi-restraints excluded: chain g residue 135 VAL Chi-restraints excluded: chain h residue 73 SER Chi-restraints excluded: chain h residue 96 ARG Chi-restraints excluded: chain i residue 29 THR Chi-restraints excluded: chain i residue 37 VAL Chi-restraints excluded: chain i residue 51 LEU Chi-restraints excluded: chain i residue 75 THR Chi-restraints excluded: chain i residue 85 PHE Chi-restraints excluded: chain j residue 26 VAL Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain k residue 66 ARG Chi-restraints excluded: chain k residue 89 VAL Chi-restraints excluded: chain k residue 96 VAL Chi-restraints excluded: chain k residue 131 VAL Chi-restraints excluded: chain l residue 33 VAL Chi-restraints excluded: chain l residue 47 SER Chi-restraints excluded: chain l residue 49 LEU Chi-restraints excluded: chain l residue 61 VAL Chi-restraints excluded: chain l residue 78 SER Chi-restraints excluded: chain m residue 4 LEU Chi-restraints excluded: chain m residue 5 VAL Chi-restraints excluded: chain m residue 7 VAL Chi-restraints excluded: chain m residue 14 ARG Chi-restraints excluded: chain m residue 69 ASP Chi-restraints excluded: chain m residue 87 TYR Chi-restraints excluded: chain n residue 53 LEU Chi-restraints excluded: chain p residue 28 ARG Chi-restraints excluded: chain p residue 30 ASP Chi-restraints excluded: chain p residue 34 ILE Chi-restraints excluded: chain p residue 35 GLU Chi-restraints excluded: chain p residue 67 THR Chi-restraints excluded: chain q residue 78 GLU Chi-restraints excluded: chain q residue 102 ASP Chi-restraints excluded: chain q residue 112 SER Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain s residue 30 VAL Chi-restraints excluded: chain s residue 62 VAL Chi-restraints excluded: chain s residue 67 VAL Chi-restraints excluded: chain t residue 19 LEU Chi-restraints excluded: chain t residue 27 SER Chi-restraints excluded: chain x residue 25 THR Chi-restraints excluded: chain x residue 47 VAL Chi-restraints excluded: chain x residue 48 LEU Chi-restraints excluded: chain x residue 148 LEU Chi-restraints excluded: chain x residue 157 VAL Chi-restraints excluded: chain x residue 160 LEU Chi-restraints excluded: chain x residue 164 GLU Chi-restraints excluded: chain x residue 173 LEU Chi-restraints excluded: chain x residue 191 ASP Chi-restraints excluded: chain x residue 265 ARG Chi-restraints excluded: chain x residue 266 LEU Chi-restraints excluded: chain x residue 321 VAL Chi-restraints excluded: chain x residue 336 LEU Chi-restraints excluded: chain x residue 349 ILE Chi-restraints excluded: chain x residue 356 ASN Chi-restraints excluded: chain x residue 378 VAL Chi-restraints excluded: chain x residue 380 VAL Chi-restraints excluded: chain x residue 390 ASP Chi-restraints excluded: chain x residue 396 ILE Chi-restraints excluded: chain x residue 404 GLU Chi-restraints excluded: chain x residue 410 LEU Chi-restraints excluded: chain x residue 427 SER Chi-restraints excluded: chain x residue 473 LEU Chi-restraints excluded: chain x residue 505 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1074 random chunks: chunk 349 optimal weight: 10.0000 chunk 934 optimal weight: 2.9990 chunk 205 optimal weight: 100.0000 chunk 609 optimal weight: 6.9990 chunk 256 optimal weight: 5.9990 chunk 1039 optimal weight: 5.9990 chunk 862 optimal weight: 1.9990 chunk 481 optimal weight: 7.9990 chunk 86 optimal weight: 10.0000 chunk 343 optimal weight: 6.9990 chunk 545 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 ASN F 142 GLN ** J 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 106 ASN M 17 GLN Q 44 ASN ** V 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 3 GLN ** d 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 93 ASN i 52 ASN ** k 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 106 ASN ** p 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 57 HIS s 83 HIS x 88 ASN ** x 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 165065 Z= 0.288 Angle : 0.644 18.337 247072 Z= 0.326 Chirality : 0.038 0.290 31508 Planarity : 0.005 0.123 13398 Dihedral : 23.164 177.630 82989 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.99 % Favored : 92.96 % Rotamer: Outliers : 4.91 % Allowed : 17.57 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.57 (0.10), residues: 6062 helix: -1.49 (0.12), residues: 1744 sheet: -1.33 (0.15), residues: 1074 loop : -1.96 (0.10), residues: 3244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP x 512 HIS 0.008 0.001 HIS U 4 PHE 0.016 0.002 PHE c 129 TYR 0.017 0.002 TYR g 85 ARG 0.012 0.001 ARG 1 8 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12124 Ramachandran restraints generated. 6062 Oldfield, 0 Emsley, 6062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12124 Ramachandran restraints generated. 6062 Oldfield, 0 Emsley, 6062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1320 residues out of total 5032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 247 poor density : 1073 time to evaluate : 5.705 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: 2 28 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.7702 (ttm110) REVERT: 2 31 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7925 (mtm-85) REVERT: 8 115 ILE cc_start: 0.7694 (mt) cc_final: 0.7364 (tt) REVERT: 8 160 LYS cc_start: 0.7920 (tmtt) cc_final: 0.7424 (tmtt) REVERT: 8 164 ARG cc_start: 0.5705 (tpt170) cc_final: 0.5410 (tpt170) REVERT: 8 198 ARG cc_start: 0.5618 (mtt-85) cc_final: 0.5119 (ttp80) REVERT: 8 199 LEU cc_start: 0.6194 (OUTLIER) cc_final: 0.5972 (mm) REVERT: C 99 ASP cc_start: 0.8341 (p0) cc_final: 0.8042 (p0) REVERT: C 205 ASN cc_start: 0.8280 (t0) cc_final: 0.7893 (t0) REVERT: E 24 ILE cc_start: 0.8140 (mm) cc_final: 0.7814 (mt) REVERT: E 81 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7701 (ptt90) REVERT: E 123 ASP cc_start: 0.7607 (t0) cc_final: 0.7327 (t0) REVERT: F 170 ASP cc_start: 0.7615 (t0) cc_final: 0.7404 (t0) REVERT: G 32 THR cc_start: 0.8215 (t) cc_final: 0.7991 (m) REVERT: G 66 HIS cc_start: 0.8112 (t70) cc_final: 0.7650 (t-170) REVERT: G 131 LYS cc_start: 0.7526 (mtmt) cc_final: 0.7196 (mtmt) REVERT: H 12 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8351 (tm) REVERT: K 105 GLU cc_start: 0.7922 (mp0) cc_final: 0.7719 (mp0) REVERT: M 10 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.7213 (mtm-85) REVERT: M 83 MET cc_start: 0.8166 (mmp) cc_final: 0.7892 (mmp) REVERT: M 120 ARG cc_start: 0.7804 (mtt-85) cc_final: 0.7225 (mtt90) REVERT: O 20 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8551 (pt) REVERT: O 59 SER cc_start: 0.8498 (m) cc_final: 0.8240 (m) REVERT: S 120 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.8362 (ptt180) REVERT: U 11 VAL cc_start: 0.8800 (t) cc_final: 0.8449 (m) REVERT: U 17 LYS cc_start: 0.8907 (tttm) cc_final: 0.8610 (ttmt) REVERT: V 44 HIS cc_start: 0.7754 (m170) cc_final: 0.7461 (m90) REVERT: V 134 GLU cc_start: 0.6165 (OUTLIER) cc_final: 0.5547 (pp20) REVERT: X 27 ARG cc_start: 0.8813 (OUTLIER) cc_final: 0.7136 (ppp80) REVERT: Y 10 LEU cc_start: 0.8964 (mp) cc_final: 0.8655 (mp) REVERT: Y 36 MET cc_start: 0.8455 (tpp) cc_final: 0.8162 (tpp) REVERT: c 30 GLU cc_start: 0.7516 (tp30) cc_final: 0.7176 (tp30) REVERT: c 58 ARG cc_start: 0.7551 (OUTLIER) cc_final: 0.6090 (mtp-110) REVERT: c 109 GLU cc_start: 0.7780 (pm20) cc_final: 0.7118 (pm20) REVERT: c 110 SER cc_start: 0.8688 (t) cc_final: 0.8270 (t) REVERT: d 197 GLU cc_start: 0.7133 (mt-10) cc_final: 0.6723 (mt-10) REVERT: e 104 ARG cc_start: 0.7844 (tpp-160) cc_final: 0.7495 (ttm-80) REVERT: e 128 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.7428 (ptp-110) REVERT: e 143 ARG cc_start: 0.7834 (mtp180) cc_final: 0.7479 (mtp85) REVERT: e 182 GLU cc_start: 0.8074 (mp0) cc_final: 0.7756 (mp0) REVERT: g 66 LEU cc_start: 0.6858 (OUTLIER) cc_final: 0.6292 (tt) REVERT: g 131 LEU cc_start: 0.8547 (mm) cc_final: 0.8213 (mp) REVERT: g 144 MET cc_start: 0.7925 (tpt) cc_final: 0.7644 (ttm) REVERT: g 149 ARG cc_start: 0.7573 (mtm180) cc_final: 0.6969 (ttp-110) REVERT: i 63 LYS cc_start: 0.8793 (mmpt) cc_final: 0.8240 (mmmt) REVERT: i 130 ARG cc_start: 0.8301 (mtp180) cc_final: 0.8026 (mtm110) REVERT: n 26 LYS cc_start: 0.8105 (OUTLIER) cc_final: 0.7721 (ttpp) REVERT: o 82 ILE cc_start: 0.8161 (OUTLIER) cc_final: 0.7810 (mm) REVERT: p 28 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.6673 (ppt-90) REVERT: p 74 LEU cc_start: 0.7050 (mt) cc_final: 0.6835 (mp) REVERT: q 115 GLU cc_start: 0.7338 (pp20) cc_final: 0.6860 (pp20) REVERT: x 4 PHE cc_start: 0.8236 (m-10) cc_final: 0.7653 (m-10) REVERT: x 175 LEU cc_start: 0.8649 (mm) cc_final: 0.8379 (mm) REVERT: x 184 ASP cc_start: 0.7214 (t0) cc_final: 0.6954 (t70) REVERT: x 196 GLN cc_start: 0.7798 (tm-30) cc_final: 0.7263 (tm-30) REVERT: x 199 GLU cc_start: 0.7130 (mt-10) cc_final: 0.6774 (mt-10) REVERT: x 404 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7702 (mp0) REVERT: x 410 LEU cc_start: 0.7632 (OUTLIER) cc_final: 0.7426 (pp) REVERT: x 412 TYR cc_start: 0.8261 (m-80) cc_final: 0.7639 (m-80) REVERT: x 419 GLU cc_start: 0.7372 (mm-30) cc_final: 0.6391 (pm20) outliers start: 247 outliers final: 194 residues processed: 1199 average time/residue: 1.2324 time to fit residues: 2527.0079 Evaluate side-chains 1251 residues out of total 5032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 1039 time to evaluate : 5.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 25 THR Chi-restraints excluded: chain 0 residue 32 VAL Chi-restraints excluded: chain 1 residue 12 THR Chi-restraints excluded: chain 1 residue 24 ILE Chi-restraints excluded: chain 2 residue 2 THR Chi-restraints excluded: chain 2 residue 23 LEU Chi-restraints excluded: chain 2 residue 28 ARG Chi-restraints excluded: chain 2 residue 31 ARG Chi-restraints excluded: chain 2 residue 32 SER Chi-restraints excluded: chain 3 residue 3 LYS Chi-restraints excluded: chain 3 residue 50 VAL Chi-restraints excluded: chain 3 residue 60 SER Chi-restraints excluded: chain 4 residue 24 MET Chi-restraints excluded: chain 8 residue 44 VAL Chi-restraints excluded: chain 8 residue 46 ILE Chi-restraints excluded: chain 8 residue 51 ASP Chi-restraints excluded: chain 8 residue 85 ASP Chi-restraints excluded: chain 8 residue 171 LEU Chi-restraints excluded: chain 8 residue 193 ILE Chi-restraints excluded: chain 8 residue 199 LEU Chi-restraints excluded: chain 8 residue 209 LEU Chi-restraints excluded: chain 8 residue 216 THR Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 143 SER Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 44 ASN Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 63 ASP Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain F residue 155 ARG Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain L residue 106 ASN Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 123 VAL Chi-restraints excluded: chain M residue 10 ARG Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 50 LEU Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain P residue 16 ILE Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 95 LEU Chi-restraints excluded: chain Q residue 112 VAL Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 30 VAL Chi-restraints excluded: chain S residue 80 VAL Chi-restraints excluded: chain S residue 120 ARG Chi-restraints excluded: chain T residue 36 ASP Chi-restraints excluded: chain T residue 59 THR Chi-restraints excluded: chain T residue 79 THR Chi-restraints excluded: chain U residue 8 THR Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 73 VAL Chi-restraints excluded: chain U residue 83 ILE Chi-restraints excluded: chain U residue 87 VAL Chi-restraints excluded: chain V residue 41 GLU Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 65 LEU Chi-restraints excluded: chain V residue 77 LEU Chi-restraints excluded: chain V residue 78 THR Chi-restraints excluded: chain V residue 111 VAL Chi-restraints excluded: chain V residue 134 GLU Chi-restraints excluded: chain W residue 12 ASN Chi-restraints excluded: chain W residue 71 ILE Chi-restraints excluded: chain X residue 27 ARG Chi-restraints excluded: chain X residue 53 THR Chi-restraints excluded: chain Y residue 38 THR Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 57 GLU Chi-restraints excluded: chain c residue 58 ARG Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 186 LEU Chi-restraints excluded: chain d residue 62 VAL Chi-restraints excluded: chain d residue 73 GLU Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 129 SER Chi-restraints excluded: chain d residue 132 VAL Chi-restraints excluded: chain d residue 140 VAL Chi-restraints excluded: chain d residue 175 VAL Chi-restraints excluded: chain d residue 180 LEU Chi-restraints excluded: chain d residue 185 GLN Chi-restraints excluded: chain d residue 188 VAL Chi-restraints excluded: chain e residue 108 ILE Chi-restraints excluded: chain e residue 128 ARG Chi-restraints excluded: chain e residue 154 ILE Chi-restraints excluded: chain f residue 8 VAL Chi-restraints excluded: chain f residue 9 ILE Chi-restraints excluded: chain f residue 27 LEU Chi-restraints excluded: chain g residue 66 LEU Chi-restraints excluded: chain g residue 87 VAL Chi-restraints excluded: chain g residue 104 LEU Chi-restraints excluded: chain g residue 108 SER Chi-restraints excluded: chain g residue 135 VAL Chi-restraints excluded: chain h residue 96 ARG Chi-restraints excluded: chain h residue 112 LEU Chi-restraints excluded: chain i residue 29 THR Chi-restraints excluded: chain i residue 37 VAL Chi-restraints excluded: chain i residue 51 LEU Chi-restraints excluded: chain i residue 54 ARG Chi-restraints excluded: chain i residue 75 THR Chi-restraints excluded: chain i residue 85 PHE Chi-restraints excluded: chain j residue 15 HIS Chi-restraints excluded: chain j residue 26 VAL Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain k residue 36 THR Chi-restraints excluded: chain k residue 66 ARG Chi-restraints excluded: chain k residue 96 VAL Chi-restraints excluded: chain k residue 115 LEU Chi-restraints excluded: chain k residue 131 VAL Chi-restraints excluded: chain l residue 33 VAL Chi-restraints excluded: chain l residue 47 SER Chi-restraints excluded: chain l residue 49 LEU Chi-restraints excluded: chain l residue 61 VAL Chi-restraints excluded: chain l residue 78 SER Chi-restraints excluded: chain l residue 115 SER Chi-restraints excluded: chain m residue 4 LEU Chi-restraints excluded: chain m residue 5 VAL Chi-restraints excluded: chain m residue 7 VAL Chi-restraints excluded: chain m residue 14 ARG Chi-restraints excluded: chain m residue 17 VAL Chi-restraints excluded: chain m residue 47 ASP Chi-restraints excluded: chain m residue 87 TYR Chi-restraints excluded: chain m residue 109 THR Chi-restraints excluded: chain n residue 18 VAL Chi-restraints excluded: chain n residue 26 LYS Chi-restraints excluded: chain o residue 82 ILE Chi-restraints excluded: chain p residue 28 ARG Chi-restraints excluded: chain p residue 30 ASP Chi-restraints excluded: chain p residue 34 ILE Chi-restraints excluded: chain p residue 35 GLU Chi-restraints excluded: chain p residue 67 THR Chi-restraints excluded: chain q residue 78 GLU Chi-restraints excluded: chain q residue 102 ASP Chi-restraints excluded: chain q residue 112 SER Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 62 VAL Chi-restraints excluded: chain s residue 67 VAL Chi-restraints excluded: chain t residue 19 LEU Chi-restraints excluded: chain t residue 27 SER Chi-restraints excluded: chain x residue 25 THR Chi-restraints excluded: chain x residue 47 VAL Chi-restraints excluded: chain x residue 48 LEU Chi-restraints excluded: chain x residue 51 MET Chi-restraints excluded: chain x residue 143 GLN Chi-restraints excluded: chain x residue 148 LEU Chi-restraints excluded: chain x residue 157 VAL Chi-restraints excluded: chain x residue 160 LEU Chi-restraints excluded: chain x residue 173 LEU Chi-restraints excluded: chain x residue 183 LEU Chi-restraints excluded: chain x residue 191 ASP Chi-restraints excluded: chain x residue 265 ARG Chi-restraints excluded: chain x residue 266 LEU Chi-restraints excluded: chain x residue 321 VAL Chi-restraints excluded: chain x residue 336 LEU Chi-restraints excluded: chain x residue 349 ILE Chi-restraints excluded: chain x residue 356 ASN Chi-restraints excluded: chain x residue 378 VAL Chi-restraints excluded: chain x residue 380 VAL Chi-restraints excluded: chain x residue 390 ASP Chi-restraints excluded: chain x residue 404 GLU Chi-restraints excluded: chain x residue 410 LEU Chi-restraints excluded: chain x residue 420 VAL Chi-restraints excluded: chain x residue 427 SER Chi-restraints excluded: chain x residue 473 LEU Chi-restraints excluded: chain x residue 505 THR Chi-restraints excluded: chain x residue 526 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1074 random chunks: chunk 1001 optimal weight: 0.9980 chunk 117 optimal weight: 6.9990 chunk 592 optimal weight: 2.9990 chunk 758 optimal weight: 50.0000 chunk 587 optimal weight: 7.9990 chunk 874 optimal weight: 5.9990 chunk 580 optimal weight: 0.3980 chunk 1035 optimal weight: 0.6980 chunk 647 optimal weight: 6.9990 chunk 631 optimal weight: 50.0000 chunk 477 optimal weight: 7.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 162 ASN C 122 ASN D 15 GLN ** J 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 106 ASN M 17 GLN ** T 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 115 HIS d 117 HIS ** g 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 93 ASN i 66 GLN k 129 ASN m 106 ASN ** p 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 497 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 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 : 0.003 0.048 165065 Z= 0.180 Angle : 0.565 18.271 247072 Z= 0.289 Chirality : 0.034 0.265 31508 Planarity : 0.005 0.121 13398 Dihedral : 23.077 178.554 82989 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.30 % Favored : 93.67 % Rotamer: Outliers : 4.07 % Allowed : 18.56 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.10), residues: 6062 helix: -1.03 (0.12), residues: 1757 sheet: -1.10 (0.15), residues: 1088 loop : -1.81 (0.10), residues: 3217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP x 512 HIS 0.006 0.001 HIS P 76 PHE 0.015 0.001 PHE e 103 TYR 0.019 0.001 TYR i 59 ARG 0.029 0.000 ARG g 149 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12124 Ramachandran restraints generated. 6062 Oldfield, 0 Emsley, 6062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12124 Ramachandran restraints generated. 6062 Oldfield, 0 Emsley, 6062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1264 residues out of total 5032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 1059 time to evaluate : 5.674 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: 2 31 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7952 (mtm-85) REVERT: 8 115 ILE cc_start: 0.7737 (mt) cc_final: 0.7461 (tt) REVERT: 8 134 ARG cc_start: 0.5206 (tpp80) cc_final: 0.4905 (mmp80) REVERT: 8 160 LYS cc_start: 0.7662 (tmtt) cc_final: 0.7446 (tmtt) REVERT: 8 164 ARG cc_start: 0.5645 (tpt170) cc_final: 0.5397 (tpt170) REVERT: 8 198 ARG cc_start: 0.5526 (mtt-85) cc_final: 0.5110 (ttp80) REVERT: 8 199 LEU cc_start: 0.6030 (OUTLIER) cc_final: 0.5796 (mm) REVERT: 8 230 ARG cc_start: 0.6642 (tpm170) cc_final: 0.5689 (mmm160) REVERT: C 205 ASN cc_start: 0.8232 (t0) cc_final: 0.7883 (t0) REVERT: E 81 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7509 (ptt90) REVERT: F 171 ASP cc_start: 0.8027 (t0) cc_final: 0.7800 (p0) REVERT: G 32 THR cc_start: 0.8169 (t) cc_final: 0.7964 (m) REVERT: G 61 ARG cc_start: 0.7757 (tpp-160) cc_final: 0.7415 (tpp-160) REVERT: G 66 HIS cc_start: 0.7970 (t70) cc_final: 0.7676 (t-170) REVERT: G 131 LYS cc_start: 0.7539 (mtmt) cc_final: 0.7060 (mmtm) REVERT: H 12 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8326 (tm) REVERT: J 143 LYS cc_start: 0.8321 (ttpt) cc_final: 0.8075 (ttpp) REVERT: K 105 GLU cc_start: 0.7925 (mp0) cc_final: 0.7724 (mp0) REVERT: M 10 ARG cc_start: 0.7510 (OUTLIER) cc_final: 0.7247 (mtm-85) REVERT: M 83 MET cc_start: 0.8047 (mmp) cc_final: 0.7753 (mmp) REVERT: S 120 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.8261 (ptt180) REVERT: T 41 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.7693 (tt0) REVERT: T 62 ARG cc_start: 0.8390 (ttm170) cc_final: 0.8070 (ttm170) REVERT: U 11 VAL cc_start: 0.8739 (t) cc_final: 0.8399 (m) REVERT: U 17 LYS cc_start: 0.8872 (tttm) cc_final: 0.8632 (ttmt) REVERT: V 44 HIS cc_start: 0.7755 (m170) cc_final: 0.7448 (m90) REVERT: X 27 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.6926 (ppp80) REVERT: Y 36 MET cc_start: 0.8518 (tpp) cc_final: 0.8176 (tpp) REVERT: c 30 GLU cc_start: 0.7438 (tp30) cc_final: 0.7087 (tp30) REVERT: c 58 ARG cc_start: 0.7508 (OUTLIER) cc_final: 0.6144 (mtp-110) REVERT: c 67 ILE cc_start: 0.7509 (OUTLIER) cc_final: 0.7084 (mt) REVERT: c 109 GLU cc_start: 0.7674 (pm20) cc_final: 0.7041 (pm20) REVERT: c 110 SER cc_start: 0.8687 (t) cc_final: 0.8252 (t) REVERT: d 64 GLU cc_start: 0.7137 (tp30) cc_final: 0.6589 (tp30) REVERT: d 65 LYS cc_start: 0.8723 (tppp) cc_final: 0.8000 (ttmt) REVERT: d 83 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7659 (pt0) REVERT: d 154 ARG cc_start: 0.7874 (tpp-160) cc_final: 0.7627 (ttp-170) REVERT: e 103 PHE cc_start: 0.8430 (p90) cc_final: 0.8127 (p90) REVERT: e 128 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.7471 (ptp-110) REVERT: e 182 GLU cc_start: 0.8066 (mp0) cc_final: 0.7762 (mp0) REVERT: f 1 MET cc_start: 0.5069 (mmm) cc_final: 0.3774 (mmm) REVERT: g 23 VAL cc_start: 0.8329 (OUTLIER) cc_final: 0.8039 (p) REVERT: g 131 LEU cc_start: 0.8547 (mm) cc_final: 0.8228 (mp) REVERT: h 112 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8143 (tp) REVERT: i 63 LYS cc_start: 0.8762 (mmpt) cc_final: 0.8205 (mmmt) REVERT: i 130 ARG cc_start: 0.8196 (mtp180) cc_final: 0.7778 (mtp-110) REVERT: n 26 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7849 (ttpp) REVERT: o 82 ILE cc_start: 0.8102 (OUTLIER) cc_final: 0.7742 (mm) REVERT: p 28 ARG cc_start: 0.7520 (ppt-90) cc_final: 0.6826 (ppt-90) REVERT: q 71 LYS cc_start: 0.7456 (mtpp) cc_final: 0.7210 (mtmt) REVERT: q 115 GLU cc_start: 0.7249 (pp20) cc_final: 0.6772 (pp20) REVERT: t 57 LYS cc_start: 0.8284 (mppt) cc_final: 0.8081 (mppt) REVERT: x 4 PHE cc_start: 0.8171 (m-10) cc_final: 0.7688 (m-10) REVERT: x 175 LEU cc_start: 0.8631 (mm) cc_final: 0.8380 (mm) REVERT: x 184 ASP cc_start: 0.7198 (t0) cc_final: 0.6932 (t70) REVERT: x 199 GLU cc_start: 0.7086 (mt-10) cc_final: 0.6760 (mt-10) REVERT: x 404 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7611 (mp0) REVERT: x 410 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7371 (pp) REVERT: x 412 TYR cc_start: 0.8300 (m-80) cc_final: 0.7695 (m-80) REVERT: x 419 GLU cc_start: 0.7262 (mm-30) cc_final: 0.6795 (mt-10) outliers start: 205 outliers final: 150 residues processed: 1164 average time/residue: 1.2259 time to fit residues: 2425.8554 Evaluate side-chains 1184 residues out of total 5032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 1017 time to evaluate : 5.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 25 THR Chi-restraints excluded: chain 0 residue 32 VAL Chi-restraints excluded: chain 1 residue 12 THR Chi-restraints excluded: chain 2 residue 7 THR Chi-restraints excluded: chain 2 residue 23 LEU Chi-restraints excluded: chain 2 residue 31 ARG Chi-restraints excluded: chain 8 residue 44 VAL Chi-restraints excluded: chain 8 residue 46 ILE Chi-restraints excluded: chain 8 residue 85 ASP Chi-restraints excluded: chain 8 residue 171 LEU Chi-restraints excluded: chain 8 residue 199 LEU Chi-restraints excluded: chain 8 residue 209 LEU Chi-restraints excluded: chain 8 residue 216 THR Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 44 ASN Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 63 ASP Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain L residue 106 ASN Chi-restraints excluded: chain L residue 123 VAL Chi-restraints excluded: chain M residue 10 ARG Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 50 LEU Chi-restraints excluded: chain P residue 7 VAL Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 74 ILE Chi-restraints excluded: chain Q residue 95 LEU Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 30 VAL Chi-restraints excluded: chain S residue 120 ARG Chi-restraints excluded: chain T residue 36 ASP Chi-restraints excluded: chain T residue 41 GLN Chi-restraints excluded: chain T residue 59 THR Chi-restraints excluded: chain U residue 8 THR Chi-restraints excluded: chain U residue 73 VAL Chi-restraints excluded: chain U residue 83 ILE Chi-restraints excluded: chain U residue 87 VAL Chi-restraints excluded: chain V residue 41 GLU Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 65 LEU Chi-restraints excluded: chain V residue 78 THR Chi-restraints excluded: chain V residue 111 VAL Chi-restraints excluded: chain W residue 12 ASN Chi-restraints excluded: chain X residue 27 ARG Chi-restraints excluded: chain X residue 53 THR Chi-restraints excluded: chain Y residue 9 GLU Chi-restraints excluded: chain Z residue 9 VAL Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain c residue 57 GLU Chi-restraints excluded: chain c residue 58 ARG Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 186 LEU Chi-restraints excluded: chain d residue 62 VAL Chi-restraints excluded: chain d residue 73 GLU Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 129 SER Chi-restraints excluded: chain d residue 132 VAL Chi-restraints excluded: chain d residue 140 VAL Chi-restraints excluded: chain d residue 175 VAL Chi-restraints excluded: chain d residue 180 LEU Chi-restraints excluded: chain d residue 185 GLN Chi-restraints excluded: chain e residue 124 VAL Chi-restraints excluded: chain e residue 128 ARG Chi-restraints excluded: chain e residue 154 ILE Chi-restraints excluded: chain f residue 9 ILE Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 87 VAL Chi-restraints excluded: chain g residue 108 SER Chi-restraints excluded: chain g residue 135 VAL Chi-restraints excluded: chain h residue 112 LEU Chi-restraints excluded: chain i residue 29 THR Chi-restraints excluded: chain i residue 37 VAL Chi-restraints excluded: chain i residue 51 LEU Chi-restraints excluded: chain i residue 54 ARG Chi-restraints excluded: chain i residue 75 THR Chi-restraints excluded: chain i residue 85 PHE Chi-restraints excluded: chain j residue 26 VAL Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain k residue 36 THR Chi-restraints excluded: chain k residue 66 ARG Chi-restraints excluded: chain k residue 69 THR Chi-restraints excluded: chain k residue 96 VAL Chi-restraints excluded: chain k residue 131 VAL Chi-restraints excluded: chain l residue 33 VAL Chi-restraints excluded: chain l residue 47 SER Chi-restraints excluded: chain l residue 49 LEU Chi-restraints excluded: chain l residue 61 VAL Chi-restraints excluded: chain l residue 78 SER Chi-restraints excluded: chain l residue 115 SER Chi-restraints excluded: chain m residue 4 LEU Chi-restraints excluded: chain m residue 5 VAL Chi-restraints excluded: chain m residue 7 VAL Chi-restraints excluded: chain m residue 14 ARG Chi-restraints excluded: chain m residue 47 ASP Chi-restraints excluded: chain m residue 69 ASP Chi-restraints excluded: chain m residue 87 TYR Chi-restraints excluded: chain n residue 18 VAL Chi-restraints excluded: chain n residue 26 LYS Chi-restraints excluded: chain o residue 82 ILE Chi-restraints excluded: chain p residue 30 ASP Chi-restraints excluded: chain p residue 35 GLU Chi-restraints excluded: chain p residue 67 THR Chi-restraints excluded: chain q residue 78 GLU Chi-restraints excluded: chain q residue 112 SER Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain s residue 30 VAL Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 62 VAL Chi-restraints excluded: chain s residue 67 VAL Chi-restraints excluded: chain t residue 19 LEU Chi-restraints excluded: chain t residue 27 SER Chi-restraints excluded: chain x residue 25 THR Chi-restraints excluded: chain x residue 51 MET Chi-restraints excluded: chain x residue 143 GLN Chi-restraints excluded: chain x residue 148 LEU Chi-restraints excluded: chain x residue 157 VAL Chi-restraints excluded: chain x residue 160 LEU Chi-restraints excluded: chain x residue 173 LEU Chi-restraints excluded: chain x residue 183 LEU Chi-restraints excluded: chain x residue 191 ASP Chi-restraints excluded: chain x residue 265 ARG Chi-restraints excluded: chain x residue 266 LEU Chi-restraints excluded: chain x residue 321 VAL Chi-restraints excluded: chain x residue 336 LEU Chi-restraints excluded: chain x residue 349 ILE Chi-restraints excluded: chain x residue 356 ASN Chi-restraints excluded: chain x residue 378 VAL Chi-restraints excluded: chain x residue 380 VAL Chi-restraints excluded: chain x residue 390 ASP Chi-restraints excluded: chain x residue 404 GLU Chi-restraints excluded: chain x residue 410 LEU Chi-restraints excluded: chain x residue 427 SER Chi-restraints excluded: chain x residue 473 LEU Chi-restraints excluded: chain x residue 505 THR Chi-restraints excluded: chain x residue 526 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1074 random chunks: chunk 640 optimal weight: 2.9990 chunk 413 optimal weight: 9.9990 chunk 618 optimal weight: 1.9990 chunk 311 optimal weight: 10.0000 chunk 203 optimal weight: 10.0000 chunk 200 optimal weight: 7.9990 chunk 658 optimal weight: 7.9990 chunk 705 optimal weight: 10.0000 chunk 511 optimal weight: 0.7980 chunk 96 optimal weight: 10.0000 chunk 813 optimal weight: 4.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 122 ASN E 127 ASN ** J 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 106 ASN M 17 GLN M 39 HIS ** T 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 66 GLN ** g 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 93 ASN m 106 ASN ** p 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 165065 Z= 0.274 Angle : 0.615 18.335 247072 Z= 0.311 Chirality : 0.036 0.276 31508 Planarity : 0.005 0.122 13398 Dihedral : 23.053 177.905 82989 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.83 % Favored : 93.12 % Rotamer: Outliers : 4.27 % Allowed : 18.92 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.10), residues: 6062 helix: -0.97 (0.12), residues: 1757 sheet: -1.12 (0.16), residues: 1076 loop : -1.74 (0.10), residues: 3229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP x 512 HIS 0.007 0.001 HIS C 231 PHE 0.015 0.002 PHE e 103 TYR 0.018 0.002 TYR S 10 ARG 0.012 0.001 ARG 1 8 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12124 Ramachandran restraints generated. 6062 Oldfield, 0 Emsley, 6062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12124 Ramachandran restraints generated. 6062 Oldfield, 0 Emsley, 6062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1231 residues out of total 5032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 1016 time to evaluate : 5.483 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: 2 28 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.7750 (ttm110) REVERT: 2 31 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7955 (mtm-85) REVERT: 8 115 ILE cc_start: 0.7756 (mt) cc_final: 0.7479 (tt) REVERT: 8 134 ARG cc_start: 0.5251 (tpp80) cc_final: 0.4612 (mmp-170) REVERT: 8 164 ARG cc_start: 0.5665 (tpt170) cc_final: 0.5344 (tpt170) REVERT: 8 198 ARG cc_start: 0.5501 (mtt-85) cc_final: 0.5064 (ttp80) REVERT: 8 199 LEU cc_start: 0.6028 (OUTLIER) cc_final: 0.5793 (mm) REVERT: 8 230 ARG cc_start: 0.6873 (tpm170) cc_final: 0.5936 (mmm160) REVERT: C 99 ASP cc_start: 0.8327 (p0) cc_final: 0.8094 (p0) REVERT: C 205 ASN cc_start: 0.8293 (t0) cc_final: 0.8039 (t0) REVERT: E 24 ILE cc_start: 0.8080 (mm) cc_final: 0.7764 (mt) REVERT: E 81 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.7726 (ptt90) REVERT: F 171 ASP cc_start: 0.8014 (t0) cc_final: 0.7809 (p0) REVERT: G 32 THR cc_start: 0.8163 (t) cc_final: 0.7953 (m) REVERT: G 60 ARG cc_start: 0.7584 (ttp80) cc_final: 0.6726 (ttp80) REVERT: G 61 ARG cc_start: 0.7835 (tpp-160) cc_final: 0.7433 (tpp-160) REVERT: G 66 HIS cc_start: 0.7972 (t70) cc_final: 0.7696 (t-170) REVERT: G 131 LYS cc_start: 0.7567 (mtmt) cc_final: 0.7250 (mtmt) REVERT: H 12 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8346 (tm) REVERT: J 143 LYS cc_start: 0.8315 (ttpt) cc_final: 0.8073 (ttpp) REVERT: K 105 GLU cc_start: 0.7939 (mp0) cc_final: 0.7737 (mp0) REVERT: M 10 ARG cc_start: 0.7462 (OUTLIER) cc_final: 0.7211 (mtm-85) REVERT: M 83 MET cc_start: 0.8135 (mmp) cc_final: 0.7848 (mmp) REVERT: O 20 LEU cc_start: 0.8745 (pp) cc_final: 0.8508 (pt) REVERT: S 120 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.8314 (ptt180) REVERT: T 41 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7693 (tt0) REVERT: T 62 ARG cc_start: 0.8425 (ttm170) cc_final: 0.8072 (ttm170) REVERT: U 11 VAL cc_start: 0.8769 (t) cc_final: 0.8420 (m) REVERT: V 44 HIS cc_start: 0.7774 (m170) cc_final: 0.7446 (m90) REVERT: X 27 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.7311 (ppp80) REVERT: Y 36 MET cc_start: 0.8556 (tpp) cc_final: 0.8191 (tpp) REVERT: c 30 GLU cc_start: 0.7484 (tp30) cc_final: 0.7118 (tp30) REVERT: c 58 ARG cc_start: 0.7562 (OUTLIER) cc_final: 0.6203 (mtp-110) REVERT: c 67 ILE cc_start: 0.7373 (OUTLIER) cc_final: 0.7014 (mt) REVERT: c 82 GLU cc_start: 0.7407 (tt0) cc_final: 0.7190 (tt0) REVERT: c 85 ARG cc_start: 0.8378 (tmm-80) cc_final: 0.8100 (tmm-80) REVERT: c 109 GLU cc_start: 0.7718 (pm20) cc_final: 0.7109 (pm20) REVERT: c 110 SER cc_start: 0.8702 (t) cc_final: 0.8186 (t) REVERT: d 11 LYS cc_start: 0.8706 (mttm) cc_final: 0.8452 (mttp) REVERT: d 65 LYS cc_start: 0.8721 (tppp) cc_final: 0.8079 (ttmt) REVERT: d 154 ARG cc_start: 0.7913 (tpp-160) cc_final: 0.7669 (ttp-170) REVERT: d 179 GLN cc_start: 0.7531 (tp-100) cc_final: 0.7313 (tp-100) REVERT: e 128 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.7491 (ptp-110) REVERT: e 182 GLU cc_start: 0.8062 (mp0) cc_final: 0.7779 (mp0) REVERT: g 23 VAL cc_start: 0.8346 (OUTLIER) cc_final: 0.8071 (p) REVERT: g 66 LEU cc_start: 0.6894 (OUTLIER) cc_final: 0.6308 (tt) REVERT: g 131 LEU cc_start: 0.8535 (mm) cc_final: 0.8213 (mp) REVERT: h 112 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8163 (tp) REVERT: i 63 LYS cc_start: 0.8789 (mmpt) cc_final: 0.8236 (mmmt) REVERT: i 130 ARG cc_start: 0.8291 (mtp180) cc_final: 0.8040 (mtm110) REVERT: l 43 LYS cc_start: 0.8069 (mmmt) cc_final: 0.7831 (mtpt) REVERT: m 15 MET cc_start: 0.8283 (tpp) cc_final: 0.8070 (mmm) REVERT: n 26 LYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7856 (ttpp) REVERT: p 28 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.6676 (ppt-90) REVERT: q 71 LYS cc_start: 0.7483 (mtpp) cc_final: 0.7261 (mtmt) REVERT: q 115 GLU cc_start: 0.7324 (pp20) cc_final: 0.6833 (pp20) REVERT: t 57 LYS cc_start: 0.8375 (mppt) cc_final: 0.8089 (mppt) REVERT: t 81 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.6501 (mp10) REVERT: x 4 PHE cc_start: 0.8214 (m-10) cc_final: 0.7717 (m-10) REVERT: x 175 LEU cc_start: 0.8642 (mm) cc_final: 0.8393 (mm) REVERT: x 184 ASP cc_start: 0.7120 (t0) cc_final: 0.6847 (t70) REVERT: x 199 GLU cc_start: 0.7066 (mt-10) cc_final: 0.6749 (mt-10) REVERT: x 200 GLN cc_start: 0.7434 (mp10) cc_final: 0.6926 (mp10) REVERT: x 299 GLU cc_start: 0.6609 (pp20) cc_final: 0.6271 (pp20) REVERT: x 404 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7634 (mp0) REVERT: x 410 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.7383 (pp) REVERT: x 412 TYR cc_start: 0.8295 (m-80) cc_final: 0.7662 (m-80) REVERT: x 419 GLU cc_start: 0.7313 (mm-30) cc_final: 0.6842 (mt-10) outliers start: 215 outliers final: 171 residues processed: 1125 average time/residue: 1.2896 time to fit residues: 2505.3828 Evaluate side-chains 1200 residues out of total 5032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 1009 time to evaluate : 5.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 25 THR Chi-restraints excluded: chain 0 residue 32 VAL Chi-restraints excluded: chain 1 residue 12 THR Chi-restraints excluded: chain 1 residue 24 ILE Chi-restraints excluded: chain 2 residue 2 THR Chi-restraints excluded: chain 2 residue 23 LEU Chi-restraints excluded: chain 2 residue 28 ARG Chi-restraints excluded: chain 2 residue 31 ARG Chi-restraints excluded: chain 3 residue 3 LYS Chi-restraints excluded: chain 4 residue 8 LYS Chi-restraints excluded: chain 8 residue 44 VAL Chi-restraints excluded: chain 8 residue 46 ILE Chi-restraints excluded: chain 8 residue 85 ASP Chi-restraints excluded: chain 8 residue 171 LEU Chi-restraints excluded: chain 8 residue 193 ILE Chi-restraints excluded: chain 8 residue 199 LEU Chi-restraints excluded: chain 8 residue 209 LEU Chi-restraints excluded: chain 8 residue 216 THR Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 44 ASN Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 63 ASP Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain F residue 155 ARG Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain L residue 123 VAL Chi-restraints excluded: chain M residue 10 ARG Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 50 LEU Chi-restraints excluded: chain P residue 16 ILE Chi-restraints excluded: chain Q residue 16 SER Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 95 LEU Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 30 VAL Chi-restraints excluded: chain S residue 80 VAL Chi-restraints excluded: chain S residue 120 ARG Chi-restraints excluded: chain T residue 36 ASP Chi-restraints excluded: chain T residue 41 GLN Chi-restraints excluded: chain T residue 59 THR Chi-restraints excluded: chain U residue 8 THR Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 73 VAL Chi-restraints excluded: chain U residue 83 ILE Chi-restraints excluded: chain U residue 87 VAL Chi-restraints excluded: chain V residue 41 GLU Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 65 LEU Chi-restraints excluded: chain V residue 78 THR Chi-restraints excluded: chain V residue 111 VAL Chi-restraints excluded: chain W residue 12 ASN Chi-restraints excluded: chain X residue 27 ARG Chi-restraints excluded: chain X residue 53 THR Chi-restraints excluded: chain Y residue 9 GLU Chi-restraints excluded: chain Z residue 9 VAL Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain c residue 57 GLU Chi-restraints excluded: chain c residue 58 ARG Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 186 LEU Chi-restraints excluded: chain d residue 62 VAL Chi-restraints excluded: chain d residue 73 GLU Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 129 SER Chi-restraints excluded: chain d residue 132 VAL Chi-restraints excluded: chain d residue 140 VAL Chi-restraints excluded: chain d residue 175 VAL Chi-restraints excluded: chain d residue 180 LEU Chi-restraints excluded: chain d residue 185 GLN Chi-restraints excluded: chain e residue 108 ILE Chi-restraints excluded: chain e residue 128 ARG Chi-restraints excluded: chain e residue 154 ILE Chi-restraints excluded: chain f residue 8 VAL Chi-restraints excluded: chain f residue 9 ILE Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 29 LYS Chi-restraints excluded: chain g residue 66 LEU Chi-restraints excluded: chain g residue 87 VAL Chi-restraints excluded: chain g residue 108 SER Chi-restraints excluded: chain g residue 135 VAL Chi-restraints excluded: chain h residue 96 ARG Chi-restraints excluded: chain h residue 112 LEU Chi-restraints excluded: chain i residue 29 THR Chi-restraints excluded: chain i residue 37 VAL Chi-restraints excluded: chain i residue 51 LEU Chi-restraints excluded: chain i residue 75 THR Chi-restraints excluded: chain i residue 85 PHE Chi-restraints excluded: chain j residue 26 VAL Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain k residue 36 THR Chi-restraints excluded: chain k residue 66 ARG Chi-restraints excluded: chain k residue 96 VAL Chi-restraints excluded: chain k residue 131 VAL Chi-restraints excluded: chain l residue 33 VAL Chi-restraints excluded: chain l residue 47 SER Chi-restraints excluded: chain l residue 49 LEU Chi-restraints excluded: chain l residue 61 VAL Chi-restraints excluded: chain l residue 78 SER Chi-restraints excluded: chain l residue 104 THR Chi-restraints excluded: chain l residue 115 SER Chi-restraints excluded: chain m residue 4 LEU Chi-restraints excluded: chain m residue 5 VAL Chi-restraints excluded: chain m residue 7 VAL Chi-restraints excluded: chain m residue 14 ARG Chi-restraints excluded: chain m residue 17 VAL Chi-restraints excluded: chain m residue 47 ASP Chi-restraints excluded: chain m residue 69 ASP Chi-restraints excluded: chain m residue 87 TYR Chi-restraints excluded: chain n residue 18 VAL Chi-restraints excluded: chain n residue 26 LYS Chi-restraints excluded: chain o residue 82 ILE Chi-restraints excluded: chain p residue 28 ARG Chi-restraints excluded: chain p residue 30 ASP Chi-restraints excluded: chain p residue 34 ILE Chi-restraints excluded: chain p residue 35 GLU Chi-restraints excluded: chain q residue 78 GLU Chi-restraints excluded: chain q residue 112 SER Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain s residue 30 VAL Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 62 VAL Chi-restraints excluded: chain s residue 67 VAL Chi-restraints excluded: chain t residue 19 LEU Chi-restraints excluded: chain t residue 27 SER Chi-restraints excluded: chain t residue 81 GLN Chi-restraints excluded: chain x residue 25 THR Chi-restraints excluded: chain x residue 51 MET Chi-restraints excluded: chain x residue 143 GLN Chi-restraints excluded: chain x residue 148 LEU Chi-restraints excluded: chain x residue 157 VAL Chi-restraints excluded: chain x residue 160 LEU Chi-restraints excluded: chain x residue 173 LEU Chi-restraints excluded: chain x residue 183 LEU Chi-restraints excluded: chain x residue 191 ASP Chi-restraints excluded: chain x residue 265 ARG Chi-restraints excluded: chain x residue 266 LEU Chi-restraints excluded: chain x residue 270 LEU Chi-restraints excluded: chain x residue 321 VAL Chi-restraints excluded: chain x residue 336 LEU Chi-restraints excluded: chain x residue 349 ILE Chi-restraints excluded: chain x residue 356 ASN Chi-restraints excluded: chain x residue 378 VAL Chi-restraints excluded: chain x residue 380 VAL Chi-restraints excluded: chain x residue 390 ASP Chi-restraints excluded: chain x residue 404 GLU Chi-restraints excluded: chain x residue 410 LEU Chi-restraints excluded: chain x residue 427 SER Chi-restraints excluded: chain x residue 473 LEU Chi-restraints excluded: chain x residue 505 THR Chi-restraints excluded: chain x residue 526 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1074 random chunks: chunk 941 optimal weight: 9.9990 chunk 991 optimal weight: 20.0000 chunk 904 optimal weight: 4.9990 chunk 964 optimal weight: 10.0000 chunk 580 optimal weight: 0.0370 chunk 420 optimal weight: 9.9990 chunk 757 optimal weight: 20.0000 chunk 296 optimal weight: 8.9990 chunk 871 optimal weight: 8.9990 chunk 912 optimal weight: 0.7980 chunk 961 optimal weight: 0.6980 overall best weight: 3.1062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 122 ASN E 127 ASN ** J 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 40 GLN X 22 HIS ** d 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 66 GLN m 106 ASN ** x 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 165065 Z= 0.234 Angle : 0.601 18.320 247072 Z= 0.305 Chirality : 0.035 0.275 31508 Planarity : 0.005 0.121 13398 Dihedral : 23.058 177.992 82989 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.65 % Favored : 93.30 % Rotamer: Outliers : 4.39 % Allowed : 19.02 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.10), residues: 6062 helix: -0.86 (0.12), residues: 1752 sheet: -1.08 (0.15), residues: 1090 loop : -1.73 (0.10), residues: 3220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP x 512 HIS 0.007 0.001 HIS e 114 PHE 0.030 0.002 PHE e 103 TYR 0.024 0.002 TYR l 117 ARG 0.012 0.000 ARG 1 8 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12124 Ramachandran restraints generated. 6062 Oldfield, 0 Emsley, 6062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12124 Ramachandran restraints generated. 6062 Oldfield, 0 Emsley, 6062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1232 residues out of total 5032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 1011 time to evaluate : 5.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 28 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.7770 (ttm110) REVERT: 2 31 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7952 (mtm-85) REVERT: 8 115 ILE cc_start: 0.7745 (mt) cc_final: 0.7470 (tt) REVERT: 8 134 ARG cc_start: 0.5233 (tpp80) cc_final: 0.4595 (mmp-170) REVERT: 8 164 ARG cc_start: 0.5669 (tpt170) cc_final: 0.5405 (tpt170) REVERT: 8 198 ARG cc_start: 0.5501 (mtt-85) cc_final: 0.5063 (ttp80) REVERT: 8 199 LEU cc_start: 0.6026 (OUTLIER) cc_final: 0.5789 (mm) REVERT: 8 230 ARG cc_start: 0.6840 (tpm170) cc_final: 0.5905 (mmm160) REVERT: C 99 ASP cc_start: 0.8328 (p0) cc_final: 0.8099 (p0) REVERT: C 205 ASN cc_start: 0.8284 (t0) cc_final: 0.7913 (t0) REVERT: E 24 ILE cc_start: 0.8072 (mm) cc_final: 0.7759 (mt) REVERT: E 81 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.7713 (ptt90) REVERT: F 171 ASP cc_start: 0.8068 (t0) cc_final: 0.7843 (p0) REVERT: G 32 THR cc_start: 0.8160 (t) cc_final: 0.7953 (m) REVERT: G 60 ARG cc_start: 0.7564 (ttp80) cc_final: 0.6796 (ttp80) REVERT: G 61 ARG cc_start: 0.7845 (tpp-160) cc_final: 0.7451 (tpp-160) REVERT: G 66 HIS cc_start: 0.7972 (t70) cc_final: 0.7715 (t-170) REVERT: G 131 LYS cc_start: 0.7554 (mtmt) cc_final: 0.7238 (mtmt) REVERT: H 12 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8342 (tm) REVERT: J 143 LYS cc_start: 0.8320 (ttpt) cc_final: 0.8084 (ttpp) REVERT: K 105 GLU cc_start: 0.7936 (mp0) cc_final: 0.7718 (mp0) REVERT: M 10 ARG cc_start: 0.7478 (OUTLIER) cc_final: 0.7228 (mtm-85) REVERT: M 83 MET cc_start: 0.8111 (mmp) cc_final: 0.7824 (mmp) REVERT: O 20 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8519 (pt) REVERT: S 120 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.8311 (ptt180) REVERT: T 41 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.7689 (tt0) REVERT: T 62 ARG cc_start: 0.8412 (ttm170) cc_final: 0.8056 (ttm170) REVERT: U 11 VAL cc_start: 0.8760 (t) cc_final: 0.8415 (m) REVERT: V 44 HIS cc_start: 0.7739 (m170) cc_final: 0.7393 (m90) REVERT: X 27 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.7185 (ppp80) REVERT: c 30 GLU cc_start: 0.7480 (tp30) cc_final: 0.7111 (tp30) REVERT: c 58 ARG cc_start: 0.7550 (OUTLIER) cc_final: 0.6183 (mtp-110) REVERT: c 67 ILE cc_start: 0.7374 (OUTLIER) cc_final: 0.7097 (mt) REVERT: c 109 GLU cc_start: 0.7702 (pm20) cc_final: 0.7132 (pm20) REVERT: c 110 SER cc_start: 0.8688 (t) cc_final: 0.8161 (t) REVERT: d 11 LYS cc_start: 0.8696 (mttm) cc_final: 0.8482 (mttp) REVERT: d 65 LYS cc_start: 0.8729 (tppp) cc_final: 0.8092 (ttmt) REVERT: d 154 ARG cc_start: 0.7907 (tpp-160) cc_final: 0.7663 (ttp-170) REVERT: d 179 GLN cc_start: 0.7542 (tp-100) cc_final: 0.7311 (tp-100) REVERT: e 128 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.7423 (ptp-110) REVERT: e 182 GLU cc_start: 0.8061 (mp0) cc_final: 0.7777 (mp0) REVERT: g 23 VAL cc_start: 0.8343 (OUTLIER) cc_final: 0.8067 (p) REVERT: g 66 LEU cc_start: 0.6884 (OUTLIER) cc_final: 0.6294 (tt) REVERT: g 131 LEU cc_start: 0.8529 (mm) cc_final: 0.8209 (mp) REVERT: h 112 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8175 (tp) REVERT: i 63 LYS cc_start: 0.8792 (mmpt) cc_final: 0.8243 (mmmt) REVERT: i 130 ARG cc_start: 0.8276 (mtp180) cc_final: 0.7925 (mtp-110) REVERT: m 15 MET cc_start: 0.8284 (tpp) cc_final: 0.8081 (mmm) REVERT: n 26 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7822 (ttpp) REVERT: p 28 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.6675 (ppt-90) REVERT: q 71 LYS cc_start: 0.7492 (mtpp) cc_final: 0.7261 (mtmt) REVERT: q 115 GLU cc_start: 0.7256 (pp20) cc_final: 0.6773 (pp20) REVERT: r 49 ARG cc_start: 0.7623 (ttm-80) cc_final: 0.7006 (ttm-80) REVERT: t 57 LYS cc_start: 0.8388 (mppt) cc_final: 0.8183 (mppt) REVERT: t 81 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.6544 (mp10) REVERT: t 86 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7472 (pp) REVERT: x 4 PHE cc_start: 0.8205 (m-10) cc_final: 0.7710 (m-10) REVERT: x 175 LEU cc_start: 0.8636 (mm) cc_final: 0.8383 (mm) REVERT: x 184 ASP cc_start: 0.7086 (t0) cc_final: 0.6806 (t70) REVERT: x 199 GLU cc_start: 0.6988 (mt-10) cc_final: 0.6682 (mt-10) REVERT: x 200 GLN cc_start: 0.7337 (mp10) cc_final: 0.6802 (mp10) REVERT: x 404 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7631 (mp0) REVERT: x 410 LEU cc_start: 0.7586 (OUTLIER) cc_final: 0.7378 (pp) REVERT: x 412 TYR cc_start: 0.8291 (m-80) cc_final: 0.7652 (m-80) REVERT: x 419 GLU cc_start: 0.7301 (mm-30) cc_final: 0.6833 (mt-10) outliers start: 221 outliers final: 177 residues processed: 1125 average time/residue: 1.2335 time to fit residues: 2368.6518 Evaluate side-chains 1202 residues out of total 5032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 1003 time to evaluate : 5.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 25 THR Chi-restraints excluded: chain 0 residue 32 VAL Chi-restraints excluded: chain 1 residue 24 ILE Chi-restraints excluded: chain 2 residue 2 THR Chi-restraints excluded: chain 2 residue 23 LEU Chi-restraints excluded: chain 2 residue 28 ARG Chi-restraints excluded: chain 2 residue 31 ARG Chi-restraints excluded: chain 3 residue 3 LYS Chi-restraints excluded: chain 4 residue 8 LYS Chi-restraints excluded: chain 4 residue 24 MET Chi-restraints excluded: chain 6 residue 26 SER Chi-restraints excluded: chain 8 residue 44 VAL Chi-restraints excluded: chain 8 residue 46 ILE Chi-restraints excluded: chain 8 residue 85 ASP Chi-restraints excluded: chain 8 residue 171 LEU Chi-restraints excluded: chain 8 residue 193 ILE Chi-restraints excluded: chain 8 residue 199 LEU Chi-restraints excluded: chain 8 residue 209 LEU Chi-restraints excluded: chain 8 residue 216 THR Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 44 ASN Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 63 ASP Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain F residue 155 ARG Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain L residue 123 VAL Chi-restraints excluded: chain M residue 10 ARG Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 132 ILE Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 50 LEU Chi-restraints excluded: chain P residue 16 ILE Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain Q residue 16 SER Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 74 ILE Chi-restraints excluded: chain Q residue 95 LEU Chi-restraints excluded: chain Q residue 112 VAL Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 30 VAL Chi-restraints excluded: chain S residue 80 VAL Chi-restraints excluded: chain S residue 120 ARG Chi-restraints excluded: chain T residue 36 ASP Chi-restraints excluded: chain T residue 41 GLN Chi-restraints excluded: chain T residue 59 THR Chi-restraints excluded: chain T residue 79 THR Chi-restraints excluded: chain U residue 8 THR Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 73 VAL Chi-restraints excluded: chain U residue 83 ILE Chi-restraints excluded: chain U residue 87 VAL Chi-restraints excluded: chain V residue 41 GLU Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain V residue 65 LEU Chi-restraints excluded: chain V residue 78 THR Chi-restraints excluded: chain V residue 111 VAL Chi-restraints excluded: chain W residue 12 ASN Chi-restraints excluded: chain X residue 27 ARG Chi-restraints excluded: chain X residue 53 THR Chi-restraints excluded: chain Y residue 9 GLU Chi-restraints excluded: chain Z residue 9 VAL Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain c residue 57 GLU Chi-restraints excluded: chain c residue 58 ARG Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 186 LEU Chi-restraints excluded: chain d residue 62 VAL Chi-restraints excluded: chain d residue 73 GLU Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 129 SER Chi-restraints excluded: chain d residue 132 VAL Chi-restraints excluded: chain d residue 140 VAL Chi-restraints excluded: chain d residue 175 VAL Chi-restraints excluded: chain d residue 180 LEU Chi-restraints excluded: chain d residue 185 GLN Chi-restraints excluded: chain e residue 108 ILE Chi-restraints excluded: chain e residue 128 ARG Chi-restraints excluded: chain e residue 154 ILE Chi-restraints excluded: chain f residue 8 VAL Chi-restraints excluded: chain f residue 9 ILE Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 66 LEU Chi-restraints excluded: chain g residue 87 VAL Chi-restraints excluded: chain g residue 108 SER Chi-restraints excluded: chain g residue 135 VAL Chi-restraints excluded: chain h residue 112 LEU Chi-restraints excluded: chain i residue 29 THR Chi-restraints excluded: chain i residue 37 VAL Chi-restraints excluded: chain i residue 51 LEU Chi-restraints excluded: chain i residue 75 THR Chi-restraints excluded: chain i residue 85 PHE Chi-restraints excluded: chain j residue 26 VAL Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain k residue 28 HIS Chi-restraints excluded: chain k residue 36 THR Chi-restraints excluded: chain k residue 66 ARG Chi-restraints excluded: chain k residue 96 VAL Chi-restraints excluded: chain k residue 115 LEU Chi-restraints excluded: chain l residue 33 VAL Chi-restraints excluded: chain l residue 47 SER Chi-restraints excluded: chain l residue 49 LEU Chi-restraints excluded: chain l residue 61 VAL Chi-restraints excluded: chain l residue 78 SER Chi-restraints excluded: chain l residue 104 THR Chi-restraints excluded: chain l residue 115 SER Chi-restraints excluded: chain m residue 4 LEU Chi-restraints excluded: chain m residue 5 VAL Chi-restraints excluded: chain m residue 7 VAL Chi-restraints excluded: chain m residue 14 ARG Chi-restraints excluded: chain m residue 47 ASP Chi-restraints excluded: chain m residue 69 ASP Chi-restraints excluded: chain m residue 87 TYR Chi-restraints excluded: chain n residue 18 VAL Chi-restraints excluded: chain n residue 26 LYS Chi-restraints excluded: chain o residue 82 ILE Chi-restraints excluded: chain p residue 28 ARG Chi-restraints excluded: chain p residue 30 ASP Chi-restraints excluded: chain p residue 34 ILE Chi-restraints excluded: chain p residue 35 GLU Chi-restraints excluded: chain p residue 67 THR Chi-restraints excluded: chain q residue 78 GLU Chi-restraints excluded: chain q residue 102 ASP Chi-restraints excluded: chain q residue 112 SER Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain s residue 30 VAL Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 62 VAL Chi-restraints excluded: chain s residue 67 VAL Chi-restraints excluded: chain t residue 19 LEU Chi-restraints excluded: chain t residue 27 SER Chi-restraints excluded: chain t residue 81 GLN Chi-restraints excluded: chain t residue 86 LEU Chi-restraints excluded: chain x residue 25 THR Chi-restraints excluded: chain x residue 143 GLN Chi-restraints excluded: chain x residue 148 LEU Chi-restraints excluded: chain x residue 157 VAL Chi-restraints excluded: chain x residue 160 LEU Chi-restraints excluded: chain x residue 173 LEU Chi-restraints excluded: chain x residue 183 LEU Chi-restraints excluded: chain x residue 191 ASP Chi-restraints excluded: chain x residue 265 ARG Chi-restraints excluded: chain x residue 266 LEU Chi-restraints excluded: chain x residue 321 VAL Chi-restraints excluded: chain x residue 336 LEU Chi-restraints excluded: chain x residue 349 ILE Chi-restraints excluded: chain x residue 356 ASN Chi-restraints excluded: chain x residue 378 VAL Chi-restraints excluded: chain x residue 380 VAL Chi-restraints excluded: chain x residue 389 VAL Chi-restraints excluded: chain x residue 390 ASP Chi-restraints excluded: chain x residue 404 GLU Chi-restraints excluded: chain x residue 410 LEU Chi-restraints excluded: chain x residue 427 SER Chi-restraints excluded: chain x residue 473 LEU Chi-restraints excluded: chain x residue 505 THR Chi-restraints excluded: chain x residue 526 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1074 random chunks: chunk 633 optimal weight: 0.8980 chunk 1020 optimal weight: 3.9990 chunk 622 optimal weight: 30.0000 chunk 483 optimal weight: 0.8980 chunk 709 optimal weight: 10.0000 chunk 1069 optimal weight: 10.0000 chunk 984 optimal weight: 7.9990 chunk 852 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 658 optimal weight: 7.9990 chunk 522 optimal weight: 10.0000 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 122 ASN E 127 ASN ** J 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 17 GLN ** V 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 66 GLN m 106 ASN ** x 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 165065 Z= 0.249 Angle : 0.606 18.341 247072 Z= 0.307 Chirality : 0.036 0.275 31508 Planarity : 0.005 0.122 13398 Dihedral : 23.046 177.911 82989 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.78 % Favored : 93.17 % Rotamer: Outliers : 4.17 % Allowed : 19.44 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.10), residues: 6062 helix: -0.80 (0.12), residues: 1754 sheet: -1.11 (0.15), residues: 1079 loop : -1.68 (0.11), residues: 3229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP x 512 HIS 0.006 0.001 HIS U 4 PHE 0.025 0.002 PHE e 103 TYR 0.021 0.002 TYR l 117 ARG 0.022 0.000 ARG 8 126 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12124 Ramachandran restraints generated. 6062 Oldfield, 0 Emsley, 6062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12124 Ramachandran restraints generated. 6062 Oldfield, 0 Emsley, 6062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1208 residues out of total 5032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 998 time to evaluate : 5.327 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: 2 28 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.7734 (ttm110) REVERT: 2 31 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7959 (mtm-85) REVERT: 8 71 LYS cc_start: 0.6852 (mttt) cc_final: 0.6508 (mttm) REVERT: 8 115 ILE cc_start: 0.7736 (mt) cc_final: 0.7463 (tt) REVERT: 8 134 ARG cc_start: 0.5121 (tpp80) cc_final: 0.4511 (mmp-170) REVERT: 8 198 ARG cc_start: 0.5487 (mtt-85) cc_final: 0.5046 (ttp80) REVERT: 8 199 LEU cc_start: 0.6024 (OUTLIER) cc_final: 0.5786 (mm) REVERT: 8 207 ARG cc_start: 0.8285 (ttp-110) cc_final: 0.7734 (mmp80) REVERT: 8 230 ARG cc_start: 0.6938 (tpm170) cc_final: 0.5813 (mmm160) REVERT: C 99 ASP cc_start: 0.8336 (p0) cc_final: 0.8111 (p0) REVERT: C 205 ASN cc_start: 0.8297 (t0) cc_final: 0.7913 (t0) REVERT: E 24 ILE cc_start: 0.8071 (mm) cc_final: 0.7759 (mt) REVERT: E 81 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.7682 (ptt90) REVERT: G 32 THR cc_start: 0.8154 (t) cc_final: 0.7953 (m) REVERT: G 60 ARG cc_start: 0.7545 (ttp80) cc_final: 0.7227 (ttp80) REVERT: G 66 HIS cc_start: 0.7973 (t70) cc_final: 0.7706 (t-170) REVERT: G 131 LYS cc_start: 0.7552 (mtmt) cc_final: 0.7239 (mtmt) REVERT: H 12 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8365 (tm) REVERT: J 143 LYS cc_start: 0.8330 (ttpt) cc_final: 0.8092 (ttpp) REVERT: K 105 GLU cc_start: 0.7927 (mp0) cc_final: 0.7711 (mp0) REVERT: M 10 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.7229 (mtm-85) REVERT: M 83 MET cc_start: 0.8115 (mmp) cc_final: 0.7827 (mmp) REVERT: S 120 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.8312 (ptt180) REVERT: T 41 GLN cc_start: 0.7940 (OUTLIER) cc_final: 0.7692 (tt0) REVERT: T 62 ARG cc_start: 0.8407 (ttm170) cc_final: 0.8052 (ttm170) REVERT: U 11 VAL cc_start: 0.8757 (t) cc_final: 0.8412 (m) REVERT: V 44 HIS cc_start: 0.7728 (m170) cc_final: 0.7418 (m90) REVERT: X 27 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.7188 (ppp80) REVERT: Y 36 MET cc_start: 0.8674 (tpp) cc_final: 0.8310 (tpt) REVERT: c 30 GLU cc_start: 0.7482 (tp30) cc_final: 0.7113 (tp30) REVERT: c 58 ARG cc_start: 0.7557 (OUTLIER) cc_final: 0.6185 (mtp-110) REVERT: c 67 ILE cc_start: 0.7379 (OUTLIER) cc_final: 0.7121 (mt) REVERT: c 109 GLU cc_start: 0.7701 (pm20) cc_final: 0.7148 (pm20) REVERT: c 110 SER cc_start: 0.8681 (t) cc_final: 0.8156 (t) REVERT: d 65 LYS cc_start: 0.8731 (tppp) cc_final: 0.8082 (ttmt) REVERT: d 179 GLN cc_start: 0.7466 (tp-100) cc_final: 0.7201 (tp-100) REVERT: d 180 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7317 (mt) REVERT: e 128 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.7447 (ptp-110) REVERT: e 143 ARG cc_start: 0.8094 (mtp85) cc_final: 0.7836 (mtp180) REVERT: e 182 GLU cc_start: 0.8063 (mp0) cc_final: 0.7780 (mp0) REVERT: g 23 VAL cc_start: 0.8346 (OUTLIER) cc_final: 0.8068 (p) REVERT: g 66 LEU cc_start: 0.6876 (OUTLIER) cc_final: 0.6288 (tt) REVERT: g 131 LEU cc_start: 0.8531 (mm) cc_final: 0.8211 (mp) REVERT: h 112 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8185 (tp) REVERT: i 63 LYS cc_start: 0.8797 (mmpt) cc_final: 0.8246 (mmmt) REVERT: i 130 ARG cc_start: 0.8280 (mtp180) cc_final: 0.7824 (mtp-110) REVERT: m 15 MET cc_start: 0.8283 (tpp) cc_final: 0.8043 (mmm) REVERT: n 26 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7823 (ttpp) REVERT: p 28 ARG cc_start: 0.7643 (OUTLIER) cc_final: 0.6684 (ppt-90) REVERT: q 71 LYS cc_start: 0.7475 (mtpp) cc_final: 0.7255 (mtmt) REVERT: q 115 GLU cc_start: 0.7262 (pp20) cc_final: 0.6782 (pp20) REVERT: r 49 ARG cc_start: 0.7731 (ttm-80) cc_final: 0.7397 (ttm-80) REVERT: s 37 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.7496 (ptm160) REVERT: t 57 LYS cc_start: 0.8410 (mppt) cc_final: 0.8199 (mppt) REVERT: t 81 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.6507 (mp10) REVERT: t 86 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7478 (pp) REVERT: x 4 PHE cc_start: 0.8211 (m-10) cc_final: 0.7712 (m-10) REVERT: x 175 LEU cc_start: 0.8664 (mm) cc_final: 0.8417 (mm) REVERT: x 184 ASP cc_start: 0.7080 (t0) cc_final: 0.6803 (t70) REVERT: x 199 GLU cc_start: 0.6987 (mt-10) cc_final: 0.6678 (mt-10) REVERT: x 200 GLN cc_start: 0.7193 (mp10) cc_final: 0.6665 (mp10) REVERT: x 404 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7648 (mp0) REVERT: x 410 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7384 (pp) REVERT: x 412 TYR cc_start: 0.8275 (m-80) cc_final: 0.7658 (m-80) REVERT: x 419 GLU cc_start: 0.7303 (mm-30) cc_final: 0.6836 (mt-10) outliers start: 210 outliers final: 177 residues processed: 1104 average time/residue: 1.3268 time to fit residues: 2530.6016 Evaluate side-chains 1195 residues out of total 5032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 995 time to evaluate : 5.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 25 THR Chi-restraints excluded: chain 0 residue 32 VAL Chi-restraints excluded: chain 1 residue 24 ILE Chi-restraints excluded: chain 2 residue 2 THR Chi-restraints excluded: chain 2 residue 23 LEU Chi-restraints excluded: chain 2 residue 28 ARG Chi-restraints excluded: chain 2 residue 31 ARG Chi-restraints excluded: chain 3 residue 3 LYS Chi-restraints excluded: chain 4 residue 8 LYS Chi-restraints excluded: chain 4 residue 24 MET Chi-restraints excluded: chain 6 residue 26 SER Chi-restraints excluded: chain 8 residue 44 VAL Chi-restraints excluded: chain 8 residue 46 ILE Chi-restraints excluded: chain 8 residue 85 ASP Chi-restraints excluded: chain 8 residue 171 LEU Chi-restraints excluded: chain 8 residue 193 ILE Chi-restraints excluded: chain 8 residue 199 LEU Chi-restraints excluded: chain 8 residue 209 LEU Chi-restraints excluded: chain 8 residue 216 THR Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 44 ASN Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain F residue 155 ARG Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain L residue 123 VAL Chi-restraints excluded: chain M residue 10 ARG Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 50 LEU Chi-restraints excluded: chain P residue 7 VAL Chi-restraints excluded: chain P residue 16 ILE Chi-restraints excluded: chain Q residue 16 SER Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 74 ILE Chi-restraints excluded: chain Q residue 95 LEU Chi-restraints excluded: chain Q residue 112 VAL Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 30 VAL Chi-restraints excluded: chain S residue 80 VAL Chi-restraints excluded: chain S residue 120 ARG Chi-restraints excluded: chain T residue 36 ASP Chi-restraints excluded: chain T residue 41 GLN Chi-restraints excluded: chain T residue 59 THR Chi-restraints excluded: chain T residue 79 THR Chi-restraints excluded: chain U residue 8 THR Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 73 VAL Chi-restraints excluded: chain U residue 83 ILE Chi-restraints excluded: chain U residue 87 VAL Chi-restraints excluded: chain V residue 41 GLU Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain V residue 65 LEU Chi-restraints excluded: chain V residue 78 THR Chi-restraints excluded: chain V residue 111 VAL Chi-restraints excluded: chain W residue 12 ASN Chi-restraints excluded: chain X residue 27 ARG Chi-restraints excluded: chain X residue 53 THR Chi-restraints excluded: chain Y residue 9 GLU Chi-restraints excluded: chain Y residue 13 LEU Chi-restraints excluded: chain Y residue 38 THR Chi-restraints excluded: chain Z residue 9 VAL Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain c residue 57 GLU Chi-restraints excluded: chain c residue 58 ARG Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 186 LEU Chi-restraints excluded: chain d residue 62 VAL Chi-restraints excluded: chain d residue 73 GLU Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 129 SER Chi-restraints excluded: chain d residue 132 VAL Chi-restraints excluded: chain d residue 140 VAL Chi-restraints excluded: chain d residue 175 VAL Chi-restraints excluded: chain d residue 180 LEU Chi-restraints excluded: chain d residue 185 GLN Chi-restraints excluded: chain e residue 108 ILE Chi-restraints excluded: chain e residue 128 ARG Chi-restraints excluded: chain e residue 154 ILE Chi-restraints excluded: chain f residue 8 VAL Chi-restraints excluded: chain f residue 9 ILE Chi-restraints excluded: chain f residue 27 LEU Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 66 LEU Chi-restraints excluded: chain g residue 87 VAL Chi-restraints excluded: chain g residue 94 ASP Chi-restraints excluded: chain g residue 108 SER Chi-restraints excluded: chain g residue 135 VAL Chi-restraints excluded: chain h residue 112 LEU Chi-restraints excluded: chain i residue 29 THR Chi-restraints excluded: chain i residue 37 VAL Chi-restraints excluded: chain i residue 51 LEU Chi-restraints excluded: chain i residue 75 THR Chi-restraints excluded: chain i residue 85 PHE Chi-restraints excluded: chain j residue 15 HIS Chi-restraints excluded: chain j residue 26 VAL Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain k residue 28 HIS Chi-restraints excluded: chain k residue 36 THR Chi-restraints excluded: chain k residue 66 ARG Chi-restraints excluded: chain k residue 96 VAL Chi-restraints excluded: chain k residue 131 VAL Chi-restraints excluded: chain l residue 33 VAL Chi-restraints excluded: chain l residue 47 SER Chi-restraints excluded: chain l residue 49 LEU Chi-restraints excluded: chain l residue 61 VAL Chi-restraints excluded: chain l residue 78 SER Chi-restraints excluded: chain l residue 104 THR Chi-restraints excluded: chain l residue 115 SER Chi-restraints excluded: chain m residue 4 LEU Chi-restraints excluded: chain m residue 5 VAL Chi-restraints excluded: chain m residue 7 VAL Chi-restraints excluded: chain m residue 14 ARG Chi-restraints excluded: chain m residue 47 ASP Chi-restraints excluded: chain m residue 69 ASP Chi-restraints excluded: chain m residue 87 TYR Chi-restraints excluded: chain n residue 18 VAL Chi-restraints excluded: chain n residue 26 LYS Chi-restraints excluded: chain o residue 82 ILE Chi-restraints excluded: chain p residue 28 ARG Chi-restraints excluded: chain p residue 30 ASP Chi-restraints excluded: chain p residue 34 ILE Chi-restraints excluded: chain p residue 35 GLU Chi-restraints excluded: chain q residue 78 GLU Chi-restraints excluded: chain q residue 102 ASP Chi-restraints excluded: chain q residue 112 SER Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain s residue 30 VAL Chi-restraints excluded: chain s residue 37 ARG Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 62 VAL Chi-restraints excluded: chain t residue 19 LEU Chi-restraints excluded: chain t residue 27 SER Chi-restraints excluded: chain t residue 81 GLN Chi-restraints excluded: chain t residue 86 LEU Chi-restraints excluded: chain x residue 25 THR Chi-restraints excluded: chain x residue 143 GLN Chi-restraints excluded: chain x residue 148 LEU Chi-restraints excluded: chain x residue 157 VAL Chi-restraints excluded: chain x residue 160 LEU Chi-restraints excluded: chain x residue 173 LEU Chi-restraints excluded: chain x residue 183 LEU Chi-restraints excluded: chain x residue 191 ASP Chi-restraints excluded: chain x residue 265 ARG Chi-restraints excluded: chain x residue 266 LEU Chi-restraints excluded: chain x residue 321 VAL Chi-restraints excluded: chain x residue 336 LEU Chi-restraints excluded: chain x residue 349 ILE Chi-restraints excluded: chain x residue 356 ASN Chi-restraints excluded: chain x residue 378 VAL Chi-restraints excluded: chain x residue 380 VAL Chi-restraints excluded: chain x residue 389 VAL Chi-restraints excluded: chain x residue 404 GLU Chi-restraints excluded: chain x residue 410 LEU Chi-restraints excluded: chain x residue 427 SER Chi-restraints excluded: chain x residue 505 THR Chi-restraints excluded: chain x residue 526 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1074 random chunks: chunk 676 optimal weight: 20.0000 chunk 907 optimal weight: 6.9990 chunk 261 optimal weight: 10.0000 chunk 785 optimal weight: 10.0000 chunk 125 optimal weight: 7.9990 chunk 236 optimal weight: 7.9990 chunk 853 optimal weight: 3.9990 chunk 357 optimal weight: 10.0000 chunk 876 optimal weight: 6.9990 chunk 108 optimal weight: 8.9990 chunk 157 optimal weight: 7.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 122 ASN D 15 GLN E 127 ASN ** J 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 17 GLN ** V 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 22 HIS m 106 ASN p 57 GLN ** x 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 471 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.120757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.081556 restraints weight = 225118.378| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 1.07 r_work: 0.2727 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.087 165065 Z= 0.476 Angle : 0.762 18.702 247072 Z= 0.375 Chirality : 0.044 0.307 31508 Planarity : 0.006 0.124 13398 Dihedral : 23.131 178.283 82989 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.40 % Favored : 91.54 % Rotamer: Outliers : 4.71 % Allowed : 19.08 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.10), residues: 6062 helix: -1.12 (0.12), residues: 1762 sheet: -1.26 (0.16), residues: 1066 loop : -1.81 (0.10), residues: 3234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP x 512 HIS 0.010 0.002 HIS C 231 PHE 0.022 0.002 PHE c 129 TYR 0.024 0.002 TYR g 85 ARG 0.017 0.001 ARG 1 8 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 38671.98 seconds wall clock time: 674 minutes 4.43 seconds (40444.43 seconds total)